Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of three methanol feed strategies for recombinant Pichia pastoris Muts fermentation

Methylotrophic yeast Pichia pastoris is an ideal host organism for recombinant protein production. However, adequate methanol feed is still a critical point of successful product formation in P. pastoris Mut S fermentations. Three methanol feed strategies were tested: an organic vapor sensor, a dissolved oxygen controlled methanol addition and a pre-determined model, as well. The organic vapor sensor proved to be unsuitable for methanol concentration measurements when samples were taken from the head space of the bioreactor, but may have the potential to substitute expensive gas analyzers in methanol fed-batch with a suitable selector submerged into the fermentation media. Dissolved oxygen and substrate consumption did not show strict mathematical relation. However, drop of dissolved oxygen tension for periodic methanol addition may be applied for the determination of the substrate concentration in the media. The rate of methanol consumption shows peaks at 0.45 and 0.95% (v/v) substrate concentrations. Th.
Aspects of the fine structure of the dauer larva of the nematode Caenorhabditis elegans

Examination of the ultrastructure of the dauer larva of Caenorhabditis elegans showed that cells in the lateral cord and body wall muscle had irregular profiles, few Golgi bodies, and cisternae of endoplasmic reticulum, but they contained abundant lipid and glycogen. These cells and the esophageal cells had mitochondria in the condensed conformation. The intestinal lumen was small and the brush border was so compact that individual microvilli were difficult to discern. Intestinal cells had cytosomes with irregular profiles and unhomogeneous matrices. The striated layer was absent from the cuticle covering the lips and papillae. These ultrastructural features are correlated with the dauer larva's low metabolic rate, its resistance to toxic chemicals and to adverse environmental conditions, and its ability to detect food and to feed soon after exposure to a hospitable environment.
Intracerebral Transplantation of BDNF-overexpressing Human Neural Stem Cells (HB1.F3.BDNF) Promotes Migration, Differentiation and Functional Recovery in a Rodent Model of Huntington's Disease

Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder caused by abnormally expanded CAG repeats in the huntingtin gene. The huntingtin gene mutation leads to the progressive degeneration of striatal GABAergic medium spiny neurons (MSN) and reduces the level of brain-derived neurotrophic factor (BDNF) in HD patient’s brain. BDNF is an essential neurotrophic factor for the cortico-striatal synaptic activity and the survival of GABAergic neurons. In this study, we transplanted BDNF-overexpressing human neural stem cells (HB1.F3.BDNF) into the contra-lateral side of unilateral quinolinic acid (QA)-lesioned striatum of HD rat model. The results of in vivo transplantation were monitored using various behavioral tests, 4.7 T animal magnetic resonance imaging (MRI) and immunohistochemical staining. We observed that the QA-lesioned rats receiving HB1.F3. BDNF cells exhibited significant behavioral improvements in the stepping, rotarod and apomorphine-induced rotation tests. Interestingly, contralaterally transplanted cells were migrated to the QA-lesioned striatum and the size of lateral ventricle was reduced. Histological analyses further revealed that the transplanted cells, which had migrated to the QA lesion site, were differentiated into the cells of GABAergic, MSN-type neurons expressing DARPP-32, and neural networks were established between the transplanted cells and the host brain, as revealed by retrograde tracing. Finally, there was a significant reduction of inflammatory response in HB1.F3. BDNF-transplanted HD animal model, compared with vehicle-transplanted group. Taken together, these results suggest that HB1.F3. BDNF can be an effective therapeutic strategy to treat HD patients in the future.
Critical Factors of Promoting Design for Safety in China’s Subway Engineering Industry

DfS (design for safety) can significantly reduce the engineering safety risk, decreasing the economic and social losses caused by safety accidents. To introduce DfS in China’s subway engineering, and with the help of a literature review and semi-structured expert interview, this study sorted out 28 promoting factors (including policy environment, practice, guidelines and tools, and education four categories) and seven impediment factors to DfS implementation. Through 80 questionnaire surveys of staff from universities, research institutes, and subway development, design, construction, and operation companies, this study screened out 26 promoting factors and seven impediment factors to assess the relationship between the two types of factors. The research provides a reference for DfS implementation in countries that have not implemented DfS before, such as China.
Driving Factors and Future Prediction of Land Use and Cover Change Based on Satellite Remote Sensing Data by the LCM Model: A Case Study from Gansu Province, China

Land use and cover change (LUCC) is an important issue affecting the global environment, climate change, and sustainable development. Detecting and predicting LUCC, a dynamic process, and its driving factors will help in formulating effective land use and planning policy suitable for local conditions, thus supporting local socioeconomic development and global environmental protection. In this study, taking Gansu Province as a case study example, we explored the LUCC pattern and its driving mechanism from 1980 to 2018, and predicted land use and cover in 2030 using the integrated LCM (Logistic-Cellular Automata-Markov chain) model and data from satellite remote sensing. The results suggest that the LUCC pattern was more reasonable in the second stage (2005 to 2018) compared with that in the first stage (1980 to 2005). This was because a large area of green lands was protected by ecological engineering in the second stage. From 1980 to 2018, in general, natural factors were the main force influencing changes in land use and cover in Gansu, while the effects of socioeconomic factors were not significant because of the slow development of economy. Landscape indices analysis indicated that predicted land use and cover in 2030 under the ecological protection scenario would be more favorable than under the historical trend scenario. Besides, results from the present study suggested that LUCC in arid and semiarid area could be well detected by the LCM model. This study would hopefully provide theoretical instructions for future land use planning and management, as well as a new methodology reference for LUCC analysis in arid and semiarid regions.
Genetic variability of tobacco streak virus in South India based on the analysis of coat protein gene

Tobacco streak virus (TSV), a member of the genus Ilarvirus, family Bromoviridae is an important viral pathogen in peanut and other crops in South India. Fifteen TSV isolates naturally infecting groundnut, sunflower, onion, black gram, green gram, jute, tagetes, calotropis, pumpkin, watermelon and kenaf plants were collected from fields in different regions of Andhra Pradesh, Tamil Nadu and Karnataka. Virus was identified as TSV by direct antigen coating enzyme linked immunosorbent assay using TSV antiserum. The CP gene from each isolate was amplified using TSV coat protein specific primers. About 700 bp product was amplified, cloned, sequenced and determined its length as 717 nucleotides and codes for 239 amino acids. The sequence analysis revealed that the CP gene shared 91–100% and 91–99% sequence identity with TSV at nucleotide and amino acid level, respectively. The phylogenetic relationship based on the nucleotide sequence of these isolates from different geographical regions was also analysed in this study.
Energetics of a host-parasite relationship as illustrated by the leech Malmiana Nuda, Richardson and the shorthorn sculpin Myoxocephalus scorpius (L.)

The weekly energy budget was balanced for two groups of the sculpin, Myoxocephalus scorpius at 10ﾟC. An accurate estimate of weekly energy expenditure could be made by calculating the metabolic energy, measuring the waste production and measuring the energy incorporated into new tissue. The metabolic energy component was measured as the difference between weekly energy input and the sum of calories of growth and calories of waste production. The logarithm of the calculated respiration rate was proportional to the logarithm of body weight, and equal to approximately twice the resting respiration rate as measured in a flowing water-type respirometer. There was no significant difference between the summed components of energy expenditure and weekly energy input. -- There was a significant difference between the expected energy expenditure and the observed energy input of fish parasitized with a known weight of the leech Malmiana nuda. This difference was proportional to the biomass of parasites and equal to 2238 calories/gram of leech. -- The resting energy consumption of the leech was estimated from measurements of resting oxygen consumption. Resting oxygen consumption was proportional to weight, and environmental temperature. It was calculated that the resting leech would consume 63 m. /gram/week at 10ﾟC. (equivalent to approximately 285 calories). At this rate of energy expenditure, there would be an additional 75 calories of waste produced. Growth would account for 1240 calories/gram of new tissue. -- The energy input also was estimated by measuring the amount of blood in the gut of recently fed leeches. It was observed that a leech would contain about 2 ml. of blood/gram. One ml. of blood was equal to 575 calories, resulting in an estimated energy input of approximately 1100 calories. This suggests that a leech continuously fed would absorb about 1600 calories of energy per week, or the equivalent of 2 3/4 ml. of blood. -- It was suggested that the ratio of energy loss from the host to energy expenditures of the parasite would be an indication of the degree of adaptation of the system. A well adapted host parasite relationship would exert a metabolic demand which is little more than the energy requirements of the parasite.
Teiresias: a Tool for Automatic Greek Handwriting Translation

The term epigraphy refers to the science that studies the written texts (epigraphs) of the diﬀerent civilizations of the past in the diﬀerent historical periods to understand the history of the ancient world. Greek epigraphs of the archaic and ancient periods contain many diﬀerent variations of each symbol; moreover, each of them is often written imperfectly or ruined by time. The goal of epigraphs is to associate these archaic symbols with the correct modern Greek letters. This work is a contribution in the direction of providing ICT facilities in the context of cultural heritage. More speciﬁcally, the paper presents a multiclass classiﬁer for the recognition of symbols belonging to the archaic Greek alphabet. The Machine Learning technique used for our classiﬁer is that of Convolutional Neural Networks (CNN). The name chosen for the tool is Teiresias, that in Greek mythology was a blind prophet of Apollo in Thebes, famous for clairvoyance and for being transformed into a woman for seven years. Teiresias’s ﬁnal aim is helping epigraphists in ﬁnding the correct association from an handwritten letter to its correspondent modern Greek letter, and therefore, in a more general context, from an handwritten script to the correspondent modern Greek script.
When Can Surfactants Enhance HydrocarbonBiodegradation In Oil Biotreatments

Petroleum hydrocarbon compounds bind to soil components and are difficult to remove and degrade. Surfactants and emulsifiers can emulsify hydrocarbons enhancing their water solubility, and increasing the displacement of oily substances from soil particles. The effects of the Ivey surfactant on oil hydrocarbon biodegradation was studied using microcosm systems containing three different soil types amended with commercial NPK fertilizer. Microbial activity was evaluated following growth of heterotrophic and degrading microorganisms, dehydrogenase activity and production of CO2. Hydrocarbon degradation was established by determining the amount of TPH (total petroleum hydrocarbon) and alkanes, the indices nC18/phytane and pristane/nC17 and the percentage of prystane and phytane. Ivey surfactant augmented the amount of hydrocarbon removed in both clay and sandy soil. This indicates that surfactant could play an important role as a biostimulating agent at the beginning of the process and in combination with a nutrient addition. Also, CG/SM analyses have shown changes in hydrocarbon composition related to the rate of biodegradation
Identification of the MAPK Cascade and its Relationship with Nitrogen Metabolism in the Green Alga Chlamydomonas reinhardtii

The mitogen activated protein kinases (MAPKs) form part of a signaling cascade through phosphorylation reactions conserved in all eukaryotic organisms. The MAPK cascades are mainly composed by three proteins, MAPKKKs, MAPKKs and MAPKs. Some signals induce MAPKKK-mediated phosphorylation and activation of MAPKK that phosphorylate and activate MAPK. Afterward, MAPKs can act either in the cytoplasm or be imported into the nucleus to activate other proteins or transcription factors. In the green microalga Chlamydomonas reinhardtii the pathway for nitrogen (N) assimilation is well characterized, yet its regulation still has many unknown features. Nitric oxide (NO) is a fundamental signal molecule for N regulation, where nitrate reductase (NR) plays a central role in its synthesis. The MAPK cascades could be regulating N assimilation, since it has been described that the phosphorylation of NR by MAPK6 promotes NO production in Arabidopsis thaliana. We have identified the proteins involved in the MAPK cascades in Chlamydomonas reinhardtii, finding 17 MAPKs, 2 MAPKKs and 108 MAPKKKs (11 MEKK-, 94 RAF- and 3 ZIK-type) that have been structurally and phylogenetically characterized. The genetic expressions of MAPKs and the MAPKK were slightly regulated by N. However, the genetic expressions of MAPKKKs RAF14 and RAF79 showed a very strong repression by ammonium, which suggests that they may have a key role in the regulation of N assimilation, encouraging to further analyze in detail the role of MAPK cascades in the regulation of N metabolism.
Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Acinetobacter baumannii Isolated from Clinical Samples in Pakistan

Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan. ABSTRACT Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan.
The Association Between Childhood Adversity and Self-Rated Physical Health in US College Students

Purpose: Adverse childhood experiences (ACEs) are related to unhealthy behaviors and poor self-rated health. Poor self-rated physical health (SRPH) is negatively associated with college students’ grades and overall academic achievement. This study examined the effects of ACEs on SRPH among undergraduate and graduate students (n = 568; 18-30 years) from a public university in the southeast. Methods: Students completed a cross-sectional online survey in October 2018. We conducted unadjusted and adjusted logistic regressions to examine the relationship between ACEs and SRPH among US college students. Results: Most participants reported 1 to 4 ACEs; one-fourth reported poor SRPH. Higher ACE exposure increased the odds for poor SRPH in a curvilinear relationship. Unadjusted results indicate ACE exposure increased risk between 82% and 228%, and that higher levels of resilience and adherence to diet and physical activity guidelines reduced risk for poor SRPH. In adjusted models, moderate ACE exposure was associated with 2.46 times greater odds (95% CI = 1.28-9.34) of reporting poor SRPH. Graduate students (odds ratio [OR] = .52, 95% CI = .27-.99) and those who met healthy diet (OR = .12, 95% CI = .02-.93) and physical activity recommendations (OR = .36, 95% CI = .23-.58) had reduced odds of poor SRPH. Conclusions: Students who have experienced ACEs are at a greater risk for poor health. Student health programs on campus should take a holistic approach by screening students for childhood adversity and promoting healthy behaviors to improve physical health.
Phenology of nutritional differences between new and mature leaves and its effect on caterpillar growth

Abstract. 1. We determined the phenology of the shrub Spiraea latifolia Ait. Bork. (Rosaceae), which has indeterminate shoot growth, and the effects of phenological changes in leaf quality on growth rate of the early‐spring feeding buckmoth caterpillars, Hemileuca lucina Hy. Edw. (Saturniidae).
Isothermal growth and stacking evolution in highly uniform AB-stacked bilayer graphene

Controlling the stacking order in bilayer graphene (BLG) allows realising unique physical properties. In particular, the possibility of tuning the band gap in AB-stacked BLG (AB-BLG) has a great technological importance for electronic and optoelectronics applications. Most of current methods to produce AB-BLG suffer from inhomogeneous layer thickness and/or coexistence with twisted BLG. Here, we demonstrate a method to synthesise highly pure large-area AB-BLG by chemical vapour deposition (CVD) using Cu-Ni films. Increasing the reaction time resulted in a gradual increase of the AB stacking, with the BLG eventually free from twist regions for the longer times (99.4 % of BLG has AB stacking), due to catalyst-assisted continuous BLG reconstruction driven by carbon dissolution-segregation processes. The band gap opening was confirmed by the electrical measurements. The concept of the continuous reconstruction to achieve highly pure AB-BLG offers a new strategy to control the stacking order of catalytically grown two-dimensional materials.
Antiobesity actions of Embelia ribes

Abstract Embelia ribes has been used as a folk medicine whole world. An aqueous extract of Embelia ribes have visceral fat accumulation and improved insulin resistance in rat model with HFD induced obesity may possibly be through down regulation of leptin, TNF-α, SREBP1γ, and PPARγ2 gene expression. The leptin might contribute to hepatic steatosis by promoting insulin resistance and also by altering insulin signaling in hepatocytes, which consequently promote increased intracellular fatty acid. Hence, drug treatment to rats with HFD prevents increase of these levels due to decrease of the body fat content. Therefore we investigated the anti-obesity effects of the aqueous extract of Embelia ribes by feeding a high-fat diet to rats for 42 weeks. Body weights at 2-6 weeks and parametrial adipose tissue weights were significantly lower in rat fed the high-fat diet containing aqueous extract of Embelia ribes than in the controls fed the high-fat diet. Our data suggest that the antiobesity effects of aqueous extract of Embelia ribes in rat fed a high-fat diet may be through down regulation of leptin, TNF-α, SREBP1γ, and PPARγ2 gene expression.
Telomere-led meiotic chromosome movements: recent update in structure and function

ABSTRACT In S. cerevisiae prophase meiotic chromosomes move by forces generated in the cytoplasm and transduced to the telomere via a protein complex located in the nuclear membrane. We know that chromosome movements require actin cytoskeleton [13,31] and the proteins Ndj1, Mps3, and Csm4. Until recently, the identity of the protein connecting Ndj1-Mps3 with the cytoskeleton components was missing. It was also not known the identity of a cytoplasmic motor responsible for interacting with the actin cytoskeleton and a protein at the outer nuclear envelope. Our recent work [36] identified Mps2 as the protein connecting Ndj1-Mps3 with cytoskeleton components; Myo2 as the cytoplasmic motor that interacts with Mps2; and Cms4 as a regulator of Mps2 and Myo2 interaction and activities (Figure 1). Below we present a model for how Mps2, Csm4, and Myo2 promote chromosome movements by providing the primary connections joining telomeres to the actin cytoskeleton through the LINC complex.
Tutorial Review of Bio-Inspired Approaches to Robotic Manipulation for Space Debris Salvage

We present a comprehensive tutorial review that explores the application of bio-inspired approaches to robot control systems for grappling and manipulating a wide range of space debris targets. Current robot manipulator control systems exploit limited techniques which can be supplemented by additional bio-inspired methods to provide a robust suite of robot manipulation technologies. In doing so, we review bio-inspired control methods because this will be the key to enabling such capabilities. In particular, force feedback control may be supplemented with predictive forward models and software emulation of viscoelastic preflexive joint behaviour. This models human manipulation capabilities as implemented by the cerebellum and muscles/joints respectively. In effect, we are proposing a three-level control strategy based on biomimetic forward models for predictive estimation, traditional feedback control and biomimetic muscle-like preflexes. We place emphasis on bio-inspired forward modelling suggesting that all roads lead to this solution for robust and adaptive manipulator control. This promises robust and adaptive manipulation for complex tasks in salvaging space debris.
Decreasing the Learning Cost of Offline Parallel Application Optimization Strategies

Many parallel applications do not scale as the number of threads increases, which means that executing them with the maximum possible number of threads will not always deliver the best outcome in performance, energy consumption, or the tradeoff between both (represented by the energy-delay product- EDP). Given that, several strategies, online and offline, have already been proposed to rightly tune the number of threads according to the application. While the former can capture some behaviors that can only be known at runtime, the latter do not impose any execution overhead and can use more efficient and costly algorithms. However, these learning algorithms in static strategics may take several hours, precluding their use or a smooth migration across different systems. In this scenario, we propose a generic methodology for such offline strategies to significantly decrease the learning time by inferring the execution behavior of parallel applications using smaller input sets than the ones used by the target applications. Through the execution of eighteen well-known benchmarks on two multicore processors, we show that our methodology is capable of converging to results that are very close to those that use the regular input set, but converging 84.7% faster, on average. We also show that such a strategy delivers better results than a dynamic one, presenting an EDP 7.7% lower, on average, when executing the applications with the number of threads found during learning. Finally, we also compare our learning methodology with an exhaustive search. It has an average learning cost (i.e., the time spent by our search algorithm to find the best configuration) of only 3.1% to optimize the EDP of the entire benchmark set1.