Miracle-dz/UniFAR-FTUs huggingface dataset:
How Integrated Management Strategies Promote Protein Quality of Cotton Embryos: High Levels of Soil Available N, N Assimilation and Protein Accumulation Rate

Cottonseed is widely used as a source of ruminant feed and for industrial purposes. Therefore, there is a tremendous need to improve the nutritional value of cotton embryos. In this study, a conventional management (CM) and two integrated cotton management strategies (IMS1, IMS2) were performed at two soil fertility levels to study the relationships among soil N, N assimilation, embryonic protein accumulation and protein quality. The levels of proteins, essential amino acids, and semi-essential amino acids, especially those of glutamate, lysine, and methionine, were higher in IMS1 and IMS2 embryos than in CM embryos. These changes were significantly positively correlated with the soil-available N content, glutamine synthetase activity and peak value of protein accumulation rate and were negatively correlated with the free amino acid level. These results illustrated that integrated management strategies, especially the rates and timing of N application, raise the level of soil available N, which is beneficial for N assimilation in developing cotton embryos. The protein content was limited by the rate of protein accumulation rather than by the free amino acid content. The combination of target yield fertilization, a growth-driven N application schedule, a high plant density and the seedling raising with bio-organic fertilizer can substantially improve protein quality in cotton embryos, especially at a soil with low soil organic matter and total nitrogen.
Fast vignetting reduction method for digital still camera

The effect of vignetting is undesirable in image processing and analysis. It cause fall-off of pixel intensity from centre towards edges of the image. In this paper, we propose a new procedure of fast vignetting reduction based on two images acquired with different camera/lens settings. The change of lens aperture or focal length will also change the effect of vignetting in images. These differences are used to estimate a vignetting function, which is used for vignetting reduction. The obtained image after vignetting reduction is not significantly different from the image without vignetting.
VLSI implementation of Piecewise Approximated antilogarithmic converter

Applications such as signal and image processing require a dedicated hardware unit for logarithmic conversion due to the large delay involved in software techniques which make them unsuitable for real time applications. In this paper, Piecewise Approximation approach based on Linear Programming technique has been proposed for antilogarithmic converter design, which achieves minimum total relative approximation error due to optimized coefficients obtained. Multipliers have been avoided in the design by utilizing shifters and adders which reduces design complexity. Hardware efficiency and high speed operation are feasible using a small LUT to store the coefficient values. The area and power requirements have been analyzed for the VLSI implementation using Cadence Encounter RTL compiler.
Genome-scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle

Bacterial cells display both spatial and temporal organization, and this complex structure is known to play a central role in cellular function. Although nearly one‐fifth of all proteins in Escherichia coli localize to specific subcellular locations, fundamental questions remain about how cellular‐scale structure is encoded at the level of molecular‐scale interactions. One significant limitation to our understanding is that the localization behavior of only a small subset of proteins has been characterized in detail. As an essential step toward a global model of protein localization in bacteria, we capture and quantitatively analyze spatial and temporal protein localization patterns throughout the cell cycle for nearly every protein in E. coli that exhibits nondiffuse localization. This genome‐scale analysis reveals significant complexity in patterning, notably in the behavior of DNA‐binding proteins. Complete cell‐cycle imaging also facilitates analysis of protein partitioning to daughter cells at division, revealing a broad and robust assortment of asymmetric partitioning behaviors.
The regional willingness to pay for a reduced eutrophication in the Stockholm archipelago

The benefits of reduced eutrophication effects in the Stockholm archipelago, Sweden, are estimated by an application of the contingent valuation method. The mean willingness to pay per adult resident in the counties of Stockholm and Uppsala is estimated to SEK 436-725 per year. This corresponds to a population estimate of SEK 506-842 million per year.
Matching Glass-Forming Ability with the Density of the Amorphous Phase

The density of the amorphous phase of metals is generally thought to be related to glass formation, but this correlation has not been demonstrated experimentally to date. In this work, systematic deflection measurements using microcantilevers and a combinatorial deposition method show a correlation between glass-forming ability and the density change upon crystallization over a broad compositional range in the copper-zirconium binary system. Distinct peaks in the density of the amorphous phase were found to correlate with specific maxima in the critical thickness for glass formation. Our findings provide quantitative data for the development of structural models of liquids that are readily quenched to the amorphous state. The experimental method developed in this work can facilitate the search for new glass-forming alloys.
Effect of Selective Cholinergic Denervation on the Serotonergic System: Implications for Learning and Memory

The cholinergic system has been widely implicated in cognitive processes and cholinergic loss is a classical hallmark in Alzheimer disease. Increasing evidence supports a role of the serotonergic system in cognition, possibly through a modulation of cholinergic activity. We compared selective cholinergic denervation by administration of the immunotoxin 192 IgG-saporin in the nucleus basalis of Meynert (NBM) with intracerebroventricular (ICV) lesions of the basal forebrain in male rats 7 days after lesioning. NBM lesions induced significant changes in cholinergic markers in the frontal cortex, whereas ICV lesions produced significant decreases in cholinergic markers both in the frontal cortex and hippocampus. Only ICV lesions lead to memory impairments in passive avoidance and Morris water maze tasks. Both models lead to reductions of serotonin levels in the frontal cortex. Similar changes in 5-hydroxytriptophan levels were observed, suggesting a downregulation of the rate-limiting enzyme for the synthesis of serotonin along with the cholinergic deficit. Neither 5-HT1A nor 5-HT1B receptors seem to mediate this process. These data imply that the serotonergic system in the frontal cortex can compensate for diminished cholinergic function and support the investigation of the serotonergic system as a therapeutic target to treat Alzheimer disease.
Impact of preoperative symptoms on survival after surgical correction of organic mitral regurgitation: rationale for optimizing surgical indications.

BACKGROUND Surgical correction of mitral regurgitation in patients with no or mild symptoms remains controversial, particularly because the impact of preoperative symptoms on postoperative outcome is unknown. METHODS AND RESULTS The long-term outcome of 478 patients with organic mitral regurgitation (199 in NYHA functional class I/II and 279 in class III/IV before surgery) operated on between 1984 and 1991 was analyzed. In patients in NYHA class I/II before surgery compared with those in class III/IV, postoperative long-term survival was higher (at 10 years, 76+/-5% versus 48+/-4%, P<0.0001), with lower operative mortality (0.5% versus 5.4%, P=0.003) and better late survival (P<0.0001). Comparison of observed and expected survival showed identical curves in patients in class I/II before surgery (P=0.18), whereas excess mortality was observed in patients in class III/IV before surgery (P<0.0001). Excess mortality associated with severe symptoms was also confirmed in all subgroups (all P<0.003) and in multivariate analysis (P=0.0036; adjusted hazard ratio [95% CI], 1.81 [1.21 to 2.70]). CONCLUSIONS In patients with organic mitral regurgitation, preoperative functional class III/IV symptoms are associated with excess short- and long-term postoperative mortality independently of all baseline characteristics. These data should lead to consideration of surgical correction of severe organic mitral regurgitation when no or minimal symptoms are present in patients at low operative risk, especially if repair is feasible.
Improvements and Extensions of Low-Rate Turbo-Hadamard Codes

In this paper, we consider a number of system improvements that have been proposed for convolutional turbo codes, and apply them to turbo-Hadamard codes (THC). Our ndings are as follows. 1. Asymmetrical THC, employing diering constituent codes, improves the waterfall region performance compared to symmetrical THC. 2. Punctured THC have improved performance in both the waterfall and error o or regions, relative to non-punctured codes of the same rate. 3. An LDPC code, when serially concatenated with an inner THC code, can correct low weight errors to improve the error o or performance. 4. Parallel-schedule decoding of THC can converge signican tly faster than conventional serial-mode decoding, leading to a reduction in decoder complexity.
Reactivity to low‐flow as a potential determinant for brachial artery flow‐mediated vasodilatation

Previous studies have reported a vasoconstrictor response in the radial artery during a cuff‐induced low‐flow condition, but a similar low‐flow condition in the brachial artery results in nonuniform reactivity. This variable reactivity to low‐flow influences the subsequent flow‐mediated dilatation (FMD) response following cuff‐release. However, it is uncertain whether reactivity to low‐flow is important in data interpretation in clinical populations and older adults. This study aimed to determine the influence of reactivity to low‐flow on the magnitude of brachial artery FMD response in middle‐aged and older individuals with diverse cardiovascular risk profiles. Data were analyzed from 165 individuals, divided into increased cardiovascular risk (CVR: n = 115, 85M, 67.0 ± 8.8 years) and healthy control (CTRL: n = 50, 30M, 63.2 ± 7.2 years) groups. Brachial artery diameter and blood velocity data obtained from Doppler ultrasound were used to calculate FMD, reactivity to low‐flow and estimated shear rate (SR) using semiautomated edge‐detection software. There was a significant association between reactivity to low‐flow and FMD in overall (r = 0.261), CTRL (r = 0.410) and CVR (r = 0.189, all P < 0.05) groups. Multivariate regression analysis found that reactivity to low‐flow, peak SR, and baseline diameter independently contributed to FMD along with sex, the presence of diabetes, and smoking (total R2 = 0.450). There was a significant association between reactivity to low‐flow and the subsequent FMD response in the overall dataset, and reactivity to low‐flow independently contributed to FMD. These findings suggest that reactivity to low‐flow plays a key role in the subsequent brachial artery FMD response and is important in the interpretation of FMD data.
Agglomerative Mean-Shift Clustering

Mean-Shift (MS) is a powerful nonparametric clustering method. Although good accuracy can be achieved, its computational cost is particularly expensive even on moderate data sets. In this paper, for the purpose of algorithmic speedup, we develop an agglomerative MS clustering method along with its performance analysis. Our method, namely Agglo-MS, is built upon an iterative query set compression mechanism which is motivated by the quadratic bounding optimization nature of MS algorithm. The whole framework can be efficiently implemented in linear running time complexity. We then extend Agglo-MS into an incremental version which performs comparably to its batch counterpart. The efficiency and accuracy of Agglo-MS are demonstrated by extensive comparing experiments on synthetic and real data sets.
Evolutionary Dynamics of Co-Segregating Gene Clusters Associated with Complex Diseases

Background The distribution of human disease-associated mutations is not random across the human genome. Despite the fact that natural selection continually removes disease-associated mutations, an enrichment of these variants can be observed in regions of low recombination. There are a number of mechanisms by which such a clustering could occur, including genetic perturbations or demographic effects within different populations. Recent genome-wide association studies (GWAS) suggest that single nucleotide polymorphisms (SNPs) associated with complex disease traits are not randomly distributed throughout the genome, but tend to cluster in regions of low recombination. Principal Findings Here we investigated whether deleterious mutations have accumulated in regions of low recombination due to the impact of recent positive selection and genetic hitchhiking. Using publicly available data on common complex diseases and population demography, we observed an enrichment of hitchhiked disease associations in conserved gene clusters subject to selection pressure. Evolutionary analysis revealed that these conserved gene clusters arose by multiple concerted rearrangements events across the vertebrate lineage. We observed distinct clustering of disease-associated SNPs in evolutionary rearranged regions of low recombination and high gene density, which harbor genes involved in immunity, that is, the interleukin cluster on 5q31 or RhoA on 3p21. Conclusions Our results suggest that multiple lineage specific rearrangements led to a physical clustering of functionally related and linked genes exhibiting an enrichment of susceptibility loci for complex traits. This implies that besides recent evolutionary adaptations other evolutionary dynamics have played a role in the formation of linked gene clusters associated with complex disease traits.
Does the Quality of Hospital Treatment Vary by Days of the Week?

This paper investigates the relationship between health outcomes and variations in staffing levels as approximated by admissions on weekdays versus admissions on weekends. Because days of admission are potentially endogenous, we instrument on emergency admissions only, which are reasonably exogenous to the time of admission. Further, we introduce a direct measure for within-diagnosis variation in severity across days of admission to control for the unobservable selection of patients.We find that after controlling for patient heterogeneity and endogeneity of the day of admission there is still a significant variation in mortality rates between weekend and weekday admissions. Patients admitted during the weekend exhibit higher in-hospital mortality rates. We also find signs of premature discharge, as patients with short lengths of stay tend to exhibit higher probability to be readmitted as emergency cases.
Ectopic engrailed 1 expression in the dorsal midline causes cell death, abnormal differentiation of circumventricular organs and errors in axonal pathfinding.

A series of gain- or loss-of-function experiments performed in different vertebrate species have demonstrated that the Engrailed genes play multiple roles during brain development. In particular, they have been implicated in the determination of the mid/hindbrain domain, in cell proliferation and survival, in neurite formation, tissue polarization and axonal pathfinding. We have analyzed the consequences of a local gain of En function within or adjacent to the endogenous expression domain in mouse and chick embryos. In WEXPZ.En1 transgenic mice (Danielian, P. S. and McMahon, A. P. (1996) Nature 383, 332-334) several genes are induced as a consequence of ectopic expression of En1 in the diencephalic roof (but in a pattern inconsistent with a local di- to mes-encephalon fate change). The development of several structures with secretory function, generated from the dorsal neuroepithelium, is severely compromised. The choroid plexus, subcommissural organ and pineal gland either fail to form or are atrophic. These defects are preceded by an increase in cell death at the dorsal midline. Comparison with the phenotype of Wnt1(sw/sw) (swaying) mutants suggests that subcommissural organ failure is the main cause of prenatal hydrocephalus observed in both strains. The formation of the posterior commissure is also delayed, and errors in axonal pathfinding are frequent. In chick, ectopic expression of En by in ovo electroporation, affects growth and differentiation of the choroid plexus.
Lattice gauge theories and the AdS / CFT correspondence

This is the write-up of a set of lectures on the comparison between Lattice Gauge Theories and AdS/CFT results for the non-perturbative behaviour of non-supersymmetric Yang Mills theories. These notes are intended for students which are assumed not to be experts in L.G. T. For this reason the first part is devoted to a pedagogical introduction to the Lattice regularization of QCD. In the second part we discuss some basic features of the AdS/CFT correspondence and compare the results obtained in the non-supersymmetric limit with those obtained on the Lattice. We discuss in particular the behaviour of the string tension and of the glueball spectrum. Lectures delivered at the School of Theoretical Physics (S.N.F.T.), Parma, September 1999.
Foundations of observing dark energy dynamics with the Wilkinson Microwave Anisotropy Probe

Detecting dark energy dynamics is the main quest of current dark energy research. Addressing the issue demands a fully consistent analysis of cosmic microwave background, large-scale structure and SN-Ia data with multiparameter freedom valid for all redshifts. Here we undertake a ten parameter analysis of general dark energy confronted with the first year Wilkinson Microwave Anisotropy Probe, 2dF galaxy survey and latest SN-Ia data. Despite the huge freedom in dark energy dynamics there are no new degeneracies with standard cosmic parameters apart from a mild degeneracy between reionization and the redshift of acceleration, both of which effectively suppress small scale power. Breaking this degeneracy will help significantly in detecting dynamics, if it exists. Our best-fit model to the data has significant late-time evolution at z<1.5. Phantom models are also considered and we find that the best-fit crosses w =-1 which, if confirmed, would be a clear signal for radically new physics. Treatment of such rapidly varying models requires careful integration of the dark energy density usually not implemented in standard codes, leading to crucial errors of up to 5%. Nevertheless cosmic variance means that standard Lambda cold dark matter models are still a very good fit to the data and evidence for dynamics is currently very weak. Independent tests of reionization or the epoch of acceleration (e.g., integrated Sachs-Wolfelarge scale structure correlations) or reduction of cosmic variance at large scales (e.g., cluster polarization at high redshift) may prove key in the hunt for dynamics.
Discovery of Fur binding site clusters in Escherichia coli by information theory models

Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence walkers, which are visual depictions of predicted binding sites, frequently appeared in clusters that fit the footprints (∼83% coverage). This indicated that the model can accurately predict Fur binding. Within the clusters, individual walkers were separated from their neighbors by exactly 3 or 6 bases, consistent with models in which Fur dimers bind on different faces of the DNA helix. When the E. coli genome was scanned, we found 363 unique clusters, which includes all known Fur-repressed genes that are involved in iron metabolism. In contrast, only a few of the known Fur-activated genes have predicted Fur binding sites at their promoters. These observations suggest that Fur is either a direct repressor or an indirect activator. The Pseudomonas aeruginosa and Bacillus subtilis Fur models are highly similar to the E. coli Fur model, suggesting that the Fur–DNA recognition mechanism may be conserved for even distantly related bacteria.
Persistent Hyperactivity of Hippocampal Dentate Interneurons After a Silent Period in the Rat Pilocarpine Model of Epilepsy

Profile of GABAergic interneuron activity after pilocarpine-induced status epilepticus (SE) was examined in the rat hippocampal dentate gyrus by analyzing immediate early gene expression and recording spontaneous firing at near resting membrane potential (REM). SE for exact 2 h or more than 2 h was induced in the male Sprague-Dawley rats by an intraperitoneal injection of pilocarpine. Expression of immediate early genes (IEGs) was examined at 1 h, 1 week, 2 weeks or more than 10 weeks after SE. For animals to be examined at 1 h after SE, SE lasted for exact 2 h was terminated by an intraperitoneal injection of diazepam. Spontaneous firing at near the REM was recorded in interneurons located along the border between the granule cell layer and the hilus more than 10 weeks after SE. Results showed that both c-fos and activity-regulated cytoskeleton associated protein (Arc) in hilar GABAergic interneurons were up-regulated after SE in a biphasic manner; they were increased at 1 h and more than 2 weeks, but not at 1 week after SE. Ten weeks after SE, nearly 60% of hilar GABAergic cells expressed c-fos. With the exception of calretinin (CR)-positive cells, percentages of hilar neuronal nitric oxide synthase (nNOS)-, neuropeptide Y (NPY)-, parvalbumin (PV)-, and somatostatin (SOM)-positive cells with c-fos expression are significantly higher than those of controls more than 10 weeks after SE. Without the REM to be more depolarizing and changed threshold potential level in SE-induced rats, cell-attached recording revealed that nearly 90% of hilar interneurons fired spontaneously at near the REM while only 22% of the same cell population did so in the controls. In conclusion, pilocarpine-induced SE eventually leads to a state in which surviving dentate GABAergic interneurons become hyperactive with a subtype-dependent manner; this implies that a fragile balance between excitation and inhibition exists in the dentate gyrus and in addition, the activity-dependent up-regulation of IEGs may underlie plastic changes seen in some types of GABAergic cells in the pilocarpine model of epilepsy.