Miracle-dz/UniFAR-FTUs huggingface dataset:
Cords, channels, corridors and conduits: critical architectural elements facilitating cell interactions in the lymph node cortex

: The lymph node cortex is a critical site for encounter between recirculating T cells and their specific antigens. Due to its extreme plasticity, little is understood of the underlying functional unit of the lymph node cortex, the paracortical cord. The idealized paracortical cord (approximately 100 nm by 1000 μm) stretches from a medullary cord to the base of a B‐cell follicle. In cross‐section, a cord can be visualized as a set of nested cylinders consisting of spaces bounded by cells. The spaces are: i) the lumen of the high endothelial venule (HEV), ii) perivenular channels ‐ narrow potential spaces (0.1 μm) tightly encircling the HEV, iii) corridors – broad spaces (10–15 μm) constituting the majority of the parenchyma, and iv) the cortical sinus. In addition to these spaces for cell traffic, the conduit (fifth space) is a special delivery system for the transit of soluble factors to the HEV and emigrating lymphocytes. The cellular barriers between these spaces are high endothelium, tibroblastic reticular cells, or sinus‐lining cells. This review describes the spaces of the paracortical cord and their cellular boundaries, outlines the movement of cells and fluids through these spaces, and discusses how this anatomy affects the efficiency of surveillance by T cells.
Influences on neural lineage and mode of division in the zebrafish retina in vivo

Cell determination in the retina has been under intense investigation since the discovery that retinal progenitors generate clones of apparently random composition (Price, J., D. Turner, and C. Cepko. 1987. Proc. Natl. Acad. Sci. USA. 84:156–160; Holt, C.E., T.W. Bertsch, H.M. Ellis, and W.A. Harris. 1988. Neuron. 1:15–26; Wetts, R., and S.E. Fraser. 1988. Science. 239:1142–1145). Examination of fixed tissue, however, sheds little light on lineage patterns or on the relationship between the orientation of division and cell fate. In this study, three-dimensional time-lapse analyses were used to trace lineages of retinal progenitors expressing green fluorescent protein under the control of the ath5 promoter. Surprisingly, these cells divide just once along the circumferential axis to produce two postmitotic daughters, one of which becomes a retinal ganglion cell (RGC). Interestingly, when these same progenitors are transplanted into a mutant environment lacking RGCs, they often divide along the central-peripheral axis and produce two RGCs. This study provides the first insight into reproducible lineage patterns of retinal progenitors in vivo and the first evidence that environmental signals influence the orientation of cell division and the lineage of neural progenitors.
Modeling direction selectivity of simple cells in striate visual cortex within the framework of the canonical microcircuit

Nearly all models of direction selectivity (DS) in visual cortex are based on feedforward connection schemes, where geniculate input provides all excitatory synaptic input to both pyramidal and inhibitory neurons. Feedforward inhibition then suppresses feedforward excitation for nonoptimal stimuli. Anatomically, however, the majority of asymmetric, excitatory, synaptic contacts onto cortical cells is provided by other cortical neurons, as embodied in the Canonical Microcircuit of Douglas and Martin (1991). In this view, weak geniculate input is strongly amplified in the preferred direction by the action of intracortical excitatory connections, while in the null direction inhibition reduces geniculate-induced excitation. We investigate analytically and through biologically realistic computer simulations the functioning of a cortical network based on massive excitatory, cortico-cortical feedback. The behavior of this network is compared to physiological data as well as to the behavior of a purely feedforward model of DS based on nonlagged input. Our model explains a number of puzzling features of direction selective simple cells, including the small somatic input conductance changes that have been measured experimentally during stimulation in the null direction, and the persistence of DS while fully blocking inhibition in a single cell. Although the operation at the heart of our network is amplification, the network passes the linearity test of (Jagadeesh et al., 1993). We make specific predictions concerning the effect of selective blockade of cortical inhibition on the velocity-response curve.
Learning Distributed Representations of Sentences from Unlabelled Data

Unsupervised methods for learning distributed representations of words are ubiquitous in today's NLP research, but far less is known about the best ways to learn distributed phrase or sentence representations from unlabelled data. This paper is a systematic comparison of models that learn such representations. We find that the optimal approach depends critically on the intended application. Deeper, more complex models are preferable for representations to be used in supervised systems, but shallow log-linear models work best for building representation spaces that can be decoded with simple spatial distance metrics. We also propose two new unsupervised representation-learning objectives designed to optimise the trade-off between training time, domain portability and performance.
Family Instability and Child Well-Being

Children who experience multiple transitions in family structure may face worse developmental outcomes than children raised in stable, two-parent families, and perhaps even worse than children raised in stable, single-parent families—a point denoted in much prior research. Multiple transitions and negative child outcomes, however, may be associated through common causal factors such as parents' antecedent behaviors and attributes. Using a nationally-representative, two-generation longitudinal survey that includes detailed information on children's behavioral and cognitive development, family history, and mothers' attributes prior to children's births, we examine these alternative hypotheses. Our results suggest that, for white children, the association between the number of family structure transitions and cognitive outcomes is largely explained by mothers' prior characteristics but that the association between the number of transitions and behavioral outcomes may be causal in part. We find no robust effects for number of transitions for black children.
Practical Feature Selection: from Correlation to Causality

Feature selection encompasses a wide variety of methods for selecting a restricted number of input variables or “features”, which are “relevant” to a problem at hand. In this report, we guide practitioners through the maze of methods, which have recently appeared in the literature, particularly for supervised feature selection. Starting from the simplest methods of feature ranking with correlation coefficients, we branch in various direction and explore various topics, including “conditional relevance”, “local relevance”, “multivariate selection”, and “causal relevance”. We make recommendations for assessment methods and stress the importance of matching the complexity of the method employed to the available amount of training data. Software and teaching material associated with this tutorial are available [12].
Quantifying loop nest locality using SPEC'95 and the perfect benchmarks

This article analyzes and quantifies the locality characteristics of numerical loop nests in order to suggest future directions for architecture and software cache optimizations. Since most programs spend the majority of their time in nests, the vast majority of cache optimization techniques target loop nests. In contrast, the locality characteristics that drive these optimizations are usually collected across the entire application rather than at the nest level. Researchers have studied numerical codes for so long that a number of commonly held assertions have emerged on their locality characteristics. In light of these assertions, we use the SPEC'95 and Perfect Benchmarks to take a new look at measuring locality on numerical codes based on references, loop nests, and program locality properties. Our results show that several popular assertions are at best overstatements. For example, although most reuse is within a loop nest, in line with popular assertions, most misses are internest capacity misses, and they correspond to potential reuse between nearby loop nests. In addition, we find that temporal and spatial reuse have balanced roles within a loop nest and that most reuse across nests and the entire program is temporal. These results are consistent with high hit rates (80&percent; or more hits), but go against the commonly held assumption that spatial reuse dominates. Our locality measurements reveal important differences between loop nests and programs, refute some popular assertions, and provide new insights for the compiler writer and the architect.
Production and optimization of cellulase from Fusarium oxysporum by submerged fermentation

Fusarium oxysporum, isolated from infected tomato plant parts, produced maximum cellulase at optimum parameters (pH, 6.0; temp., 50°C; and incubation period, 12 d) in cellulase enzyme production broth having 1% CMC (carboxy methyl cellulose) as a cellulose substrate. Activities of purified cellulases (mol wt, 24, 29 and 45 kDa) were stimulated by concentrations (0-70 mM) of Na + and Mg ++ , while EDTA inhibited enzyme activity at all concentrations.
Projective Structure from Uncalibrated Images: Structure From Motion and Recognition

Address the problem of reconstructing 3-D space in a projective framework from two or more views, and the problem of artificially generating novel views of the scene from two given views (reprojection). The author describes an invariance relation that provides a new description of structure, which the author calls projective depth, that is captured by a single equation relating image point correspondences across two or more views and the homographics of two arbitrary virtual planes. The framework is based on knowledge of correspondence of features across views, is linear and extremely simple, and the computations of structure readily extend to overdetermination using multiple views. Experimental results demonstrate a high degree of accuracy in both tasks: reconstruction and reprojection. >
Are oral and dental diseases linked to cancer?

OBJECTIVE Infection and inflammation play a role in carcinogenesis, and highly prevalent oral and dental diseases have been significantly linked to some types of cancer. This article reviews current literature in this area. MATERIALS AND METHODS Open literature review using the PubMed database and focused on publications from 2000 to 2010. RESULTS Numerous potential mechanisms are implicated in the oral disease/carcinogenesis paradigm, including infection- and inflammation-associated cell pathology and microbial carcinogen metabolism. Poor oral hygiene is associated with oral cancer, but there is also evidence of a possible link between oral or dental infections and malignancies in general. CONCLUSION Oral infections may trigger malignant transformation in tissues of the mouth and other organs. However, scientific evidence to date remains weak and further well-conducted studies are warranted before cancer can be properly added to the list of oral infection-related systemic diseases.
A facile method of shielding from UV damage by polymer photonic crystals

BACKGROUND: UV radiation is a potent and ubiquitous carcinogen, which is responsible for most of the skin cancer in the human population. General UV protection materials may produce dangerous degradation products under UV irradiation; therefore, safe, nontoxic and simple UV protection approaches are urgent requirements. RESULTS: A series of photonic crystals with stopband covering the range 200–400 nm have been fabricated which can shield radiation from the whole UV range. Both UV-visible and 1H NMR results confirm the effective protection from UV light of 254 nm. CONCLUSIONS: A facile method for UV protection has been demonstrated by utilizing the unusual optical properties of photonic crystals that can inhibit light propagation at a given frequency without specific requirement of chemical composition. This approach opens a new way to protect from UV damage using safe materials, which is of great significance for extending the practical applications of photonic crystals. Copyright © 2007 Society of Chemical Industry
Randomness is Linear in Space

We show that any randomized algorithm that runs in spaceSand timeTand uses poly(S) random bits can be simulated using onlyO(S) random bits in spaceSand timeT+poly(S). A deterministic simulation in spaceSfollows. Of independent interest is our main technical tool: a procedure which extracts randomness from a defective random source using a small additional number of truly random bits.
Validity and power in hemodynamic response modeling: A comparison study and a new approach

One of the advantages of event‐related functional MRI (fMRI) is that it permits estimation of the shape of the hemodynamic response function (HRF) elicited by cognitive events. Although studies to date have focused almost exclusively on the magnitude of evoked HRFs across different tasks, there is growing interest in testing other statistics, such as the time‐to‐peak and duration of activation as well. Although there are many ways to estimate such parameters, we suggest three criteria for optimal estimation: 1) the relationship between parameter estimates and neural activity must be as transparent as possible; 2) parameter estimates should be independent of one another, so that true differences among conditions in one parameter (e.g., hemodynamic response delay) are not confused for apparent differences in other parameters (e.g., magnitude); and 3) statistical power should be maximized. In this work, we introduce a new modeling technique, based on the superposition of three inverse logit functions (IL), designed to achieve these criteria. In simulations based on real fMRI data, we compare the IL model with several other popular methods, including smooth finite impulse response (FIR) models, the canonical HRF with derivatives, nonlinear fits using a canonical HRF, and a standard canonical model. The IL model achieves the best overall balance between parameter interpretability and power. The FIR model was the next‐best choice, with gains in power at some cost to parameter independence. We provide software implementing the IL model. Hum Brain Mapp 2006. © 2006 Wiley‐Liss, Inc.
A new flavonoid and other constituents from Centaurea nicaeensis All. var. walliana M.

A new flavone glucoside, apigenin 4′-(6″-methylglucuronide) (1), together with six known compounds, cirsilineol, jaceosidin, melitensin, apigenin, apigenin 7-(6″-methylglucuronide) and prunasin, were isolated from the ethanolic extract of the aerial parts of Centaurea nicaeensis All. var. walliana M. (Asteraceae) collected from Souk-Ahras, eastern Algeria. The structures were established by spectral analysis, mainly HRESI-MS, UV and 2D-NMR experiments (COSY, HSQC and HMBC).
Interdependencies of Critical Radius, Critical Energy and Surface Energy (CRESE) in Silicon Self-Assembled Nanodots

The interdependence parameters in the growth of silicon self-assembled nanodots are investigated. Accordingly, the critical radius, critical energy change and surface energy can be interpreted in terms of cubic function, where it produced a critical surface energy NS* and the corresponding r* and G*, called a CRESE point at a fixed growth temperature T when solved mathematically. It is defined as a limiting point at which equilibrium of the critical parameters take place at a constant temperature. Experiments were performed on the samples of amorphous silicon nanodots fabricated onto different non-crystalline substrates. A further analysis on the NS*-T plots revealed inverse linear relationships which converged at a CID point (o*,T*) when projected near the solidification temperature of silicon. The results suggested strong influence of atomic bonding at the nucleus-surface interface combined with higher surface roughness. In conclusion, there exists an equilibrium condition among the growth parameters which stabilizes the growth of amorphous silicon nanodots, as well as the existence of CRESE’s ideal destination (CID).
Altered Cardiac Repolarization in Association with Air Pollution and Air Temperature among Myocardial Infarction Survivors

Background Epidemiological studies have shown that ambient particulate matter (PM) and changes in air temperature are associated with increased cardiopulmonary events. Objective We hypothesized that patients with previous myocardial infarction (MI) experience changes in heart rate (HR) and repolarization parameters, such as Bazett-corrected QT interval (QTc), and T-wave amplitude (Tamp), in association with increases in air pollution and temperature changes. Methods Between May 2003 and February 2004, 67 MI survivors from the Augsburg KORA-MI registry repeatedly sent 16 sec electrocardiograms (ECGs) with a personal transmitter (Viapac) via telephone to the Philips Monitoring Center, where ECG parameters were immediately analyzed. Meteorological data and air pollutants were acquired from fixed monitoring sites on an hourly basis. Additive mixed models were used for analysis. Effect modification by patient characteristics was investigated. Results The analysis of the 1,745 ECGs revealed an increased HR associated with interquartile range (IQR) increases in PM levels among participants not using beta-adrenergic receptor blockers and among those with body mass index ≥ 30 kg/m2. We observed a 24- to 47-hr lagged QTc prolongation [0.5% change (95% confidence interval, 0.0–1.0%)] in association with IQR increases in levels of PM ≤ 2.5 μm in aerodynamic diameter, especially in patients with one [0.6% (0.1–1.0%)] or two [1.2% (0.4–2.1%)] minor alleles of the nuclear factor (erythroid-derived 2)-like 2 (NFE2L2) single-nucleotide polymorphism rs2364725. Positive immediate (0–23 hr) and inverse delayed (48–71 hr up to 96–119 hr) associations were evident between PM and Tamp. We detected an inverse U-shaped association between temperature and Tamp, with a maximum Tamp at 5°C. Conclusions Increased air pollution levels and temperature changes may lead to changes in HR and repolarization parameters that may be precursors of cardiac problems.
A Comparative Study of the Sedative Effect of Oral Midazolam and Oral Promethazine Medication in Lumbar Puncture

Objective Lumbar puncture (LP) essentially is a painful and stressful procedure, however indicated for diagnosis and therapeutic purposes. One way to reduce the anxiety is to administer an oral premedication. The aim of this study is to compare clinical effects of oral midazolam and oral promethazine in LP. Materials & Methods This prospective randomized controlled clinical trial study was performed on 80 children aged 2-7 years that were candidate for LP. They were divided into two randomized equal groups. First group received oral midazolam syrup 0.5 mg/kg and the other group received oral promethazine syrup 1mg/kg. Level of sedation, hemodynamic changes and any other complications were monitored every 5 minutes from 30 minutes before the start of the procedure. Results Midazolam group and promethazine group were similar in age, gender and weight. Midazolam had significantly shorter onset of sedation and also shorter duration to maximal sedation. The two groups were similar with respect to sedative effect at all time. The only complication that was significantly more in midazolam group was nausea and vomiting. Conclusion Midazolam syrup and promethazine syrup have same sedative effect in children. Both of these medications are easy to use in preschool children and none of them appeared to be superior to another.
Low‐affinity nerve growth factor receptor (P75 NGFR) as a marker of perineural invasion in malignant melanomas

Background: Perineural invasion (PNI) is a well‐recognized route of tumor extension in cutaneous neoplasms. Despite an established association with increased local recurrences and metastases, the mechanisms responsible for PNI have yet to be elucidated. We hypothesize that P75 NGFR, a nerve growth factor receptor, may be implicated in the pathogenesis of PNI in these tumors.
Modelling Genetic Susceptibility to Multiple Sclerosis with Family Data

A genetic contribution to susceptibility is well established in multiple sclerosis (MS) and 57 associated genetic loci have been identified. We have undertaken a meta-analysis of familial risk studies with the aims of providing definitive figures for risks to relatives, performing a segregation analysis and estimating the proportion of the overall genetic risk that currently identified genes represent. We have used standard methods of meta-analysis combined with novel approaches to age adjustment to provide directly comparable estimates of lifetime risk. The overall recurrence risk for monozygotic twins was 18.2% and for siblings 2.7%. The recurrence risk for dizygotic twins was significantly higher than for siblings. The overall estimate of sibling relative risk (λS) was 16.8. Risks for older relatives (parents, siblings, aunts, uncles and cousins) show a latitudinal gradient, in line with population risk. No latitudinal gradient for λS was seen. Segregation analysis supports a multiplicative model of one locus of moderate effect with many loci of small effect. The estimated contribution of the 57 known MS loci is 18–24% of λS. This meta-analysis supports the notion of MS being in part the result of multiple genetic susceptibility factors and environmental factors.
Subtype-Specific Sorting of the ETA Endothelin Receptor by a Novel Endocytic Recycling Signal for G Protein-Coupled Receptors

We have previously reported that endocytic sorting of ETA endothelin receptors to the recycling pathway is dependent on a signal residing in the cytoplasmic carboxyl-terminal region. The aim of the present work was to characterize the carboxyl-terminal recycling motif of the ETA receptor. Assay of truncation mutants of the ETA receptor with increasing deletions of the carboxyl-terminal tail revealed that amino acids 390 to 406 contained information critical for the ability of the receptor to recycle. This peptide sequence displayed significant sequence similarity to several protein segments confirmed by X-ray crystallography to adopt antiparallel β-strand structures (β-finger). One of these segments was the β-finger motif of neuronal nitric-oxide synthase reported to function as an internal PDZ (postsynaptic density-95/disc-large/zona occludens) domain-binding ligand. Based on these findings, the three-dimensional structure of the recycling motif of ETA receptor was predicted to attain a β-finger conformation acting as an internal PDZ ligand. Site-directed mutagenesis at residues that would be crucial to the structural integrity of the putative β-finger conformation or PDZ ligand function prevented recycling of the ETA receptor. Analysis of more than 300 G protein-coupled receptors (GPCRs) identified 35 different human GPCRs with carboxylterminal sequence patterns that fulfilled the structural criteria of an internal PDZ ligand. Among these are several receptors reported to follow a recycling pathway. In conclusion, recycling of ETA receptor is mediated by a motif with the structural characteristics of an internal PDZ ligand. This structural motif may represent a more general principle of endocytic sorting of GPCRs.