Folding Lennard-Jones proteins by a contact potential

We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native) conformations were then identified by Molecular Dynamics. Then we turned to investigate whether one can find a pairwise contact potential, whose ground states are the contact maps associated with these native conformations. We show that such a requirement cannot be satisfied exactly - i.e. no such contact parameters exist. Nevertheless, we found that one can find contact energy parameters for which an energy minimization procedure, acting in the space of contact maps, yields maps whose corresponding structures are close to the native ones. Finally we show that when these structures are used as the initial point of a Molecular Dynamics energy minimization process, the correct native folds are recovered with high probability.Comment: submitted to "Proteins: Structure, Function, and Genetics

Self-Templated Nucleation in Peptide and Protein aggregation

Peptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of disordered oligomeric assemblies. This process has received much attention because disordered oligomeric aggregates have been associated with neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Here we describe a self-templated nucleation mechanism that determines the transition between the initial condensation of polypeptide chains into disordered assemblies and their reordering into fibrillar structures. The results that we present show that at the molecular level this transition is due to the ability of polypeptide chains to reorder within oligomers into fibrillar assemblies whose surfaces act as templates that stabilise the disordered assemblies.Comment: 4 pages, 3 figure

Degradation processes of reinforced concretes by combined sulfate--phosphate attack

A novel form of alteration due to the interaction between hydrated cement phases and sulfate and phosphate-based pollutants is described, through the characterization of concrete samples from an industrial reinforced concrete building. Decalcification of the cement matrices was observed, with secondary sulfate and phosphate-based mineral formation, according to a marked mineralogical and textural zoning. Five alteration layers may be detected: the two outermost layers are characterized by the presence of gypsum–brushite solid solution phases associated with anhydrous calcium sulfates and phosphates, respectively, while a progressive increase in apatite and ammonium magnesium phosphates is observable in the three innermost layers, associated with specific apatite precursors (brushite, octacalcium phosphate and amorphous calcium phosphate, respectively). The heterogeneous microstructural development of secondary phases is related to the chemical, pH and thermal gradients in the attacked cementitious systems, caused by different sources of pollutants and the exposure to the sun's radiation

Lithium Exposure During Pregnancy and the Postpartum Period: A Systematic Review and Meta-Analysis of Safety and Efficacy Outcomes

OBJECTIVE: Uncertainty surrounds the risks of lithium use during pregnancy in women with bipolar disorder. The authors sought to provide a critical appraisal of the evidence related to the efficacy and safety of lithium treatment during the peripartum period, focusing on women with bipolar disorder and their offspring. METHODS: The authors conducted a systematic review and random-effects meta-analysis assessing case-control, cohort, and interventional studies reporting on the safety (primary outcome, any congenital anomaly) or efficacy (primary outcome, mood relapse prevention) of lithium treatment during pregnancy and the postpartum period. The Newcastle-Ottawa Scale and the Cochrane risk of bias tools were used to assess the quality of available PubMed and Scopus records through October 2018. RESULTS: Twenty-nine studies were included in the analyses (20 studies were of good quality, and six were of poor quality; one study had an unclear risk of bias, and two had a high risk of bias). Thirteen of the 29 studies could be included in the quantitative analysis. Lithium prescribed during pregnancy was associated with higher odds of any congenital anomaly (N=23,300, k=11; prevalence=4.1%, k=11; odds ratio=1.81, 95% CI=1.35-2.41; number needed to harm (NNH)=33, 95% CI=22-77) and of cardiac anomalies (N=1,348,475, k=12; prevalence=1.2%, k=9; odds ratio=1.86, 95% CI=1.16-2.96; NNH=71, 95% CI=48-167). Lithium exposure during the first trimester was associated with higher odds of spontaneous abortion (N=1,289, k=3, prevalence=8.1%; odds ratio=3.77, 95% CI=1.15-12.39; NNH=15, 95% CI=8-111). Comparing lithium-exposed with unexposed pregnancies, significance remained for any malformation (exposure during any pregnancy period or the first trimester) and cardiac malformations (exposure during the first trimester), but not for spontaneous abortion (exposure during the first trimester) and cardiac malformations (exposure during any pregnancy period). Lithium was more effective than no lithium in preventing postpartum relapse (N=48, k=2; odds ratio=0.16, 95% CI=0.03-0.89; number needed to treat=3, 95% CI=1-12). The qualitative synthesis showed that mothers with serum lithium levels <0.64 mEq/L and dosages <600 mg/day had more reactive newborns without an increased risk of cardiac malformations. CONCLUSIONS: The risk associated with lithium exposure at any time during pregnancy is low, and the risk is higher for first-trimester or higher-dosage exposure. Ideally, pregnancy should be planned during remission from bipolar disorder and lithium prescribed within the lowest therapeutic range throughout pregnancy, particularly during the first trimester and the days immediately preceding delivery, balancing the safety and efficacy profile for the individual patient

The Botanical Record of Archaeobotany Italian Network - BRAIN: a cooperative network, database and website

Con autorización de la revista para autores CSIC[EN] The BRAIN (Botanical Records of Archaeobotany Italian Network) database and network was developed by the cooperation of archaeobotanists working on Italian archaeological sites. Examples of recent research including pollen or other plant remains in analytical and synthetic papers are reported as an exemplar reference list. This paper retraces the main steps of the creation of BRAIN, from the scientific need for the first research cooperation to the website which has a free online access since 2015.Peer reviewe

Semi, frutti e altri resti da una capanna medievale a Montegrotto Terme (Padova)

Attività di ricerca archeobotanica per lo studio di una capanna medievale portata alla luce nella campagna 2006, e in particolare della sua superficie di calpestio (US 2004 e US 2019) nell'area di scavo in via Neroniana nel territorio di Montegrotto Terme

Il contributo dell'analisi di macroresti vegetali nella ricostruzione paleoambientale e delle attività umane presso un sito archeologico in area termale euganea

The contribute of plant macrofossil analysis to the palaeoenvironment reconstruction of an archaeological site in the thermal area of Euganean Hills This thesis is the contribute of plant macrofossil analysis to the multi-disciplinary study started in 2005 in the archaeological site of via Neroniana (Montegrotto Terme) ( “Acquae Patavinae” Project), in the thermal area of the Euganean Hills. There is a variety of studies concerning this area, e.g. archaeological, botanical, geological and geomorphological studies, but none of them concerns archaeobotany. The participation to this project has been an interesting occasion to study the unusual environment of the thermal springs, and to contribute with archaeobotanical data to the regional history. The archaeological evidence of via Neroniana are dated to the Copper, Bronze, Roman and Medieval age. Deep and archaeological sediments were investigated, and also the infilling of two archaeological structures. The research aimed to reconstruct the palaeoenvironment and to know the principal human activities in the site, by means of the plant macro-remain analysis. Firstly the evolution and spatial localization of water bodies of thermal origin has been studied. A particolar interest has been devoted to the alophilous taxa of the typical plant community that lived near the natural thermal springs before hurbanization in order to use them as proxies of the thermal environment, today no longer existing in the area. Then the human activities in the Roman and Medieval Age have been suggested in the context of the local historical records. The results of this research within the framework of a multidisciplinary study, provided evidence of water bodies fed by thermal waters during the Last Glacial Maximum (18000-24000 years ago) and in the Roman Age. These results documented also the presence of vineyard, in the area, before the construction of the Roman Imperial building, the remains of which have been put on light during the archaeological excavation. Almost all the sediments sampled from the archaeological context have revealed to be sterile,, except the fillings of a silos and an elongated ditch (IX-XIV cent. a.D.). The plant remains suggest cultivations of cereals, grapevine and linen, probably for food, textile and dying activities. The findings of linen in the site are particularly interesting, because the line cultivation is historically well documented in the near area of Padova and Monselice during the Medioeval Ages, when it played an important economical role. The proximity of the hot springs should have been an advantage for the retting of linen plants in thermal water, as it is documented in other similar contexts in ItalyLa tesi presenta il contributo archeobotanico allo studio multidisciplinare in atto dal 2005 nel sito di via Neroniana a Montegrotto Terme (Progetto “Aquae Patavinae”), nell’area termale euganea. Sono numerosissimi gli studi archeologici, geologici e geostratigrafici pubblicati su quest’area, ma non sono note indagini archeobotaniche. L’occasione di partecipare al progetto ha rappresentato un’interessante opportunità di studiare un contesto ambientale insolito, come è quello termale, e di ampliare le conoscenze archeobotaniche nella regione. Il sito ha restituito tracce di frequentazioni dell’età del rame, del bronzo, di epoca romana e medievale. La ricerca ha interessato sia i sedimenti profondi che i sedimenti archeologici e sub archeologici del sito. Gli obiettivi che il presente studio si è posto sono stati principalmente due. Il primo è stato la ricostruzione del paleoambiente, con una particolare attenzione alla ricostruzione dei limiti e dell’evoluzione nel tempo dei corpi d’acqua di origine termale, che caratterizzavano il sito. All’interno di questo obiettivo si è posta una particolare attenzione alle piante appartenenti alla flora alofila tipica delle sorgenti termali naturali, al fine di utilizzarle come proxy di quell’ambiente, studiando sia la letteratura botanica classica sia la ricca documenzione storica sull’ ambiente termale euganeo, oggi scomparso. Il secondo obiettivo della tesi è stato la ricostruzione delle attività umane, produttive e culturali nei periodi di occupazione del sito, attraverso lo studio dei macroresti nei contesti antropici e la loro contestualizzazione nelle fonti storiche locali. I risultati della ricerca, nell’ambito delle ricerche multidisciplinari hanno permesso di ricostruire la presenza di un bacino alimentato da acque termali nell’area durante l’ultimo massimo glaciale (18000-24000 anni fa). La ricerca carpologica nei sedimenti sottostanti la villa di età romana portata alla luce nello scavo, ha permesso di evidenziare una negativa antropica precedente o coeva alla costruzione della struttura, documentando anche in questo periodo l’afflusso di acqua termale nell’area e soprattutto la presenza di attività agricole, legate alla coltura della vite e datate tra il I e il II sec. d.C. delle quali non vi erano indicazioni precedenti. I sedimenti archeologici si sono rivelati per la maggior parte sterili, ma i carporesti ritrovati nei riempimenti di un silos e di una fossa allungata di età medievale (IX-XIV sec. d.C.) suggeriscono la presenza in sito di coltivazioni cerealicole, viticoltura e probabile vinificazione, coltivazione del lino a scopo sia tessile che alimentare e attività tintorie. Il ritrovamento del lino è di particolare interesse per via dell’importanza che ha avuto nell’area del padovano e nel Monselicense in età medievale, e il suo ritrovamento in un contesto termale euganeo suggerisce anche attività di uso improprio delle acque termali per la macerazione delle sue fibre, come in altri contesti simili italian

Hot sandpiles

A temperature-like parameter is introduced in ordinary sandpiles models. A temperature-dependent probability distribution is assigned for the sand toppling on sites of any height. In mean-field theory criticality is obtained for all the values of temperature and no characteristic avalanche size appears. Numerical simulations support the existence of criticality at any temperature with apparently continuously varying critical exponents