Miracle-dz/UniFAR-FTUs huggingface dataset:
Postnatal development of dendritic spines on olfactory bulb granule cells in rats

Postnatal morphological changes in granule cell dendritic spines and filopodia (collectively referred to as “spines/filopodia”) were examined in the rat main olfactory bulb to characterize the development of the neural circuitry for olfaction. Granule cells were labeled with a membrane dye and confocal laser scanning microscope images of labeled spines/filopodia were acquired in the following three dendritic domains: apical dendrites in the external plexiform layer, those in the granule cell layer, and basal dendrites. In all three domains the proportion of typical spines slightly increased during development, with a concomitant decrease in the proportion of “stubby” spines lacking a neck; the proportion of filopodia remained unchanged, accounting for 20–40% of all protrusions. The mean diameter and length of the spine/filopodium population were nearly constant throughout development. On the other hand, the developmental pattern of the spine/filopodium density varied markedly, depending on the domain of the dendrites. In the external plexiform layer, the density did not change remarkably during development. The density in apical dendrites in the granule cell layer increased during the initial 2 postnatal weeks, then gradually decreased. The spine/filopodium density in basal dendrites, however, continued to increase until 4 weeks of age, and then began to decrease. These results suggest that a substantial amount of input‐specific synaptic remodeling occurs in granule cells during development, which proceeds from superficial dendritic domains to deeper ones, occurring most prominently in the basal dendrites. J. Comp. Neurol. 473:553–561, 2004. © 2004 Wiley‐Liss, Inc.
correspondence: Incidence of leukaemia in patients with primary myelofibrosis and RBC–transfusion‐dependence

Berliner, N. , Horwitz, M. & Loughran, Jr, T.P. (2004) Congenital and acquired neutropenia. The American Society of Hematology Education Program, 2004, 63–79. Karsunky, H. , Zeng, H. , Schmidt, T. , Zevnik, B. , Kluge, R. , Schmid, K.W. , Duhrsen, U. & Moroy, T. (2002) Inflammatory reactions and severe neutropenia in mice lacking the transcriptional repressor Gfi1. Nature Genetics, 30, 295–300. Kollner, I. , Sodeik, B. , Schreek, S. , Heyn, H. , von Neuhoff, N. , Germeshausen, M. , Zeidler, C. , Kruger, M. , Schlegelberger, B. , Welte, K. & Beger, C. (2006) Mutations in neutrophil elastase causing congenital neutropenia lead to cytoplasmic protein accumulation and induction of the unfolded protein response. Blood, 108, 493–500. Loughran, Jr, T.P. & Hammond, W.P.t. (1986) Adult-onset cyclic neutropenia is a benign neoplasm associated with clonal proliferation of large granular lymphocytes. Journal of Experimental Medicine, 164, 2089–2094. Molldrem, J.J., Lee, P.P., Wang, C. , Champlin, R.E. & Davis, M.M. (1999) A PR1-human leukocyte antigen-A2 tetramer can be used to isolate low-frequency cytotoxic T lymphocytes from healthy donors that selectively lyse chronic myelogenous leukemia. Cancer Research, 59, 2675–2681. Molldrem, J.J., Lee, P.P., Wang, C. , Felio, K. , Kantarjian, H.M. , Champlin, R.E. & Davis, M.M. (2000) Evidence that specific T lymphocytes may participate in the elimination of chronic myelogenous leukemia. Nature Medicine, 6, 1018–1023. Person, R.E. , Li, F.Q. , Duan, Z. , Benson, K.F. , Wechsler, J., Papadaki, H.A. , Eliopoulos, G. , Kaufman, C. , Bertolone, S.J., Nakamoto, B. , Papayannopoulou, T. , Grimes, H.L. & Horwitz, M. (2003) Mutations in proto-oncogene GFI1 cause human neutropenia and target ELA2. Nature Genetics, 34, 308–312. Salipante, S.J., Rojas, M.E. , Korkmaz, B. , Duan, Z. , Wechsler, J., Benson, K.F. , Person, R.E. , Grimes, H.L. & Horwitz, M.S. (2009) Contributions to neutropenia from PFAAP5 (N4BP2L2), a novel protein mediating transcriptional repressor cooperation between Gfi1 and neutrophil elastase. Molecular and Cellular Biology, 29, 4394–4405. Schnakenberg, J. (1979) Simple chemical reaction systems with limit cycle behaviour. Journal of Theoretical Biology, 81, 389–400. Zarebski, A. , Velu, C.S. , Baktula, A.M., Bourdeau, T. , Horman, S.R. , Basu, S. , Bertolone, S.J., Horwitz, M. , Hildeman, D.A. , Trent, J.O. & Grimes, H.L. (2008) Mutations in growth factor independent-1 associated with human neutropenia block murine granulopoiesis through colony stimulating factor-1. Immunity, 28, 370–380.
Effect of catechol and ethanol with and without methylamylnitrosamine on esophageal carcinogenesis in the rat.

Alcohol consumption and cigarette smoking are synergistic etiologic factors for squamous cell carcinoma of the esophagus in Western countries. Catechol, a constituent of cigarette smoke, was previously found to be a co-carcinogen with methyl-n-amylnitrosamine (MNAN) for esophageal tumors in rats, when it was given in the diet. Here we tested whether the inclusion of ethanol in a similar system had an additional promoting effect on esophageal carcinogenesis. Male MRC - Wistar rats were injected three times i.p. with 25 mg MNAN/kg starting from 7 weeks of age. A second group of rats was injected similarly with MNAN and treated for life with 10% ethanol and 0.2% catechol in the drinking water, starting at 6 weeks of age. One or more test chemicals were omitted in other groups. The rats were maintained until they died and were necropsied. The number of esophageal papillomas/rat was 2.18 +/- 0.36, 4.27 +/- 0.53, 2.54 +/- 0.48 and 3.21 +/- 0.52 (mean +/- SE) in groups treated with MNAN alone, MNAN + ethanol + catechol, MNAN + ethanol and MNAN + catechol, respectively. Esophageal carcinomas showed a similar trend, with the number of carcinomas/rat equal to 0.23 +/- 0.08 in the MNAN alone group and 0.50 +/- 0.14 in the MNAN + ethanol + catechol group. Tumor multiplicities for the esophageal papillomas and carcinomas were significantly (P < 0.05) greater in the MNAN + ethanol + catechol group than in the MNAN group. These findings indicate that, in the esophagus, catechol alone was not significantly co-carcinogenic with MNAN when it was given in the drinking water (unlike when given in the diet in our previous study), but that ethanol + catechol given in the water was co-carcinogenic with MNAN. Seven of 19 rats given ethanol + catechol without MNAN developed esophageal papillomas, as compared to zero incidence in untreated controls (P = 0.06). Forestomach papillomas occurred in 22% of all rats given catechol. Hence, for esophageal tumor induction, ethanol and catechol were co-carcinogenic with MNAN and appeared to be tumorigenic when given without MNAN. Ethanol and catechol could have increased the carcinogenicity because they affected MNAN metabolism. As a partial test of this possibility, the effect of feeding these compounds for 5-7 weeks separately or together was examined on 2-, 3-, 4-and 5-hydroxy-MNAN (HO-MNAN) production from MNAN by the esophagus and liver slices from freshly killed rats. (ABSTRACT TRUNCATED AT 400 WORDS)
A Tunable Dual-Fed Self-Diplexing Patch Antenna

We propose a simple and compact design of a tunable self-diplexing patch antenna. Two U-shapes are etched on the same platform to locate the radiating patches which are excited separately using two feed ports. Metalized vias acting like metal walls are applied to reduce the antenna footprint, and to avoid coupling effects when the frequency ratio (fr) approaches 2. The tuning process is achieved by using two varactors properly inserted into the radiating structure. The operating frequencies can be tuned independently with high isolation level. Simulation and measurement results are quite consistent. Measured results show that the lower frequency band ranges from 3.9 to 4.37 GHz with measured peak gain and efficiency of 3.82 dBi–65%, while the upper band ranges from 4.63 to 5.34 GHz with peak gain of 4.48 dBi and peak efficiency of 64%. The self-diplexing antenna achieves an isolation level better than 22 and 32 dB for the lowest fr of 1.05, and the highest fr of 1.37, respectively. The radiation pattern is unidirectional and extremely stable during the frequency tuning of both bands.
Influence of the diameter and growth conditions on the magnetic properties of cobalt nanowires

Arrays of cobalt nanowires of diameter 23-70 nm were grown by electrodeposition. Their magnetic properties are probed using ferromagnetic resonance. Depending on the solution pH and deposition rate, the orientation of the dense planes of the hexagonal structure can be controlled so that its c-axis is oriented either parallel or perpendicular to the wires axis. In particular, the effects of the pH and deposition current on the structural and magnetic properties are considered and it is shown that the wire diameter plays an important role in the final preferred structure by inducing local changes of the pH within the pores.
Mesenchymal stem cells induce the ramification of microglia via the small RhoGTPases Cdc42 and Rac1

Activated microglia play a central role in the course of neurodegenerative diseases as they secrete cytotoxic substances which lead to neuronal cell death. Understanding the mechanisms that drive activation of microglia is essential to reverse this phenotype and to protect from neurodegeneration. With some exceptions, evidence indicates that changes in cell morphology from a star shape to a round and flat shape accompany the process of activation in microglia. In this study, we investigated the effect of adipose‐tissue‐derived mesenchymal stem cells (ASCs), which exert important anti‐inflammatory actions, in microglia morphology. Microglia exposed to ASCs or their secreted factors (conditioned medium) underwent a cell shape change into a ramifying morphology in basal and inflammatory conditions, similar to that observed in microglia found in healthy brain. Colony‐stimulating factor‐1 secreted by ASCs played a critical role in the induction of this phenotype. Importantly, ASCs reversed the activated round phenotype induced in microglia by bacterial endotoxins. The ramifying morphology of microglia induced by ASCs was associated with a decrease of the proinflammatory cytokines tumor necrosis factor‐α and interleukin‐6, an increase in phagocytic activity, and the upregulation of neurotrophic factors and of Arginase‐1, a marker for M2‐like regulatory microglia. In addition, activation of the phosphoinositide‐3‐kinase/Akt pathway and the RhoGTPases Rac1 and Cdc42 played a major role in the acquisition of this phenotype. Therefore, these RhoGTPases emerge as key players in the ramification of microglia by anti‐inflammatory agents like ASCs, being fundamental to maintain the tissue‐surveying, central nervous system supporting state of microglia in healthy conditions. GLIA 2014;62:1932–1942
Detection of Planetary Emission from TrES-2 using Spitzer/IRAC

Abstract We present here results from observations of TrES-2 made using the Infrared Array Camera on the Spitzer Space Telescope. We monitored this transiting system during two secondary eclipses, when the planetary emission is blocked by the star. The resulting decrease in flux is 0.135 ± 0.036%, 0.245 ± 0.027%, 0.162 ± 0.064%, and 0.295 ± 0.066%, at 3.6-μm, 4.5-μm, 5.8-μm, and 8.0-μm, respectively. We find evidence for a temperature inversion in the atmosphere of TrES-2, which is predicted by Fortney and collaborators based on the proposed importance of TiO and VO opacities for this highly irradiated gas giant. We also find the time of the center of the eclipse to be consistent with predictions from transit timing observations of TrES-2. This implies that TrES-2 most likely has a circular orbit, and thus does not obtain additional thermal energy from tidal dissipation of a non-zero orbital eccentricity, a proposed explanation of the large planetary radius.
DOUBLE DEGENERATE MERGERS AS PROGENITORS OF HIGH-FIELD MAGNETIC WHITE DWARFS

High-field magnetic white dwarfs have been long suspected to be the result of stellar mergers. However, the nature of the coalescing stars and the precise mechanism that produces the magnetic field are still unknown. Here, we show that the hot, convective, differentially rotating corona present in the outer layers of the remnant of the merger of two degenerate cores can produce magnetic fields of the required strength that do not decay for long timescales. Using a state-of-the-art Monte Carlo simulator, we also show that the expected number of high-field magnetic white dwarfs produced in this way is consistent with that found in the solar neighborhood.
Myocardial apoptosis in a heterotopic murine heart transplantation model of chronic rejection and graft vasculopathy.

BACKGROUND Apoptosis has been implicated in myocardial reperfusion injury and in experimental transplantation rejection. One mechanism of apoptosis is through the interaction of the cell-surface Fas receptor on target cells and the Fas ligand that is expressed on cytotoxic T cells. The purpose of this study was to look for evidence of myocardial Fas receptor, Fas ligand, and apoptosis in a murine heterotopic heart transplantation model of chronic rejection/graft vasculopathy. METHODS Using the nick-end labeling technique, we examined a murine heterotopic heart transplantation model of chronic rejection/graft vasculopathy (strain B10.A to B10.BR) histologically for evidence of DNA fragmentation. MRNA for the Fas receptor, Fas ligand, and beta-actin was detected with reverse transcription-polymerase chain reaction. RESULTS Hearts harvested after 30 and 60 days showed an intimal index of the allografts (0.5 +/- 0.1) (mean +/- standard error) that was at least five times more than syngeneic grafts and native (nontransplanted) hearts (p < 0.01). In situ nick end-labeling of partially degraded DNA with terminal deoxynucleotydil transferase showed an increase in apoptotic cells in allografts and syngeneic grafts compared with native hearts. Reverse transcription-polymerase chain reaction detected equal myocardial RNA signal intensity of Fas receptor and beta-actin in allografts, syngeneic grafts, and native hearts. In contrast, allografts showed a strong signal for the Fas ligand mRNA, a signal not seen in syngeneic grafts or native hearts. CONCLUSIONS Apoptosis is occurring in both allografts and syngeneic grafts in this murine model of chronic rejection/graft vasculopathy, although distinct mechanisms may be involved.
Porcine malignant hyperthermia: Cell injury enhances halothane sensitivity of biopsies

A possible relationship between muscle cell injury or deterioration and enhanced halothane sensitivity was studied by monitoring mechanical responses of skeletal muscles from normal pigs and pigs susceptible to malignant hyperthermia (MH). Increased time postbiopsy and decreased maximum control tetanic tension both correlated significently with enhanced sensitivity to halothane. In both normal and MHsusceptible (MHS) muscles, greater halothane sensitivity was observed in cut cell than in intact cell bundles and in low tetanic tension as compared to high tension preparations. Subsequent to halothane exposure, twitches of high tension (≥ 1.75 kg · cm −2) intact bundles of both normal and MHS muscles were potentiated. Tetani of normal intact bundles were not altered, whereas those of MHS bundles were depressed after halothane exposure. Control twitch‐to‐tetanus ratios (twitch ratios) were higher in MHS (0.23) than in normal (0.12) intact bundles. According to discriminant analysis, the best distinction between normal and MHS muscles, either cut or intact, was obtained by comparing halothane‐induced changes in tetanic tension and control twitch ratios.
Early Growth Response Gene 3 Regulates Thymocyte Proliferation during the Transition from CD4−CD8− to CD4+CD8+1

In thymocytes developing in the αβ lineage, the transition from CD4, CD8 double negative (DN) to CD4, CD8 double positive (DP) is associated with several rounds of cell division and changes in the expression of multiple genes. This transition is induced by the formation of a pre-TCR that includes a rearranged TCR β-chain and the pre-TCR α-chain. The mechanism by which the pre-TCR influences both gene expression and proliferation has not been defined. We have evaluated the role played by early growth response gene 3 (Egr3) in translating pre-TCR signals into differentiation and proliferation. Egr3 is a transcriptional regulator that contains a zinc-finger DNA binding domain. We find that Egr3-deficient mice have a reduced number of thymocytes compared with wild-type mice, and that this is due to poor proliferation during the DN to DP transition. Treatment of both Egr3+/+ and Egr3−/− mice on the Rag1−/− background with anti-CD3ε Ab in vivo results in similar differentiation events, but reduced cell recovery in the Egr3−/− mice. We have also generated transgenic mice that express high levels of Egr3 constitutively, and when these mice are bred onto a Rag1−/− background they exhibit increased proliferation in the absence of stimulation and have pre-TCR α-chain and CD25 down-regulation, as well as increased Cα expression. The results show that Egr3 is an important regulator of proliferation in response to pre-TCR signals, and that it also may regulate some specific aspects of differentiation.
State-Level Treatment Outcome Studies Using Administrative Databases

State substance dependence administrative databases contain both administrative and clinical information on large numbers of patients collected over extended time periods. Access to other state databases—employment, criminal behavior, and Medicaid—has also been achieved in some instances. Such data could prove an important source for the evaluation of long-term treatment outcomes and their determinants. This selected review describes and evaluates the treatment outcome and cost-related findings of the most advanced studies using these databases. A number of these studies have shown that completion of substance dependence treatment is associated with reduced societal costs. Some of these studies have focused on significant subpopulations of patients, including pregnant women and adolescents. A shortcoming of the findings of most of these studies concerns their use of noncompleter or nonrandomly collected comparison groups. The utility of these databases can be enhanced by coupling them with clinical research treatment outcome evaluation approaches.
Influence of the timing of fluid ingestion on temperature regulation during exercise.

The purpose of this investigation was to determine whether the timing of fluid ingestion affects thermoregulation during exercise-heat stress. On four occasions, seven endurance-trained cyclists [age 25 +/- 2 (SE) yr, body weight 70.5 +/- 3.3 kg, maximal O2 uptake (VO2max) 4.69 +/- 0.11 l/min] performed 140 min of cycle ergometer exercise at 62-66% of VO2max in a hot environment (33 degrees C dry bulb, 51% relative humidity, wind speed 2.5 m/s). The subjects drank 1,173 +/- 44 ml of a carbohydrate-electrolyte beverage after 0 min (D0), 40 min (D40), or 80 min (D80) of exercise or consumed the same total volume in small aliquots throughout exercise (DT). The exercise-heat stress resulted in calculated sweating rates of approximately 1,200 ml/h and a body weight loss of 2.9 +/- 0.1% after 140 min of exercise. After fluid intake in the D0, D40, and D80 trials, there was a time period (approximately 40 min) in which the increases in serum osmolality and sodium concentration and the reduction in blood volume were attenuated. During that same time period, there was an attenuated rise in esophageal temperature (Tes; P < 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
Systematic reconstruction of splicing regulatory modules by integrating many RNA-seq datasets

Alternative splicing is a ubiquitous gene regulatory mechanism that dramatically increases the complexity of the proteome. In this paper we study splicing module, which we define as a set of cassette exons co-regulated by the same splicing factors. We have designed a tensor-based approach to identify co-splicing clusters that appear frequently across multiple conditions, thus very likely to represent splicing modules - a unit in the splicing regulatory network. In particular, we model each RNA-seq dataset as a co-splicing network, where the nodes represent exons and the edges are weighted by the correlations between exon inclusion rate profiles. We apply our tensor-based method to the 19 co-splicing networks derived from RNA-seq datasets and identify an atlas of frequent co-splicing clusters. We demonstrate that these identified clusters represent splicing modules by validating against four biological knowledge databases. The likelihood that a frequent co-splicing cluster is biologically meaningful increases with its recurrence across multiple datasets, highlighting the importance of the integrative approach. We also demonstrate that the co-splicing clusters reveal novel functional groups which cannot be identified by co-expression clusters, and that the same exons can dynamically participate in different pathways depending on different conditions and different other exons that are co-spliced.
TTW life sign detection by means of CW X-band radar, homeland security and rescue applications

The aim of this research works is to developed a very simple and efficient strategy to detect vital life signs in Through the wall (TTW) scenarios, by taking advantage of a simple detection scheme and by exploiting a properly designed measurement set-up working in X-band regime. In the proposed method of a light weight microwave system based on continuous wave X-Band rescue radar, implementation has been done through proper experimental set-up and a new model of detection schema has been performed. The information of life signal has been extracted from the backscattered electromagnetic field employing independent component analysis (ICA) algorithm which works as an effective blind source separation technique to separate vital sign through complex noise, interference and clutter removing. Comparing among different algorithm like ICA, ACMA, EFFICA, the most efficient one gives the expected outcome was ICA.
Stringer Gate FinFET on Bulk Substrate

A gate stringer normally considered parasitic is used as a subthreshold leakage suppressor in a bulk FinFET. The gate stringer remaining along the source/drain extension suppresses the formation of a sub-fin leakage path and improves the subthreshold slope. The stringer gate structure is implemented by simple process modification in the gate etch step while the other process steps are unchanged. The fabricated stringer gate FinFET shows 35% reduction in the OFF-state leakage current compared with a conventional FinFET without a retrograde well process at the expense of only 5% increase in parasitic capacitance. The power-delay product enhancement at reduced drive voltage characteristics exhibits that the stringer gate FinFET can be an attractive candidate for low standby power and subthreshold logic applications.
Waveguide-Integrated Si Nano-Photodiode with Surface-Plasmon Antenna and its Application to On-chip Optical Clock Distribution

We developed a waveguide-integrated Si nano-photodiode (PD) with a surface plasmon (SP) antenna for on-chip optical clock distribution. The interfacial periodic nano-scale metal–semiconductor–metal Schottky electrodes were shown to function as an SP optical antenna and also as an optical coupler between a SiON waveguide and a very thin Si-absorption layer. Furthermore, a very high speed response of 17 ps as well as enhanced photoresponsivity was achieved for a 10-µm coupling length. By using this technology, we fabricated a prototype of a large-scale-integration (LSI) on-chip optical clock system and demonstrated 5 GHz of optical clock circuit operation connected with a 4-branching H-tree structure.