Miracle-dz/UniFAR-FTUs huggingface dataset:
Thyrocytes Responding to IFN-γ Are Essential for Development of Lymphocytic Spontaneous Autoimmune Thyroiditis and Inhibition of Thyrocyte Hyperplasia1

IFN-γ promotes the development of lymphocytic spontaneous autoimmune thyroiditis (L-SAT) in NOD.H-2h4 mice and inhibits the development of thyrocyte hyperplasia and proliferation (TEC H/P). The precise mechanisms by which IFN-γ promotes L-SAT and inhibits TEC H/P are unknown. To determine whether responsiveness of lymphocytes or thyrocytes to IFN-γ is important for the development of these lesions, IFN-γR−/− mice, which develop TEC H/P similar to IFN-γ−/− mice, were used as recipients for adoptive cell transfer. Wild-type (WT) splenocytes or bone marrow induced L-SAT and inhibited TEC H/P in IFN-γ−/−, but not IFN-γR−/− recipients. IFN-γR−/− recipients of WT cells developed severe TEC H/P, but did not develop L-SAT, suggesting that thyrocytes responding to IFN-γ are important for inhibition of TEC H/P. Unexpectedly, IFN-γR−/− splenocytes or bone marrow did not induce L-SAT in IFN-γ−/− or WT mice even though IFN-γR−/− lymphocyte donors produced as much IFN-γ as lymphocytes from WT donors, and thyrocytes could respond to IFN-γ. Real-time PCR indicated that recipients of IFN-γR−/− bone marrow expressed less mRNA for IFN-γ-inducible chemokines compared with recipients of WT bone marrow. This might limit the migration of IFN-γR−/− lymphocytes to thyroids. Few IFN-γR−/− lymphocytes infiltrated thyroids even in the presence of WT lymphocytes, suggesting that lymphocytes unable to respond to IFN-γ are not induced to migrate to thyroids. These results suggest that thyrocytes must be able to respond to IFN-γ for the development of L-SAT and inhibition of TEC H/P, and lymphocytes must be able to respond to IFN-γ to induce L-SAT.
One approach to HTML wrappers creation: using Document Object Model tree

Most of the Internet sources are in unstructured HTML format, which is often difficult to process further. Content extraction from such sources is usually carried out by wrappers. There are various approaches to wrapper construction. The method proposed in this paper utilizes valued Document Object Model (DOM) trees. For each tag in the DOM tree a hash is computed from the sequence of parent tags, tag attributes, its values and the tag sub-tree. This conception ensures that same hashes will be computed for the particular wrapper even for different queries. Proposed solution has been implemented and verified.
Computational modelling of double focus in American English

This study investigated how double focus in English statements and questions can be computationally modelled. PENTAtrainer2 was used to learn syllable-sized multi-functional targets from a corpus of 1960 English utterances, with controlled variations in lexical stress, focus, modality, and sentence length. The results showed that the learned targets could generate F0 contours close to the original. In particular, the asymmetry in the interaction between focus and modality was effectively simulated.
“Once upon a Time in the Mediterranean” Long Term Trends of Mediterranean Fisheries Resources Based on Fishers’ Traditional Ecological Knowledge

We investigate long-term changes in the Mediterranean marine resources driving the trawl fisheries by analysing fishers’ perceptions (Traditional Ecological Knowledge, TEK) throughout the Mediterranean Sea during the last 80 years. To this end, we conducted an extended set of interviews with experienced fishers that enabled us to classify species (or taxa) as ‘decreasing’ or ‘increasing’ both in terms of abundance, as well as average size in the catch. The aspect that most clearly emerged in all the investigated areas over time was the notable increase of fishing capacity indicators, such as engine power and fishing depth range. Atlantic mackerel, poor cod, scorpionfishes, striped seabream, and John Dory demonstrated a decreasing trend in the fishers’ perceived abundance, while Mediterranean parrotfish, common pandora, cuttlefish, blue and red shrimp, and mullets gave indications of an increasing temporal trend. Although, as a rule, trawler captains did not report any cataclysmic changes (e.g. extinctions), when they were invited to estimate total catches, a clear decreasing pattern emerged; this being a notable finding taking into account the steep escalation of fishing efficiency during the past century. The overall deteriorating status of stocks in most Mediterranean regions calls for responsible management and design of rebuilding plans. This should include historical information accounting for past exploitation patterns that could help defining a baseline of fish abundance prior to heavy industrial fisheries exploitation.
New Arabidopsis cue mutants suggest a close connection between plastid- and phytochrome regulation of nuclear gene expression.

We searched for new components that are involved in the positive regulation of nuclear gene expression by light by extending a screen for Arabidopsis cue (chlorophyll a/b-binding [CAB] protein-underexpressed) mutants (H.-M. Li, K. Culligan, R.A. Dixon, J. Chory [1995] Plant Cell 7: 1599-1610). cue mutants display reduced expression of the CAB3 gene, which encodes light-harvesting chlorophyll protein, the main chloroplast antenna. The new mutants can be divided into (a) phytochrome-deficient mutants (hy1 and phyB), (b) virescent or delayed-greening mutants (cue3, cue6, and cue8), and (c) uniformly pale mutants (cue4 and cue9). For each of the mutants, the reduction in CAB expression correlates with the visible phenotype, defective chloroplast development, and reduced abundance of the light-harvesting chlorophyll protein. Levels of protochlorophyllide oxidoreductase (POR) were reduced to varying degrees in etiolated mutant seedlings. In the dark, whereas the virescent mutants displayed reduced CAB expression and the lowest levels of POR protein, the other mutants expressed CAB and accumulated POR at near wild-type levels. All of the mutants, with the exception of cue6, were compromised in their ability to derepress CAB expression in response to phytochrome activation. Based on these results, we propose that the previously postulated plastid-derived signal is closely involved in the pathway through which phytochrome regulates the expression of nuclear genes encoding plastid proteins.
Optimal Caching and Scheduling for Cache-Enabled D2D Communications

To maximize offloading gain of cache-enabled device-to-device (D2D) communications, content placement and delivery should be jointly designed. In this letter, we jointly optimize caching and scheduling policies to maximize successful offloading probability, defined as the probability that a user can obtain desired file in local cache or via D2D link with data rate larger than a given threshold. We obtain the optimal scheduling factor for a random scheduling policy that can control interference in a distributed manner, and a low complexity solution to compute caching distribution. We show that the offloading gain can be remarkably improved by the joint optimization.
MAC Access Delay In IEEE 802.11e EDCA

In this paper, we analyze the MAC access delay of the EDCA mechanism in the IEEE 802.11e standard under saturation. We model the effect of differentiation based on both contention window size and inter-frame spacing. Explicit expressions for the mean, the standard deviation and the generating function of the distribution of the access delay are obtained. By applying numerical inversion on the generating function, we are able to compute values of the distribution. We show that our analytical model is accurate through comparison with simulation.
Characterization of Reemerging Chikungunya Virus

An unprecedented epidemic of chikungunya virus (CHIKV) infection recently started in countries of the Indian Ocean area, causing an acute and painful syndrome with strong fever, asthenia, skin rash, polyarthritis, and lethal cases of encephalitis. The basis for chikungunya disease and the tropism of CHIKV remain unknown. Here, we describe the replication characteristics of recent clinical CHIKV strains. Human epithelial and endothelial cells, primary fibroblasts and, to a lesser extent, monocyte-derived macrophages, were susceptible to infection and allowed viral production. In contrast, CHIKV did not replicate in lymphoid and monocytoid cell lines, primary lymphocytes and monocytes, or monocyte-derived dendritic cells. CHIKV replication was cytopathic and associated with an induction of apoptosis in infected cells. Chloroquine, bafilomycin-A1, and short hairpin RNAs against dynamin-2 inhibited viral production, indicating that viral entry occurs through pH-dependent endocytosis. CHIKV was highly sensitive to the antiviral activity of type I and II interferons. These results provide a general insight into the interaction between CHIKV and its mammalian host.
Is Model-Based Development a Favorable Approach for Complex and Safety-Critical Computer Systems on Commercial Aircraft?

Abstract A system is safety-critical if its failure can endanger human life or cause significant damage to property or the environment. State-of-the-art computer systems on commercial aircraft are highly complex, software-intensive, functionally integrated, an d network-centric systems of systems. Ensuring that such systems are safe and comply with existing safety regulations is costly and time-consuming as the level of rigor in the development process, especially the validation and verification activities, is determined by considerations of syst em complexity and safety criticality. A significant degree of care and deep insight into the operational principles of these systems is required to ensure adequate coverage of all design implications relevant to system safety. Model-based development methodologies, methods, tools, and techniques facilitate collaboration and enable the use of common design artifacts among groups dealing with different aspects of the development of a system. This paper examines the application of model-based development to complex and safety-critical aircraft computer systems. Benefits and detriments are identified and an overall assessment of the approach is given.
Semantic Web-based Source Code Search

The ability to search for source code on the Internet has proven to be essential for many common software development and maintenance tasks. However, available code search engines are typically limited to lexical searches and do not take in consideration the underlying semantics of source code such as the program structure or language. Especially object-oriented source code, which includes inheritance and polymorphism, is often not modeled to a level in which it can be queried sufficiently. In this paper, we present a Semantic Web-based approach to source code search that uses ontologies to model and connect source code fragments extracted from repositories on the Internet. This modeling approach allows us to reason and search across project boundaries while dealing with incomplete knowledge and ambiguities. In comparison with other search tools, we incrementally build our knowledge base without the need to re-visit fragments or compile the source code. Our search engine is scalable and allows us to process and query a large code base collected from opensource projects.
Systemic Stimulation of TLR2 Impairs Neonatal Mouse Brain Development

Background Inflammation is associated with perinatal brain injury but the underlying mechanisms are not completely characterized. Stimulation of Toll-like receptors (TLRs) through specific agonists induces inflammatory responses that trigger both innate and adaptive immune responses. The impact of engagement of TLR2 signaling pathways on the neonatal brain is still unclear. The aim of this study was to investigate the potential effect of a TLR2 agonist on neonatal brain development. Methodology/Principal Findings Mice were injected intraperitoneally (i.p.) once a day from postnatal day (PND) 3 to PND11 with endotoxin-free saline, a TLR2 agonist Pam3CSK4 (5 mg/kg) or Lipopolysaccharide (LPS, 0.3 mg/kg). Pups were sacrificed at PND12 or PND53 and brain, spleen and liver were collected and weighed. Brain sections were stained for brain injury markers. Long-term effects on memory function were assessed using the Trace Fear Conditioning test at PND50. After 9 days of Pam3CSK4 administration, we found a decreased volume of cerebral gray matter, white matter in the forebrain and cerebellar molecular layer that was accompanied by an increase in spleen and liver weight at PND12. Such effects were not observed in Pam3CSK4-treated TLR 2-deficient mice. Pam3CSK4-treated mice also displayed decreased hippocampus neuronal density, and increased cerebral microglia density, while there was no effect on caspase-3 or general cell proliferation at PND12. Significantly elevated levels of IL-1β, IL-6, KC, and MCP-1 were detected after the first Pam3CSK4 injection in brain homogenates of PND3 mice. Pam3CSK4 administration did not affect long-term memory function nor the volume of gray or white matter. Conclusions/Significance Repeated systemic exposure to the TLR2 agonist Pam3CSK4 can have a short-term negative impact on the neonatal mouse brain.
Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells

Adenoviruses replicate primarily in the host cell nucleus, and it is well established that adenovirus infection affects the structure and function of host cell nucleoli in addition to coding for a number of nucleolar targeted viral proteins. Here we used unbiased proteomics methods, including high throughput mass spectrometry coupled with stable isotope labeling by amino acids in cell culture (SILAC) and traditional two-dimensional gel electrophoresis, to identify quantitative changes in the protein composition of the nucleolus during adenovirus infection. Two-dimensional gel analysis revealed changes in six proteins. By contrast, SILAC-based approaches identified 351 proteins with 24 proteins showing at least a 2-fold change after infection. Of those, four were previously reported to have aberrant localization and/or functional relevance during adenovirus infection. In total, 15 proteins identified as changing in amount by proteomics methods were examined in infected cells using confocal microscopy. Eleven of these proteins showed altered patterns of localization in adenovirus-infected cells. Comparing our data with the effects of actinomycin D on the nucleolar proteome revealed that adenovirus infection apparently specifically targets a relatively small subset of nucleolar antigens at the time point examined.
Types of Property Pairs and Alignment on Linked Datasets - A Preliminary Analysis

Dataset publication on the Web has been greatly influenced by the Linked Open Data (LOD) project. Many interlinked datasets have become freely available on the Web creating a structured and distributed knowledge representation. Analysis and aligning of concepts and instances in these interconnected datasets have received a lot of attention in the recent past compared to properties. We identify three different categories of property pairs found in the alignment process and study their relative distribution among well known LOD datasets. We also provide comparative analysis of state-of-the-art techniques with regard to different categories, highlighting their capabilities. This could lead to more realistic and useful alignment of properties in LOD and similar datasets.
High‐speed atmospheric atomic layer deposition of ultra thin amorphous TiO2 blocking layers at 100 °C for inverted bulk heterojunction solar cells

Ultrafast, spatial atmospheric atomic layer deposition, which does not involve vacuum steps and is compatible with roll‐to‐roll processing, is used to grow high quality TiO2 blocking layers for organic solar cells. Dense, uniform thin TiO2 films are grown at temperatures as low as 100 °C in only 37 s (~20 nm/min growth rate). Incorporation of these films in P3HT‐PCBM‐based solar cells shows performances comparable with cells made using TiO2 films deposited with much longer processing times and/or higher temperatures. Copyright © 2013 John Wiley & Sons, Ltd.
Combined Data Mining Approach for Intrusion Detection

This paper presents the results of the project MIAU, a data mining approach for intrusion detection alert correlation. MIAU combines different data mining techniques in order to properly solve some existing problems in the management and analysis of alerts generated by actual intrusion detection systems. Some of these data mining methods and their application to MIAU are introduced in this paper. Experiments have been carried out with the purpose of demonstrating the validity of the proposed model and some conclusions about them are extracted. Finally, some possible improvements for the system and further work are exposed.
Acetylation of a Specific Promoter Nucleosome Accompanies Activation of the ɛ-Globin Gene by β-Globin Locus Control Region HS2

ABSTRACT On stably replicating episomes, transcriptional activation of the ɛ-globin promoter by the β-globin locus control region HS2 enhancer is correlated with an increase in nuclease sensitivity which is limited to the TATA-proximal nucleosome (N1). To elucidate what underlies this increase in nuclease sensitivity and the link between chromatin modification and gene expression, we examined the nucleoprotein composition and histone acetylation status of transcriptionally active and inactive promoters. Micrococcal nuclease digestion of active promoters in nuclei released few nucleosome-like nucleoprotein complexes containing N1 sequences in comparison to results with inactive promoters. We also observed that N1 DNA fragments from active promoters are of a subnucleosomal length. Nevertheless, chromatin immunoprecipitation experiments indicate that histones H3 and H4 are present on N1 sequences from active promoters, with H3 being dramatically hyperacetylated compared with that from inactive promoters and vector sequences. Strikingly, H3 in the adjacent upstream nucleosome (N2) does not appear to be differentially acetylated in active and inactive promoters, indicating that the nucleosome modification of the promoter that accompanies transactivation by HS2 is highly directed and specific. However, global acetylation of histones in vivo by trichostatin A did not activate transcription in the absence of HS2, suggesting that HS2 contributes additional activities necessary for transactivation. N1 sequences from active promoters also contain reduced levels of linker histone H1. The detection of a protected subnucleosomal sized N1 DNA fragment and the recovery of N1 DNA sequences in immunoprecipitations using anti-acetylated H3 and H4 antibodies argue that N1 is present, but in an altered conformation, in the active promoters.
Bilattice-based Logical Reasoning for Human Detection

The capacity to robustly detect humans in video is a critical component of automated visual surveillance systems. This paper describes a bilattice based logical reasoning approach that exploits contextual information and knowledge about interactions between humans, and augments it with the output of different low level detectors for human detection. Detections from low level parts-based detectors are treated as logical facts and used to reason explicitly about the presence or absence of humans in the scene. Positive and negative information from different sources, as well as uncertainties from detections and logical rules, are integrated within the bilattice framework. This approach also generates proofs or justifications for each hypothesis it proposes. These justifications (or lack thereof) are further employed by the system to explain and validate, or reject potential hypotheses. This allows the system to explicitly reason about complex interactions between humans and handle occlusions. These proofs are also available to the end user as an explanation of why the system thinks a particular hypothesis is actually a human. We employ a boosted cascade of gradient histograms based detector to detect individual body parts. We have applied this framework to analyze the presence of humans in static images from different datasets.
Overview and progress of the pallid sturgeon assessment framework redesign process

The Pallid Sturgeon Population Assessment Program (PSPAP) was initiated in 2003, and full implementation began in 2006, to monitor the trend of Scaphirhynchus albus (pallid sturgeon) and native fish communities in the Upper and Lower Missouri River Basins. The original PSPAP (v. 1.0) was a catch-effort based monitoring program where population abundance and trend were monitored using a relative index, catch per unit effort. In 2013, the Missouri River Recovery Program (MRRP), led by the U.S. Army Corps of Engineers (USACE) and the U.S. Fish and Wildlife Service (USFWS), began a reassessment of science and monitoring approaches to support a new river management plan. The need to redesign the PSPAP was triggered by the recognition that the PSPAP v. 1.0 would not be optimally effective in contributing information needed to make decisions about the pallid sturgeon fundamental management objective—to avoid jeopardizing the continued existence of the pallid sturgeon from USACE actions in the Missouri River—identified in the Missouri River Science and Adaptive Management Plan. The fundamental management objective includes two management subobjectives: (1) increase pallid sturgeon recruitment to age 1 and (2) maintain or increase numbers of pallid sturgeon as an interim measure until sufficient and sustained natural recruitment occurs. These two management subobjectives motivated the development of two fundamental information objectives for PSPAP v. 2.0: (1) to provide information needed to quantify recruitment to age 1 and (2) to quantify pallid sturgeon population abundance and trend. The charge to the authors of this report was to develop an approach to monitoring the pallid sturgeon population in the Missouri River that would contribute information toward gauging overall performance of management actions to achieve the fundamental objectives of the MRRP and to potentially improve understanding of linkages from the management activities to population responses. We used transparent and robust processes to identify alternative monitoring designs that meet the fundamental objectives for managing pallid sturgeon in the MRRP, with a focus on simulation models to evaluate the performance of varying monitoring. This report documents the process of comparing potential alternative monitoring design abilities to provide decision-relevant information for management of the species. The process includes 1Mississippi State University. 2U.S. Geological Survey. 3U.S. Fish and Wildlife Service. 4Nebraska Game and Parks Commission. 5U.S. Army Corps of Engineers.
Spatial separation of multi-user MIMO channels

Since multi-antenna (MIMO) systems are becoming more popular thanks to their inherent potential for capacity improvement, interference from MIMO transceivers is an increasingly serious concern. Spatial multiplexing schemes are particularly vulnerable to multi-user interference. Fortunately, this interference can be mitigated, when the channel matrices show a sufficient spatial separation. In this paper, we quantify the separability of multi-user MIMO channels using actual measurements in a scenario where a single outdoor base station transmits to two indoor mobile receivers. To quantify the spatial distance between the two users, we compare the spatial correlation matrices using two simple measures: (i) matrix collinearity, and (ii) the condition number ratio. Both measures are directly linked to MIMO system performance. Our measurement-based evaluations demonstrate that the downlink channels of different users can have a significantly different spatial structure, even when the users are in the same room. This leads to the following conclusions: (i) new multi-user MIMO models are needed to describe the spatial characteristics of different users, and (ii) spatial interference can be well managed by appropriate scheduling and precoding algorithms.