Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteolytic processing of the primary translation products of cowpea mosaic virus RNAs

Cowpea mosaic virus (CPMV) is the type member of a group of plant viruses, the comoviruses, with a genome consisting of two single stranded RNA molecules separately encapsidated in icosahedral particles. A characteristic feature of the two genome RNAs is that they are both polyadenylated at their 3'-terminus and supplied with a small protein at their 5'end. The genetic information encoded in the virus RNAs is expressed by translation of each RNA into large-sized proteins referred to as polyproteins because these primary translation products are subsequently cleaved by specific proteolytic cleavages ("proteolytic processing") into a number of smaller-sized proteins, each with a specific function during virus multiplication. The research reported in this thesis deals with the identification of the proteolytic activities involved in this processing and their specificity. We have been able to demonstrate that the larger of the two virus RNAs, which contains the information necessary for virus RNA replication, also encodes two different proteolytic activities. One proteolytic activity is responsible for the cleavage of the overlapping polyproteins produced by the smaller of two virus RNAs and releases the two capsid proteins, encoded by this RNA (Chapter III and V), whereas the other proteolytic activity achieves the processing of the polyprotein produced by the larger RNA (Chapter VII). Besides this functional difference the two proteolytic activities recognise peptide bounds between different specific amino acid pairs (Chapter VI and VIII). The results of our studies have led to a detailed model for the processing of the proteins encoded on the two CM RNAs. The striking analogy between the plant comoviruses and the animal picornaviruses, like poliovirus and foot-and-mouth- disease virus, with regard to genome structure, replication, expression strategy and functional organisation of genes has prompted us to study the homology in amino acid sequences between corresponding proteins of the two groups of virus. It was found that some of the non-structural proteins of CM and the picornaviruses exhibit significant homology in amino acid se quence (Chapter VIII). These results suggest that animal picornaviruses and plant comoviruses have a common ancestor and throw a light on the evolution of RNA viruses.
Prediction of the service life of deep-sea conical acrylic portholes at designing

Conical deep-sea portholes (CDSP) from acrylic are widely used in underwater equipment. Due to the specific properties of acrylic, operating conditions and the stress-strain state of CDSP, it is difficult to evaluate service life and choose optimal geometric characteristics. The experimental studies and numerical calculations of the stress-strain state of CDSP from acrylic under various levels of hydrostatic pressure were made to develop an optimal design method of CDSP considering operating conditions. CDSP from acrylic were exposed to long-term (up to 7 days) and cyclic (up to 2000 cycles) hydrostatic pressure of 40, 60, 70 and 80 MPa. The deformation of the CDSP was periodically determined at no less than 20 experimental points with the help of displacement sensors. Experimental dependences of the CDSP displacements were obtained under long-term and cyclic exposure to hydrostatic pressure. According to the method of stress-time analogy, a forecast of the CDSP deformability for 10 years is made. The series of CDSP calculations with cone angles of 60–150° and relative thicknesses of 0.35–0.60 using the finite-element method was made. The calculations obtained by the finite-element method coincide with the experimental results, which demonstrated the adequacy of the adopted CDSP design scheme – continuous sliding of the translucent element with friction along the supporting surface of the porthole body. It is shown that an increase in the cone angle reduces the deflection of the CDSP, and equivalent stresses are minimal at cone angles of 75–105°. The synthesis of stress-strain state calculations by the finite-element method in aggregate with the prediction based on short-term tests allows selecting the optimal geometric characteristics of CDSP, depending on the operating conditions
Comparative analysis of cellular proteins in stably and transiently produced lentiviral vectors

Lentiviral vectors (LVs) are successfully used in clinical trials showing long term therapeutic benefits. Studying the role of cellular proteins during replication of lentivirus HIV-1 helped to understand virus assembly and budding. Knowing what cellular proteins interact with viral proteins and identifying interactions that promote formation of functional particles can be valuable for improving LV production in Gene Therapy. The cellular protein composition of LVs produced by two different methods was compared, the transient transfection system producing vectors pseudotyped with the VSV-G envelope and a stable producer cell system producing vectors pseudotyped with the non-toxic retroviral envelope, RDpro. Lentiviral vectors were purified using size exclusion chromatography (SEC). The number of purified LVs produced by transient transfection was six fold higher compared to stably produced particles. For linear ion trap-orbitrap tandem mass spectrometry (LTQ-MS/MS) a comparable amount of SEC purified LVs was analysed, detecting a smaller number of cellular protein species in stably compared to transiently produced vector samples. The greater numbers of host proteins in purified transiently produced samples may due to the presence of co-purified VSV-G vesicles. On the other hand, a large number of proteins we identified had also been detected in studies of wild type viruses and HIV-1 derived vectors indicating a role in vector formation, such as viral protein transport to the assembly site in producer cells. The potential role in LV particle production of selected identified proteins was assessed. Whilst some proteins that have been detected in studies on wild type HIV-1 were found in all our samples, such as ALIX, AHNAK was unique to stably produced, RDpro pseudotyped vector samples, and thus selected for further investigation. In summary, knock down of ALIX, AHNAK and TSG101 host cell proteins in vector producer cells did not result in a significant difference in vector production.
Study on the Steepness of Landslide-Induced Wave and Nonlinear Motion of Container Ships

Large-scale instability of a landslide body, sliding down a bank slope and entering water at a high speed, arouses landslide surges. Taking the water entry point as a source point, they spread rapidly to surrounding areas, increasing the danger risk of vessel passages in the water area. In this paper, adopting an orthogonal experimental design method, based on the test data, the Three Gorges Reservoir area was derived in order to calculate the height of the first wave of the bank landslide surge: to analyze the slope angle, the geological environment, the volume of the landslide surge, and the landslide surge wave steepness; to study the landslide volume effect on ship rolling and the swaying motion rule; and to explore the landslide surge in different ship rolling positions and transverse oscillation characteristics. This study can provide theoretical support for the navigation safety of ships in landslide surge waters.
Complicating parents’ gender and sexual expectations for children: A comparison of biological parents and stepparents

When social scientists argue that “families” reproduce and sometimes challenge gender and sexual norms, they tend to refer to biological, cisgender, and heterosexual families. We consider how one alternative family form—stepfamilies—might, like gay and lesbian families, challenge these norms. Interviews with 20 biological and stepparents reveal that whereas biological parents held relatively intense feelings about their children’s gender and sexual conformity, stepparents were indifferent and far less inclined to police their children’s behavior. We conclude that stepfamilies, similar to gay and lesbian families, might be a source of less rigid expectations and greater liberty than biological families, and we consider the implications for the future of traditional gender and sexual norms in the face of the proliferation of alternative family forms.
The role of immune inhibitory receptors in age-associatedimmune decline

The balance between signals delivered by positive and negative costimulatory molecules is crucial to the ultimate fate of cellular immune responses. Manipulation of T cell costimulatory pathways may offer a novel approach for reinvigorating exhausted T cell responses, especially in the context of chronic infections. T cells also display profound exhaustion in old age and this thesis investigates the hypothesis that T cell inhibitory receptor upregulation may define a reversible defect in age onset immune decline. Data presented here illustrate how T cells utilise different inhibitory receptors as they differentiate and that KLRG1 signalling is causative of dysfunctions in highly differentiated CD8+ T cells. The inhibitory receptors KLRG1 and CTLA-4 are revealed to undergo age-associated upregulations on CD8+ T cells but their blockade does not reverse the characteristic hypo-responsiveness of CD8+ T cells amongst old donors. The dysregulated immune response to lifelong chronic cytomegalovirus (CMV) infection is thought to play a major role in driving age related immune dysfunctions. We found that CMV accelerates age-associated telomere attrition amongst CD8+ and CD4+ T cells. CMV infection is also shown to drive CTLA-4, PD-1 and KLRG1 upregulation on both CD4+ and CD8+ T cells. Moreover, the PD-1/Ligand (L) inhibitory pathway defines a reversible proliferative dysfunction in the responses of CMV specific CD8+ T cells. Specifically, the CD45RA re-expressing memory subset exhibits a proliferative deficiency, relative to their central and effector memory counterparts, that is reversible upon PD-L blockade. However, this augmented proliferative response was not accompanied by increased telomerase function, suggesting this does not result in true reversal of exhaustion. In summary, the dysfunctions of highly differentiated and CMV specific CD8+ T cells can be at least partially reversed by perturbation of inhibitory receptor pathways, whose further manipulation may provide a therapeutic modality to combat age-associated immune decline.
Uncertainty Quantification in Machine Learning Modeling for Multi-Step Time Series Forecasting: Example of Recurrent Neural Networks in Discharge Simulations

As a revolutionary tool leading to substantial changes across many areas, Machine Learning (ML) techniques have obtained growing attention in the field of hydrology due to their potentials to forecast time series. Moreover, a subfield of ML, Deep Learning (DL) is more concerned with datasets, algorithms and layered structures. Despite numerous applications of novel ML/DL techniques in discharge simulation, the uncertainty involved in ML/DL modeling has not drawn much attention, although it is an important issue. In this study, a framework is proposed to quantify uncertainty contributions of the sample set, ML approach, ML architecture and their interactions to multi-step time-series forecasting based on the analysis of variance (ANOVA) theory. Then a discharge simulation, using Recurrent Neural Networks (RNNs), is taken as an example. Long Short-Term Memory (LSTM) network, a state-of-the-art DL approach, was selected due to its outstanding performance in time-series forecasting, and compared with simple RNN. Besides, novel discharge forecasting architecture is designed by combining the expertise of hydrology and stacked DL structure, and compared with conventional design. Taking hourly discharge simulations of Anhe (China) catchment as a case study, we constructed five sample sets, chose two RNN approaches and designed two ML architectures. The results indicate that none of the investigated uncertainty sources are negligible and the influence of uncertainty sources varies with lead-times and discharges. LSTM demonstrates its superiority in discharge simulations, and the ML architecture is as important as the ML approach. In addition, some of the uncertainty is attributable to interactions rather than individual modeling components. The proposed framework can both reveal uncertainty quantification in ML/DL modeling and provide references for ML approach evaluation and architecture design in discharge simulations. It indicates uncertainty quantification is an indispensable task for a successful application of ML/DL.
First record of Dictyocaulus capreolus (Gibbons and Höglund 2002) in roe deer (Capreolus capreolus) from Turkey.

Il Cevre ve Orman Mudurlugu tarafindan fakultemiz kliniklerine agir yarali olarak getirilip olen bir disi karaca, olum sonrasi parazitolojik acidan sistematik olarak muayene edilmis ve akcigerde brons ve bronsiollerden 42 (14 ♂, 27 ♀ ve 1 larva) nematod toplanmistir. Tumu Dictyocaulus capreolus olarak tanimlanan parazitler Turkiye icin ilk kayittir
Development of beneficial residual stresses in glass fiber epoxy composites through fiber prestressing

The undesired residual stresses in fiber reinforced polymer composites are developed during their manufacturing processes due to the thermal and chemical shrinkage of the polymer matrix, which negatively affect the performance of the composites. Applying tensile stress to the reinforcement fibers during the curing of the matrix can reduce or eliminate the undesired residual stresses. Furthermore, the undesired tensile residual stress within the matrix can be replaced with beneficial compressive residual stress which can improve the mechanical properties of the composites. In this study, theoretical stress analysis was performed in order to determine the value of the optimum compressive residual stress that is associated with the highest tensile strength. This value was determined based on the tensile testing result of prestressed composites with a 40% fiber volume fraction. For the composites with different fiber volume fractions, a new approach was introduced to estimate the optimum fiber prestressing level which generates the optimum compressive residual stress within the matrix and consequently, the highest tensile strength can be achieved. In order to validate this approach experimentally, prestressed composites with 25 and 30% fiber volume fraction were prepared by applying the estimated optimum fiber prestressing levels during curing of matrix and tensile testing was performed. The result of the stress analysis showed that the value of the optimum compressive residual stress corresponding to the highest tensile strength is 2.5 MPa approximately. The tensile testing results confirmed the validity of the new approach in estimating the optimum fiber prestressing level for the composites with different fiber volume fractions. For both prestressed composites with 25 and 30% fiber volume fraction, the highest tensile strength was achieved when the theoretically estimated optimum fiber prestressing level was applied to the fibers during the curing of the matrix.
The invasive apple snail Pomacea canaliculata in Indonesia: a case study in Lake Rawa Pening, Central Java

The occurrence of the invasive apple snail Pomacea canaliculata in Indonesia was first reported in 1984. The species was introduced as an ornamental aquarium pet. Since then, people have begun to culture the snail in ponds usually adjacent to rice fields. When it was realized that the species multiplied rapidly and was a serious pest, this invasive apple snail had already spread widely. There are many cultural methods of controlling and preventing its distribution, but none are effective in keeping them at non-damaging levels. We mapped the distribution of P. canaliculata in Indonesia from the MZB’s collections as well as literature references and found that the snail invaded almost all large islands, such as Sumatra, Java, Kalimantan, Sulawesi, Maluku, and West Papua. We also studied the impact of P. canaliculata on the native apple snails P. ampullacea, P. scutata, and P. virescens in Lake Rawa Pening (a popular tourism destination) as a case study. The results showed that two species of Pila already disappeared from Lake Rawa Pening. Only P. scutata occurs still in the region and was found alive usually in shallow water and rice fields surrounding the lake. To resolve the problem we recommend that cleaning the lake periodically from the invasive aquatic weed Eichhornia crassipes (known to locals as “eceng gondok”) by a private company and harvesting the weeds for the local small craft industry by the local fishermen could be an alternative measure to reduce the population of the P. canaliculata, as well as collecting P. canaliculata for local food or for feeding ducks. Rearranging the number of fish-pens “karamba” and their location in the lake could be seen as an alternative way also for reducing the population of P. canaliculata, since the snails lay their egg masses on the bamboo stakes of “karamba. ” Such rearrangement could make the landscape more attractive for tourism.
Topical Delivery of 3-O-ethyl l-ascorbic Acid from Complex Solvent Systems

3-O-ethyl l-ascorbic acid (EA), an ether derivative of Vitamin C, is widely used in skincare formulations. Previously, we reported the effects of neat solvents on EA percutaneous absorption and observed that 0.6–7.5% of the applied EA was delivered through the skin over 24 h. In this work, we designed complex formulations using combinations of solvents that may act synergistically and examined their impact on EA permeation in porcine skin in vitro under finite dose conditions. Binary combinations of propylene glycol (PG) with propylene glycol monolaurate (PGML) were effective in enhancing skin permeation of EA compared with individual solvents (p 0.05). Addition of the volatile solvent isopropyl alcohol (IPA) to PG solutions also did not improve EA skin delivery compared with neat PG. Ternary solvent systems containing PG:PGML were subsequently prepared by the addition of a lipophilic solvent, either isopropyl myristate (IPM), medium-chain triglycerides (MCT) or isostearyl isostearate (ISIS). The optimum vehicle, PG:PGML:IPM, promoted up to 70.9% skin delivery of EA. The PG:PGML:ISIS vehicles also promoted EA permeation across the skin, but to a significantly lesser extent than the IPM-containing vehicles. No enhancement of EA delivery was noted for the PG:PGML:MCT mixtures. These results will inform the development of targeted formulations for EA in the future.
The practicality of mathematics learning module on triangles using GeoGebra

The 2013 curriculum in Indonesia requires students to be able to develop knowledge independently, creatively and skillfully in solving mathematics problems. One way that can be taken by professional mathematics teachers to support the curriculum is to develop precise learning modules that integrate software dynamically and open source, such as GeoGebra. This study aims to determine the practicality of the module developed in mathematics teaching and learning on triangles using GeoGebra. The study used the Plomp development model, which consists of three phases, namely preliminary research, prototyping phase, and assessment phase. The test trial was conducted four times on students of class VII SMP Negeri1 Idi Rayeuk, Aceh. The results showed that the mathematics teaching and learning module using GeoGebra software fulfilled valid and practical criteria. The validity of the module is obtained based on the results of validation by five validators. Meanwhile, the practicality of the module is achieved based on the recommendations of five validators stated that the module could be used with a minor revision and the level of implementation of learning using the module is good. For future research, it is crucial to apply this study on a broader scale to determine the effectiveness of the module.
Effect of the addition of diatoms (Navicula spp.) and rotifers (Brachionus plicatilis) on water quality and growth of the Litopenaeus vannamei postlarvae reared in a biofloc system

The aim of this study was to evaluate the effect of the addition of Navicula spp. and Brachionus plicatilis on water quality and growth of postlarvae shrimp Litopenaeus vannamei reared in a biofloc system. Four treatments were considered: a control (biofloc system – BFT); BFT with the addition of Navicula spp. (BFT-N); BFT with the addition of Brachionus plicatilis (BFT-B) and BFT with the addition of Navicula spp. and Brachionus plicatilis (BFT-NB), each in triplicate. Shrimp (16.2 ± 0.03 mg) were stocked at a density of 2500 shrimp m−3 and plankton were added on days 1, 5, 10, 15, 20, 25 and 30 at a density of 5 × 104 cells mL−1 (Navicula spp.) and 30 organisms L−1 (Brachionus plicatilis). The shrimp were fed a formulated feed in four daily rations composed of 40% crude protein and 8% lipids. Significant differences between treatments were observed for final weight, yield, feed conversion ratio, specific growth rate, protein efficiency ratio and protein content of the shrimp. The combined plankton addition of Navicula spp. and B. plicatilis had better performance parameters, indicating their benefit as natural food sources for postlarvae L. vannamei in biofloc systems.
Repellent effect of ethanol extracts from plants of the family Lamiaceae on Colorado Potato Beetle adults (Leptinotarsa decemlineata SAY)

The effect of ethanol extracts, from 9 plants of the family Lamiaceae applied on potato leaves, on the feeding behaviour of adult individuals of Colorado potato beetle was studied in laboratory. Extracts of Salvia splendens, Origanum majorana, Hyssopus officinalis, Salvia officinalis and Marrubium vulgare were strongly repellent (84-98 % repellency). Thymus vulgaris, Ocimum bassilicum and Origanum vulgare showed a medium repellency (61-74%) and Mellisa officinalis had a weak repellency (28%). After 24 and 48 hours there were 50 and 90%, respectively, of control leaves eaten. Leaves with extracts of S. splendens, O. majorana, H. officinalis, S. officinalis and M. vulgare showed long antifeedant activity as they were not eaten at all or a little (less than 7%) even after 48 hours of exposure. Leaves treated by T vulgaris and O. bassilicum had a medium antifeedant activity - eaten by less than 28%. Finally, leaves treated by O. vulgare and M. officinalis showed weak antifeedant effect as being eaten by 46-71%.