bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of drosophila kinship from three regions in East Java, Indonesia
Authors: Agustin M , Zubaidah S , Susanto H , Habiddin  
Published: March 2024

Abstract

Drosophila has a massive number of members and a wide range of habitats. Different natural conditions make it possible to find diverse Drosophila populations, although several types of Drosophila are cosmopolitan. Drosophila diversity is characterized by morphological variations. The structural similarity of an individual can be used to determine various kinship relations between organisms. This research aimed to determine the relation between Drosophila from three regions in East Java, Indonesia, namely Malang, Mojokerto, and Pasuruan, based on similarities in morphological characteristics. Samples were taken from these three areas, and observations were carried out from January to May 2023 at the Genetics Laboratory, Biology Department, FMIPA UM. Identification of Drosophila is based on an identification key consisting of 52 traits. Drosophila was purified to the third generation to achieve a homogeneity of 87.5%. The kinship relation is sought by calculating the association coefficient and similarity index as a reference in preparing the dendrogram. The dendrogram illustrates that Drosophila from Malang had a closer relationship with Drosophila from the Pasuruan area than from the Mojokerto area. Drosophila kinship relations are influenced by internal and external factors, which include gene flow, mobility, distance, and natural conditions.
Variance analysis and heritability estimation of growth and yield parameter of sweet cassava promising clones in two environments
Authors: Wahyuni T S , Sholihin  , Noerwijati K , Indriani F C , Mejaya M J , Solikin  
Published: March 2024

Abstract
Planting a good variety is important thing in increasing the productivity of cassava’s productivity. Selection and evaluation are needed for development of new variety. The evaluations were done in Malang (Entisol soil) and Probolinggo (Alfisol soil). The evaluation used an RCBD with three replications. Plants were planted on rows with distance 100 cm between rows and 80 cm within rows. Twelve clones (8 promising clones and four released variety) were used in this evaluation. Results can be seen that the variance of genotype was bigger than the variance of genotype x environment interaction for fresh tuber yield, starch content, long of tuber, diameter of tuber, tuber number/plant in eight months and plant height in 4 months, means genetic potency of clones tested more important compared to effect of genotype x environment interaction. This result indicated that clone tested have low chance to be a specific adaptation. The genotypic variance and the heritability for fresh tuber yield, diameter of tuber and tuber number/plant in eight months in Malang were higher than that in Probolinggo.
Viability test of yeast encapsulation (Candida tropicalis) using sodium alginate polymer in bread production
Authors: Utami U , Putra D C W , Harianie L 
Published: March 2024

Abstract
This study explores sodium alginate encapsulation’s impact on Candida tropicalis yeast cell viability and its influence on bread making. Encapsulation protects yeast cells from damage during drying and storage. The research used 10% and 15% sodium alginate for two isolates and one control. Statistical analysis, including Kruskal Wallis and Mann-Whitney tests in Microsoft Excel SPSS, showed significant effects. Sodium alginate encapsulation notably improved Candida tropicalis yeast cell viability and final bread swelling, especially at 15% concentration. Mann-Whitney tests on organoleptic parameters revealed panelist preferences: Candida tropicalis 2 with 15% sodium alginate for color, taste, and texture, while Candida tropicalis 1 with 15% sodium alginate for aroma. This study suggests sodium alginate’s potential to enhance yeast viability and improve bread quality, offering insights for food processing and preservation applications. The research findings may contribute to developing effective encapsulation techniques for yeast-based products.
Chisocheton pentandrus (Blanco) Merr. leaf as a potential antioxidant and α-glucosidase inhibitory agent
Authors: Wibawa I P A H , Hanafi M , Minarti  , Li’aini A S , Rahayu A , Semarayani C I M , Lugrayasa I N , Butardo V M , Mahon P J 
Published: March 2024

Abstract
Indonesia is one of the countries with the highest diversity of plants worldwide, including the Chisocheton genus. The Chisocheton genus has been widely used in traditional medicine due to a variety of compounds with different activities, such as antiplasmodial, antiviral, and anti-inflammatory. The focus of this research is to determine the antioxidant, anti-diabetic, and anti-bacterial activity of Chisocheton pentandrus leaf extract from the Bali Botanic Garden plant collection, as well as the chemical compounds contained in the extract. The antioxidant activity test was carried out by capturing DPPH-free radicals, the antidiabetic test was carried out by assaying its inhibitory activity toward α-glucosidase enzyme, the antibacterial test was carried out using the agar diffusion method, while LC-MS/MS was used to determine the compounds contained in the extract. The results showed that the C. pentandrus leaf methanol extract showed the highest inhibitory activity as an antioxidant and inhibitor of the α-glucosidase enzyme in the very strong category; however, the extract is not effective in inhibiting bacterial growth.
Application of life cycle assessment in measuring the environmental impact of waste cooking oil utilization for biodiesel - a review
Authors: Febijanto I , Indrijarso S , Siswanto  , Kusrestuwardhani  , Trihadi S E Y , Ulfah F , Oktaufik M A M , Dharmawan  , Raharjo P , Barkah A , Iskandar M S , Hermawan T 
Published: March 2024

Abstract
Utilizing waste cooking oil for fuel is one of the steps to reduce the uncontrolled environmental impact due to the disposal of waste cooking oil into water bodies and onto the ground. Utilization as fuel will contribute to achieving net zero emissions and reducing global warming as the primary target. With increasing attention to the environment, the extent to which the process of making waste cooking oil impacts the environment has also been widely discussed. Using the Life Cycle Assessment (LCA) methodology as a strong tool to assess the environmental impact, many previous studies have carried out the environmental impact concerning waste cooking oil utilization for biodiesel. This paper reviews previous research from around the world in the 2008-2023 period related to the environmental impact assessment of using LCA in manufacturing waste cooking oil for biodiesel. The review results are divided into scope and technology used, manufacturing raw materials, research locations, functional units, system boundaries (cradle to grave, gate to gate, and gate to grave), software used, midpoint impact assessment, impact assessment method, and impact category.
The utilization of Binahong leaves as medicinal plants for livestock production and health
Authors: Rohaeni E S , Widiawati Y , Setiasih  , Bakrie B , Wardi  , Anggraeny Y N , Hatta M , Shiddieqy M I , Ahmad S N , Widodo S , Firsoni  , Evvyernie D , Yolanda D E 
Published: March 2024

Abstract
The utilization of Binahong leaves or Anredera cordifolia (Ten.) Stennis as a medicinal plant in livestock production and health, has garnered significant attention in recent years. This review paper aims to comprehensively analyze the diverse potential benefits of Binahong leaves in enhancing livestock well-being and productivity. With a focus on its applications in the livestock sector, this review encompasses multiple facets, including the phytochemical composition of Binahong leaves, their pharmacological activities, and their impact on animal health and production. The phytochemical profile of Binahong leaves is examined in detail, highlighting the presence of bioactive compounds such as flavonoids, saponins, and alkaloids, which contribute to their medicinal properties. These compounds exhibit antioxidant, anti-inflammatory, antimicrobial, and immunomodulatory activities, making Binahong leaves a promising natural remedy for addressing health challenges in livestock. Furthermore, the review explores the potential mechanisms by which Binahong leaves can improve livestock health. These mechanisms involve the enhancement of immune responses, the reduction of oxidative stress, and the mitigation of common ailments in animals. Additionally, the effects of Binahong leaves on livestock growth, reproduction, and overall production are discussed, emphasizing their role in sustainable livestock farming. In ruminants, Binahong is beneficial for therapy in Gastroenteritis caused by Bacillus subtilis, for the treatment of eye infections, for overcoming drug resistance in E. coli, and for mastitis therapy in dairy cattle. This review paper suggests the potential utilization of Binahong as an herbal plant or alternative medicine for general health and, specifically, for enhancing livestock productivity.
Thermal enhancement of microchannel heat sink using pin-fin configurations and geometric optimization
Authors: Wazir Muhammad Anas , Akhtar Kareem , Ghani Usman , Wajib Mohsin , Shaukat Shahmir , Ali Haseeb 
Published: March 2024

Abstract
The microchannel heat sink (MCHS) is a robust cooling technique that ensures the efficiency and reliability of compact electronic devices by dissipating a large amount of heat because of its high surface area-to-volume ratio. This study proposes a novel modification of the pin-fins geometry in MCHS, and geometric optimization using response surface methodology (RSM) to build a low thermal resistant MCHS with enhanced heat transfer efficiency with low-pressure drop. Three dimensional numerical simulations using ANSYS FLUENT 2021 R2 are performed on three pin-fins configurations, i.e., MC-BW (pins mounted transversely to the bottom wall), MC-SW (pins mounted transversely to the side wall), and MC-Mixed (pins mounted transversely to the bottom and side wall). The thermal and flow characteristics are investigated using a laminar conjugate heat transfer model at Reynolds numbers 100–1000. Results show that introducing pin-fins significantly enhances heat dissipation as it continuously breaks the boundary layer and generates flow separation downstream of the pin-fins, which enhances fluid mixing and increases heat transfer augmentation inside MCHS. Among different configurations, the MC-Mixed gives the highest improvement of 50% in the convective heat transfer coefficient at Re = 1000. The highest thermal enhancement factor of η = 1.4 is obtained for the MC-Mixed configuration at Re = 600. For the base wall pin fin configuration RSM yields optimized values of 2.50 mm, 0.25 mm, and 0.045 mm for transverse pitch, longitudinal pitch, and diameter of pin respectively, and for the mixed pin fin configuration it gives 1.0 mm, 0.150 mm, 0.035 mm and 1.250 mm values for transverse pitch, longitudinal pitch, diameter of pin and pitch of side wall pins respectively for the maximum heat transfer and minimum pressure drop.
Neuromorphic auditory classification based on a single dynamical electrochemical memristor
Authors: Chen Peng , Xiong Xuehao , Zhang Bihua , Ye Yuxuan , Pan Gang , Lin Peng 
Published: March 2024

Abstract
Designing compact computing hardware and systems is highly desired for resource-restricted edge computing applications. Utilizing the rich dynamics in a physical device for computing is a unique approach in creating complex functionalities with miniaturized footprint. In this work, we developed a dynamical electrochemical memristor from a static memristor by replacing the gate material. The dynamical device possessed short-term fading dynamics and exhibited distinct frequency-dependent responses to varying input signals, enabling its use as a single device-based frequency classifier. Simulation showed that the device responses to different frequency components in a mixed-frequency signal were additive with nonlinear attenuation at higher frequency, providing a guideline in designing the system to process complex signals. We used a rate-coding scheme to convert real world auditory recordings into fixed amplitude spike trains to decouple amplitude-based information and frequency-based information and was able to demonstrate auditory classification of different animals. The work provides a new building block for temporal information processing.
Local climate and vernalization sensitivity predict the latitudinal patterns of flowering onset in the crop wild relative Linum bienne Mill.
Authors: Landoni Beatrice , Suárez-Montes Pilar , Habeahan Rico H F , Brennan Adrian C , Pérez-Barrales Rocío 
Published: March 2024

Abstract

Background and Aims
The timing of flowering onset is often correlated with latitude, indicative of climatic gradients. Flowering onset in temperate species commonly requires exposure to cold temperatures, known as vernalization. Hence, population differentiation of flowering onset with latitude might reflect adaptation to the local climatic conditions experienced by populations.

Methods
Within its western range, seeds from Linum bienne populations (the wild relative of cultivated Linum usitatissimum) were used to describe the latitudinal differentiation of flowering onset to determine its association with the local climate of the population. A vernalization experiment including different crop cultivars was used to determine how vernalization accelerates flowering onset, in addition to the vernalization sensitivity response among populations and cultivars. Additionally, genetic differentiation of L. bienne populations along the latitudinal range was scrutinized using microsatellite markers.

Key Results
Flowering onset varied with latitude of origin, with southern populations flowering earlier than their northern counterparts. Vernalization reduced the number of days to flowering onset, but vernalization sensitivity was greater in northern populations compared with southern ones. Conversely, vernalization delayed flowering onset in the crop, exhibiting less variation in sensitivity. In L. bienne, both flowering onset and vernalization sensitivity were better predicted by the local climate of the population than by latitude itself. Microsatellite data unveiled genetic differentiation of populations, forming two groups geographically partitioned along latitude.

Conclusions
The consistent finding of latitudinal variation across experiments suggests that both flowering onset and vernalization sensitivity in L. bienne populations are under genetic regulation and might depend on climatic cues at the place of origin. The association with climatic gradients along latitude suggests that the climate experienced locally drives population differentiation of the flowering onset and vernalization sensitivity patterns. The genetic population structure suggests that past population history could have influenced the flowering initiation patterns detected, which deserves further work.
SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy
Authors: Grexa Istvan , Iván Zsanett Zsófia , Migh Ede , Kovács Ferenc , Bolck Hella A , Zheng Xiang , Mund Andreas , Moshkov Nikita , Miczán Vivien , Koos Krisztian , Horvath Peter 
Published: March 2024

Abstract
Numerous imaging techniques are available for observing and interrogating biological samples, and several of them can be used consecutively to enable correlative analysis of different image modalities with varying resolutions and the inclusion of structural or molecular information. Achieving accurate registration of multimodal images is essential for the correlative analysis process, but it remains a challenging computer vision task with no widely accepted solution. Moreover, supervised registration methods require annotated data produced by experts, which is limited. To address this challenge, we propose a general unsupervised pipeline for multimodal image registration using deep learning. We provide a comprehensive evaluation of the proposed pipeline versus the current state-of-the-art image registration and style transfer methods on four types of biological problems utilizing different microscopy modalities. We found that style transfer of modality domains paired with fully unsupervised training leads to comparable image registration accuracy to supervised methods and, most importantly, does not require human intervention.
Ovarian cancer is detectable from peripheral blood using machine learning over T-cell receptor repertoires
Authors: Zuckerbrot-Schuldenfrei Miriam , Aviel-Ronen Sarit , Zilberberg Alona , Efroni Sol 
Published: March 2024

Abstract
The extraordinary diversity of T cells and B cells is critical for body maintenance. This diversity has an important role in protecting against tumor formation. In humans, the T-cell receptor (TCR) repertoire is generated through a striking stochastic process called V(D)J recombination, in which different gene segments are assembled and modified, leading to extensive variety. In ovarian cancer (OC), an unfortunate 80% of cases are detected late, leading to poor survival outcomes. However, when detected early, approximately 94% of patients live longer than 5 years after diagnosis. Thus, early detection is critical for patient survival. To determine whether the TCR repertoire obtained from peripheral blood is associated with tumor status, we collected blood samples from 85 women with or without OC and obtained TCR information. We then used machine learning to learn the characteristics of samples and to finally predict, over a set of unseen samples, whether the person is with or without OC. We successfully stratified the two groups, thereby associating the peripheral blood TCR repertoire with the formation of OC tumors. A careful study of the origin of the set of T cells most informative for the signature indicated the involvement of a specific invariant natural killer T (iNKT) clone and a specific mucosal-associated invariant T (MAIT) clone. Our findings here support the proposition that tumor-relevant signal is maintained by the immune system and is coded in the T-cell repertoire available in peripheral blood. It is also possible that the immune system detects tumors early enough for repertoire technologies to inform us near the beginning of tumor formation. Although such detection is made by the immune system, we might be able to identify it, using repertoire data from peripheral blood, to offer a pragmatic way to search for early signs of cancer with minimal patient burden, possibly with enhanced sensitivity.
CAFA-evaluator: a Python tool for benchmarking ontological classification methods
Authors: Piovesan Damiano , Zago Davide , Joshi Parnal , De Paolis Kaluza M Clara , Mehdiabadi Mahta , Ramola Rashika , Monzon Alexander Miguel , Reade Walter , Friedberg Iddo , Radivojac Predrag , Tosatto Silvio C E 
Published: March 2024

Abstract

We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the prediction targets are drawn from a directed acyclic graph and achieves high efficiency by leveraging matrix computation and topological sorting. The program requirements include a small number of standard Python libraries, making CAFA-evaluator easy to maintain. The code replicates the Critical Assessment of protein Function Annotation (CAFA) benchmarking, which evaluates predictions of the consistent subgraphs in Gene Ontology. Owing to its reliability and accuracy, the organizers have selected CAFA-evaluator as the official CAFA evaluation software.

Availability and implementation
https://pypi.org/project/cafaeval
Acetic Acid Enables Molecular Enumeration of Mycobacterium tuberculosis from Sputum and Eliminates the Need for a Biosafety Level 3 Laboratory
Authors: Palekyte Ana , Morkowska Anna , Billington Owen , Morris-Jones Stephen , Millard James , Marakalala Mohlopheni J , Owolabi Olumuyiwa , Sambou Basil , Zumla Alimuddin , Sutherland Jayne S , McHugh Timothy D , Honeyborne Isobella 
Published: March 2024

Abstract

Background
Improved monitoring of Mycobacterium tuberculosis response to treatment is urgently required. We previously developed the molecular bacterial load assay (MBLA), but it is challenging to integrate into the clinical diagnostic laboratory due to a labor-intensive protocol required at biosafety level 3 (BSL-3). A modified assay was needed.

Methods
The rapid enumeration and diagnostic for tuberculosis (READ-TB) assay was developed. Acetic acid was tested and compared to 4 M guanidine thiocyanate to be simultaneously bactericidal and preserve mycobacterial RNA. The extraction was based on silica column technology and incorporated low-cost reagents: 3 M sodium acetate and ethanol for the RNA extraction to replace phenol–chloroform. READ-TB was fully validated and compared directly to the MBLA using sputa collected from individuals with tuberculosis.

Results
Acetic acid was bactericidal to M. tuberculosis with no significant loss in 16S rRNA or an unprotected mRNA fragment when sputum was stored in acetic acid at 25°C for 2 weeks or −20°C for 1 year. This novel use of acetic acid allows processing of sputum for READ-TB at biosafety level 2 (BSL-2) on sample receipt. READ-TB is semiautomated and rapid. READ-TB correlated with the MBLA when 85 human sputum samples were directly compared (R2 = 0.74).

Conclusions
READ-TB is an improved version of the MBLA and is available to be adopted by clinical microbiology laboratories as a tool for tuberculosis treatment monitoring. READ-TB will have a particular impact in low- and middle-income countries (LMICs) for laboratories with no BSL-3 laboratory and for clinical trials testing new combinations of anti-tuberculosis drugs.
Using modified trapping regimes to understand the behavioral and spatial ecology of Philornis downsi (Diptera: Muscidae)
Authors: Boulton Rebecca A , Cahuana Andrea , Lahuatte Paola F , Ramírez Erika , Sevilla Christian , Causton Charlotte E 
Published: March 2024

Abstract
The avian vampire fly Philornis downsi (Dodge & Aitken) (Diptera: Muscidae) is native to continental South America and the Caribbean, but invasive in the Galapagos Archipelago. The larvae of P. downsi feed on the blood and tissues of the nestlings of 75% of the small land bird species that are endemic or native to Galapagos, causing high in-nest mortality and severe population declines in some species. Efficient trapping techniques are vital to safeguarding these birds in the short term as well as for monitoring fly populations, but basic information about the ecology of the fly is still needed to help develop a species-appropriate trapping method. In this study, we used a novel trapping regime with a vertical distribution to make inferences about P. downsi’s behavioral and spatial ecology and to optimize trap catch. Our results showed that male and female P. downsi were trapped in greater numbers below the canopy (3.1–7.5 m), lower down than other commonly caught insect species (5.1–11.5 m). Notably, the effect of trap height remained consistent across seasons and different weather conditions. These findings suggest that P. downsi tend to move at heights where their hosts nest (at or below the canopy) and do not spend time above the canopy. This also makes it unlikely that strategies such as hill-topping or aerial swarming are being used to locate mates. As such, trapping and control efforts should be focused below the canopy in forests with similar canopy heights to effectively capture P. downsi and reduce bycatch of other insects.