Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic editing: towards realization of the curable genome concept

Recent developments in biotechnology have enabled scientists to modulate DNA sequences in a precise way. These genome engineering technologies also open new possibilities to alter the epigenetic composition of the genome at any given genomic location thereby changing gene expression patterns, while leaving the primary DNA sequence intact. This new approach, so-called epigenetic editing, holds great promise to permanently reprogram cell identity. As reprogramming the epigenetic composition, and hence gene expression patterns is now technically feasible, the society needs to consider to what extent interference at the epigenetic level can be accepted. In this review, we discuss the potential epigenetic editing holds for research and therapy, and also touch upon societal implications of this rapidly growing research field.
Inward tubulation of the plasma membrane expedites membrane exchange and receptor presentation

The plasma membrane is a crucial barrier between the cell and its external environment, and it also enables efficient passage of materials and information. Membrane vesicle trafficking allows precise delivery of materials but is rather inefficient. The mechanism for efficient membrane exchange remains elusive. Here we describe inward tubulation of the plasma membrane (PM tubes) that extends deep into the cytoplasm. These widespread PM tubes elongate along microtubules and are stabilized by actin filaments and cholesterol. PM tubes are preferred sites for connection between the endoplasmic reticulum and the plasma membrane. PM tubes facilitate receptor presentation at the surface of cells, possibly also shortening the distance for transported cargo to reach the external environment. In Brief A new type of tubular membrane structures was discovered in cells, revealing a shortcut that cells employ to expedite material exchange with their external environment. Highlights Inward tubulation of the plasma membrane (PM tubes), transiently interacts with the Golgi apparatus Microtubule side-binding proteins pull PM tubes, while actin filaments and cholesterol stabilize PM tubes PM tubes are preferred sites where ER-PM contacts form in response to increased cytoplasmic calcium concentration PM tubes are preferred sites for the surface presentation of GLUT1 upon glucose deprivation
Noninvasive age estimation in rodents by measuring incisors width, with the Zaisan mole vole (Ellobius tancrei) as an example

Abstract Non-invasive age estimation is critically important for many field studies but often it represents a significant challenge. In rodents, upper incisors represent a part of a cranium which can be readily measured in an alive animal. We propose an age estimation method based on the measurements of both upper incisors’ width (IW) for a subterranean rodent, Ellobius tancrei. The IW measurements for 77 laboratory-born females and 81 males were fitted, separately for the sexes, by sigmoidal Gompertz growth functions to obtain the asymptotic values. Based on the data set encompassing pre-asymptotic ages, we then derived a polynomial regression model with log-transformed age as а predictor. The analysis revealed no statistically significant sex difference in growth patterns. Derived model explained 91% of IW variation and was used to obtain predicted values of age and their 95% prediction intervals through inverse calculations. We conclude that IW is a potentially useful age indicator for mole voles and possibly other rodents in cases when invasive or time-consuming methods are non-appropriate.
Sewage Sludge Valorization via Hydrothermal Carbonization: Optimizing Dewaterability and Phosphorus Release

As the use of sewage sludge as a fertilizer in agriculture is increasingly restricted in the European Union, other ways to utilize this waste stream need to be developed. Sewage sludge is an ideal input material for the process of hydrothermal carbonization, as it can convert wet biomass into a solid energy carrier with increased mechanical dewaterability. Digested sewage sludge was hydrothermally carbonized at 160–200 °C for 30–60 min with initial pH levels of 1.93–8.08 to determine optimal reaction conditions for enhanced dewaterability and phosphorus release into the liquid phase. Design of experiments was used to develop response surface models, which can be applied to optimize the process conditions. For optimal dewaterability and phosphorus release, low initial pH values (pH 1.93) and mild temperatures around 170 °C are favorable. Because holding time had no statistically relevant effect, a dependency of reaction time was investigated. Though it did not yield substantially different results, it could be included in investigations of short reaction times prospectively. Low reaction temperatures and short holding times are desirable considering economic reasons for scale-up, while the high acid consumption necessary to achieve these results is unfavorable.
Vulnerability to climate change and sea-level rise of the 35th biodiversity hotspot, the Forests of East Australia

SUMMARY There is an urgent need to understand how climate change, including sea-level rise, is likely to threaten biodiversity and cause secondary effects, such as agro-ecosystem alteration and human displacement. The consequences of climate change, and the resulting sea-level rise within the Forests of East Australia biodiversity hotspot, were modelled and assessed for the 2070–2099 period. Climate change effects were predicted to affect c. 100000 km2, and a rise in sea level an area of 860 km2; this could potentially lead to the displacement of 20600 inhabitants. The two threats were projected to mainly affect natural and agricultural areas. The greatest conservation benefits would be obtained by either maintaining or increasing the conservation status of areas in the northern (Wet Tropics) or southern (Sydney Basin) extremities of the hotspot, as they constitute about half of the area predicted to be affected by climate change, and both areas harbour high species richness. Increasing the connectivity of protected areas for Wet Tropics and Sydney Basin species to enable them to move into new habitat areas is also important. This study provides a basis for future research on the effects on local biodiversity and agriculture.
Investigation on a Shallow Water Annular Tuned Liquid Damper for Suppressing Vibration of Wind Tower

Although the annular tuned liquid damper (ATLD) filling with shallow water is helpful in mitigating the vibration response of wind tower, it’s challenging in predicting the interface force between the ATLD and its supporting system and evaluating the damping contribution of the ATLD to the dynamic response of tower. In this study, we developed an approach to investigate the damping performance of the ATLD base on the cooperation between the smoothed particle hydrodynamics method (SPH) and the equivalent tuned mass damper model (TMD). Herein the SPH method is employed to numerically investigate the non-linear behaviour of sloshing waves in the damper and calculate the interface force, while the TMD method is used to express the TLD properties. Based on this approach, a series of numerical simulations of liquid sloshing in a shallow water ATLD with different excitation periods are carried out. The equivalent damping ratios of ATLD are calculated to quantitatively analyse the suppression effect of ATLD on the vibration response of a wind tower.
Pathogenesis of Avian Influenza Virus Subtype H9N2 in Turkeys and Evaluation of Inactivated Vaccine Efficacy

SUMMARY. Avian influenza H9N2 viruses circulate in all types of poultry species, including turkeys, and cause significant losses for the poultry industry in many parts of the word. The aim of this study was to assess the pathogenesis of the Moroccan avian influenza virus (AIV) H9N2 under experimental conditions in turkeys and the protection efficacy of an inactivated commercial vaccine against AIV H9N2. Unvaccinated turkeys showed marked depression sinusitis, respiratory distress characterized by bronchiolar and tracheal rales of moderate severity, and a mortality rate of 50%. Postmortem examinations of dead and euthanatized birds revealed the presence of fibrinous tracheitis and airsacculitis lesions. Vaccination reduced the mortality rate to 20%. Vaccinated birds recovered at day 10 postchallenge, and only 12.5% (1/8) and 37.5% of birds still displayed fibrinous and nonfibrinous airsacculitis lesions, respectively, at day 15 postinoculation. Viral shedding in cloacal and tracheal swabs was lower in vaccinated than in control birds. Although viral RNA was detected in the cloacal swabs of all unvaccinated turkeys at day 3 postinoculation, only 50% of the vaccinated turkeys were positive for virus detection. At day 11 postinoculation, no viral RNA was detected in oropharyngeal swabs of vaccinated turkeys, whereas 40% of the unvaccinated turkeys were still shedding virus.
Molecular phylogenetics and microsatellite analysis reveal a new pathogenic Ceratocystis species in the Asian‐Australian clade

The National Natural Science Foundation of China (NSFC; project numbers: 31622019 and 31400546), the International Science & Technology Cooperation Program of China (project number: 2012DFG31830), the Tree Protection and Cooperation Programme (TPCP) and the National Research Foundation (NRF), South Africa.
Can We Exploit Machine Learning to Predict Congestion over mmWave 5G Channels?

It is well known that transport protocol performance is severely hindered by wireless channel impairments. We study the applicability of Machine Learning (ML) techniques to predict congestion status of 5G access networks, in particular mmWave links. We use realistic traces, using the 3GPP channel models, without being affected using legacy congestion-control solutions. We start by identifying the metrics that might be exploited from the transport layer to learn the congestion state: delay and inter-arrival time. We formally study their correlation with the perceived congestion, which we ascertain based on buffer length variation. Then, we conduct an extensive analysis of various unsupervised and supervised solutions, which are used as a benchmark. The results yield that unsupervised ML solutions can detect a large percentage of congestion situations and they could thus bring interesting possibilities when designing congestion-control solutions for next-generation transport protocols.
Comparing Two Methods of Usability Testing in Saudi Arabia: Concurrent Think-Aloud vs. Co-Discovery

ABSTRACT This paper presents the results of a study that aimed to compare the utility and validity of the traditional concurrent think-aloud and the co-discovery usability testing methods. The study was conducted in Saudi Arabia and involved three points of comparison: number and nature of usability problems discovered, test participants’ experiences, and overall task performance. The results show significant differences between the two types of testing methods. The co-discovery method led to the detection of a greater number of minor usability problems relating to layout and functionality. The participants also found the co-discovery method to be easier and less tiring to perform and more natural for them than the concurrent think-aloud method. No difference was found between the methods in terms of participants’ task performance. The study concludes that the co-discovery method seems to be appropriate for identifying numerous minor issues and ensuring that the usability testing experience is as natural as possible for participants. However, the classic method seems to be a more cost-effective method, as it is equally useful in revealing high-severity problems and requires only one participant per test session.
Mountaintop removal mining alters stream salamander population dynamics

Population dynamics are often tightly linked to the condition of the landscape. Focusing on a landscape impacted by mountaintop removal coal mining (MTR), we ask the following questions: (1) How does MTR influence vital rates including occupancy, colonization and persistence probabilities, and conditional abundance of stream salamander species and life stages? (2) Do species and life stages respond similar to MTR mining or is there significant variation among species and life stages?
Organizational Change Associated With DPT Curricular Transformation: A Qualitative Study of Faculty Experiences in One Program

Introduction. Faculty perceptions of organizational change and culture shifts created by major curricular revision in higher education have been described. However, there are no similar descriptions for faculty in physical therapist education. Methods. All faculty from one Doctor of Physical erapy program were recruited and agreed to participate in this study (n = 19). A qualitative thematic approach was applied to deidentified transcripts of faculty interviews conducted at the end of the first year (round 1) of a new curriculum and again after all academic courses had been taught at least once (round 2). Independently coded themes were discussed and further refined iteratively. All data and themes were sent to an external reviewer with feedback incorporated into findings. Results. Ten themes emerged from the analysis of the interviews—7 from round 1 interviews and 3 additional themes from round 2 interviews, including Convoluted Planning Process, Challenging Management Processes & Structure, Overwhelming Workload, New Pedagogy, Integrated Curricular Structure, Crucial Teamwork and Communication, Insufficient Resources, Evolving Attitudes and Approaches, Personal & Professional Growth, and Cautious Optimism. Discussion and Conclusion. e themes that emerged from this study—as well as faculty observations, insights, and concerns—parallel those experienced by non-PT faculty going through similar changes to innovative curricula although with greater levels of angst than evident elsewhere in the literature. e themes alsofit the framework by Armenakis and Bedeian that identified 4 common issues across the organizational change literature. Most of our faculty remained hopeful that the original goal of a patient-centered, integrated, active learning curriculum could be reached with continued curricular development and faculty growth. ere are increasingly urgent calls to rethink physical therapy education to better prepare graduates for a dynamic health care environment, to respond to emerging biopsychosocial research and pandemic demands, and to reduce graduate indebtedness. ese will likely lead to extensive curricular change across programs in the near future. Our findings may facilitate more realistic expectations of physical therapy faculty when facing the challenges of major curriculum change.
Evaluation of Land Fertility Status in Tirtomoyo District, Wonogiri Regency, Indonesia

Evaluation of soil fertility status on agricultural is to know the fertility of soil chemically through soil analysis or soil test. This is done to obtain estimates data of land characteristics based on parameters observed and tested for various alternative uses based on specific objectives. Parameters used to assess soil fertility status are Cation Exchange Capacity (CEC); Bases Saturation (BS); Organic Carbon; Total P and K levels. Evaluation of soil fertility status is needed as an effort to know the potential and direction of the management of production land on the cultivation of agricultural crops, and to know the factor of fertility that limits on the land. Based on the above description, it is necessary to evaluate the status of soil fertility in Tirtomoyo District in order to be used in the effort to provide and increase food sustainability for Wonogiri region and able to increase the economy level and income for the farmers. The results showed that the soil fertility status in all areas of Tirtomoyo District classified into the low category. This is due to the low value shown in almost all observation parameters; Cation Exchange Capacity (CEC); Base Saturation (BS); Organic Carbon; Total P and K levels. The limiting factor of soil fertility status caused by a very low Total P value of 2.16 mg 100 g -1 to 14.19 mg 100 g -1 , and Organic Carbon which is low with 0.4% to 1.7%.
Effect of amylase activity in germinated maize flour on viscosity, energy and nutrient density of complementary porridge

This study aimed at determining amylase activity in different maize varieties during germination and developing an energy and nutrient dense maize complementary porridge using different amounts of germinated maize flour. Two varieties of maize grains were collected, cleaned, and soaked for 24 hours at room temperature (25±2°C). Each variety was germinated for 168 hours (7 days) separately at soaking temperature, dried using a conventional oven at 60°C for 24 hours, and milled into flour. Standard procedures were used to determine the amylase activity of the two varieties. Results showed that amylase activity in the two varieties increased consistency until the fourth day and then decreased thereafter. The yellow maize flour had average amylase activity of 12.41CU/g compared to the white maize flour (10.73CU/g). Addition of germinated maize flour at 5%, 10%, 15% and 20% rates yielded porridges with viscosities of 2130, 1860, 1326 and 1230 cP, and energy and nutrient density of 376.59, 375.35, 372.24 and 377.22 kcal/100g, respectively. Since these porridges were developed targeting children in the age range of 6-24 months, the porridges have appropriate, viscosities, energy and nutrient densities which will supply the needs of the target group especially children aged 9-11 months, both for milk breastfed and complementary fed.
The Development of a European and Mediterranean Chickpea Association Panel (EMCAP)

Association panels represent a useful tool for quantitative trait loci (QTL) mapping and pre-breeding. In this study, we report on the development of a European and Mediterranean chickpea association panel as a useful tool for gene discovery and breeding. Chickpea (Cicer arietinum L.) is one of the most important food legumes worldwide and a key crop in the Mediterranean environments. The selection of genotypes followed criteria aimed to build a set of materials representative of the genetic diversity of chickpea germplasm focusing on the European and Mediterranean environments, which have largely been ignored to date. This tool can help breeders to develop novel varieties adapted to European and Mediterranean agro-ecosystems. Initially, 1931 chickpea accessions were phenotypically evaluated in a field trial in central Italy. From these, an association panel composed by 480 genotypes derived from single-seed descent was identified and phenotypically evaluated. Current and future phenotypic data combined with the genotypic characterization of the association panel will allow to dissect the genetic architecture of important adaptive and quality traits and accelerate breeding. This information can be used to predict phenotypes of unexploited chickpea genetic resources available in genebanks for breeding.
Lion Densities in Selous Game Reserve, Tanzania

Lion densities in Selous Game Reserve, Tanzania William-Georges Crosmary* ( ), Dennis Ikanda, Fredrick Ambwene Ligate, Pietro Sandini, Imani Mkasanga, Lameck Mkuburo, Richard Lyamuya, Kelvin Ngongolo & Philippe Chardonnet Fondation Internationale pour la Gestion de la Faune under the auspices of the Fondation François Sommer, 56 rue Beaubourg, 75003 Paris, France. Tanzania Wildlife Research Institute, P.O. Box 661, Arusha, Tanzania Wildlife Division, Ministry of Natural Resources and Tourism, Mpingo House, 40 Julius Nyerere Road, 15472 Dar es Salaam, Tanzania Southern Tanzania Elephant Program, P.O. Box 2494, Iringa, Tanzania University of Dodoma, Department of Conservation Biology, P.O. Box 259, Dodoma, Tanzania
Vibration characteristics of multiple functionally graded nonuniform beams

Based on the Euler–Bernoulli beam theory, the natural vibration behavior of functionally graded nonuniform multiple beams has been investigated. It is assumed that the beams are joined by elastic translational springs, and the properties of the beams vary along the axial direction. The Chebyshev spectral collocation method has been used to convert the governing differential equations of transverse motion into a system of algebraic equations that are put in the matrix–vector form. Then, the dimensionless transverse frequencies are obtained by solving the eigenvalue problem. The influence of several factors, such as the stiffness parameters of the coupling translational springs, the properties of the cross section of the beams, and the boundary conditions on the frequencies, has been carried out. The results generated from the Chebyshev spectral collocation method have been verified by comparing them with those reported in other studies and references from the literature. Several numerical examples have been presented and discussed to analyze the system under consideration. The authors hope that the findings of the current study are helpful in designing and characterizing multiple nonuniform thin engineering structures.
Environment Affects White Drupelet Disorder Expression on Three Blackberry Cultivars in South Mississippi

S . White drupelet disorder (WDD) is a problem that occurs during the ripening stage in some blackberry ( Rubus subgenus Rubus ) cultivars. Although berries affected with a few white drupelets may taste ﬁne, they are unpleasant aesthetically, and this may lead to negative consumer perceptions and economic ramiﬁcations. During 2 years of observational studies and ﬁeld trials (2016 and 2017), we evaluated changes in three susceptible cultivars in Mississippi affected by WDD. ‘Chickasaw’, ‘Kiowa’, and ‘Sweetie Pie’ berries were harvested twice per week and assessed for WDD. Weather conditions differed substantially during harvest in 2016 and 2017, with 2017 being cooler and rainier which resulted in a lower incidence of WDD. Compared with 2016, in 2017, the overall percentage of berries exhibiting WDD dropped from 22% to 12% for ‘Sweetie Pie’, 6% to 3% for ‘Chickasaw’, and 8% to 3% for ‘Kiowa’. The soluble solids concentration was highest in ‘Sweetie Pie’, 11.9% and 9.5% for 2016 and 2017, respectively. For all cultivars examined, the soluble solids concentration of extracted white drupelets was substantially lower than regular drupelets. The value for skin break force for white drupelets was higher than that for black drupelets, 0.99 N vs. 0.29 N, respectively. In 2017, an about 30% shadecloth treatment had a signiﬁcantly positive impact by decreasing WDD symptoms in all cultivars by 63% when compared with non-shaded plants, but soluble solids concentration was lower. Our results indicate that rain and shadecloth decrease symptoms of WDD. Therefore, growers may be able to use overhead irrigation and shade to reduce WDD symptoms.
Impact of Direction Parameter in Performance of Modified AODV in VANET

A vehicular ad hoc network (VANET) is a technology in which moving cars are used as routers (nodes) to establish a reliable mobile communication network among the vehicles. Some of the drawbacks of the routing protocol, Ad hoc On-Demand Distance Vector (AODV), associated with VANETs are the end-to-end delay and packet loss. We modified the AODV routing protocols to reduce the number of route request (RREQ) and route reply (RREP) messages by adding direction parameters and two-step filtering. The two-step filtering process reduces the number of RREQ and RREP packets, reduces the packet overhead, and helps to select the stable route. In this study, we show the impact of the direction parameter in reducing the end-to-end delay and the packet loss in AODV. The simulation results show a 1.4% reduction in packet loss, an 11% reduction in the end-to-end delay, and an increase in throughput.