Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of asymptomatic genital tract infections on in vitro Fertilization (IVF) outcome

Background Infertility is estimated to affect approximately 9–30% of reproductive-aged couples. Several conditions involving one or both partners may contribute to infertility. The aim of this study is to evaluate the role of asymptomatic genital tract infections in the outcome of In Vitro Fertilization (IVF) in couples with infertility. Methods A total of 285 infertile couples were enrolled in the study. Vaginal/endocervical swabs and semen samples were collected and subjected to microbiological analysis. Spermiograms were carried out on semen specimens, and lactobacilli were quantified in vaginal swabs. Data were associated with IVF results and analysed by using non parametric tests and multivariate analysis. Results Microbiological analysis showed that 46.3% of couples presented with an asymptomatic genital tract infection. Spermiogram results showed a significantly diminished motility of sperm cells in samples positive to microbiological testing compared to negative specimens. Enterococcus faecalis was the most prevalent species (11.6%) in positive semen samples and was found to negatively affect both sperm morphology (p = 0.026) and motility (p = 0.003). Analysis of genital swabs from females showed that the presence of E. faecalis (p<0.0001), Escherichia coli (p = 0.0123), Streptococcus agalactiae (p<0.0001), and Gardnerella vaginalis (p = 0.0003) was significantly associated to reduced levels of vaginal lactobacilli. Association of microbiological data with IVF outcome showed that 85.7% of IVF+ couples was microbiologically negative, while IVF was successful in just 7.5% of couples infected with E. faecalis and/or U. urealyticum and/or M. hominis (p = 0.02). Conclusions The results show the negative impact of E. faecalis on sperm quality and the association of definite bacterial pathogens with reduced levels of vaginal lactobacilli. The presence of E. faecalis and/or U. urealyticum and/or M. hominis in genital samples of infertile couples is predictive for a negative outcome of IVF.
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis

Motivation Genome-scale metabolic networks and transcriptomic data represent complementary sources of knowledge about an organism’s metabolism, yet their integration to achieve biological insight remains challenging. Results We investigate here condition-specific series of metabolic sub-networks constructed by successively removing genes from a comprehensive network. The optimal order of gene removal is deduced from transcriptomic data. The sub-networks are evaluated via a fitness function, which estimates their degree of alteration. We then consider how a gene set, i.e. a group of genes contributing to a common biological function, is depleted in different series of sub-networks to detect the difference between experimental conditions. The method, named metaboGSE, is validated on public data for Yarrowia lipolytica and mouse. It is shown to produce GO terms of higher specificity compared to popular gene set enrichment methods like GSEA or topGO. Availability The metaboGSE R package is available at https://cran.r-project.org/web/packages/metaboGSE.
The multiple merger assembly of a hyperluminous obscured quasar at redshift 4.6

Mergers drive a powerful dusty quasar Massive galaxies in the early Universe host supermassive black holes at their centers. When material falls toward the black hole, it releases energy and is observed as a quasar. Astronomers found a population of powerful distant quasars that are obscured by dust, but it has been unclear how they are formed. Díaz-Santos et al. observed the dust-obscured quasar WISE J224607.56-052634.9 at submillimeter wavelengths, finding three small companion galaxies connected to the quasar by bridges of gas and dust. They inferred that galaxy mergers can provide both the raw material to power a quasar and large quantities of dust to obscure it. Science, this issue p. 1034 Galaxy mergers can provide the raw materials to drive powerful dust-observed quasars in the early Universe. Galaxy mergers and gas accretion from the cosmic web drove the growth of galaxies and their central black holes at early epochs. We report spectroscopic imaging of a multiple merger event in the most luminous known galaxy, WISE J224607.56−052634.9 (W2246−0526), a dust-obscured quasar at redshift 4.6, 1.3 billion years after the Big Bang. Far-infrared dust continuum observations show three galaxy companions around W2246−0526 with disturbed morphologies, connected by streams of dust likely produced by the dynamical interaction. The detection of tidal dusty bridges shows that W2246−0526 is accreting its neighbors, suggesting that merger activity may be a dominant mechanism through which the most luminous galaxies simultaneously obscure and feed their central supermassive black holes.
Prevalence of heart failure and the diagnostic value of MR‐proANP in outpatients with type 2 diabetes

The prevalence of heart failure (HF) in patients with type 2 diabetes (T2DM) is debatable and no data exist concerning the diagnostic value of mid‐regional pro‐atrial natriuretic peptide (MR‐proANP). We aimed to identify HF prevalence and evaluate the diagnostic value of MR‐proANP in outpatients followed in two specialized diabetes clinics. HF was pre‐defined as HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF). The prevalence of HFrEF and HFpEF was 2.4% and 17.5%, respectively. An MR‐proANP <60 pmol/L ruled out HFrEF in the total population (n = 806) and in patients reporting dyspnea (n = 311) with a sensitivity of 94.7% and 87.5%, a negative predictive value of 99.7% and 99.0%, a specificity of 39.5% and 33.0%, and a positive predictive value of 3.6% and 3.3%, respectively. In a multivariable model including age, sex, T2DM duration, albuminuria, uncontrolled systolic blood pressure, abnormal electrocardiogram and ischaemic heart disease for diagnosis of HF in patients reporting dyspnea, adding MR‐proANP increased the area under the curve from 0.69 to 0.78 (P < 0.001). In conclusion, HFrEF was rare among outpatients with T2DM. MR‐proANP rules out HFrEF and contributes independent information relevant to diagnosis of HF in patients reporting dyspnea.
Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) stereotyped subsets #6 and #8 include cases expressing unmutated B cell receptor immunoglobulin (BcR IG) (U‐CLL). Subset #6 (IGHV1‐69/IGKV3‐20) is less aggressive compared to subset #8 (IGHV4‐39/IGKV1(D)‐39) which has the highest risk for Richter's transformation among all CLL. The underlying reasons for this divergent clinical behavior are not fully elucidated. To gain insight into this issue, here we focused on epigenomic signatures and their links with gene expression, particularly investigating genome‐wide DNA methylation profiles in subsets #6 and #8 as well as other U‐CLL cases not expressing stereotyped BcR IG. We found that subset #8 showed a distinctive DNA methylation profile compared to all other U‐CLL cases, including subset #6. Integrated analysis of DNA methylation and gene expression revealed significant correlation for several genes, particularly highlighting a relevant role for the TP63 gene which was hypomethylated and overexpressed in subset #8. This observation was validated by quantitative PCR, which also revealed TP63 mRNA overexpression in additional nonsubset U‐CLL cases. BcR stimulation had distinct effects on p63 protein expression, particularly leading to induction in subset #8, accompanied by increased CLL cell survival. This pro‐survival effect was also supported by siRNA‐mediated downregulation of p63 expression resulting in increased apoptosis. In conclusion, we report that DNA methylation profiles may vary even among CLL patients with similar somatic hypermutation status, supporting a compartmentalized approach to dissecting CLL biology. Furthermore, we highlight p63 as a novel prosurvival factor in CLL, thus identifying another piece of the complex puzzle of clinical aggressiveness.
Mobile Mammography Participation Among Medically Underserved Women: A Systematic Review

Introduction Although breast cancer deaths have declined, the mortality rate among women from medically underserved communities is disproportionally high. Screening mammography is the most effective tool for detecting breast cancer in its early stages, yet many women from medically underserved communities do not have adequate access to screening mammograms. Mobile mammography may be able to bridge this gap by providing screening mammograms at no cost or low cost and delivering services to women in their own neighborhoods, thus eliminating cost and transportation barriers. The objective of this systematic review was to describe the scope and impact of mobile mammography programs in promoting mammographic screening participation among medically underserved women. Methods We searched electronic databases for English-language articles published in the United States from January 2010 through March 2018 by using the terms “mobile health unit,” “mammogram,” “mammography,” and “breast cancer screening. ” Of the 93 articles initially identified, we screened 55; 16 were eligible to be assessed and 10 qualified for full text review and data extraction. Each study was coded for study purpose, research design, data collection, population targeted, location, sample size, outcomes, predictors, analytical methods, and findings. Results Of the 10 studies that qualified for review, 4 compared mobile mammography users with users of fixed units, and the other 6 characterized mobile mammography users only. All the mobile mammography units included reached underserved women. Most of the women screened in mobile units were African American or Latina, low income, and/or uninsured. Mobile mammography users reported low adherence to 1-year (12%–34%) and 2-year (40%–48%) screening guidelines. Some difficulties faced by mobile clinics were patient retention, patient follow-up of abnormal or inconclusive findings, and women inaccurately perceiving their breast cancer risk. Conclusion Mobile mammography clinics may be effective at reaching medically underserved women. Adding patient navigation to mobile mammography programs may promote attendance at mobile sites and increase follow-up adherence. Efforts to promote mammographic screening should target women from racial/ethnic minority groups, women from low-income households, and uninsured women. Future research is needed to understand how to best improve visits to mobile mammography clinics.
Assessment of lower incisor alveolar bone width using cone-beam computed tomography images in skeletal Class III adults of different vertical patterns

Objective This study was performed to investigate the alveolar bone of lower incisors in skeletal Class III adults of different vertical facial patterns and to compare it with that of Class I adults using cone-beam computed tomography (CBCT) images. Methods CBCT images of 90 skeletal Class III and 29 Class I patients were evaluated. Class III subjects were divided by mandibular plane angle: high (SN-MP > 38.0°), normal (30.0° < SN-MP < 37.0°), and low (SN-MP < 28.0°) groups. Buccolingual alveolar bone thickness was measured using CBCT images of mandibular incisors at alveolar crest and 3, 6, and 9 mm apical levels. Linear mixed model, Bonferroni post-hoc test, and Pearson correlation analysis were used for statistical significance. Results Buccolingual alveolar bone in Class III high, normal and low angle subjects was not significantly different at alveolar crest and 3 mm apical level while lingual bone was thicker at 6 and 9 mm apical levels than on buccal side. Class III high angle group had thinner alveolar bone at all levels except at buccal alveolar crest and 9 mm apical level on lingual side compared to the Class I group. Class III high angle group showed thinner alveolar bone than the Class III normal or low angle groups in most regions. Mandibular plane angle showed negative correlations with mandibular anterior alveolar bone thickness. Conclusions Skeletal Class III subjects with high mandibular plane angles showed thinner mandibular alveolar bone in most areas compared to normal or low angle subjects. Mandibular plane angle was negatively correlated with buccolingual alveolar bone thickness.
Complexity, Regularity and Non-Linear Behavior in Human Eye Movements: Analyzing the Dynamics of Gaze in Virtual Sailing Programs

The non-linear analysis of the behavior of biological signals in humans is studied from different scientific disciplines. The aim of this study was to analyze the possible non-linear behavior present in eye movements during eye-tracking tasks in simulated sailing. Thirty young sailors were selected. Fuzzy entropy and detrended fluctuation analyses were applied to quantify the regularity and complexity of eye movements. The results show that neither experience nor ranking affect the regularity or the complexity of eye movement positions or velocities. Younger age is related to more regular visual behavior. At younger ages, eye positions present more complex behavior. Eye positions show more complex behavior than eye velocities. This complexity would allow for a more functional exploration of the environment by sailors. Eye movement velocity presents the greatest irregularity, with significantly higher values than eye movement position. This irregularity would facilitate the visual perception of the environment. All these findings could be related to the sailors’ functional behavior, based on complexity and stability, which has been associated with the ability of human beings to adapt to the environment.
Some Linguistic Neutrosophic Cubic Mean Operators and Entropy with Applications in a Corporation to Choose an Area Supervisor

In this paper, we combined entropy with linguisti neutrosophic cubic numbers and used it in daily life problems related to a corporation that is going to choose an area supervisor, which is the main target of our proposed model. For this, we first develop the theory of linguistic neutrosophic cubic numbers, which explains the indeterminate and incomplete information by truth, indeterminacy and falsity linguistic variables (LVs) for the past, present, as well as for the future time very effectively. After giving the definitions, we initiate some basic operations and properties of linguistic neutrosophic cubic numbers. We also define the linguistic neutrosophic cubic Hamy mean operator and weighted linguistic neutrosophic cubic Hamy mean (WLNCHM) operator with some properties, which can handle multi-input agents with respect to the different time frame. Finally, as an application, we give a numerical example in order to test the applicability of our proposed model.
Noninvasive peripheral vascular function and atrial fibrillation in the general population

Background: Arterial stiffness is a strong predictor of atrial fibrillation in the community. Whether noninvasively measured conduit artery function and peripheral vascular reactivity are related to atrial fibrillation remains unknown. Methods and results: In 15 010 individuals of the population-based Gutenberg Health Study, mean age 55 ± 11 years, 50.5% men, we determined noninvasive vascular function by flow-mediated dilation (FMD) and peripheral arterial tonometry (PAT) in relation to manifest atrial fibrillation (N = 466). Patients with atrial fibrillation exhibited a higher mean brachial artery diameter [4.81 mm (4.17, 5.33) in atrial fibrillation vs. 4.31 mm (3.67, 4.93)] and baseline pulse amplitude in arbitrary units [6.35 (5.76, 6.78) in atrial fibrillation vs. 6.09 (5.36, 6.71)] as well as a reduced FMD in arbitrary units [1.29 (1.26, 1.33) in atrial fibrillation vs. (1.31 (1.26, 1.37)] and PAT ratio [0.42 (0.19, 0.77) in atrial fibrillation vs. 0.67 (0.33, 0.94)] compared with individuals without atrial fibrillation (all PWilcoxon rank-sum test). In age-adjusted and sex-adjusted logistic regression analyses, only baseline brachial artery diameter [odds ratio (OR) per standard deviation 1.19; 95% confidence interval (CI), 1.04–1.37; P = 0.012] and PAT ratio (OR 0.83; 0.74–0.94; P = 0.0029) were associated with atrial fibrillation. In risk factor and heart rate-adjusted models, there was no statistically significant correlation of atrial fibrillation and brachial artery diameter, FMD and PAT ratio while baseline pulse amplitude was reduced in individuals with atrial fibrillation (OR 0.81; 95% CI 0.71–0.93; P = 0.0034). Conclusion: In our large contemporary cohort, peripheral vascular function was compromised in individuals with atrial fibrillation. However, observed associations were mediated by age and classical risk factors. Noninvasive vascular function measures did not improve discriminatory ability for atrial fibrillation.
A Batteryless, Wireless Strain Sensor Using Resonant Frequency Modulation

In this study, we demonstrated the feasibility of a wireless strain sensor using resonant frequency modulation through tensile impedance test and wireless sensing test. To achieve a high stretchability, the sensor was fabricated by embedding a copper wire with high conductivity in a silicone rubber with high stretchability, in which the resonant frequency can be modulated according to changes in strain. The characteristics of the sensor and the behavior of wireless sensing were calculated based on equations and simulated using finite element method. As the strain of the sensor increased, the inductance increased, resulting in the modulation of resonant frequency. In experimental measurement, as the strain of the sensor increased from 0% to 110%, its inductance was increased from 192 nH to 220 nH, changed by 14.5%, and the resonant frequency was shifted from 13.56 MHz to 12.72 MHz, decreased by 6.2%. It was demonstrated that using the proposed sensor, strains up to 110% could be detected wirelessly up to a few centimeters.
Slick, Stretchy Fascia Underlies the Sliding Tongue of Rorquals

The tongue of rorqual (balaenopterid) whales slides far down the throat into the expanded oral pouch as an enormous mouthful of water is engulfed during gulp feeding. As the tongue and adjacent oral floor expands and slides caudoventrally, it glides along a more superficial (outer) layer of ventral body wall musculature, just deep to the accordion‐like ventral throat pleats. We hypothesize that this sliding movement of adjacent musculature is facilitated by a slick, stretchy layer of loose areolar connective tissue that binds the muscle fibers and reduces friction: fascia. Gross anatomical examination of the gular region of adult minke, fin, and humpback whales confirms the presence of a discrete, three‐layered sublingual fascia interposed between adhering fasciae of the tongue and body wall. Histological analysis of this sublingual fascia reveals collagen and elastin fibers loosely organized in a random feltwork along with numerous fibroblasts in a watery extracellular matrix. Biomechanical testing of tissue samples in the field and laboratory, via machine‐controlled or manual stretching, demonstrates expansion of the sublingual fascia and its three layers up to 250% beyond resting dimensions, with slightly more extension observed in anteroposterior (rather than mediolateral or oblique) stretching, and with the most superficial of the fascia's three layers. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc. Anat Rec, 302:735–744, 2019. © 2018 Wiley Periodicals, Inc.
Cortisol secretion moderates the association between mother–infant attachment at 17 months and child behavior at age 5 years

This study examined infant cortisol secretion as a moderator of the association between mother-infant attachment security at age 17 months and child behavior at age 5 years. A longitudinal community sample of 96 mother-child dyads participated in the strange situation procedure (SSP) at age 17 months. Cortisol was collected at baseline, and at 20 and 40 min post-SSP. Maternal reports of child behavior were collected at age 5 years. Results revealed that the associations between nonsecure mother-infant attachment and higher total, internalizing, and externalizing behavior were stronger for infants with high cortisol secretion, relative to infants with low cortisol secretion. The model of interaction differed depending on the outcome, with diathesis-stress explaining variance in total as well as internalizing behavior, and with differential susceptibility explaining variance in externalizing behavior. These findings augment our understanding of risk and resilience to the impact of the early rearing environment on later psychopathology.
The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure

Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. To address this, quantitative analysis of single cell responses can help characterize the redundancy within gene families. We developed high‐throughput quantitative imaging of stomatal closure, a response of plant guard cells, and performed a reverse genetic screen in a group of Arabidopsis mutants to five stimuli. Focussing on the intersection between guard cell signalling and the endomembrane system, we identified eight clusters based on the mutant stomatal responses. Mutants generally affected in stomatal closure were mostly in genes encoding SNARE and SCAMP membrane regulators. By contrast, mutants in RAB5 GTPase genes played specific roles in stomatal closure to microbial but not drought stress. Together with timed quantitative imaging of endosomes revealing sequential patterns in FLS2 trafficking, our imaging pipeline can resolve non‐redundant functions of the RAB5 GTPase gene family. Finally, we provide a valuable image‐based tool to dissect guard cell responses and outline a genetic framework of stomatal closure.
Listeriolysin O-dependent host surfaceome remodeling modulates Listeria monocytogenes invasion

Abstract Listeria monocytogenes is a pathogenic bacterium that invades epithelial cells by activating host signaling cascades, which promote bacterial engulfment within a phagosome. The pore-forming toxin listeriolysin O (LLO), which is required for bacteria phagosomal escape, has also been associated with the activation of several signaling pathways when secreted by extracellular bacteria, including Ca2+ influx and promotion of L. monocytogenes entry. Quantitative host surfaceome analysis revealed significant quantitative remodeling of a defined set of cell surface glycoproteins upon LLO treatment, including a subset previously identified to play a role in the L. monocytogenes infection process. Our data further shows that the lysosomal-associated membrane proteins LAMP-1 and LAMP-2 are translocated to the cellular surface and those LLO-induced Ca2+ fluxes are required to trigger the surface relocalization of LAMP-1. Finally, we identify late endosomes/lysosomes as the major donor compartments of LAMP-1 upon LLO treatment and by perturbing their function, we suggest that these organelles participate in L. monocytogenes invasion.
The genomic landscape of plasma cells in systemic light chain amyloidosis.

TO THE EDITOR: The key event in the pathogenesis of systemic light chain amyloidosis (AL) is an unstable misfolded secondary or tertiary structure of a monoclonal immunoglobulin (IG) light chain that precipitates in the extracellular compartments. [1][1] The plasma cell disorder underlying AL is