Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways

Abstract Acinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an Acinetobacter baumannii strain, belonging to the ST25IP (Institut Pasteur) sequence type recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPFI conjugative transfer system. The plasmid carries the aacA1, aacC2, sul2, strAB, and tetA(B) antibiotic resistance genes. pCl107 region encompassing the sul2, strAB, tetA(B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in A. baumannii strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a ptx phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of Acinetobacter spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.
Simplifying quantum gravity calculations

The Einstein-Hilbert Lagrangian for gravity is non-renormalizable at loop level. However, it can be treated in the effective field theory framework which means that gravity as an effective theory can be renormalized when a proper expansion of the effective Lagrangian is made. At the same time, the Feynman rules for gravity are very complicated, although the resulting amplitudes do not have the same complications. Therefore, in this thesis we want to simplify the Feynman rules as much as possible by using the most general parameterized gauge condition, adding all possible parameterized total derivative terms and redefining the gravitational, ghosts and scalar fields in a general parameterization way. By choosing the parameters in a specific way, we obtain simplified Feynman rules, especially the triple and quadruple graviton vertices are simplified. In addition, we verify our simplified rules by calculating the amplitudes of scalar-graviton and graviton-graviton scattering at tree level using the simplified and standard Feynman rules. Finally, we show the utility of these simplified rules by calculating some one-loop diagrams for scalar-graviton scattering and comparing to the standard Feynman rules. (Less)
Newton polygons as lattice points

Let M be the reduction modulo p of a Shimura variety, and let N ( M ) be the partially ordered set predicted to be the set of all types occurring in the stratification of M by Newton polygons, in the context of F -isocrystals with additional structures. We prove that N ( M ) is ranked (or catenary ), in the sense that any two maximal chains have the same length. We also give a Lie-theoretic formula for the distance between two comparable elements in N ( M ). This formula can be used to give the expected dimension of the Newton strata of M .
Cornelian Cherry (Cornus mas L.): Insight into its Phytochemistry and Bioactivity

: Cornus mas L. (Cornelian cherry) (family Cornaceae) is one of the important medicinal plants with a rich phytochemical profile. It is an ornamental plant with edible fruits possessing therapeutic and nutritional values. The fruits have been used in folk medicine since ancient times. They are red-colored, pear-shaped, oval, and sour taste and are often used in the form of beverages, marmalade, and jams, as well as utilized in the cosmetic industry. Phytochemicals reported for C. mas are phenolic acids, flavonoids, organic acids, anthocyanins, tannins, fatty acids, iridoids, and carotenoids. Especially, the fruits are rich in anthocyanins, vitamin C, and phenolic compounds. The extracts and compounds from C. mas have been investigated for antimicrobial, cytotoxic, anti-inflammatory, antioxidant, antiatherosclerotic, antihyperlipidemic, antidiabetic, anti-colitis, neuroprotective, hepatoprotective, cardioprotective, and nephroprotective activities. The objective of the present review is to summarize the recent studies on the phytoconstituents of C. mas and their biological effects.
Chemical diversity of floral scents in 9 species of Philodendron (Araceae) from French Guiana

ABSTRACT We provide a characterization of the floral scent chemistry of nine species of Philodendron present in French Guiana. The scent samples were obtained by dynamic headspace, in situ in French Guiana, or from plants in the living aroid collection at the Botanical Garden of the University of Brasilia. Overall, we identified 43 volatile organic compounds (VOCs) belonging to the compound classes of monoterpenes, sesquiterpenes, irregular terpenes, benzenoids, aliphatics, jasmone derivatives, and nitrogen-containing compounds. Five of these floral VOCs are new reports for Philodendron. Interestingly, the floral blends in the investigated species were comprised of 3–22 VOCs; but when considering only major VOCs (≥5%), each fragrant blend could be summarized into one up to four constituents. Except for P. acutatum and P. billietiae, whose floral scents were largely dominated (≥93%) by 4-vinylanisole, fragrances of the investigated species were dominated (≥62%) each by a different VOC (i.e. dehydrojasmone, dihydro-β-ionone, (E)-4,8-dimethylnona-1,3,7-trien-5-yl acetate, methyl benzoate, 1,3,5-trimethoxybenzene, dihydrobovolide, or (Z)-jasmone). Consequently, all floral scent compositions significantly differed from one other. We compare our results to published data to provide an insight into the floral scent chemistry within the genus Philodendron. We further discuss the diversity of VOCs in cyclocephaline scarab-pollinated aroids.
Evaluation of seagrass beds as a foraging and nursery habitat based on the structure of the fish community in Nusmapi Island, West Papua, Indonesia

Abstract. Manangkalangi E, Sembel L, Tebaiy S, Manuputty A, Rumayomi MR, Musyeri P, Sawaki D, Orissu D, Manumpil AW, Kaber Y. 2022. Evaluation of seagrass beds as a foraging and nursery habitat based on the structure of the fish community in Nusmapi Island, West Papua, Indonesia. Biodiversitas 23: 5539-5550. Seagrass beds are one of the ecosystems inhabited by various coastal aquatic fauna, including fish. However, information on the temporal role of this ecosystem for fish fauna, particularly diurnal and nocturnal, is still limited. Therefore, this study was conducted to describe daily variations in the fish species composition, their ecological index, developmental stages, and trophic groups in a seagrass bed on Nusmapi Isl. , Manokwari. The species composition differed between day and night sampling periods based on the results obtained from 40 species of fish belonging to 21 families and 7 orders. Furthermore, fish species consisted of three trophic groups (omnivores, carnivores, and herbivores), with omnivores and carnivores dominating during the day and at night by 48.6% and 87.5%, respectively. Species found in seagrass beds majorly consisted of juvenile stage individuals (65.9%). Individual abundance varied from day to night and was mainly found among group-forming species, such as S. spinus, S. trilineata, S. punctatissimum, and M. pralinia. The index of diversity, evenness, and dominance at the two relatively similar sampling times described the overall stability of fish communities in seagrass beds. The results indicate that seagrass beds serve as foraging and nursery grounds for many fish species in coastal waters. In addition, the management and protection of fish biodiversity and coastal fishery resources are affected by the ecosystem function.
Cost-Effectiveness of Abemaciclib in Early Breast Cancer Patients: One Size Fits All or Tailoring to Patients’ Needs?

Purpose The addition of two years of abemaciclib treatment to standard adjuvant endocrine therapy in all patients with high risk ER+, HER2- early breast cancer (EBC) has been approved by the US Food and Drug Administration (FDA). Pre-selection of patients with an immediate risk of recurrence within the group of clinically high risk patients using detection of minimal residual disease (MRD) using patient-informed circulating tumor DNA assays during follow-up could enhance efficacy. Here, we investigate the cost-effectiveness of the addition of two years abemaciclib in all high risk HR+, HER2- patients and in MRD-guided high risk patients only. Methods Two semi-Markov models were developed to evaluate the cost-effectiveness of adding two years of abemaciclib compared to “standard treatment”: 1) “abemaciclib all” and 2) “MRD-guided abemaciclib” using MRD-guidance. Data of the MonarchE trial were used to model the invasive disease-free survival (iDFS). Since iDFS and overall survival (OS) data of abemaciclib were currently limited, abemaciclib effects were extrapolated using a favorable, intermediate and unfavorable effect scenario. Results The addition of abemaciclib in all high-risk EBC patients prolonged iDFS slightly (0.04 additional quality adjusted life years (QALYs)) and led to higher costs compared to standard ET, leading to a high incremental cost effectiveness ratio (ICER) of €1,551,876/QALY. Neither the favorable effect scenario (additional 1.09 QALYs) was cost-effective (ICER €62,935/QALY), using a willingness-to-pay threshold of €50,000/QALY. The “MRD-guided abemaciclib” strategy resulted in lower costs and an increase in QALYs (1.27) compared to “standard treatment” in the unfavorable effect scenario. Conclusion The addition of abemaciclib to adjuvant endocrine therapy in all high-risk ER+, HER2- EBC patients is not cost-effective. However, using MRD detection to justify the addition of abemaciclib treatment dominates standard treatment in this cost-effectiveness analysis. Further evaluation of MRD detection in EBC by means of prospective clinical trials assessing clinical utility is recommended and promising in terms of cost-effectiveness.
A Review on Stimuli-Actuated 3D Micro/Nanostructures for Tissue Engineering and the Potential of Laser-Direct Writing via Two-Photon Polymerization for Structure Fabrication

In this review, we present the most recent and relevant research that has been done regarding the fabrication of 3D micro/nanostructures for tissue engineering applications. First, we make an overview of 3D micro/nanostructures that act as backbone constructs where the seeded cells can attach, proliferate and differentiate towards the formation of new tissue. Then, we describe the fabrication of 3D micro/nanostructures that are able to control the cellular processes leading to faster tissue regeneration, by actuation using topographical, mechanical, chemical, electric or magnetic stimuli. An in-depth analysis of the actuation of the 3D micro/nanostructures using each of the above-mentioned stimuli for controlling the behavior of the seeded cells is provided. For each type of stimulus, a particular recent application is presented and discussed, such as controlling the cell proliferation and avoiding the formation of a necrotic core (topographic stimulation), controlling the cell adhesion (nanostructuring), supporting the cell differentiation via nuclei deformation (mechanical stimulation), improving the osteogenesis (chemical and magnetic stimulation), controlled drug-delivery systems (electric stimulation) and fastening tissue formation (magnetic stimulation). The existing techniques used for the fabrication of such stimuli-actuated 3D micro/nanostructures, are briefly summarized. Special attention is dedicated to structures’ fabrication using laser-assisted technologies. The performances of stimuli-actuated 3D micro/nanostructures fabricated by laser-direct writing via two-photon polymerization are particularly emphasized.
A transient variable 6 Hz QPO from GX 339-4

We report the results of an observation with the Rossi X-ray Timing Explorer of the black hole candidate GX 339-4 during its 2002/2003 outburst. This observation took place during a spectral transition from the hard to the soft state. A strong (6% rms) transient quasi-periodic oscillation (QPO) appears suddenly in the power density spectrum during this observation. The QPO centroid is ∼6 Hz, but it varies significantly between 5 and 7 Hz with a characteristic time scale of ∼10 s, correlated with the 2-30 keV count rate. The appearance of the QPO is related to spectral hardening of the flux, due to a change in the relative contribution of the soft and hard spectral components. We compare this peculiar behavior with results from other systems that show similar low frequency QPO peaks, and discuss the results in terms of possible theoretical models for QPO production.
Occupation-Centered Anatomy and Applied Biomechanics Courses: Design and Outcomes

Abstract Occupation-centered course design allows occupational therapy (OT) educators to differentiate ourselves from other professions while communicating the distinct value of occupation to our students. While there have been numerous calls to action for centering occupation in the OT classroom and proposed models to approach course design, there is limited literature on occupation-centered course design in specific courses, notably foundational science courses like anatomy and applied biomechanics. In this study, we outline our course design process in two courses taught concurrently, as well as our prospective study to determine if an occupation-centered course design allowed students to meet objectives and the effect of undergraduate preparation on objective achievement. We also explored students’ agreement with importance of occupation-centered instruction, and our ability to stay occupation-centered. Fifty-five students completed pre and post course surveys rating their ability to perform the five objectives for each course and their level of agreement about the role of occupation in these courses. We found statistically significant increases in all objective ratings, with some ratings more than doubling. Post-course ratings among students with different undergraduate backgrounds were similar despite being statistically different at baseline. Students placed high value in occupation-centered course design at both time points. Students rated the ability to stay occupation-centered lowest in the first few weeks, with Anatomy rated lower than Applied Biomechanics in all weeks. This suggests that the incremental improvements made in the course delivery were effective; however, it was more challenging to create an occupation-centered course in Anatomy.
Carbon nanotube thermal transport: Ballistic to diffusive

We propose the expression l0∕(l0+L) for the energy transmission covering both ballistic and diffusive regimes, where l0 is mean free path and L is system length. With this formula, calculations of thermal conduction in carbon nanotubes (CNTs) show: (1) Thermal conductance at room temperature is proportional to the diameter for single-walled CNTs (SWCNTs) and to the square of diameter for multiwalled CNTs. (2) Interfaces play an important role in thermal conduction in CNTs due to their symmetry of vibrational modes. (3) For CNTs in ballistic-diffusive regime, thermal conductivity κ goes as Lα. The exponent α is found to decrease with increasing temperature and is insensitive to the diameter of SWCNTs for the Umklapp process, α≈0.8 for short SWCNTs at room temperature. These results are consistent with recent experimental findings.
Electric-Magnetic Duality, Matrices, & Emergent Spacetime

This is a rough transcript of talks given at the Workshop on Groups & Algebras in M Theory at Rutgers University, May 31--Jun 04, 2005. We review the basic motivation for a pre-geometric formulation of nonperturbative String/M theory, and for an underlying eleven-dimensional electric-magnetic duality, based on our current understanding of the String/M Duality Web. We explain the concept of an emerging spacetime geometry in the large N limit of a U(N) flavor matrix Lagrangian, distinguishing our proposal from generic proposals for quantum geometry, and explaining why it can incorporate curved spacetime backgrounds. We assess the significance of the extended symmetry algebra of the matrix Lagrangian, raising the question of whether our goal should be a duality covariant, or merely duality invariant, Lagrangian. We explain the conjectured isomorphism between the O(1/N) corrections in any given large N scaling limit of the matrix Lagrangian, and the corresponding alpha' corrections in a string effective Lagrangian describing some weak-coupling limit of the String/M Duality Web.
Ga-polar (In,Ga)N/GaN quantum wells vs. N-polar (In,Ga)N quantum disks in GaN nanowires: Comparative analysis of carrier recombination, diffusion, and radiative efficiency

We investigate the radiative and nonradiative recombination processes in planar (In,Ga)N/GaN(0001) quantum wells and (In,Ga)N quantum disks embedded in GaN$(000\bar{1})$ nanowires using photoluminescence spectroscopy under both continuous-wave and pulsed excitation. The photoluminescence intensities of these two samples quench only slightly between 10 and 300 K, which is commonly taken as evidence for high internal quantum efficiencies. However, a side-by-side comparison shows that the absolute intensity of the Ga-polar quantum wells is two orders of magnitude higher than that of the N-polar quantum disks. A similar difference is observed for the initial decay time of photoluminescence transients obtained by time-resolved measurements, indicating the presence of a highly efficient nonradiative decay channel for the quantum disks. In apparent contradiction to this conjecture, the decay of both samples is observed to slow down dramatically after the initial rapid decay. Independent of temperature, the transients approach a power law for longer decay times, reflecting that recombination occurs between individual electrons and holes with varying spatial separation. Employing a coupled system of stochastic integro-differential equations taking into account both radiative and nonradiative Shockley-Read-Hall recombination of spatially separate electrons and holes as well as their diffusion, we obtain simulated transients matching the experimentally obtained ones. The results reveal that even dominant nonradiative recombination conserves the power law decay for (In,Ga)N/GaN{0001} quantum wells and disks.
Influence of supplementation of Spirulina platensis on nutritional, physiological and metabolic performance of GIFT Tilapia (Oreochromis niloticus)

An eight weeks feeding trial was conducted to assess the influence of supplementation of Spirulina platensis on nutritional, physiological and metabolic performance of GIFT Tilapia (Oreochromis niloticus). Fingerlings (120; Initial body weight 3.4±0.01 g) were randomly assigned to four dietary treatments, viz. control (0%), T1 (1%), T2 (3%) and T3 (5% S. platensis meal) in triplicates. The animals were fed with a ration at 5% body weight twice a day throughout the trial. The results indicated that, final body proximate composition, growth performance and nutrients digestibility coefficient were higher in T2 group compared to other treatments and the control. At this level of inclusion, fish digestive enzymes, such as amylase, protease and lipase were significantly higher between control and treatments however, metabolic enzyme activities were not influenced by dietary treatments. The liver and intestinal histology were not affected by dietary treatments, however the intestinal tissues showed a higher intestinal villi length and muscular layer thickness than the control group. It can be concluded that, S. plantesis meal can be supplemented up to 3% without compromising the overall performance of GIFT tilapia.
Teachers’ Knowledge of Green Chemistry in Senior Secondary Schools in Kwara State, Nigeria

There have been series of advocacies all over the world to prepare future scientists who would take up the challenge of eradicating environmental pollution through the deployment of scientific knowledge such as green chemistry. This study investigated teachers’ knowledge of green chemistry in Kwara State, Nigeria. The Green Chemistry Knowledge Questionnaire (GCKQ) was used to collect the data. Answers were provided to the research questions using the mean and percentage, while the research hypotheses were subjected to t-Test and ANOVA. Findings from the study revealed that the teachers’ knowledge of green chemistry was high and significantly higher among experienced teachers. It is recommended that the chemistry teachers should endeavor to pass green chemistry ideas to the students and that the experienced chemistry teachers should carry the less experienced teachers along in the course of passing across the knowledge of green chemistry.
Spin Seebeck effect and ballistic transport of quasi-acoustic magnons in room-temperature yttrium iron garnet films

We studied the transient behavior of the spin current generated by the longitudinal spin Seebeck effect (LSSE) in a set of platinum-coated yttrium iron garnet (YIG) films of different thicknesses. The LSSE was induced by means of pulsed microwave heating of the Pt layer and the spin currents were measured electrically using the inverse spin Hall effect in the same layer. We demonstrate that the time evolution of the LSSE is determined by the evolution of the thermal gradient triggering the flux of thermal magnons in the vicinity of the YIG/Pt interface. These magnons move ballistically within the YIG film with a constant group velocity, while their number decays exponentially within an effective propagation length. The ballistic flight of the magnons with energies above 20 K is a result of their almost linear dispersion law, similar to that of acoustic phonons. By fitting the time-dependent LSSE signal for different film thicknesses varying by almost an order of magnitude, we found that the effective propagation length is practically independent of the YIG film thickness. We consider this fact as strong support of a ballistic transport scenario—the ballistic propagation of quasi-acoustic magnons in room temperature YIG.