Miracle-dz/UniFAR-FTUs huggingface dataset:
Short-Term High-Fat Feeding Does Not Alter Mitochondrial Lipid Respiratory Capacity but Triggers Mitophagy Response in Skeletal Muscle of Mice

Lipid overload of the mitochondria is linked to the development of insulin resistance in skeletal muscle which may be a contributing factor to the progression of type 2 diabetes during obesity. The targeted degradation of mitochondria through autophagy, termed mitophagy, contributes to the mitochondrial adaptive response to changes in dietary fat. Our previous work demonstrates long-term (2-4 months) consumption of a high-fat diet increases mitochondrial lipid oxidation capacity but does not alter markers of mitophagy in mice. The purpose of this study was to investigate initial stages of mitochondrial respiratory adaptations to high-fat diet and the activation of mitophagy. C57BL/6J mice consumed either a low-fat diet (LFD, 10% fat) or high-fat diet (HFD, 60% fat) for 3 or 7 days. We measured skeletal muscle mitochondrial respiration and protein markers of mitophagy in a mitochondrial-enriched fraction of skeletal muscle. After 3 days of HFD, mice had lower lipid-supported oxidative phosphorylation alongside greater electron leak compared with the LFD group. After 7 days, there were no differences in mitochondrial respiration between diet groups. HFD mice had greater autophagosome formation potential (Beclin-1) and greater activation of mitochondrial autophagy receptors (Bnip3, p62) in isolated mitochondria, but no difference in downstream autophagosome (LC3II) or lysosome (Lamp1) abundance after both 3 and 7 days compared with the LFD groups. In cultured myotubes, palmitate treatment decreased mitochondrial membrane potential and hydrogen peroxide treatment increased accumulation of upstream mitophagy markers. We conclude that several days of high-fat feeding stimulated upstream activation of skeletal muscle mitophagy, potentially through lipid-induced oxidative stress, without downstream changes in respiration.
Dynamic Responses of Barley Root Succinyl-Proteome to Short-Term Phosphate Starvation and Recovery

Barley (Hordeum vulgare L.)—a major cereal crop—has low Pi demand, which is a distinct advantage for studying the tolerance mechanisms of phosphorus deficiency. We surveyed dynamic protein succinylation events in barley roots in response to and recovery from Pi starvation by firstly evaluating the impact of Pi starvation in a Pi-tolerant (GN121) and Pi-sensitive (GN42) barley genotype exposed to long-term low Pi (40 d) followed by a high-Pi recovery for 10 d. An integrated proteomics approach involving label-free, immune-affinity enrichment, and high-resolution LC-MS/MS spectrometric analysis was then used to quantify succinylome and proteome in GN121 roots under short-term Pi starvation (6, 48 h) and Pi recovery (6, 48 h). We identified 2,840 succinylation sites (Ksuc) across 884 proteins; of which, 11 representative Ksuc motifs had the preferred amino acid residue (lysine). Furthermore, there were 81 differentially abundant succinylated proteins (DFASPs) from 119 succinylated sites, 83 DFASPs from 110 succinylated sites, 93 DFASPs from 139 succinylated sites, and 91 DFASPs from 123 succinylated sites during Pi starvation for 6 and 48 h and during Pi recovery for 6 and 48 h, respectively. Pi starvation enriched ribosome pathways, glycolysis, and RNA degradation. Pi recovery enriched the TCA cycle, glycolysis, and oxidative phosphorylation. Importantly, many of the DFASPs identified during Pi starvation were significantly overexpressed during Pi recovery. These results suggest that barley roots can regulate specific Ksuc site changes in response to Pi stress as well as specific metabolic processes. Resolving the metabolic pathways of succinylated protein regulation characteristics will improve phosphate acquisition and utilization efficiency in crops.
Effects of Location and Season on Seaweed Spectral Signatures

Remote sensing is an effective tool for applications such as discriminating plant species, detecting plant diseases or drought, and mapping aquatic vegetation such as seagrasses and seaweeds. Each plant species has a unique spectral reflectance which can be used with remote sensing to map them. However, variations in season, illumination, phenological stages, turbidity or location may affect the spectral reflectance. The aim of this study is to understand the spatial and seasonal effect on two commonly found New Zealand native seaweed species, Ecklonia radiata (C. Agardh) J. Agardh. and Carpophyllum maschalocarpum (Turner) Grev. We collected hyperspectral data (using ASD Handheld2 Field spectrometer with wavelength range 325–1,075 nm) of the seaweed species from four locations across four seasons and used mixed effects modelling to determine the model that best described the spectral data of each seaweed species. The results showed some seasonal pattern across the four locations. In general, summer has an effect on both the species in all four locations; likely due to the higher rates of photosynthesis. However, location did not effect the spectral signature of either species in winter. This study shows the potential for analysis of other micro-and macro-environment factors of different species and provides an understanding of the degree of natural spectral variation in seaweeds enabling further assessment of the impact of anthropogenic activities and changing environment on their spectral characteristics and health. It also identifies a general trend for best season to collect data for better classification accuracy across larger areas.
Microenvironmental Regulation of Macrophage Transcriptomic and Metabolomic Profiles in Pulmonary Hypertension

The recruitment and subsequent polarization of inflammatory monocytes/macrophages in the perivascular regions of pulmonary arteries is a key feature of pulmonary hypertension (PH). However, the mechanisms driving macrophage polarization within the adventitial microenvironment during PH progression remain unclear. We previously established that reciprocal interactions between fibroblasts and macrophages are essential in driving the activated phenotype of both cell types although the signals involved in these interactions remain undefined. We sought to test the hypothesis that adventitial fibroblasts produce a complex array of metabolites and proteins that coordinately direct metabolomic and transcriptomic re-programming of naïve macrophages to recapitulate the pathophysiologic phenotype observed in PH. Media conditioned by pulmonary artery adventitial fibroblasts isolated from pulmonary hypertensive (PH-CM) or age-matched control (CO-CM) calves were used to activate bone marrow derived macrophages. RNA-Seq and mass spectrometry-based metabolomics analyses were performed. Fibroblast conditioned medium from patients with idiopathic pulmonary arterial hypertension or controls were used to validate transcriptional findings. The microenvironment was targeted in vitro using a fibroblast-macrophage co-culture system and in vivo in a mouse model of hypoxia-induced PH. Both CO-CM and PH-CM actively, yet distinctly regulated macrophage transcriptomic and metabolomic profiles. Network integration revealed coordinated rewiring of pro-inflammatory and pro-remodeling gene regulation in concert with altered mitochondrial and intermediary metabolism in response to PH-CM. Pro-inflammation and metabolism are key regulators of macrophage phenotype in vitro, and are closely related to in vivo flow sorted lung interstitial/perivascular macrophages from hypoxic mice. Metabolic changes are accompanied by increased free NADH levels and increased expression of a metabolic sensor and transcriptional co-repressor, C-terminal binding protein 1 (CtBP1), a mechanism shared with adventitial PH-fibroblasts. Targeting the microenvironment created by both cell types with the CtBP1 inhibitor MTOB, inhibited macrophage pro-inflammatory and metabolic re-programming both in vitro and in vivo. In conclusion, coordinated transcriptional and metabolic reprogramming is a critical mechanism regulating macrophage polarization in response to the complex adventitial microenvironment in PH. Targeting the adventitial microenvironment can return activated macrophages toward quiescence and attenuate pathological remodeling that drives PH progression.
Pregnancy or Psychological Outcomes of Psychotherapy Interventions for Infertility: A Meta-Analysis

Background: The pregnancy and psychological status of infertile couples has always been a concern, but there is no clear evidence for the efficacy of psychotherapy for infertile couples. This study aimed to summarize the current evidence of the effects of psychotherapy on psychological and pregnancy outcomes for infertile couples. Method: We searched Ovid MEDLINE, Ovid EMbase, The Cochrane Library, and Web of Science (ISI) for articles published from 1946 to June 26, 2020. The pregnancy outcomes, psychological outcomes, and acceptability were involved in the study. Results: Overall, 29 studies with a combined total of 3,522 adult participants were included in the meta-analysis. Compared with a placebo, psychotherapy was associated with the pregnancy rate [risk ratio (RR) = 1.43, 95% CI [1.07, 1.93]], total psychological scales associated with infertility [standardized mean difference (SMD) = −0.33 95% CI [−0.63, −0.02]], subsymptoms of psychological scores using the 28-item version of GHQ (including social function [MD = −3.10, 95% CI [−4.30, −1.90]] and depression [MD = −3.90, 95% CI [−5.36, −2.44]], and depression [MD = 3.60, 95% CI [2.25, 4.95]] using the 14-item version of Hospital Anxiety and Depression Scale, but it had no statistically significant association with the other outcomes. In the stratified analyses, the pregnancy rate using assisted reproduction, cognitive behavioral therapy (CBT), and the integrative body–mind–spirit (BMS); total psychological scales associated with infertility using other treatments and more than a month; and anxiety using BMS had significant statistical significance. The funnel plots of all outcomes were approximately symmetrical, and no significant publication bias was found. Conclusions: The study showed that psychotherapy can lead to improvements in the pregnancy rate for infertile patients, especially for patients receiving assisted fertility. In addition, it may help improve total psychological scales associated with infertility and depression. CBT and BMS play an important role in improving rate of pregnancy, and BMS is associated with reducing anxiety. Although psychological interventions had limited effects on the pregnancy outcomes of infertility, our study still recommended that psychotherapies, in particular CBT and BMS, were applied to the therapeutic regimen for infertility, especially for patients receiving assisted fertility.
ViscoCam: Smartphone-based Drink Viscosity Control Assistant for Dysphagia Patients

Dysphagia patients need to carefully control their intake liquid’s viscosity to reduce choking and aspiration risks. However, accurate liquid viscosity measurement requires expensive rheometers still unavailable in daily life. Though the existing approximate testing methods are low-cost, they are not convenient for everyday use as they require either tedious procedures or dedicated apparatus. This paper presents ViscoCam, the first liquid viscosity classification system for dysphagia patients or carers, which only requires a smartphone. It is easy to operate, widely deployable, and robust for daily use. ViscoCam classifies visually indistinguishable liquid of various viscosity levels by exploiting the fact that the sloshing motion of viscous liquid decays faster than thin liquid. To perform a measurement, the user shakes a cup of liquid and their smartphone to induce the liquid sloshing motion. Then, ViscoCam senses the cup’s motion using the smartphone’s built-in accelerometer or microphone and infers liquid viscosity from the fluid surface motion captured by flashlight camera. To combat changes in camera position, lighting conditions, and liquid sloshing motion, a 3D convolutional neural network is trained to extract reliable motion features for classification. We evaluate ViscoCam’s performance in classifying three levels in the IDDSI standard, which is the most up-to-date and internationally adopted one for dysphagia patients. Results show that ViscoCam achieves an overall accuracy of 96.52% in controlled cases. It is robust to unseen liquid heights or container sizes, and >81% accuracy is maintained under extreme testing cases.
Role of invariant water molecules in retaining the active site geometry of β-lactamase: a molecular dynamics simulation study

Water molecules play a critical role in stabilising the three-dimensional architecture, dynamics and function of biological macromolecules. Comparative analysis of structurally similar proteins has shown that there are water molecules conserved in the same relative positions and make similar hydrogen bonds with proteins in all crystal structures. These invariant water molecules are essential for the maintenance of the native structure of proteins. The present study explores the role of invariant water molecules to maintain the active site geometry of β-lactamase enzyme. Thirteen crystal structures of class-A β-lactamase from Staphylococcus aureus have been used in this study. Molecular dynamics simulations of the protein structures were performed in hydrated as well as in dehydrated conditions. The analysis showed that significant changes occur in the active site geometry due to dehydration. These changes can be attributed to the removal of water molecules at the active site.
Effect of Weak Acids as a Catalyst on the Transesterification of Soybean Oil in Supercritical Methanol

To obtain a high biodiesel yield, the conditions of transesterification of vegetable oil with supercritical methanol are harsh. The reaction temperature is required between 350 and 400 °C, and the reaction pressure is required above 20 MPa. To reduce the operating temperature and pressure, many researchers adopted various methods, such as the selection of a new reactor, the addition of a co-solvent, or the usage of microwave irradiation. According to the characteristics of transesterification, a small amount of organic or inorgnic acid was added into the reaction system, and the effects of an acidic condition on transesterification was investigated in this paper. The experiment was conducted in a continuous flow tubular reactor; the temperature ranged from 270 to 350 °C; the pressure covered the range from the normal pressure to 15 MPa; the molar ratio of methanol/oil was from 20:1 to 60:1; and the acidity of acidified soybean oil was from 5 to 30 mg of KOH/g. The results showed that the higher yield of b.
Soil and foliar application of nitrogen for Boro rice (BRRIdhan 29)

An experiment was conducted at the Soil Science Field Laboratory of Bangladesh Agricultural University, Mymensingh during Boro season of 2008 with a view to examining the effect of soil and foliar application of urea on the yield and nutrient uptake of BRRIdhan 29 and to evaluate whether urea foliar application (FA) could replace its soil application (SA) in the rice cultivation. The experiment was laid out in a randomized complete block design (RCBD) with eight treatments, each treatment replicated thrice. The treatments were: T 1 (control), T 2 (282 kg urea ha -1 SA), T 3 (1% urea solution FA), T 4 (2% urea solution FA), T 5 (3% urea solution FA), T 6 (94 kg urea ha -1 SA + 1% urea solution FA), T 7 (94 kg urea ha -1 SA + 2% urea solution FA) and T 8 (94 kg urea ha -1 SA + 3% urea solution FA). The results showed that soil and foliar application of nitrogen significantly influenced the growth and yield of crop. The treatment T 2 (282 kg urea ha -1 ) produced the highest grain yield (5.34 t ha -1 ). The T 6 (94 kg urea ha -1 + 1% urea solution FA) produced the highest straw yield (6.58 t ha -1 ) of the crop. The lowest grain yield (3.20 t ha -1 ) and the lowest straw yield (4.19 t ha -1 ) were recorded with T 1 (control). Economic analysis showed that treatment T 2 gave the highest marginal benefit cost ratio (7.65) while the lowest value (2.71) was observed with T 5 treatment. The overall results demonstrated that soil application of 282 kg urea ha -1 was the best treatment for obtaining higher grain yield, higher nitrogen content of rice and higher marginal benefit cost ratio, and soil application is better than foliar application of urea. Keywords: Urea, Nitrogen; Foliar application; Soil application DOI: 10.3329/jbau.v8i2. 7925 J. Bangladesh Agril. Univ. 8(2): 199-202, 2010
Integrating SDGs in Higher Education—Case of Climate Change Awareness and Gender Equality in a Developing Country According to RMEI-TARGET Strategy

Universities play an essential role in spreading climate change awareness. However, slight information on climate change and environmental issues had been integrated into the curricula. Moreover, minimal research had been carried out to understand university role in spreading awareness, and students level of awareness and daily behaviour towards climate change, especially in developing countries. This paper aims to investigate the aforementioned issues. An experimental study was carried out on 448 undergraduate students enrolled at An-Najah National University Palestine. The study aimed to examine students’ knowledge and daily behaviour towards climate change, and the important role the university and students’ societies play in terms of spreading and enhancing awareness. The results revealed that female and male students had a non satisfactory interest level in environmental topics and activities, and gender equality did not seem to be an issue. Moreover, female students tend to have a significantly lower level of awareness on climate change compared to male students. On the other hand, being an engineering students or a member in students’ societies had a positive impact on students’ level of awareness and especially females. The results revealed that female students who are enrolled in the engineering faculty or members of students’ societies had a significantly higher level of awareness compared to female students who are enrolled in other faculties or not members of students’ societies. In general, students had a low level of awareness regardless of gender or faculty and universities should offer undergraduate students and especially female students’ opportunities to learn more about climate change by integrating climate change topics into higher education. Moreover, universities should support extracurricular activities held by student societies, and some of these activities should be directed towards environmental and climate change issues. This study entails the activities of the Mediterranean Gender Equality Community of Practice co-created by the Mediterranean Network of Engineering Schools (RMEI), where An-Najah University is an active member, with the support of the EU TARGET project entitled ’Taking a reflexive approach to gender equality at Institutional transformation’.
Satisﬁability of Propositional Projection Temporal Logic (cid:63)

This paper investigates the decision procedure for checking the satisﬁability of Propositional Projection Temporal Logic (PPTL). The syntax, semantics and logic laws of PPTL are presented. Within this logic, besides the usual logic connectives, two basic temporal operators, (cid:176) and prj are introduced. A normal form of PPTL is formalized and a proof for transforming a formula of PPTL into the normal form is given by induction on the structure of formulas in details. An algorithm transforming a formula into the normal form is presented. To ﬁnd out a model for a given formula, the notation of Normal Form Graph (NFG) and an algorithm constructing NFG for the formula are introduced. A decision procedure for checking the satisﬁability of PPTL formulas with ﬁnite models is demonstrated and some examples are given to illustrate how the algorithms work.
A Book Chapter Entitled, “Do They Make Sense Anywhere Else? Urban Theories in Action: Bahir Dar City in Focus”

Urbanization, as a major demographic trend, has become a global phenomenon. The year 2007, being taken as a tipping point where global urban population outnumbered the rural one for the first time, has been followed by increase in the magnitude of regional and global urbanization (Orum 2005). Ethiopia, with a projected 18% urban population in 2018, has also been urbanizing fast. Its urban growth implicates, inter alia, increase in urban areas of which Bahir Dar is among the most important ones. Bahir Dar has been urbanizing fast. Its population size increased from 167,261 in 2005 to 249,125 in 2013 and total area from 28 Km2 in 2005 to 286.6 Km2 in 2006 and then after. According to the city administration, Bahir Dar is also witnessing high rate of urbanization, 6.4 percent in 2017. Built up area has also shown large increase, especially, over the past three decades (Abraham 2020). Focusing on urban growth in the city in the post revolution period, especially since the city’s designation as the capital of Amhara region in 1993, the study assessed the nature of urbanization and urbanism in the city by through the lenses of urban sociological theories.
NUMAscope: Capturing and Visualizing Hardware Metrics on Large ccNUMA Systems

Cache-coherent non-uniform memory access (ccNUMA) systems enable parallel applications to scale-up to thousands of cores and many terabytes of main memory. However, since remote accesses come at an increased cost, extra measures are necessitated to scale the applications to high core-counts and process far greater amounts of data than a typical server can hold. In a similar manner to how applications are optimized to improve cache utilization, applications also need to be optimized to improve data-locality on ccNUMA systems to use larger topologies effectively. The first step to optimizing an application is to understand what slows it down. Consequently, profiling tools, or manual instrumentation, are necessary to achieve this. When optimizing applications on large ccNUMA systems, however, there are limited mechanisms to capture and present actionable telemetry. This is partially driven by the proprietary nature of such interconnects, but also by the lack of development of a common and accessible (read open-source) framework that developers or vendors can leverage. In this paper, we present an open-source, extensible framework that captures high-rate on-chip events with low overhead (<10% single-core utilization). The presented framework can operate in live or record mode, allowing both real-time monitoring or capture for later post-workload or offline analysis. High-resolution visualization is available either through a standards-based (web) interactive graphical interface or through a convenient textual interface for quick-look analysis.