Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental Exposure of Mice to Dioxin Promotes Transgenerational Testicular Inflammation and an Increased Risk of Preterm Birth in Unexposed Mating Partners

TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin, commonly known as dioxin) is a ubiquitous environmental contaminant and known endocrine disruptor. Using a mouse model, we previously found that adult female mice exposed in utero to TCDD (F1 generation) as well as multiple subsequent generations (F2-F4) exhibited reduced fertility and an increased incidence of spontaneous preterm birth. Additional studies revealed that male F1 mice with a similar in utero/developmental TCDD exposure also exhibited diminished fertility and conferred an increased risk of preterm birth to their unexposed mating partners. Herein, we extend these previous observations, reporting that reduced fertility in male F1 mice is linked to testicular inflammation which coincides with apoptosis of developing spermatocytes, sub-fertility and an increased risk of preterm birth in their unexposed mating partners. Significantly, in the absence of additional toxicant exposure, testicular inflammation and reduced fertility persisted in F2 and F3 males and their control mating partners also frequently exhibited spontaneous preterm birth. Although a steady, global decline in male fertility has been noted over the last few decades, the reasons for these changes have not been firmly established. Likewise, the PTB rate in the U.S. and other countries has paralleled industrial development, suggesting a possible relationship between environmental toxicant exposure and adverse pregnancy outcomes. Most current clinical strategies to prevent preterm birth are focused solely on the mother and have yielded limited benefits. In contrast, our studies strongly suggest that the preconception testicular health of the father is a critical determinant of pregnancy outcomes in mice. Future clinical studies should examine the potential contribution of the male to gestation length in women and whether efforts to reduce the incidence of preterm birth should be initiated in both parents prior to pregnancy.
Biomimetic molecularly imprinted polymers : a new quorum sensing capturing agent to prevent bacterial biofilm formation

ii Preface . iv Table of contents . v List of tables. viii List of figures . ix List of abbreviations . xiii Acknowledgements . xv Dedication . xvii Chapter 1: Introduction . 1 Chapter 2: Hypotheses and objectives . 4 2.1 Hypotheses . 4 2.2 Objectives . 4 Chapter 3: Literature review . 6 3.1 Quorum sensing . 6 3.1.1 Mechanism of quorum sensing . 6 3.1.2 Quorum sensing autoinducers . 7 3.2 Bacterial biofilm . 13 3.2.1 Prevalence and hazards of biofilms in the food industry . 13 3.2.2 Process of biofilm formation . 15 3.2.3 Pseudomonas aeruginosa: an example of the relationship between QS and biofilm formation . 17 3.2. 4 Antimicrobial resistance . 22 vi 3.3 Current strategies to control biofilm: QS interruption . 24 3.3.1 Three major QS interruption strategies . 25 3.3.2 Limitation . 26 3.4 A novel biofilm inhibition strategy: application of MIPs . 26 3.4.1 Principle and categories . 27 3.4.2 Important factors in polymerization. 30 3.4.3 Previous applications of imprinted polymers in biofilm inhibition . 33 Chapter 4: Materials and methods . 37 4.1 Chemicals . 37 4.2 Synthesis of MIPs . 37 4.2.1 Polymerization condition . 38 4.2.2 Ratio of AHL: IA: EGDMA . 39 4.2.3 Ratio of AHL: HEMA: EGDMA . 40 4.3 Effect of MIPs on capturing 3-oxo-C12-AHL . 41 4.3.1 Equilibrium rebinding study . 41 4.3.2 High performance liquid chromatographic condition . 42 4.4 Effect of MIPs on P. aeruginosa biofilm formation . 42 4.4.1 Media, bacterial strain and culture preparation . 42 4.4.2 Anti-biofilm activity test . 43 4.4.2.1 Immobilization and sterilization of MIPs . 43 4.4.2.2 Biofilm cultivation with MIPs . 43 4.4.2.3 Biofilm quantification . 44 4.4.3 Antimicrobial activity test. 46 vii 4.5 Statistical analysis . 46 Chapter 5: Results and discussion. 47 5.1 Effect of MIPs on capturing 3-oxo-C12-AHL . 47 5.1.1 Effect of polymerization condition on 3-oxo-C12-AHL stability . 47 5.1.2 Synthesis and characterization of IA-based polymers . 50 5.1. 3 Synthesis and characterization of HEMA-based polymers . 56 5.1. 4 Summary . 62 5.2 Effect of MIPs on P. aeruginosa biofilm formation . 62 5.2.1 Anti-biofilm activity . 62 5.2.1.1 Crystal violet assay . 63 5.2.1.2 TTC assay . 67 5.2.2 Antimicrobial activity . 73 5.2.3 Summary . 75 Chapter 6: Conclusion. 77 6.1 Study outcomes . 77 6.2 Future directions . 78 Bibliography . 81
Motility of Electric Cable Bacteria

ABSTRACT Cable bacteria are filamentous bacteria that electrically couple sulfide oxidation and oxygen reduction at centimeter distances, and observations in sediment environments have suggested that they are motile. By time-lapse microscopy, we found that cable bacteria used gliding motility on surfaces with a highly variable speed of 0.5 ± 0.3 μm s−1 (mean ± standard deviation) and time between reversals of 155 ± 108 s. They frequently moved forward in loops, and formation of twisted loops revealed helical rotation of the filaments. Cable bacteria responded to chemical gradients in their environment, and around the oxic-anoxic interface, they curled and piled up, with straight parts connecting back to the source of sulfide. Thus, it appears that motility serves the cable bacteria in establishing and keeping optimal connections between their distant electron donor and acceptors in a dynamic sediment environment. IMPORTANCE This study reports on the motility of cable bacteria, capable of transmitting electrons over centimeter distances. It gives us a new insight into their behavior in sediments and explains previously puzzling findings. Cable bacteria greatly influence their environment, and this article adds significantly to the body of knowledge about this organism.
Enterovirus 71 3 C Inhibits Cytokine Expression through Cleavage of the TAK 1 / TAB 1 / TAB 2 / TAB 3 Complex

Enterovirus 71 (EV71) causes hand, foot, and mouth disease in young children and infants. Severe infection with EV71 can lead to various neurological complications or fatal diseases. However, the mechanism of EV71 pathogenesis is poorly understood. Emerging evidence suggests that EV71 modulates type I interferon (IFN) and cytokine responses. Here, we show that EV71 disables components of the TAB2 complex through the 3C protein. When expressed in mammalian cells, EV71 3C interacts with TAB2 and TAK1, which inhibits NFB activation. Furthermore, 3C mediates cleavage of TAB2 and its partners, which requires the protease activity. H40D or C147S substitution in the 3C active sites abolishes its activity, whereas R84Q or V154S substitution in the RNA binding domain has no effect. The 3C protein targets TAB2 at Q113-S114, TAK1 at Q360-S361, TAB1 both at Q414-G415 and Q451-S452, and TAB3 at Q173-G174 and Q343-G344. Importantly, overexpression of TAB2 inhibits EV71 replication, whereas addition of cleaved fragments has no effect. Thus, an equilibrium between the TAB2 complex and EV71 3C represents a control point of viral infection. These results suggest that TAK1/TAB1/TAB2/TAB3 cleavage mediated by EV71 may be a mechanism to interfere with inflammatory responses.
L1 penalized Cox regression to characterize cardiovascular events in hypertensive patients

Reliable cardiovascular risk stratification of hypertensive patients is essential to provide appropriate clinical management. However, traditional statistical approaches may ignore important information from datasets and overlook possible interactions among covariates when dealing with high-dimensional data. Regularization techniques, such as least absolute shrinkage and selection operator (LASSO), may improve the prediction accuracy and inter-pretability of regression models. Our aim is to identify the most relevant features to predict cardiovascular (CV) events in hypertensive patients by using the L1-penalized Cox regression. We use clinical records of 1664 patients of the Mostoles University Hospital whose CV status was determined by clinical variables and biomarkers including body index mass, blood pressure, cholesterol, albumin/creatinine ratio, and kidney function. By monotoni-cally tuning its regularization parameter, the LASSO approach put forth is able to identify the most predictive features, with "cystanin C-based glomerular filtration" being the single most relevant predictor for CV events.
Relationship of Serum Vitamin D Concentrations and Allostatic Load as a Measure of Cumulative Biological Risk among the US Population: A Cross-Sectional Study

Introduction The allostatic load (AL) index is a multi-systemic measure of physiologic dysregulation known to be associated with chronic exposure to stress and adverse health outcomes. We examined the relationship between AL and serum 25-hydroxyvitamin D (25(OH)D) concentration in non-institutionalized US adults. Methods Data from the Third National Health and Nutrition Examination Survey (NHANES III, 1988–94) were used to calculate two versions of AL including 9 biomarkers and another two with 14 biomarkers (systolic and diastolic blood pressure, pulse rate, serum cholesterol, serum HDL-cholesterol, glycated hemoglobin, sex-specific waist-to-hip ratio, serum albumin, and serum C-reactive protein for AL1, and, additionally body mass index, serum triglyceride, serum creatinine, and serum herpes I & II antibodies for AL2), each set defined by predefined cut-offs or by quartiles. Serum vitamin D concentration was ranked into quartiles. Logistic regression, Poisson regression and linear regression were used to examine the association of serum 25(OH)D concentrations on AL, after adjusting for biological, physiological, socioeconomic, lifestyle, and health variables. Results Odds Ratios (OR) for high AL of the lowest 25(OH)D serum quartile were between 1.45 (95% CI: 1.28, 1.67) and 1.79 (95% CI: 1.39, 2.32) for the fully adjusted model, depending on AL version. Inverse relationships between vitamin D serum concentrations were observed for all AL versions and every adjustment. This relationship was consistent after stratification by sex, age or ethnic background. Sensitivity to low 25(OH)D concentrations was highest among the youngest group (20–39 years) with an OR of 2.11 (95% CI: 1.63, 2.73) for the lowest vitamin D quartile Q1. Conclusions Vitamin D had a consistent and statistically significant inverse association with all tested models of high AL, which remained consistent after adjusting for biological, socioeconomic, lifestyle and health variables. Our study adds evidence linking low 25(OH)D concentrations with poorer health, further-reaching than bone health.
Effect of Incubation on Bacterial Communities of Eggshells in a Temperate Bird, the Eurasian Magpie (Pica pica)

Inhibitory effect of incubation on microbial growth has extensively been studied in wild bird populations using culture-based methods and conflicting results exist on whether incubation selectively affects the growth of microbes on the egg surface. In this study, we employed culture-independent methods, quantitative PCR and 16S rRNA gene pyrosequencing, to elucidate the effect of incubation on the bacterial abundance and bacterial community composition on the eggshells of the Eurasian Magpie (Pica pica). We found that total bacterial abundance increased and diversity decreased on incubated eggs while there were no changes on non-incubated eggs. Interestingly, Gram-positive Bacillus, which include mostly harmless species, became dominant and genus Pseudomonas, which include opportunistic avian egg pathogens, were significantly reduced after incubation. These results suggest that avian incubation in temperate regions may promote the growth of harmless (or benevolent) bacteria and suppress the growth of pathogenic bacterial taxa and consequently reduce the diversity of microbes on the egg surface. We hypothesize that this may occur due to difference in sensitivity to dehydration on the egg surface among microbes, combined with the introduction of Bacillus from bird feathers and due to the presence of antibiotics that certain bacteria produce.
Semantic Edge Based Disparity Estimation Using Adaptive Dynamic Programming for Binocular Sensors

Disparity calculation is crucial for binocular sensor ranging. The disparity estimation based on edges is an important branch in the research of sparse stereo matching and plays an important role in visual navigation. In this paper, we propose a robust sparse stereo matching method based on the semantic edges. Some simple matching costs are used first, and then a novel adaptive dynamic programming algorithm is proposed to obtain optimal solutions. This algorithm makes use of the disparity or semantic consistency constraint between the stereo images to adaptively search parameters, which can improve the robustness of our method. The proposed method is compared quantitatively and qualitatively with the traditional dynamic programming method, some dense stereo matching methods, and the advanced edge-based method respectively. Experiments show that our method can provide superior performance on the above comparison.
Use of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) as Non-Invasive Approach for Dietary Analysis of Svalbard Reindeer, Rangifer tarandus platyrhynchus

To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components.
Seeing in the deep-sea: visual adaptations in lanternfishes

Ecological and behavioural constraints play a major role in shaping the visual system of different organisms. In the mesopelagic zone of the deep- sea, between 200 and 1000 m, very low intensities of downwelling light remain, creating one of the dimmest habitats in the world. This ambient light is, however, enhanced by a multitude of bioluminescent signals emitted by its inhabitants, but these are generally dim and intermittent. As a result, the visual system of mesopelagic organisms has been pushed to its sensitivity limits in order to function in this extreme environment. This review covers the current body of knowledge on the visual system of one of the most abundant and intensely studied groups of mesopelagic fishes: the lanternfish (Myctophidae). We discuss how the plasticity, performance and novelty of its visual adaptations, compared with other deep-sea fishes, might have contributed to the diversity and abundance of this family. This article is part of the themed issue ‘Vision in dim light’.
Detection Threshold and Reproducibility of 68Ga-PSMA11 PET/CT in a Mouse Model of Prostate Cancer

To improve prostate-specific membrane antigen (PSMA)–targeted theranostic approaches, robust murine models of prostate cancer are needed. However, important characteristics of preclinical PSMA imaging—that is, the reproducibility of the imaging signal and the relationship between quantitative cell surface PSMA expression and lesion detectability with small-animal PET/CT—have not been defined yet. Methods: Murine prostate cancer RM1 sublines (ras myc transformed cells of C57BL/6 prostate origin) expressing varying levels of human PSMA were injected into the shoulder of C57BL/6 mice on day 0. 68Ga-PSMA11 PET/CT was performed on days 7 and 8 and interpreted by 2 masked readers to determine interday and interreader reproducibility. PSMA expression was quantified on days 7 and 8 by flow cytometry of fine-needle aspiration tumor biopsy samples. Cell surface PSMA expression was correlated with PET signal. The threshold for PET positivity was based on the clinical Prostate Cancer Molecular Imaging Standardized Evaluation (PROMISE) criteria. Results: The maximum and average percentages of injected 68Ga-PSMA11 activity per gram of tissue (%IA/g) correlated nearly perfectly as determined by 2 independent readers and on 2 separate days (intraclass correlation coefficient, 1.00/0.89 and 0.95/0.88, respectively). The number of PSMA molecules per cell increased from the RM1-yellow fluorescent protein subline (PSMA−; 2,000/cell) to the RM1-low subline (PSMA+; 17,000/cell), the RM1-medium subline (PSMA++; 22,000/cell), and the RM1-PGLS subline (PSMA-positive, green fluorescent protein–positive, and luciferase-positive; PSMA+++; 45,000/cell). Expression levels correlated with the visual positivity rate on 68Ga-PSMA11 PET and with the PSMA PET %IA/g. The PSMA threshold for PET positivity was approximately 20,000 per cell. Signal correlation was close at lower PSMA levels (RM1-low to RM1-medium; 10–23 %IA/g) but was lost at higher PSMA levels (RM1-medium to RM1-PGLS; 23–27 %IA/g). Conclusion: The in vivo relationship between 68Ga-PSMA11 PET/CT and PSMA expression level in a murine model of prostate cancer was robust for lower cell surface PSMA expression levels (≤22,000/cell). Thus, preclinical 68Ga-PSMA11 PET/CT can be used as an imaging biomarker to test PSMA-targeted interventions in murine models.
Systolic Blood Pressure Response in SPRINT (Systolic Blood Pressure Intervention Trial) and ACCORD (Action to Control Cardiovascular Risk in Diabetes): A Possible Explanation for Discordant Trial Results

Background SPRINT (Systolic Blood Pressure Intervention Trial) and the ACCORD (Action to Control Cardiovascular Risk in Diabetes) blood pressure trial used similar interventions but produced discordant results. We investigated whether differences in systolic blood pressure (SBP) response contributed to the discordant trial results. Methods and Results We evaluated the distributions of SBP response during the first year for the intensive and standard treatment groups of SPRINT and ACCORD using growth mixture models. We assessed whether significant differences existed between trials in the distributions of SBP achieved at 1 year and the treatment‐independent relationships of achieved SBP with risks of primary outcomes defined in each trial, heart failure, stroke, and all‐cause death. We examined whether visit‐to‐visit variability was associated with heterogeneous treatment effects. Among the included 9027 SPRINT and 4575 ACCORD participants, the difference in mean SBP achieved between treatment groups was 15.7 mm Hg in SPRINT and 14.2 mm Hg in ACCORD, but SPRINT had significantly less between‐group overlap in the achieved SBP (standard deviations of intensive and standard groups, respectively: 6.7 and 5.9 mm Hg in SPRINT versus 8.8 and 8.2 mm Hg in ACCORD; P<0.001). The relationship between achieved SBP and outcomes was consistent across trials except for stroke and all‐cause death. Higher visit‐to‐visit variability was more common in SPRINT but without treatment‐effect heterogeneity. Conclusions SPRINT and ACCORD had different degrees of separation in achieved SBP between treatment groups, even as they had similar mean differences. The greater between‐group overlap of achieved SBP may have contributed to the discordant trial results.
A Short-Range Inertial Sensor Exploiting Magnetic Levitation and an Inductive Readout Strategy

This paper demonstrates a methodology, exploiting a low-cost levitation architecture, for the implementation of a highly sensitive inertial sensor to measure displacement and acceleration. The system uses a graphite tile suspended over four NdFeB magnets and a differential inductive readout strategy to implement the sensing mechanism. The main claims of the developed sensor are related to the levitation mechanism, which leads to a suitable responsivity and resolution for the device. Moreover, the passive inductive sensing strategy allows for static displacement measurement, which is a unique feature in the field of levitating systems. The mechanical decoupling between the graphite sensing element and the inductive readout electronics is another interesting characteristic of the device enhancing the device reliability and life time, since the low-cost sensing element (the graphite tile) can be easily replaced if damaged. It is also worth considering that the inductive sensing strategy has been realized by a low-cost technology. The device has been characterized as a short-range accelerometer and displacement sensor. The responsivity and the resolution in these two operating modes are (1.17 V/m/s<sup>2</sup>, <inline-formula> <tex-math notation="LaTeX">$1 \times 10^{-4}$ </tex-math></inline-formula> m/s<sup>2</sup>) and (0.61 V/mm, <inline-formula> <tex-math notation="LaTeX">$1.9 \times 10^{-4}$ </tex-math></inline-formula> mm), respectively.
Long‐Term Impacts of Poaching on Relatedness, Stress Physiology, and Reproductive Output of Adult Female African Elephants

Abstract: Widespread poaching prior to the 1989 ivory ban greatly altered the demographic structure of matrilineal African elephant (Loxodonta africana) family groups in many populations by decreasing the number of old, adult females. We assessed the long‐term impacts of poaching by investigating genetic, physiological, and reproductive correlates of a disturbed social structure resulting from heavy poaching of an African elephant population in Mikumi National Park, Tanzania, prior to 1989. We examined fecal glucocorticoid levels and reproductive output among 218 adult female elephants from 109 groups differing in size, age structure, and average genetic relatedness over 25 months from 2003 to 2005. The distribution in group size has changed little since 1989, but the number of families with tusked old matriarchs has increased by 14.2%. Females from groups that lacked an old matriarch, first‐order adult relatives, and strong social bonds had significantly higher fecal glucocorticoid values than those from groups with these features (all females R2= 0.31; females in multiadult groups R2= 0.46). Females that frequented isolated areas with historically high poaching risk had higher fecal glucocorticoid values than those in low poaching risk areas. Females with weak bonds and low group relatedness had significantly lower reproductive output (R2[U]=0.21). Females from disrupted groups, defined as having observed average group relatedness 1 SD below the expected mean for a simulated unpoached family, had significantly lower reproductive output than females from intact groups, despite many being in their reproductive prime. These results suggest that long‐term negative impacts from poaching of old, related matriarchs have persisted among adult female elephants 1.5 decades after the 1989 ivory ban was implemented.