bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of Genetic Divergence in Chickpea (Cicer arietinum L.) Germplasm
Authors: Swetha Dokku Baby , Kumam Sanjay , Kumar Anand
Published: March 2024

A field experiment was carried out to assess the nature and magnitude of genetic divergence in forty genotypes of desi chickpea using Mahalanobis’s D2 Statistics. High magnitude of heritability (bs) was recorded for plant height, days to 50% flowering, biological yield, harvest index, number of pods per plant, seed yield per plot, 100 seed weight and seed yield per plant. High heritability coupled with high genetic advance was observed for seed yield per plant, seed yield per plot, number of pods per plant, 100 seed weight, harvest index, biological yield and plant height suggesting that, the role of additive gene effect and possibilities of achieving high genetic progress through selection. The forty chickpea genotypes were grouped into seven clusters suggesting considerable amount of genetic diversity in the material. The cluster III has a total of 10 genotypes, followed by cluster II with nine, cluster VI with seven, cluster IV and V with four, and cluster I and VII with three genotypes, respectively. The intra-cluster D2 value ranged from 148.25 to 491.49 while, inter-cluster D2value ranged from 386.99 to 2141.49. The maximum intra cluster distance was found in cluster I followed by cluster VII and VI, indicating that cross combinations may occur through hybridization between genotypes from the same clusters. The highest inter-cluster distance was observed between cluster I and V (2141.49), followed by cluster I and IV (1590.64), cluster II and V (1271.17) and cluster I and VII (1184.91) suggesting that the genetic architecture of the genotypes in one cluster differ entirely from those included in other clusters. These lines may be utilized in further breeding programe for the exploitation of hybrid vigour and suggesting wide diversity between them and crossings between genetically diverse lines will result in heterotic segregants, genotypes in these clusters could be employed as parents in a hybridization program to develop desirable plant types. Among the ten traits studied, maximum contribution was made by harvest index (21.28 %) followed by number of pods per plant (19.36%), biological yield (15.13%), plant height (14.87%), days to 50% flowering (12.18%) and seed yield per plant (8.08%). The genotypes ICC15921, ICC15903, K1058 and ICC15926, ICC15226, ICC7549, ICC15855 were identified as genetically diverse parents, which can be utilized for future crop improvement programe in chickpea. The aforementioned findings show that these genotypes contain the greatest genetic diversity and are useful for creating a large number of segregants through a crossing program.
Green Synthesis of Zinc Oxide Nanoparticles using Allium sativum Plant Extract and Photocatalytic Activity of Rhodamine B
Authors: Vithalani Priya , Bhatt Nikhil
Published: March 2024

The green approach is regarded as an economical and environmentally responsible way to create nanoparticles. In the field of dye degradation, the photocatalytic degradation mediated by nanoparticles is an effective method. Rhodamine B is a dye that, even at very low concentrations, is highly mutagenic and carcinogenic. Prior to discharge, Rhodamine B must be removed from wastewater. A low-cost plant employed in the manufacture of zinc oxide nanoparticles is Allium sativum. By using XRD and SEM, the synthesized nanoparticles were identified. Rhodamine B was eliminated using zinc oxide nanoparticles. The results demonstrated 99.99% Rhodamine B decolorization at reaction rates of 0.028 mg/L/min for 180 min at 5 ppm dye concentration, 1 g/L catalyst concentration, and pH 6. Analysis using FTIR, HPTLC and UV-Visible spectrophotometers proved Rhodamine degradation. Vigna radiata L, a key agricultural plant, was used to test the toxicity of Rhodamine B and treated effluent. The findings supported the treated effluent’s lower toxicity than the original chemical by showing that the plant and soil had a less harmful reaction to being irrigated with treated water.
Using ARIMA Model to forecast production of kharif sweet potato in Odisha
Authors: Pradhan Jayashree , Dash Abhiram
Published: March 2024

Sweet potato, which is frequently referred to as a small farmers crop, is a major vegetable crop of Odisha. In India, Odisha is producing the most sweet potatoes. During the kharif season (June to August), sweet potatoes are grown as rain fed crop. A timely and accurate forecast of the area and production of such major vegetable crop is helpful for making agricultural policy decisions and giving nutrients to the population as the sweet potato occupies a key place among vegetable crops in Odisha. The objective of the present research is to predict the area, yield, and production of kharif sweet potato in Odisha by applying the most widely used forecasting model, ARIMA model. ACF and PACF plots and secondary data on the area, yield, and production of kharif sweet potato were collected from 1970–1971 to 2019–20 to fit the models that were determined to be appropriate. The best fit model was chosen based on the importance of the estimated coefficients, model diagnostic tests, and model fit statistics. By refitting the model with data from the most recent 4 years, 3 years, 2 years and 1 year, as well as by making one step ahead forecasts for the years 2016–17 to 2019–20, and the best fit model was cross-validated. The models with the best fits for the area, yield, and production of kharif sweet potatoes were found to be ARIMA (1,0,0) with constant model, ARIMA (0,1,1) without constant model, and ARIMA (0,1,1) without constant without constant. The forecast values show that the area, yield, and production of kharif sweet potatoes in Odisha will remain constant in future years, regardless of variation in the lower and upper class interval of the forecast values.
Half quantized Hall effect
Authors: Shen Shun-Qing
Published: March 2024

Here we report a half-quantized Hall effect in a metal or semimetal. The Hall conductance is half quantized and the longitudinal conductance is nonzero. Consequently, the Hall resistivity is not quantized. The half quantization occurs when the parity symmetry or time reversal symmetry emerges near the Fermi surface or Fermi level while the symmetry is broken in the whole system. A recent experiment reports the observation of the half-quantized Hall conductance in a magnetically-doped topological insulator. We discover that a single gapless Dirac cone exists in the band structure and has half-quantized conductance when the Fermi level intercepts the gapless surface states in which the parity symmetry is invariant. As there are no localized chiral edge states in the gapless and metallic system, we find that the chiral edge current is carried by the gapless surface states. The current density peaks at the edge and decays in a power law rather than the exponential decay as in the conventional quantum anomalous Hall effect. The half quantized Hall conductance is a signature of parity anomaly in a single gapless Dirac cone on a lattice. We term the nontrivial quantum phase as “parity anomalous semimetal”. The work opens the door to exploring novel topological states of matter with fractional topological invariants.
Adherencia al tratamiento antituberculoso. Una revisión de las estrategias desde la intersectorialidad
Authors: Manosalvas Jaramillo Lucía Abigail
Published: March 2024

Antecedentes El personal de enfermería juega un papel crucial en el cuidado, apoyo de los pacientes y en la adherencia al tratamiento de diferentes enfermedades.
Objetivo Examinar las dinámicas de los actores involucrados en el proceso de gestión intersectorial frente a la adherencia al tratamiento antituberculoso.
Métodos Se llevó a cabo una revisión en Google Académico, BVS, PubMed, Scielo, Redalyc, Latindex, Medigraphic, MedLine, Scopus, Elsevier y fuentes complementarias. Tras filtrar, se seleccionaron 41 artículos publicados entre 2015 y 2020.
Resultados Se hallaron diferentes iniciativas de países suramericanos, también estrategias de adherencia al tratamiento como el DOTS, protección social, cooperación, educación para la salud, visitas domiciliarias y seguimiento continuo. También se destacó la intervención de diversos actores sociales, como los ministerios, grupos comunitarios y la familia.
Conclusiones La literatura revela cuán importante es la adherencia al tratamiento antifímico para combatir la tuberculosis desde el rol de la enfermería, a nivel de instituciones de salud y en el plano gubernamental o sector público. Esto, aún representa un desafío en materia de intersectorialidad.
Assessing Physical and Demographic Conditions of Freshman "15" Male Medical Students
Authors: Sharif Mohammad Reza , Sayyah Mansour
Published: March 2024

Objectives: Anthropometric conditions of college students following their admission to college programs is one of the concerns of health authorities as well as the health policy makers. The concept of ‘Freshman 15’ is a popular term that describes dramatic weight gain of college students. This research was designed to examine the anthropometric conditions of newly admitted medical students. Methods: 51 male students aged 19 - 21 years old admitted to the undergraduate programs in colleges of medicine at Kashan University of Medical Sciences participated in this cross sectional study. Demographic characteristics of the participants including age, weight, waist and hip circumferences sizes were measured and recorded. Flexible tape was used to measure waist and hip circumferences sizes in centimeter. The data were analyzed using ANOVA and Pearson correlation tests with the significant levels of P ≤ 0.05. Results: The result indicated that only 16 (34.4 percent) of the admitted students had normal weight while 26 (51 percent) were overweight and 8 (15.7 percent) were fat. In addition, 18 (35.3 percent) were in age 18 group, 15 (29.4 percent) in age 19 and 18 (35.3 percent) were in age 20 group. The result of one-way ANOVA suggested that there was a significant difference between the BMI of the age group of 18 to the 19 and 20 years old (respectively, P = 0.02, P = 0.03), while no significant differences was found between the age group 19 and 20 years old (P > 0.05). Conclusions: The result suggested that a considerable proportion of newly admitted male medical students are already overweight or fat prior to starting their medical education. Further research is needed to follow the weight changes after they start their medical education.
Eight Weeks of Aerobic Exercises Improves the Quality of Life in Healthy Aged Sedentary Men
Authors: Amini Mojtaba , Mirmoezzi Masoud , Salmanpour Maryam , Khorshidi Davood
Published: March 2024

Objectives: Advancements in health care systems and technologies have lowered the rate of mortality leading to an accelerated increase of aged population in Iran and worldwide. Therefore, the aim of the study was to investigate the effect of aerobic exercises on quality of life in healthy aged sedentary men. Methods: In this randomized controlled trial, 26 healthy aged men living in Qazvin nursing home participated voluntarily and were randomly assigned in two experimental (n = 13) and control (n = 13) groups. The experimental group performed aerobic exercise protocol three sessions a week for two months. The quality of life was assessed Using SF-36 health survey before and after exercise intervention. The data were analyzed by paired and independent t-tests. Results: The results suggested that quality of life was improved significantly after exercise program (P = 0.001), while no significant change was found in the quality of life in the control group (P = 0.34). Conclusions: Taken together, 8 Week of aerobic exercise program significantly improves the quality of life among the aged persons Additional research with a greater number of subjects and different exercise protocols are required to make crucial decisions regarding the effectiveness of similar exercise programs on aged persons.
Identifying and Quantifying the Difference between Adenomatous Colon Polyps and Normal Colon Tissue from Clinical Histological Images
Authors: Nasser Esgiar Abdelrahim
Published: March 2024

This study aimed to evaluate automated image analysis as a tool for differentiating normal tissue from adenomatous polyp lesions. Images of colon surgical pathology samples from 140 patients (70 normal subjects and 70 polyp subjects) were captured on a personal computer using an Olympus DP20 digital photomicrography apparatus mounted on an Olympus light microscope (trinocular) at 1200×1800 dots per inch resolution, with the high power magnification of ×400. The complexity of image patterns was studied. In particular, image features of Fractal Dimension (FD) and Lacunarity (Lac) were extracted by using non-overlapping and sliding box-counting techniques. There were highly significant differences between the two clinical groups for both techniques, with polyp images in comparison with normal tissue images having significantly greater FD (1.83±0.04 v 1.73±0.08 p<0.0001) and significantly smaller Lac (0.28±0.08 v 0.42±0.12 p<0.0001) by using the non-overlapping box-counting method, and similar results by using the sliding box-counting method (1.86±0.09 v 1.78±0.08 p<0.0001, and 0.26±0.08 v 0.37±0.12 p<0.0001, respectively). These results encourage the use of computer automation, as normal colon tissue and adenomatous polyp tissue can be significantly differentiated
A Joint Model of Entity Linking for RFC Protocols Knowledge Graph Construction
Authors: Li Shoubin , Luan Tao
Published: March 2024

Applying knowledge representation and reasoning to downstream tasks has been considered a promising research direction, as it enables semantic analysis of network protocols. Knowledge Graph is a new way of collecting knowledge, and building a protocol knowledge graph based on RFCs can help us study and analyze network protocols more effectively. However, automatically constructing a protocol knowledge graph from RFCs poses a major challenge, particularly in terms of extracting and linking protocol entities, due to the semi-structured nature of RFC documents. In this paper, we propose a model that combines a fine-tuned language model with an RFC Domain Model to link entities in RFCs to categories in the protocol knowledge base. Firstly, we design a protocol knowledge base as the schema for protocol entity linking. Secondly, we use heuristic methods to identify protocol entities and infer their descriptions from the nearby contexts of their header fields. Finally, we conduct comprehensive experiments on the RFC dataset using our joint model and baseline methods for protocol entity linking. Experimental results demonstrate that our model achieves state-of-the-art performance in entity linking on the RFC dataset, outperforming all baseline methods. In addition, we release a protocol knowledge graph, RFC-KG1.
Evaluation of the Environmental Impact of Oil Pollution from Maritime Transportation
Authors: Asan Cihat
Published: March 2024

Maritime transportation, which has a growing share in global transportation, and especially ships with large carrying capacities, increases the risk of marine environment pollution. The fact that maritime transport takes place not only in the open seas, but also in coastal waters, narrow waters with high navigational risk, and sea areas in the vicinity of ecologically sensitive zones necessitates prediction and calculation of this risk, as well as taking precautionary measures. This study seeks to identify optimal intervention strategies and determine where and when interventions should take place to minimize the adverse effects of potential oil pollution on the marine environment, utilizing a simulation model based on the example of Istanbul's Tuzla shipyard region. The Potential Incident Simulation and Evaluation System (PISCES) decision support system, which predicts the spread of pollution based on the behavior of oil in water, was used in the simulation. As oil weathering processes, which result in evaporation, emulsification, and dispersion, vary depending on the type of oil, weather, and oceanographic conditions, their seasonal average values were obtained from the relevant institutions and entered into the simulation. In the dispersion of oil, the surface current structure, which plays the most pivotal role, has been established by PISCES, based on the reference vector obtained from the relevant institute.Given that, once the oil disperses, starts to submerge and sedimentation occurs, intervention becomes impossible, leading to long-lasting negative impacts on the marine ecosystem, timely response to marine pollution caused by ships is of utmost importance. Intervention strategies should be selected based on dispersion time and quantity, as well as the duration of the interaction of oil with the coast. Another consequence is that oil pollution can affect not only the marine environment but other areas as well, such as adjacent environmentally sensitive areas, causing devastation to the marine habitat.
Optimizing Postprocessing of Range-Gated Viewing Data for Maritime Search and Rescue Operations at Night and in Bad Weather Conditions
Authors: Preis Tristan , Schmidt Jendrik , Klein Alexander , Peters Enno , Lübcke Thomas , Stephan Maurice
Published: March 2024

At night and in bad weather conditions the detection of persons and objects floating in the sea represents a major challenge for search and rescue operations (SAR). If conventional searchlights are used, backscattering from rain, fog and snow decreases detection range. Therefore, a compact and inexpensive range-gated viewing system which significantly reduces atmospheric backscattering was developed. The instrument was designed for detection ranges of several hundred meters. In this study, different image processing techniques were analyzed in terms of improved object detectability for a human observer and for a machine learning-based object detector, based on a real-world image dataset. On the one hand, noise of the camera is reduced by performing a non-uniformity correction (NUC) and on the other, the dynamic range of the images is adjusted and dark objects are accentuated by equalizing (EQ). The aim of this field study with the subsequent post processing steps was to improve visibility for both human observers and machine learning-based object detectors with low computing power, based on real-world image datasets. The results show that processing requirements are different in both cases, mainly due to human eye perception, which an automated detector does not rely on and therefore the performance of the object detector before the equalizing step is slightly better. However, the NUC improves the image quality in any case.
Risk-indicative or sustainable consumption? Consumers’ risk perception on conventional and organic food products in Poland
Authors: Mazur-Włodarczyk Katarzyna , Wódkowska Agata , Gruszecka-Kosowska Agnieszka
Published: March 2024

The consumption of organic food is becoming increasingly popular and, to avoid numerous threats to human health and the natural environment, the issues devoted to it require greater attention from decision-makers, producers, and consumers. Consumer decisions have an impact on shaping food consumption patterns and recently the trend of the consumption of conventional versus organic food products has been widely discussed. This is especially true given the fact that the area of human health is strongly related to the consumption of food products produced under the challenges of environmental protection and sustainability. The study aimed to investigate if the perception of consumption among Polish respondents was risk-indicative or sustainable based on the animal, fruit, and vegetable products purchased from conventional or organic production. The results revealed that fruit and vegetable consumption was not identically related with socio-demographic features, but the income level equally affected consumer choices regarding the purchase of organic food products. Gender and marital status only influenced decisions regarding the purchase of organic fruit. The consumption of animal products regarding the frequency of their consumption did not reveal the features of sustainability. The metal accumulation index (MAI) for conventionally cultivated vegetables was not higher for all of the investigated vegetables, namely pumpkin, spring onion, cabbage, lettuce, spinach, and garlic. Our study contributes to addressing the knowledge gap on consumer choices about organic food products in Poland.
Multi-stage fault formation and REE distribution in the surrounding Devonian dolomites in the south-eastern part of the Holy Cross Mountains (Poland)
Authors: Nieć Marek , Pawlikowski Maciej , Sermet Edyta
Published: March 2024

Metallogenic studies carried out in the Holy Cross Mountains indicate a relationship between mineralization and fault tectonics in Devonian formations. The impact of fault formation on the geochemistry of host rocks has not yet been studied. Mineralogical and geochemical studies of fault core gouges and damage zones in the fault walls of Devonian dolomites in the Budy and Jurkowice quarries were carried out. In the clay-carbonate filling of the fault fissure, the presence of two generations of Fe sulfides, the increased content of Zr, Nb, U and Th in relation to the surrounding rocks was noted. In the fault walls of the dolomites, iron sulfide and hematite mineralization were found. Research on the REE content indicates that it is lower in the fault walls than in those located far from it, while it is clearly higher in the fault gouge, especially in terms of the content of “heavy” elements (HREE). This indicates both the supply of some components to the fault zone from external sources and their displacement from the surrounding rocks. It was also found that the fault was renewed before and after the Neogene at least twice (Badenian)
Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model
Authors: Llambrich Sergi , Tielemans Birger , Saliën Ellen , Atzori Marta , Wouters Kaat , Van Bulck Vicky , Platt Mark , Vanherp Laure , Gallego Fernandez Nuria , Grau de la Fuente Laura , Poptani Harish , Verlinden Lieve , Himmelreich Uwe , Croitor Anca , Attanasio Catia , Callaerts-Vegh Zsuzsanna , Gsell Willy , Martínez-Abadías Neus , Vande Velde Greetje
Published: March 2024

Down syndrome (DS) is characterized by skeletal and brain structural malformations, cognitive impairment, altered hippocampal metabolite concentration and gene expression imbalance. These alterations were usually investigated separately, and the potential rescuing effects of green tea extracts enriched in epigallocatechin-3-gallate (GTE-EGCG) provided disparate results due to different experimental conditions. We overcame these limitations by conducting the first longitudinal controlled experiment evaluating genotype and GTE-EGCG prenatal chronic treatment effects before and after treatment discontinuation. Our findings revealed that the Ts65Dn mouse model reflected the pleiotropic nature of DS, exhibiting brachycephalic skull, ventriculomegaly, neurodevelopmental delay, hyperactivity, and impaired memory robustness with altered hippocampal metabolite concentration and gene expression. GTE-EGCG treatment modulated most systems simultaneously but did not rescue DS phenotypes. On the contrary, the treatment exacerbated trisomic phenotypes including body weight, tibia microarchitecture, neurodevelopment, adult cognition, and metabolite concentration, not supporting the therapeutic use of GTE-EGCG as a prenatal chronic treatment. Our results highlight the importance of longitudinal experiments assessing the co-modulation of multiple systems throughout development when characterizing preclinical models in complex disorders and evaluating the pleiotropic effects and general safety of pharmacological treatments.
Habitat loss weakens the positive relationship between grassland plant richness and above-ground biomass
Authors: Yan Yongzhi , Jarvie Scott , Zhang Qing
Published: March 2024

Habitat loss and fragmentation per se have been shown to be a major threat to global biodiversity and ecosystem function. However, little is known about how habitat loss and fragmentation per se alters the relationship between biodiversity and ecosystem function (BEF relationship) in the natural landscape context. Based on 130 landscapes identified by a stratified random sampling in the agro-pastoral ecotone of northern China, we investigated the effects of landscape context (habitat loss and fragmentation per se) on plant richness, above-ground biomass, and the relationship between them in grassland communities using a structural equation model. We found that habitat loss directly decreased plant richness and hence decreased above-ground biomass, while fragmentation per se directly increased plant richness and hence increased above-ground biomass. Fragmentation per se also directly decreased soil water content and hence decreased above-ground biomass. Meanwhile, habitat loss decreased the magnitude of the positive relationship between plant richness and above-ground biomass by reducing the percentage of grassland specialists in the community, while fragmentation per se had no significant modulating effect on this relationship. These results demonstrate that habitat loss and fragmentation per se have inconsistent effects on BEF, with the BEF relationship being modulated by landscape context. Our findings emphasise that habitat loss rather than fragmentation per se can weaken the positive BEF relationship by decreasing the degree of habitat specialisation of the community.
Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers
Authors: Kim Jee Min , Carcamo Claudia C , Jazani Sina , Xie Zepei , Feng Xinyu A , Yamadi Maryam , Poyton Matthew , Holland Katie L , Grimm Jonathan B , Lavis Luke D , Ha Taekjip , Wu Carl
Published: March 2024

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push–pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
Caspase-1 activates gasdermin A in non-mammals
Authors: Billman Zachary Paul , Kovacs Stephen Bela , Wei Bo , Kang Kidong , Cissé Ousmane H , Miao Edward A
Published: March 2024

Gasdermins oligomerize to form pores in the cell membrane, causing regulated lytic cell death called pyroptosis. Mammals encode five gasdermins that can trigger pyroptosis: GSDMA, B, C, D, and E. Caspase and granzyme proteases cleave the linker regions of and activate GSDMB, C, D, and E, but no endogenous activation pathways are yet known for GSDMA. Here, we perform a comprehensive evolutionary analysis of the gasdermin family. A gene duplication of GSDMA in the common ancestor of caecilian amphibians, reptiles, and birds gave rise to GSDMA–D in mammals. Uniquely in our tree, amphibian, reptile, and bird GSDMA group in a separate clade than mammal GSDMA. Remarkably, GSDMA in numerous bird species contain caspase-1 cleavage sites like YVAD or FASD in the linker. We show that GSDMA from birds, amphibians, and reptiles are all cleaved by caspase-1. Thus, GSDMA was originally cleaved by the host-encoded protease caspase-1. In mammals the caspase-1 cleavage site in GSDMA is disrupted; instead, a new protein, GSDMD, is the target of caspase-1. Mammal caspase-1 uses exosite interactions with the GSDMD C-terminal domain to confer the specificity of this interaction, whereas we show that bird caspase-1 uses a stereotypical tetrapeptide sequence to confer specificity for bird GSDMA. Our results reveal an evolutionarily stable association between caspase-1 and the gasdermin family, albeit a shifting one. Caspase-1 repeatedly changes its target gasdermin over evolutionary time at speciation junctures, initially cleaving GSDME in fish, then GSDMA in amphibians/reptiles/birds, and finally GSDMD in mammals.
Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity
Authors: Hu Chongbin , Zhang Nan , Hong Yun , Tie Ruxiu , Fan Dongdong , Lin Aifu , Chen Ye , Xiang Li-xin , Shao Jian-zhong
Published: March 2024

The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of the kidney in fish immune systems remains to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cells types from zebrafish kidneys via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in the kidney, suggesting the kidney acts as a secondary lymphoid organ. These results indicated that the fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune systems, and highlighted the multifaced biology of kidneys in ancient vertebrates.
Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs
Authors: Schmidlin Kara , Apodaca Sam , Newell Daphne , Sastokas Alexander , Kinsler Grant , Geiler-Samerotte Kerry
Published: March 2024

There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common in evolution and occur when, for example, resistance to one drug results in sensitivity to another. Major questions remain about the extent to which tradeoffs are reliable, specifically, whether the mutants that provide resistance to a given drug all suffer similar tradeoffs. This question is difficult because the drug-resistant mutants observed in the clinic, and even those evolved in controlled laboratory settings, are often biased towards those that provide large fitness benefits. Thus, the mutations (and mechanisms) that provide drug resistance may be more diverse than current data suggests. Here, we perform evolution experiments utilizing lineage-tracking to capture a fuller spectrum of mutations that give yeast cells a fitness advantage in fluconazole, a common antifungal drug. We then quantify fitness tradeoffs for each of 774 evolved mutants across 12 environments, finding these mutants group into classes with characteristically different tradeoffs. Their unique tradeoffs may imply that each group of mutants affects fitness through different underlying mechanisms. Some of the groupings we find are surprising. For example, we find some mutants that resist single drugs do not resist their combination, while others do. And some mutants to the same gene have different tradeoffs than others. These findings, on one hand, demonstrate the difficulty in relying on consistent or intuitive tradeoffs when designing multidrug treatments. On the other hand, by demonstrating that hundreds of adaptive mutations can be reduced to a few groups with characteristic tradeoffs, our findings may yet empower multidrug strategies that leverage tradeoffs to combat resistance. More generally speaking, by grouping mutants that likely affect fitness through similar underlying mechanisms, our work guides efforts to map the phenotypic effects of mutation.
Growth in early infancy drives optimal brain functional connectivity which predicts cognitive flexibility in later childhood
Authors: Bulgarelli Chiara , Blasi Anna , McCann Samantha , Milosavljevic Bosiljka , Ghillia Giulia , Mbye Ebrima , Touray Ebou , Fadera Tijan , Acolatse Lena , Moore Sophie E. , Lloyd-Fox Sarah , Elwell Clare E. , Eggebrecht Adam T. ,   the BRIGHT Study Team
Published: March 2024

Functional brain network organization, measured by functional connectivity (FC), reflects key neurodevelopmental processes for healthy development. Early exposure to adversity, e.g. undernutrition, affects neurodevelopment, observable via disrupted FC, and leads to poorer outcomes from preschool age onward. We assessed longitudinally the impact of early growth trajectories on developmental FC in a rural Gambian population from age 5 to 24 months. To investigate how these early trajectories relate to later childhood outcomes, we assessed cognitive flexibility at 3-5 years. We observed that early physical growth before the fifth month of life drove optimal developmental trajectories of FC that in turn predicted cognitive flexibility at pre-school age. In contrast to previously studied developmental populations, this Gambian sample exhibited long-range interhemispheric FC that decreased with age. Our results highlight the measurable effects that poor growth in early infancy has on brain development and the subsequent impact on pre-school age cognitive development, underscoring the need for early life interventions throughout global settings of adversity.
Performance discrepancy mitigation in heart disease prediction for multisensory inter-datasets
Authors: Hasan Mahmudul , Sahid Md Abdus , Uddin Md Palash , Marjan Md Abu , Kadry Seifedine , Kim Jungeun
Published: March 2024

Heart disease is one of the primary causes of morbidity and death worldwide. Millions of people have had heart attacks every year, and only early-stage predictions can help to reduce the number. Researchers are working on designing and developing early-stage prediction systems using different advanced technologies, and machine learning (ML) is one of them. Almost all existing ML-based works consider the same dataset (intra-dataset) for the training and validation of their method. In particular, they do not consider inter-dataset performance checks, where different datasets are used in the training and testing phases. In inter-dataset setup, existing ML models show a poor performance named the inter-dataset discrepancy problem. This work focuses on mitigating the inter-dataset discrepancy problem by considering five available heart disease datasets and their combined form. All potential training and testing mode combinations are systematically executed to assess discrepancies before and after applying the proposed methods. Imbalance data handling using SMOTE-Tomek, feature selection using random forest (RF), and feature extraction using principle component analysis (PCA) with a long preprocessing pipeline are used to mitigate the inter-dataset discrepancy problem. The preprocessing pipeline builds on missing value handling using RF regression, log transformation, outlier removal, normalization, and data balancing that convert the datasets to more ML-centric. Support vector machine, K-nearest neighbors, decision tree, RF, eXtreme Gradient Boosting, Gaussian naive Bayes, logistic regression, and multilayer perceptron are used as classifiers. Experimental results show that feature selection and classification using RF produce better results than other combination strategies in both single- and inter-dataset setups. In certain configurations of individual datasets, RF demonstrates 100% accuracy and 96% accuracy during the feature selection phase in an inter-dataset setup, exhibiting commendable precision, recall, F1 score, specificity, and AUC score. The results indicate that an effective preprocessing technique has the potential to improve the performance of the ML model without necessitating the development of intricate prediction models. Addressing inter-dataset discrepancies introduces a novel research avenue, enabling the amalgamation of identical features from various datasets to construct a comprehensive global dataset within a specific domain.
Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma
Authors: Zhou Zhijia , Gao Yanan , Deng Longxin , Lu Xiaole , Lai Yancheng , Wu Jieke , Chen Shaodong , Li Chengzhong , Liang Huiqing
Published: March 2024

Background

The incidence of non-alcoholic fatty liver disease (NAFLD) associated hepatocellular carcinoma (HCC) has been increasing. However, the role of glycosylation, an important modification that alters cellular differentiation and immune regulation, in the progression of NAFLD to HCC is rare.

Methods

We used the NAFLD-HCC single-cell dataset to identify variation in the expression of glycosylation patterns between different cells and used the HCC bulk dataset to establish a link between these variations and the prognosis of HCC patients. Then, machine learning algorithms were used to identify those glycosylation-related signatures with prognostic significance and to construct a model for predicting the prognosis of HCC patients. Moreover, it was validated in high-fat diet-induced mice and clinical cohorts.

Results

The NAFLD-HCC Glycogene Risk Model (NHGRM) signature included the following genes: SPP1, SOCS2, SAPCD2, S100A9, RAMP3, and CSAD. The higher NHGRM scores were associated with a poorer prognosis, stronger immune-related features, immune cell infiltration and immunity scores. Animal experiments, external and clinical cohorts confirmed the expression of these genes.

Conclusion

The genetic signature we identified may serve as a potential indicator of survival in patients with NAFLD-HCC and provide new perspectives for elucidating the role of glycosylation-related signatures in this pathologic process.
Changes in hamstring contractile properties during the competitive season in young football players
Authors: Pakosz Paweł , Konieczny Mariusz , Domaszewski Przemysław , Dybek Tomasz , Gnoiński Mariusz , Skorupska Elżbieta
Published: March 2024

Background

The study aimed to examine alterations and imbalances in hamstring muscle contractile properties among young football players throughout their competitive season, and to understand how these changes might contribute to the risk of muscle injuries. Hamstring injuries are particularly common in football, yet the underlying causes and effective prevention methods remain unclear.

Methods

The research involved 74 young footballers who were assessed before the season (pre-test) and after 12 weeks of training (post-test). To evaluate changes in hamstring muscle contractile properties, specifically the left and right biceps femoris (BF) and semitendinosus (ST), tensiomyography (TMG) parameters were utilized.

Results

In comparison to the BF muscle, significant differences in time delay (Td) between the left and right sides in the post-test (p = 0.0193), and maximal displacement (Dm) between the left and right sides at the pre-test (p = 0.0395). However, significant differences in Dm were observed only in the left ST muscle between the pre- and post-tests (p = 0.0081). Regarding lateral symmetry, BF registered measurements of 79.7 ± 13.43 (pre-test) and 77.4 ± 14.82 (post-test), whereas ST showed measurements of 87.0 ± 9.79 (pre-test) and 87.5 ± 9.60 (post-test).

Conclusions

These assessments provided TMG reference data for hamstring muscles in young footballers, both before the season and after 12 weeks of in-season training. The observed changes in the contractile properties and decrease in lateral symmetry of the BF in both tests suggest an increased risk of injury.
An algorithm for block diagram processing and the DiaBloS tool for systems simulation
Authors:   , Rojas Sepúlveda Matías Nicolás Alejandro
Published: March 2024

Visual diagrammatic programming and block diagrams have been a valuable tool for systems modeling and simulation for several decades in research, development, and educational purposes. Despite the existing mature commercial and free software tools, there is no such kind of tool for the Python programming environment. Little information concerning algorithms to process block diagrams that represent dynamical systems and simulate the corresponding models can be found in the public domain. This is likely because simulation systems based on block diagram descriptions that have become de facto industry standards use proprietary solutions, even if their origins can be traced back to work done in research centers and universities more than seven decades ago. Therefore, the main contributions of this work can be summarized in: i) the development of an algorithm and its detailed description for processing block diagrams (multigraphs), ii) the development of DiaBloS, an open source software tool for Python that implements a diagrammatic visual programming interface and the associated block diagram processing algorithms. The latter contribution aims at code design simplicity, modularity, portability, extensibility of its functionality, and providing an open source tool for Python that could satisfy educational purposes while contributing to the understanding of algorithms for processing block diagrams. Other goals like performance, interface responsiveness aesthetics and code optimization were intentionally treated as secondary goals. We expect this contribution will not only serve as a basis for new developments in visual programming systems, but also provide a free open tool accessible to educators in many areas involving systems modeling and simulation. The numerical accuracy of DiaBloS has been validated to be the same as that achieved by commercial and open code-based existing integration routines implementing the fixed-step RK45 method. Application examples are also provided to demonstrate its capabilities and simplicity. This work also provides an overview of the evolution of existing graph-based modeling paradigms. This overview could also have a reference value, as it brings together many ideas that are connected, but spread in such a way that it becomes difficult to have a general articulated picture of the developments in the field of graphical programming tools and algorithms for processing multigraphs.
Managing stakeholder deliberation using NLP in policymaking
Authors:   , Zamora Arriagada Catalina
Published: March 2024

Relacionarse con múltiples grupos de interés es una tendencia creciente en políticas de ciencia y tecnología. Para los formuladores de políticas, dar sentido a los datos participativos es una tarea compleja. El Procesamiento del Lenguaje Natural (NLP) puede ayudar a procesar estos datos, reducir la sobrecarga cognitiva y respaldar la participación de múltiples partes interesadas. Sin embargo, implementar NLP puede ser un desafío en entornos con recursos, conocimientos o infraestructura limitados. Este estudio utiliza métodos mixtos para analizar la viabilidad y las limitaciones del uso de la Latent Dirichlet Allocation (LDA), un algoritmo de NLP, de trabajar con datos de deliberación pública durante la creación de la Política de Inteligencia Artificial (IA) de Chile. Este caso es único ya que más de 1.700 personas deliberaron a través de procesos estructurados y no estructurados, y sus reflexiones variaban en formato, calidad, profundidad y extensión. Comparamos el contenido del borrador de la política de IA de Chile, escrito por expertos, con los resultados del algoritmo LDA aplicado a los datos de deliberación pública. LDA detectó efectivamente el 87% de los temas en el borrador y solo requirió evaluar manualmente el 26% de los documentos para entregar ese resultado. LDA fue robusta ante ambos formatos de deliberación. Para comprender cómo interactúan los formuladores de políticas con el algoritmo, realizamos entrevistas semiestructuradas a cuatro personas que participaron en la creación de la política. Los formuladores de políticas valoraron el potencial de este algoritmo para rastrear el progreso, sistematizar y reducir el tiempo en la revisión de documentos, sugiriendo que reduciría su sobrecarga cognitiva. Sin embargo, los formuladores de políticas expresaron su preocupación por la simplificación de las opiniones de los ciudadanos a palabras clave y posibles sesgos del algoritmo en contra de las minorías. Discutimos el potencial y las limitaciones del uso de LDA en la formulación de políticas tecnológicas y contribuimos mostrando cómo puede ayudar en la gestión estratégica de las partes interesadas en un entorno del mundo real con recursos limitados.
Modeling and Optimization of Groundnut Production in Vijayapura District of Karnataka, India
Authors: Biradar Sampatkumar S , Ragini H. R.  , Harshith K. V.
Published: March 2024

Groundnut is a significant oilseed crop in India, with Karnataka being one of the largest producers. The agricultural economy of Vijayapura district relies heavily on crop production, including groundnut. Understanding the production patterns and forecasting future yields is crucial for agricultural planning and economic sustainability. The study aimed to investigate the production patterns and forecast the groundnut yield in Vijayapura district, Karnataka. The research problem focused on understanding the trends in groundnut area, production, and productivity over time and developing a forecasting model for future yields. Secondary data from 1966-67 to 2020-21 was collected from various sources. Statistical models including linear, quadratic, cubic, exponential, log-logistic and GAM were used to analyze the trends. The ARIMA method was employed for forecasting. The models' adequacy was assessed using MAPE, R2, AIC, and BIC criteria. The log-logistic model was found to be the best fit for groundnut area trends, while the cubic model and GAM were best for productivity and production, respectively. Forecasting using ARIMA initially indicated a slight increase in groundnut yield, but the GAM model predicted a decrease in future production. The findings provide insights for policymakers, agricultural extension services and farmers to make informed decisions regarding crop planning, resource allocation and economic sustainability. Understanding the production patterns and forecasting future yields is crucial for agricultural planning and economic sustainability in Vijayapura district.