Miracle-dz/UniFAR-FTUs huggingface dataset:
Attenuated Listeria monocytogenescarrier strains can deliver an HIV‐1 gp120 T helper epitope to MHC class II‐restricted human CD4+ T cells

Listeria monocytogenes is a facultative intracellular pathogen which, following uptake by macrophages, escapes from the phagosome and replicates in the cytoplasm. This property has been exploited using recombinant L. monocytogenes as a carrier for the intracytoplasmic expression of antigens when MHC class I‐restricted cytotoxic T lymphocyte responses are required. Much less is known of the ability of these bacteria to trigger MHC class II‐restricted responses. Here, we demonstrate that after ingestion of L. monocytogenes expressing a T helper epitope from the gp120 envelope glycoprotein of HIV, human adherent macrophages and dendritic cells can process and present the epitope to a specific CD4+ T cell line in the context of MHC class II molecules. No significant differences were observed when the attenuated strains were trapped in the phagolysosome or impaired in the capacity to spread intracellularly or from cell to cell. Similar results were obtained using carrier proteins that were either secreted, associated with the bacterial surface, or restricted to the bacterial cytoplasm. A dominant expression of the TCR Vβ 22 gene subfamily was observed in specific T cell lines generated after stimulation with the recombinant strains or with soluble gp120. Our data show that in this in vitro system L. monocytogenes can efficiently deliver antigens to the MHC class II pathway, in addition to the well‐established MHC class I pathway. The eukaryotic cell compartment in which the antigen is synthesized, and the mode of display seem to play a minor role in the overall efficiency of epitope processing and presentation.
Ideology AND Health Reporting

The majority of research studies analysing the types of information and messages disseminated about health issues in the entertainment and news media employ quantitative methods to identify surface patterns in coverage. This article introduces a further, ideological, dimension to the analysis of the portrayal of health issues in the news media. It is argued that within the field of health communication there needs to be a greater emphasis upon using more interpretative and critical methods of textual analysis. The present discussion reviews research which has attempted to identify the sub textual meanings in press accounts of risks, health, disease and illness.
Graphlets versus node2vec and struc2vec in the task of network alignment

Network embedding aims to represent each node in a network as a low-dimensional feature vector that summarizes the given node's (extended) network neighborhood. The nodes' feature vectors can then be used in various downstream machine learning tasks. Recently, many embedding methods that automatically learn the features of nodes have emerged, such as node2vec and struc2vec, which have been used in tasks such as node classification, link prediction, and node clustering, mainly in the social network domain. There are also other embedding methods that explicitly look at the connections between nodes, i.e., the nodes' network neighborhoods, such as graphlets. Graphlets have been used in many tasks such as network comparison, link prediction, and network clustering, mainly in the computational biology domain. Even though the two types of embedding methods (node2vec/struct2vec versus graphlets) have a similar goal -- to represent nodes as features vectors, no comparisons have been made between them, possibly because they have originated in the different domains. Therefore, in this study, we compare graphlets to node2vec and struc2vec, and we do so in the task of network alignment. In evaluations on synthetic and real-world biological networks, we find that graphlets are both more accurate and faster than node2vec and struc2vec.
Clinical significance of pre-surgical serum lipid levels in patients with glioblastoma

Accumulating evidence demonstrates that pre-surgical serum lipid levels are linked to the clinical outcome of different types of human malignant tumors, but few studies have explored the prognostic value of these easily accessible parameters in glioblastoma. The aim of the current study was to validate the association between pre-surgical serum lipid levels and the clinical outcome of patients with glioblastoma. The pre-surgical serum lipid levels (triglycerides, total cholesterol, high-density lipoprotein [HDL] cholesterol, and low-density lipoprotein [LDL] cholesterol) of 125 patients with glioblastoma, who underwent surgery between January 2015 and May 2016, were retrospectively evaluated. The correlation between pre-surgical serum lipid levels and overall survival (OS) was examined using the Kaplan-Meier method and Cox proportional hazards regression model. Univariate analysis showed that lipids associated with OS were total cholesterol, HDL cholesterol, and LDL cholesterol levels. Results of multivariate analysis identified LDL cholesterol level as an independent prognostic factor for OS in patients with glioblastoma (hazard ratio: 0.412; 95% confidence interval: 0.211-0.801; P = 0.009). Total cholesterol and HDL cholesterol levels were predictive factors only in univariate analysis, but not in multivariate analysis. The current study demonstrated that pre-surgical serum LDL cholesterol level is an independent prognostic factor for clinical outcomes of patients with glioblastoma. Pre-surgical serum LDL cholesterol level might provide valuable prognostic information for patients with glioblastoma that could be applied in clinical practice.
EFFECTS OF THE ELECTRONIC SPIN TRANSITIONS OF IRON IN LOWER MANTLE MINERALS: IMPLICATIONS FOR DEEP MANTLE GEOPHYSICS AND GEOCHEMISTRY

We have critically reviewed and discussed currently available information regarding the spin and valence states of iron in lower mantle minerals and the associated effects of the spin transitions on physical, chemical, and transport properties of the deep Earth. A high‐spin to low‐spin crossover of Fe2+ in ferropericlase has been observed to occur at pressure‐temperature conditions corresponding to the middle part of the lower mantle. In contrast, recent studies consistently show that Fe2+ predominantly exhibits extremely high quadrupole splitting values in the pseudo‐dodecahedral site (A site) of perovskite and post‐perovskite, indicative of a strong lattice distortion. Fe3+ in the A site of these structures likely remains in the high‐spin state, while a high‐spin to low‐spin transition of Fe3+ in the octahedral site of perovskite occurs at pressures of 15–50 GPa. In post‐perovskite, the octahedral‐site Fe3+ remains in the low‐spin state at the pressure conditions of the lowermost mantle. These changes in the spin and valence states of iron as a function of pressure and temperature have been reported to affect physical, chemical, rheological, and transport properties of the lower mantle minerals. The spin crossover of Fe2+ in ferropericlase has been documented to affect these properties and is discussed in depth here, whereas the effects of the spin transition of iron in perovskite and post‐perovskite are much more complex and remain debated. The consequences of the transitions are evaluated in terms of their implications to deep Earth geophysics, geochemistry, and geodynamics including elasticity, element partitioning, fractionation and diffusion, and rheological and transport properties.
Outcomes After Transcatheter Aortic Valve Replacement: A Propensity Matched Retrospective Cohort Study.

OBJECTIVES To examine patient acuity and perioperative outcomes in a contemporary cohort of patients undergoing either transcatheter aortic valve replacement (TAVR) or surgical aortic valve replacement (SAVR). DESIGN A retrospective propensity-matched cohort study with univariable logistic regression to assess postoperative outcomes. SETTING Hospitals participating in the American College of Surgeons National Surgical Quality Improvement Program. PARTICIPANTS The study comprised 2,043 patients who underwent either TAVR or SAVR that was reported in the American College of Surgeons-National Surgical Quality Improvement Program. INTERVENTIONS None. MEASUREMENT AND MAIN RESULTS Age greater than 65 years, patients with dyspnea with moderate exertion or dependence in activities of daily living, high American Society of Anesthesiologists physical status classification, and history of chronic obstructive pulmonary disease were associated with TAVR, whereas body mass index greater than 25 was associated with SAVR. After propensity matching, no differences in 30-day mortality, length of stay, or most postoperative outcomes were observed between the 2 cohorts. Patients undergoing TAVR were less likely to require a perioperative blood transfusion and on an individual patient basis had a lower number of complications than patients in the SAVR group. CONCLUSIONS Patients undergoing TAVR have similar mortality, length of stay, and risk for postoperative complications as do patients undergoing SAVR, but patients undergoing TAVR are less likely to have blood transfused.
CuckooQ Hashing

Cuckoo hashing is an efficient scheme that guarantees worst case constant lookup time. But the insertion delay is significant in cuckoo hashing when the table is highly occupied. This project explores a modification to cuckoo hashing, called CuckooQ. CuckooQ exploits “the power of two choices paradigm” during insertions to reduce the insertion delay in cuckoo hashing, without affecting the lookup time of the existing scheme. When compared to cuckoo hashing, thus, CuckooQ shows a 28 percent speedup on average during insertions. But this comes at the cost of additional rehashes that result in larger tables.
Liquefaction Probability Curves for Surficial Geologic Deposits

Liquefaction probability curves that predict the probability of surface manifestations of earthquake-induced liquefaction are developed for 14 different types of surficial geologic units. The units consist of alluvial fan, beach ridge, river delta topset and foreset beds, eolian dune, point bar, flood basin, natural river and alluvial fan levees, abandoned river channel, deep-water lake, lagoonal, sandy artificial fill, and valley train deposits. Probability is conditioned on earthquake magnitude and peak ground acceleration. Curves are developed for water table depths of 1.5 and 5.0 m. Probabilities are derived from complementary cumulative frequency distributions of the liquefaction potential index (LPI) that were computed from 927 cone penetration tests. For natural deposits with a water table at 1.5 m and subjected to a M7.5 earthquake with peak ground acceleration (PGA) = 0.25 g , probabilities range from 0.5 for beach ridge, point bar, and deltaic deposits. The curves also were used to assign ranges of liquefaction probabilities to the susceptibility categories proposed previously for different geologic deposits. For the earthquake described here, probabilities for susceptibility categories have ranges of 0–0.08 for low, 0.09–0.30 for moderate, 0.31–0.62 for high, and 0.63–1.00 for very high. Retrospective predictions of liquefaction during historical earthquakes based on the curves compare favorably to observations.
A phase II double-blind study to investigate efficacy and safety of two doses of the triple angiokinase inhibitor BIBF 1120 in patients with relapsed advanced non-small-cell lung cancer.

BACKGROUND To assess the efficacy, safety, tolerability and pharmacokinetics of BIBF 1120 in patients with stage IIIB/IV non-small-cell lung cancer (NSCLC). METHODS Patients with locally advanced or metastatic relapsed NSCLC in whom first- or second-line platinum-based chemotherapy failed were randomly allocated to daily 250 mg BIBF 1120 b.i. d. or 150 mg BIBF 1120 b.i. d. Primary end points were progression-free survival (PFS) and objective tumour response (RECIST). Incidence and severity of adverse events (AEs) were reported. RESULTS Seventy-three patients received BIBF 1120. Median PFS was 6.9 weeks, with no significant difference between treatment arms. Median overall survival (OS) was 21.9 weeks. Eastern Cooperative Oncology Group (ECOG) 0-1 patients (n = 56) had a median PFS of 11.6 weeks and a median OS of 37.7 weeks. Tumour stabilisation was achieved in 46% of patients (ECOG 0-1 patients: 59%), with one confirmed partial response (250 mg b.i.d.). Most commonly reported drug-related AEs were nausea (57.5%), diarrhoea (47.9%), vomiting (42.5%), anorexia (28.8%), abdominal pain (13.7%) and reversible alanine transaminase (13.7%) and aspartate aminotransferase elevations (9.6%). BIBF 1120 displayed dose-linear pharmacokinetic characteristics. CONCLUSION Continuous treatment with BIBF 1120 was well tolerated, with no difference in efficacy between treatment arms. PFS and objective response with single-agent treatment in advanced disease warrants further exploration.
Phosphatidylinositol-4,5-biphosphate-dependent rearrangement of TRPV4 cytosolic tails enables channel activation by physiological stimuli

Most transient receptor potential (TRP) channels are regulated by phosphatidylinositol-4,5-biphosphate (PIP2), although the structural rearrangements occurring on PIP2 binding are currently far from clear. Here we report that activation of the TRP vanilloid 4 (TRPV4) channel by hypotonic and heat stimuli requires PIP2 binding to and rearrangement of the cytosolic tails. Neutralization of the positive charges within the sequence 121KRWRK125, which resembles a phosphoinositide-binding site, rendered the channel unresponsive to hypotonicity and heat but responsive to 4α-phorbol 12,13-didecanoate, an agonist that binds directly to transmembrane domains. Similar channel response was obtained by depletion of PIP2 from the plasma membrane with translocatable phosphatases in heterologous expression systems or by activation of phospholipase C in native ciliated epithelial cells. PIP2 facilitated TRPV4 activation by the osmotransducing cytosolic messenger 5′-6’-epoxyeicosatrienoic acid and allowed channel activation by heat in inside-out patches. Protease protection assays demonstrated a PIP2-binding site within the N-tail. The proximity of TRPV4 tails, analyzed by fluorescence resonance energy transfer, increased by depleting PIP2 mutations in the phosphoinositide site or by coexpression with protein kinase C and casein kinase substrate in neurons 3 (PACSIN3), a regulatory molecule that binds TRPV4 N-tails and abrogates activation by cell swelling and heat. PACSIN3 lacking the Bin-Amphiphysin-Rvs (F-BAR) domain interacted with TRPV4 without affecting channel activation or tail rearrangement. Thus, mutations weakening the TRPV4–PIP2 interacting site and conditions that deplete PIP2 or restrict access of TRPV4 to PIP2—in the case of PACSIN3—change tail conformation and negatively affect channel activation by hypotonicity and heat.
Constrained Maximum Likelihood Estimation for Model Calibration Using Summary-Level Information From External Big Data Sources

Information from various public and private data sources of extremely large sample sizes are now increasingly available for research purposes. Statistical methods are needed for using information from such big data sources while analyzing data from individual studies that may collect more detailed information required for addressing specific hypotheses of interest. In this article, we consider the problem of building regression models based on individual-level data from an “internal” study while using summary-level information, such as information on parameters for reduced models, from an “external” big data source. We identify a set of very general constraints that link internal and external models. These constraints are used to develop a framework for semiparametric maximum likelihood inference that allows the distribution of covariates to be estimated using either the internal sample or an external reference sample. We develop extensions for handling complex stratified sampling designs, such as case-control sampling, for the internal study. Asymptotic theory and variance estimators are developed for each case. We use simulation studies and a real data application to assess the performance of the proposed methods in contrast to the generalized regression calibration methodology that is popular in the sample survey literature. Supplementary materials for this article are available online.
Ray Specialized Contraction on Bounding Volume Hierarchies

In this paper we propose a simple but effective method to modify a BVH based on ray distribution for improved ray tracing performance. Our method starts with an initial BVH generated by any state‐of‐the‐art offline algorithm. Then by traversing a small set of sample rays we collect statistics at each node of the BVH. Finally, a simple but ultra‐fast BVH contraction algorithm modifies the initial binary BVH to a multi‐way BVH. The overall acceleration for ray‐primitive testing is about 25% for incoherent diffuse rays and 30% for shadow rays, which is significant as a data structure optimization. Similar results are also presented for packet ray tracing, and for Quad‐BVHs the improvement is 10% to 15%. The approach has the advantages of being simple, and compatible with almost any existing BVH and ray tracing techniques, and it require very little extra work to generate the modified tree.
ACUTE RESPIRATORY DISEASE IN NORMAL VOLUNTEERS ASSOCIATED WITH COXSACKIEA-21 VIRAL INFECTION

Four strains of an unclassified human virus were isolated in 1958 by Lennette, Fox, Schmidt, and Culver and given the name Coe virus (1). This agent multiplied in tissues of human but not of simian origin, and could not be adapted to serial propagation of suckling mice. Subsequently, Pereira and Pereira demonstrated that the virus was approximately 25 mu in diameter, ether-resistant, and enterovirus-like in cytopathic effect in human tissue culture (2). Further serologic testing has shown the Coe virus to be indistinguishable from the enterovirus Coxsackie A-21 (3). In addition to the initial isolation from military recruits by Lennette and associates, Coxsackie A-21 has been isolated by others from throat specimens of military personnel with mild respiratory illness (4-7). Parsons. Bynoe, Pereira, and Tyrrell (8) conducted a volunteer study using Coxsackie A-2 1 virus and showed that this agent could produce a mild upper respiratory illness in young adults after an incubation period of 2 to 4 days. Virus was detected in pharyngeal specimens over a 6-day period of observation, but was less often found in fecal specimens. In two recent reports (5, 6), Coxsackie A-21 virus was associated with mild upper respiratory illness in military personnel at Camp Lejeune, North Carolina. Virus was readily recovered from pharyngeal specimens of ill recruits, and significant rises in neutralizing and hemagglutination-inhibiting antibodies were demonstrated. The evidence that this agent was a cause of human disease suggested the need for additional knowledge of its effects in man. Accordingly, studies were made in normal volunteers in which virus was administered by the nasopharyngeal route, or directly into the intestinal tract in subjects with no, intermediate, or high titers of homologous antibody. The study revealed that nasopharyngeal inoculation of subjects without measurable prechallenge antibody was followed by a systemic illness with fever and myalgia that was more severe when the inoculum was large. The presence of intermediate amounts of antibody before inoculation was associated with a syndrome of common cold, whereas men with high titers exhibited no illness. It was also found that the agent, although designated an enterovirus, was isolated most frequently from throat swabs. This finding was confirmed when it was found that direct intestinal inoculation produced only transient infection and no illness or antibody response. These findings are described in the following report.
The IMF and OECD versus Consensus Forecasts

This paper compares the accuracy and information content of macroeconomic economic forecasts for G7 countries made in the 1990s by the OECD and IMF. The benchmarks for comparison are the average forecasts of private sector economists published by Consensus Economics. With few exceptions, the private sector forecasts are less biased and more accurate in terms of mean absolute error and root mean square error. Formal tests show that there is little information in the OECD and IMF forecasts that could be used to reduce significantly the error in the private sector forecasts.
The Most Important Virulence Markers of Yersinia enterocolitica and Their Role during Infection

Yersinia enterocolitica is the causative agent of yersiniosis, a zoonotic disease of growing epidemiological importance with significant consequences for public health. This pathogenic species has been intensively studied for many years. Six biotypes (1A, 1B, 2, 3, 4, 5) and more than 70 serotypes of Y. enterocolitica have been identified to date. The biotypes of Y. enterocolitica are divided according to their pathogenic properties: the non-pathogenic biotype 1A, weakly pathogenic biotypes 2–5, and the highly pathogenic biotype 1B. Due to the complex pathogenesis of yersiniosis, further research is needed to expand our knowledge of the molecular mechanisms involved in the infection process and the clinical course of the disease. Many factors, both plasmid and chromosomal, significantly influence these processes. The aim of this study was to present the most important virulence markers of Y. enterocolitica and their role during infection.
Non-stationary texture synthesis by adversarial expansion

The real world exhibits an abundance of non-stationary textures. Examples include textures with large scale structures, as well as spatially variant and inhomogeneous textures. While existing example-based texture synthesis methods can cope well with stationary textures, non-stationary textures still pose a considerable challenge, which remains unresolved. In this paper, we propose a new approach for example-based non-stationary texture synthesis. Our approach uses a generative adversarial network (GAN), trained to double the spatial extent of texture blocks extracted from a specific texture exemplar. Once trained, the fully convolutional generator is able to expand the size of the entire exemplar, as well as of any of its sub-blocks. We demonstrate that this conceptually simple approach is highly effective for capturing large scale structures, as well as other non-stationary attributes of the input exemplar. As a result, it can cope with challenging textures, which, to our knowledge, no other existing method can handle.
Effect of effluent from a nitrogen fertilizer factory and a pulp mill on the distribution and abundance of Aeromonas hydrophila in Albemarle Sound, North Carolina

The density of Aeromonas hydrophila, standard count bacteria, fecal coliform bacteria, and 18 physical and chemical parameters were measured simultaneously at six sites for 12 months in Albemarle Sound, N.C. One site was above and two sites were below the discharge plume of a Kraft pulping process paper mill. The fourth site was above and the remaining two sites were below the discharge point of a nitrogen fertilizer factory. The impact of the pulp mill on water quality was acute, whereas that of the nitrogen fertilizer factory was chronic and much more subtle. Diffusion chamber studies indicated that A. hydrophila survival is increased by pulp mill effluent and decreased by nitrogen fertilizer factory effluent. From correlation and regression analysis, A. hydrophila was found to be directly affected by phytoplankton density and, thus, indirectly by concentrations of phosphate, nitrate, and total organic carbon. These two point sources are suspect as indirect causes of red-sore disease epizootics, a disease of fish caused by A. hydrophila.