bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of Institutions in the Downstream Agribusiness Palm oil (Elaeis Sp) Subsystem
Authors: Jafar Rayhana , Khaerunnisa  , Sutrisno Adi , Sulistyo Anang , Mubarak Ahmad , Kurniasih Nia , Nurlela M , Abimayu Sakti
Published: October 2022

Palm oil is one of the leading commodities of Nunukan Regency. However, problems related to institutions that play a role in the downstream agribusiness subsystem are not running optimally. This is due to limited information, weak coordination between institutions, weak capacity and optimization of farmer institutions. Therefore, this study aims to analyze the institutions that play a role in the downstream agribusiness subsystem. The research was conducted in Nunukan Regency, North Kalimantan Province. Data collection was carried out using a descriptive method through an expert system approach with a survey method. Data analysis with Interpretative Structural Modeling (ISM). The results showed that 11 institutions that have an important role in the Downstream Oil Palm Agribusiness Subsystem in Nunukan Regency are (1). Department of Agriculture and Plantation, (2). Agricultural Extension, (3). Bank Rakyat Indonesia Nunukan Regency, (4).GAPOKTAN/Women’s Farmer’s Group/Farmers’ Group, (5) Middlemen, (6) Cooperative Service, (7).Community Empowerment Agency and Village Government, (8). Cooperative Business Unit, (9). Palm Oil Company, (10). Central Bureau of Statistics (11). Agricultural Quarantine Center. Pemberdayaan Masyarakat dan Pemerintah Desa (BPMD), (8). Unit Usaha Koperasi, (9). Perusahaan Sawit, (10). Badan Pusat Statistik (11). Balai Karantina Pertanian.
Characterization of powdered S. japonica as carrier material for natural food preservatives
Authors: Putra Y , Siahaan E A , Pangestuti R , Ali L , Wahab A
Published: October 2022

S. japonica, an edible brown seaweed, has been used as an efficient biosorbent for its ability in compound adsorption and desorption. Our previous study has demonstrated that natural preservatives (AITC) could be loaded into basic and processed S. japonica via vapor and solution deposition methods. S. japonica carried AITC was successful in inhibiting several foodborne pathogens. According to our previous findings, we proposed this edible brown seaweed suitable for a delivery system of volatile antimicrobials. A comprehensive study was carried out to investigate the absorption and desorption behavior of S. japonica and its porosity. Basic and processed materials of S. japonica were prepared and analyzed. The BET technique was used to determine the surface area and pore size distribution of basic and processed S. japonica. The processed S. japonica powders showed an improvement of pore volume (0.113 cm3/g), pore diameter (0.938 nm), and surface area (5.439 m2/g); while the basic powders showed dense and smoother surface with smaller pore volume (0.077 cm3/g), pore diameter (0.245 nm), and surface area of 0.4529 m2/g. It is suggested that the removal of lipid material may contribute to the improvement of pore size distribution.
Heavy Metal Contents of Hg, Cd, Pb, and Cu in Mud Crab (Scylla Serrata) in Banten Bay, Indonesia
Authors: Fatryani Dita , Sulistiono  , Batu Djamar TF Lumban
Published: October 2022

The development of industry and residential areas around the waters of Banten Bay can increase the input of heavy metal waste and cause accumulation in aquatic biota, especially in mud crab (Scylla serrata). This study aims to determine the level of accumulation of heavy metals (Hg, Cd, Pb, and Cu) contained in mud crab meat in Bojonegara Coastal Waters, Banten Bay. Sampling of the mud crabs was carried out monthly for three months, from August to October 2020 in the waters. The research method consists of the calculation of Bioconcentration Factor (BCF), Maximum Weekly Intake (MWI), and Maximum Tolerable Intake (MTI). According to the analysis, content of heavy metals Hg, Cd, and Pb in mud crab was under the AAS sensitivity value used, which was <0.001 mg/kg, <0.005 mg/kg, <0.030 mg/kg, respectively, while for heavy metal Cu ranged from 4.44 to 13.52 mg/kg. The bioconcentration factor of the heavy metals Hg, Cd, and Pb in the water was classified as low accumulation, while heavy metal Cu in water was classified as medium to high accumulation. The safe limit for consumption of the mud crab meat taken in the waters was 12.94 kg meat/week (adults) and 3.88 kg meat/week (children).
Effect of Maturity Level and Fruit Size on Mechanical Properties of Tomato Fruit (Solanum lycopersicum)
Authors: Safitri Y , Bintoro N , Karyadi J N W
Published: October 2022

Knowledge of the mechanical properties of fruit is an important parameter for post-harvest handling in order to minimize damage to the product. The purpose of this study was to analyze the effect of maturity level and fruit size on the changes in the mechanical properties of tomatoes (Solanum lycopersicum). The study was conducted on three levels of maturities, namely green, turning, and red as well as three kinds of fruit sizes, namely small, medium, and large with a completely randomized design in three replications. Measurement was done by compressing the tomato samples using a compression machine equipped with a loadcell (Loadstar 10kg) and a linear variable deformation transformer (KTC 50mm). Obtained data were than analyzed according to the ASAE S368.4 DEC2000 (R2008) to determine modulus of elasticity, contact area, and maximum compression stress. The results showed that the modulus of elasticity was significantly affected by the maturity level, whereas Smax was significantly affected by both the size and maturity level, and the contact area only affected by the size of the sample. The interaction of the size and maturity level was found to be significant for the modulus of elasticity and Smax values. It was also observed that the tomato of green maturity had the highest modulus of elasticity than tomatoes at turning and red ripeness levels. The smallest modulus of elasticity was 0.5758 MPa for small red tomato, while the largest was 1.9694 MPa for small green tomato. For the contact area, it was found that as the size of the sample increased, the value of the contact area was also increased. The smallest value of contact area was found for small red tomato, which was 0,0006 m2 and the largest value was for large red tomatoes which was 0,0018 m2. The green tomatoes had the largest Smax, followed by turning tomatoes and the last one was red tomatoes. The smallest Smax was 0.1081MPa for large red tomato, while the largest was 0.6427 MPa for small green tomato.
Morphological adaptation of cocoa fine roots under shaded of langsat tree in exploring stony soil
Authors: Saleh AR , Gusli S , Ala A , Neswati R , Sudewi S
Published: October 2022

Cocoa fine roots are responsive to changes in the soil environment to maximize nutrient and water absorption for plant growth. The presence of rock increases soil density and decreases available water content, promoting modification of fine root development. The purpose of this study was to clarify the effect of the physical properties of stony soil on the morphological properties of fine roots. In three land-use systems, soil samples were taken from four depths using a sample core measuring 385 cm3 in three land-use systems. Fine roots were extracted by the immersion method, to measure the length of fine roots from five classes of orders based on diameter. We notes, the bulk density of stony soil increases as the rock mass increases, and the depth increases. The available water content decreases with the increase in bulk density, and this decrease is more pronounced in the lower soil layer. Fine root length was found more in the lower order diameter class, decreasing soil moisture against the bulk density gradient. The bulk density in the topsoil layer reaches 1.71 g cm-3, increasing to 1.84 g cm-3 in the lower soil layer. It seems unreasonable, when compared to the general density of soil mass. Still, this result is solely due to the high fraction of rock with a higher density. Fine roots were dominated by orders 1 and 2 with root diameters < 0.25 mm and < 0.50 mm, reaching 70% of the total fine root length. Fine roots in this diameter class act as absorbent roots, acquiring water and nutrients from the soil.
Antibacterial Activity of Garlic Extract (Allium Sativum) using Fermentation and Non Fermentation towards Propionibacterium Acne
Authors: Fajryana Annisa , Ginting Chrismis Novalinda , Chiuman Linda , Ginting Sahna Ferdinand
Published: October 2022

This study aims to reveal the relationship between responses, where the taken response is the inflammatory response, especially on acne (Acne vulgaris). Simply, acne can also promotes the presence of Propionibacterium acne colonies. Therefore, inhibitor test is needed to reduce the number of Propionibacterium acne, hence in the end it has effect to help reliving the inflammation. These efforts encourage a utilization on the potential of natural materials to be able to suppress the growth rate of bacteria. This research is an experiment with an analytical laboratory quantitative approach by using a static group comparison experimental research design. This study conduct the experiments on potential natural ingredients from several concentrations of extracting garlic (Allium sativum) toward the bacteria Propionibacterium acnes. This test was carried out by observing the results research on antibacterial activity inside garlic (Allium sativum) using fermentation of tempe mushrooms and non-fermented garlic towards Propionibacterium acnes bacteria. The results indicated that there was an effect related to the average diameter of the formed inhibited zone.
Relationship of diatom phytoplankton (Bacillariophyceae) diversity with water quality and heavy metal in Angke and Grogol Rivers, Jakarta City
Authors: Sukma Ayu Maulida , Takarina Noverita Dian
Published: October 2022

Jakarta City is passing by 2 rivers, they are Angke and Grogol Rivers. These rivers are a source of phytoplankton including diatom Bacillariophyceae. Whereas recently, those rivers have received heavy metal inputs that may affect the water quality and also the diatom diversity. Then this study aims to assess the relationship of diatom phytoplankton belonging to Bacillariophyceae diversity with water quality and heavy metal in Angke and Grogol Rivers, Jakarta City. The diversity was quantified using the Shannon-Wiener index (H’) and the relationships were analyzed using Principal Component Analysis (PCA). The results show the diversity of diatoms in both rivers were significantly different (P < 0.05) with the diatom diversity in Grogol (H’ = 1.175) being higher than in Angke (H’ = 0.8175). Mean heavy metal values in Grogol River were recorded higher (P < 0.05) than in Angke as observed in Cu (0.61 mg/L) and Pb. According to the PCA results, water turbidity along with Zn and Cu were the limiting factors for the diversity of diatom Bacillariophyceae.
A Detection Technique Using Dual Authentication Stages Framework for Rogue Access Point Identification
Authors: Arisandia Diki , Ahmad Nazrul Muhaimin , Kannan Subarmaniam
Published: October 2022

Wi-Fi hotspot or Access point indicates many threats that lead to compromise a user’s identity, personal data, and network integrity. Therefore, this will uncover the users to the adversaries who deploy Rogue Access Point (RAP) by purpose to pilfer sensitive information. Hence, the adversaries can exchange the communication anonymously or mimic it as a client to pose a threat to public safety. The research aims to propose a new approach based on the beacon frame anomaly to detect the threats of RAP in the Wi-Fi hotspot. This research uses dual-pass identification steps to detect the RAP to identify the anomalies between the first and second responses. First, the identification will check the AP legitimacy to uncover the true identity of an AP. Second, the connection type of RAP is necessary to identify once the AP is determined as a rogue. The five (5) features have been selected in this research: the beacon response, OUI Number, address 1-4, retry bit, and IBSS status. The combination of all the features was 100% successfully detected the presence of RAP and identify its connection source.
Validation of CHIRPS Estimation Rainfall Data Using Numerical Accuracy Test with Precitipation Observation Data
Authors: Saragih Naikson Fendier , Sitepu Surianto , Simanungkalit Geraldi Titus , Sinambela Marzuki , Rajagukguk Edward , Larosa Frati Gratianus , Jaya Indra Kelana
Published: October 2022

Rainfall is the dominant and most studied weather and climate factor in Indonesia. The use of global satellite estimation data is a solution to overcome the constraints of limited observational rainfall data. Although the global data can be extracted according to the desired location, the data still has to be validated with observational data. This study was conducted to validate the CHIRPS rainfall estimation data with observation rainfall data at the Central MKG Region I Medan. Estimation data used is CHIRPS daily estimation data version 2.0 with a spatial resolution of 0.05°, and validator data is daily observation data of Central MKG Region I Medan for the period 2017- 2019. Validation was done by calculating Pearson correlation, accuracy, bias, mean error (ME), mean absolute error (MAE), and root mean square error (RMSE) values, and using simple linear regression to see overestimated or underestimated estimation data on observation data. Results of this study indicated that the CHIRPS data has a low correlation with the observation data. Large MAE and RMSE values of CHIRPS indicated that the average error of CHIRPS is quite large. Estimation of CHIRPS was underestimated to the observation data so that it is not suitable for daily rainfall forecasting in Medan City. High accuracy value of CHIRPS indicated that CHIRPS was able to detect rain events based on a threshold of 1 mm.
Elemental composition of the oligotrophic peat soils in Yamalo-Nenets Autonomous District (Western Siberia)
Authors: Sokolov D A , Ivanova I S , Siromlya T I , Soldatova E A , Kolubaeva Yu V
Published: October 2022

The research aimed to evaluate the specifics of the elemental composition of oligotrophic peat soils (Cryic Histosols) in Yamalo-Nenets Autonomous district. The content of 32 chemical elements was analyzed in the soil samples using CHN Elemental Analyzer and the atomic emission method. The soil density, ash and organic carbon content were measured along with elemental composition. The ratio of TC/TN (total carbon to total nitrogen) and the degree of pedogenic maturity (degree of organic matter intramolecular oxidation) were calculated. The research shows that the elemental composition of the oligotrophic peat soils of flat-mound frost bogs in Yamalo-Nenets Autonomous District varies widely, and it is closely connected with organic matter features. The content of Ca, Cd, Pb, and Zn correlates negatively (ρ are from -0.71 to -0.63) with the total carbon content. Accordingly, the same elements interconnect with the degree of pedogenic maturity (ρ are from 0.66 to 0.74). Still, there is no dependency between the organic carbon content and the elemental composition of the peat soils. The following factors may result in this: residual eutrophication; the release of elements trace from permafrost sediments and their involvement in local hydrogeochemical fluxes; local geochemical features (for example, the proximity of the Polar Urals).
Algae and cyanoprokaryotes in raised swamps of KMAO – Yugra, Russia
Authors: Skorobogatova O N , Semochkina M A , Yumagulova E R
Published: October 2022

This paper reports a 2015-2019 study of freshwater algae found in seven typical sphagnum bogs in Khanty-Mansi Autonomous Okrug – Yugra, Russia. The algocenoses were studied using conventional methods of algology. Microscopes Nikon ECLIPSE E200 and OLYMPUS SX4 were used. The identified species are named considering the recent changes in the global algal database AlgaeBase. The chemical composition of the swamp mass is presented. In total, 459 algae and cyanobacteria were identified in conditions of low salinity (40–70 mg/L), acidified waters (pH 2.4–5.4) and a wide temperature range (2–31 °C). The analysis of the algae composition was performed.Species-rich classes, families and genera, and species-poor taxa were found. The eco-geographical and saprobiological analyses were performed. A very low similarity of algal floras in individual swamps was revealed during assessment of the algal floras using the Chekanovsky-Sorensen similarity index.
Main ecological-geographical factors of mire vegetation syntaxa differentiation in Southern Urals
Authors: Ivchenko T G , Znamenskiy S R
Published: October 2022

Using gradient analysis and indicator values, it was revealed that the main factors of syntaxa differentiation of mire communities in the South Ural region are acidity and mineral composition of mire-ground waters, variability of habitat moisture and thermo-climatic factors. To a lesser extent, the ordination of mire vegetation syntaxa depends on the general moisture of the habitats and the light factor. The identified nine groups of syntaxa are ordered in the axes of the main ecological factors and are characterized by formations of indicator species. They have clear differences in floristic composition and reflect the specific ecological conditions of mire habitats.
Nutrients in streams draining the different types of wetlands in Western Siberian Plain
Authors: Tokareva I V , Korets M A , Prokushkin A S
Published: October 2022

Two second order streams were compared to test the influence of peatbog type (minerotrophic vs. oligotrophic) on dissolved nutrient composition and dynamics during several hydrologic years. A significant spatio-temporal variation in the concentration of nutrients in the channel runoff is shown. It depends on the catchment characteristics and the hydrological period of the year. In general, the concentrations of phosphates, nitrates and nitrites are lower in the stream draining an area dominated by a minerotrophic bog that indicates nutrients removal by more intense microbiological activity. This is also confirmed by the greater amount of ammonium nitrogen present in the streamflow. In the annual runoff of both streams, the ammonium form dominates dissolved inorganic nitrogen. The minimum concentration of phosphates is observed in winter, and ammonium in the spring flood. In the territory with a predominance of minerotrophic bogs the stream runoff is enriched in calcium, magnesium and silicon indicating specific major cation-rich groundwater input.
On distribution, ecology and conservation of rare moss Tomentypnum nitens (Hedw.) Loeske in Republic of Bashkortostan (Southern Urals region)
Authors: Baisheva E Z
Published: October 2022

The distribution of rare moss Tomentypnum nitens in the Republic of Bashkortostan has been studied. 13 subpopulations have been found in the minerotrophic mires, and only six of them occur within special nature protected areas. The distribution map of the species and the precise locality data are provided. The conservation status of this species is assessed as Near Threatened in the republic, and it should be included into the next edition of the regional Red Data book.
Soil carbon and nitrogen stocks in polygonal-fissure mires of southern tundra in Western Siberia
Authors: Golubyatnikov L L , Zarov E A
Published: October 2022

Based on the experimental data, soil carbon and nitrogen stocks are estimated in polygonal-fissure mires of southern tundra in the north-eastern part of Western Siberia. The field experiments were carried out in 2014-2017 at the site located in tundra zone of the Yamal-Nenets Autonomous District. Active soil layer (seasonally thaw) and upper frozen layer are investigated. The seasonally thaw layer of tundra soils has been subdivided into two horizons: active upper layer (down to 15 cm depth) and active lower layer (from 15 cm down to the permafrost). Our research has shown that the values of organic carbon and total nitrogen storages in mires under study can be estimated as 14.1±3.6 kgC/m2 and 0.4±0.1 kgN/m2 for the active soil layer and 12.9±2.8 kgC/m2 and 0.5±0.1 kgN/m2 for the upper frozen layer. Organic carbon and total nitrogen stocks for the active soil layer and upper frozen layer in polygonal-fissure mires are evaluated as 172.0±29.1 ktC and 5.4±1.2 ktN.
Species composition of the bryophytes in mires of Big Shantar Island (National Park «Shantarskie ostrova»)
Authors: Kuptsova V A , Chakov V V
Published: October 2022

The article presents the results investigating the species composition of the bryophytes based on field research of mire ecosystems of the Big Shantar Island. This study found a total of 75 bryophyte species, including 60 species of which belong to mosses and 15 species of liverworts. The most species-rich family of bryophytes of the National Park, Sphagnaceae includes 22 species. The sections Cuspidata comprises 8 species and Acutifolia – 8 species. Calliergonaceae (7 species) is the most represented family of the Bryopsida (38 species), and Scapaniaceae (5 species) and Cephaloziaceae (4 species) are the largest taxa of liverworts. The distribution of the identified species is considered in relation to the sites of mires.
Generation of all-fiber ultrafast pulses at 2 μm by soliton self-frequency shift in highly nonlinear silica fiber
Authors: Marqués-García Jorge , Jarabo Sebastián
Published: October 2022

An efficient and straightforward method to obtain all-fiber pulsed sources at 2 μm is presented and experimentally demonstrated. It is based on the soliton self-frequency shift effect in a highly nonlinear fiber. The output power of a supercontinuum source is previously increased by an optimized homemade thulium-doped fiber amplifier. By coupling the amplified output power in a highly nonlinear fiber, the spectrum is shifted toward 130 nm and the spectral peak is located at 2014 nm. The power conversion factor reaches values as high as 0.93, without employing additional amplifiers. The mean spectral power of the 2 μm source reaches −4.6 dBm nm−1 (0.35 mW nm−1), its output power is 38 mW and the peak power of each pulse is higher than 27 kW.
Nasal and Plasma Severe Acute Respiratory Syndrome Coronavirus 2 RNA Levels Are Associated With Timing of Symptom Resolution in the ACTIV-2 Trial of Nonhospitalized Adults With Coronavirus Disease 2019
Authors: Li Yijia , Harrison Linda J , Chew Kara W , Currier Judy S , Wohl David A , Daar Eric S , Evering Teresa H , Wu Ryan , Giganti Mark , Ritz Justin , Javan Arzhang Cyrus , Coombs Robert W , Moser Carlee , Hughes Michael D , Eron Joseph J , Smith Davey M , Li Jonathan Z
Published: October 2022

Acute Coronavirus Disease 2019 symptoms limit daily activities, but little is known about its association with severe acute respiratory syndrome coronavirus 2 viral burden. In this exploratory analysis of placebo recipients in the ACTIV-2/A5401 platform trial, we showed that high anterior nasal RNA levels and detectable plasma RNA were associated with delayed symptom improvement.

Clinical Trials Registration. https://clinicaltrials.gov/ct2/show/NCT04518410.
miRNA analysis reveals novel dysregulated pathways in amyotrophic lateral sclerosis
Authors: Hur Junguk , Paez-Colasante Ximena , Figueroa-Romero Claudia , Lo Ting-wen , Barmada Sami J , Paulsen Michelle T , Ljungman Mats , Alakwaa Fadhl M , Savelieff Masha G , Goutman Stephen A , Feldman Eva L
Published: October 2022

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Its complex pathogenesis and phenotypic heterogeneity hinder therapeutic development and early diagnosis. Altered RNA metabolism is a recurrent pathophysiologic theme, including distinct microRNA (miRNA) profiles in ALS tissues. We profiled miRNAs in accessible biosamples, including skin fibroblasts and whole blood and compared them in age- and sex-matched healthy controls versus ALS participants with and without repeat expansions to chromosome 9 open reading frame 72 (C9orf72; C9-ALS and nonC9-ALS), the most frequent ALS mutation. We identified unique and shared profiles of differential miRNA (DmiRNA) levels in each C9-ALS and nonC9-ALS tissues versus controls. Fibroblast DmiRNAs were validated by quantitative real-time PCR and their target mRNAs by 5-bromouridine and 5-bromouridine-chase sequencing. We also performed pathway analysis to infer biological meaning, revealing anticipated, tissue-specific pathways and pathways previously linked to ALS, as well as novel pathways that could inform future research directions. Overall, we report a comprehensive study of a miRNA profile dataset from C9-ALS and nonC9-ALS participants across two accessible biosamples, providing evidence of dysregulated miRNAs in ALS and possible targets of interest. Distinct miRNA patterns in accessible tissues may also be leveraged to distinguish ALS participants from healthy controls for earlier diagnosis. Future directions may look at potential correlations of miRNA profiles with clinical parameters.
Development of an Accessible and Scalable Quantitative Polymerase Chain Reaction Assay for Monkeypox Virus Detection
Authors: Porzucek Abigail J , Proctor Abigale M , Klinkhammer Katharina E , Tritsch Sarah R , Robertson Molly A , Bashor Jonathan P , Villani Jack , Sepulveda Jorge L , Mores Christopher N
Published: October 2022

During the 2022 monkeypox (MPX) outbreak, testing has been limited and results delayed, allowing ongoing transmission. Gold-standard quantitative polymerase chain reaction (qPCR) diagnostics are difficult to obtain. This research adapted the June 2022 CDC MPX qPCR assay for broad implementation. Validated using MPX stocks in a matrix with multiple sample types, MPX was detected with cycle threshold (Ct) values 17.46–35.59 and titer equivalents 8.01 × 106 to 2.45 × 100 plaque–forming unit (PFU)/mL. The detection limit was 3.59 PFU/mL. Sensitivity and specificity were both 100%. This qPCR assay can be quickly and broadly implemented in research and public health laboratories to increase diagnostic capacity amid the growing MPX outbreak.
Sniffing out Stingray Noses: The Functional Morphology of Batoid Olfaction
Authors: Rutledge K M
Published: October 2022

Synopsis

Batoid fishes (rays, skates, sawfishes, and guitarfishes) are macrosmatic, meaning they rely on their sense of smell as one of the primary senses for survival and reproduction. Olfaction is important for long-distance tracking and navigation, predator and prey recognition, and conspecific signaling. However, the mechanisms by which batoids harness odorants is unknown. Without a direct pump-like system, it is hypothesized that batoids irrigate their nostrils via one or a combination of the following: the motion pump, buccopharyngeal pump, pressure (ex. pitot-like mechanism), or a shearing force (ex. viscous entrainment). These mechanisms rely on the size, shape, and position of the nostrils with respect to the head and to each other. Batoids are united as a group by their dorsoventrally compressed body plans, with nostrils on the ventral side of their body. This position presents several challenges for odor capture and likely limits the effectivity of the motion pump. Batoid fishes display an expansive nasal morphology, with inlet nostrils ranging from thin, vertical slits to wide, horizontal ovals to protruding, tube-like funnels, and more. In this paper, a morphometric model is developed to quantify the vast diversity in batoid nose shapes, sizes, and positions on the head in an ecological and functional framework. Specifically, swimming mode, lifestyle, habitat, and diet are examined for correlations with observed nasal morphotypes. Morphometric measurements were taken on all 4 orders present in Batoidea to broadly encompass batoid nasal diversity (Rhinopristiformes 4/5 families; Rajiformes 2/4 families; Torpediniformes 4/4 families; Myliobatiformes 8/11 families). All batoid external nasal diversity was found to be categorized into 5 major morphological groups and were termed: flush nare [circle, comma, intermediate], open nare, and protruding nare. Several morphometric traits remained significant when accounting for shared ancestry, including the position and angle of the nostril on the head, the width of the inlet hole, and the spacing of the nostrils from each other. These measurements were found to be closely correlated and statistically significant with the swimming mode of the animal. This study provides the first crucial step in understanding batoid olfaction, by understanding the diversity of the morphology of the system. Because odor capture is a strictly hydrodynamic process, it may be that factors relating more directly to the fluid dynamics (i.e., swimming mode, velocity, Reynolds number) may be more important in shaping the evolution of the diversity of batoid noses than other ecological factors like habitat and diet.
Appropriateness of surgical antimicrobial prophylaxis in a teaching hospital in Ghana: findings and implications
Authors: Sefah Israel Abebrese , Denoo Edinam Yawo , Bangalee Varsha , Kurdi Amanj , Sneddon Jacqueline , Godman Brian
Published: October 2022

Background

Surgical site infections (SSIs) are among the most common infections seen in hospitalized patients in low- and middle-income countries (LMICs), accounting for up to 60% of hospital-acquired infections. Surgical antimicrobial prophylaxis (SAP) has shown to be an effective intervention for reducing SSIs and their impact. There are concerns of inappropriate use of SAP in Ghana and therefore our audit in this teaching hospital.

Methods

A retrospective cross sectional clinical audit of medical records of patients undergoing surgery over a 5 month duration from January to May 2021 in Ho Teaching Hospital. A data collection form was designed to collect key information including the age and gender of patients, type and duration of surgery, choice and duration of SAP. The collected data was assessed for the proportion of SAP compliance with Ghana Standard Treatment Guidelines (STGs) and any association with various patient, surgical wound and drug characteristics.

Results

Of the 597 medical records assessed, the mean age of patients was 35.6 ± 12.2 years with 86.8% (n = 518) female. Overall SAP compliance with the STG was 2.5% (n = 15). SAP compliance due to appropriate choice of antimicrobials was 67.0% (n = 400) and duration at 8.7% (n = 52). SAP compliance was predicted by duration of SAP (P < 0.000) and postoperative hospitalization duration (P = 0.005).

Conclusions

SAP compliance rate was suboptimal, principally due to a longer duration of prescription. Quality improvement measures such as education of front-line staff on guideline compliance, coupled with clinical audit and regular updates, are urgently needed to combat inappropriate prescribing and rising resistance rates.
Unique features of regulation of sulfate assimilation in monocots
Authors: Rahimzadeh Karvansara Parisa , Kelly Ciaran , Krone Raissa , Zenzen Ivan , Ristova Daniela , Silz Emely , Jobe Timothy O , Kopriva Stanislav
Published: October 2022

Sulfate assimilation is an essential pathway of plant primary metabolism, regulated by the demand for reduced sulfur (S). The S-containing tripeptide glutathione (GSH) is the key signal for such regulation in Arabidopsis, but little is known about the conservation of these regulatory mechanisms beyond this model species. Using two model monocot species, C3 rice (Oryza sativa) and C4Setaria viridis, and feeding of cysteine or GSH, we aimed to find out how conserved are the regulatory mechanisms described for Arabidopsis in these species. We showed that while in principle the regulation is similar, there are many species-specific differences. For example, thiols supplied by the roots are translocated to the shoots in rice but remain in the roots of Setaria. Cysteine and GSH concentrations are highly correlated in Setaria, but not in rice. In both rice and Setaria, GSH seems to be the signal for demand-driven regulation of sulfate assimilation. Unexpectedly, we observed cysteine oxidation to sulfate in both species, a reaction that does not occur in Arabidopsis. This reaction is dependent on sulfite oxidase, but the enzyme(s) releasing sulfite from cysteine still need to be identified. Altogether our data reveal a number of unique features in the regulation of S metabolism in the monocot species and indicate the need for using multiple taxonomically distinct models to better understand the control of nutrient homeostasis, which is important for generating low-input crop varieties.
Robust sampling for weak lensing and clustering analyses with the Dark Energy Survey
Authors: Lemos P , Weaverdyck N , Rollins R P , Muir J , Ferté A , Liddle A R , Campos A , Huterer D , Raveri M , Zuntz J , Valentino E Di , Fang X , Hartley W G , Aguena M , Allam S , Annis J , Bertin E , Bocquet S , Brooks D , Burke D L , Rosell A Carnero , Kind M Carrasco , Carretero J , Castander F J , Choi A , Costanzi M , Crocce M , da Costa L N , Pereira M E S , Dietrich J P , Everett S , Ferrero I , Frieman J , García-Bellido J , Gatti M , Gaztanaga E , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Kuropatkin N , Lima M , March M , Melchior P , Menanteau F , Miquel R , Morgan R , Palmese A , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Porredon A , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Smith M , Suchyta E , Swanson M E C , Tarle G , Thomas D , To C , Varga T N , Weller J ,   (DES Collaboration)
Published: October 2022

Recent cosmological analyses rely on the ability to accurately sample from high-dimensional posterior distributions. A variety of algorithms have been applied in the field, but justification of the particular sampler choice and settings is often lacking. Here, we investigate three such samplers to motivate and validate the algorithm and settings used for the Dark Energy Survey (DES) analyses of the first 3 yr (Y3) of data from combined measurements of weak lensing and galaxy clustering. We employ the full DES Year 1 likelihood alongside a much faster approximate likelihood, which enables us to assess the outcomes from each sampler choice and demonstrate the robustness of our full results. We find that the ellipsoidal nested sampling algorithm multinest reports inconsistent estimates of the Bayesian evidence and somewhat narrower parameter credible intervals than the sliced nested sampling implemented in polychord. We compare the findings from multinest and polychord with parameter inference from the Metropolis–Hastings algorithm, finding good agreement. We determine that polychord provides a good balance of speed and robustness for posterior and evidence estimation, and recommend different settings for testing purposes and final chains for analyses with DES Y3 data. Our methodology can readily be reproduced to obtain suitable sampler settings for future surveys.
Full-shape galaxy power spectra and the curvature tension
Authors: Glanville Aaron , Howlett Cullan , Davis Tamara
Published: October 2022

With recent evidence for a possible ‘curvature tension’ among early and late universe cosmological probes, Effective Field Theories of Large Scale Structure (EFTofLSS) have emerged as a promising new framework to generate constraints on Ωk that are independent of both CMB measurements, and some of the assumptions of flatness that enter into other large-scale structure analyses. In this work we use EFTofLSS to simultaneously constrain measurements from the 6dFGS, BOSS, and eBOSS catalogues, representing the most expansive full-shape investigation of curvature to date. Using the Bayesian evidence ratio our full-shape data assigns betting odds of 2:1 in favour of curvature, indicating present measurements remain broadly compatible with both flat and curved cosmological models. When our full-shape sample is combined with Planck 2018 CMB measurements, we break the geometric degeneracy and recover a joint fit on Ωk of $-0.0037^{+0.0025}_{-0.0026}$. Using the suspiciousness statistic we find evidence for a moderate tension between Planck 2018 and our suite of full-shape measurements, at a significance of $1.86 ^{+0.13}_{-0.11} \sigma$ (p ∼ 0.06 ± 0.02). These results demonstrate the usefulness of full-shape clustering measurements as a CMB independent probe of curvature in the ongoing curvature tension debate.
Grantecan spectroscopic observations and confirmations of planetary nebulae candidates in the Northern Galactic Plane
Authors: Ritter Andreas , Parker Q A , Sabin L , Le Dû P , Mulato L , Patchick D
Published: October 2022

We present Gran Telescopio Canarias (GTC) spectroscopic confirmations of 55 faint Planetary Nebulae (PNe) candidates discovered largely in the INT Photometric H α Survey (IPHAS) of the Northern Galactic Plane by our pro-am collaboration. We confirm 46 of them as ‘True’ (T), 4 as ‘Likely’ (L), and 5 as ‘Possible’ (P) PNe and including 5 new PNe central star (CSPN) discoveries. This was from observations of 62 new candidates yielding a maximum PN discovery success rate of 89 per cent. The sensitivity and longer wavelength coverage of IPHAS allows PNe to be found in regions of greater extinction and at these lower Galactic latitudes, including PNe in a more advanced evolutionary state and at larger distances compared to previously known Galactic PNe. We use a holistic set of observed characteristics and optical emission-line diagnostics to confirm candidates. Plasma properties have been determined in a self-consistent way using pyneb. This work is facilitated by the functionality of our powerful, multiwavelength database ‘HASH’ (Hong Kong, Australian Astronomical Observatory, Strasbourg Observatory H-alpha Planetary Nebula catalogue) that federates known imaging, spectroscopy, and other pertinent data for all Galactic T, L, P PNe, and the significant numbers of mimics. Reddenings, corrected radial velocities, and PNe electron density and temperature estimates are provided for these new PNe wherever possible.
Stochastic dynamical description of κ and ρ bursting classes of the microquasar GRS 1915+105
Authors: Alberti Tommaso , Massaro Enrico , Mineo Teresa , Feroci Marco
Published: October 2022

We applied a stochastic analysis based on the Langevin equation to some bursting X-ray light curves of the bright microquasar GRS 1915+105. These time series, obtained with the PCA instrument onboard Rossi-XTE, are typical of the ρ and κ classes, which are characterized by several recurring bursts with different profiles and recurrence times. We computed the state functions which are able to capture the main dynamical properties of these light curves. In the case of the κ class, the state functions in four energy bands have a double-well structure (two stable states with an unstable one in between) and the system oscillates from one to the other minimum describing a typical hysteresis cycle, as in the case of a stochastic resonance under a forcing input. For the ρ class, the functions have only one stable state followed by an unstable interval, and the system describes a limit cycle. We also performed a new spectral analysis of these data with a multitemperature zero torque accretion disc model and used the resulting parameters for interpreting the main properties of the stochastic description.
Classification of local ultraluminous infrared galaxies and quasars with kernel principal component analysis
Authors: Papaefthymiou Evangelos S , Michos Ioannis , Pavlou Orestis , Papadopoulou Lesta Vicky , Efstathiou Andreas
Published: October 2022

We present a new diagnostic diagram for local ultraluminous infrared galaxies (ULIRGs) and quasars, analysing particularly the Spitzer Space Telescope’s infrared spectrograph spectra of 102 local ULIRGs and 37 Palomar Green quasars. Our diagram is based on a special non-linear mapping of these data, employing the kernel principal component analysis method. The novelty of this map lies in the fact that it distributes the galaxies under study on the surface of a well-defined ellipsoid, which, in turn, links basic concepts from geometry to physical properties of the galaxies. Particularly, we have found that the equatorial direction of the ellipsoid corresponds to the evolution of the power source of ULIRGs, starting from the pre-merger phase, moving through the starburst-dominated coalescing stage towards the active galactic nucleus-dominated phase, and finally terminating with the post-merger quasar phase. On the other hand, the meridian directions distinguish deeply obscured power sources of the galaxies from unobscured ones. These observations have also been verified by comparison with simulated ULIRGs and quasars using radiative transfer models. The diagram correctly identifies unique galaxies with extreme features that lie distinctly away from the main distribution of the galaxies. Furthermore, special two-dimensional projections of the ellipsoid recover almost monotonic variations of the two main physical properties of the galaxies, the silicate and polycyclic aromatic hydrocarbon features. This suggests that our diagram naturally extends the well-known Spoon diagram and it can serve as a diagnostic tool for existing and future infrared spectroscopic data, such as those provided by the James Webb Space Telescope.
CottonMD: a multi-omics database for cotton biological study
Authors: Yang Zhiquan , Wang Jing , Huang Yiming , Wang Shengbo , Wei Lulu , Liu Dongxu , Weng Yonglin , Xiang Jinhai , Zhu Qiang , Yang Zhaoen , Nie Xinhui , Yu Yu , Yang Zuoren , Yang Qing-Yong
Published: October 2022

Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http://yanglab.hzau.edu.cn/CottonMD/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.
AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics
Authors: Lund Jesper B , Lindberg Eric L , Maatz Henrike , Pottbaecker Fabian , Hübner Norbert , Lippert Christoph
Published: October 2022

With the current surge of spatial transcriptomics (ST) studies, researchers are exploring the deep interactive cell-play directly in tissues, in situ. However, with the current technologies, measurements consist of mRNA transcript profiles of mixed origin. Recently, applications have been proposed to tackle the deconvolution process, to gain knowledge about which cell types (SC) are found within. This is usually done by incorporating metrics from single-cell (SC) RNA, from similar tissues. Yet, most existing tools are cumbersome, and we found them hard to integrate and properly utilize. Therefore, we present AntiSplodge, a simple feed-forward neural-network-based pipeline designed to effective deconvolute ST profiles by utilizing synthetic ST profiles derived from real-life SC datasets. AntiSplodge is designed to be easy, fast and intuitive while still being lightweight. To demonstrate AntiSplodge, we deconvolute the human heart and verify correctness across time points. We further deconvolute the mouse brain, where spot patterns correctly follow that of the underlying tissue. In particular, for the hippocampus from where the cells originate. Furthermore, AntiSplodge demonstrates top of the line performance when compared to current state-of-the-art tools. Software availability: https://github.com/HealthML/AntiSplodge/.
Physician Perspectives on Reducing Curative Cancer Treatment Intensity for Populations Underrepresented in Clinical Trials
Authors: Rocque Gabrielle B , Andrews Courtney , Lawhon Valerie M , Ingram Stacey A , Frazier Rachel M , Smith Mary Lou , Wagner Lynne I , Zubkoff Lisa , Wallner Lauren P , Wolff Antonio C
Published: October 2022

Background

Historically, clinical trials involved adding novel agents to standard of care to improve survival. There has been a shift to an individualized approach with testing less intense treatment, particularly in breast cancer where risk of recurrence is low. Little is known about physician perspectives on delivering less intense treatment for patients who are not well represented in clinical trials.

Methods

Open-ended, individual qualitative interviews with medical oncologists explored their perspectives on trials that test less intense treatment for patients with cancer, with a focus on breast cancer. Interviews were audio-recorded and transcribed. Four independent coders utilized a content analysis approach to analyze transcripts using NVivo. Major themes and exemplary quotes were extracted.

Results

Of the 39 participating physicians, 61.5% felt comfortable extrapolating, 30.8% were hesitant, and 7.7% would not feel comfortable extrapolating trial outcomes to underrepresented populations. Facilitators of comfort included the sentiment that “biology is biology” (such that the cancer characteristics were what mattered), the strength of the evidence, inclusion of subset analysis on underrepresented populations, and prior experience making decisions with limited data. Barriers to extrapolation included potential harm over the patient’s lifetime, concerns about groups that had minimal participants, application to younger patients, and extending findings to diverse populations. Universally, broader inclusion in trials testing lowering chemotherapy was desired.

Conclusions

The majority (92%) of physicians reported that they would de-implement treatment for patients poorly represented in clinical trials testing less treatment, while expressing concerns about applicability to specific subpopulations. Further work is needed to increase clinical trial representation of diverse populations to safely and effectively optimize treatment for patients with cancer.

Trial registration

NCT03248258