Miracle-dz/UniFAR-FTUs huggingface dataset:
Human cystic echinococcosis in southwest Iran: a 15-year retrospective epidemiological analysis of 501 consecutive hospitalized cases (2004-2018)

Background: Cystic echinococcosis (CE) is considered a neglected disease with significant mortality and morbidity in most of the developing countries. The current study aimed to retrospectively assess the epidemiologic and clinical features of human CE in a 15-year period in Fars province, southwestern Iran. Methods: Hospital records of patients undergone surgeries for CE in two main hospitals in Fars Province, southwestern Iran in a 15-year period (2004-2018) were reviewed and data concerning the patients' demographical and clinical features were retrieved from each record. Results: A total of 501 CE surgical cases were recorded during a 15-year period, giving an average annual incidence of 33.4 cases in which 242 (48.6%) were male and 256 (52.4%) were female. Patients' age ranged from 2 to 96 years, with a mean age of 34.92 (±19.87) years. A significantly higher rate of CE cases was noted in subjects ≥ 50 years of age. The highest frequency of cases (62: 12.5%) was recorded in the year 2017. The most commonly involved organs were liver (339 cases; 57.8%), and lung (279 cases; 47.6%). Concurrent involvement of two organs was seen in 58 (9.9%) cases of both lung and liver, 10 (1.6%) cases of lung and other locations (but not liver) and 23 (3.9%) cases of liver and other locations (but not lung). Recurrence was noted in 67 (13.37%) of the cases. The size of the lung hydatid cyst varied, ranging between 2 to 24 cm (mean = 7.33, SD= 3.737). The size of liver hydatid cysts ranged from 1 to 26 cm (mean: 9.04, SD= 4.275). Conclusion: The findings of the current study demonstrated a nearly constant prevalence of CE during the last 15 years in southern Iran. Further studies are needed to find out the reasons behind the recurrence of the disease, which is substantial, in surgically-treated patients.
Evaluation of Machine Learning Methods Developed for Prediction of Diabetes Complications: A Systematic Review

Background: With the rising prevalence of diabetes, machine learning (ML) models have been increasingly used for prediction of diabetes and its complications, due to their ability to handle large complex data sets. This study aims to evaluate the quality and performance of ML models developed to predict microvascular and macrovascular diabetes complications in an adult Type 2 diabetes population. Methods: A systematic review was conducted in MEDLINE®, Embase®, the Cochrane® Library, Web of Science®, and DBLP Computer Science Bibliography databases according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) checklist. Studies that developed or validated ML prediction models for microvascular or macrovascular complications in people with Type 2 diabetes were included. Prediction performance was evaluated using area under the receiver operating characteristic curve (AUC). An AUC >0.75 indicates clearly useful discrimination performance, while a positive mean relative AUC difference indicates better comparative model performance. Results: Of 13 606 articles screened, 32 studies comprising 87 ML models were included. Neural networks (n = 15) were the most frequently utilized. Age, duration of diabetes, and body mass index were common predictors in ML models. Across predicted outcomes, 36% of the models demonstrated clearly useful discrimination. Most ML models reported positive mean relative AUC compared with non-ML methods, with random forest showing the best overall performance for microvascular and macrovascular outcomes. Majority (n = 31) of studies had high risk of bias. Conclusions: Random forest was found to have the overall best prediction performance. Current ML prediction models remain largely exploratory, and external validation studies are required before their clinical implementation. Protocol Registration: Open Science Framework (registration number: 10.17605/OSF.IO/UP49X).
Probing the metabolism of γ-glutamyl peptides in cyanobacteria via metabolite profiling and 13 C labeling.

Cyanobacteria are attractive model organisms for studies of photosynthesis and diurnal metabolism and as hosts for photoautotrophic production of chemicals. Exposure to bright light, environmental pollutants, and diurnal lifestyle of these prokaryotes may result in significant oxidative stress. Glutathione is a widely studied gamma-glutamyl peptide that plays a key role in managing oxidative stress and detoxification of xenobiotics in cyanobacteria. The functional role and biosynthetic pathways of this tripeptide have been studied in detail in various phyla, including cyanobacteria. However, other γ-glutamyl peptides remain largely unexplored. We use an integrated approach to identify a number of γ-glutamyl peptides based on signature mass fragments and mass shifts in them in 13 C and 15 N enriched metabolite extracts. The newly identified compounds include γ-glutamyl dipeptides and derivatives of glutathione. Carbon backbones of the former turn over much faster than that of glutathione suggesting that they follow a distinct biosynthetic pathway. Further, transients of isotopic 13 C enrichment show positional labeling in these peptides which allow us to delineate between the alternative biosynthetic pathways. Importantly, the amino acid of γ-glutamyl dipeptides shows much faster turnover compared to the glutamate moiety. The significant accumulation of γ-glutamyl dipeptides under slow-growth conditions combined with the results from dynamic 13 C labeling suggests that these compounds may act as reservoirs of amino acids in cyanobacteria.
DAY-TO-DAY DYNAMICS OF COMMUTER ROUTE CHOICE BEHAVIOUR UNDER REAL-TIME INFORMATION

In this paper, the experimental data collected from a dynamic simulator are used to develop a nd calibrate commuter behavior models under a multinomial probit (MNP) model framework. The goal is to take into account travelers' learning from past experience with the system and to gain insights into the day-to-day dynamics of traveler decision process under Advanced Traveler Information Systems (ATIS). A description of the laboratory experiment is presented, followed by framework for the day-to- day commuter route switching models under ATIS. A brief discussion and interpretation of the model specification is then presented. The paper concludes with a discussion of the estimated results.
Reply to the discussion by Das and Sivakugan on “Intelligent computing for modeling axial capacity of pile foundations”Appears in Canadian Geotechnical Journal, 47(8): 928–930.

The author welcomes and appreciates the interest and comments of the discussers, and the issues that they have raised are responded to as follows. The discussers recommend scaling the inputs and outputs data between [–1, 1] rather than [0, 1] because the transfer function used in the hidden layer was tanh, which is bounded by [–1, 1]. It should be noted that the sigmoid transfer function was used in the output layer and thus, the outputs must be scaled between [0, 1], commensurate with the limits of the sigmoid transfer function. Using the tanh transfer function in the output layer is not acceptable, as it does not comply with the underlying physical meaning of the bearing capacity problem. To explain this, consider the minimum value of ultimate bearing capacity of 290 kN and the maximum value of 4500 kN that was used in the driven piles model. If these two values are to be scaled between [–1, 1], the minimum ultimate bearing capacity will be equal to –1 and the maximum ultimate bearing capacity will be equal to 1. This means that, during artificial neural network (ANN) model training, the impact of the minimum ultimate bearing capacity will be as if it is exactly opposite to the impact of the maximum ultimate bearing capacity, which is not true from the physical point of view. In the hidden layer, however, the tanh transfer function was used, as it was found to
Deep learning based ultrasonic dynamic video detection and segmentation of thyroid gland and its surrounding cervical soft tissues.

BACKGROUND The prevalence of thyroid diseases has been increasing year by year. In this study, we established and validated a deep learning method (Cascade region-based convolutional neural network, R-CNN) based on ultrasound videos for automatic detection and segmentation of the thyroid gland and its surrounding tissues in order to reduce the workload of radiologists and improve the detection and diagnosis rate of thyroid disease. METHODS 71 patients with normal thyroid ultrasound were included. The ultrasound videos of 59 patients were used as the training dataset, the data of 12 patients were used as the validation dataset, and in addition, the data of 9 patents were used as the testing dataset. Ultrasound videos of thyroid examination, including five standard sections (left and right lobe transverse scan, central isthmus transverse scan, left and right lobe longitudinal scan), were collected from all patients. The radiologists labeled the neck tissues, including anterior cervical muscle, cricoid cartilage, trachea, thyroid gland, endothyroid vessels, carotid artery, internal jugular vein, and esophagus. A large dataset was constructed to train and test the deep learning method. The performance was evaluated using the COCO metrics AP, AP50, and AP75. We compared the Cascade R-CNN with a state-of-the-art method CenterMask in the test dataset. RESULTS We annotated 166817, 34364 and 29227 regions in training, validation and testing samples. The model could achieve a good detection performance for the thyroid left lobe, right lobe, isthmus, muscles, trachea, carotid artery, and jugular vein; the AP50 of these tissues were 86.5%, 87.5%, 89.1%, 96.1%, 96.6%, 97.7%, and 91.8%, respectively. In addition, the model showed good segmentation performance for the muscles, trachea, and carotid artery; the AP50 of these tissues were 96%, 96.6%, and 97.8%, respectively. For the left lobe, right lobe, isthmus, esophagus, and jugular vein, AP50 was ≥86%. However, the segmentation results for the cricoid cartilage and endothyroid vessels were not high (AP50 of 53.9% and 48.5%, respectively). For fair comparison, the performance of Cascade R-CNN is better than that of CenterMask for detection and segmentation tasks. The difference was statistically significant (P < 0.05). CONCLUSIONS The new method could successfully detect and segment the thyroid gland and its surrounding tissues. This article is protected by copyright. All rights reserved.
The measurement of underwater noise radiated by dredging vessels during aggregate extraction operations

The total marine aggregate extracted from the seabed in UK waters can exceed 20 million tonnes each year, and there is a need to understand the noise generated during the extraction process in order to evaluate any potential impact on the marine environment. For aggregate extraction, the type of vessel used is a trailing suction hopper dredger, which lowers a drag head and suction pipe to the sea floor to extract the sand or gravel, depositing it in a hopper on the vessel, whilst returning unwanted material and water over the side of the vessel. There are a number of potential noise generation mechanisms during this type of dredging activity. This paper presents the results of underwater noise measurements for six different dredgers measured in three locations around the UK, with aggregate type varying from sand to coarse gravel. One vessel was measured in two different areas with different aggregate types. The methodology used to derive the source level for the dredgers is described, and the results of an investigation into the origin of the radiated noise are given. Measurements were made at frequencies up to 100 kHz. Noise levels are shown for the same dredger under different operational modes, illustrating that the noise output is partially dependent upon the mode of operation and the aggregate type being extracted.
Are cyclic plant and animal behaviours driven by gravimetric mechanical forces?

Abstract The celestial mechanics of the Sun, Moon, and Earth dominate the variations in gravitational force that all matter, live or inert, experiences on Earth. Expressed as gravimetric tides, these variations are pervasive and have forever been part of the physical ecology with which organisms evolved. Here, we first offer a brief review of previously proposed explanations that gravimetric tides constitute a tangible and potent force shaping the rhythmic activities of organisms. Through meta-analysis, we then interrogate data from three study cases and show the close association between the omnipresent gravimetric tides and cyclic activity. As exemplified by free-running cyclic locomotor activity in isopods, reproductive effort in coral, and modulation of growth in seedlings, biological rhythms coincide with temporal patterns of the local gravimetric tide. These data reveal that, in the presumed absence of rhythmic cues such as light and temperature, local gravimetric tide is sufficient to entrain cyclic behaviour. The present evidence thus questions the phenomenological significance of so-called free-run experiments.
Study on Improvement of Main Protection for Converter Ground Faults for Some HVDC Projects in China

The dc differential protection with one stage needs to react all inverter ground faults under various fault conditions in some HVDC projects in China. The protection setting values of action value and delay time are set low and short, respectively, in order to satisfy the protection speedy and sensitivity, which reduces the protection reliability and induces protection mal-operation. Based on the relationship between fault influence level and protection action quantity, this paper improved the dc differential protection from one stage to two stages, in wihich high-value and low-value stages are used to guarantee the protection speedy and the protection sensitivity and reliability, respectively. Then, by using analysis results from the characteristics of inverter ground fault and the influence of ground resistance, this paper obtained the worst fault conditions, which helped setting calculation of the two-stage protection improved. The PSCAD/EMTDC simulation model of Guiguang II HVDC Project was established and used to verify the improvement on the main protection for converter ground faults. The simulation results showed that the improvement was correct and reasonable, and can be helpful to resolve the contradiction among the speedy, sensitivity and reliability of protection performance. Streszczenie. W artykule przedstawiono ulepszony sposob ochrony roznicowoprądowej dla ukladow HVDC. W rozwiązaniu zastosowano dwa stopnie ochrony, wysoki i niski, w celu zapewnienia odpowiedniej szybkości, czulości i odporności ukladu. Na podstawie charakterystyk zwarc doziemnych w falownikach oraz wplywu rezystancji uziemienia, wyznaczono najgorszy przypadek awarii. Wykonano badania symulacyjne, proponowanego rozwiązania, ktore potwierdzily skutecznośc dzialania. (Badanie ulepszonego glownego systemu ochrony w zwarciach doziemnych w ukladach HVDC w Chinach).
Transcriptional repression of E‐cadherin in nickel‐exposed lung epithelial cells mediated by loss of Sp1 binding at the promoter

E‐cadherin plays a central role in the stability of epithelial tissues by facilitating cell‐cell adhesion. Loss of E‐cadherin expression is a hallmark of epithelial‐mesenchymal transition (EMT), a major event in the pathogenesis of several lung diseases. Our earlier studies showed that nickel, a ubiquitous environmental toxicant, induced EMT by persistently downregulating E‐cadherin expression in human lung epithelial cells and that the EMT remained irreversible postexposure. However, the molecular basis of persistent E‐cadherin downregulation by nickel exposure is not understood. Here, our studies show that the binding of transcription factor Sp1 to the promoter of E‐cadherin encoding gene, CDH1, is essential for its expression. Nickel exposure caused a loss of Sp1 binding at the CDH1 promoter, resulting in its downregulation and EMT induction. Loss of Sp1 binding at the CDH1 promoter was associated with an increase in the binding of ZEB1 adjacent to the Sp1 binding site. ZEB1, an EMT master regulator persistently upregulated by nickel exposure, is a negative regulator of CDH1. CRISPR‐Cas9‐mediated knockout of ZEB1 restored Sp1 binding at the CDH1 promoter. Furthermore, ZEB1 knockout rescued E‐cadherin expression and re‐established the epithelial phenotype. Since EMT is associated with a number of nickel‐exposure‐associated chronic inflammatory lung diseases including asthma, fibrosis and cancer and metastasis, our findings provide new insights into the mechanisms associated with nickel pathogenesis.
The Genetics and Biology of FOXL2

FOXL2 encodes a transcription factor that regulates a wide array of target genes including those involved in sex development, eyelid development, ovarian function and maintenance, genomic integrity as well as cellular pathways such as cell-cycle progression, proliferation, and apoptosis. The role of FOXL2 has been widely studied in humans and animals. Consistent with its role in ovarian and eyelid development, over 100 germline variants in FOXL2 are associated with blepharophimosis, ptosis, and epicanthus inversus syndrome in humans, an autosomal dominant condition characterised by ovarian dysgenesis/premature ovarian insufficiency, as well as defective eyelid development. Reflecting its role in apoptosis and proliferation, a somatic variant in FOXL2 causes adult granulosa cell tumours in humans. Despite being widely studied and having clear relevance to human disease, much remains unknown about the genes FOXL2 regulates and how it exerts its wide-reaching effect on multiple organs. This review focuses on FOXL2 and its varied roles as a transcription factor in sex determination, ovarian maintenance and function, eyelid development, genome integrity, and cell regulation, followed by discussion of the in vivo disruption of FOXL2 in humans and other species.
Feline atopic syndrome - An update.

T he International Committee on Allergic Diseases of Animals (ICADA) recently published 4 foundational review papers related to feline allergic disease (1–4). The committee performed a thorough literature review of available publications and prepared detailed guidelines on clinical signs, diagnosis, immunopathogenesis, and treatment of the newly coined Feline Atopic Syndrome (FAS). By reviewing and summarizing all published work related to feline allergic disease, these papers provide a comprehensive overview of available scientific information for feline allergies (1–4). This work also identifies limitations in the available knowledge base, and therefore should guide future feline allergy specific research and knowledge, rather than relying on information extrapolated from allergies in dogs and humans. Following is a brief summary of the current ICADA guidelines, including proposed terminology. Interested readers are encouraged to retrieve and read the ICADA review papers (1–4).
Host Restriction Factor A3G Inhibits the Replication of Enterovirus D68 by Competitively Binding the 5′ Untranslated Region with PCBP1

As the two major pathogens causing hand, foot, and mouth disease (HFMD), enterovirus 71 (EV71) and coxsackievirus A16 (CA16) attract a lot of attention for the study of their pathogenesis, their involvement with cellular proteins, and so on. However, other EVs such as CA6 and EVD68 constantly occur sporadically or have spread worldwide in recent years. ABSTRACT The host restriction factor APOBEC3G (A3G) inhibits an extensive variety of viruses, including retroviruses, DNA viruses, and RNA viruses. Our study shows that A3G inhibits enterovirus 71 (EV71) and coxsackievirus A16 (CA16) via competitively binding the 5′ untranslated region (UTR) with the host protein poly(C)-binding protein 1 (PCBP1), which is required for the replication of multiple EVs. However, whether A3G inhibits other EVs in addition to EV71 and CA16 has not been investigated. Here, we demonstrate that A3G could inhibit the replication of EVD68, which requires PCBP1 for its replication, but not CA6, which does not require PCBP1 for replication. Further investigation revealed that the nucleic-acid-binding activity of A3G is required for EVD68 restriction, similar to the mechanism presented for EV71 restriction. Mechanistically, A3G competitively binds to the cloverleaf (1 to 123 nucleotides [nt]) and the stem-loop IV (234 to 446 nt) domains of the EVD68 5′ UTR with PCBP1, thereby inhibiting the 5′ UTR activity of EVD68; by contrast, A3G does not interact with CA6 5′ UTR, resulting in no effect on CA6 replication. Moreover, the nonstructural protein 2C, encoded by EVD68, overcomes A3G suppression by inducing A3G degradation via the autophagy-lysosome pathway. Our findings revealed that A3G might have broad-spectrum antiviral activity against multiple EVs through this general mechanism, and they might provide important information for the development of an anti-EV strategy. IMPORTANCE As the two major pathogens causing hand, foot, and mouth disease (HFMD), enterovirus 71 (EV71) and coxsackievirus A16 (CA16) attract a lot of attention for the study of their pathogenesis, their involvement with cellular proteins, and so on. However, other EVs such as CA6 and EVD68 constantly occur sporadically or have spread worldwide in recent years. Therefore, more information related to these EVs is needed in order to develop a broad-spectrum anti-EV inhibitor. In this study, we first reveal that the protein poly(C)-binding protein 1 (PCBP1), involved in PV- and EV71 virus replication, is also required for the replication of EVD68, but not for the replication of CA6. Next, we found that the host-restriction factor A3G specifically inhibits the replication of EVD68, but not the replication of CA6, by competitively binding to the 5′ UTR of EVD68 along with PCBP1. Our findings broaden knowledge related to EV replication and the interplay between EVs and host factors.
THE URBAN TRANSPORTATION SYSTEM

SEVENTY-FIVE PERCENT OF CANADIANS LIVE IN AN URBAN SYSTEM, THE ELEMENTS OF WHICH ARE (1) PEOPLE, (2) PHYSICAL FEATURES, (3) FUNCTIONS. THESE ELEMENTS ARE SUBJECT TO FORCES WHICH DERIVE FROM THE GOALS OF MANY INDIVUDUALS OR GROUPS. AN EQUILIBRIUM IS MAINTAINED BETWEEN THESE CONFLICTING FORCES. A TRANSPORTATION SYSTEM EXISTS PRIMARILY TO MOVE PERSONS AND OBJECTS: TO MINIMIZE TIME AND COST AND TO MAXIMIA MOBILITY AND FREEDOM OF THE INDIVIDUAL THUS MOVING THE EQUILIBRIUM POINT TO A MORE BEARABLE POSITION. A SYSTEM MUST BE FOUND WHICH COMBINES HIGH SPEED AND HIGH CAPACITY. UNFORTUNATELY MONEY IS TIGHT, AND THERE ARE MANY HUMAN CONSIDERATIONS (E.G. ACCELERATION, COMFORT AND NOISE LEVELS) WHICH MUST BE EFFICIENTLY DEALT WITH. THE DEVELOPMENT OF SUCH A SYSTEM WILL TAKE MUCH TIME AND EXPERIMENTATION. HIGH SPEED SYSTEMS WILL EVENTUALLY COME, BUT MUST BE COUPLED WITH INCREASED CAPACITY. THIS SYSTEM WILL BE EVOLUTIONARY AND MUST BE FLEXIBLE. IT MUST HAVE INDIVIDUAL CONTROL AS TO THE TIME OF TRAVEL, COMFORT CONVENIENCE AND BE EASY TO USE. /CGRA/