Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Sciences Prediction of Protein S-nitrosylation Sites Based on Adapted Normal Distribution Bi-profile Bayes and Chou's Pseudo Amino Acid Composition

Protein S-nitrosylation is a reversible post-translational modification by covalent modification on the thiol group of cysteine residues by nitric oxide. Growing evidence shows that protein S-nitrosylation plays an important role in normal cellular function as well as in various pathophysiologic conditions. Because of the inherent chemical instability of the S-NO bond and the low abundance of endogenous S-nitrosylated proteins, the unambiguous identification of S-nitrosylation sites by commonly used proteomic approaches remains challenging. Therefore, computational prediction of S-nitrosylation sites has been considered as a powerful auxiliary tool. In this work, we mainly adopted an adapted normal distribution bi-profile Bayes (ANBPB) feature extraction model to characterize the distinction of position-specific amino acids in 784 S-nitrosylated and 1568 non-S-nitrosylated peptide sequences. We developed a support vector machine prediction model, iSNO-ANBPB, by incorporating ANBPB with the Chou's pseudo amino acid composition. In jackknife cross-validation experiments, iSNO-ANBPB yielded an accuracy of 65.39% and a Matthew's correlation coefficient (MCC) of 0.3014. When tested on an independent dataset, iSNO-ANBPB achieved an accuracy of 63.41% and a MCC of 0.2984, which are much higher than the values achieved by the existing predictors SNOSite, iSNO-PseAAC, the Li et al. algorithm, and iSNO-AAPair. On another training dataset, iSNO-ANBPB also outperformed GPS-SNO and iSNO-PseAAC in the 10-fold crossvalidation test.
Comparative and functional genomics of the innate immune system in the malaria vector Anopheles gambiae

Summary: In much of Africa, the mosquito Anopheles gambiae is the major vector of human malaria, a devastating infectious disease caused by Plasmodium parasites. Vector and parasite interact at multiple stages and locations, and the nature and effectiveness of this reciprocal interaction determines the success of transmission. Many of the interactions engage the mosquito's innate immunity, a primitive but very effective defense system. In some cases, the mosquito kills the parasite, thus blocking the transmission cycle. However, not all interactions are antagonistic; some represent immune evasion. The sequence of the A. gambiae genome revealed numerous potential components of the innate immune system, and it established that they evolve rapidly, as summarized in the present review. Their rapid evolution by gene family expansion diversification as well as the prevalence of haplotype alleles in the best‐studied families may reflect selective adaptation of the immune system to the exigencies of multiple immune challenges in a variety of ecologic niches. As a follow‐up to the comparative genomic analysis, the development of functional genomic methodologies has provided novel opportunities for understanding the immune system and the nature of its interactions with the parasite. In this context, identification of both Plasmodium antagonists and protectors in the mosquito represents a significant conceptual advance. In addition to providing fundamental understanding of primitive immune systems, studies of mosquito interactions with the parasite open unprecedented opportunities for novel interventions against malaria transmission. The generation of transgenic mosquitoes that resist malaria infection in the wild and the development of antimalarial ‘smart sprays’ capable of disrupting interactions that are protective of the parasite, or reinforcing others that are antagonistic, represent technical challenges but also immense opportunities for improvement of global health.
Sem1 is a functional component of the nuclear pore complex–associated messenger RNA export machinery

The evolutionarily conserved protein Sem1/Dss1 is a subunit of the regulatory particle (RP) of the proteasome, and, in mammalian cells, binds the tumor suppressor protein BRCA2. Here, we describe a new function for yeast Sem1. We show that sem1 mutants are impaired in messenger RNA (mRNA) export and transcription elongation, and induce strong transcription-associated hyper-recombination phenotypes. Importantly, Sem1, independent of the RP, is functionally linked to the mRNA export pathway. Biochemical analyses revealed that, in addition to the RP, Sem1 coenriches with components of two other multisubunit complexes: the nuclear pore complex (NPC)-associated TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation. Notably, targeting of Thp1, a TREX-2 component, to the NPC is perturbed in a sem1 mutant. These findings reveal an unexpected nonproteasomal function of Sem1 in mRNA export and in prevention of transcription-associated genome instability. Thus, Sem1 is a versatile protein that might stabilize multiple protein complexes involved in diverse pathways.
Solar irradiance estimation based on photovoltaic module short circuit current measurement

This paper presents the estimation method of solar irradiance in W/m2 based on the short circuit current output produce by the photovoltaic module. The proposed solar irradiance estimation method is derived using photovoltaic mathematical model. Therefore, photovoltaic module modeling is required to develop the proposed estimation method. The modeling includes the identification of photovoltaic module diode ideality factor using recursive iteration and series resistance identification using photovoltaic model equation. The reminding modeling parameters can be obtained from the given photovoltaic module manufacturer datasheet. With all the required parameters in place the solar irradiance can be estimated using equation derived from the photovoltaic model. The proposed solar irradiance estimation method is evaluated using a 80W 36 cells polycrystalline photovoltaic module in the field and the results are validated with a World Meteorological Organization certified second class pyranometer. This paper demonstrates that the solar irradiance can be estimated by the short circuit current output measured from the photovoltaic module with acceptable accuracy. This contributes to the elimination of the installation of expensive pyranometer.
Study on Dynamical Mechanism of Industrial Agglomeration Innovation System

The innovative advantages of industrial agglomeration lie in innovation cluster. From the perspective of innovation network system, industrial agglomeration innovation system is a special system,which includes enterprises, governments,universities, research institutes, financial institutions, and intermediary service agencies. The realization of industrial agglomeration innovation depends on the stress and motivity inspired by the clusters' innovation.It is affected by special requirement, promotion from competition and cooperation, cluster learning mechanism, organization innovation mechanism, as well as the stimulation of local resources and industrial circumstances.So we should apply the dynamical mechanisms of industrial agglomeration innovation,and take some appropriate measures to ensure the effective operation of the mechanism.
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification

Abstract Motivation Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process. Results Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results. Availability and implementation ClinOmicsTrailbc can be freely accessed at https://clinomicstrail.bioinf. uni-sb.de. Supplementary information Supplementary data are available at Bioinformatics online.
Isolation and Characterization of Two Members of the Siderophore-Microcin Family , Microcins M and H 47

In this paper we provide the first biochemical evidence of the existence of a family of structure-related antimicrobial peptides, the siderophore-microcins, in the Enterobacteriaceae family. We isolated and characterized two novel siderophore-microcins, MccM and MccH47, previously characterized through genetic studies. MccM and MccH47 were expressed from several Escherichia coli strains containing the microcin gene clusters. The spectra of their bactericidal activities were found to be restricted to some species of the Enterobacteriaceae. MccM and MccH47 were unable to inhibit the growth of strains carrying mutations in the fepA, cir, and fiu genes, which showed the requirement of the iron-catecholate receptors for their recognition. The MccM and MccH47 peptide moieties contain 77 and 60 residues, respectively, and are derived from the microcin precursors McmA and MchB, respectively. In addition, both peptides carried a C-terminal posttranslational modification containing a salmochelin-like siderophore moiety also found in MccE492 (X. Thomas et al., J. Biol. Chem., 279:28233–28242, 2004). Interestingly, when MccM was isolated from E. coli Nissle 1917, which lacks the two genes necessary for modification biosynthesis, it was devoid of posttranslational modification. Those two genes could be complemented by their homologues from the MccH47 gene cluster, thereby showing their functional interchangeability between at least two members of the siderophore-microcin family. Finally, from the sequence analysis of the MccE492 gene cluster, we hypothesized the existence of an additional member of the siderophore-microcin family. Therefore, we propose that the siderophore-microcin family contains five representatives.
Moniliformin production and toxicity of different Fusarium species from Southern Africa

Four new moniliformin-producing species of Fusarium were found, viz., F. acuminatum, F. concolor, F. equiseti, and F. semitectum. Isolates of F. acuminatum and F. concolor produced large amounts of moniliformin (3.4 and 9.5 g/kg, respectively), whereas isolates of the other three species yielded less than 30 mg/kg. The production of moniliformin by isolates of F. oxysporum and F. avenaceum from southern Africa is described. All 14 toxic isolates of F. oxysporum produced moniliformin. Most isolates of F. fusarioides and all six isolates of Fusarium moniliforme va. subglutinans tested produced moniliformin, as did 28 of 36 toxic isolates of F. moniliforme. A number of F. moniliforme isolates produced greater than 10 g/kg, and one isolate yielded 33.7 g/kg in corn after incubation for 5 weeks at 25 degrees C. Moniliformin production in the field in corn ears was shown by inoculating plants with known moniliformin-producing isolates of three Fusarium species. Yields of up to 645 mg/kg were recorded. Isolates of F. acuminatum, F. equiseti, F. fusarioides, and F. moniliforme were found that were highly toxic to ducklings but which did not produce moniliformin.
Phase II Study of Lutetium-177–Labeled Anti-Prostate-Specific Membrane Antigen Monoclonal Antibody J591 for Metastatic Castration-Resistant Prostate Cancer

Purpose: To assess the efficacy of a single infusion of radiolabeled anti-prostate-specific membrane antigen (PSMA) monoclonal antibody J591 (lutetium-177; 177Lu) by prostate-specific antigen (PSA) decline, measurable disease response, and survival. Experimental Design: In this dual-center phase II study, two cohorts with progressive metastatic castration-resistant prostate cancer received one dose of 177Lu-J591 (15 patients at 65 mCi/m2, 17 at 70 mCi/m2) with radionuclide imaging. Expansion cohort (n = 15) received 70 mCi/m2 to verify response rate and examine biomarkers. Results: Forty-seven patients who progressed after hormonal therapies (55.3% also received prior chemotherapy) received 177Lu-J591. A total of 10.6% experienced ≥50% decline in PSA, 36.2% experienced ≥30% decline, and 59.6% experienced any PSA decline following their single treatment. One of 12 with measurable disease experienced a partial radiographic response (8 with stable disease). Sites of prostate cancer metastases were targeted in 44 of 47 (93.6%) as determined by planar imaging. All experienced reversible hematologic toxicity, with grade 4 thrombocytopenia occurring in 46.8% (29.8% received platelet transfusions) without significant hemorrhage. A total of 25.5% experienced grade 4 neutropenia, with one episode of febrile neutropenia. The phase I maximum tolerated dose (70 mCi/m2) resulted in more 30% PSA declines (46.9% vs. 13.3%, P = 0.048) and longer survival (21.8 vs. 11.9 months, P = 0.03), but also more grade 4 hematologic toxicity and platelet transfusions. No serious nonhematologic toxicity occurred. Those with poor PSMA imaging were less likely to respond. Conclusion: A single dose of 177Lu-J591 was well tolerated with reversible myelosuppression. Accurate tumor targeting and PSA responses were seen with evidence of dose response. Imaging biomarkers seem promising. Clin Cancer Res; 19(18); 5182–91. ©2013 AACR.
Putting the Scientist in the Loop -- Accelerating Scientific Progress with Interactive Machine Learning

Technology drives advances in science. Giving scientists access to more powerful tools for collecting and understanding data enables them to both ask and answer new kinds questions that were previously beyond their reach. Of these new tools at their disposal, machine learning offers the opportunity to understand and analyze data at unprecedented scales and levels of detail. The standard machine learning pipeline consists of data labeling, feature extraction, training, and evaluation. However, without expert machine learning knowledge, it is difficult for scientists to optimally construct this pipeline to fully leverage machine learning in their work. Using ecology as a motivating example, we analyze a typical scientist's data collection and processing workflow and highlight many problems facing practitioners when attempting to capitalize on advances in machine learning and pattern recognition. Understanding these shortcomings allows us to outline several novel and underexplored research directions. We end with recommendations to motivate progress in future cross-disciplinary work.
Transparent Exploration of Remote Environments by Internet Telepresence

This paper presents control methods for haptic telepresence and teleaction systems with Internet communication. Human rescuing systems are considered as one of the important application areas of telepresence technology. The stability and performance of telepresence systems with kinesthetic (force) feedback operated via a communication network with time-varying delay and underlying packet nature as for example the Internet is discussed. A stability condition in discrete time is derived from the continuous time case for time varying delays. In experiments being the first steps towards a multimodal telepresence system with rescue and other applications the system performance in terms of transparency is compared for the standard velocity/force architecture and the newly proposed position/velocity/force architecture.
Emerging and re-emerging viruses of the honey bee (Apis mellifera L.)

Until the late 1980s, specific viral infections of the honey bee were generally considered harmless in all countries. Then, with the worldwide introduction of the ectoparasite mite Varroa destructor, beekeepers encountered increasing difficulties in maintaining their colonies. Epidemiological surveys and laboratory experiments have demonstrated that the newly acquired virulence of several viruses belonging to the family Dicistroviridae (acute bee paralysis virus, Kashmir bee virus and Israeli acute paralysis virus) in Europe and the USA had been observed in relation with V. destructor acting as a disseminator of these viruses between and within bee colonies and as an activator of virus multiplication in the infected individuals: bee larvae and adults. Equal emphasis is given to deformed wing virus (DWV) belonging to the Iflaviridae. Overt outbreaks of DWV infections have been shown to be linked to the ability of V. destructor to act not only as a mechanical vector of DWV but also as a biological vector. Its replication in mites prior to its vectoring into pupae seemed to be necessary and sufficient for the induction of a overt infection in pupae developing in non-viable bees with deformed wings. DWV in V. destructor infested colonies is now considered as one of the key players of the final collapse. Various approaches for combating bee viral diseases are described: they include selection of tolerant bees, RNA interference and prevention of new pathogen introduction. None of these approaches are expected to lead to enhanced bee-health in the short term.
Ranolazine ( Ranexa ® ) for Chronic Stable Angina Issues in Emerging Health Technologies Summary

In three randomized controlled trials (RCTs), ranolazine, in combination with standard antianginal medications, led to modest but statistically significant improvements in exercise duration, and reductions in the frequency of angina episodes and nitroglycerin consumption, when compared to standard antianginal medications only. The clinical significance of these improvements is unknown. Most of the participants in studies were male and Caucasian. Thus, there are questions about the drug’s efficacy in other populations.
Dynamic Buffer Management for Multimedia QoS in Beyond 3G Wireless Networks

This paper investigates a dynamic buffer man- agement scheme for QoS control of multimedia services in be- yond 3G wireless systems. The scheme is studied in the context of the state-of-the-art 3.5G system i.e. the High Speed Downlink Packet Access (HSDPA) which enhances 3G UMTS to support high-speed packet switched services. Unlike earlier systems, UMTS-evolved systems from HSDPA and beyond incorporate mechanisms such as packet scheduling and HARQ in the base station necessitating data buffering at the air interface. This introduces a potential bottleneck to end-to-end communication. Hence, buffer management at the air interface is crucial for end-to-end QoS support of multimedia services with multi- plexed parallel diverse flows such as video and data in the same end-user session. The dynamic buffer management scheme for HSDPA multimedia sessions with aggregated real-time and non real-time flows is investigated via extensive HSDPA simulations. The impact of the scheme on end-to-end traffic performance is evaluated with an example multimedia session comprising a real-time streaming flow concurrent with TCP-based non real-time flow. Results demonstrate that the scheme can guar- antee the end-to-end QoS of the real-time streaming flow, whilst simultaneously protecting the non real-time flow from starva- tion resulting in improved end-to-end throughput performance.
Optimal Vehicle Routing and Scheduling with Precedence Constraints and Location Choice

To realize the vision of intelligent transportation systems with fully automated vehicles, there is a need for highlevel planning for single vehicles as well as fleets of vehicles. This paper addresses the problem of optimally assigning and scheduling a set of spatially distributed tasks to a fleet of vehicles working together to achieve a high-level goal, in domains where tasks may be related by precedence or synchronization constraints and might have a choice of locations at which they can be performed. Such problems may arise, for example, in disaster preparedness planning, transportation of people, and delivery of supplies. We present a novel mathematical model of the problem and describe how it can be solved optimally in a branch-and-price framework.
Frontal lobe neurology and the creative mind

Concepts from cognitive neuroscience strongly suggest that the prefrontal cortex (PFC) plays a crucial role in the cognitive functions necessary for creative thinking. Functional imaging studies have repeatedly demonstrated the involvement of PFC in creativity tasks. Patient studies have demonstrated that frontal damage due to focal lesions or neurodegenerative diseases are associated with impairments in various creativity tasks. However, against all odds, a series of clinical observations has reported the facilitation of artistic production in patients with neurodegenerative diseases affecting PFC, such as frontotemporal dementia (FTD). An exacerbation of creativity in frontal diseases would challenge neuroimaging findings in controls and patients, as well as the theoretical role of prefrontal functions in creativity processes. To explore this paradox, we reported the history of a FTD patient who exhibited the emergence of visual artistic productions during the course of the disease. The patient produced a large amount of drawings, which have been evaluated by a group of professional artists who were blind to the diagnosis. We also reviewed the published clinical cases reporting a change in the artistic abilities in patients with neurological diseases. We attempted to reconcile these clinical observations to previous experimental findings by addressing several questions raised by our review. For instance, to what extent can the cognitive, conative, and affective changes following frontal damage explain changes in artistic abilities? Does artistic exacerbation truly reflect increased creative capacities? These considerations could help to clarify the place of creativity—as it has been defined and explored by cognitive neuroscience—in artistic creation and may provide leads for future lesion studies.
The potential for reducing differences in life expectancy between educational groups in five European countries: the effects of obesity, physical inactivity and smoking

Introduction This study assesses the effects of obesity, physical inactivity and smoking on life expectancy (LE) differences between educational groups in five European countries in the early 2000s. Methods We estimate the contribution of risk factors on LE differences between educational groups using the observed risk factor distributions and under a hypothetically more optimal risk factor distribution. Data on risk factor prevalence were obtained from the Survey of Health, Ageing and Retirement in Europe study, and data on mortality from census-linked data sets for the age between 50 and 79 according to sex and education. Results Substantial differences in LE of up to 2.8 years emerged between men with a low and a high level of education in Denmark, Austria and France, and smaller differences among men in Italy and Spain. The educational differences in LE were not as large among women. The largest potential for reducing educational differences was in Denmark (25% among men and 41% among women) and Italy (14% among men). Conclusions The magnitude of the effect of unhealthy behaviours on educational differences in LE varied between countries. LE among those with a low or medium level of education could increase in some European countries if the behavioural risk factor distributions were similar to those observed among the highly educated.