bluuebunny/crossref_metadata_2025 huggingface dataset:
Rheological and functional characteristics of starch and flour on different drying methods from Beneng Taro as sustainability products from agricultural in Banten
Authors: Jufrinaldi  , Sitanggang Azis Boing , Purwani Endang Yuli , Budijanto Slamet
Published: October 2023

Beneng Taro is a type of taro found in Banten agricultural but has not been appropriately utilized. The drying process is critical since temperature changes will result in various properties. This research aimed to evaluate the rheology and functional characteristics of starch and flour made from Beneng Taro dried in the sunlight and hot air as sustainability products of it. This research contains the extraction of starch, the production of flour, and characterizing the starch and flour produced. The rheological characteristics of the flour and starch from the can be model using the Herschel-Bulkley. Starch and flour showed non-Newtonian shear-thinning flow characteristics, according to the flow behavior index. The difference in the consistency index value of flour is significant, where flour dried with sunlight shows a higher value. Both starch and flour show a sharp decrease in viscosity at low shear rates. The value of the starch and flour’s swelling power shown that cabinet drying was superior to drying outdoors in the sun. The solubility index undergoes the same phenomenon. In contrast to water and oil holding capacity, sun drying shows a higher value. Knowing the characteristics of the starch and flour produced can be applied as a food source.
Calcium oxalate levels, glucomannan levels, and antioxidative activities of different sized Amorphophallus oncophyllus particles and the maceration of Strobilanthes crispus
Authors: Aprilia V , Kusumawardani N , Fauzi R , Estiningsih D , Kusumawati D
Published: October 2023

Porang (Amorphophallus oncophyllus) is a type of tuber widely planted in Indonesia. It has a high glucomannan content, but its use is limited due to high calcium oxalate content. However, it has previously been shown that the maceration of porang with the ethanolic extract of Strobilanthes crispus (SC) can serve to reduce its calcium oxalate content. This study sought to determine the impact of sieving in combination with ethanolic extract of SC maceration on the calcium oxalate levels, glucomannan levels, and antioxidant activities of different sized particles of porang. The calcium oxalate levels were analyzed by the atomic absorption method, whereas the glucomannan levels were determined based on the yield of glucomannan derived from the ethanolic extraction process. The porang particles were then analyzed to assess their antioxidant activities using DPPH (1,1-diphenyl-2-picrylhydrazyl). The particles were grouped into six in different particle size and maceration: AX, AY, AN, BY, and BN. The results revealed that porang with a particle size of <40 mesh that was macerated with SC exhibited lower calcium oxalate levels and higher glucomannan levels than porang with a particle size of >40 mesh. The antioxidant activity of the porang decreased after maceration with the ethanolic extract of SC.
Physicochemical and organoleptic characterization of dried tapioca noodles with sorghum-moringa substitution
Authors: Hamidah R S , Sadek N F , Murwani I A
Published: October 2023

Sorghum and moringa leaf are rich in macro- and micronutrients and bioactive components, known to have health-functional benefits. This research aimed to characterize tapioca noodles’ physicochemical and sensory acceptance after sorghum and moringa substitution. In this study, four noodle formulations were made based on the basic mixture composition, namely the ratio of tapioca flour and sorghum flour, each of 80:20 (S2T8); 70:30 (S3T7), 60:40 (S4T6), and 50:50 (S5T5). Five percent of moringa leaf flour was added to the formulation. The dried noodles were then analyzed for their physical characteristics (texture and color), cooking quality (water absorption, volume increase, and cooking loss), and sensory acceptance using a hedonic test. Increased sorghum proportion resulted in increased yellowness and cooking loss and decreased elongation, hardness, and overall acceptance of the product. The de Garmo effectiveness index calculation found that 20% sorghum substitution with 5% moringa leaf powder (S2T8) showed the best performance of dried tapioca noodles.
Effect of various packaging on the quality of Gayo arabica coffee processed using full-washed method
Authors: Sinaga H , Karo-Karo T , Nurminah M , Hilman A , Sitanggang A E
Published: October 2023

Gayo Arabica coffee is known as one of the best quality coffees in the world. This study examined physical and chemical properties of Gayo Arabica coffee which was processed using the full-washed method after being stored for 4 months in several types of packaging (Grain Pro, Aluminum Foil, Plastic sack, Cloth sack, and Ramie sack). The parameters analyzed were moisture content, ash content, lipid content, protein content, caffeine content, total phenol, pH along with color and specific volume. After being stored for 4 months at room temperature, different type of packaging gave a significant effect on moisture, ash, lipid, protein, caffeine, total phenol and pH of the coffee. In addition, various packaging carried out in this experiment did not change the color and specific volume of the bean. Coffee plantations in Indonesia are very wide, so that the plants will certainly have a positive impact on the surrounding environment and support biodiversity. Further research is continued by extending stored period of the green bean and knowing the impact of packaging on the coffee quality.
Color stability of anthocyanin extract from wastewater of purple sweet potato starch processing
Authors: Julianti E , Ridwansyah  , Yusraini E
Published: October 2023

The wastewater from PSP starch extraction was then filtered, concentrated in a rotary evaporator at 55°C, and investigated to evaluate its stability which was influenced by pH, light, storage temperature, heat, sugar, and salt concentrations. The results showed that the highest anthocyanin content, antioxidant activity and color stability were found in wastewater extracted from starch using water as an insulating agent for starch. The color of PSP starch wastewater using water as starch isolation agent has good stability for 15 days of storage at dark room temperature, and is stable at pH 3.0 – 9.0, heated at 100°C for 15 minutes, and in a solution of 10-50% and 10-30 % each concentration of sugar and salt.
Feasibility of utilization of eucalyptus leaves (Eucalyptus spp) from logging waste in industrial plantation forests to produce essential oils
Authors: Purwoko A , Azhar I , Damanik S E , Taufik W B N E
Published: October 2023

Eucalyptus is a type of industrial plantation forest (HTI) tree that has high economic value. Almost all parts of eucalyptus can be used. In addition, wood can be used as raw material for pulp, leaves and twigs containing cineol can be used as raw material for essential oils. This study aims to analyze the feasibility of using eucalyptus leaves from a financial perspective for essential oil production in the plantation forest area of PT. Toba Pulp Lestari Tbk. The analytical method used is descriptive analysis, financial analysis with two selling price scenarios, namely the high target scenario and the low target scenario with the criteria of Net Present Value (NPV), Benefit Cost Ratio (BCR), and Internal Rate of Return (IRR). The results showed that the use of eucalyptus leaves as a raw material for essential oils from logging waste in plantation forest areas is financially feasible. With details of the high target scenario, it produces an NPV value of IDR 134,903,510,450 (USD 8,895,714.5), an IRR value of 33.01% and a BCR value of 3.76. The NPV value for the low target scenario is IDR 84,029,947,498 (USD 5,541,045), the IRR value is 21.90% and the BCR value is 2.72.
Use of Yellow Sticky Trap (YST) and coffee experts (pakar kopi) reduces coffee pest attacks in Perteguhan Hamlet, Telagah Villages, Langkat District, North Sumatra
Authors: Siregar A Z , Tulus
Published: October 2023

Telagah is one of the village located in Sei Binge Subdistrict, Langkat District, North Sumatra Province with coordinate 03 18 43.26” North and latitude 98 23 47.70” East Longitude. The area of Telagah village reaches 53.38 km with a height of the place reaches 823.7m above sea level. The beauty of nature with cool air through the seasons is a magnet for nature and adventures visitors because this is the ‘home’ to see how the ecosystem is extraordinary. The tour starts from a phenomenal matchmaking view, Adem Peak in Perteguhan Hamlet with coffee plantations of farmers in the middle of a wild forest so exotic, stunning and challenging. Otherwise, use of Yellow Sticky Trap (YST) catches 6 pests, such as: Hypothenemus hampeii, Xylosandrus compactus, Coccus viridis, Pseudococcus citri, Zeuzera coffeae and Sanurus indecora, while used by ethanol and methanol attractant showed variances of trapped pests. The Coffee Expert (Pakar Kopi) recorded 6 pests, 5 diseases and 28 symptoms for detecting pests and diseases in agricultural and plantation crop commodities are very helpful for human work and farmers in the future.
Mapping spatial patterns in Tinondo Swamp, East Kolaka Regency to increase land productivity
Authors: Syaf H , Saili T , Taridala S , Yasin A
Published: October 2023

The development of land use activities in the Tinondo Swamp promotes the acceleration of spatial planning to ensure sustainability. This research aimed to evaluate land use in Tinondo Swamp and to provide alternative areas in the spatial plan of the east Kolaka regency. Primary and secondary data were collected using survey methods. The research used qualitative and quantitative methods to analyze the deepening and scanning of autopilot aircraft, the environmental carrying capacity, linkages and existence of linkages with the community, the needs of facilities and infrastructure, and spatial analysis. The results showed that the survey area of the Tinondo Swamp was 5,699.41 hectares, consisting of 11 land-use types. There are swamps with an area of 1,999.34 hectares (35.08%), settlements of 133.41 hectares (2.34%), the company’s Base Camp of 0.94 acres, the forest of 104.65 hectares (1.84%), swamp forests of 178.02 hectares (3.12%), roads of 26.22 hectares (0.46%), canals of 51.59 hectares (0.91%), mixed gardens of 489.88 hectares (8.60%), oil palm plantations of 1,178,298 hectares (20.67%), rice fields of 1,536,096 hectares (26.95%), and open land of 0.96 hectares. Furthermore, the total survey area that is available and planned for was 1,999.34 hectares.
Diversity, distribution and conservation status of the world’s smallest fish, Paedocypris progenetica
Authors: Hussin N J , Azmir I A , Esa Y , Ahmad A
Published: October 2023

Paedocypris progenetica, the smallest fish in the world and recorded as Near Threatened by the IUCN Red List due to a large population declined. This condition caused survival threats on the population of Paedocypris. Thus, the objective of this study is to examine the species of Paedocypris in the selected peat swamp area based on their diversity, distribution, and conservation status. A total of 66 individuals were collected from February 2019 to September 2021 from three out of four selected sampling area, comprising of two species namely Paedocypris progenetica (TL: 6.63-12.50 mm) and Paedocypris mircromegethes (TL: 8.89-10.60 mm). The results displayed that P. progenetica was found at two sampling locations and dsitinguished the greater in local distribution (LD) which is 50% followed by P. micromgethes (25%) represented the lowest distribution. Moreover, parameter measurements (in situ) of water quality in the blackwater peat swamp revealed temperatures ranging from 23°C to 25.3°C while pH between 4.0-6.9. The population trend for Paedocypris genus is declining due to continuing loss and degradation of blackwater peat swamp habitat which is considered to be the greatest threat.
Growth of seaweed Kappaphycus alvarezii co-cultivated with Sargassum plagiophyllum using the long line method
Authors: Setiawan F , Aslan L O M , Iba W , Yusnaini  , Ruslaini  , Balubi M , Hafid Harapin
Published: October 2023

The use of smaller seed weights < 20g has never been done for cultivating S. plagiophyllum. The study of cultivation of both species S. plagiophyllum (SP) and K. alvarezii (KA) simultaneously had never been done previously. This research was conducted in Bungin Permai coastal waters, South Konawe regency. This research aim was to examine the most suitable wet initial weight for better growth (10,15, 20g) on the growth of both species’ seaweed. The collecting data were analyzed by factorial completely randomized design with three replications. Yields were observed every 9,18,27,36,45 days of the growth period. The results showed that S. plagiophyllum had significantly higher different DGR than those of K. alvarezii (P<0.05) during cultivation period. No interaction between species and wet initial weight was found (P>0.05). In addition, the species of seeds influence the DGR. Seed of SP had higher DGR than KA, but the initial wet weight of the seeds only influences at the initial cultivation period (9th day). Broken thallus was found in the 10,15,20g seeds. The percentage of thallus damage in SP tends to be higher than KA. DGR at 10g seed weight of both species was significantly higher than other seed weights (15g and 20g; P<0.05).
Seasonal grass production and carrying capacity of buffalo grazing area in Paminggir, South Kalimantan
Authors: Sumantri I , Widi T S M , Prastowo S , Hanafi
Published: October 2023

The population and performance of Kalimantan swamp buffalo are declining. Diminishing grazing area and pasture biomass availability, especially in the rainy season, contribute to inadequate buffalo feed consumption. This study was conducted to investigate the seasonal productivity of palatable native grasses and to estimate the carrying capacity of the swamp grazing area. One year of observation indicated that kumpai banta and sumpilang had higher dry matter production in the deep-water season, whereas kumpai minyak was in the shallow-water season, and padi hiyang had similar production in both seasons. Dry matter production in the deep-water season was higher than in the shallow-water season (1.29 vs 1.15 ton DM/ha/month) as well as for the carrying capacity of swamp grazing area (0.044 vs 0.029 AU/year). It is concluded that the swamp grazing area in the Paminggir sub-district could not carry the existing buffalo population.
The biology and preying abilities of ladybird beetle (Coccinella transversalis Fabricius) on Myzus persicae (Homoptera: Aphididae)
Authors: Sidauruk L , Panjaitan E , Sipayung P
Published: October 2023

The use of predators in biological control has been widely known to reduce pest populations. The research aim is to determine the biology and preying abilities ladybird beetle, a species of family Coccinellidae named Coccinella transversalis Fabricius which can be used to mass rearing on laboratory for augmentation and conservation purpose. This study directed at research facility at Methodist University of Indonesia with descriptive methods. Samples collecting from horticultural cultivation at Karo District, then kept in maintenance jar with substitute food and real food Myzuz persicae as standard mass rearing technique for the coccinellid. The results showed that egg incubation was 3.2±0.76 days. There are four instars of larval with lifetime 2.67±0.20 days, 2.87±0.26 days, 2.91±0.53 and 3.42±0.75 days respectively. Prepupae was 1.62±0.56 days and pupae was 3.11±0.81 days. Life period of female was 35.05±3.80 days and male 25.75±3.14 days. The female potential produce egg was 118.4±20.14 eggs and percentage of egg hatching 85.0±6.37%. The survival rate from larvae to imago was 48.8±5.84%, which means half of the larvae succeeded becoming an imago. Preying abilities for aphid at larva instar I until instar IV, female and male were 24.55±3.28, 44.55±6.63, 89.90±13.41, 174.50±27.7, 973.67±29.21 and 786.31±14.77 aphids respectively.
Identification of adulterated rice bran with rice husks by using the image analytics
Authors: Albarki H R , Agustin A F , Permana A T , Jayanegara A
Published: October 2023

Rice bran is often adulterated with milled rice husks which can lead to losses and decreased production of livestock. Testing of rice bran adulteration is still carried out manually which is quite subjective, and thus it is necessary to test using the image analysis method based on convolutional neural network (CNN) through a visual image analysis process. The purpose of this study was to evaluate the accuracy of training, validation, and test data on rice bran adulteration with rich husks using the CNN-based image analysis. This study employed staining treatment using phloroglucinol. The stages of this research consisted of the process of mixing forgery, colouring treatment, taking pictures, sharing data, and building the CNN model. This study found that the results of the accuracy of training data, validation data, and test data with phloroglucinol staining treatment had accuracy that was still far from 100% accuracy. This result is due to the epoch value, quantity of datasets, and the different viewing angles when capturing an image.
Effectiveness equilibration time on the quality of sperm buffalo in diluent tris yolk eggs with 4 % extract skin mangosteen (Garcinia mangostana L.)
Authors: Yendraliza  , Nurcholish F , Handoko J , Sianturi R S G , Kusumaningrum D A
Published: October 2023

A comfortable livestock environment will produce good sperm productivity. Sperm dilution is done so that rural communities can feel the benefits. This study aims to determine the best equilibration time to produce high motility, intact plasma membrane values with low abnormality values in buffalo spermatozoa. This research used a completely randomized design (CRD) with four treatments and ten replications. Sperm came from three buffalo kept at the Ciawi Balitnak. The research treatment consisted of equilibration times of two, three, four and five hours. The parameters measured were sperm motility, abnormality, and intact plasma membrane (IPM). Equilibrium time does not affect buffalo sperm motility, abnormalities, and IPM. The range of motility, abnormalities, and IPM was 43.75%-55.00%; 20.25%-29.00%; 71.75%-74.75%. Conclusion; An equilibration time of two hours can maintain motility, abnormality, the intact plasma membrane of buffalo sperm with egg yolk tris diluent, and the addition of 4% mangosteen peel extract which was suitable for artificial insemination. The application can improve the standard of living of the community through increased meat production.
Preliminary study on local Indonesian sheep MC4R gene as a prospective marker for sustainable high production trait
Authors: Adani F , Maharani D , L Sari A P Z N , Ibrahim A , Panjono
Published: October 2023

A prospective genetic marker to archive for sustainable growth traits of local Indonesian sheep is the Melanocortin-4 Receptor (MC4R) gene, which arrange feeding behavior. This study were examined the MC4R gene of Indonesian sheep for polymorphism and restriction enzyme for PCR-RFLP within the partial coding sequence (CDS) and 3’UTR regions. A 642 bp of PCR product was amplified from sixteen blood samples (Sakub: 2, Wonosobo: 3, Sapudi: 3, Garut:3, and Garut-Dorper cross: 2). Sequence alignments between the samples and GenBank (NC_056076) discovered five SNPs (CDS: SNPs 1039A>G and 1068G>C, 3’UTR region: SNPs 1403G>A, 1511C>A and 1526G>C). The SNP 1039A>G was categorized as a missense mutation (Met to Val). However, SNP 1068G>C was a silent mutation (Ala to Ala). The restriction enzyme analysis showed that SNPs 1039A>G and 1403G>A were recognized by BssSI and SfaNI. SNPs 1068G>C, 1511C>A and 1526G>C were not recognized by the enzyme. In conclusion, the MC4R gene of Indonesian has five SNPs discovered, among other two SNPs in CDS and three SNPs in 3’UTR region. BssSI and SfaNI enzymes are eligible for further genotyping of sheep samples using the PCR-RFLP method.
A simple method to prepare carbon-based mesoporous materials by coal gasification of fine slag and its application in phenol adsorption
Authors: Guo Lei , Zhang Tong , Dai Xiaomin , Cao Baowei , Xu Yunhua , Yang Yonglin
Published: October 2023

Phenol is a common organic pollutant that is difficult to degrade and widely exists in all kinds of wastewater. In this study, an economical and environmentally friendly alternative process for phenol-containing wastewater has been developed using porous nano-adsorption material (PNAM) prepared from coal gasification fine slag. The morphology, crystal structure, surface functional groups, gap structure, and specific surface area of PNAM were characterized by SEM, XRD, FT-IR, and BET. The effects of adsorbent dosage, temperature, pH, and reaction time on adsorption were further investigated. In addition, the adsorption kinetics, thermodynamics, and adsorption mechanism were explored. The results show that the surface area of PNAM is high, up to 602 m2 g−1, and the pore volume is 0.507 cm3 g−1. Adsorption processes mainly occur in mesopores between 2 and 5 nm, including physical and chemical adsorption, and here chemical adsorption plays a significant role. The adsorption rate of phenol in a 1000 mg l−1 simulated phenol solution by PNAM reaches 96.14%, while the unit adsorption capacity is 32.045 mg g−1. As a result, it is expected that employing coal gasification fine slag to prepare adsorption materials for phenol-containing wastewater treatment may be an economically feasible and environmentally sustainable strategy.
Contamination reduction for 150 mm SiC substrates by integrating CMP and Post-CMP cleaning
Authors: Hsieh Chi-Hsiang , Lee Ming-Hsun , Chen Chao-Chang A , Tu Chang-Ching , Kuo Hao-Chung
Published: October 2023

The quality of silicon carbide (SiC) substrates has great influence on the quality of the epitaxial layers atop. During the epitaxial growth, crystallographic defects and substrate contaminations may transform to various surface defects, such as carrots, polytype inclusions and scratches, which are detrimental to the performance and reliability of SiC devices. In general, chemical mechanical polishing (CMP) and post-CMP cleaning are the last two steps before the epitaxial growth, playing critical roles in controlling the scratch and contamination levels on the SiC substrates. In this article, the methods for reducing the aluminum (Al) and manganese (Mn) metal contaminations as well as other surface particle contaminations are investigated. We found that different commercial CMP slurries may lead to different contamination levels. Most importantly, by adding a scrubber cleaning step prior to the conventional RCA cleaning process, the contamination levels can be greatly reduced, achieving the quality for mass production.
Monitoring of thermo-cycles in fibre laser welding of duplex stainless steel 2205 sheets and its correlation with microstructures and mechanical properties
Authors: Ahmad Gulshad Nawaz , Singh Nirmal Kumar , Tripathi Brajendra Nath , Askari Syed Sadique Anwer , Pandey Shatrudhan , Zare Ali , Hasnain S M Mozammil
Published: October 2023

The study reports the influence of change in the heat supplied (43 J mm−1 to 18.5 J mm−1) on the microstructures as well as mechanical properties of weld joints obtained by welding of Duplex stainless steel 2205 using fibre laser. In-process thermal monitoring of the molten weld pool was carried out using IR pyrometer. Cooling rates (i.e. solidification and solid) were calculated from the thermo-profiles of weld pool, and it increases with the decrease in heat input. From the optical images, it is observed that columnar grains originated from the fusion zone walls and merged at the center. Since, solidification front velocity is comparable on both sides’ leads to a central edge. Ferrite phase content observed in fusion zone microstructure, increases with the increase in solid cooling rate. The result suggests that the joints fabricated at lowest heat input displayed highest tensile strength. The maximum tensile strength been reported to be 872.5 ± 10.8 MPa, and failure occurred at parent metal. Tensile strength of weld joints of DSS 2205 was found to have improved with increasing cooling rate. Higher cooling rate results in the formation of fine dendritic grains as well as higher ferrite content in the weld metal.
Design and analysis of multi-material structures of 3D printed implants of mandible
Authors: K Kalaithendral , Karuppudaiyan S , Roy Sandipan
Published: October 2023

Significant advances in 3D printing technology have paved the way for improvements in the integrity and biological characteristics of polymer implants. The principal objective of this research is the construction of a heterogeneous implant structure using a multi-material approach and 3D printing. Due to their advantageous strength-to-weight ratio, biocompatible polymers have an increasing application in the field of medicine. The osteo-integration process, in which implants bind to the bone over time, can be made more effective by incorporating these materials into implants. In this work, we focused especially on analyzing the strength and integrity of polymer material implants that were created using a combination of different materials, and their stress distribution, and the deformation of these multi-material structures when they were subjected to physiological loading through finite element analysis. The evidence from the frontal bite condition has led to some fascinating conclusions. The variations in stress were observed in homogenous structures, with values ranging from 37.42 MPa for the TPU to 41.07 MPa for the PETG. In contrast, stress distributions in multi-material constructions ranged from 52.31 MPa (in the case of TPU +TPU) to 73.55 MPa (in the case of PLA+ PCL). Similarly, the maximum deformation in homogeneous constructions ranged from 0.81mm (PLA) to 6.85mm (PCL). The deformation of multi-material structures composed of several different materials ranged from 0.68mm (PLA+ PLA) to 5.74 mm (PCL+PCL).These findings provide conclusive evidence that multi-material architectures have a considerable impact on known stress and strain levels. Particularly noteworthy is the fact that the combination of PLA+PLA and PLA+PETG displayed deformation that was equivalent to that of the intact bone model while having lower stress levels. The results of this study provide useful information that can be used to select optimal multi-material combinations that can be 3D printed for implants.
Assessing dynamic energy efficiency in the organization for economic Co-operation and development (OECD) countries and China during COVID-19
Authors: Wu Dan , Hung Fang-Chen , Lin I-Fang , Lu Ching-Cheng
Published: October 2023

According to the October 2021 Glasgow Climate Agreement reaffirming the cooling goals of the Paris Agreement and the Glasgow Leaders Declaration on Forests and Land Use, this research applies the Super-D-DDF model to non-oriented variable returns to scale to evaluate the Organization for Economic Cooperation and Development (OECD) and China (38 countries in total), collect important production and energy variables from 2016 to 2020, and measure the total efficiency of energy dynamics and its changes during COVID-19. The empirical results are as follows. (1) Comparing energy efficiency from 2016 to 2018 and 2019 to 2020 (during COVID-19), we find that most countries (22 countries) changed from high efficiency to low efficiency, showing a decrease in energy efficiency. (2) The emissions of carbon dioxide in China in 2020 are close to the sum of OECD carbon dioxide emissions, highlighting that the energy policy in China should be adjusted appropriately. (3) From 2016 to 2020, the forest area of various countries has a significant impact on overall energy efficiency performance. In line with the United Nations’ policy goals, countries should adjust forest protection policies to effectively reduce carbon emissions.
OffRisk: a docker image for annotating CRISPR off-target sites in the human genome
Authors: Barkai Gil-ad , Malul Tal , Eliaz Yossi , Eyal Eran , Veksler-Lublinsky Isana
Published: October 2023

The CRISPR-Cas9 system has been adapted to achieve targeted genome editing as well as transcriptional control by customizing 20-nt guide RNA (gRNA) molecules for desired regions in the target genome. Designing gRNAs must consider nonspecific and unintended binding, known as off-targets, since these may have potentially harmful effects. To assist in gRNA design, we have developed OffRisk. This Docker-based tool annotates off-target sites in the human genome and assigns them a potential risk label by incorporating functional and regulatory information at different molecular levels.

Availability and implementation

OffRisk is available at https://github.com/IsanaVekslerLublinsky/OffRisk and https://github.com/IsanaVekslerLublinsky/OffRisk-ui (including code, user guide, docker installation guide, and running examples).

All processed datasets are available at https://zenodo.org/record/8289271.
Aliro: an automated machine learning tool leveraging large language models
Authors: Choi Hyunjun , Moran Jay , Matsumoto Nicholas , Hernandez Miguel E , Moore Jason H
Published: October 2023

Motivation

Biomedical and healthcare domains generate vast amounts of complex data that can be challenging to analyze using machine learning tools, especially for researchers without computer science training.

Results

Aliro is an open-source software package designed to automate machine learning analysis through a clean web interface. By infusing the power of large language models, the user can interact with their data by seamlessly retrieving and executing code pulled from the large language model, accelerating automated discovery of new insights from data. Aliro includes a pre-trained machine learning recommendation system that can assist the user to automate the selection of machine learning algorithms and its hyperparameters and provides visualization of the evaluated model and data.

Availability and implementation

Aliro is deployed by running its custom Docker containers. Aliro is available as open-source from GitHub at: https://github.com/EpistasisLab/Aliro.
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data
Authors: Hsieh Ping-Han , Lopes-Ramos Camila Miranda , Zucknick Manuela , Sandve Geir Kjetil , Glass Kimberly , Kuijjer Marieke Lydia
Published: October 2023

Motivation

Gene co-expression measurements are widely used in computational biology to identify coordinated expression patterns across a group of samples. Coordinated expression of genes may indicate that they are controlled by the same transcriptional regulatory program, or involved in common biological processes. Gene co-expression is generally estimated from RNA-Sequencing data, which are commonly normalized to remove technical variability. Here, we demonstrate that certain normalization methods, in particular quantile-based methods, can introduce false-positive associations between genes. These false-positive associations can consequently hamper downstream co-expression network analysis. Quantile-based normalization can, however, be extremely powerful. In particular, when preprocessing large-scale heterogeneous data, quantile-based normalization methods such as smooth quantile normalization can be applied to remove technical variability while maintaining global differences in expression for samples with different biological attributes.

Results

We developed SNAIL (Smooth-quantile Normalization Adaptation for the Inference of co-expression Links), a normalization method based on smooth quantile normalization specifically designed for modeling of co-expression measurements. We show that SNAIL avoids formation of false-positive associations in co-expression as well as in downstream network analyses. Using SNAIL, one can avoid arbitrary gene filtering and retain associations to genes that only express in small subgroups of samples. This highlights the method’s potential future impact on network modeling and other association-based approaches in large-scale heterogeneous data.

Availability and implementation

The implementation of the SNAIL algorithm and code to reproduce the analyses described in this work can be found in the GitHub repository https://github.com/kuijjerlab/PySNAIL.
Geographical patterns in mandible variation of the common shrew (Sorex araneus) in Europe
Authors: Farková Lucie , Lázaro Javier , Kryštufek Boris , Vohralík Vladimír
Published: October 2023

The common shrew (Sorex araneus) is one of the most studied shrew species of the Western Palaearctic. Despite this, the general drivers underlying morphological variation still remain unclear. Here we provide evidence for contradictory effects of climatic and geographical factors on the mandible of the common shrew. At the continental scale there is a negative correlation between body- and skull-size and latitude and longitude but at regional scales such an association is often not apparent; in fact, in some cases body size and skull size follow the opposite trend and observations at various scales yielded contradictory results. We studied shrew mandibles using geometric morphometrics and tested for correlations of their size and shape with selected geographical and climatic variables. We examined 1155 mandibles from 29 European localities and found significant interpopulation differences in both size and shape. Centroid size negatively correlated with latitude. We also found that centroid size was significantly correlated with altitude and annual precipitation. Our results confirmed an inverse Bergmann’s rule relationship in S. araneus along the transect from the Baltic to the Adriatic Sea. Regarding mandible shape, Slovenian shrews were the most distant from all other studied populations. We discuss how altitude and precipitation can influence the morphology of the common shrew.
Disease from opposing forces in regulatory control
Authors: Frank Steven A
Published: October 2023

Danger requires a strong rapid response. Speedy triggers are prone to false signals. False alarms can be costly, requiring strong negative regulators to oppose the initial triggers. Strongly opposed forces can easily be perturbed, leading to imbalance and disease. For example, immunity and fear response balance strong rapid triggers against widespread slow negative regulators. Diseases of immunity and behavior arise from imbalance. A different opposition of forces occurs in mammalian growth, which balances strong paternally expressed accelerators against maternally expressed suppressors. Diseases of overgrowth or undergrowth arise from imbalance. Other examples of opposing forces and disease include control of dopamine expression and male versus female favored traits.
Nationwide time trends in patients hospitalized for acute coronary syndrome: a worrying generational and social effect among women
Authors: Grave Clémence , Gabet Amélie , Cinaud Alexandre , Tuppin Philippe , Blacher Jacques , Olié Valérie
Published: October 2023

Aims

To estimate the time trends in the annual incidence of patients hospitalized for acute coronary syndrome (ACS) in France from 2009 to 2021 and to analyse the current sex and social differences in ACS, management, and prognosis.

Methods and results

All patients hospitalized for ACS in France were selected from the comprehensive National Health Insurance database. Age-standardized rates were computed overall and according to age group (over or under 65 years), sex, proxy of socioeconomic status, and ACS subtype [ST-segment elevation (STSE) and non-ST-segment elevation]. Patient characteristics and outcomes were described for patients hospitalized in 2019. Differences in management (coronarography, revascularization), and prognosis were analysed by sex, adjusting for cofonders. In 2019, 143,670 patients were hospitalized for ACS, including 53,227 STSE-ACS (mean age = 68.8 years; 32% women). Higher standardized incidence rates among the most socially deprived people were observed. Women were less likely to receive coronarography and revascularization but had a higher excess in-hospital mortality. In 2019, the age-standardized rate for hospitalized ACS patients reached 210 per 100 000 person-year. Between 2009 and 2019, these rates decreased by 11.4% (men: −11.2%; women: −14.0%). Differences in trends of age-standardized incidence rate have been observed according to sex, age, and social status. Middle aged women (45–64 years) showing more unfavourable trends than in other age classes or in men. In addition, among women the temporal trends were more unfavourable as social deprivation increased.

Conclusion

Despite encouraging overall trends in patients hospitalized for ACS rates, the increasing trends observed among middle-aged women, especially socially deprived women, is worrying. Targeted cardiovascular prevention and close surveillance of this population should be encouraged.
IRplus: An Augmented Tool to Detect Inverted Repeats in Plastid Genomes
Authors: Díez Menéndez Carmen , Poczai Peter , Williams Bernardo , Myllys Leena , Amiryousefi Ali
Published: October 2023

High-throughput sequencing methods have increased the accessibility of plastid genomes, which are crucial for clarifying phylogenetic relationships. Current large sequencing efforts require software tools for routine display of their distinctive quadripartite structure, which is denoted by four junction sites. By concentrating on these junctions and their close vicinity, IRscope has emerged as the standard tool for detection of this structure and creating simplified comparative graphical maps of plastid genomes. Here, we provide an augmented version (IRplus) that encompasses a novel set of functions such as integrated error detection, flexible color schemes, and an upgraded method to detect inverted repeats in genomic sequences. Spanning across the plant tree of life, IRplus allows the quick visualization of various sets of plastid genomes and features, next to smooth interoperability with other widely used annotation file formats and platforms. The IRplus can be accessed at https://irscope.shinyapps.io/IRplus/, and source codes are freely available at https://github.com/AmiryousefiLab/IRplus.
Life Events and Loneliness Transitions Among Middle-Aged and Older Adults Around the World
Authors: Sheftel Mara Getz , Margolis Rachel , Verdery Ashton M
Published: October 2023

Objectives

Adult loneliness is a substantial social problem and a growing point of concern for policymakers around the world. We assess whether the predictors of loneliness onset among middle-aged and older adults vary from country to country in a large array of settings across world regions. Taking a life course perspective, we focus on common life events in our focal age range, including changes in partnership, coresidence, work, and health, and we test whether changes in them have comparable prospective associations with loneliness onset in different countries.

Methods

We draw on respondent-level data from a diversity of world regions surveyed in 7 harmonized cross-national studies in 20 countries, representing 47% of the global population over the age of 50. Our innovative longitudinal approach estimates prospective transition probability models that examine how each life event predicts the transition into loneliness.

Results

Despite substantial variation in the prevalence of loneliness and life events across the range of countries in our sample, our results highlight consistency in the predictors of loneliness transitions. Family and household changes like divorce, coresidence, and especially widowhood are paramount predictors of loneliness transition across settings, with changes in work and health playing more minor and less universal roles.

Discussion

The results demonstrate the importance that family and household connections play in determining loneliness at these ages. These findings suggest that addressing late-life loneliness may require a focus on key life events, especially those concerning changes in families and households.
Locating tectonic tremors with uncertainty estimates: time- and amplitude-difference optimization, wave propagation-based quality control and Bayesian inversion
Authors: Akuhara Takeshi , Yamashita Yusuke , Sugioka Hiroko , Shinohara Masanao
Published: October 2023

The accurate location of tectonic tremors helps improve understanding of their underlying physical processes. However, current location methods often do not statistically evaluate uncertainties to a satisfactory degree and do not account for potential biases due to subsurface structures not included in the model. To address these issues, we propose a novel three-step process for locating tectonic tremors. First, the measured time- and amplitude differences between station pairs are optimized to obtain station-specific relative time and amplitude measurements with uncertainty estimates. Secondly, the time– and amplitude–distance relationships in the optimized data are used to roughly estimate the propagation speed (i.e. shear wave velocity) and attenuation strength. Linear regression is applied to each event, and the resulting velocity and attenuation strength are used for quality control. Finally, the tremor location problem is formulated within a Bayesian framework where the model parameters include the source locations, local site delay/amplification factors, shear wave velocity and attenuation strength. The Markov chain Monte Carlo algorithm is used to sample the posterior probability and is augmented by a parallel tempering scheme for an efficient global search. We tested the proposed method on ocean-bottom data indicating an intense episode of tectonic tremors in Kumano-nada within the Nankai Trough subduction zone. The results show that the range of the 95 per cent confidence interval is typically <7 km horizontally and <10 km vertically. A series of experiments with different inversion settings reveals that adopting amplitude data and site correction factors help reduce random error and systematic bias, respectively. Probabilistic sampling allows us to spatially map the probability of a tremor occurring at a given location. The probability map is used to identify lineaments of tremor sources, which provides insights into structural factors that favour tremor activity.
Cupferron impairs the growth and virulence of Escherichia coli clinical isolates
Authors: Palma Francesca , Dell'Annunziata Federica , Folliero Veronica , Foglia Francesco , Marca Roberta Della , Zannella Carla , De Filippis Anna , Franci Gianluigi , Galdiero Massimiliano
Published: October 2023

Aims

Multidrug resistance is a worrying problem worldwide. The lack of readily available drugs to counter nosocomial infections requires the need for new interventional strategies. Drug repurposing represents a valid alternative to using commercial molecules as antimicrobial agents in a short time and with low costs. Contextually, the present study focused on the antibacterial potential of the ammonium salt N-nitroso-N-phenylhydroxylamine (Cupferron), evaluating the ability to inhibit microbial growth and influence the main virulence factors.

Methods and results

Cupferron cytotoxicity was checked via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and hemolysis assays. The antimicrobial activity was assessed through the Kirby-Bauer disk diffusion test, broth microdilution method, and time-killing kinetics. Furthermore, the impact on different stages of the biofilm life cycle, catalase, swimming, and swarming motility was estimated via MTT and crystal violet (CV) assay, H2O2 sensitivity, and motility tests, respectively. Cupferron exhibited <15% cytotoxicity at 200 µg/mL concentration. The 90% bacterial growth inhibitory concentrations (MIC90) values recorded after 24 hours of exposure were 200 and 100 µg/mL for multidrug-resistant (MDR) and sensitive strains, respectively, exerting a bacteriostatic action. Cupferron-treated bacteria showed increased susceptibility to biofilm production, oxidative stress, and impaired bacterial motility in a dose-dependent manner.

Conclusions

In the new antimicrobial compounds active research scenario, the results indicated that Cupferron could be an interesting candidate for tackling Escherichia coli infections.
Grit and Health-Related Quality of Life in Adolescents and Young Adults with Cancer: Mediating Role of Health Self-Efficacy and Treatment Adherence
Authors: McKelvey Elise R , Zelikovksy Nataliya , Psihogios Alexandra M
Published: October 2023

Objective

Challenges with health-related quality of life (HRQOL) are common among adolescents and young adults (AYA) with cancer. Literature on HRQOL has largely been focused on individual deficits, rather than individual strengths. The present study investigated the relations between a strengths-based concept called grit (i.e., perseverance and passion for long-term goals), self-management (i.e., health self-efficacy and adherence), and HRQOL among AYA with cancer.

Methods

Sixty-seven AYA receiving cancer treatment (Mage=17.1; 50.7% female; 25.4% Black, Hispanic, Asian, or a race other than white) and their caregivers (73.0% mothers) completed a semistructured, validated interview about adherence. AYA also completed self-report questionnaires about perceptions of their grit, health self-efficacy, and HRQOL.

Results

After controlling for sex, health self-efficacy (i.e., a cognitive self-management variable) mediated the relation between grit and HRQOL (95% confidence interval = .74–6.52). When testing adherence to medications, diet, or physical activity as mediators of the relation between grit and HRQOL, mediation models were non-significant.

Conclusions

Among AYA with cancer, this study identified grit as an individual strength associated with more positive self-management beliefs, which in turn, related to better HRQOL. This adds to a growing body of literature supporting the need for resiliency-oriented, strengths-based approaches to AYA HRQOL research. Future directions include exploring the role of caregiver grit in relation to AYA cancer self-management, given that caregivers have demonstrated a high degree of involvement in AYA cancer care.