Miracle-dz/UniFAR-FTUs huggingface dataset:
A method for reduced-order modeling and simulation of large interconnect circuits and its application to PEEC models with retardation

The continuous improvement in the performance and the increases in the sizes of VLSI systems make electrical interconnect and package (EIP) design and modeling increasingly more important. Special software tools must be used for the design of high-performance VLSI systems. Furthermore, larger and faster systems require larger and more accurate circuit models. The partial element equivalent circuit (PEEC) technique is used for modeling such systems with three-dimensional full wave models. In this paper, we present a practical, readily parallelizable procedure for generating reduced-order frequency-domain models from general full wave PEEC systems. We use multiple expansion points, and piecemeal construction of pole-residue approximations to transfer functions of the PEEC systems, as was used in the complex frequency hopping algorithms. We consider general, multiple-input/multiple-output PEEC systems. Our block procedure consists of an outer loop of local approximations to the PEEC system, coupled with an inner loop where an iterative model-reduction method is applied to the local approximations. We systematically divide the complex frequency region of interest into small regions and construct local approximations to the PEEC system in each subregion. The local approximations are constructed so that the matrix factorizations associated with each of them are the size of the original system and independent of the order of the approximation. Results of computations on these local systems are combined to obtain a reduced-order model for the original PEEC system. We demonstrate the usefulness of our approach with three interesting examples.
Genetic Variation in Cytokine-Related Genes and Migraine Susceptibility

Migraine is classified by the World Health Organization (WHO) as being one of the top 20 most debilitating diseases. According to the neurovascular hypothesis, neuroinflammation may promote the activation and sensitisation of meningeal nociceptors, inducing the persistent throbbing headache characterized in migraine. The tumor necrosis factor (TNF) gene cluster, made up of TNFα, lymphotoxin α (LTA), and lymphotoxin β (LTB), has been implicated to influence the intensity and duration of local inflammation. It is thought that sterile inflammation mediated by LTA, LTB, and TNFα contributes to threshold brain excitability, propagation of neuronal hyperexcitability and thus initiation and maintenance of a migraine attack. Previous studies have investigated variants within the TNF gene cluster region in relation to migraine susceptibility, with largely conflicting results. The aim of this study was to expand on previous research and utilize a large case-control cohort and range of variants within the TNF gene cluster to investigate the role of the TNF gene cluster in migraine. Nine single nucleotide polymorphisms (SNPs) were selected for investigation as follows: rs1800683, rs2229094, rs2009658, rs2071590, rs2239704, rs909253, rs1800630, rs1800629, and rs3093664. No significant association with migraine susceptibility was found for any of the SNPs tested, with further testing according to migraine subtype and gender also showing no association for disease risk. Haplotype analysis showed that none of the tested haplotypes were significantly associated with migraine.
STUDY OF BRAZILIAN COMMERCIAL ORIENTED STRAND BOARD PANELS USING STRESS WAVE

ABSTRACT Today lumber industry has shown a clearly evident trend towards wood based panels’ production; and, among them, Oriented Strand Board (OSB) has become more and more prominent. Nondestructive Testing (NDT) such as stress wave is one of the possible ways to make their mechanical characterization. This study aimed to investigate the efficiency of NDT stress wave to estimate mechanical parameters of Brazilian commercial OSB panels. National commercial OSB panels (15 and 25 mm in thickness) were tested by standard methods, EN codes, and non-destructive tests employing Stress Wave Timer, METRIGUARD, model 239 A. Data obtained in tests were analyzed using mean comparison by analysis of variance (ANOVA) and Tukey method. R² values greater than those established by EN 326-2 2002 to determine correlation between mechanical properties in bending (f m and E m ), obtained by the standard and non-destructive testing, suggest the possibility of using stress wave for quality control in OSB industry. KEYWORDS: Oriented strand board, nondestructive testing, stress wave, static mechanical properties.
BCL-2 Family protein expression in initial and recurrent glioblastomas: modulation by radiochemotherapy

OBJECTIVE In vitro studies indicate a role of apoptosis regulatory proteins of the BCL-2 family in the resistance of glioblastoma multiforme to irradiation and chemotherapy. To date, no study has compared the expression of these proteins in initial and recurrent tumours. The differences of expression of BCL-2, BCL-X, BAX, and MCL-1 proteins of paired first resection and recurrence glioblastoma specimens were examined. METHODS Immunohistochemistry was performed in 37 cases of glioblastoma multiforme with paraffin embedded tissue from first resections and their recurrences in three treatment groups (15 radiochemotherapy, 15 irradiation, seven untreated). Ten high power fields were evaluated with an arbitrary score (< 5%=1, 5–50%=2, >50%=3), and cumulative scores for each antigen calculated. RESULTS In the whole group, we found a significant up regulation of antiapoptotic BCL-2 (median cumulative score of 15 in the primary, 19 at recurrence; p<0.0001 in the Wilcoxon test), BCLX (median scores 20 and 25, respectively, p<0.0001), and MCL-1 (median scores 11 and 14, p=0.0395), and a significant down regulation of proapoptotic BAX (median scores 14 and 11, p<0.0001). In the subgroups, these trends were also found. No association between protein expression and treatment regimen was found, although significant changes were restricted to the subgroups that received adjuvant chemotherapy. No significant correlation with clinical prognosis was detected with the Kaplan-Meier method. CONCLUSIONS In the development from initial to recurrent glioblastoma multiforme, the BCL-2 family rheostat shifts towards antiapoptotic adjustment in vivo. Importantly, the changes in BCL-2 family protein expression characterised here were also seen in the subgroup of patients who did not receive adjuvant radiotherapy or chemotherapy, suggesting that the changes of BCL-2 family protein expression result not only from radiochemotherapy but also reflect the natural course of disease.
Bound on errors in particle filtering with incorrect model assumptions and its implication for change detection

We study the errors in particle filtering with incorrect system model parameters. The total error in approximating the posterior distribution of the actual process (state), given noisy observations, can be split into modeling error and particle filtering error in tracking with the incorrect model. We show that the bound on both errors is a monotonically increasing function of the error in the system model per time step. The bound on the particle filtering error blows up very quickly since it has increasing derivatives of all orders. We apply this result to bounding the errors in approximating our statistic for slow change detection in nonlinear systems.
Adiponectin Haploinsufficiency Promotes Mammary Tumor Development in MMTV-PyVT Mice by Modulation of Phosphatase and Tensin Homolog Activities

Background Adiponectin is an adipokine possessing beneficial effects on obesity-related medical complications. A negative association of adiponectin levels with breast cancer development has been demonstrated. However, the precise role of adiponectin deficiency in mammary carcinogenesis remains elusive. Methodology/Principal Findings In the present study, MMTV-polyomavirus middle T antigen (MMTV-PyVT) transgenic mice with reduced adiponectin expressions were established and the stromal effects of adiponectin haploinsufficiency on mammary tumor development evaluated. In mice from both FVB/N and C57BL/6J backgrounds, insufficient adiponectin production promoted mammary tumor onset and development. A distinctive basal-like subtype of tumors, with a more aggressive phenotype, was derived from adiponectin haplodeficient MMTV-PyVT mice. Comparing with those from control MMTV-PyVT mice, the isolated mammary tumor cells showed enhanced tumor progression in re-implanted nude mice, accelerated proliferation in primary cultures, and hyperactivated phosphatidylinositol-3-kinase (PI3K)/Akt/beta-catenin signaling, which at least partly attributed to the decreased phosphatase and tensin homolog (PTEN) activities. Further analysis revealed that PTEN was inactivated by a redox-regulated mechanism. Increased association of PTEN-thioredoxin complexes was detected in tumors derived from mice with reduced adiponectin levels. The activities of thioredoxin (Trx1) and thioredoxin reductase (TrxR1) were significantly elevated, whereas treatment with either curcumin, an irreversible inhibitor of TrxR1, or adiponectin largely attenuated their activities and resulted in the re-activation of PTEN in these tumor cells. Moreover, adiponectin could inhibit TrxR1 promoter-mediated transcription and restore the mRNA expressions of TrxR1. Conclusion Adiponectin haploinsufficiency facilitated mammary tumorigenesis by down-regulation of PTEN activity and activation of PI3K/Akt signalling pathway through a mechanism involving Trx1/TrxR1 redox regulations.
Prevention of Intestinal Allergy in Mice by rflaA:Ova Is Associated with Enforced Antigen Processing and TLR5-Dependent IL-10 Secretion by mDC

Conjugated vaccines consisting of flagellin and antigen activate TLR5 and induce strong innate and adaptive immune responses. Objective of the present study was to gain further insight into the mechanisms by which flagellin fusion proteins mediate their immune modulating effects. In a mouse model of Ova-induced intestinal allergy a fusion protein of flagellin and Ova (rflaA:Ova) was used for intranasal and intraperitoneal vaccination. Aggregation status of flaA, Ova and flaA:Ova were compared by light scattering, uptake of fluorescence labeled proteins into mDC was analyzed, processing was investigated by microsomal digestion experiments. Mechanism of DC-activation was investigated using proteasome and inflammasome inhibitors. Immune responses of wildtype, IL-10−/−, TLR5−/− mDCs and Ova-transgenic T cells were investigated. Mucosal and i.p.-application of rflaA:Ova were able to prevent allergic sensitization, suppress disease-related symptoms, prevent body weight loss and reduction in food uptake. Intranasal vaccination resulted in strongest suppression of Ova-specific IgE production. These protective effects were associated with increased aggregation of rflaA:Ova and accompanied by tenfold higher uptake rates into mDC compared to the mixture of both proteins. Microsomal digestion showed that stimulation with rflaA:Ova resulted in faster degradation and the generation of different peptides compared to rOva. rflaA:Ova-mediated activation of mDC could be suppressed in a dose-dependent manner by the application of both inflammasome and proteasome inhibitors. Using TLR5−/− mDC the rflaA:Ova induced IL-10 secretion was shown to be TLR5 dependent. In co-cultures of IL-10−/− mDC with DO11.10 T cells the lack of rflaA:Ova-mediated IL-10 secretion resulted in enhanced levels of both TH2 (IL-4, IL-5) and TH1 (IL-2 and IFN-y) cytokines. In summary, mucosal vaccination with flaA:Ova showed strongest preventive effect. Stimulation with rflaA:Ova results in strong immune modulation mediated by enhanced uptake of the aggregated fusion protein, likely resulting in a different processing by DC as well as stronger TLR5 mediated cell activation.
Parallelization of the NASA Goddard Cumulus Ensemble Model for Massively Parallel Computing

Massively parallel computing, using a message passing interface (MPI), has been implemented into a three-dimensional version of the Goddard Cumulus Ensemble (GCE) model. The implementation uses the domainresemble concept to design a code structure for both the whole domain and sub-domains after decomposition. Instead of inserting a group of MPI related statements into the model routine, these statements are packed into a single routine. In other words, only a single call statement to the model code is utilized once in a place, thus there is minimal impact on the original code. Therefore, the model is easily modified and/or managed by the model developers and/or users, who have little knowledge of massively parallel computing. The model decomposition is highly flexible such that the entire model domain can be sliced into any number of partial domains in one- or twodimensional decomposition. Data exchange is through a halo-region, which is overlaid with neighboring partial domains. A halo-region is also known as a ghost-cell region. For reproducibility purposes, transposing data among tasks into different decompositions is required, such as Fourier transform and full domain summation.
Comparative neurobiology of the basal ganglia

Basal Ganglia and Vertebrate Phylogeny Telencephalic Organization in Fishes Telencephalic Organization in Amphibians Basal Ganglia in Reptiles Basal Ganglia in Birds Basal Ganglia in Mammals: An Overview Mammalian Striatum: A Highly Heterogeneous Structure Mammalian Pallidum: A Source of Redundancy Mammalian Substantia Nigra A Dual Structure Basal Ganglia versus Limbic Structure References Indexes.
Strategies to Increase Research-based Practice: Interplay With Unit Culture

Purpose: A major focus of clinical nurse specialist nursing practice is the integration of research findings into practice. The purpose of this study was to describe strategies used to facilitate research utilization (RU) by nurses in a practice setting. Design: This multiple-case study identified the strategies that clinical nurse specialists and master's degree-prepared nurse educators, working collaboratively, used to facilitate RU. Setting/Sample: The setting included 8 units in 4 sites of a university hospital with all willing nurses participating. Methods: Open-ended focus groups and individual interviews and observational sessions were conducted using investigator-designed interview guides. Comprehensive qualitative analysis led to identification of categories and themes related to RU and the unit culture that supported it. Findings: Findings demonstrated that strategies to facilitate RU by staff at the unit level included conducting original research, supporting nurses participating in research, assessing and meeting staff learning needs, promoting staff attendance at conferences, stimulating goal-setting for presentations and publications, encouraging and responding to new ideas, questioning practice and stimulating inquiry, capitalizing on expertise in research knowledge and skills, and generating information and material resources. Characteristics of unit culture were linked to varying degrees of success with these strategies. The interplay of strategies with unit culture and research-based practice is described. Conclusion: A wide repertoire of strategies is needed to facilitate RU, and the outcome of these strategies is influenced by the unit culture. Implications for Practice: Consideration of the findings and the scope of the strategies used by nurses in the study can help clinical nurse specialist and other nursing leaders facilitate the building of practice on research.
Drivers of bacterial β-diversity depend on spatial scale

The factors driving β-diversity (variation in community composition) yield insights into the maintenance of biodiversity on the planet. Here we tested whether the mechanisms that underlie bacterial β-diversity vary over centimeters to continental spatial scales by comparing the composition of ammonia-oxidizing bacteria communities in salt marsh sediments. As observed in studies of macroorganisms, the drivers of salt marsh bacterial β-diversity depend on spatial scale. In contrast to macroorganism studies, however, we found no evidence of evolutionary diversification of ammonia-oxidizing bacteria taxa at the continental scale, despite an overall relationship between geographic distance and community similarity. Our data are consistent with the idea that dispersal limitation at local scales can contribute to β-diversity, even though the 16S rRNA genes of the relatively common taxa are globally distributed. These results highlight the importance of considering multiple spatial scales for understanding microbial biogeography.
Induction of Glutamate Dehydrogenase in the Ovine Fetal Liver by Dexamethasone Infusion during Late Gestation1

Glucocorticoids near term are known to upregulate many important enzyme systems prior to birth. Glutamate dehydrogenase (GDH) is a mitochondrial enzyme that catalyzes both the reversible conversion of ammonium nitrogen into organic nitrogen (glutamate production) and the oxidative deamination of glutamate resulting in 2-oxoglutarate. The activity of this enzyme is considered to be of major importance in the development of catabolic conditions leading to gluconeogenesis prior to birth. Ovine hepatic GDH mRNA expression and activity were determined in near-term (130 days of gestation, term 147 ± 4 days) control and acutely dexamethasone-treated (0.07 mg–1 hr–1 for 26 hr) fetuses. Dexamethasone infusion had no effect on placental or fetal liver weights. Dexamethasone infusion for 26 hr significantly increased hepatic GDH mRNA expression. This increased GDH mRNA expression was accompanied by an increase in hepatic mitochondrial GDH activity, from 30.0 ± 7.4 to 58.2 ± 8.1 U GDH/U CS (citrate synthase), and there was a significant correlation between GDH mRNA expression and GDH activity. The generated ovine GDH sequence displayed significant similarity with published human, rat, and murine GDH sequence. These data are consistent with the in vivo studies that have shown a redirection of glutamine carbon away from net hepatic glutamate release and into the citric acid cycle through the forward reaction catalyzed by GDH, i.e., glutamate to oxoglutarate.
Low-Complexity Direction-of-Arrival Estimation Based on Wideband Co-Prime Arrays

A class of low-complexity compressive sensing-based direction-of-arrival (DOA) estimation methods for wideband co-prime arrays is proposed. It is based on a recently proposed narrowband estimation method, where a virtual array model is generated by directly vectorizing the covariance matrix and then using a sparse signal recovery method to obtain the estimation result. As there are a large number of redundant entries in both the auto-correlation and cross-correlation matrices of the two sub-arrays, they can be combined together to form a model with a significantly reduced dimension, thereby leading to a solution with much lower computational complexity without sacrificing performance. A further reduction in complexity is achieved by removing noise power estimation from the formulation. Then, the two proposed low-complexity methods are extended to the wideband realm utilizing a group sparsity based signal reconstruction method. A particular advantage of group sparsity is that it allows a much larger unit inter-element spacing than the standard co-prime array and therefore leads to further improved performance.
Overexpression of N-Acetylglucosaminyltransferase III Enhances the Epidermal Growth Factor-induced Phosphorylation of ERK in HeLaS3 Cells by Up-regulation of the Internalization Rate of the Receptors*

N-Acetylglucosaminyltransferase III (GnT-III) is a key enzyme that inhibits the extension ofN-glycans by introducing a bisectingN-acetylglucosamine residue. In this study we investigated the effect of GnT-III on epidermal growth factor (EGF) signaling in HeLaS3 cells. Although the binding of EGF to the epidermal growth factor receptor (EGFR) was decreased in GnT-III transfectants to a level of about 60% of control cells, the EGF-induced activation of extracellular signal-regulated kinase (ERK) in GnT-III transfectants was enhanced to ∼1.4-fold that of the control cells. A binding analysis revealed that only low affinity binding of EGF was decreased in the GnT-III transfectants, whereas high affinity binding, which is considered to be responsible for the downstream signaling, was not altered. EGF-induced autophosphorylation and dimerization of the EGFR in the GnT-III transfectants were the same levels as found in the controls. The internalization rate of EGFR was, however, enhanced in the GnT-III transfectants as judged by the uptake of125I-EGF and Oregon Green-labeled EGF. When the EGFR internalization was delayed by dansylcadaverine, the up-regulation of ERK phosphorylation in GnT-III transfectants was completely suppressed to the same level as control cells. These results suggest that GnT-III overexpression in HeLaS3 cells resulted in an enhancement of EGF-induced ERK phosphorylation at least in part by the up-regulation of the endocytosis of EGFR.
Anti-Human Platelet Antigen-1a Immunoglobulin G Preparation Intended to Prevent Fetal and Neonatal Alloimmune Thrombocytopenia

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is a severe disease that is caused by maternal alloantibodies generated during pregnancy or at delivery as a result of incompatibility between maternal and fetal human platelet antigens (HPAs) inherited from the father. Antibody-mediated immune suppression using anti-HPA-1a immunoglobulins is thought to be able to prevent FNAIT caused by HPA-1a. A fractionation process to prepare anti-HPA-1a immunoglobulin (Ig) G (IgG) from human plasma was therefore developed. Anti-HPA-1a plasma was obtained from volunteer mothers who underwent alloimmunization against HPA-1a during a previous pregnancy. Plasma was cryoprecipitated and the supernatant treated with caprylic acid and solvent/detergent (S/D), purified by chromatography, nanofiltered, concentrated, and sterile-filtered. The anti-HPA-1a immunoglobulin fraction was characterized for purity and safety. PAK12 and quantitative monoclonal antibody immobilization of platelet antigen (MAIPA) assays were used to detect anti-HPA-1a IgG. Hepatitis C virus (HCV) removal during nanofiltration was assessed by spiking experiments, using cell culture-derived reporter HCV and luciferase analysis. The caprylic acid treatment precipitated non-Ig proteins yielding a 90% pure Ig supernatant. S-HyperCel chromatography of the S/D-treated supernatant followed by HyperCel STAR AX provided high IgG recovery (>80%) and purity (>99.5%), and efficient IgA and IgM removal. Concentrations of complement factors C3 and C4 were < 0.5 and < 0.4 mg/dL, respectively. The final IgG could be nanofiltered on Planova 20N under conditions removing more than 3 log HCV infectivity to baseline mock infection level, and concentrated to ca. 30 g/L. Proteolytic activity and thrombin generation were low in the final fraction. The Pak12 and MAIPA assays showed good recovery of anti-HPA-1a throughout the process. Clinical-grade HPA-1a IgG can be prepared using a process compliant with current quality requirements opening perspectives for the prevention of FNAIT.