Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators

We present an approach to the estimate of the potential of mean force along a generic reaction coordinate based on maximum likelihood methods and path-ensemble averages in systems driven far from equilibrium. Following similar arguments, various free energy estimators can be recovered, all providing comparable computational accuracy. The method, applied to the unfolding process of the alpha-helix form of an alanine deca-peptide, gives results in good agreement with thermodynamic integration.Comment: 9 pages, 3 figures; important changes (figure 2, demonstration of Eq. 16, figure 3 and related discussion); style correction

Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone

Protein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein-protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.We thank F. Abascal and M. L. Tress for helpful discussions. This work was supported by Spanish Ministry of Economy and Competitiveness Projects BFU2015-71241-R and BIO2012-40205, cofunded by the European Regional Development Fund.S

Clinical Aspects and Management of Levodopa-Induced Dyskinesia

In Parkinson's disease, one of the most troublesome dilemmas is the treatment of levodopa-induced dyskinesia. After a few years, chronic treatment with levodopa is associated with the development of dyskinesias. Strategies to delay or to reduce dyskinesias are based on the change of levodopa dosing or the early use of dopamine agonists. Dopamine agonists with different pharmacological profile are available. Our paper was aimed to analyse the clinical impact and the management of dyskinesias with dopamine agonists

Comparative analysis of local angular rotation between the Ring Laser Gyroscope GINGERINO and GNSS stations

The study of local deformations is a hot topic in geodesy. Local rotations of the crust around the vertical axis can be caused by deformations. In the Gran Sasso area the ring laser prototype GINGERINO and the GNSS array are operative. One year of data of GINGERINO is compared with the ones from the GNSS stations, homogeneously selected around the position of GINGERINO, aiming at looking for rotational signals with period of days common to both systems. At that purpose the rotational component of the area circumscribed by the GNSS stations has been evaluated and compared with the GINGERINO data. The coherences between the signals show structures that even exceed 60$\%$ coherence over the 6-60 days period; to validate this unprecedented analysis two different methods have been used to evaluate the local rotation using the GNSS stations. The analysis reveals that the shared rotational signal's amplitude in both instruments is approximately $10^{-13} rad/s$, an order of magnitude lower than the amplitudes of the signals examined using the coherence method. The ring laser array GINGER is at present under construction, and the confrontation of the ring laser data with GNSS antennas provides evidence of the fruibility and validity of the ring laser data for very low frequency investigation

Demonstration of sub-3 ps temporal resolution with a superconducting nanowire single-photon detector

Improvements in temporal resolution of single-photon detectors enable increased data rates and transmission distances for both classical and quantum optical communication systems, higher spatial resolution in laser ranging, and observation of shorter-lived fluorophores in biomedical imaging. In recent years, superconducting nanowire single-photon detectors (SNSPDs) have emerged as the most efficient time-resolving single-photon-counting detectors available in the near-infrared, but understanding of the fundamental limits of timing resolution in these devices has been limited due to a lack of investigations into the timescales involved in the detection process. We introduce an experimental technique to probe the detection latency in SNSPDs and show that the key to achieving low timing jitter is the use of materials with low latency. By using a specialized niobium nitride SNSPD we demonstrate that the system temporal resolution can be as good as 2.6 ± 0.2 ps for visible wavelengths and 4.3 ± 0.2 ps at 1,550 nm

Demonstration of sub-3 ps temporal resolution with a superconducting nanowire single-photon detector

Improvements in temporal resolution of single-photon detectors enable increased data rates and transmission distances for both classical and quantum optical communication systems, higher spatial resolution in laser ranging, and observation of shorter-lived fluorophores in biomedical imaging. In recent years, superconducting nanowire single-photon detectors (SNSPDs) have emerged as the most efficient time-resolving single-photon-counting detectors available in the near-infrared, but understanding of the fundamental limits of timing resolution in these devices has been limited due to a lack of investigations into the timescales involved in the detection process. We introduce an experimental technique to probe the detection latency in SNSPDs and show that the key to achieving low timing jitter is the use of materials with low latency. By using a specialized niobium nitride SNSPD we demonstrate that the system temporal resolution can be as good as 2.6 ± 0.2 ps for visible wavelengths and 4.3 ± 0.2 ps at 1,550 nm

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe