Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal expression of type I interferon responsive genes in systemic lupus erythematosus

Cross-sectional studies of patients with systemic lupus erythematosus (SLE) have demonstrated an association between activation of type I interferon (IFN) pathway and disease activity. This study examined longitudinal changes in IFN-regulated gene expression in peripheral blood using microarrays. A cross-section of 66 patients from the Autoimmune Biomarkers Collaborative Network SLE archive was evaluated. We also examined paired samples from a 15 patient subset collected during a period of low disease activity (Baseline) and at a subsequent flare event, and baseline scores of 29 patients who maintained low disease activity. IFN response (IFNr) scores were calculated from three IFN-regulated genes. Overall, higher IFNr scores were associated with increased disease activity. However, IFNr scores were not significantly different between the paired Baseline and Flare samples. An extended longitudinal analysis in 11 patients indicated little change in IFNr scores over time, even during dynamic disease activity. In patients with low disease activity, IFNr scores were not different between patients who experienced a subsequent flare and those who maintained low disease activity. In summary, although higher IFNr scores were associated with greater disease activity, IFNr scores of individual patients did not correlate with changes in disease severity or flare risk.
Measurement of Specific Absorption Rate and Thermal Simulation for Arterial Embolization Hyperthermia in the Maghemite-Gelled Model

Theoretical models are designed to be applied in hyperthermia treatment planning and to help optimize the surgical treatment procedures. However, it is difficult to obtain every physical parameter of the magnetic field in the living tissue in detail, which is necessary for the calculation. We therefore investigated the simulation of thermal distribution in arterial embolization hyperthermia (AEH) stimulated by the external ferrite-core applicator, and measured specific absorption rate (SAR) of magnetic nanoparticles in the maghemtite-gelled composite model. We used fiber optic temperature sensors (FOTS) to measure the values of SAR, which depend on the microstructure and sizes of particles and the intensity and frequency of external ac magnetic field. Detailed tests indicated that the attenuation of magnetic field was mainly focused on the vertical distance in the aperture of the apparatus. We built a simplified cylindrical phantom containing maghemite particles of 20 nm for thermal field simulation on the basis of SAR measurement. The results of simulation indicated that temperature elevation, induced by nanoparticles inside tumors under ac magnetic field, was dose-dependent. The temperature data acquired from the experiment were compatible with the theoretical results, which demonstrated that the current model considering the inhomogenous heat generation could provide accurate and reliable simulation results and a theoretical and technical basis for controlling temperature during AEH therapy
Multi-Grained Block Management to Enhance the Space Utilization of File Systems on PCM Storages

Phase-change memory (PCM) is a promising candidate as a storage medium to resolve the performance gap between main memory and storage in battery-powered mobile computing systems. However, it is more expensive than flash memory, and thus introduces a more serious storage capacity issue for low-cost solutions. This issue is further exacerbated by the fact that existing file systems are usually designed to trade space utilization for performance over block-oriented storage devices. In this work, we propose a multi-grained block management strategy to improve the space utilization of file systems over PCM-based storage systems. By utilizing the byte-addressability and fast read/write feature of PCM, a methodology is proposed to dynamically allocate multiple sizes of blocks to fit the size of each file, so as to resolve the space fragmentation issue with minimized space and management overheads. The space utilization of file systems is analyzed with consideration of block sizes. A series of experiments was conducted to evaluate the efficacy of the proposed strategy, and the results show that the proposed strategy can significantly improve the space utilization of file systems.
Fusion of Hematopoietic Cells with Purkinje Neurons Does Not Lead to Stable Heterokaryon Formation under Noninvasive Conditions

Transplanted hematopoietic cells have previously been shown to contribute to cells of other tissues by cell fusion. We wanted to elucidate whether this phenomenon of cell fusion also occurs under physiological conditions. Using a transgenic mouse reporter system to irreversibly label cells of the hematopoietic lineage, we were able to test their contribution to other tissues in the absence of any additional and potentially confounding factors such as irradiation or chemoablation. We found genetically marked, fused Purkinje neurons as well as hepatocytes in numbers comparable to previous bone marrow transplantation studies. The number of fused Purkinje neurons increased after intrathecal administration of bacterial lipopolysaccharide, suggesting that cell fusion can be induced by inflammation. In contrast to previous studies, however, genetically labeled Purkinje neurons never contained more than one nucleus, and we found only a single cell containing two Y-chromosomes in a male mouse. Consistent with results from the mouse model and unlike human bone marrow transplant recipients, postmortem adult human cerebelli of nontransplanted individuals were devoid of binucleated or polyploid Purkinje neurons. Therefore, our data suggests that fusion of hematopoietic cells with Purkinje neurons is only transient and does not lead to stable heterokaryon formation under noninvasive conditions.
Percutaneous microwave ablation of thyroid nodules: effects on thyroid function and antibodies

Abstract Purpose: Microwave ablation (MWA) is a new minimally invasive method for thermal ablation of benign thyroid nodules with promising results. The aim of this study was to investigate whether MWA has an impact on thyroid function. Materials and methods: Thirty patients with a total of 34 benign thyroid nodules underwent MWA between January 2013 and July 2014. Serum levels of triiodothyronine (T3), thyroxine (T4), thyrotropin (TSH), thyroglobuline (Tg) and additionally antibodies against Tg (anti-Tg), thyrotropin receptors (TRAb) and thyroid peroxidase (anti-TPO) were measured at enrolment, 24 h after MWA, as well as at the 3-month and 6-month follow-up. Moreover, the nodule volume was evaluated to determine effectiveness. Results: Serum TSH, T4, T3 and Tg levels did not change significantly at the 3-month or 6-month follow-up (p > 0.05); thyroid function was not affected by MWA. Antibody levels did not change significantly either; however, two patients developed antibodies after treatment. A volume reduction of 51.4% or 7.85 mL could be demonstrated after 3 months and a reduction of 55.8% or 14.0 mL after 6 months. Slight complications such as mild pain during the ablation or superficial haematomas emerged. The development of Graves’ disease and mild Horner’s syndrome were observed as more severe side effects. Conclusions: The data suggest MWA as an alternative for the treatment of benign thyroid nodules. While first results for preservation of thyroid function are positive, further measurements of laboratory data and especially antibodies are necessary.
Regional Variation in Interhemispheric Coordination of Intrinsic Hemodynamic Fluctuations

Electrophysiological studies have long demonstrated a high degree of correlated activity between the left and right hemispheres, however little is known about regional variation in this interhemispheric coordination. Whereas cognitive models and neuroanatomical evidence suggest differences in coordination across primary sensory-motor cortices versus higher-order association areas, these have not been characterized. Here, we used resting-state functional magnetic resonance imaging data acquired from 62 healthy volunteers to examine interregional correlation in spontaneous low-frequency hemodynamic fluctuations. Using a probabilistic atlas, we correlated probability-weighted time series from 112 regions comprising the entire cerebrum. We then examined regional variation in correlated activity between homotopic regions, contrasting primary sensory-motor cortices, unimodal association areas, and heteromodal association areas. Consistent with previous studies, robustly correlated spontaneous activity was noted between all homotopic regions, which was significantly higher than that between nonhomotopic (heterotopic and intrahemispheric) regions. We further demonstrated substantial regional variation in homotopic interhemispheric correlations that was highly consistent across subjects. Specifically, there was a gradient of interhemispheric correlation, with highest correlations across primary sensory-motor cortices (0.758, SD = 0.152), significantly lower correlations across unimodal association areas (0.597, SD = 0.230) and still lower correlations across heteromodal association areas (0.517, SD = 0.226). These results demonstrate functional differences in interhemispheric coordination related to the brain's hierarchical subdivisions. Synchrony across primary cortices may reflect networks engaged in bilateral sensory integration and motor coordination, whereas lower coordination across heteromodal association areas is consistent with functional lateralization of these regions. This novel method of examining interhemispheric coordination may yield insights regarding diverse disease processes as well as healthy development.
Rule learning by Habituation can be Simulated in Neural Networks

Contrary to a recent claim that neural network models are unable to account for data on infant habituation to artificial language sentences, the present simulations show successful coverage with cascade-correlation networks using analog encoding. The results demonstrate that a symbolic rule-based account is not required by the infant data. One of the fundamental issues of cognitive science continues to revolve around which type of theoretical model better accounts for human cognition -- a symbolic rulebased account or a sub-symbolic neural network account. A recent study of infant habituation to expressions in an artificial language claims to have struck a damaging blow to the neural network approach (Marcus, Vijayan, Rao, & Vishton, 1999). The results of their study show that 7month-old infants attend longer to sentences with unfamiliar structures than to sentences with familiar structures. Because of certain features of their experimental design and their own unsuccessful neural network models, Marcus et al. conclude that neural networks cannot simulate these results and that infants possess a rule -learning capability unavailable to neural networks. A companion article suggests that rule learning is an innately provided capacity of the human mind, distinct from associative learning mechanisms like those in neural networks (Pinker, 1999). My paper presents neural network simulations of the key features of the Marcus et al. (1999) experiment, thus showing that their infant data do not uniquely support a rule-based account.
Different Atmospheric Methane-Oxidizing Communities in European Beech and Norway Spruce Soils

ABSTRACT Norway spruce (Picea abies) forests exhibit lower annual atmospheric methane consumption rates than do European beech (Fagus sylvatica) forests. In the current study, pmoA (encoding a subunit of membrane-bound CH4 monooxygenase) genes from three temperate forest ecosystems with both beech and spruce stands were analyzed to assess the potential effect of tree species on methanotrophic communities. A pmoA sequence difference of 7% at the derived protein level correlated with the species-level distance cutoff value of 3% based on the 16S rRNA gene. Applying this distance cutoff, higher numbers of species-level pmoA genotypes were detected in beech than in spruce soil samples, all affiliating with upland soil cluster α (USCα). Additionally, two deep-branching genotypes (named 6 and 7) were present in various soil samples not affiliating with pmoA or amoA. Abundance of USCα pmoA genes was higher in beech soils and reached up to (1.2 ± 0.2) × 108pmoA genes per g of dry weight. Calculated atmospheric methane oxidation rates per cell yielded the same trend. However, these values were below the theoretical threshold necessary for facilitating cell maintenance, suggesting that USCα species might require alternative carbon or energy sources to thrive in forest soils. These collective results indicate that the methanotrophic diversity and abundance in spruce soils are lower than those of beech soils, suggesting that tree species-related factors might influence the in situ activity of methanotrophs.
Alternative Implementations of Two-Level Adaptive Branch Prediction

As the issue rate and depth of pipelining of high performance Superscalar processors increase, the importance of an excellent branch predictor becomes more vital to delivering the potential performance of a wide-issue, deep pipelined microarchitecture. We propose a new dynamic branch predictor (Two-Level Adaptive Branch Prediction) that achieves substantially higher accuracy than any other scheme reported in the literature. The mechanism uses two levels of branch history information to make predictions, the history of the last k branches encountered, and the branch behavior for the last s occurrences of the specific pattern of these k branches. We have identified three variations of the Two-Level Adaptive Branch Prediction, depending on how finely we re- solve the history information gathered. We compute the hardware costs of implementing each of the three variations, and use these costs in evaluating their relative effectiveness. We measure the branch prediction accuracy of the three variations of Two-Level Adaptive Branch Prediction, along with several other popular proposed dynamic and static prediction schemes, on the SPEC benchmarks. We show that the average prediction accuracy for Two-Level Adaptive Branch Prediction is 97 percent, while the other known schemes achieve at most 94.4 percent average prediction accuracy. We measure the effectiveness of different prediction algorithms and different amounts of history and pattern information. We measure the costs of each variation to obtain the same prediction accuracy.
Microbiologically documented infections in patients undergoing high‐dose melphalan and autologous stem cell transplantation for the treatment of light chain amyloidosis

Immunoglobulin light chain (AL) amyloidosis can be treated with high‐dose melphalan and autologous stem cell transplantation (HDM/SCT). Risk factors for infections may include hyposplenism, hypogammaglobulinemia, treatment‐related neutropenia, melphalan‐induced mucositis, and nosocomial exposures.
Fetal nigral grafts survive and mediate clinical benefit in a patient with Parkinson's disease

We have previously demonstrated that fetal nigral grafts can survive, reinnervate the striatum, and mediate clinically relevant recovery in a patient with Parkinson's disease (PD). 1 Most previous autopsy cases have failed to identify meaningful numbers of viable grafted cells suggesting that differences in critical transplant variables determine graft viability. 2–4 The present study evaluated the structural and functional correlates of fetal nigral transplantation in a second PD patient who received fetal nigral grafts according to our previously published transplant protocol. 5 A 61‐year‐old woman with severe PD received bilateral fetal nigral grafts to the post commissural putamen from seven donor fetuses (four right side and three left side) aged 6.5‐9 weeks postconception. This patient died 19 months after surgery from a cause unrelated to the transplant surgery. Her postoperative clinical course was characterized by improved motor and activities of daily living scores during “off time,” reduced “off time,” and increased “on” time without dyskinesia. Positron emission tomography (PET) scans revealed a bilateral and progressive increase in fluorodopa (FD) uptake within the grafted putamen. Postmortem examination of the right hemisphere revealed large ovalshaped grafts containing more than 138,000 tyrosinehydroxylase‐immunoreactive (TH‐ir) neurons. Grafted cells formed a seamless border with the host and provided dense TH‐ir innervation to 78% of the host postcommissural putamen. Graft‐mediated sprouting of host fibers was not observed. These data provide essential confirmation that, under appropriate transplant conditions, grafted nigral neurons can survive, reinnervate the host striatum, and provide clinical benefit to PD patients. These findings also support the concept that improved motor function and striatal FD uptake on PET after nigral grafting in PD are the result of the viability of grafted neurons and graft‐derived reinnervation of the host striatum.
Dynamically Integrating Cross-Domain Translation Memory into Phrase-Based Machine Translation during Decoding

Our previous work focuses on combining translation memory (TM) and statistical machine translation (SMT) when the TM database and the SMT training set are the same. However, the TM database will deviate from the SMT training set in the real task when time goes by. In this work, we concentrate on the task when the TM database and the SMT training set are different and even from different domains. Firstly, we dynamically merge the matched TM phrase-pairs into the SMT phrase table to meet the real application. Secondly, we propose an improved integrated model to distinguish the original and the newly-added phrase-pairs. Thirdly, a simple but effective TM adaptation method is adopted to favor the consistent translations in cross-domain test. Our experiments have shown that merging the TM phrasepairs achieves significant improvements. Furthermore, the proposed approaches are significantly better than the TM, the SMT and previous integration works for both in-domain and cross-domain tests.
Fourier transform rheology of complex, filled rubber materials

The presence of reinforcing fillers has a tremendous impact on the structure and the rheological properties of rubber materials. In this work, the nonlinear viscoelastic properties of two types of complex rubber materials, thermoplastic elastomers synthesized by anionic polymerization and carbon black filled SBR, were investigated by means of Fourier transform rheology. The results indicate a large influence of the interface on the third higher harmonic contribution.
Multi-agent systems to build a computational middleware: A chatterbot case study

In this work we argue that the shift from computer networks to agent networks is an important improvement of the network programming technology. Its due the fact that agents are well suited for modeling, designing and implementing scalable, flexible and secure distributed systems over a computing environment. Based on this agent-paradigm, our proposal is to make a case study of a chatterbot prototype. This chatterbot can be utilized in educational virtual environments to provide an interface to guide the student in the explanation of the FAQs.
Integral transforms, convolution products, and first variations

We establish the various relationships that exist among the integral transform ℱα,βF, the convolution product (F∗G)α, and the first variation δF for a class of functionals defined on K[0,T], the space of complex-valued continuous functions on [0,T] which vanish at zero.
Activation of the prefrontal cortex during the Trail‐Making Test detected with multichannel near‐infrared spectroscopy

Abstract The Trail‐Making Test (TMT) is a neuropsychological test for evaluating executive function, and the TMT Part B reflects more complex cognitive processes including cognitive set shifting. The prefrontal cortex (PFC) is thought to be involved in these cognitive processes. The purpose of the present paper was to investigate PFC activation during performance of the TMT Part A and Part B using multichannel near‐infrared spectroscopy (NIRS). Subjects were 41 healthy right‐handed volunteers. The hemodynamic changes in the PFC during the TMT were measured on a 22‐channel NIRS machine. The subjects had a greater increase of oxygenated hemoglobin ([oxyHb]) during the TMT Part B than during Part A in the PFC. Twenty‐seven out of the 41 subjects had a bilateral increase of [oxyHb] in the PFC during Part B according to laterality index. NIRS detected activation in the PFC during the performance of the TMT Part B and this PFC activation may reflect executive functions including cognitive set shifting involved in the TMT Part B.
Effects of mTOR Inhibitor Everolimus (RAD001) on Bladder Cancer Cells

Purpose: We investigated the effect of the mTOR inhibitor RAD001 (everolimus) on human bladder cancer (BC) cells in vitro and in vivo. Experimental Design: The effect of RAD001 on the growth of UM-UC-3, UM-UC-6, UM-UC-9, and UM-UC-14 BC cells were assessed by crystal violet and [3H]thymidine incorporation assays. Flow cytometric cell-cycle analyses were done to measure the apoptotic cell fraction. Protein synthesis was measured using tritium-labeled leucine incorporation assays. The effects of RAD001 on the mTOR pathway were analyzed by Western blotting. To test the effects of RAD001 in vivo, UM-UC-3, UM-UC-6, and UM-UC-9 cells were subcutaneously implanted into nude mice. Tumor-bearing mice were treated orally with RAD001 or placebo. Tumors were harvested for immunohistochemical analysis. Results:In vitro, RAD001 transiently inhibited BC cell growth in a dose-dependent manner. This effect was augmented by re-treatment of cells after 3 days. UM-UC-14 cells were the most sensitive to RAD001, whereas UM-UC-9 cells were the least sensitive. After re-treatment with RAD001, only sensitive cell lines showed G1-phase arrest, with no evidence of apoptosis. RAD001 significantly inhibited the growth of tumors that were subcutaneously implanted in mice. Inhibition of protein synthesis through the S6K and 4EBP1 pathways seems to be the main mechanism for the RAD001-induced growth inhibition. However, inhibition of angiogenesis was the predominant mechanism of the effect of RAD001 on UM-UC-9 cells. Conclusions: The mTOR inhibitor RAD001 inhibits growth of BC cells in vitro. RAD001 is effective in treating BC tumors in an in vivo nude mouse model despite the heterogeneity of in vitro responses. Clin Cancer Res; 17(9); 2863–73. ©2011 AACR.
Localization of type IV collagen, laminin, heparan sulfate proteoglycan, and fibronectin to the basal lamina of basement membranes

Electron microscopic immunostaining of rat duodenum and incisor tooth was used to examine the location of four known components of the basement-membrane region: type IV collagen, laminin, heparan sulfate proteoglycan, and fibronectin. Antibodies or antisera against these substances were localized by direct or indirect peroxidase methods on 60-microns thick slices of formaldehyde-fixed tissues. In the basement- membrane region of the duodenal epithelium, enamel-organ epithelium, and blood-vessel endothelium, immunostaining for all four components was observed in the basal lamina (also called lamina densa). The bulk of the lamina lucida (rara) was unstained, but it was traversed by narrow projections of the basal lamina that were immunostained for all four components. In the subbasement-membrane fibrous elements or reticular lamina, immunostaining was confined to occasional "bridges" extending from the epithelial basal-lamina to that of adjacent capillaries. The joint presence of type IV collagen, laminin, heparan sulfate proteoglycan, and fibronectin in the basal lamina indicates that these substances do not occur in separate layers but are integrated into a common structure.