bluuebunny/crossref_metadata_2025 huggingface dataset:
Increasing yield of paddy rice on peat soil using steel slag
Authors: Suwarno
Published: January 2023

Peat soil is one marginal soil having the potential for paddy rice cultivation. Peat soil has a low content of total Si and available copper and zinc. Steel slag is the typical source of Si elements. Two experiments were carried out to determine steel slag supplementation effects on the growth and development of paddy rice on peat soil. Experiment 1 was a greenhouse pot experiment to evaluate three steel slag dosages (i.e., 0.0, 2.5, and 5.0 %). Experiment 2 was a field experiment to validate the effects of five steel slag dosages (i.e., 0, 2.5, 5.0, 7.5, and 10-tons ha−1). In experiment 1, applying steel slag at 2.5 and 5.0 % dosages significantly increased paddy rice development. In experiment 2, paddy rice development was significantly increased with steel slag. Grain yield increased from 65 to 96 % with steel slag 2.5 to 10 tons ha−1. The response of paddy rice on peat soil to steel slag in experiments 1 and 2 was associated with increasing soil pH and availability of Si, Mg, and Ca.
Essence, principle, and technique in utilization and converting vinasse waste to bio-organic fertilizer
Authors: Rachman L M , Hartono A , Hazra F , Noorwicaksono T , Wasono K B , Adityasari A D , Prabowo B , Putri N , Davik
Published: January 2023

The increased need for energy resources that reduce the emission of greenhouse gases triggers ethanol demand has increased. Production of ethanol from biomass produces by-product waste (vinasse). Vinasse waste management could be a great opportunity. It is about 6 trillion liters of these materials will need to be managed in 2023 since each liter of bioethanol produced around 9-14 liters of vinasse. Converting vinasse to bio-organic fertilizer needs proper waste management. This study aims to describe the essence, fundamentals, importance, benefits, and challenges together with the principles, stages, and techniques required to convert vinasse waste into bio-organic fertilizer. The fundamental of converting vinasse waste into bio-organic fertilizer includes 1) taming the toxic elements and other contaminants and 2) enriching and elevating its organic and nutrient contents to fulfill its function as an excellent fertilizer. The data from the laboratory analysis result showed that vinasse waste contains: 1) heavy metals As, Hg, Pb, Cr, and Ni that are still lower than the permissible threshold index, 2) high organic and N-organic ingredients, 3) high main macronutrients (N-P-K), 4) low level of main micronutrients of Fe, Cu, Zn and Mo and a moderate level of Mn and B. The proposed ultimate steps required to covert vinasse waste to bio-organic fertilizer are: 1) physical detoxication/decontamination by soaking in zeolite rock fraction, 2) preparation of techniques and formulas to tame the toxic and contaminants and enhancing macronutrients and micronutrients, 3) testing the effect of the produced bio-organic fertilizer on soil and plants on a greenhouse scale, 4) testing the effect of the produced bio-organic fertilizers on soil and plants on a field scale, 5) evaluating and improving the bio-organic fertilizer formulas.
Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae): Attacks and their natural enemies on corn plantations in Munte Village, Munte Sub-district, Karo District, North Sumatera.
Authors: Tarigan S , Maryana N , Mubin N
Published: January 2023

Spodoptera frugiperda (Lepidoptera: Noctuidae) is a relatively new pest in Indonesia and an important pest of corn. Corn cultivation is dominant in Munte Village, Karo District, North Sumatera. This study aimed to estimate the damage caused by S. frugiperda, and observe its natural enemies in Munte Village. Damage observations were four times over two weeks on 100 sample plants. Eggs and larvae of S. frugiperda were collected from the cultivation and reared in the laboratory until the parasitoids emerged. Insects that can act as predators and entomopathogens that attack S. frugiperda were also observed. The intensity of damage due to S. frugiperda in each observation was more than 30%. Parasitoids found during the observation were Telenomus sp. (Hymenoptera: Scelionidae), Trichogramma sp. (Hymenoptera: Trichogrammatidae), Microplitis sp. (Hymenoptera: Braconidae), Charops sp., Anomaloninae (Hymenoptera: Ichneumonidae), Megaselia sp. (Diptera: Phoridae), and Tachinidae (Diptera), with parasitization levels of 29.71, 3.40, 1.65, 0.41, 1.23, 0.41, and 0.41% respectively. The other natural enemies found were predators, i.e. Doru sp. (Dermaptera: Forficulidae), Oxyopes sp. (Araneae: Oxyopidae), and entomopathogenic fungi Metarhizium sp. Telenomus was the most dominant natural enemy found during the observation.
The abundance of phytonematodes associated with ginger plants in the District of Bogor, Cianjur, and Sukabumi, West Java
Authors: Almursyidi H H , Munif A , Triwidodo H
Published: January 2023

Phytonematodes are a severe threat that can cause damage to ginger plants, decreasing the quality and quantity of ginger production. Lack of information regarding ginger’s association and abundance of phytonematodes is a challenge in phytonematode management. The research objective was to study the abundance and identify associated phytonematodes in ginger plantations. Samples of rhizomes, roots, and soil were taken from symptomatic ginger plantations in major ginger production areas in Bogor, Cianjur, and Sukabumi, West Java. Phytonematodes from rhizomes and roots samples were extracted using the mist chamber technique and phytonematodes from soil samples were removed with the centrifugal flotation technique. The phytonematodes suspension obtained was observed using a stereo microscope. Identification book The Pictorial Key To Genera of Plant-parasitic Nematodes and related journals for genus and species identification were used to identify nematodes. Each nematode sample received was calculated as a phytonematodes population. The results showed that based on morphological characteristics, seven species of phytonematodes were found in the rhizomes, roots, and soil of ginger plants, namely Aphelenchoides bicaudatus, Hoplolaimus sp., Helichotylenchus sp., Meloidogyne sp., Pratylenchus sp., Radopholus similis, and Rotylenchulus reniformis. R. similis was found to dominate from Bogor’s rhizomes, roots, and soil samples. The highest nematode population was Meloidogyne sp., with at least 821 nematodes per10 g of roots associated with ginger in Sukabumi.
Aflatoxin in rice: a publication review
Authors: Kristiningrum Ellia , Nurcahyo Rahmat , Susanto DanarAgus , Isharyadi Febrian , Budi Mulyono Ary , Anggraeni Putty , Dulbert Tampubolon Biatna , Harjanto Singgih , Wahyu Hapsari Bety , Yusuf Muhamad
Published: January 2023

Contamination of food products by various types of fungi can pose a severe health threat to humans and livestock. Aflatoxin (AFS) is a toxic and carcinogenic metabolite of the Aspergillus fungus that can occur in rice. Many studies have been conducted on the content of aflatoxins in staple foods, including rice. A literature analysis was performed to get an overview of the development of aflatoxin publication in rice using the Scopus database (Elsevier) between 2010 - 2021. In this article, we describe the focus of trends and characteristics of publications and visualize the growing network. The analysis includes descriptive analysis, keyword network, author collaboration network, and country/regional cooperation analysis. Research on the content of aflatoxins in rice has increased sharply in the last 20 years. The cause of aflatoxins is that fungi can potentially infect food crops, posing a significant health risk to humans and livestock. Aflatoxins are also thought to inhibit growth (growth retardation), resulting in stunting or failure to thrive. The main areas of study for aflatoxins can be separated into four categories: (a) types of aflatoxins; (b) origin and development process of aflatoxins; (c) test methods; and (d) type of product.
Potential of Dioscorea bulbifera L. as a bio-insecticide in controlling dry wood termites (Cryptotermes cynocephalus Ligh.)
Authors: Oksari A A , Susanty D , Rizki F H , Wanda I F , Arinana  , Dadang
Published: January 2023

Currently, chemical control techniques prevent termite attacks, but these chemicals’ effects are concerning because they negatively impact human health and the environment. Therefore, pest control is focused on alternative insecticides that are effective, selective, biodegradable, and environmentally friendly. Several secondary metabolites from the methanolic extract of Dioscorea bulbifera leaves have insecticidal activities. This study aimed to examine the potential of D. bulbifera extract as a bio-insecticide in controlling dry-wood termites (Cryptotermes cynocephalus Light.). The study was conducted using a Completely Randomized Design (CRD) with seven treatments and three replications. The treatment in this study was a combination of concentration and source of D. bulbifera extract. Parameters observed were termite mortality, weight loss percentage of the paper disc, and damage degree. Based on the One-Way ANOVA test at a 5% significance level, the treatment had a significant effect on mortality but had no significant effect on the weight loss percentage and the degree of damage. A concentration of 50% from D. bulbifera extract leaves was able to control dry wood termites with mortality of 70.97%., a weight loss percentage of 33.88%, and a degree of damage of 65.05%. This result indicates that D. bulbifera has the potential as a bio-insecticide in controlling dry wood termites.
Understanding indigenous knowledge in sustainable management of NTFPs agroforestry in Indonesia: a case of Southern Sumatra
Authors: Lestari Sri , Winarno Bondan
Published: January 2023

Peoples’ utilization and management of non-timber forest products in a sustainable manner is influenced by traditional knowledge and regulations. Communities near forests in Southern Sumatra, Indonesia, continue to rely on forest resources to cover their basic needs. However, as more people use the forests to collect non-timber forest products, their availability is decreasing. Qualitative research methods and literature studies were applied in this paper to document local communities in the provinces of South Sumatra, Bengkulu, and Jambi in applying their traditional knowledge and local wisdom to manage dragon’s blood (Daemonorops spp.) and cinnamon (Cinnamomum burmanii Blume). These priceless NTFPs (non-timber forest products) played a significant role in supporting people’s livelihoods and protecting the natural resources in their forest area. The community implemented a sustainable harvesting system to maintain the availability of resources so that the community still has the opportunity to collect NTFPs as a source of income in the future. Along with the decrease in these natural resources, the community has begun to develop an agroforestry system of NTFPs, coffee, and other crops. This domestication activity was expected to ensure the sustainability of production and to prevent overexploitation of forest resources. In the long run, involving indigenous knowledge was needed in maintaining natural resources to achieve sustainable development of NTFPs agroforestry in Indonesia.
Morphology of hybrid orchid induced by polyploidy using colchicine
Authors: Hartati S , Samanhudi  , Cahyono O , Wibowo A , Muliawati E S , Andarrini A A
Published: January 2023

Phalaenopsis orchid flower is one of the essential aspects that has received significant attention from orchid breeders and farmers. Undesirable floral characters can be improved and enhanced by polyploidization using chemically induced antimitotic compounds such as colchicine. This reserach aimed to determine the morphological characteristics of orchids after being colchicine. This research was conducted on December 2021-February 2022 in Screen House, Faculty of Agriculture, Universitas Sebelas Maret, Surakarta. In this research, three orchids of different types were used, that is P. Ox Black Face Ox 1647, P. Ox Spot Queen Ox Rouge Ox 1460, and P. Chain Xen Moment. This experimental study uses three samples of orchids given colchicine and orchids without colchicine. Each sample was repeated three times. The treatment was carried out by dripping colchicine 1,250 ppm on the buds of the three varieties, then covered with cotton and carbon paper. This study used descriptive analysis with data collection techniques, including direct observation and morphological documentation of three varieties of orchids. The results of this research indicated the success of P. Ox Spot Queen Ox Rouge Ox 1460, which had larger flower widths and lengths, that is, 9 cm long and 20 cm wide, and had an average flower autumn time of 60 days longer than the other two varieties.
Analysis of seed viability through respiration metabolism using CO2 sensors and internet of things (IoT) system
Authors: Widajati Eny , Putro T Y , Dewi E M , Aini M A , Mahardhika A
Published: January 2023

The respiration metabolism is an indicator of seed viability. The respiration process can be measured through the production of CO2 during the seed germination process. The respiration process can be measured through the production of CO2 during the seed germination process. This study aims to create a CO2 measuring device that can measure in real-time using a CO2 sensor and an IoT system. The study consisted of two experiments. The first experiment was to create a seed respiration measuring device using a CO2 sensor and an IoT system. The second experiment was to validate. The first experiment’s results were that a device can detect carbon dioxide levels automatically in the measurement range from 400 ppm to 5000 ppm. The device had online data storage through a database that can be monitored using the IoT system and is equipped with backup data storage using an SD card to avoid data loss in the cloud due to internet connection failure. The second experiment used a randomized complete block design. The treatment consisted of six levels of soybean seed viability (94.8%, 92.4%, 90.4%, 88.4%, 66.0%, 40.8% based on germination test). The results showed that the CO2 measurement could differentiate the viability of seeds.
Linear spectral mixture analysis of land cover for assessment level sub-pixel using PlanetScope imagery in Dieng Plateau
Authors: Priana A , Danoedoro P , Kamal M
Published: January 2023

Information on the land cover is essential as thematic information for planning, controlling, and spatial planning to create sustainable development. Remote sensing is a tool used to solve a problem related to space, environment, and zoning. One of the obstacles in using remote sensing data is the presence of mixed pixels. This research was conducted in the Dieng Plateau. This research aims to calculate accuracy assessment and land cover map fraction using PlanetScope imagery in Dieng Plateau. The remote sensing image is PlanetScope, recorded November 19, 2020. Topographic correction is carried out using the cosine correction method. The Linear Spectral Mixture Analysis (LSMA) method determines each endmember percentage land cover fraction. The field survey was conducted with 74 samples for accuracy testing. Each sample plot measures 10 m x 10 m. The topographic correction results can significantly affect land cover classification results. The result of the LSMA method classification used PlanetScope images to determine the percentage land cover map fraction of bare soil, impervious surface, vegetation, and water in one pixel with an accuracy of MAE 99.76%.
Preface of the Proceedings of 14th International Conference on Hydroinformatics – HIC 2022
Authors: Georgescu Andrei-Mugur , Georgescu Sanda-Carmen
Published: January 2023

The present volume contains the Proceedings of the 14th International Conference on Hydroinformatics – HIC 2022, held from the 4th to the 8th of July 2022 in Bucharest, Romania. The conference was jointly organised by the Technical University of Civil Engineering Bucharest and the University “Politehnica” of Bucharest.
A complete digital water experience to support real leakage management planning
Authors: Laucelli Daniele , Spagnuolo Serena , Rinaldi Antonio , Perrone Gianluca , Berardi Luigi , Giustolisi Orazio
Published: January 2023

In the next years digital transition of Water Distribution Networks (WDNs) will represent a long-standing challenge for triggering innovations in the WDNs management tasks. The ongoing impulse for innovation, boosted also by the economic resources for post-pandemic recovery, is opening novel opportunities for technicians and researchers in the context of Digital Water. This work reports the key steps where novel concepts and tools of Digital Water have been used to support consultant companies in designing WDN leakage management actions in a real WDN managed by Acquedotto Pugliese, in Southern Italy. The Digital Water Services (DWSs) were used to support key phases of the workflow, including validation of topological data and integration of georeferenced connection to private properties; calibration of advanced hydraulic model exploiting mass-balance in pressure-driven analysis; the application of strategies for DMA design and pressure control; and the planning of pipe rehabilitation. WDNetXL platform was used to develop WDN Digital Twin and exploit the DWSs. Applying the Digital Water experience to multiple WDNs managed by the same provider also enabled planning the best courses of actions accounting for investments vs. expected leakage reduction at global scale.
Profiling urban water consumption using autoencoders and time-series clustering techniques
Authors: Lange Danillo , Ribalta Marc , Echeverria Lluís , Pocock Joshua
Published: January 2023

Nowadays, water utilities face the rising challenge of ensuring water availability amidst a rapidly growing society and a shifting climate. Our research aims to develop a household clustering solution based on water consumption behaviour in Southwest England, to enable utilities to identify different profiles and enhance customized control of household consumption, resulting in improved resource management. The solution is composed of three modules. The first one is based on a K-Means clustering model, designed to group domestic water use behaviours. This module uses the Dynamic Time Wrapping algorithm as a similarity mechanism to process the high-resolution water meter data. In parallel, the second module processes the market segmentation data through an Autoencoder, a specific Neural Network architecture used to reduce the high dimensionality of such data to a low dimension dataset by extracting its latent encoded space. Finally, to assemble the final household water use profiles, a blending K-Means algorithm is used to merge previous modules outputs, based on the Euclidean distance. The solution provides insightful information to water companies to better understand consumer behaviour, habits, and routines.
Smart water chain: Immutable, distributed and decentralized water transaction ledgers
Authors: Satilmisoglu Talat Kemal , Keskin Huzur
Published: January 2023

Blockchain is a transactional data storage system where data can be stored reliably without the need for a central database or trusted authority. The data can be anything like financial transactions, supply chain processes or medical records. It is similar to a classical database but uses a decentralized ledger and allowing each participant in the network to have their own copy of the ledger and be able to see all transactions. Data stored in the distributed ledger can only be read or written, not deleted or updated unlike traditional central database. Reliable data is essential for the water industry for information about the current status of any water system, to build trust between stakeholders at all scales, and for effective forecasting and future scenarios by reducing uncertainty. The aim of this study is to examine the potential of using blockchain-based algorithms (smart contracts, chain codes, decentralised identifiers etc.) for the water industry on the edge of digital transformation, and to propose water-related data processing system architectures for different water quantity-quality based scenarios.
Hydroinformatics tools used to quantify the impact of urban expansion on water bodies, in the context of the intensification of extreme phenomena (Bacău urbanization case study)
Authors: Marcoie Nicolae , Toma Daniel , Boboc Valentin , Hrăniciuc Tomi Alexăndrel , Balan Cătălin Dumitrel
Published: January 2023

The present study presents the results of the use of hydraulic and hydrological modeling in order to maintain the quantitative and qualitative parameters of the groundwater Capture Front Gherăeşti, Bacau County. With the help of specialized hydro-computer programs such as: Visual MODFLOW for groundwater dynamics, and Mike 11 for hydraulic modeling, the impact of urban development projects on surface and groundwater bodies can be simulated and anticipated. The results obtained are used in the Project to assess the impact of the project on water bodies (SEICA). SEICA contributes significantly to maintaining the quality of water bodies by making reasoned decisions that ensure the sustainability of urban development projects.
Performance of water valves required by water supply network digitalization process
Authors: Safta Carmen Anca , Cococi Valentin Nicolae , Călinoiu Constantin , Marin Alexandru
Published: January 2023

Digitalization process has the capacity to increase productivity and efficiency, to improve the business and reducing costs. Working with big data, using sensors, meters, digital controls and analytic tools, or artificial intelligence in smart water management, the water industry has known a profound transformation with the aim to improve the water services and consumption in the context of our day’s water threats. The water supply networks are exposed permanently to more leaks when water pressures are high which mean higher energy costs and more water losses. For this reason, water supply systems need to monitor in real time the main hydraulic parameters and to control and drive all the hydraulic equipment, to predict consumption and to anticipate the problems. The new water technology is using valves which regulate the water inlet to a system and receiving real-time wireless pressure values. Staring from the quality of services in water distribution systems, the present paper presents a pneumatic actuator used to control and drive water valves. The pneumatic actuator is controlled by a proportional valve. The numerical simulation results highlight the pneumatic actuator performance regarding the dynamic behaviour.
Parametrization of a wastewater hydraulic model under incomplete data constraint
Authors: Belghaddar Yassine , Delenne Carole , Chahinian Nanée , Seriai Abderrahmane , Begdouri Ahlame
Published: January 2023

Hydraulic simulation represents a powerful tool for studying wastewater networks. In order to achieve this target, hydraulic software require a set of parameters such as pipe slopes, roughness, diameters, etc. However, these pieces of information are rarely known for each and every pipe. Moreover, underground networks are frequently expanded, repaired and improved and these changes are not always reported in databases. The task of completing the required data represents the most time-consuming part of model implementation. In this context, we present algorithms that complete missing data required by hydraulic software. We automated this data insertion and transformation in SWMM© format to make it quicker and easier for the user. This automated solution was compared with manually estimated inputs. The simulation results show a coherent hydraulic behaviour.
Assessment of heavy metals removal in a wastewater using aquatic ferns
Authors: Hajiali Amir , Robescu Lăcrămioara Diana
Published: January 2023

Aquatic ferns, which due to their rapid growth on the surface of the water in aquatic areas in many countries as an invasive species threaten the aquatic life and ecosystem of the regions, have the ability to remove heavy metals in wastewater. In this study, their use in removal of existing heavy metals in a domestic wastewater was experimented and the results proved their remarkable efficiency in treating such a wastewater. This research was conducted in two steps; laboratory and semi-industrial. Applying a jar testing apparatus was the first attempt in laboratory scale and optimization of the following four different factors by a routine procedure was the further goal: pH-value, reaction time, absorbent, pollutant concentration. Afterwards, it was scaled up by a real wastewater and removal efficiency was evaluated under optimum conditions designed by the basic experiments. In the second stage, the reactor was designed and constructed on a semi-industrial scale and the removal rate of contaminated metals was achieved. Focusing on the energy efficiency after the heavy metal removal in this method in comparison with another method (active sludge) can be considered to be suggested for treating domestic wastewaters which include considerable contents of heavy metals.
Numerical modelling of the cooling water system of a 106MW Hydro-Power Plant using EPANET
Authors: Milcă Alexandru-Spiridon , Dunca Georgiana , Pitorac Livia
Published: January 2023

The present paper studies the behavior of the new proposed cooling water pumps for a 106 MW Hydro-Power Plant using EPANET. This case-study Hydropower Plant, located in the south of Romania and equipped with two Francis units 53 MW each, processing a 269m gross head, presently goes through a rehabilitation process. The cooling water system of this Hydro-Power Plant consists in four centrifugal pumps, two for each unit, and two additional pumps for the 130 MVA step-up transformer. The rehabilitation process involves the replacement of these pumps. A numerical model following the exact configuration of the cooling water system in what regards pipes diameters, lengths and roughness was designed in EPANET. The focus is to verify if the required pressure is ensured at the cooling water consumers of the plant considering their specific flow demand and if the velocity in the system pipes is within the acceptable limits during the power production process.
The secret agent of galaxy evolution
Authors: Owen Ellis
Published: January 2023

Ellis Owen discusses how cosmic rays can shape galaxy evolution, and the exciting opportunities to study their effects
Do we have a standard model of cosmology?
Authors: Efstathiou George
Published: January 2023

George Efstathiou, recipient of the 2022 RAS Gold Medal in Astronomy, discusses the paradigm shifts that have led to the LCDM cosmology
Where past meets future
Authors: Burton Michael
Published: January 2023

Ireland's historic astronomical observatories at Armagh, Birr and Dunsink are embarking on the process of seeking UNESCO World Heritage Status. Michael Burton examines the deep astronomical heritage that they embody.
Cameron Patterson: Riding the rails to AGU
Authors: Patterson Cameron
Published: January 2023

Sue Bowler talks to Cameron Patterson about putting plans for sustainable research travel into action
A cloud-based pipeline for analysis of FHIR and long-read data
Authors: Dunn Tim , Cosgun Erdal
Published: January 2023

Motivation

As genome sequencing becomes cheaper and more accurate, it is becoming increasingly viable to merge this data with electronic health information to inform clinical decisions.

Results

In this work, we demonstrate a full pipeline for working with both PacBio sequencing data and clinical FHIR® data, from initial data to tertiary analysis. The electronic health records are stored in FHIR® (Fast Healthcare Interoperability Resource) format, the current leading standard for healthcare data exchange. For the genomic data, we perform variant calling on long-read PacBio HiFi data using Cromwell on Azure. Both data formats are parsed, processed and merged in a single scalable pipeline which securely performs tertiary analyses using cloud-based Jupyter notebooks. We include three example applications: exporting patient information to a database, clustering patients and performing a simple pharmacogenomic study.

Availability and implementation

https://github.com/microsoft/genomicsnotebook/tree/main/fhirgenomics

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
SBML2HYB: a Python interface for SBML compatible hybrid modeling
Authors: Pinto José , Costa Rafael S , Alexandre Leonardo , Ramos João , Oliveira Rui
Published: January 2023

Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML) into hybrid semiparametric models that combine mechanistic functions with machine learning (ML). The so-formed hybrid models can be trained and stored back in databases in SBML format. The tool supports a user-friendly export interface with an internal format validator. Two case studies illustrate the use of the sbml2hyb tool. Additionally, we describe HMOD, a new model format designed to support and facilitate hybrid models building. It aggregates the mechanistic model information with the ML information and follows as close as possible the SBML rules. We expect the sbml2hyb tool and HMOD to greatly facilitate the widespread usage of hybrid modeling techniques for biological systems analysis.

Availability and implementation

The Python interface, source code and the example models used for the case studies are accessible at: https://github.com/r-costa/sbml2hyb.

Supplementary information

Supplementary data are available at Bioinformatics online.
Has the core outcome (domain) set for vitiligo been implemented? An updated systematic review on outcomes and outcome measures in vitiligo randomized clinical trials
Authors: Eleftheriadou Viktoria , Bergqvist Christina , Kechichian Elio , Shourick Jason , Ju Hyun-Jeong , van Geel Nanja , Bae Jung Min , Ezzedine Khaled
Published: January 2023

Background

In 2015, a major achievement in vitiligo research was the development of an internationally agreed upon core outcome domain set for randomized clinical trials (RCTs). Three outcomes were identified as being essential: repigmentation, side-effects/harms and maintenance of gained repigmentation. Four items were further recommended for inclusion. The following recommendations then followed: repigmentation should be assessed by measuring the percentage of repigmentation in quartiles (0–25%, 26–50%, 51–79%, 80–100%) and cosmetic acceptability of the results should be assessed using the Vitiligo Noticeability Scale.

Objectives

The primary objective of this study was to assess uptake of the core outcome domain set for RCTs in vitiligo. Secondary objectives were to update the systematic review on outcomes reported in vitiligo RCTs, and to assess whether repigmentation and cosmetic acceptability of the results were measured using the above-mentioned recommended scales.

Methods

We searched PubMed, Cochrane Library (CENTRAL and Systematic Reviews) and ClinicalTrials.gov for vitiligo RCTs between November 2009 and March 2021. Screening and data extraction were independently performed on title and summary by two researchers. All outcomes and outcome measures reported in eligible RCTs were retrieved and collated.

Results

In total, 174 RCTs were identified: 62 were published between 2009 and 2015, and 112 were published between 2016 and 2021.Thirty-eight different outcomes were reported. Repigmentation was the primary outcome in 89% of trials (150 of 169). Forty-nine different tools were used to measure repigmentation. Side-effects and harms were reported in 78% of trials (136 of 174). Maintenance of gained repigmentation was reported in only 11% of trials (20 of 174) and duration of follow-up varied greatly from 1 to 14 months. Cosmetic acceptability of the results and cessation of disease activity were assessed in only 2% of trials (four of 174). Quality of life of patients with vitiligo was assessed in 13% of trials (22 of 174). Finally, only 11 of 112 RCTs (10%) published between 2016 and 2021 reported all three essential core outcome domains (repigmentation, side-effects and maintenance of gained repigmentation) and none of the trials reported both essential and recommended core outcome domains.

Conclusions

Efforts are still needed to close the gap between set recommendations and RCT outcome reporting.
A clinician-to-clinician universal electronic consultation programme at the cardiology department of a Galician healthcare area improves healthcare accessibility and outcomes in elderly patients
Authors: Mazón-Ramos Pilar , Cinza-Sanjurjo Sergio , Garcia-Vega David , Portela-Romero Manuel , Sanmartin-Pena Juan C , Rey-Aldana Daniel , Martinez-Monzonis Amparo , Espasandín-Domínguez Jenifer , Gude-Sampedro Francisco , González-Juanatey José R
Published: January 2023

Aims

We aimed to assess longer-term results (accessibility, hospital admissions, and mortality) in elderly patients referred to a cardiology department (CD) from primary care using e-consultation in outpatient care.

Methods and results

We included 9963 patients >80 years from 1 January 2010 to 31 December 2019. Until 2012, all patients attended an in-person consultation (2010–2012). In 2013, we instituted an e-consult programme (2013–2019) for all primary care referrals to cardiologists that preceded a patient’s in-person consultation when considered. We used an interrupted time series (ITS) regression approach to investigate the impact of e-consultation on (i) cardiovascular hospital admissions and mortality. We also analysed (ii) the total number and referral rate (population-adjusted referred rate) in both periods, and (iii) the accessibility was measured as the number of consultations and variation according to the distance from the municipality and reference hospital. During e-consultation, the demand for care increased (12.8 ± 4.3% vs. 25.5 ± 11.1% per 1000 inhabitants, P < 0.001) and referrals from different areas were equalized. After the implementation of e-consultation, we observed that the increase in hospital admissions and mortality were stabilized [incidence rate ratio (iRR): 1.351 (95% CI, 0.787, 2.317), P = 0.874] and [iRR: 1.925 (95% CI: 0.889, 4.168), P = 0.096], respectively. The geographic variabilities in hospital admissions and mortality seen during the in-person consultation were stabilized after e-consultation implementation.

Conclusions

Implementation of a clinician-to-clinician e-consultation programme in outpatient care was associated with improved accessibility to cardiology healthcare in elderly patients. After e-consultations were implemented, hospital admissions and mortality were stabilized.
Rehabilitation services must include support for sexual and gender-based violence survivors in Ukraine and other war- and conflict-affected countries
Authors: Morgan Rosemary , Asiimwe Lillian , Ager Amanda L , Haq Zuhra , Thumba Linda , Shcherbinina Diana
Published: January 2023

Sexual and gender-based violence (SGBV)—both during times of war and peace—can have impactful negative social and health outcomes. Reports of rape being used as an act of war in Ukraine are drawing global attention to the need for specialized care for SGBV survivors during times of war and thereafter. While data remain limited, in 3 November 2022, 7 million people in Ukraine were reported to need SGBV prevention and response services. Services offered by the government and civil society include a coordination centre of free legal aid, online and mobile platforms, chat-bots, hotlines, assistance centres, shelters, crisis rooms and mobile brigades. Rehabilitation services to support women and girls who have experienced SGBV during times of conflict and war, however, remain limited. We must make sure that our understanding of rehabilitation extends beyond providing physical modalities or recovery after surgery and that SGBV survivors are not excluded from necessary care. This is particularly important if we want to ensure that rehabilitation services are meeting the needs of the most vulnerable populations. We call on the international rehabilitation community to ensure the availability of and access to these vital life-changing services.
Critical role of the RpoE stress response pathway in polymyxin resistance of Escherichia coli
Authors: Zeng Ximin , Hinenoya Atsushi , Guan Ziqiang , Xu Fuzhou , Lin Jun
Published: January 2023

Objectives

Polymyxins, including colistin, are the drugs of last resort to treat MDR bacterial infections in humans. In-depth understanding of the molecular basis and regulation of polymyxin resistance would provide new therapeutic opportunities to combat increasing polymyxin resistance. Here we aimed to identify novel targets that are crucial for polymyxin resistance using Escherichia coli BL21(DE3), a unique colistin-resistant model strain.

Methods

BL21(DE3) was subjected to random transposon mutagenesis for screening colistin-susceptible mutants. The insertion sites of desired mutants were mapped; the key genes of interest were also inactivated in different strains to examine functional conservation. Specific genes in the known PmrAB and PhoPQ regulatory network were inactivated to examine crosstalk among different pathways. Lipid A species and membrane phospholipids were analysed by normal phase LC/MS.

Results

Among eight mutants with increased susceptibility to colistin, five mutants contained different mutations in three genes (rseP, degS and surA) that belong to the RpoE stress response pathway. Inactivation of rpoE, pmrB, eptA or pmrD led to significantly increased susceptibility to colistin; however, inactivation of phoQ or eptB did not change colistin MIC. RpoE mutation in different E. coli and Salmonella resistant strains all led to significant reduction in colistin MIC (16–32-fold). Inactivation of rpoE did not change the lipid A profile but significantly altered the phospholipid profile.

Conclusions

Inactivation of the important members of the RpoE regulon in polymyxin-resistant strains led to a drastic reduction in polymyxin MIC and an increase of lysophospholipids with no change in lipid A modifications.
Insect PRXamides: Evolutionary Divergence, Novelty, and Loss in a Conserved Neuropeptide System
Authors: Farris Sarah M
Published: January 2023

The PRXamide neuropeptides have been described in both protostome and deuterostome species, including all major groups of the Panarthropoda. Best studied are the insect PRXamides consisting of three genes: pk/pban, capa, and eth, each encoding multiple short peptides that are cleaved post-translationally. Comparisons of genome and transcriptome sequences reveal that while retaining its fundamental ancestral organization, the products of the pk/pban gene have undergone significant change in the insect Order Diptera. Basal dipteran pk/pban genes are much like those of other holometabolous insects, while more crown species have lost two peptide coding sequences including the otherwise ubiquitous pheromone biosynthesis activating neuropeptide (PBAN). In the genomic model species Drosophila melanogaster, one of the remaining peptides (hugin) plays a potentially novel role in feeding and locomotor regulation tied to circadian rhythms. Comparison of peptide coding sequences of pk/pban across the Diptera pinpoints the acquisition or loss of the hugin and PBAN peptide sequences respectively, and provides clues to associated changes in life history, physiology, and/or behavior. Interestingly, the neural circuitry underlying pk/pban function is highly conserved across the insects regardless of the composition of the pk/pban gene. The rapid evolution and diversification of the Diptera provide many instances of adaptive novelties from genes to behavior that can be placed in the context of emerging selective pressures at key points in their phylogeny; further study of changing functional roles of pk/pban may then be facilitated by the high-resolution genetic tools available in Drosophila melanogaster.
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410–DNA interaction using small angle X-ray scattering
Authors: Kaur Gundeep , Ren Ren , Hammel Michal , Horton John R , Yang Jie , Cao Yu , He Chenxi , Lan Fei , Lan Xianjiang , Blobel Gerd A , Blumenthal Robert M , Zhang Xing , Cheng Xiaodong
Published: January 2023

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.
Optimizing the order of actions in a model of contact tracing
Authors: Meister Michela , Kleinberg Jon
Published: January 2023

Contact tracing is a key tool for managing epidemic diseases like HIV, tuberculosis, COVID-19, and monkeypox. Manual investigations by human-contact tracers remain a dominant way in which this is carried out. This process is limited by the number of contact tracers available, who are often overburdened during an outbreak or epidemic. As a result, a crucial decision in any contact tracing strategy is, given a set of contacts, which person should a tracer trace next? In this work, we develop a formal model that articulates these questions and provides a framework for comparing contact tracing strategies. Through analyzing our model, we give provably optimal prioritization policies via a clean connection to a tool from operations research called a “branching bandit”. Examining these policies gives qualitative insight into trade-offs in contact tracing applications.
The Clinical Evaluation of a Modified Fmp in Infant Auditory Brainstem Response Tests
Authors: Lightfoot Guy , Georga Constantina , Ferm Inga , Beeby Rachel
Published: January 2023

Objective:

The performance of a modified calculation of F statistic using multiple points (Fmp) in auditory brainstem response (ABR) tests in infants was evaluated.

Design:

Using UK national guidelines, the ABR threshold was established on 50 infant ears at 4 kHz and 41 infant ears at 1 kHz. A specificity-based Fmp criterion for response presence was established from the distribution of no-response values. This criterion was then applied to determine the sensitivity of Fmp in detecting responses.

Results:

A 97.5% true negative rate in no-response waveforms corresponded to an Fmp of 2.2. This criterion detected 85% of 4 kHz and 68% of 1 kHz responses at 10 dB above the ABR threshold but only 51% of 4 kHz and 32% of 1 kHz responses at the ABR threshold.

Conclusions:

Fmp has reasonable clinical utility at stimulus levels above the ABR threshold but is not an adequate replacement for strictly applied conventional waveform interpretation at the ABR threshold. A proposal is offered that should improve Fmp sensitivity.
Chronic Achilles Tendon Repair: Minimally Invasive Turndown Technique With Flexor Hallucis Longus Tendon Transfer
Authors: Pyle Casey , Meyers Andrew
Published: January 2023

Achilles tendon ruptures have shown an increased incidence over the past decades. Of those, an estimated 25% are missed at the first presentation. Chronic Achilles tendon ruptures are routinely retracted and unable to be primarily repaired end-to-end. To provide enough length to allow repair, procedures such as V-Y lengthening, central turndown, or grafting are often necessary. Several lengthening techniques have been described, but there is no gold standard. Complications associated with these varying techniques include wound necrosis and infection. We describe a minimally invasive Achilles tendon central turndown technique for performing chronic Achilles tendon repairs while minimizing wound risk and avoiding use of allograft.

Level of Evidence: Level V.
Modification in Applying Appendix D of 40 CFR Part 61 to Heated Solid Radionuclide Materials With High Melting and Boiling Points
Authors: Smith Linda L. , McCarter William (Bill) L. , Barnett J. Matthew
Published: January 2023

Appendix D of Title 40 Part 61 of the US Code of Federal Regulations (CFR) provides a procedure that US Department of Energy (US DOE) facility owners and operators can use to estimate radionuclide emissions to the atmosphere for dose calculations instead of measuring emissions for minor sources under the 40 CFR Part 61, Subpart H, National Emission Standards for Emissions of Radionuclides Other Than Radon From Department of Energy Facilities, regulation. The procedure assumes that any radioactive material heated above 100 °C is completely vaporized and emitted to the atmosphere. In 1991, the US DOE Oak Ridge Reservation (ORR) requested approval to use different release fractions (RFs) for uranium because of its high melting and boiling points. In response to the request, the US Environmental Protection Agency (US EPA) Region IV approved the use of modified RFs for elemental uranium provided no reaction had taken place to alter its chemical form. In 2015, the ORR requested approval to use different RFs for tungsten, again because of its high melting and boiling points. EPA Region IV approved the use of modified RFs for heated radioactive tungsten metal. In accordance with the two precedents set for heating uranium and radioactive tungsten metals, in 2016, the ORR requested approval to use modified RFs in a similar fashion for other radioactive solid metals and compounds with melting and boiling points above 500 °C that might be heated above 100 °C in future research projects and experiments. EPA Region IV again granted approval to use modified RFs for the list of compounds. This note discusses the proposed modified RFs and their development.