Miracle-dz/UniFAR-FTUs huggingface dataset:
A Genome-Wide Expression Profile of Salt-Responsive Genes in the Apple Rootstock Malus zumi

In some areas of cultivation, a lack of salt tolerance severely affects plant productivity. Apple, Malus x domestica Borkh. , is sensitive to salt, and, as a perennial woody plant the mechanism of salt stress adaption will be different from that of annual herbal model plants, such as Arabidopsis. Malus zumi is a salt tolerant apple rootstock, which survives high salinity (up to 0.6% NaCl). To examine the mechanism underlying this tolerance, a genome-wide expression analysis was performed, using a cDNA library constructed from salt-treated seedlings of Malus zumi. A total of 15,000 cDNA clones were selected for microarray analysis. In total a group of 576 cDNAs, of which expression changed more than four-fold, were sequenced and 18 genes were selected to verify their expression pattern under salt stress by semi-quantitative RT-PCR. Our genome-wide expression analysis resulted in the isolation of 50 novel Malus genes and the elucidation of a new apple-specific mechanism of salt tolerance, including the stabilization of photosynthesis under stress, involvement of phenolic compounds, and sorbitol in ROS scavenging and osmoprotection. The promoter regions of 111 genes were analyzed by PlantCARE, suggesting an intensive cross-talking of abiotic stress in Malus zumi. An interaction network of salt responsive genes was constructed and molecular regulatory pathways of apple were deduced. Our research will contribute to gene function analysis and further the understanding of salt-tolerance mechanisms in fruit trees.
Morphology and burrowing energetics of semi-fossorial skinks (Liopholis spp.)

ABSTRACT Burrowing is an important form of locomotion in reptiles, but no study has examined the energetic cost of burrowing for reptiles. This is significant because burrowing is the most energetically expensive mode of locomotion undertaken by animals and many burrowing species therefore show specialisations for their subterranean lifestyle. We examined the effect of temperature and substrate characteristics (coarse sand or fine sand) on the net energetic cost of burrowing (NCOB) and burrowing rate in two species of the Egernia group of skinks (Liopholis striata and Liopholis inornata) compared with other burrowing animals. We further tested for morphological specialisations among burrowing species by comparing the relationship between body shape and retreat preference in Egernia group skinks. For L. striata and L. inornata, NCOB is 350 times more expensive than the predicted cost of pedestrian terrestrial locomotion. Temperature had a positive effect on burrowing rate for both species, and a negative effect on NCOB for L. striata but not L. inornata. Both NCOB and burrowing rate were independent of substrate type. Burrows constructed by skinks had a smaller cross-sectional area than those constructed by mammals of comparable mass, and NCOB of skinks was lower than that of mammals of similar mass. After accounting for body size, retreat preference was significantly correlated with body shape in Egernia group skinks. Species of Egernia group skinks that use burrows for retreats have narrower bodies and shorter front limbs than other species. We conclude that the morphological specialisations of burrowing skinks allow them to construct relatively narrow burrows, thereby reducing NCOB and the total cost of constructing their burrow retreats. Summary: Burrowing skinks have a lower net cost of burrowing than tunnel-constructing endotherms and exhibit morphological specialisation associated with burrowing.
Immune Response to Inactivated Newcastle Disease Virus by Electrolysed Catholyte Anolyte and Binary Ethylenimine in Specific Pathogen Free Chickens

This study aimed to investigate the immunogenicity of Newcastle disease virus (NDV) in specificpathogen-free (SPF) chickens. The NDV was inactivated using either Binary ethyleneimine (BEI) or Electrolysed water-Catholyte-Anolyte (ECA). Complete inactivation of NDV occurred after 24 hours with either BEI or ECA. Prepared inactivated NDV vaccines were tested for their efficiency in generating humoral immune response in different groups of specific pathogen free (SPF) chicks. Test groups received 0.2 ml BEI inactivated NDV (NDVBEI) and ECA (NDVECA) subcutaneously. No significant ELISA total mean titer between NDVBEI group (11303 ± 4515) and NDVECA (12131 ± 1932) (p<0.05) at two week post inoculation. BEI and ECA inactivated vaccine gave higher antibody titers and preserves both structural integrity and antigenicity of the virus. Thus, it might be possible to use these compounds as an inactivator agent for commercial NDV inactivated vaccines in future.
Graph spectral compressed sensing for sensor networks

Consider a wireless sensor network with N sensor nodes measuring data which are correlated temporally or spatially. We consider the problem of reconstructing the original data by only transmitting M ≪ N sensor readings while guaranteeing that the reconstruction error is small. Assuming the original signal is “smooth” with respect to the network topology, our approach is to gather measurements from a random subset of nodes and then interpolate with respect to the graph Laplacian eigenbasis, leveraging ideas from compressed sensing. We propose algorithms for both temporally and spatially correlated signals, and the performance of these algorithms is verified using both synthesized data and real world data. Significant savings are made in terms of energy resources, bandwidth, and query latency.
Tysnd1 Deficiency in Mice Interferes with the Peroxisomal Localization of PTS2 Enzymes, Causing Lipid Metabolic Abnormalities and Male Infertility

Peroxisomes are subcellular organelles involved in lipid metabolic processes, including those of very-long-chain fatty acids and branched-chain fatty acids, among others. Peroxisome matrix proteins are synthesized in the cytoplasm. Targeting signals (PTS or peroxisomal targeting signal) at the C-terminus (PTS1) or N-terminus (PTS2) of peroxisomal matrix proteins mediate their import into the organelle. In the case of PTS2-containing proteins, the PTS2 signal is cleaved from the protein when transported into peroxisomes. The functional mechanism of PTS2 processing, however, is poorly understood. Previously we identified Tysnd1 (Trypsin domain containing 1) and biochemically characterized it as a peroxisomal cysteine endopeptidase that directly processes PTS2-containing prethiolase Acaa1 and PTS1-containing Acox1, Hsd17b4, and ScpX. The latter three enzymes are crucial components of the very-long-chain fatty acids β-oxidation pathway. To clarify the in vivo functions and physiological role of Tysnd1, we analyzed the phenotype of Tysnd1−/− mice. Male Tysnd1−/− mice are infertile, and the epididymal sperms lack the acrosomal cap. These phenotypic features are most likely the result of changes in the molecular species composition of choline and ethanolamine plasmalogens. Tysnd1−/− mice also developed liver dysfunctions when the phytanic acid precursor phytol was orally administered. Phyh and Agps are known PTS2-containing proteins, but were identified as novel Tysnd1 substrates. Loss of Tysnd1 interferes with the peroxisomal localization of Acaa1, Phyh, and Agps, which might cause the mild Zellweger syndrome spectrum-resembling phenotypes. Our data established that peroxisomal processing protease Tysnd1 is necessary to mediate the physiological functions of PTS2-containing substrates.
Evaluating the Quality of Process Models : Empirical Analysis of a Quality Framework

This paper conducts an empirical analysis of the quality framework proposed by Lindland et al (1994) for evaluating the quality of conceptual models. 194 participants were trained in the concepts of the quality framework, and then used it to evaluate models in an extended ER language. A randomised, double-blind design was used, and the results evaluated by a combination of quantitative and qualitative analysis. Finally, an analysis was conducted of the framework’s perceived ease of use, usefulness and likelihood of adoption in practice. The study provides strong support for the validity of the framework and suggests that it is likely to be adopted in practice, but raises questions about its reliability. The research findings provide clear direction for further refinements of the framework to improve its reliability.
Precision measurement of cosmic magnification from 21 cm emitting galaxies

We show how precision lensing measurements can be obtained through the lensing magnification effect in high-redshift 21-cm emission from galaxies. Previously, cosmic magnification measurements have been seriously complicated by galaxy clustering. With precise redshifts obtained using the 21-cm emission line wavelength, one can correlate galaxies at different source planes, or exclude close pairs to eliminate such contamination. We provide forecasts for future surveys, specifically the Square Kilometer Array (SKA) and the Canadian Large Adaptive Reflector (CLAR). SKA can achieve ∼1 per cent precision on the dark-matter power spectrum and the galaxy dark-matter cross-correlation power spectrum, while CLAR can measure an accurate cross-correlation power spectrum. The neutral hydrogen fraction was most likely significantly higher at high redshifts, which increases the number of observed galaxies significantly, such that CLAR can also measure the dark-matter lensing power spectrum. SKA can also allow precise measurement of bispectrum lensing.
Limits of translates of plane curves -- on a paper of Aldo Ghizzetti

We study the limits of PGL(3) translates of an arbitrary plane curve, giving a description of all possible limits of a given curve and computing the multiplicities of corresponding components in the normal cone to the base scheme of a related linear system. This information is a key step in the computation of the degree of the closure of the linear orbit of an arbitrary plane curve. Our analysis recovers and extends results obtained by Aldo Ghizzetti in the 1930's.
Dysentery Caused by Escherichia coli (S102-9) in Calves: Natural and Experimental Disease

A dysentery syndrome was recognized among the Institute's calves at 18 to 21 days of age. It was reproduced experimentally in gnotobiotic calves with an atypical Escherichia coli (S102-9) isolated from the affected calves. In both natural and experimental disease the calves passed copious bright red blood in the feces and developed diarrhea. Walls of the colon and rectum were thickened, and the mucosa was reddened and covered by an exudate that contained mucus and blood clots. Bacteria were seen closely adherent to the luminal surfaces of enterocytes, often in cup-shaped depressions or on cytoplasmic pedestals. Microvilli were distorted, disorientated or absent. There was exfoliation of infected enterocytes and a mild acute inflammation of the underlying lamina. In two of five calves with natural disease, the adherent bacteria did not stain by the immunoperoxidase method with antisera raised against E. coli (S102-9). This indicated that there was possibly more than one bacterial cause of the syndrome. Lesions in experimentally infected calves were indistinguishable from those produced by some E. coli which are enteropathogenic for man, rabbits, and pigs.
Thermodynamic properties of QCD in external magnetic fields

We consider the effect of strong external electromagnetic fields on thermodynamic observables in QCD, through lattice simulations with 1+1+1 flavors of staggered quarks at physical quark masses. Continuum extrapolated results are presented for the light quark condensates and for their tensor polarizations, as functions of the temperature and the magnetic field. We find the light condensates to undergo inverse magnetic catalysis in the transition region, in a manner that the transition temperature decreases with growing magnetic field. We also compare the results to other approaches and lattice simulations. Furthermore, we relate the tensor polarization to the spin part of the magnetic susceptibility of the QCD vacuum, and show that this contribution is diamagnetic.
Simultaneous detection and genotyping of three genomic groups of Borrelia burgdorferi sensu lato in Dutch Ixodes ricinus ticks by characterization of the amplified intergenic spacer region between 5S and 23S rRNA genes

We developed a rapid and reliable method for the identification Borrelia burgdorferi sensu lato species in ticks. We used the DNA sequence polymorphism of the spacer region between 5S and 23S rRNA genes, which has been shown to be able to discriminate between eight genomic groups of B. burgdorferi sensu lato (D. Postic, M. Assous, P. A. D. Grimont, and G. Baranton, Int. J. Syst. Bacteriol. 44:743-752, 1994). Spacer DNA was amplified by PCR and was then hybridized to five membrane-bound oligonucleotides. The oligonucleotides were specific for B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii, and group VS116. A probe which reacted with all genomic groups of B. burgdorferi sensu lato was also used. Ninety-six ticks collected in the field were destructed by bead beating, and the supernatant was used directly in a PCR. B. burgdorferi sensu lato DNA was detected in 6 of 57 adult ticks (11%) and 9 of 39 nymphs (23%). B. garinii was found in three nymphs and four adults, three nymphs carried B. afzelii, and one adult and one nymph carried group VS116. Double infections with B. afzelii and group VS116 were found in two nymphs and one adult. Thus, our method can simultaneously identify three genomic groups of B. burgdorferi sensu lato in ticks collected in the field. This technique provides new ways to study the association of genomic groups present in ticks and the risk of Lyme borreliosis.
Coming of Age in Times of Uncertainty

Adulthood is taken for granted. It connotes the end of childhood, the resolution to the "storm and stress" period of adolescence. This conception is strongly entrenched in the sociology of youth and the sociology of the life course as well as in the policy arena. At the same time, adulthood itself remains unarticulated; journey's end remains conceptually fixed and theoretically uncontested. Adulthood, then, is both central to the social imagination and neglected as an area of sociological investigation, something that has been noted by sociologists over the last four decades. Going beyond the overwhelmingly psychological literature, this book draws on original qualitative research and theories of social recognition and thus presents a first step towards filling an important gap in our understanding of the meaning of adulthood.
modeling in physiology The hot IVGTT two-compartment minimal model : indexes of glucose effectiveness and insulin sensitivity

Vicini, Paolo, Andrea Caumo, and Claudio Cobelli. Hot IVGTT two-compartment minimal model: indexes of glucose effectiveness and insulin sensitivity. Am. J. Physiol. 273 (Endocrinol. Metab. 36): E1024–E1032, 1997. —A twocompartment minimal model (2CMM) has been proposed [A. Caumo and C. Cobelli. Am. J. Physiol. 264 (Endocrinol. Metab. 27): E829–E841, 1993] to describe intravenous glucose tolerance test (IVGTT) labeled (hereafter hot) glucose kinetics. This model, at variance with the one-compartment minimal model (1CMM), allows the estimation of a plausible profile of glucose production. The aim of this study is to show that the 2CMM also allows the assessment of insulin sensitivity (SI 2*), glucose effectiveness (SG 2*), and plasma clearance rate (PCR). The 2CMM was identified on stable-isotope IVGTTs performed in normal subjects (n 5 14). Results were (means 6 SE) SG 2* 5 0.85 6 0.14 ml·kg21 ·min21, PCR 5 2.02 6 0.14 ml·kg21 ·min21, and SI 2* 5 13.83 6 2.54 3 1022 ml·kg21 · min21·μU21·ml. The 1CMM was also identified; glucose effectiveness and insulin sensitivity indexes were S*GV 5 1.36 6 0.08 ml·kg21 ·min21 and S*IV 5 12.98 6 2.21 3 1022 ml·kg21 · min21 ·μU21 ·ml, respectively, where V is the 1CMM glucose distribution volume. S*GV was lower than PCR and higher than SG 2* and did not correlate with either [r 5 0.45 (NS) and r 5 0.50 (NS), respectively], whereas S*IV was not different from and was correlated with SI 2* (r 5 0.95; P , 0.001). S*G compares well (r 5 0.78; P , 0.001) with PCR normalized by the 2CMM total glucose distribution volume. In conclusion, the 2CMM is a powerful tool to assess glucose metabolism in vivo.
Clinical effectiveness of CBT-based guided self-help for anxiety and depression: does it work in practice and what helps people to benefit?

1 1. SYSTEMATIC REVIEW 2 1.1 Abstract 3 1.2 Introduction 5 1.3 Method 7 1.3. 1 Inclusion and exclusion criteria 7 1.3. 1.1 Study design 7 1.3. 1.2 Population 7 1.3. 1.3 Interventions 8 1.3. 1.4 Outcome measures 9 1.3. 2 Literature search strategies 9 1.3. 3 Assessment of quality of included studies 12 1.4 Results 14 1.4. 1 Characteristics of included studies 14 1.4. 2 Quality of included studies 17 1.4. 3 Meta-analysis 20 1.5 Discussion 22 1.5. 1 Strengths of review 24 1.5. 2 Limitations of review 25 1.5. 3 Implications for research, clinical practice and policy 26 1.6 Conclusions 29 1.7 Acknowledgements 30 1.8 References 30
L-optimal transportation for Ricci flow

We introduce the notion of L-optimal transportation, and use it to construct a natural monotonic quantity for Ricci flow which includes a selection of other monotonicity results, including some key discoveries of Perelman [13] (both related to entropy and to L-length) and a recent result of McCann and the author [11].
Testing for Inherited Thrombophilias in Arterial Stroke: Can It Cause More Harm Than Good?

Background and Purpose— Despite a paucity of evidence supporting a true association of ischemic stroke and the inherited thrombophilias, it is common practice for many neurologists to order these tests as part of the work-up of ischemic stroke, especially in young patients. Treatment with oral anticoagulation is often used in patients with positive results for the inherited thrombophilias. Methods— We reviewed the literature focusing on case-control studies of the 5 most commonly inherited disorders of coagulation: protein C deficiency, protein S deficiency, antithrombin deficiency, and the factor V Leiden and prothrombin gene mutations in patients with stroke. We also analyzed the available data on stroke patients with inherited thrombophilia and patent foramen ovale. Results— Multiple case-control studies have not convincingly shown an association of the inherited thrombophilias with ischemic stroke, even in young patients and patients with patent foramen ovale. Conclusion— If there is an association between the inherited thrombophilias and arterial stroke, then it is a weak one, likely enhanced by other prothrombotic risk factors. The consequences of ordering these tests and attributing causality to an arterial event can result in significant costs to the health care system and pose a potential risk to patients, because this may lead to inappropriate use of long-term oral anticoagulants, exposing patients to harm without a clearly defined benefit.
Campylobacter pylori isolated from the stomach of the monkey, Macaca nemestrina

Campylobacter pylori was isolated from the gastric mucosa in 6 of 24 pigtailed macaques (Macaca nemestrina) examined by gastric biopsy and culture; 3 isolates were recovered during gastroendoscopy, and 3 were recovered at necropsy. The isolates were morphologically and biochemically similar to the human type strain NCTC 11638, differing only in colony diameter, pigmentation, and rate of growth. Identity of the isolates was confirmed by whole-genomic DNA-DNA hybridization with the type strain. Colonization of the monkey stomachs was associated with hypochlorhydria and histologic features resembling type B chronic gastritis in humans. Host animals exhibited no morbid clinical effects of colonization, although endoscopy revealed inflammation, erythema, and friable tissue in some animals. The discovery of C. pylori occurring spontaneously in M. nemestrina extends the known range of the hosts of the organism and offers the possibility of a natural or experimental model of the infection in monkeys.
Gene K of bacteriophage phi X174 codes for a protein which affects the burst size of phage production

Site-directed mutagenesis has been used to produce a T----A change at nucleotide 70 of phi X174 genome. This generates an am codon, TAG, in the gene K reading frame without affecting the amino acid, leucine, encoded by the overlapping gene A. The gene K mutant produces small plaques on su- hosts. It has an identical latent period, but a more reduced burst size than that of the wild-type phi X174. The reduced burst size in the gene K mutant suggests that the gene K protein, although not essential, has a role in increasing infectivity by increasing the burst size three- to sixfold.
High-Efficiency Wideband 3-D On-Chip Antennas for Subterahertz Applications Demonstrated at 200 GHz

This work presents an efficient method for realizing a laterally radiating 3-D monopole antenna for millimeter-wave and terahertz applications. The vertical antenna rod is formed with a standard <inline-formula> <tex-math notation="LaTeX">$\text{17-}{\mu} \text{m}$</tex-math></inline-formula> aluminum wire on a programmable semiautomatic ultrasonic wedge bonder, which allows for a good reproducibility. The key features are a high gain of up to 4.9 dBi, a <inline-formula><tex-math notation="LaTeX">${\text{360}}^{\circ }$</tex-math></inline-formula> azimuthal coverage, an estimated radiation efficiency of around 90%, a uniform behavior over a wide frequency range of 60 GHz, and a low chip area requirement of <inline-formula><tex-math notation="LaTeX">${\text{0.06}}\ \text{mm}^{2}$ </tex-math></inline-formula>. The on-chip structure offers the unique ability to be alternatively utilized for direct characterization with standard measurement probes. In addition, an analytic model is derived and compared to electromagnetic field simulations. To verify the radiation performance, a physical transmission link is demonstrated for distances between 5 and 15 mm and for a frequency ranging from 140 to 220 GHz. The obtained results agree well with the theoretical and simulated estimations.
Cryostratigraphy and Permafrost Evolution in the Lacustrine Lowlands of West‐Central Alaska

The influence of permafrost growth and thaw on the evolution of ice‐rich lowland terrain in the Koyukuk‐Innoko region of interior Alaska is fundamental but poorly understood. To elucidate this influence, the cryostratigraphy and properties of perennially frozen sediments from three areas in this region are described and interpreted in terms of permafrost history. The upper part of the late Quaternary sediments at the Koyukuk and Innoko Flats comprise frozen organic soils up to 4.5 m thick underlain by ice‐rich silt characterised by layered and reticulate cryostructures. The volume of visible segregated ice in silt locally reaches 50 per cent, with ice lenses up to 10 cm thick.