Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in broilers.
Rapid RFID tag collision resolution with the frame slotted ALOHA protocol

RFID holds the promise to provide a bridge between the physical item world and the digital virtual space. One of the key issues that affect this promise to become a reality is the tag collision. When multiple tags try to transmit their digital identifiers simultaneously to the reader, tag collision will occur. In this paper, based on the analysis of the frame slotted ALOHA protocol commonly used for tag collision resolution, the optimal frame size for the protocol to adopt in resolving the collisions caused by different number of tags is calculated, and two enhanced frame slotted ALOHA protocols are proposed for the rapid resolution of collisions caused by a large amount RFID tags. The performances of these protocols are evaluated and it is verified that this protocols outperforms the traditional frame slotted ALOHA protocols.
On Instance-level Update and Erasure in Description Logic Ontologies

A Description Logic (DL) ontology is constituted by two components, a TBox that expresses general knowledge about the concepts and their relationships, and an ABox that describes the properties of individuals that are instances of concepts. We address the problem of how to deal with changes to a DL ontology, when these changes affect only the ABox, i.e. when the TBox is considered invariant. We consider two basic changes, namely instance-level update and instance-level erasure, roughly corresponding to the addition and the deletion of a set of facts involving individuals. We characterize the semantics of instance-level update and erasure on the basis of the approaches proposed by Winslett and by Katsuno and Mendelzon. Interestingly, DLs are typically not closed with respect to instance-level update and erasure, in the sense that the set of models corresponding to the application of any of these operations to a knowledge base in a DL L may not be expressible by ABoxes in L. In particular, we show that this is true for DL-LiteF, a tractable DL that is oriented towards data-intensive applications. To deal with this problem, we first introduce DL-LiteFS, a DL that minimally extends DL-LiteF and is closed with respect to instance-level update, and present a polynomial algorithm for computing instance-level update in this logic. Then, we provide a principled notion of best approximation with respect to a fixed language L of instance-level update and erasure, and exploit the algorithm for instance-level update for DL-LiteFS to get polynomial algorithms for approximated instance-level update and erasure for DL-LiteF. These results confirm the nice computational properties of DL-LiteF for data intensive applications, even where information about instances is not only read, but also written.
Efficient Induction of Apoptosis by Wee1 Kinase Inhibition in Hepatocellular Carcinoma Cells

Transforming growth factor-β1 (TGF-β1) potently inhibits human hepatocellular carcinoma (HCC) cell growth. Here we demonstrated that TGF-β1-induced apoptosis is mediated by decreased phosphorylation of cdc2 at Tyr15 accompanied by down-regulation of Wee1 kinase expression. As expected from these results, a Wee1 kinase inhibitor efficiently induced apoptosis in HCC cells in the absence of TGF-β1 treatment. In surgically resected samples, Wee1 kinase was expressed in moderately to poorly differentiated HCC, whereas no Wee1 kinase expression was observed in non-cancerous tissue, including cirrhotic tissue. Our results suggest that Wee1 kinase inhibitors may be a practical novel therapeutic option against advanced HCC.
Stage-Specific Expression of Smad2 and Smad3 During Folliculogenesis1

Abstract Paracrine and autocrine growth factors can affect many different aspects of ovarian follicle development. Many members of the transforming growth factor β (TGFβ) family of growth factors and their receptors are expressed in developing follicles. However, the presence and function of the family of the TGFβ signaling molecules known as Smads have not been evaluated during follicle development. We have demonstrated that two Smad family members that function as mediators for both activin and TGFβ are expressed in granulosa cells of preantral follicles but not in large antral follicles. Smad2 expression, but not Smad3 expression, returns in luteal cells. Both Smad2 and Smad3 are translocated to the nucleus of granulosa cells in response to treatment with either TGFβ or activin. However, Smad2 is more responsive to activin stimulation, and Smad3 is more responsive to TGFβ stimulation. Stage-specific expression and differing ligand sensitivity of signaling molecules may work together to allow different effects of TGFβ family ligands using the same signaling pathways over the course of follicular development.
Activation and Cleavage of Caspase-3 in Apoptosis Induced by Experimental Cerebral Ischemia

We examined the expression, activation, and cellular localization of caspase-3 (CPP32) using immunohistochemistry, immunoblots, and cleavage of the fluorogenic substrateN-benzyloxycarbonyl-Asp-Glu-Val-Asp-7-amino-4-trifluoromethyl coumarin (zDEVD-afc) in adult mouse brain after temporary (2 hr) middle cerebral artery occlusion produced by filament insertion into the carotid artery. Immunoreactive caspase-3p32 but not its cleavage product caspase-3p20 was constitutively expressed in neurons throughout brain and was most prominent in neuronal perikarya within piriform cortex. Caspase-like enzyme activity was elevated in brain homogenate 0–3 hr after reperfusion and reached a peak within 30 to 60 min. Caspase-3p20 immunoreactivity became prominent in neuronal perikarya within the middle cerebral artery territory at the time of reperfusion and on immunoblots 1–12 hr later. DNA laddering (agarose gels) and terminal deoxynucleotidyl transferase-mediated dUTP—biotin nick-end labeling (TUNEL)-stained cells were detected 6–24 hr after reperfusion. At 12–24 hr, immunoreactive p20 was visualized in TUNEL-positive cells, a finding also observed in apoptotic mouse cerebellar granule cells on postnatal day 5. Together, these observations suggest the existence of a time-dependent evolution of ischemic injury characterized by the close correspondence between caspase-like enzyme activation and an associated increase in immunoreactive product (caspase-3p20) beginning at or before reperfusion and followed several hours later by morphological and biochemical features of apoptosis.
Hypoxia stimulates neural stem cell proliferation by increasing HIF‑1α expression and activating Wnt/β-catenin signaling.

Evidence indicates that after brain injury, neurogenesis is enhanced in regions such as hippocampus, striatum, and cortex. To study the role of hypoxia-inducible factor-1 (HIF‑1α) and Wnt signaling in cerebral ischemia/hypoxia-induced proliferation of neural stem cells (NSCs), we investigated the proliferation of NSCs, expression of HIF‑1α, and activation of Wnt signaling under conditions of pathologic hypoxia in vitro. NSCs were isolated from 30-day-old Sprague-Dawley rats and subjected to 0.3% oxygen in a microaerophilic incubation system. Cell proliferation was evaluated by measuring the diameter of neurospheres and by bromodeoxyuridine incorporation assays. Real-time quantitative PCR and Western blotting were used to detect mRNA and protein levels of HIF-1α, β-catenin, and cyclin D1 in the NSCs. The results showed that hypoxia increased NSC proliferation and the levels of HIF-1α, β‑catenin, and cyclin D1 (p < 0.05). Blockade of the Wnt signaling pathway decreased hypoxia-induced NSC proliferation, whereas activation of this pathway increased hypoxia-induced NSC proliferation (p < 0.05). Knockdown of HIF-1α with HIF-1α siRNA decreased β‑catenin nuclear translocation and cyclin D1 expression, and inhibited proliferation of NSCs (p < 0.05). These findings indicate that pathologic hypoxia stimulates NSC proliferation by increasing expression of HIF-1α and activating the Wnt/β-catenin signaling pathway. The data suggest that Wnt/β-catenin signaling may play a key role in NSC proliferation under conditions of pathologic hypoxia.
End-to-End ARQ: Transport-Layer Reliability for Airborne Telemetry Networks

Due to the mission-critical nature of command-and-control traffic in the telemetry environment, it is imperative that reliable transfer be supported. The AeroTP disruption-tolerant transport protocol is intended for this environment. The mechanism for reliable transfer is ARQ with end-to-end acknowledgments. This has significant performance limitations resulting from the highly-dynamic nature of airborne telemetry networks, since end-to-end paths may not persist long enough for retransmissions to be received. We use ns-3 to analyze the AeroTP ARQ mechanism, along with tunable parameters that may improve performance in reliable transfer mode.
Simultaneous Vt selection and assignment for leakage optimization

This paper presents a novel approach for leakage optimization through simultaneous V/sub t/ selection and assignment. V/sub t/ selection implies deciding the right value for V/sub t/ and assignment implies deciding which gates should be assigned which threshold value. The proposed algorithm is a general mathematical formulation that can be trivially extended to multiple threshold voltages (more than two). Traditional leakage optimization strategies either assume the prespecification of threshold values or are good only for two thresholds. The presented formulation is based on a linear programming approach under the piecewise linear approximation of delay/leakage vs threshold curves. The algorithm was incorporated in SIS. Experimental results indicate that on some benchmarks having more that two thresholds was beneficial for leakage.
Cognitive Behavior Therapy with Internet Addicts: Treatment Outcomes and Implications

Research over the last decade has identified Internet addiction as a new and often unrecognized clinical disorder that impact a user's ability to control online use to the extent that it can cause relational, occupational, and social problems. While much of the literature explores the psychological and social factors underlying Internet addiction, little if any empirical evidence exists that examines specific treatment outcomes to deal with this new client population. Researchers have suggested using cognitive behavioral therapy (CBT) as the treatment of choice for Internet addiction, and addiction recovery in general has utilized CBT as part of treatment planning. To investigate the efficacy of using CBT with Internet addicts, this study investigated 114 clients who suffered from Internet addiction and received CBT at the Center for Online Addiction. This study employed a survey research design, and outcome variables such as client motivation, online time management, improved social relationships, improved sexual functioning, engagement in offline activities, and ability to abstain from problematic applications were evaluated on the 3rd, 8th, and 12th sessions and over a 6-month follow-up. Results suggested that Caucasian, middle-aged males with at least a 4-year degree were most likely to suffer from some form of Internet addiction. Preliminary analyses indicated that most clients were able to manage their presenting complaints by the eighth session, and symptom management was sustained upon a 6-month follow-up. As the field of Internet addiction continues to grow, such outcome data will be useful in treatment planning with evidenced-based protocols unique to this emergent client population.
Dividing Businesses into Processes Foundations for Modelling Essentials

One important part of infonnation systems development work is business modelling. Traditionally businesses have been regarded as systems consisting of sub-systems. During the 90' s a number of process-oriented approaches for business modelling have gained a lot of interest. One problem about dividing businesses into processes is that there resolves controversy around the number of processes appropriate to a given organisation. The difficulty derives from the fact that processes are almost infinitely divisible. It is therefore a need to find basis of division when adopting a process-oriented view on the organisation. This paper reports on ongoing research concerning understanding businesses by using the notion of business processes. Results reported on are a further developed notion of business processes, a reference model for process determination, criteria for process determination and a theory of imperceivable business systems. These results are generated through a dialectic approach where both transfonnational and communicational aspects of business processes are taken into consideration as well as the notion of systems for perceiving businesses. By using this theory of imperceivable business systems for business modelling essential characteristics of businesses can be focused on different levels of abstraction.
Flyback Mode for Improved Low-Power Efficiency in the Dual-Active-Bridge Converter for Bidirectional PV Microinverters With Integrated Storage

This paper targets photovoltaic microinverters (MIVs) with integrated battery storage. The dual-active-bridge (DAB) topology provides bidirectional power flow; however, it generally suffers from poor efficiency and limited regulation accuracy at low power. It is shown that by modifying one switch, the DAB converter can operate as a two-transistor flyback to resolve these two issues. In addition, the dc-link voltage in the two-stage MIV can be dynamically adjusted for optimal performance in DAB mode. The proposed dual-mode control scheme is demonstrated experimentally on a 100-W prototype, with up to 8% increase in converter efficiency at low power.
A Comparative Study for the Evaluation of Two Doses of Ellagic Acid on Hepatic Drug Metabolizing and Antioxidant Enzymes in the Rat

The present study was designed to evaluate different doses of ellagic acid (EA) in vivo in rats for its potential to modulate hepatic phases I, II, and antioxidant enzymes. EA (10 or 30 mg/kg/day, intragastrically) was administered for 14 consecutive days, and activity, protein, and mRNA levels were determined. Although the cytochrome P450 (CYP) 2B and CYP2E enzyme activities were decreased significantly, the activities of all other enzymes were unchanged with the 10 mg/kg/day EA. In addition, western-blot and qRT-PCR results clearly corroborated the above enzyme expressions. On the other hand, while the NAD(P)H:quinone oxidoreductase 1 (NQO1), catalase (CAT), glutathione peroxidase (GPX), and glutathione S-transferase (GST) activities were increased significantly, CYP1A, 2B, 2C, 2E, and 19 enzyme activities were reduced significantly with 30 mg/kg/day EA. In addition, CYP2B, 2C6, 2E1, and 19 protein and mRNA levels were substantially decreased by the 30 mg/kg/day dose of EA, but the CYP1A protein, and mRNA levels were not changed. CYP3A enzyme activity, protein and mRNA levels were not altered by neither 10 nor 30 mg/kg/day ellagic acid. These results indicate that EA exerts a dose-dependent impact on the metabolism of chemical carcinogens and drugs by affecting the enzymes involved in xenobiotics activation/detoxification and antioxidant pathways.
Defining the roles of Asn-128, Glu-129 and Phe-130 in loop A of the 5-HT3 receptor

The ligand binding pocket of Cys-loop receptors consists of a number of binding loops termed A–F. Here we examine the 5-HT3 receptor loop A residues Asn-128, Glu-129 and Phe-130 using modelling, mutagenesis, radioligand binding and functional studies on HEK 293 cells. Replacement of Asn-128 results in receptors that have wild type [3H]granisetron binding characteristics but large changes (ranging from a five-fold decrease to a 1500-fold increase) in the 5-HT EC50 when compared to wild type receptors. Phe-130 mutant receptors show both increases and decreases in Kd and EC50 values, depending on the amino acid substituted. The most critical of these residues appears to be Glu-129; its replacement with a range of other amino acids results in non-binding and non-functional receptors. Lack of binding and function in some, but not all, of these receptors is due to poor membrane expression. These data suggest that Glu-129 is important primarily for receptor expression, although it may also play a role in ligand binding; Phe-130 is important for both ligand binding and receptor function, and Asn-128 plays a larger role in receptor function than ligand binding. In light of these results, we have created two new homology models of the 5-HT3 receptor, with alternative positions of loop A. In our preferred model Glu-129 and Phe-130 contribute to the binding site, while the location of Asn-128 immediately behind the binding pocket could contribute to the conformation changes that result in receptor gating. This study provides a new model of the 5-HT3 receptor binding pocket, and also highlights the importance of experimental data to support modelling studies.
Modulation of phenolic metabolism under stress conditions in a Lotus japonicus mutant lacking plastidic glutamine synthetase

This paper was aimed to investigate the possible implications of the lack of plastidic glutamine synthetase (GS2) in phenolic metabolism during stress responses in the model legume Lotus japonicus. Important changes in the transcriptome were detected in a GS2 mutant called Ljgln2-2, compared to the wild type, in response to two separate stress conditions, such as drought or the result of the impairment of the photorespiratory cycle. Detailed transcriptomic analysis showed that the biosynthesis of phenolic compounds was affected in the mutant plants in these two different types of stress situations. For this reason, the genes and metabolites related to this metabolic route were further investigated using a combined approach of gene expression analysis and metabolite profiling. A high induction of the expression of several genes for the biosynthesis of different branches of the phenolic biosynthetic pathway was detected by qRT-PCR. The extent of induction was always higher in Ljgln2-2, probably reflecting the higher stress levels present in this genotype. This was paralleled by accumulation of several kaempferol and quercetine glycosides, some of them described for the first time in L. japonicus, and of high levels of the isoflavonoid vestitol. The results obtained indicate that the absence of GS2 affects different aspects of phenolic metabolism in L. japonicus plants in response to stress.
On-line identification of robotic ubiquitous cognitive network with erasure channels

Nowadays the Robotic Ubiquitous Cognitive network (RUBICON) has raised great attentions in robotics area. In this paper we explore and first propose a timely identification method of RUBICON with erasure channels. Firstly, the complex cognitive network is simplified into a single close-loop communicating network for identification. Then inspired by the interactive cognitive method, we propose recursive network identification method containing feedback mechanism. Three key problems of this method - dense format of transmitting messages, selection of prior packet for identification and the detailed network identification procedure - and their solving methods are presented. Finally, we make a simulation about the parameters identification of RUBICON which contains 8 sensors/actuator nodes. The simulated results show that the proposed algorithm can balance the difference of the identification results for every sensor node and enhance the unique convergence effect.
TOWARDS THE CONSTRUCTION OF WIGHTMAN FUNCTIONS OF INTEGRABLE QUANTUM FIELD THEORIES

The purpose of the "bootstrap program" for integrable quantum field theories in 1+1 dimensions is to construct a model in terms of its Wightman functions explicitly. In this article, the program is mainly illustrated in terms of the sine-Gordon and the sinh-Gordon model and (as an exercise) the scaling Ising model. We review some previous results on sine-Gordon breather form factors and quantum operator equations. The problem to sum over intermediate states is attacked in the short distance limit of the two point Wightman function for the sinh-Gordon and the scaling Ising model.
UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge

The DDIExtraction 2013 task in the SemEval conference concerns the detection of drug names and statements of drug-drug interactions (DDI) from text. Extraction of DDIs is important for providing up-to-date knowledge on adverse interactions between coadministered drugs. We apply the machine learning based Turku Event Extraction System to both tasks. We evaluate three feature sets, syntactic features derived from deep parsing, enhanced optionally with features derived from DrugBank or from both DrugBank and MetaMap. TEES achieves F-scores of 60% for the drug name recognition task and 59% for the DDI extraction task.
A Multi-classifier Approach to support Coreference Resolution in a Vector Space Model

In this paper a different machine learning approach is presented to deal with the coreference resolution task. This approach consists of a multi-classifier system that classifies mention-pairs in a reduced dimensional vector space. The vector representation for mentionpairs is generated using a rich set of linguistic features. The SVD technique is used to generate the reduced dimensional vector space. The approach is applied to the OntoNotes v4.0 Release Corpus for the column-format files used in CONLL-2011 coreference resolution shared task. The results obtained show that the reduced dimensional representation obtained by SVD is very adequate to appropriately classify mention-pair vectors. Moreover, we can state that the multi-classifier plays an important role in improving the results.