AREA Science Park

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

BACKGROUND: Fatty liver (FL) is the most frequent liver disease in Western countries. We used data from the Dionysos Nutrition & Liver Study to develop a simple algorithm for the prediction of FL in the general population. METHODS: 216 subjects with and 280 without suspected liver disease were studied. FL was diagnosed by ultrasonography and alcohol intake was assessed using a 7-day diary. Bootstrapped stepwise logistic regression was used to identify potential predictors of FL among 13 variables of interest [gender, age, ethanol intake, alanine transaminase, aspartate transaminase, gamma-glutamyl-transferase (GGT), body mass index (BMI), waist circumference, sum of 4 skinfolds, glucose, insulin, triglycerides, and cholesterol]. Potential predictors were entered into stepwise logistic regression models with the aim of obtaining the most simple and accurate algorithm for the prediction of FL. RESULTS: An algorithm based on BMI, waist circumference, triglycerides and GGT had an accuracy of 0.84 (95%CI 0.81-0.87) in detecting FL. We used this algorithm to develop the "fatty liver index" (FLI), which varies between 0 and 100. A FLI < 30 (negative likelihood ratio = 0.2) rules out and a FLI > or = 60 (positive likelihood ratio = 4.3) rules in fatty liver. CONCLUSION: FLI is simple to obtain and may help physicians select subjects for liver ultrasonography and intensified lifestyle counseling, and researchers to select patients for epidemiologic studies. Validation of FLI in external populations is needed before it can be employed for these purposes.

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

The prevalence of and the risk factors for fatty liver have not undergone a formal evaluation in a representative sample of the general population. We therefore performed a cross-sectional study in the town of Campogalliano (Modena, Italy), within the context of the Dionysos Project. Of 5,780 eligible persons aged 18 to 75 years, 3,345 (58%) agreed to participate in the study. Subjects with suspected liver disease (SLD), defined on the basis of elevated serum alanine aminotransferase (ALT) and gamma-glutamyl-transferase (GGT) activity, hepatitis B surface antigen (HBsAg), or hepatitis C virus (HCV)-RNA positivity, were matched with randomly selected subjects of the same age and sex without SLD. A total of 311 subjects with and 287 without SLD underwent a detailed clinical, laboratory, and anthropometrical evaluation. Fatty liver was diagnosed by ultrasonography, and alcohol intake was assessed by using a 7-day diary. Multinomial logistic regression was used to detect risk factors for normal liver versus nonalcoholic fatty liver disease (NAFLD) and for alcoholic fatty liver (AFLD) versus NAFLD. The prevalence of NAFLD was similar in subjects with and without SLD (25 vs. 20%, P = .203). At multivariable analysis, normal liver was more likely than NAFLD in older subjects and less likely in the presence of obesity, hyperglycemia, hyperinsulinemia, hypertriglyceridemia, and systolic hypertension; AFLD was more likely than NAFLD in older subjects, males, and in the presence of elevated GGT and hypertriglyceridemia, and less likely in the presence of obesity and hyperglycemia. In conclusion, NAFLD is highly prevalent in the general population, is not associated with SLD, but is associated with many features of the metabolic syndrome.

The isotropic magnetic moment of a free atom is shown to develop giant magnetic anisotropy energy due to symmetry reduction at an atomically ordered surface. Single cobalt atoms deposited onto platinum (111) are found to have a magnetic anisotropy energy of 9 millielectron volts per atom arising from the combination of unquenched orbital moments (1.1 Bohr magnetons) and strong spin-orbit coupling induced by the platinum substrate. By assembling cobalt nanoparticles containing up to 40 atoms, the magnetic anisotropy energy is further shown to be dependent on single-atom coordination changes. These results confirm theoretical predictions and are of fundamental value to understanding how magnetic anisotropy develops in finite-sized magnetic particles.

BACKGROUND: SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. METHODS: We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann-Whitney and Fisher-Exact tests were used to assess statistical significance. RESULTS: We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001). CONCLUSIONS: These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates.

Cathelicidins comprise a family of mammalian proteins containing a C-terminal cationic antimicrobial domain that becomes active after being freed from the N-terminal cathelin portion of the holoprotein. Many other members of this family have been identified since the first cathelicidin sequences were reported 10 years ago. The mature peptides generally show a wide spectrum of antimicrobial activity and, more recently, some of them have also been found to exert other biological activities. The human cathelicidin peptide LL-37 is chemotactic for neutrophils, monocytes, mast cells, and T cells; induces degranulation of mast cells; alters transcriptional responses in macrophages; stimulates wound vascularization and re-epithelialization of healing skin. The porcine PR-39 has also been involved in a variety of processes, including promotion of wound repair, induction of angiogenesis, neutrophils chemotaxis, and inhibition of the phagocyte NADPH oxidase activity, whereas the bovine BMAP-28 induces apoptosis in transformed cell lines and activated lymphocytes and may thus help with clearance of unwanted cells at inflammation sites. These multiple actions provide evidence for active participation of cathelicidin peptides in the regulation of the antimicrobial host defenses.

&lt;p&gt;The aim of this review article is to assess the descriptive capabilities of the Hubbard-rooted LDA+U method and to clarify the conditions under which it can be expected to be most predictive. The article illustrates the theoretical foundation of LDA+U and prototypical applications to the study of correlated materials, discusses the most relevant approximations used in its formulation, and makes a comparison with other approaches also developed for similar purposes. Open “issues” of the method are also discussed, including the calculation of the electronic couplings (the Hubbard U), the precise expression of the corrective functional and the possibility to use LDA+U for other classes of materials. The second part of the article presents recent extensions to the method and illustrates the significant improvements they have obtained in the description of several classes of different systems. The conclusive section finally discusses possible future developments of LDA+U to further enlarge its predictive power and its range of applicability.&lt;/p&gt;

Forty years of research have established that the p53 tumor suppressor provides a major barrier to neoplastic transformation and tumor progression by its unique ability to act as an extremely sensitive collector of stress inputs, and to coordinate a complex framework of diverse effector pathways and processes that protect cellular homeostasis and genome stability. Missense mutations in the TP53 gene are extremely widespread in human cancers and give rise to mutant p53 proteins that lose tumor suppressive activities, and some of which exert trans-dominant repression over the wild-type counterpart. Cancer cells acquire selective advantages by retaining mutant forms of the protein, which radically subvert the nature of the p53 pathway by promoting invasion, metastasis and chemoresistance. In this review, we consider available evidence suggesting that mutant p53 proteins can favor cancer cell survival and tumor progression by acting as homeostatic factors that sense and protect cancer cells from transformation-related stress stimuli, including DNA lesions, oxidative and proteotoxic stress, metabolic inbalance, interaction with the tumor microenvironment, and the immune system. These activities of mutant p53 may explain cancer cell addiction to this particular oncogene, and their study may disclose tumor vulnerabilities and synthetic lethalities that could be exploited for hitting tumors bearing missense TP53 mutations.

A novel strategy for efficient growth of nitrogen-doped graphene (N-graphene) on a large scale from s-triazine molecules is presented. The growth process has been unveiled in situ using time-dependent photoemission. It has been established that a postannealing of N-graphene after gold intercalation causes a conversion of the N environment from pyridinic to graphitic, allowing to obtain more than 80% of all embedded nitrogen in graphitic form, which is essential for the electron doping in graphene. A band gap, a doping level of 300 meV, and a charge-carrier concentration of ∼8×10(12) electrons per cm2, induced by 0.4 atom % of graphitic nitrogen, have been detected by angle-resolved photoemission spectroscopy, which offers great promise for implementation of this system in next generation electronic devices.

The adsorption of several common gas molecules over boron-, nitrogen-, aluminum-, and sulfur-doped graphene was theoretically studied using density-functional theory. B- and N-doped graphene retain a planar form, while Al and S atoms protrude out of the graphene layer. We find that only NO and NO2 bind to B-doped graphene, while only NO2 binds to S-doped graphene. Al-doped graphene is much more reactive and binds many more gases, including O2. We suggest that B- and S-doped graphene could be a good sensor for polluting gases such as NO and NO2.

We present a simple revision of the VV10 nonlocal density functional by Vydrov and Van Voorhis [J. Chem. Phys. 133, 244103 (2010)] for dispersion interactions. Unlike the original functional our modification allows nonlocal correlation energy and its derivatives to be efficiently evaluated in a plane wave framework along the lines pioneered by Rom\'an-P\'erez and Soler [Phys. Rev. Lett. 103, 096102 (2009)]. Our revised functional maintains the outstanding precision of the original VV10 in noncovalently bound complexes and performs well in representative covalent, ionic, and metallic solids.

Bulk and surface sensitive x-ray spectroscopic techniques are applied in tandem to show that the valence band edge for In2O3 is found significantly closer to the bottom of the conduction band than expected on the basis of the widely quoted bulk band gap of 3.75 eV. First-principles theory shows that the upper valence bands of In2O3 exhibit a small dispersion and the conduction band minimum is positioned at Gamma. However, direct optical transitions give a minimal dipole intensity until 0.8 eV below the valence band maximum. The results set an upper limit on the fundamental band gap of 2.9 eV.

We report on the electronic properties of straight, 1.6 nm wide, silicene nanoribbons on Ag(110), arranged in a one-dimensional grating with a pitch of 2 nm, whose high-resolution scanning tunneling microscopy images reveal a honeycomb geometry. Angle-resolved photoemission shows quantum confined electronic states of one-dimensional character. The silicon band dispersion along the direction of the nanoribbons suggests a behavior analogous to the Dirac cones of graphene on different substrates.

Two new transition metal nitrides, IrN2 and OsN2, were synthesized at high pressures and temperatures using laser-heated diamond-anvil cell techniques. Synchrotron x-ray diffraction was used to determine the structures of novel nitrides and the equations of states of both the parent metals as well as the newly synthesized materials. The compounds have bulk moduli comparable with those of the traditional superhard materials. For IrN2, the measured bulk modulus [K0 = 428(12) GPa] is second only to that of diamond (K0 = 440 GPa). Ab initio calculations indicate that both compounds have a metal:nitrogen stoichiometry of 1:2 and that nitrogen intercalates in the lattice of the parent metal in the form of single-bonded N-N units.

Optimal control theory is a promising candidate for a drastic improvement of the performance of quantum information tasks. We explore its ultimate limit in paradigmatic cases, and demonstrate that it coincides with the maximum speed limit allowed by quantum evolution.

Graphene is easily produced by thermally reducing graphene oxide. However, defect formation in the C network during deoxygenation compromises the charge carrier mobility in the reduced material. Understanding the mechanisms of the thermal reactions is essential for defining alternative routes able to limit the density of defects generated by carbon evolution. Here, we identify a dual path mechanism in the thermal reduction of graphene oxide driven by the oxygen coverage: at low surface density, the O atoms adsorbed as epoxy groups evolve as O(2) leaving the C network unmodified. At higher coverage, the formation of other O-containing species opens competing reaction channels, which consume the C backbone. We combined spectroscopic tools and ab initio calculations to probe the species residing on the surface and those released in the gas phase during heating and to identify reaction pathways and rate-limiting steps. Our results illuminate the current puzzling scenario of the low temperature gasification of graphene oxide.

BACKGROUND: Gut microbiota modifiers may have beneficial effects of non-alcoholic fatty liver disease (NAFLD) but randomised controlled trials (RCT) are lacking in children. AIM: To perform a double-blind RCT of VSL#3 vs. placebo in obese children with biopsy-proven NAFLD. METHODS: Of 48 randomised children, 44 (22 VSL#3 and 22 placebo) completed the study. The main outcome was the change in fatty liver severity at 4 months as detected by ultrasonography. Secondary outcomes were the changes in triglycerides, insulin resistance as detected by the homoeostasis model assessment (HOMA), alanine transaminase (ALT), body mass index (BMI), glucagon-like peptide 1 (GLP-1) and activated GLP-1 (aGLP-1). Ordinal and linear models with cluster confidence intervals were used to evaluate the efficacy of VSL#3 vs. placebo at 4 months. RESULTS: At baseline, moderate and severe NAFLD were present in 64% and 36% of PLA children and in 55% and 45% of VSL#3 children. The probability that children supplemented with VSL#3 had none, light, moderate or severe FL at the end of the study was 21%, 70%, 9% and 0% respectively with corresponding values of 0%, 7%, 76% and 17% for the placebo group (P < 0.001). No between-group differences were detected in triglycerides, HOMA and ALT while BMI decreased and GLP-1 and aGLP1 increased in the VSL#3 group (P < 0.001 for all comparisons). CONCLUSIONS: A 4-month supplement of VSL#3 significantly improves NAFLD in children. The VSL#3-dependent GLP-1 increase could be responsible for these beneficial effects. Trial identifier: NCT01650025 (www.clinicaltrial.gov).

BACKGROUND: Recent studies suggest a role of n-3 long-chain polyunsaturated fatty acids (n-3 PUFA) as peroxisome proliferator-activated receptor-alpha ligands in improving non-alcoholic fatty liver disease (NAFLD) in rodents. However, data in humans are still lacking. AIM: To evaluate the efficacy of prolonged PUFA supplementation in patients with NAFLD. METHODS: Fifty-six patients with NAFLD were enrolled. Among the overall eligible patients, 42 assumed n-3 PUFA 1-g capsule daily for 12 months, whereas 14 refused the treatment and were analysed as controls. All patients underwent haematochemical and ultrasound follow-up. RESULTS: Polyunsaturated fatty acid supplementation significantly decreased serum aspartate transaminase (P = 0.003), alanine transaminase (P = 0.002), gamma-glutamyl transpeptidase (P = 0.03), triglycerides (P = 0.02) and fasting glucose (P = 0.02) in comparison with controls. Circulating arachidonate and n-6/n-3 fatty acid ratio was reduced (P = 0.0002, and P = 0.0001 respectively) in treated patients. Moreover, ultrasonography demonstrated improvement of liver echotexture after PUFA (P = 0.0001), and increase of Doppler perfusion index (P = 0.001), whereas no significant changes occurred in controls. CONCLUSIONS: Supplementation with n-3 PUFA improves biochemical, ultrasonographic and haemodynamic features of liver steatosis. Our study supports the efficacy of n-3 PUFA as a new therapeutic approach in the treatment of NAFLD.