Miracle-dz/UniFAR-FTUs huggingface dataset:
Gestational weight gain and risk of autism spectrum disorders in offspring: a systematic review and meta-analysis

Abstract It has been revealed that gestational weight gain (GWG) influences the risk of autism spectrum disorder (ASD) in the offspring, but the findings are inconsistent. The current study aimed to evaluate the relationship between GWG and risk of ASD in offspring. Four electronic databases were searched up to August 28 2018 to identify observational studies reporting the association between GWG and risk of ASD in the offspring. Nine studies which met the inclusion criteria were included in the systematic review. Finally, five studies with a total of 3793 children with ASD were included in the meta-analysis. The-results indicated that excessive GWG might increase the risk of ASD in offspring (p = .0008, OR = 1.23, 95% confidence interval (CI) 1.09–1.38). More high quality cohort studies are needed to confirm this result. This research has the potential to inspire new research on ASD and promote efforts to design appropriate interventions against excessive GWG. Impact statement What is already known on this subject? It has been revealed that gestational weight gain (GWG) influences the risk of autism spectrum disorder (ASD) in the offspring, but the findings are inconsistent. What the results of this study add? This is the first systematic review and meta-analysis on the association between GWG and ASDs in offspring. This study suggested that excessive GWG was associated with higher risk of ASD in offspring. What the implications are of these findings for clinical practice and/or further research? More high quality cohort studies are needed to confirm this result. This research has the potential to inspire new research on ASD and promote efforts to design appropriate interventions against excessive GWG.
Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite

Abstract Motivation RNA 5-methylcytosine (m5C) is a type of post-transcriptional modification that may be involved in numerous biological processes and tumorigenesis. RNA m5C can be profiled at single-nucleotide resolution by high-throughput sequencing of RNA treated with bisulfite (RNA-BisSeq). However, the exploration of transcriptome-wide profile and potential function of m5C in splicing remains to be elucidated due to lack of isoform level m5C quantification tool. Results We developed a computational package to quantify Epitranscriptomal RNA m5C at the transcript isoform level (named Episo). Episo consists of three tools: mapper, quant and Bisulfitefq, for mapping, quantifying and simulating RNA-BisSeq data, respectively. The high accuracy of Episo was validated using an improved m5C-specific methylated RNA immunoprecipitation (meRIP) protocol, as well as a set of in silico experiments. By applying Episo to public human and mouse RNA-BisSeq data, we found that the RNA m5C is not evenly distributed among the transcript isoforms, implying the m5C may subject to be regulated at isoform level. Availability and implementation Episo is released under the GNU GPLv3+ license. The resource code Episo is freely accessible from https://github.com/liujunfengtop/Episo (with Tophat/cufflink) and https://github.com/liujunfengtop/Episo/tree/master/Episo_Kallisto (with Kallisto). Supplementary information Supplementary data are available at Bioinformatics online.
AN ANALYSIS OF CHINESE UNIVERSITY ENGLISH ENTRANCE EXAMINATIONS FROM THE VIEWPOINT OF CULTURE AND COUNTRIES

Teaching culture is an important policy of high-school English education in China, and the country experiences significant washback effects of university entrance examinations on high-school English education. However, there has been little research on the content of Chinese university English entrance examinations in terms of cultural topics, although the source of washback is test content. Therefore, we analyzed university entrance examinations administered in Beijing and Shanghai from the perspective of cultural topic categories, the source-culture country, and the three concentric circles (Inner, Outer, and Expanding Circles). The results showed that both two tests had the same preferences in favor of particular topics as well as countries: Topics related to society and daily life frequently appeared. The U.S. and UK appeared far more frequently than other countries in both examinations, while Outerand Expanding-Circle countries rarely appeared. The source-culture country did not appear at all. On the other hand, a few differences were also found in these tests: In the Beijing tests, topics related to social problems often appeared; on the other hand, in the Shanghai tests, career-related topics frequently appeared. This difference might have arisen because the former city is the center of politics, and the latter is the center of commerce. In the Beijing tests, the U.S.A. appeared far more frequently than the UK; the reason might be that the former is politically more important to Beijing, which is the center of politics in China. This study implies that English entrance exam constructors in China should include cultural topics and countries that were not found very often or at all in this study in their tests. This is to ensure that both high-school students and teachers will pay more attention to more diverse cultural topics and countries, which is necessary in learning English as an international language.
A virtual & an augmented reality application of the Rashid Agha's diwakhana in the citadel of erbil using 360° 3D Lidar

Preserving the historical monuments as archaeological heritage has cultural and financial significance. However, the fragility of these constructions does not help in intrusive human intervention to preserve them. For example, intrusive research or the use of mechanical or chemical activities could damage the archaeological site entirely or partially. Modern technologies have helped to modernize archaeological research, documentation and restoration by finding alternative nonintrusive precise methods for object identification, modelling and virtualisation without damaging them. Nowadays, Lidar (Light detection and ranging) is a significant technology for archaeological research that provides detailed data of the site for wide-ranging spatial locations. It can achieve images in three dimensions with the help of hardware established on ground or a drone or even an airplane. The precise 3D information (point cloud) provided by the Lidar are used later for virtual reconstruction or restoration in case of unwanted destructive invasive catastrophes. Moreover, the acquired point cloud can also be utilised to design an augmented reality (AR) and a (VR) virtual reality application to be used on various platforms. In this work, an experimental setup is suggested, using a Lidar device, to scan façades of an archaeological site, obtaining the point cloud and virtualising as 3D model so that it can be used in AR and VR applications. This setup is used for one of the houses in Erbil's Citadel which is classified as a world archaeological heritage by UNISCO.
Towards Globally Optimal full 3D reconstruction of scenes with complex reflectance using Helmholtz Stereopsis

Many 3D reconstruction techniques are based on the assumption of prior knowledge of the object’s surface reflectance, which severely restricts the scope of scenes that can be reconstructed. In contrast, Helmholtz Stereopsis (HS) employs Helmholtz Reciprocity to compute the scene geometry regardless of its Bidirectional Reflectance Distribution Function (BRDF). Despite this advantage, most HS implementations to date have been limited to 2.5D reconstruction, with the few extensions to full 3D being generally limited to a local refinement due to the nature of the optimisers they rely on. In this paper, we propose a novel approach to full 3D HS based on Markov Random Field (MRF) optimisation. After defining a solution space that contains the surface of the object, the energy function to be minimised is computed based on the HS quality measure and a normal consistency term computed across neighbouring surface points. This new method offers several key advantages with respect to previous work: the optimisation is performed globally instead of locally; a more discriminative energy function is used, allowing for better and faster convergence; a novel visibility handling approach to take advantage of Helmholtz reciprocity is proposed; and surface integration is performed implicitly as part of the optimisation process, thereby avoiding the need for an additional step. The approach is evaluated on both synthetic and real scenes, with an analysis of the sensitivity to input noise performed in the synthetic case. Accurate results are obtained on both types of scenes. Further, experimental results indicate that the proposed approach significantly outperforms previous work in terms of geometric and normal accuracy.
Drug Metabolism by the Mitochondrial Amidoxime Reducing Component (mARC): Rapid Assay and Identification of New Substrates.

For the development of new drugs, the investigation of their metabolism is of central importance. In the past, the focus was mostly on the consideration of established enzymes leading to oxidations such as cytochrome P450. However, reductive metabolism by the mARC enzyme system can play an important role in particular for nitrogen containing functional groups. A rapid test was established to give developers of new drugs in the preclinical stage the opportunity to test the metabolism by mARC. In order to demonstrate the relevance and validity of the new test system, known and potential substrates were applied to this new assay. All known substrates could be detected by the system. Furthermore, several new substrates were found including long-established drugs such as hydroxyurea and new compounds in development such as epacdadostat.
Simulation on metro railway induced vibration. Part II: effect of corrugated rail

The deterioration of running surface, including out-of-round wheels and corrugated rails. The effect of out-of-round wheels on simulation of rail dynamic behavior was presented in a companion paper [1]. In this paper, the effect of corrugated rails was discussed. Considering a perfect round wheels moving on different irregularities rail surface, including perfect smooth rail, irregularities generated from a US PSD, measurement data from corrugated rails. Calculation result indicated that (1) the traditional used irregularity generated from US-PSD would not satisfy the requirement simulation on rolling noise and vibration generation in high frequency range; (2) corrugated rail plays the dominant role on the vibration which obviously related to its typical wavelength.
Effort-based information retrieval evaluation with varied evaluation depth and topic sizes

The information retrieval accessed globally is a vital productivity boost for most organization. However, the outcome of information retrieval system evaluation does not agree with the real user's satisfaction. Information retrieval systems retrieving low effort documents are preferred by users as effort factor influences user satisfaction. However, there lacks evaluation on deeper depth and reduced topic sizes with the incorporation of effort in evaluating the information retrieval systems. Therefore, this study aims to measure the effectiveness of evaluating information retrieval systems using effort-based relevance judgment with varied evaluation depth, and reduced topic sizes using effort-based relevance judgment. The evaluation depth is varied from 10, 100 and 1000, and the correlation coefficient between the baseline and those generated using effort-based relevance judgment is evaluated. Topic sizes smaller than 50 were also considered and measured to observe changes in correlation coefficient due to effort. As a result, standard evaluation depth, and reduced topic sizes are sufficient for evaluation using effort-based relevance judgment.
Results from one-year use of an electronic Clinical Decision Support System in a post-conflict context: An implementation research

Background In 2017, the Adamawa State Primary Healthcare Development Agency introduced ALMANACH, an electronic clinical decision support system based on a modified version of IMCI. The target area was the Federal State of Adamawa (Nigeria), a region recovering after the Boko Haram insurgency. The aim of this implementation research was to assess the improvement in terms of quality care offered after one year of utilization of the tool. Methods We carried out two cross-sectional studies in six Primary Health Care Centres to assess the improvements in comparison with the baseline carried out before the implementation. One survey was carried out inside the consultation room and was based on the direct observation of 235 consultations of children aged from 2 to 59 months old. The second survey questioned 189 caregivers outside the health facility for their opinion about the consultation carried out through using the tablet, the prescriptions and medications given. Results In comparison with the baseline, more children were checked for danger signs (60.0% vs. 37.1% at baseline) and in addition, children were actually weighed (61.1% vs. 27.7%) during consultation. Malnutrition screening was performed in 35.1% of children (vs. 12.1%). Through ALMANACH, also performance of preventive measures was significantly improved (p<0.01): vaccination status was checked in 39.8% of cases (vs. 10.6% at baseline), and deworming and vitamin A prescription was increased to 46.5% (vs. 0.7%) and 48.3% (vs. 2.8%) respectively. Furthermore, children received a complete physical examination (58.3% vs. 45.5%, p<0.01) and correct treatment (48.4% vs. 29.5%, p<0.01). Regarding antibiotic prescription, 69.3% patients received at least one antibiotic (baseline 77.7%, p<0.05). Conclusions Our findings highlight major improvements in terms of quality of care despite many questions still pending to be answered in relation to a full integration of the tool in the Adamawa health system.
The efficacy of conditioned medium released by tonsil-derived mesenchymal stem cells in a chronic murine colitis model

Tonsil-derived mesenchymal stem cells (TMSC) have characteristics of MSC and have many advantages. In our previous studies, intraperitoneal (IP) injection of TMSC in acute and chronic colitis mouse models improved the disease activity index, colon length, and the expression levels of proinflammatory cytokines. However, TMSC were not observed to migrate to the inflammation site in the intestine. The aim of this study was to verify the therapeutic effect of conditioned medium (CM) released by TMSC (TMSC-CM) in a mouse model of dextran sulfate sodium (DSS)-induced chronic colitis. TMSC-CM was used after seeding 5×105 cells onto a 100 mm dish and culturing for 5–7 days. TMSC-CM was concentrated (TMSC-CM-conc) by three times using a 100 kDa cut-off centrifugal filter. Seven-week-old C57BL/6 mice were randomly assigned to the following 5 groups: 1) normal, 2) colitis, 3) TMSC, 4) TMSC-CM, and 5) TMSC-CM-conc. Chronic colitis was induced by continuous oral administration of 1.5% dextran sulfate sodium (DSS) for 5 days, followed by 5 additional days of tap water feeding. This cycle was repeated two more times (total 30 days). Phosphate buffered saline (in the colitis group), TMSC, TMSC-CM, and TMSC-CM-conc were injected via IP route 4, 4, 12, and 4 times, respectively. Reduction of disease activity index, weight gain, recovery of colon length, and decreased in the expression level of the proinflammatory cytokines, interleukin (IL)-1β, IL-6, and IL-17 were observed at day 30 in the treatment groups, compared to control. However, histological colitis scoring and the expression level of tumor necrosis factor α and IL-10 did not differ significantly between each group. TMSC-CM showed an equivalent effect to TMSC related to the improvement of inflammation in the chronic colitis mouse model. The data obtained support the use of TMSC-CM to treat inflammatory bowel disease without any cell transplantation.
Down‐regulation of miR‐3068‐3p enhances kcnip4‐regulated A‐type potassium current to protect against glutamate‐induced excitotoxicity

The main cause of excitotoxic neuronal death in ischemic stroke is the massive release of glutamate. Recently, microRNAs (miRNAs) have been found to play an essential role in stroke pathology, although the molecular mechanisms remain to be investigated. Here, to identify potential candidate miRNAs involved in excitotoxicity, we treated rat primary cortical neurons with glutamate and found that miR‐3068‐3p, a novel miRNA, was up‐regulated. We hypothesized that restoring miR‐3068‐3p expression might influence the neuronal injury outcomes. The inhibition of miR‐3068‐3p, using tough decoy lentiviruses, significantly attenuated the effects of glutamate on neuronal viability and intracellular calcium overload. To unravel the mechanisms, we employed bioinformatics analysis and RNA sequencing to identify downstream target genes. Additional luciferase assays and western blots validated kcnip4, a Kv4‐mediated A‐type potassium current (IA) regulator, as a direct target of miR‐3068‐3p. The inhibition of miR‐3068‐3p increased kcnip4 expression and vice versa. In addition, the knockdown of kcnip4 by shRNA abolished the protective effect of miR‐3068‐3p, and over‐expressing kcnip4 alone was sufficient to play a neuroprotective role in excitotoxicity. Moreover the inhibition of miR‐3068‐3p enhanced the IA density, and the pharmacological inhibition of IA abrogated the protective role of miR‐3068‐3p inhibition and kcnip4 over‐expression. Therefore, we conclude that inhibition of miR‐3068‐3p protects against excitotoxicity via its target gene, kcnip4, and kcnip4‐regulated IA. Our data suggest that the miR‐3068‐3p/kcnip4 axis may serve as a novel target for the treatment of ischemic stroke.
Need Assessment for Master of Science in Family Nursing Curriculum: Using Delphi Technique

Background & Aims: Our country needs nurses who are expert in family nursing. Accordingly, we need to determine their professional tasks as a basis for future planning regarding establishment of family nursing discipline in Iran. This study was a need assessment for family nursing curriculum using the viewpoints of nursing experts. Material & Methods: It was a need assessment study using Delphi technique. Study population included nursing experts such as members of nursing board in Ministry of Health and Medical Education, vice dean for education and head of the departments in nursing schools in Iran who were selected through cluster multistage sampling and 93 experts participated in the first stage of the study. Data was gathered through Delphi technique and using questionnaire in two stages. The questionnaires were send by post. Focus groups viewpoints were used to complete and finalize the tasks. Data was analyzed using SPSS- PC by calculating mean and standard deviation for each statement. Results: In the first stage of Delphi 56 items in care domain, 34 items in consultation domain, 14 items in research domain and 15 items in management domain were determined. In the second phase of Delphi all tasks received a mean score more than4. At last, 15, 11, 5, and 5 tasks were determined and finalized in care, consultation, and research and management domains, respectively. Conclusion: Findings of the study revealed the importance of family nursing role in care domain especially regarding the care of patients suffering from chronic diseases. The results of this study could be used in curriculum development of family nursing discipline.
Neutrophils suppress tumor‐infiltrating T cells in colon cancer via matrix metalloproteinase‐mediated activation of TGFβ

High T‐cell infiltration in colorectal cancer (CRC) correlates with a favorable disease outcome and immunotherapy response. This, however, is only observed in a small subset of CRC patients. A better understanding of the factors influencing tumor T‐cell responses in CRC could inspire novel therapeutic approaches to achieve broader immunotherapy responsiveness. Here, we investigated T cell‐suppressive properties of different myeloid cell types in an inducible colon tumor mouse model. The most potent inhibitors of T‐cell activity were tumor‐infiltrating neutrophils. Gene expression analysis and combined in vitro and in vivo tests indicated that T‐cell suppression is mediated by neutrophil‐secreted metalloproteinase activation of latent TGFβ. CRC patient neutrophils similarly suppressed T cells via TGFβ in vitro, and public gene expression datasets suggested that T‐cell activity is lowest in CRCs with combined neutrophil infiltration and TGFβ activation. Thus, the interaction of neutrophils with a TGFβ‐rich tumor microenvironment may represent a conserved immunosuppressive mechanism in CRC.
MHC-II-restricted, CD4+ T cell-dependent and -independent mechanisms are required for vaccine-induced protective immunity against Coxiella burnetii.

To understand the role of major histocompatibility complex class I (MHC-I) and class II (MHC-II) in vaccine-mediated protection against C. burnetii, we evaluated the protective efficacy of a formalin-inactivated C. burnetii Nine Mile phase I vaccine (PIV) in beta-2-microglobulin-deficient (B2m KO) and MHC-II-deficient (MHC-II KO) mice. Vaccination reduced disease severity in wild-type (WT) and B2m KO mice, but failed to reduce bacterial burden in MHC-II KO mice. This suggests that the MHC-II antigen presentation pathway is required for PIV-mediated protection against C. burnetii infection. MHC-I and MHC-II affect antibody isotype switching, as both PIV-vaccinated B2m KO and MHC-II KO mice produced less Coxiella-specific IgG than PIV-vaccinated WT mice. Interestingly, MHC-II and CD4 deficiency were not equivalent in terms of splenomegaly and bacterial clearance. This demonstrates a partial role for CD4+ T cells while revealing MHC-II-restricted, CD4-independent mechanisms. Adoptive transfer of CD4+ T cells from PIV-vaccinated WT mice to naïve CD4-deficient (CD4 KO) mice demonstrated that antigen-experienced CD4+ T cells are sufficient to generate protection. Conversely, transfer of naïve CD4+ T cells to PIV-vaccinated CD4 KO mice exacerbates disease. Using Tbet-deficient mice (Tbet KO), we showed a partial role for Th1 subset CD4+ T cells in vaccine protection. Furthermore, Th1-independent roles for Tbet were suggested by significant differences in disease between PIV-vaccinated Tbet KO and CD4 KO mice. Interferon-gamma (IFN-γ) was shown to contribute to the host inflammatory response, but not bacterial clearance. Collectively, these findings suggest that vaccine-induced protective immunity against a murine model of experimental Q fever requires MHC-II-restricted, CD4+ T cell-dependent and -independent mechanisms that can be exploited for a new-generation human Q fever vaccine.