Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards a Positive Welfare Protocol for Cattle: A Critical Review of Indicators and Suggestion of How We Might Proceed

Current animal welfare protocols focus on demonstrating the absence (or at least low levels) of indicators of poor welfare, potentially creating a mismatch between what is expected by society (an assurance of good animal welfare) and what is actually being delivered (an assurance of the absence of welfare problems). This paper explores how far we have come, and what work still needs to be done, if we are to develop a protocol for use on commercial dairy farms where the aim is to demonstrate the presence of positive welfare. Following conceptual considerations around a perceived “ideal” protocol, we propose that a future protocol should be constructed (i) of animal-based measures, (ii) of indicators of affective state, and (iii) be structured according to indicators of short-term emotion, medium-term moods and long-term cumulative assessment of negative and positive experiences of an animal's life until now (in contrast to the current focus on indicators that represent different domains/criteria of welfare). These three conditions imposed the overall structure within which we selected our indicators. The paper includes a critical review of the literature on potential indicators of positive affective states in cattle. Based on evidence about the validity and reliability of the different indicators, we select ear position, play, allogrooming, brush use and QBA as candidate indicators that we suggest could form a prototype positive welfare protocol. We emphasise that this prototype protocol has not been tested in practice and so it is perhaps not the protocol itself that is the main outcome of this paper, but the process of trying to develop it. In a final section of this paper, we reflect on some of the lessons learnt from this exercise and speculate on future perspectives. For example, while we consider we have moved towards a prototype positive welfare protocol for short-term affective states, future research energy should be directed towards valid indicators for the medium and long-term.
Climate Change in Fisheries and Aquaculture: Analysis of the Impact Caused by Idai and Kenneth Cyclones in Mozambique

Fisheries and Aquaculture are among the most popular activities in coastal regions of the world. In addition, both correspond to high-risk activities within a climate change context as they are vulnerable to environmental changes that threaten the socio-economic sustainability of the fishing communities that depend on fish for food security and income generation. In 2019, the central part of Mozambique was hit by two unprecedented cyclones: Idai and Kenneth that killed over 600 people and left nearly 2.2 million people in need of urgent assistance. The aim of the present study was to investigate the impacts these cyclones had on fisheries and aquaculture in the provinces of Sofala and Zambézia in Mozambique. The study further seeks to propose strategies that could be adopted by the communities to minimize the risks in the future. For the construction of the database, both secondary and primary data collection approaches were used to characterize the cyclone events. Secondary data was collected through sector reports and previously published articles, while primary data was collected through interviews with fishers, sector employees, and aquaculture producers in the affected provinces. The results revealed that these natural events had both a direct and indirect impact on fishing, as they affected more than 1,440 fishermen that lost 590 vessels, 1,800 fishing gear, and 67 boat engines in Sofala province. In Zambézia province, aquaculture producers lost 169 fish ponds, two cages, and 606,000 lost fry, while in Sofala province, 58 fish tanks, 204 cages, and 257,500 fish fry were lost. Overall, our study reveals the vulnerability of fisheries and aquaculture to extreme events particularly the cyclones in Mozambique. Lack of knowledge regarding climate change, advanced preventive measures, and poor adaptive capacity makes the sectors more vulnerable to disasters. Therefore, it is recommended to improve awareness programs, introduce measures and policies that promote resilience and optimum adaptive efficiency.
Metabolomics Analysis Discovers Estrogen Altering Cell Proliferation via the Pentose Phosphate Pathway in Infertility Patient Endometria

Estrogen therapy is widely used as a supplementary treatment after hysteroscopy for female infertility patients owing to its protective function that improves endometrial regeneration and menstruation, inhibits recurrent adhesions, and improves subsequent conception rate. The endometrial protective function of such estrogen administration pre-surgery is still controversial. In the current study, 12 infertility patients were enrolled, who were treated with estrogen before hysteroscopy surgery. Using cutting-edge metabolomic analysis, we observed alterations in the pentose phosphate pathway (PPP) intermediates of the patient’s endometrial tissues. Furthermore, using Ishikawa endometrial cells, we validated our clinical discovery and identified estrogen–ESR–G6PD–PPP axial function, which promotes estrogen-induced cell proliferation.
Proportional Changes in Cognitive Subdomains During Normal Brain Aging

Background: Neuroscience lacks a reliable method of screening the early stages of dementia. Objective: To improve the diagnostics of age-related cognitive functions by developing insight into the proportionality of age-related changes in cognitive subdomains. Materials and Methods: We composed a battery of psychophysiological tests and collected an open-access psychophysiological outcomes of brain atrophy (POBA) dataset by testing individuals without dementia. To extend the utility of machine learning (ML) classification in cognitive studies, we proposed estimates of the disproportional changes in cognitive functions: an index of simple reaction time to decision-making time (ISD), ISD with the accuracy performance (ISDA), and an index of performance in simple and complex visual-motor reaction with account for accuracy (ISCA). Studying the distribution of the values of the indices over age allowed us to verify whether diverse cognitive functions decline equally throughout life or there is a divergence in age-related cognitive changes. Results: Unsupervised ML clustering shows that the optimal number of homogeneous age groups is four. The sample is segregated into the following age-groups: Adolescents ∈ [0, 20), Young adults ∈ [20, 40), Midlife adults ∈ [40, 60) and Older adults ≥60 year of age. For ISD, ISDA, and ISCA values, only the median of the Adolescents group is different from that of the other three age-groups sharing a similar distribution pattern (p > 0.01). After neurodevelopment and maturation, the indices preserve almost constant values with a slight trend toward functional decline. The reaction to a moving object (RMO) test results (RMO_mean) follow another tendency. The Midlife adults group's median significantly differs from the remaining three age subsamples (p < 0.01). No general trend in age-related changes of this dependent variable is observed. For all the data (ISD, ISDA, ISCA, and RMO_mean), Levene's test reveals no significant changes of the variances in age-groups (p > 0.05). Homoscedasticity also supports our assumption about a linear dependency between the observed features and age. Conclusion: In healthy brain aging, there are proportional age-related changes in the time estimates of information processing speed and inhibitory control in task switching. Future studies should test patients with dementia to determine whether the changes of the aforementioned indicators follow different patterns.
Valorization of Urban Street Tree Pruning Residues in Biorefineries by Steam Refining: Conversion Into Fibers, Emulsifiers, and Biogas

Street tree pruning residues are a widely available and currently undervalorized bioresource. Their utilization could help alleviate an increasing biomass shortage and offset costs of the pruning process for the municipalities. In this work, a holistic valorization pathway of pruning residues leading to fibers, oligosaccharides, biogas, and compost is presented. For this, representative mixtures of tree pruning materials from the most prevalent street tree genera (oak, linden, maple) found in Hamburg (Germany) were prepared by shredding and cleaning procedures. Collection of sample material was performed in summer and winter to account for seasonality. A steam-based fractionation was conducted using treatment severities ranging from log R0 = 2.5 to 4.0. At the highest severity, a fiber yield of around 66%, and liquor yield of 26–30% was determined. The fibers were evaluated with respect to their properties for paper product applications, with higher treatment severities leading to higher paper strengths. From the oligosaccharide-rich liquor, emulsions were created, which showed promising stability properties over 8 weeks of storage. The liquors and the rejects from the material preparation also displayed good potential for biomethane production. Overall, the differences between material collected in summer and winter were found to be small, indicating the possibility for a year-round utilization of pruning residues. For the presented utilization pathway, high severity treatments were the most promising, featuring a high liquor yield, good biomethane potential, and the highest paper strengths.
The Antioxidant Guaiacol Exerts Fungicidal Activity Against Fungal Growth and Deoxynivalenol Production in Fusarium graminearum

The main component of creosote obtained from dry wood distillation—guaiacol—is a natural antioxidant that has been widely used in pharmaceutical and food preservation applications. However, the antifungal mechanism of guaiacol against phytopathogens remains unclear. In this study, we found that guaiacol exerts inhibitory effects against mycelial growth, conidial formation and germination, and deoxynivalenol (DON) biosynthesis in Fusarium graminearum in a dose-dependent manner. The median effective concentration (EC50) value of guaiacol for the standard F. graminearum strain PH-1 was 1.838 mM. Guaiacol strongly inhibited conidial production and germination. The antifungal effects of guaiacol may be attributed to its capability to cause damage to the cell membrane by disrupting Ca2+ transport channels. In addition, the decreased malondialdehyde (MDA) levels and catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activity by guaiacol treatment indicate that guaiacol displays activity against DON production by modulating the oxidative response in F. graminearum. Taken together, this study revealed the potentials of antioxidant in inhibiting mycotoxins in F. graminearum.
Obesity Prolongs the Inflammatory Response in Mice After Severe Trauma and Attenuates the Splenic Response to the Inflammatory Reflex

Thoracic traumas with extra-thoracic injuries result in an immediate, complex host response. The immune response requires tight regulation and can be influenced by additional risk factors such as obesity, which is considered a state of chronic inflammation. Utilizing high-dimensional mass and regular flow cytometry, we define key signatures of obesity-related alterations of the immune system during the response to the trauma. In this context, we report a modification in important components of the splenic response to the inflammatory reflex in obese mice. Furthermore, during the response to trauma, obese mice exhibit a prolonged increase of neutrophils and an early accumulation of inflammation associated CCR2+CD62L+Ly6Chi monocytes in the blood, contributing to a persistent inflammatory phase. Moreover, these mice exhibit differences in migration patterns of monocytes to the traumatized lung, resulting in decreased numbers of regenerative macrophages and an impaired M1/M2 switch in traumatized lungs. The findings presented in this study reveal an attenuation of the inflammatory reflex in obese mice, as well as a disturbance of the monocytic compartment contributing to a prolonged inflammation phase resulting in fewer phenotypically regenerative macrophages in the lung of obese mice.
Epithelial Aryl Hydrocarbon Receptor Protects From Mucus Production by Inhibiting ROS-Triggered NLRP3 Inflammasome in Asthma

Background Despite long-standing recognition in the significance of mucus overproduction in asthma, its etiology remains poorly understood. Muc5ac is a secretory mucin that has been associated with reduced pulmonary function and asthma exacerbations. Objectives We sought to investigate the immunological pathway that controls Muc5ac expression and allergic airway inflammation in asthma. Methods Cockroach allergen-induced Muc5ac expression and aryl hydrocarbon receptor (AhR) signaling activation was examined in the human bronchial epithelial cells (HBECs) and mouse model of asthma. AhR regulation of Muc5ac expression, mitochondrial ROS (Mito-ROS) generation, and NLRP3 inflammasome was determined by AhR knockdown, the antagonist CH223191, and AhR-/- mice. The role of NLRP3 inflammasome in Muc5ac expression and airway inflammation was also investigated. Results Cockroach allergen induced Muc5ac overexpression in HBECs and airways of asthma mouse model. Increased expression of AhR and its downstream genes CYP1A1 and CYP1B1 was also observed. Mice with AhR deletion showed increased allergic airway inflammation and MUC5AC expression. Moreover, cockroach allergen induced epithelial NLRP3 inflammasome activation (e.g., NLRP3, Caspase-1, and IL-1β), which was enhanced by AhR knockdown or the antagonist CH223191. Furthermore, AhR deletion in HBECs led to enhanced ROS generation, particularly Mito-ROS, and inhibition of ROS or Mito-ROS subsequently suppressed the inflammasome activation. Importantly, inhibition of the inflammasome with MCC950, a NLRP3-specifc inhibitor, attenuated allergic airway inflammation and Muc5ac expression. IL-1β generated by the activated inflammasomes mediated cockroach allergen-induced Muc5ac expression in HBECs. Conclusions These results reveal a previously unidentified functional axis of AhR-ROS-NLRP3 inflammasome in regulating Muc5ac expression and airway inflammation.
The Half-Life-Extended IL21 can Be Combined With Multiple Checkpoint Inhibitors for Tumor Immunotherapy

In the era of immune checkpoint blockade cancer therapy, cytokines have become an attractive immune therapeutics to increase response rates. Interleukin 21 (IL21) as a single agent has been evaluated for cancer treatment with good clinical efficacy. However, the clinical application of IL21 is limited by a short half-life and concern about potential immune suppressive effect on dendritic cells. Here, we examined the antitumor function of a half-life extended IL21 alone and in combination with PD-1 blockade using preclinical mouse tumor models. We also determined the immune mechanisms of combination therapy. We found that combination therapy additively inhibited the growth of mouse tumors by increasing the effector function of type 1 lymphocytes. Combination therapy also increased the fraction of type 1 dendritic cells (DC1s) and M1 macrophages in the tumor microenvironment (TME). However, combination therapy also induced immune regulatory mechanisms, including the checkpoint molecules Tim-3, Lag-3, and CD39, as well as myeloid derived suppressor cells (MDSC). This study reveals the mechanisms of IL21/PD-1 cooperation and shed light on rational design of novel combination cancer immunotherapy.
The use of project management mechanisms in software development and their relationship to organisational distance : an emperical investigation

Page xiv the data provided both quantitative and qualitative data that enabled three separate ways to investigate the research questions. The empirical research found that project managers do not rely on a single mechanism to monitor, control or coordinate a software development project but employ multiple mechanisms. While the portfolio of mechanisms for both monitoring and control comprised a relatively narrow selection, the portfolio of coordination mechanisms was more diverse. Project monitoring mechanisms were employed to first detect any project problems then to respond to those problems. This contrasts with monitoring systems designed to provide all the information about both the existence and probable causes of project problems. Project control mechanisms reflected the origin of the control. The constraints imposed on the project by the organization and used by the project manager to direct the project tended to be outcome related, for example budget and schedule. The behaviour of the project team, even across significant organizational distances, was controlled through the use of project plans that determined when different tasks would be performed. Project coordination mechanisms reflected the different types of dependencies between software development activities. The most common was using a project work breakdown structure, expressed in the project schedule, to resolve sequential and pooled resource dependencies. Mutual dependencies tended to be resolved using interactive mechanisms such as co-location, conversations and meetings. The empirical evidence did not find any difference between co-located projects and distributed projects so far as the choice of project management mechanisms were concerned. Distributed and globally outsourced software development projects may encounter many difficulties that a fully co-located project does not, but the response to those difficulties appears to lie with the implementation of project management mechanisms and not their selection.
How Does the Gradient Measure of the Lung SBRT Treatment Plan Depend on the Tumor Volume and Shape?

Purpose Gradient measure (GM) is a critical index related to normal tissue sparing in radiosurgery. This study aims to describe the dependence of GM on target volume and target shape for lung stereotactic body radiation therapy (SBRT) treatment plans. Methods A total of 307 peripheral and 119 central lung SBRT treatment plans were enrolled for this study. A least-squares regression was used for data analysis. First, the equations with different functional forms were established to determine the dependence of GM on a univariaty (VP or Sp) and bivariaty (VP and Sp), respectively. Then, the correlation coefficients and p-values of variables for all equations were compared and analyzed to determine the dependence of GM on PTV volume (VP) and sphericity (Sp). Results The power equations had the highest coefficient of determination (R2) in the dependence results of GM on univariate VP. The equations were GM = 0.674 V P 0.178 and GM = 0.660 V P 0.185 for peripheral and central lesions, respectively. On the other hand, the R2 of all functional forms were less than 0.25 when the relationship of GM versus univariate Sp was analyzed. Similarly, the power equation also obtained the highest R2 in bivariaty VP and Sp analysis, whether for central or peripheral. However, the R2 of the bivariate equations were not improved compared with those of univariate equations. Moreover, the p-values of the variable Sp were greater than 0.05. Conclusions The GM of the lung SBRT plan is shape-independent and volume-dependent. The dependence of GM on PTV volume for peripheral and central lung cancer can be described by two different power equations. The results of this study can be used as a potential tool to assist dosimetric quality control during the radiosurgery process.
Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains

Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis, including essD, uhpt, sdrF, sdrG, fbe, and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF, sdrG, fbe, and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources.
Value of Echocardiography in the Treatment of Patients With Acute Heart Failure

Heart failure (HF) is a burden in pandemic medicine resulting in high mortality and morbidity. Because acute HF is a life-threatening event, its diagnosis and choice of optimal treatment are important to improve outcomes. Furthermore, understanding the cause and hemodynamics of acute HF is important in selecting the optimal treatment for these patients. Echocardiography is widely used in daily clinical practice because of its non-invasive nature and excellent portability to understand cardiac function and hemodynamics. Echocardiography is highly recommended by guidelines in the practice of HF, but evidence is limited. In this review, I would like to share clinical value of echocardiography in the treatment of patients with acute HF and discuss the usefulness of echocardiography.