Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular Adenosine Triphosphate (ATP) Concentration: A Switch in the Decision Between Apoptosis and Necrosis

Apoptosis and necrosis are considered conceptually and morphologically distinct forms of cell death. Here, we report that demise of human T cells caused by two classic apoptotic triggers (staurosporin and CD95 stimulation) changed from apoptosis to necrosis, when cells were preemptied of adenosine triphosphate (ATP). Nuclear condensation and DNA fragmentation did not occur in cells predepleted of ATP and treated with either of the two inducers, although the kinetics of cell death were unchanged. Selective and graded repletion of the extramitochondrial ATP/pool with glucose prevented necrosis and restored the ability of the cells to undergo apoptosis. Pulsed ATP/depletion/repletion experiments also showed that ATP generation either by glycolysis or by mitochondria was required for the active execution of the final phase of apoptosis, which involves nuclear condensation and DNA degradation.
Lipschitz Continuity of Optimal Controls for State Constrained Problems

This paper provides new conditions under which optimal controls are Lipschitz continuous for dynamic optimization problems with functional inequality constraints, a control constraint expressed in terms of a general closed convex set and a coercive cost function. It is shown that the linear independence condition on active state constraints, present in the earlier literature, can be replaced by a less restrictive, positive linear independence condition that requires linear independence merely with respect to nonnegative weighting parameters. Smoothness conditions on the data, imposed in earlier work, are also relaxed. The new conditions for Lipschitz continuity of optimal controls are obtained by a detailed analysis of the implications of first order optimality conditions in the form of a nonsmooth maximum principle.
The Contribution of Family, School and Community Characteristics to Inequality in Education and Labor Market Outcomes

This paper examines the impact of high school quality on three subsequent outcomes of concern to economists and policymakers: high school graduation, college enrollment, and adult wages. We isolate the causal impact of school/neighborhood combinations from student sorting among schools by exploiting panel data from three national longitudinal surveys. We decompose each of our three outcomes into the withinand between-school contributions of both observed and unobserved student and family characteristics, as well as the contributions of observed and unobserved school and neighborhood variables that vary only across schools. Instead of attempting to disentangle school averages of individual-level unobservable inputs from school-level unobservable inputs, we estimate upper and lower bounds on the contribution of school quality to student outcomes. On the one hand, the vast majority of the variation in students’ outcomes can be attributed to some combination of student inputs, parent inputs, and quality of schooling prior to high school. On the other hand, the small fraction of the variance attributable to differences in school quality translates into substantial impacts on high school graduation and college enrollment, since large numbers of students seem to be near the decision margin. Our lower bound estimates of the average increase in the probability of graduation from moving a student from a school at the 10th percentile of the quality distribution to a school at the 90th percentile range from . 06 to . 13, with the corresponding lower bound estimates for college enrollment ranging from . 14 to . 23. The upper bound estimates are a few points higher. We also find a substantial effect of schools on adult wage rates. Finally, we find that the impact of attending a high quality school on college enrollment increased between 1972 and 1988, but remained stable between 1988 and 2000. ∗Yale University and NBER. ∗∗Yale University. We thank Rebecca Blank, Greg Duncan, Richard Murnane, Lawrence Katz, Jesse Rothstein, and participants in a conference at the Brookings Institution (November 2009) and a seminar at Yale (June 2010) for helpful comments. We are responsible for the remaining shortcomings of the paper.
Two-Photon Microscopy for Imaging of the (Atherosclerotic) Vascular Wall: A Proof of Concept Study

Background: Understanding atherogenesis will benefit significantly from simultaneous imaging, both ex vivo and in vivo, of structural and functional information at the (sub)cellular level within intact arteries. Due to limited penetration depth and loss of resolution with depth, intravital and confocal fluorescence microscopy are not suitable to study (sub)cellular details in arteries with wall thicknesses above 50 µm. Methods: Using two-photon laser scanning microscopy (TPLSM), which combines 3D resolution and large penetration depth, we imaged mouse carotid arteries. Results: In thin slices, (sub)cellular structures identified using histochemical techniques could also be identified using TPLSM. Ex vivo, structural experiments on intact atherosclerotic arteries of Apo-E–/– mice demonstrated that in contrast to confocal or wide-field microscopy, TPLSM can be used to visualize (sub) cellular structural details of atherosclerotic plaques. In vivo, pilot experiments were carried out on healthy arteries of wild-type C57BL6 and atherosclerotic arteries of Apo-E–/– mice. As an example of functional measurements, we visualized fluorescently labeled leukocytes in vivo in the lumen. Additionally, detailed morphological information of vessel wall and atherosclerotic plaque was obtained after topical staining. Conclusions: Thus, TPLSM potentially allows combined functional and structural studies and can therefore be eminently suitable for investigating structure-function relationships at the cellular level in atherogenesis in the mouse.
Rice Yellow Mottle Virus, an RNA Plant Virus, Evolves as Rapidly as Most RNA Animal Viruses

ABSTRACT The rate of evolution of an RNA plant virus has never been estimated using temporally spaced sequence data, by contrast to the information available on an increasing range of animal viruses. Accordingly, the evolution rate of Rice yellow mottle virus (RYMV) was calculated from sequences of the coat protein gene of isolates collected from rice over a 40-year period in different parts of Africa. The evolution rate of RYMV was estimated by pairwise distance linear regression on five phylogeographically defined groups comprising a total of 135 isolates. It was further assessed from 253 isolates collected all over Africa by Bayesian coalescent methods under strict and relaxed molecular clock models and under constant size and skyline population genetic models. Consistent estimates of the evolution rate between 4 × 10−4 and 8 × 10−4 nucleotides (nt)/site/year were obtained whatever method and model were applied. The synonymous evolution rate was between 8 × 10−4 and 11 × 10−4 nt/site/year. The overall and synonymous evolution rates of RYMV were within the range of the rates of 50 RNA animal viruses, below the average but above the distribution median. Experimentally, in host change studies, substitutions accumulated at an even higher rate. The results show that an RNA plant virus such as RYMV evolves as rapidly as most RNA animal viruses. Knowledge of the molecular clock of plant viruses provides methods for testing a wide range of biological hypotheses.
Annexin V binding to platelets is agonist, time and temperature dependent

Platelets bind annexin V when stimulated with combinations of platelet agonists such as collagen and thrombin. Previous studies have demonstrated significant heterogeneity of platelets binding annexin V. The relative role of the thrombin protease-activated receptors (PARs), PAR1 and PAR4, together with different methods of platelet preparation on annexin V binding to platelets is unclear. We therefore investigated the role of PAR1- and PAR4-activating peptides in combination with collagen-related peptide on annexin V binding. In diluted whole blood, PAR1- and PAR4-activating peptides were as effective as thrombin in inducing annexin V binding. However, in washed platelets, PAR-activating peptides were less potent than thrombin at inducing annexin V binding. This difference was more pronounced when experiments were performed at 37°C compared to room temperature. In studies of diluted whole blood, platelet rich plasma and washed platelets, platelets incubated at room temperature bound more annexin V than platelets incubated at 37°C. We also saw a significant effect of time on annexin V binding, in that more annexin V bound to platelets with longer incubation times. In conclusion, PAR1 and PAR4-activating peptides were as effective as thrombin in inducing annexin V binding in combination with collagen-related peptide in diluted whole blood and platelet rich plasma, but not in washed platelets. In addition, incubation temperature and time has a strong influence on annexin V binding to platelets. Thus variations in these conditions may explain the differences observed between previous studies.
Survey and benchmark of block ciphers for wireless sensor networks

Cryptographic algorithms play an important role in the security architecture of wireless sensor networks (WSNs). Choosing the most storage- and energy-efficient block cipher is essential, due to the facts that these networks are meant to operate without human intervention for a long period of time with little energy supply, and that available storage is scarce on these sensor nodes. However, to our knowledge, no systematic work has been done in this area so far. We construct an evaluation framework in which we first identify the candidates of block ciphers suitable for WSNs, based on existing literature and authoritative recommendations. For evaluating and assessing these candidates, we not only consider the security properties but also the storage- and energy-efficiency of the candidates. Finally, based on the evaluation results, we select the most suitable ciphers for WSNs, namely Skipjack, MISTY1, and Rijndael, depending on the combination of available memory and required security (energy efficiency being implicit). In terms of operation mode, we recommend Output Feedback Mode for pairwise links but Cipher Block Chaining for group communications.
Electron acceleration behind the dipolarization fronts in the magnetotail

Summary form only given. We investigate the electron acceleration behind dipolarization fronts (DFs) in the magnetotail from -25 RE to -10RE through the examination of the energetic electron energy flux (>30 keV) with the observations from THEMIS satellites. Statistical results of 133 DF events are presented based on the dataset from January to April of the years 2008 and 2009. As the DFs propagate earthward, the acceleration of energetic electrons behind the DFs is found to take place over several RE along the tail. The increase in energetic electron energy flux can reach 2~4 orders of magnitude. The dominant acceleration mechanisms are different in the mid-tail (XGSM ≤-15RE) and the near-Earth region (-15<;XGSM ≤-10RE). In the mid-tail, the majority of DF events show that the dominant electron acceleration mechanism is betatron acceleration. In the near-Earth region, betatron acceleration is dominant in ~46% DF events while Fermi acceleration is dominant in ~39% DF events.
Genetic counseling and presymptomatic testing programs for Machado-Joseph Disease: lessons from Brazil and Portugal

Machado-Joseph disease (MJD) is an autosomal dominant, late-onset neurological disorder and the most common form of spinocerebellar ataxia (SCA) worldwide. Diagnostic genetic testing is available to detect the disease-causing mutation by direct sizing of the CAG repeat tract in the ataxin 3 gene. Presymptomatic testing (PST) can be used to identify persons at risk of developing the disease. Genetic counseling provides patients with information about the disease, genetic risks, PST, and the decision-making process. In this study, we present the protocol used in PST for MJD and the relevant observations from two centers: Brazil (Porto Alegre) and Portugal (Porto). We provide a case report that illustrates the significant ethical and psychological issues related to PST in late-onset neurological disorders. In both centers, counseling and PST are performed by a multidisciplinary team, and genetic testing is conducted at the same institutions. From 1999 to 2012, 343 individuals sought PST in Porto Alegre; 263 (77%) of these individuals were from families with MJD. In Porto, 1,530 individuals sought PST between 1996 and 2013, but only 66 (4%) individuals were from families with MJD. In Brazil, approximately 50% of the people seeking PST eventually took the test and received their results, whereas 77% took the test in Portugal. In this case report, we highlight several issues that might be raised by the consultand and how the team can extract significant information. Literature about PST testing for MJD and other SCAs is scarce, and we hope this report will encourage similar studies and enable the implementation of PST protocols in other populations, mainly in Latin America.
Pulmonary Function and Incidence of Selected Respiratory Diseases Depending on the Exposure to Ambient PM10

It is essential in pulmonary disease research to take into account traffic-related air pollutant exposure among urban inhabitants. In our study, 4985 people were examined for spirometric parameters in the presented research which was conducted in the years 2008–2012. The research group was divided into urban and rural residents. Traffic density, traffic structure and velocity, as well as concentrations of selected air pollutants (CO, NO2 and PM10) were measured at selected areas. Among people who live in the city, lower percentages of predicted values of spirometric parameters were noticed in comparison to residents of rural areas. Taking into account that the difference in the five-year mean concentration of PM10 in the considered city and rural areas was over 17 μg/m3, each increase of PM10 by 10 μg/m3 is associated with the decline in FEV1 (forced expiratory volume during the first second of expiration) by 1.68%. These findings demonstrate that traffic-related air pollutants may have a significant influence on the decline of pulmonary function and the growing rate of respiratory diseases.
Analysis of precipitation strengthening process in 2xxx aluminium alloys

This paper is showing the results of study devoted to determination of the chemical composition and strengthening process parameters effect on the precipitation sequence of intermetallic phases in the supersaturated 2xxx aluminium alloys. This study was based on a calorimetric study where temperature’s effects were determined when precipitation process occurred during heating with different heating rate of the supersaturated alloys group of 2xxx. Based on the calorimetric curves and estimated values of ln(Q/T2) and 1000/RT an activation energy for precipitation and dissolution of phase components were evaluated.
X-band MMIC power amplifier with an on-chip temperature compensation circuit

An X-band MMIC power amplifier with an on-chip temperature compensation circuit has been presented. The temperature compensation circuit is composed of a diode and a resistor. The compensation circuit is applied to a 4 stage X-band MMIC power amplifier. The gain variation is improved from 5.5 dB to 1.3 dB in the temperature range between -10 degC and +80 degC.
Graph Sampling for Covariance Estimation

In this paper, the focus is on subsampling as well as reconstructing the second-order statistics of signals residing on nodes of arbitrary undirected graphs. Second-order stationary graph signals may be obtained by graph filtering zero-mean white noise and they admit a well-defined power spectrum whose shape is determined by the frequency response of the graph filter. Estimating the graph power spectrum forms an important component of stationary graph signal processing and related inference tasks such as Wiener prediction or inpainting on graphs. The central result of this paper is that by sampling a significantly smaller subset of vertices and using simple least squares, we can reconstruct the second-order statistics of the graph signal from the subsampled observations, and more importantly, without any spectral priors. To this end, both a nonparametric approach as well as parametric approaches including moving average and autoregressive models for the graph power spectrum are considered. The results specialize for undirected circulant graphs in that the graph nodes leading to the best compression rates are given by the so-called minimal sparse rulers. A near-optimal greedy algorithm is developed to design the subsampling scheme for the nonparametric and the moving average models, whereas a particular subsampling scheme that allows linear estimation for the autoregressive model is proposed. Numerical experiments on synthetic as well as real datasets related to climatology and processing handwritten digits are provided to demonstrate the developed theory.
Prodigiosin production from Serratia marcescens strains obtained from farm soil

Prodigiosin is a red color pigment produced by the bacterium Serratia marcescens. Prodigiosin is emerging as a valuable molecule because of its large applications. The pigment is anticancer, immunosuppressant, antifungal, algicidal and many more applications are still to be studied. It has already been proved that pigmented strain of Serratia marcescens is less virulent than non-pigmented strains. Moreover the strain we have obtained is from farm soil which indicates that prodigiosin production can be carried safely using this strain. In present study we employed an already characterized pigmented strain which was confirmed by morphological, biochemical and phylogenetic studies. A non-pigmented strain was used as negative control. The levels of prodigiosin are studied in peptone glycerol broth and nutrient broth. Influence of aeration is also studied which indicates that higher levels of prodigiosin are found in the media kept for aeration. We found that the prodigiosin production is increasing gradually after 48h and were maximum towards 72h thereafter the production was decreasing towards 92h in both media. Prodigiosin was nil after 24h also. Greater levels of prodigiosin were observed inn nutrient broth which is quite significant. Generally oils are required for prodigiosin production but the strain is producing prodigiosin in nutrient broth which is indicative of wild type prodigiosin producing strain.
Major Genes for Major Affective Disorder?

Some authorities view the history of science as a sort of saltatory process in which periods of modest gain and of plodding ‘normal science’ are interrupted by dramatic leaps forward and episodes of ‘revolution’ (Kuhn, 1962). If this is so then genetics has, for the past several years, been in a phase of remarkably sustained and continuous revolution. The advent of the ‘new genetics' of recombinant DNA has resulted in new discoveries occurring at a breath-taking pace, many of which have important clinical implications. Recent findings of psychiatric relevance have included the localisation of the gene for Huntington's chorea on the short arm of chromosome 4 (Gusella et al, 1983) and the use of DNA probes in predictive testing (Harper, 1986). Advances have been achieved in the understanding of the molecular biology of Alzheimer's disease, and at least some of the familial forms of the condition appear to be linked to a gene on chromosome 21 (St George-Hyslop et al, 1987). However, perhaps the most exciting development for most psychiatrists has been the report (Egeland et al, 1987) of a major gene for manic-depressive illness linked to a marker on the short arm of chromosome 11. Could this signal the leap of biological psychiatry into a revolutionary phase? It is perhaps appropriate before attempting to answer this that we give some consideration to the recent historical background.
Fc gamma RII/III and CD2 expression mark distinct subpopulations of immature CD4-CD8- murine thymocytes: in vivo developmental kinetics and T cell receptor beta chain rearrangement status

We have recently identified a dominant wave of CD4-CD8- (double- negative [DN]) thymocytes in early murine fetal development that express low affinity Fc gamma receptors (Fc gamma RII/III) and contain precursors for Ti alpha/beta lineage T cells. Here we show that Fc gamma RII/III is expressed in very immature CD4low single-positive (SP) thymocytes and that Fc gamma RII/III expression is downregulated within the DN subpopulation and before the CD3-CD8low SP stage in T cell receptor (TCR)-alpha/beta lineage-committed thymocytes. DN Fc gamma RII/III+ thymocytes also contain a small fraction of TCR-gamma/delta lineage cells in addition to TCR-alpha/beta progenitors. Fetal day 15.5 DN TCR-alpha/beta lineage progenitors can be subdivided into three major subpopulations as characterized by cell surface expression of Fc gamma RII/III vs. CD2 (Fc gamma RII/III+CD2-, Fc gamma RII/III+CD2+, Fc gamma RII/III-CD2+). Phenotypic analysis during fetal development as well as adoptive transfer of isolated fetal thymocyte subpopulations derived from C57B1/6 (Ly5.1) mice into normal, nonirradiated Ly5.2 congenic recipient mice identifies one early differentiation sequence (Fc gamma RII/III+CD2(-)-->Fc gamma RII/III+CD2(+)-->Fc gamma RII/III- CD2+) that precedes the entry of DN thymocytes into the CD4+CD8+ double- positive (DP) TCRlow/- stage. Unseparated day 15.5 fetal thymocytes develop into DP thymocytes within 2.5 d and remain at the DP stage for > 48 h before being selected into either CD4+ or CD8+ SP thymocytes. In contrast, Fc gamma RII/III+CD2- DN thymocytes follow this same developmental pathway but are delayed by approximately 24 h before entering the DP compartment, while Fc gamma RII/III-CD2+ display accelerated development by approximately 24 h compared with total day 15.5 thymocytes. Fc gamma RII/III-CD2+ are also more developmentally advanced than Fc gamma RII/III+CD2- fetal thymocytes with respect to their TCR beta chain V(D)J rearrangement. At day 15.5 in gestation, beta chain V(D)J rearrangement is mostly, if not entirely, restricted to the Fc gamma RII/III-CD2+ subset of DN fetal thymocytes. Consistent with this analysis in fetal thymocytes, > 90% of adult thymocytes derived from mice carrying a disrupting mutation at the recombination- activating gene 2 locus (RAG-2-/-) on both alleles are developmentally arrested at the DN CD2- stage. In addition, there is a fivefold increase in the relative percentage of thymocytes expressing Fc gamma RII/III in TCR and immunoglobulin gene rearrangement-incompetent homozygous RAG-2-/- mice (15% Fc gamma RII/III+) versus rearrangement- competent heterozygous RAG-2+/- mice (< 3% Fc gamma RII/III+). Thus, Fc gamma RII/III expression defines an early DN stage preceding V beta(D beta)I beta rearrangement, which in turn is followed by surface expression of CD2. Loss of Fc gamma RII/III and acquisition of CD2 expression characterize a late DN stage immediately before the conversion into DP thymocytes.