Miracle-dz/UniFAR-FTUs huggingface dataset:
Degradation of Pheromone and Plant Volatile Components by a Same Odorant-Degrading Enzyme in the Cotton Leafworm, Spodoptera littoralis

Background Odorant-Degrading Enzymes (ODEs) are supposed to be involved in the signal inactivation step within the olfactory sensilla of insects by quickly removing odorant molecules from the vicinity of the olfactory receptors. Only three ODEs have been both identified at the molecular level and functionally characterized: two were specialized in the degradation of pheromone compounds and the last one was shown to degrade a plant odorant. Methodology Previous work has shown that the antennae of the cotton leafworm Spodoptera littoralis, a worldwide pest of agricultural crops, express numerous candidate ODEs. We focused on an esterase overexpressed in males antennae, namely SlCXE7. We studied its expression patterns and tested its catalytic properties towards three odorants, i.e. the two female sex pheromone components and a green leaf volatile emitted by host plants. Conclusion SlCXE7 expression was concomitant during development with male responsiveness to odorants and during adult scotophase with the period of male most active sexual behaviour. Furthermore, SlCXE7 transcription could be induced by male exposure to the main pheromone component, suggesting a role of Pheromone-Degrading Enzyme. Interestingly, recombinant SlCXE7 was able to efficiently hydrolyze the pheromone compounds but also the plant volatile, with a higher affinity for the pheromone than for the plant compound. In male antennae, SlCXE7 expression was associated with both long and short sensilla, tuned to sex pheromones or plant odours, respectively. Our results thus suggested that a same ODE could have a dual function depending of it sensillar localisation. Within the pheromone-sensitive sensilla, SlCXE7 may play a role in pheromone signal termination and in reduction of odorant background noise, whereas it could be involved in plant odorant inactivation within the short sensilla.
Phytoremediation Potential of Plants Growing on the Pb-Contaminated Soil at the Song Tho Pb Mine, Thailand

ABSTRACT The contamination of lead (Pb) is one of the main environmental problems on a global scale. This study assessed the potential of native metallophytes growing on the Song Tho Pb mine in Kanchanaburi province, Thailand, by a field survey. Plants and the associated soil samples were collected. Total Pb concentrations were analyzed by a flame atomic absorption spectrophotometer after a microwave-assisted acid digestion. While total Pb concentrations of top soils varied from 4881 to 16,720 mg/kg, those in soil around the roots ranged from 421 to 48,883 mg/kg. A total of 12 species belonging to eight families accumulated Pb concentrations in roots (47–32,633 mg/kg) which were higher than those in shoots (non-detected values – 1489 mg/kg). Bidens pilosa, with Pb accumulation in shoots > 1000 mg/kg and translocation factor (TF) > 1, could be useful in phytoextraction as a hyperaccumulator. Thysanolaena latifolia and Mimosa pudica with bioconcentration factor > 1 and TF < 1 could be useful in phytostabilization as excluders. So far, not many Pb hyperaccumulators are reported. The results from this study proposed a new candidate, B. pilosa, for Pb extraction. The potential use of these three phytoremediators should be further investigated using hydroponic and pot experiments.
Nitric oxide and oxygen utilization: exercise, heart failure and diabetes.

In addition to regulating vascular tone, there is increasing evidence for the involvement of NO in the modulation of oxygen consumption. Our in-vitro studies indicated that exogenous and endogenous NO reduces the consumption of oxygen in isolated canine skeletal and cardiac muscle, which is probably related to its direct effect on mitochondria, i.e. cytochrome oxidase. In resting, conscious dogs, the blockade of NO synthesis results in an increase in total oxygen consumption. During exercise, there is a significant increase in the release of NO from the coronary circulation in conscious dogs, and there are greater increases in total oxygen consumption, and oxygen consumption in skeletal muscle and in the heart when NO synthesis is blocked. Our results suggest that NO plays a role in matching blood flow to tissue metabolism at rest and during exercise. The modulation of the consumption of O2 by endogenous NO in skeletal or cardiac muscle is blunted after the development of heart failure or diabetes. After heart failure, the heart switches from fatty acid to glucose metabolism, suggesting that NO also plays a role in the regulation of metabolism in the heart.
Base of the Measles Virus Fusion Trimer Head Receives the Signal That Triggers Membrane Fusion*

Background: A homology model of the trimeric measles virus fusion protein predicts a cavity in the base of the head. Results: Hydrophobic residues required for interactions with the hemagglutinin map to this cavity. Conclusion: The base of the measles virus fusion protein trimer head receives the signal that triggers membrane fusion. Significance: Emerging, re-emerging, and prevalent paramyxoviruses may operate based on similar signal transmission mechanisms. The measles virus (MV) fusion (F) protein trimer executes membrane fusion after receiving a signal elicited by receptor binding to the hemagglutinin (H) tetramer. Where and how this signal is received is understood neither for MV nor for other paramyxoviruses. Because only the prefusion structure of the parainfluenza virus 5 (PIV5) F-trimer is available, to study signal receipt by the MV F-trimer, we generated and energy-refined a homology model. We used two approaches to predict surface residues of the model interacting with other proteins. Both approaches measured interface propensity values for patches of residues. The second approach identified, in addition, individual residues based on the conservation of physical chemical properties among F-proteins. Altogether, about 50 candidate interactive residues were identified. Through iterative cycles of mutagenesis and functional analysis, we characterized six residues that are required specifically for signal transmission; their mutation interferes with fusion, although still allowing efficient F-protein processing and cell surface transport. One residue is located adjacent to the fusion peptide, four line a cavity in the base of the F-trimer head, while the sixth residue is located near this cavity. Hydrophobic interactions in the cavity sustain the fusion process and contacts with H. The cavity is flanked by two different subunits of the F-trimer. Tetrameric H-stalks may be lodged in apposed cavities of two F-trimers. Because these insights are based on a PIV5 homology model, the signal receipt mechanism may be conserved among paramyxoviruses.
Differential Regulation of Brain-Derived Neurotrophic Factor in Term and Preterm Preeclampsia

Our earlier studies in preeclampsia (PE) suggest a causal relationship between altered angiogenic factors and birth outcomes. Recent studies suggest that brain-derived neurotrophic factor (BDNF) can stimulate angiogenesis. The present study examines the levels of maternal and cord BDNF in women with PE (n = 106; full term [n = 60] and preterm [n = 46]) and normotensive women (n = 95; control) delivering at term. Maternal BDNF levels were lower (P < .05) in women with PE when compared to normotensive women. Cord BDNF levels were higher (P < .01) in women with PE delivering at term, while it was lower (P < .01) in women delivering preterm. Maternal BDNF levels were negatively associated with systolic and diastolic blood pressure (P < .01 for both). Our data for the first time suggest a possible role for BDNF in the pathophysiology of PE. Differential regulation of cord BDNF levels in preterm PE suggests a need to follow-up children to assess the neurodevelopmental effects in later life.
Javert: fully automatic mining of general temporal properties from dynamic traces

Program specifications are important for many tasks during software design, development, and maintenance. Among these, temporal specifications are particularly useful. They express formal correctness requirements of an application's ordering of specific actions and events during execution, such as the strict alternation of acquisition and release of locks. Despite their importance, temporal specifications are often missing, incomplete, or described only informally. Many techniques have been proposed that mine such specifications from execution traces or program source code. However, existing techniques mine only simple patterns, or they mine a single complex pattern that is restricted to a particular set of manually selected events. There is no practical, automatic technique that can mine general temporal properties from execution traces. In this paper, we present Javert, the first general specification mining framework that can learn, fully automatically, complex temporal properties from execution traces. The key insight behind Javert is that real, complex specifications can be formed by composing instances of small generic patterns, such as the alternating pattern ((ab)) and the resource usage pattern ((ab c)). In particular, Javert learns simple generic patterns and composes them using sound rules to construct large, complex specifications. We have implemented the algorithm in a practical tool and conducted an extensive empirical evaluation on several open source software projects. Our results are promising; they show that Javert is scalable, general, and precise. It discovered many interesting, nontrivial specifications in real-world code that are beyond the reach of existing automatic techniques.
Transgenic Expression of Bcl-2 Modulates Energy Metabolism, Prevents Cytosolic Acidification During Ischemia, and Reduces Ischemia/Reperfusion Injury

The antiapoptotic protein Bcl-2 is targeted to the mitochondria, but it is uncertain whether Bcl-2 affects only myocyte survival after ischemia, or whether it also affects metabolic functions of mitochondria during ischemia. Hearts from mice overexpressing human Bcl-2 and from their wild-type littermates (WT) were subjected to 24 minutes of global ischemia followed by reperfusion. During ischemia, the decrease in pHi and the initial rate of decline in ATP were significantly reduced in Bcl-2 hearts compared with WT hearts (P <0.05). The reduced acidification during ischemia was dependent on the activity of mitochondrial F1F0-ATPase. In the presence of oligomycin (Oligo), an F1F0-ATPase inhibitor, the decrease in pHi was attenuated in WT hearts, but in Bcl-2 hearts, Oligo had no additional effect on pHi during ischemia. Likewise, addition of Oligo to WT hearts slowed the rate of decline in ATP during ischemia to a level similar to that observed in Bcl-2 hearts, but addition of Oligo had no significant effect on the rate of decline in ATP in Bcl-2 hearts during ischemia. These data are consistent with Bcl-2–mediated inhibition of consumption of glycolytic ATP. Furthermore, mitochondria from Bcl-2 hearts have a reduced rate of consumption of ATP on uncoupler addition. This could be accomplished by limiting ATP entry into the mitochondria through the voltage-dependent anion channel, and/or the adenine nucleotide transporter, or by direct inhibition of the F1F0-ATPase. Immunoprecipitation showed greater interaction between Bcl-2 and voltage-dependent anion channel during ischemia. These data indicate that Bcl-2 modulation of metabolism contributes to cardioprotection.
A Model Evaluation of Biological Effects on Seasonal Variation of Air–Sea CO2 Flux in the Yellow and East China Seas

ABSTRACT Based on a coupled physical-biogeochemical model of the Yellow and East China Seas (YECS), the influence of biological activity on the seasonal variation of the air–sea CO2 flux is evaluated. The solution of a sensitivity experiment that excludes biological activity is compared with that of a reference experiment that includes the full processes. The comparison reveals that biological activity results in a much stronger seasonal variation of surface dissolved inorganic carbon (DIC) and, hence, the ratio of total alkalinity to DIC in the northern parts of the YECS. The increased ratio resulting from biological DIC consumption contributes to the undersaturated partial pressure of CO2 at the sea surface with respect to the atmosphere, causing the central Yellow Sea in summer and autumn to shift from being a CO2 source to a sink; this same shift also occurs over the Changjiang Bank in summer. In the southern YECS, the biological effect is relatively weak. The comparison further reveals that low water temperature, instead of biological activity, is the dominant factor causing the YECS to become a carbon sink in spring. The biological effect on the variation of DIC (both at the surface and in the water column) differs greatly among the three representative regions of the YECS because of differences in primary production and hydrodynamic conditions. Particle-tracking simulations quantify the regional difference in horizontal advection. In the northern region, weaker horizontal advection causes the longer residence time of low DIC water induced by biological consumption. Over the entire YECS, biological activity contributes to about one-third of the total annual absorption of atmospheric CO2.
Marine Mammal Impacts in Exploited Ecosystems: Would Large Scale Culling Benefit Fisheries?

Competition between marine mammals and fisheries for marine resources—whether real or perceived—has become a major issue for several countries and in international fora. We examined trophic interactions between marine mammals and fisheries based on a resource overlap index, using seven Ecopath models including marine mammal groups. On a global scale, most food consumed by marine mammals consisted of prey types that were not the main target of fisheries. For each ecosystem, the primary production required (PPR) to sustain marine mammals was less than half the PPR to sustain fisheries catches. We also developed an index representing the mean trophic level of marine mammal's consumption (TLQ) and compared it with the mean trophic level of fisheries' catches (TLC). Our results showed that overall TLQ was lower than TLC (2.88 versus 3.42). As fisheries increasingly exploit lower-trophic level species, the competition with marine mammals may become more important. We used mixed trophic impact analysis to evaluate indirect trophic effects of marine mammals, and in some cases found beneficial effects on some prey. Finally, we assessed the change in the trophic structure of an ecosystem after a simulated extirpation of marine mammal populations. We found that this lead to alterations in the structure of the ecosystems, and that there was no clear and direct relationship between marine mammals' predation and the potential catch by fisheries. Indeed, total biomass, with no marine mammals in the ecosystem, generally remained surprisingly similar, or even decreased for some species.
Neonatal maternal separation alters adult eyeblink conditioning and glucocorticoid receptor expression in the interpositus nucleus of the cerebellum

Neonatal maternal separation alters learning and memory. Glucocorticoids also modulate adult learning and memory, and neonatal maternal separation alters forebrain glucocorticoid receptor (GR) concentrations. We used eyeblink classical conditioning to assess the effect of neonatal maternal separation on associative learning. We assessed delay eyeblink conditioning, GR expression, and total neuron number in the interpositus nucleus, a critical site of plasticity in eyeblink conditioning, in adult rats that had undergone either standard animal facilities rearing, handling for 15 min, or maternal separation for either 15 or 60 min per day on postnatal days 2–14. At 2–3 months of age, delay eyeblink classical conditioning was assessed. Brains were processed for GR immunohistochemistry, and GR expression in the interpositus nucleus was assessed using a computer‐based densitometry system. Neuron counts and nuclear volumes were obtained from an alternate series of thionin‐stained sections. Maternal separation significantly impaired eyeblink conditioning in male but not female rats. Handling and maternal separation did not significantly affect interpositus neuron number and volume. However, prolonged maternal separation significantly increased GR expression in the posterior interpositus in males, and increases were correlated with eyeblink conditioning. In female rats, maternal separation and handling did not significantly alter interpositus neuron number, volume, or GR protein expression, and GR expression did not correlate with eyeblink conditioning. Thus, neonatal maternal separation produces adult deficits in eyeblink conditioning and alterations in GR expression in its neural substrate in a sex‐dependent manner. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Philos. Trans. R Universal Turing Machine

The networking solution to DHTs is defined not only by the refinement of active networks, but also by the confusing need for simulated annealing. After years of significant research into the location-identity split, we verify the investigation of IPv4, which embodies the typical principles of pipelined machine learning. We motivate a heuristic for the exploration of semaphores, which we call Sun.
A novel bipartite mode of binding of M. smegmatis topoisomerase I to its recognition sequence.

We have investigated interaction of Mycobacterium smegmatis topoisomerase I at its specific recognition sequence. DNase I footprinting demonstrates a large region of protection on both the scissile and non-scissile strands of DNA. Methylation protection and interference analyses reveal base-specific contacts within the recognition sequence. Missing contact analyses reveal additional interactions with the residues in both single and double-stranded DNA, and hence underline the role for the functional groups associated with those bases. These interactions are supplemented by phosphate contacts in the scissile strand. Conformation specific probes reveal protein-induced structural distortion of the DNA helix at the T-A-T-A sequence 11 bp upstream to the recognition sequence. Based on these footprinting analyses that define parameters of topoisomerase I-DNA interactions, a model of topoisomerase I binding to its substrate is presented. Within the large protected region of 30 bp, the enzyme makes direct contact at two locations in the scissile strand, one around the cleavage site and the other 8-12 bases upstream. Thus the enzyme makes asymmetric recognition of DNA and could carry out DNA relaxation by either of the two proposed mechanisms: enzyme bridged and restricted rotation.
Bayesian inference of visual motion boundaries

This chapter addresses an open problem in visual motion analysis, the estimation of image motion in the vicinity of occlusion boundaries. With a Bayesian formulation, local image motion is explained in terms of multiple, competing, nonlinear models, including models for smooth (translational) motion and for motion boundaries. The generative model for motion boundaries explicitly encodes the orientation of the boundary, the velocities on either side, the motion of the occluding edge over time, and the appearance/disappearance of pixels at the boundary. We formulate the posterior probability distribution over the models and model parameters, conditioned on the image sequence. Approximate inference is achieved with a combination of tools: A Bayesian filter provides for online computation; factored sampling allows us to represent multimodal non-Gaussian distributions and to propagate beliefs with nonlinear dynamics from one time to the next; and mixture models are used to simplify the computation of joint prediction distributions in the Bayesian filter. To efficiently represent such a high-dimensional space, we also initialize samples using the responses of a low-level motion-discontinuity detector. The basic formulation and computational model provide a general probabilistic framework for motion estimation with multiple, nonlinear models.
Expression of CHOP in Squamous Tumor of the Uterine Cervix

Background High-risk human papillomavirus (HR-HPV) infection and abnormal p53 expression are closely involved in carcinogenesis of squamous cell carcinoma (SqCC) of uterine cervix. Recent studies have suggested that virus-induced endoplasmic reticulum (ER) stress modulates various cell survival and cell death signaling pathways. The C/EBP homologous protein (CHOP) is associated with ER stress-mediated apoptosis and is also involved in carcinogenesis of several human cancers. We hypothesized that CHOP is involved in the carcinogenesis of uterine cervical cancer in association with HR-HPV and/or p53. Methods Immunohistochemistry was used to analyze CHOP and p53 protein expression of tissue sections from 191 patients with invasive cancer or preinvasive lesions of the uterine cervix (61 cases of SqCC, 66 cases of cervical intraepithelial neoplasia [CIN] III, and 64 cases of CIN I). Results CHOP was expressed in 59.4% of CIN I, 48.5% of CIN III, and 70.5% of SqCC cases. It was also significantly more frequent in invasive SqCC than in preinvasive lesions (p=0.042). Moreover, CHOP expression significantly correlated with HR-HPV infection and p53 expression (p=0.009 and p=0.038, respectively). Conclusions Our results suggest that CHOP is involved in the carcinogenesis of the uterine cervix SqCC via association with HR-HPV and p53.
Pre–T Cell Receptor (Tcr) and Tcr-Controlled Checkpoints in T Cell Differentiation Are Set by Ikaros

T cell differentiation relies on pre–T cell receptor (TCR) and TCR signaling events that take place at successive steps of the pathway. Here, we show that two of these T cell differentiation checkpoints are regulated by Ikaros. In the absence of Ikaros, double negative thymocytes can differentiate to the double positive stage without expression of a pre-TCR complex. Subsequent events in T cell development mediated by TCR involving transition from the double positive to the single positive stage are also regulated by Ikaros. Nonetheless, in Ikaros-deficient thymocytes, the requirement of pre-TCR expression for expansion of immature thymocytes as they progress to the double positive stage is still maintained, and the T cell malignancies that invariably arise in the thymus of Ikaros-deficient mice are dependent on either pre-TCR or TCR signaling. We conclude that Ikaros regulates T cell differentiation, selection, and homeostasis by providing signaling thresholds for pre-TCR and TCR.