Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and antigenic characterization of a novel genotype of Mfa1 fimbriae in Porphyromonas gingivalis

ABSTRACT Background Mfa1 fimbriae of the periodontal pathogen Porphyromonas gingivalis are responsible for biofilm formation and comprise five proteins: Mfa1–5. Two major genotypes, mfa170 and mfa153, encode major fimbrillin. The mfa170 genotype is further divided into the mfa170A and mfa170B subtypes. The properties of the novel mfa170B remain unclear. Methods Fimbriae were purified from P. gingivalis strains JI-1 (mfa170A), 1439 (mfa170B), and Ando (mfa153), and their components and their structures were analyzed. Protein expression and variability in the antigenic specificity of fimbrillins were compared using Coomassie staining and western blotting using polyclonal antibodies against Mfa170A, Mfa170B, and Mfa153 proteins. Cell surface expression levels of fimbriae were analyzed by filtration enzyme-linked immunosorbent assays. Results The composition and structure of the purified Mfa1 fimbriae of 1439 was similar to that of JI-1. However, each Mfa1 protein of differential subtype/genotype was specifically detected by western blotting. Mfa170B fimbriae were expressed in several strains such as 1439, JKG9, B42, 1436, and Kyudai-3. Differential protein expression and antigenic heterogeneities were detected in Mfa2–5 between strains. Conclusion Mfa1 fimbriae from the mfa170A and mfa170B genotypes indicated an antigenic differencesuggesting the mfa170B, is to be utilized for the novel classification of P. gingivalis.
The Underlying Mechanism of Duanteng Yimu Decoction in Inhibiting Synovial Hyperplasia in Rheumatoid Arthritis

Dysregulation of microRNAs (miRNAs) is associated with the pathogenesis of rheumatoid arthritis (RA). Our previous studies confirmed that Duanteng Yimu decoction (DTYMT) effectively inhibits RA fibroblast-like synoviocyte (FLS) proliferation. In this study, we investigated the influence of DTYMT on miR-221 in RA individuals. Hematoxylin–eosin (HE) staining was performed to assess histopathological alterations in collagen-induced arthritis (CIA) mice. The expression of miR-221-3p and TLR4 in PBMC, FLS, and cartilage was measured by RT-qPCR. In the in vitro experiments, DTYMT-containing serum was incubated with FLS-transfected miR-221 mimic or inhibitor. CCK-8 was performed to determine FLS proliferation, and the secretion of IL-1β, IL-6, IL-18, and TNF-α was quantified by ELISA assay. In addition, the regulation of miR-221 expression on FLS apoptosis was assessed using flow cytometry. Finally, western blot was employed to reflect TLR4/MyD88 protein levels. HE results showed that DTYMT effectively reduced synovial hyperplasia in the joints of CIA mice. RT-qPCR assay of FLS and cartilage of the model group showed that miR-221-3p and TLR4 significantly increased compared with those in the normal group. All outcomes were improved by DTYMT. The miR-221 mimic reversed the inhibitory effect of DTYMT-containing serum on FLS proliferation, the release of IL-1β, IL-18, IL-6, and TNF-α, and FLS apoptosis, as well as TLR4/MyD88 protein levels. The results showed that miR-221 promotes the activity of RA-FLS by activating TLR4/MyD88 signaling, and DTYMT treats RA by reducing miR-221 in CIA mice.
Surrogate markers of metabolic syndrome (MetS) and insulin resistance (IR) in children and young adults with type 1 diabetes: A systematic review & meta-analysis

Introduction: Metabolic syndrome (MetS), a collection of risk factors for cardiovascular disease, and Insulin resistance (IR) are associated with diabetes. The diagnosis of both these conditions are based on specific clinical parameters. However, the efficacy of these parameters has not been systematically studied in paediatric population with T1DM. Methodology: We performed a systematic review and meta-analysis in paediatric populations of type 1 diabetes. We assessed the strength of association of the parameters of MetS and IR. The meta-analysis was performed using a metaphor package in R. A random effect model was used to study the strength of association by estimating Hedges g. Results: The systematic review resulted in identification of 30 studies on MetS and IR in paediatric patients with T1DM. Insulin dosage and HbA1C, markers for glycaemic condition showed no association with MetS in patients with T1DM. In the lipid profile, increased triglyceride (TG) and low-density lipoprotein (LDL) showed better effect size than reduced high-density lipoprotein (HDL). In case of insulin resistance, heterogeneous nature of studies made it difficult to carry out a meta-analysis. A descriptive review of existing and novel markers is thus provided. Conclusion: Lack of association between markers of glycaemic condition suggested that MetS may develop independently of glycaemic control in children with T1DM. Other than TG and HDL, LDL may be used in the diagnosis of MetS. From the descriptive analysis it could be observed that a standard protocol for the diagnosis of IR is needed.
Immune checkpoint inhibitors combined with antiangiogenic drugs in the treatment of unresectable locally advanced / distant metastatic esophageal squamous cell carcinoma: a systematic review protocol

Background and purpose Esophageal cancer has the seventh highest incidence and sixth highest fatality rate of all malignant tumors. It's a type of cancer that has a greater fatality rate than morbidity. In the treatment of advanced esophageal and squamous cell carcinoma, targeted and immune checkpoint inhibitors have showed promising outcomes in recent years. The aim of this research was to examine the effectiveness and safety of immune checkpoint inhibitors in combination with antiangiogenic medicines in the treatment of unresectable patients with locally progressed / distant metastatic esophageal squamous cell carcinoma. Methods Before April 15, 2022, randomized controlled trials of immune checkpoint inhibitors combined with anti-angiogenic drugs in the treatment of esophageal cancer will be searched on PubMed, Cochrane Library, EMBASE, WebofScience, China Knowledge Network, Wanfang Data Knowledge Service Platform, and VIP. The two authors independently extracted the data, checked the data, and used the "bias risk" tool in the Cochrane intervention system evaluation manual to independently evaluate the bias included in the study. When the extracted data were similar enough, the Revman5.4 software was used for meta analysis. If the summary data could not be collected for meta analysis, the results would be summarized in a narrative way. Discussion This paper introduces in detail the systematic review and design method of immune checkpoint inhibitors mixture with antiangiogenic drugs in the treatment of unresectable locally advanced / distant metastatic esophageal squamous cell carcinoma.
Life-table parameters of Plodia interpunctella (Lepidoptera: Pyralidae) on different stored date palm fruits under laboratory conditions

Abstract Indian meal moth, Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae), is a polyphagous insect pest that causes serious damage to various food crops in storage. This study aimed to investigate the life-history and demographic parameters of P. interpunctella on 5 varieties of date palm fruits (Phoenix dactylifera L.), including Dayri, Estemaran, Fersi, Halavi, and Zahedi under laboratory conditions. Data were analyzed and compared using the age–stage, 2-sex life table. Plodia interpunctella completed its development on all date varieties. The shortest and longest pre-adult periods were recorded on Zahedi (38.47 days) and Estemaran (44.65 days) varieties, respectively. The net reproductive rates (R0) were 82.51, 59.05, 63.61, 102.27, and 114.86 offspring on Dayri, Estemaran, Fersi, Halavi, and Zahedi varieties, respectively. The intrinsic rate of increase (r) were 0.098, 0.085, 0.089, 0.109, and 0.113 day−1 on Dayri, Estemaran, Fersi, Halavi, and Zahedi varieties, respectively. The female fecundity ranged from 133.4 to 259.24 eggs on Estemaran and Zahedi varieties, respectively. The highest mean generation time (T) was obtained on Estemaran (47.984 days), and the lowest value of this parameter was obtained on Zahedi (41.722 days) variety. The results indicated that Zahedi and Halavi varieties were the susceptible hosts for P. interpunctella. In contrast, the Estemaran and Fersi were the most resistant varieties against P. interpunctella, which can be used for integrated management programs to decrease the damage of this pest.
APE1 recruits ATRIP to ssDNA in an RPA-dependent and -independent manner to promote the ATR DNA damage response

Cells have evolved the DNA damage response (DDR) pathways in response to DNA replication stress or DNA damage. In the ATR-Chk1 DDR pathway, it has been proposed that ATR is recruited to RPA-coated single-stranded DNA (ssDNA) by direct ATRIP-RPA interaction. However, it remains elusive how ATRIP is recruited to ssDNA in an RPA-independent manner. Here, we provide evidence that APE1 directly associates ssDNA to recruit ATRIP onto ssDNA in an RPA-independent fashion. The N-terminal motif within APE1 is required and sufficient for the APE1-ATRIP interaction in vitro and the distinct APE1-ATRIP interaction is required for ATRIP recruitment to ssDNA and the ATR-Chk1 DDR pathway activation in Xenopus egg extracts. In addition, APE1 directly associates with RPA70 and RPA32 via two distinct motifs. Taken together, our evidence suggests that APE1 recruits ATRIP onto ssDNA in an RPA-dependent and -independent manner in the ATR DDR pathway.
Epidemiological analysis of African swine fever in the European Union during 2022

Abstract This report presents the epidemiological analysis of African swine fever (ASF) during 2022 based on the surveillance and pig population data submitted by the European Union (EU) affected countries and one neighbouring country. Coinciding with regulatory changes and an important decrease in ASF outbreaks in 2022 in the EU, the number of domestic pig samples tested as part of active surveillance decreased by 80%, while the number of samples from passive surveillance almost doubled compared with 2021. Most outbreaks among domestic pigs in the EU were detected by testing clinical suspicions (93% of outbreaks), followed by tracing activities (5%) and weekly testing of the first two dead pigs per establishment (2%). Although most of the wild boar samples came from hunted animals, the probability of detecting PCR‐positive animals was much higher in wild boar found dead. The ASF outbreaks among domestic pigs in the EU decreased by 79% while a decrease of 40% in the wild boar cases was observed in comparison with 2021. This was strongly marked in Romania, Poland and Bulgaria, with a reduction of 50–80% compared with 2021. In many countries, an important decrease in the number of pig establishments was observed, especially of small establishments with fewer than 100 pigs. The regional between farm incidence and proportion of pigs lost due to ASF in the EU was in general very low (average of 1%) apart from some regions in Romania. The impact of ASF on wild boar populations was variable, with a decline in wild boar abundance observed in certain countries versus a stable or even increased population after ASF introduction. This supports the negative relationship observed in this report between the proportion of the country with restricted zones due to ASF in wild boar and wild boar hunting bags.
Functional impacts of polyaniline in composite matrix of photocatalysts: an instrumental overview

The challenges associated with photocatalysts including their agglomeration, electron–hole recombination and limited optoelectronic reactivity to visible light during the photocatalysis of dye-laden effluent make it necessary to fabricate versatile polymeric composite photocatalysts, and in this case the incredibly reactive conducting polyaniline can be employed. The selection of polyaniline among the conducting polymers is based on its proficient functional impacts in composite blends and proficient synergism with other nanomaterials, especially semiconductor catalysts, resulting in a high photocatalytic performance for the degradation of dyes. However, the impacts of PANI in the composite matrix, which result in the desired photocatalytic activities, can only be assessed using multiple characterization techniques, involving both microscopic and spectroscopic assessment. The characterization results play a significant role in the detection of possible points of agglomeration, surface tunability and improved reactivity during the fabrication of composites, which are necessary to improve their performance in the photocatalysis of dyes. Accordingly, studies revealed the functional impacts of polyaniline in composites including morphological transformation, improved surface functionality, reduction in agglomeration and lowered bandgap potential employing different characterization techniques. In this review, we present the most proficient fabrication techniques based on the in situ approach to achieve improved functional and reactive features and efficiencies of 93, 95, 96, 98.6 and 99% for composites in dye photocatalysis.
Bioengineering liver microtissues for modeling non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) has become the world's most common chronic liver disease. However, due to the lack of reliable in vitro NAFLD models, drug development studies have faced many limitations, and there is no food and drug administration-approved medicine for NAFLD treatment. A functional biomimetic in vitro human liver model requires an optimized natural microenvironment using appropriate cellular composition, to provide constructive cell-cell interactions, and niche-specific bio-molecules to supply crucial cues as cell-matrix interplay. Such a suitable liver model could employ appropriate and desired biochemical, mechanical, and physical properties similar to native tissue. Moreover, bioengineered three-dimensional tissues, specially microtissues and organoids, and more recently using infusion-based cultivation systems such as microfluidics can mimic natural tissue conditions and facilitate the exchange of nutrients and soluble factors to improve physiological function in the in vitro generated constructs. This review highlights the key players involved in NAFLD initiation and progression and discussed the available cells and matrices for in vitro NAFLD modeling. The strategies for optimizing the liver microenvironment to generate a powerful and biomimetic in vitro NAFLD model were described as well. Finally, the current challenges and future perospective for promotion in this subject were discussed.
Tocilizumab in the Treatment of Eosinophilic Fasciitis: A Case Study and Review of Literature

Eosinophilic fasciitis (EF) is a rare connective-tissue disorder that is characterised by subacute onset of erythema, oedema, and induration of the skin and soft tissues of the limbs and trunk. Although several triggers have been hypothesised to be associated with EF, the aetiology of eosinophilic fasciitis (EF) is still unclear, and several treatment regimens have been proposed to treat this disease. In this article, we report a case of a 72-year-old gentleman with multiple comorbidities who presented to the clinic for diffuse skin thickening present on his forearms, thighs, legs bilaterally, and over the pelvis. The patient was diagnosed with EF and failed multiple treatment regimens including prednisone, methotrexate, rituximab, but finally responded and was maintained on tocilizumab. In this article, we will review the current understanding of EF, diagnostic approach, popular treatments and review other cases of EF in which tocilizumab was used.
Experimental investigations of turbulent wake behind porous disks

Turbulent wake plays an important role in optimizing turbine layout in tidal farms and in understanding turbine‐seabed interactions. Although porous disk models are frequently used in experiments and numerical simulations to represent turbines, how well and to what extent the wake of a disk model can represent that of a prototype turbine is not well understood. In this work, laboratory-scale experiments of porous disks in isolated deployment and in an array are conducted in a circulating water channel to investigate the effects of porous structures and array on the characteristics of near wake. It is found that the porous structures on the disk drastically decrease the velocity deficit, the rate of velocity recovery, and the turbulence production in the wake. The array effects decrease the velocity deficit and the rate of velocity recovery, but increases the turbulence production. The experiments also show that the wake of flow past three disks is nearly fully developed and adequately represents that of a disk in an infinite array.
Functional analysis of three new alpha-thalassemia deletions involving MCS-R2 reveals the presence of an additional enhancer element in the 5’ boundary region

We report three novel deletions involving the Multispecies Conserved Sequences (MCS) R2, also known as the Major Regulative Element (MRE), in patients showing the α-thalassemia phenotype. The three new rearrangements showed peculiar positions of the breakpoints. 1) The (αα)ES is a telomeric 110 kb deletion ending inside the MCS-R3 element. 2) The (αα)FG, 984 bp-long, ends 51 bp upstream to MCS-R2; both are associated with a severe α-thalassemia phenotype. 3) The (αα)CT, 5058 bp-long starts at position +93 of MCS-R2 and is the only one associated to a mild α-thalassemia phenotype. To understand the specific role of different segments of the MCS-R2 element and of its boundary regions we carried out transcriptional and expression analysis. Transcriptional analysis of patients’ reticulocytes showed that (αα)ES was unable to produce α2-globin mRNA, while a high level of expression of the α2-globin genes (56%) was detected in (αα)CT deletion, characterized by the presence of the first 93 bp of MCS-R2. Expression analysis of constructs containing breakpoints and boundary regions of the deletions (αα)CT and (αα)FG, showed comparable activity both for MCS-R2 and the boundary region (-682/-8). Considering that the (αα)CT deletion, almost entirely removing MCS-R2, has a less severe phenotype than the (αα)FG α0thalassemia deletion, removing both MCS-R2 almost entirely and an upstream 679 bp, we infer for the first time that an enhancer element must exist in this region that helps to increase the expression of the α-globin genes. The genotype-phenotype relationship of other previously published MCS-R2 deletions strengthened our hypothesis.
TRIPBASE: a database for identifying the human genomic DNA and lncRNA triplexes

Abstract Long-non-coding RNAs (lncRNAs) are defined as RNA sequences which are >200 nt with no coding capacity. These lncRNAs participate in various biological mechanisms, and are widely abundant in a diversity of species. There is well-documented evidence that lncRNAs can interact with genomic DNAs by forming triple helices (triplexes). Previously, several computational methods have been designed based on the Hoogsteen base-pair rule to find theoretical RNA–DNA:DNA triplexes. While powerful, these methods suffer from a high false-positive rate between the predicted triplexes and the biological experiments. To address this issue, we first collected the experimental data of genomic RNA-DNA triplexes from antisense oligonucleotide (ASO)-mediated capture assays and used Triplexator, the most widely used tool for lncRNA–DNA interaction, to reveal the intrinsic information on true triplex binding potential. Based on the analysis, we proposed six computational attributes as filters to improve the in-silico triplex prediction by removing most false positives. Further, we have built a new database, TRIPBASE, as the first comprehensive collection of genome-wide triplex predictions of human lncRNAs. In TRIPBASE, the user interface allows scientists to apply customized filtering criteria to access the potential triplexes of human lncRNAs in the cis-regulatory regions of the human genome. TRIPBASE can be accessed at https://tripbase.iis. sinica.edu. tw/.
The financial performance of private hospitals in Saudi Arabia: An investigation into the role of internal control and financial accountability

The aim of this study was to examine the relationship between internal control, financial accountability, and financial performance in the private healthcare sector in the Kingdom of Saudi Arabia (KSA) through a questionnaire survey of 78 private hospitals. Drawing on agency theory, the study utilized structural equation modelling with partial least-squares technique to test multiple hypotheses. Results indicate a significant positive relationship between internal control and financial performance, with financial accountability acting as a mediator. Additionally, financial accountability was found to have a direct positive effect on financial performance. These findings provide new evidence for improving financial performance in private hospitals in the KSA through the implementation of internal control and financial accountability measures. Further research could examine additional factors that may impact financial performance in the healthcare sector.
Spatial predictions of tree density and tree height across Mexico forests using ensemble learning and forest inventory data

Abstract The National Forestry Commission of Mexico continuously monitors forest structure within the country's continental territory by the implementation of the National Forest and Soils Inventory (INFyS). Due to the challenges involved in collecting data exclusively from field surveys, there are spatial information gaps for important forest attributes. This can produce bias or increase uncertainty when generating estimates required to support forest management decisions. Our objective is to predict the spatial distribution of tree height and tree density in all Mexican forests. We performed wall‐to‐wall spatial predictions of both attributes in 1‐km grids, using ensemble machine learning across each forest type in Mexico. Predictor variables include remote sensing imagery and other geospatial data (e.g., mean precipitation, surface temperature, canopy cover). Training data is from the 2009 to 2014 cycle (n > 26,000 sampling plots). Spatial cross validation suggested that the model had a better performance when predicting tree height r 2 = . 35 [. 12, . 51] (mean [min, max]) than for tree density r 2 = . 23 [. 05, . 42]. The best predictive performance when mapping tree height was for broadleaf and coniferous‐broadleaf forests (model explained ~50% of variance). The best predictive performance when mapping tree density was for tropical forest (model explained ~40% of variance). Although most forests had relatively low uncertainty for tree height predictions, e.g., values <60%, arid and semiarid ecosystems had high uncertainty, e.g., values >80%. Uncertainty values for tree density predictions were >80% in most forests. The applied open science approach we present is easily replicable and scalable, thus it is helpful to assist in the decision‐making and future of the National Forest and Soils Inventory. This work highlights the need for analytical tools that help us exploit the full potential of the Mexican forest inventory datasets.