Miracle-dz/UniFAR-FTUs huggingface dataset:
How ancient DNA may help in understanding the origin and spread of agriculture

The origin and spread of agriculture have been central questions in archaeology for the last 75 years and are increasingly being addressed by a multidisciplinary approach involving biologists, ecologists, geographers and anthropologists as well as archaeologists. Molecular genetics has the potential to make an important contribution, especially by enabling the number of times that a crop or animal was domesticated to be determined. Molecular genetics can also assign approximate dates to domestication events, identify the wild progenitor of a domesticate, and provide new forms of evidence relevant to agricultural spread. With wheat, molecular genetical studies of modern plants have suggested that einkorn was domesticated just once but that emmer might have been domesticated more than once. Ancient DNA studies of animal remains have benefited from progress made with equivalent analyses of human bones, and with plant material there have been clear demonstrations of DNA preservation in desiccated seeds. Charred remains have also been shown to contain ancient DNA but this finding is unexpected in view of the high temperatures to which these seeds have supposedly been exposed. Ancient DNA studies of wheat remains have been used in taxonomic identification and in assessment of the possible bread–making quality of the wheat grown at an Early Bronze Age site in Greece.
How Should the Value Relevance Research Employ Book Value of Equity

Design/methodology/approach – As the Price Model employs reported earnings together with book value of equity (BVE), it induces a mechanical interdependency since earnings are partially integrated to BVE via the net income available to owners of parent item. We suggest researchers subtract this item from BVE prior to analyses. We perform analyses by employing the Price Model with the unadjusted (or reported) version BVE and the Price Model with the adjusted version of BVE.
Purification and partial characterization of phospholipases A2 from Bothrops asper (barba amarilla) snake venom from Chiriguaná (Cesar, Colombia)

Components with phospholipase A2 activity were isolated by gel filtration and cationic exchange chromatography from the venom of Bothrops asper snakes from Chiriguana, Colombia (9°22´N; 73°37´W). Five fractions were obtained by the gel filtration, and PLA2 activity was found in fraction 3 (F3). In the cationic exchange chromatography, F3 showed eight components with PLA2 activity. Six of these components appeared as one band in polyacrylamide gel electrophoresis (SDS-PAGE). Fractions II and VII exhibited an optimal activity at pH 9 and 52oC. The optimum calcium concentration for fraction II was 48 mM and for fraction VII, 384 mM. Both fractions showed thermal stability. Fraction II was stable at pH values between 2.5 and 9, and fraction VII, between 2.5 and 8. The Michaelis Menten constant (KM) was 3.5x10-3 M for fraction II and 1.6x10-3 M for fraction VII. The molecular weight was 16,000 Dalton for fraction II and 17,000 Dalton for fraction VII. Both isoenzymes did not show any toxic activity (DL50) at 5.3 and 4 µg/g. The two fractions showed different kinetic constant (KM), calcium requirement, and substrate specificity for haemolytic activity.
Interaction of DNA and polyethylenimine: Fourier-transform infrared (FTIR) and differential scanning calorimetry (DSC) studies

Polyplexes, which are formed spontaneously between cationic polymer and negatively charged nucleic acids, are commonly used for gene and oligonucleotide delivery in vitroand in vivo. Many kinds of cationic polymers have been used to condense DNA by electrostatic interaction into small particles (Polyplexes), for protecting the DNA from degradation and enhancing its uptake via endocytosis. Polyethylenimine (PEI) appears to be one of the most advanced delivery materials that can condense DNA efficiently forming PEI/DNA complexes. The PEI/DNA interaction was evaluated by measuring zeta potential and DNA secondary structures using Fourier-transform infrared (FTIR) technique. IR results show that the antisymmetric PO2- vibration of DNA (at 1236 cm-1) shifts toward lower frequencies when complexed with PEI. The secondary conformation of DNA in aqueous solution clearly remains in B-form. Thermal behaviors of plasmid DNA, polymer and their formed complexes were recorded to give insights into their conformational changes when temperature was raised. DSC results showed a disappearance of the main DNA transition band at 94°C at all examined N/P (0.3 to 5) ratios of PEI/DNA complexes. These findings could be useful for the developing polymer-based gene delivery systems with better in vitro and in vivo performance. Key words: Polyethylenimine, DNA, Fourier-transform infrared (FTIR), differential scanning calorimetry (DSC), zeta potential.
Self-Guided and Self-Regularized Actor-Critic

Deep reinforcement learning (DRL) algorithms have successfully been demon-1 strated on a range of challenging decision making and control tasks. One dominant 2 component of recent deep reinforcement learning algorithms is the target network 3 which mitigates the divergence when learning the Q function. However, target 4 networks can slow down the learning process due to delayed function updates. An-5 other dominant component especially in continuous domains is the policy gradient 6 method which models and optimizes the policy directly. However, when Q func-7 tions are approximated with neural networks, their landscapes can be complex and 8 therefore mislead the local gradient. In this work, we propose a self-regularized and 9 self-guided actor-critic method. We introduce a self-regularization term within the 10 TD-error minimization and remove the need for the target network. In addition, we 11 propose a self-guided policy improvement method by combining policy-gradient 12 with zero-order optimization such as the Cross Entropy Method. It helps to search 13 for actions associated with higher Q-values in a broad neighborhood and is robust 14 to local noise in the Q function approximation. These actions help to guide the 15 updates of our actor network. We evaluate our method on the suite of OpenAI gym 16 tasks, achieving or outperforming state of the art in every environment tested. 17
Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea

Climate, which sets broad limits for migrating species, is considered a key filter to species migration between contrasting marine environments. The Southeast Mediterranean Sea (SEMS) is one of the regions where ocean temperatures are rising the fastest under recent climate change. Also, it is the most vulnerable marine region to species introductions. Here, we explore the factors which enabled the colonization of the endemic Red Sea octocoral Melithaea erythraea (Ehrenberg, 1834) along the SEMS coast, using sclerite oxygen and carbon stable isotope composition (δ18OSC and δ13CSC), morphology, and crystallography. The unique conditions presented by the SEMS include a greater temperature range (∼15 °C) and ultra-oligotrophy, and these are reflected by the lower δ13CSCvalues. This is indicative of a larger metabolic carbon intake during calcification, as well as an increase in crystal size, a decrease of octocoral wart density and thickness of the migrating octocoral sclerites compared to the Red Sea samples. This suggests increased stress conditions, affecting sclerite deposition of the SEMS migrating octocoral. The δ18Osc range of the migrating M. erythraea indicates a preference for warm water sclerite deposition, similar to the native depositional temperature range of 21–28 °C. These findings are associated with the observed increase of minimum temperatures in winter for this region, at a rate of 0.35 ± 0.27 °C decade−1 over the last 30 years, and thus the region is becoming more hospitable to the Indo-Pacific M. erythraea. This study shows a clear case study of “tropicalization” of the Mediterranean Sea due to recent warming.
Identifying Crowding Impact on Departure Time Choice of Commuters in Urban Rail Transit

Crowding in urban rail transit is an inevitable issue for most of the high-density cities across the world, especially during peak time. For commuters who have considerably fixed destination arrival times, departure time choice is an important tool to adjust their trips. The ignorance of crowding impact on commuters’ departure time choice in urban rail transit may cause errors in forecasting dynamic passenger flow during peak time in urban rail transit. The paper develops a mixed logit model to identify how crowding impacts the departure time choice of commuters and their taste variation. Arrival time value was firstly measured in a submodel by applying the reference point approach and then integrated to the main model. Considering the characteristics of human perception, we divided crowding into five grades with distinct circumstances. All parameter distributions were assumed based on their empirical distributions revealed through resampling. The data from Shanghai Metro used for estimation were collected by a specifically designed survey, which combines revealed preference questions and stated preference experiments to investigate the willingness and extent of changing departure time choice of passengers who experienced various grades and duration of crowding in the most crowded part. The result shows that an asymmetric valuation model with preferred arrival time as the only reference point best captured commuters’ responses to arrival time. The departure time choice model clearly identified that only crowding ranging from Grades 3 to 5 had an impact on commuters’ departure time choice. The parameters of crowding costs can be assumed to follow transformed lognormal distributions. It is found that the higher the grade of crowding is, the bigger the impact each unit of crowding cost has on commuters’ departure time choice, while commuters’ tastes get more concentrated when crowded situation upgrades. The model in this paper can help policymakers better understand the interaction between commuters’ departure time choice and crowding alleviation.
Evolutionary tempo in Jurassic and Cretaceous ammonites

Stage-level range data for 983 Jurassic and Cretaceous ammonite genera, distributed within 83 families, were analyzed by assigning absolute ages to stages or substages. We found ammonite genera to have a mean generic range of 7.3 Myr/ammonite genus. Using a similar methodology, mean generic range per family was also computed. The distribution of long-ranging genera (arbitrarily chosen as those ammonite genera ranging for 12 Myr or more) among families was found to be nonrandom. Instead, long-ranging genera were found to be concentrated in a few families, resulting in significant heterogeneity in the distribution of generic longevities within families (taxotely sensu Raup and Marshall 1980). Although some of the long-ranging genera were found to be morphologically simpler than shorter-ranging genera, others were equally or even more complex, indicating that longevity among ammonite genera is not merely a taxonomic artifact, dependent on degree of differentiable conch morphology. Those Cretaceous families composed of a large number of long-ranging genera were also among the leaders in mean species longevity per family, based on species-level range data for Cretaceous ammonites of the Great Valley Sequence of California. Many of the long-ranging genera and species possess a similar morphologic attribute: siphuncular tubes (connecting rings) of small diameter but high wall thickness.
Fat uptake evaluation in fried fish fillet by using Scanning Electron Microscopy (SEM)

The aim of this study was to investigate the effects of breading materials and two different frying oils on the fat up-take in the fish fillets during frying process. Breaded and non-breaded black pomfret (Parastromateus niger) fillets were fried in sunflower oil and palm olein. Fat content by Soxhelet method and scanning electron microscopy (SEM) was studied. Results from Soxhelet method showed that fat content in the nonbreaded fried fillets was significantly (P<0.05) higher than breaded fillets. This was confirmed by the SEM. Observations from the SEM micrographs showed that some gas cell can be seen in the non-breaded fried fillets. Presence of these cells in the nonbreaded fillets resulted in the higher fat uptake than that of fish muscle fillets. Observation by the SEM also showed that the surfaces of the non-breaded fried fillets highly deformed. However, this deformation in the breaded fried fillets was significantly lower.
A New Alligator Lizard from Northeastern Mexico

Abstract A new alligator lizard is described from the Chihuahuan Desert in southwestern Tamaulipas, Mexico. This lizard appears to be most closely related to the smooth-scaled, relatively small-bodied alligator lizards Gerrhonotus lugoi, from the Cuatro Ciénegas Basin of central Coahuila, and G. parvus, from the central part of Nuevo León, but differs from these species, especially G. parvus, in a number of morphological characters. We tentatively place our new species in the genus Gerrhonotus alongside G. lugoi and G. parvus, but concede that future research is needed to ascertain the phylogenetic placement of these smooth-scaled gerrhonotine lizards.
Mining Students’ Data to Analyse Usage Patterns in eLearning System of Secondary Schools in Tanzania

The adoption and use of various eLearning systems to enhance the quality of education in secondary schools in Tanzania is becoming common. However, there is little evidence to suggest that students are actually use them. Existing studies tend to focused on investigating students’ attitude towards using these systems through surveys. Nonetheless, data from surveys is normally subject to the possibility of distortion, low reliability, and rarely indicate the causal effects. This study adopted WEKA and Keel as data mining tools to analyze students’ usage patterns and trends using 6,8827 individual records from log file of Halostudy system implemented in secondary schools in Tanzania. The study found that the system usage is moderate and, in the decline. There is also variability in the usage of multimedia elements with biology having the highest number while mathematics had the lowest. Students from Dar es Salaam, Mwanza, and Arusha in that order had the highest system usage with the lowest being from the peripheral regions. The possible challenges limiting system usage are discussed. These findings show that data mining tools can be used to indicate usage patterns of systems implemented in sub-Saharan Africa and help educators to find ways of maximizing systems usage.
Crowd Behavior Cognitive Model Architecture Design

Our United States military is increasingly engaged in urban combat or peace-keeping missions. As a result, soldiers are also increasingly engaged with the civilian non-combatant inhabitants of various nations. Yet, current military simulation models have little or no representation of these effects which can lead to suboptimal training or experimentation results. More realistic and sophisticated crowd models are desired to address this growing need. It is unlikely that one crowd model will meet all our military’s crowd requirements since models are needed with a variety of behaviors depending upon the type of mission, the size of encounters, and the user application. A federate that may be used to provide such variety of civilian behaviors in a crowd context would need to be flexible, configurable, and extensible. In this paper, we report about one such instantiation and the framework and cognitive model that support it. The framework is a layered architecture that is composed of a physical layer in which movements and other actions of the crowd are manifested; and also a cognitive layer in which the motivations of these activities are generated and propagated. Connecting these two layers is an API layer that provides mapping and communication services for the stimuli, activities, and accompanying parameters that are crowd behavior centric. We focus especially on the details about the cognitive model architecture (CMA) and the design process used to achieve it.
Phase Opposition Disposition PWM Strategy and Capacitor Voltage Control for Modular Multilevel Converters

This paper focuses on the carrier disposition Pulse Width Modulation (PWM) strategies for Modular Multilevel Converters (MMC). The authors propose a new Phase Opposition Disposition PWM (PODPWM) scheme applicable regardless of the converter’s sub-modules number. Moreover, a capacitor voltage sorting algorithm is synthesized aiming to ensure the converter’s balanced operation. Simulation results of a 3.6 MVA, 3-SM-MMC are presented and discussed.
Legacies of past land use challenge grassland recovery – An example from dry grasslands on ancient burial mounds

Due to large-scale agricultural intensification, grasslands are often restricted to habitat islands in human-transformed landscapes. There are approximately half a million ancient burial mounds built by nomadic steppic tribes in the Eurasian steppe and forest steppe zones, which act as habitat islands for dry grassland vegetation. Land use intensification, such as arable farming and afforestation by non-native woody species are amongst the major threats for Eurasian dry grasslands, including grasslands on mounds. After the launch of the Good Agricultural and Environmental Condition framework of the European Union, in Hungary there is a tendency for ceasing crop production and cutting non-native woody plantations, in order to conserve these unique landmarks and restore the historical grassland vegetation on the mounds. In this study, restoration prospects of dry grassland habitats were studied on kurgans formerly covered by croplands and Robinia pseudoacacia plantations. Soil and vegetation characteristics were studied in thespontaneously recovering grasslands. The following questions were addressed: 1; How does site history affect the spontaneous grassland recovery? 2; Do residual soil nutrients play a role in grassland recovery? In former croplands, excess phosphorus, while in former Robinia plantations, excess nitrogen was present in the soil even four years after the land use change and grassland vegetation was in an early or mid-successional stage both on the mounds. The results showed that, without proper management measures, recovery of grassland vegetation is slow on mounds formerly used as cropland or black locust plantation. However, restoration efforts, focused on the restoration of mounds formerly covered by croplands, can be more effective compared to the restoration of mounds formerly covered by forest plantations.
An investigation into the role of syntaxin 16 in GLUT4 trafficking

In muscle and fat cells, insulin stimulates the translocation of GLUT4 from unique intracellular storage site(s) to the cell surface. In type II diabetes this translocation is impaired. The translocation of GLUT4 in response to insulin is an example of regulated membrane trafficking. Membrane trafficking involves the fusion of vesicles with specific target membranes and is mediated by SNARE proteins. The SNARE proteins involved in the intracellular trafficking of GLUT4 are poorly understood. Stx 16 is a t-SNARE located in the TGN which has been proposed to have a role in GLUT4 trafficking. Previous work has shown that expression of the cytosolic domain of stx 16 significantly slows the reversal of insulin-stimulated glucose transport and depletion of stx 16 using morpholino antisense oligonucleotides reduces glucose transport over a range of insulin concentrations. Stx 16 knockdown also reduces total cellular levels of GLUT4. It has been suggested that stx 16 has a role in sequestration of GLUT4 in its storage site(s). In this thesis the role of stx 16 in GLUT4 trafficking was further investigated. First of all, stx 16 expression was stably depleted in 3T3-L1 adipocytes using a shRNA approach. Knockdown of stx 16 reduced the total GLUT4 cellular levels by 20% and the majority of GLUT4 appeared to be lost from fractions which included GSVs. Stx 16 depletion also resulted in a reduction in stx 6 levels and reduced recruitment of mVps45 to the membrane. Also, assays were developed to investigate GLUT4 trafficking kinetics using 3T3-L1 adipocytes expressing HA-GLUT4-GFP. Stx 16 is phosphorylated under basal conditions and insulin stimulation decreases this phosphorylation. It is thought that this dephosphorylation regulates an important membrane trafficking event in GLUT4 sorting. Potential phosphorylation sites have been previously identified. Screening of phosphorylation site mutants in yeast suggested that stx 16 may be phosphorylated at Ser 95. Unfortunately it was not possible to confirm this in 3T3-L1 adipocytes. In summary the data in this thesis suggests that stx 16 has a role in sorting GLUT4 to its storage site(s). The precise role of stx 16 will need to be further examined to determine the how stx 16 depletion affects GLUT4 trafficking kinetics. The work presented in this thesis also suggests that stx 16 may be phosphorylated at Ser 95. This will need to be confirmed in 3T3-L1 adipocytes and the effect of stx 16 phosphorylation on GLUT4 trafficking examined.
Cross-Species amplification of Catla catla microsatellite locus in Labeo rohita

Successful cross-species amplification of microsatellites of a particular locus in Labeo rohita using primers of specific microsatellite loci from Catla catla is reported. This is the first report on amplification of microsatellites in Labeo rohita. The locus was found to be polymorphic (p<0.95) in the samples from the two rivers, Satlej and Rapti belonging to different river systems of Indus and Ganges rivers and a total of 4 alleles were found. This validates the utility of the microsatellite locus for screening genetic variability in wild stocks of L. rohita.
Using Machine Learning Techniques for Supercell Tornado Prediction with Environmental Sounding Data

This work is supported by the grant “CyberTraining: DSE: Cross-Training of Researchers in Computing, Applied Mathematics and Atmospheric Sciences using Advanced Cyberinfrastructure Resources” from the National Science Foundation (grant no. OAC–1730250). The hardware used in the computational studies is part of the UMBC High Performance Computing Facility (HPCF). The facility is supported by the U.S. National Science Foundation through the MRI program (grant nos. CNS–0821258, CNS–1228778, and OAC–1726023) and the SCREMS program (grant no. DMS– 0821311), with additional substantial support from the University of Maryland, Baltimore County (UMBC). See hpcf.umbc. edu for more information on HPCF and the projects using its resources. Co-author Carlos Barajas additionally acknowledges support as HPCF and CyberTraining RA.
Numerical Simulations for the Port Structures Damaged Due to Ground Motion During the 2011 Off the Pacific Coast of Tohoku Earthquake

Many port structures were damaged over a wide area by the 2011 off the Pacific Coast of Tohoku earthquake. Especially the quay walls damaged by both the ground motion and the tsunami were observed more remarkably in the south of the epicenter. Although it is supposed that the damage due to liquefaction before the tsunami induced severer damage, it is unknown how severely liquefaction and damage to the quay walls occurred during the earthquake. In order to clarify it, this study examined some numerical simulations using the strain space multiple mechanism model (called the cocktail glass model) as a geotechnical constitutive model for the port structures. Based on the results of this study, it was found that the cocktail glass model taking permeability into account is applicable to evaluate seismic performance such as deformation of the port structures against strong and long duration ground motion.