Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational studies on cyclic imide formation mechanism of glutamic acid residues catalyzed by two water molecules

Aspartic acid (Asp) residues in peptides and proteins are prone to nonenzymatic stereoinversion and/or isomerization to form three types of isomerized Asp residues (L-β-Asp, D-α-Asp, and D-β-Asp) via a five-membered ring succinimide intermediate. These isomerized Asp residues are detected more frequently in aged tissues. However, stereoinversion and/or isomerization of glutamic acid (Glu) residues having a chemical structure similar to Asp residues are hardly detected in proteins. In this study, we investigate computationally the formation mechanism of the cyclic imide, i.e., amino-glutarimidyl (Agl) from Glu residues, with water molecules as catalyst. We study the reaction mechanism by using quantum chemical B3LYP/6-31+G(d,p) density functional theory calculations. All calculations are performed by using model compounds in which a Glu residue is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Agl formation consists of the three steps of iminolization, cyclization, and dehydration, and two water molecules acting as proton-relay mediators catalyze all three steps. The calculated activation energy for Agl formation from Glu residues is 30.3 kcal mol−1, which is somewhat greater than found experimentally for Asp-residue stereoinversion. This calculation suggests that in vivo Glu-residue stereoinversion is unlikely to occur because of the high activation barrier.
A CROSS-SECTIONAL STUDY TO DETERMINE THE ACCURACY OF HIGH FREQUENCY USG AMONG PATIENTS WITH MENISCAL INJURIES

: Objective: The objective of the research was to determine the correctness of high-frequency ultrasonography in knee joint meniscal injuries in matured patients verified on magnetic resonance imaging. Material and Method: This cross-sectional research was carried out at Mayo Hospital, Lahore from September 2018 to May 2019. The numbers of patients enrolled for research were one hundred with the supposition of meniscal injuries. The age of the enrolled patients was between fifteen to fifty years and comprising of both the genders. A researcher not included those patients in his research who have open wound over the knee, cases with former meniscal tears follow up and those patients having disease mimicking meniscal wounds. Researcher compares the ultrasonography results with the results of MRI which was carried out and explained by radiologist. Results: Among one hundred enrolled patients for research, ultrasound displayed meniscal injuries in seventy-five percent cases. Magnetic resonance imaging verified meniscal injuries in seventy-seven percent of patients. However, twenty-three percent displayed no meniscal injuries. In ultrasonography positive cases, the percentage of true positive and false positive cases was 72% & 3% respectively. Moreover, in twenty-five ultrasonography negative cases, five percent (false negative) has meniscal injuries verified through magnetic resonance imaging whereas twenty percent true negative had nil meniscal injury on magnetic resonance imaging. Therefore, negative and positive predictive value, specificity, diagnostic correctness, sensitivity in detecting meniscal injuries via ultrasonography was 80%, 96%, 86.96%, 92% and 93.50% respectively. Conclusion: This research determines that high-resolution ultrasonography emerges as safe, trustable, precise, available with ease as well as cost-effective procedure utilized for the assessment of meniscal injuries in the zone of low resources, however, MRI is costly and reachable to few ones.
Roads support the spread of invasive Asclepias syriaca in Austria

Summary Asclepias syriaca is an invasive alien plant that has recently spread in Central Europe. The spatiotemporal spread of A. syriaca was reconstructed based on the distribution data for Austria. A. syriaca has increased in abundance and range, especially after the year 2005. At present, the species occurs primarily in eastern Austria (Vienna, Lower Austria), while it was rarely recorded in southern and western Austria. Further spread and range filling is probable. Moreover, the distribution of A. syriaca along roadsides and the role of road type and adjoining land use in facilitating its spread were studied in an area of high presence of the species in Lower Austria in 2018. It was shown that A. syriaca occurred regularly along roadsides and the chance of finding A. syriaca was higher along unpaved roads and along roadsides bordered by forests and grassland. The results indicate that the road network contributes to the spread of A. syriaca in the study area, most likely by providing suitable and well connected habitats. If A. syriaca densities are to be lowered, emphasis should be placed on both a proper roadside management (e.g., mowing regimes) and on the control of the species in the respective adjacent habitat.
Infections, immunity and anthropogenesis

The presented investigation revealed for the first time the creative function of infections and inherent immunity on initial (molecular) stages of anthropogenesis. This approach allows explain the extraordinariness of both intensification of natural selection among primates and subsequent tens-fold acceleration of human evolution during Pliocene and Pleistocene epochs. Its results provide a new perspective upon both the molecular timing of the preceding evolution of Homo sapiens, and the evolutionary significance ofmodern epidemics. In addition, this perspective includes a revision of both the strategy and routine praxis of protective medicine.
Coding advantage of grid cell orientation under noisy conditions

Grid cells constitute a crucial component of the “GPS” in the mammalian brain. Recent experiments revealed that grid cell activity is anchored to environmental boundaries. More specifically, these results revealed a slight yet consistent offset of 8 degrees relative to boundaries of a square environment. The causes and possible functional roles of this orientation are still unclear. Here we propose that this phenomenon maximizes the spatial information conveyed by grid cells. Computer simulations of the grid cell network reveal that the universal grid orientation at 8 degrees optimizes spatial coding specifically in the presence of noise. Our model also predicts the minimum number of grid cells in each module. In addition, analytical results and a dynamical reinforcement learning model reveal the mechanism underlying the noise-induced orientation preference at 8 degrees. Together, these results suggest that the experimentally observed common orientation of grid cells serves to maximize spatial information in the presence of noise. Author summary Spatial navigation depends on several specialized cell types including place and grid cells. Grid cells have multiple firing fields that are arranged in a regular hexagonal pattern. The axes of this pattern are anchored to environmental boundaries at a universal angle of 8°. Here, we combine computer simulations of the grid cell network with analytical derivations and a reinforcement learning model to explain the functional relevance of this universal grid cell orientation. We show that spatial information provided by grid cells is maximized at the experimentally observed grid orientation within a broad parameter range. This relationship occurs only in the presence of noise. The model allows for several experimentally testable predictions including the number of grid cells.
Myosin Orientation in a Muscle Fiber Determined with High Angular Resolution Using Bifunctional Spin Labels

We have measured the orientation of the myosin light chain domain in demembranated muscle fibers by electron paramagnetic resonance (EPR), using a bifunctional spin label (BSL), with angular resolution of 4 degrees. Despite advances in X-ray crystallography, cryo-electron microscopy (cryo-EM), and fluorescence polarization, none of these techniques provide high-resolution structural information about the myosin light chain domain under ambient conditions in fiber. Two cysteines, 4 residues apart, were engineered on an α helix in the myosin regulatory light chain (RLC), permitting stereoselective site-directed labeling with BSL. By exchanging BSL-labeled RLC onto oriented muscle fibers, we obtained EPR spectra that resolved angular distributions in several biochemical states. The accurate determination of BSL’s angular coordinates allowed us to determine the orientation of individual structural elements with respect to the muscle fiber axis. The addition of ATP, in the absence of Ca2+, shifted the orientation to a much more disordered distribution. We resolved an oriented population with lever arm oriented perpendicular to the muscle fiber axis, a state previously observed directly in insect flight muscle, but not in fibers having isolated myosin heads (S1) attached to actin. Summary We used electron paramagnetic resonance to determine the orientation of elements within the myosin regulatory light chain in skinned skeletal muscle fibers. A bifunctional spin label provided sufficient resolution to detect an ordered population of lever arms perpendicular to actin.
On the Dynamics of (Anti)competitive Behaviour in the Airline Industry

This thesis consists of three empirical studies that examine the relationship between different forms of rivalry in monopoly and oligopoly airline markets and the resulting market price outcomes. The ultimate goal of this work is to empirically distinguish the concept of competition from the market structure, which is often conceived as a combination of the number of firms present in a market and their relative market share or dominance. These studies build on economic theory of imperfect competition to determine the incentives for rivalry in each context and in turn develop a measure of the intensity of competition in order to study its effect on market price outcomes. A large part of this thesis focuses on forms and instruments of rivalry that firms may deploy to maintain or expand their market dominance and restrain competition. It therefore studies the dynamics of both competitive and plausibly anticompetitive behaviour in the airline industry.
The complete mitochondrial genome of the giant clam, Tridacna maxima (Tridacnidae Tridacna)

Abstract In this study, we present the first complete mitochondrial genome sequence of the giant clam Tridacna maxima. The total length of the mitogenome is 18,632 bp. It contains the typical mitochondrial genomic structure, including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Mitogenome base composition is biased toward A + T content, at 61.54%. A phylogenetic tree based on complete mitogenome sequences revealed that, within the genus Tridacna, T. maxima is closely related to T. squamosa and T. derasa.
Développement de la fabrication additive par procédé arc-fil pour les aciers : caractérisation microstructurale et mécanique des dépôts en nuances ER100 et 316L pour la validation des propriétés d'emploi de pièces industrielles

L'arc-fil est un nouveau procede de fabrication additive utilisant une cellule desoudage robotisee pour la fabrication, couche par couche, de pieces de grandes dimensions. Ilpermet de realiser des ebauches de pieces unitaires ou de petites series avec des couts et desdelais de fabrication reduits. Les premiers developpements se sont principalement orientes sur larealisation de pieces a forte valeur ajoutee en alliage de titane et d’aluminium pour le secteuraeronautique et aerospatial, et interessent maintenant d’autres secteurs tels que les industriesnavales, petrolieres, ferroviaires et mecaniques utilisant des aciers. Ce travail propose unemethodologie de selection des parametres et des strategies de depots, avec le controle final despieces fabriquees. Il porte sur deux materiaux : un acier C-Mn a haute limite d’elasticite(ER100) et un acier inoxydable austenitique (316LSi). Le resultat des caracterisations permetd’etablir le lien entre les conditions de fabrication, les dimensions geometriques et les proprietesmicrostructurales et mecaniques des pieces obtenues, ce qui conduit au final a une demarchepermettant de faire evoluer le procede vers l’industrialisation.
Self-Selection and Recruit Quality in Sweden’s All Volunteer Force: Do Civilian Opportunities Matter?

ABSTRACT This paper studies how local labour market conditions influence the quality composition of those who volunteer for military service in Sweden. A fixed-effects regression model is estimated on a panel data set containing IQ scores for those who applied for military basic training across Swedish municipalities during the period 2010 to 2016. The main finding is that low civilian employment rates at the local level tend to increase the mean IQ score of those who volunteer for military service, whereas the opposite is true if employment rates in the civilian labour market move in a more favourable direction. As such, the results suggest that the negative impact of a strong civilian economy on recruitment volumes is reinforced by a deterioration in recruit quality.
The chloroplast genome of a landscape tree Zelkova serrata (Ulmaceae)

Abstract We reported the complete chloroplast genome for Zelkova serrata, the first in the distinctive genus Zelkova to be sequenced in the family Ulmaceae. The plastome is totally 158,495 bp in length, containing a pair of inverted repeats (IRs), a large single-copy region (LSR) and a small single-copy region (SSR), which are 26,456 bp, 86,921 bp and 18,684 bp, respectively. A total of 103 unique genes were identified in Z. serrata chloroplast genome, of which 88 are single-copy genes, while15 are duplicated in IR regions. Further, maximum-likelihood phylogenetic analyses were conducted using eight complete plastomes of the Ulmaceae, which support close relationships between Z. serrata, Ulmus gaussenii, and U. chenmoui.
Distinct Subgroups in Hypertrophic Cardiomyopathy: Baseline Results From HCMR

Background: The Hypertrophic Cardiomyopathy Registry (HCMR) is an NHLBI-funded, prospective registry of 2755 patients with HCM recruited from 44 sites in 6 countries. Objectives: HCMR was designed to improve risk prediction in HCM by incorporating cardiovascular magnetic resonance (CMR), genetic, and biomarker data. Methods: Demographic and echocardiographic data were collected. Patients underwent CMR including cine imaging, late gadolinium enhancement imaging (LGE, replacement fibrosis) and T1 mapping for measurement of extracellular volume (ECV) as a measure of interstitial fibrosis. Blood was drawn for biomarker (N-terminal pro brain natriuretic peptide, NTproBNP and high sensitivity troponin T, cTnT) and genetic analysis. Results: A total of 2755 patients were studied. Mean age was 49±11 years, 71% were male, and 17% non-white. Mean ESC risk score was 2.48±0.56. Twenty four % had a resting left ventricular outflow tract (LVOT) gradient ≥ 30mmHg. Thirty six percent had a sarcomere mutation identified. Fifty percent had any LGE, which was more common and extensive in patients who were sarcomere mutation (+), had reverse septal curvature morphology and no significant resting LVOT obstruction. Those without LGE were more likely sarcomere mutation (-), had isolated basal septal hypertrophy, and more LVOT obstruction. Interstitial fibrosis was present in segments both with and without LGE. Serum NTproBNP and cTnT levels correlated with increasing LGE and ECV in a graded fashion. Conclusions: The HCMR population has characteristics of mild-to-moderate risk HCM. Baseline data separated patients broadly into 2 categories. One group was sarcomere mutation (+), more likely had reverse septal curvature morphology, more fibrosis, but less resting sarcomere mutation more likely had isolated basal septal obstruction but less fibrosis. Further follow-up will allow better understanding of these subgroups and development of an improved risk prediction model incorporating all of these markers. Abstract HCMR is a prospective registry of 2755 hypertrophic cardiomyopathy patients from 44 sites in 6 countries. Patients underwent cardiovascular magnetic resonance including cine imaging, late gadolinium enhancement imaging (LGE), and T1 mapping for measurement of extracellular volume and had blood drawn for biomarkers and genetics. Patients with sarcomere mutations more commonly had LGE and reverse septal curvature morphology but less resting outflow obstruction. Serum biomarkers correlated with the extent of LGE and ECV. Further follow-up will allow development of a useful risk prediction model incorporating these markers. biomarker and genetic variables that best predict risk of major adverse cardiac events in mild-to-moderate risk HCM.
Recherche de marqueurs biochimiques et génétiques de l'adaptation des caféiers cultivés aux variations climatiques

La baisse de la production et la proliferation des maladies engendrees par le changement climatique dans la cafeiculture, particulierement pour Coffea arabica, conduit a chercher de nouvelles pratiques culturales et etudier la reponse adaptative des cafeiers aux modifications environnementales. En se basant sur l’importance des composes phenoliques dans la reponse des plantes aux stress et sur la richesse des cafeiers en ces composes antioxydants, la reponse adaptative des cafeiers cultives en plein champ a ete etudiee en s’interessant a l’evolution du contenu des feuilles en ces composes dans differentes conditions de culture simulees par un gradient altitudinal, des cultures sous ombrage ou l’obtention de plants greffes. Les analyses biochimiques montrent que certains composes phenoliques s’accumulent dans les feuilles en reponse a la modification d’un parametre meteorologique specifique. Ainsi, acides chlorogeniques et flavanols sont plus accumules en cas de secheresse alors que les flavonols glycosyles s’accumulent sous forte radiation solaire. La comparaison avec C. canephora permet de valider ces marqueurs. Les analyses transcriptomiques indiquent une difference d’expression des genes de biosynthese de ces composes suivant le stade de croissance de la feuille. Elles montrent egalement que la reponse a la lumiere passe par la surexpression de nombreux genes codant des HSP ainsi que ceux impliques dans la photosynthese et la glycosylation des flavonoides. Enfin, ces resultats montrent l’interet, suivant l’altitude, de l’ombrage et du greffage pour la culture de C. arabica.
Busier bees: increasing nest traffic in commercial bumblebee colonies

Commercially-reared bumblebee colonies contribute to the pollination of crops globally. If the efficiency of commercial colonies at providing pollination services could be increased, it would have implications for agricultural outputs. Commercial colonies are sold with an internal nectar reservoir on which bees can forage from within the nest. Nectar stores in naturally-produced nectar pots of colonies can affect forager recruitment and activity outside the nest. Thus, it is possible that artificial nectar reservoirs could impact the foraging activity of colonies. To investigate this, commercial Bombus terrestris audax colonies were placed in a university parkland campus. Colonies were split into three treatment groups: those with (1) access to an unaltered nectar reservoir; (2) access to a diluted reservoir; and (3) no reservoir access. Foraging observations were made for all colonies over a 19-day period. The mass of each colony was measured and demographic data were collected. Colonies with diluted reservoirs had 131% and 39% more bees entering and leaving than colonies with no reservoir access and unaltered reservoirs respectively. Both treatments with access to a nectar reservoir gained more mass, had a higher proportion of pollen foraging bees, and had more workers, males, larvae and pupae, than colonies with no access to a reservoir. These results demonstrate that manipulating the availability and concentration of internal nectar reservoirs of commercial B. terrestris colonies significantly affects the number of bees entering and leaving the colony. Dilution of the nectar reservoir could be a strategy for increasing the pollination services commercial colonies provide to crops. Further research in commercial crops is required before such a strategy could be implemented on farms.
Etude mecanistique et modelisation de la retention de radionucleides par les silicates de calcium hydrates (csh) des ciments

L'objectif de cette etude a ete d'elaborer un modele capable de predire quantitativement la fixation de radionucleides (rn) (cs +, pb 2 + et eu 3 +) par une matrice cimentaire hydratee, dans le cadre de la conception des barrieres ouvragees de site de stockage de dechets radioactifs (centres de surface ou faisabilite d'un stockage en formation geologique profonde). La methodologie de l'etude a consiste a : - etablir un modele caracterisant la chimie de surface des csh (choisi comme simulant des ciments) - etudier la fixation des rn par analyse de solide pour identifier les mecanismes de fixation - utiliser les deux premieres etapes, associees a un bilan en solution, pour etablir un modele de retention des rn. Les resultats obtenus sont : 1 - un modele thermodynamique de speciation de surface des csh, qui rend compte des equilibres acide-base et de sorption des ions calcium labiles, sur les sites silanols de surface des csh. Ce modele est applicable sans ajustement sur toute la gamme ca/si et a ete confirme par des tests predictifs. 2 - la retention de cs + est le resultat d'une sorption sur deux types de sites. Un site faible qui est identifie aux sites silanols dont la concentration elevee (10 sites. Nm 2) permet d'expliquer l'absence de saturation. Un site fort identifie comme un site de bord. Le modele de fixation de cs + par les csh, etabli a partir du modele de speciation de surface, permet des calculs predictifs avec differentes forces ioniques et differents ratios ca/si (valides par des donnees experimentales). 3 - la modelisation de la retention de pb 2 + est etablie en couplant des equilibres de surface et un equilibre de precipitation et le modele est egalement confirme par des essais predictifs sur des ratios ca/si differents et des forces ioniques differentes. 4 - l'etude de la retention de eu 3 + est basee sur des analyses du solide par spectro-luminescence laser a resolution temporelle (slrt), xps et meb-eds. Il a ete montre que eu 3 + n'etait pas retenu dans la matrice csh par precipitation mais par affinite avec le csh. Il est majoritairement fixe a la surface du solide (un environnement -oh important) et minoritairement par insertion dans le solide.
Challenges associated with ceftriaxone resistance in Salmonella

ABSTRACT Salmonella is the leading cause of typhoidal and non-typhoidal infections in the world. The entry of Salmonella into the bloodstream causes an invasive disease state, resulting to high morbidity and mortality rates, especially in children. Owing to the misuse of antibiotics, certain Salmonella serovars are multi-drug resistant and do not respond to traditional antibiotics, such as ampicillin and trimethoprim-sulphamethoxazole, presenting a significant challenge for healthcare practitioners in treating and controlling the spread of this disease. Therefore, expensive third-generation cephalosporins, such as ceftriaxone, are currently used to treat Salmonella infection. However, a novel serovar of Salmonella that resists ceftriaxone was recently identified in Saudi Arabia, indicating wide spread Salmonella resistance. A comprehensive literature review on ceftriaxone resistance in Salmonella is therefore necessary to reflect upon current challenges. In this report, we provide a summary of Salmonella incidence, mechanisms of ceftriaxone resistance in Salmonella, and current treatment options.