Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Genetic Characterization of Smooth Cordgrass for Coastal Wetland Restoration

1 , B. C. VENUTO 2 ABSTRACT Spartina alterniflora (Loisel.), smooth cordgrass, is a domi- nant perennial salt marshgrass native to tidal wetland plant communities along the Atlantic and Gulf coasts of North America. It is an important plant species for coastal reclama- tion and restoration efforts. It spreads quickly by rhizomes and tolerates a wide range of saline, anoxic, and sulfidic soils. However, because of poor seed production this species is propagated vegetatively for reclamation or restoration projects. Current practices reduce genetic diversity of the spe- cies by utilizing a single vegetatively propagated genotype. The objectives of this study were; 1) identify multiple geno- types of S. alterniflora for use in restoration efforts and 2) as- sess genetic variability of these genotypes at the molecular level. Identification of desirable plants was based on plant growth characteristics and reproductive traits. Growth charac- ters were plant height, spread, rust reaction, and vigor. Re- productive traits were seed set, germination, kernel weight, seed weight, and total seed per plant. This process resulted in seven plants, descended from seven different original source populations, which demonstrated superior performance for vegetative and reproductive traits. Molecular marker analysis revealed that genetic diversity, essential for success in the res- toration projects, was maintained in selected plants. These plants offer an enhanced germplasm base for current restora- tion efforts. Research is continuing on the feasibility of devel- oping seed based populations that would add even greater genetic diversity to the current accepted restoration practices.
Estimating internal waves and diapycnal mixing from conventional mooring data in a lake

A methodology is described to analyze and interpret the temporal variation; of temperature and current measured in lakes or on the continental shelf by generally available standard and robusi equipment, a single thermistor chain, and current meters. It is assumed that variations are mainly produced by internal wave modes propagating in the mean flow and mean stratification. The analysis provides estimates of the propagation characteristics, energy density, and directional flux of the internal waves, as well as the temporal and vertical distribution of Richardson number, Ri, on scales that may be smaller than those separating the measuring instruments. The method is tested with measurements made in Lake Geneva, and provides realistic quantitative estimates of the rate of dissipation of turbulent kinetic energy per unit mass, ϵ, and of the vertical diffusivity, Kv, which are useful in establishing the processes leading to diapycnal mixing.
Distribution and turnover of dissolved DMSP and its relationship with bacterial production and dimethylsulfide in the Gulf of Mexico

We measured the distribution of particulate and dissolved pools of the phytoplankton osmolyte dimethylsulfoniopropionate (DMSP) in the euphotic zone at a series of shelf (<40 m total water depth) and oceanic (>500 m depth) stations in the northern Gulf of Mexico. We also measured turnover rates of the dissolved DMSP pools (DMSPd) with tracer additions of 35S‐DMSPd and short‐term (<1 h) incubations, with the aim of examining the relationship between DMSPd turnover and bacterial production. Particulate DMSP concentrations were relatively low (<25 nM) throughout the study area with about twofold higher mean concentration at the shelf sites (15 nM) compared with the oligotrophic oceanic sites (7 nM). DMSPd concentrations averaged 3.0 nM in shelf waters and 1.3 nM in oceanic waters. Concentrations of dimethylsulfide (DMS), a degradation product of DMSP, also were low throughout the Gulf, averaging 2.0 nM for all depths sampled and 2.5 nM in surface waters. Microbial assem‐blages metabolized 35S‐DMSPd with the sulfur being incorporated into biomass, volatile compounds (DMS and methanethiol), and other dissolved products. DMSPd turnover was relatively slow (mean of 3.8 nM d−1) in oligotrophic oceanic waters and averaged 10‐fold higher (39 nM d−1) in mesotrophic shelf waters. DMS concentrations ranged from 0.2 to 5.1 nM in oceanic waters and appeared to be weakly related to DMSP turnover. In contrast, DMS concentrations in shelf waters fell within a narrow range (0.8–2.8 nM) and showed no relationship at all with DMSPd turnover. DMSPd turnover rates were high enough to sustain the measured concentrations and estimated turnover of DMS, even if the conversion efficiency of DMSPd into DMS was only 10%. DMSPd turnover was significantly correlated with bacterial production (as measured by 3H‐thymidine incorporation) and we estimate that DMSPd turnover contributed a mean of 3.4% of the carbon and ~100% of the sulfur required for bacterial growth in Gulf of Mexico surface waters. In addition to its role as a precursor of DMS, DMSP deserves attention as an important substrate for bacterioplankton in the euphotic zone.
Climate system response to stratospheric sulfate aerosols: sensitivity to altitude of aerosol layer

Abstract. Reduction of surface temperatures of the planet by injecting sulfate aerosols in the stratosphere has been suggested as an option to reduce the amount of human-induced climate warming. Several previous studies have shown that for a specified amount of injection, aerosols injected at a higher altitude in the stratosphere would produce more cooling because aerosol sedimentation would take longer. In this study, we isolate and assess the sensitivity of stratospheric aerosol radiative forcing and the resulting climate change to the altitude of the aerosol layer. We study this by prescribing a specified amount of sulfate aerosols, of a size typical of what is produced by volcanoes, distributed uniformly at different levels in the stratosphere. We find that stratospheric sulfate aerosols are more effective in cooling climate when they reside higher in the stratosphere. We explain this sensitivity in terms of effective radiative forcing: volcanic aerosols heat the stratospheric layers where they reside, altering stratospheric water vapor content, tropospheric stability, and clouds, and consequently the effective radiative forcing. We show that the magnitude of the effective radiative forcing is larger when aerosols are prescribed at higher altitudes and the differences in radiative forcing due to fast adjustment processes can account for a substantial part of the dependence of the amount of cooling on aerosol altitude. These altitude effects would be additional to dependences on aerosol microphysics, transport, and sedimentation, which are outside the scope of this study. The cooling effectiveness of stratospheric sulfate aerosols likely increases with the altitude of the aerosol layer both because aerosols higher in the stratosphere have larger effective radiative forcing and because they have higher stratospheric residence time; these two effects are likely to be of comparable importance.
Application of the conductometric method for differentiation of proteins and peptides

The aim of this work was to use the conductometry method for the differentiation of the chemically- and enzymatically-modified food proteins. The protein extracts of soybean, bean pea, maize and rice seeds, 3 varieties “Tonacja”, “Nawra” and “Sukces” of wheat, as well bovine serum albumin, pepsin trypsin and acid protein hydrolyzates were investigated. Additionally, proteins were glycated by glucose. It was found that differences of the electrolytic conductivity between native proteins and their hydrolyzates were statistically significant; the electrolytic conductivity of the water protein solutions was directly proportional to the concentration of protein. It was also proved that the concentration of glucose in the protein solution modified its electrolytic conductivity. Moreover, statistically significant differences were observed between native and glycated proteins. Finally, it was stated that the electrolytic conductivity can be a tool for the differentiation of the native and modified proteins.
Synthesis of New Star-Shaped Liquid Crystalline Cyclotriphosphazene Derivatives with Fire Retardancy Bearing Amide-Azo and Azo-Azo Linking Units

Two series of new hexasubstituted cyclotriphosphazene derivatives were successfully synthesized and characterized. These derivatives are differentiated by two types of linking units in the molecules such as amide-azo (6a–j) and azo-azo (8a–j). The homologues of the same series contain different terminal substituents such as heptyl, nonyl, decyl, dodecyl, tetradecyl, hydroxyl, carboxyl, chloro, nitro, and amino groups. All the intermediates and final compounds were characterized using Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance spectroscopy (NMR), and Carbon, Hydrogen, and Nitrogen (CHN) elemental analysis. Liquid crystal properties for all compounds were determined using polarized optical microscope (POM). It was found that only intermediates 2a–e with nitro and alkoxyl terminal chains showed a smectic A phase. All the final compounds with alkoxyl substituents are mesogenic with either smectic A or C phases. However, other intermediates and compounds were found to be non-mesogenic. The study on the fire retardancy of final compounds was determined using limiting oxygen index (LOI) method. The LOI value of pure polyester resin (22.53%) was increased up to 24.71% after treating with 1 wt% of hexachlorocyclotriphosphazene (HCCP). Moreover, all the compounds gave positive results on the LOI values and compound 6i with the nitro terminal substituent showed the highest LOI value of 27.54%.
Maternal undernutrition during mid-pregnancy in sheep: variable effects on placental growth

SUMMARY The effect of maternal undernutrition between the 30th and 96th day of pregnancy on placental growth in single-bearing ewes was determined separately in two experiments in consecutive years (1986 and 1987) at Mount Derrimut Field Station, Deer Park, Australia. In the first experiment, placental growth measured on the 96th day of pregnancy was reduced (473 v. 596 g) by maternal undernutrition, while in the second, placental growth was increased (600 v. 496 g). Foetal weight and its linear dimensions on the 96th day of pregnancy were not significantly affected by maternal u dernutrition in either experiment. The only significant difference in the animals and experimental conditions between the two studies was the liveweight of the ewes at mating, which was c. 10 kg higher in the second experiment compared with the first (P < 0·01). Body condition score and the change in condition score during the respective nutritional treatments were not significantly different between the two experiments. The results suggest that maternal liveweight, possibly body reserves not quantifiable by condition score, protects and even enhances placental growth during a period of maternal undernutrition.
Effect of Flap Design for Enamel Matrix Derivative Application in Intraosseous Defects

Objective: To systematically review the literature addressing the focused question: What is the effectiveness of different surgical and nonsurgical procedures combined with enamel matrix derivative (EMD) on clinical, radiographic, and patient-centered outcomes in intraosseous defects? Methods: Electronic (Medline, Scopus, and Cochrane databases) and hand literature searches were performed for studies including at least 1 treatment arm where EMD had been applied according to 1 of the following procedures: modified Widman flap; papilla preservation variants (PPVs), including papilla preservation technique, modified papilla preservation technique, and simplified papilla preservation technique; minimally invasive variants, including minimally invasive surgical approach and minimally invasive surgical technique; single-flap variants (SFVs), including single-flap approach and modified minimally invasive surgical technique; or nonsurgical application (flapless approach). Data from 42 selected articles were used to perform a network meta-analysis, and a hierarchy of surgical and nonsurgical applications of EMD was built separately for EMD and EMD + graft based on 6- to 12-mo clinical and radiographic outcomes. Results: Among surgical approaches, EMD was associated with best regenerative outcomes when applied through SFVs, with a mean clinical attachment level gain of 3.93 mm and a reduction in the intrabony component of the defect of 3.35 mm. For EMD + graft, limited differences in regenerative outcomes were observed among surgical procedures. PPVs were associated with the highest residual probing depth for EMD (4.08 mm) and EMD + graft (4.32 mm). Conclusions: In the treatment of periodontal intraosseous defects, 1) SFVs appear to optimize the regenerative outcomes of EMD; 2) substantial regenerative outcomes can be obtained with SFVs and conservative double flaps (i.e., PPVs and minimally invasive variants) when EMD is combined with a graft; and 3) residual probing depth was higher following PPVs for EMD and EMD + graft. Knowledge Transfer Statement: The results of the present systematic review and meta-analysis can be used by clinicians to identify the most effective surgical or nonsurgical procedure to treat an intraosseous defect with EMD or EMD + graft. The main findings indicate that when EMD application is indicated, surgical access based on a single flap seems the most appropriate to optimize clinical outcomes. The application of EMD + graft can be effectively combined with single flaps and conservative double flaps.
Comparative Life History of Liriomyza trifolii and Liriomyza huidobrensis (Diptera: Agromyzidae) on Beans: Effect of Temperature on Development

Abstract The influence of four constant temperatures (15, 20, 25, and 30°C) on development time and survivorship of Liriomyza trifolii (Burgess) and Liriomyza huidobrensis (Blanchard) was studied in laboratory experiments. L. huidobrensis required more time for embryonic development at 25 and 30°C, and less time at 15°C, compared with L. trifolii; at 20°C there were no differences between the two species. Larval development time for L. huidobrensis was longer than for L. trifolii at 20, 25, and 30°C. At 15°C no differences were detected. Pupal development of L. huidobrensis was always faster at 15, 20, and 25°C than that of L. trifolii. Total preimaginal development time was quicker at 15 and 20°C in L. huidobrensis than in L. trifolii; at 25°C no significant differences were found. Highest survival of L. trifolii (68%) occurred at 20°C, while that of L. huidobrensis (61%) occurred at 15°C. At 30°C no adults of L. huidobrensis emerged. The estimated lower threshold temperatures for egg, larva, pupa and total development of L. huidobrensis ranged between 7.3 and 8.1°C, and they were always lower than L. trifolii thresholds, which ranged between 9.9 and 10.7°C. The Logan model was used to describe the relationship between development rate and temperature. The quantification of development times presented in this study, combined with fecundity under different temperatures, could be incorporated into a phenological model that will aid in predicting population charges of leafminers.
Characterization of Extremely Drug-Resistant and Hypervirulent Acinetobacter baumannii AB030

Acinetobacter baumannii is an important nosocomial bacterial pathogen. Multidrug-resistant isolates of A. baumannii are reported worldwide. Some A. baumannii isolates display resistance to nearly all antibiotics, making treatment of infections very challenging. As the need for new and effective antibiotics against A. baumannii becomes increasingly urgent, there is a need to understand the mechanisms of antibiotic resistance and virulence in this organism. In this work, comparative genomics was used to understand the mechanisms of antibiotic resistance and virulence in AB030, an extremely drug-resistant and hypervirulent strain of A. baumannii that is a representative of a recently emerged lineage of A. baumannii International Clone V. In order to characterize AB030, we carried out a genomic and phenotypic comparison with LAC-4, a previously described hyper-resistant and hypervirulent isolate. AB030 contains a number of antibiotic resistance- and virulence-associated genes that are not present in LAC-4. A number of these genes are present on mobile elements. This work shows the importance of characterizing the members of new lineages of A. baumannii in order to determine the development of antibiotic resistance and virulence in this organism.
Spiking network optimized for word recognition in noise predicts auditory system hierarchy

The auditory neural code is resilient to acoustic variability and capable of recognizing sounds amongst competing sound sources, yet, the transformations enabling noise robust abilities are largely unknown. We report that a hierarchical spiking neural network (HSNN) optimized to maximize word recognition accuracy in noise and multiple talkers predicts organizational hierarchy of the ascending auditory pathway. Comparisons with data from auditory nerve, midbrain, thalamus and cortex reveals that the optimal HSNN predicts several transformations of the ascending auditory pathway including a sequential loss of temporal resolution and synchronization ability, increasing sparseness, and selectivity. The optimal organizational scheme enhances performance by selectively filtering out noise and fast temporal cues such as voicing periodicity, that are not directly relevant to the word recognition task. An identical network arranged to enable high information transfer fails to predict auditory pathway organization and has substantially poorer performance. Furthermore, conventional single-layer linear and nonlinear receptive field networks that capture the overall feature extraction of the HSNN fail to achieve similar performance. The findings suggest that the auditory pathway hierarchy and its sequential nonlinear feature extraction computations enhance relevant cues while removing non-informative sources of noise, thus enhancing the representation of sounds in noise impoverished conditions.
Computational Drug Repositioning for Chagas Disease Using Protein-Ligand Interaction Profiling

Chagas disease, caused by Trypanosoma cruzi (T. cruzi), affects nearly eight million people worldwide. There are currently only limited treatment options, which cause several side effects and have drug resistance. Thus, there is a great need for a novel, improved Chagas treatment. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) has emerged as a promising pharmacological target. Moreover, some human dihydrofolate reductase (HsDHFR) inhibitors such as trimetrexate also inhibit T. cruzi DHFR-TS (TcDHFR-TS). These compounds serve as a starting point and a reference in a screening campaign to search for new TcDHFR-TS inhibitors. In this paper, a novel virtual screening approach was developed that combines classical docking with protein-ligand interaction profiling to identify drug repositioning opportunities against T. cruzi infection. In this approach, some food and drug administration (FDA)-approved drugs that were predicted to bind with high affinity to TcDHFR-TS and whose predicted molecular interactions are conserved among known inhibitors were selected. Overall, ten putative TcDHFR-TS inhibitors were identified. These exhibited a similar interaction profile and a higher computed binding affinity, compared to trimetrexate. Nilotinib, glipizide, glyburide and gliquidone were tested on T. cruzi epimastigotes and showed growth inhibitory activity in the micromolar range. Therefore, these compounds could lead to the development of new treatment options for Chagas disease.
Preparation and properties of physically modified banana starch prepared by alcoholic-alkaline treatment

Granular cold-water-soluble (GCWS) starches were prepared from banana starch treating it with 40 and 60% aqueous ethanol at two controlled temperatures (25 and 35 °C). GCWS starches prepared at 25 °C and with 40 and 60% aqueous ethanol had the lowest cold-water solubility, that prepared with 40% aqueous ethanol at 35 °C and stored at room temperature showed low tendency to retrogradation, as assessed by transmittance. Solubility and swelling profiles were similar for GCWS starches and the freeze-thaw stability of GCWS starches was increased as compared with native starch. The apparent viscosity of GCWS banana starches was higher than that of its native starch counterpart.
EMT and EndMT: Emerging Roles in Age-Related Macular Degeneration

Epithelial–mesenchymal transition (EMT) and endothelial–mesenchymal transition (EndMT) are physiological processes required for normal embryogenesis. However, these processes can be hijacked in pathological conditions to facilitate tissue fibrosis and cancer metastasis. In the eye, EMT and EndMT play key roles in the pathogenesis of subretinal fibrosis, the end-stage of age-related macular degeneration (AMD) that leads to profound and permanent vision loss. Predominant in subretinal fibrotic lesions are matrix-producing mesenchymal cells believed to originate from the retinal pigment epithelium (RPE) and/or choroidal endothelial cells (CECs) through EMT and EndMT, respectively. Recent evidence suggests that EMT of RPE may also be implicated during the early stages of AMD. Transforming growth factor-beta (TGFβ) is a key cytokine orchestrating both EMT and EndMT. Investigations in the molecular mechanisms underpinning EMT and EndMT in AMD have implicated a myriad of contributing factors including signaling pathways, extracellular matrix remodelling, oxidative stress, inflammation, autophagy, metabolism and mitochondrial dysfunction. Questions arise as to differences in the mesenchymal cells derived from these two processes and their distinct mechanistic contributions to the pathogenesis of AMD. Detailed discussion on the AMD microenvironment highlights the synergistic interactions between RPE and CECs that may augment the EMT and EndMT processes in vivo. Understanding the differential regulatory networks of EMT and EndMT and their contributions to both the dry and wet forms of AMD can aid the development of therapeutic strategies targeting both RPE and CECs to potentially reverse the aberrant cellular transdifferentiation processes, regenerate the retina and thus restore vision.