Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity hotspots and refugia identified by mapping multi-plant species haplotype diversity in China

Historical processes during the Quaternary are likely to have left a signature on the geographical distribution of intraspecific genetic variation. In particular, high genetic uniqueness could be expected within glacial refugia for multiple species. We aimed to test this for plants in China and whether multi-species hotspots of genetic diversity are good indicators of glacial refugia in this region. From chloroplast DNA haplotype data for 116 species we calculated two local genetic diversity metrics for each species: haplotype genetic richness and genetic uniqueness. From these two, only uniqueness could reliably identify refugia, whereas richness may indicate either glacial refugia or areas recolonized by genetic lineages from different refugia in the postglacial period. Our results suggest the occurrence of numerous cryptic refugia and their likely importance in the maintenance and evolution of the Chinese flora, and indicate that an approach that locates geographic hotspots of genetic diversity data can reliably identify refugia.
The MRL/MpJ Mouse Strain Is Not Protected From Muscle Atrophy And Weakness After Rotator Cuff Tear

Chronic rotator cuff tears are a common source of shoulder pain and disability. Patients with rotator cuff tears often have substantial weakness, fibrosis, and fat accumulation which limit successful surgical repair and postoperative rehabilitation. The Murphy Roths Large (MRL) strain of mice have demonstrated superior healing and protection against pathological changes in several disease and injury conditions. We tested the hypothesis that, compared to the commonly used C57Bl/6 (B6) strain, MRL mice would have less muscle fiber atrophy and fat accumulation, and be protected against the loss in force production that occurs after cuff tear. Adult male mice B6 and MRL mice were subjected to a rotator cuff tear, and changes in muscle fiber contractility and histology were measured. RNA sequencing, and shotgun metabolomics and lipidomics were also performed. Muscles were harvested one month after tear. B6 and MRL mice had a 40% reduction in relative muscle force production after rotator cuff tear. RNA sequencing identified an increase in fibrosis-associated genes and a reduction in mitochondrial metabolism genes. Markers of glycolytic metabolism increased in B6 mice, while MRL mice appeared to increase amino acid metabolism after tear. There was an accumulation of lipid after injury, although there was a divergent response between B6 and MRL mice in the types of lipid species that accrued. There were strain-specific differences between the transcriptome, metabolome, and lipidome of B6 and MRL mice, but these differences did not protect MRL mice from weakness and pathological changes after rotator cuff tear.
Search For Gut Microbiota-Mediated Composition And Influence In Type 2 Diabetes

Type 2 diabetes mellitus (T2DM) has proven to be of utmost importance in clinical care, having been diagnosed in more than 29 million Americans in 2012 ("Statistics about Diabetes," 2012). The microbiome has a strong influence in the development of diabetes, but the relationship is not well understood. Methods: This current study utilized diabetic and nondiabetic porcine fecal samples, focusing on bacteria of interest from pre-existing studies to observe bacterial changes in the gut related to type 2 diabetes. We aimed to characterize the microbiota both compositionally and functionally. Relative abundance comparisons and retrospective analysis of the literature allowed a preliminary analysis of the alteration of the microbiota which may contribute to the consequent dysglycemia characteristic of type 2 diabetes. Results: Our results revealed, at the genus level, a significant decrease of intestinal bacterium Roseburia (p<0.0001) and Bacteroides (p=0.018) in the gut microbiome of diabetic compared to the non-diabetic porcine. Conclusion: This study revealed preliminary relationships between gut microbiome and diabetes in a prorcine model. Roseburia, which was decreased in the diabetic microbiome, has been associated with anti-inflammatory mechanisms activated by the short chain fatty acid (SCFA) butyrate. This study found the pig to be a strong model for analysis. Further study may help with understanding potential mechanisms linking SCFA, the microbiome and diabetes. A more comprehensive analysis of taxonomic resolution of the gut microbiome to better define these complex interconnections is needed. A deeper understanding of the impact of this interaction on diabetes could help with the development of more targeted prevention mechanisms for at-risk populations and better management for diabetic patients.
Primary cilia deficiency in neural crest cells causes Anterior Segment Dysgenesis

During eye embryogenesis, neural crest cells (NCC) of the periocular mesenchyme (POM) migrate to the anterior segment (AS) of the eye and then differentiate into the corneal stroma and endothelium, ciliary body, iris stroma, and the trabecular meshwork. Defective development of these structures leads to anterior segment dysgenesis (ASD) that in 50% of the cases leads to glaucoma, a leading cause of blindness. Here, we show that the primary cilium is indispensable for normal AS development and that its ablation in NCC induces ASD phenotypes including; small and thin cornea, impaired stromal keratocyte organization, abnormal iridocorneal angle with reduced anterior chamber and corneal neovascularization. These defects are similar to those described in patients with AS conditions such as Axenfeld-Rieger syndrome and Peter’s anomaly. Mechanistically, disruption of the primary cilium in the NCC resulted in reduced hedgehog (Hh) signaling in the POM, canonically activated by the Indian Hedgehog ligand expressed by endothelial cells of the choroid. This caused decreased cell proliferation in a subpopulation of POM cells surrounding the retinal pigmented epithelium. Moreover, primary cilium ablation in NCC also led to a decreased expression of Foxc1 and Pitx2, two transcription factors identified as major ASD causative genes. These findings suggest that primary cilia are indispensable for NCC to form normal AS structures via Hh signaling. Defects in primary cilia could, therefore, contribute to the pathogenesis of ASD, and to their complications such as congenital glaucoma.
Evaluation of Isfahan Inhabitant Attitude About Brucellosis and Common its Herbal Treatment

treatment. Patients and Methods: This evaluation was a simple random sample study, which was carried out on 162 people in the city of Isfahan, Iran, by means of questionnaires. The data was analyzed using SPSS for Windows (Version 21.0). Results: Of 162 people that were interviewed, 90 (55.6%) patients were male and the other were female. Of these, 74 (45.7%) patients were single and 88 (54.3%) were married. Forty-three (26.5%) participants lived in the city. The average age of participants was 11.51 ± 29.11 years. There is no significant relationship between age, gender, education level, residence, and people familiar with the disease brucellosis, herbal treatment for brucellosis (P > 0.05). Conclusions: Our data suggest that the demographic and socioeconomic characteristics of people in Isfahan, Iran, show no relationship with the attitude of individuals regarding brucellosis and towards common herbal treatments for the disease.
Gut-Liver physiomimetics reveal paradoxical modulation of IBD-related inflammation by short-chain fatty acids

Association between the microbiome, IBD and liver diseases are known, yet cause and effect remain elusive. By connecting human microphysiological systems of the gut, liver and circulating Treg/Th17 cells, we modeled progression of ulcerative colitis (UC) ex vivo. We show that microbiome-derived short-chain fatty acids (SCFA) may either improve or worsen disease severity, depending on the activation state of CD4 T cells. Employing multiomics, we found SCFA increased production of ketone bodies, glycolysis and lipogenesis, while markedly reducing innate immune activation of the UC gut. However, during acute T cell-mediated inflammation, SCFA exacerbated CD4+ T cell effector function, partially through metabolic reprograming, leading to gut barrier disruption and hepatic injury. These paradoxical findings underscore the emerging utility of human physiomimetic technology in combination with systems immunology to study causality and the fundamental entanglement of immunity, metabolism and tissue homeostasis.
Neuroblastoma rat sarcoma mutated melanoma: That’s what we got so far

Neuroblastoma rat sarcoma (NRAS) mutation, occurring in about 20%–30% of cutaneous melanomas, leads to activation of RAS‐RAF‐MAPK cascade and represents a clear distinct clinicopathological entity in melanoma. In contrast with BRAF mutant melanoma, no specific target therapies are available outside the setting of clinical trials. In the field of immunoncology, the predictive role of NRAS mutation with respect to checkpoint inhibitors treatment has not clearly established and deserves further investigation. At present, the standard treatment is the same as for BRAF wild type melanoma. Ongoing trials are exploring novel combination strategies among patients with advanced NRAS mutant melanoma.
Phylogenetic history of Auroraceratops rugosus (Ceratopsia: Ornithischia) from the Lower Cretaceous of Gansu Province, China

Abstract Basal neoceratopsians are a relatively diverse group of small- to medium-sized herbivorous dinosaurs from the Early to Late Cretaceous of Asia and North America. Although known for over a century, this group has only relatively recently received intense independent study, tied to the rapid increase in known diversity since 1997. Auroraceratops rugosus is one of these recently discovered species and is one of the best-known basal neoceratopsians, being represented by over 80 specimens, and is also the most completely represented neoceratopsian from the Early Cretaceous. A phylogenetic analysis focusing on non-ceratopsid ceratopsians examines the phylogenetic context of Auroraceratops. The analysis is based on a new matrix of 41 taxa and 257 characters. The results recover an Auroraceratops-Aquilops-ZPAL MgD-I/156 clade within basal Neoceratopsia that is sister to a clade composed of Asiaceratops, Yamaceratops, Mosaiceratops, and the larger clades Leptoceratopsidae and Coronosauria. This phylogeny recovers a monophyletic Coronosauria, Leptoceratopsidae, and Protoceratopsidae. Helioceratops is recovered as sister to the rest of Leptoceratopsidae, Ischioceratops is recovered nested within Leptoceratopsidae, and the enigmatic genus Mosaiceratops is recovered as a basal neoceratopsian, sister to Yamaceratops. Yinlong, and Hualianceratops are recovered in an expanded Chaoyangsauridae, and the genus Psittacosaurus is recovered as the earliest diverging lineage in Ceratopsia. Ajkaceratops, the only European ceratopsian, is robustly recovered as sister to the rest of Ceratopsoidea. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline. com/UJVP Citation for this article: Morschhauser, E. M. , H. You, D. Li, and P. Dodson. 2019. Phylogenetic history of Auroraceratops rugosus (Ceratopsia: Ornithischia) from the Lower Cretaceous of Gansu Province, China; pp. 117–147 in Hailu You, Peter Dodson, and Eric Morschhauser (eds.), Auroraceratops rugosus (Ornithischia, Ceratopsia) from the Early Cretaceous of northwestern Gansu Province, China. Society of Vertebrate Paleontology Memoir 18. Journal of Vertebrate Paleontology 38(Supplement). DOI: 10.1080/02724634.2017. 1509866.
THE ASSOCIATION OF ORPHAN AND VULNERABLE CHILD (OVC) PRIMARY CAREGIVING, HOUSEHOLD WEALTH, AND FEMALE AUTONOMY ON WOMEN'S BODY MASS INDEX IN NAMIBIA, SWAZILAND AND ZAMBIA

Background: This dissertation investigates factors associated with orphan and vulnerable child (OVC) caregivers' body mass index (BMI) in Namibia, Swaziland and Zambia. Methods: Secondary analyses were performed using cross-sectional data from Demographic Health Surveys conducted in 2006 and 2007. Manuscript 1 included de facto women from Namibia (n=6,638), Swaziland (n=3,285), and Zambia (n=4,497). Manuscript 2 included de jure women from Namibia (n=6,305), Swaziland (n=2,786), and Zambia (n=4,389). Manuscript 3 included married de jure women from Namibia (n=2,633), Swaziland (n=1,395), and Zambia (n=2,920). Statistical analyses using data from 20-49 year old women included weighted marginal means, logistic regression, and Sobel and Goodman tests. Results: Manuscript 1. OVC caregivers' overweight prevalence ranged from 26.98% (Namibia) to 61.3% (Swaziland). Namibian OVC caregivers were less likely to be overweight than non-OVC caregivers and non-caregivers not living with OVC. Swazi and Zambian OVC caregivers were more likely to be overweight than non-caregivers. In Namibia, women's age modified the effect of the association between OVC caregiving and overweight status. Manuscript 2. Namibian and Swazi OVC caregivers had lower Absolute Wealth Index (AWI) mean scores than non-OVC caregivers and non-caregivers. In Zambia, OVC caregivers had a lower mean AWI score than non-caregivers living with an OVC but a higher mean AWI score than non-OVC caregivers. In all countries, even small increases in household wealth (e.g., being a poorer women - 2 to 3 AWI items) were associated with higher odds for being overweight regardless of women's caregiving status. Manuscript 3. Women's educational attainment increased the odds for being overweight in Swaziland and Zambia, and decreased the odds for being underweight in Namibia. Decision-making autonomy mediated the association between AWI and OVC caregivers' BMI in Zambia (Z=2.13, p=0.03). Conclusions. As Africa is experiencing a nutritional and HIV/AIDS transition, overweight problems among OVC caregivers has emerged and should be addressed. These findings support the World Health Organization's recommendations that African countries should focus on addressing infectious diseases as well as the emergence of chronic diseases. Some African public health systems and OVC programs may face a new overweight epidemic alongside existing ones such as HIV/AIDS, tuberculosis, and malaria.
Supply chain management : a model for implementation for SMEs in Saudi Arabia

With markets going global and competitions turning intense, Organizations are fast realizing the immense potential of a proactive Supply Chain Management (SCM) to improving their market positions in this cut-throat business environment. The research aims at developing a supply chain framework model that enables SMEs to improve their SCM performance and to have a sustainable business growth in dynamic environment. To fulfill the foremost aim, the following objectives have been set as follows. To fulfill the foremost aim, the following objectives have been set: 1. To contribute to the bod of knowledge to the both Supply Chain Management and Saudi Arabian SMEs manufacturing by reviewing pertinent literature of the same field. Knowledge in this study refers to as information, understanding and skills that one gain during research and education. 2. To investigate the current SCM practice of Saudi Arabia SMEs manufacturing sector by explorative approach, broad reliable and valid survey questionnaires distributed to 320 SMEs companies (Chapter 4). 3. To identify the gap within the current supply chain dimensions of SMEs against world class companies (Chapter 5) by statistical analyzing the survey questionnaires developed in chapter four. 4. To suggest appropriate methodological design using robust techniques that is to developed framework model (Chapter 6). 5. To develop qualitative assessment approach in the form of focus group to theoretically and practically validate and test the framework model ( Chapter 6). 6. To benchmark the developed model with different model in the same field. A sample of 150 of Saudi Arabia SMEs within the manufacturing sector was surveyed aimed at identifying the gap between SCM practices as adopted by the world class organizations and the actual practices adopted by SMEs under investigation. The research carried out using multiple research methods, i.e. quantitative and qualitative methods. This is mainly to gain multiple perspectives on the issue and filter out the real problem to be understood and worked upon. The framework model was developed based on literature review, other works in the same field, and the results of the field work study (survey) and the working experience of the researcher in the manufacturing sector for more than 20 years. The model was validated theoretically and practically with a predetermined selected manufacturing company. The significance of the research work could be best understood from the overall results which make important contributions to supply chain management system. The study is significant as it aids in better understanding of an issue which is of increasing importance to both the organizational practice and academic literature.
Frequency and variation of neural tube defects at Liaquat University Hospital Jamshoro, Sindh, Pakistan

Background: Neural tube defects (NTDs) are a group of congenital malformations of the neural tube. The incidence of NTDs in Pakistan is 13.90 per 1000 deliveries. Such type of study in our setup is conducted for the first time which shows that different varieties of (NTDs) are seen commonly in our setup also. Methods: This descriptive study was conducted in department of Neurosurgery of Liaquat University Hospital Jamshoro, Sindh Pakistan with collaboration of department of Anatomy of Liaquat University of Medical and Health Sciences Jamshoro to determine the frequency and variations of neural tube defects seen in this institution. 45 patients with (NTDs) were included in the study. O ut of 45 patients 18 were males and 27 were females. All were admitted through the outpatient department. The type of anomaly was recorded with other bio data. Results: In this study Hydrocephalous accounts for 25 cases (55.5%), hydrocephalus with meningocele in 01 case (2.2%) and hydrocephalus with encephalocele in 02 cases (4.4%) in addition is seen. Myelomeningocele seen in 04 cases (8.8%), Meningocele in 06 cases (13.3%), congenital dermal sinus and dandy walker syndrome 01 (2.2%) cases of each, also seen in this study 01 cases of Lipomyelocele with mengiocele and 01 case of Encephalocele with microcephaly which accounts for 2.2% of all neural tube defects. Conclusions: The high occurrence of NTDs observed in this study calls for a special attention. A nationwide surveillance can recognize the disease burden in pre & post-natal period and related risk factors to plan future strategies for prevention, early diagnosis and timely management.
Enhancement of H2O2 decomposition by the synergistic effect on CuO-MnFe2O4 nanoparticles for sulfamethoxazole degradation over a wide pH range

Abstract Advanced treatment of micro-polluted water is a hot research topic at present. The construction of transition metal oxide-based Fenton-like reaction can effectively remove antibiotics from micro-polluted water. Magnetic CuO-MnFe2O4 nanoparticles, a type of nontoxic trimetallic transition metal oxides, is a promising heterogeneous catalyst for H2O2 activation over a wide pH range. In this study, the activation of H2O2 by CuO-MnFe2O4 nanoparticles is evaluated using sulfamethoxazole as a model reactant. The as-prepared CuO-MnFe2O4 nanoparticles exhibited excellent capability for sulfamethoxazole degradation over a wide pH range. Under the optimal conditions (0.5 g/L catalyst, 10 mM H2O2 and 5 mg/L SMX), 99.2% removal efficiency and 58.5% TOC removal were achieved within 30 minutes. According to quenching experiments and ESR analysis, ·O2 −/·OH/1O2 were generated in CuO-MnFe2O4/H2O2 system, ·OH and 1O2 were main active species. XPS analysis indicated that there existed a synergistic effect between CuO and MnFe2O4, while the generated 1O2 were probably derived from lattice oxygen and hydroxylate oxygen in CuO-MnFe2O4 nanoparticles. The CuO-MnFe2O4 nanoparticles are effective, environmental friendliness and low-cost catalysts for H2O2 activation over a wide pH range. These features make CuO-MnFe2O4 nanoparticles be a promising heterogeneous catalyst in Fenton-like reaction to process sulfamethoxazole in micro-polluted water. Graphical Abstract
Enhanced Nonlinear Yield from Barium Titanate Metasurface Down to the Near Ultraviolet

Metasurfaces are artificial nanopatterned 2D architectures that can offer a solution to the bottleneck problem of bulky optical elements. They have the ability of wavefront shaping and light sub‐wavelength manipulation because they are formed of resonantly scattering elements. Recently, the properties of metasurfaces gained interest for nonlinear optics in the efforts to miniaturize nonlinear optical devices while maintaining high photon–photon interactions. Herein, a new type of nonlinear metasurface based on the metal oxide barium titanate is developed, which demonstrates an efficient nonlinear optical response over a broad spectral range, from near‐ultraviolet to the visible range, where metals and semiconductors typically have losses. Contrary to previously demonstrated nonlinear plasmonic metasurfaces, these dielectric metasurfaces are less sensitive to surface roughness and gain their optical nonlinearity from the noncentrosymmetric crystal structure of the ferroelectric barium titanate.
Plasma‐activated methane partial oxidation reaction to oxygenate platform chemicals over Fe, Mo, Pd and zeolite catalysts

Natural gas from stranded sources is being predominantly flared, and there is a growing demand for new technologies for its utilisation, where electrification, flexibility, and modularity play an important role. Plasma‐activated methane partial oxidation reaction was studied in a designed dielectric barrier discharge ionisation reactor unit, producing value‐added platform chemicals, namely, methanol, formaldehyde, intermediate formic acid, acetic acid, and paraformaldehyde at ambient temperature and atmospheric pressure. The effects of various process parameters, such as voltage, total convertible gas flow rate, and reagent ratio relationship, were considered. In addition, coupling of the following catalytic materials with plasma was examined: alumina (Al2O3), chabazite, ferrierite, microporous beta zeolite, silica (SiO2) glass beads, ZSM‐5 (MFI), Fe on H‐ZSM‐5 and Al2O3, Mo on H‐ZSM‐5, TiO2 and SiO2, and Pd on Al2O3. In the liquid product, 21.5% CH3OH, 20.4% CH2O, 0.3% HCOOH, and 2.4% CH3COOH were measured when using pure plasma, and a maximum aggregate yield of the organic oxygenate compounds of 5.21 mol. % was achieved. The usage of shaped silicate surface increased the selectivity towards synthesised oxygen‐containing structures, while the application of alumino‐silicate mixture constituents reduced it. It was determined that elementary covalently bonded carbon was formed inside pores when pure zeolites were used. Fe‐ and Pd‐based heterogeneous catalysts favoured the complete exothermic combustion of CH4 feedstock reactant species, and the liquid product consisted only of water in the Pd‐ case. The utilisation of Mo/H‐ZSM‐5 resulted in a 46% increased yield of formalin. A mechanism for the role of Mo was proposed, where Mo oxidises methanol to formaldehyde and the metal is reoxidised in plasma.