bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiological diagnosis of endophthalmitis using nanopore targeted sequencing
Authors: Huang Qiong , Fu Aisi , Wang Yiyan , Zhang Jie , Zhao Wanxu , Cheng Yang 
Published: August 2021

AbstractBackgroundMicroorganism identification is critical for the early diagnosis and management of infectious endophthalmitis, but traditional culture can yield false‐negative results. Nanopore targeted sequencing (NTS) is a third‐generation sequencing technique with multiple advantages. This study aimed to test aqueous humour or vitreous fluid samples from presumed cases of infectious endophthalmitis using NTS to evaluate the feasibility of NTS in diagnosing endophthalmitis, especially for culture‐negative cases.MethodsThis prospective study enrolled patients who presented to the Department of Ophthalmology of Union Hospital (Wuhan, China) between June 2018 and December 2020. The samples were sent immediately for routine microbiology culture processing and NTS assay.ResultsNTS identified microorganisms in 17 of 18 cases (94.4%) (eight culture‐positive cases, nine culture‐negative cases, and one case unavailable for culture). There was a high‐quality match between culture and NTS for culture‐positive cases. In the eight culture‐negative cases and the case unavailable for culture, NTS detected either bacteria, fungi, or a mixture of bacteria and fungi in the intraocular fluids. The average waiting times for the results of bacterial and fungal cultures were 48 and 72 h, respectively. The average time for the NTS results was 12 h.ConclusionsNTS appears to be a promising diagnostic platform for diagnosing infectious endophthalmitis, even for culture‐negative cases.
Urban Precarity: The Destructiveness of Neoliberalism and Possibilities for Transformation
Authors: Susser Ida 
Published: August 2021

AbstractAs neoliberalism has torn apart the policies of social and collective stability integral to the visions of welfare states post‐World War II, precarity has become central to the study of advanced capitalist societies. This contribution invokes literary explorations of urbanity to argue that the anthropological analysis of the “urban” is pivotal to the understanding of how contemporary precarity is made and experienced. It draws on my fieldwork with the French Gilets Jaunes movement. The study of the urban has a long history both outside Europe and the United States as well as within. By contrast, precarity has emerged as a key word in the historic centers of capital where states have abandoned aspirations for expanding wellbeing. The papers presented here explore the relevance of this concept to post‐colonial countries where life, as many have pointed out, has always been precarious.
Patch characteristics and domestic dogs differentially affect carnivore space use in fragmented landscapes in southern Chile
Authors: Malhotra Rumaan , Jiménez Jaime E. , Harris Nyeema C. 
Published: August 2021

AbstractAimIn an increasingly anthropogenic world, species face multiple interacting threats. Habitat fragmentation and domestic dogs are two perturbations threatening terrestrial mammals globally. Our aim was to determine whether (a) the spatial use of domestic dogs increases with habitat destruction, and (b) domestic dogs and habitat destruction drive the spatial use of native carnivores in a heavily degraded agricultural landscape.LocationCentral valley/Andean foothills transition of Los Lagos, Chile.MethodsWe implemented a camera trap survey in a fragmented landscape comprised of native forest patches amidst a matrix of pastureland. We used single‐species occupancy models to assess the impact of domestic dogs and habitat destruction on three mesocarnivores—the foxes, culpeo (Lycalopex culpaeus) and chilla (Lycalopex griseus) and the wild cat güiña (Leopardus guigna). Additionally, we compared temporal activity of all study species including domestic dogs.ResultsDetection rates for both the foxes increased with domestic dog occupancy, while factors driving occupancy differed for each of the native species. We found that a 12% projected increase in domestic dog occupancy negatively impacted the spatial use of the culpeo. Habitat loss and fragmentation were positive drivers for chilla and domestic dog occupancy. The güiña did not respond to fragmentation and other habitat covariates or domestic dog occupancy. All native carnivore species were primarily nocturnal, while the domestic dog was almost entirely diurnal.Main ConclusionsWe highlight that domestic dog occupancy was positively correlated with habitat loss. Native species showed varied tolerance to domestic dog occupancy and no negative response to habitat destruction. Future conditions of increased fragmentation and habitat loss will likely increase the potential contact between domestic dogs and native carnivores.
Is the severity of initial sensitization to diphenylcyclopropenone in alopecia areata patients predictive of the final clinical response?
Authors: Ghandi Narges , Seifi Golnoosh , Nasimi Maryam , Abedini Robabeh , Mirabedian Soheila , Etesami Ifa , Ehsani Amirhooshang 
Published: August 2021

AbstractImmunotherapy by diphenylcyclopropenone (DPCP) is generally started with 2% DPCP sensitization, however in recent years studies have questioned the necessity of sensitization that may cause patients severe reactions and troubles at the onset of therapy. The purpose of the present study was to evaluate the association between the severity of initial reaction to 2% DPCP sensitization in AA patients and clinical response. In this retrospective study, 110 AA patients who continued therapy for at least 6 months were enrolled. Hair loss and hair regrowth rates were calculated based on the Severity of Alopecia Tool (SALT) scoring system. Initial reaction to 2% DPCP sensitization after 2 weeks was graded as negative reaction (absence of any reaction), doubtful reaction (mild erythema, pruritus, and irritation for minutes after test), weak (erythema, mild edema, and scaling), and strong to extreme reaction (vesicles, bullae, ulcer, and discharge). The degrees of the initial reaction to 2% DPCP after 2 weeks were negative reaction 13 (11.81%), doubtful reaction 40 (36.36%), weak reaction 33 (30%), and strong to extreme reaction 24 (21.81%). Patients were divided into two groups: (A) patients with less than 12‐month therapy (75 of 110), (B) patients with more than 12‐month therapy (35 of 110). Initial reaction to 2% DPCP sensitization was not correlated with hair regrowth rate in either group (group A: Spearman's rho = 0.194, p = 0.095; group B: Spearman's rho = 0.063 p = 0.720). After 12‐month treatment with DPCP, hair regrowth rate was significantly greater than 6‐months therapy (group A: 17.03 ± 37.78, group B: 49.26 ± 36.34; p = 0.003). The severity of hair loss at the onset of treatment was significantly associated with the response rate in both groups (p‐value <0.002). Based on our results, it is the initial severity of the disease and not the initial reaction to 2% DPCP sensitization that predicts the clinical response to DPCP immunotherapy.
The Attitude towards Polypills Questionnaire (APPQ): a phase I–III development and validation study in patients with cerebrovascular disease
Authors: Lehmann Jens , Riedl David , Sztankay Monika , Boehme Christian , Fischnaller Julian , Kiechl Stefan , Holzner Bernhard , Knoflach Michael , Rumpold Gerhard 
Published: August 2021

AbstractBackground and purposeThe polypill approach has been proposed to reduce patients’ pill burden, increase medication adherence and lower stroke incidence. However, little is known about patients’ attitudes towards polypills for cerebrovascular medication.MethodsBased on the European Organization for Research and Treatment of Cancer Quality of Life Group questionnaire development guidelines, a questionnaire to measure patients’ attitudes towards polypills for the secondary prevention of stroke (phase I–III) was developed. In phase I, issues were generated via literature review and interviews with patients and healthcare professionals. The issues were operationalized into items in phase II. In phase III the questionnaire was validated in a large single‐centre sample, and test–retest and internal validity were evaluated.ResultsIn phase I, 34 relevant issues were identified through literature search and interviews. Pre‐testing the questionnaire indicated high applicability and comprehensibility. The final Attitudes towards Polypills Questionnaire was tested in N = 260 patients and showed a two‐factor structure. The factors were labelled ‘concerns’ and ‘benefits’. The scales showed acceptable and good internal validity (concerns, Cronbach's α = 0.85; benefits, α = 0.93), but the scales’ test–retest validity was ambiguous. On a 0 to 3 rating scale, concerns were rated lower than benefits (mean 1.07, SD 0.69 vs. mean 1.87, SD 0.89).ConclusionsThe Attitudes towards Polypills Questionnaire showed high comprehensibility and content validity to assess German language patients’ attitudes towards a polypill medication. Our data and questionnaire may aid the implementation of polypill treatments in clinical practice and can be used in the design of future clinical trials on polypill therapy. Further validation of the questionnaire is advised.
Level of local human disturbance and feeding state determines escape behaviour in Eurasian Oystercatchers
Authors: Azaki Bukola DA , Cresswell Will 
Published: August 2021

AbstractHuman disturbances may constitute a significant stressor for wildlife, especially where human recreational activities overlap with fitness‐enhancing activities such as feeding. Disturbances cause an animal to flee from the perceived predation risk, using energy, rather than remaining and gaining energy. Such reactions are, however, context‐dependent, as predicted by optimal escape theory: animals should only flee when the perceived risk of predation of remaining exceeds the risk of starvation of leaving. Animals may also learn that humans do not generally represent a predation risk after repeated false alarms and then learn to only respond when approached deliberately and closely. We tested the Flight Initiation Distance (FID; distance at which an approached animal begins escape) of feeding or roosting Eurasian Oystercatchers Haematopus ostralegus (oystercatchers) to a human (as a simulated predator) in areas with or without humans on beaches in south‐east Scotland. We predicted roosting oystercatchers to respond earlier (greater FID) than feeding birds because the risk of starvation will be lower, and earlier on beaches where there were no humans at the start of the experiment because a human will then represent a more novel predator signal. As predicted, oystercatchers escaped at greater distances away from the perceived threat when feeding and in areas with humans. We found that escape distances decreased (greater tolerance of the perceived threat) as the number of people in an area increased, but people being present or not explained more of the variation in the data. The results show that oystercatchers habituate on a short timescale to non‐lethal human presence and generally respond to perceived predation risk in accordance with the predictions of optimal escape theory.
Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA
Authors: Fairfield Eleanor A. , Richardson David S. , Daniels Carly L. , Butler Christopher L. , Bell Ewen , Taylor Martin I. 
Published: August 2021

AbstractCrustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality‐filtered loci in the economically important European lobster (Homarus gammarus). Across 0‐ to 51‐month‐old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality‐filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8–55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known‐age individuals and tissue types before the model can be used in fisheries management.
Traditional and deep‐based techniques for end‐to‐end automated karyotyping: A review
Authors: Remani Sathyan Remya , Chandrasekhara Menon Gopakumar , S Hariharan , Thampi Rakhi , Duraisamy Jude Hemanth 
Published: August 2021

AbstractIn the field of cytogenetics, chromosome image analysis or karyotyping from metaphase images plays an imperative role in the diagnosis, prognosis and treatment assessment of different genetic disorders and cancers. This paper is a comprehensive review on different traditional and deep‐based techniques, which are utilized in the design of automated karyotyping systems (AKSs). By this review, a detailed methodology is suggested for the design of end‐to‐end automated karyotyping system (EEAKS) which portrays a sequential multi stage approach. Methods related to all the stages in EEAKS are systematically surveyed by exploring the state of the art literature. Datasets and performance measures incorporated in the past studies are explored. Even though numerous methods were proposed throughout the past three decades, a completely automated framework has not yet been acknowledged. Inferences from this study show that, while various traditional image processing strategies are utilized for pre‐processing and segmentation, machine learning techniques are used only for the classification purpose. In conventional classifiers, artificial neural networks are generally utilized even when the peak performance is given by support vector machines. However, owing to the recent prodigious breakthrough in computer vision, deep neural networks are progressively utilized for developing automated systems. It is seen that deep neural networks are not yet explored in the realm of pre‐processing stage of EEAKS. However, limited number of methods based on convolutional neural networks (CNN) are utilized in all other stages. This review recommends a hybrid CNN for the design of EEAKS, in which all the stages can be automated by sub CNNs. Methodology for generating sufficient datasets is also discussed here which is, indeed, required for further research in this area. This paper concludes with future research directions for the development of a fully automated end‐to‐end karyotyping system.
Local community assembly processes shape β‐diversity of soil phoD‐harbouring communities in the Northern Hemisphere steppes
Authors: Xu Lin , He Nianpeng , Li Xiangzhen , Cao Huili , Li Chaonan , Wang Ruili , Wang Changhui , Yao Minjie , Zhou Shungui , Wang Junming 
Published: August 2021

AbstractAimThe contemporary coexistence theory suggests that species pool, environmental filtering, dispersal assembly processes, ecological drift and biotic interactions collectively determine the β‐diversity of communities. However, we know little about the biogeographical patterns of the β‐diversity of microbial communities harbouring the alkaline phosphatase phoD gene (phoD communities, hereafter) and whether these mechanisms are all‐important in shaping phoD communities’ β‐diversity in natural steppe ecosystems.LocationNorthern Hemisphere steppes.Time periodJuly to August 2018.Major taxa studiedAlkaline phosphatase (phoD gene) encoding community.MethodsUsing the high throughput amplicon sequencing method, soil phoD communities were comparatively studied along three representative regions of the Northern Hemisphere steppes, namely the Qinghai‐Tibetan Plateau, Inner Mongolian Plateau and the Loess Plateau. Each region harbours three types of steppes (habitats): meadow, typical and desert steppes.ResultsWe observed significantly higher phoD β‐diversity in the Qinghai‐Tibetan than in the Loess and Inner Mongolian Plateaus and significantly lower β‐diversity in the typical steppes than in other steppe types. The decay rates of phoD β‐diversity with geographical distance varied in different steppe regions and types. The phoD β‐diversity was not significantly influenced by species pool; instead, environmental filtering, dispersal assembly processes, ecological drift and biotic interactions jointly shaped the β‐diversity patterns. The β‐deviation variations (β‐diversity excluding the effects of species pool) were influenced by spatial and environmental factors and biotic interactions, among which soil pH was the key environmental determinant. The soil pH driving β‐diversity mechanism was steppe region and habitat specific.Main conclusionsThe biogeographical patterns of phoD β‐diversity were mainly driven by local community assembly processes in the Northern Hemisphere steppes.
Rapid Mapping of Hydrological Systems in Tanzania Using a Towed Transient Electromagnetic System
Authors: Grombacher Denys , Maurya Pradip Kumar , Lind Johan Christensen , Lane John , Auken Esben 
Published: August 2021

AbstractLimited knowledge of local groundwater systems often results in the failure of boreholes to yield water of the required quantity and quality. This is particularly problematic in the developing world, where financial resources are often limited, and failed wells represent a significant financial burden. To enhance understanding of local hydrological systems, noninvasive geophysical methods can aid the understanding of hydrogeological structures and identification of groundwater sources needed to optimize siting of wells. Here, we highlight the utility of a relatively new towed‐transient electromagnetic system, called tTEM. This system is a rapidly deployable mobile geophysical method well‐suited to cost‐efficient characterization of local‐to‐regional groundwater systems. Results from tTEM surveys conducted in two refugee camps and several host communities in western Tanzania demonstrate the capability of the method to characterize shallow aquifer systems with high lateral and vertical resolution, with data collection typically exceeding 15 to 20 line‐kilometers (km) per day. This work focuses on tTEM's ability to provide semiquantitative insights into regional hydrogeological settings when supporting data required for more rigorous interpretation/modeling is lacking. The system provided useful data within communities with low density of electrification and near buildings with metal roofs and walls. tTEM‐derived resistivity profiles were correlated with limited local borehole lithologic information to develop conceptual models of the local groundwater systems. These models were used to successfully guide the siting of a production well and to identify future drilling targets in the refugee camps and surrounding communities.
Advanced extraction techniques for Berberis species phytochemicals: A review
Authors: Ali Redha Ali , Siddiqui Shahida A. , Ibrahim Salam A. 
Published: August 2021

SummaryBerberis species are known for their functional and nutraceutical properties. For example, different Berberis species have shown a wide range of pharmacological activities and they have been used in food industries as additives, preservatives and antioxidants. The functional property of any herb is influenced by many factors including the extraction process of its active components. Consequently, new extraction methodologies have been investigated to increase the efficiency of extracting bioactive compounds. In this review, we examine all the recent extraction techniques and advanced technologies that have been applied for the extraction of phytochemicals from different Berberis species. The five following techniques have been included for this purpose: ultrasound‐, microwave‐, pulsed electric field‐assisted, supercritical carbon dioxide and subcritical water extraction. These techniques have been used to extract phenolics, flavonoids, anthocyanins and berberine from different parts of various Berberis species which include B. vulgaris, B. jaeschkeana, B. aristata, B. integerrima, B. dasystachya and B. koreana. Microwave‐assisted extraction (MAE) has been well studied, optimised and evaluated. Yet, the present research considering other techniques are limited, and require further investigation and optimisation. In addition, the application of green solvents such as natural deep eutectic solvents could be considered in further developing MAE.
l‐glutamate inhibits blue mould caused by Penicillium expansum in apple fruits by altering the primary nitrogen and carbon metabolisms
Authors: Yang Jiali , Wang Tengfei , Di Jianbing , Liu Yaping , Hao Xiaoling , Wang Yu 
Published: August 2021

SummaryAlthough several studies have shown the ability of l‐glutamate (glutamate) to mitigate the stress imposed by pathogens, the underlying mechanism is still in its infancy. To gain further knowledge, this study focussed on the effect of glutamate on primary nitrogen and carbon metabolisms during apple‐Penicillium expansum interaction. The obtained result showed that glutamate could effectively restrict blue mould rot development in apples, but had no direct impact on fungal growth in vitro. The application of glutamate increased the level of nitrogen in apples, resulting in a disrupted balance of carbon and nitrogen. Consistently, the key enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) involved in the GS/GOGAT cycle, and the deaminating activity of glutamate dehydrogenase (GDH), forming 2‐oxoglutarate and ammonium from glutamate, were promptly stimulated by glutamate. Interestingly, glutamate led to considerable consumption of the tricarboxylic acid (TCA) cycle intermediates, such as isocitric acid and citric acid, accompanied by the enhancement of malate dehydrogenase and succinate dehydrogenase activities. Collectively, exogenous application of glutamate might confer blue mould resistance in apples, at least in part, by redirecting host’s primary nitrogen and carbon metabolisms, such as the activation of the GS/GOGAT cycle, deaminating activity of GDH and the TCA cycle.
Replacement of buckwheat by black sorghum flour on soba‐type noodles
Authors: Johnson Stuart K. , Kaur Gurpreet , Luitel Smriti , Hoang Le Anh Phuoc , Bhattarai Rewati R. 
Published: August 2021

AbstractIncorporation of black sorghum flour containing high levels of polyphenols and slowly digestible starch could provide opportunity to enhance nutritional functionality of noodles. Soba‐type noodles were prepared based on a typical wheat‐buckwheat (65:35) formulation by replacement of buckwheat flour with black sorghum flour at 0%, 25%, 50%, 75% and 100%. Noodle colour, texture, total phenolics, antioxidant capacity, in vitro starch digestibility and sensory acceptability were evaluated. Increasing the addition of black sorghum flour significantly (P < 0.05) decreased the firmness (g) in noodles and imparted a darker colour but increased total polyphenolics and antioxidant capacity. Significantly (P < 0.05) lower rapidly digestible starch and higher resistant starch was found in noodles with >50% replacement with black sorghum flour. Overall acceptability of noodles showed preference for noodles containing 25%–75% black sorghum flour. This study demonstrates the potential of using black sorghum as a novel functional food ingredient in noodle manufacturing.