Miracle-dz/UniFAR-FTUs huggingface dataset:
Neonatal maternal deprivation triggers long term alterations in colonic epithelial barrier and mucosal immunity in rats

Background: Stressful events in the early period of life (for example, maternal deprivation) have been shown to modify adult immune and gastrointestinal tract functions. The present study aimed to establish whether maternal deprivation affects colonic epithelial barrier and the development of an experimental colitis in adult rats. Methods: Male Wistar rat pups were separated during postnatal days 2–14 or left undisturbed with their dam. At 12 weeks of age, we assessed colonic paracellular permeability, bacterial translocation, myeloperoxidase (MPO) activity, mucosal mast cell density, cytokine (interleukin (IL)-1β, IL-2, IL-4, IL-10, and interferon γ (IFN-γ)) mRNA expression, and macroscopic damage. Total gut permeability, MPO activity, and macroscopic damage were also assessed four days after intracolonic administration of 2,4,6-trinitrobenzenesulphonic acid (TNBS). Results: Maternal deprivation triggered a significant increase in colonic permeability associated with bacterial translocation into the mesenteric lymph nodes, liver, and spleen. These alterations were associated with some macroscopic damage and an increase in colonic MPO activity, mucosal mast cell density, and cytokine mRNA expression. Intracolonic infusion of TNBS induced a significantly higher inflammatory reaction in separated animals, as judged by enhanced MPO colonic levels, total gut permeability, and macroscopic lesions. Conclusions: Maternal deprivation promotes long term alterations in the colonic epithelial barrier associated with an exaggerated immune response to an external immune stimulus. This suggests a role for early psychological factors in the regulation of colonic mucosal barrier in later life.
Two-dimensional arrays of ordered, highly dense and ultra small Ge nanocrystals on thin SiO 2 layers

In this work, we have developed two original processes for the fabrication of 2-dimensional arrays of ordered Ge nanocrystals embedded in thin SiO2 layers for their use in nanocrystal floating gate memories. Ordering is achieved by a combination of focused ion beam nano-patterning and self assembly of Ge islands on the patterned SiO2 surface. In the first process the Ge islands are grown by selective chemical vapor deposition of Si/Ge/Si on Si holes fabricated by FIB patterning, while the second process uses solid phase epitaxy by MBE of amorphous Ge on SiO2 at room temperature, followed by annealing for crystallization. Highly ordered and highly dense (1.5 × 1011/cm2) ultra-small (~20 nm) Ge dots on SiO2 were achieved by both processes. This work has been carried out within the European IST project FORUM FIB: Fabrication, Organisation and Use of Memories obtained by Focused Ion Beams.
Morphological analysis of isolated rhoptries from Plasmodium yoelii, P. berghei, and P. chabaudi merozoites.

Abstract Sam-Yellowe, T. Y. , Fujioka, H. , and Aikawa, M. 1999. Morphological analysis of isolated rhoptries from Plasmodium yoelii , P. berghei , and P. chabaudi merozoites. Experimental Parasitology 92, 275–278.
Regulation of nitrogen metabolism in Escherichia coli and Klebsiella aerogenes: studies with the continuous-culture technique

Ammonia-nitrogen-limited continuous cultures of Escherichia coli and Klebsiella aerogenes contain induced levels of glutamine synthetase that is deadenylyated (i.e., fully active). In the presence of excess ammonia or glutamate in glucose-limited cultures of E. coli, glutamine synthetase is repressed and adenylylated (inactive). The average state of adenylylation (n) is a linear function of the specific growth rate. At low specific growth rates, glutamine synthetase is adenylylated; as the specific growth rate increases, n decreases, approaching 0 to 2 at rapid growth rates. The average state of adenylylation correlates well with the intracellular concentrations and ratios of alpha-ketoglutarate and glutamine, which are key effectors in the adenylylation-deadenylylation systems. E. coli and K. aerogenes differ markedly in their growth yields, growth rates, and enzymatic composition during nitrogen limitation. The data suggest that, unlike K. aerogenes, E. coli W uses glutamate dehydrogenase to incorporate ammonia during nitrogen limitation. In E. coli, glutamate dehydrogenase is progressively induced during nitrogen limitation when mu (growth rate) approaches mumax. In contrast, in K. aerogenes glutamate dehydrogenase is repressed during nitrogen limitation, whereas glutamate synthase, an alternative supplier of glutamate to the cell, is induced. Data are presented that support the regulatory schemes proposed for the control of glutamine synthetase activity by induction-repression phenomena and adenylylation-deadenylylation reaction. We propose that the intracellular ratio of alpha-ketoglutarate to glutamine may be the most important physiological parameter in determining the activity of glutamine synthetase.
Centralized Lifetime Maximizing Tree For Wireless Sensor Networks

To enable data aggregation among the event sources in wireless sensor networks and to reduce the communication cost there is a need to establish a coveraged tree structure inside any given event region to allow data reports to be aggregated at a single processing point prior to transmission to the network. In this paper we propose a novel technique to create one such tree which maximizes the lifetime of the event sources while they are constantly transmitting for data aggregation. We use the term Centralized Lifetime Maximizing Tree (CLMT) to denote this tree. CLMT features with identification of bottleneck node among the given set of nodes. This node collects the data from every other node via routes with the highest branch energy subject to condition loop is not created. By constructing tree in such a way, protocol is able to reduce the frequency of tree reconstruction, minimize the delay and maximize the functional lifetime of source nodes by minimizing the additional energy involved in tree reconstruction.
Drosophila Biology in the Genomic Age

Over the course of the past century, flies in the family Drosophilidae have been important models for understanding genetic, developmental, cellular, ecological, and evolutionary processes. Full genome sequences from a total of 12 species promise to extend this work by facilitating comparative studies of gene expression, of molecules such as proteins, of developmental mechanisms, and of ecological adaptation. Here we review basic biological and ecological information of the species whose genomes have recently been completely sequenced in the context of current research.
Framework for Design Validation of Security Architectures

New security architectures are dicult to prototype and test. They require interactions between hardware, operating systems, and applications, making them hard to simulate and monitor. We have designed and prototyped a testing framework using a virtualization platform which emulates the behavior of new hardware security architecture in the virtual CPU, and performs a wide range of hardware and software attacks on the system under test. Our testing framework significantly speeds up development of the testing environment and infrastructure, and provides APIs for launching attacks and monitoring the eects of an attack on the hardware and software layers, which is especially convenient during the design and validation phases for new hardwaresoftware architectural solutions. We have used our testing framework to test the trust chain of the SP architecture [1] as an example.
Attack Detection over Network based on C45 and RF Algorithms

In this paper, Intrusion detection is to detect attacks(Intrusions) against a computer system. In the highly networked modern world, conventional techniques of network security such as cryptography, user authentication and intrusion prevention techniques like firewalls are not sufficient to detect new attacks. In this paper, we perform experiments on the kddcup99 data set. We perform dimensionality reduction of the data set using PCA (principal Component Analysis) and clear distinction between normal and anomalous data is observed by using supervised data mining techniques. Primarily experiments with kddcup99 network data show that the supervised techniques such as Naive Bayesian, C4.5 can effectively detect anomalous attacks and achieve a low false positive rate. In this thesis optimization technique such as Random Forest has applied to improve the efficiency of detection rate and achieve a low false positive rate. This mechanism can effectively tolerate intrusion.
Design of low voltage low power CMOS OP-AMPS with rail-to-rail input/output swing

A novel input and output biasing circuit to extend the input common mode (CM) voltage range and the output swing to rail-to-rail in a low voltage op-amp in standard CMOS technology is presented. The input biasing circuit uses a Switched Capacitor Based Attenuator (SCBA) approach to establish rail-to-rail common mode input voltage range. And the output biasing circuit uses an Output Driver (OD), with floating bias to give the rail-to-rail swing at output stage. Three different OD schemes in operational amplifier have been proposed and tested the performance with SCBA. The simulation results justify the theoretical analysis.
A Canonical Model of Multistability and Scale-Invariance in Biological Systems

Multistability and scale-invariant fluctuations occur in a wide variety of biological organisms from bacteria to humans as well as financial, chemical and complex physical systems. Multistability refers to noise driven switches between multiple weakly stable states. Scale-invariant fluctuations arise when there is an approximately constant ratio between the mean and standard deviation of a system's fluctuations. Both are an important property of human perception, movement, decision making and computation and they occur together in the human alpha rhythm, imparting it with complex dynamical behavior. Here, we elucidate their fundamental dynamical mechanisms in a canonical model of nonlinear bifurcations under stochastic fluctuations. We find that the co-occurrence of multistability and scale-invariant fluctuations mandates two important dynamical properties: Multistability arises in the presence of a subcritical Hopf bifurcation, which generates co-existing attractors, whilst the introduction of multiplicative (state-dependent) noise ensures that as the system jumps between these attractors, fluctuations remain in constant proportion to their mean and their temporal statistics become long-tailed. The simple algebraic construction of this model affords a systematic analysis of the contribution of stochastic and nonlinear processes to cortical rhythms, complementing a recently proposed biophysical model. Similar dynamics also occur in a kinetic model of gene regulation, suggesting universality across a broad class of biological phenomena.
The ethics of wasting the donor’s gift of buffy coat

Dear Editor, Schrezenmeier and Seifried [1] observed that – albeit rare – donor reactions with plateletapheresis collections can be more frequent ⁄ severe compared with whole-blood collections. They then argued that – because all platelet transfusion needs of patients not alloimmunized to HLA antigens can be met by pooling (already-available) buffy coats from the whole-blood donations – donor reactions to any plateletapheresis collections represent an ‘additional’ (hence unnecessary and hard to justify) risk. As Table 1 shows for the US [2], any country with a North-American ⁄ Western-European health-care system requires several times more red-blood-cell (RBC) than platelet or fresh frozen plasma (FFP) doses to meet the needs of all its transfusion recipients. Modern apheresis technology permits blood operators to collect large-size units of plasma, as well as ‘double’ RBCs, in addition to single-donor platelets. Furthermore, it allows blood operators to collect RBCs along with platelets and ⁄ or plasma [3, 4]. Thus, modern apheresis technology could enable national blood services to provide for all of a country’s RBC, platelet, and plasma needs by subjecting a number of donors to the rare risks of donation, which would not exceed the number of donors bled today by the same blood services to produce components from whole-blood collections. Importantly, and in contrast to the historical literature on donor reactions reviewed by Schrezenmeier and Seifried [1], this modern approach to meeting all of a country’s needs should not be associated with any increase in donor reactions. In the largest reported multivariate analysis of moderate and severe donor reactions, Kamel et al. [5] observed no increase in donor reactions following each of three types of apheresis collections compared with wholeblood donation (Table 2). Even if donor reactions were higher with plateletapheresis (compared with whole-blood) collections in Germany today [1], the rights of transfusion recipients supersede any rights of donors who have given informed consent for the procedure and are aware of its risks [6]. The duty of national blood operators in countries with North-American ⁄ Western-European health-care systems is to maximize the safety and efficacy of all transfused blood components for the benefit of transfusion recipients. Although Schrezenmeier and Seifried [1] correctly assess that – based on the available data – the efficacy of buffy-coat PWBD vs. single-donor platelet concentrates does not differ, there is a ‡ 2-fold difference in the safety of the two components with regard to emerging transfusion-transmitted infections; and, in countries that use platelets from first-time wholeblood donors in buffy-coat pools, a ‡ 2-fold difference in the risk of human immunodeficiency virus, hepatitis C Table 1 Number of therapeutic doses of each blood component transfused in the US in 2006
Head movement artifact removal in EEG signals using Empirical Mode Decomposition and Pearson Correlation

This paper presents an approach on head movement artifact removal from EEG signals, in the context of an ongoing brain computer interface project. The proposed artifact removal scheme is based on Empirical Mode Decomposition (EMD) applied to the signals obtained from each electrode. Correlation analysis using Pearson coefficient allows identification of those intrinsic mode functions related to common artifacts, which are associated to head movement. The goal of this experiment is separation of signals corresponding to single and double blinking from head movement artifacts. Once the preprocessing is applied, blinking detection is reduced to threshold operations. Final selection step based on Mahalanobis distance provides a detection rate of 95% in average.
Musical Data Mining Pattern Matching Apriori and DHP Algorithm

Musical data mining is not a new invention, but as a nationwide resource of this type it breaks new ground by providing researchers with new ways to analyze musical data. It was Toiviainen and Eerola s idea to combine specific information with a geographical coordinate database. Now geographical comparisons can be made it is possible to follow the geographical variation of musical features. For instance, schools can now identify and trace folk tune originating from their own regions. Musical Data Mining is used for discovering any kind of relevant similarity between music titles. Several algorithms like Apriori, PHP, partition, sampling and some other parallel algorithm have been developed. In this thesis, Apriori and DHP are implemented. To extract the similarity between music titles and to manipulate their relationships two techniques are used cooccurrence analysis and correlation analysis. By the use of these two techniques it is capable to access the database and then find whether any similarity exist between the music titles. For the purpose of finding a match within the titles in the database Pattern matching is used using the Apriori and DHP algorithms
Dyeing Rate of Nylon 6 Yarn with p-Aminoazobenzene

The dyeing rate of p-aminoazobenzene on nylon 6 yarn at 40°C has been investigated. The apparent diffusion coefficient and the diffusional boundary layer parameter are estimated in such a way that the experimental data fit with the theoretical rate curve based on the diffusional boundary layer model. The dyeing behavior of the yarn is discussed in relation to the pore size of the spaces between individual filaments.
First Isolation of Hepatitis E Virus Genotype 4 in Europe through Swine Surveillance in the Netherlands and Belgium

Hepatitis E virus (HEV) genotypes 3 and 4 are a cause of human hepatitis and swine are considered the main reservoir. To study the HEV prevalence and characterize circulating HEV strains, fecal samples from swine in the Netherlands and Belgium were tested by RT-PCR. HEV prevalence in swine was 7–15%. The Dutch strains were characterized as genotype 3, subgroups 3a, 3c and 3f, closely related to sequences found in humans and swine earlier. The HEV strains found in Belgium belonged to genotypes 3f and 4b. The HEV genotype 4 strain was the first ever reported in swine in Europe and an experimental infection in pigs was performed to isolate the virus. The genotype 4 strain readily infected piglets and caused fever and virus shedding. Since HEV4 infections have been reported to run a more severe clinical course in humans this observation may have public health implications.
The connection between elastic scattering cross sections and acoustic vibrations of an embedded nanoparticle

Arbitrary waves incident on a solid embedded nanoparticle are studied. The acoustic vibrational frequencies are shown to correspond to the poles of the scattering cross section in the complex frequency plane. The location of the poles is unchanged even if the incident wave is nonplanar. A second approach approximating the infinite matrix as a very large shell surrounding the nanoparticle provides an alternate way of predicting the mode frequencies. The wave function of the vibration is also provided. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Productivity Effects of Organizational Change: Microeconometric Evidence

This paper analyzes the relationship between investment in information and communication technologies (ICT), non-ICT investment, labor productivity, and workplace reorganization. Firms are assumed to reorganize workplaces if the productivity gains arising from workplace reorganization exceed the associated reorganization costs. Two different types of organizational change are considered: enhancement group work and flattening of hierarchies. Empirical evidence is provided for a sample of 411 firms from the German business-related services sector.We develop and estimate a model for labor productivity and firms' decision to reorganize workplaces that allows workplace reorganization to affect any parameter of the labor productivity equation. Our general and flexible methodology allows us to properly take account of strategic complementarities between the input factors and workplace reorganization. The estimation results show that changes in human resources practices do not significantly affect firms' output elasticities with respect to ICT, non-ICT capital, and labor, although most of the point estimates of the individual output elasticities and of the control variables for observable firm heterogeneity are larger if workplace reorganization is realized. We therefore apply the Kernel density-estimation technique and demonstrate that for firms with organizational change, theentire labor productivity distribution shifts significantly out to the right if workplace reorganization takes place, indicating that workplace reorganization induces an increase in labor productivity that is attributable to complementarities between the various input factors and workplace reorganization. By contrast, firms without organizational change would not have realized significant productivity gains if they had reorganized workplaces.
Stable shRNA Silencing of Lactate Dehydrogenase A (LDHA) in Human MDA-MB-231 Breast Cancer Cells Fails to Alter Lactic Acid Production, Glycolytic Activity, ATP or Survival.

BACKGROUND In the US, African Americans have a high death rate from triple-negative breast cancer (TNBC), characterized by lack of hormone receptors (ER, PR, HER2/ERRB2) which are otherwise valuable targets of chemotherapy. There is a need to identify novel targets that negatively impact TNBC tumorigenesis. TNBCs release an abundance of lactic acid, under normoxic, hypoxic and hyperoxic conditions; this referred to as the Warburg effect. Accumulated lactic acid sustains peri-cellular acidity which propels metastatic invasion and malignant aggressive transformation. The source of lactic acid is believed to be via conversion of pyruvate by lactate dehydrogenase (LDH) in the last step of glycolysis, with most studies focusing on the LDHA isoform. MATERIALS AND METHODS In this study, LDHA was silenced using long-term MISSION® shRNA lentivirus in human breast cancer MDA-MB-231 cells. Down-regulation of LDHA transcription and protein expression was confirmed by western blot, immunocytochemistry and qPCR. A number of parameters were measured in fully viable vector controls versus knock-down (KD) clones, including levels of lactic acid produced, glucose consumed, ATP and basic metabolic rates. RESULTS The data show that lentivirus V-165 generated a knock-down clone most effective in reducing both gene and protein levels to less than 1% of vector controls. Stable KD showed absolutely no changes in cell viability, lactic acid production, ATP, glucose consumption or basic metabolic rate. Given the complete absence of impact on any observed parameter by LDH-A KD and this being somewhat contrary to findings in the literature, further analysis was required to determine why. Whole-transcriptome analytic profile on MDA-MB-231 for LDH subtypes using Agilent Human Genome 4×44k microarrays, where the data show the following component breakdown. Transcripts: 30.47 % LDHA, 69.36% LDHB, 0.12% LDHC and 0.05% LDHD. CONCLUSION These findings underscore the importance of alternative isoforms of LDH in cancer cells to produce lactic acid, when LDHA is silenced or inhibited. LDHA silencing alone is not effective in hampering or inducing changes in survival, metabolism or lactic acid produced in a cell line with high concentrations of LDHB. Future research will be required to confirm effects of dual LDHA/B knockdown and further confirm that the sole source of lactic acid produced occurs through LDH (all isoforms) in breast cancer cells.