Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of the Extracellular Matrix Molecule Thrombospondin 1 and Its Pericellular Association in the Brain Using a Semiautomated Computerized Approach

The structure and functions of the extracellular matrix (ECM), its spatial distribution and pericellular association of ECM molecules remain poorly understood. Colocalization of ECM molecules with cell phenotypes through immunohistochemistry can provide crucial insights into their juxtacrine signaling role as well as their structural relevance to tissue architecture. As manual quantification of images introduces intra- and inter-user bias and is cumbersome for high-throughput approaches, we implemented an automated high-throughput method to quantify the spatial distribution and cellular association of one ECM molecule, thrombospondin 1 (TSP1) with two major cell phenotypes, neurons, and astrocytes. The distribution of TSP1 was homogeneous throughout the striatum and cortex along the anterior–posterior axis. TSP1 occupied 8.85% of the striatum and 7.40% in the cortex. TSP1 also associated with 94.58% and 88.45% of neurons in the striatum and cortex. The association with astrocytes was significantly lower at 47.55% and 28.09%. These findings highlight the key role that TSP1 plays in neuron physiology in a healthy brain, but also highlights key regional difference in astrocytes secreting ECM molecules. The semiautomated approach implemented here will improve the throughput and reliability of measuring the distribution and cellular colocalization of ECM molecules.
131I SPECT/CT in the follow-up of patients with differentiated thyroid carcinoma.

PURPOSE 131I SPECT/Spiral-CT has been shown to be superior to planar imaging in staging of differentiated thyroid carcinoma (DTC) at first radioablation. The purpose of this study was to investigate whether this is also true in the further follow-up of patients with DTC. METHODS From our clinical database, all patients with DTC who underwent planar scintigraphy as well as SPECT/low-dose spiral CT during follow-up between June 2005 and August 2010 were selected. Iodine-positive foci on the planar images as well as on the SPECT/CT data sets were classified as benign or equivocal/malignant. The criterion standard was provided by histology, other imaging modalities, and clinical and serological follow-up of at least 6 months. RESULTS A total of 123 patients with altogether 139 studies met the selection criteria. Whereas the sensitivities of SPECT/CT and planar imaging did not differ significantly (both 62%), the specificity of SPECT/CT was significantly higher than that of planar imaging (98 vs 78%, P < 0.01). SPECT/CT yielded a gain in diagnostic information in 20 (16.3%) of 123 patients (95% confidence interval, 10.8%-23.8%). Hybrid imaging led to a change of diagnosis in none of the patients in whom planar imaging result was normal, in 16% of patients with foci in the neck, and in 26% of patients with extracervical foci. CONCLUSIONS In the follow-up of patients with DTC, SPECT/CT significantly improves specificity compared with planar imaging. Incremental diagnostic value is higher in lesions outside the neck than in those in the neck and absent in patients without iodine-positive foci on planar imaging.
Blood flow restricted and traditional resistance training performed to fatigue produce equal muscle hypertrophy

This study investigated the hypertrophic potential of load‐matched blood‐flow restricted resistance training (BFR) vs free‐flow traditional resistance training (low‐load TRT) performed to fatigue. Ten healthy young subjects performed unilateral BFR and contralateral low‐load TRT elbow flexor dumbbell curl with 40% of one repetition maximum until volitional concentric failure 3 days per week for 6 weeks. Prior to and at 3 (post‐3) and 10 (post‐10) days post‐training, magnetic resonance imaging (MRI) was used to estimate elbow flexor muscle volume and muscle water content accumulation through training. Acute changes in muscle thickness following an early vs a late exercise bout were measured with ultrasound to determine muscle swelling during the immediate 0–48 h post‐exercise. Total work was threefold lower for BFR compared with low‐load TRT (P < 0.001). Both BRF and low‐load TRT increased muscle volume by approximately 12% at post‐3 and post‐10 (P < 0.01) with no changes in MRI‐determined water content. Training increased muscle thickness during the immediate 48 h post‐exercise (P < 0.001) and to greater extent with BRF (P < 0.05) in the early training phase. In conclusion, BFR and low‐load TRT, when performed to fatigue, produce equal muscle hypertrophy, which may partly rely on transient exercise‐induced increases in muscle water content.
A comprehensive analysis of TCP congestion control schemes in wireless mesh networks

TCP is the standard transport protocol for reliable data communication over the internet. However, TCP behaviour over wireless mesh networks encounters random losses due to channel errors, changing topology and node distance. This paper aims to perform a comparison of TCP Old Tahoe and Tahoe in wireless mesh networks and analyze the throughput, propagation delay, packets retransmitted and number of duplicate acknowledgements received for varying node densities. The anomalous behaviour of TCP in the wireless network is documented, and probable explanations are provided. A comparison of the most suitable variant for each case is concluded. Overall, Tahoe shows 52% lower average throughput and 14% lower delay as compared to Old Tahoe. TCP Old Tahoe appears to be more suitable for lower density networks, whereas TCP Tahoe gives better results for higher density networks.
Purified vesicles of tobacco cell vacuolar and plasma membranes exhibit dramatically different water permeability and water channel activity.

The vacuolar membrane or tonoplast (TP) and the plasma membrane (PM) of tobacco suspension cells were purified by free-flow electrophoresis (FFE) and aqueous two-phase partitioning, with enrichment factors from a crude microsomal fraction of >/=4- to 5-fold and reduced contamination by other cellular membranes. For each purified fraction, the mean apparent diameter of membrane vesicles was determined by freeze-fracture electron microscopy, and the osmotic shrinking kinetics of the vesicles were characterized by stopped-flow light scattering. Osmotic water permeability coefficients (Pf) of 6.1 +/- 0.2 and 7.6 +/- 0.9 microm . s(-1) were deduced for PM-enriched vesicles purified by FFE and phase partitioning, respectively. The associated activation energies (Ea; 13.7 +/- 1.0 and 13.4 +/- 1.4 kcal . mol(-1), respectively) suggest that water transport in the purified PM occurs mostly by diffusion across the lipid matrix. In contrast, water transport in TP vesicles purified by FFE was characterized by (i) a 100-fold higher Pf of 690 +/- 35 microm . s(-1), (ii) a reduced Ea of 2.5 +/- 1.3 kcal . mol(-1), and (iii) a reversible inhibition by mercuric chloride, up to 83% at 1 mM. These results provide functional evidence for channel-mediated water transport in the TP, and more generally in a higher plant membrane. A high TP Pf suggests a role for the vacuole in buffering osmotic fluctuations occurring in the cytoplasm. Thus, the differential water permeabilities and water channel activities observed in the tobacco TP and PM point to an original osmoregulatory function for water channels in relation to the typical compartmentation of plant cells.
Self- versus physician-collected samples for the follow-up of human papillomavirus-positive women in sub-Saharan Africa

Introduction Human papillomavirus (HPV) testing is a suitable tool for primary cervical cancer (CC) screening and follow-up in low-resource settings. Vaginal samples taken by women themselves (Self-HPV) are an interesting alternative to physician-performed sampling (Dr-HPV). Our aim was to assess the performance of Self-HPV and Dr-HPV at 6 and 12 months following a CC screening campaign. Methods This study was carried out at the Dschang District Hospital, Cameroon. Women aged 30–49 years were recruited in a CC screening campaign. HPV-positive women, of whom 2/3 were treated with thermoablation because of abnormal results at baseline screening, were invited to participate in a follow-up study. Self- and Dr-HPV, as well as cytology, were performed at 6 and 12 months. HPV samples were analyzed using the Xpert HPV assay. Sensitivity and specificity for the detection of low-grade squamous intraepithelial lesion or worse and of high-grade squamous intraepithelial lesion or worse were calculated for Self-HPV and Dr-HPV, using cytology as the reference diagnosis. Results Overall, 188 HPV-positive women were invited to attend follow-up. The obtained follow-up visits’ attendance was 154 (81.9%) and 131 (69.7%) at 6 and 12 months, respectively. While the overall performance of Dr-HPV at 6 months was slightly superior, Self-HPV showed an improved sensitivity for HSIL+ detection at 12 months when compared with Dr-HPV (83.3% [95% CI 41.8–98.9] versus 71.4% [95% CI 21.5–95.8], respectively). The overall HPV positivity agreement between Self- and Dr-HPV at 6 and 12 months corresponded to a κ value of 0.62 and 0.52, respectively. Among women treated with thermoablation (n=121) at baseline screening, Self-HPV was as sensitive as Dr-HPV, although less specific (P=0.003). Conclusion Self-HPV is a valuable tool for the follow-up of HPV-positive women in low-resource settings. Larger, randomized trials are needed to confirm the validity of our findings.
Fault-tolerant valve-based microfluidic routing fabric for droplet barcoding in single-cell analysis

High-throughput single-cell genomics is used to gain insights into diseases such as cancer. Motivated by this important application, microfluidics has emerged as a key technology for developing comprehensive biochemical procedures for studying DNA, RNA, proteins, and many other cellular components. Recently, a hybrid microfluidic platform has been proposed to efficiently automate the analysis of a heterogeneous sequence of cells. In this design, a valve-based routing fabric based on transposers is used to label/barcode the target cells. However, the design proposed in prior work overlooked defects that are likely to occur during chip fabrication and system integration. We address the above limitation by investigating the fault tolerance of the valve-based routing fabric. We develop a theory of failure assessment and introduce a design technique for achieving fault tolerance. Simulation results show that the proposed method leads to a slight increase in the fabric size and decrease in cell-analysis throughput, but this is only a small price to pay for the added assurance of fault tolerance in the new design.
Immunization with pVAXhsp65 Decreases Inflammation and Modulates Immune Response in Experimental Encephalomyelitis

Background: A DNA vaccine (pVAXhsp65) containing the gene of a heat-shock protein (hsp65) from Mycobacterium leprae showed high immunogenicity and protective efficacy against tuberculosis in BALB/c mice. A possible deleterious effect related to autoimmunity needed to be tested because hsp65 is highly homologous to the correspondent mammalian protein. In this investigation we tested the effect of a previous immunization with DNAhsp65 in the development of experimental autoimmune encephalomyelitis (EAE), a rat model of multiple sclerosis. Methods: Female Lewis rats were immunized with 3 pVAXhsp65 doses by intramuscular route. Fifteen days after the last DNA dose the animals were evaluated for specific immunity or submitted to induction of EAE. Animals were evaluated daily for weight loss and clinical score, and euthanized during the recovery phase to assess the immune response and inflammatory infiltration at the central nervous system. Results: Immunization with pVAXhsp65 induced a specific immune response characterized by production of IgG2b anti-hsp65 antibodies and IFN-γ secretion. Previous immunization with pVAXhsp65 did not change EAE clinical manifestations (weight and clinical score). However, the vaccine clearly decreased brain and lumbar spinal cord inflammation. In addition, it downmodulated IFN-γ and IL-10 production by peripheral lymphoid organs. Conclusion: Our data demonstrated that this vaccine does not trigger a deleterious effect on EAE development and also points to a potential protective effect.
2016 Ieee International Conference on Big Data (big Data) Text Mining and Sentiment Extraction in Central Bank Documents

—The deep transformation induced by the World Wide Web (WWW) revolution has thoroughly impacted a relevant part of the social interactions in our present global society. The huge amount of unstructured information available on blogs, forum and public institution web sites puts forward different challenges and opportunities. Starting from these considerations, in this paper we pursue a twofold goal. Firstly we review some of the main methodologies employed in text mining and for the extraction of sentiment and emotions from textual sources. Secondly we provide an empirical application by considering the latest 20 issues of the Bank of Italy Governor's concluding remarks from 1996 to 2015. By taking advantage of the open source software package R, we show the following: 1) checking the word frequency distribution features of the documents; 2) extracting the evolution of the sentiment and the polarity orientation in the texts; 3) evaluating the evolution of an index for the readability and the formality level of the texts; 4) attempting to measure the popularity gained from the documents in the web. The results of the empirical analysis show the feasibility in extracting the main topics from the considered corpus. Moreover it is shown how to check for positive and negative terms in order to gauge the polarity of statements and whole documents. The evaluation of these synthetic indexes is quite relevant for increasing the transparency of the central banks' communications.
Health and disease in 85 year olds: baseline findings from the Newcastle 85+ cohort study

Objectives The Newcastle 85+ Study aims to systematically study the clinical, biological, and psychosocial attributes of an unselected cohort of 85 year olds and to examine subsequent health trajectories as the cohort ages; health at baseline is reported. Design Cross sectional analysis of baseline data from a cohort study. Setting Newcastle upon Tyne and North Tyneside primary care trusts, United Kingdom. Participants 1042 people born in 1921 and registered with the participating general practices. Main outcome measures Detailed health assessment and review of general practice records (disease, medication, and use of general practice services); participants could decline elements of the protocol. Results Of the 1453 eligible people, 851 (58.6%) were recruited to health assessment plus record review, 188 (12.9%) to record review only, and 3 (0.2%) to health assessment only. Data from record review are reported on a maximum of 1030 and from health assessment on a maximum of 853; individual denominators differ owing to withdrawal and missing values. Of the health assessment sample (n=853), 62.1% (n=530) were women and 10.4% (n=89) were in institutional care. The most prevalent diseases were hypertension (57.5%, 592/1030) and osteoarthritis (51.8%, 534/1030). Moderate or severe cognitive impairment was present in 11.7% (96/824) of participants, severe or profound urinary incontinence in 21.3% (173/813), hearing impairment in 59.6% (505/848), and visual impairment in 37.2% (309/831). Health assessment identified participants with possible disease but without a previous diagnosis in their medical record for hypertension (25.1%, 206/821), ischaemic heart disease (12.6%, 99/788), depression (6.9%, 53/772), dementia (6.7%, 56/840), and atrial fibrillation (3.8%, 30/788). Undiagnosed diabetes mellitus and thyroid disease were rare (1%, 7/717 and 6/762, respectively). A median of 3 (interquartile range 1-8) activities of daily living were undertaken with difficulty. Overall, 77.6% (646/832) of participants rated their health compared with others of the same age as good, very good, or excellent. High contact rates in the previous year with general practitioners (93.8%, 960/1024) were recorded. Women had significantly higher disease counts (medians: women 5, men 4; P=0.033) and disability scores (medians: women 4, men 2; P=0.0006) than men, but were less likely to have attended outpatient clinics in the previous three months (women 29% (150/524), men 37% (118/320), odds ratio 0.7, 95% confidence interval 0.5 to 0.9). Conclusions This large cohort of 85 year olds showed good levels of both self rated health and functional ability despite significant levels of disease and impairment. Hypertension, ischaemic heart disease, atrial fibrillation, depression, and dementia may be underdiagnosed. Notable differences were found between the sexes: women outnumbered men and had more disease and disability.
ASCL1 regulates proliferation of NG2‐glia in the embryonic and adult spinal cord

NG2‐glia are highly proliferative oligodendrocyte precursor cells (OPCs) that are widely distributed throughout the central nervous system (CNS). During development, NG2‐glia predominantly differentiate into oligodendrocytes (OLs) to myelinate axon fibers, but they can also remain as OPCs persisting into the mature CNS. Interestingly, NG2‐glia in the gray matter (GM) are intrinsically different from those in the white matter (WM) in terms of proliferation, differentiation, gene expression, and electrophysiological properties. Here we investigate the role of the transcriptional regulator, ASCL1, in controlling NG2‐glia distribution and development in the GM and WM. In the spinal cord, ASCL1 levels are higher in WM NG2‐glia than those in the GM. This differential level of ASCL1 in WM and GM NG2‐glia is maintained into adult stages. Long‐term clonal lineage analysis reveals that the progeny of single ASCL1+ oligodendrocyte progenitors (OLPs) and NG2‐glia are primarily restricted to the GM or WM, even though they undergo extensive proliferation to give rise to large clusters of OLs in the postnatal spinal cord. Conditional deletion of Ascl1 specifically in NG2‐glia in the embryonic or adult spinal cord resulted in a significant reduction in the proliferation but not differentiation of these cells. These findings illustrate that ASCL1 is an intrinsic regulator of the proliferative property of NG2‐glia in the CNS.
Assessing the anomalous superdiffusive heat transport in a single one-dimensional PEDOT chain

We present a computational investigation on heat transport in a single polymer chain of poly-3,4ethylenedioxythiophene (PEDOT). By applying equilibrium and nonequilibrium molecular dynamics simulations to evaluate the thermal conductivity, as well as by investigating how the polymer chain approaches equilibrium upon a local thermal excitation, we provide a robust picture assessing the anomalous superdiffusive (i.e., intermediate between ballistic and diffusive) character of its thermal transport. This assessment is provided by the present simulations showing that three scaling laws with unlike physical meaning and characterizing the thermal energy transport in one-dimensional systems indeed occur in the very same polymer chain with consistent critical exponents. In order to disentangle the effect of dimensionality, we perform a systematic comparison of transport features for a single one-dimensional (1D) PEDOT chain and a three-dimensional (3D) PEDOT crystal. Present simulations suggest that by increasing the dimensionality, the anomalous regime is completely removed as due to the occurrence of strong interchains anharmonic interactions. Finally, we prove that thermal transport in isolated single PEDOT chains belongs to a novel universality class of superdiffusion characterized by a critical exponent β = 1/2.
Actor-Critic Algorithms for Learning Nash Equilibria in N-player General-Sum Games

We consider the problem of finding stationary Nash equilibria (NE) in a finite discounted general-sum stochastic game. We first generalize a non-linear optimization problem from Filar and Vrieze [2004] to a $N$-player setting and break down this problem into simpler sub-problems that ensure there is no Bellman error for a given state and an agent. We then provide a characterization of solution points of these sub-problems that correspond to Nash equilibria of the underlying game and for this purpose, we derive a set of necessary and sufficient SG-SP (Stochastic Game - Sub-Problem) conditions. Using these conditions, we develop two actor-critic algorithms: OFF-SGSP (model-based) and ON-SGSP (model-free). Both algorithms use a critic that estimates the value function for a fixed policy and an actor that performs descent in the policy space using a descent direction that avoids local minima. We establish that both algorithms converge, in self-play, to the equilibria of a certain ordinary differential equation (ODE), whose stable limit points coincide with stationary NE of the underlying general-sum stochastic game. On a single state non-generic game (see Hart and Mas-Colell [2005]) as well as on a synthetic two-player game setup with $810,000$ states, we establish that ON-SGSP consistently outperforms NashQ ([Hu and Wellman, 2003] and FFQ [Littman, 2001] algorithms.
Voxel-wise magnetization transfer imaging study of effects of natalizumab and IFNβ-1a in multiple sclerosis

Objective: To determine the effects of intravenous natalizumab and intramuscular interferon beta-1a (IFNβ-1a) on the volume of white-matter (WM) lesions and normal appearing brain tissue (NABT) undergoing voxel-wise (VW) increases in magnetization transfer ratio (MTR) suggestive of remyelination in patients with relapsing multiple sclerosis. Methods: This prospective, open-label, single-blinded study enrolled patients with relapsing–remitting multiple sclerosis (RRMS) and relapsing secondary progressive multiple sclerosis (RSPMS) as well as a group of age/sex-matched healthy controls (n=22). Patients with multiple sclerosis were assigned to receive natalizumab monotherapy (n=77; RRMS/RSPMS) or intramuscular IFNβ-1a (n=26) as either monotherapy (RRMS) or combined with pulsed i.v. methylprednisolone, as needed (RSPMS). The primary endpoint was the two-year change in volume of NABT VWMTR, by quantifying the number of voxels that increased (suggesting remyelination) or decreased (suggesting demyelination) in their MTR value. Results: The volume of tissue undergoing increases in VWMTR was significantly larger in natalizumab compared with IFNβ-1a-treated patients (year 1: p=0.001 in NABT and p<0.006 in WM lesions; year 2: p=0.008 in NABT) and compared with healthy control subjects (year 1: p=0.05 and year 2: p=0.007 in NABT). The larger volume within NABT undergoing decreases in VWMTR was detected in multiple sclerosis patients compared with healthy controls (p<0.001), and in the IFNβ-1a group compared with the natalizumab group (year 1: p=0.05; year 2: p=0.002). One patient on natalizumab died from progressive multifocal leukoencephalopathy eight months after completing the study. Conclusion: Natalizumab may promote remyelination and stabilize demyelination in lesions and NABT in relapsing multiple sclerosis, compared with intramuscular IFNβ-1a.