EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays

Multiomic droplet-based technologies allow different molecular modalities, such as chromatin accessibility and gene expression (scATAC-seq and scRNA-seq), to be probed in the same nucleus. We develop EmptyDropsMultiome, an approach that distinguishes true nuclei-containing droplets from background. Using simulations, we show that EmptyDropsMultiome has higher statistical power and accuracy than existing approaches, including CellRanger-arc and EmptyDrops. On real datasets, we observe that CellRanger-arc misses more than half of the nuclei identified by EmptyDropsMultiome and, moreover, is biased against certain cell types, some of which have a retrieval rate lower than 20%.

Effects of vaccination timing and target pathogens on performances and antimicrobial use in long-transported Charolais beef cattle from France to Italy - A retrospective study

Antimicrobial use (AMU) in the livestock sector is a major driver of antimicrobial resistance. Italian beef industry strongly relies on the import of young cattle from France, which are commingled in sorting facilities before transportation to Italy. Both commingling and transportation are stressors for animals and lead to higher risk of bovine respiratory disease (BRD), which in turn increases the risk of AMU. This study aimed to investigate how the timing of first BRD vaccination and the different vaccination target pathogens affect AMU and performance of young Charolais beef cattle imported from France to Italy. Information on animal performance, antimicrobial treatments, and vaccinations was available for 60,726 Charolais cattle belonging to 1449 batches in 33 Italian specialised fattening farms between January 2016 and December 2021. Antimicrobial use was estimated using the treatment incidence 100 adapted for Italy (TI100it). A mixed linear model was used to quantify the effects of the vaccination and the time of first administration on slaughter age, carcase weight, and average daily carcase gain. Similarly, a generalised linear mixed model was used to analyse the TI100it. The vaccination programme was usually applied the first day after the animals' arrival to the Italian fattening farms. Most animals were vaccinated with a polyvalent vaccine against infectious bovine rhinotracheitis (IBR), bovine parainfluenza type 3 virus (PI-3), bovine viral diarrhoea virus type 1 and 2 (BVDV), and bovine respiratory syncytial virus (BRSV). The most used class of antimicrobials to treat BRD were the macrolides, followed by aminoglycosides, amphenicols, tetracyclines, aminopenicillins, and fluoroquinolones. Animals that got vaccinated against any of the considered BRD pathogens upon arrival had significantly lower TI100it, greater average daily carcase gain, and reached slaughter age earlier than animals that got vaccinated later. Animals that received the vaccination against BVDV had lower TI100it and greater average daily carcase gain, and animals that received the vaccination against BRSV were younger at slaughter than unvaccinated animals. The vaccination against Mannheimia haemolytica significantly decreased the slaughter age and increased the carcase weight and average daily carcase gain, and the vaccination against PI-3 and Histophilus somni significantly increased the slaughter age. Thus, even if the vaccination programme is essential to tackle BRD, this practice is questionable if applied at arrival to the Italian fattening farms and it is advisable that the vaccination programme is planned before the commingling procedure in France.

Tracking flowpaths in a complex karst system through tracer test and hydrogeochemical monitoring: Implications for groundwater protection (Gran Sasso, Italy)

Groundwater in karst aquifers is frequently tapped for drinking purposes, due to frequent huge volumes of resources. Unfortunately, vulnerability of these aquifers can be high, due to possible fast transfer of recharge water on springs by the karst network. On Gran Sasso Mountain regional aquifer, several springs are subjected to drinking withdrawal and an updated evaluation of their potential is now a fundamental issue to be considered, facing climate change effects, which reflect on variation of discharge regimen and values. To distinguish between different contribution of spring recharge, a tracer test has been carried out on the Vitella d'Oro spring, fed both by the regional aquifer and by a local system exposed to karst features developed in the Rigopiano Conglomerates formation. Thanks to hydrogeological, hydrogeochemical and isotopic data, a conceptual model of spring recharge has been proposed and subsequently validated by the tracer test results. All information confirms the superimposition on the regional base flow, by a relevant contribution of the karst network, influencing the spring discharge in recharge periods. In detail, a fast flow component is responsible for discharge peaks and frequently of turbidity events, having a mean velocity ranging from 30 to 70 m/h in the aquifer. Besides of this fast flow, an additional aliquot of the recharge is due to the same local aquifer, but slower flow clearly identifiable by hydrochemistry and isotopic data. Thanks to these findings, a renewed management of the spring has been suggested, considering the different degrees of aquifer vulnerability (turbidity occurrence) directly related to the discharge regimen.

Farmed fish welfare during slaughter in Italy: survey on stunning and killing methods and indicators of unconsciousness

Information on slaughter procedures for farmed fish in aquaculture is limited, both in Europe and in Italy, due to a general lack of field data. The aim of this study was to gather information on the procedures used to slaughter fish in Italy and to discuss them considering the WOAH and EFSA recommendations on fish welfare. Using a questionnaire survey, data were collected by official veterinarians in 64 slaughtering facilities where 20 different species of fish were slaughtered. The main species slaughtered were rainbow trout (Oncorhynchus mykiss; 29/64), followed by European sea bass (Dicentrarchus labrax; 21/64), sea bream (Sparus aurata; 21/64), Arctic char (Salvelinus alpinus; 14/64), European eel (Anguilla anguilla; 11/64), sturgeon (Acipenser spp; 11/64), common carp (Cyprinus carpio; 6/64), and brown trout (Salmo trutta fario L.; 5/64). The most applied stunning/killing methods were "asphyxia in ice/thermal shock" and "electric in water bath," followed by "percussion," "asphyxia in air," and "electric dry system." After the application of the method, the assessment of the fish level of unconsciousness was practiced in 72% of the facilities using more than one indicator, with "breathing" and "coordinated movements" the most practiced. The collected data showed a discrepancy between the available recommendations about the welfare of fish at slaughter and what is practiced in many production sites, but for many species precise recommendations are still not available.

DMRT1 regulates human germline commitment

Germline commitment following primordial germ cell (PGC) specification during early human development establishes an epigenetic programme and competence for gametogenesis. Here we follow the progression of nascent PGC-like cells derived from human embryonic stem cells in vitro. We show that switching from BMP signalling for PGC specification to Activin A and retinoic acid resulted in DMRT1 and CDH5 expression, the indicators of migratory PGCs in vivo. Moreover, the induction of DMRT1 and SOX17 in PGC-like cells promoted epigenetic resetting with striking global enrichment of 5-hydroxymethylcytosine and locus-specific loss of 5-methylcytosine at DMRT1 binding sites and the expression of DAZL representing DNA methylation-sensitive genes, a hallmark of the germline commitment programme. We provide insight into the unique role of DMRT1 in germline development for advances in human germ cell biology and in vitro gametogenesis.

Yolk sac cell atlas reveals multiorgan functions during human early development

The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds.

Paratuberculosis, Animal Welfare and Biosecurity: A Survey in 33 Northern Italy Dairy Goat Farms

Paratuberculosis is a notable infectious disease of ruminants. Goats appear to be particularly susceptible. The survey aimed to investigate the spread of paratuberculosis in Italian goat farming and evaluate whether the presence of the disease could be influenced by welfare and biosecurity deficiencies. A serological survey for paratuberculosis in 33 dairy farms in northern Italy was conducted. Contextually, animal welfare and biosecurity were assessed, using a standardized protocol of 36 welfare indicators and 15 biosecurity indicators which assigns to each farm a welfare and biosecurity score from 0 (any application) to 100% (full application). An overall result of less than 60% was considered insufficient. Nineteen farms (58%) tested positive for paratuberculosis, with a mean intra-herd seroprevalence of 7.4%. Total welfare ranged from 39.56 to 90.7% (mean 68.64%). Biosecurity scores ranged from 10.04 to 90.01% (mean 57.57%). Eight farms (24%) showed poor welfare conditions (welfare score < 60%) and 19 (58%) an unsatisfactory biosecurity condition (biosecurity score < 60%). With respect to the explorative character of the study, an indicative association between seven welfare and biosecurity indicators and paratuberculosis seropositivity was identified. The presence of paratuberculosis in northern Italy dairy goat farms was confirmed. The welfare and biosecurity assessment protocol proved to be an accurate tool, capable of identifying critical points for managing health, welfare and productivity.

Safety Evaluation and Probabilistic Health Risk Assessment of Cow Milk Produced in Northern Italy According to Dioxins and PCBs Contamination Levels

Contamination levels of dioxins and polychlorinated biphenyls (PCBs) were monitored over 2018-2021 in 214 bovine milk samples from farms located in two regions in northern Italy (Lombardy and Emilia-Romagna). The average concentrations of the sum of dioxins and dioxin-like PCBs (0.78 ± 0.55 pg TEQ/g fat) and six non-dioxin-like PCBs (6.55 ± 2.24 ng/g fat) were largely below the maximum, and action limits established at European level, confirming a decreasing trend observed both locally and across Europe in recent years. The impact of contamination levels on chronic dietary exposure of the Italian population to dioxins and PCBs was found to be highly variable based on the type of cow milk (skimmed, semi-skimmed, or whole-fat milk) and the population age group considered. Indeed, a first-tier screening of the potential exposure via determinist methods allowed for the identification of the youngest population as the group with the worst risk profile. The refinement of exposure assessment via Monte Carlo probabilistic methods suggested that, at the less pessimistic middle-bound simulation scenario, infants, toddlers, and children consuming whole cow milk may be exposed to dioxins and PCBs levels above the toxicological reference values with a probability of 76, 56, and 22%, respectively.

Brain-Derived Neurotrophic Factor, Kynurenine Pathway, and Lipid-Profiling Alterations as Potential Animal Welfare Indicators in Dairy Cattle

Complete animal welfare evaluation in intensive farming is challenging. With this study, we investigate new biomarkers for animal physical and mental health by comparing plasma expression of biochemical indicators in dairy cows reared in three different systems: (A) semi-intensive free-stall, (B) non-intensive tie-stall, and (C) intensive free-stall. Additionally, protein levels of mature brain-derived neurotrophic factor (mBDNF) and its precursor form (proBDNF) and indoleamine 2,3-dioxygenase (IDO1) specific activity were evaluated in brain samples collected from 12 cattle culled between 73 and 138 months of age. Alterations in plasma lipid composition and in the kynurenine pathway of tryptophan metabolism were observed in the tie-stall-reared animals. The total plasma BDNF concentration was higher in tie-stall group compared to the two free-housing groups. Brain analysis of the tie-stall animals revealed a different mBDNF/proBDNF ratio, with a higher level of proBDNF (p < 0.001). Our data are similar to previous studies on animal models of depression, which reported that inhibition of the conversion of proBDNF in its mature form and/or elevated peripheral kynurenine pathway activation may underlie cerebral biochemical changes and induce depressive-like state behavior in animals.

Staphylococcus aureus adlb gene is associated with high prevalence of intramammary infection in dairy herds of northern Italy: A cross-sectional study

Staphylococcus aureus is a major mastitis pathogen in dairy cattle worldwide, responsible for substantial economic losses. Environmental factors, milking routine, and good maintenance of milking equipment have been described as important factors to prevent intramammary infections (IMI). Staphylococcus aureus IMI can be widespread within the farm or the infection can be limited to few animals. Several studies have reported that Staph. aureus genotypes differ in their ability to spread within a herd. In particular, Staph. aureus belonging to ribosomal spacer PCR genotype B (GTB)/clonal complex 8 (CC8) is associated with high within-herd prevalence of IMI, whereas other genotypes are generally associated with individual cow disease. The adlb gene seems to be strictly related to Staph. aureus GTB/CC8, and is a potential marker of contagiousness. We investigated Staph. aureus IMI prevalence in 60 herds in northern Italy. In the same farms, we assessed specific indicators linked to milking management (e.g., teat condition score and udder hygiene score) and additional milking risk factors for IMI spread. Ribosomal spacer-PCR and adlb-targeted PCR were performed on 262 Staph. aureus isolates, of which 77 underwent multilocus sequence typing. In most of the herds (90%), a predominant genotype was identified, especially Staph. aureus CC8 (30%). In 19 of 60 herds, the predominant circulating Staph. aureus was adlb-positive and the observed IMI prevalence was relevant. Moreover, the adlb gene was detected only in genotypes of CC8 and CC97. Statistical analysis showed a strong association between the prevalence of Staph. aureus IMI, the specific CCs, and carriage of adlb, with the predominant circulating CC and presence of the gene alone explaining the total variation. Interestingly, the difference in the odds ratio obtained in the models for CC8 and CC97 suggests that it is carriage of the adlb gene, rather than the circulation of these CCs per se, that leads to higher within-herd prevalence of Staph. aureus. In addition, the model showed that environmental and milking management factors had no or minimal effect on Staph. aureus IMI prevalence. In conclusion, the circulation of adlb-positive Staph. aureus strains within a herd has a strong effect on the prevalence of IMI. Thus, adlb can be proposed as a genetic marker of contagiousness for Staph. aureus IMI in cattle. However, further analyses using whole-genome sequencing are required to understand the role of genes other than adlb that may be involved in the mechanisms of contagiousness of Staph. aureus strains associated with high prevalence of IMI.

Single-cell roadmap of human gonadal development

Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries¹. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal-mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15⁺ and TREM2⁺ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.

Robust temporal map of human in vitro myelopoiesis using single-cell genomics

Myeloid cells are central to homeostasis and immunity. Characterising in vitro myelopoiesis protocols is imperative for their use in research, immunotherapies, and understanding human myelopoiesis. Here, we generate a >470K cells molecular map of human induced pluripotent stem cells (iPSC) differentiation into macrophages. Integration with in vivo single-cell atlases shows in vitro differentiation recapitulates features of yolk sac hematopoiesis, before definitive hematopoietic stem cells (HSC) emerge. The diversity of myeloid cells generated, including mast cells and monocytes, suggests that HSC-independent hematopoiesis can produce multiple myeloid lineages. We uncover poorly described myeloid progenitors and conservation between in vivo and in vitro regulatory programs. Additionally, we develop a protocol to produce iPSC-derived dendritic cells (DC) resembling cDC2. Using CRISPR/Cas9 knock-outs, we validate the effects of key transcription factors in macrophage and DC ontogeny. This roadmap of myeloid differentiation is an important resource for investigating human fetal hematopoiesis and new therapeutic opportunities.

Mapping Human Reproduction with Single-Cell Genomics

The trillions of cells in the human body develop as a result of the fusion of two extremely specialized cells: an oocyte and a sperm. This process is essential for the continuation of our species, as it ensures that parental genetic information is mixed and passed on from generation to generation. In addition to producing oocytes, the female reproductive system must provide the environment for the appropriate development of the fetus until birth. New genomic and computational tools offer unique opportunities to study the tight spatiotemporal regulatory mechanisms that are required for the cycle of human reproduction. This review explores how single-cell technologies have been used to build cellular atlases of the human reproductive system across the life span and how these maps have proven useful to better understand reproductive pathologies and dissect the heterogeneity of in vitro model systems. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Promoting Judicious Antimicrobial Use in Beef Production: The Role of Quarantine

Judicious antimicrobial stewardship in livestock industry is needed to reduce the use of antimicrobials (AMU) and the associated risk of antimicrobial resistance. Biosecurity measures are acknowledged for their role against the spread of diseases and the importance in reducing AMU in different species. However, their effectiveness in beef production has been scarcely considered. The aim of this study was to investigate the effect of the quarantine strategy on AMU in beef cattle. A total of 1206 Charolaise animals in five farms were included in the trial. Roughly half of the animals followed the standard procedure of the fattening cycle (no-quarantine; NO-QUA group) and half followed a 30-day period of quarantine (QUA group) since their arrival. Performance and antimicrobial data were recorded and a treatment incidence 100 (TI100it) per animal was calculated. Penicillins was the most used class of antimicrobials. Differences between groups were significant for males only, with NO-QUA group having greater TI100it (3.76 vs. 3.24; p < 0.05) and lower body weight at slaughter (713.4 vs. 723.7 kg; p < 0.05) than QUA group. Results suggest that quarantine strategy can reduce AMU in males without compromising their performance, whereas further investigation is needed for females.

OUP accepted manuscript

Motivation

Wikipedia is one of the most important channels for the public communication of science and is frequently accessed as an educational resource in computational biology. Joint efforts between the International Society for Computational Biology (ISCB) and the Computational Biology taskforce of WikiProject Molecular Biology (a group of expert Wikipedia editors) have considerably improved computational biology representation on Wikipedia in recent years. However, there is still an urgent need for further improvement in quality, especially when compared to related scientific fields such as genetics and medicine. Facilitating involvement of members from ISCB Communities of Special Interest (COSIs) would improve a vital open education resource in computational biology, additionally allowing COSIs to provide a quality educational resource highly specific to their subfield.

Results

We generate a list of around 1500 English Wikipedia articles relating to computational biology and describe the development of a binary COSI-Article matrix, linking COSIs to relevant articles and thereby defining domain-specific open educational resources. Our analysis of the COSI-Article matrix data provides a quantitative assessment of computational biology representation on Wikipedia against other fields and at a COSI-specific level. Furthermore, we conducted similarity analysis and subsequent clustering of COSI-Article data to provide insight into potential relationships between COSIs. Finally, based on our analysis, we suggest courses of action to improve the quality of computational biology representation on Wikipedia.

The influence of different production systems on dioxin and PCB levels in chicken eggs from Emilia-Romagna and Lombardy regions (Italy) over 2017-2019 and consequent dietary exposure assessment

Hen eggs from farms with different production systems (organic, free range, barn, and in cage) sited in two regions of Italy (Emilia-Romagna and Lombardy) were collected from 2017 to 2019 to monitor the levels of 17 polychlorinated dibenzo-p-dioxin/dibenzofurans (PCDD/Fs), 12 dioxin-like polychlorinated biphenyls (dl-PCBs) and the 6 non-dioxin-like polychlorinated biphenyl indicators (ndl-PCBs). Average concentrations of PCDD/Fs (0.21 pg WHO₍₂₀₀₅₎-TEQ/g fat), PCDD/Fs + dl-PCBs (0.43 pg WHO₍₂₀₀₅₎-TEQ/g fat) and ndl-PCBs (6.41 ng/g fat) were below the maximum limits established at European level in eggs, but significantly higher amounts of PCDD/Fs and PCDD/Fs + dl-PCBs were found in eggs from free-range housing system compared to barn, cage, and organic ones. The potential dietary intake of the monitored contaminants by Italian population age groups through the consumption of locally produced eggs was also evaluated. Exposure levels to PCDD/Fs plus dl-PCBs were below the tolerable weekly intake (TWI) of 2 pg WHO₍₂₀₀₅₎-TEQ/kg bw/week recently set by the European Food Safety Authority (EFSA). However, the younger population was found to be more vulnerable than other age groups to exposure to these contaminants. Specifically, the preferential consumption of free-range eggs by infants, toddlers, and children contributed more than 30% to the TWI. The results confirm the need to continuously monitor the levels of chemical contaminants in the environment and provide a reminder of the importance of targeted intervention measures aimed to reduce their occurrence in food and feed, firstly by improving the management practices on egg-producing farms.

Best Farming Practices for the Welfare of Dairy Cows, Heifers and Calves

Simple Summary

The evolving change in societal attitudes regarding animal care and use has led to two main streams of thought. On one hand, there is the concept of “animal rights”, emphasizing that animals should have the same rights as humans, and as such should never be used to benefit humans (e.g., for food, clothing, entertainment, education, research, and even pet ownership). Animals should be able to live a life free of human interference and exploitation. On the other hand, many people agree that humans are responsible for animals and for their care; animals can be used to benefit humans if properly cared for, and their needs are met; abuse and neglect are banned. This is the “animal welfare” (AW) point of view, based on humane treatment, ensuring the physical and mental fitness of animals, as required by current EU legislation. Now, the point is that to fulfill the basic requirements of animal welfare animals are ensured a life worth living, especially given that they can feel emotions. In view of ensuring not only compliance with minimum legislative requirements, but also optimal farming conditions (above minimum legislative requirements), growing attention is attributed to best farming practices. In this work, a list of best practices proposed by the Italian National Reference Centre for Animal Welfare (CReNBA) has been collected to ensure a good quality of life for dairy cows, heifers and calves kept in intensive rearing systems.

Abstract

The concept of animal welfare (AW) has many meanings. Traditionally, AW has been considered as freedom from disease and suffering. Nowadays, growing attention goes to the concept of “positive animal welfare” (PAW), which can be interpreted within the concept of quality of life (QoL), thinking about a “balance of positives over negatives” and a “life worth living”. In this vision, where the QoL represents a continuum between positives and negatives, the Italian National Reference Centre for Animal Welfare (CReNBA), within the Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), has developed a welfare assessment protocol for dairy cows, heifers, and calves in loose housing systems, including both animal-based and non-animal-based indicators, in which not only hazards but also benefits are identified. This protocol is part of an integrated monitoring system called “ClassyFarm”, belonging to the Italian Ministry of Health and developed by IZSLER. The aim of this paper is to extrapolate from the mentioned protocol, a list of 38 best farming practices (on managerial and equipment factors) for ensuring a high level of welfare in dairy cattle. All stakeholders (veterinarians, farmers, competent authorities, consumers, etc.) can benefit of these best practices as a guide or toolbox to ensure a life worth living for these animals.

The Relationship between Animal Welfare and Antimicrobial Use in Italian Dairy Farms

Information regarding the relationship between animal welfare (AW) and antimicrobial use (AMU) in dairy cows is limited. The current study aimed to investigate this relationship on Italian farms and to identify potential targets of AMU reduction. The study was performed at 79 Italian dairy farms housing over 15,000 cows during 2019. AW was scored with an on-farm protocol assessing farm management and staff training, housing systems, and animal-based measures. AMU was estimated using a defined daily dose per kg of animal biomass (DDDAit/biomass) for Italy. The median AW score was 73% (range: 56.6-86.8%). The median AMU was 4.8 DDDAit/biomass (range: 0-11.8). No relationship between the total AMU and AW was found. Management and staff training were positively associated with the use of the European Medicines Agency's category B antimicrobials, which are critical for human medicine, and with intramammary products for dry cow therapy. In those farms, antimicrobial stewardship should aim to reduce the category B antimicrobials and selective dry cow therapy. Our results underline the importance of implementing both an integrated monitoring system (AW, AMU, etc.) and antimicrobial stewardship tailored to the specific needs of each dairy farm.

Welfare Assessment: Correspondence Analysis of Welfare Score and Hematological and Biochemical Profiles of Dairy Cows in Sardinia, Italy

The need for animal welfare definition and assessment is increasing worldwide, and several studies have been conducted to help fill the knowledge gaps regarding the welfare of cattle. However, further studies are needed to provide valid synthetized measures for welfare evaluation. The aim of this study was to assess the welfare status of 16 Sardinian dairy cattle farms, based on the developed Animal Welfare and Biosecurity Evaluation checklist (AWB-EF) and the corresponding hematological, biochemical, and electrophoretic profiles of these animals. Considering the AWB-EF as gold standard, blood samples were collected from 230 Holstein breed dairy cattle, aged between 3 and 8 years, out of the periparturient period, and with no clinical signs of specific pathologies. Principal Component (PC) and correlation analyses were performed to simplify phenomena interpretation and assess positive/negative associations. Four PCs were able to explain 76% of the total variability, and six laboratory parameters were strongly associated with the AWB-EF score (Spearman's correlation coefficient ≥ 0.40, p-Value < 0.05), reflecting the real health status of the animals. Given the complexity of animal welfare as a multidimensional concept and the need to include both animal-based and non-based measures in welfare evaluation, the present work represents a sound basis for future evaluation and veterinary health planning.

Animal welfare and biosecurity assessment: a comparison between Italian and Irish beef cattle rearing systems

Context European beef production is facing fresh challenges on various fronts: increasing public concern on animal welfare; declining EU meat consumption; and, conversely, expected growth in global demand for meat. The Italian National Reference Centre for Animal Welfare (CReNBA) has developed an assessment protocol for collecting information about beef cattle welfare and biosecurity conditions, with the intention of better understanding animal needs and disseminating best practices. Aims The protocol was applied on Italian and Irish farms, and the results were used as a starting point for a specific statistical analysis for comparing animal welfare and biosecurity levels in the two countries. Methods The protocol consists of animal-based measures and non-animal-based measures (management-based and resource-based indicators) and has been designed to determine the major hazards and benefits that can influence cattle health and welfare, including the presence of biosecurity issues. The outcomes of welfare and biosecurity assessments conducted during November 2016–July 2017 of 40 Irish beef herds reared indoors were compared with those of 85 Italian beef units assessed over the same period. Differences obtained within each beef-unit distribution were calculated by the VARNC index (diversity index), and a distance estimate of the beef-unit distribution from a hypothetical ideal condition was calculated by using the distance from ideal (dfi) index. Key results The dfi index revealed that Irish farms were closer to the ideal condition for the measures ‘experience and training of stockpersons’, ‘water provision’, ‘handling facilities’, ‘restraint facilities’, and ‘temperature, humidity and ventilations conditions’. Italian farms were closer to the ideal condition for ‘diet calculation and feed quality’, ‘feeding management’, ‘feeding place dimension’, ‘cleanliness of water points’, ‘cleanliness of floors’, ‘type of floors’, ‘cleanliness of animals’, and ‘integument alterations’. In contrast to the Italian farms, there was particular awareness of the importance of biosecurity on Irish farms. Conclusions The results revealed intrinsic management and housing differences between the two rearing systems, although only few dissimilarities were found in the animal outcomes: in fact, the assessment of the animal-based measures gave very similar results for the two countries, except for ‘cleanliness of the animals’ and ‘integument alterations’. Implications In the face of global challenges affecting the pursuit of farming sustainability, farmers should be encouraged to improve safeguards for animal welfare and reduce the spread of animal diseases. This can be achieved by facilitating knowledge exchange internationally.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma.

Effect of welfare standards and biosecurity practices on antimicrobial use in beef cattle

Antimicrobial use (AMU) in livestock species and the associated antimicrobial resistance are a global concern, thus strategies for their reduction and a more judicious use are needed. Previous research has revealed a link between improved animal welfare, biosecurity and AMU reduction in pig and dairy sectors, however, little is known about the beef sector. This study aimed to investigate the impact of welfare standards and biosecurity on AMU in beef cattle. Data on performance traits and AMU were collected over a 3.5 year time from 27 specialised beef farms and a treatment incidence was calculated using the defined daily dose for animals. An on-farm assessment was carried out by assigning a score from 0 (very poor) to 100% (very good) to 3 sections: welfare, biosecurity and emergency management. The highest average score was obtained for the welfare section (76%) followed by emergency management (39%) and biosecurity (24%). This suggests that major focus on strategies for the implementation of biosecurity measures and emergency management is needed, due to the low scores reported. A statistically significant lower AMU was observed with improved level of welfare. These results may be helpful for farm benchmarking and highlight the importance of improved animal welfare for an efficient antimicrobial stewardship.

“Nudge” in Lucca’s Hospital: separate waste collection improvement and cigarettes dumping reduction

Background

Positive behaviour and user's collaboration improved by using choices orientation techniques; in Lucca's Hospital (North-West Tuscany Sanitary Authority) this approach has improved separate waste collection execution and has decreased cigarettes dumping in commons areas.

Objectives

Phase 1 (May 2019): amendment of choices architecture recyclable waste bins in commons areas and into the wards were boosted, with “islands” clearly visible from any point of common paths; in the transit areas were installed exclusively multi-material and paper bins, equipped with signs that clearly indicate which products deliver; residual waste bins were allowed exclusively in certain points.ashtrays at the hospital entrances were eliminated and replaced with signage indicating smoking cessation benefits and the presence of areas “put your cigarette out” along the structure approach routes.

Phase 2 (scheduled for May 2020): “nudge” action

Spreading in community (using press and social-media) and locally (using poster) of the slogan “In San Luca we are taking a step forward: don't lag behind!”. This message stimulate the perception of an ongoing change to join.

Results

A decrease in residual waste collection and in instances of non-compliance in separate waste collection was detected. Decorum in the outdoor environments improved, with a reduction of user's reports and extra-cleaning interventions.

Conclusions

The described actions have improved user's collaboration, management efficiency of waste disposal and cleaning service, perceived quality and cost.

Key messages

Imitating a social model appears to be successful motivator of virtuous behaviours. Choices architecture and “nudge” techniques may improve citizens’ care pathways governance.

PCDD/Fs, DL-PCBs, and NDL-PCBs in Dairy Cows: Carryover in Milk from a Controlled Feeding Study

A feeding study was carried out to investigate the kinetics in cow milk of the 17 polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), the 12 dioxin-like polychlorinated biphenyls (DL-PCBs), and the 6 non-dioxin-like PCBs (NDL-PCBs) regulated by the European (EU) legislation. A fortified ration (ΣPCDD/Fs and DL-PCBs: 24.68 ng TEQ/day/cow; ΣNDL-PCBs: 163.99 μg/day/cow) was given to the animals for 49 days, followed by 42 days on clean feed. EU maximum limit for TEQ_{PCDD/F+DL-PCB} was exceeded in milk after 1 week of exposure, while for ΣNDL-PCBs, after 5 weeks. Milk compliance was restored after 1 week on clean feed, but to return to the basal TEQ_{PCDD/F+DL-PCB} it took 42 days. At the end of the study, ΣNDL-PCBs had not yet reached the basal level. The carryover rate of ΣNDL-PCBs was 25.4%, while the carryover rate of TEQ_{PCDD/F+DL-PCB} was 36.9%. The latter was mainly affected by the 12 congeners contributing most to the toxic equivalent (TEQ) level, explaining the fast overcome of the maximum limit in milk.

Diagnostic value of composite milk sample vs single quarter milk sample for the detection of Staphylococcus aureus intra-mammary infections in cattle

Staphylococcus aureus (S. aureus) is one of the most important causes of mastitis in dairy cattle. Control and eradication programs of S. aureus intra-mammary infections (IMI) are based on different factors included the correct detection and management of the infected cows. The present study aimed at evaluating the efficacy of composite milk samples (CMS) analysis, compared to quarter milk samples (QMS) analysis, for the bacteriological detection of S. aureus intra-mammary infections. During 2016, 661 CMS (hygienically collected) and 2644 QMS (aseptically collected) were obtained from 661 cows in 5 herds. All the samples were submitted to S. aureus bacteriological culture and somatic cell count (SCC) analysis. QMS bacteriological analysis on blood agar plates was able to detect 236 cows excreting S. aureus, while the bacteriological analysis of CMS, using selective agar, identified 229 positive cows. The concordance was 95% with an excellent Cohen's κ (0.89). Relative sensitivity and specificity of CMS vs QMS, considered as the reference test, were 91.5% ± 2.1 and 96.9% ± 1.3 (CI 95%), respectively. In addition, the relative sensitivity of CMS improved as the number of infected quarters per cow and the number of colony forming units (cfu) per sample increased. The predictive value of CMS results was better when paired with SCC data, in particular CMS showed better negative predictive value when SCC was <200,000 cells/mL and better positive predictive value when SCC was>200,000 cells/mL. The probability for a cow to be S. aureus positive was 56.4% in case of SCC > 200,000 cells/mL, while it was 18.6% in case of SCC < 200,000 cells/mL. The average SCC in CMS was significantly higher in positive cows and the value rose as the number of infected quarters per cow increased. Given the intermittent excretion of S. aureus in milk from dairy cows, it could be more advantageous to carry out several serial CMS, rather than few QMS, being CMS an easier to collect and less expensive milk sampling method. Thus, bacteriological examination of CMS, combined with SCC data of the same sample, could be extremely useful for the success of S. aureus IMI control plans, because repeated CMS are easier to be performed and could be more easily proposed to the farmers.

Key role of hydrogen peroxide in antimicrobial activity of spring, Honeydew maquis and chestnut grove Corsican honeys on Pseudomonas aeruginosa DNA

In honeys, several molecules have been known for their antibacterial or wound healing properties. Corsican honeys just began to be tested for their antimicrobial activity with promising results on Pseudomonas aeruginosa. So, identification of active molecules and their mode of action was determined. Hydrogen peroxide concentrations were evaluated and, in parallel, the minimal inhibitory concentrations (MIC) values were performed with and without catalase. More, the quantity of phenolic compounds and ORAC assay were measured. Observation of antibacterial action was done using scanning electron microscopy (SEM) followed by plasmidic DNA extraction. MIC values of chestnut grove and honeydew maquis honeys vary between 7 and 8%, showing a strong antimicrobial capacity, associated with a plasmidic DNA degradation. When catalase is added, MIC values significatively increase (25%) without damaging DNA, proving the importance of H₂ O₂ . This hypothesis is confirmed by SEM micrographies which did not show any morphological damages but a depletion in bacterial population. Although, such low concentrations of H₂ O₂ (between 23 μmol l^-1 and 54 μmol l^-1 ) cannot explain antimicrobial activity and might be correlated with phenolic compounds concentration. Thus, Corsican honeys seem to induce DNA damage when H₂ O₂ and phenolic compounds act in synergy by a putative pro-oxidant effect.

SIGNIFICANCE AND IMPACT OF THE STUDY

We started to determine the antibacterial efficiency of Corsican chestnut grove and honeydew maquis honeys on Pseudomonas aeruginosa. No morphological alteration of the bacterial surface was observed. Antimicrobial action seems to be related to the synergy between hydrogen peroxide and phenolic compounds. The exerted pro-oxidant activity leads to a degradation of P. aeruginosa plasmidic DNA. This is the first study that investigate the primary antibacterial mechanism of Corsican honeys.

Disease risk assessment by clinical immunology analyses in periparturient dairy cows

A disease prediction system was investigated in a case-control study in the dry period of high-yielding dairy cows. Blood samples of 75 cows from 26 herds were collected before calving between -23 and -33 days (T1) and also between -2 and -6 days (T2) to investigate a panel of clinical immunology and chemistry parameters. Cows with abnormal serum lysozyme and interleukin-6 concentrations showed a greater disease prevalence until the 60th day in milk compared with non-responder cows (P<0.05 and lower at T1). Differences in disease prevalence were observed on the basis of T1 data, and also by combining the results at T1 and T2. The other laboratory parameters under study were not predictive of a disease risk. Results indicate that environmental stressors in the dry period may cause a negative imprinting of the innate immune response, underlying predisposition to later disease occurrence.

Case-study and risk management of dioxins and PCBs bovine milk contaminations in a high industrialized area in Northern Italy

Milk supplied to a dairy plant in Brescia City (Northern Italy) was found to be contaminated by dioxin like PCBs at levels above the European (EU) action limit (2 pg WHO-TEQ/g fat). As a consequence, 14 dairy farms were sampled individually, in order to identify and possibly eliminate the source of contamination. All the farms were located in Brescia or just nearby, an area that is characterized by a strong industrialization. Four out of the 14 farms showed contamination levels above the legal maximum limit set by European Commission at 5.5 pg WHO-TEQ/g fat for the sum of dioxins and DL-PCBs. Concentrations of 8.16, 6.83, 5.71 and 5.65 pg WHO-TEQ/g fat were detected. In the three most polluted farms, cow ration was substituted with feed coming from uncontaminated areas and the time needed to reduce milk pollution was evaluated. In all the three farms, contamination levels dropped below the EU legal limit after only 1 month from the removal of the pollution source. In each sampled farm, DL-PCBs were the major contributors to the total WHO-TEQ level, with percentages up to 87% in the most contaminated one. PCB 126 WHO-TEQ value explained by itself large part of this contamination, and its decrease was fundamental for the reduction of milk contamination levels. This study provides an example of an on-field successful emergency intervention that succeeded in decontamination of dairy cows, allowing a fast restart of their production activity.

Innate and adaptive immune mechanisms are effectively induced in ileal Peyer's patches of Salmonella typhimurium infected pigs

In this report we employed laser-capture microdissection (LCM) coupled to qPCR technology and bioinformatic analysis to characterize, for the first time, the response of Peyer's patches (PP) from orally infected animals to Salmonella typhimurium, in a model of non-typhoidal salmonellosis. Pathogen was highly found in the cytoplasm of phagocytes in PP and differential gene expression analysis indicated an up-regulation of proinflammatory molecules, establishment of a Th1 driven response and triggering of DC and T-cell activity. Furthermore, predictions by bioinformatic analysis pointed to an activation of processes regarding stimulation and maturation of DC, influx of leukocytes in tissue and T lymphocytes priming and differentiation. In short, the approach used in this study proved to be a promising strategy to explore infectious processes. Indeed, it revealed an effective induction of innate and adaptive immune mechanisms in swine PP which appear to be distinct from those observed in mesenteric lymph nodes and closely related to response of gut mucosa.

Diurnal patterns and sex differences in cortisol, 11-ketotestosterone, testosterone, and 17beta-estradiol in the bluebanded goby (Lythrypnus dalli)

The primary goals of this study were to evaluate diurnal patterns of and sex differences in the levels of cortisol, 11-ketotestosterone, testosterone, and 17beta-estradiol in the sex-changing bluebanded goby Lythrypnus dalli. Steroid hormones were collected from water samples and analyzed by enzyme immunoassay. During the breeding season, hormones were sampled from both males and females at seven time points between 0600 and 2000 h. When comparing each time point separately, there were significant overall time effects for cortisol and 17beta-estradiol. Cortisol concentrations were lowest at the 0800-1000 h sampling point and showed a qualitative peak in late morning (1000-1200 h). Concentrations of 17beta-estradiol were elevated at the last sampling point (1800-2000 h). Broader temporal trends were revealed for testosterone and 11-ketotestosterone concentrations, both of which were elevated in the morning. There were no sex differences in overall hormone concentrations or temporal profiles for cortisol, 11-ketotestosterone, or testosterone. Males and females showed similar diurnal patterns of 17beta-estradiol but females had significantly higher water-borne 17beta-estradiol levels than males. The results show the presence of diurnal changes in steroid hormone levels in male and female bluebanded gobies. The lack of sex differences in androgens suggests that males of this species, and perhaps other bi-directional sex-changing species in which males do not exhibit prominent secondary sexual characteristics, do not require persistent elevations in 11-ketotestosterone or testosterone to maintain the male phenotype. Although the role of 17beta-estradiol in maintaining sex differences in sexually plastic species is unclear, our results suggest that, of the hormones measured, 17beta-estradiol has the greatest potential for future studies interested in this question.

A giant outburst two years before the core-collapse of a massive star

The death of massive stars produces a variety of supernovae, which are linked to the structure of the exploding stars. The detection of several precursor stars of type II supernovae has been reported (see, for example, ref. 3), but we do not yet have direct information on the progenitors of the hydrogen-deficient type Ib and Ic supernovae. Here we report that the peculiar type Ib supernova SN 2006jc is spatially coincident with a bright optical transient that occurred in 2004. Spectroscopic and photometric monitoring of the supernova leads us to suggest that the progenitor was a carbon-oxygen Wolf-Rayet star embedded within a helium-rich circumstellar medium. There are different possible explanations for this pre-explosion transient. It appears similar to the giant outbursts of luminous blue variable stars (LBVs) of 60-100 solar masses, but the progenitor of SN 2006jc was helium- and hydrogen-deficient (unlike LBVs). An LBV-like outburst of a Wolf-Rayet star could be invoked, but this would be the first observational evidence of such a phenomenon. Alternatively, a massive binary system composed of an LBV that erupted in 2004, and a Wolf-Rayet star exploding as SN 2006jc, could explain the observations.

Purification, product characterization and kinetic properties of lipoxygenase from olive fruit (Olea europaea L.)

Lipoxygenase from olive fruit was purified to homogeneity for the first time after differential centrifugations and by hydrophobic chromatography. The enzyme had a molecular mass of 98 kDa and exhibited a maximal activity at pH 6. Lipoxygenase had a better affinity for linoleic acid (Km=82.44 microM) than for linolenic acid (Km = 306.26 microM). It is inhibited by linoleate:oxygen oxidoreductase (LOX) inhibitors like nordihydroguaiaretic acid (NDGA) or propyl gallate. The reaction product was 13-hydroperoxy octadecadienoic acid when linoleic acid was used as substrate.

Amifostine: potential for clinically useful cytoprotection

The ability to target malignant cells for cytotoxicity while sparing normal host tissues has proven to be limited. These limitations have resulted in unacceptable toxicity or insufficiently effective therapy. Continuing investigation of new, potentially useful cytotoxic agents must continue. An alternative approach, also worthy of study, is the selective protection of normal tissues. This approach, used in conjunction with available therapeutic agents, may open the therapeutic window and incrementally enhance the effectiveness of cytotoxic therapy. A variety of methods have been used to protect normal tissues selectively. Regional protection can be used for certain organ systems, such as the oral mucosa. Selective protection on a systemic level is more difficult but agents that seem to protect normal but not malignant tissues selectively are being developed. Among these is amifostine, which was originally selected by the U.S. defense department for study as a radioprotectant. Pre-clinical studies have suggested that amifostine is differentially concentrated in normal tissues but not in malignant tissues. Tissue-specific differences in the activity of alkaline phosphatase, which dephosphorylates amifostine to its active metabolite WR-1065, and in pH are thought to be involved in this relative specificity. Clinical studies indicate that amifostine can reduce the myelosuppression produced by cyclosphosphamide, the combination of cyclophosphamide and cisplatin, and, perhaps, carboplatin. The protective effects of amifostine on nonhematopoietic toxicities are being investigated. Future trials will investigate the integration of amifostine with cytokine-based supportive care in order to define the role of this potentially clinically useful cytoprotectant agent.

Phase I trial of subcutaneous recombinant macrophage colony-stimulating factor: clinical and immunomodulatory effects

PURPOSE

Recombinant human macrophage colony-stimulating factor (rM-CSF) has been demonstrated to control the growth, differentiation, and function of mononuclear phagocytes. Preclinical studies have indicated antitumor effects, and therefore a phase I trial of rM-CSF in patients with malignancy was initiated. The toxicity and hematologic and immunologic effects were investigated.

PATIENTS AND METHODS

rM-CSF was administered as a subcutaneous injection on days 1 through 5 and 8 through 12. Cycles were repeated every 28 days. Cohorts of four to seven patients received rM-CSF at dose levels from 0.1 to 25.6 mg/m2/d. Forty-two patients received 88 cycles of rM-CSF. All patients had metastatic solid tumors refractory to standard therapy.

RESULTS

The toxicity of rM-CSF was mild. Dose-limiting toxicity included thrombocytopenia (two patients) and iritis (one patient) occurring at a dose of 25.6 mg/m2/d. Hematologic studies demonstrated dose-related monocytosis occurring routinely at doses > or = 3.2 mg/m2/d, and thrombocytopenia. Immunologic studies demonstrated enhanced secretion of tumor necrosis factor-alpha (TNF-alpha) and interleukin-1-beta (IL-1 beta) by monocytes after in vitro stimulation with lipopolysaccharide, and increased expression of TNF-alpha mRNA at higher rM-CSF dose levels. Pharmacokinetic studies demonstrated that the systemic clearance rate of M-CSF increases during week 1 of therapy, resulting in lower blood levels of M-CSF during the second week of therapy.

CONCLUSION

rM-CSF can be safely administered to patients, and has biologic activity on peripheral-blood monocytes.