Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of MicroRNAs as biomarkers in the early diagnosis of prostate cancer

Introduction: Prostate cancer (PCa) is a common type of cancer in western countries and prominent cause of mortality in men. The aim of the study was to evaluate miRNAs as biomarkers in PCa in healthy individuals and prostate cancer with patients, and examined the effect of miRNA levels on tumour mass. Material and methods: Twenty prostate cases, age (mean and range) 61,4±12.1 (45-73), and twenty healthy men, age 59,3±11.2 (44-70) were included to the study. Seven miRNAs including two internal controls (Let7c, miR125b, miR141, miR145, miR 155, miR181 ve miR192) were evaluated in two groups. Results: The mean and range of prostate spesific antigen (PSA) in cancer cases and healthy individuals were 6.79±2.84 ng/ml (2.25-14.7) and 3.8±2.2 ng/ml (1.3-7.8) respectively. The level of miR141 was significantly lower in PCa cases than healthy individuals (p=0,004), and miR155 was significantly higher (p=0,005) in PCa cases. Both miRNAs were explored sensitive and specific in the ROC analysis. Tumour mass were found to be associated with the level of miR-125b and miR-145. Conclusion: validation studies are required in wider patient groups in the subject of tumor effect and miRNA biomarkers in prostate cancer.
Modelling air pollution around nuclear power plants: validation of dispersion models using tracer data

The Šoštanj exercise of the Modelling and Data for Radiological Impact Assessments I Urban Environments Working Group took advantage of a set of measurement data from a 1991 tracer experiment to test atmospheric dispersion models for emissions from point sources over complex terrain. The data set included emissions of SO2 from the stacks of the Šoštanj Thermal Power Plant in Slovenia, measurements of the SO2 at a number of locations in the surrounding area up to 7 km from the plant, and meteorological data from several monitoring stations, all as measured half-hour average values. Two sets of meteorological conditions were modelled: (a) a simple situation with a strong wind blowing from a point source directly towards a monitoring station; and (b) a complex situation involving a temperature inversion and convective mixing. The modelling results enable the assessment of the capabilities of various dispersion models in handling both complex terrain and complex meteorological situations.
Habitat alteration and fecal deposition by geese alter tundra invertebrate communities: Implications for diets of sympatric birds

Over the last 60 years, Arctic goose populations have increased while many sympatric tundra nesting bird populations have declined. Hyperabundant geese have well-documented effects on tundra habitats, which can alter habitat use by sympatric bird species. These habitat changes may also alter invertebrate communities and abundances, with potentially important, but as of yet, undocumented effects on insectivorous birds such as shorebirds. Here, we determined the effects of goose-induced habitat alteration on invertebrate communities and relate the observed changes to shorebird diet. At sites and habitat types representing a gradient of goose influence, we identified goose-related changes in ground cover and linked these factors to variation in invertebrate communities. We then used DNA metabarcoding to characterize the diet of six shorebird species across sites and identify inter-site variation in abundance, biomass, and timing of emergence of dominant shorebird prey items. Invertebrate diversity and richness did not vary either among sites or habitat types. However, for prey items identified as part of the shorebird diet, we found significantly higher abundances and biomasses at a moderately goose-influenced site than at either low or high goose-influenced sites. Biomass of Tipulidae, the dominant prey taxon for shorebirds at the study sites, was 7.5 times higher at the moderately goose-influenced site compared to the site where goose influence was minor. We attribute this enhancement of prey biomass to both the fertilizing effect of goose fecal pellets and the moderate grazing pressure. Many studies have documented adverse effects of overabundant geese, but here we show that a moderate degree of goose grazing can lead to enhanced biomass of invertebrates, with the potential for improved shorebird foraging success and chick growth. These benefits, however, might be outweighed by negative effects of goose-induced habitat alteration and predation pressure.
Assessment of foodborne transmission of Salmonella enteritidis in hens and eggs in Bangladesh

Abstract Objectives Salmonella is considered one of the leading causes of foodborne illnesses worldwide. Information about the transmission of pathogens to poultry and poultry products is necessary to implement control measures for reducing both human exposure and economic loss. The aim of this study was to analyze and evaluate the transmission characteristics of Salmonella enteritidis to laying‐type hen flocks and their laid eggs. Materials and methods For this purpose, 15 pairs of laying hens were used in which each pair consisted of one inoculated and one contact exposed hen. The eggs and cloacal swabs from these hens were subsequently analyzed. Results Of the 15 in‐contact hens tested, 60% were found to be positive for S. enteritidis within 61 days postinoculation, of which 26.7% transmission occurred within the first 31 days postinoculation. Among the collected laid eggs tested, S. enteritidis was detected on 58% eggshells and 5.33% eggs internal contents. We also observed a 33.33% reduction in egg production from S. enteritidis‐infected hens. In a cross‐contamination study, we demonstrated that an experimentally inoculated container can act as a potential source of Salmonella spp. infection. Conclusions Our results will help establish effective monitoring programs to reduce the transmission of Salmonella spp. in poultry and poultry products.
The impact of monosomies, trisomies and segmental aneuploidies on chromosomal stability

Aneuploidy and chromosomal instability are both commonly found in cancer. Chromosomal instability leads to karyotype heterogeneity in tumors and is associated with therapy resistance, metastasis and poor prognosis. It has been hypothesized that aneuploidy per se is sufficient to drive CIN, however due to limited models and heterogenous results, it has remained controversial which aspects of aneuploidy can drive CIN. In this study we systematically tested the impact of different types of aneuploidies on the induction of CIN. We generated a plethora of isogenic aneuploid clones harboring whole chromosome or segmental aneuploidies in human p53-deficient RPE-1 cells. We observed increased segregation errors in cells harboring trisomies that strongly correlated to the number of gained genes. Strikingly, we found that clones harboring only monosomies do not induce a CIN phenotype. Finally, we found that an initial chromosome breakage event and subsequent fusion can instigate breakage-fusion-bridge cycles. By investigating the impact of monosomies, trisomies and segmental aneuploidies on chromosomal instability we further deciphered the complex relationship between aneuploidy and CIN.
Quantum Monte Carlo for accurate energies and materials design

Quantum Monte Carlo (QMC) is an electronic structure calculation method that is capable of calculating incredibly accurate solutions of Schrodinger equation of quantum mechanics for real systems. However, QMC is computationally very expensive compared to density functional theory (DFT) method, such that its application has been limited. In addition, QMC is a stochastic (Monte Carlo) method, meaning that the way calculations are initialized, where a lot of user effort is invested, is crucial for getting accurate results. Computational expense can be justified if the data would be used repeatedly, however the lack of automatization is a severe problem, if QMC would be used in materials discovery. In Chapter 4, we show our automated calculation strategy for formation energy of periodic materials using QMC. We show that our method performs almost by an order of a magnitude more accurate, compared to high throughput DFT strategies having empirical corrections. Nevertheless, it would be beneficial to understand when DFT methods fail such that QMC is used only when the computational expense is justified. A single DFT functional rarely performs uniformly accurate accross different materials and properties due to nonsystematic errors. In Chapter 5, we investigate one specific example: dihydroazulene ring opening photoisomerization, where different substitutions on the ring opening moiety introduce isomerization enthalpy errors up to 0.8 eV. We show that GGA exchange is the main reason for failure in B3LYP, PBE and TPSSH functionals. However, performing a test, similar to the Chapter 5, on each chemical reaction can be an intimidating task where the benchmark set must be carefully devised by an expert in the field. In the absence of experiments, the DFT functional choice is still often done in heuristic way. In Chapter 6, we demonstrate how we can systematically analyze benchmark sets using machine learning to provide highly accurate reaction energies and provide DFT functional selection for different classes of materials when high accuracy calculations or experiments are not available. Our approach provides probabilities of getting accurate results for a reaction that is investigated using each DFT functional.
From decoding the perception of tightness to a clinical proof of soothing effects derived from natural ingredients in a moisturizer

To decode the feeling of skin tightness after application of a cosmetic product and how to soothe this discomfort. To pursue this aim, we considered the ingredient's effect on stratum corneum (SC) biomechanics to differentiate between consumers prone to tightness from those that are not and correlate these effects with mechanoreceptor activation.
Negative effects during multicomponent group-based treatment: A multisite study

ABSTRACT Objective Negative effects (NEs) in group treatments remain an under-researched area. This study aimed to explore the prevalence of various types of NEs in a multicomponent group-based treatment and to determine their predictors. Method: A total of 330 patients participating in a multicomponent group-based treatment were recruited across seven clinical sites. At the end of treatment, the Negative Effects Questionnaire (NEQ) was used to measure NEs. Item-level descriptive analysis was conducted to explore the prevalence of various types of NEs, and structural equation modeling was used to determine predictors of these NEs. Results: The most frequently reported type of NEs was the worsening of symptoms, and the single most frequently reported item was the resurfacing of unpleasant memories. Predictors of NEs included the overall distress level, alexithymia, attachment avoidance, low working alliance, problem actuation, and worse outcomes; psychological mindedness was a protective factor. Conclusion: Patients who experience higher levels of distress at the beginning of treatment, who perceive the group working alliance as problematic, and who experience high in-session emotional arousal related to their problem seem to be especially prone to reporting NEs. Furthermore, the findings do not support the assumption that NEs are a prerequisite for therapeutic change. Trial registration: ISRCTN.org identifier: ISRCTN13532466.
Adherence, Effectiveness and Safety of Dolutegravir Based Antiretroviral Regimens among HIV Infected Children and Adolescents in Tanzania

Objectives:This study aimed at assessing adherence, effectiveness, and safety of DTG-based HAART regimens among HIV-infected children and adolescents in Tanzania. Methods: This was a single-center prospective cohort study, conducted at the pediatric HIV Clinic in Mbeya, Tanzania. A binary logistic regression model was used to determine predictors of undetectable viral load at week 24. The results were significant when P-value was <0.05. Results: A total of 200 patients were enrolled with the majority (85.5%) being treatment experienced. High adherence levels (71%) were observed using the pharmacy refill method. At week 24, the overall proportion of patients with undetectable viral load was 70.2%. The predictors of undetectable viral load were age, World Health Organization (WHO) clinical stage, baseline VL and adherence to pharmacy refill. Conclusion: The majority of patients attained undetectable viral load 6 months after using DTG based regimen. DTG-based regimens were generally safe with few ADEs reported.
Impact of lower urinary tract symptoms in women with multiple sclerosis: an observational cross-sectional study

ABSTRACT Background Lower urinary tract symptoms (LUTS) are common in women with multiple sclerosis. Objective To investigate the impact of LUTS on pelvic floor muscle contraction, sexual function, and quality of life in women with multiple sclerosis. Methods Thirty-nine women with relapsing-remitting multiple sclerosis were enrolled in this study. Participants were divided into the presence or not of LUTS. Assessments involved the Expanded Disability Status Scale score, the NEW PERFECT scheme, the Female Sexual Function Index, and the Qualiveen Questionnaire. Statistical procedures involved Student t-tests, chi-squared, and regression analyses (R2). Results Nineteen women (48.7%) presented LUTS. Women with LUTS were in a more advanced stage of multiple sclerosis (p = .029), presented weaker pelvic muscle contraction (p = .009), less sexual function satisfaction (p = .018), and more limitations in the quality of life (p = .001) than women without LUTS. Regression analyses pointed out that the quality of life and sexual function of women with multiple sclerosis are affected by intercourse pain (R2 = 12.9) and perineal contraction force (R2 = 19.2). Conclusion LUTS affects pelvic floor muscle contraction, sexual function, and quality of life in women with multiple sclerosis. A multi-professional rehabilitation team should assist women with multiple sclerosis, taking special care of LUTS.
How scared are Americans of the Zika virus? The role of threat, efficacy, and third-person perception to induce protective behaviors

Abstract This study examines how public perception of threat and efficacy (on self and others) influence their tendency to take preventive action against the Zika virus by surveying 1,152 U.S. adults in Texas and Florida. Findings show that individuals were likely to take protective actions when they: (1) saw a high risk of the disease (high threat) and were confident about their ability to reduce the danger (high efficacy); and (2) perceived others as having a high risk (high threat), but lacked the ability to reduce the danger (low efficacy). Further, the study discusses practical implications for the design of public health campaigns.
Glycoengineered anti-CD39 promotes anticancer responses by depleting suppressive cells and inhibiting angiogenesis in tumor models

Immunosuppressive cells accumulating in the tumor microenvironment constitute a formidable barrier that interferes with current immunotherapeutic approaches. A unifying feature of these tumor-associated immune and vascular endothelial cells appears to be the elevated expression of ectonucleotidase CD39, which in tandem with ecto-5′-nucleotidase CD73, catalyzes the conversion of extracellular ATP into adenosine. We glycoengineered an afucosylated anti-CD39 IgG2c and tested this reagent in mouse melanoma and colorectal tumor models. We identified major biological effects of this approach on cancer growth, associated with depletion of immunosuppressive cells, mediated through enhanced Fcγ receptor–directed (FcγR-directed), antibody-dependent cellular cytotoxicity (ADCC). Furthermore, regulatory/exhausted T cells lost CD39 expression, as a consequence of antibody-mediated trogocytosis. Most strikingly, tumor-associated macrophages and endothelial cells with high CD39 expression were effectively depleted following antibody treatment, thereby blocking angiogenesis. Tumor site–specific cellular modulation and lack of angiogenesis synergized with chemotherapy and anti–PD-L1 immunotherapy in experimental tumor models. We conclude that depleting suppressive cells and targeting tumor vasculature, through administration of afucosylated anti-CD39 antibody and the activation of ADCC, comprises an improved, purinergic system–modulating strategy for cancer therapy.
A localized calcium transient and polar body abscission

ABSTRACT Polar body emission is a special form of cytokinesis in oocyte meiosis that ensures the correct number of chromosomes in reproduction-competent eggs. The molecular mechanism of the last step, polar body abscission, is poorly understood. While it has been proposed that Ca2+ signaling plays important roles in embryonic cytokinesis, to date transient increases in intracellular free Ca2+ have been difficult to document in oocyte meiosis except for the global Ca2+ wave induced by sperm at fertilization. Here, we find that microinjection of the calcium chelator dibromo-BAPTA inhibits polar body abscission in Xenopus laevis oocytes. Using a novel, microtubule-targeted ratio-metric calcium sensor, we detected a calcium transient that is focused at the contractile ring-associated plasma membrane and which occurred after anaphase and constriction of the contractile ring but prior to abscission. This calcium transient was confirmed by mobile calcium probes. Further, the Ca2+-sensitive protein kinase Cβ C2 domain transiently translocated to the contractile ring-associated membrane simultaneously with the calcium transient. Collectively, these results demonstrate that a calcium transient, apparently originating at the contractile ring-associated plasma membrane, promotes polar body abscission.
Electron-impact ionization cross sections of small molecules containing Fe and Cr

We present the electron-impact ionization cross sections (EICSs) of iron and chromium hydrides, nitrides, and oxides. The motivation of this work stems from the fact that chemical sputtering from a steel surface exposed to a hot plasma can create these molecules which in turn influence the composition and energy balance of the plasma. The latter influence is quantified by the EICS which we derive by using two semi-empirical methods which can be employed in the relevant energy range of 10–1000 eV. They are important molecular properties for plasma- and materials science. We discuss the foundations of the methods and present the cross sections of the high- and low-spin states of the species in their neutral ground states and of their cations.
Comparing Emotional Valence Scores of Twitter Posts from Manual Coding and Machine Learning Algorithms to Gain Insights to Refine Interventions for Family Caregivers of Persons with Dementia

We randomly extracted Korean-language Tweets mentioning dementia/Alzheimer's disease (n= 12,413) from November 28 to December 9, 2020. We independently applied three machine learning algorithms (Afinn, Syuzhet, and Bing) using natural language processing (NLP) techniques and qualitative manual scoring to assign emotional valence scores to Tweets. We then compared the means and distributions of the four emotional valence scores. Visual examination of the graphs produced indicated that each method exhibited unique patterns. The aggregated mean emotional valence scores from the NLP methods were mostly neutral, vs. slightly negative for manual coding (Afinn 0.029, 95% CI [-0.019, 0.077]; Syuzhet 0.266, [0.236, 0.295]; Bing -0.271, [-0.289, -0.252]; manual coding -1.601, [-1.632, -1.569]). One-way analysis of variance (ANOVA) showed no statistically significant differences among the four means after normalization. These findings suggest that the application of NLP can be fairly effective in extracting emotional valence scores from Korean-language Twitter content to gain insights regarding family caregiving for a person with dementia.
Seasonal roost selection and activity of a remnant population of northern myotis in Pennsylvania

The decline in northern myotis (Myotis septentrionalis) populations due to the disease white-nose syndrome (WNS) has led to the species receiving federal protection in the United States and Canada, requiring conservation of critical habitats. However, considerably more is known about summer habitat preferences of northern myotis compared to late summer through winter. Our goal was to describe the seasonal presence and habitat use of a remnant colony of northern myotis in central Pennsylvania. We radio-tagged 31 northern myotis and established 6 acoustic monitoring stations to document activity from 2017–2021. We found that roost trees used during the maternity season by reproductive females were occupied by bats during both summer (21 June–14 August) and autumn (15 August–31 October), indicating similar habitat use patterns between seasons. During this time, both males and females preferred to roost in dead and declining trees. No other variable influenced male use, but females also preferred trees located close to water and in forest stands with higher basal area than randomly located trees. Northern myotis with active transmitters never left the study area and were tracked to roosts until early November. During October and November, a female and male were tracked to an underground network of air-filled voids (the Milieu Souterrain Superficiel) we presume to be a hibernaculum. Northern myotis calls were recorded outside this roost between March and October, and bats were observed emerging from this roost during spring and autumn but not summer. Acoustic activity at this site exhibited a seasonal pattern that differed from acoustic activity near roost trees and foraging areas, with a peak of activity during late summer when northern myotis are known to swarm. These data show that northern myotis maternity roosts are used extensively outside of summer and may be vulnerable to forestry practices that occur even outside of the pup-rearing season. These data also support the growing evidence that some northern myotis hibernate outside of caves and mines.
Motor overflow in the lower limb after stroke: Insights into mechanisms

Motor overflow (involuntary muscle activation) is common after stroke, particularly in the non‐paretic upper limb. Two potential cortical mechanisms are as follows: (1) The contralesional hemisphere controls both limbs, and (2) inhibition from the ipsilesional to the contralesional hemisphere is diminished. Few studies have differentiated between these hypotheses or investigated motor overflow in the lower limb after stroke. To investigate these potential mechanisms, individuals with chronic stroke performed unilateral isometric and dynamic dorsiflexion. Motor overflow was quantified in the contralateral, resting (non‐target) ankle. Transcranial magnetic stimulation (TMS) was applied, and responses were measured in both legs. Relations between motor overflow, excitability of ipsilateral motor pathways, and interhemispheric inhibition were assessed. Non‐target muscle activity (motor overflow) was greater during isometric and dynamic conditions than rest in both legs (p ≤ 0.001) and was higher in the non‐paretic than the paretic leg (p = 0.03). Some participants (25%) had motor overflow >4SD above the group mean in the non‐paretic leg. Greater motor overflow in the non‐paretic leg was associated with lesser inhibition from the ipsilesional to the contralesional hemisphere (p = 0.04). In both legs, non‐target TMS responses were greater during the isometric and dynamic than the rest condition (p ≤ 0.01) but not when normalized to background muscle activity. Overall, motor overflow occurred in both legs after stroke, suggesting a common bilateral mechanism. Our correlational results suggest that alterations in interhemispheric inhibition may contribute to motor overflow. Furthermore, the lack of differences in non‐target motor evoked potentials MEPs between rest, isometric, and dynamic conditions suggests that subcortical and/or spinal pathways may contribute to motor overflow.