Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of an optimal lysis method for the study of thymus and thymoma by mass spectrometry-based proteomics

Background: Thymoma is the most common disease in the anterior mediastinum with malignant potentials even with low overall incidence. Although a few studies on genetic aberrations involved in thymoma have been published, a proteomic study on the landscape of the protein profiles that contributes to the systematic understanding of development of thymomas remains unseen. This is partly due to lack of generic protocols in efficiently extracting proteins from both thymus and thymoma tissues. In this paper, a one-step and highly efficient protein preparation protocol has been established and evaluated. With the use of the presented protocol, it is for the first time that over 2,900 proteins with various molecular functions and cellular locations were identified from human thymoma and thymus tissues. Application of such protocol would allow researchers to study thymus and its carcinogenesis in a comprehensive and systematic manner. Methods: Three representative human tissue types, namely normal (thymus), Thymoma and Para-tumor were applied. Three groups of experimental procedures using different protein extraction buffers including: (I) tris buffer followed by chloroform/methanol extraction; (II) a modified RIPA buffer; (III) buffer with different concentrations of acid-labile surfactant (ALS) were compared. In total, eleven experimental settings were evaluated to optimize the protocol and the proteomes of these three tissue types were profiled using high resolution (HR) tandem mass spectrometry (MS). Results: In this study, we found that chloroform/methanol extraction removed lipids and some lipoprotein efficiently but also resulted in a significant protein loss during the protein extraction. The modified RIPA buffer provided the highest protein yield in the extraction step but after an additional acetone precipitation step required for MS analysis, the total protein yield was significantly compromised and therefore was not considered for further applications. Using the buffers with various ALS concentrations, proteins were extracted in a reliable manner, which showed a positive correlation between the amounts of extracted proteins and the applied ALS concentrations. Proteomics analysis of all the three tissues lysed by ALS led to the identification of 2,902 proteins in total, of which about 1,271 (43.8%) proteins were identified only in thymoma. Conclusions: We present here a simple protein extraction protocol, specifically designed for proteomics analysis for human thymus and thymoma tissues. Application of this method in together with an HR-MS analysis using Orbitrap Fusion, has led to identification of 2,000+ proteins from the thymoma tissue and 1,000+ proteins from the thymus tissue. Comprehensive proteomic profiling of such a large number of proteins with various molecular functions and cellular locations could significantly broaden and deepen our understanding of the mechanisms about thymus carcinogenesis, metastasis, and possible recurrence.
How purchasing departments facilitate organizational ambidexterity

Abstract Companies must pursue both exploration and exploitation of supplier’s knowledge in increasingly competitive and complex production environments. This has been referred to as pursuing an ambidextrous supply strategy, extending the mobilisation of resources in pursuit of both aims beyond the borders of the lead manufacturer and into supplier organizations as well. Purchasing and supply management plays an increasingly central role in mobilizing and involving the suppliers in the pursuit of this agenda. The purpose of this paper is to contribute to the literature on organizational ambidexterity and operations management by exploring how purchasing departments contribute to the organizational pursuit of organizational ambidexterity. We explore practices followed by purchasing departments for mediating tensions between supply networks and organizational functions.
Changes in pollution indicators in Lake Victoria, Kenya and their implications for lake and catchment management

Monitoring of aquatic pollution is important for ascertaining the relationship between fisheries and the general ecosystem health of a lake. This study evaluated the use of changes in pollution indicators in Lake Victoria, Kenya, as a decision support tool for fisheries management and productivity. Principal component analysis (PCA; R2 ≥ 0.5, P < 0.05) of physical and chemical parameters delineated sampling sites into ecological cluster zones consisting of the inner gulf (C1), mid-gulf (C2) and open lake (C3). Test results for lead (Pb) and mercury (Hg) levels in the Nile perch tissues were found to be compliant with EU standards. The inner and mid-gulfs of the Winam Gulf had high levels of total (1818.8 ± 102–1937.78 ± 94 cfu 100 mL−1) and faecal (390 ± 21 cfu 100 mL−1) coliforms attributable to urban sewage and industrial effluents exceeded WHO standards. Similarly, Winam Gulf was more polluted than the open lake, with higher total phosphorus and nitrogen concentrations, turbidity levels and electrical conductivity. Low phytoplankton biovolume and a low number of macroinvertebrates genera, and high zooplankton densities and pollution-tolerant catfishes (e.g., Schilbe victoriae; Clarias gariepinus) were observed in Winam Gulf. Faecal coliforms and dissolved oxygen influenced the abundance of tolerant fish species (e.g., S. victoriae) in the lake. This study indicated a declining trend of ecological integrity in the Winam Gulf, compared with the open waters of Lake Victoria. An integrated management approach directed to minimizing pollution levels, especially in the Winam Gulf, is recommended to enhance fishery production.
Development of a single nucleotide polymorphism-based DNA marker for fall armyworm (Lepidoptera: Noctuidae) biotyping: a case study from the fall armyworm outbreak in Sri Lanka

Abstract Crop damage caused by fall armyworm (FAW), Spodoptera frugipera J.E. Smith (1797) (Lepidoptera: Noctuidae), has generated concern among agriculturists globally. In 2019, FAW was first reported in Sri Lanka, where it caused significant losses to corn crops. However, given that the two FAW biotypes – “rice strain” (R-FAW) and “corn strain” (C-FAW) – are morphologically identical, the biotype(s) present in Sri Lanka were unknown. The current study used the mitochondrial cytochrome c oxidase subunit I gene (mt-CO1) of FAW to biotype nine FAW samples collected in Sri Lanka. The resulting molecular phylogeny revealed that both R-FAW and C-FAW biotypes were present among the samples. In addition, we used the temperature-switch polymerase chain reaction (PCR) technique to develop a gel-based molecular marker. Two fragments were successfully amplified by the newly developed marker ABUOP0002, with fragment sizes of 341 bp from R-FAW and 204 bp from C-FAW. This demonstrates that ABUOP0002 can serve as a diagnostic gel-based molecular marker to identify the R-FAW and C-FAW biotypes from samples already identified to species level as S. frugiperda through taxonomical keys and provides a possible alternative to more expensive sequencing-based assays.
Topographer Reveals Dynamic Mechanisms of Cell Fate Decisions from Single-Cell Transcriptomic Data

Cell fate decisions play a pivotal role in development but technologies for dissecting them are limited. We developed a multifunction new method, Topographer to construct a ‘quantitative’ Waddington’s landscape of single-cell transcriptomic data. This method is able to identify complex cell-state transition trajectories and to estimate complex cell-type dynamics characterized by fate and transition probabilities. It also infers both marker gene networks and their dynamic changes as well as dynamic characteristics of transcriptional bursting along the cell-state transition trajectories. Applying this method to single-cell RNA-seq data on the differentiation of primary human myoblasts, we not only identified three known cell types but also estimated both their fate probabilities and transition probabilities among them. We found that the percent of genes expressed in a bursty manner is significantly higher at (or near) the branch point (∼97%) than before or after branch (below 80%), and that both gene-gene and cell-cell correlation degrees are apparently lower near the branch point than away from the branching. Topographer allows revealing of cell fate mechanisms in a coherent way at three scales: cell lineage (macroscopic), gene network (mesoscopic) and gene expression (microscopic).
Invasive plant feedbacks promote alternative states in California vernal pools

Invasive species have the potential to create positive feedbacks and push an ecosystem into an alternative state through a variety of mechanisms. Unless the drivers behind these feedbacks are understood, restoring a system to a more desirable state may not be possible. We used a long‐term vernal pool restoration project based out of Travis Airforce Base, Fairfield, CA, U.S.A. to examine natural pools dominated by either invasive or native plant communities, and restored pools predominately composed of invasive plants. We determined that plant community structure is drastically altered towards invasive grasses with the addition of a single centimeter of litter. In the absence of this litter layer, community structure was driven by a non‐native forb rather than native species. We also found that native plant‐dominated vernal pools have a longer inundation duration and are deeper compared to invasive‐dominated pools, regardless of construction status. These results suggest that once invasive grasses establish through lower inundation depths, their litter deposition can initiate a positive feedback to maintain an invasive alternative state. However, even after litter removal, non‐native forbs can replace the grasses causing a second alternative state still separate from the most desirable native dominated state. This study directly demonstrates that invasive species, and their positive feedbacks, may limit the success of ecological restoration. To effectively restore a system all constraints must be identified and removed before successful restoration can occur.
Aging in a Digital Society: Exploring How Canadian and Australian Public Library Systems Program for Older Adults

ABSTRACT Amid global population aging and technological advancement, this article seeks to support public librarians in innovating programs for older adults. It compares how Canadian and Australian public libraries approach this task using environmental scans and thematic analyses within both countries. Findings reveal that Canadian and Australian librarians similarly seek to craft programs that target the informational interests of older adults, increase digital literacy, mitigate social isolation, and combat ageism by means of community engagement, strategic partnerships, and experimentation. Findings highlight similar approaches to overcoming programming challenges and differences in how they market older adult specific programs.
Information Type Influences Students’ Perceptions of Faculty Self-Disclosures

Background: Faculty might disclose personal information in order to illustrate a concept related to course material. However, the impact of self-disclosing potentially personal information (e.g., medical or mental health) is unclear. Objective: The purpose of this study was to determine how students perceive professors who self-disclose personal information during lectures, given that some conditions may be viewed negatively. Method: Introductory psychology students (N = 137) completed an online survey in which they rated female professors in vignettes describing course lectures. Each lecture was one of the following topics: bipolar disorder, opioid addiction, breast cancer, brain tumor, and animal learning (control). At the end of each vignette, the professor self-disclosed personal information related to that lecture. Results: Overall, students perceived professors who disclosed physical (breast cancer and brain tumor) conditions more positively compared to psychological (bipolar and opioid addiction) conditions. Highest approval ratings were given to the professor with breast cancer. Conclusion: Students’ perceptions of self-disclosure depended on the type of personal information, providing a springboard for future studies on this topic. Teaching Implications: Given the different levels of approval for each professor, we cannot make a blanket recommendation as to whether personal information should be shared in the classroom.
Vitamins, Amino Acids, Lipids and Sterols of Eggs from Three Different Birds Genotypes

The study compared the nutritional and physical quality of whole raw and cooked eggs of birds collected from three different genotypes as well as environments,namely (Broiler chicken (Gallus gallus), quail (Coturnix coturnix japonica ) and Local chicken or indigenous (Gallus gallus domesticus). The eggs were divided into two portions one portion was cooked for 30 minutes. Furthermore the whole boiled and cooked of these eggs were characterized with respect to their vitamins and amino acids and the oils extracted from them were analyzed for individual fatty acid and sterols. Among all the vitamins analyzed for vitamin B5 that was highest and ranged 1.409mg/l00g in raw boiler eggs to I . 529mg/100g in boiled quail eggs. Amino acid profile compared well among all the eggs analyzed for with minimal differences in their concentrations. However, among all the amino acid, glutamate had highest concentration ranged 13.8114. 94g/100g protein and the least concentrated was tryptophan and ranged 0.66-0.82g/100g protein. The saturated fatty acids (SFA) were (in % of total fatty acid) had the best level 46.888mg/l00g in raw quail egg and the lowest level of 4 l.8l3mg/l00g was found in raw broiler egg. MUFA was highest in raw local chicken egg 43.267g/. The range in PUFA, AA/DGLA, EPA/PHA LA/ALA, n-6/n-3, PUFA/SFA MUFA/SFA and EPSI were 12.03420. 474, 0.219-0.506; 0.0150. 615; 2436.4-9683.0; 7.670-14.574; 0.883 0.993 and 0.2910. 0.552g/l00g respectively. The only sterol of significance was cholesterol with a range of 269.9 -357.2mg/l00g.The study indicated that the thre different eggs analyzed contained high nutritional contents of vitamins, amino acids, fatty acids and sterols irrespective of the environment however, heat had effect on the nutrients especially the vitamins.
A Morphological Process of Derivational Affixes in Popular LINE Webtoon: The Annarasumanara

This research tries to analyze the morphological process of derivational affixes in a popular LINE Webtoon comic titled Annarasumanara authored by Il Kwon Ha. This research uses a synchronic descriptive approach in which data are collected and explained naturally. The objects of this research are the conversations in Annarasumanara from episode 1 to 10. The results of the research are 53 words that changed word classes, involving 7 derivational prefixes and 47 derivational suffixes. The suffix “-ly” is the most dominantly used in the Webtoon. This study revealed not only the detailed morphological process of affix analysis but also the grammatical categories of words and meanings.
Growth, Yield and Quality of Maize under Ozone and Carbon Dioxide Interaction in North West India

ABSTRACT Maize is an important C4 crop and how it will respond to elevated atmospheric carbon dioxide and ozone levels is not well documented. To understand how the growth and nutritional quality of maize will be affected under elevated carbon dioxide (CO2) and tropospheric ozone (O3) interaction, a field experiment was conducted under free air O3 and CO2 enrichment rings (FAOCE) growing HQPM-1 and PMH-1 maize cultivars at New Delhi, India. Each cultivar was exposed to ambient and elevated CO2 (559ppm) alone and along with ambient and elevated O3 (71.8 ppb) throughout the growing period. Elevated CO2 (EC) significantly increased the leaf area index (10.8-22.5%), chlorophyll (11.2-17.3%) and photosynthetic rate (12.1-16.5%) in the two cultivars over the ambient. O3 exposure of 27 ppmhr (AOT4O) under elevated O3 (EO) treatment led to a significant decline in yield (p<0.01) by 9.2% in HQPM-1 and 9.8% in PMH-1. Under elevated CO2 the increase in grain yield was higher under HQPM-1 (25.4%) as compared to PMH-1 (9.04%). The protein content increased under EO (8.1-12.5%) and decreased under EC (13.4-13.6%) in the two maize cultivars due to yield dilution effect. Lysine, phosphorus and potassium content of the grain significantly decreased in both the cultivars under elevated CO2. Carbohydrate and amylose concentrations in grains increased (9.9-15.5%) under EC and decreased (10.8-16.7%) under EO, however, no significant change in yield, protein, amylase, carbohydrate, lysine, potassium and phosphorus was observed under the interaction treatment ECO as compared to the ambient. After two years of study we could conclude that elevated CO2 (559 ppm) was able to offset the negative effect of elevated O3 (71 ppb) on grain yield by 11.2% in PMH-1 and by 18.8% in HQPM-1 without significantly affecting the grain quality in both the maize cultivars
Therapeutic Electrical Stimulation Currents in Chronic Non-specific Low Back Pain: Designing a Systematic Review

Introduction. The aim of this study will be to evaluate the effect of electrical stimulation currents on the pain and function in subjects with chronic non-specific low back pain. Methods. Pubmed, ISI Web of Science, Scopus, Clinical Key, Science Direct, Medline, Embase, PEDro, ProQuest, the Cochrane Library, PROSPERO, and also the MOH Thesis, MOH Articles, Magiran, and SID as the national databases will be searched. Also, Google Scholar search engine will be used. All study types except Qualitative Studies, and Narrative Reviews, i.e . Clinical Trials, Cohort, Case-controls, Cross-sectionals, Observational Descriptive, Case Report, Case Series, Ecological Studies, Systematic Reviews, thesis and dissertation, in English and Persian will be retrieved. The publication date should not be after August 2019. To ensure all the publication has been reached, search will be extended to three years before the publication date of first article found for each type of electrical stimulation currents. The search will be limited to human studies of subjects between 18-65, regardless of gender and race. The search strategy will cover PICO. The quality of studies will be determined using Consort, STROBE, NHLBI, PEDro and CASP checklists in expert consensus. Dissemination. The results of this plan will clarify which electrical stimulation current will improve pain and function in chronic non-specific low back pain. This is valuable in clinical practice to optimize therapeutic planning.
Nestedness of eco‐industrial networks: Exploring linkage distribution to promote sustainable industrial growth

Eco‐industrial networks (EINs, of which eco‐industrial parks are a subset) have gained support as a solution that simultaneously reduces environmental burdens and promotes economic interests. EINs operate under a mutualistic framework, where waste materials and energy are exchanged between industries to their mutual benefit, creating a diverse web of flows. Recent studies have focused on analogies between food webs (FWs) and EINs, measuring a network's success at ecological imitation as representative of its sustainability. Studies have focused heavily on the number of links and nodes in a network, but have neglected the economic reality that each investment comes at the opportunity cost of all alternatives. This analysis focuses on the nestedness metric as used by ecologists to address this pivotal facet to the FW‐EIN analogy. Nestedness describes an ecological strategy for the position of links between nodes in a network in a way that maximizes network cycling for a given number of connections. This metric presents many advantages for EIN design and analysis, including maturity independence, size normalization, and a strong statistical record in highly mutualistic ecological systems. Application of nestedness to EINs indicates a lower presence of nested structures and more randomness than what is typically seen in FWs. The industrial networks also display a correlation between high nestedness and internal cycles, suggesting that the reuse of materials and energy in EINs can be improved upon by increasing the nestedness of structures.
Structural modification of Quercus petraea leaf caused by Cynips quercusfolii – histological study of galls

ABSTRACT Galls formed by the interaction of insects on plant tissues are an example of the unusual transformation and use of plants by insects. The aim of this study was to characterize the structure of galls formed by Cynips quercusfolii L. on sessile oak leaves. In the structure of galls, we distinguished the following: (1) the protective ‘first contact zone’ created by epidermal and sub-epidermal sclerenchyma rings, (2) the wide parenchymatous ring, (3) the internal protective zone created by the sclerenchyma ring, and (4) the nutritional zone consisting of cells filled with amyloplasts containing starch. A characteristic for galls in the development stage is the centripetal starch gradient in which starch accumulates in a ‘ring of amyloplasts’ in the larval chamber.
Evidence of Climate Change Engagement Behaviour on a Facebook Fan-Based Page

Climate change has become one of the most debated topics in recent times. The social media platforms have given the general public the power and propensity to share and express concerns about climate change. However, climate change awareness created on social media depends on user engagement with the contents modulated by emotions. Much has been researched in this area using Twitter, but Facebook fan-based pages have not been extensively explored in the past. In this study, we investigate the engagement behaviour of users on a Facebook fan-based page titled “Global Climate Change Awareness” by analysing user insights data for two years starting from April 2018 to April 2020. Results show that the frequency of posts made to the page did not significantly promote engagement but improved visibility of the contents to the users. Overall, fan growth was attributed more to increased post visibility that enhanced post engagement. Hashtags associated with climate change had a significant reach amongst users, but those associated with disasters where the page expressed sadness and informed users about taking precautions had the highest engagement rate. Likewise, users from developing countries, especially from the small islands, were more engaged with climate change awareness. This study did not assess negative responses from users (possible deniers of climate change) and other Facebook fan-based pages due to data privacy and stringent Facebook policy.
An epidemiological study of malnutrition in children from six months to five years of age to assess the prevalence and factors related to it, in a rural area of Palghar district of Maharashtra

High economic growth in India in the last two decades has unfortunately not been translated into satisfactory progress on reducing hunger and malnutrition. India occupies a hot spot in the global map of childhood stunting as 61 million (37%) of the 165 million stunted children aged under five years globally are Indian children (UNICEF 2014). We cannot hope for a healthy future for our country with a large number of malnourished children, the problem of malnutrition is a matter of ‘National shame’ despite of impressive growth in our GDP (Dr. Manmohan Singh, Ex. Prime Minister, India). India remains home to one third of the world’s stunted children (UNICEF 2016), it therefore falls into serious category, 38.7% of Indian children under 5 are stunted reflecting chronic malnutrition, and 4.8% of children die before 5 years of age. NFHS4 (national family health survey) data shows high prevalence of malnutrition among rural India, prevalence of underweight, stunting, and wasting for rural area was 40%, 38.4% and 26.1% respectively; and for urban area it ABSTRACT