Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphotectonic analysis of the East Anatolian Fault, Turkey

The East Anatolian Fault (EAF) is a morphologically distinct and seismically active left-lateral strike-slip fault that extends for ~400 km and forms the Arabian/Anatolian plate boundary in southeastern Turkey. The EAF together with its conjugate fault, the North Anatolian Fault, help accommodate the westward escape of the Anatolian plate from the Arabian/Eurasian collision zone. Morphotectonic features along the EAF provide insights into the nature of landscape development and aid in understanding variations in tectonic activity and fault evolution. Several geomorphic indices, namely stream length-gradient index, mountain-front sinuosity, valley width to valley height ratio, basin asymmetry factor, and drainage density, and hypsometric analysis were examined using digital elevation models. The EAF can be divided into five segments based on its tectonic geomorphology. The stream length-gradient index values are between 50 and 350 along the five segments. Mountain-front sinuosity varies from 1.01 to 1.46 on the five segments. The mean ratio of valley floor width to valley height along the studied segments ranges from 0.11 to 1.32, which is well correlated with the mountain-front sinuosity values. Basin asymmetry factors for 18 catchments range from 1.88 to 26.25 along the study fault zone. Drainage density values for the studied catchments range from 3.5 to 5.6. Finally, the hypsometric analysis index of the 18 catchments indicates high, intermediate, and low relative tectonic activity. The results show that all geomorphic indices are remarkably uniform along the entire length of the fault, thus indicating that fault development was essentially coeval along its length, which supports the view that the present-day Arabian/Anatolian plate boundary (delimited by the EAF) jumped eastwards from the Malatya-Ovacik Fault at ~3 Ma. This is in good agreement with the nearly uniform geological offsets and the GPS-determined present-day slip rate of ~10 mm/year along the entire fault.
ERD-Based Online Brain–Machine Interfaces (BMI) in the Context of Neurorehabilitation: Optimizing BMI Learning and Performance

Event-related desynchronization (ERD) of sensori-motor rhythms (SMR) can be used for online brain-machine interface (BMI) control, but yields challenges related to the stability of ERD and feedback strategy to optimize BMI learning. Here, we compared two approaches to this challenge in 20 right-handed healthy subjects (HS, five sessions each, S1-S5) and four stroke patients (SP, 15 sessions each, S1-S15). ERD was recorded from a 275-sensor MEG system. During daily training, motor imagery-induced ERD led to visual and proprioceptive feedback delivered through an orthotic device attached to the subjects' hand and fingers. Group A trained with a heterogeneous reference value (RV) for ERD detection with binary feedback and Group B with a homogenous RV and graded feedback (10 HS and 2 SP in each group). HS in Group B showed better BMI performance than Group A (p <; 0.001) and improved BMI control from S1 to S5 ( p=0.012) while Group A did not. In spite of the small n, SP in Group B showed a trend for a higher BMI performance ( p=0.06) and learning was significantly better ( p <; 0.05). Using a homogeneous RV and graded feedback led to improved modulation of ipsilesional activity resulting in superior BMI learning relative to use of a heterogeneous RV and binary feedback.
Pericardial Fat and Myocardial Perfusion in Asymptomatic Adults from the Multi-Ethnic Study of Atherosclerosis

Background Pericardial fat has adverse effects on the surrounding vasculature. Previous studies suggest that pericardial fat may contribute to myocardial ischemia in symptomatic individuals. However, it is unknown if pericardial fat has similar effects in asymptomatic individuals. Methods We determined the association between pericardial fat and myocardial blood flow (MBF) in 214 adults with no prior history of cardiovascular disease from the Minnesota field center of the Multi-Ethnic Study of Atherosclerosis (43% female, 56% Caucasian, 44% Hispanic). Pericardial fat volume was measured by computed tomography. MBF was measured by MRI at rest and during adenosine-induced hyperemia. Myocardial perfusion reserve (PR) was calculated as the ratio of hyperemic to resting MBF. Results Gender-stratified analyses revealed significant differences between men and women including less pericardial fat (71.9±31.3 vs. 105.2±57.5 cm3, p<0.0001) and higher resting MBF (1.12±0.23 vs. 0.93±0.19 ml/min/g, p<0.0001), hyperemic MBF (3.49±0.76 vs. 2.65±0.72 ml/min/g, p<0.0001), and PR (3.19±0.78 vs. 2.93±0.89, p = 0.03) in women. Correlations between pericardial fat and clinical and hemodynamic variables were stronger in women. In women only (p = 0.01 for gender interaction) higher pericardial fat was associated with higher resting MBF (p = 0.008). However, this association was attenuated after accounting for body mass index or rate-pressure product. There were no significant associations between pericardial fat and hyperemic MBF or PR after multivariate adjustment in either gender. In logistic regression analyses there was also no association between impaired coronary vasoreactivity, defined as having a PR <2.5, and pericardial fat in men (OR, 1.18; 95% CI, 0.82–1.70) or women (OR, 1.11; 95% CI, 0.68–1.82). Conclusions Our data fail to support an independent association between pericardial fat and myocardial perfusion in adults without symptomatic cardiovascular disease. Nevertheless, these findings highlight potentially important differences between asymptomatic and symptomatic individuals with respect to the underlying subclinical disease burden.
Dental Follicle Cells Participate in Tooth Eruption via the RUNX2-MiR-31-SATB2 Loop

Cleidocranial dysplasia (CCD) is characterized by the runt-related transcription factor 2 (RUNX2) mutation, which results in delayed tooth eruption due to disturbed functions of dental follicle. Accumulating evidence has revealed a key regulatory circuit, including RUNX2, miR-31, and special AT-rich binding protein 2 (SATB2) acting in concert in mesenchymal stem cell homeostasis and functions. However, whether such a regulatory loop works in dental follicle cells (DFCs) remains unknown. Herein, we investigated the roles of RUNX2-miR-31-SATB2 in DFCs from patients with CCD (DFCs-CCD) to advance our understanding regarding physical tooth eruption. We identified a novel mutation on exon 5 (c.634T>G, p.T212P) in RUNX2 via exome sequencing in the CCD patient with typical clinical presentations. Compared with DFCs from healthy donors, DFCs-CCD displayed significantly lower osteogenic, osteoclast-inductive, and matrix-degrading capacities and had lower RUNX2 (a transcriptional inhibitor of miR-31), higher miR-31, and downregulated SATB2. Lower ratios of RANKL/OPG and RANKL/RANK, as well as decreased expression of matrix metalloproteinase 9 (MMP9) and matrix metalloproteinase 2 (MMP2), would lead to inactivation of osteoclasts and suppression of bone matrix remodeling in DFCs-CCD. Furthermore, the roles of the RUNX2-miR-31-SATB2 loop in DFCs-CCD were revealed by endogenous miR-31 knockdown, which resulted in increased SATB2 and RUNX2, as well as osteoclast-inductive and matrix degradation capacities. Conversely, SATB2, RUNX2, MMP9, MMP2, and osteoclast-inductive factors expression declined upon ectopic miR-31 overexpression in normal DFCs. Importantly, neonatal mice with in vivo siRUNX2 delivery exhibited less activated osteoclasts around dental follicles and delayed tooth eruption. Together, these results suggest that RUNX2 mutation/haploinsufficiency disturbs osteoclast-inductive signaling in DFCs, which may be responsible for delayed tooth eruption in CCD patients. Manipulation of the RUNX2-miR-31-SATB2 loop may be a potential way to facilitate tooth eruption in CCD patients.
Seroprevalence and molecular diagnosis of Toxoplasma gondii infection among blood donors in southern Iran.

INTRODUCTION Toxoplasma gondii is a protozoan parasite which can be transmitted to human through a variety of routes including blood transfusion. This cross sectional study aimed to evaluate the seroprevalence of Toxoplasma infection and related epidemiological features among healthy blood donors. METHODOLOGY A total of 1,480 healthy blood donors from five blood service centers in Fars province were analyzed for anti-Toxoplasma antibodies. Blood samples were tested for anti-T. gondii IgG and IgM antibodies by enzyme immunoassay. IgM-positive samples were also tested for the presence of Toxoplasma DNA by Polymerase Chain Reaction (PCR). Demographic characteristics of participants were also recorded during samples collection. RESULTS Anti T. gondii antibodies were detected in sera of 286 out of 1,480 blood donors corresponding to an overall seroprevalence of 19.3% in this population. From these, 182 (12.3%) were seropositive only for IgG, 81 (5.47%) were seropositive only for IgM and 23 (1.6%) were positive for both IgG and IgM. PCR detected active parasitemia in two (1.9%) of the IgM-positive subjects. Age, place of residence and level of education were statistically significant (p < 0.05) with seropositivity to Toxoplasma. CONCLUSIONS Our results highlighted that asymptomatic blood donors, especially those with active parasitemia, may constitute a significant risk of transmitting toxoplasmosis to susceptible recipients.
Prevention and Reduction: A review of strategies for intervening early to prevent or reduce youth crime and anti-social behaviour

We are not here concerned with programmes that target infants and very young children with the aim of improving outcomes on a whole range of dimensions: those have already been discussed in the Allen review. Instead, we are concerned with programmes and practices for which the primary aim is to have an impact on the development of antisocial and criminal behaviour in young people aged 8 and above.
Ceramic-Coated Implant Systems

Practitioners have used hydroxyapatite-coated (HA-coated) endosseous and subperiosteal implants in various forms for many years. These have included root forms in both screw and cylindrical shapes, blades, and subperiosteals. The clinical predictability remains controversial and subject to claims and counterclaims. The early days of dental implantology involving root-form implants recommended their placement in fully edentulous cases only, and anterior to the maxillary sinus and mental foramen. Today's philosophy and rationale of dental implantology include the placement of a single implant replacing a missing natural tooth (especially where the teeth adjacent to the edentulous site have no caries or restorative experience). Implants are used to replace the natural dentition in one quadrant/segment, often preceded or accompanied by ridge augmentation and/or sinus grafting if sufficient bone is not present. So we have to address the clinical predictability of survival in terms of indications, quantity, and quality of bone. Clinical data and experience suggest that hydroxyapatite-coated (HA) dental implants may (and possibly should) be used in (1) Type IV bone, (2) fresh extraction sites, (3) grafted maxillary and/or nasal sinuses, or (4) with short implants (≤ 10 mm in length).
Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.
Temporal differentiation and spatial coexistence of sexual and facultative asexual lineages of an aphid species at mating sites

Cases of coexisting sexual and asexual relatives are puzzling, as evolutionary theory predicts that competition for the same ecological niches should lead to the exclusion of one or the other population. In the cyclically parthenogenetic aphid, Rhopalosiphum padi, sexual and facultative asexual lineages are admixed in space at the time of sexual reproduction. We investigated how the interaction of reproductive mode and environment can lead to temporal niche differentiation. We demonstrated theoretically that differential sensitivity of sexual and facultatively asexual aphids to an environmental parameter (mating host suitability) shapes the two strategies: whereas the sexual lineages switch earlier to the production of sexual forms, the facultative asexual lineages delay and spread out their investment in sexual reproduction. This predicted pattern of niche specialization is in agreement with the temporal structure revealed in natura by demographic and genetic data. We propose that partial loss of sex by one pool of aphids and subsequent reduction in gene flow between lineages may favour temporal specialization through disruptive selection.
Nox 2 , Ca 2 , and Protein Kinase C Play a Role in Angiotensin II – Induced Free Radical Production in Nucleus Tractus Solitarius

The dorsomedial portion of the nucleus tractus solitarius (dmNTS) is the site of termination of baroreceptor and cardiorespiratory vagal afferents and plays a critical role in cardiovascular regulation. Angiotensin II (Ang II) is a powerful signaling molecule in dmNTS neurons and exerts some of its biological effects by modulating Ca currents via reactive oxygen species (ROS) derived from reduced nicotinamide-adenine dinucleotide phosphate (NADPH) oxidase. We investigated whether a Nox2-containing NADPH oxidase is the source of the Ang II—induced ROS production and whether the signaling mechanisms of its activation require intracellular Ca or protein kinase C (PKC). Second-order dmNTS neurons were anterogradely labeled with 4-(4-[didecylamino]styryl)-N-methylpyridinium iodide transported from the vagus and isolated from the brain stem. ROS production was assessed in 4-(4[didecylamino]styryl)-N-methylpyridinium iodide–positive dmNTS neurons using the fluorescent dye 6-carboxy-2 ,7 dichlorodihydro-fluorescein di(acetoxymethyl ester). Ang II (3 to 2000 nmol/L) increased ROS production in dmNTS neurons (EC50 38.3 nmol/L). The effect was abolished by the ROS scavenger Mn (III) porphyrin 5,10,20-tetrakis (benzoic acid) porphyrin manganese (III), the Ang II type 1 receptor antagonist losartan, or the NADPH oxidase inhibitors apocynin or gp91ds-tat. Ang II failed to increase ROS production or to potentiate L-type Ca currents in dmNTS neurons of mice lacking Nox2. The PKC inhibitor GF109203X or depletion of intracellular Ca attenuated Ang II–elicited ROS production. We conclude that the powerful effects of Ang II on Ca currents in dmNTS neurons are mediated by PKC activation leading to ROS production via Nox2. Thus, a Nox2-containing NADPH oxidase is the critical link between Ang II and the enhancement of Ca currents that underlie the actions of Ang II on central autonomic regulation. (Hypertension. 2006;48:482-489.)
TCR Binding Kinetics Measured with MHC Class I Tetramers Reveal a Positive Selecting Peptide with Relatively High Affinity for TCR 1

The interaction between TCR and peptide-MHC (pMHC) complexes is crucial for the activation of T cells as well as for positive and negative selection in the thymus. The kinetics and affinity of this interaction and the densities of TCR and pMHC complexes on the cell surface are determining factors for different outcomes during thymic selection. In general, it is thought that agonist pMHC, which cause negative selection, have higher affinities and, in particular, slower off-rates than partial or weak agonists and antagonists, which cause positive selection. In this study, we have used pMHC tetramers to investigate the kinetics of TCR-pMHC interaction for agonist, weak agonist, and antagonist ligands of the anti-lymphocytic choriomeningitis virus P14 TCR. Kinetics determined on the cell surface may be biologically more relevant than methods using soluble proteins. We can distinguish between agonists and weak agonists or antagonists based on the half-life and the avidity of tetramer-TCR interaction. Furthermore, we show that a weak agonist self-peptide that positively selects P14 TCR+ thymocytes has a tetramer half-life and avidity only slightly weaker than strong agonists. We show that, in fact, it can act as quite a strong agonist, but that its poor ability to stabilize MHC causes it instead to have a weak agonist phenotype.
Spectral characteristics of water megamaser galaxies - II. ESO 103-G035, TXS 2226-184, and IC 1481

Long-slit optical emission-line spectra of the H 2 O megamaser galaxies ESO 103-G035, TXS 2226-184, and IC 1481 are evaluated in order to look for characteristics typical for water-megamaser galaxies. We present rotation curves, line ratios, electron densities, temperatures, and H β luminosities. The successful line-profile decompositions rest on d -Lorentzians with an additional parameter d to adjust the wings, rather than Gaussians or Lorentzians as basic functions. No significant velocity gradient is found along the major axis in the innermost 2 kpc of TXS 2226-184. IC 1481 reveals a spectrum suggestive of a vigorous starburst in the central kiloparsec 10 8 years ago. None of the three galaxies shows any hints for outflows nor special features which could give clues to the presence of H 2 O megamaser emission. The galaxies are of normal Seyfert-2 (ESO 103-G035) or LINER (TXS 2226-184, IC 1481) type.
Sidedness of (Calcium, Magnesium) Adenosine Triphosphatase of Purified Torpedo Synaptic Vesicles

Abstract: Purified Torpedo synaptic vesicles contain ouabain‐insensitive Mg2+τ and Ca2+‐stimulated ATPase activity. The sidedness of the ATPase on the vesicular membranes was investigated. Addition of ATP and Mg2+ or Ca2+ to intact vesicles results in activation of the ATPase. Exposure of the vesicles to low concentrations of Lubrol‐PX and Triton X‐100, which do not solubilize the activity, results in the concurrent release of the vesicular contents and in an increase of the Mg2+‐ATPase activity, whereas the Ca2+‐dependent activity is drastically decreased. p‐Chloromercuribenzene sulphonate (PCMBS) almost completely inhibits the activity of detergent‐treated vesicles whereas that of the native material is only slightly affected. Tryptic digestion of intact vesicles and of vesicular ghosts results in partial reduction of the ATPase activity. These results suggest that the vesicles contain an outward oriented Ca2+/Mg2+ ATPase activity which can be modulated by detergents.
Roles of the Catalytic Domain and Two Cellulose Binding Domains of Thermomonospora fusca E4 in Cellulose Hydrolysis

ABSTRACT Thermomonospora fusca E4 is an unusual 90.4-kDa endocellulase comprised of a catalytic domain (CD), an internal family IIIc cellulose binding domain (CBD), a fibronectinlike domain, and a family II CBD. Constructs containing the CD alone (E4-51), the CD plus the family IIIc CBD (E4-68), and the CD plus the fibronectinlike domain plus the family II CBD (E4-74) were made by using recombinant DNA techniques. The activities of each purified protein on bacterial microcrystalline cellulose (BMCC), filter paper, swollen cellulose, and carboxymethyl cellulose were measured. Only the whole enzyme, E4-90, could reach the target digestion of 4.5% on filter paper. Removal of the internal family IIIc CBD (E4-51 and E4-74) decreased activity markedly on every substrate. E4-74 did bind to BMCC but had almost no hydrolytic activity, while E4-68 retained 32% of the activity on BMCC even though it did not bind. A low-activity mutant of one of the catalytic bases, E4-68 (Asp55Cys), did bind to BMCC, although E4-51 (Asp55Cys) did not. The ratios of soluble to insoluble reducing sugar produced after filter paper hydrolysis by E4-90, E4-68, E4-74, and E4-51 were 6.9, 3.5, 1.3, and 0.6, respectively, indicating that the family IIIc CBD is important for E4 processivity.
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae)

Abstract The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3′H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3′5′H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3′H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.
Nonlinear actuator fault estimation observer: An inverse system approach via a T-S fuzzy model

Nonlinear actuator fault estimation observer: An inverse system approach via a T-S fuzzy model Based on a Takagi-Sugeno (T-S) fuzzy model and an inverse system method, this paper deals with the problem of actuator fault estimation for a class of nonlinear dynamic systems. Two different estimation strategies are developed. Firstly, T-S fuzzy models are used to describe nonlinear dynamic systems with an actuator fault. Then, a robust sliding mode observer is designed based on a T-S fuzzy model, and an inverse system method is used to estimate the actuator fault. Next, the second fault estimation strategy is developed. Compared with some existing techniques, such as adaptive and sliding mode methods, the one presented in this paper is easier to be implemented in practice. Finally, two numerical examples are given to demonstrate the efficiency of the proposed techniques.