bluuebunny/crossref_metadata_2025_split huggingface dataset:
Counting animals in aerial images with a density map estimation model
Authors: Qian Yifei , Humphries Grant R. W. , Trathan Philip N. , Lowther Andrew , Donovan Carl R. 
Published: April 2023

AbstractAnimal abundance estimation is increasingly based on drone or aerial survey photography. Manual postprocessing has been used extensively; however, volumes of such data are increasing, necessitating some level of automation, either for complete counting, or as a labour‐saving tool. Any automated processing can be challenging when using such tools on species that nest in close formation such as Pygoscelis penguins. We present here a customized CNN‐based density map estimation method for counting of penguins from low‐resolution aerial photography. Our model, an indirect regression algorithm, performed significantly better in terms of counting accuracy than standard detection algorithm (Faster‐RCNN) when counting small objects from low‐resolution images and gave an error rate of only 0.8 percent. Density map estimation methods as demonstrated here can vastly improve our ability to count animals in tight aggregations and demonstrably improve monitoring efforts from aerial imagery.
Effects of large‐scale disturbance on animal space use: Functional responses by greater sage‐grouse after megafire
Authors: Stevens Bryan S. , Roberts Shane B. , Conway Courtney J. , Englestead Devin K. 
Published: April 2023

AbstractGlobal change has altered the nature of disturbance regimes, and megafire events are increasingly common. Megafires result in immediate changes to habitat available to terrestrial wildlife over broad landscapes, yet we know surprisingly little about how such changes shape space use of sensitive species in habitat that remains. Functional responses provide a framework for understanding and predicting changes in space use following habitat alteration, but no previous studies have assessed functional responses as a consequence of megafire. We studied space use and tested for functional responses in habitat use by breeding greater sage‐grouse (Centrocercus urophasianus) before and after landscape‐level changes induced by a >40,000 ha, high‐intensity megafire that burned sagebrush steppe in eastern Idaho, USA. We also incorporated functional responses into predictive resource selection functions (RSFs) to map breeding habitat before and after the fire. Megafire had strong effects on the distribution of available resources and resulted in context‐dependent habitat use that was heterogeneous across different components of habitat. We observed functional responses in the use and selection of a variety of resources (shrubs and herbaceous vegetation) for both nesting and brood rearing. Functional responses in the use of nesting habitat were influenced by the overarching effect of megafire on vegetation, whereas responses during brood rearing appeared to be driven by individual variation in available resources that were conditional on nest locations. Importantly, RSFs built using data collected prior to the burn also had poor transferability for predicting space use in a post‐megafire landscape. These results have strong implications for understanding and predicting how animals respond to a rapidly changing environment, given that increased severity, frequency, and extent of wildfire are consequences of global change with the capacity to reshape ecosystems. We therefore demonstrate a conceptual framework to better understand space use and aid habitat conservation for wildlife in a rapidly changing world.
Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae
Authors: Teklemariam Daniel M. , Gailing Oliver , Siregar Iskandar Z. , Amandita Fitri Yola , Moura Carina C. M. 
Published: April 2023

AbstractThe high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short‐lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.
Satellite telemetry reveals habitat selection decisions by black oystercatchers across seasonal, diel, and tidal cycles
Authors: Ware Lena , Hipfner John Mark , Green David J. 
Published: April 2023

AbstractHabitat use of indicator species is used to prioritize management activities. However, habitat use can vary temporally in response to changes in predation risk and foraging rewards. We deployed satellite tags on 20 black oystercatchers (Haematopus bachmani) in four regions of British Columbia, Canada, to examine habitat use and selection decisions across seasonal, diel and tidal cycles. We characterized the shoreline in each region and used GLMMs to investigate how habitat characteristics influenced shoreline use by tracked birds. For individuals, we estimated home range size and the frequency key features of the shoreline were re‐visited. Black oystercatchers generally made greater‐than‐expected use of rocky islets and shoreline with freshwater outflows, less tree cover and greater intertidal area. However, while black oystercatchers preferred islets and shoreline with less tree cover at most/all time periods, they only exhibited preferences for greater intertidal area during low tides, and preferences for shoreline with freshwater outflows during the nonbreeding season, day, and high tides. Individual home ranges, on average, contained 46 km of shoreline (range: 12–156 km) and individuals used 10.4 km (range: 6.7–13.9 km). Individuals made greater use of larger islets with less tree cover that were closer to outflows, and greater use of outflows associated with larger streams, greater intertidal areas and gravel substrates. Black oystercatchers' habitat preferences likely reduce predation risk (rocky islets and shoreline with less tree cover) and increase foraging rewards (shoreline with freshwater outflows, greater intertidal area, and gravel substrates). However, habitat preferences appear sensitive to constraints on movement in the breeding season and changes in foraging rewards across the diel and tidal cycle, highlighting the importance of examining habitat use at multiple temporal scales. Black oystercatchers are considered indicators of rocky intertidal health; therefore, critical habitat is expected to be important for a suite of wildlife dependent on safe and productive coastline.
Bait attractiveness changes community metrics in dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae)
Authors: Bach Andressa , Mateus Lúcia A. F. , Peres Carlos A. , Haugaasen Torbjørn , Louzada Julio , Hawes Joseph E. , Azevedo Renato A. , Lucena Emanuelly F. , Ferreira José Victor A. , Vaz‐de‐Mello Fernando Z. 
Published: April 2023

AbstractSpecies relative abundance (SRA) is an essential attribute of biotic communities, which can provide an accurate description of community structure. However, the sampling method used may have a direct influence on SRA quantification, since the use of attractants (e.g., baits, light, and pheromones) can introduce additional sources of variation in trap performance. We tested how sampling aided by baits affect community data and therefore alter derived metrics. We tested our hypothesis on dung beetles using data from flight interception traps (FITs) as a baseline to evaluate baited pitfall trap performance. Our objective was to assess the effect of bait attractiveness on estimates of SRA and assemblage metrics when sampled by pitfall traps baited with human feces.Dung beetles were sampled at threeterra firmeprimary forest sites in the Brazilian Amazon. To achieve our objective, we (i) identified species with variable levels of attraction to pitfall baited with human feces; (ii) assessed differences in SRA; and (iii) assessed the effect of bait on the most commonly used diversity metrics derived from relative abundance (Shannon and Simpson indices). We identified species less and highly attracted to the baits used, because most attracted species showed greater relative abundances within baited pitfall traps samples compared with our baseline. Assemblages sampled by baited pitfall traps tend to show lower diversity and higher dominance than those sampled by unbaited FITs. Our findings suggest that for ecological questions focused on species relative abundance, baited pitfall traps may lead to inaccurate conclusions regarding assemblage structure. Although tested on dung beetles, we suggest that the same effect could be observed for other insect taxa that are also sampled with baited traps. We highlight a need for further studies on other groups to elucidate any potential effects of using baits.
Factors influencing mammalian community occupancy in Dhorpatan Hunting Reserve, Nepal
Authors: Regmi Sandeep , Belant Jerrold L. , Pant Bindu , Sharma Hari Prasad 
Published: April 2023

AbstractThe decline in mammalian species diversity is increasing worldwide, with areas characterized by high human activities experiencing more prominent effects. Knowledge of spatial distributions of species and factors acting on them is necessary for effective management. We evaluated community‐level occupancy of mammal species in Dhorpatan Hunting Reserve (DHR), Nepal using remote cameras during 15 March–15 June 2022. We used mammal species detections from remote cameras and multispecies hierarchical occupancy modeling to assess the effects of environmental and anthropogenic variables on community‐level occupancy of detected mammal species. We identified a highly heterogeneous mammal species community at DHR with greatest detection probability (0.21) for red fox (Vulpes vulpes) and lowest (0.08) for blue sheep (Pseudois nayaur). Naïve occupancy ranged from 0.31 for giant‐flying squirrel (Petaurista magnificus) to 0.84 for red fox. Mammal community occupancy increased with increasing canopy cover and number of livestock detections, but overall occupancy declined close to human settlements. The findings of this study can be used for developing policy at DHR for the management of mammal species through reducing the potential increase of human settlements or livestock grazing.
Riparian cottonwood mortality following compound impacts from river water withdrawal and hydroclimatic variation
Authors: Rood Stewart B. , Mahoney John M. 
Published: April 2023

AbstractOriginating in Glacier Park, Montana, the transboundary St. Mary River has provided a focus for international water sharing for a century. It was dammed and diverted in the USA, and more extensively in Alberta, where it supports Canada's centre for agricultural irrigation. Following water withdrawals, the riparian cottonwoods (Populus angustifolia) collapsed, and we assessed the woodland decline downstream from the St. Mary Dam, through eight sets of aerial photographs over seven decades. These revealed 88% woodland loss from 1951 to 1999 (R2 = 0.984), including a steeper decline with the 1980s drought. Following the implementation of an environmental flow regime that increased minimum flows after 1993, the remnant woodlands were stabilized, with a slight recovery by 2022. Analyses of the historical hydrology revealed compound contributions to the woodland mortality. (1) Annual river flows declined with increasing water diversion, and (2) late summer flows were particularly depleted. (3) Dam operations resulted in abrupt stage recessions and irregular spikes. (4) Accompanying climate warming, the spring snowmelt advanced and late summer flows declined. (5) The greatest climatic influence involved multiple‐year clusters with high versus low flows, corresponding with the Pacific decadal oscillation (PDO) from 1920 to 1990 (R2 = 0.365), but less coupled thereafter. This long‐term study demonstrates the coordination between hydroclimatic variation, water management and the fate of riparian woodlands, which reveal ecosystem health. An environmental flow regime provided benefit, and for other regulated rivers in dry ecoregions, we recommend functional flow regimes that provide sufficient minimum flows and avoid abrupt flow recession or irregular spikes.
Nonreplicating synthetic mRNA vaccines: A journey through the European (Journal of Immunology) history
Authors: Pascolo Steve 
Published: April 2023

AbstractThe first worldwide article reporting that injections of synthetic nonreplicating mRNA could be used as a vaccine, which originated from a French team located in Paris, was published in the European Journal of Immunology (EJI) in 1993. It relied on work conducted by several research groups in a handful of countries since the 1960s, which put forward the precise description of eukaryotic mRNA and the method to reproduce this molecule in vitro as well as how to transfect it into mammalian cells. Thereafter, the first industrial development of this technology began in Germany in 2000, with the founding of CureVac, which stemmed from another description of a synthetic mRNA vaccine published in EJI in 2000. The first clinical studies investigating mRNA vaccines in humans were performed as collaboration between CureVac and the University of Tübingen in Germany as early as 2003. Finally, the first worldwide approved mRNA vaccine (an anti‐COVID‐19 vaccine) is based on the mRNA technologies developed by BioNTech since its 2008 foundation in Mainz, Germany, and earlier by the pioneering academic work of its founders. In addition to the past, present, and future of mRNA‐based vaccines, the article aims to present the geographical distribution of the early work, how the development of the technology was implemented by several independent and internationally distributed research teams, as well as the controversies on the optimal way to design or formulate and administer mRNA vaccines.
Stability and Bioaccessibility of β‐Carotene in Oil in Water Emulsions: Impact of Antioxidant Type and Emulsifier
Authors: Li Jing , Chen Xianxin , Li Chen , Xiong Hua , Mu Guangqing , Zhu Xuemei 
Published: April 2023

AbstractThe objective of this study is to explore the influence of proteins type and antioxidants on the physicochemical properties, in vitro digestion, and bioaccessibility of β‐carotene laden emulsions. The combination of rutin and whey protein isolate provides optimal bioaccessibility while also stabilizing the emulsion system and effectively preventing β‐carotene degradation. This is due to the amphiphilic rutin adsorbed into the interface of the emulsion stabilized by whey protein, resulting in partially replacing and further improving the physical and oxidative stability of the β‐carotene emulsion. Meanwhile, the rutin emulsions remain stable and carotene content is still higher (22.38–32.07%) than others even after digestion. Hence, these emulsions show great potential to be applied for delivering β‐carotene based on oil‐in‐water emulsions. This study provides valuable information to build up stable excipient emulsions for functional foods and nutraceuticals.Practical applications: β‐carotene is being exploited for a range of biomedical applications. Concentrate on the blend of antioxidants and proteins displaying various properties in β‐carotene O/W emulsions that can more likely convey β‐carotene to the body and better keep up with natural movement.
Rapid quality assessment of Gentianae Macrophyllae Radix based on near‐infrared spectroscopy and capillary electrophoresis
Authors: Zhang Zhiyong , Hao Nan , Wang Long , Li Shunan , Yan Xinhao , Guo Xuting , Lian Yunlan , Li Wenlong 
Published: April 2023

AbstractThe aim of this study was to establish a rapid quality assessment method for Gentianae Macrophyllae Radix (RGM) using near‐infrared (NIR) spectra combined with chemometric analysis. The NIR spectra were acquired using an integrating sphere diffuse reflectance module, using air as the reference. Capillary electrophoresis (CE) analyses were performed on a model P/ACE MDQ Plus system. Partial least squares‐discriminant analysis qualitative model was developed to distinguish different species of RGM samples, and the prediction accuracy for all samples was 91%. The CE response values at each retention time were predicted by building a partial least squares regression (PLSR) calibration model with the CE data set as the Y matrix and the NIR spectra data set as the X matrix. The converted CE fingerprints basically match the real ones, and the six main peaks can be accurately predicted. Transforming NIR spectra fingerprints into the form of CE fingerprints increases its interpretability and more intuitively demonstrates the components that cause diversity among samples of different species and origins. Loganic acid, gentiopicroside, and roburic acid were considered quality indicators of RGM and calibration models were built using PLSR algorithm. The developed models gave root mean square error of prediction of 0.2592% for loganic acid, 0.5341% for gentiopicroside, and 0.0846% for roburic acid. The overall results demonstrate that the rapid quality assessment system can be used for quality control of RGM.
Developmental and epileptic encephalopathy 89: A novel bi‐allelic variant, molecular dynamics simulation, and a comprehensive clinical and molecular profile
Authors: Khorram Erfan , Amini Masoomeh , Khorrami Mehdi 
Published: April 2023

AbstractObjectiveGamma‐aminobutyric acid (GABA), the major inhibitory neurotransmitter in the adult central nervous system, plays an important role during embryonic neural network formation. GAD67 is the rate‐limiting enzyme in GABA synthesis, and its deficiency leads to developmental and epileptic encephalopathy 89 (DEE 89). Patients who suffered from this syndrome generally manifested severe to profound neurodevelopmental delay, seizures, and often congenital anomalies such as the cleft palate or/and omphalocele. Up to now, only three papers on this syndrome have been published, and our knowledge about the disease's clinical course and pathophysiology is in its infancy.MethodsWe used whole‐exome sequencing (WES) and multiple in‐silico tools to detect a potential causative variant in a patient with severe neurodevelopmental delay and refractory epilepsy. Moreover, by molecular docking and molecular dynamics simulation, we investigate the effect of the candidate variant on the GAD67 function and structure.ResultsWES data analysis revealed a novel deleterious variant (NM_000817.3: c.850C>T; p.Leu284Phe) in the GAD1 gene, which encodes the GAD67 enzyme. Molecular docking and molecular dynamics simulation showed that this variant has deleterious effects on the structure and function of the GAD67. This study's patient, in addition to typical symptoms of the DEE89, showed microcephaly and clonus in the toe, which were novel clinical findings.SignificanceOur findings expand the mutational and clinical spectrum of DEE 89. Also, by gathering clinical symptoms and genetic findings of previously reported cases, moreover providing a comprehensive clinical picture of the disease, we found that there was no common drug therapy among patients whose epilepsy was controlled. Furthermore, the comparison of clinical symptoms between patients with missense and truncating mutations did not show any significant clinical difference, except that patients with missense mutations did not show cleft palates or omphaloceles.
1H nuclear magnetic resonance‐based metabolomics study of serum and pectoralis major for different commercial chicken breeds
Authors: Tan Chengkeng , Selamat Jinap , Jambari Nuzul Noorahya , Sukor Rashidah , Murugesu Suganya , Muhamad Azira , Khatib Alfi 
Published: April 2023

AbstractThis study aimed to characterize the metabolic composition of four types of commercially available chicken breeds [village chicken, colored broiler (Hubbard), broiler (Cobb), and spent layers (Dekalb)] by 1H NMR coupling and discriminate them using multivariate analysis. Five chickens were collected for each chicken breed based on the marketing age from the respective commercial farms. The orthogonal partial least squares discriminant analysis (OPLS‐DA) results showed an obvious separation of local village chickens from the other breeds based on the metabolites present in their serum and meat (pectoralis major). The cumulative values of Q2, R2X, and R2Y of the OPLS‐DA model for chicken serum were 0.722, 0.877, and 0.841. For the pectoralis major muscle, the cumulative values of Q2, R2X, and R2Y of the OPLS‐DA model were reported as 0.684, 0.781, and 0.786, respectively. The quality of both OPLS‐DA models was accepted by the cumulative values of Q2 ≥ 0.5 and R2 ≥ 0.65. The 1H NMR result with multivariate analysis has successfully distinguished local village chicken from the other three commercial chicken breeds based on serum and pectoralis major muscle. Nonetheless, colored broiler (Hubbard) was not distinguished from broiler (Cobb) and spent layers (Dekalb) in serum and pectoralis major, respectively. The OPLS‐DA assessment in this study identified 19 and 15 potential metabolites for discriminating different chicken breeds in serum and pectoralis major muscle, respectively. Some of the prominent metabolites identified include amino acids (betaine, glycine, glutamine, guanidoacetate, phenylalanine, and valine), nucleotides (IMP and NAD+), organic acids (lactate, malate, and succinate), peptide (anserine), and sugar alcohol (myo‐inositol).