Miracle-dz/UniFAR-FTUs huggingface dataset:
Fibronectin‐bound TNF‐α stimulates monocyte matrix metalloproteinase‐9 expression and regulates chemotaxis

Tumor necrosis factor α (TNF‐α) is a proinflammatory cytokine implicated in the stimulation of matrix metalloproteinase (MMP) production by several cell types. Our previous studies demonstrated that TNF‐α avidly binds fibronectin (FN) and laminin, major adhesive glycoproteins of extracellular matrix (ECM) and basement membranes. These findings suggested that TNF‐α complexing to insoluble ECM components may serve to concentrate its activities to distinct inflamed sites. Herein, we explored the bioactivity and possible function of ECM‐bound TNF‐α by examining its effects on MMP‐9 secretion by monocytes. Immunofluorescent staining indicated that LPS‐activated monocytes deposited newly synthesized TNF‐α into ECM‐FN. FN‐bound TNF‐α (FN/TNF‐α) significantly up‐regulated MMP‐9 expression and secretion by the human monocytic cell line MonoMac‐6 and peripheral blood monocytes. Such secretion could be inhibited by antibodies that block TNF‐α activity and binding to its receptors TNF RI (p55) and TNF RII (p75). Chemotaxis through ECM gels in the presence of soluble or bound TNF‐α was inhibited by a hydroxamic acid inhibitor of MMPs (GM6001). It is interesting that, although the adhesion of MonoMac‐6 cells to FN/TNF‐α required functional activated β1 integrins, FN/TNF‐α‐induced MMP‐9 secretion was independent of binding to β1 integrins, since MMP‐9 secretion was unaffected by: (1) neutralizing mAb to α4, α5, and β1 subunits, which blocked cell adhesion; (2) a mAb that stimulated β1 integrin‐mediated adhesion; and (3) binding TNF‐α to the 30‐kDa amino‐terminal fragment of FN, which lacks the major cell adhesive binding sites. Thus, in addition to their cell‐adhesive roles, ECM glycoproteins, such as FN, may play a pivotal role in presenting proinflammatory cytokines to leukocytes within the actual inflamed tissue, thereby affecting their capacities to secrete ECM‐degrading enzymes. These TNF‐α‐ECM interactions may serve to limit the cytokine’s availability and bioactivity to target areas of inflammation.
Association of Cerebral Small Vessel Disease Burden and Health-Related Quality of Life after Acute Ischemic Stroke

Objective: Cerebral small vessel disease (SVD) is associated with increased mortality, disability and cognitive decline, depression in stroke survivors. This study examined the association between SVD burden, defined by a combination of SVD markers, and health-related quality of life (HRQoL) in acute ischemic stroke. Methods: Patients admitted with acute ischemic stroke of any etiology were prospectively screened between January 2010 to December 2014 and enrolled in the study if they met study entry criteria. HRQoL was evaluated with the 12-item Stroke Specific Quality of Life (SSQoL) at 3 months after the onset of acute ischemic stroke. SVD was ascertained by the presence of any of the SVD markers including lacune, white matter hyperintensities (WMH), cerebral microbleeds (CMB) and enlarged perivascular spaces (EPVS) in the basal ganglia or their combinations on brain magnetic resonance imaging (MRI). The presence of each individual marker scored 1 point and was summed up to generate an ordinal “SVD score” (0–4) capturing total SVD burden. Linear regression was used to determine the associations between SVD burden and HRQoL. Results: Of the743 acute ischemic stroke patients that formed he study sample (mean age: 66.3 ± 10.6 years; 41.7% women), 49.3%, 22.5%, 16.0%, 9.2% and 3.1% had SVD scores of 0, 1, 2, 3 and 4, respectively. After adjusting for demographic, clinical and imaging variables, the SVD score was independently associated with lower overall score of SSQoL (B = −1.39, SE = 0.56, p = 0.01), and its domains of mobility (B = −0.41, SE = 0.10, p < 0.001) and vision (B = −0.12, SE = 0.06, p = 0.03). Acute infract volume (B = −1.44, SE = 0.54, p = 0.01), functional independence (B = 5.69, SE = 0.34, p < 0.001) and anxious (B = −1.13, SE = 0.23, p < 0.001) and depressive symptoms (B = −3.41, SE = 0.22, p < 0.001) were also the significant predictors of the overall score of SSQoL. Conclusion: The brain’s SVD burden predicts lower HRQoL, predominantly in domains of mobility and vision at 3 months after acute ischemic stroke. The evaluation of SVD burden could facilitate developing individual treatment strategies.
Long-term Impact of a “3 + 0” Schedule for 7- and 13-Valent Pneumococcal Conjugate Vaccines on Invasive Pneumococcal Disease in Australia, 2002–2014

Background. Australia introduced universal 7-valent pneumococcal conjugate vaccine (PCV7) from 2005, replaced by 13-valent PCV (PCV13) in 2011, uniquely among high-income countries giving doses at 2, 4, and 6 months (3 + 0 schedule). Data on impact of a timely 3 + 0 PCV schedule with high coverage are sparse, with none for PCV13. Methods. We used national surveillance of invasive pneumococcal disease (IPD) from 2002 for baseline and appropriate later comparison periods to calculate incidence rate ratios (IRRs) by serotype and age using a Poisson model. PCV coverage was assessed from the Australian Childhood Immunisation Register. Results. After 9 years of timely 3-dose PCV coverage of >92%, all-age IPD in Australia almost halved (IRR, 0.53; 95% confidence interval [CI], .50–.57), but differed by PCV era. Reductions in IPD due to vaccine serotypes from PCV7 (IRR, 0.20; CI, .17–.22) were about 2-fold greater than for IPD due to extra serotypes in PCV13 (13v-non7v) in a similar period (IRR, 0.58; CI, .51–.66). Post-PCV13 declines in serotype 19A IPD in persons aged <2 years (IRR, 0.23; CI, .13–.35) and ≥2 years (IRR, 0.35; CI, .28–.44) differed from other 13v-non7v IPD (IRR, 0.73; CI, .35–1.48 for those aged <2 years and IRR, 0.96; CI, .81–1.15 for those ≥2 years). Meningitis due to vaccine serotypes nearly disappeared in children eligible for 3 PCV13 doses. IPD due to non-PCV13 serotypes increased by 30% compared with 76% for non-PCV7 serotypes in equivalent period of vaccine use. Conclusions. Reductions in vaccine-type IPD post-PCV13 were inferior to Australian experience with PCV7 and reports from high-income countries giving a PCV booster dose. Applicability of findings to other settings would depend on age of IPD onset, serotype profile, and timeliness of vaccination.
Application of Visible and Near-Infrared Hyperspectral Imaging to Determine Soluble Protein Content in Oilseed Rape Leaves

Visible and near-infrared hyperspectral imaging covering spectral range of 380–1030 nm as a rapid and non-destructive method was applied to estimate the soluble protein content of oilseed rape leaves. Average spectrum (500–900 nm) of the region of interest (ROI) of each sample was extracted, and four samples out of 128 samples were defined as outliers by Monte Carlo-partial least squares (MCPLS). Partial least squares (PLS) model using full spectra obtained dependable performance with the correlation coefficient (rp) of 0.9441, root mean square error of prediction (RMSEP) of 0.1658 mg/g and residual prediction deviation (RPD) of 2.98. The weighted regression coefficient (Bw), successive projections algorithm (SPA) and genetic algorithm-partial least squares (GAPLS) selected 18, 15, and 16 sensitive wavelengths, respectively. SPA-PLS model obtained the best performance with rp of 0.9554, RMSEP of 0.1538 mg/g and RPD of 3.25. Distribution of protein content within the rape leaves were visualized and mapped on the basis of the SPA-PLS model. The overall results indicated that hyperspectral imaging could be used to determine and visualize the soluble protein content of rape leaves.
Topological correlations of structural and functional networks in patients with traumatic brain injury

Despite an increasing amount of specific correlation studies between structural and functional connectivity, there is still a need for combined studies, especially in pathological conditions. Impairments of brain white matter (WM) and diffuse axonal injuries are commonly suspected to be responsible for the disconnection hypothesis in traumatic brain injury (TBI) patients. Moreover, our previous research on TBI patients shows a strong relationship between abnormalities in topological organization of brain networks and behavioral deficits. In this study, we combined task-related functional connectivity (using event-related fMRI) with structural connectivity (derived from fiber tractography using diffusion MRI data) estimates in the same participants (17 adults with TBI and 16 controls), allowing for direct comparison between graph metrics of the different imaging modalities. Connectivity matrices were computed covering the switching motor network, which includes the basal ganglia, anterior cingulate cortex/supplementary motor area, and anterior insula/inferior frontal gyrus. The edges constituting this network consisted of the partial correlations between the fMRI time series from each node of the switching motor network. The interregional anatomical connections between the switching-related areas were determined using the fiber tractography results. We found that graph metrics and hubs obtained showed no agreement in both groups. The topological properties of brain functional networks could not be solely accounted for by the properties of the underlying structural networks. However, combining complementary information from both imaging modalities could improve accuracy in prediction of switching performance. Direct comparison between functional task-related and anatomical structural connectivity, presented here for the first time in TBI patients, links two powerful approaches to map the patterns of brain connectivity that may underlie behavioral deficits in brain-injured patients.
Construction and validation of anisotropic and orthotropic ventricular geometries for quantitative predictive cardiac electrophysiology

Reaction–diffusion computational models of cardiac electrophysiology require both dynamic excitation models that reconstruct the action potentials of myocytes as well as datasets of cardiac geometry and architecture that provide the electrical diffusion tensor D, which determines how excitation spreads through the tissue. We illustrate an experimental pipeline we have developed in our laboratories for constructing and validating such datasets. The tensor D changes with location in the myocardium, and is determined by tissue architecture. Diffusion tensor magnetic resonance imaging (DT-MRI) provides three eigenvectors ei and eigenvalues λi at each voxel throughout the tissue that can be used to reconstruct this architecture. The primary eigenvector e1 is a histologically validated measure of myocyte orientation (responsible for anisotropic propagation). The secondary and tertiary eigenvectors (e2 and e3) specify the directions of any orthotropic structure if λ2 is significantly greater than λ3—this orthotropy has been identified with sheets or cleavage planes. For simulations, the components of D are scaled in the fibre and cross-fibre directions for anisotropic simulations (or fibre, sheet and sheet normal directions for orthotropic tissues) so that simulated conduction velocities match values from optical imaging or plunge electrode experiments. The simulated pattern of propagation of action potentials in the models is partially validated by optical recordings of spatio-temporal activity on the surfaces of hearts. We also describe several techniques that enhance components of the pipeline, or that allow the pipeline to be applied to different areas of research: Q ball imaging provides evidence for multi-modal orientation distributions within a fraction of voxels, infarcts can be identified by changes in the anisotropic structure—irregularity in myocyte orientation and a decrease in fractional anisotropy, clinical imaging provides human ventricular geometry and can identify ischaemic and infarcted regions, and simulations in human geometries examine the roles of anisotropic and orthotropic architecture in the initiation of arrhythmias.
Association of Earthworm-Denitrifier Interactions with Increased Emission of Nitrous Oxide from Soil Mesocosms Amended with Crop Residue

ABSTRACT Earthworm activity is known to increase emissions of nitrous oxide (N2O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N2O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N2O emissions from the soil. We set up a 90-day mesocosm experiment in which 15N-labeled maize (Zea mays L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm Lumbricus rubellus and/or the endogeic earthworm Aporrectodea caliginosa. We measured N2O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes nirS and nosZ through real-time quantitative PCR. Compared to the control, L. rubellus increased denitrification enzyme activity and N2O emissions on days 21 and 90 (day 21, P = 0.034 and P = 0.002, respectively; day 90, P = 0.001 and P = 0.007, respectively), as well as cumulative N2O emissions (76%; P = 0.014). A. caliginosa activity led to a transient increase of N2O emissions on days 8 to 18 of the experiment. Abundance of nosZ was significantly increased (100%) on day 90 in the treatment mixture containing L. rubellus alone. We conclude that L. rubellus increased cumulative N2O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source.
Magnetic and mechanical characterisation of natural rubber coprecipitated barium ferrite composites at high loading

The influence of coprecipitated barium ferrite (BaF) on the magnetic and mechanical properties of natural rubber–ferrite composites (RFCs) has been studied. Unusual characteristics of the BaF particles were revealed by a scanning electron microscope. The results show that the saturation magnetisation increases with increasing the ferrite content even for the considerably high BaF loading samples, whereas the coercivity is almost unchanged. The present RFCs recorded relatively low density 1·95 g cm−3 with high stored energy 1·26 MGOe at the maximum BaF loading of 220 phr. Both of the tensile strength and the elongation at break decrease with increasing BaF content. Evaluation of the swelling ratio was carried out to have an insight into the change in the mechanical properties of the RFCs at high BaF loading.
The effect of molecular architecture on the properties of propylene impact copolymers

Impact polypropylene copolymers (IPPC) are important commercial materials, but their morphology and molecular architecture are not yet fully understood. In this study the focus was on selectively removing specific fractions from the original IPPC, recombining the remaining fractions, and studying the properties of these recombined polymers. It was found that some properties of the samples changed remarkably, depending on the fraction of material that was removed before recombination. For example, the degree of phase separation and the crystalline morphology of the recombined materials varied noticeably. During the study an effective way of staining samples for transmission electron microscopy (TEM) was developed. Furthermore, a comparison of fourier transform infrared spectroscopy (FTIR), with TEM and scanning electron microscopy (SEM) results, revealed a hitherto unreported relationship between phase separation. Absorption bands appeared at 1100 cm and 1080 cm in the FTIR spectra and appear to be an indication of phase separation. It was further established that specific copolymer fractions present in the original polymer affect not only the morphology of the final polymer, but also the hardness and impact resistance.
Maturation of transmission in reinnervated mouse soleus muscle

After the tibial nerve of the mouse was cut unilaterally and immediately resutured, reinnervation of soleus muscle proceeded rapidly and muscle isometric contraction characteristics reached normal levels within 2 months. In contrast, synaptic transmission remained immature since resistance to presynaptic (magnesium) or postsynaptic (curare) blocking solutions remained reduced. Results suggest that release probability and transmitter stores were smaller than normal. To study the effect of training, animals were allowed to run in wheels. Running caused a delay in reinnervation at 18–20 days, which was, however, abolished by 4 weeks. On the other hand, exercise counteracted development of denervation atrophy. The safety margin of transmission in runners was higher than in nonrunners at 4 weeks, indicating enhanced maturation, but was lower at 2 months of reinnervation. These results suggest that recovery of muscle precedes maturation of synaptic transmission.
Working memory impairment as a common component in recurrent depressive disorder and certain somatic diseases.

OBJECTIVES Deterioration of the working memory is regarded as one of the most important deficits in a number of somatic diseases. The purpose of the present study was to compare the effectiveness of working memory in 4 groups of patients: 1) diagnosed with recurrent depressive disorder (rDD), 2) with diabetes type 1 (DM1), 3) with diabetes type 2 (DM2), 4) with arterial hypertension (HA) and in healthy controls (HC). METHODS The study comprised 300 subjects: rDD (n=99), DM1 (n=31), DM2 (n=31), HA (n=30) and HC (n=109). Cognitive function assessment was based on Trail Making Test (TMT) and the Stroop test. RESULTS Analysis of variance (ANOVA) indicated statistically significant differences of the mean values among particular groups for each of the analysed results of the Stroop Test and TMT (p<0.0001). Patients with DM1 performed better in both TMT and Stroop tests, when compared to those diagnosed with HA. Patients with HA obtained better results than patients with DM2. Patients with rDD performed significantly worse than those with DM1 in both parts of TMT (A/time: p=0.022, B/time: p<0.001) and in the Stroop test (RCNb/time: p<0.001; NCWd/time: p=0.001; NCWd/errors: p=0.443). They also obtained worse results than patients with DM2 and HA, however, the differences were not statistically significant. CONCLUSIONS 1) Our study has confirmed previous results showing association between depressive disorder and cognitive impairment. 2) Patients with rDD had worse performance on working memory tasks than the patients with DM type 1, DM type 2 and HA. 3) Further investigation is needed to clarify the role of inflammatory and oxidative and nitrosative stress (O&NS) processes in neurocognitive dysfunctions occurring in recurrent depression and somatic disease.
Strong assortative mating between allopatric sticklebacks as a by-product of adaptation to different environments

Speciation involves the evolution of reproductive isolation between populations. One potentially important mechanism is the evolution of pre- or postzygotic isolation between populations as a by-product of adaptation to different environments. In this paper, we tested for assortative mating between allopatric stickleback populations adapted to different ecological niches. Our experimental design controlled for interpopulation interactions and non-adaptive explanations for assortative mating. We found that prezygotic isolation was surprisingly strong: when given a choice, the majority of matings occurred between individuals from similar environments. Our results indicate that the by-product mechanism is a potent source of reproductive isolation, and likely contributed to the origin of sympatric species of sticklebacks.
Hippocampal episode fields develop with learning

Several recent studies have shown that hippocampal neurons fire during the delay period in between trials and that these firing patterns differ when different behaviors are required, suggesting that the neuronal responses may be involved in maintaining the memories needed for the upcoming trial. In particular, one study found that hippocampal neurons reliably fired at particular times, referred to as “episode fields” (EFs), during the delay period of a spatial alternation task (Pastalkova et al. ( 2008 ) Science 321:1322–1327). The firing of these neurons resulted in distinct sequential firing patterns on left and right turn trials, and these firing patterns could be used to predict the upcoming behavioral response. In this study, we examined neuronal firing during the delay period of a hippocampus‐dependent plus maze task, which involved learning to approach two different reward locations (east and west), and we examined the development of these firing patterns with learning. As in the previous study, hippocampal neurons exhibited discrete periods of elevated firing during the delay (EFs) and the firing patterns were distinct on the east and west trials. Moreover, these firing patterns emerged and began to differentiate the east and west conditions during the first training session and continued to develop as the rats learned the task. The finding of similar firing patterns in different tasks suggests that the EFs are a robust phenomenon, which may occur whenever subjects must maintain distinct memory representations during a delay period. Additionally, in the previous study (Pastalkova et al. ( 2008 ) Science 321:1322–1327), the distinct firing patterns could have been due to the differing goal locations, behavioral responses (left or right turns), or trajectories. In this study, neuronal firing varied with the goal location regardless of the trajectories or responses, suggesting that the firing patterns encode the behavioral context rather than specific behaviors. ©2010 Wiley Periodicals, Inc.