Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing and maintaining protective CD8+ memory T cells

Summary: A critical aim of vaccine‐related research is to identify the mechanisms by which memory T cells are formed and maintained over long periods of time. In recent years, we have designed experiments aimed at addressing two key questions: (i) what are the factors that maintain functionally responsive CD8+ memory cells over long periods of time, and (ii) what are the signals during the early stages of infection that drive the differentiation of long‐lived CD8+ memory T cells? We have identified a role for CD4+ T cells in the generation of CD8+ T‐cell‐mediated protection from secondary challenge. While CD4+ T cells appear to play a role in the programme of CD8 memory, we find that they are also required for the long‐term maintenance of CD8+ memory T‐cell numbers and function. This property is independent of CD40–CD40L interactions, and we propose a role for CD4+ T cells in maintaining the ability of CD8+ memory T cells to respond to interleukin‐7 (IL‐7) and IL‐15. By manipulating both the time course of infection and the timing of antigen presentation to newly recruited CD8+ T cells, we also demonstrate that the programming of effector and memory potential are at least partially distinct processes.
Molecular cloning of cDNA for caltractin, a basal body-associated Ca2+- binding protein: homology in its protein sequence with calmodulin and the yeast CDC31 gene product

An extended synthetic oligonucleotide (59-mer) was used to isolate a Chlamydomonas cDNA containing the entire coding region for a novel basal body-associated 20-kD calcium-binding protein (CaBP). DNA and RNA blot analysis indicate that the 20-kD CaBP is encoded by a single copy gene from which is derived an approximately 1.1-kb-long transcript. The deduced amino acid sequence for the protein shows a linear relatedness with calmodulin from Chlamydomonas and other organisms (45-48% identity). The primary protein sequence of the 20-kD CaBP and its predicted secondary structure suggests that the protein is likely to contain four homologous calcium-binding domains that conform to the helix-loop-helix (or EF hand) structure found in calmodulin and related calcium-modulated proteins. The major difference between the protein and calmodulin is an amino-terminal domain of 21 amino acids present on the 20-kD CaBP. In addition to its relatedness to calmodulin, the Chlamydomonas 20-kD CaBP shows a strong sequence identity (50%) with the yeast Saccharomyces cerevisiae CDC31 gene product required for spindle pole body duplication. The association of these sequence- related calcium-binding proteins to microtubule-organizing centers of divergent structure suggests a potential conserved function for the proteins.
Human Action Recognition Using Adaptive Local Motion Descriptor in Spark

Human action recognition plays a significant part in the computer vision and multimedia research society due to its numerous applications. However, despite different approaches proposed to address this problem, some issues regarding the robustness and efficiency of the action recognition still need to be solved. Moreover, due to the speedy development of multimedia applications from numerous origins, e.g., CCTV or video surveillance, there is an increasing demand for parallel processing of the large-scale video data. In this paper, we introduce a novel approach to recognize the human actions. First, we explore Apache spark with in-memory computing, to resolve the task of human action recognition in the distributed environment. Secondly, we introduce a novel feature descriptor, namely, adaptive local motion descriptor (ALMD) by considering motion and appearance, which is an extension of local ternary pattern used for static texture analysis, and ALMD also generate persistent codes to describe the local-textures. Finally, the spark machine learning library random forest is employed to recognize the human actions. Experimental results show the superiority of the proposed approach over other state-of-the-arts.
Synthesis of New Hydrated Geranylphenols and in Vitro Antifungal Activity against Botrytis cinerea

Geranylated hydroquinones and other geranylated compounds isolated from Aplydium species have shown interesting biological activities. This fact has prompted a number of studies where geranylated phenol derivatives have been synthesized in order to assay their bioactivities. In this work, we report the synthesis of a series of new hydrated geranylphenols using two different synthetic approaches and their inhibitory effects on the mycelial growth of Botrytis cinerea. Five new hydrated geranylphenols were obtained by direct coupling reaction between geraniol and phenol in dioxane/water and using BF3·Et2O as the catalyst or by the reaction of a geranylated phenol with BF3·Et2O. Two new geranylated quinones were also obtained. The synthesis and structural elucidation of all new compounds is presented. All hydrated geranylphenols efficiently inhibit the mycelial growth of B. cinerea. Their activity is higher than that observed for non-hydrated compounds. These results indicate that structural modification on the geranyl chain brings about an enhancement of the inhibition effect of geranylated phenol derivatives.
IgA-dependent, monocyte-mediated, antibacterial activity

IgA purified from the sera of patients convalescing from disseminated group C meningococcal disease induced human monocyte-mediated anti- meningococcal activity in vitro in the absence of complement. Both IgA- and IgG-dependent activity were directed against the group C meningococcal polysaccharide (Csss) capsule. The amount of IgA that was effective bound less than 1 ng of Csss. Antibacterial activity was dependent upon the length and the temperature of the test incubation and on the concentration of monocytes. The implications of this mechanism for local cell-mediated antibacterial immunity are discussed.
The 0.4 < z < 1.3 star formation history of the Universe as viewed in the far-infrared

Aims. We use the deepest existing mid- and far-infrared observations (reaching ∼3 mJy at 70 μm) obtained with Spitzer in the Great Observatories Origins Deep Survey (GOODS) and Far Infrared Deep Extragalactic Legacy survey (FIDEL) fields to derive the evolution of the rest-frame 15 μm, 35 μm, and total infrared luminosity functions of galaxies spanning z < 1.3. We thereby quantify the fractional contribution of infrared luminous galaxies to the comoving star formation rate density over this redshift range. In comparison with previous studies, the present one takes advantage of deep 70 μm observations that provide a more robust infrared luminosity indicator than 24 μm affected by the emission of PAHs at high redshift (z ∼ 1), and we use several independent fields to control cosmic variance. Methods. We used a new extraction technique based on the well-determined positions of galaxies at shorter wavelengths to extract the 24 and 70 μm flux densities of galaxies. It is found that sources separated by a minimum of 0.5 x FWHM are deblended by this technique, which facilitates multi-wavelength associations of counterparts. Using a combination of photometric and spectroscopic redshifts that exist for ∼80% of the sources in our sample, we are able to estimate the rest-frame luminosities of galaxies at 15 μm and 35 μm. By complementing direct detections with a careful stacking analysis, we measured the mid- and far-infrared luminosity functions of galaxies over a factor ∼100 in luminosity (1011 L ⊙ <∼ L IR <∼ 10 13 L ⊙ ) at z < 1.3. A stacking analysis was performed to validate the bolometric corrections and to compute comoving star-formation rate densities in three redshift bins 0.4 < z < 0.7, 0.7 < z < 1.0 and, 1.0 < z < 1.3. Results. We find that the average infrared spectral energy distribution of galaxies over the last 2/3 of the cosmic time is consistent with that of local galaxies, although individual sources do present significant scatter. We also measured both the bright and faint ends of the infrared luminosity functions and find no evidence for a change in the slope of the double power law used to characterize the luminosity function. The redshift evolution of infrared luminous galaxies is consistent with pure luminosity evolution proportional to (1 + z ) 3.6±0.4 up to z ∼ 1.3. We do not find evidence of differential evolution between LIRGs and ULIRGs up to z ∼ 1.3, in contrast with previous claims. The comoving number density of infrared luminous galaxies has increased by a factor of ∼100 between 0 < z < 1. By z ∼ 1.0, LIRGs produce half of the total comoving infrared luminosity density.
Hormonal carcinogenesis and socio‐biological development factors in endometrial cancer: A clinical review

Objective. Endometrial cancer is one of the most common invasive gynecologic malignancies in developed countries and the eighth leading cause of cancer death in women; it typically arises in the sixth or seventh decade of life. The aim of this review was to evaluate possible roles of genetic and socio‐biological factors in type I endometrial cancer, largely confined to pre‐ and perimenopausal women, with a history of estrogen exposure and/or endometrial hyperplasia. Methods. An extensive literature review, from 1990 to 2007 was performed on modifiable risk factors for type I endometrial cancer. Additionally, carcinogenesis mechanisms, biomarker and hormonal and biomolecular approaches to cancer detection, progression and monitoring and socio‐biological factors were reviewed. Results. Several socio‐biological and lifestyle characteristics, such as hormone replacement therapy, glycemic index, obesity, alcohol use, antipsychotic medication, melatonin, physical activity and variants in hormone metabolism genes have been identified as risk factors for developing endometrial cancer of type I, the majority of which are associated with excess estrogens causing continued stimulation of the endometrium. There is a genetic link to non‐polyposis colorectal cancer syndrome, but association of endometrial cancer risk to other genetic polymorphisms has yielded conflicting results. Conclusions. Many factors linked to hormonal imbalance, such as obesity, weight change, body size, alcohol, hyper‐androgenic states, glycemic index and antidepressant agents, influence the endometrial cancer risk, central to which are endogenous and exogenous estrogen hyperstimulation of the endometrium. Conversely, smoking cigarettes, diet, physical activity and melatonin production seem to reduce the risk of cancer development. Other external factors fit well with the unopposed estrogen theory, but more studies are needed to investigate modifiable and added risk factors for endometrial cancer.
Inhibition of Ca2+ Signaling by Mycobacterium tuberculosisIs Associated with Reduced Phagosome–Lysosome Fusion and Increased Survival within Human Macrophages

Complement receptor (CR)-mediated phagocytosis of Mycobacterium tuberculosis by macrophages results in intracellular survival, suggesting that M. tuberculosis interferes with macrophage microbicidal mechanisms. As increases in cytosolic Ca2+ concentration ([Ca2+]c) promote phagocyte antimicrobial responses, we hypothesized that CR phagocytosis of M. tuberculosis is accompanied by altered Ca2+ signaling. Whereas the control complement (C)-opsonized particle zymosan (COZ) induced a 4.6-fold increase in [Ca2+]c in human macrophages, no change in [Ca2+]c occurred upon addition of live, C-opsonized virulent M. tuberculosis. Viability of M. tuberculosis and ingestion via CRs was required for infection of macrophages in the absence of increased [Ca2+]c, as killed M. tuberculosis or antibody (Ab)-opsonized, live M. tuberculosis induced elevations in [Ca2+]c similar to COZ. Increased [Ca2+]c induced by Ab-opsonized bacilli was associated with a 76% reduction in intracellular survival, compared with C-opsonized M. tuberculosis. Similarly, reversible elevation of macrophage [Ca2+]c with the ionophore A23187 reduced intracellular viability by 50%. Ionophore-mediated elevation of [Ca2+]c promoted the maturation of phagosomes containing live C-opsonized bacilli, as evidenced by acidification and accumulation of lysosomal protein markers. These data demonstrate that M. tuberculosis inhibits CR-mediated Ca2+ signaling and indicate that this alteration of macrophage activation contributes to inhibition of phagosome–lysosome fusion and promotion of intracellular mycobacterial survival.
Archaefructaceae, a New Basal Angiosperm Family

Archaefructaceae is proposed as a new basal angiosperm family of herbaceous aquatic plants. This family consists of the fossilsArchaefructus liaoningensis and A.sinensis sp. nov. Complete plants from roots to fertile shoots are known. Their age is a minimum of 124.6 million years from the Yixian Formation, Liaoning, China. They are a sister clade to all angiosperms when their characters are included in a combined three-gene molecular and morphological analysis. Their reproductive axes lack petals and sepals and bear stamens in pairs below conduplicate carpels.
Power spectrum analysis for classification of heart sound recording

This study assessed the feasibility of using power spectrum analysis to compute additional features from heart sound recordings that can be used for normal / abnormal classification in the PhysioNet/Computing in Cardiology Challenge 2016. Our approach relies on the segmentation of the heart sound recording into the 4 distinct Fundamental Heart Sounds (FHS) states. Based on the FHS states, the heart sound recording is divided into multiple segments — each segment corresponds to 1 FHS state in 1 cardiac cycle. A fast Fourier transform is then performed on each of these segments. For each FHS state, we compute the ratio between the sum of the powers in the N highest peaks in the power spectrum to that of the entire power spectrum. The rationale is that the most dominant frequencies in the heart sound recording can potentially contain relevant information useful for classification. These additional features are subsequently combined with the features computed from the intervals of the 4 distinct FHS states. This enlarged set of features is used to train a feed forward neural network with 1 hidden layer for heart sound clarification. The scores of our neural network on a random subset of the test data are as follows: Sensitivity = 0.747; Specificity = 0.788; Overall = 0.767.
A meta-analysis of voucher-based reinforcement therapy for substance use disorders.

AIMS To systematically investigate the effectiveness of voucher-based reinforcement therapy for the treatment of substance use disorders. METHODS Effect sizes and 95% confidence intervals were calculated for studies published between January 1991 and March 2004 that utilized voucher-based reinforcement therapy (VBRT) or related monetary-based incentives to treat substance use disorders (SUDs). FINDINGS Thirty studies involved interventions targeting abstinence from drug use using experimental designs where effects on treatment outcome could be attributed to the VBRT intervention. The estimated average effect size (r) for those studies was 0.32 (95% CI 0.26-0.38). Analyses of variables thought to moderate VBRT effect sizes revealed that more immediate voucher delivery and greater monetary value of the voucher were associated with larger effect sizes. Additional studies were identified wherein VBRT was used to target clinic attendance (n = 6) or medication compliance (n = 4). VBRT studies targeting attendance produced average effect sizes of 0.15 (95% CI 0.02-0.28), while those that targeted medication compliance produced an average effect of 0.32 (95% CI 0.15-0.47). No significant moderators were identified for these 10 studies. CONCLUSIONS Overall, VBRT generated significantly better outcomes than did control treatments. These results further support the efficacy of VBRT, quantify the magnitude of its effects, identify significant moderators and suggest potential directions for future research.
Displacement and velocity of the coronary arteries: cardiac and respiratory motion

This paper presents measurements of three-dimensional (3-D) displacements and velocities of the coronary arteries due to the myocardial beating motion and due to breathing. Data were acquired by reconstructing the coronary arteries and their motion from biplane angiograms in 10 patients. A parametric motion model was used to separate the cardiac and breathing motion fields. The arteries move consistently toward the left, inferior, and anterior during a cardiac contraction. The displacement and velocity of the right coronary artery during a cardiac contraction was larger than measured for the left coronary tree. Cardiac motion dominates the respiratory motion of the coronary arteries during spontaneous breathing. On inspiration, the arteries move caudally, but the motion in the left-right and anterior-posterior axes was variable. Spatial variation in respiratory displacement and velocity of the coronary arteries indicates that the breathing motion of the heart is more complex than a 3-D translation.
Lambek grammars are context free

Basic categorial grammars are the context-free ones. Another kind of categorial grammars was introduced by J. Lambek (1958). These grammars are based on a syntactic calculus, known as the Lambek calculus. Chomsky (1963) conjectured that these grammars are also equivalent to context-free ones. Every basic categorial grammar (and thus every context-free grammar) is equivalent to a Lambek grammar. Conversely, some special kinds of Lambek grammars are context-free. These grammars use weakly unidirectional types, or types of order at most two. The main result of this paper says that Lambek grammars generate only context-free languages. Thus they are equivalent to context-free grammars and also to basic categorial grammars. The Chomsky conjecture, that all languages recognized by the Lambek calculus are context-free, is thus proved. <<ETX>>
Regulation of peripheral T cell activation by calreticulin

Regulated expression of positive and negative regulatory factors controls the extent and duration of T cell adaptive immune response preserving the organism's integrity. Calreticulin (CRT) is a major Ca2+ buffering chaperone in the lumen of the endoplasmic reticulum. Here we investigated the impact of CRT deficiency on T cell function in immunodeficient mice reconstituted with fetal liver crt −/− hemopoietic progenitors. These chimeric mice displayed severe immunopathological traits, which correlated with a lower threshold of T cell receptor (TCR) activation and exaggerated peripheral T cell response to antigen with enhanced secretion of inflammatory cytokines. In crt −/− T cells TCR stimulation induced pulsatile cytosolic elevations of Ca2+ concentration and protracted accumulation of nuclear factor of activated T cells in the nucleus as well as sustained activation of the mitogen-activated protein kinase pathways. These observations support the hypothesis that CRT-dependent shaping of Ca2+ signaling critically contributes to the modulation of the T cell adaptive immune response.
TripleBit: a Fast and Compact System for Large Scale RDF Data

The volume of RDF data continues to grow over the past decade and many known RDF datasets have billions of triples. A grant challenge of managing this huge RDF data is how to access this big RDF data efficiently. A popular approach to addressing the problem is to build a full set of permutations of (S, P, O) indexes. Although this approach has shown to accelerate joins by orders of magnitude, the large space overhead limits the scalability of this approach and makes it heavyweight. In this paper, we present TripleBit, a fast and compact system for storing and accessing RDF data. The design of TripleBit has three salient features. First, the compact design of TripleBit reduces both the size of stored RDF data and the size of its indexes. Second, TripleBit introduces two auxiliary index structures, ID-Chunk bit matrix and ID-Predicate bit matrix, to minimize the cost of index selection during query evaluation. Third, its query processor dynamically generates an optimal execution ordering for join queries, leading to fast query execution and effective reduction on the size of intermediate results. Our experiments show that TripleBit outperforms RDF-3X, MonetDB, BitMat on LUBM, UniProt and BTC 2012 benchmark queries and it offers orders of mangnitude performance improvement for some complex join queries.
Evaluation of forensic cases admitted to pediatric intensive care unit.

AIM This study aimed to determine the epidemiological and clinical characteristics of pediatric forensic cases to contribute to the literature and to preventive health care services. MATERIAL AND METHODS Pediatric forensic cases hospitalized in our pediatric intensive care unit below the age of 17 years were reviewed retrospectively (January 2009-June 2014) . The patients were evaluated in two groups as physical traumas (Group A) and poisonings (Group B). The patients' age, gender, complaints at presentation, time of presentation and referral (season, time) and, mortality rates were determined. Cases of physical trauma (Group A) were classified as traffic accidents, falling down from height, falling of device, drowning, electric shock, burns and child abuse. Poisonings (Group B) were classified as pharmaceuticals, pesticides, other chemicals and unknown drug poisonings. RESULTS Two hundred twenthy cases were included. The mean age was 5.1+3.1 years. One hundred fifteen (%52.5) of the cases were male and 105 (%47.5) were female. Group A consisted of 62 patients and Group B consisted of 158 patients. The patients presented most frequently in summer months. The most common reason for presentation was falling down from height (12.7%) in Group A and accidental drug poisoning (most frequently antidepressants) in Group B. The mortality rate was 5%. CONCLUSION Forensic cases in the pediatric population (physical trauma and poisoning) are preventable health problems. Especially, preventive approach to improve the environment for falling down from height must be a priority. Increasing the awareness of families and the community on this issue, in summer months during which forensic cases are observed most frequently can contribute to a reduction in the number of cases.
Highly Selective Receptive Fields in Mouse Visual Cortex

Genetic methods available in mice are likely to be powerful tools in dissecting cortical circuits. However, the visual cortex, in which sensory coding has been most thoroughly studied in other species, has essentially been neglected in mice perhaps because of their poor spatial acuity and the lack of columnar organization such as orientation maps. We have now applied quantitative methods to characterize visual receptive fields in mouse primary visual cortex V1 by making extracellular recordings with silicon electrode arrays in anesthetized mice. We used current source density analysis to determine laminar location and spike waveforms to discriminate putative excitatory and inhibitory units. We find that, although the spatial scale of mouse receptive fields is up to one or two orders of magnitude larger, neurons show selectivity for stimulus parameters such as orientation and spatial frequency that is near to that found in other species. Furthermore, typical response properties such as linear versus nonlinear spatial summation (i.e., simple and complex cells) and contrastinvariant tuning are also present in mouse V1 and correlate with laminar position and cell type. Interestingly, we find that putative inhibitory neurons generally have less selective, and nonlinear, responses. This quantitative description of receptive field properties should facilitate the use of mouse visual cortex as a system to address longstanding questions of visual neuroscience and cortical processing.