bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of Rice Straw Adequacy as Ruminants Feed-in Java Based on Yield Area Conversion
Authors: Nugraha R I , Shiddieqy M I , Laconi E B , Jayanegara A
Published: May 2023

Java is considered a center for the ruminant population and supplies cattle and buffalo to several parts of Indonesia. Livestock population increment needs the adequacy of feed, both quantity and quality. Potential sources of feeds are therefore needed to be inventoried to ensure the sustainability of feed adequacy. This study aimed to estimate the potential amount of feed from rice straw in Java for supporting ruminant production in the region. The method of this study was descriptive and quantitative, using secondary data. The potential amount of rice straw as cattle and buffalo feed ingredients was calculated using the yield area of rice. The yield area was converted to grain production, which led to the rice straw production as feed availability. Dry matter (DM), crude protein (CP), and total digestible nutrient (TDN) contents were used as a parameter. The percentage of the three parameters was collected from previous studies. The availability of DM, CP, and TDN from rice straws was then calculated based on the Animal Unit (AU). On the other hand, feed requirement was derived from the cattle and buffalo population. The population data were converted to AU, and then the total DM, CP, and TDN requirements were calculated based on previous studies (6.25 kg DM.AU-1, 0.66 kg CP.AU -1, and 4.3 kg TDN.AU-1). The feed availability and condition in Java province were compared and classified into three categories: surplus, sufficient, and deficit. The results showed that Banten, West Java, and Central Java provinces were sufficient to feed adequacy, whereas East Java and Yogyakarta provinces were deficient. This study suggests each province should utilize alternative feed resources in addition to rice straws to ensuring a sufficient feed supply for a ruminant.
Cinnamon Java Roll Modification as Alternative Sweet Snack for Diabetes Mellitus Patients
Authors: Hangesti Emi Widyasari R. A. , Widodo Gatot , Devy  , Nurdialy Mela
Published: May 2023

One of the healthy lifestyles that continues to grow is consuming healthy food. The consumption of sweet bread in Indonesia continues to increase, and as a result, the cases of people with diabetes mellitus in Indonesia have also experienced a significant increase, for it is not recommended for people with diabetes mellitus to consume excessive amounts of sweet bread. A cinnamon roll is a dough roll sheet consisting of the cinnamon and sugar mixture (raisins or other sweet fruit ingredients) which are sprinkled on top of a thin layer of butter. Cinnamon Java Roll is a modified product of cinnamon roll with cinnamon and palm sugar with lower sugar content due to the ingredients in it, where there is a modification of the ingredients by adding palm sugar which has a lower glycemic index, and the addition of sliced dates as an additional sweetener and almond nuts for nutritional enrichment. One slice of bread contains 137 Cal of energy, 2.59 grams of protein, 4.93 grams of fat, and 22.36 grams of carbohydrates with a sugar content of 8.37 grams/serving (1 slice) and 75.34 grams/recipe (9 slices).
Scale-up of citric acid production by utilizing rice husk waste and purification using ion exchange chromatography
Authors: Siagian A A , Manurung A , Martgrita M M
Published: May 2023

Citric acid is one of the essential organic acids in human life and rice husk has the potential to be used as a substrate because it contains about 28.6-43.3% cellulose, and its use, does not compete with human needs. This research aims to increase citric acid production by using rice husk as a substrate, with a working volume of 2000 mL. In this study, it produced citric acid using submerged fermentation and Aspergillus niger at 22.42% w/v rice husk conditions, 10% w/v sucrose, 3% v/v methanol, and 400 rpm agitation. The results showed that the citric acid pH value on day 18 of fermentation was 1.9, and the concentration of citric acid after purification was 162.667 g/L, while the concentration of citric acid before purification was 148.639 g/L. The specific growth rate of Aspergillus niger obtained was 0.0863 cells/day, and the rate of reducing sugar consumption was 0.1283 g/day. The yield of Aspergillus niger biomass produced is 1.1258 cells for each g of reducing sugar, and the yield of citric acid production is 16.8144 g for each g of cell and 18.9301 g for each g of reducing sugar.
Extraction of Bio-pigments from the Green Microalgae Chlorella pyrenoidosa Under Different Solvent Ratios
Authors: Farobie Obie , Anis Latifah Aisya , Nurcahyani Puji Rahmawati , Hartulistiyoso Edy , Rahman Delicia Yunita , Fatriasari Widya , Nafisyah Ayu Lana , Amrullah Apip , Aziz Muhammad
Published: May 2023

Nowadays, the use of microalgae biomass is evolving rapidly for their various applications such as food, pharmaceutical, and cosmetics. One of the essential compounds in microalgae that have good perspectives in the market is pigment since it can be used as a natural colorant in food or cosmetics. However, the extraction of bio-pigments from the green microalgae Chlorella pyrenoidosa under different solvent ratios is still rarely reported. Therefore, this study aims to investigate the bio-pigment potential from C. pyrenoidosa extracted under different ethanol ratios. The algae-to-ethanol ratios of 1:5, 1:7.5, and 1:10 were employed in this study. Overall, C. pyrenoidosa contains total chlorophyll content much higher than carotenoids due to the fact that C. pyrenoidosa is the autotrophic microorganism that performs photosynthesis. The total chlorophyll content decreased with an increase in ethanol ratio, i.e., 134.47, 133.74, and 129.46 μg/mL at the ratio of 1:5, 1:7.5, and 1:10, respectively. In contrast, the carotenoid content slightly increased with an increase in ethanol ratio, i.e., 86.64, 87.08, 88.45 μg/mL at the ratio of 1:5, 1:7.5, and 1:10, respectively. The main chlorophyll compounds in the ethanol extract with the algae-to-ethanol molar ratio of 1:5 were identified as chlorophyll c (47.09 μg/mL), followed by chlorophyll b (38.50 μg/mL), chlorophyll a (28.67 μg/mL), and chlorophyll d (20.23 μg/mL).
A Review on used cooking oil as a sustainable biodiesel feedstock in Indonesia
Authors: Febijanto Irhan , Ulfah Fathiah , Kusrestuwardhani  , Siswanto  , Yuwono Trihadi Sudarwaji Edi
Published: May 2023

Indonesia is the world’s largest producer and consumer of palm oil. Its residents are accustomed to frying food in its food culture, hence the massive generation of used cooking oil (UCO). However, UCO has not been optimally utilized. Most is dumped into the environment, causing uncontrolled environmental pollution. The utilization of UCO as biodiesel feedstock is one solution to overcome environmental pollution while increasing its economic value. This utilization contributes to the Nationally Determined Contribution (NDC) target while simultaneously providing an additional global supply of biodiesel feedstock. The amount of UCO for biodiesel raw materials is potential to be increased further. However, the UCO collection system is extremely dependent on the existing collection system, socio-cultural and education aspects of the local community, as well as support from the local government. In Indonesia, UCO collection remains limited in a local context and is carried out partially. This study reviews several previous studies related to the potential of UCO and the environmental impact of UCO use for biodiesel. The improvement of the UCO collection management system in alignment with local socio-cultural conditions is also proposed. This paper is expected to offer a useful reference for decision-makers in updating and implementing the UCO collection method for sustainable biodiesel feedstock.
Utilization of Indigofera Leaves as Natural Dyes for Silk Fabrics
Authors: Erdawati  , Lisdiana Hayyun , Saefurahman Ganjar
Published: May 2023

Indigo is a natural blue dye produced from the leaves of the Indigofera plant, which is environmentally friendly and non-carcinogenic. This study aimed to determine the reduction potential value of molasses and brown sugar as reducing agents, to examine the effect of the hydrochloric acid concentrations and aeration time on the amount of indigo, and to test the fastness of rubbing against solar heat, dry, wet and acid on silk fabrics that were dyed by indigo with various fixators. To extract the indigo dye, the Indian glycosides contained in Indigofera leaves were hydrolyzed to indoxyl and glucose using hydrochloric acid. Indoxyl was then oxidized to indigo using molasses as a polysaccharide compound. The results showed that the concentration of 0.01 M hydrochloric acid produced the highest indigo content of 26.83 ppm, and the best aeration time was 4 hours to produce indigo with a concentration of 22.32 ppm. The effect of the fixator types produced different colors. The fixator of ferrous sulfate produced a dark blue-green color, limestone produced a light blue color, while alum produced a bright blue color. The fastness test showed the same result as the gray sale value of 4-5 meaning that there was a slight fading.
Thermogravimetric assessment for combustion characteristic of torrefied pellet biomass from agricultural solid waste
Authors: Iryani Dewi A , Rakaseri Isyaeboni , Azhar Azhar , Haryanto Agus , Hidayat Wahyu , Hasanudin Udin
Published: May 2023

This present paper is focused on the investigation of combustion characteristics of torrefied pellet biomass from agricultural waste. Four biomass pellet samples such as sugarcane bagasse, Napier grass, Palm Empty Fruit Bunches, and Cassava stem were torrefied in a designed cylinder tubular pyrolysis reactor. The reactor was set up under 30 min of residence time, and the temperature reaction was varied at 200, 250, and 300 °C in an inert atmosphere. The torrefied products were then characterized in terms of their psychochemical properties such as proximate, ultimate, calorific value, and combustion properties. The combustion properties of raw and torrefied biomass pellets during the combustion process were investigated by the thermogravimetric analyzer Exstar SII TG/DTA7300. The samples were heated at an ambient temperature up to 800 °C at a constant heating rate of airflow at 10 °C/min in airflow. The results showed that the moisture content and volatile matter of torrefied pellets decreased by 2 to 5% and 8 to 14%, subsequently. Otherwise, the fixed carbon content is up to three times higher than the raw material. The study conclusively that torrefaction can also able to enhance combustion performance in terms of ignition and burnout temperature, ignition and burnout index, and combustion rate. The results shows that, the ignition and burnout temperatures of torrefied pellets are higher than raw material. The ignition and combustion index of torrefied pellets are lower than raw material, and the torrefied pellets have a longer burning time and a higher combustion temperature.
Characterization of Gasoline, Ethanol, and Methanol Blends (GEM) With Calculation RON Target
Authors: Hanifuddin M. , Gibran Hario , Galvin Ronald , Muhammad Zaim Kamil , Anggarani Riesta , Wibowo Cahyo Setyo , Sugiarto Bambang
Published: May 2023

Fossil fuels still dominate future energy needs, while oil production has shown a declining trend over the past ten years. One solution to this condition is using new and renewable energy sources. In the transportation sector, one of the most common environmental problems resulting from the combustion of fossil fuels in internal combustion engines is emission. Mixing gasoline with alcohol is based on this problem. This paper calculates the composition of gasoline-ethanol-methanol with target RON 92, 95, and 98 with RON-based 89. The composition of this blend is calculated with linear molar calculation. Blending ethanol and methanol in gasoline also influences their chemical and physical properties. The characteristics, i.e., research octane number (RON) and density of gasoline-ethanol-methanol fuel blends of RON target 92, 95, and 98, are presented. The results of this calculation will be compared with the experiment. RON is one of the critical characteristics of the internal combustion engine’s compression ratio and combustion quality. The obtained result revealed that the average difference from the calculation with the experiment on RON is 0.73, and the density is 0.36.
Digital monitoring system for anaerobic bioreactor conditions based on information on biogas volume, biogas pressure and methane gas content
Authors: Soehartanto Totok , Putu Eka Widya Pratama I , Tanaya Jamal Fikri , Sumirman Edy
Published: May 2023

The operational conditions of the anaerobic bioreactor can be predicted using three parameters, such as biogas pressure, biogas mass flow rate, and methane gas content. This research will present a monitoring system for the operational conditions of an anaerobic bioreactor through the measurement of those operational parameters based on knowledge data. The knowledge-based monitoring system is equipped with an interface for connectivity with pressure sensor, mass flow rate and methane gas content sensor, so that it can monitor the condition of the bioreactor in real time. The implementation of bioreactor monitoring is applied at bioreactors in Pakal Benowo Forest, Surabaya. The trial test was carried out under three different conditions: In the morning (around 08.00 AM) indicated information on the methane gas content of 72.5% LEL, biogas pressure 7.3 kPa and mass flow rate biogas 0.3 liters per minute. The second one during the day (around 11.00 AM) indicates information on the methane gas content of 56.5% LEL, biogas pressure 1.1 kPa and biogas mass flow rate of 0.3 liters per minute. The last, in the afternoon (around 03.00 PM) indicates information on the methane gas content of 51.1% LEL, biogas pressure of 1.1 kPa and biogas mass flow rate of 0.3 liters per minute. From those results, our monitoring system is able to identify the operational conditions of the anaerobic bioreactor.
Determination of optimum technologies implementation scenarios toward net zero emissions in palm oil biodiesel production
Authors: Prasetya H , Apriyanto H , Agustina L
Published: May 2023

Increasing bioenergy use is one of the strategies for achieving net zero emissions by 2060. Palm oil biodiesel is a type of bioenergy that has the potential to be applied to achieve this target. On the other side, there are several sources of emission along the palm oil biodiesel (POB) production chain. These potential emissions can be reduced by applying various technologies along the production chain. This study aims to develop a model for reducing emissions from palm oil biodiesel. The model developed was a combination of life cycle assessment and genetic algorithms. Two objectives are defined in this model, namely: maximizing greenhouse gas (GHG) emission reduction through technology implementation and minimizing mitigation costs in its implementation. A combination of technology implementations was represented as chromosomes generated through crossover and mutation. By running more than 1000 iterations, a combination of optimal technology implementation can be obtained with the smallest emissions and minimal mitigation costs.
The Emission Effect of Utilization of Gasoline, Ethanol, and Methanol (GEM) Blend in Passenger Car
Authors: Agama Askar Adika , Sugiarto Bambang , Mokhtar  , Sukmono Anis , Igorio Kevan Jeremy , Fathoni Muhammad Her Perwito , Muhammad Fadhel
Published: May 2023

The energy demand for fuel is increasing as the vehicle population increases. Until 2035, it is projected that energy use will still be dominated by fossil energy. This needs to be addressed to diversify the use of energy which should be renewable energy (RE) to get a larger portion than at this time, RE has only utilized 5% of all fossil energy used. The higher the use of fuel, the emission of combustion gases is one of the impacts that will accompany it. So, it is necessary to look for renewable and environmentally friendly energy. Ethanol and Methanol are alcoholic chemical compounds, which contain hydrocarbons that can be used as fuel. This study looks for the fuel consumption, emissions, and performance resulting from the use of Ethanol and Methanol as a gasoline fuel mixture in the passenger car. The method used is UN-ECE R101 for fuel consumption and UN-ECE R83 for emission tests. The based and comparison fuel used is gasoline with RON 90 produced by PT. Pertamina and the mixture used is GEM. The car used is Toyota Kijang LGX. As a result, fuel consumption is still better using based fuel with a difference of 18% decreased from M1010. Meanwhile, for cleaner emissions, GEM has reduced CO and HC levels, respectively 43% in E15M5 blend, than 18% in E10M10, while NOx increased by 30% in E10M10 and E15M5 blend. The performance result is GEM better than based.
Generation of a spatially multiplexed perfect vortex beam for digital data transmission
Authors: Gangwar Swati , Jaiswal V K , Mehrotra Ranjana , Saha Shibu , Sharma Parag
Published: May 2023

A perfect vortex beam (PVB) has emerged as a potential candidate for optical communication as its intensity profile remains invariant for different orbital angular momenta being carried by the beam. The present study proposes a simple technique to enhance the data handling capacity of the beam through its spatial multiplexing. The variation of the ring radius of the PVB under Fourier transformation, with different focal lengths, has been used to generate multiple PVBs of different annular radii, and then combined into a single beam to produce a concentric PVB (CPVB). Each ring may represent one bit of digital data. A simple experimental setup was used to generate the beam, which has also been validated through theoretical simulation. Further studies confirm that each ring of the CPVB has the same phase profile, with impeccable spatial alignment. Spatial multiplexing of the PVB adds an additional degree which can multiply the data handling capacity of the PVB, as a result of which it can prove to be a potential candidate for optical data transmission.
Effect of Al2TiO5 powder coating on the tribological, corrosion and mechanical properties of AISI 316L stainless steel
Authors: Kumar J Jagadesh , Satyanarayana Vaddi Venkata , Reddy Gundeti Sreeram , Reddy B Ravinder , Dharmavarapu Pratibha
Published: May 2023

The aim of the current research is to examine the tribological, corrosion and mechanical properties of AISI 316L stainless steel without and with Al2TiO5 surface coating. AISI 316L is selected for the study, owing to its extensive usage in power plant and marine members that are usually subjected to wear, fatigue and corrosion either separately or in a combinatorial mode from mild to severe intensities. Al2TiO5 coating is provided to components to improve their tribological, corrosion and mechanical properties. Being a ceramic material, Al2TiO5 coating is expected to improve the properties under consideration. The coated specimens are analyzed by considering two factors viz. ‘speed of rotation of job’ and ‘axial speed of the spray gun’, applying Taguchi L4 array. Coating of Al2TiO5 on AISI 316L substrate increased the corrosion resistance, coefficient of friction and micro-hardness, however the wear rate and fatigue life decreased. Twenty times reduction in wear rate is recorded with the coating of Al2TiO5 on the base material when compared to the uncoated counterpart. The wear rate has also decreased by 16% with the increase in coating thickness from 300 to 375 μm. The fatigue life of the coated specimens reduced by around 12% while their corrosion resistance increased by 20% when compared to the uncoated specimens.
Photocatalytic degradation of ethylene by mesoporous nano silica loaded chlorin e6
Authors: Jia Liangyu , Jin Weihao , Zhang Weiwei , Wang Jun , Li Wanzhen , Tao Yugui
Published: May 2023

Green foods are usually harvested and stored before ripening, but excessive ethylene generated during storage can lead to the loss of vegetables and fruits. Photocatalytic oxidation provides a promising method to remove ethylene and extend the shelf life of green foods. In this study, a mesoporous nanosilica-loaded Ce6 composite nanomaterial (Ce6@SiO2) was designed and synthesized to adsorb ethylene into its pores and then degrade it under visible light illumination. The photosensitizer Ce6 in the mesopore produced large amounts of reactive oxygen species that degraded ethylene. The specific surface area was greatly increased by coating the material on the surface of a sodium alginate (SA) hydrogel membrane. This improved its degradation efficiency and facilitated the adsorption and degradation of ethylene during fruit storage. The ethylene removal capacity was studied by measuring the ethylene concentration and increases in the humidity in Tedlar gas bags. Practical applications were tested by observing color changes and surface decay of tomatoes stored with and without SA/Ce6@SiO2. The results showed the system may be used in practical commercial preservation systems.
Shellac as dielectric materials in organic field-effect transistors: from silicon to paper substrates
Authors: Skaf Daniella , Gomes Tiago Carneiro , Majidzadeh Robabeh , Hussein Rahaf Nafez , Carmichael Tricia Breen , Rondeau-Gagné Simon
Published: May 2023

Recent advances in the design and preparation of electroactive materials, particularly semiconducting and conductive polymers, have resulted in the creation of novel organic electronics with advanced functionality and performance competitive with that of devices made of silicon. With an increasing number of organic and printed electronics being engineered and produced at a larger scale, the environmental cost of the final organic electronic devices (life cycle, environmental impact, etc) needs to be considered. While e-waste is already a growing global problem, improving the sustainability of emerging electronics through a careful materials selection is highly desirable. In this work, we explore the use of shellac as a sustainable greener dielectric material in organic field-effect transistors. A careful examination of shellac in combination with diketopyrrolopyrrole-based semiconducting polymers was performed on rigid substrates through atomic force microscopy (AFM) and the fabrication of thin film transistors. All devices made from this green dielectric showed good performance and device characteristics. Building from this investigation, shellac was further integrated with paper substrates to fabricate paper-based thin film transistors. Thin film samples based on shellac on both silicon wafer and paper substrates were characterized by AFM to investigate solid-state morphology of shellac and selected semiconducting materials. Through careful optimization of the device architecture and processing time, device characteristics and performances on paper substrates (average charge mobilities and on/off current ratios) were comparable to those of devices prepared on silicon wafers, confirming that shellac, in combination with organic semiconducting polymers, can be an advantageous dielectric material to be used for the fabrication of greener and sustainable thin film electronics from renewable feedstocks and components.
Valuation of pollination services from habitat management: a case study of utility scale solar energy facilities in the United States
Authors: Mishra Shruti Khadka , Zhu Minjia , Bernknopf Richard L , Walston Leeroy J
Published: May 2023

Creating and maintaining pollinator habitats following the ecological infrastructure concept in degraded or unutilized land, such as solar energy facilities, is a practical way to synergistically advance the food, energy, and ecology nexus. Given the large land-use requirements for solar farming—the fastest growing renewable energy technology–considerable attention has been focused on strategies to maximize multiple ecosystem services. In this study, we coupled the principles of agronomy and ecology with economics and integrated national-scale data on crops, pollinators, and solar facilities to identify locations for creating pollinator habitats and estimating the economic value of pollination from the habitats. We examined opportunities for pollination services from pollinator-friendly utility-scale solar facilities adjacent to 42 million hectares of pollination-dependent crops in the conterminous United States at high resolution of 1 ha. We used the net income method to estimate the potential economic value of creating habitat in the land adjacent to solar facilities in the eight states with the greatest number of solar installations. Creating pollinator habitats at the 217 utility-scale solar facilities in these states could support adjacent 80,000 hectares of high pollinator dependent crops, which could potentially generate a pollination value of $120 to $264 million USD. The location-specific information and high-resolution maps generated for the United States demonstrate integration of grey and green infrastructure to support the food, energy, and environment nexus.
Improved the heterodimer protein complex prediction with protein language models
Authors: Chen Bo , Xie Ziwei , Qiu Jiezhong , Ye Zhaofeng , Xu Jinbo , Tang Jie
Published: May 2023

AlphaFold-Multimer has greatly improved the protein complex structure prediction, but its accuracy also depends on the quality of the multiple sequence alignment (MSA) formed by the interacting homologs (i.e. interologs) of the complex under prediction. Here we propose a novel method, ESMPair, that can identify interologs of a complex using protein language models. We show that ESMPair can generate better interologs than the default MSA generation method in AlphaFold-Multimer. Our method results in better complex structure prediction than AlphaFold-Multimer by a large margin (+10.7% in terms of the Top-5 best DockQ), especially when the predicted complex structures have low confidence. We further show that by combining several MSA generation methods, we may yield even better complex structure prediction accuracy than Alphafold-Multimer (+22% in terms of the Top-5 best DockQ). By systematically analyzing the impact factors of our algorithm we find that the diversity of MSA of interologs significantly affects the prediction accuracy. Moreover, we show that ESMPair performs particularly well on complexes in eucaryotes.
C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data
Authors: Ibéné Mandy , Legendre Audrey , Postic Guillaume , Angel Eric , Tahi Fariza
Published: May 2023

RNAs can interact with other molecules in their environment, such as ions, proteins or other RNAs, to form complexes with important biological roles. The prediction of the structure of these complexes is therefore an important issue and a difficult task. We are interested in RNA complexes composed of several (more than two) interacting RNAs. We show how available knowledge on the considered RNAs can help predict their secondary structure. We propose an interactive tool for the prediction of RNA complexes, called C-RCPRed, that considers user knowledge and probing data (which can be generated experimentally or artificially). C-RCPred is based on a multi-objective optimization algorithm. Through an extensive benchmarking procedure, which includes state-of-the-art methods, we show the efficiency of the multi-objective approach and the positive impact of considering user knowledge and probing data on the prediction results. C-RCPred is freely available as an open-source program and web server on the EvryRNA website (https://evryrna.ibisc.univ-evry.fr).
Similarity measures-based graph co-contrastive learning for drug–disease association prediction
Authors: Gao Zihao , Ma Huifang , Zhang Xiaohui , Wang Yike , Wu Zheyu
Published: May 2023

Motivation

An imperative step in drug discovery is the prediction of drug–disease associations (DDAs), which tries to uncover potential therapeutic possibilities for already validated drugs. It is costly and time-consuming to predict DDAs using wet experiments. Graph Neural Networks as an emerging technique have shown superior capacity of dealing with DDA prediction. However, existing Graph Neural Networks-based DDA prediction methods suffer from sparse supervised signals. As graph contrastive learning has shined in mitigating sparse supervised signals, we seek to leverage graph contrastive learning to enhance the prediction of DDAs. Unfortunately, most conventional graph contrastive learning-based models corrupt the raw data graph to augment data, which are unsuitable for DDA prediction. Meanwhile, these methods could not model the interactions between nodes effectively, thereby reducing the accuracy of association predictions.

Results

A model is proposed to tap potential drug candidates for diseases, which is called Similarity Measures-based Graph Co-contrastive Learning (SMGCL). For learning embeddings from complicated network topologies, SMGCL includes three essential processes: (i) constructs three views based on similarities between drugs and diseases and DDA information; (ii) two graph encoders are performed over the three views, so as to model both local and global topologies simultaneously; and (iii) a graph co-contrastive learning method is introduced, which co-trains the representations of nodes to maximize the agreement between them, thus generating high-quality prediction results. Contrastive learning serves as an auxiliary task for improving DDA predictions. Evaluated by cross-validations, SMGCL achieves pleasing comprehensive performances. Further proof of the SMGCL’s practicality is provided by case study of Alzheimer’s disease.

Availability and implementation

https://github.com/Jcmorz/SMGCL.
Consistency enhancement of model prediction on document-level named entity recognition
Authors: Jeong Minbyul , Kang Jaewoo
Published: May 2023

Biomedical named entity recognition (NER) plays a crucial role in extracting information from documents in biomedical applications. However, many of these applications require NER models to operate at a document level, rather than just a sentence level. This presents a challenge, as the extension from a sentence model to a document model is not always straightforward. Despite the existence of document NER models that are able to make consistent predictions, they still fall short of meeting the expectations of researchers and practitioners in the field. To address this issue, we have undertaken an investigation into the underlying causes of inconsistent predictions. Our research has led us to believe that the use of adjectives and prepositions within entities may be contributing to low label consistency. In this article, we present our method, ConNER, to enhance a label consistency of modifiers such as adjectives and prepositions. By refining the labels of these modifiers, ConNER is able to improve representations of biomedical entities. The effectiveness of our method is demonstrated on four popular biomedical NER datasets. On three datasets, we achieve a higher F1 score than the previous state-of-the-art model. Our method shows its efficacy on two datasets, resulting in 7.5%–8.6% absolute improvements in the F1 score. Our findings suggest that our ConNER method is effective on datasets with intrinsically low label consistency. Through qualitative analysis, we demonstrate how our approach helps the NER model generate more consistent predictions.

Availability and implementation

Our code and resources are available at https://github.com/dmis-lab/ConNER/.
Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data
Authors: Kuo Albert , Hansen Kasper D , Hicks Stephanie C
Published: May 2023

In complex tissues containing cells that are difficult to dissociate, single-nucleus RNA-sequencing (snRNA-seq) has become the preferred experimental technology over single-cell RNA-sequencing (scRNA-seq) to measure gene expression. To accurately model these data in downstream analyses, previous work has shown that droplet-based scRNA-seq data are not zero-inflated, but whether droplet-based snRNA-seq data follow the same probability distributions has not been systematically evaluated. Using pseudonegative control data from nuclei in mouse cortex sequenced with the 10x Genomics Chromium system and mouse kidney sequenced with the DropSeq system, we found that droplet-based snRNA-seq data follow a negative binomial distribution, suggesting that parametric statistical models applied to scRNA-seq are transferable to snRNA-seq. Furthermore, we found that the quantification choices in adapting quantification mapping strategies from scRNA-seq to snRNA-seq can play a significant role in downstream analyses and biological interpretation. In particular, reference transcriptomes that do not include intronic regions result in significantly smaller library sizes and incongruous cell type classifications. We also confirmed the presence of a gene length bias in snRNA-seq data, which we show is present in both exonic and intronic reads, and investigate potential causes for the bias.
Porous Penality and the Myth of Liberal Punishment: Lessons from South Africa
Authors: Super Gail
Published: May 2023

Drawing on Walter Benjamin, this paper discusses the relationships between law, violence, and punishment. The main argument I make is that state punishment is BOTH a violent and logically contradictory practice and that the state’s legal right to punish often spills over into extralegal penal violence, perpetrated by a range of actors against the racialized poor. I use the term penal violence to refer to all forms of violence which are aimed at enforcing law or punishing a perceived transgression of law or norms. The paper focuses on the infliction of penal violence in South Africa on/in three different scales and jurisdictions: Makwanyane and violence in prisons; police and prosecutorial violence; and extralegal civilian violence.
Mechanical bowel preparation and antibiotics in elective colorectal surgery: network meta-analysis
Authors: Tan Jonavan , Ryan Éanna J , Davey Matthew G , McHugh Fiachra T , Creavin Ben , Whelan Maria C , Kelly Michael E , Neary Paul C , Kavanagh Dara O , O’Riordan James M
Published: May 2023

Background

The use of intravenous antibiotics at anaesthetic induction in colorectal surgery is the standard of care. However, the role of mechanical bowel preparation, enemas, and oral antibiotics in surgical site infection, anastomotic leak, and other perioperative outcomes remains controversial. The aim of this study was to determine the optimal preoperative bowel preparation strategy in elective colorectal surgery.

Methods

A systematic review and network meta-analysis of RCTs was performed with searches from PubMed/MEDLINE, Scopus, Embase, and the Cochrane Central Register of Controlled Trials from inception to December 2022. Primary outcomes included surgical site infection and anastomotic leak. Secondary outcomes included 30-day mortality rate, ileus, length of stay, return to theatre, other infections, and side effects of antibiotic therapy or bowel preparation.

Results

Sixty RCTs involving 16 314 patients were included in the final analysis: 3465 (21.2 per cent) had intravenous antibiotics alone, 5268 (32.3 per cent) had intravenous antibiotics + mechanical bowel preparation, 1710 (10.5 per cent) had intravenous antibiotics + oral antibiotics, 4183 (25.6 per cent) had intravenous antibiotics + oral antibiotics + mechanical bowel preparation, 262 (1.6 per cent) had intravenous antibiotics + enemas, and 1426 (8.7 per cent) had oral antibiotics + mechanical bowel preparation. With intravenous antibiotics as a baseline comparator, network meta-analysis demonstrated a significant reduction in total surgical site infection risk with intravenous antibiotics + oral antibiotics (OR 0.47 (95 per cent c.i. 0.32 to 0.68)) and intravenous antibiotics + oral antibiotics + mechanical bowel preparation (OR 0.55 (95 per cent c.i. 0.40 to 0.76)), whereas oral antibiotics + mechanical bowel preparation resulted in a higher surgical site infection rate compared with intravenous antibiotics alone (OR 1.84 (95 per cent c.i. 1.20 to 2.81)). Anastomotic leak rates were lower with intravenous antibiotics + oral antibiotics (OR 0.63 (95 per cent c.i. 0.44 to 0.90)) and intravenous antibiotics + oral antibiotics + mechanical bowel preparation (OR 0.62 (95 per cent c.i. 0.41 to 0.94)) compared with intravenous antibiotics alone. There was no significant difference in outcomes with mechanical bowel preparation in the absence of intravenous antibiotics and oral antibiotics in the main analysis.

Conclusion

A bowel preparation strategy with intravenous antibiotics + oral antibiotics, with or without mechanical bowel preparation, should represent the standard of care for patients undergoing elective colorectal surgery.
A structural magnetic resonance imaging review of clinical motor outcomes from deep brain stimulation in movement disorders
Authors: Andrews Luke , Keller Simon S , Osman-Farah Jibril , Macerollo Antonella
Published: May 2023

Patients with movement disorders treated by deep brain stimulation do not always achieve successful therapeutic alleviation of motor symptoms, even in cases where surgery is without complications. Magnetic resonance imaging (MRI) offers methods to investigate structural brain-related factors that may be predictive of clinical motor outcomes. This review aimed to identify features which have been associated with variability in clinical post-operative motor outcomes in patients with Parkinson’s disease, dystonia, and essential tremor from structural MRI modalities. We performed a literature search for articles published between 1 January 2000 and 1 April 2022 and identified 5197 articles. Following screening through our inclusion criteria, we identified 60 total studies (39 = Parkinson’s disease, 11 = dystonia syndromes and 10 = essential tremor). The review captured a range of structural MRI methods and analysis techniques used to identify factors related to clinical post-operative motor outcomes from deep brain stimulation. Morphometric markers, including volume and cortical thickness were commonly identified in studies focused on patients with Parkinson’s disease and dystonia syndromes. Reduced metrics in basal ganglia, sensorimotor and frontal regions showed frequent associations with reduced motor outcomes. Increased structural connectivity to subcortical nuclei, sensorimotor and frontal regions was also associated with greater motor outcomes. In patients with tremor, increased structural connectivity to the cerebellum and cortical motor regions showed high prevalence across studies for greater clinical motor outcomes. In addition, we highlight conceptual issues for studies assessing clinical response with structural MRI and discuss future approaches towards optimizing individualized therapeutic benefits. Although quantitative MRI markers are in their infancy for clinical purposes in movement disorder treatments, structural features obtained from MRI offer the powerful potential to identify candidates who are more likely to benefit from deep brain stimulation and provide insight into the complexity of disorder pathophysiology.
Comprehensive volumetric phenotyping of the neonatal brain in Down syndrome
Authors: Fukami-Gartner Abi , Baburamani Ana A , Dimitrova Ralica , Patkee Prachi A , Ojinaga-Alfageme Olatz , Bonthrone Alexandra F , Cromb Daniel , Uus Alena U , Counsell Serena J , Hajnal Joseph V , O’Muircheartaigh Jonathan , Rutherford Mary A
Published: May 2023

Down syndrome (DS) is the most common genetic cause of intellectual disability with a wide range of neurodevelopmental outcomes. To date, there have been very few in vivo neuroimaging studies of the neonatal brain in DS. In this study we used a cross-sectional sample of 493 preterm- to term-born control neonates from the developing Human Connectome Project to perform normative modeling of regional brain tissue volumes from 32 to 46 weeks postmenstrual age, accounting for sex and age variables. Deviation from the normative mean was quantified in 25 neonates with DS with postnatally confirmed karyotypes from the Early Brain Imaging in DS study. Here, we provide the first comprehensive volumetric phenotyping of the neonatal brain in DS, which is characterized by significantly reduced whole brain, cerebral white matter, and cerebellar volumes; reduced relative frontal and occipital lobar volumes, in contrast with enlarged relative temporal and parietal lobar volumes; enlarged relative deep gray matter volume (particularly the lentiform nuclei); and enlargement of the lateral ventricles, amongst other features. In future, the ability to assess phenotypic severity at the neonatal stage may help guide early interventions and, ultimately, help improve neurodevelopmental outcomes in children with DS.
Impact of Point-of-Care Rapid Diagnostic Tests on Antibiotic Prescription Among Patients Aged <18 Years in Primary Healthcare Settings in 2 Peri-Urban Districts in Ghana: Randomized Controlled Trial Results
Authors: Adjei Alexander , Kukula Vida , Narh Clement Tetteh , Odopey Selase , Arthur Emmanuel , Odonkor Gabriel , Mensah Michael Matey , Olliaro Piero , Horgan Philip , Dittrich Sabine , Moore Catrin E , Salami Olawale , Awini Elizabeth , Nkeramahame Juvenal , Williams John , Baiden Rita
Published: May 2023

Background

Inappropriate antibiotic prescriptions are a known driver of antimicrobial resistance in settings with limited diagnostic capacity. This study aimed to assess the impact of diagnostic algorithms incorporating rapid diagnostic tests on clinical outcomes and antibiotic prescriptions compared with standard-of-care practices, of acute febrile illness cases at outpatient clinics in Shai-Osudoku and Prampram districts in Ghana.

Methods

This was an open-label, centrally randomized controlled trial in 4 health facilities. Participants aged 6 months to <18 years of both sexes with acute febrile illness were randomized to receive a package of interventions to guide antibiotic prescriptions or standard care. Clinical outcomes were assessed on day 7.

Results

In total, 1512 patients were randomized to either the intervention (n = 761) or control (n = 751) group. Majority were children aged <5 years (1154 of 1512, 76.3%) and male (809 of 1512, 53.5%). There was 11% relative risk reduction of antibiotic prescription in intervention group (RR, 0.89; 95% CI, .79 to 1.01); 14% in children aged <5 years (RR, 0.86; 95% CI, .75 to .98), 15% in nonmalaria patients (RR, 0.85; 95% CI, .75 to .96), and 16% in patients with respiratory symptoms (RR, 0.84; 95% CI, .73 to .96). Almost all participants had favorable outcomes (759 of 761, 99.7% vs 747 of 751, 99.4%).

Conclusions

In low- and middle-income countries, the combination of point-of-care diagnostics, diagnostic algorithms, and communication training can be used at the primary healthcare level to reduce antibiotic prescriptions among children with acute febrile illness, patients with nonmalarial fevers, and respiratory symptoms.

Clinical Trials Registration

NCT04081051.
Understanding the Decline of Incident, Active Tuberculosis in People With Human Immunodeficiency Virus in Switzerland
Authors: Zeeb Marius , Tepekule Burcu , Kusejko Katharina , Reiber Claudine , Kälin Marisa , Bartl Lena , Notter Julia , Furrer Hansjakob , Hoffmann Matthias , Hirsch Hans H , Calmy Alexandra , Cavassini Matthias , Labhardt Niklaus D , Bernasconi Enos , Braun Dominique L , Günthard Huldrych F , Kouyos Roger D , Nemeth Johannes ,   the Swiss HIV Cohort Study, Meier Jan , Schäfer Yves , Follonier Océane , Perraudin Danièle , Amstad Marianne
Published: May 2023

Background

People with human immunodeficiency virus type 1 (HIV-1) (PWH) are frequently coinfected with Mycobacterium tuberculosis (MTB) and at risk for progressing from asymptomatic latent TB infection (LTBI) to active tuberculosis (TB). LTBI testing and preventive treatment (TB specific prevention) are recommended, but its efficacy in low transmission settings is unclear.

Methods

We included PWH enrolled from 1988 to 2022 in the Swiss HIV Cohort study (SHCS). The outcome, incident TB, was defined as TB ≥6 months after SHCS inclusion. We assessed its risk factors using a time-updated hazard regression, modeled the potential impact of modifiable factors on TB incidence, performed mediation analysis to assess underlying causes of time trends, and evaluated preventive measures.

Results

In 21 528 PWH, LTBI prevalence declined from 15.1% in 2001% to 4.6% in 2021. Incident TB declined from 90.8 cases/1000 person-years in 1989 to 0.1 in 2021. A positive LTBI test showed a higher risk for incident TB (hazard ratio [HR] 9.8, 5.8–16.5) but only 10.5% of PWH with incident TB were tested positive. Preventive treatment reduced the risk in LTBI test positive PWH for active TB (relative risk reduction, 28.1%, absolute risk reduction 0.9%). On population level, the increase of CD4 T-cells and reduction of HIV viral load were the main driver of TB decrease.

Conclusions

TB specific prevention is effective in selected patient groups. On a population level, control of HIV-1 remains the most important factor for incident TB reduction. Accurate identification of PWH at highest risk for TB is an unmet clinical need.
First report on the serum chemistry and haematology of free-ranging dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) sharks in the eastern Mediterranean Sea
Authors: Starostinetsky-Malonek Tal , Scheinin Aviad , Aroch Itamar , Davidovich Nadav , Bigal Eyal , Livne Leigh , Hauser-Davis Rachel Ann , Wosnick Natascha , Tchernov Dan , Morick Danny
Published: May 2023

Shark assessments in the Mediterranean Sea are still scarce, and serum chemistry and haematological data have yet to be reported for wild dusky (Carcharhinus obscurus) or sandbar (Carcharhinus plumbeus) shark populations in the Mediterranean Sea. Herein, blood samples were obtained from adult dusky (n = 23) and sandbar (n = 14) sharks from an aggregation site near the Hadera power and desalination plants in Israel in the winters of 2016–20. Several serum chemistry analytes were characterized with relation to stress, body size and environmental conditions. Glucose concentrations were higher, while total cholesterol concentrations were lower in dusky sharks than in sandbar sharks, potentially due to distinct metabolic pathways utilized during the capture-related activity by both species. However, differences in sex and size are noted and should be considered. The blood cell morphology of both species was consistent with previous findings for sandbar sharks. Atypical monocytes were noted in one dusky shark. Preliminary and exploratory reference intervals for female dusky sharks were calculated for glucose, triglycerides, total cholesterol, total protein and creatine kinase. These data must be viewed with caution due to the potential influence of capture-related stress on analyte concentrations and activities and the fact that only females were employed in the calculations. Moreover, the sampling site is adjacent to coastal power and desalination plants, which may significantly affect shark physiology. Although limited, this novel database on dusky and sandbar shark serum chemistry and haematology aspects is essential as a first attempt to obtain data on these species in the eastern Mediterranean Sea and for future conservation and long-term biomonitoring efforts.