Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors contributing to the inaccuracy and lack of repeatability with the traditional subjective heterophoria measurements

(vergence) to the object of interest in the real world thereby maintaining clear and single binocular vision. Any inaccuracies in the alignment would lead to eye deviations which can be broadly classified into three types: heterophoria, fixation disparity and heterotropia (strabismus). Heterophoria is the relative misalignment of the eyes in the absence of fusion. In other words, it is the eye misalignment measured under dissociated conditions. It can be horizontal, vertical, cyclo deviated or any combination of the above and is typically compensated by the eye’s fusional vergence in the presence of fusion. An inability to compensate this eye misalignment would lead to a manifest deviation called heterotropia or strabismus. Fixation disparity, on the other hand, is the relative misalignment of the eyes in the presence of fusion. This deviation is typically less than the Panum’s fusional area therefore objects in space do not appear double. Conditions related to phoria or fixation disparity are clinically referred to as non-strabismic binocular vision disorders.
Real-time assessment of plant photosynthetic pigment contents with an artificial intelligence approach in a mobile application

The assessment of the photosynthetic pigment contents in plants is a common procedure in agricultural studies and can describe plant conditions, such as their nutritional status, response to environmental changes, senescence, disease status and so forth. In this report, we show how the photosynthetic pigment contents in plant leaves can be predicted non-destructively and in real-time with an artificial intelligence approach. Using a convolutional neural network (CNN) model that was embedded in an Androidbased mobile application, a digital image of a leaf was processed to predict the three main photosynthetic pigment contents: chlorophyll, carotenoid and anthocyanin. The data representation, low sample size handling and developmental strategies of the best CNN model are discussed in this report. Our CNN model, photosynthetic pigment prediction network (P3Net), could accurately predict the chlorophyll, carotenoid and anthocyanin contents simultaneously. The prediction error for anthocyanin was ±2.93 mg/g (in the range of 0-345.45 mg/g), that for carotenoid was ±2.14 mg/g (in the range of 0-211.30 mg/g) and that for chlorophyll was ±5.75 mg/g (in the range of 0-892.25 mg/g). This is a promising result as a baseline for the future development of IoT smart devices in precision agriculture.
Complete mitochondrial genome of Cyclograpsus intermedius Ortmann, 1894 (Crustacea: Decapoda: Grapsoidea) specimen collected in South Korea

Abstract In this study, the complete 16,184 bp mitochondrial genome of Cyclograpsus intermedius was determined from a specimen collected in South Korea. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and a non-coding A + T rich region. The base composition of the heavy strand in the mitochondrial genome was 34.7% A, 10.7% G, 18.7% C, and 35.9% T, resulting in a G + C content of 29.4%. A maximum-likelihood phylogenetic tree based on the 13 mitochondrial protein-coding genes showed that C. intermedius clustered together with the Varunidae. These molecular data will be useful for studying the evolutionary relationships among crab species.
The complete chloroplast genome sequence of Camellia sinensis cv. Dahongpao: a most famous variety of Wuyi tea (Synonym: Thea bohea L.)

Abstract Here, combining PacBio and Illumina sequencing data, we reported the complete chloroplast genome of the first Wuyi tea (Bohea), Camellia sinensis cv. Dahongpao (DHP) with very high economic value. The chloroplast genome was 157,077 bp in length, with a large single copy (LSC) region of 86,633 bp, a small single-copy (SSC) region of 18,282 bp, separated by two inverted repeat (IR) regions of 26,081 bp each. It contained a total of 137 genes, with an overall GC content of 37.29%. The phylogenetic analysis showed that DHP was sister to C. sinensis cv. Longjing.
The Prevalence of Fibromyalgia Among Medical Students at King Abdulaziz University: A Cross-Sectional Study

Background and objective Fibromyalgia (FM) is a chronic, multifactorial pain condition. The latest literature suggests that genetic and environmental factors including continuous stress contribute significantly to FM's pathophysiology. In this study, we aimed to investigate the prevalence of FM among medical students as they are considered a population significantly at risk of developing the condition. Methods This cross-sectional study was conducted at King Abdulaziz University. Medical students included in the study were recruited through a random stratified sampling method. A self-administered questionnaire was distributed to the participants; it included questions related to widespread pain index (WPI) and symptom severity scale (SSS) to assess the symptoms and diagnosis of FM, which were established based on the current diagnostic criteria. All first-year students were excluded from this research. Results A total of 450 participants were recruited for the study. Among them, 291 (64.7%) were females and 159 (35.3%) were males. Their ages ranged from 18 to 26 years, and the mean age was 21.52 years (SD: ±1.52). They came from different academic levels: 97 (21.6%) were in the second year, 79 (17.6%) were in the third year, 70 (15.6%) were in the fourth year, 99 (22%) were in the fifth year, and 105 (23.3%) were in the sixth year. The overall prevalence of FM was found to be 43 (9.6%). It was established based on the number of students who fulfilled the diagnostic criteria or were previously diagnosed with FM by a professional physician. Conclusion FM is highly prevalent among medical students. Our findings demonstrate the likelihood of the influence of medical school on causing the condition, as it has a stressful education system with high academic expectations. We recommend that this issue be seriously addressed since FM leads to a significant burden on the students and can negatively affect their future medical practice.
Chloroplast genome structure and phylogenetic position of Lophatherum gracile

Abstract Lophatherum gracile is distributed in south China, Japan and South Asia, and it is wild in the valley, stream, woodland, forest edge and gully edge. In this study, the complete chloroplast genome sequence of Lophatherum gracile was successfully obtained using Illumina sequencing. The full length of the chloroplast genome length was 137,749 bp with a typical quadripartite structure: one large single copy (LSC) region (80,610 bp), one small single copy (SSC) region (12,429 bp), and a pair of inverted repeats (IRs) (22,355 bp each). The GC content of this genome was 38.64%. The whole genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that Lophatherum gracile was closely related to Cenchrus americanus and Cenchrus longispinus.
Quasi-physical model for fast resist contour simulation: importance of lens aberrations and acid diffusion in LSI pattern design

The aberration in optics and acid diffusion in resist films have a great influence on proximity effects in optical lithography. Our analysis clarified that (1) a local (random) pupil-phase variation (higher-order aberration) degrades imaging performance under highly coherent illumination often used with periodic phase-shifting masks, and (2) in some positive-tone chemically amplified resists, the non-Fickean diffusion process changes effective image distributions, depending on the patterns features and mask tonality. Although the latter has a potential to achieve high resolution capability for isolated bright features, these effects generally pronounce proximity effects and make their correction difficult. Simple modeling of these effects and their simulation implementation are also discussed.
The complete chloroplast genome of Cymbidium hookerianum (Orchidaceae): genome structure and basic analysis

Abstract Cymbidium hookerianum Rchb.f. is an ornamental orchid with large flowers and delicate aroma. Here, we reported the complete chloroplast genome sequence of C. hookerianum. The total chloroplast genome cycle was 155,447 bp. It displayed a typical structure including one large single-copy (LSC, 84,186 bp) region, one small single-copy (SSC, 17,839 bp) region, and two inverted repeat (IRs, 26,711 bp). 124 genes (78 CDSs, 38 tRNAs, 8 rRNAs) were encoded by the cp genome. The average GC content of this sequence was 36.8%. The phylogenetic analysis revealed C. hookerianum and C. changningense are sisters. The groundwork of chloroplast genome would provide available reference for molecular taxonomy and breeding.
Enterococcus faecalis shifts macrophage polarization toward M1-like phenotype with an altered cytokine profile

ABSTRACT Background: The macrophage is an innate immune defense cell involved in pathogen recognition and clearance. Aim: In view of the diversity of the macrophage phenotype and function, the present study investigated how Enterococcus faecalis infection affects the differentiation, phenotype and cytokine profile of macrophages. Methods: Murine bone marrow-derived stem cells were co-cultured with E. faecalis before and after differentiation. Macrophage M0 polarization towards M1 or M2 was initiated at day 6 by addition of LPS and INF-γ, or IL-4 and IL-13, respectively. Results: E. faecalis did not inhibit macrophage differentiation and were identified within macrophages. Viability of the macrophages infected with E. faecalis prior to differentiation was enhanced, evidenced by apoptosis inhibition, as was expression of CD38 and IRF5 proteins, indicators of M1-like polarization. These M1-like macrophages expressed an aberrant cytokine mRNA profile, with reduction in inflammatory cytokines IL-1β and IL-12 and increase in regulatory cytokine IL-10. No changes in TNF-α or TGF-β1 were detected, compared with the control groups. This atypical M1-like phenotype was retained even upon stimulation with growth factors that normally trigger their development into M2 macrophages. Conclusions: These findings suggested that E. faecalis infection of bone marrow-derived stem cells during differentiation into macrophages induces an atypical M1-like phenotype associated with intracellular bacterial survival.
Risk Factors Associated with Helminthic Intestinal Infection in Lurambi Subcounty, Kakamega, Kenya

Background Soil-transmitted helminths (STHs) and schistosome infections have been known to be major causes of morbidity and mortality in sub-Saharan countries. School aged and preschool children are known to be at high risk of infection. Therefore, the aim of this study was to determine the prevalence and risk factors associated with soil-transmitted helminths among school-going children in Lurambi Subcounty, Kakamega, Kenya. Method A cross-sectional study was conducted from Jan 2020 to Feb 2020 among 392 randomly selected primary school-going children aged 5 to 14 years old in six primary schools. Risk factors associated with STH infection were obtained using a structured questionnaire answered by the children's caregivers. Stool samples were examined using the standard quantitative Kato-Katz technique. The data was analyzed using SPSS version 20 and Epi Info version 7.2. 3.1. Result A total of 278 children provided stool samples for analysis. The overall prevalence of intestinal helminths was 14.4% (40/278). The prevalence of Ascaris lumbricoides was 11.5% (32/278), 0.4% (1/278) for hookworm, 0.4% (1/278) for Trichuris trichiura, and 2.1% (6/278) for Schistosoma mansoni; coinfection was detected in 0.4% (1/278). The intensity of infection ranged between light and moderate. Significant risk factors for STH infection included failure to wash hands before eating (OR: 3.529; P = 0.041), failure to wash fruits and vegetables before eating (OR: 2.3129; P = 0.005), and not washing hands after soil contact (OR: 2.1529; P = 0.005). Age (Z = 2.4006, P = 0.0164) was a risk factor only for infection with Schistosoma mansoni. Conclusion Preventive chemotherapy and proper hygienic and sanitation practices should be integrated to achieve elimination of STH and Schistosoma mansoni in Lurambi Subcounty and at large in Kenya.
17-Hydroxyprogesterone Caproate for the Prevention of Recurrent Preterm Birth – A Systematic Review and Meta-analysis Taking into Account the PROLONG Trial

Background Prior spontaneous preterm birth is a strong risk factor for the recurrence of spontaneous preterm birth in a subsequent pregnancy and has been evaluated in prevention studies using progesterone (natural progesterone administered orally or vaginally, and 17-hydroxyprogesterone caproate [17-OHPC]) as a selection criterion. Based on the findings of a randomized, placebo-controlled study, 17-OHPC was approved for use in 2011 by the Food and Drug Administration in the USA for the prevention of recurrent preterm birth. The approval was granted with qualification that a subsequent confirmatory study would need to be carried out, the results of which have just been published (PROLONG trial). Method A systematic literature search for the period from 1970 to April 2020 using the search terms “preterm birth” and “17-OHPC” or “progesterone” was carried out. Only randomized, placebo-controlled studies of women with singleton pregnancies who received 17-OHPC to prevent recurrent preterm birth were included in the subsequent meta-analysis. The relative risk and associated 95% confidence intervals were calculated. The heterogeneity between studies was evaluated with I 2 statistics. Results In addition to the original study used for the approval and the PROLONG trial, only one other study was found which met the inclusion criteria (total number of patients: 2221). With considerable heterogeneity between the studies, particularly with respect to the risk factors for preterm birth, the comparison between 17-OHPC and placebo showed no significant reduction in preterm birth rates before 37, 35 and 32 weeks of gestation and no significant differences with regard to the prevalence of miscarriage before 20 weeks of gestation or fetal deaths (antepartum or intrapartum) after 20 weeks of gestation and neonatal morbidity. Conclusion Based on the currently available data, 17-OHPC cannot be recommended for the prevention of recurrent preterm birth. Further randomized, placebo-controlled studies with clearly defined, comparable risk factors are required to identify the group of pregnant women which could benefit from the use of 17-OHPC to prevent preterm birth.
NAMPT/SIRT1 Attenuate Ang II-Induced Vascular Remodeling and Vulnerability to Hypertension by Inhibiting the ROS/MAPK Pathway

Hypertension is characterized by endothelial dysfunction, vascular remodeling, and rearrangement of the extracellular matrix. Besides, the pathogenesis of hypertension is closely related to excess generation of reactive oxygen species (ROS). Nicotinamide phosphoribosyltransferase (NAMPT) is a rate-limiting enzyme in nicotinamide adenine dinucleotide (NAD) biosynthesis that influences the activity of NAD-dependent enzymes, such as sirtuins, which possess NAD-dependent protein deacetylase activity and cleave NAD during the deacetylation cycle. Recently, NAMPT has been shown to play a crucial role in various diseases associated with oxidative stress. However, the function and regulation of NAMPT in hypertension have not been extensively explored. In the present study, we identified NAMPT as a crucial regulator of hypertension, because NAMPT expression was significantly downregulated in both patients with hypertension and experimental animals. NAMPT knockout (NAMPT+/-) mice exhibited a significantly higher blood pressure and ROS levels after stimulation with angiotensin II (Ang II) than wild-type mice, and the administration of recombinant human NAMPT (rhNAMPT) reversed this effect. In vivo, overexpression of NAMPT protected against angiotensin II- (Ang II-) induced hypertension by inhibiting ROS production via sirtuin 1 in mouse aortic endothelial cells (MAECs) and mouse aortic vascular smooth muscle cells (MOVAs). In turn, NAMPT alleviated the ROS-induced mitogen-activated protein kinase (MAPK) pathway. In conclusion, NAMPT might be a novel biomarker and a therapeutic target in hypertension.
NR2F1-AS1/miR-140/HK2 Axis Regulates Hypoxia-Induced Glycolysis and Migration in Hepatocellular Carcinoma

Background Hypoxia is an important feature for the progression of hepatocellular carcinoma (HCC). Long noncoding RNA nuclear receptor subfamily 2 group F member 1 antisense RNA 1 (NR2F1-AS1) is dysregulated in HCC. However, the role and mechanism of N2RF1-AS1 in hypoxia-induced glycolysis and migration remain unclear. Materials and Methods Tumor tissues and adjacent samples were harvested from 40 HCC patients. HCC cells were treated by hypoxia. The levels of NR2F1-AS1, microRNA (miR)-140, and hexokinase 2 (HK2) were examined via quantitative reverse transcription polymerase chain reaction or Western blot. Glycolysis was analyzed via glucose uptake, lactate production, and adenosine triphosphate (ATP) levels. Cell migration was analyzed via transwell assay. The target association was analyzed via dual-luciferase reporter assay and RNA immunoprecipitation. Results NR2F1-AS1 level was enhanced in HCC tissues and cells. High expression of NR2F1-AS1 indicated poor overall survival. Silence of NR2F1-AS1 repressed hypoxia-induced glycolysis and migration in HCC cells. NR2F1-AS1 could regulate HK2 expression by modulating miR-140. miR-140 down-regulation or HK2 up-regulation mitigated the influence of NR2F1-AS1 silence on hypoxia-induced glycolysis and migration in HCC cells. Conclusion NR2F1-AS1 knockdown restrained hypoxia-induced glycolysis and migration in HCC cells via increasing miR-140 and decreasing HK2.
Ophiopogonin D Increases SERCA2a Interaction with Phospholamban by Promoting CYP2J3 Upregulation

Ophiopogonin D (OPD), a compound from the Chinese herb Radix Ophiopogonis, reportedly induces increased levels of cytochrome P450 2J3 (CYP2J3)/epoxyeicosatrienoic acids (EETs) and Ca2+ in rat cardiomyocytes. Little is known regarding the specific mechanism between CYP2J3 and Ca2+ homeostasis. Here, we investigated whether CYP2J3 is involved in the protective action of OPD on the myocardium by activating the Ca2+ homeostasis-related protein complex (SERCA2a and PLB) in H9c2 rat cardiomyoblast cells. The interaction between SERCA2a and PLB was measured using fluorescence resonance energy transfer. OPD attenuated heart failure and catalyzed the active transport of Ca2+ into the sarcoplasmic reticulum by inducing the phosphorylation of PLB and promoting the SERCA2a activity. These beneficial effects of OPD on heart failure were abolished after knockdown of CYP2J3 in a model of heart failure. Together, our results identify CYP2J3 as a critical intracellular target for OPD and unravel a mechanism of CYP2J3-dependent regulation of intracellular Ca2+.
Characterization of the complete mitochondrial genome of Ostorhinchus novemfasciatus and phylogenetic studies of Apogoninae

Abstract The complete mitochondrial genome of Ostorhinchus novemfasciatus was first presented in this study. The full length of the mitochondrial genome was 16,779 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.0% A, 30.2% C, 26.2% T and 17.5% G. 12 PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of O. novemfasciatus described in this study could be a useful basis for the management of this species and laid a foundation for further research involved with phylogenetic relationship within Apogoninae.
Silica−Dimethylsiloxane HybridsNon-Hydrolytic Sol−Gel Synthesis and Characterization by NMR Spectroscopy

The non-hydrolytic sol−gel process provides a facile route to silica−dimethylsiloxane (DMS) hybrids starting from silicon(IV) chloride, tetraethoxysilane (TEOS), and hexamethylcyclotrisiloxane, D3. Both the non-hydrolytic sol−gel silica synthesis and ring-opening polymerization of the D3 are initiated simultaneously by the presence of an iron(III) chloride catalyst. Evidence for the structures of these hybrids is presented from the results of solid-state 2D NMR correlation spectroscopy. The siloxane component consists of short D units, which show good compatibility with the silica on a molecular level, probably as a result of copolymerization between Q and D units.
Decreased Ecological Resistance of the Gut Microbiota in Response to Clindamycin Challenge in Mice Colonized with the Fungus Candida albicans

Candida albicans is the most common fungal member of the human gut microbiota, yet its ability to interact with and affect the bacterial gut microbiota is largely uncharacterized. Previous reports showed limited changes in microbiota composition as defined by bacterial species abundance as a consequence of C. albicans colonization. ABSTRACT The mammalian gut microbiota is a complex community of microorganisms which typically exhibits remarkable stability. As the gut microbiota has been shown to affect many aspects of host health, the molecular keys to developing and maintaining a “healthy” gut microbiota are highly sought after. Yet, the qualities that define a microbiota as healthy remain elusive. We used the ability to resist change in response to antibiotic disruption, a quality we refer to as ecological resistance, as a metric for the health of the bacterial microbiota. Using a mouse model, we found that colonization with the commensal fungus Candida albicans decreased the ecological resistance of the bacterial microbiota in response to the antibiotic clindamycin such that increased microbiota disruption was observed in C. albicans-colonized mice compared to that in uncolonized mice. C. albicans colonization resulted in decreased alpha diversity and small changes in abundance of bacterial genera prior to clindamycin challenge. Strikingly, co-occurrence network analysis demonstrated that C. albicans colonization resulted in sweeping changes to the co-occurrence network structure, including decreased modularity and centrality and increased density. Thus, C. albicans colonization resulted in changes to the bacterial microbiota community and reduced its ecological resistance. IMPORTANCE Candida albicans is the most common fungal member of the human gut microbiota, yet its ability to interact with and affect the bacterial gut microbiota is largely uncharacterized. Previous reports showed limited changes in microbiota composition as defined by bacterial species abundance as a consequence of C. albicans colonization. We also observed only a few bacterial genera that were significantly altered in abundance in C. albicans-colonized mice; however, C. albicans colonization significantly changed the structure of the bacterial microbiota co-occurrence network. Additionally, C. albicans colonization changed the response of the bacterial microbiota ecosystem to a clinically relevant perturbation, challenge with the antibiotic clindamycin.