Miracle-dz/UniFAR-FTUs huggingface dataset:
Focus on quantum effects and noise in biomolecules

The role of quantum mechanics in biological organisms has been a fundamental question of twentieth-century biology. It is only now, however, with modern experimental techniques, that it is possible to observe quantum mechanical effects in bio-molecular complexes directly. Indeed, recent experiments have provided evidence that quantum effects such as wave-like motion of excitonic energy flow, delocalization and entanglement can be seen even in complex and noisy biological environments (Engel et al 2007 Nature 446 782; Collini et al 2010 Nature 463 644; Panitchayangkoon et al 2010 Proc. Natl Acad. Sci. USA 107 12766). Motivated by these observations, theoretical work has highlighted the importance of an interplay between environmental noise and quantum coherence in such systems (Mohseni et al 2008 J. Chem. Phys. 129 174106; Plenio and Huelga 2008 New J. Phys. 10 113019; Olaya-Castro et al 2008 Phys. Rev. B 78 085115; Rebentrost et al 2009 New J. Phys. 11 033003; Caruso et al 2009 J. Chem. Phys. 131 105106; Ishizaki and Fleming 2009 J. Chem. Phys. 130 234111). All of this has led to a surge of interest in the exploration of quantum effects in biological systems in order to understand the possible relevance of non-trivial quantum features and to establish a potential link between quantum coherence and biological function. These studies include not only exciton transfer across light harvesting complexes, but also the avian compass (Ritz et al 2000 Biophys. J. 78 707), and the olfactory system (Turin 1996 Chem. Sens. 21 773; Chin et al 2010 New J. Phys. 12 065002). These examples show that the full understanding of the dynamics at bio-molecular length (10 Å) and timescales (sub picosecond) in noisy biological systems can uncover novel phenomena and concepts and hence present a fertile ground for truly multidisciplinary research.
Socio-economic consequences of rheumatoid arthritis in the first years of the disease.

OBJECTIVE Few data have been presented to document the impact of rheumatoid arthritis (RA) on socio-economic well-being. In this study, exact figures on socio-economic consequences were assessed. METHODS The socio-economic consequences were studied in an inception cohort (186 early RA patients, mean disease duration 3 yr) by measuring the change in work capability, income, rest during the daytime, leisure time activity, transport mobility, housing and social support occurring in the first years of the disease. RESULTS For 89% of the patients, RA had an impact on one of the socio-economic items; for 58%, at least three of these items were affected simultaneously. Work disability appeared to be 4-15 times higher than in the general population. After 3 yr, 42% of the patients were registered as work disabled. Nearly a quarter of the patients experienced income reduction. Over 40% of the patients claimed extra rest during the daytime. Leisure activity changed towards activities with a lower joint load. There was a decline in transport mobility for 52% of the patients. Social support increased strongly. CONCLUSIONS Socio-economic change already presents in the first years of RA and appears to be influenced by age, gender, marital status and work disability. Furthermore, physical limitation appeared to be predictive for work-related income reduction, reduced transport mobility and development of social dependency.
Analysis of latency-aware caching strategies in information-centric networking

5G has loudly ambitioned to achieve extremely low latency in mobile networks. To this aim, we have recently introduced two novel latency-aware caching heuristics, LAC and LAC+ and we showed through simulations in Information-Centric Networks their good performance figures. In this paper, we present an insight on their operations: a mathematical analysis of these caching systems led us to novel results that we validate in simulation. The advantages of these algorithms come (i) on one side from the fact they are distributed and lightweight and (ii) from the ability to quickly adapt to content popularity and network congestion, with no signaling nor explicit coordination between the network nodes. In this paper we provide analytical bounds of latency aware caching policies and evaluate their performance by network simulations. The proposed mechanisms can halve the mean and standard deviation of content delivery time with respect to approximations of LFU as leave a copy probabilistically.
CRANIAL NERVE PRESERVATION AND OUTCOMES AFTER STEREOTACTIC RADIOSURGERY FOR JUGULAR FORAMEN SCHWANNOMAS

OBJECTIVE Jugular foramen region schwannomas are rare intracranial tumors that usually present with multiple lower cranial nerve deficits. For some patients, complete surgical resection is possible but may be associated with significant morbidity. Stereotactic radiosurgery is a minimally invasive alternative or adjunct to microsurgery for such tumors. We reviewed our clinical and imaging outcomes after patients underwent gamma knife radiosurgery for management of jugular foramen schwannomas. METHODS Thirty-four patients with 35 tumors (one patient had bilateral tumors) underwent radiosurgery between May 1990 and December 2005. Twenty-two patients had previous microsurgical resection and all patients experienced various cranial neuropathies. A median of six isocenters were used. Median marginal and maximum doses were 14 and 28 Gy, respectively. RESULTS None of the patients were lost to evaluation and the mean duration of follow-up was 83 months. Tumors regressed in 17 patients, remained stable in 16, and progressed in two. Five- and 10-year actuarial control rates were 97 and 94%, respectively. Preexisting cranial neuropathies improved in 20% and remained stable in 77% after radiosurgery. One patient worsened. The function of all previous intact nerves was preserved after radiosurgery. CONCLUSION Stereotactic radiosurgery proved to be a safe and effective management for newly diagnosed or residual jugular foramen schwannomas. Long-term tumor control rates and stability or improvement in cranial nerve function was confirmed.
A grid enabled PSE for medical imaging: experiences on MedIGrid

A key issue in designing applications codes which are able to effectively take advantage of grid computing environments is to deal and manage all the software components complexity, this is even more true for medical imaging applications. We are concerned with development of a medical imaging PSE for advanced and grid computing environments. Specifically, MedIGrid is a distributed application for the management, processing and visualization of biomedical images that integrates a set of software and hardware components, or, more specifically, a set of grid collaborative applications useful to nuclear doctors. It results from the interaction of computing scientists devoted to the design and deployment of new tomographic reconstruction algorithms techniques, computer scientists researchers in the field of distributed and parallel architectures and physicians involved in nuclear medicine. We'll describe MedIGrid general architecture, as well as improvements and enhancements, essentially regarding the semantic power of the GUI (the Portal) (its language and its realization), and the entire phase of monitoring and migration of the parallel computational kernel for images reconstruction, mainly based on a performance contract inked taking into account historical performances and an ad hoc developed performance model.
What Is the Subjective Cost of Cognitive Effort? Load, Trait, and Aging Effects Revealed by Economic Preference

It has long been assumed that people treat cognitive effort as costly, but also that such effort costs may vary greatly across individuals. Individual differences in subjective effort could present a major and pervasive confound in behavioral and neuroscience assessments, by conflating cognitive ability with cognitive motivation. Self-report cognitive effort scales have been developed, but objective measures are lacking. In this study, we use the behavioral economic approach of revealed preferences to quantify subjective effort. Specifically, we adapted a well-established discounting paradigm to measure the extent to which cognitive effort causes participants to discount monetary rewards. The resulting metrics are sensitive to both within-individual factors, including objective load and reward amount, and between-individual factors, including age and trait cognitive engagement. We further validate cognitive effort discounting by benchmarking it against well-established measures of delay discounting. The results highlight the promise and utility of behavioral economic tools for assessing trait and state influences on cognitive motivation.
Global Survey of Corneal Transplantation and Eye Banking.

IMPORTANCE Corneal transplantation restores visual function when visual impairment caused by a corneal disease becomes too severe. It is considered the world's most frequent type of transplantation, but, to our knowledge, there are no exhaustive data allowing measurement of supply and demand, although such data are essential in defining local, national, and global strategies to fight corneal blindness. OBJECTIVE To describe the worldwide situation of corneal transplantation supply and demand. DESIGN, SETTING, AND PARTICIPANTS Data were collected between August 2012 and August 2013 from a systematic review of published literature in parallel with national and international reports on corneal transplantation and eye banking. In a second step, eye bank staff and/or corneal surgeons were interviewed on their local activities. Interviews were performed during international ophthalmology or eye-banking congresses or by telephone or email. Countries' national supply/demand status was classified using a 7-grade system. Data were collected from 148 countries. MAIN OUTCOMES AND MEASURES Corneal transplantation and corneal procurements per capita in each country. RESULTS In 2012, we identified 184,576 corneal transplants performed in 116 countries. These were procured from 283,530 corneas and stored in 742 eye banks. The top indications were Fuchs dystrophy (39% of all corneal transplants performed), a primary corneal edema mostly affecting elderly individuals; keratoconus (27%), a corneal disease that slowly deforms the cornea in young people; and sequellae of infectious keratitis (20%). The United States, with 199.10-6 corneal transplants per capita, had the highest transplantation rate, followed by Lebanon (122.10-6) and Canada (117.10-6), while the median of the 116 transplanting countries was 19.10-6. Corneas were procured in only 82 countries. Only the United States and Sri Lanka exported large numbers of donor corneas. About 53% of the world's population had no access to corneal transplantation. CONCLUSIONS AND RELEVANCE Our survey globally quantified the considerable shortage of corneal graft tissue, with only 1 cornea available for 70 needed. Efforts to encourage cornea donation must continue in all countries, but it is also essential to develop alternative and/or complementary solutions, such as corneal bioengineering.
Redactor: Reconcile network control with declarative control programs In SDN

With SDN control programs from multi-domains configuring the network, it is inevitable that control programs make conflicting control decisions, which probably lead to misconfiguration or performance degradation. Existing control coordination approaches either compose control programs to derive consistent solutions jointly or examine the generated rules of each control program to ensure they are consistent. However, the former is usually of great complexity and hard to be conducted automatically, and the latter probably results in suboptimal solutions due to the independent execution of control programs. Moreover, these approaches all fail to consider the control utility of control programs. In this paper, we propose Redactor to optimize the consistency and utility of network control in an automatic and dynamic manner. To make network control consistent, we implement SDN control programs with declarative language Prolog, and compose control programs automatically to execute together to make consistent decisions. When conflicts occur, we use a heuristic approach to compromise a subset of control programs to maximize the control utility. We compare Redactor with the static priority mechanism and Athens [1], and the results show that Redactor always satisfies more control objectives to achieve better control consistency and utility.
Fast accurate evaluation of protein solvent exposure

Protein solvation energies are often taken to be proportional to solvent‐accessible surface areas. Computation of these areas is numerically demanding and may become a bottleneck for folding and design applications. Fast graph‐based methods, such as dead‐end elimination (DEE), become possible if all energies, including solvation energies, are expressed as single‐residue and pair‐residue terms. To this end, Street and Mayo originated a pair‐residue approximation for solvent‐accessible surface areas (Street AG, Mayo SL. Pairwise calculation of protein solvent accessible surface areas. Fold Des 1998;3:253–258). The dominant source of error in this method is the overlapping burial of side‐chain surfaces in the protein core. Here we report a new pair‐residue approximation, which greatly reduces this overlap error by the use of optimized generic side‐chains. We have tested the generic‐side‐chain method for the ten proteins studied by Street and Mayo and for 377 single‐domain proteins from the CATH database (Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH‐A hierarchic classification of protein domain structures. Structure 1997;5:1093–1108). With little additional cost in computation, the new method consistently reduces error for total areas and residue‐by‐residue areas by more than a factor of two. For example, the residue‐by‐residue error (for buried area) is reduced from 7.42 Å2 to 3.70 Å2. This difference translates into a solvation energy difference of ∼0.2 kcal/mol per residue, amounting to a reduction in root‐mean‐square energy error of 2 kcal/mol for a 100 residue chain, a potentially critical difference for both protein folding and design applications. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Ensuring Multi Messages Broadcasting in Mobile Ad Hoc Network using Network Coding Approach

Problem statement: In mobile adhoc network, broadcasting is a common operation for route establishment and for sending control and emergency messages. Most of the existing broadcasting algorithms consider broadcasting from single source node and consider only single message broadcasting. Initiating multiple messages broadcasting from multiple sources is a challenging task which requires minimum number of retransmission made by the forwarding nodes. Approach: Network coding-based broadcasting was proposed which focuses on reducing the number of transmissions each forwarding node performs in the multiple source/multiple message broadcast application, where each forwarding node combines some of the received messages for transmission. We exploit the usage of directional antennas to network coding-based broadcasting to further reduce energy consumption. A node equipped with directional antennas could divided the omni directional transmission range into several sectors and turns some of them on for transmission. In the proposed scheme using a directional antenna, forwarding nodes selected locally only need to transmit broadcast messages, original or coded, to restricted sectors. Results: Simulation results show that the proposed method maximizes packet delivery ratio and throughput with reduced packet drop. Conclusion: The proposed network coding based broadcasting method reduces the total number of retransmissions made by the forwarding nodes compared to broadcasting using the same forwarding nodes without coding. Directional antennas are used to select the forwarding node set to maximize the throughput with minimal packet drop.
Perceptual disorders in schizophrenia.

Schizophrenia may involve a perceptual distortion characterized by an ontogenetically more primitive mode of perception in which parts of a whole are seen as separate and unrelated. In this study of perceptual distortion among four groups of patients, acute schizophrenic patients were least able to organize perceptual parts into a whole correctly. Chronic and recovered schizophrenic patients did better, although their responses still showed greater fragmentation of percepts than did those of the nonschizophrenic control group.
Backbone dynamics of Fusarium solani pisi cutinase probed by nuclear magnetic resonance: the lack of interfacial activation revisited.

The backbone dynamics of Fusarium solani pisi cutinase has been studied by a variety of nuclear magnetic resonance experiments to probe internal motions on different time scales. The core of cutinase appears to be highly rigid. The binding site, including the oxyanion hole, is mobile on the microsecond to millisecond time scale, in contrast to the well-defined active site and preformed oxyanion hole elucidated by X-ray crystallography [Martinez, C. , de Geus, P., Lauwereys, M. , Matthyssens, G. , and Cambillau, C. (1992) Nature 356, 615-618]. In this crystal structure, cutinase has a rather open conformation, in which the hydrophobic binding site is exposed. The observed mobility in solution most likely represents the interconversion between open and more closed conformations, like in a true lipase. The opening and closing motions are on a time scale which corresponds with the kinetics of the hydrolysis reaction, i.e., the millisecond range, which suggests that these conformational rearrangements form the rate-limiting step in catalysis. We conclude that the crystal structure probably represents one of the multiple conformations present in solution, which fortuitously is the active conformation. The implications of our findings are discussed with particular reference to the explanation of the lack of interfacial activation as found for cutinase.
Molecular Cloning and Characterization of the oprQ Gene Coding for Outer Membrane Protein OprE3 of Pseudomonas aeruginosa

We cloned and characterized the oprQ gene coding for outer membrane protein OprE3 of Pseudomonas aeruginosa PAO1. The oprQ gene was composed of 1,275 base pairs including a sequence encoding for the signal sequence and a mature protein with a Mr of 44,602. Computer‐aided alignment and hydropathy analyses of the predicted amino acid sequences suggested that OprE3 is a transmembrane protein homologous to outer membrane proteins of P. aeruginosa such as OprD2 (OprD) porin and OprE1 (OprE) porin. Susceptibility to several antibiotics of the strains lacking or overproducing OprE3 was indistinguishable from that of the wild‐type strain, suggesting that OprE3 is unlikely involved in the diffusion of carbapenems and other β‐lactam antibiotics.
Improved long-term survival after intra-operative single high-dose ATG-Fresenius induction in renal transplantation: a single centre experience.

BACKGROUND In organ grafts donor-specific sensitization is initiated immediately after revascularization. Therefore, in 1990 we introduced the intra-operative single high-dose ATG-Fresenius (ATG-F) induction in addition to standard triple drug therapy (TDT) consisting of steroids, azathioprine and cyclosporin. A total of 778 first renal transplantations from deceased donors, performed between 1987 and 1998, were included in this evaluation. MATERIAL/METHODS This retrospective analysis of clinic records and electronic databases presents data of all recipients of first kidney grafts who received two different ATG-F inductions (1(st) group: 9 mg/kg body weight as single high-dose intra-operatively, n=484; 2(nd) group: 3 mg/kg body weight on 7 or 8 consecutive days as multiple-dose starting also intra-operatively, n=78) and standard TDT alone (3(rd) group: TDT alone, n=216). RESULTS The 10-year patient survival rates were 72.6+/-2.6% (TDT + ATG-F single high-dose), 79.5+/-5.1% (TDT + ATG-F multiple-dose) and 67.2+/-3.7%% (TDT alone; Kaplan-Meier estimates with standard errors; ATG-F vs TDT alone, p=0.001). The 10-year graft survival rates with censoring of patients that died with a functioning graft were 73.8+/-2.4%, 57.7+/-5.8% and 58.4+/-3.6% (Kaplan-Meier estimates with standard errors; 1(st) vs 2(nd )and 3(rd) group, respectively, p<0.001) and the 10-year graft survival rates with patient death counted as graft failure were 58.3+/-2.7%, 55.7+/-5.8% and 48.2+/-3.5% (Kaplan-Meier estimates with standard errors; ATG-F single high-dose vs TDT, p=0.023). In pre-sensitized recipients there were also significant differences in favour of ATG-F, more notably in the single high-dose ATG-F induction. A total of 69% of the patients in the two cohorts receiving ATG-F did not experience any transplant rejections compared to 56% in patients undergoing TDT alone (p=0.018). The incidence of infectious complications was comparable across all groups. CONCLUSIONS According to evidence obtained from the routine documentation of 778 renal transplantations, ATG-F induction therapy administered as a part of immunosuppressive therapy significantly improves patient survival and reduces the risk of graft failure and transplant rejections.
On the Transient Behavior of Large-Scale Distribution Networks During Automatic Feeder Reconfiguration

The paper presents an in-depth analysis of the automatic reconfiguration and self-healing principles of the next generation (3G) smart grid of a real metropolitan distribution network. The large network is to be divided dynamically and remotely controlled into three smaller subnetworks to further increase the reliability of electrical power distribution secondary networks. When one subsection is experiencing difficulties, there is no longer the need to de-energize the entire network. A time-domain (EMTP) model has been developed and validated by comparing simulations with recordings of actual transient events. Different switching and fault scenarios are investigated using this model. Analysis of the results provides important conclusions on equipment rating, relay protection coordination, voltage regulation, switching and operation strategies which are discussed in the paper. A subset of these results is presented for illustration. This extensive study of a complex urban network suggests that: 1) before implementation of smart grid principles, it would be prudent to supplement steady-state analysis with time-domain analysis to avoid problems, such as installation of improperly rated equipment, and improper relay-protection coordination; and 2) EMTP-type programs may be used to conduct the time-domain analysis, despite the enormous number of elements contained in an urban network.
Emotion modeling using Fuzzy Cognitive Maps

In this study, Fuzzy Cognitive Map (FCM) modeling technique on emotion recognition problem with regression of arousal and valence values is applied and Big Bang - Big Crunch learning method is used for developing the model. Emotions play a critical role of humans' behaviors, beliefs, motivations and decisions. Developing a model between bodily responses and emotional states of a human is an extremely challenging problem in affective computing area. In this study, DEAP dataset, which is publicly available, is used as a dataset. The set contains the recordings of physiological modalities for participant, each participant viewing video clips and reporting emotional states with using self assessment manikins. The results of various simulations show that FCM is a useful and convenient tool for emotion modeling.