Miracle-dz/UniFAR-FTUs huggingface dataset:
High Eomesodermin Expression among CD57+ CD8+ T Cells Identifies a CD8+ T Cell Subset Associated with Viral Control during Chronic Human Immunodeficiency Virus Infection

ABSTRACT During HIV infection, increased CD57 expression among CD8+ T cells has been associated with immune senescence and defective immune responses. Interestingly, CD57-expressing CD8+ T cells exhibit a dual profile, being simultaneously highly cytotoxic (terminally differentiated effectors) and poorly proliferative (replicative senescent). Recent publications point toward a positive role of CD57-expressing CD8+ T cell subsets, presumably due to their high cytolytic activity. We further investigated the phenotype of CD57-expressing CD8+ T cells in healthy donors and during HIV infection combining CD57 expression to Eomesodermin (EOMES), a T box transcription factor which determines, coordinately with T-bet, effector and memory CD8+ T cell differentiation. We defined in healthy donors two functionally distinct CD57-expressing CD8+ T cell subsets exhibiting different levels of EOMES expression: EOMEShi CD57+ and EOMESint CD57+ CD8+ T cells. EOMEShi CD57+ cells exhibited low cytotoxic activity but preserved proliferative capacity and interleukin 7 (IL-7) receptor expression, whereas EOMESint CD57+ cells exhibited obvious cytotoxic functions and a more terminally differentiated phenotype. We next performed a similar analysis in different contexts of HIV infection: primary infected patients, long-term viremic patients, aviremic patients treated with antiretroviral therapy, and HIV controllers; we demonstrated a higher percentage of CD57-expressing cells in all HIV-infected patients regardless of virological status. When heterogeneity in EOMES expression among CD57 cells was taken into account, we detected significantly higher proportions of EOMEShi CD57+ cells among HIV-specific and nonspecific CD8+ T cells from HIV controllers than in aviremic antiretroviral-treated patients and viremic patients. Importantly, such a peculiar non-terminally differentiated EOMEShi CD57+ phenotypic profile was associated with viral control. IMPORTANCE This study demonstrates that functional heterogeneity exists among CD57-expressing CD8 T cells, which include both terminally differentiated, highly cytotoxic EOMESint CD57+ CD8+ T cells and less differentiated EOMEShi CD57+ CD8 T cells, which do not exhibit immediate cytotoxic functions but present high proliferative capacity. Interestingly, HIV controllers present a high proportion of EOMEShi CD57 cells among CD57-expressing HIV-specific CD8 T cells compared to both long-term viremic and aviremic antiretroviral therapy (ART)-treated patients, suggesting a beneficial role for this cell subset in viral control.
Seoul National University Renal Stone Complexity Score for Predicting Stone-Free Rate after Percutaneous Nephrolithotomy

Objectives Currently, no standardized method is available to predict success rate after percutaneous nephrolithotomy. We devised and validated the Seoul National University Renal Stone Complexity (S-ReSC) scoring system for predicting the stone-free rate after single-tract percutaneous nephrolithotomy (sPCNL). Patients and Methods The data of 155 consecutive patients who underwent sPCNL were retrospectively analyzed. Preoperative computed tomography images were reviewed. The S-ReSC score was assigned from 1 to 9 based on the number of sites involved in the renal pelvis (#1), superior and inferior major calyceal groups (#2–3), and anterior and posterior minor calyceal groups of the superior (#4–5), middle (#6–7), and inferior calyx (#8–9). The inter- and intra-observer agreements were accessed using the weighted kappa (κ). The stone-free rate and complication rate were evaluated according to the S-ReSC score. The predictive accuracy of the S-ReSC score was assessed using the area under the receiver operating characteristic curve (AUC). Results The overall SFR was 72.3%. The mean S-ReSC score was 3.15±2.1. The weighted kappas for the inter- and intra-observer agreements were 0.832 and 0.982, respectively. The SFRs in low (1 and 2), medium (3 and 4), and high (5 or higher) S-ReSC scores were 96.0%, 69.0%, and 28.9%, respectively (p<0.001). The predictive accuracy was very high (AUC 0.860). After adjusting for other variables, the S-ReSC score was still a significant predictor of the SFR by multiple logistic regression. The complication rates were increased to low (18.7%), medium (28.6%), and high (34.2%) (p = 0.166). Conclusions The S-ReSC scoring system is easy to use and reproducible. This score accurately predicts the stone-free rate after sPCNL. Furthermore, this score represents the complexity of surgery.
On How Insulin May Influence Ageing and Become Atherogenic throughout the Insulin-Like Growth Factor-1 Receptor Pathway: In vitro Studies with Human Vascular Smooth Muscle Cells

Background: It is known that growth factors play a role in ageing and atherogenesis, and insulin develops mitogenic activity in vitro. Objectives: This study focusses on the pathway by which insulin induces proliferation and mobility in vascular smooth muscle cells (SMCs) compared with that of insulin-like growth factor-1 (IGF-1), because they are two basic phenomena for atherogenesis that could also help to understand the role of insulin in the ageing process. Methods: Bromodeoxyuridine DNA incorporation, chemotaxis and the appearance of membrane ruffles were measured in cultured SMCs after incubation with insulin or IGF-1 in the presence of insulin or IGF-1 receptor-blocking antibodies. Results: Insulin-induced SMC proliferation through the IGF-1 receptors; indeed, the blockade of insulin receptors does not inhibit the mitogenic influence of insulin. On the contrary, insulin-induced cell migration was inhibited by blocking the insulin receptor but not the IGF-1 receptor. Nevertheless, in less differentiated SMCs from non-confluent cultures, the migratory response was significantly higher and insulin lost its receptor specificity. It was stimulated through receptors both for insulin and IGF-1. In these cases the IGF-1 action was similar. Insulin-induced F-actin rearrangements took place through both types of receptors, but IGF-1 was a little more specific through its own receptors. Conclusion: The pathway activated by insulin to induce SMC proliferation is not different from that of IGF-1, whereas the unspecific mechanism inducing mobility in growing cells seems to be related to a higher sensitivity response. Cells with the highest mitotic activity have the highest mobility in which stimulation of receptor specificity is lost for either insulin or IGF-1. Extrapolating these results to in vivo, insulin could become relevant for inducing stabilization and also side effects in ageing.
Unsupervised and knowledge-poor approaches to sentiment analysis

Sentiment analysis focuses upon automatic classiffication of a document's sentiment (and more generally extraction of opinion from text). Ways of expressing sentiment have been shown to be dependent on what a document is about (domain-dependency). This complicates supervised methods for sentiment analysis which rely on extensive use of training data or linguistic resources that are usually either domain-specific or generic. Both kinds of resources prevent classiffiers from performing well across a range of domains, as this requires appropriate in-domain (domain-specific) data. This thesis presents a novel unsupervised, knowledge-poor approach to sentiment analysis aimed at creating a domain-independent and multilingual sentiment analysis system. The approach extracts domain-specific resources from documents that are to be processed, and uses them for sentiment analysis. This approach does not require any training corpora, large sets of rules or generic sentiment lexicons, which makes it domain- and languageindependent but at the same time able to utilise domain- and language-specific information. The thesis describes and tests the approach, which is applied to diffeerent data, including customer reviews of various types of products, reviews of films and books, and news items; and to four languages: Chinese, English, Russian and Japanese. The approach is applied not only to binary sentiment classiffication, but also to three-way sentiment classiffication (positive, negative and neutral), subjectivity classifiation of documents and sentences, and to the extraction of opinion holders and opinion targets. Experimental results suggest that the approach is often a viable alternative to supervised systems, especially when applied to large document collections.
Compressibility behaviour of remoulded, fine-grained soils and correlation with index properties

Cherubini et al. have discussed in great detail the merits and demerits of various statistical procedures which can be used to analyze the experimental data and may help to relatively place the various correlation of compression index with the various index properties available in the geotechnical literature. The Authors do agree that the statistical method used by them need not be the best one, but they made use of it for a relative comparison. However, a qualitative look at the plot between compression index Cc and the index property to which it is correlated itself can show which index property is better.
Pliocene-Pleistocene Orbital Cyclostratigraphy and Glacial Evolution of the East Antarctic Ice Sheet from Continental Rise IODP Site U1361, Wilkes Land Margin, East Antarctica

Stability of the East Antarctic Ice Sheet (EAIS), in response to the orbitally-paced cooling climate of the Late Neogene, is largely unknown. The Wilkes Land margin of East Antarctica, largely grounded below sea level, has previously been proposed to respond dynamically during the warmer climate of the Pliocene, similarly to other marine based sectors of Antarctica (i.e. West Antarctica). Sediment deposition on the Wilkes Land continental rise, recovered in Integrated Ocean Drilling Program U1361A drillcore provides a distal but continuous record of EAIS fluctuations. Changes in sedimentary depositional environments at U1361A core site, were determined through analysis of lithofacies and physical property logs: natural gamma-ray (NGR), gamma-ray attenuation bulk density (GRA), magnetic susceptibility (MS) and L* colour reflectance. NGR primarily reflected biogenic content and a synchronous relationship between NGR, GRA and MS was used to identify interglacial and glacial phases, whereby decreased NGR, GRA and MS values indicated an increase in biogenic material. L* colour reflectance was more variable through time, displayed higher frequency fluctuations and a changing relationship with the other physical property logs down core. Two depositional models, based on facies interpretations and the defined physical property relationships, were produced for the Middle Late Pleistocene (last ~550 kyr; model A) and mid-Pliocene (~4.2-3.6 Ma; model B), which represent end members. Depositional processes common to both models occurred in the intervening core, spanning the Late Pliocene-Early Pleistocene (3-1 Ma). Model A, applied to the Middle Late Pleistocene, shows that alternating diatom-rich clays to silty clays in the upper 9 m of core U1361A, reflect the large amplitude ~100 kyr paced glacial-interglacial cycles, which is confirmed by spectral analysis of the physical properties for this interval. Model B, applied to the Early Pliocene, suggest that the depositional processes recorded by facies may have been less sensitive to EAIS fluctuations, probably due to the fact that the ice margin was generally more distal to the core site during glacial-interglacial cycles of advance and retreat. Nevertheless, these more subtle changes in lithology were characterised by variations in the physical property logs, and spectral analysis of these time series implied orbital pacing was still influential on depositional processes at this time (displaying power in precession and obliquity frequencies). Spectral analysis of the physical property logs and visual correlations to the benthic δ18O stack, confirmed the 4.2-1 Ma interval was paced by ~40 kyr and implies obliquity-paced oscillations of the margin of the EAIS. Precession periodicities, significant in spectra throughout the 4.2 Myr record, are proposed to be the response of phytoplankton productivity in response to seasonal insolation controlling sea-ice extent.
Attenuated recombinant vaccinia virus expressing oncofetal antigen (tumor-associated antigen) 5T4 induces active therapy of established tumors.

The human oncofetal antigen 5T4 (h5T4) is a transmembrane glycoprotein overexpressed by a wide spectrum of cancers, including colorectal, ovarian, and gastric, but with a limited normal tissue expression. Such properties make 5T4 an excellent putative target for cancer immunotherapy. The murine homologue of 5T4 (m5T4) has been cloned and characterized, which allows for the evaluation of immune intervention strategies in "self-antigen" in vivo tumor models. We have constructed recombinant vaccinia viruses based on the highly attenuated and modified vaccinia virus ankara (MVA strain), expressing h5T4 (MVA-h5T4), m5T4 (MVA-m5T4), and Escherichia coli LacZ (MVA-LacZ). Immunization of BALB/c and C57BL/6 mice with MVA-h5T4 and MVA-m5T4 constructs induced antibody responses to human and mouse 5T4, respectively. C57BL/6 and BALB/c mice vaccinated with MVA-h5T4 were challenged with syngeneic tumor line transfectants, B16 melanoma, and CT26 colorectal cells that express h5T4. MVA-h5T4-vaccinated mice showed significant tumor retardation compared with mice vaccinated with MVA-LacZ or PBS. In active treatment studies, inoculation with MVA-h5T4 was able to treat established CT26-h5T4 lung tumor and to a lesser extent B16.h5T4 s.c. tumors. Additionally, when C57BL/6 mice vaccinated with MVA-m5T4 were challenged with B16 cells expressing m5T4, resulting growth of the tumors was significantly retarded compared with control animals. Furthermore, mice vaccinated with MVA-m5T4 showed no signs of autoimmune toxicity. These data support the use of MVA-5T4 for tumor immunotherapy.
The TokuFS Streaming File System

The TokuFS file system outperforms write-optimized file systems by an order of magnitude on microdata write workloads, and outperforms read-optimized file systems by an order of magnitude on read workloads. Microdata write workloads include creating and destroying many small files, performing small unaligned writes within large files, and updating metadata. TokuFS is implemented using Fractal Tree indexes, which are primarily used in databases. TokuFS employs block-level compression to reduce its disk usage.
Open trial of interpersonal psychotherapy for the treatment of social phobia.

OBJECTIVE Interpersonal psychotherapy is a time-limited treatment initially developed to treat depression. It has not been studied for the treatment of anxiety disorders. METHOD Interpersonal psychotherapy was modified and tested in a 14-week, open trial of nine patients with DSM-IV social phobia. RESULTS At termination, seven (78%) were independently rated as much or very much improved on overall social phobia symptoms. Nearly all clinician ratings and self-ratings of social phobia symptoms significantly improved. Changes approximated those of established treatments for social phobia. CONCLUSIONS Interpersonal psychotherapy may have efficacy for the treatment of social phobia. Further study in a comparison trial is warranted.
[A study of expression of p53, c-myc and PCNA in retinoblastoma].

OBJECTIVE To investigate the expressions of p53, c-myc (oncogene) and proliferating cell nuclear antigen (PCNA) in retinoblastoma (Rb) and the relationships of the expression to the degree of differentiation and optic nerve infiltration. METHOD The expressions of p53, c-myc and PCNA in Rb tissues of 31 cases were analyzed by using LSAB immunohistochemical method. RESULTS The positive rates of p53, c-myc and PCNA in Rb were respectively 51.6%, 45.2% and 67.7% and all the expressions were significantly related to the differentiation degree of Rb (all P < 0.05). The expression of PCNA was significantly related to the optic nerve infiltration of Rb (P < 0.05). Both the expressions of p53 and c-myc in Rb were markedly correlated with the expression of PCNA (all P < 0.05). CONCLUSIONS The occurrence of Rb is the result of multiple gene mutations. The determinations of p53, c-myc and PCNA are of significance for evaluating the histologic characteristics and biological behavior of Rb.
Vertebrate fauna at the Allosaurus fossil-site of Andrés (Upper Jurassic), Pombal, Portugal

An overview of the faunistic diversity of the Andres fossil-site from the Portuguese Upper Jurassic is presented. This work provides a preliminary approach on the vertebrate fauna known at present. Although this quarry is known since the 1990’s, due to the description on the first robust evidence of a member of the neotetanuran genus Allosaurus outside North America, the results presented here are mainly derived from the analysis of the elements found during the second and third field seasons in 2005. At the moment, among the material collected from Andres it was identified remains that represent a diverse vertebrate fauna, including fishes, sphenodonts, crocodrylomorphs, pterosaurs, and at least, seven distinct dinosaur forms. The recovery of this diverse and abundant osteological collection from one unique fossil-site is noteworthy for the Upper Jurassic Portuguese record, and only comparable with those from the Guimarota coalmine. Due to these two features plus the good preservation of the fossils, the Andres quarry may be a site of reference for the analysis of vertebrate ecosystems from the Portuguese Upper Jurassic. Dinosaur elements are the most abundant fossils, and among them it is particulary common the presence of remains identified as Allosaurus. These new evidences allow testing the previus phylogenetical hypothesys ascribing the firsts theropod remains from Andres to A. fragilis, a species described in synchronic levels of the North American Morrison Formation. The similarity between the Allosaurus remains collected in Andres and some specimens from the Morrison Formation seems to point the existence of a genetic flow between some continental vertebrates on both sides of the proto-north Atlantic during the Upper Jurassic. Favourable tectonic conditions for the occurrence of punctual contacts between the two continents is, at present, the best scenario for explain this situation.
The length of the magnetospheric tail

Dessler's [1964] theoretical reasonings lead him to conclude that the magnetosphere has a tail of astronomical length. If the ‘open model’ [Dungey, 1963] is assumed, however, an empirical estimate can be obtained very simply, and it is more reasonable. A line of force of the interplanetary field becomes attached to the earth in the region of local noon and 75° geomagnetic latitude. The terrestrial end of the line then moves over the pole to the night side and the line becomes detached again when the terrestrial end reaches a geomagnetic latitude of about 67°.
Implantation and explantation of a wireless epiretinal retina implant device: observations during the EPIRET3 prospective clinical trial.

PURPOSE Visual sensations in patients with blindness and retinal degenerations may be restored by electrical stimulation of retinal neurons with implantable microelectrode arrays. A prospective trial was initiated to evaluate the safety and efficacy of a wireless intraocular retinal implant (EPIRET3) in six volunteers with blindness and RP. METHODS The implant is a remotely controlled, fully intraocular wireless device consisting of a receiver and a stimulator module. The stimulator is placed on the retinal surface. Data and energy are transmitted via an inductive link from outside the eye to the implant. Surgery included removal of the lens, vitrectomy, and implantation of the EPIRET3 device through a corneal incision. The clinical outcome after implantation and explantation of the device was determined. The implant was removed after 4 weeks, according to the study protocol. RESULTS Implantation was successful in all six patients. While the anterior part was fixed with transscleral sutures, the stimulating foil was placed onto the posterior pole and fixed with retinal tacks. The implant was well tolerated, causing temporary moderate postoperative inflammation, whereas the position of the implant remained stable until surgical removal. In all cases explantation of the device was performed successfully. Adverse events were a sterile hypopyon effectively treated with steroids and antibiotics in one case and a retinal break in a second case during explantation requiring silicone oil surgery. CONCLUSIONS The EPIRET3 system can be successfully implanted and explanted in patients with blindness and RP. The surgical steps are feasible, and the postoperative follow-up disclosed an acceptable range of adverse events.
Hypoxemia in healthy subjects at moderate altitude.

BACKGROUND Healthy individuals are known to have significantly reduced oxygen saturations at rest when acutely exposed to moderate altitudes, such as during commercial flight. There is a paucity of data on the response of healthy individuals to exercise at these altitudes. The aim of this study was to establish the normal response to exercise during acute, moderate altitude exposure with regard to oxygen saturations. Secondary aims were to establish if this response can be predicted from pulmonary function measurements at sea level. METHODS At sea level, 20 subjects performed pulmonary function tests, including submaximal steady state exercise, followed by replication of submaximal steady state exercise during acute altitude exposure at 6844 ft (2086 m). RESULTS Mean resting oxygen saturation at 6844 ft (2086 m) was 96%, a significant reduction from the sea level value of 99%. Mean nadir oxygen saturation during steady state exercise at moderate altitude was 89%. There was a weak negative correlation between aerobic capacity and end exercise oxygen saturation at altitude. Modified BORG dyspnea scores were unchanged at rest at 6844 ft (2086 m) and higher post-exercise at 6844 ft (2086 m) when compared to sea level, although absolute values were low. DISCUSSION Healthy individuals desaturate at rest and upon exercise during acute altitude exposure at 6844 ft (2086 m). A quarter of participants experienced SpO2 < or = 85% upon exercise at altitude, although this had no correlation with dyspnea scores or baseline pulmonary function measurements. The weak negative correlation between aerobic capacity and end exercise oxygen saturation is unexplained and merits further research.
Alert: An Adaptive Low-Latency Event-Driven MAC Protocol for Wireless Sensor Networks

Collection of rare but delay-critical messages from a group of sensor nodes is a key process in many wireless sensor network applications. This is particularly important for security related applications like intrusion detection and fire alarm systems. An event sensed by multiple sensor nodes in the network can trigger many messages to be sent simultaneously. We present Alert, a MAC protocol for collecting event-triggered urgent messages from a group of sensor nodes with minimum latency and without requiring any cooperation or pre-scheduling among the senders or between senders and receiver during protocol execution. Alert is designed to handle multiple simultaneous messages efficiently and reliably minimizing the overall delay to collect all messages along with the delay to get the first message. Moreover, the ability to handle a large number of simultaneous messages does not come at the cost of excessive delays when only a few messages need to be handled. We analyze Alert and evaluate its feasibility and performance with an implementation on commodity hardware. We further compare Alert with existing approaches through simulations and show the performance improvement possible through Alert.