Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistence of Pathogens on Inanimate Surfaces: A Narrative Review

For the prevention of infectious diseases, knowledge about transmission routes is essential. In addition to respiratory, fecal–oral, and sexual transmission, the transfer of pathogens via surfaces plays a vital role for human pathogenic infections—especially nosocomial pathogens. Therefore, information about the survival of pathogens on surfaces can have direct implications on clinical measures, including hygiene guidelines and disinfection strategies. In this review, we reviewed the existing literature regarding viral, bacterial, and fungal persistence on inanimate surfaces. In particular, the current knowledge of the survival time and conditions of clinically relevant pathogens is summarized. While many pathogens persist only for hours, common nosocomial pathogens can survive for days to weeks under laboratory conditions and thereby potentially form a continuous source of transmission if no adequate inactivation procedures are performed.
The prevalence of human leucocyte antigen and human papillomavirus DNA in penile intraepithelial neoplasia in England 2011–2012

Background: The pathogenesis of penile intraepithelial neoplasia (PeIN) is unclear but human papillomavirus (HPV) infection and polymorphisms in human leucocyte antigen (HLA). Objectives: To examine the prevalence of HPV DNA and HLA in PeIN. Methods: Adult Caucasian men with a clinical and histological diagnosis of PeIN, that is, Bowenoid papulosis (BP), Bowen’s disease of penis (BDP) and erythroplasia of Queyrat (EQ) were selected and phenotyped from the clinical records. DNA was extracted from blood and paraffin-embedded sections for HLA and HPV typing, respectively. Human leucocyte antigen allele frequencies were compared with those derived from the UK–based Caucasian population. Results: Seventy-two cases of PeIN (20 BP, 34 BDP and 18 EQ) were studied. Human papillomavirus DNA was identified in 65/72 (90.2%) PeIN; Alphapapillomavirus types were detected in 62/72 (85%) followed by Betapapillomavirus types in 9/72 (12.5%) and cutaneous types in 7/72 (9.7%); HPV16 was the most prevalent genotype at 35/72 (48.6%) followed by HPV33 at 7/72 (9.7%); multiple infections were seen in 18/72 (25%) PeIN. HLA-C*15 (Bonferroni corrected p = 0.049) confers susceptibility to PeIN, whereas HLA-DQA1*01 (corrected p = 0.02) protects against PeIN. HPV16-associated PeIN cases showed no statistically significant association with HLA genotype after multiple corrections. Conclusion: Human papillomavirus is involved in the pathogenesis of PeIN. Immunogenotype may play a role in the pathogenesis of PeIN.
Disruption of pH Dynamics Suppresses Proliferation and Potentiates Doxorubicin Cytotoxicity in Breast Cancer Cells

The reverse pH gradient is a major feature associated with cancer cell reprogrammed metabolism. This phenotype is supported by increased activity of pH regulators like ATPases, carbonic anhydrases (CAs), monocarboxylate transporters (MCTs) and sodium–proton exchangers (NHEs) that induce an acidic tumor microenvironment, responsible for the cancer acid-resistant phenotype. In this work, we analyzed the expression of these pH regulators and explored their inhibition in breast cancer cells as a strategy to enhance the sensitivity to chemotherapy. Expression of the different pH regulators was evaluated by immunofluorescence and Western blot in two breast cancer cell lines (MDA-MB-231 and MCF-7) and by immunohistochemistry in human breast cancer tissues. Cell viability, migration and invasion were evaluated upon exposure to the pH regulator inhibitors (PRIs) concanamycin-A, cariporide, acetazolamide and cyano-4-hydroxycinnamate. Additionally, PRIs were combined with doxorubicin to analyze the effect of cell pH dynamic disruption on doxorubicin sensitivity. Both cancer cell lines expressed all pH regulators, except for MCT1 and CAXII, only expressed in MCF-7 cells. There was higher plasma membrane expression of the pH regulators in human breast cancer tissues than in normal breast epithelium. Additionally, pH regulator expression was significantly associated with different molecular subtypes of breast cancer. pH regulator inhibition decreased cancer cell aggressiveness, with a higher effect in MDA-MB-231. A synergistic inhibitory effect was observed when PRIs were combined with doxorubicin in the breast cancer cell line viability. Our results support proton dynamic disruption as a breast cancer antitumor strategy and the use of PRIs to boost the activity of conventional therapy.
Development of parvalbumin neurons and perineuronal nets in the visual cortex of normal and dark‐exposed cats

During development, the visual system maintains a high capacity for modification by expressing characteristics permissive for plasticity, enabling neural circuits to be refined by visual experience to achieve their mature form. This period is followed by the emergence of characteristics that stabilize the brain to consolidate for lifetime connections that were informed by experience. Attenuation of plasticity potential is thought to derive from an accumulation of plasticity‐inhibiting characteristics that appear at ages beyond the peak of plasticity. Perineuronal nets (PNNs) are molecular aggregations that primarily surround fast‐spiking inhibitory neurons called parvalbumin (PV) cells, which exhibit properties congruent with a plasticity inhibitor. In this study, we examined the development of PNNs and PV cells in the primary visual cortex of a highly visual mammal, and assessed the impact that 10 days of darkness had on both characteristics. Here, we show that labeling for PV expression emerges earlier and reaches adult levels sooner than PNNs. We also demonstrate that darkness, a condition known to enhance plasticity, significantly reduces the density of PNNs and the size of PV cell somata but does not alter the number of PV cells in the visual cortex. The darkness‐induced reduction of PV cell size occurred irrespective of whether neurons were surrounded by a PNN, suggesting that PNNs have a restricted capacity to inhibit plasticity. Finally, we show that PV cells surrounded by a PNN were significantly larger than those without one, supporting the view that PNNs may mediate trophic support to the cells they surround.
Prognostic Value of the Hemoglobin/Red Cell Distribution Width Ratio in Resected Lung Adenocarcinoma

Simple Summary Low hemoglobin (Hb) values—indicating a condition of anemia—are related to impaired nutrition and immune system status, suggesting reduced tolerance to therapies in oncologic patients. In fact, it has been shown that pre-treatment anemia predicts poor outcomes in many neoplastic diseases. Similarly, red cell distribution width—which is a measure of the size of variation of circulating erythrocytes—has been shown to be closely related to poor prognosis both in cardiovascular and in oncologic diseases. The use of the Hb-to-red cell distribution width (RDW) ratio (HRR)—which merges data coming from the two blood parameters—is a prognostic marker in esophageal squamous cell carcinoma, small cell lung cancer, and several other types of solid tumors, emerging as an independent prognostic factor for overall survival and disease-free survival. The aim of the present study was to investigate the prognostic role of pre-operative HRR in resected-pulmonary adenocarcinoma patients undergoing a multidisciplinary treatment. Abstract Background: The ratio of hemoglobin to red cell distribution width (HRR) has been described as an effective prognostic factor in several types of cancer. The aim of this study was to investigate the prognostic role of preoperative HRR in resected-lung-adenocarcinoma patients. Methods: We enrolled 342 consecutive patients. Age, sex, surgical resection, adjuvant treatments, pathological stage, preoperative hemoglobin, red cell distribution width, and their ratio were recorded for each patient. Results: Mean age was 66 years (SD: 9.0). There were 163 females (47.1%); 169 patients (49.4%) had tumors at stage I, 71 (20.8%) at stage II, and 102 (29.8%) at stage III. In total, 318 patients (93.0%) underwent lobectomy, and 24 (7.0%) pneumonectomy. Disease-free survival multivariable analysis disclosed an increased hazard ratio (HR) of relapse for preoperative HRR lower than 1.01 (HR = 2.20, 95%CI: (1.30–3.72), p = 0.004), as well as for N1 single-node (HR = 2.55, 95%CI: (1.33–4.90), p = 0.005) and multiple-level lymph node involvement compared to N0 for both N1 (HR = 9.16, 95%CI:(3.65–23.0), p < 0.001) and N2 (HR = 10.5, 95%CI:(3.44–32.2, p < 0.001). Conclusion: Pre-operative HRR is an effective prognostic factor of disease-free survival in resected-lung-adenocarcinoma patients, together with the level of pathologic node involvement.
Cross-sectional and prospective relationships of endogenous progestogens and estrogens with glucose metabolism in men and women: a KORA F4/FF4 Study

Introduction Relationships between endogenous female sex hormones and glycemic traits remain understudied, especially in men. We examined whether endogenous 17α-hydroxyprogesterone (17-OHP), progesterone, estradiol (E2), and free estradiol (fE2) were associated with glycemic traits and glycemic deterioration. Research design and methods 921 mainly middle-aged and elderly men and 390 perimenopausal/postmenopausal women from the German population-based Cooperative Health Research in the Region of Augsburg (KORA) F4/FF4 cohort study were followed up for a median of 6.4 years. Sex hormones were measured at baseline using mass spectrometry. We calculated regression coefficients (β) and ORs with 95% CIs using multivariable-adjusted linear and logistic regression models for Z-standardized hormones and glycemic traits or glycemic deterioration (ie, worsening of categorized glucose tolerance status), respectively. Results In the cross-sectional analysis (n=1222 men and n=594 women), in men, 17-OHP was inversely associated with 2h-glucose (2hG) (β=−0.067, 95% CI −0.120 to −0.013) and fasting insulin (β=−0.074, 95% CI −0.118 to −0.030), and positively associated with Quantitative Insulin Sensitivity Check Index (QUICKI) (β=0.061, 95% CI 0.018 to 0.105). Progesterone was inversely associated with fasting insulin (β=−0.047, 95% CI −0.088 to −0.006) and positively associated with QUICKI (β=0.041, 95% CI 0.001 to 0.082). E2 was inversely associated with fasting insulin (β=−0.068, 95% CI −0.116 to −0.020) and positively associated with QUICKI (β=0.059, 95% CI 0.012 to 0.107). fE2 was positively associated with glycated hemoglobin (HbA1c) (β=0.079, 95% CI 0.027 to 0.132). In women, 17-OHP was positively associated with fasting glucose (FG) (β=0.068, 95% CI 0.014 to 0.123). fE2 was positively associated with FG (β=0.080, 95% CI 0.020 to 0.141) and HbA1c (β=0.121, 95% CI 0.062 to 0.180). In the sensitivity analyses restricted to postmenopausal women, we observed a positive association between 17-OHP and glycemic deterioration (OR=1.518, 95% CI 1.033 to 2.264). Conclusions Inter-relations exist between female sex hormones and glucose-related traits among perimenopausal/postmenopausal women and insulin-related traits among men. Endogenous progestogens and estrogens appear to be involved in glucose homeostasis not only in women but in men as well. Further well-powered studies assessing causal associations between endogenous female sex hormones and glycemic traits are warranted.
Caputo Fractional Derivative and Quantum-Like Coherence

We study two forms of anomalous diffusion, one equivalent to replacing the ordinary time derivative of the standard diffusion equation with the Caputo fractional derivative, and the other equivalent to replacing the time independent diffusion coefficient of the standard diffusion equation with a monotonic time dependence. We discuss the joint use of these prescriptions, with a phenomenological method and a theoretical projection method, leading to two apparently different diffusion equations. We prove that the two diffusion equations are equivalent and design a time series that corresponds to the anomalous diffusion equation proposed. We discuss these results in the framework of the growing interest in fractional derivatives and the emergence of cognition in nature. We conclude that the Caputo fractional derivative is a signature of the connection between cognition and self-organization, a form of cognition emergence different from the other source of anomalous diffusion, which is closely related to quantum coherence. We propose a criterion to detect the action of self-organization even in the presence of significant quantum coherence. We argue that statistical analysis of data using diffusion entropy should help the analysis of physiological processes hosting both forms of deviation from ordinary scaling.
Gluten and Autism Spectrum Disorder

An expanding body of literature is examining connections between Autism Spectrum Disorder (ASD) and dietary interventions. While a number of specialist diets have been suggested as beneficial in ASD, gluten has received particularly close attention as a potentially exacerbating factor. Reports exist suggesting a beneficial effect of the gluten-free diet (GFD) in ameliorating behavioural and intellectual problems associated with ASD, while epidemiological research has also shown a comorbidity between ASD and coeliac disease. However, both caregivers and clinicians have expressed an uncertainty of the value of people with ASD going gluten-free, and as the GFD otherwise receives considerable public attention a discussion which focuses specifically on the interaction between ASD and gluten is warranted. In this review we discuss the historical context of ASD and gluten-related studies, and expand this to include an overview of epidemiological links, hypotheses of shared pathological mechanisms, and ultimately the evidence around the use and adoption of the GFD in people with ASD.
From the Horse’s Perspective: Investigating Attachment Behaviour and the Effect of Training Method on Fear Reactions and Ease of Handling—A Pilot Study

Simple Summary Optimising horse–human relationships can promote positive experiences and advance the welfare and safety of both dyad members. Attachment and bonding are key components in such relationships, and horses are good candidate subjects for studying bonding processes due to their social nature, artificial selection for trainability and their dependence on human care in a domestic context. However, the factors that contribute to successful relationships remain unclear. This preliminary study on 12 horses investigated whether horses develop an attachment bond with their trainer after a short period of frequent interactions. The study also aimed to explore how the type of training method (negative reinforcement and two types of combined reinforcement) may affect the horse–human relationship and how this manifests as ease of handling in a novel environment. The horses showed reduced reactions in both the fear test (encountering novel objects with the trainer and a stranger present while moving freely) and handling test (encountering novel objects while being led by the trainer versus a stranger) after training compared to before training. However, we could not provide conclusive evidence that horse–human relationships established during training constitute an attachment. Suggestions for future studies are provided. Abstract The study investigated equine responses to novelty and handling, aiming to reveal whether horse–human relationships reflect criteria of an attachment bond. Twelve adult Standardbreds were subjected to a fear-eliciting test (novel objects presented close to two humans) and a handling test (being led passing novel objects) to study attachment-related behaviours and ease of handling. The tests were performed both before (pre-test) and after (post-test) horses had been trained by the same female handler (10 sessions of 15 min). Horses were assigned to three groups of four, each of which underwent different operant conditioning protocols: negative reinforcement (NR; pressure, release of lead, and whip tap signals) or combined NR with either positive reinforcement using food (PRf) or wither scratching (PRs). Results showed that neither familiarity of the person nor training method had a significant impact on the horses’ behavioural responses in the post-tests. However, horses showed decreased heart rates between pre- and post-tests, which may indicate habituation, an effect of training per se, or that the presence of the familiar trainer served to calm the horses during the challenging situations. There were large individual variations among the horses’ responses and further studies are needed to increase our understanding of horse–human relationships.
LAMA: automated image analysis for the developmental phenotyping of mouse embryos

ABSTRACT Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.
Deriving fine-scale models of human mobility from aggregated origin-destination flow data

The spatial dynamics of epidemics are fundamentally affected by patterns of human mobility. Mobile phone call detail records (CDRs) are a rich source of mobility data, and allow semi-mechanistic models of movement to be parameterised even for resource-poor settings. While the gravity model typically reproduces human movement reasonably well at the administrative level spatial scale, past studies suggest that parameter estimates vary with the level of spatial discretisation at which models are fitted. Given that privacy concerns usually preclude public release of very fine-scale movement data, such variation would be problematic for individual-based simulations of epidemic spread parametrised at a fine spatial scale. We therefore present new methods to fit fine-scale mathematical mobility models (here we implement variants of the gravity and radiation models) to spatially aggregated movement data and investigate how model parameter estimates vary with spatial resolution. We use gridded population data at 1km resolution to derive population counts at different spatial scales (down to ∼ 5km grids) and implement mobility models at each scale. Parameters are estimated from administrative-level flow data between overnight locations in Kenya and Namibia derived from CDRs: where the model spatial resolution exceeds that of the mobility data, we compare the flow data between a particular origin and destination with the sum of all model flows between cells that lie within those particular origin and destination administrative units. Clear evidence of over-dispersion supports the use of negative binomial instead of Poisson likelihood for count data with high values. Radiation models use fewer parameters than the gravity model and better predict trips between overnight locations for both considered countries. Results show that estimates for some parameters change between countries and with spatial resolution and highlight how imperfect flow data and spatial population distribution can influence model fit.
Effect of Omega-3 Supplementation in Pregnant Women with Obesity on Newborn Body Composition, Growth and Length of Gestation: A Randomized Controlled Pilot Study

Maternal obesity, a state of chronic low-grade metabolic inflammation, is a growing health burden associated with offspring adiposity, abnormal fetal growth and prematurity, which are all linked to adverse offspring cardiometabolic health. Higher intake of anti-inflammatory omega-3 (n-3) polyunsaturated fatty acids (PUFA) in pregnancy has been associated with lower adiposity, higher birthweight and longer gestation. However, the effects of n-3 supplementation specifically in pregnant women with overweight and obesity (OWOB) have not been explored. We conducted a pilot double-blind randomized controlled trial of 72 pregnant women with first trimester body mass index (BMI) ≥ 25 kg/m2 to explore preliminary efficacy of n-3 supplementation. Participants were randomized to daily DHA plus EPA (2 g/d) or placebo (wheat germ oil) from 10–16 weeks gestation to delivery. Neonatal body composition, fetal growth and length of gestation were assessed. For the 48 dyads with outcome data, median (IQR) maternal BMI was 30.2 (28.2, 35.4) kg/m2. In sex-adjusted analyses, n-3 supplementation was associated with higher neonatal fat-free mass (β: 218 g; 95% CI 49, 387) but not with % body fat or fat mass. Birthweight for gestational age z-score (−0.17 ± 0.67 vs. −0.61 ± 0.61 SD unit, p = 0.02) was higher, and gestation longer (40 (38.5, 40.1) vs. 39 (38, 39.4) weeks, p = 0.02), in the treatment vs. placebo group. Supplementation with n-3 PUFA in women with OWOB led to higher lean mass accrual at birth as well as improved fetal growth and longer gestation. Larger well-powered trials of n-3 PUFA supplementation specifically in pregnant women with OWOB should be conducted to confirm these findings and explore the long-term impact on offspring obesity and cardiometabolic health.
Microelectrochemical Systems on Silicon Chips for the Detection of Pollutants in Seawater

The ever-growing demand for simple, fast and reliable techniques for the detection of pollutants and contaminants in the environment has sparked the development of remote detection and monitoring systems which include application specific sensors, instrumentation and signal processing. We report here the design, fabrication and characterisation of four designs of microelectrochemical systems on silicon chip for the detection of pollutants in artificial seawater. These systems were fabricated by photolithography and incorporate a Pt working microelectrode array (squares or bands), a Pt counter electrode and a Ag|AgCl reference electrode. They have been characterised by cyclic voltammetry of ferricyanide and behaved in good agreement with the theory. These systems were evaluated over 72 hours and showed good stability. Underpotential Deposition – Stripping Voltammetry experiments of Cu2+ in artificial seawater have been carried out at an array of 35 microsquares of 20 µm × 20 µm. The sensitivity achieved was (2.93±0.14) µA cm−2 µM−1, with 1 µM being the lowest Cu2+ concentration measured. These devices provide the basis for the development into sensor systems for remote analysis applications.