Miracle-dz/UniFAR-FTUs huggingface dataset:
Difficulties in diagnostics of lung tumours in biopsies: an interpathologist concordance study evaluating the international diagnostic guidelines

Aims Accurate and reliable diagnosis is essential for lung cancer treatment. The study aim was to investigate interpathologist diagnostic concordance for pulmonary tumours according to WHO diagnostic criteria. Methods Fifty-two unselected lung and bronchial biopsies were diagnosed by a thoracic pathologist based on a broad spectrum of immunohistochemical (IHC) stainings, molecular data and clinical/radiological information. Slides stained with H&E, thyroid transcription factor-1 (TTF-1) clone SPT24 and p40 were scanned and provided digitally to 20 pathologists unaware of reference diagnoses. The pathologists independently diagnosed the cases and stated if further diagnostic markers were deemed necessary. Results In 31 (60%) of the cases, ≥80% of the pathologists agreed with each other and with the reference diagnosis. Lower agreement was seen in non-small cell neuroendocrine tumours and in squamous cell carcinoma with diffuse TTF-1 positivity. Agreement with the reference diagnosis ranged from 26 to 45 (50%–87%) for the individual pathologists. The pathologists requested additional IHC staining in 15–44 (29%–85%) of the 52 cases. In nearly half (17 of 36) of the malignant cases, one or more pathologist advocated for a different final diagnosis than the reference without need of additional IHC markers, potentially leading to different clinical treatment. Conclusions Interpathologist diagnostic agreement is moderate for small unselected bronchial and lung biopsies based on a minimal panel of markers. Neuroendocrine morphology is sometimes missed and TTF-1 clone SPT24 should be interpreted with caution. Our results suggest an intensified education need for thoracic pathologists and a more generous use of diagnostic IHC markers.
Fetal Sex-Dependent Associations Between Gestational Hormone Concentrations and Adverse Birth Outcomes

Adverse birth outcomes remain significant public health problems that can have long-lasting impacts on mother and child. Understanding biological mechanisms underlying these outcomes, including altered endocrine function, can inform prevention efforts. The aim of this study was to evaluate associations between hormones at two times points during mid-gestation and adverse birth outcomes, and to assess effect modification by fetal sex. Repeated gestational hormone measurements (at 18 and 26 weeks) and birth outcomes were assessed among 976 women in PROTECT, a longitudinal prospective birth cohort in northern Puerto Rico, from 2011 to 2018. Birth outcomes assessed included preterm and spontaneous preterm birth (PTB), preeclampsia, gestational diabetes mellitus (GDM), small/large for gestational age (SGA, LGA), birthweight z-score, and gestational age at birth. Multivariate logistic and linear regressions were fit using visit-specific concentrations of hormones. We also conducted sensitivity analyses assessing impacts of fetal sex on observed associations. All models were adjusted for maternal age and education, and other confounders were assessed separately between birth outcomes based on a priori knowledge and observed associations with exposure and outcome measures. We observed increased odds of spontaneous PTB with IQR increases in progesterone (OR: 2.12, 95% CI: 1.29, 3.47), fT4 (OR: 1.73, 95% CI: 1.04, 2.86), and the ratio of progesterone to estriol (OR: 1.63, 95% CI: 1.05, 2.54) at 26 weeks. Elevated estriol was protective against preeclampsia at 26 weeks (OR: 0.42, 95% CI: 0.17, 0.99). Increases in TSH and T3 conferred greater risk of GDM at 18 weeks. Many associations were modified by fetal sex, with hormone alterations during male pregnancies conferring greater risk of PTB, spontaneous PTB, and GDM. In conclusion, associations between hormones and birth outcomes vary based on timing of hormone measurement and fetal sex. Future studies are needed to understand mechanisms involved in adverse birth outcomes and fetal sex differences.
Ethnoveterinary practice of medicinal plants in Chhatradev Rural Municipality, Arghakhanchi District of Western Nepal

Abstract. Dhakal A, Khanal S, Pandey M. 2021. Ethnoveterinary practice of medicinal plants in Chhatradev Rural Municipality, Arghakhanchi District of Western Nepal. Nusantara Bioscience 13: 29-40. The use of medicinal plants is a traditional system in treating domestic animals in Nepal. This study was done to investigate and document knowledge about using different plants with medicinal value to cure different animal ailments in Chhatradev Rural Municipality, Arghakhanchi district of western Nepal. A total of 100 elderly people rearing domestic animals and having traditional knowledge of ethnoveterinary plants were selected for interview. A semi-structured questionnaire was employed, and interviews were conducted for addressing detailed ethnoveterinary information. The uses of 103 plant species belonging to 56 families were documented for the treatment of 21 animal ailments. Fabaceae was found to be a dominant family with 10 plant species followed by Poaceae (8 species). The most commonly used plant parts were leaf, seed, and fruit. Herbs were dominant with 44 plant species followed by trees (32 species), shrubs (14 species), and climbers (13 species). The wide application of the medicinal plants as the form of paste formulation was observed for 41 plant species, while 25 plant species were used as powder formulation followed by Juice (21 species), raw (20 species), decoction (19 species), infusion (5 species), and roasted formulation (3 species). Oral route was the most common route followed by dermal and ocular. It was found that the informant consensus factor (ICF) values varied from 0.858 to 0.96. A high informant consensus factor was found for ailment of reproductive category (0.96) followed by respiratory (0.957), gastrointestinal (0.949) while the least was in urinary problem category (0.858). The highest citation frequency was found for Trachyspermum ammi (L.) Sprague (247) followed by Myristica fragrans Houtt. (111), Sesamum indicum L. (109), Saccharum officinarum L. (107) and Zea mays L. (97). The wide use and rich knowledge of ethnoveterinary practice were found in the study area. This study might be handy to discover useful ethnopharmaceutical agents applicable in the livestock industry. Conservation programs should be done from the government level and study on the use of medicinal plants for treating animal diseases is recommended.
Marginal Vertical Convergence: New Approach in Real Convergence Analysis

: Purpose: The main aim of this paper is to present a concept of marginal vertical income convergence. This method allows to determine the individual contribution of the objects (countries, regions) to the observed general process of real convergence. Design/Methodology/Approach: Proposed methodology allows to avoid the limitations of the classical analysis of income convergence. To check the cross-country stability of the parameters and to assess an individual contribution to convergence process, separate regressions for all EU member states was provided. The differences between coefficients of the model based on full sample and coefficients specific for a particular country indicate this individual effect. Findings: The empirical results show that in 1993-2018 we can observe an absolute 𝛽 income convergence within the European Union, accelerated after 2008-2009’s crisis period. However, the main conclusion is that the contribution to the overall process of levelling out GDP per capita within the EU was different from one member state to another. Received results confirmed that outliers removing allows to increase the quality of used models and the reliability of formulated interpretations. Practical Implications: Different values of marginal vertical income convergence are caused by differences in the dynamics of economic growth of individual countries, their different resistance to economic shocks, as well as different levels of inequality and distribution of income and wealth. Recognition of such differences is the first step in developing policies aimed at reducing discrepancies among national behaviours that could be observed as a background of a general convergence process. Originality/value: This research presents new concept of cross-sectional real convergence analysis built on the long period sample covering pre- and post-crisis time for all EU member countries. Additional contribution of the undergone study is robustness analysis that make allowances of outlier’s impact.
Student score and responses to the analogy approach in learning physics in terms of gender and parents’ work

This study aims to identify the types of analogy approaches required in learning physics and analyze physics scores of students based on gender and parent’s occupation. This research uses quantitative and qualitative approaches. Quantitative data is in the form of primary and secondary data. Primary data were collected using a questionnaire, while secondary data were from a teacher. Meanwhile, the qualitative data were collected using an open questionnaire. Quantitative analysis use using non-parametric statistics (Mann-Whitney) with the help of IBM SPSS version 24, while qualitative analysis is descriptive. The results of the study (with a significance of 0.05) showed that gender (sig.-value = 0.584 for PA and 0.874 for physical grades, greater than 0.05) and the type of work of parents (sig.-value = 0.303 for PA and 0.528 for physics scores, greater than 0.05) did not affect student responses about the analogy approach and to the students’ physics scores. Meanwhile, the the open questionnaire results generally stated that the students were happy, interesting, motivated, easier, clearer, more meaningful, more understanding of concepts, effective, and efficient in learning physics. The recommendation is that this analogy approach needs to be developed on other physics concepts and implemented in physics learning.
Can arbuscular mycorrhizal fungi speed up carbon sequestration by enhanced weathering?

Climate change is one of the most pressing environmental and societal issues currently faced by humanity (IPCC, 2018). At the 2015 climate summit in Paris, nearly all world leaders committed themselves to limit global warming to well below 2°C (UNFCCC, 2015). Achieving this target requires rapid and complete decarbonization of all sectors. Current policies focus on conventional mitigation to reduce emissions, yet scenario analyses and model projections unveiled that conventional mitigation alone Received: 14 August 2020 | Revised: 31 October 2020 | Accepted: 10 December 2020 DOI: 10.1002/ppp3.10179
A historical reconstruction of cropland in China from 1900 to 2016

Abstract. A spatially-explicit cropland distribution time-series dataset is the basis for the accurate assessment of biogeochemical processes in terrestrial ecosystems and their feedback to the climate system; however, this type of dataset is lacking in China. Existing cropland maps have a coarse resolution, are intermittently covered, or the data are inconsistent. We reconstructed a continuously covered cropland distribution dataset in China spanning from 1900 to 2016 by assimilating multiple data sources. In total, national cropland acreage expanded from 77.72 Mha in 1900 to the peak of 151.00 Mha in 1979, but it consistently decreased thereafter to 134.92 Mha in 2016. The cropland was primarily distributed in three historically cultivated plains in China: the Sichuan Plain, the Northern China Plain, and the Northeast China Plain. Cropland abandonment was approximately 29.90 Mha; it was mainly concentrated in the Northern China Plain and the Sichuan Plain and occurred during the 1990–2010 period. Cropland expansion was over 74.30 Mha; it was primarily found in the southeast, northern central, and northeast regions of China and occurred before 1950. In comparison, the national total and spatial-distribution of cropland in the Food and Agriculture Organization (FAO) of the United Nations and the History Database of the Global Environment (HYDE) were distorted during the period of 1960–1980 due to the biased signal from the Chinese Agricultural Yearbook. We advocate that newly reconstructed cropland data, in which the bias has been corrected, should be used as the updated data for regional and global assessments, such as greenhouse gas emission accountings and food production simulations. The cropland dataset is available via an open-data repository (https://doi.org/10.6084/m9.figshare.13356680) (Yu et al., 2020).
Using DHS and MICS data to complement or replace NGO baseline health data: an exploratory study

Background: Non-government organizations (NGOs) spend substantial time and resources collecting baseline data in order to plan and implement health interventions with marginalized populations. Typically interviews with households, often mothers, take over an hour, placing a burden on the respondents. Meanwhile, estimates of numerous health and social indicators in many countries already exist in publicly available datasets, such as the Demographic and Health Surveys (DHS) and the Multiple Indicator Cluster Surveys (MICS), and it is worth considering whether these could serve as estimates of baseline conditions. The objective of this study was to compare indicator estimates from non-governmental organizations (NGO) health projects’ baseline reports with estimates calculated using the Demographic and Health Surveys (DHS) or the Multiple Indicator Cluster Surveys (MICS), matching for location, year, and season of data collection. Methods: We extracted estimates of 129 indicators from 46 NGO baseline reports, 25 DHS datasets and three MICS datasets, generating 1,996 pairs of matched DHS/MICS and NGO indicators. We subtracted NGO from DHS/MICS estimates to yield difference and absolute difference, exploring differences by indicator. We partitioned variance of the differences by geographical level, year, and season using ANOVA. Results: Differences between NGO and DHS/MICS estimates were large for many indicators but 33% fell within 5% of one another. Differences were smaller for indicators with prevalence <15% or >85%. Difference between estimates increased with increasing year and geographical level differences. However, <1% of the variance of the differences was explained by year, geographical level, and season. Conclusions: There are situations where publicly available data could complement NGO baseline survey data, most importantly when the NGO has tolerance for estimates of low or unknown accuracy.
A Comprehensive Study of Franki pile with the other pile models Embedded within cohesionless soils

Frankie pile is classified as a large displacement pile cast in place with a concrete mixture. This paper dealt with the laboratory work to produce a model of the Franki pile similar to the full-scale production process in the field to investigate its behaviour and make a comparison study with the other familiar types of piles models (precast concrete pile, closed-ended steel pipe pile, and bored pile with the same surface and cross-sectional area). The investigation occurred within dry sandy soil with two different relative densities (30 and 60) % will be denoted as (S1) and (S2) respectively. Axial compressive piles load tests were performed for embedded piles models in sandy soils at relative densities of 30% and 60%. Several interpretations have been used to estimate the ultimate capacity of pile models from the results of pile load tests. It was found that the Davisson, De Beer, Fuller and Hoy, and Tangent Methods gives an approximate acceptable result for all typical pile load tests, so average values of theses methods were adopted for comparisons. It was observed that the ultimate bearing load value at a Franki pile was greater than the other types of piles models in both densities. The for precast concrete pile, 2.98 for close ended pipe pile and 5.5 for bored piles for low relative density. While for high relative density the bearing ratio of Franki pile over other pile models were 0.94 for precast concrete pile, 2.26 for pipe pile model and 3.16 for bored pile model. During this study, it was found that a Franki pile was more effective in weak granular soils.
Interaction of Factors Influencing the Sustainability of Water, Sanitation, and Hygiene (WASH) Services in Rural Indonesia: Evidence from Small Surveys of WASH-Related Stakeholders in Indonesia

It is argued that there are interconnected and dynamic factors that influence the sustainability of water, sanitation, and hygiene (WASH) services in developing countries. Five sustainability factors are often mentioned by literature: financial, institutional, environmental, technical, and social (FIETS) factors. This article aims to understand the interaction of those five sustainability factors in the context of WASH services in Indonesia. A system approach, in the form of a “modified” causal loop diagram, was utilized to analyze this interaction. The strength of influence from one factor to others were obtained from small surveys of 16 WASH practitioners and experts from international and national non-governmental organizations (NGOs) based in Indonesia and national government institutions related to WASH. It was found that institutional factor is the “leverage” factor, i.e., the most influential and least dependent, in the WASH services system in Indonesia. It means that WASH institutional strengthening is necessary to sustain WASH services in Indonesia. Furthermore, the most important feedback loop is social–WASH services. This depicts the importance of the bi-directional effect of WASH services and the social conditions of the community, i.e., the more supportive the community is, the higher the likelihood of the sustainability of WASH services, and then positively influence back the social conditions of the community. Moreover, the relationship between factors varies across context or location. Finally, this paper shows that the sustainability of WASH services involves complex interactions of the sustainability factors and understanding these interactions is critical to sustaining the WASH services or program in rural Indonesia.
Prevalence, Species Distribution and Antifungal Susceptibility Profile of Candida Species Isolated from Bloodstream of Critical Care Unit Patients in a Tertiary Care Hospital in Kenya

The upsurge of candidemia in the past years has been an immense encumbrance on public health and the number of deaths caused by candidemia particularly in critical care unit patients is devastating. Candida species harbor a 30% - 60% mortality rate and compared to stable people or those with less serious illnesses, this ranges from 60% to 80% of those who are chronically ill patients. Grounded on a recent report from a tertiary care hospital in Kenya showing the emergence of previously unobserved species: Candida auris, this study aimed to determine the prevalence, species distribution, and antifungal susceptibility profile of candidemia in critical care unit patients of the hospital. 378 Critical Care Unit patients were enrolled for the study from January 2019 to January 2020. Positive archived isolates were sub-cultured using Saboraud Dextrose Agar. Candida species were identified utilizing API20C AUX and Vitek-2. Antifungal susceptibility testing was conducted using the Liofilchem MIC Test strip. Out of 378 patients, thirty-one presented a positive culture for Candida species. The prevalence of Candidemia was 8.2% with 9 (29.03%) Candida auris, 8 (25.81%) Candida albicans, 6 (19.35%) Candida parapsilosis, 3 (9.68%) Candida famata, 3 (9.68%) Candida tropicalis, 1 (3.23%) Candida duobushaemolumonii, and 1 (3.23%) Candida lusitaniae. A resistance pattern to Fluconazole was observed among Candida auris and Candida parapsilosis, and resistance to Flucytosine was observed in Candida tropicalis, whereas susceptible MIC values were obtained for the other drugs. There is an increase in candidemia among critical care unit patients in the health facility posing a public health challenge. Moreover, the onset of new species Candida auris which is unprecedented in Kenya warrants enhanced infection control, and the uniform resistance of Candida auris, Candida parapsilosis, and Candida tropicalis towards Fluconazole and Flucytosine necessitate constant drug monitoring for empirical treatment regime. In contrast, the high potency of Echinocandins and Amphotericin-B demonstrate them as the drug of choice.
A polyphasic approach to the characterization of potential silver-nanoparticles–producing and non-producing isolates of Alternaria species and antifungal activity against mycotoxigenic fungi

Abstract A polyphasic approach consisting of physical, chemical and molecular characterization was applied to three Alternaria species, A. alternata, A. chlamydospora and A. solani, to characterize and identify isolates producing and non-producing silver nanoparticles (AgNPs). Based on physical characters, the synthesized AgNPs were characterized by transmission electron microscopy and formation of spherical AgNPs sized 5 nm to 60 nm. Scanning electron microscopy (SEM) of the AgNPs did not show a uniform surface; the shape was irregular, like a coral reef. Energy Dispersive Spectroscopy (EDS) showed the presence of Ag element. Fourier transform-infrared spectroscopy (FTIR) confirmed the conversion of Ag ions to AgNPs by fungal metabolites. A. alternata PNU75 non-producing AgNPs showed negative results when characterized by physical devices. Chemical characterization involved the screening of three Alternaria species for fatty acids (FAs) with similar FAs composition while different in terms of relative concentration. The principal FAs were palmitic, stearic, oleic acid and linoleic acid, which comprised 90% or more of the total FAs composition of these species. Molecularly, the fungal protein pattern of the three Alternaria species showed changes against the control by finding 6 proteins associated with AgNPs-producing species. Inter simple sequence repeats (ISSR) analysis using ten primers indicated a high level of genetic variability of three Alternaria species producing and non-producing AgNPs. The results also indicated that the AgNPs synthesized by A. alternata at the concentration 100 mg/L gave the highest inhibition zone against Aspegillus flavus and Aaltenaria alternata, where the percentages of reduction were 77.1% and 87.6% respectively.
Assessment of fertilizers usage and cropping patterns in study area of Naypyitaw, Myanmar

A study was conducted to observe the demographic characteristics of farmers, to assess the use of fertilizers application by farmer and to identify the current status of cropping pattern in the study area. The demographic profiles of 60 respondents stated that the age ranged from 30 to 78 years and land holding ranged from 0.10 to 2.80 ha. The majority of farmers (40%) had a primary educational level. Farmers utilized the different kinds of fertilizers (urea, NPK compound, phosphorous, special potash and foliar) depending on crops and time of applications, and 68% of respondents used cattle manure as basal. Response on farming experience indicated that six different levels of 3 to 60 years. The most cropping patterns observed in the study area were rice-black gram, rice-fallow, maize-tomato, maize- tomato and lablab bean intercropping, maize-lablab bean, okra-tomato. In addition, some of the farmers cultivated horticultural crops such as banana, guava and ambarella. There is a highly significant positive relationship on farm size with cropping pattern. This study suggested that farm size, inputs, market price, labors and farmer’s willingness would influence the fertilizer usage and cropping patterns. Key words: Demographic characteristics, fertilizer use, cropping patterns.