Miracle-dz/UniFAR-FTUs huggingface dataset:
The first isolation and detection of Ornithobacterium rhinotracheale from swollen head syndrome-infected broiler flocks in Iraq

Abstract Background and Aim: The swollen head syndrome (SHS) makes up complex diseases that infect the upper respiratory tract in poultry and causes several economic losses. Furthermore, this syndrome is considered one of the multifactorial etiological agents. Therefore, this study isolated and molecularly detected Ornithobacterium rhinotracheale (ORT) in poultry. Materials and Methods: This study was conducted at 67 broiler farms that had birds observed to be infected with the SHS from September 2018 until August 2019. Subsequently, swabs were collected from their trachea, infraorbital sinuses, and lungs, after which obtained samples were treated through two methods: (a) The direct method, by uploading samples on FTA cards, and the indirect method using a transport media. Afterward, reverse transcription-polymerase chain reaction (RT-PCR) was used to analyze the directly treated samples; howeverAQ1, the culture method, followed by PCR, was used to analyze the indirectly treated samples. Next, a partial 16S RNA gene was isolated using four positive PCR products, after which the effect of 16 antibiotics was studied on the seven local ORT strains isolated. Results: The quantity of ORT isolated using the direct method was 28 (41.7%) samples, which were all positive for the strain. Identification was by direct molecular identification (RT-PCR) from samples loaded on FTA cards. Alternatively, 7 (10.4%) ORTs were detected from the indirect method, as obtained using the culture method and biochemical tests. Then, PCR was subsequently used to confirm the results. As observed, 784 bp bands were shown for all seven ORT isolates. Furthermore, results revealed a significant difference in the detection of ORT strains between direct and indirect methods, with p-value (<0.05) and standard deviation of the error±0.038 for the direct, then ±0.061 for the indirect method. For further analysis on the strain types, four 784 bp PCR products were taken, then partial 16S ribosomal sequence typing was conducted. All these four strains were found to be recorded in NCBI for the 1st time as a local Iraqi strain, with accession numbers (MN931657, MN931656, MN931655, and MN931654). Notably, results also showed that all isolated strains were multidrug-resistant. Conclusion: From the results, ORT is proposed to be implicated as one of the etiological factors that cause SHSs in poultry. Phylogenetic analysis of the current ORT bacterial strains also showed that they are closely related to the Egyptian isolates.
Open Information Extraction in Digital Libraries: Current Challenges and Open Research Questions

A central challenge for digital libraries is to provide effective access paths to ever-growing collections of mostly textual, i.e., unstructured information. The traditional, yet expensive way to manage, categorize, and annotate such collections is extensivemanualmetadata curationtosemanticallyenrichlibrary items. Theabilitytoconverttextual informationautomat-ically into a structured representation would be extremely beneficial, allowing for novel access paths as well as supporting semantically meaningful discovery. This paper investigates opportunities and challenges that the latest techniques for open information extraction offer for digital libraries. Open information extraction promises to work out-of-the-box and does not require domain-specific training data. To evaluate how well such tools perform, we perform a qualitative evaluation in two domains: general news and biomedicine. Our research shows current benefits, but also reveals serious challenges for practical applications. In particular three research questions still have to be addressed to reliably use open information extraction in digital library projects.
Pleiotropic benefits and utility of angiotensin converting enzyme inhibitors in current practice

The renin-angiotensin-aldosterone system (RAAS) is responsible for maintaining hemodynamic stability and thereby impacts multiple organ systems, such as the central nervous system, heart, and kidneys. Angiotensin II (ang II) is the main effector of the RAAS. However, overactivity of the RAAS can give rise to cardiovascular disorders, stroke, and nephrosclerosis. Unfavorable effects on cardiovascular system are attributed to ang II. RAAS activation also results in release and increased activity of several hormonal and inflammatory mediators, trigger formation of a number of secondary messengers and/or activate pathways, which negatively affects blood vessels and tissue. RAAS inhibitors, such as angiotensin-converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs), and calcium channel blockers can protect various organs from damage by blocking the protean manifestation of RAAS activity, either in its circulating or its locally tissue-active form. This review explains on the pleiotropic effects and benefits that go beyond mere blood pressure control. ACEIs in terms of mortality reduction, long-term survival benefits, cardioprotective and vasculo-protective effects as well as improve fibrinolytic balance. Ramipril has been clinically proven to reduce rates of mortality, myocardial infarction, and stroke. ACEIs and ARBs were associated with lesser risks of COVID-19 infection.
Theoretical and Experimental Investigation of Warpage Evolution of Flip Chip Package on Packaging during Fabrication

This study attempts to investigate the warpage behavior of a flip chip package-on-package (FCPoP) assembly during fabrication process. A process simulation framework that integrates thermal and mechanical finite element analysis (FEA), effective modeling and ANSYS element death-birth technique is introduced for effectively predicting the process-induced warpage. The mechanical FEA takes into account the viscoelastic behavior and cure shrinkage of the epoxy molding compound. In order to enhance the computational and modeling efficiency and retain the prediction accuracy at the same time, this study proposes a novel effective approach that combines the trace mapping method, rule of mixture and FEA to estimate the effective orthotropic elastic properties of the coreless substrate and core interposer. The study begins with experimental measurement of the temperature-dependent elastic and viscoelastic properties of the components in the assembly, followed by the prediction of the effective elastic properties of the orthotropic interposer and substrate. The predicted effective results are compared against the results of the ROM/analytical estimate and the FEA-based effective approach. Moreover, the warpages obtained from the proposed process simulation framework are validated by the in-line measurement data, and good agreement is presented. Finally, key factors that may influence process-induced warpage are examined via parametric analysis.
Influence of Sampling Methods and Storage Condition on Volatile Methyl Siloxanes Quantification in Biogas

Siloxanes are widely distributed in biogas and have a negative impact on energy applications of biogas. So far, there is no standard method for the sampling and analysis of siloxanes in biogas. The appropriate sampling method must ensure that the composition of samples collected in siloxanes does not change during sampling and analysis. To this end, three sampling methods (two-tandem (section A and B) impingers with acetone as adsorbent (TTIA), coconut activated carbon adsorbent tubes (CACT), and silica gel adsorbent tubes (SGT)) were evaluated in this paper. Hexamethyldisiloxane (L2), hexamethylcyclotrisiloxane (D3), octamethylcyclotetrasiloxane (D4), and decamethylcyclopentasiloxane (D5) detected in section B were less than 7% of those in section A of three methods. The gas chromatography coupled with mass spectrometry (GC-MS) was used for quantitative analysis of the siloxane in samples. The results demonstrated that target compounds were completely adsorbed by three methods. For D3, D4, and D5, there was no significant difference between recovery rates of CACT and SGT, whereas they were higher than those of TTIA. The siloxane contents in dry synthesis gas collected by three methods were generally higher than those in wet synthesis gas. The effect of storage time and temperature on the short-term stability of siloxanes in SGT was further investigated. The contents of D3, D4, and D5 did not change significantly with storage temperatures except L2. However, the content of D3 stored at 25 ℃ was not stable over time, which reduced by 16.2% on average at 12 h.
AUTOMATIC QUESTION GENERATION MODEL BASED ON DEEP LEARNING APPROACH

: Nowadays, students face many difficulties to practice for exams. Professors and teachers spend a lot of time and effort to make exams. Automatic Question Generation Model proposes a solution to save time, effort, and student’s learning process which helps in educational purposes. AQGM is user-friendly which is implemented as a GUI-based system that generates Wh-questions which mean” WH” (” What”,” Who”, and” Where”) and formatted into two types of templates, Question Bank template, and Exam template. Exams have different difficulty levels (Easy, Medium, and Hard). Therefore, students can measure their level and teachers will know to what extent the students understand the course. Researches have shown that this method is helpful and successful for educational purposes. AQGM generates questions automatically by using its model that generated by using sequence-to-sequence approach specially encoder-decoder technique with copy mechanism and attention decoder. AQGM model uses SQuAD as a training dataset which helps to get more accurate results. This model gets a BLEU-4 score 11.3 which is good according to it generated automatically using deep learning approaches.
HIF-1α Activation Promotes Luteolysis by Enhancing ROS Levels in the Corpus Luteum of Pseudopregnant Rats

The increase of oxidative stress is one of the important characteristics of mammalian luteal regression. Previous investigations have revealed the essential role of reactive oxygen species (ROS) in luteal cell death during luteolysis, while it is unknown how ROS is regulated in this process. Considering the decrease of blood flow and increase of PGF2α during luteolysis, we hypothesized that the HIF-1α pathway may be involved in the regulation of ROS in the luteal cell of the late corpus luteum (CL). Here, by using a pseudopregnant rat model, we showed that the level of both HIF-1α and its downstream BNIP3 was increased during luteal regression. Consistently, we observed the increase of autophagy level during luteolysis, which is regulated in a Beclin1-independent manner. Comparing with early (Day 7 of pseudopregnancy) and middle CL (Day 14), the level of ROS was significantly increased in late CL, indicating the contribution of oxidative stress in luteolysis. Inhibition of HIF-1α by echinomycin (Ech), a potent HIF-1α inhibitor, ameliorated the upregulation of BNIP3 and NIX, as well as the induction of autophagy and the accumulation of ROS in luteal cells on Day 21 of pseudopregnancy. Morphologically, Ech treatment delayed the atrophy of the luteal structure at the late-luteal stage. An in vitro study indicated that inhibition of HIF-1α can also attenuate PGF2α-induced ROS and luteal cell apoptosis. Furthermore, the decrease of cell apoptosis can also be observed by ROS inhibition under PGF2α treatment. Taken together, our results indicated that HIF-1α signaling is involved in the regression of CL by modulating ROS production via orchestrating autophagy. Inhibition of HIF-1α could obviously hamper the apoptosis of luteal cells and the process of luteal regression.
Síndrome de Miller Fisher tratado con plasmaféresis durante el embarazo: reporte de un caso y revisión de la literatura

Resumen Objetivo: Reportar el caso de una paciente gestante con síndrome de Guillain-Barré (SGB) presentado en la variante denominada síndrome de Miller Fisher (SMF), y realizar una revisión en torno al diagnóstico, tratamiento y pronóstico de esta variedad de SGB durante la gestación. Materiales y métodos: Se presenta el caso de una gestante de 27 semanas con síndrome de Miller Fisher, quien fue tratada con plasmaféresis en un hospital militar de referencia, con evolución satisfactoria a los 15 días y continuación normal del embarazo, parto a las 38 semanas con recién nacido sano. Se realizó una búsqueda bibliográfica en bases de datos electrónicas: Medline vía PubMed, Lilacs, SciELO, ScienceDirect, Ovid, con los términos “Embarazo”, “Síndrome de Miller Fisher”, “Síndrome de Guillain-Barré”. Se incluyeron cohortes, series y reportes de casos de mujeres gestantes con síndrome de Miller Fisher; se extrajo información sobre los métodos diagnósticos, el tratamiento utilizado y el pronóstico materno y perinatal. La búsqueda se hizo en junio de 2020, sin restricción por fecha, pero sí por tipo de idioma (español e inglés). Resultados: Se identificaron 423 títulos, tres estudios cumplieron los criterios de inclusión, los tres correspondieron a reportes de caso. Todos los casos mostraron seropositividad para antigangliósidos GQ1b positivos; en ningún caso hubo alteración imagenológica. Dos pacientes recibieron inmunoglobulina intravenosa y la tercera paciente se dejó en observación. Hasta el momento no se documentan complicaciones obstétricas. Conclusión: Existen pocos casos reportados de SMF durante la gestación, el diagnóstico se basa en el examen clínico; el tratamiento con inmunoglobulina IV representa la alternativa utilizada con mayor frecuencia. En el caso presentado se utilizó la plasmaféresis. Se desconoce el impacto de la variedad del síndrome de Miller Fisher sobre el curso normal de la gestación y sobre los resultados perinatales a largo plazo. Se requieren más estudios que aborden el diagnóstico, el tratamiento y el pronóstico de esta entidad.
NEDD4L-induced β-catenin ubiquitination suppresses the formation and progression of interstitial pulmonary fibrosis via inhibiting the CTHRC1/HIF-1α axis

Interstitial pulmonary fibrosis (IPF) is a severe progressive lung disease with limited therapeutic options and poor prognosis. Initially, we found the downregulated level of neural precursor cell expressed developmentally down-regulated 4-like protein (NEDD4L) in IPF-related expression microarray dataset, and this study was thus performed to explore the molecular mechanism of NEDD4L in IPF. The expression of NEDD4L was subsequently validated in lung tissues of IPF patients and mouse models. Then, mouse primary lung fibroblasts (LFs) were collected for in vitro functional experiments, with CCK-8, Transwell, and immunofluorescence assays used to examine the viability, migration, and differentiation of LFs. The in vitro findings were further assessed using in vivo mouse models. The expression of NEDD4L was down-regulated in lung tissues of IPF patients and mouse models. Overexpression of NEDD4L restricted the formation and progression of IPF in mice and attenuated the proliferative, invasive and differentiative abilities of LFs. Further, NEDD4L halted LFs activity by enhancing β-catenin ubiquitination and down-regulating the CTHRC1/HIF-1α axis. Also, in vivo experiments then validated that NEDD4L silencing repressed β-catenin ubiquitination and activated the CTHRC1/HIF-1α axis, thereby aggravating IPF in mice. NEDD4L may suppress the formation and progression of IPF through augmenting β-catenin ubiquitination and inhibiting the CTHRC1/HIF-1α axis.
The Role of Intestinal Permeability in Gastrointestinal Disorders and Current Methods of Evaluation

An increased intestinal permeability has been described in various gastrointestinal and non-gastrointestinal disorders. Nevertheless, the concept and definition of intestinal permeability is relatively broad and includes not only an altered paracellular route, regulated by tight junction proteins, but also the transcellular route involving membrane transporters and channels, and endocytic mechanisms. Paracellular intestinal permeability can be assessed in vivo by using different molecules (e.g., sugars, polyethylene glycols, 51Cr-EDTA) and ex vivo in Ussing chambers combining electrophysiology and probes of different molecular sizes. The latter is still the gold standard technique for assessing the epithelial barrier function, whereas in vivo techniques, including putative blood biomarkers such as intestinal fatty acid-binding protein and zonulin, are broadly used despite limitations. In the second part of the review, the current evidence of the role of impaired barrier function in the pathophysiology of selected gastrointestinal and liver diseases is discussed. Celiac disease is one of the conditions with the best evidence for impaired barrier function playing a crucial role with zonulin as its proposed regulator. Increased permeability is clearly present in inflammatory bowel disease, but the question of whether this is a primary event or a consequence of inflammation remains unsolved. The gut-liver axis with a crucial role in impaired intestinal barrier function is increasingly recognized in chronic alcoholic and metabolic liver disease. Finally, the current evidence does not support an important role for increased permeability in bile acid diarrhea.
Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration

Diabetes mellitus (DM) is a complex metabolic disorder. Long-term hyperglycemia may induce diabetic keratopathy (DK), which is mainly characterized by delayed corneal epithelial regeneration. MicroRNAs (miRNAs) have been reported to play regulatory roles during tissue regeneration. However, the molecular mechanism by which miRNAs influence epithelial regeneration in DK is largely unknown. In this study, we performed miRNA and mRNA sequencing of regenerative corneal epithelium tissue from streptozotocin-induced type 1 diabetic (T1DM) and wild-type mice to screen for differentially expressed miRNAs and mRNAs. Based on regulatory network analysis, miR-223-5p was selected for subsequent experiments and Hpgds was then identified as a direct target gene. MiR-223-5p downregulation significantly promoted diabetic corneal epithelial wound healing and nerve regeneration. However, the beneficial effects of miR-223-5p inhibition were abolished by an Hpgds inhibitor. Furthermore, mechanistic studies demonstrated that miR-223-5p suppression ameliorated inflammation and enhanced cell proliferation signaling in DK. Taken together, our findings revealed that the regulatory role of miR-223-5p in diabetic corneal epithelial and nerve regeneration by mediating inflammatory processes and cell proliferation signaling. And silencing miR-223-5p may contribute to the development of potential therapeutic strategies for DK.
High-Level Serum Fibroblast Growth Factor 21 Concentration Is Closely Associated With an Increased Risk of Cardiovascular Diseases: A Systematic Review and Meta-Analysis

Background: The association between fibroblast growth factor 21 (FGF21) and cardiovascular disease (CVD) risk remains unclear. We conducted this systematic review and meta-analysis to evaluate the association between FGF21 and CVDs, and relevant vascular parameters. Methods: PubMed and Web of Science databases were systematically searched to identify relevant studies published before March 2021. The FGF21 concentration was compared between individuals with and without CVDs. The effect of FGF21 on CVD risk was assessed by using hazard ratio (HR) and odds ratio (OR). The association between FGF21 and vascular parameters was assessed by Pearson's r. Study quality was assessed using Newcastle–Ottawa Scale and Joanna Briggs Institution Checklist. Results: A total of 29,156 individuals from 30 studies were included. Overall, the serum FGF21 concentration was significantly higher in CVD patients (p < 0.001), especially for coronary artery disease (CAD) (p < 0.001) and hypertension (p < 0.001). The pooled OR (p = 0.009) and HR (p < 0.001) showed that the risk of CVDs increased with FGF21. The linear association between FGF21 and vascular parameters, including pulse wave velocity (r = 0.32), carotid intima-media thickness (r = 0.21), ankle-brachial index (r = 0.33), systolic blood pressure (r = 0.13), and diastolic blood pressure (r = 0.05), was insignificant. The incidence of overall CVDs (p = 0.03) was significantly higher in individuals with higher FGF21 levels. Conclusion: High-level serum FGF21 concentration is closely associated with an increased risk of CVDs, which may be independent of vascular parameters. A standard FGF21 classification threshold needs to be established before clinical use for CVD risk assessment. Systematic Review Registration: https://www.crd. york.ac. uk/prospero/display_record. php? RecordID=241968, identifier: CRD42021241968.
A New Story of the Three Magi: Scaffolding Proteins and lncRNA Suppressors of Cancer

Simple Summary MAGI1, 2, and 3 belong to a subgroup of the MAGUK family of scaffolding proteins, and are comprised of 6 PDZ domains, 2 WW domains, and 1 GUK domain. MAGIs associate with cell surface receptors, junctional complexes, and interact selectively with a wide range of effectors, including the PTEN tumor suppressor, the β-catenin, and YAP1 proto-oncogenes. The regulation of the PI3K/AKT, the Wnt, and the Hippo signaling pathways, on the one hand, the downmodulation of MAGIs in various types of cancers, and its physiopathological significance, on the other, make these scaffolding proteins considered to be tumor suppressors. Interestingly, MAGI1 and MAGI2 genetic loci generate a series of long non-coding RNAs (lncRNAs) that act as promoters or suppressors of tumors in a tissue-dependent manner by sponging some sets of miRNAs or by regulating epigenetic processes. This review details current knowledge of paths followed by the three MAGIs to control carcinogenesis. Abstract Scaffolding molecules exert a critical role in orchestrating cellular response through the spatiotemporal assembly of effector proteins as signalosomes. By increasing the efficiency and selectivity of intracellular signaling, these molecules can exert (anti/pro)oncogenic activities. As an archetype of scaffolding proteins with tumor suppressor property, the present review focuses on MAGI1, 2, and 3 (membrane-associated guanylate kinase inverted), a subgroup of the MAGUK protein family, that mediate networks involving receptors, junctional complexes, signaling molecules, and the cytoskeleton. MAGI1, 2, and 3 are comprised of 6 PDZ domains, 2 WW domains, and 1 GUK domain. These 9 protein binding modules allow selective interactions with a wide range of effectors, including the PTEN tumor suppressor, the β-catenin and YAP1 proto-oncogenes, and the regulation of the PI3K/AKT, the Wnt, and the Hippo signaling pathways. The frequent downmodulation of MAGIs in various human malignancies makes these scaffolding molecules and their ligands putative therapeutic targets. Interestingly, MAGI1 and MAGI2 genetic loci generate a series of long non-coding RNAs that act as a tumor promoter or suppressor in a tissue-dependent manner, by selectively sponging some miRNAs or by regulating epigenetic processes. Here, we discuss the different paths followed by the three MAGIs to control carcinogenesis.