jimnoneill/paper-to-field-training huggingface dataset:
Dissection of the mutation accumulation process during bacterial range expansions

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Abstract

Background Recent experimental work has shown that the evolutionary dynamics of bacteria expanding across space can differ dramatically from what we expect under well-mixed conditions. During spatial expansion, deleterious mutations can accumulate due to inefficient selection on the expansion front, potentially interfering with and modifying adaptive evolutionary processes. Results We used whole genome sequencing to follow the genomic evolution of 10 mutator Escherichia coli lines during 39 days (∼1650 generations) of a spatial expansion, which allowed us to gain a temporal perspective on the interaction of adaptive and non-adaptive evolutionary processes during range expansions. We used elastic net regression to infer the positive or negative effects of mutations on colony growth. The colony size, measured after three day of growth, decreased at the end of the experiment in all 10 lines, and mutations accumulated at a nearly constant rate over the whole experiment. We find evidence that beneficial mutations accumulate primarily at an early stage of the experiment, leading to a non-linear change of colony size over time. Indeed, the rate of colony size expansion remains almost constant at the beginning of the experiment and then decreases after ∼12 days of evolution. We also find that beneficial mutations are enriched in genes encoding transport proteins, and genes coding for the membrane structure, whereas deleterious mutations show no enrichment for any biological process. Conclusions Our experiment shows that beneficial mutations target specific biological functions mostly involved in inter or extra membrane processes, whereas deleterious mutations are randomly distributed over the whole genome. It thus appears that the interaction between genetic drift and the availability or depletion of beneficial mutations determines the change in fitness of bacterial populations during range expansion.
Using Stress Factors for Storage of Withania somnifera L. Hairy Roots without Passages

Field: Agricultural and Biological Sciences (Life Sciences)

Hairy root cultures are widely used both for fundamental and practical purposes as a source of valuable secondary metabolites. Hairy roots require frequent passages to fresh nutrient medium due to their rapid growth. Cryopreservation of the most productive hairy root lines for a long time (some years) is a resource-consuming task. In this regard, it is especially important to develop alternative methods for short-term (few months) storage of hairy roots without the loss of their properties and viability. In this study hairy roots of Withania somnifera L. were used as an experimental object to test different stressful conditions for short-term preservation. Effects of increased content of mannitol and NaCl in the medium, oxygen and sucrose deficiency and cold stress on the root growth parameters were evaluated. Nutrient medium with high content of NaCl and reduced concentration of sucrose was the most suitable for the short-term preservation of hairy roots. All cultures survived in the presence of either 300 mM NaCl or 1.875 g/L sucrose for three months. Standard activity of catalases and peroxidases, malondialdehyde content and total antioxidant capacities were completely restored in the cultures after they were returned to normal conditions. Moreover, these hairy roots maintained the same growth rate they had before the treatment. According to these results, we propose new, simple and inexpensive methods for long-term storage of hairy roots at room temperature.
Effects of enzymatic degradation on the subunit composition and biologic properties of human factor VIII

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Human factor VIII was purified from cryoprecipitate and subjected to enzymatic degradation with plasmin, trypsin, chymotrypsin, and thrombin. The reactions were monitored by sodium dodecyl sulfate (SDS)-Polyacrylamide gel electrophoresis and by measurement of four biologic properties, namely, procoagulant activity, ristocetin cofactor activity, precipitation by heterologous antibody, and neutralization of a human factor VIII inhibitor. The electrophoretic patterns of reduced digests showed a reproducible sequence of degradation of the 215,000 molecular weight subunit by plasmin, trypsin, and chymotrypsin, each with well-defined intermediate and enzyme-resistant chain remnants. There were striking similarities in the sizes of several intermediate chain remnants produced by these three enzymes, suggesting the presence of regions on the factor VIII molecule that are especially susceptible to enzymatic degradation, but each enzyme also produced distinctive proteolytic derivatives. The most obvious differences included (1) a single-chained 40,000 molecular weight remnant cleaved by plasmin and trypsin which was either absent or degraded in chymotryptic digests, (2) large intermediate chain remnants of 176,000 and 157,000 molecular weight which were produced only by trypsin, and (3) differences in size and content of nonreduced fragments in the final digests. Thrombin caused no detectable change in electrophoretic patterns. The immunoprecipitation reaction was sensitive to minor degrees of proteolytic cleavage, showing a marked increase in rocket size even when the SDS-treated subunit chains showed virtually no change in electrophoretic mobility. Procoagulant and inhibitor neutralizing activities were rapidly destroyed by trypsin and plasmin, but this destruction did not correlate with specific changes in electrophoretic patterns. Both thrombin and chymotrypsin caused an increase in procoagulant activity prior to destruction of activity; changes in this property were therefore unrelated to changes in the protein visualized by gel electrophoresis. Ristocetin cofactor activity was considerably more resistant to plasmin than to trypsin or chymotrypsin, and roughly paralleled the persistence of highly aggregated forms in the digests.
Rancang Bangun Aplikasi Sistem Informasi Pariwisata di Kabupaten Maluku Tenggara Berbasis Web dengan Metode User Centered Design (UCD)

Field: Computer Science (Physical Sciences)

This research is motivated by the necessity for an information system capable of providing comprehensive, fast, and accurate tourism information for Southeast Maluku Regency. The current dissemination of tourism information within the regency is limited, hindering potential visitors from outside the area from accessing valuable insights. The proposed information system aims to bridge this gap by offering a web-based platform that facilitates the management of tourism and cultural information by the local government’s tourism and culture department. Utilizing the user-centered design (UCD) methodology, the system is developed using programming languages such as PHP and is supported by a MySQL database for data storage. This tourism information system includes features that allow users to search for information related to cultural tourism and culinary experiences in the region. It is anticipated that the implementation of this system will significantly enhance the promotion of Southeast Maluku tourism sector to a wider audience.
Retrieval and Assimilation of Storm Characteristics from Both In-Cloud and Cloud-to-Ground Lightning Data to Improve Mesoscale Model Forecasts

Field: Earth and Planetary Sciences (Physical Sciences)

Abstract : To improve the accuracy of regional weather forecasts, we (1) obtained and operated a lightning mapping system that detects all types of lightning to provide data for this project, (2) quantified and tested relationships between lightning and other storm properties that will be useful for assimilation, and (3) developed techniques for assimilating data from all types of lightning into COAMPS. Observational data analysis and storm simulations showed that total lightning flash rates were correlated with a storms mass and volume of graupel, updraft mass flux through the mixed phase region, and the volume of updraft exceeding 10 m/s. Gridded lightning data were assimilated into COAMPS by nudging the trigger function of the Kain-Fritsch subgrid-scale convective parameterization. In a test case from the central United States in July 2000, assimilation of lightning data greatly improved the surface moisture, the intensity and location of surface cold pools, and the location of deep convection at the time of forecast initialization. The best results were obtained when convection was completely suppressed where no lightning was observed.
Models of European Identity: Reconciling Universalism and Particularism

Field: Social Sciences (Social Sciences)

Abstract The paper offers an analysis of the four main conceptions of European identity, which can be termed: moral universalism, post‐national universalism, cultural particularism and pragmatism. The first three of these models can be analysed in terms of an emphasis either on universalism or on particularism. In this paper it is argued that these three models suffer from an excessive concern with either ‘thin’ univeralistic conceptions of identity or with ‘thick’ particularistic identities and that the fourth possibility does not offer a satisfactory alternative. What is neglected in all four models is the potential for pluralisation that is expressed in an alternative model of European identity. The paper offers a defence of this in terms of a pluralised cosmopolitan European identity.
A Self Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations

Field: Computer Science (Physical Sciences)

There are currently over 160,000 protein crystal structures obtained by X-ray diffraction with resolutions of 1.5Å or greater in the Protein Data Bank. At these resolutions hydrogen atoms do not resolve and heavy atoms such as oxygen, carbon, and nitrogen are indistinguishable. This leads to ambiguity in the rotamer and protonation states of multiple amino acids, notably asparagine, glutamine, histidine, serine, tyrosine, and threonine. When the rotamer and protonation states of these residues changes, so too does the electrochemical surface of a binding site. A variety of computational tools have been developed to assign these states for these residues based on a crystal protein structure by evaluating the possible states and typically deciding on one single state for each residue. We posit that multiple rotamer and protonation states of residues are consistent with the resolved structure of the proteins and introduce a protonation and rotamer assignment tool that identifies an ensemble of rotamer and protonation states that are consistent with the X-ray scattering data of the protein. Here, we present a Rotamer and Protonation state Assignment (RAPA) tool that analyzes local hydrogen bonding environments in the resolved structures of proteins and identifies a set of unique rotamer and protonation states that are energetically consistent with the crystal structure. We evaluate all RAPA predicted states in unrestrained molecular dynamics simulations and find that there are multiple configurations for each protein which match the X-ray results with RMSDs of less than 1.0Å for the atoms with the lowest 90% B-factors. We find that for most protein systems (62 of 77) there are 8 or fewer possible states suggesting that there is no combinatorial explosion of accessible configurations for a majority of proteins. This suggests that investigating all energetically accessible rotamer and protonation states for most proteins is computationally feasible and that the selection of single states is arbitrary.
A Threshold Key Management Scheme for Mobile Ad Hoc Networks Using Elliptic Curve Dlog-Based Cryptosystem

Field: Computer Science (Physical Sciences)

In mobile ad-hoc networks (MANETs), traditional security solutions are not adequate due to the lack of infrastructure and the absence of centralized administration. In this paper, a threshold key management scheme for MANETs is presented. The proposed scheme is implemented using elliptic curve dlog-based cryptosystem. In this scheme, an off-line central authority is required in the initialization phase before network deployment. The central authority creates and preloads the shares matrix for each mobile node in the network initialization phase. Each session member generates its private/public keypair, and the session public key by collaborating with its trusted neighbors. The generation of the node private/public key pair,and the session public key is performed without any prior-communication between session members. The advantages of the proposed scheme are justified through extensive timing and network simulations.
On the oil of the living egg of salmon (Oncorhynchus Keta)

Field: Agricultural and Biological Sciences (Life Sciences)

Living subsance contains three main organic constituents. Of these the proteins and carbohydrates are typically water soluble substance. The third (lipids) is distinguished by insolubility in water, but soluble in fat solvent. Though lipids are insoluble in water, they are nevertheless finally dispersed in protoplasm. This is in part due to the fact that the lipids are emulsified, in part, also to the fact that the lipids may combine with proteins to form water soluble compounds. The nature of these compounds is not well known, but it is certain that they can be found in protoplasm (Heilbrunn. '36, '38). The present study deals with the general characters of oil of salmon egg and the relation between oil and proteins in egg. With the lapse of time, the larger oil drops grow in their diameters, while the oil granules decrease in number (Table 1, 2), and the amount of oil increases in total (Table 3). The similar increase of oil was also observed in eggs immersed in NH4Cl-, 0.5% saponin Ringer-, various Ph- (Ph 5, 8), alcohol Ringer-or ether Ringer-isotonic solut6ions as well as in eggs treated with heat (at 20°C) (Table 5-9). On the contrary, when the egg has been immersed in 0.5% chloreton Ringer the oil decreases (Table 6). The isotonic solution of salts such as NaCl, KCl, CaCl2, MgCl2 is not effective on the oil volume (Table 4). The increase of oil may due to the oil freed from the protein lipid as the result of denature of protoplasm, and as soon as the denature has been occured, the fertilizability of egg falls suddenly.
Length–weight relationship and condition factor for 7 loliginid squid species in Mexican waters

Field: Agricultural and Biological Sciences (Life Sciences)

The length–weight relationship and the condition factor are key parameters in stock assessment. Despite the fisheries potential loliginid squids have in Mexico, the group is scarcely known and no formal management has been implemented. A total of 1,105 squids captured on the Pacific and Atlantic coasts of Mexico were measured to estimate length–weight relations and condition factors. Except for Lolliguncula brevis and Lolliguncula argus, all species showed negative allometric growth. The 2 species with isometric growth showed a poor condition, according to Fulton’s condition factor, and the rest of the species were in good health, according to the relative condition factor. The type of growth exhibited by the species identified in this study could be associated with their swimming habits or otherwise be affected by the same variables that determine the type of growth of other squid found in Mexican waters. The parameters evaluated in this research are now available for incorporation in further fishery stock assessment models for loliginid squids.
Effect of Rhizome Fragmentation, Clover Competition, Shoot-Cutting Frequency, and Cutting Height on Quackgrass (Elymus repens)

Field: Agricultural and Biological Sciences (Life Sciences)

Quackgrass is a problematic agricultural weed in the temperate zones of the world and is difficult to control without herbicides or intensive tillage. However, it may be possible to control quackgrass with less environmental impact by combining multiple low-intensity control methods. A pot experiment was conducted in July to October 2012 and repeated in June to September 2013 to investigate the effect of rhizome fragmentation, competition from white clover, shoot-cutting frequency, and cutting height on quackgrass. Rhizome fragmentation was expected to result in more, but weaker, quackgrass shoots that would be more vulnerable to shoot cutting and competition. However, by 20 d past planting, rhizome fragmentation did not change the total number of quackgrass shoots per pot, because an increase in main shoots was offset by a decrease in tiller numbers. Rhizome fragmentation did not reduce quackgrass biomass acquisition during the experimental period. Although rhizome fragmentation did reduce total fructan content, it did not enhance the effect of clover competition, shoot-cutting frequency, or shoot-cutting height. Clover competition by itself reduced quackgrass shoot numbers by 72%, rhizome biomass by 81%, and belowground fructan concentration by 10 percentage points, compared with no competition. The more frequently quackgrass shoots were cut, the less biomass quackgrass acquired, and a high shoot-cutting frequency (each time quackgrass reached 2 leaves) resulted in a lower belowground fructan concentration than a low shoot-cutting frequency (at 8 leaves). However, in pots without competition, a higher shoot-cutting frequency resulted in more quackgrass shoots. A lower shoot-cutting height (25 mm) had more impact when shoot cutting was more frequent. In conclusion, rhizome fragmentation did not reduce the number of quackgrass shoots or rhizome biomass, but competition from white clover, a high shoot-cutting frequency, and a low shoot-cutting height strongly suppressed quackgrass biomass and fructan acquisition.
Low-noise supercontinuum generation in chiral all-normal dispersion photonic crystal fibers

Field: Physics and Astronomy (Physical Sciences)

We present the advantages of supercontinuum generation in chiral, therefore circularly birefringent, all-normal dispersion fibers. Due to the absence of nonlinear power transfer between the polarization eigenstates of the fiber, chiral all-normal dispersion fibers do not exhibit any polarization instabilities and thus are an ideal platform for low-noise supercontinuum generation. By pumping a chiral all-normal dispersion fiber at 802 nm, we obtained an octave-spanning, robustly circularly polarized supercontinuum with low-noise.
A review and analysis of Title IX of the Education Amendments of 1972

Field: Social Sciences (Social Sciences)

Title IX of the Education Amendments of 1972 has become synonymous with expanding the athletic opportunities for females. Often misunderstood by educational administrators and the general public, this study attempts to review and analyze the historical development of Title IX with specific attention given to athletics at the collegiate and scholastic levels. Throughout this study, the historical and current status of the Title IX is evaluated as well as a thorough comparison between the law’s current administration with the historical evidence of Title IX’s legislative intent. With the most recent actions involving Title IX in March of 2005, the law’s recent publicity demonstrates the ever increasing importance of understanding the legality of various actions by educational institutions as well as high school athletic associations.
Hepatorenal Toxicity Induced by Maternal Exposure to Topical Betamethasone Prior to Fertilization in Newborn Rabbits

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Background: Synthetic glucocorticoids, such as Betamethasone, are used for treatment of skin disease including Psoriasis. No enough evidences are present about the side effect of maternal exposure to betamethasone, before fertilization, on new-born. So, the goal of the present study was to determine these side effects on liver and kidney. Methods: In the present study, two doses of betamethasone (0.02 and 0.2 mg/kg b.w) were used. At the end of the experimental period (after 3 weeks of delivery), six new-born rabbits of both sexes (1 newborn rabbit per mother) were dissected under light anesthesia and blood, liver and kidney samples were collected. All the measurements were performed in one assay. Result: Maternal exposure to betamethasone, for 2 months before fertilization, induced toxicity in new-born rabbits and decrease the relative organ weight of liver and kidney in new-born rabbits. The biochemical changes involved induction of oxidative, alterations in hepatic and renal parameters. Moreover, structural changes in liver and kidney new-born rabbits were observed. So, this study suggested that females must take care in using treatment with betamethasone before fertilization to avoid toxicity of their offspring.
Removal of Pharmaceuticals in a Macrophyte Pond-Constructed Wetland System and the Effect of a Low Effluent Recirculation

Field: Environmental Science (Physical Sciences)

Waste stabilization ponds and constructed wetlands (CWs) are effective at eliminating pharmaceutical residues, but removals are not usually complete. Their combination is regarded as an efficient, robust wastewater treatment method, but their efficiency in the removal of pharmaceuticals and the effect of a mild effluent recirculation has not been sufficiently studied in full-scale systems. Effluent recirculation can help to improve performance by increasing hydraulic residence time and, eventually, dissolved oxygen concentration. In this work, the presence of pharmaceuticals in wastewater from a university campus, their removal in a macrophyte pond–CW system, and the effect of effluent recirculation on removal and ecological risk were evaluated. Stimulants (caffeine and nicotine) and non-steroidal anti-inflammatories (naproxen and ibuprofen) were the most detected compounds in the influent and showed the highest concentrations, ranging from 0.5 to 300 µg·L−1. The pond–CW combination showed notable elimination for these compounds, achieving 87% on average. The ecological risk was also reduced by between 5.5 and 12.4 times, but it was still over values that indicates high ecological risk, mainly because of the concentrations of nicotine and ibuprofen. The effect of effluent recirculation was not as high as expected since the removals of caffeine, paraxanthine and naproxen were significantly improved, but those of atenolol and ibuprofen were lower. These results suggest that a higher recirculation ratio should be tested.