Miracle-dz/UniFAR-FTUs huggingface dataset:
Cooperative contributions of structural and functional connectivity to successful memory in aging

Understanding the precise relation between functional connectivity and structural (white-matter) connectivity and how these relationships account for cognitive changes in older adults are major challenges for neuroscience. We investigate these issues using a new approach in which structural equation modeling (SEM) is employed to integrate functional and structural connectivity data analyzed with a common framework based on regions connected by canonical tract groups (CTGs). CTGs (e.g., uncinate fasciculus, cingulum, etc.) serve as a common currency between functional and structural connectivity matrices, and ensures that the same amount of data contributing to brain-behavior relationships. We used this approach to investigate the neural mechanisms supporting memory for items and memory for associations, and how they are affected by healthy aging. Our results are threefold. Firstly, structural and functional CTGs made independent contributions to associative memory performance, suggesting that both forms of connectivity underlie age-related changes in associative memory. Secondly, distinct groups of CTGs supported associative versus item memory. Lastly, the relationship between functional and structural connectivity was best explained by the relationship between latent variables describing functional and structural CTGs based on a constrained set of tracts—but no one specific CTG group—suggesting that age effects in connectivity are constrained to specific pathways. These results provide further insights into the interplay between structural and functional connectivity patterns, and help to elucidate their relative contribution to age-related changes in associative memory performance.
Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

Abstract The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
Cross-Sectional Associations between Dietary Fat-Related Behaviors and Continuous Metabolic Syndrome Score among Young Australian Adults

Dietary guidelines recommend removing visible fat from meat, choosing low-fat options and cooking with oil instead of butter. This study examined cross-sectional associations between fat-related eating behaviors and a continuous metabolic syndrome (cMetSyn) score among young adults. During 2004–2006, 2071 participants aged 26–36 years reported how often they trimmed fat from meat, consumed low-fat dairy products and used different types of fat for cooking. A fasting blood sample was collected. Blood pressure, weight and height were measured. To create the cMetSyn score, sex-specific principal component analysis was applied to normalized risk factors of the harmonized definition of metabolic syndrome. Higher score indicates higher risk. For each behavior, differences in mean cMetSyn score were calculated using linear regression adjusted for confounders. Analyses were stratified by weight status (Body mass index (BMI) < 25 kg/m2 or ≥ 25 kg/m2). Mean cMetSyn score was positively associated with consumption of low-fat oily dressing (PTrend = 0.013) among participants who were healthy weight and frequency of using canola/sunflower oil for cooking (PTrend = 0.008) among participants who were overweight/obese. Trimming fat from meat, cooking with olive oil, cooking with butter, and consuming low-fat dairy products were not associated with cMetSyn score. Among young adults, following fat-related dietary recommendations tended to not be associated with metabolic risk.
Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability

Eutrophication and climate warming, induced by anthropogenic activities, are simultaneously occurring worldwide and jointly affecting soil carbon stability. Therefore, it is of great interest to examine whether and how they interactively affect soil microbial community, a major soil carbon driver. Here, we showed that climate warming, simulated by southward transferring Mollisol soil in agricultural ecosystems from the cold temperate climate zone (N) to warm temperate climate (C) and subtropical climate zone (S), decreased soil organic matter (SOM) by 6%-12%. In contrast, amendment with nitrogen, phosphorus and potassium enhanced plant biomass by 97% and SOM by 6% at the N site, thus stimulating copiotrophic taxa but reducing oligotrophic taxa in relative abundance. However, microbial responses to nutrient amendment were overridden by soil transfer in that nutrient amendment had little effect at the C site but increased recalcitrant carbon-degrading fungal Agaricomycetes and Microbotryomycetes taxa derived from Basidiomycota by 4-17 folds and recalcitrant carbon-degrading genes by 23%-40% at the S site, implying a possible priming effect. Consequently, SOM at the S site was not increased by nutrient amendment despite increased plant biomass by 108%. Collectively, we demonstrate that soil transfer to warmer regions overrides microbial responses to nutrient amendment and weakens soil carbon sequestration.
Temporal and spatial dynamics in microbial community composition within a temperate stream network

The water column of streams hosts a unique microbial community that is distinct from the microbial communities of the stream benthos and surrounding soil. This community is shaped by complex interacting forces, including microbial dispersal from surrounding environments and in-stream selection. However, how the processes structuring stream communities change over space and time remains poorly understood. In this study, we characterize spatial and temporal trends in microbial community composition throughout a stream network spanning first through fifth order streams. We found that the microbial communities of headwater streams are compositionally diverse, with low representation of freshwater microbial taxa and high representation of soil and sediment-associated taxa. In three out of five seasonal samplings, a successional pattern was identified in which phylotype richness and compositional heterogeneity decreased while the proportion of known freshwater taxa increased with increasing cumulative upstream dendritic distance. However, in two samplings, streams instead exhibited uniformly high microbial diversity across the watershed, and the fraction of freshwater taxa showed no relationship with dendritic distance. Overall, our data suggest that the successional processes that drive microbial diversity in streams are highly dynamic and can be disrupted at landscape scales, potentially in response to variation in temperature and precipitation.
Artificial light at night decreases metamorphic duration and juvenile growth in a widespread amphibian

Artificial light at night (ALAN) affects over 20% of the earth's surface and is estimated to increase 6% per year. Most studies of ALAN have focused on a single mechanism or life stage. We tested for indirect and direct ALAN effects that occurred by altering American toads' (Anaxyrus americanus) ecological interactions or by altering toad development and growth, respectively. We conducted an experiment over two life stages using outdoor mesocosms and indoor terraria. In the first phase, the presence of ALAN reduced metamorphic duration and periphyton biomass. The effects of ALAN appeared to be mediated through direct effects on toad development, and we found no evidence for indirect effects of ALAN acting through altered ecological interactions or colonization. In the second phase, post-metamorphic toad growth was reduced by 15% in the ALAN treatment. Juvenile-stage ALAN also affected toad activity: in natural light, toads retreated into leaf litter at night whereas ALAN toads did not change behaviour. Carry-over effects of ALAN were also present; juvenile toads that had been exposed to larval ALAN exhibited marginally increased activity. In this time frame and system, our experiments suggested ALAN's effects act primarily through direct effects, rather than indirect effects, and can persist across life stages.
Effect of self-monitoring on long-term patient engagement with mobile health applications

Despite the growing adoption of the mobile health (mHealth) applications (apps), few studies address concerns with low retention rates. This study aimed to investigate how the usage patterns of mHealth app functions affect user retention. We collected individual usage logs for 1,439 users of single tethered personal health record app, which spanned an 18-months period from August 2011 to January 2013. The user logs contained timestamps whenever an individual uses each function, which enables us to identify the usage patterns based on the intensity of using a particular function in the app. We then estimated how these patterns were related to 1) the app usage over time (using the random effect model) and 2) the probability of stopping the use of the application (using the Cox proportional hazard model). The analyses suggested that the users utilize the app most at the time of the adoption and gradually reduce their usage over time. The average duration of use after starting the app was 25.62 weeks (SD: 18.41). The degree of the usage reduction, however, decreases as the self-monitoring function is more frequently used (coefficient = 0.002, P = 0.013); none of the other functions has this effect. Moreover, engaging with the self-monitoring function frequently (coefficient = −0.18, P = 0.003) and regularly (coefficient = 0.10, P = 0.001) significantly also reduces the probability of abandoning the application. Specifically, the estimated survival rate indicates that, after 40 weeks since the adoption, the probability of the regular users of self-monitoring to stay in use was about 80% while that of non-user was about 60%. This study provides the empirical evidence that sustained use of mHealth app is closely linked to the regular usage on self-monitoring function. The implications can be extended to the education of users and physicians to produce better outcomes as well as application development for effective user interfaces.
Identifying misclassified bug reports

The data mining methodology for identification and detection of bugs is an important application. Especially separating bugs from non-bugs is a general challenge. When software developers classify bug reports, they may misclassify bug reports with bias and errors. All issue reports are analyzed by combining the classification rules from open-ihm project and Herzig et al. (2012). A comparison on the classification results of different authors has been extracted which shows the misclassification rate. Depending on the percent of misclassification rates, it is concluded that the classification of bugs in Herzig et al. (2012) can be applied to the open-ihm project and it exhibited the similar proportion of misclassified bugs as reported in Herzig et al. (2012).
A functional siRNA screen identifies RhoGTPase-associated genes involved in thrombin-induced endothelial permeability

Thrombin and other inflammatory mediators may induce vascular permeability through the disruption of adherens junctions between adjacent endothelial cells. If uncontrolled, hyperpermeability leads to an impaired barrier, fluid leakage and edema, which can contribute to multi-organ failure and death. RhoGTPases control cytoskeletal dynamics, adhesion and migration and are known regulators of endothelial integrity. Knowledge of the precise role of each RhoGTPase, and their associated regulatory and effector genes, in endothelial integrity is incomplete. Using a combination of a RNAi screen with electrical impedance measurements, we quantified the effect of individually silencing 270 Rho-associated genes on the barrier function of thrombin-activated, primary endothelial cells. Known and novel RhoGTPase-associated regulators that modulate the response to thrombin were identified (RTKN, TIAM2, MLC1, ARPC1B, SEPT2, SLC9A3R1, RACGAP1, RAPGEF2, RHOD, PREX1, ARHGEF7, PLXNB2, ARHGAP45, SRGAP2, ARHGEF5). In conclusion, with this siRNA screen, we confirmed the roles of known regulators of endothelial integrity but also identified new, potential key players in thrombin-induced endothelial signaling.
Architecture of structures in the urogenital triangle of young adult males; comparison with females

The fibro‐muscular architecture of the urogenital triangle remains contentious. Reasons are small size of the constituting structures and poor visibility with most imaging methods. We reinvestigated the area in serial sections of three males (21–38 years old) of the American and Chinese Visible Human Projects and two 26‐week‐old male fetuses, and compared the findings with earlier observations in females. The mass of the levator ani muscle was approximately twofold smaller and its funnel shape steeper in males than females. In the levator hiatus, a strand of the smooth longitudinal muscle layer of the rectum, the ‘rectourethral (RU) muscle’, extended anteriorly from the anorectal bend to the penile bulb. Fibrous tissue that formed in the inferior reach of the fetal RU muscle identified the location of the developing perineal body (PB) and divided the muscle into posterior ‘rectoperineal’ and anterior ‘deep perineal’ portions. In males, the PB remained small and bipartite, so that the RU muscle presented as an undivided midline structure. The well‐developed female PB, instead, intertwined with the deep perineal muscle and both structures passed the vagina bilaterally to form the perineal membrane in the posterior portion of the urogenital triangle. The urethral rhabdosphincter extended in the anterior portion of the urogenital triangle between the penile bulb inferiorly and the bladder neck superiorly, and consisted of a well‐developed circular ‘membranous’ portion with bilateral posteroinferior ‘wings’ and a thinner ‘prostatic’ portion on the prostate anterior side. In men, muscles occupy the urogenital triangle, but additional tightening of the locally fibrous adipose tissue by the superficial transverse perineal muscle appears necessary to generate functional support in women. An interactive 3D pdf file with these anatomical details (available online) should allow more accurate interpretation of ultrasound, computed tomography and magnetic resonance images.
Five-Year Longitudinal Study of Neck Vessel Cross-Sectional Area in Multiple Sclerosis

BACKGROUND AND PURPOSE: Alterations of neck vessel cross-sectional area in multiple sclerosis have been reported. Our aim was to investigate the evolution of the neck vessel cross-sectional area in patients with MS and healthy controls during 5 years. MATERIALS AND METHODS: Sixty-nine patients with MS (44 relapsing-remitting MS, 25 progressive MS) and 22 age- and sex-matched healthy controls were examined twice, 5 years apart, on a 3T MR imaging scanner using 2D neck MR angiography. Cross-sectional areas were computed for the common carotid/internal carotid arteries, vertebral arteries, and internal jugular veins for all slices between the C3 and C7 cervical levels. Longitudinal cross-sectional area differences at each cervical level and the whole-vessel course were tested within study groups and between patients with MS with and without cardiovascular disease using mixed-model analysis and the related-samples Wilcoxon singed rank test. The Benjamini-Hochberg procedure was performed to correct for multiple comparisons. RESULTS: No significant cross-sectional area differences were seen between patients with MS and healthy controls at baseline or at follow-up. During the follow-up, significant cross-sectional area decrease was found in patients with MS for the common carotid artery–ICAs (C4: P = .048; C7: P = .005; whole vessel: P = .012), for vertebral arteries (C3: P = .028; C4: P = .028; C7: P = .028; whole vessel: P = .012), and for the internal jugular veins (C3: P = .014; C4: P = .008; C5: P = .010; C6: P = .010; C7: P = .008; whole vessel: P = .002). Patients with MS without cardiovascular disease had significantly greater change than patients with MS with cardiovascular disease for internal jugular veins at all levels. CONCLUSIONS: For 5 years, patients with MS showed significant cross-sectional area decrease of all major neck vessels, regardless of the disease course and cardiovascular status.
Adaptation processes in the auditory system of a beluga whale Delphinapterus leucas

The effects of prolonged sound stimuli (tone pip trains) on evoked potentials (the rate following response, RFR) were investigated in a beluga whale. The stimuli (rhythmic tone pips) were of 64 kHz frequency at levels from 80 to 140 dB re 1 μPa. During stimulation, every 1000 ms stimulus level either was kept constant (the steady-state stimulation) or changed up/down by 20 or 40 dB. With such stimulus presentation manner, RFR amplitude varied as follows. (i) After a stimulus level increase, the response amplitude increased quickly and then decayed slowly. The more the level increased, the higher the response amplitude increased. (ii) After a stimulus level decrease, the response amplitude was suppressed and then recovered slowly. The more the level decreased, the stronger was the response suppression. (iii) At the end of the 1000 ms window, the response amplitude approached, but did not reach, the amplitude characteristic of the steady-state stimulation. As a result, both after a sound level increase and decrease, the responses were almost stabilized during an analysis time as short as 1 s. This stabilization is attributed to an adaptation process. RFR decay after initial increase could be approximated by an exponent with a time constant of 59.4 ±1.8 (standard error) ms; RFR recovery after initial decrease could be approximated by an exponent with a time constant of 139.2 ±9.9 ms.
Knockdown of HIF‐1α impairs post‐ischemic vascular reconstruction in the brain via deficient homing and sprouting bmEPCs

Although the critical role of hypoxia inducible factor‐1α (HIF‐1α) in cerebral neovascularization after stroke has been well characterized, the details regarding the regulation of endothelial progenitor cell (EPC)‐dependent neovascularization by HIF‐1α are not completely understood. Using lentiviral shRNA to knockdown HIF‐1α, we showed that HIF‐1α plays a central role in bone marrow‐derived EPC (bmEPC) homing and sprouting in the post‐acute stage of ischemic Sprague Dawley (SD) rat brains. First, knockdown of HIF‐1α decreased the homing of both endogenous and exogenous bmEPCs to the ischemic brain. Additionally, the knockdown impaired the incorporation and sprouting of bmEPCs in the ischemic brain. In vitro, knockdown of HIF‐1α inhibited the spheroid sprouting and tube formation of bmEPCs. Mechanically, the HIF‐1α‐dependent recruitment of bmEPCs to the ischemic brain was relative to the CXCL12/CXCR4 axis and HMGB1, which were relative to astrocytes. In addition, the loss of HIF‐1α resulted in deficient expression levels of VEGF‐A, Flk‐1, NRP1, and Dll4 in the ischemic brains, bmEPCs, and astrocytes. These findings suggested that HIF‐1α implicates in bmEPC homing via CXCL12/CXCR4 and HMGB1 and that it promotes bmEPC sprouting via VEGF‐A/flk1‐NRP1/Dll4.
Clinical and biochemical characteristics of familial type 1 diabetes mellitus (FT1DM) compared to non-familial type 1 DM (NFT1DM)

Introduction: Familial type 1 diabetes mellitus (FT1DM) comprises parent-offspring and sib-pair subgroups. The clinical and genetic characteristics of FT1DM cases with and without affected family members have been previously studied with varying results. Some investigators found similarity of presenting features whereas others reported significant differences between the two groups.Objective:To describe the clinical and biochemical characteristics of children with FT1DM in comparison with those with non-familial type 1 diabetes mellitus (NFT1DM). Patients and Methods: We performed a cross-sectional retrospective study in a cohort of children and adolescents with T1DM (n=424) aged between 6 months - 16 years attending to Hamad General Hospital Pediatric Diabetes Center, Doha (Qatar) from 2012-2016. They were divided into 2 groups. Group 1 consisted of 62 children and adolescent with FT1DM (parent-offspring or sib-pair). The other group (Group 2) consisted of 362 patients with NFT1DM. The clinical presentation and prevalence of β-cell autoimmunity (anti-glutamic acid decarboxylase (GAD) antibodies, anti-islet cell and anti-insulin antibodies), thyroid function (Free thyroxine: FT4 and thyroid-stimulating hormone: TSH), anti-thyroid peroxidase antibody (TPO) and anti-tissue transglutaminase (ATT) at their first presentation were recorded, described and analyzed. Results:FT1 DM was more prevalent in boys versus girls (1.4:1, respectively) whereas the prevalence of NFT1DM did not differ between genders (1:1.1, respectively). F1DM occurred relatively early in childhood (40.7% before the age of 4 years and 72% before 9 years of age) versus NFT1DM which occurred relatively later in life (80% after the age of 4 years and 40% after the age of 9 years). 35.2% of FT1DM presented with diabetic ketoacidosis (DKA) versus 32.5% of T1DM patients. Anti-islet antibodies (Ab) were detected more frequently in FT1DM versus NFT1DM. The prevalence of positive anti-insulin and anti- GAD antibodies did not differ between the two groups. Anti TPO were detected in 27.2% of NFT1DM and 35.5% of FT1DM. A primary hypothyroidism, with positive ATPO, was more prevalent in FT1DM versus NFT1DM. ATT IgA was high in 5% of NFT1DM and 19.8% of FT1DM whereas ATT IgG was high in 4.4 % of NFT1DM and 15.4% of FT1DM. Conclusions:FT1DM is more prevalent in boys versus girls and occurs earlier in childhood compared to NFT1DM. Primary hypothyroidism was more prevalent in NFT1DM versus FT1DM. Anti-islet Ab and ATT antibodies were more prevalent in the FT1DM versus NFT1DM. The genetic background may explain some differences between FT1DM and NFT1DM including the age of onset, gender affection, as well as associated autoimmune disorders. (www.actabiomedica.it)