Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Aggregates and Aggresomes of C-Terminal Truncated Human αA-Crystallins in Mammalian Cells and Protection by αB-Crystallin

Background Cleavage of 11 (αA162), 5 (αA168) and 1 (αA172) residues from the C-terminus of αA-crystallin creates structurally and functionally different proteins. The formation of these post-translationally modified αA-crystallins is enhanced in diabetes. In the present study, the fate of the truncated αA-crystallins expressed in living mammalian cells in the presence and absence of native αA- or αB-crystallin has been studied by laser scanning confocal microscopy (LSM). Methodology/Principal Findings YFP tagged αAwt, αA162, αA168 and αA172, were individually transfected or co-transfected with CFP tagged αAwt or αBwt, expressed in HeLa cells and studied by LSM. Difference in protein aggregation was not caused by different level of α-crystallin expression because Western blotting results showed nearly same level of expression of the various α-crystallins. The FRET-acceptor photo-bleaching protocol was followed to study in situ protein-protein interaction. αA172 interacted with αAwt and αBwt better than αA168 and αA162, interaction of αBwt being two-fold stronger than that of αAwt. Furthermore, aggresomes were detected in cells individually expressing αA162 and αA168 constructs and co-expression with αBwt significantly sequestered the aggresomes. There was no sequestration of aggresomes with αAwt co-expression with the truncated constructs, αA162 and αA168. Double immunocytochemistry technique was used for co-localization of γ-tubulin with αA-crystallin to demonstrate the perinuclear aggregates were aggresomes. Conclusions/Significance αA172 showed the strongest interaction with both αAwt and αBwt. Native αB-crystallin provided protection to partially unfolded truncated αA-crystallins whereas native αA-crystallin did not. Aggresomes were detected in cells expressing αA162 and αA168 and αBwt co-expression with these constructs diminished the aggresome formation. Co-localization of γ-tubulin in perinuclear aggregates validates for aggresomes.
Capacitive behaviour in Super Junction trench MOSFET devices

This paper exploits for the first time the capacitive behaviour of Super Junction (SJ) Trench Power MOSFETs as a characterization method to determine their Charge Balance (CB). Differently from blocking voltage methods, the capacitive method allows the CB extraction in 800 V SJ devices by using low voltage systems (<30 V) to extract the drain-source capacitance (Cds) in function of the drain-source voltage (Vds). Hence, the device-under-test is never stressed in avalanche, avoiding device degradation and/or destruction. The correlation between the minimum Cds value at 25 V and the optimum CB is demonstrated by TCAD simulations and measurements. As a result, the highest breakdown voltage (Vbd), corresponding to the optimum CB, is determined by measuring Cds at 25 V. Moreover, the maximum Vds pinch voltage (Vpinch) exhibits a maximum value when Cds at 25 V is minimum, thus also being an interesting parameter to monitor.
Factorial Scaled Hidden Markov Model for polyphonic audio representation and source separation

We present a new probabilistic model for polyphonic audio termed factorial scaled hidden Markov model (FS-HMM), which generalizes several existing models, notably the Gaussian scaled mixture model and the Itakura-Saito nonnegative matrix factorization (NMF) model. We describe two expectation-maximization (EM) algorithms for maximum likelihood estimation, which differ by the choice of complete data set. The second EM algorithm, based on a reduced complete data set and multiplicative updates inspired from NMF methodology, exhibits much faster convergence. We consider the FS-HMM in different configurations for the difficult problem of speech/music separation from a single channel and report satisfying results.
Immediate response to nonsurgical periodontal treatment in subjects with diabetes mellitus.

The short-term response (3-4 months) to non-surgical periodontal treatment, i.e., oral hygiene instruction, scaling and root planing, was determined in 34 diabetic and 45 control subjects. Measurements of probing pocket depth and gingival bleeding (%) were used for evaluation. No significant difference could be observed in the response to non-surgical periodontal treatment between the diabetics and controls.
Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria

ABSTRACT The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [13C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.
A Framework for Collision-Tolerant Optimal Trajectory Planning of Autonomous Vehicles

Collision-tolerant trajectory planning is the consideration that collisions, if they are planned appropriately, enable more effective path planning for robots capable of handling them. A mixed integer programming (MIP) optimization formulation demonstrates the computational practicality of optimizing trajectories that comprise planned collisions. A damage quantification function is proposed, and the influence of damage functions constraints on the trajectory are studied in simulation. Using a simple example, an increase in performance is achieved under this schema as compared to collision-free optimal trajectories.
Bulletin of Electrical Engineering and Informatics

Rasim Azeez Kadhim, Yaseen Naser Jurn, Mohammed Taih Gatte Department of Information Networks, College of Information Technology, University of Babylon, Hilla, Iraq Department of Mobile Communication and Computing Engineering (MCCE), College of Engineering, University of Information Technology and Communications, Baghdad, Iraq Department Electrical Engineering, College of Engineering, University of Babylon, Hilla, Iraq
Analysis of Pigtail Macaque Major Histocompatibility Complex Class I Molecules Presenting Immunodominant Simian Immunodeficiency Virus Epitopes

ABSTRACT Successful human immunodeficiency virus (HIV) vaccines will need to induce effective T-cell immunity. We studied immunodominant simian immunodeficiency virus (SIV) Gag-specific T-cell responses and their restricting major histocompatibility complex (MHC) class I alleles in pigtail macaques (Macaca nemestrina), an increasingly common primate model for the study of HIV infection of humans. CD8+ T-cell responses to an SIV epitope, Gag164-172KP9, were present in at least 15 of 36 outbred pigtail macaques. The immunodominant KP9-specific response accounted for the majority (mean, 63%) of the SIV Gag response. Sequencing from six macaques identified 7 new Mane-A and 13 new Mane-B MHC class I alleles. One new allele, Mane-A*10, was common to four macaques that responded to the KP9 epitope. We adapted reference strand-mediated conformational analysis (RSCA) to MHC class I genotype M. nemestrina. Mane-A*10 was detected in macaques presenting KP9 studied by RSCA but was absent from non-KP9-presenting macaques. Expressed on class I-deficient cells, Mane-A*10, but not other pigtail macaque MHC class I molecules, efficiently presented KP9 to responder T cells, confirming that Mane-A*10 restricts the KP9 epitope. Importantly, naïve pigtail macaques infected with SIVmac251 that respond to KP9 had significantly reduced plasma SIV viral levels (log10 0.87 copies/ml; P = 0.025) compared to those of macaques not responding to KP9. The identification of this common M. nemestrina MHC class I allele restricting a functionally important immunodominant SIV Gag epitope establishes a basis for studying CD8+ T-cell responses against AIDS in an important, widely available nonhuman primate species.
Epigenetic and immune function profiles associated with posttraumatic stress disorder

The biologic underpinnings of posttraumatic stress disorder (PTSD) have not been fully elucidated. Previous work suggests that alterations in the immune system are characteristic of the disorder. Identifying the biologic mechanisms by which such alterations occur could provide fundamental insights into the etiology and treatment of PTSD. Here we identify specific epigenetic profiles underlying immune system changes associated with PTSD. Using blood samples (n = 100) obtained from an ongoing, prospective epidemiologic study in Detroit, the Detroit Neighborhood Health Study, we applied methylation microarrays to assay CpG sites from more than 14,000 genes among 23 PTSD-affected and 77 PTSD-unaffected individuals. We show that immune system functions are significantly overrepresented among the annotations associated with genes uniquely unmethylated among those with PTSD. We further demonstrate that genes whose methylation levels are significantly and negatively correlated with traumatic burden show a similar strong signal of immune function among the PTSD affected. The observed epigenetic variability in immune function by PTSD is corroborated using an independent biologic marker of immune response to infection, CMV—a typically latent herpesvirus whose activity was significantly higher among those with PTSD. This report of peripheral epigenomic and CMV profiles associated with mental illness suggests a biologic model of PTSD etiology in which an externally experienced traumatic event induces downstream alterations in immune function by reducing methylation levels of immune-related genes.
Immunocytochemical characterization of macular hole opercula.

OBJECTIVES To immunocytochemically characterize the neural and glial elements of idiopathic full-thickness macular hole (FTMH) opercula excised during vitrectomy, and to correlate them with the outcome of surgery. METHODS Opercula were collected from eyes undergoing vitrectomy for stage 3 FTMH and processed for transmission electron microscopy, light epifluorescence, and laser scanning confocal microscopy. Glia were identified using anti-glial fibrillary acid protein (GFAP), antivimentin, and anti-cellular retinaldehyde binding protein antibodies. Anti-phosphodiesterase gamma and antirhodopsin were used for cone and rod photoreceptors, and anticytokeratin was used for retinal pigment epithelium. The findings were correlated with the clinical data before and after surgery. For statistical analysis, data were combined with those of a previous study by the authors of 18 opercula. RESULTS Opercula from 12 consecutive eyes of 12 patients were studied. In all opercula, GFAP, vimentin, and cellular retinaldehyde binding protein-positive glia were present. Six (50%) of 12 opercula contained more than 5 photoreceptors with somata and internal photoreceptor fibres, but lacking outer segments, demonstrating strong immunoreactivity to anti-phosphodiesterase gamma without antirhodopsin reactivity consistent with cones. Further, 2 (17%) of 12 opercula showed few cones (1-5 cones), and 4 (33%) of 12 contained only glia. Clinicopathologic correlation of the 30 opercula from the 2 studies showed that eyes with opercula containing more than 5 photoreceptors were associated with a worse anatomical closure rate after initial surgery, compared with those with fewer than 5 photoreceptors (P =.004). Once closure had been achieved with reoperation, median postoperative vision was similar in both groups (20/40 and 20/60, respectively). CONCLUSIONS A spectrum of opercula occur in FTMH ranging from those containing only glia to those containing numerous cones. The extent of foveal neuroretinal tissue loss may affect the outcome of surgery.
Inhaled corticosteroids and growth of airway function in asthmatic children

Airway inflammation and remodelling play an important role in the pathophysiology of asthma. Remodelling may affect childhood lung function, and this process may be reversed by anti-inflammatory treatment. The current study assessed longitudinally whether asthma affects growth of airway function relative to airspaces, and if so whether this is redressed by inhaled corticosteroids (ICS). Every 4 months for up to 3 yrs, lung function was assessed in 54 asthmatic children (initial age 7–16 yrs), who inhaled 0.2 mg salbutamol t.i. d. and 0.2 mg budesonide t.i. d. (β2‐agonist (BA)+ICS), or placebo (PL) t.i. d. (BA+PL) in a randomised, double-blind design. Measurements were carried out before and after maximal bronchodilation. Airway growth was assessed from the change of forced expiratory volume in one second and of maximal expiratory flows (at 60% and 40% of total lung capacity (TLC) remaining in the lung) relative to TLC, as measures of more central, intermediate and more peripheral airways. Growth patterns were compared with the longitudinal findings in 376 healthy children. Airway patency after maximal bronchodilation in patients on BA+PL remained reduced compared to healthy subjects, whereas in patients on BA+ICS a marked improvement was observed to subnormal. No differences between patients and controls could be demonstrated for growth patterns of central and intermediate airway function. Compliance with BA+ICS was 75% of the prescribed dose, resulting in significant, sustained improvement of symptoms and postbronchodilator calibre of central and intermediate airways to subnormal within 2 months, but postbronchodilator small airway patency remained reduced, though improved compared to patients on BA+PL. Anti-inflammatory treatment of asthmatic children is associated with normal functional development of central and intermediate airways. The persistently reduced postbronchodilator patency of peripheral airways may reflect remodelling, or insufficient anti-inflammatory treatment.
RNS multi-voltage low-power multiply-add unit

In this paper an efficient way to exploit multi-Vdd standard-cell libraries is quantitatively investigated as a means to reduce power consumption of multiply-add units. It is shown that multi-Vdd library-based design is suitable for RNS systems due to their inherent modular organization. In particular the paths defined by the isolated moduli channels are clearly distinguished and the designer can easily and efficiently determine high- and low-voltage areas in the design. A five-moduli RNS system has been implemented including RNS-to-Binary and Binary-to-RNS converters.
Activation of either ERK1/2 or ERK5 MAP kinase pathways can lead to disruption of the actin cytoskeleton

Oncogenic transformation often leads to the disruption of the actin cytoskeleton. Activation of the classical Ras-Raf-MEK1/2-ERK1/2 signalling cascade has been implicated in the effects of oncogenes such as Ras and Src on the cytoskeleton. Many of the studies of the effects of oncogenes on the cytoskeleton have made use of chemical inhibitors of MEK1/2 but it is now clear that these inhibitors also inactivate MEK5 in the MEK5-ERK5 MAP kinase pathway raising the possibility that this pathway may also be involved in oncogenic transformation. We therefore investigated whether activation of ERK5 can lead to disruption of the actin cytoskeleton. We show that activation of ERK5 can lead to loss of actin stress fibres, but by a distinct mechanism to ERK1/2. We demonstrate that ERK5 is activated by oncogenic Src as demonstrated by translocation of endogenous ERK5 from the cytoplasm to nucleus and activation of an ERK5-dependent transcriptional reporter and that ERK5 activation is required for Src-mediated transformation. We also show that in Src-transformed cells inhibition of ERK1/2 signalling is not sufficient for reappearance of the actin cytoskeleton and that ERK5 activation contributes to cytoskeletal disruption by Src. Our results suggest that multiple MAP kinase pathways downstream of oncogenes participate in cytoskeletal alterations.
MODELING SUBSURFACE DRIP APPLICATION OF ONSITE WASTEWATER TREATMENT SYSTEM EFFLUENT

The use of subsurface drip irrigation for the disposal/reuse of septic tank effluent began to gaininterest in the 1990s. Using subsurface drip irrigation, effluent can be applied at a lower rateover a larger area and in a more biologically active part of the soil profile than with standarddeep infiltration trenches. Subsurface drip irrigation also makes the water and nutrientspotentially more available for uptake by plants. Various models developed over the years havebeen applied to model infiltration, soil nitrogen, and general vadose zone transport scenarios.Based on an evaluation of available models, Hydrus 2D was selected as being capable ofadequately modeling the geometry and transport, and having many specific useful features formodeling subsurface drip irrigation. Modeling was then performed for various soils, emitterspacings, depths, and loading rates. Modeling results showed that a system designed for efficientirrigation generally minimized annual nitrate percolation. Nitrification of septic tank effluentprior to subsurface drip application increased nitrate percolation. Nitrification and denitrificationrates in the soil profile were enhanced when effluent was applied in a brief daily pulse rather thancontinuously. Finer soil texture also minimized nitrate percolation. Other results and plans forcontrolled soil bed tests are presented.
Nanofiber-expanded human umbilical cord blood–derived CD34+ cell therapy accelerates cutaneous wound closure in NOD/SCID mice

Nanofiber‐expanded human umbilical cord blood–derived CD34+ cell therapy has been shown to have potential applications for peripheral and myocardial ischaemic diseases. However, the efficacies of expanded CD34+ cell therapy for treating cutaneous wounds and its mechanisms of action have yet to be established. Using an excisional wound model in non‐obese diabetic/severe combined immune deficient mice, we show herein that CD34+ cells accelerate the wound‐healing process by enhancing collagen synthesis, and increasing fibroblast cell migration within the wound bed. Concomitantly, reduced levels of matrix metalloproteinase (MMPs) such as MMP1, MMP3, MMP9 and MMP13 were detected in the wound beds of animals treated with CD34+ cells compared with vehicle‐treated controls. CD34+ cells were found to mediate enhanced migration and proliferation of dermal fibroblast cells in vitro. Moreover, CD34+ cells secrete collagen in a serum‐deprived environment. In mechanistic studies, co‐culture of CD34+ cells with primary skin fibroblasts increased the expression of collagen1A1, a component of type 1 collagen, and decreased the expression of MMP1 in fibroblast cells in the presence of a proteasome inhibitor. Finally, CD34+ cell–mediated functions were transcriptionally regulated by the c‐Jun N‐terminal kinases pathway. Collectively, these data provide evidence of therapeutic efficacy and a novel mechanism of nanofiber‐expanded CD34+ cell–mediated accelerated wound healing.
A hybrid model of speculative execution and scout threading for auto-memoization processor

We have proposed an auto-memoization processor based on computation reuse, and merged it with speculative multi-threading based on value prediction into a parallel speculative execution. In the parallel speculative execution model, speculative cores do not work when the target instruction region is not suitable for computation reuse. This paper proposes a new parallel speculative execution model where the idle speculative cores execute scout threads for reducing cache miss penalties. The scout thread is based on value prediction, and can handle an instruction region which accesses the addresses with several strides. It also can reduce execution cycles by raising computation reuse ratio. The result of the experiment with SPEC CPU95 FP suite benchmarks shows that the new hybrid model of parallel speculative execution and scout threading improves the maximum speedup from 40.6% to 41.3%, and the average speedup from 15.0% to 19.1%.
Private equity ownership and nursing home financial performance.

BACKGROUND Private equity has acquired multiple large nursing home chains within the last few years; by 2009, it owned nearly 1,900 nursing homes. Private equity is said to improve the financial performance of acquired facilities. However, no study has yet examined the financial performance of private equity nursing homes, ergo this study. PURPOSE The primary purpose of this study is to understand the financial performance of private equity nursing homes and how it compares with other investor-owned facilities. It also seeks to understand the approach favored by private equity to improve financial performance-for instance, whether they prefer to cut costs or maximize revenues or follow a mixed approach. METHODOLOGY/APPROACH Secondary data from Medicare cost reports, the Online Survey, Certification and Reporting, Area Resource File, and Brown University's Long-term Care Focus data set are combined to construct a longitudinal data set for the study period 2000-2007. The final sample is 2,822 observations after eliminating all not-for-profit, independent, and hospital-based facilities. Dependent financial variables consist of operating revenues and costs, operating and total margins, payer mix (census Medicare, census Medicaid, census other), and acuity index. Independent variables primarily reflect private equity ownership. The study was analyzed using ordinary least squares, gamma distribution with log link, logit with binomial family link, and logistic regression. FINDINGS Private equity nursing homes have higher operating margin as well as total margin; they also report higher operating revenues and costs. No significant differences in payer mix are noted. PRACTICE IMPLICATIONS Results suggest that private equity delivers superior financial performance compared with other investor-owned nursing homes. However, causes for concern remain particularly with the long-term financial sustainability of these facilities.