Miracle-dz/UniFAR-FTUs huggingface dataset:
Live cell imaging of Plasmodiophora brassicae—host plant interactions based on a two‐step axenic culture system

Plasmodiophora brassicae, a parasitic protist, induces club‐shaped tumor‐like growth of host Brassicas roots and hypocotyls after infection. Due to its soil‐borne nature and intracellular, biotrophic parasitism the infection biology and early pathogenesis remains in doubt. In this study, we have established a new protocol, based on a two‐step axenic culture of P. brassicae with its host tissues, for easy and in planta observation of cellular interactions between P. brassicae and host plants: first, coculture of P. brassicae with infected canola root tissues, on growth‐medium plates, enables the propagation of P. brassicae that serves as pure inoculum for pathogenicity assays, and second, the pure inoculum is subsequently used for pathogenicity tests on both canola and Arabidopsis seedlings grown on medium plates in Petri dishes. During the first axenic culture, we established a staining protocol by which the pathogen was fluorescently labeled with Nile red and calcofluor white, thus allowing in planta observation of pathogen development. In the pathogenicity assays, our results showed that axenic cultures of P. brassicae, in calli, remains fully virulent and completes its life cycle in both canola and Arabidopsis roots grown in Petri dishes. Combining visualization of fluorescent probe‐labeled P. brassicae structures with fluorescent protein tagging of Arabidopsis cellular components, further revealed dynamic responses of host cells at the early stages of P. brassicae infection. Thus, established protocols for in planta detection of P. brassicae structures and the live cell imaging of P. brassicae—Arabidopsis interactions provide a novel strategy for improving our detailed knowledge of P. brassicae infection in host tissues.
A prospective study of transmission of Multidrug-Resistant Organisms (MDROs) between environmental sites and hospitalized patients—the TransFER study

Abstract Objective Hospital environmental surfaces are frequently contaminated by microorganisms. However, the causal mechanism of bacterial contamination of the environment as a source of transmission is still debated. This prospective study was performed to characterize the nature of multidrug-resistant organism (MDRO) transmission between the environment and patients using standard microbiological and molecular techniques. Setting Prospective cohort study at 2 academic medical centers. Design A prospective multicenter study to characterize the nature of bacterial transfer events between patients and environmental surfaces in rooms that previously housed patients with 1 of 4 ‘marker’ MDROs: methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, Clostridium difficile, and MDR Acinetobacter baumannii. Environmental and patient microbiological samples were obtained on admission into a freshly disinfected inpatient room. Repeat samples from room surfaces and patients were taken on days 3 and 7 and each week the patient stayed in the same room. The bacterial identity, antibiotic susceptibility, and molecular sequences were compared between organisms found in the environment samples and patient sources. Results We enrolled 80 patient–room admissions; 9 of these patients (11.3%) were asymptomatically colonized with MDROs at study entry. Hospital room surfaces were contaminated with MDROs despite terminal disinfection in 44 cases (55%). Microbiological Bacterial Transfer events either to the patient, the environment, or both occurred in 12 patient encounters (18.5%) from the microbiologically evaluable cohort. Conclusions Microbiological Bacterial Transfer events between patients and the environment were observed in 18.5% of patient encounters and occurred early in the admission. This study suggests that research on prevention methods beyond the standard practice of room disinfection at the end of a patient’s stay is needed to better prevent acquisition of MDROs through the environment.
CCL2 induces resistance to the antiproliferative effect of cabazitaxel in prostate cancer cells

Understanding the mechanism of chemoresistance and disease progression in patients with prostate cancer is important for developing novel treatment strategies. In particular, developing resistance to cabazitaxel is a major challenge in patients with docetaxel‐resistant and castration‐resistant prostate cancer (CRPC) because cabazitaxel is often administered as a last resort. However, the mechanism by which cabazitaxel resistance develops is still unclear. C‐C motif chemokine ligands (CCL) were shown to contribute to the castration resistance of prostate cancer cells via an autocrine mechanism. Therefore, we focused on CCL as key factors of chemoresistance in prostate cancer cells. We previously established a cabazitaxel‐resistant cell line, DU145‐TxR/CxR, from a previously established paclitaxel‐resistant cell line, DU145‐TxR. cDNA microarray analysis revealed that the expression of CCL2 was upregulated in both DU145‐TxR and DU145‐TxR/CxR cells compared with DU145 cells. The secreted CCL2 protein level in DU145‐TxR and DU145‐TxR/CxR cells was also higher than in parental DU145 cells. The stimulation of DU145 cells with CCL2 increased the proliferation rate under treatments with cabazitaxel, and a CCR2 (a specific receptor of CCL2) antagonist suppressed the proliferation of DU145‐TxR and DU145‐TxR/CxR cells under treatments of cabazitaxel. The CCL2‐CCR2 axis decreased apoptosis through the inhibition of caspase‐3 and poly(ADP‐ribose) polymerase (PARP). CCL2 is apparently a key contributor to cabazitaxel resistance in prostate cancer cells. Inhibition of the CCL2‐CCR2 axis may be a potential therapeutic strategy against chemoresistant CRPC in combination with cabazitaxel.
MKL1/miR34a/FOXP3 axis regulates cell proliferation in gastric cancer

Megakaryoblastic leukemia 1 (MKL1) was closely related to the pathogenesis of various human malignant cancers. MiR34a was reported to be closely related to cancer cell proliferation. Forkhead box protein 3 (FOXP3) was a transcription factor that played a different role in different cancer types. CDK6 was involved in cell cycle progression and was upregulated in several types of cancers. The present study investigated the effects of MKL1/miR34a/FOXP3 axis on cell proliferation in MGC803 gastric cancer cells. Our results demonstrated that overexpression of MKL1 promoted proliferation of MGC80‐3 cells, MKL1 directly binding to the promoter of CDK6 to increase its expression. Knockdown of FOXP3 promoted proliferation of MGC80‐3 cells and MKL1 inhibited the expression of FOXP3 via miR‐34a. The finding can contribute to elucidating the regulatory mechanism involved in the cell cycle progression of gastric cancer cells and may aid in screening potential gene targets for the biological therapy of gastric cancer.
A DIC-Based Study on Fatigue Damage Evolution in Pre-Corroded Aluminum Alloy 2024-T4

This paper investigates the fatigue damage and cracking behavior of aluminum alloy 2024-T4 with different levels of prior corrosion. Damage evolution, crack initiation and propagation were experimentally analyzed by digital image correlation, scanning electron microscopy and damage curves. Prior corrosion is shown to cause accelerated damage accumulation, inducing premature fatigue crack initiation, and affecting crack nucleation location, crack orientation and fracture path. For the pre-corrosion condition, although multiple cracks were observed, only one corrosion-initiated primary crack dominates the failure process, in contrast to the plain fatigue cases, where multiple cracks propagated simultaneously leading to final coalescence and fracture. Based on the experimental observations, a mixed-mode fracture model is proposed and shown to successfully predict fatigue crack growth and failure from the single dominant localized corrosion region.
QTL Mapping Reveals the Relationship between Pasting Properties and Malt Extract in Barley

Pasting properties are important characteristics of barley starch from a processing standpoint. Many studies reported the close relationship between pasting properties and malting quality, especially malt extract. However, most conclusions were derived from the correlation between pasting properties and malting quality using a set of cultivars or breeding lines. In this study, a doubled haploid population of 150 lines from a cross between a Japanese malting barley and a Chinese feed barley was grown in four different environments (two sites × two years). Based on average values from all different environments, 17 significant quantitative trait loci (QTL) were identified for pasting properties. The genetic variance explained by these QTL varied from 7.0 to 23.2%. Most QTL controlling pasting properties were located on 1H, 2H, 5H, and 7H. Results confirmed the linkage between pasting properties and malt extract, with most of the QTL for pasting properties becoming nonsignificant when using malt extract as a covariate. Breakdown showed the closest correlation with malt extract. Molecular markers closely linked to the QTL can be used to select desired pasting properties to improve malting quality.
Kat2a and Kat2b Acetyltransferase Activity Regulates Craniofacial Cartilage and Bone Differentiation in Zebrafish and Mice

Cranial neural crest cells undergo cellular growth, patterning, and differentiation within the branchial arches to form cartilage and bone, resulting in a precise pattern of skeletal elements forming the craniofacial skeleton. However, it is unclear how cranial neural crest cells are regulated to give rise to the different shapes and sizes of the bone and cartilage. Epigenetic regulators are good candidates to be involved in this regulation, since they can exert both broad as well as precise control on pattern formation. Here, we investigated the role of the histone acetyltransferases Kat2a and Kat2b in craniofacial development using TALEN/CRISPR/Cas9 mutagenesis in zebrafish and the Kat2ahat/hat (also called Gcn5) allele in mice. kat2a and kat2b are broadly expressed during embryogenesis within the central nervous system and craniofacial region. Single and double kat2a and kat2b zebrafish mutants have an overall shortening and hypoplastic nature of the cartilage elements and disruption of the posterior ceratobranchial cartilages, likely due to smaller domains of expression of both cartilage- and bone-specific markers, including sox9a and col2a1, and runx2a and runx2b, respectively. Similarly, in mice we observe defects in the craniofacial skeleton, including hypoplastic bone and cartilage and altered expression of Runx2 and cartilage markers (Sox9, Col2a1). In addition, we determined that following the loss of Kat2a activity, overall histone 3 lysine 9 (H3K9) acetylation, the main epigenetic target of Kat2a/Kat2b, was decreased. These results suggest that Kat2a and Kat2b are required for growth and differentiation of craniofacial cartilage and bone in both zebrafish and mice by regulating H3K9 acetylation.
Levels of total antioxidant capacity and 8-hydroxy-2′-deoxyguanosine of serum and follicular fluid in women undergoing in vitro fertilization: focusing on endometriosis

Abstract This study was designed to evaluate the levels of oxidative stress (OS) markers, total non-enzymatic antioxidant capacity (TAC) and 8-hydroxy-2′-deoxyguanosine (8-OHdG) in the serum and follicular fluid (FF) of patients undergoing in vitro fertilization (IVF). The impact of these biomarkers on IVF outcome was also analysed. Samples were obtained from 61 patients (age: 36.40 ± 4.99 years; BMI: 22.54 ± 2.46; infertility: 3.7 ± 2.5 years [mean ± SD]) before and after controlled ovarian hyperstimulation (COH). Patients with and without endometriosis were also evaluated separately. TAC was quantified by enhanced chemiluminescence assay and 8-OHdG was measured by enzyme-linked immunosorbent assay. It was demonstrated that these biomarkers responded to COH differently. No relationship could be detected in their FF levels, although their cumulative serum levels were inversely related. Both FF TAC and FF 8-OHdG had a negative impact on the number of good quality embryos, but an effect of Serum TAC and 8-OHdG could not be observed. When women with and without endometriosis were evaluated separately, inconsistent results were obtained. However, women without endometriosis had higher levels of serum and FF TAC when they progressed to clinical pregnancy. Our findings support the notion that OS has an important contribution to the reproductive potential in IVF patients, the ideal biomarkers of outcome measures, however, need to be further explored.
Human Protein Reference Database—2009 update

Human Protein Reference Database (HPRD—http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system—Human Proteinpedia (http://www.humanproteinpedia.org/)—through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15 000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.
Resuscitation of Out-of-Hospital Cardiac Arrest Victims in Lebanon: The Experience and Views of Prehospital Providers

Background: The survival rate of out-of-hospital cardiac arrest (OHCA) victims in Lebanon is much lower than those seen internationally. In this study, we examined the attitudes and practices of prehospital providers in resuscitation. Methods: We devised a cross-sectional survey with questions adopted from the literature including a study out of Lebanon. Questionnaires were mailed to 300 volunteers who were recruited from 10 centers of local emergency medical services (EMS). Results: A total of 258 questionnaires were returned (86% response rate). Most participants (>80%) were younger than 30 years, and males (60%). Over half reported witnessing up to 10 arrests per year, with 72.5% reporting prehospital return of spontaneous circulation in <6% of cases. Futile resuscitation was frequently (91%) practiced. Participants believed resuscitation should be withdrawn when prolonged (55.4%) or in the presence of advanced directives (34.1%) or terminal illness (27.5%). Reported resuscitation challenges were related to the reaction of witnesses (70.1%), to delay in calling EMS (84.4%), and to traffic delays (30%). Participants recommended training lay persons in resuscitation (79%), training prehospital providers in advanced airway management (68.2%) and intravenous skills (60.1%), providing medications in ambulances (57.7%), and adjusting traffic laws (52%). Conclusion: Prehospital providers in Lebanon face several challenges in their resuscitation practices. A multi-faceted strategy to improve resuscitation practices is needed in Lebanon. In addition to policy development, structural changes should be put in place for improved outcomes in OHCA victims.
Bayesian Reinforcement Learning in Factored POMDPs

Model-based Bayesian Reinforcement Learning (BRL) provides a principled solution to dealing with the exploration-exploitation trade-off, but such methods typically assume a fully observable environments. The few Bayesian RL methods that are applicable in partially observable domains, such as the Bayes-Adaptive POMDP (BA-POMDP), scale poorly. To address this issue, we introduce the Factored BA-POMDP model (FBA-POMDP), a framework that is able to learn a compact model of the dynamics by exploiting the underlying structure of a POMDP. The FBA-POMDP framework casts the problem as a planning task, for which we adapt the Monte-Carlo Tree Search planning algorithm and develop a belief tracking method to approximate the joint posterior over the state and model variables. Our empirical results show that this method outperforms a number of BRL baselines and is able to learn efficiently when the factorization is known, as well as learn both the factorization and the model parameters simultaneously.
Towards the use of multidimensional performance indicators in football small-sided games: the effects of pitch orientation

ABSTRACT This study aimed to compare youth football players’ performance during two small-sided games with different pitch orientation: i) 40x30m and ii) 30x40m formats. Twenty under-15 players (age = 14.1 ± 0.5 years) participated in nine GK+4vs4+GK situations in each format, with the duration of six minutes each. Positional data were collected using individual GPS units, and computed for tactical and physical performance indicators. The SSG were video recorded, using notational analysis for collecting technical indicators. A novel method that incorporates time dependent notational information with spatiotemporal data was used to compute multidimensional parameters. Standardised effect sizes and non-clinical magnitude-based inferences were used to compare formats. Results showed that players covered more distance at higher intensities, presented more passes and dribbles and were more synchronised in the longitudinal axis while playing in the 40x30m pitch. In the 30x40m pitch, results showed a lower distance between team centroids, higher number of shots, more lateral passes and a wider team positioning. Multidimensional indicators, as players position and distance to the closest defender while shooting, revealed a more constant distance between attacker and defender in the 40x30m pitch. These results highlight the importance of integrating information from different indicators for a contextually valid information.
Spectral change and duration as cues in Australian English listeners' front vowel categorization.

Australian English /iː/, /ɪ/, and /ɪə/ exhibit almost identical average first (F1) and second (F2) formant frequencies and differ in duration and vowel inherent spectral change (VISC). The cues of duration, F1 × F2 trajectory direction (TD) and trajectory length (TL) were assessed in listeners' categorization of /iː/ and /ɪə/ compared to /ɪ/. Duration was important for distinguishing both /iː/ and /ɪə/ from /ɪ/. TD and TL were important for categorizing /iː/ versus /ɪ/, whereas only TL was important for /ɪə/ versus /ɪ/. Finally, listeners' use of duration and VISC was not mutually affected for either vowel compared to /ɪ/.
MopA, the Mn Oxidizing Protein From Erythrobacter sp. SD-21, Requires Heme and NAD+ for Mn(II) Oxidation

Bacterial manganese (Mn) oxidation is catalyzed by a diverse group of microbes and can affect the fate of other elements in the environment. Yet, we understand little about the enzymes that catalyze this reaction. The Mn oxidizing protein MopA, from Erythrobacter sp. strain SD-21, is a heme peroxidase capable of Mn(II) oxidation. Unlike Mn oxidizing multicopper oxidase enzymes, an understanding of MopA is very limited. Sequence analysis indicates that MopA contains an N-terminal heme peroxidase domain and a C-terminal calcium binding domain. Heterologous expression and nickel affinity chromatography purification of the N-terminal peroxidase domain (MopA-hp) from Erythrobacter sp. strain SD-21 led to partial purification. MopA-hp is a heme binding protein that requires heme, NAD+, and calcium (Ca2+) for activity. Mn oxidation is also stimulated by the presence of pyrroloquinoline quinone. MopA-hp has a KM for Mn(II) of 154 ± 46 μM and kcat = 1.6 min−1. Although oxygen requiring MopA-hp is homologous to peroxidases based on sequence, addition of hydrogen peroxide and hydrogen peroxide scavengers had little effect on Mn oxidation, suggesting this is not the oxidizing agent. These studies provide insight into the mechanism by which MopA oxidizes Mn.
Informed consent and ethics committee approval in laboratory medicine

Informed consent is a process in which a human subject who is to participate in research needs to give his or her consent after being properly informed of the expected benefits as well as the potential harm of the research that will be performed. The function and purpose of the research ethics committee is to ensure that the research that will take place is in accordance with the relevant ethical standards. This means that the committee must assess the appropriateness of the design of the study reviewed. Research in the field of laboratory medicine has specific features, i.e. the use of samples that remain after routine analysis, data collection from databases containing patient information, data mining, collection of laboratory management data, method/instrument comparisons and validation, etc. As most of such research is either retrospective or not directly associated with patients, the question arises as to whether all types of research require informed consent and ethics committee approval. This article aims to clarify what is specific about obtaining informed consent and ethical approval in laboratory medicine, to provide general guidance on informed consent and ethical approval requirements based on the type of study, and what information should be included in applications for ethical approval and informed consent. This could also provide some guidance for future contributors to the Biochemia Medica.
Using Google Trends to Examine the Spatio-Temporal Incidence and Behavioral Patterns of Dengue Disease: A Case Study in Metropolitan Manila, Philippines

Dengue is a major public health concern and an economic burden in the Philippines. Despite the country’s improved dengue surveillance, it still suffers from various setbacks and therefore needs to be complemented with alternative approaches. Previous studies have demonstrated the potential of internet-based surveillance such as Google Dengue Trends (GDT) in supplementing current epidemiological methods for predicting future dengue outbreaks and patterns. With this, our study aims to assess the temporal relationship of GDT and dengue incidence in Metropolitan Manila from previous years and examine web search behavior of the population towards the disease. The study collated and organized the population statistics and reported dengue cases in Metropolitan Manila from respective government agencies to calculate the spatial and temporal dengue incidence. The relative search volume of the term ‘dengue’ and top dengue-related search queries in Metropolitan Manila were obtained and organized from the Google trends platform. Data processing of GDT and dengue incidence was performed by conducting an ‘adjustment’ procedure and subsequently used for correlation and cross-correlation analyses. Moreover, a thematic analysis was employed on the top dengue-related search queries. Results revealed a high temporal relationship between GDT and dengue incidence when either one of the variables is adjusted. Cross-correlation showed that there is delayed effect (1-2 weeks) of GDT to dengue incidence, demonstrating its potential in predicting future dengue outbreaks and patterns in Metropolitan Manila. Thematic analysis of dengue-related search queries indicated 5 categories namely; (a) dengue, (b) sign and symptoms of dengue, (c) treatment and prevention, (d) mosquito and (e) other diseases where the majority of the search queries was ‘signs and symptoms’ which indicate the health-seeking behavior of the population towards the disease.