Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: a molecular dynamics study

We present here a structural analysis of ten extensive all-atom molecular dynamics simulations of the monomeric protein FtsZ in various binding states. Since the polymerization and GTPase activities of FtsZ depend on the nature of a bound nucleotide as well as on the presence of a magnesium ion, we studied the structural differences between the average conformations of the following five systems: FtsZ-Apo, FtsZ-GTP, FtsZ-GDP, FtsZ-GTP-Mg, and FtsZ-GDP-Mg. The in silico solvated average structure of FtsZ-Apo significantly differs from the crystallographic structure 1W59 of FtsZ which was crystallized in a dimeric form without nucleotide and magnesium. The simulated Apo form of the protein also clearly differs from the FtsZ structures when it is bound to its ligand, the most important discrepancies being located in the loops surrounding the nucleotide binding pocket. The three average structures of FtsZ-GTP, FtsZ-GDP, and FtsZ-GTP-Mg are overall similar, except for the loop T7 located at the opposite side of the binding pocket and whose conformation in FtsZ-GDP notably differs from the one in FtsZ-GTP and FtsZ-GTP-Mg. The presence of a magnesium ion in the binding pocket has no impact on the FtsZ conformation when it is bound to GTP. In contrast, when the protein is bound to GDP, the divalent cation causes a translation of the nucleotide outwards the pocket, inducing a significant conformational change of the loop H6-H7 and the top of helix H7.
Rabbit supraspinatus tendon detachment: Effects of size and time after tenotomy on morphometric changes in the muscle

We studied the effects of size and time after rabbit supraspinatus tenotomy (group A - small tenotomy, group B - large tenotomy) on muscle morphometric changes in 48 rabbits. Animals were killed 6 (subgroups A1 and B1), 12 (subgroups A2 and B2) and 24 weeks (subgroups A3 and B3) after tendon detachment. Statistically significantly greater increases in interstitium volume were noted in subgroups A1-A3 and B1-B3 than in controls. Reductions in type I and II fiber diameters were mainly due to the length of observation. However, statistically significant differences in comparison with controls appeared earlier after large tenotomy. The size of the tenotomy primarily affected muscle fiber composition. Our results suggest that these changes were caused by fiber transformation from type I to type II and vice versa. These findings indicate that the interdigitations between the supraspinatus and infraspinatus and between the supraspinatus and subscapularis tendons are important in dynamics and the degree of morphometric changes in the rabbit supraspinatus after tenotomy.
Antigenotoxic and Free Radical Scavenging Activities of Extracts from Moricandia arvensis

This study evaluates genotoxic and antigenotoxic effects of extracts from leaves of Moricandia arvensis, which are used in traditional cooking and medicines. Extracts showed no genotoxicity when tested with the SOS Chromotest using E. coli PQ37 and PQ35 strains, except for the total oligomers flavonoids enriched extract. Petroleum ether and methanol extracts are the most active in reducing nitrofurantoin genotoxicity, whereas methanol and total oligomers flavonoids enriched extracts showed the most important inhibitory effect of H2O2 genotoxicity. In addition, these two extracts showed important free radical scavenging activity toward the DPPH· radical, whereas the chloroform extract exhibited the highest value of TEAC against ABTS+· radical.
Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing

The ribosome small subunit is expressed in all living cells. It performs numerous essential functions during translation, including formation of the initiation complex and proofreading of base-pairs between mRNA codons and tRNA anticodons. The core constituent of the small ribosomal subunit is a ∼1.5 kb RNA strand in prokaryotes (16S rRNA) and a homologous ∼1.8 kb RNA strand in eukaryotes (18S rRNA). Traditional sequencing-by-synthesis (SBS) of rRNA genes or rRNA cDNA copies has achieved wide use as a ‘molecular chronometer’ for phylogenetic studies 1, and as a tool for identifying infectious organisms in the clinic 2. However, epigenetic modifications on rRNA are erased by SBS methods. Here we describe direct MinION nanopore sequencing of individual, full-length 16S rRNA absent reverse transcription or amplification. As little as 5 picograms (∼10 attomole) of E. coli 16S rRNA was detected in 4.5 micrograms of total human RNA. Nanopore ionic current traces that deviated from canonical patterns revealed conserved 16S rRNA base modifications, and a 7-methylguanosine modification that confers aminoglycoside resistance to some pathological E. coli strains. This direct RNA sequencing technology has promise for rapid identification of microbes in the environment and in patient samples.
Characterization and comparison of microsatellite markers derived from genomic and expressed libraries for the desert locust

The desert locust (Schistocerca gregaria) has been feared agricultural pest since early civilization, with plagues documented in ancient texts. Population genetic studies of the desert locust are needed to determine genetic variation and movement pattern for efficient control of the pest. In this study, we complemented the limited available microsatellite collection for the desert locust with 34 new polymorphic and multiplexed microsatellite loci. To this aim, we screened an expressed sequence tags library and constructed a partial genomic library enriched for dinucleotide repeats to develop high‐throughput and high‐quality genotyping assays. We then paid particular attention to quality control and carefully validated 26 of these novel microsatellites and six previously described loci for the absence of null alleles in Western African field populations. This large panel of high‐quality microsatellite markers provides new opportunity to infer dispersal rates between populations of the desert locust and help prioritize early monitoring and control. Furthermore, high potential for cross‐taxa utility of markers was observed within Schistocerca genus, which includes other locust pest species, with reliable amplification achieved for at least ten of loci per species. Microsatellite markers developed from transcriptome resources were largely devoid of null alleles and were conserved across species compared with those derived from traditional genomic libraries. Accordingly, the number of highly reliable microsatellite markers was greatly improved compared with that of previous studies on Orthopteran species, and this strategy might be broadly applied in other insect species prone to null alleles.
Improved beam search with constrained softmax for NMT

We propose an improved beam search decoding algorithm with constrained softmax operations for neural machine translation (NMT). NMT is a newly emerging approach to predict the best translation by building a neural network instead of a log-linear model. It has achieved comparable translation quality to the existing phrase-based statistical machine translation systems. However, how to perform efﬁcient decoding for NMT is still challenging, especially for commercial systems which provide real-time translation service. Unlike the standard beam search algorithm, we use a priority queue to choose the best hypothesis for the next search, which drastically reduces search space. Another time consuming factor is the softmax operation in the output layer because of the large target vocabulary size. To solve this problem, we introduce a limited word set of translation candidates to greatly reduce the computation complexity. Our experiments show that, under the GPU environment, our method achieves a speed about 3.5 times faster than the well optimized baseline system without sacriﬁcing the translation quality. Our method translates about 117 words per second, beating the real-time translation requirements for practical MT systems.
Large Amounts of Reactivated Virus in Tears Precedes Recurrent Herpes Stromal Keratitis in Stressed Rabbits Latently Infected with Herpes Simplex Virus

Abstract Aim: Recurrent herpetic stromal keratitis (rHSK), due to an immune response to reactivation of herpes simplex virus (HSV-1), can cause corneal blindness. The development of therapeutic interventions such as drugs and vaccines to decrease rHSK have been hampered by the lack of a small and reliable animal model in which rHSK occurs at a high frequency during HSV-1 latency. The aim of this study is to develop a rabbit model of rHSK in which stress from elevated temperatures increases the frequency of HSV-1 reactivations and rHSK. Materials and methods: Rabbits latently infected with HSV-1 were subjected to elevated temperatures and the frequency of viral reactivations and rHSK were determined. Results: In an experiment in which rabbits latently infected with HSV-1 were subjected to ill-defined stress as a result of failure of the vivarium air conditioning system, reactivation of HSV-1 occurred at over twice the normal frequency. In addition, 60% of eyes developed severe rHSK compared to <1% of eyes normally. All episodes of rHSK were preceded four to five days prior by an unusually large amount of reactivated virus in the tears of that eye and whenever this unusually large amount of reactivated virus was detected in tears, rHSK always appeared 4–5 days later. In subsequent experiments using well defined heat stress the reactivation frequency was similarly increased, but no eyes developed rHSK. Conclusions: The results reported here support the hypothesis that rHSK is associated not simply with elevated reactivation frequency, but rather with rare episodes of very high levels of reactivated virus in tears 4–5 days earlier.
Thyroid hormone early adjustment in pregnancy (the THERAPY) trial.

BACKGROUND Thyroid hormone requirement increases 20-40% during gestation. Women with treated hypothyroidism must increase their l-T(4) in pregnancy to prevent maternal hypothyroidism, although how this should be accomplished is unclear. METHODS We prospectively enrolled 60 women with treated hypothyroidism seeking pregnancy. Once pregnant, women were randomized to increase l-T(4) by either two tablets/wk (group A) or three tablets/wk (group B). Thyroid function was tested biweekly through midpregnancy and at 30 wk gestation. Levothyroxine was adjusted to maintain goal TSH concentrations. The primary objective was to assess efficacy in preventing maternal hypothyroidism and the safety of this intervention. RESULTS Forty-eight women completed the protocol. Increasing the l-T(4) dose once pregnant (regardless of study arm) prevented TSH elevation over 5.0 mIU/liter throughout the first trimester and replicated physiological changes of pregnancy. The early l-T(4) increase caused TSH suppression below 0.5 mIU/liter in eight of 25 women in group A compared with 15 of 23 women in group B (P < 0.01). This risk was significantly increased in athyreotic patients [odds ratio (OR) = 3.3; 95% confidence interval (CI) = 1.1-11.1], those with prepregnancy TSH less than 1.5 mIU/liter (OR = 4.6; 1.3-16.2), and those receiving prepregnancy l-T(4) doses of 100 microg/d or more (OR = 7.2; 1.7-30.6). However, if a trimester-specific TSH lower reference range of 0.1 mIU/liter was used, only two patients (8%) in group A required dose reduction. TSH testing every 4 wk identifies 92% of abnormal values. CONCLUSIONS A two-tablet increase in l-T(4) initiated at confirmation of pregnancy significantly reduces the risk of maternal hypothyroidism during the first trimester and mimics normal physiology. Monitoring TSH every 4 wk through midgestation is recommended.
Quantitative Microscopic Approaches for Studying Kidney Functions

Intravital ratiometric microscopy is a powerful method for quantitative study of kidney functions. As demonstrated in the examples, both the generalized polarity and direct ratio imaging approaches allow investigators to address basic and important questions such as those related to filtration, permeability and reabsorption. Both approaches have similar advantageous for in vivo imaging. However, they have different sensitivities and responses to the component intensity changes. Therefore, investigators must design their experiments based on the characteristics of the generalized polarity function and direct ratio approach.
The effects of canrenone on inflammatory markers in patients with metabolic syndrome

Abstract Aim. To evaluate the effects of canrenone compared to placebo on blood pressure control, some non-conventional biomarkers in cardiovascular stratification, and on metalloproteinases in patients affected by metabolic syndrome. Methods. A total of 156 Caucasian patients were treated with placebo or canrenone, 50 mg once a day, for 3 months and then 50 mg twice a day, till the end of the study. We evaluated: systolic (SBP) and diastolic blood pressure (DBP), body weight, body mass index (BMI), fasting plasma glucose (FPG), lipid profile, plasma aldosterone, creatinine, potassium, brain natriuretic peptide (BNP), metalloproteinases 2 and 9 (MMP-2 and -9), lipoprotein (a) (Lp(a)), and serum myeloperoxidase (MPO). Results. We observed a significant decrease of SBP and DBP in the canrenone group compared to baseline. Canrenone gave a significant decrease of MMP-2 and -9, Lp(a), and MPO compared to baseline, not observed with placebo. Plasma aldosterone, but not BNP, decreased with canrenone, both compared to baseline and to placebo. Conclusion. Canrenone seems to be effective in reducing blood pressure in patients with metabolic syndrome. Moreover, canrenone seems also to improve MPO, Lp(a), and metalloproteinases in these patients. Trial registration: ClinicalTrials.gov identifier: NCT02064218.
Hybrid Integration of Differential Evolution with Artificial Bee Colony for Global Optimization

In this paper, we investigate the hybridization of a swarm intelligence algorithm and an evolutionary algorithm, namely, the Artificial Bee Colony (ABC) algorithm and Differential Evolution (DE), to solve continuous optimization problems. This Hybrid Integration of DE and ABC (HIDEABC) technique is based on integrating the DE algorithm with the principle of ABC to improve the neighborhood search for each particle in ABC. The swarm intelligence of the ABC algorithm and the global information obtained by the DE population approach facilitate balanced exploration and exploitation using the HIDEABC algorithm. All algorithms were applied to five benchmark functions and were compared using several different metrics.
Endogenous gamma interferon is essential in granuloma formation induced by glycolipid-containing mycolic acid in mice

The present study examined the role of endogenous gamma interferon (IFN-gamma) in the formation of granulomas in mice which had been given a single intravenous injection of glycolipid-containing mycolic acid (trehalose 2,3,6'-trimycolate) purified from cell walls of Rhodococcus aurantiacus (Gordona aurantiaca) (GaGM) in the form of liposome. The histological status of granuloma formation in the livers, spleens, and lungs of GaGM-injected mice was studied at weeks 1 through 5, and the titers of endogenous IFN-gamma in all of these organ extracts and in the sera were determined by enzyme-linked immunosorbent assay. The granulomas, composed of epithelioid cells, developed until 3 weeks postinjection, and thereafter the granulomas regressed. The production of endogenous IFN-gamma was biphasic, with an early phase detected at days 1 through 3 and a late phase detected at weeks 1 through 5. The latter peak of endogenous IFN-gamma production proceeded in parallel with granuloma formation. Both the areas of granulomas and titers of IFN-gamma in these organs were dependent on the doses of GaGM used for injection. The cells which produce endogenous IFN-gamma in the spleens appear within the granulomas. To study the role of endogenous IFN-gamma in granuloma formation, the in vivo administration of rat anti-mouse IFN-gamma monoclonal antibody was carried out. Anti-mouse IFN-gamma monoclonal antibody neutralized endogenous IFN-gamma and resulted in the suppression of the number of granulomas and the size of each granuloma. These findings suggest that biphasic production of endogenous IFN-gamma in the local lesions may be crucial to the formation and development of the granulomas.
Mitral valve annuloplasty: comparison of the mural annulus shortening suture (MASS) with the Carpentier-Edwards prosthetic ring.

BACKGROUND AND AIM OF THE STUDY Although mitral annuloplasty is an important element of mitral valve repair, the technique employed remains controversial. In this prospective study, we compared two different annuloplasty techniques with regard to hemodynamic performance. METHODS Between October 1995 and December 1998, 109 consecutive patients underwent mitral valve repair for mitral regurgitation. One group of patients (n = 55) received a Carpentier-Edwards (CE) ring for annuloplasty, and a second group (n = 54) underwent the mural annulus shortening suture (MASS) to reinforce the posterior circumference of the annulus. All patients were investigated prospectively by Doppler echocardiography before discharge and annually thereafter. The mean follow up was 22.7+/-11.6 months. RESULTS The early mortality rate was 3.7%, with four early deaths in the CE group, and no early death in the MASS group. There was one late death in each group. One patient in each group required reoperation for severe mitral regurgitation after 19 and 30 months, respectively. Postoperative (12 months) Doppler echocardiography showed mean mitral valve gradients to be significantly lower (1.7+/-0.7 versus 2.7+/-1.7 mmHg; p <0.01) and mitral valve areas significantly larger (3.3+/-1.0 versus 2.6+/-0.7 cm2; p <0.01) in MASS patients compared with CE patients. There was no significant difference in mean postoperative mitral regurgitation between the two groups (0.5+/-0.2 versus 0.4+/-0.2). CONCLUSION Both annuloplasty techniques showed excellent results; however, hemodynamic performance of MASS was superior to that of the rigid CE ring, while not increasing postoperative mitral regurgitation. Therefore, MASS may be recommended as an alternative to annuloplasty rings, if future long-term follow up studies confirm the durability of the technique.
Process Management Conceptual Evolution Map

Process management concepts have been present within the modern organizational development since its early days. Since then, we have been able to detect many changes, challenges and improvements that occurred in the field during the past century with the primary aim remaining unchanged: defining and optimizing organizational processes in order to achieve better business results. This paper discusses the field of process management from three angles: the evolution through time, the architecture of the concepts and the notable interaction within the scope of its evolution. The significant contribution of this paper is a development of the graphical conceptual evolution map built on the basis of the three perspectives, revealing the complexity and the impact of the process management in last two decades as well as the indication for the future development. It is a simple tool for improving the understanding of how the conceptual evolution has influenced what are today known as Business process management systems. During the research phase we concluded that relations, connections and time scopes of many different approaches under the concept of process management have not been specifically evaluated or discussed. This providedthe framework for the proposed conceptual evolution map with the opportunity for future expansion and additional shaping with new details.
The accessibility of vulnerable groups to health services in Greece: a Delphi study on the perceptions of health professionals.

BACKGROUND Problems of accessibility to healthcare services notably affect certain population groups such as poor and unemployed people, migrants and minorities, thus having a negative impact on their health. The aim of this study was to investigate these problems from the perspective of health professionals and to formulate empirically informed suggestions to solve the issue. METHODS Primary data were collected in 2010-2011 by using a panel of 36 experienced health professionals around Greece. A two-round Delphi method was undertaken to achieve the objectives of the study. The first questionnaire investigated the factors that hinder accessibility to health services. The second round aimed at determining the relative importance of each of the factors emerging in the first round. RESULTS The group of experts identified 345 factors in the first round, which were grouped in 55 statements. Consensus was achieved in 22 statements. The study revealed important issues, and health professionals proposed a number of actions to eliminate the accessibility problems. CONCLUSIONS The use of medical interpreters and cultural mediators, transcultural education and stronger linkages among medical facilities are important to reduce accessibility problems. Restructuring primary healthcare and better documenting of the beneficiaries could also improve the quality of provided healthcare services.
Distributed Secondary Control for Islanded MicroGrids - A Novel Approach

 Abstract — This paper presents a novel approach to conceive the secondary control in droop-controlled MicroGrids. The conventional approach is based on restoring the frequency and amplitude deviations produced by the local droop controllers by using a MicroGrid Central Controller (MGCC). A distributed networked control system is used in order to implement a distributed secondary control (DSC) thus avoiding its implementation in MGCC. The proposed approach is not only able to restore frequency and voltage of the MicroGrid but also ensures reactive power sharing. The distributed secondary control does not rely on a central control, so that the failure of a single unit will not produce the fail down of the whole system. Experimental results are presented to show the feasibility of the DSC. The time latency and data drop-out limits of the communication systems are studied as well.
Effect of Interplanetary Shocks on the AL and Dst Indices

The question of how much interplanetary shock (IP) events contribute to the geoeffectiveness of solar wind drivers is assessed through numerical experiments using the WINDMI model, a physics‐based model of the solar wind‐driven magnetosphere‐ionosphere system. Analytic fits to solar wind input parameters (B⊥IMF, usw, nsw) allowed shocks and associated shock‐sheath plasma to be removed while leaving other features of the solar wind driver undisturbed. Percent changes in WINDMI‐derived AL and Dst indices between runs with and without the observed shock and sheath signatures were taken as a measure of its relative contribution to the geoeffectiveness. The major magnetic storms during 15–24 April 2002 and 3–6 October 2000 were selected for this experiment. In both cases, the IP shock and sheath features contributed significantly to the geoeffectiveness of the solar wind driver. The magnetic field compressional jump is important to producing the changes in the AL during these two storm intervals.