Miracle-dz/UniFAR-FTUs huggingface dataset:
The three-dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity.

The RNase 4 family is unique among RNase enzymes, displaying the highest level of sequence similarity and encompassing the shortest polypeptide chain. It is the only one showing high specificity. The human representative is an intracellular and plasma enzyme, first isolated from colon adenocarcinoma cell line HT-29. The crystal structures of human recombinant RNase 4, unliganded and in complex with d(Up), have been determined, revealing in the unique active site an explanation for the uridine specificity. Arg101, at a position not involved in catalysis in the other RNase enzymes, penetrates the enzyme moiety shaping the recognition pocket, a flip that is mediated by the interaction with the (shorter chain) C-terminal carboxylate group, providing an anchoring point for the O4 atom of the substrate uridine. The bulky Phe42 side-chain forces Asp80 to be in the chi1=-72.49 degrees rotamer, accepting a hydrogen bond from Thr44, further converting the latter into a hydrogen bond acceptor. This favours an interaction with the -NH-donor group of uridine at position 3 over that with the =N-acceptor of cytidine. The two chemical groups that distinguish uracyl from cytosine are used by the enzyme to discriminate between these two bases.
A Novel LBP-1-mediated Restriction of HIV-1 Transcription at the Level of Elongation in Vitro(*)

The cellular factor, LBP-1, can repress HIV-1 transcription by preventing the binding of TFIID to the promoter. Here we have analyzed the effect of recombinant LBP-1 on HIV-1 transcription in vitro by using a “pulse-chase” assay. LBP-1 had no effect on initiation from a preformed preinitiation complex and elongation to position +13 (“pulse”). However, addition of LBP-1 after RNA polymerase was stalled at +13 strongly inhibited further elongation (“chase”) by reducing RNA polymerase processivity. Severe mutations of the high affinity LBP-1 binding sites between −4 and +21 did not relieve the LBP-1-dependent block. However, LBP-1 could bind independently to upstream low affinity sites (−80 to −4), suggesting that these sites mediate the effect of LBP-1 on elongation. These results demonstrate a novel function of LBP-1, restricting HIV-1 transcription at the level of elongation. In addition, Tat was found to suppress the antiprocessivity effect of LBP-1 on HIV-1 transcription in nuclear extracts. These findings strongly suggest that LBP-1 may provide a natural mechanism for restricting the elongation of HIV-1 transcripts and that this may be a target for the action of Tat in enhancing transcription.
Bateman's Principle in Cooperatively Breeding Vertebrates: The Effects of Non-breeding Alloparents on Variability in Female and Male Reproductive Success1

Abstract The sex-specific slopes of Bateman's gradients have important implications for understanding animal mating systems, including patterns of sexual selection and reproductive competition. Intersexual differences in the fitness benefits derived from mating with multiple partners are expected to yield distinct patterns of reproductive success for males and females, with variance in direct fitness predicted to be greater among males. These analyses assume that typically all adults are reproductive and that failure to produce offspring is non-adaptive. Among some species of cooperatively breeding birds and mammals, however, non-breeding adult alloparents are common and may comprise the majority of individuals in social groups. The presence of a large number of non-breeding adults, particularly when coupled with greater social suppression of reproduction among females, may alter the relative variance in direct fitness between the sexes, thereby generating an apparent contradiction to Bateman's Paradigm. To explore quantitatively the effects of non-breeding alloparents on variance in reproductive success, we used genetic estimates of parentage and reproductive success drawn from the literature to calculate the relative variability in direct fitness for females and males in alloparental and “other” societies of birds and mammals. Our analyses indicate that in mammals and, to a lesser extent, in birds, variability in direct fitness is greater among females in species characterized by the presence of non-breeding alloparents. These data suggest that social interactions, including social suppression of reproduction, are powerful determinants of individual direct fitness that may modify sex-specific patterns of reproductive variance from those described by Bateman.
Modified Methods of Generating Saliency Maps Based on Superpixels

Various types of approaches that can model a human visual attention have been already proposed. However, a model that could perfectly simulate the human perception and methods of computer prediction of human visual attention belongs to one of the high focused research areas. Our work is aimed at methods of generating a saliency map which will detect the areas in the picture that could most likely attract a human attention. The basis of our work is method of saliency detection using superpixels published by authors Z. Liu, O. Meur and S. Luo. Several modifications of this method with the aim to improve the results have been proposed, tested and evaluated in our experiments. In this paper, we present our proposed modification based on border prior and statistical evaluation of the saliency central position in the used dataset. This center position will be expressed using a fitted Gaussian function. Results of all experiments are evaluated and presented in the following paper.
Combining genetic algorithm and compressed sensing for features and operators selection in symbolic regression

Symbolic-inference methods have recently found a broad application in materials science. In particular, the Sure-Independence Screening and Sparsifying Operator (SISSO) performs symbolic regression and classification by adopting compressed sensing for the selection of an optimized subset of features and mathematical operators out of a given set of candidates. However, SISSO becomes computationally unpractical when the set of candidate features and operators exceeds the size of few tens. In the present work, we combine SISSO with a genetic algorithm (GA) for the global search of the optimal subset of features and operators. We demonstrate that GA-SISSO efficiently finds more accurate predictive models than the original SISSO, due to the possibility to access a larger input feature and operator space. GA-SISSO was applied for the search of the model for the prediction of carbon-dioxide adsorption energies on semiconductor oxides. The obtained with GA-SISSO model has much higher accuracy compared to models previously discussed in the literature (based solely on the O 2p-band center). The analysis of features importance shows that, besides the O 2p-band center, the contribution of the electrostatic potential above adsorption sites and the surface formation energies are also important.
Stability Analysis of Two-Terminal VSC-HVDC Systems Using the Net-Damping Criterion

This paper performs a frequency-domain investigation in two-terminal voltage-source-converter-HVDC (VSC-HVDC) systems, focusing on the use of the net-damping criterion to investigate poorly damped conditions and closed-loop stability. The system is represented as a feedback interconnection of two subsystems, defined in this paper as: 1) a dc-grid input impedance and 2) a VSC input admittance. The damping characteristics of the two subsystems are defined at critical frequencies and their separate contribution to the closed-loop stability is assessed by the net-damping criterion. A variety of study cases demonstrates the effectiveness of the latter as a powerful tool for stability investigation, while a correlation has been derived between the net-damping value and the damping factor of the poorly damped poles of the system.
Ensuring Disturbance Rejection Performance by Synthesizing Grid-Following and Grid-Forming Inverters in Power Systems

To satisfy dynamic requirements of power systems, it is imperative for grid-tied inverters to ensure good disturbance rejection performance (DRP) under variable grid conditions. This letter discovers and theoretically proves that for general networks, synthesizing grid-following (GFL) inverters and grid-forming (GFM) inverters can always more effectively ensure the DRP of multiple inverters, as compared to homogeneous inverter-based systems that solely utilize either GFL or GFM inverters. The synthesis of GFL inverters and GFM inverters can concurrently increase the smallest eigenvalue and decrease the largest eigenvalue of the network grounded Laplacian matrix. This can be equivalent to rematching the proper short-circuit ratio (SCR) for GFL and GFM inverters, thereby ensuring the DRP of inverters both in weak and strong grids. The results reveal the necessity of synthesizing diverse inverter control schemes from the network-based perspective. Sensitivity function-based tests and real-time simulations validate our results.
Cryptanalysis aspects in 3-D watermarking

3-D object security is increasingly brought to the attention of the public by the expansion of new multimedia technologies such as the 3-D printing. In the development of crypto-security systems of 3-D objects, we can identify two major directions represented by the cryptography and digital watermarking. A good security system has to be format compliant, has to preserve the original bit rate and, whenever possible, it should be reversible. Watermarking methodology has the advantage of ensuring that the embedded hidden message can be verified at any processing stage such as the transmission, storage and when visualizing the embedding media. In this paper, we review the previous work in 3-D security and analyze the crypto-security of a 3-D watermarking method which embeds information by mesh surface distortion minimization. Then, we discuss future avenues of research by presenting emerging applications.
Deep Regression Forests for Age Estimation

Age estimation from facial images is typically cast as a nonlinear regression problem. The main challenge of this problem is the facial feature space w.r. t. ages is inhomogeneous, due to the large variation in facial appearance across different persons of the same age and the non-stationary property of aging patterns. In this paper, we propose Deep Regression Forests (DRFs), an end-to-end model, for age estimation. DRFs connect the split nodes to a fully connected layer of a convolutional neural network (CNN) and deal with inhomogeneous data by jointly learning input-dependant data partitions at the split nodes and data abstractions at the leaf nodes. This joint learning follows an alternating strategy: First, by fixing the leaf nodes, the split nodes as well as the CNN parameters are optimized by Back-propagation; Then, by fixing the split nodes, the leaf nodes are optimized by iterating a step-size free update rule derived from Variational Bounding. We verify the proposed DRFs on three standard age estimation benchmarks and achieve state-of-the-art results on all of them.
Orbital-ordering driven structural distortion in metallic SrCrO3

In contrast to the previous reports that the divalent perovskite ${\text{SrCrO}}_{3}$ was believed to be cubic structure and nonmagnetic metal, recent measurements suggest coexistence of majority tetragonally distorted weak antiferromagnetic phase and minority nonmagnetic cubic phase. Within the local (spin) density approximation [L(S)DA] our calculations confirm that a slightly tetragonally distorted phase indeed is energetically favored. Using the correlated band theory method $(\text{LDA}+\text{Hubbard}\text{ }U)$ as seems to be justified by the unusual behavior observed in ${\text{SrCrO}}_{3}$, above the critical value ${U}_{c}=4\text{ }\text{eV}$ only the distorted phase undergoes an orbital-ordering transition, resulting in ${t}_{2g}^{2}\ensuremath{\rightarrow}{d}_{xy}^{1}{({d}_{xz}{d}_{yz})}^{1}$ corresponding to the filling of the ${d}_{xy}$ orbital but leaving the other two degenerate. The Fermi surfaces of the cubic phase are simple with nesting features, although the nesting wave vectors do not correlate with known data. This is not uncommon in perovskites; the strongly directional $d\ensuremath{-}d$ bonding often leads to boxlike Fermi surfaces and either the nesting is not strong enough or the matrix elements are not large enough to promote instabilities. Fixed spin moment calculations indicate the cubic structure is just beyond a ferromagnetic Stoner instability $[IN(0)\ensuremath{\approx}1.1]$ in L(S)DA and that the energy is unusually weakly dependent on the moment out to $1.5{\ensuremath{\mu}}_{B}/\text{Cr}$ (varying only by 11 meV/Cr), reflecting low-energy long-wavelength magnetic fluctuations. We observe that this system shows strong magnetophonon coupling (change in Cr local moment is $\ensuremath{\sim}7.3{\ensuremath{\mu}}_{B}/\text{\AA{}}$) for breathing phonon modes.
The selective PPARgamma antagonist GW9662 reverses the protection of LPS in a model of renal ischemia-reperfusion.

BACKGROUND We have recently reported that pretreatment of rats with endotoxin (lipopolysaccharide, LPS) and selective agonists of the nuclear receptor peroxisome proliferator-activated receptor-gamma (PPARgamma) protect the kidney against ischemia/reperfusion (I/R) injury. Here we investigate the hypothesis that the renoprotective effects of LPS may be due to an enhanced formation of endogenous ligands of PPARgamma, rather than an up-regulation of PPARgamma expression. METHODS Rats were pretreated with LPS (1 mg/kg, IP, 24 hours prior to ischemia) in the absence (control) or presence of the selective PPARgamma antagonist GW9662 (1 mg/kg, IP, 24 and 12 hours prior to ischemia). Twenty-four hours after injection of LPS, rats were subjected to 60 minutes of bilateral renal ischemia, followed by 6 hours of reperfusion. Serum and urinary indicators of renal injury and dysfunction were measured, specifically serum creatinine, aspartate aminotransferase, and gamma-glutamyl-transferase, creatinine clearance, urine flow, and fractional excretion of sodium. Kidney PPARgamma1 mRNA levels were determined by reverse transcriptase-polymerase chain reaction. RESULTS Pretreatment with LPS significantly attenuated all markers of renal injury and dysfunction caused by I/R. Most notably, GW9662 abolished the protective effects of LPS. Additionally, I/R caused an up-regulation of kidney PPARgamma1 mRNA levels compared to sham animals, which were unchanged in rats pretreated with LPS. CONCLUSION We document here for the first time that endogenous ligands of PPARgamma may contribute to the protection against renal I/R injury afforded by LPS pretreatment in the rat.
Comparison between effects of various partial inferior turbinectomy options on nasal airflow: a computer simulation study

Partial inferior turbinectomy is typically performed on patients suffering from chronic nasal obstruction due to hypertrophy of inferior turbinates and is refractory to other more conservative treatments. The effects of the various options of incision performed on the inferior turbinate in terms of the resulting nasal airflow pattern are examined using computational fluid mechanics. The pressure drops across the severely blocked nose and healthy nose models were found to be 32.3 and 12.3 Pa, respectively, whereas the pressure drops across the nasal cavity following one-third turbinate resection, total turbinate resection and front-end resection were obtained as 5.8, 6.1 and 30.5 Pa correspondingly. Based on the total pressure drop results, the one-third resection option seems to be better than the front-end surgery and the total turbinate resection.
The effect of budesonide on orthodontic induced root resorption

Background: The aim of this study was to evaluate the hypothesis that budesonide increases the susceptibility of teeth to root resorption during the course of orthodontic treatment. Materials and Methods: A randomized controlled trial design (animal study) was employed. Budesonide was administered in test group for 14 days during which orthodontic force was applied to upper right molar. Afterwards, root resorption was measured on mesio-cervical and disto-apical parts of the mesial root on transverse histological sections. ANOVA and Bonfferoni tests were used. Statistical significance was considered to be P ≤ 0.05. Results: In general, the subgroups in which the force was applied showed significantly greater root resorption. Where force was applied there was no significant difference, whether budesonide was administered or not. While where there was no force, a group who received budesonide showed significantly greater root resorption than the other, unless at the coronal level where the difference was not significant. Conclusion: Within the limitations of this study, it seems budesonide could increase root resorption, but in the presence of orthodontic force this effect is negligible.
Daytime Solar Heating Controls Downy Mildew Peronospora belbahrii in Sweet Basil

The biotrophic oomycete Peronospora belbahrii causes a devastating downy mildew disease in sweet basil. Due to the lack of resistant cultivars current control measures rely heavily on fungicides. However, resistance to fungicides and strict regulation on their deployment greatly restrict their use. Here we report on a ‘green’ method to control this disease. Growth chamber studies showed that P. belbahrii could hardly withstand exposure to high temperatures; exposure of spores, infected leaves, or infected plants to 35-45°C for 6-9 hours suppressed its survival. Therefore, daytime solar heating was employed in the field to control the downy mildew disease it causes in basil. Covering growth houses of sweet basil already infected with downy mildew with transparent infra-red-impermeable, transparent polyethylene sheets raised the daily maximal temperature during sunny hours by 11-22°C reaching 40-58°C (greenhouse effect). Such coverage, applied for a few hours during 1-3 consecutive days, had a detrimental effect on the survival of P. belbahrii: killing the pathogen and/or suppressing disease progress while enhancing growth of the host basil plants.
Multi-Objective Evolutionary Optimization of Probabilistic Neural Network

In this paper the major principles to effectively design a parameter-less, multi-objective evolutionary algorithm that optimizes a population of probabilistic neural network (PNN) classifier models are articulated; PNN is an example of an exemplar-based classifier. These design principles are extracted from experiences, discussed in this paper, which guided the creation of the parameter-less multi-objective evolutionary algorithm, named MO-EPNN (multi-objective evolutionary probabilistic neural network). Furthermore, these design principles are also corroborated by similar principles used for an earlier design of a parameter-less, multi-objective genetic algorithm used to optimize a population of ART (adaptive resonance theory) models, named MO-GART (multi-objective genetically optimized ART); the ART classifier model is another example of an exemplar-based classifier model. MO-EPNN’s performance is compared to other popular classifier models, such as SVM (Support Vector Machines) and CART (Classification and Regression Trees), as well as to an alternate competitive method to genetically optimize the PNN. These comparisons indicate that MO-EPNN’s performance (generalization on unseen data and size) compares favorably to the aforementioned classifier models and to the alternate genetically optimized PNN approach. MO-EPPN’s good performance, and MO-GART’s earlier reported good performance, both of whose design relies on the same principles, gives credence to these design principles, delineated in this paper.
Highly Active Antiretroviral Therapy (HAART) and Metabolic Complications

The overwhelming impact the Human Immunodeficiency Virus (HIV) has on the world is undeniable – by the end of 2009 there were 33.3 million people living with HIV in the world, with 1.8 million deaths in that year alone (WHO 2010). In addition, the high rate of deaths can be directly attributed to the lack of available medications – only 36% of the infected population received adequate antiretroviral therapy (WHO 2009). Besides the known political and monetary issues at hand, the multiple number of HIV virus subtypes and subsubtypes that have been described are overwhelming pharmaceutical availability. In fact, most research completed on HIV therapies has occurred, and continues to occur, in Europe and America, targeting the HIV-1 strain, although much of the world population is also afflicted by HIV-2. To combat viral strain mutations, Highly Active Antiretroviral Therapy (HAART) has increased in complexity and effectively decreased deaths from opportunistic infections in those that are candidates for this treatment. However, these advances are tainted with metabolic long-term side effects, some of which are directly attributed to HIV Protease Inhibitors (PIs). HAART has been linked to cardiovascular complications in HIV-1 patients, and recent studies have shown that HIV PIs play critical roles in insulin resistance, dysregulation of lipid metabolism, and inflammation, which are all cornerstones of cardiovascular complications. In addition, HIV PI-induced atherosclerotic cardiovascular disease is becoming the leading cause of mortality in HIV-1 infected persons in developed countries. During the last decade, an extensive effort has been put forth to study HAART-induced side effects. Both in vitro and in vivo animal studies from our laboratory and others’ have linked HIV PIs with the activation of endoplasmic reticulum (ER) stress and oxidative stress as well as an increase in inflammatory cytokine production from several cell types including macrophages, hepatocytes, intestinal epithelial cells and adipocytes. However, the underlying cellular and molecular mechanisms remain to be fully identified and therapeutic strategies are currently unavailable. Understanding the root causes of HAART-associated metabolic syndrome and its potential implications for HIV-infected patients will be critical to the design of effective interventions to combat the metabolic and cardiovascular diseases
Intermediate structures in radiation damaged titanite (CaTiSiO5): a Raman spectroscopic study

Effects of radiation damage and thermal annealing on the crystal structure of natural titanite (CaTiSiO5) were studied using Raman spectroscopy. The results show that well crystallized natural titanites generally have the P21/a structure at the unit cell level, in contrast to the A2/a symmetry reported previously. Radiation caused by naturally incorporated impurities (such as U and Th) leads to structural damage and amorphization in titanite, as evidenced by a significant loss of band intensity, spectral broadening and frequency shifts. Additional bands (e.g. near 574 and 650 cm−1) occur in weakly or partially metamict titanite due to the formation of an intermediate phase (with the A2/a symmetry). Raman spectra of titanite thermal glasses showed features different from those of metamict titanite, especially in the Ti–O and Si–O stretching regions. The effect of thermal annealing is strongly affected by the initial degrees of damage that the sample experienced. Weakly damaged titanite samples showed that annealing leads to a structural recovery, and the spectral patterns of these recovered crystals are consistent with the P21/a symmetry. Highly damaged titanite starts to recrystallize into an A2/a phase near 700–800 K, and additional structural modification occurs when annealed at 1300–1400 K, which involves significant change in broad Ti–O features. However, in terms of bandwidths, the metamict samples are far from fully recovered even on being annealed at 1300–1400 K.