Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical evaluation of commonly used methods to determine the concordance between sonography and magnetic resonance imaging: A comparative study

Introduction An increasing number of studies investigate the influence of training interventions on muscle thickness (MT) by using ultrasonography. Ultrasonography is stated as a reliable and valid tool to examine muscle morphology. Researches investigating the effects of a training intervention lasting a few weeks need a very precise measurement since increases in MT can be assumed as small. Therefore, the aim of the present work was to investigate the concordance between MT via sonography and muscle cross-sectional area (MCSA) determined via MRI imaging (gold standard) in the calf muscle. Methods Reliability of sonography measurement and the concordance correlation coefficient, the mean error (ME), mean absolute error (MAE) and the mean absolute percentage error (MAPE) between sonography and MRI were determined. Results Results show intraclass correlation coefficients (ICC) of 0.88–0.95 and MAPE of 4.63–8.57%. Concordance between MT and MCSA was examined showing ρ = 0.69–0.75 for the medial head and 0.39–0.51 c for the lateral head of the gastrocnemius. A MAPE of 15.88–19.94% between measurements were determined. Based on this, assuming small increases in MT due to training interventions, even with an ICC of 0.95, MAPE shows a high error between two investigators and therefore limited objectivity. Discussion The high MAPE of 15.88–19.94% as well as CCC of ρc = 0.39–0.75 exhibit that there are significant differences between MRI and sonography. Therefore, data from short term interventions using sonography to detect changes in the MT should be handled with caution.
Latency-associated upregulation of SERBP1 is important for the recruitment of transcriptional repressors to the viral major immediate early promoter of human cytomegalovirus during latent carriage

Suppression of human cytomegalovirus (HCMV) major immediate early gene (IE) expression from the viral major immediate early promoter (MIEP) is known to be crucial for the establishment and maintenance of HCMV latency in myeloid progenitor cells and their undifferentiated derivatives. This suppression of the MIEP during latent infection is known to result from epigenetic histone modification imparting a repressive chromatin structure around the MIEP in undifferentiated myeloid cells. In contrast, reactivation, resulting from, e.g., myeloid cell differentiation, is associated with activatory chromatin marks around the MIEP. Recently, recruitment of the transcriptional repressor SETDB1, via KAP1, to latent HCMV genomes was shown to be involved in latency-associated MIEP suppression in CD34+ progenitor cells. KAP1 is also known to associate with Chromodomain-helicase-DNA-binding protein 3 (CHD3) as part of the NuRD complex which can aid transcriptional silencing. We now show that the cellular protein Plasminogen activator inhibitor 1 RNA-binding protein (SERBP1), a known interactor of CHD3, is significantly upregulated during HCMV latency and that this protein is required for MIEP suppression during latent infection of myeloid cells. We further show that SERBP1 mediates CHD3 association with the MIEP as well as KAP1 association with viral genomic DNA. We suggest that SERBP1 functions as a scaffold protein to recruit transcriptional repressors to the latent viral genome and to mediate transcriptional silencing of the MIEP during latent carriage.
A new NLR disease resistance gene Xa47 confers durable and broad-spectrum resistance to bacterial blight in rice

Bacterial blight (BB) induced by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating bacterial disease in rice. The use of disease resistance (R) genes is the most efficient method to control BB. Members of the nucleotide-binding domain and leucine-rich repeat containing protein (NLR) family have significant roles in plant defense. In this study, Xa47, a new bacterial blight R gene encoding a typical NLR, was isolated from G252 rice material, and XA47 was localized in the nucleus and cytoplasm. Among 180 rice materials tested, Xa47 was discovered in certain BB-resistant materials. Compared with the wild-type G252, the knockout mutants of Xa47 was more susceptible to Xoo. By contrast, overexpression of Xa47 in the susceptible rice material JG30 increased BB resistance. The findings indicate that Xa47 positively regulates the Xoo stress response. Consequently, Xa47 may have application potential in the genetic improvement of plant disease resistance. The molecular mechanism of Xa47 regulation merits additional examination.
Bounding the first Dirichlet eigenvalue of a tube around a complex submanifold of $CP^n$ by the degrees of the polynomials defining it

We obtain upper bounds for the first Dirichlet eigenvalue of a tube around a complex submanifold $P$ of $CP^n$ which depends only on the radius of the tube, the degrees of the polynomials defining $P$ and the first eigenvalue of some model centers of the tube. The bounds are sharp on these models. Moreover, when the models used are $CP^q$ or the complex hyperquadric, these bounds also give gap phenomena and comparison results.
Quantitative analysis of Robertsonian chromosomes inherited by descendants from multiple Rb heterozygotes of Mus m. Domesticus

Robertsonian translocation is the most common chromosomal rearrangement in mammals, and represents the type of chromosomal change that most effectively contributes to speciation in natural populations. Rb translocations involve double-strand DNA breaks at the centromere level in two telocentric chromosomes, followed by repair ligation of the respective long arms, creating a metacentric Rb chromosome. Many different chromosomal races have been described in Mus musculus domesticus that show reduced chromosome numbers due to the presence of Rb metacentric chromosomes. The crossroads between ancestral telocentrics and the new metacentric chromosomes should be resolved in the meiotic cells of the heterozygote individuals, which form trivalents. The preferential segregation of metacentric chromosomes to the egg during female meiosis I has been proposed to favor their fixation and eventual conversion of a telocentric karyotype to a metacentric karyotype. This biased segregation, a form of meiotic drive, explains the karyotype changes in mammalian species that have accumulated Rb fusions. We studied and compared the number of Rb chromosomes inherited by the offspring of multiple Rb heterozygous of M. domesticus in reciprocal crosses. We did not find that the Rb chromosomes were inherited preferentially with respect to the telocentric chromosomes; therefore, we found no evidence for the meiotic drive, nor was there a random distribution of Rb chromosomes inherited by the descendants.
The effects and mechanism of taxanes on chemotherapy-associated ovarian damage: A review of current evidence

Chemotherapy is often a cause of premature ovarian insufficiency and infertility since the ovarian follicles are extremely sensitive to the effects of chemotherapeutic agents. Different chemotherapeutic agents with varying mechanisms of action may damage ovarian function differently. Taxanes are widely used in clinical cancer treatment, but the specific reproductive toxicological information is still controversial. This review described the impact and duration of taxanes on ovarian function in women and analyzed the possible reasons for different conclusions. Furthermore, the toxicity of taxanes on ovarian function and its possible mechanisms were discussed. The potential protective strategies and agents against ovarian damage induced by taxanes are also reviewed.
Assessing the effects of land transfer marketization on green total factor productivity from the perspective of resource allocation: Evidence from China

Exploring the determinants of green total factor productivity (green TFP) is of great importance to economic performance and ecological sustainability. Based on the data of 30 provincial units in China from 2004 to 2016, this study first analyzes the mechanism of land transfer marketization (LTM) affecting green TFP through resource allocation, then the regional resource allocation level is measured using the indicator of factor market distortion, and regional green TFP is estimated by the slack-based measure (SBM) directional distance function and Malmquist–Luenberger (ML) index. On the basis of that, a panel threshold regression model is used to empirically examine the theoretical mechanism of LTM affecting green TFP through the intermediate variable of resource allocation. We find that there is one single-threshold effect between LTM, resource allocation, and green TFP taking resource allocation as the threshold variable. Specifically, while the degree of resource mismatch is lower than 0.1371, the coefficient of LTM on green TFP is 0.1553; otherwise, the coefficient changes to −0.2776. This study concludes that LTM would significantly increase green TFP when the degree of regional resource mismatch is below the threshold; otherwise, it would have an inhibitory effect on the development of green TFP. In addition, the economic development level, R&D investment, and infrastructure level can, to a certain extent, contribute to the improvement of green TFP. The findings have three important policy implications for the land transfer policy of local governments, investment strategies of enterprises, and differentiated policy services.
Strings, fermions and the topology of curves on annuli

In previous work with Schoenfeld, we considered a string-type chain complex of curves on surfaces, with differential given by resolving crossings, and computed the homology of this complex for discs. In this paper we consider the corresponding "string homology" of annuli. We find this homology has a rich algebraic structure which can be described, in various senses, as fermionic. While for discs we found an isomorphism between string homology and the sutured Floer homology of a related 3-manifold, in the case of annuli we find the relationship is more complex, with string homology containing further higher-order structure.
Amplitude damping for single-qubit system with single-qubit mixed-state environment

We study a generalized amplitude damping channel when environment is initially in the single-qubit mixed state. Representing the affine transformation of the generalized amplitude damping by a three-dimensional volume, we plot explicitly the volume occupied by the channels simulatable by a single-qubit mixed-state environment. As expected, this volume is embedded in the total volume by the channels which is simulated by a two-qubit enviroment. The volume ratio is approximately 0.08 which is much smaller than 3/8, the volume ratio for generalized depolarizing channels.
The interaction of ABA and ROS in plant growth and stress resistances

The plant hormone ABA (abscisic acid) plays an extremely important role in plant growth and adaptive stress, including but are not limited to seed germination, stomatal closure, pathogen infection, drought and cold stresses. Reactive oxygen species (ROS) are response molecules widely produced by plant cells under biotic and abiotic stress conditions. The production of apoplast ROS is induced and regulated by ABA, and participates in the ABA signaling pathway and its regulated plant immune system. In this review, we summarize ABA and ROS in apoplast ROS production, plant response to biotic and abiotic stresses, plant growth regulation, ABA signal transduction, and the regulatory relationship between ABA and other plant hormones. In addition, we also discuss the effects of protein post-translational modifications on ABA and ROS related factors.
Equine Gastric Ulcer Syndrome affects fitness parameters in poorly performing Standardbred racehorses

Introduction Equine Gastric Ulcer Syndrome (EGUS) is a highly prevalent disorder in horses, which can be classified, based on the localization of the lesions, as Equine Squamous Gastric Disease (ESGD) or Equine Glandular Gastric Disease (EGGD). Although EGUS is recognized as a common cause of poor performance in racehorses, objective investigations about its relation with athletic capacity are lacking. Therefore, the present retrospective study aims to evaluate the associations between EGUS severity and some fitness parameters measured during an incremental treadmill test in Standardbred racehorses in training. Methods With this aim, data from 87 Standard bred racehorses which underwent a complete diagnostic evaluation for poor performance was reviewed. During gastroscopic examination, a 0-4 score was assigned to ESGD, while EGGD was evaluated for absence/presence; a total EGUS score was obtained by adding 1 point to ESGD score in horses showing concomitant EGGD. Fitness parameters obtained during incremental treadmill test included speed at a heart rate of 200 bpm (V200), speed and heart rate at a blood lactate of 4 mmol/L (VLa4, HRLa4), peak lactate, lactate and heart rate at 30 minutes post-exercise, maximum speed, minimum pH and maximum hematocrit. The associations between fitness parameters and EGUS and ESGD scores were evaluated by Spearman correlation, while Mann-Whitney test was used to compare them between horses with or without EGGD. Statistical significance was set at p<0.05. Results EGUS grade was inversely correlated with V200 (p = 0.0025) and minimum pH (p = 0.0469); ESGD grade was inversely correlated with V200 (p = 0.0025) and VLa4 (p = 0.0363). Although a trend was observed, no significant differences in V200 were observed between horses with or without EGGD (p = 0.073); horses with EGGD reached a lower minimum pH (p = 0.0087). Discussion These results show a negative association between aerobic capacity and EGUS, in particular ESGD. Although different hypotheses have been proposed, including abdominal pain and decreased appetite due to lactate accumulation, the underlying mechanisms are still unknown, and it is not clear whether EGUS represents a cause or a consequence of an early lactate accumulation and post-exercise acidosis.
Transcriptome analysis revealed the role of mTOR and MAPK signaling pathways in the white strain of Hypsizygus marmoreus extracts-induced cell death of human hepatoma Hep3B cells

The aim of this study was to investigate the anticancer mechanisms of white genius mushroom (WGM). WGM is a popular edible mushroom in Taiwan and has been demonstrated to mediate potent antiproliferation effects against human Hep3B liver cancer cells in our previous study. According to next generation sequencing technology and KEGG pathway enrichment analysis, mTOR and MAPK signaling pathways were markedly changed during treatment with WGM extracts in Hep3B cells. Therefore, this study examined the effects of WGM extracts on the expression of mTOR and MAPK signaling pathway-related proteins, such as PI3K, Akt, mTOR, Ras, Raf, MEK, ERK, p38 and JNK in Hep3B cells. According to the results of immunoblotting, we demonstrated that the protein expression of the members of PI3K/Akt/mTOR and MAPK signaling pathways were involved in WGM extracts-induced cell death. Furthermore, the inhibitors of PI3K/Akt/mTOR and MAPK signaling pathways such as rapamycin, MK2206, LY3214996 and SB202190, blocked the induction of cell death and vacuoles formation induced by WGM extracts. This study also demonstrated that WGM extracts is able to inhibit Hep3B cell migration and colony formation in a dose-dependent manner. In addition to being a very popular food, WGM should be a pharmacologically safe natural agent for cancer treatment. Therefore, WGM might be designed to develop into a dietary chemopreventive agent for the cancer treatment.
Long-term variations in water discharge and sediment load of the Pearl River Estuary: Implications for sustainable development of the Greater Bay Area

The water discharge and sediment load have been increasingly altered by climate change and human activities in recent decades. For the Pearl River, however, long-term variations in the sediment regime, especially in the last decade, remain poorly known. Here we updated knowledge of the temporal trends in the sediment regime of the Pearl River at annual, seasonal and monthly time scales from the 1950s to 2020. Results show that the annual sediment load and suspended sediment concentration (SSC) exhibited drastically decreased, regardless of water discharge. Compared with previous studies, we also found that sediment load and SSC reached a conspicuous peak in the 1980s, and showed a significant decline starting in the 2000s and 1990s, respectively. In the last decade, however, water discharge and sediment load showed slightly increasing trends. At the seasonal scale, the wet-season water discharge displays a decreasing trend, while the dry-season water discharge is increasing. At the monthly scale, the flood seasons in the North and East Rivers typically occur one month earlier than that in the West River due to the different precipitation regimes. Precipitation was responsible for the long-term change of discharge, while human activities (e.g. dam construction and land use change) exerted different effects on the variations in sediment load among different periods. Changes in the sediment regime have exerted substantial influences on downstream channel morphology and saltwater intrusion in the Greater Bay Area. Our study proposes a watershed-based solution, and provides scientific guidelines for the sustainable development of the Greater Bay Area.
Synergistic relationship of endophyte-nanomaterials to alleviate abiotic stress in plants

Plant responses to abiotic stresses through diverse mechanisms and strategic measures in utilizing nanomaterials have positively impacted crop productivity. Stress can cause membrane depletion, reactive oxygen species formation, cell toxicity and death, and reduction in plant growth. However, nanomaterials can mitigate some of the negative impacts of abiotic stresses and enhance crop yield. Some endophytic microbes can synthesize nanomaterials, which can maintain and enhance plant health and growth via nitrogen fixation, siderophore production, phytohormones synthesis, and enzyme production without any pathological effects. Nanoparticle-synthesizing endophytes also help boost plant biochemical and physiological functions by ameliorating the impact of abiotic stresses. The increase in the use and implementation of nano-growth enhancers from beneficial microbes, such as nano-biofertilizers, nano-pesticides, nano-herbicides, and nano-fungicides are considered safe and eco-friendly in ensuring sustainable agriculture and reduction of agrochemical usage. Promisingly, nanotechnology concepts in agriculture aim to sustain plant health and protect plants from oxidative stresses through the activation of anti-oxidative enzymes. The mechanisms and the use of nanomaterials to relieve abiotic plant stress still require further discussion in the literature. Therefore, this review is focused on endophytic microbes, the induction of abiotic stress tolerance in plants, and the use of nanomaterials to relieve abiotic plant stresses.
Examining the Impacts of Green and Blue Biophilic Landscapes on University Students’ Stress and Anxiety

The current study explored how viewing green or blue biophilic outdoor landscapes impacts university students’ stress and anxiety? To operate the study, we hypothesized that a combination of green and blue biophilic landscapes would reduce stress and anxiety to a greater extent than individual elements or non-biophilic urban landscapes. We conducted an online experiment using a between-subject design on the UBC Qualtrics Platform. Participants were randomly assigned to one of the four conditions with different pictorial window views (ocean view, forest view, combined view and urban view) and asked to imagine studying and living in the environments shown in the pictures. Their stress and anxiety levels were measured using the Depression Anxiety Stress Scale (DASS-21) questionnaire. An one-way between groups ANOVA and post hoc Turkey test revealed that participants in the forest view condition showed the greatest reduction of stress and anxiety, followed by the ocean view and combined view condition. Therefore, the results do not support our hypothesis. This can be due to the lack of ecological validity of pictures used and sampling bias. The current research can be applied to future residential zoning plans at UBC to maximize the forest and ocean views exposed to students.
Some Musings on Galaxy Morphology, Galactic Colors, and the Environments of Galaxies

Careful inspection of large-scale photographs of Shapley-Ames galaxies seems to show a smooth transition between the morphological characteristics of galaxies located on the narrow red and on the broad blue sequences in the galaxian color-magnitude diagram. In other words, there does not appear to be a dichotomy between blue and red galaxies. Both the colors and the morphologies of galaxies are found to correlate strongly with their environments. Red and early-type Shapley-Ames galaxies are dominant in clusters, whereas blue late-type star-forming objects dominate the general field. Interestingly, the colors and morphologies of galaxies in small groups resemble the field and differ from those in clusters. As noted by Baade, the presence of dust and star formation are very closely correlated, except in a few galaxies that probably had unusual evolutionary histories. Over the entire range from S0 to Sc there is no significant difference between the integrated colors of normal and barred objects, suggesting that the formation of a bar does not significantly affect the stellar evolutionary history of a galaxy.
Keasaman dan Susut Masak Daging Ayam Broiler dengan Lama Pendinginan dan Jenis Kemasan Plastik Berbeda (Acidity And Cooking Losses Of Broiler Chicken Meet With Cooling Time And Different Types Of Plastic Packaging)

The purpose of this study was to determine the effect of interaction between packaging plastic types and storage time and the different acidity and cooking shrinkage of broiler chicken meat. This study used a factorial randomized complete design method consisting of two factors, namely storage time (factor A) and type of packaging (Factor B). The storage time factor consists of 4 levels, while the plastic type of packaging consists of 3 levels. Each treatment combination was repeated 3 times. The results showed that the interaction between storage time and type of packaging did not significantly affect pH, and cooking loss of broiler chicken meat. Independently the storage time had a significant effect (p<0.05) on pH but did not give a significant effect (p> 0.05) on cooking losses. Likewise the type of packaging has no significant effect (p> 0.05) with pH and cooking loss of broiler chicken meat. It was concluded that the plastic packaging of PE (Polyethylene) and PP (Polypropylene) is suitable for packing meat / carcass broiler chicken for up to four days.
Two-dimensional photonic crystals designed by evolutionary algorithms

We use evolutionary algorithms to design photonic crystal structures with large band gaps. Starting from randomly generated photonic crystals, the algorithm yielded a photonic crystal with a band gap (defined as the gap to midgap ratio) as large as 0.3189. This band gap is an improvement of 12.5% over the best human design using the same index contrast platform.