Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical manipulation of the Escherichia coli chromosome reveals its soft nature

Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In this work, we demonstrate experimentally the fundamentally soft nature of the bacterial chromosome and the entropic forces that can compact it in a crowded intracellular environment. We developed a unique “micropiston” and measured the force-compression behavior of single Escherichia coli chromosomes in confinement. Our data show that forces on the order of 100 pN and free energies on the order of 105 kBT are sufficient to compress the chromosome to its in vivo size. For comparison, the pressure required to hold the chromosome at this size is a thousand-fold smaller than the surrounding turgor pressure inside the cell. Furthermore, by manipulation of molecular crowding conditions (entropic forces), we were able to observe in real time fast (approximately 10 s), abrupt, reversible, and repeatable compaction–decompaction cycles of individual chromosomes in confinement. In contrast, we observed much slower dissociation kinetics of a histone-like protein HU from the whole chromosome during its in vivo to in vitro transition. These results for the first time provide quantitative, experimental support for a physical model in which the bacterial chromosome behaves as a loaded entropic spring in vivo.
In-network guide performance in wireless multi-hop cache networks

In wireless multi-hop networks, content servers are generally located outside a wireless multi-hop network and a user accesses these servers through a gateway node. So, content traffic has a tendency to be concentrated at a gateway node, which might cause throughput degradation in a whole wireless multi-hop network. Caching network is one promising way to resolve this technical problem. However, caching network has a limitation of cache availability on a default-path. For wired networks, Breadcrumbs has been proposed as in-network guide for cached contents. In this paper, we evaluate Breadcrumbs in wireless multi-hop networks. Our simulation results show that Breadcrumbs improves total throughput performance of wireless multi-hop networks. And also they surprisingly show that not only popular content throughput but also unpopular content throughput is improved.
Multimodal Distributional Semantics

Distributional semantic models derive computational representations of word meaning from the patterns of co-occurrence of words in text. Such models have been a success story of computational linguistics, being able to provide reliable estimates of semantic relatedness for the many semantic tasks requiring them. However, distributional models extract meaning information exclusively from text, which is an extremely impoverished basis compared to the rich perceptual sources that ground human semantic knowledge. We address the lack of perceptual grounding of distributional models by exploiting computer vision techniques that automatically identify discrete "visual words" in images, so that the distributional representation of a word can be extended to also encompass its co-occurrence with the visual words of images it is associated with. We propose a flexible architecture to integrate text- and image-based distributional information, and we show in a set of empirical tests that our integrated model is superior to the purely text-based approach, and it provides somewhat complementary semantic information with respect to the latter.
3D curved multiplanar cone beam CT reconstruction for intracochlear position assessment of straight electrodes array. A temporal bone and clinical study

SUMMARY A retrospective review of post-op cone beam CT (CBCT) of 8 adult patients and 14 fresh temporal bones that underwent cochlear implantation with straight flexible electrodes array was performed to determine if the position of a long and flexible electrodes array within the cochlear scalae could be reliably assessed with CBCT. An oto-radiologist and two otologists examined the images and assessed the electrodes position. The temporal bone specimens underwent histological analysis for confirm the exact position. The position of the electrodes was rated as scala tympani, scala vestibule, or intermediate position for the electrodes at 180°, 360° and for the apical electrode. In the patient group, for the electrodes at 180° all observers agreed for scala tympani position except for 1 evaluation, while a discrepancy in 3 patients both for the 360° and for the apical electrode assessment were found. In five temporal bones the evaluations were in discrepancy for the 180° electrode, while at 360° a disagreement between raters on the scalar positioning was seen in six temporal bones. A higher discrepancy between was found in assessment of the scalar position of the apical electrode (average pairwise agreement 45.4%, Fleiss k = 0.13). A good concordance was found between the histological results and the consensus between raters for the electrodes in the basal turn, while low agreement (Cohen's k 0.31, pairwise agreement 50%) was found in the identification of the apical electrode position confirming the difficulty to correct identify the electrode position in the second cochlear turn in temporal bones. In conclusion, CBCT is a reliable radiologic exam to correctly evaluate the position of a lateral wall flexible array in implanted patients using the proposed imaging reconstruction method, while some artefacts impede exact evaluation of the position of the apical electrode in temporal bone and other radiological techniques should be preferred in ex vivo studies.
EEG microstate sequences in healthy humans at rest reveal scale-free dynamics

Recent findings identified electroencephalography (EEG) microstates as the electrophysiological correlates of fMRI resting-state networks. Microstates are defined as short periods (100 ms) during which the EEG scalp topography remains quasi-stable; that is, the global topography is fixed but strength might vary and polarity invert. Microstates represent the subsecond coherent activation within global functional brain networks. Surprisingly, these rapidly changing EEG microstates correlate significantly with activity in fMRI resting-state networks after convolution with the hemodynamic response function that constitutes a strong temporal smoothing filter. We postulate here that microstate sequences should reveal scale-free, self-similar dynamics to explain this remarkable effect and thus that microstate time series show dependencies over long time ranges. To that aim, we deploy wavelet-based fractal analysis that allows determining scale-free behavior. We find strong statistical evidence that microstate sequences are scale free over six dyadic scales covering the 256-ms to 16-s range. The degree of long-range dependency is maintained when shuffling the local microstate labels but becomes indistinguishable from white noise when equalizing microstate durations, which indicates that temporal dynamics are their key characteristic. These results advance the understanding of temporal dynamics of brain-scale neuronal network models such as the global workspace model. Whereas microstates can be considered the “atoms of thoughts,” the shortest constituting elements of cognition, they carry a dynamic signature that is reminiscent at characteristic timescales up to multiple seconds. The scale-free dynamics of the microstates might be the basis for the rapid reorganization and adaptation of the functional networks of the brain.
Meeting madness: counterproductive meeting behaviours and personality traits

When used effectively, workplace meetings serve as an invaluable opportunity for co-workers to achieve organisational objectives. However, meetings are often regarded as inefficient, unproductive, and a waste of time. Owing to meeting attendee frustration, there can be detrimental impact on employee wellbeing. In this paper, we examine the impact of a specific type of meeting behaviour, counterproductive meeting behaviours (CMBs), which include non-constructive criticism and complaints on perceptions of meeting effectiveness. Additionally, we explore the potential moderating influence of personality characteristics on this relationship. While meeting leaders may take great efforts in designing meetings based on good meeting practices supported by research, meeting outcomes could be largely influenced by the individual personality characteristics of meeting attendees. This research is aimed at developing a greater understanding of how individual differences, namely personality traits, play a role in meeting interactions and outcomes. Respondents completed a survey that measured CMBs, personality characteristics, and meeting effectiveness. Our findings indicate CMBs are negatively related to perceived meeting effectiveness. Additionally, the negative relationship was stronger for individuals who possess higher levels of agreeableness and stronger for individuals possessing lower levels of extraversion. We discuss implications for managers and meeting attendees.
Analysis of Scan Blindness in a Linearly Polarized Tapered-Slot Phased Array in Triangular Lattice—Performance Improvement With Parasitic Notches

Various types of scan blindness are analyzed in a single-polarized tapered-slot phased array with triangular lattice arrangement, and a scan blindness removal strategy is proposed. In the presented analysis, two types of scan blindness are observed which have not been previously reported. First, a special case of parallel plate cavity resonance is demonstrated to cause scan blindness at a fixed frequency for E-plane scanning. Second, another cause for E-plane scan blindness is extended from previous observations, by including the fundamental mode of a half-mode open waveguide. This type of leaky-wave-induced scan blindness is limited to triangular lattices and can occur at lower frequencies compared to other types of leaky-wave blindness. In the second part of this paper, parasitic notches are proposed as an effective measure to significantly improve the E-plane scanning characteristics of the considered array by reducing the magnitude of the leaky modes. As a beneficial side-effect, these parasitic notches are also proven to improve the H-plane scanning characteristics by suppressing resonances within the stripline substrate cavity of the individual tapered-slot elements. Numerical simulations and measurements performed on a 169-element array prototype validate the analysis and confirm the effectiveness of the proposed concept for scan blindness suppression.
Epigenetics-related genes in prostate cancer: Expression profile in prostate cancer tissues, androgen-sensitive and -insensitive cell lines

Epigenetic changes have been suggested to drive prostate cancer (PCa) development and progression. Therefore, in this study, we aimed to identify novel epigenetics-related genes in PCa tissues, and to examine their expression in metastatic PCa cell lines. We analyzed the expression of epigenetics-related genes via a clustering analysis based on gene function in moderately and poorly differentiated PCa glands compared to normal glands of the peripheral zone (prostate proper) from PCa patients using Whole Human Genome Oligo Microarrays. Our analysis identified 12 epigenetics-related genes with a more than 2-fold increase or decrease in expression and a p-value <0.01. In moderately differentiated tumors compared to normal glands of the peripheral zone, we found the genes, TDRD1, IGF2, DICER1, ADARB1, HILS1, GLMN and TRIM27, to be upregulated, whereas TNRC6A and DGCR8 were found to be downregulated. In poorly differentiated tumors, we found TDRD1, ADARB and RBM3 to be upregulated, whereas DGCR8, PIWIL2 and BC069781 were downregulated. Our analysis of the expression level for each gene in the metastatic androgen-sensitive VCaP and LNCaP, and -insensitive PC3 and DU-145 PCa cell lines revealed differences in expression among the cell lines which may reflect the different biological properties of each cell line, and the potential role of each gene at different metastatic sites. The novel epigenetics-related genes that we identified in primary PCa tissues may provide further insight into the role that epigenetic changes play in PCa. Moreover, some of the genes that we identified may play important roles in primary PCa and metastasis, in primary PCa only, or in metastasis only. Follow-up studies are required to investigate the functional role and the role that the expression of these genes play in the outcome and progression of PCa using tissue microarrays.
Incidence of cardiovascular disease and cancer in advanced age: prospective cohort study

Objective To investigate the influence of increasing age on the incidence and remaining lifetime risk of cardiovascular disease and cancer in a cohort of older men. Design Prospective cohort study. Setting United States. Participants 22 048 male doctors aged 40-84 who were free of major disease in 1982. Main outcome measures Incidence and remaining lifetime risk of major cardiovascular disease (myocardial infarction, stroke, and death from cardiovascular disease) and cancer. Results 3252 major cardiovascular events and 5400 incident cancers were confirmed over 23 years of follow-up. The incidence of major cardiovascular disease continued to increase to age 100. Beginning at age 80, however, major cardiovascular disease was more likely to be diagnosed at death. The incidence of cancer peaked in those aged 80-89 and then declined. Cancers detected by screening accounted for most of the decline, whereas most cancers for which there was no screening continued to increase to age 100. Unadjusted cumulative incidence overestimated the risk of cardiovascular disease by 16% and cancer by 8.5%. The remaining lifetime risk of cancer at age 40 was 45.1% (95% confidence interval 43.8% to 46.3%) and at age 90 was 9.6% (7.2% to 11.9%). The remaining lifetime risk of major cardiovascular disease at age 40 was 34.8% (33.1% to 36.5%) and at age 90 was 16.7% (12.9% to 20.6%). Conclusions In this prospective cohort of men, the incidence of new cardiovascular disease continued to increase after age 80 but was most often diagnosed at death. The decrease in incidence of cancer late in life seemed largely due to a decline in cancers usually detected by screening. These findings suggest that people aged 80 and older have a substantial amount of undiagnosed disease. The remaining lifetime risk of both diseases approached a plateau in the 10th decade. This may be due to decreased detection of disease and reporting of symptoms and increased resistance to disease in those who survive to old age. Accurate estimates of disease risk in an aging population require adjustment for competing risks of mortality.
The Polymodal Ion Channel Transient Receptor Potential Vanilloid 4 Modulates Calcium Flux, Spiking Rate, and Apoptosis of Mouse Retinal Ganglion Cells

Sustained increase in intraocular pressure represents a major risk factor for eye disease, yet the cellular mechanisms of pressure transduction in the posterior eye are essentially unknown. Here we show that the mouse retina expresses mRNA and protein for the polymodal transient receptor potential vanilloid 4 (TRPV4) cation channel known to mediate osmotransduction and mechanotransduction. TRPV4 antibodies labeled perikarya, axons, and dendrites of retinal ganglion cells (RGCs) and intensely immunostained the optic nerve head. Müller glial cells, but not retinal astrocytes or microglia, also expressed TRPV4 immunoreactivity. The selective TRPV4 agonists 4α-PDD and GSK1016790A elevated [Ca2+]i in dissociated RGCs in a dose-dependent manner, whereas the TRPV1 agonist capsaicin had no effect on [Ca2+]RGC. Exposure to hypotonic stimulation evoked robust increases in [Ca2+]RGC. RGC responses to TRPV4-selective agonists and hypotonic stimulation were absent in Ca2+-free saline and were antagonized by the nonselective TRP channel antagonists Ruthenium Red and gadolinium, but were unaffected by the TRPV1 antagonist capsazepine. TRPV4-selective agonists increased the spiking frequency recorded from intact retinas recorded with multielectrode arrays. Sustained exposure to TRPV4 agonists evoked dose-dependent apoptosis of RGCs. Our results demonstrate functional TRPV4 expression in RGCs and suggest that its activation mediates response to membrane stretch leading to elevated [Ca2+]i and augmented excitability. Excessive Ca2+ influx through TRPV4 predisposes RGCs to activation of Ca2+-dependent proapoptotic signaling pathways, indicating that TRPV4 is a component of the response mechanism to pathological elevations of intraocular pressure.
COSMOLOGY WITH STRONG-LENSING SYSTEMS

In this paper, we assemble a catalog of 118 strong gravitational lensing systems from the Sloan Lens ACS Survey, BOSS emission-line lens survey, Lens Structure and Dynamics, and Strong Lensing Legacy Survey and use them to constrain the cosmic equation of state. In particular, we consider two cases of dark energy phenomenology: the XCDM model, where dark energy is modeled by a fluid with constant w equation-of-state parameter, and in the Chevalier–Polarski–Linder (CPL) parameterization, where w is allowed to evolve with redshift, w ( z ) = w 0 + w 1 z 1 + z ? > . We assume spherically symmetric mass distribution in lensing galaxies, but we relax the rigid assumption of the SIS model in favor of a more general power-law index γ, also allowing it to evolve with redshifts γ ( z ) ? > . Our results for the XCDM cosmology show agreement with values (concerning both w and γ parameters) obtained by other authors. We go further and constrain the CPL parameters jointly with γ ( z ) ? > . The resulting confidence regions for the parameters are much better than those obtained with a similar method in the past. They are also showing a trend of being complementary to the Type Ia supernova data. Our analysis demonstrates that strong gravitational lensing systems can be used to probe cosmological parameters like the cosmic equation of state for dark energy. Moreover, they have a potential to judge whether the cosmic equation of state evolved with time or not.
Birth Weight, Postnatal Weight Gain, and Childhood Adiposity in Relation to Lipid Profile and Blood Pressure During Early Adolescence

Background Different pathways likely underlie the association between early weight gain and cardiovascular disease risk. We examined whether birth weight for length relationship and weight gain up to 2 years of age are associated with lipid profiles and blood pressure (BP) in early adolescence and determined whether childhood adiposity mediates these associations. Methods and Results Data from QUALITY (Quebec Adipose and Lifestyle Investigation in Youth), a cohort of white children with parental history of obesity, were analyzed (n=395). Sex‐specific weight for length z scores from birth to 2 years were computed. Rate of postnatal weight gain was estimated using individual slopes of weight for length z‐score measurements. Percentage of body fat was measured at 8 to 10 years. Fasting lipids and BP were measured at 10 to 12 years. Using path analysis, we found indirect effects of postnatal weight gain, through childhood adiposity, on all outcomes: Rate of postnatal weight for length gain was positively associated with childhood adiposity, which in turn was associated with unfavorable lipid and BP levels in early adolescence. In contrast, small beneficial direct effects on diastolic BP z scores, independent of weight at other time points, were found for birth weight for length (β=−0.05, 95% CI, −0.09 to −0.002) and for postnatal weight gain (β=−0.02, 95% CI, −0.03 to −0.002). Conclusions Among children with at least 1 obese parent, faster postnatal weight gain leads to cardiovascular risk factors in early adolescence through its effect on childhood adiposity. Although heavier newborns may have lower BP in early adolescence, this protective direct effect could be offset by a deleterious indirect effect linking birth weight to later adiposity.
evelopment and evaluation of a nutrient cycling extension for the LANDIS-II andscape simulation model

Long-term nutrient cycling dynamics are the result of interactions between forest succession, disturbance, nutrient cycling, and other forest processes. We developed NuCycling-Succession, a simple nutrient cycling and succession extension for the LANDIS-II landscape model of forest dynamics, to examine the interactions between these forest processes in order to develop more realistic predictions of forest response to management practices and global change. NuCycling-Succession models carbon, nitrogen, and phosphorus nutrient fluxes and masses associated with the living biomass, dead biomass, soil organic matter, soil mineral N and P, charcoal, and bedrock nutrient pools. It includes direct effects of disturbance events on nutrient cycling as well as indirect effects mediated through changes in forest composition and structure. NuCycling-Succession represents the continuum of decomposition and associated changes in chemistry using annual cohorts of leaf and fine root litter. This formulation includes the interaction of decomposition dynamics with disturbances that affect the forest floor, such as fire. Evaluation of model utrient cycling results relative to field data and results reported in the literature indicate the model adequately represents nutrient pools and fluxes. We present a case study of the effects of changing fire and biomass harvesting regimes on nutrient cycling in the Lake Tahoe Basin. Model results suggest that fire exclusion has resulted in substantially increased mass of nutrient pools. The NuCycling-Succession extension provides a useful simulation framework for exploring how global change factors (climate change, altered disturbance regimes) may influence nutrient cycling processes and nutrient budgets in forested ecosystems.
Xanthine oxidase inhibitory activity of the methanolic extracts of selected Jordanian medicinal plants

Background: The search for novel xanthine oxidase (XO) inhibitors with a higher therapeutic activity and fewer side effects are desired not only to treat gout but also to combat various other diseases associated with the XO activity. At present, the potential of developing successful natural products for the management of XO-related diseases is still largely unexplored. In the present study, we have screened the methanolic extracts of various Jordanian medicinal plants for their XO inhibitory activities using an optimized protocol. Materials and Methods: The methanolic extracts of 23 medicinal plants, belonging to 12 families, were tested in vitro, at 200 μg/ml concentrations, for their XO inhibitory potential. The dose-dependent inhibition profiles of the most active plants were further evaluated by estimating the IC50 values of their corresponding extracts. Results: Six plants were found most active (% inhibition more than 39%). These plants are Salvia spinosa L. (IC50 = 53.7 μg/ml), Anthemis palestina Boiss. (168.0 μg/ml), Chrysanthemum coronarium L. (199.5 μg/ml), Achillea biebersteinii Afansiev (360.0 μg/ml), Rosmarinus officinalis L. (650.0 μg/ml), and Ginkgo biloba L. (595.8 μg/ml). Moreover, four more plants, namely Lavandula angustifolia Mill. (28.7% inhibition), Helianthemum ledifolium (L.) Mill. (28.4%), Majorana syriaca (L.) Kostel. (25.1%), and Mentha spicata L. (22.5%) showed a XO inhibitory activity in the range of 22–30%. Conclusion: The study showed that many of the tested plant species are potential sources of natural XO inhibitors that can be developed, upon further investigation, into successful herbal drugs for treatment of gout and other XO-related disorders.