Miracle-dz/UniFAR-FTUs huggingface dataset:
The auxin influx carriers AUX1 and LAX3 are involved in auxin-ethylene interactions during apical hook development in Arabidopsis thaliana seedlings

Dark-grown dicotyledonous seedlings form a hook-like structure at the top of the hypocotyl, which is controlled by the hormones auxin and ethylene. Hook formation is dependent on an auxin signal gradient, whereas hook exaggeration is part of the triple response provoked by ethylene in dark-grown Arabidopsis seedlings. Several other hormones and light are also known to be involved in hook development, but the molecular mechanisms that lead to the initial installation of an auxin gradient are still poorly understood. In this study, we aimed to unravel the cross-talk between auxin and ethylene in the apical hook. Auxin measurements, the expression pattern of the auxin reporter DR5::GUS and the localization of auxin biosynthesis enzymes and influx carriers collectively indicate the necessity for auxin biosynthesis and efficient auxin translocation from the cotyledons and meristem into the hypocotyl in order to support proper hook development. Auxin accumulation in the meristem and cotyledons and in the hypocotyl is increased ∼2-fold upon treatment with ethylene. In addition, a strong ethylene signal leads to enhanced auxin biosynthesis at the inner side of the hook. Finally, mutant analysis demonstrates that the auxin influx carrier LAX3 is indispensable for proper hook formation, whereas the auxin influx carrier AUX1 is involved in the hook exaggeration phenotype induced by ethylene.
Study of circulating prohepcidin in association with insulin sensitivity and changing iron stores.

BACKGROUND Liver synthesizes hepcidin in response to iron overload, leading to down-regulation of duodenal iron absorption. The pathophysiology of type 2 diabetes is associated with increased iron stores. We aimed to study circulating prohepcidin in association with insulin sensitivity and parameters of glucose and iron metabolism. METHODS Serum prohepcidin was evaluated in three cohorts: 1) a cross-sectional study (cohort 1, men from the general population; n = 135); 2) after decreasing iron stores in men with "high-ferritin" type 2 diabetes (cohort 2; n = 13); and 3) after decreasing iron stores in men carrying HFE gene mutations (cohort 3; n = 16). Insulin sensitivity was measured using either the minimal model or the clamp technique. RESULTS Circulating prohepcidin correlated significantly with glycated hemoglobin (P < 0.0001), fasting glucose (P = 0.002), triglycerides (P = 0.007), high-density lipoprotein-cholesterol (P = 0.01), ferritin (P = 0.01), and soluble transferrin receptor concentration (P = 0.001) in subjects from cohort 1. Prohepcidin decreased significantly after iron depletion in patients with type 2 diabetes (P = 0.04) (cohort 2) and in carriers of HFE gene mutations (P = 0.03) (cohort 3). In the latter subjects, the change in serum prohepcidin after iron depletion was associated with the change in both fasting glucose transferrin (r = 0.58; P = 0.02) and saturation (r = 0.68; P = 0.005). The changes in insulin sensitivity were associated with those of liver iron content (r = -0.64; P = 0.007) and with those of serum prohepcidin (r = -0.50; P = 0.04) (cohort 3). CONCLUSIONS These associations suggest that circulating prohepcidin concentration is pathophysiologically associated with parameters of glucose and iron metabolism. A failure to increase prohepcidin synthesis is hypothesized to contribute to iron-induced disorders of glucose metabolism.
Seroprevelance of Hepatitis B Surface Antigen in Hospital based Population in Southern Rajasthan, India

Hepatitis B virus is a partially doublestranded circular DNA virus and is a member of the Hepadnaviridae family. The virus consists of a core capsid which contains viral DNA and this is surrounded by an envelope containing surface antigen (HBsAg). The HBsAg particles vary greatly in morphology and are found in high concentrations in early acute infection and continue to be produced in chronic disease. HBsAg is the most commonly used marker of infection for diagnostic and blood screening. An individual positive for HBsAg is considered to be infected with HBV, and is therefore potentially infectious (World Health Organization, 2004). Of the approximately 2 billion people, who have been infected worldwide more than 350 million are chronic carriers of HBV. (Behel et al., 2008)
Cutting Edge: Prolonged Antigen Presentation after Herpes Simplex Virus-1 Skin Infection1

It has been reported that MHC class I-restricted Ag presentation persists for only a short period following infection with certain pathogens, declining in parallel with the emergence of specific CTL activity. We have examined this issue in the case of murine infection with HSV-1. We found that the period of Ag presentation capable of priming naive CD8+ T cells is comparatively prolonged, persisting for at least 7 days after infection, and continuing despite the appearance of localized CTL activity. Ag presentation was abbreviated to 3 or 4 days postinfection by surgical excision of the inoculation site early after infection. This intervention attenuated the size of the primary CTL response, implying that prolonged presentation is necessary to drive maximal CTL expansion. Combined, these data show that, in some types of infection, CTL priming can extend well beyond the first 24–48 h after primary inoculation.
Analysis and removal of multiply scattered tube waves

Because of irregularities in or near the borehole, vertical seismic profiling (VSP) or crosswell data can be contaminated with scattered tube waves. These can have a large amplitude and can interfere with weaker upcoming reflections, destroying their continuity. This type of organized noise cannot always be removed with filtering methods currently in use. We propose a method based on modeling the scattered tube‐wave field and then subtracting it from the total data set. We assume that the scattering occurs close to the borehole axis and therefore use a 1-D impedance function to characterize borehole irregularities. Estimation of this impedance function is one of the first steps. Our method also accounts for multiply scattered tube waves. We apply the method to an actual VSP data set and conclude that the continuity of reflected, upcoming events improves significantly in a washout zone.
Determination of cholesterol oxides by gas chromatography‐flame ionization detection/mass selective detection and their occurence in lanolin‐containing cosmetics and ointments

Cholesterol oxides (COPs) are thought to be of toxicological relevance in cholesterol‐containing foods. For cholesterol‐containing cosmetics and the like, no information is available up to this date. Therefore, the first of two main aims of this study was to develop and validate a method for determining COPs in lanolin‐containing cosmetics such as lipsticks and fatty creams as well as in nipple ointments. The second aim was to study the occurrence of COPs and their concentration levels in the respective product classes.
Interactions of Tone and Intonation in Whispered Mandarin

A previous study has found that whispered Mandarin, though still allowing listeners to perceive tones to a certain degree, does not carry acoustic cues that are special to whispered tones. That conclusion, however, was based on data from only one speaker. The present study attempted to verify the earlier finding with data from more speakers, with an additional goal to find out if there are acoustic cues to intonation in whispered Mandarin and whether they interact with tonal cues. Twelve Mandarin speakers produced tonal as well as intonational contrasts in both phonated and whispered speech. Acoustic analyses found that whispered questions had longer duration, greater intensity and shallower spectral tilt than statements. However, a perception experiment with 20 native listeners showed a strong bias toward hearing statement in whispers, so that questions were identified well below chance. Thus the acoustic properties in whisper were countering each other as cues to intonation. There was also an interaction of tone and intonation in whispers in that Tone 2 and question help each other while Tone 4 and question hinder each other in their perceptual identification. Overall, therefore, there do not seem to be special perceptual cues to whispered intonation either.
Correlates of prolonged swimming performance in F2 hybrids of migratory and non-migratory threespine stickleback

SUMMARY Determining which underlying traits contribute to differences in whole-animal performance can be difficult when many traits differ between individuals with high and low capacities. We have previously found that migratory (anadromous marine) and non-migratory (stream-resident) threespine stickleback (Gasterosteus aculeatus) populations have genetically based differences in prolonged swimming performance (Ucrit) that are associated with divergence of a number of candidate morphological and physiological traits (pectoral fin size and shape, body shape, pectoral muscle and heart size, and pectoral muscle metabolic enzyme activities). Here, we use F2 hybrid crosses to determine which traits are correlated with Ucrit when expressed in a largely randomized genetic background and a range of trait values for other divergent traits. We found that four of our 12 candidate traits were positively correlated with Ucrit in F2 hybrids and that the combined effects of ventricle mass, pectoral adductor mass and adductor citrate synthase activity accounted for 17.9% of the variation in Ucrit. These data provide additional support for a causal role of muscle and heart size in mediating intraspecific differences in Ucrit, but indicate that many candidate morphological and biochemical traits do not have a strong effect on Ucrit when disassociated from other divergent traits. However, the limited variation in Ucrit in our F2 hybrid families may have decreased our ability to detect correlations among these candidate traits and Ucrit. These data suggest that many traits, interactions among traits and traits not measured in this study affect prolonged swimming performance in threespine stickleback.
Computationally efficient scheduling with the physical interference model for throughput improvement in wireless mesh networks

Wireless mesh networks are expected to be widely used to provide Internet access in the near future. In order to fulfill the expectations, these networks should provide high throughput simultaneously to many users. Recent research has indicated that, due to its conservative CSMA/CA channel access scheme and RTS/CTS mechanism, 802.11 is not suitable to achieve this goal.In this paper, we investigate throughput improvements achievable by replacing CSMA/CA with an STDMA scheme where transmissions are scheduled according to the physical interference model. To this end, we present a computationally efficient heuristic for computing a feasible schedule under the physical interference model and we prove, under uniform random node distribution, an approximation factor for the length of this schedule relative to the shortest schedule possible with physical interference. This represents the first known polynomial-time algorithm for this problem with a proven approximation factor.We also evaluate the throughput and execution time of this algorithm on representative wireless mesh network scenarios through packet-level simulations. The results show that throughput with STDMA and physical-interference-based scheduling can be up to three times higher than 802.11 for the parameter values simulated. The results also show that our scheduling algorithm can schedule networks with 2000 nodes in about 2.5 minutes.
Sex-related differences in morphological, physiological, and ultrastructural responses of Populus cathayana to chilling

Low temperature is one of the abiotic factors limiting plant growth and productivity. Yet, knowledge about sex-related responses to low temperature is very limited. In our study, the effects of low, non-freezing temperature on morphological, physiological, and ultrastructural traits of leaves in Populus cathayana Rehd. males and females were investigated. The results showed that 4 °C temperature caused a chilling stress, and females suffered from greater negative effects than did males. At the early growth stage of development, chilling (4 °C) significantly inhibited plant growth, decreased net photosynthesis rate (Pn), stomatal conductance (gs), transpiration (E), and chlorophyll pigments (Chl), and increased intercellular CO2 concentration (Ci), chlorophyll a/b (Chl a/b), proline, soluble sugar and H2O2 contents, and ascorbate peroxidase (APX) activity in both sexes, whereas peroxidase (POD) and glutathione reductase (GR) activities decreased and thiobarbituric acid reactive substance (TBARS) content increased only in females. Chilling stress also caused chloroplast changes and an accumulation of numerous plastoglobules and small vesicles in both sexes. However, disintegrated chloroplasts and numerous tilted grana stacks were only found in chilling-stressed females. Under chilling stress, males showed higher Chl and soluble sugar contents, and higher superoxide dismutase (SOD), POD, and GR activities than did females. In addition, males exhibited a better chloroplast structure and more intact plasma membranes than did females under chilling stress. These results suggest that sexually different responses to chilling are significant and males possess a better self-protection mechanism than do females in P. cathayana.
Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations

A possible consequence of planting genetically modified organisms (GMOs) in centres of crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence of the transgenic 35S promoter in maize landraces sampled in 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample taken from the same region in 2003 and 2004 could not confirm the existence of transgenes, thereby casting doubt on the earlier results. These two studies were based on different sampling and analytical procedures and are thus hard to compare. Here, we present new molecular data for this region that confirm the presence of transgenes in three of 23 localities sampled in 2001. Transgene sequences were not detected in samples taken in 2002 from nine localities, while directed samples taken in 2004 from two of the positive 2001 localities were again found to contain transgenic sequences. These findings suggest the persistence or re‐introduction of transgenes up until 2004 in this area. We address variability in recombinant sequence detection by analyzing the consistency of current molecular assays. We also present theoretical results on the limitations of estimating the probability of transgene detection in samples taken from landraces. The inclusion of a limited number of female gametes and, more importantly, aggregated transgene distributions may significantly lower detection probabilities. Our analytical and sampling considerations help explain discrepancies among different detection efforts, including the one presented here, and provide considerations for the establishment of monitoring protocols to detect the presence of transgenes among structured populations of landraces.
Rapeseed Oil and Sunflower Oil Diets Enhance Platelet In Vitro Aggregation and Thromboxane Production in Healthy Men when Compared with Milk Fat or Habitual Diets

Summary In this highly controlled trial, 26 normolipidemic men (average age 28 years, range 18 to 60) were fed a baseline diet high in milk fat (MF) (fat 36% of energy, saturates 19%, monounsaturates 11%, polyunsaturates 4%), followed by a diet high in sunflower oil (SO) (fat 38% of energy, saturates 13%, monounsaturates 10%, polyunsaturates 13%) and another diet high in low erucic-acid rapeseed oil (RO) (fat 38% of energy, saturates 12%, monounsaturates 16%, polyunsaturates 8%). All diets were mixed natural diets with the same cholesterol contents. The baseline milk fat diet was given for 14 days and the oil diets for 24 days in a blind cross-over design. The platelet in vitro aggregation (slope %/min) induced by 1, 2 and 3 pM ADP and collagen (25 pg/ml PRP) was highly significantly (p <0.001) increased after both oil diets when compared with the results from the milk fat diet. The aggregation pattern determined by threshold collagen concentration confirmed increased collagen sensitivity of the platelets after the rapeseed oil diet (p <0.001). The enhancement of platelet aggregation was associated with increased in vitro platelet thromboxane production after the oil diets vs. the milk fat diet (p <0.05 after the sunflower oil diet and p <0.001 after the rapeseed oil diet).
Investigation of Genetic Structure between Deep and Shallow Populations of the Southern Rock Lobster, Jasus edwardsii in Tasmania, Australia

The southern rock lobster, Jasus edwardsii, shows clear phenotypic differences between shallow water (red coloured) and deeper water (pale coloured) individuals. Translocations of individuals from deeper water to shallower waters are currently being trialled as a management strategy to facilitate a phenotypic change from lower value pale colouration, common in deeper waters, to the higher value red colouration found in shallow waters. Although panmixia across the J. edwardsii range has been long assumed, it is critical to assess the genetic variability of the species to ensure that the level of population connectivity is appropriately understood and translocations do not have unintended consequences. Eight microsatellite loci were used to investigate genetic differentiation between six sites (three shallow, three deep) across southern Tasmania, Australia, and one from New Zealand. Based on analyses the assumption of panmixia was rejected, revealing small levels of genetic differentiation across southern Tasmania, significant levels of differentiation between Tasmania and New Zealand, and high levels of asymmetric gene flow in an easterly direction from Tasmania into New Zealand. These results suggest that translocation among Tasmanian populations are not likely to be problematic, however, a re-consideration of panmictic stock structure for this species is necessary.
Modelling of high velocity impact on composite materials for airframe structures application

This thesis presents a new lamina material model that addresses shortfalls identified in advanced material models for use in composite impact predictions. The new model combines the ease of use of the Matzenmiller-Lubliner-Taylor model with the robustness of the Baz̆ant crack band method. A material model interpolation scheme is also presented to allow for the simulation of high strain rate loading events with the new lamina material model. The proposed lamina model is implemented in a commercial Finite Element Method (FEM) code and used in combination with a stack shell approach using cohesive zone elements to predict delamination damage. The proposed material model and chosen discretization enable for the prediction of high velocity through thickness impacts, which lead to the perforation of the targets. To validate the newmaterial model, experimental tests are performed on three woven composite materials. These tests consist in perpendicular impacts on Carbon Fiber Reinforced Polymer (CFRP) panels using an elongated aluminium impactor. The elongated projectile is required to record the projectiles’ deceleration histories during the impact event. Postmortem inspections of the panels are also undertaken to quantify the damage sustained by the CFRP targets. Projected delamination areas are quantified through C-Scan inspection of the targets, followed by visual inspection of the impact sites’ cross sections. Numerical simulations are next carried out using different in-plane and outof-plane discretization approaches. Three material formulations are also investigated: brittle, the proposed model and the proposed model with high strain rate parameters. The results of these simulations are compared to the results obtained experimentally. The new model is found to predict reasonably well the damage encountered in the experimental test and to greatly diminish the mesh size sensitivity of the FEM approach. Areas requiring further attention are identified to further move composite material failure prediction from laboratory to industrial applications.
Issues affecting the level of prosthetics research evidence: Secondary analysis of a systematic review

Background: Systematic reviews of scientific literature are valuable sources of synthesized knowledge. Systematic review results may also be used to inform readers about challenges inherent to an area of research, guide future research efforts, and facilitate improvements in evidence quality. Objectives: To identify methodological issues that affected the overall level of scientific evidence reported in a contemporary systematic review and to offer suggestions for enhancing publications’ contribution to the overall evidence. Study design: Secondary analysis of a systematic review. Methods: Publications included in a systematic review related to microprocessor-controlled prosthetic knees were analyzed with respect to established methodological quality criteria. Common issues were identified and discussed. Results: Internal validity was commonly affected by variable comparison conditions, limited justification of accommodation time, potential fatigue and learning effects, lack of blinding, small sample sizes, limited evidence of measurement reliability, subject attrition, and limited descriptions of selection criteria. Similarly, external validity was affected by limited descriptions of the study sample, indeterminate representativeness, and suboptimal description of the interventions. Conclusion: Results suggest that efforts to address methodological limitations, educate evidence consumers, and improve research reporting are needed to advance the quality and use of evidence in the field of prosthetics. Clinical relevance Critical analysis of the strengths and limitations of publications included in a systematic review can inform evidence consumers and contributors about challenges inherent to a field of research. Results of this analysis suggest that efforts to address identified limitations are needed to enhance the overall level of prosthetics evidence.
Improved Climate Risk Simulations for Rice in Arid Environments

We integrated recent research on cardinal temperatures for phenology and early leaf growth, spikelet formation, early morning flowering, transpirational cooling, and heat- and cold-induced sterility into an existing to crop growth model ORYZA2000. We compared for an arid environment observed potential yields with yields simulated with default ORYZA2000, with modified subversions of ORYZA2000 and with ORYZA_S, a model developed for the region of interest in the 1990s. Rice variety ‘IR64’ was sown monthly 15-times in a row in two locations in Senegal. The Senegal River Valley is located in the Sahel, near the Sahara desert with extreme temperatures during day and night. The existing subroutines underestimated cold stress and overestimated heat stress. Forcing the model to use observed spikelet number and phenology and replacing the existing heat and cold subroutines improved accuracy of yield simulation from EF = −0.32 to EF =0.70 (EF is modelling efficiency). The main causes of improved accuracy were that the new model subversions take into account transpirational cooling (which is high in arid environments) and early morning flowering for heat sterility, and minimum rather than average temperature for cold sterility. Simulations were less accurate when also spikelet number and phenology were simulated. Model efficiency was 0.14 with new heat and cold routines and improved to 0.48 when using new cardinal temperatures for phenology and early leaf growth. The new adapted subversion of ORYZA2000 offers a powerful analytic tool for climate change impact assessment and cropping calendar optimisation in arid regions.