Miracle-dz/UniFAR-FTUs huggingface dataset:
Lamina Propria CCL25-Deficient Intestinal Epithelium and CD8 Lymphocytes in Chemokine Impaired Accumulation of Antigen-Specific

CCL25 and CCR9 constitute a chemokine/receptor pair involved in T cell development and in gut-associated immune responses. In this study, we generated CCL25 (cid:1) / (cid:1) mice to answer questions that could not be addressed with existing CCR9 (cid:1) / (cid:1) mice. Similar phenotypes were observed for both CCL25 (cid:1) / (cid:1) and CCR9 (cid:1) / (cid:1) mice, consistent with the notion that CCL25 and CCR9 interact with each other exclusively. We assessed the requirement for CCL25 in generating CCR9 high CD8 intestinal memory-phenotype T cells and the subsequent accumulation of these cells within effector sites. TCR-transgenic naive CD8 T cells were transferred into wild-type or CCL25-deﬁcient hosts. Oral sensitization with Ag allowed these naive donor cells to efﬁciently differentiate into CCR9 high memory-phenotype cells within the mesenteric lymph nodes of wild-type hosts. This differentiation event occurred with equal efﬁciency in the MLN of CCL25-deﬁcient hosts, demonstrating that CCL25 is not required to induce the CCR9 high memory phenotype in vivo. However, we found that CCL25 deﬁciency severely impaired the Ag-dependent accumulation of donor-derived CD8 T cells within both lamina propria and epithelium of the small intestine. Thus, although CCL25 is not necessary for generating memory-phenotype CD8 T cells with “gut-homing” properties, this chemokine is indispensable for their trafﬁcking to the small intestine. The Journal of Immunology, 2007, 178: 7598–7606. nteractions between the chemokine CCL25
Exploiting text mining techniques in the analysis of execution traces

The analysis of execution traces can be useful in many software engineering activities including debugging, feature enhancement, performance analysis, and any other task that requires some degree of understanding of the way a system behaves. Traces, however, tend to be considerably large, which often hinders effective analysis of their content. There is a need to investigate ways to help software engineers find and understand important information conveyed in a trace despite the trace being massive. Motivated by the work done in the area of text mining, we propose, in this paper, a trace exploration approach based on examining the trace execution phases. The approach consists of automatically identifying relevant information about the phases as well as the ability to provide an efficient representation of the flow of phases by detecting redundant phases using a cosine similarity metric. We applied our approach to large traces generated from two different systems and were able to quickly understand their content and extract higher level views that characterize the essence of the information conveyed in these traces.
Hydrogen sulfide and radon in and over the western North Atlantic Ocean

Atmospheric measurements of radon and hydrogen sulfide, and seawater measurements of total sulfide, free sulfide, and carbonyl sulfide, were made on a cruise in the western North Atlantic Ocean (October 24 to November 9, 1989). Measured values for 222Rn ranged from 3 to 70 pCi m−3, those for atmospheric hydrogen sulfide from 1 to 85 parts per trillion, and those for dissolved total and free sulfide in seawater from 33 to 930 pmol L−1 and 0 to 73 pmol L−1, respectively. A positive correlation between 222Rn and atmospheric H2S was observed. Both 222Rn and H2S were high in air masses traced back to North America. Measurements in seawater showed that uncomplexed sulfides were approximately 13% of total sulfide at 2 m depth. Atmospheric H2S and dissolved H2S in seawater were usually not far from saturation equilibrium. Our results indicate that the ocean acted at some times as a source of atmospheric H2S but more frequently as a sink. Hydrolysis of COS and atmospheric deposition of H2S both may contribute to the budget of dissolved sulfide in seawater of the western North Atlantic Ocean. On a global scale the ocean/atmosphere exchange of H2S appears to play a minor role in the atmospheric sulfur cycle.
Demodulating subsampled Direct Sequence Spread Spectrum signals using compressive signal processing

We show that to lower the sampling rate in a spread spectrum communication system using Direct Sequence Spread Spectrum (DSSS), compressive signal processing can be applied to demodulate the received signal. This may lead to a decrease in the power consumption or the manufacturing price of wireless receivers using spread spectrum technology. The main novelty of this paper is the discovery that in spread spectrum systems it is possible to apply compressive sensing with a much simpler hardware architecture than in other systems, making the implementation both simpler and more energy efficient. Our theoretical work is exemplified with a numerical experiment using the IEEE 802.15. 4 standard's 2.4 GHz band specification. The numerical results support our theoretical findings and indicate that compressive sensing may be used successfully in spread spectrum communication systems. The results obtained here may also be applicable in other spread spectrum technologies, such as Code Division Multiple Access (CDMA) systems.
Micro-milling of unreinforced and reinforced polypropylene

It is essential to determine the micro-machinability performance of polymer and glass fiber–reinforced polymer composite in order to effectively utilize the polymer and its composite as an engineering material at the micro-scale world. However, a literature survey revealed that not much work was done on the micro-milling of polymer and its composite. In the light of literature surveys, it can be said that the novelty of this study is to investigate the micro-milling performance of polypropylene and glass fiber–reinforced polypropylene manufactured with plastic injection molding process. The tests were performed at different feed rates and spindle speeds and the effect of these parameters on tool wear, burr width and micro-milling forces was investigated. In general, it was concluded that wear and forces in micro-milling of reinforced polypropylene composite were higher than that of unreinforced polypropylene. Micro-milling forces increased with feed rate and spindle speed for both materials. The lowest top burr size and force values were obtained at the feed of 50 mm/min and the spindle speed of 20,000 r/min. Unreinforced polypropylene gave better performance with respect to glass fiber–reinforced polypropylene composite from micro-machinability aspect.
Protein Characterization of a Candidate Mechanism SNP for Crohn's Disease: The Macrophage Stimulating Protein R689C Substitution

High throughput genome wide associations studies (GWAS) are now identifying a large number of genome loci related to risk of common human disease. Each such locus presents a challenge in identifying the relevant underlying mechanism. Here we report the experimental characterization of a proposed causal single nucleotide polymorphism (SNP) in a locus related to risk of Crohn's disease and ulcerative colitis. The SNP lies in the MST1 gene encoding Macrophage Stimulating Protein (MSP), and results in an R689C amino acid substitution within the β-chain of MSP (MSPβ). MSP binding to the RON receptor tyrosine kinase activates signaling pathways involved in the inflammatory response. We have purified wild-type and mutant MSPβ proteins and compared biochemical and biophysical properties that might impact the MSP/RON signaling pathway. Surface plasmon resonance (SPR) binding studies showed that MSPβ R689C affinity to RON is approximately 10-fold lower than that of the wild-type MSPβ and differential scanning fluorimetry (DSF) showed that the thermal stability of the mutant MSPβ was slightly lower than that of wild-type MSPβ, by 1.6 K. The substitution was found not to impair the specific Arg483-Val484 peptide bond cleavage by matriptase-1, required for MSP activation, and mass spectrometry of tryptic fragments of the mutated protein showed that the free thiol introduced by the R689C mutation did not form an aberrant disulfide bond. Together, the studies indicate that the missense SNP impairs MSP function by reducing its affinity to RON and perhaps through a secondary effect on in vivo concentration arising from reduced thermodynamic stability, resulting in down-regulation of the MSP/RON signaling pathway.
Leaf morphology shift: new data and analysis support climate link

Links between leaf morphology and temperature have been established at a range of ecological scales [[1][1],[2][2]]. Narrower leaves can lose heat without evapotranspiration during hot, dry summers [[3][3]]. We proposed that an observed decrease in leaf width in Dodonaea viscosa subsp. angustissima
Key-Based Dynamic Functional Obfuscation of Integrated Circuits Using Sequentially Triggered Mode-Based Design

This paper proposes a novel technique for hardware obfuscation termed <italic>dynamic functional obfuscation</italic>. Hardware obfuscation refers to a set of countermeasures used against IC counterfeiting and illegal overproduction. Traditionally, obfuscation encrypts semiconductor circuits using <italic>key</italic> inputs which must be set to a correct value to operate the circuit correctly. By keeping the key values secret during the manufacturing process, any attempt by unauthorized parties to overproduce chips or pirate designs is thwarted. The proposed dynamic technique differs from existing fixed obfuscation schemes as the obfuscating signals change over time. This results in inconsistent circuit behavior upon input of incorrect key, where the chip operates correctly sometimes and fails sometimes. The advantage of dynamic obfuscation is that it results in stronger obfuscation by increasing the time complexity of deciphering the correct key using brute-force attack, even with shorter keys. Moreover, the dynamic nature of these circuits also makes them resistant to reverse engineering and SAT solver-based attacks. To achieve dynamic obfuscation, ideas from hardware Trojan literature and sequentially triggered counters are utilized. A demonstration of obfuscation on sequential circuits implementing fast Fourier transform (FFT) algorithm and Ethernet IP shows low overall area and power overheads of less than 1%. Security in terms of time to attack for the FFT circuit (for a key size of 30 bits and a system operating at 100 MHz) is increased to 1 021,055 years using dynamic obfuscation compared with only 5.36 s using fixed obfuscation schemes. For the Ethernet IP core, time to attack of dynamic obfuscation with a key size of 32 bits is 1 046,423, 135 years compared with 21.47s with fixed obfuscation. It is also shown that for a key size of <inline-formula> <tex-math notation="LaTeX">$K$ </tex-math></inline-formula> bits, the lower bound for time to attack using brute-force is proportional to <inline-formula> <tex-math notation="LaTeX">$K 2^{K}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$K 2^{2K}$ </tex-math></inline-formula> for the proposed design using one and two random number generators, respectively.
Influence of Viscoelastic properties of Solid Propellants on Starting Transient of Solid Rocket Motors

In this paper a critical review has been carried out on the influence of viscoelastic properties of propellants on starting transient of solid rocket motors and further numerical studies have been carried out for the thermo viscoelastic characterization of an idealized solid propellant grain using Prony series viscoelastic model. Parametric analytical studies have been carried out in simulated tubular specimens with different internal pressures and thermal loadings at various propellant properties. Non-linear pressure input is specified as steps of linear pressure inputs at various time intervals and accordingly continuous grain deformations has been evaluated using the Prony series viscoelastic model. We have observed that at certain conditions of internal pressure and thermal loadings coupled with certain range of material properties, the solid propellant grain might alter its initial shape non-linearly prior to the ignition due to the pre-ignition chamber pressurization and thermal loading. Such non-linear variations of the inner surface area of the solid rocket motors lead to undesirable starting transient. We concluded that the solid rocket motor with actual grain geometry with internal pressurization is a realistic method for the thermo viscoelastic characterization of solid propellant grains for generating data for an accurate prediction of the starting transient and the reduction of ignition pressure peak often observed in certain class of solid propellant rocket motors.
Drosophila spectrin: the membrane skeleton during embryogenesis

The distribution of alpha-spectrin in Drosophila embryos was determined by immunofluorescence using affinity-purified polyclonal or monoclonal antibodies. During early development, spectrin is concentrated near the inner surface of the plasma membrane, in cytoplasmic islands around the syncytial nuclei, and, at lower concentrations, throughout the remainder of the cytoplasm of preblastoderm embryos. As embryogenesis proceeds, the distribution of spectrin shifts with the migrating nuclei toward the embryo surface so that, by nuclear cycle 9, a larger proportion of the spectrin is concentrated near the plasma membrane. During nuclear cycles 9 and 10, as the nuclei reach the cell surface, the plasma membrane-associated spectrin becomes concentrated into caps above the somatic nuclei. Concurrent with the mitotic events of the syncytial blastoderm period, the spectrin caps elongate at interphase and prophase, and divide as metaphase and anaphase progress. During cellularization, the regions of spectrin concentration appear to shift: spectrin increases near the growing furrow canal and concomitantly increases at the embryo surface. In the final phase of furrow growth, the shift in spectrin concentration is reversed: spectrin decreases near the furrow canal and concomitantly increases at the embryo surface. In gastrulae, spectrin accumulates near the embryo surface, especially at the forming amnioproctodeal invagination and cephalic furrow. During the germband elongation stage, the total amount of spectrin in the embryo increases significantly and becomes uniformly distributed at the plasma membrane of almost all cell types. The highest levels of spectrin are in the respiratory tract cells; the lowest levels are in parts of the forming gut. The spatial and temporal changes in spectrin localization suggest that this protein plays a role in stabilizing rather than initiating changes in structural organization in the embryo.
Stereotype Threat and Race of Interviewer Effects in a Survey on Political Knowledge

Social desirability is generally thought to underlie the propensity for survey respondents to tailor their answers to what they think would satisfy or please the interviewer. While this may in fact be the underlying motivation, especially on attitudinal and opinion questions, social desirability does not seem to be an adequate explanation for interviewer effects on factual questions. Borrowing from the social psychology literature on stereotype threat, we test an alternative account of the race-ofinterviewer effects. Stereotype threat maintains that the pressure to disconfirm and to avoid being judged by negative and potentially degrading stereotypes interferes with the processing of information. We argue that the survey context contains many parallels to a testing environment in which stereotype threat might alter responses to factual questions. Through a series of framing experiments in a public opinion survey and the reliance on the sensitivity to the race of the interviewer, our results are consistent with expectations based on a theory of “stereotype threat. ” African American respondents to a battery of questions about political knowledge get fewer answers right when interviewed by a white interviewer than when interviewed by an African American interviewer. The observed differences in performance on the political knowledge questions cannot be accounted for by differences in the educational background or gender of the respondents.
Development of the pelvis and posterior part of the vertebral column in the Anura

The anuran pelvic girdle is unique among all amphibians in that its acetabular portion is located far posterior to the sacrum, lateral to the postsacral (= caudal) vertebral column, which is reduced to a single rod‐like element called the urostyle. This situation in the adult is strikingly different not only from that in ancestral temnospondyls but also in other modern amphibians. Because there is no fossil that would document this evolutionary anatomical modification except for Triadobatrachus, the only data may be inferred from development in modern anurans. We chose seven anuran species (belonging to the genera Discoglossus, Bombina, Pelobates, Bufo, Rana and Xenopus), representing the principal locomotory types (saltation, swimming, crawling and burrowing). Development of the pelvic girdle was studied on cleared and stained whole mounts and partly on serial histological sections. The basic developmental pattern was similar in all species: the pelvis on both sides develops from two centres (puboischiadic and iliac, respectively). The ilium then extends vertically towards the sacral vertebra and later rotates posteriorly so that ultimately the acetabulum is lateral to the tail (= urostyle). Only minor deviations from this pattern were found, mainly associated with differences in water and terrestrial dwelling.
Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae

The 25S rRNA of yeast contains several base modifications in the functionally important regions. The enzymes responsible for most of these base modifications remained unknown. Recently, we identified Rrp8 as a methyltransferase involved in m1A645 modification of 25S rRNA. Here, we discovered a previously uncharacterized gene YBR141C to be responsible for second m1A2142 modification of helix 65 of 25S rRNA. The gene was identified by reversed phase–HPLC screening of all deletion mutants of putative RNA methyltransferase and was confirmed by gene complementation and phenotypic characterization. Because of the function of its encoded protein, YBR141C was named BMT2 (base methyltransferase of 25S RNA). Helix 65 belongs to domain IV, which accounts for most of the intersubunit surface of the large subunit. The 3D structure prediction of Bmt2 supported it to be an Ado Met methyltransferase belonging to Rossmann fold superfamily. In addition, we demonstrated that the substitution of G180R in the S-adenosyl-l-methionine–binding motif drastically reduces the catalytic function of the protein in vivo. Furthermore, we analysed the significance of m1A2142 modification in ribosome synthesis and translation. Intriguingly, the loss of m1A2142 modification confers anisomycin and peroxide sensitivity to the cells. Our results underline the importance of RNA modifications in cellular physiology.
Heme Binding Proteins of Bartonella henselae Are Required when Undergoing Oxidative Stress During Cell and Flea Invasion

Bartonella are hemotropic bacteria responsible for emerging zoonoses. These heme auxotroph alphaproteobacteria must import heme for their growth, since they cannot synthesize it. To import exogenous heme, Bartonella genomes encode for a complete heme uptake system enabling transportation of this compound into the cytoplasm and degrading it to release iron. In addition, these bacteria encode for four or five outer membrane heme binding proteins (Hbps). The structural genes of these highly homologous proteins are expressed differently depending on oxygen, temperature and heme concentrations. These proteins were hypothesized as being involved in various cellular processes according to their ability to bind heme and their regulation profile. In this report, we investigated the roles of the four Hbps of Bartonella henselae, responsible for cat scratch disease. We show that Hbps can bind heme in vitro. They are able to enhance the efficiency of heme uptake when co-expressed with a heme transporter in Escherichia coli. Using B. henselae Hbp knockdown mutants, we show that these proteins are involved in defense against the oxidative stress, colonization of human endothelial cell and survival in the flea.
Visual Selection and Shifting Mechanisms Based on a Network of Chaotic Wilson-Cowan Oscillators

In this paper, a Visual Selection and a Shifting Mechanisms based on a lattice of coupled chaotic Wilson-Cowan oscillators is proposed. The oscillators representing each object in a given visual scene are synchronized to produce a chaotic trajectory. A cooperation and competition mechanisms are also introduced to accelerate oscillating frequency of the salient object as well as to slow down other objects in the same scene. The model can not only discriminate each object among others in a given visual scene, but also deliver the focus of attention to a salient object in an instant of time. In comparison to other visual selection approaches, this model presents at least three new features. First, it is able to highlight objects in complex forms, including those that are non-linear separable. Second, a shifting mechanism used to change the focus of attention among the objects. Lastly, oscillators representing the salient object will jump from chaotic phase to periodic phase. This behavior matches well to biological experiments on pattern recognition of rabbit. Computer simulations are performed and the results show that the proposed model is promising as a Selection Mechanism with Shifting embedded in a Visual Attention System.
Development of a noninvasive system for monitoring dairy cattle sleep.

Limited research has been conducted to assess sleep in production livestock primarily because of limitations with monitoring capabilities. Consequently, biological understanding of production circumstances and facility options that affect sleep is limited. The objective of this study was to assess if data collected from a proof-of-concept, noninvasive 3-axis accelerometer device are correlated with sleep and wake-like behaviors in dairy cattle. Four Holstein dairy cows housed at the University of Kentucky Coldstream Dairy in September 2013 were visually observed for 2 consecutive 24-h periods. The accelerometer device was attached to a harness positioned on the right side of each cow's neck. Times of classified behaviors of wake (standing, head up, alert, eyes open) or sleep-like behaviors (lying, still, head resting on ground, eyes closed) were recorded continuously by 2 observers who each watched 2 cows at a time. The radial signal was extracted from 3 different axes of the accelerometer to obtain a motion signal independent of direction of movement. Radial signal features were examined for maximizing the performance of detecting sleep-like behaviors using a Fisher's linear discriminant analysis classifier. The study included 652min of high-activity wake behaviors and 107min of sleep-like behavior among 4 cows. Results from a bootstrapping analysis showed an agreement between human observation and the linear discriminant analysis classifier, with an accuracy of 93.7±0.7% for wake behavior and 92.2±0.8% for sleep-like behavior (±95% confidence interval). This prototype shows promise in measuring sleep-like behaviors. Improvements to both hardware and software should allow more accurate determinations of subtle head movements and respiratory movements that will further improve the assessment of these sleep-like behaviors, including estimates of deep, light, and rapid eye movement sleep. These future studies will require simultaneous electroencephalography and electromyography measures and perhaps additional measures of arousal thresholds to validate this system for measuring true sleep.