bluuebunny/crossref_metadata_2025_split huggingface dataset:
Library size confounds biology in spatial transcriptomics data
Authors: Bhuva Dharmesh D. , Tan Chin Wee , Marceaux Claire , Chen Jinjin , Kharbanda Malvika , Jin Xinyi , Liu Ning , Feher Kristen , Putri Givanna , Asselin-Labat Marie-Liesse , Phipson Belinda , Davis Melissa J. 
Published: March 2023

AbstractSpatial molecular technologies have revolutionised the study of disease microenvironments by providing spatial context to tissue heterogeneity. Recent spatial technologies are increasing the throughput and spatial resolution of measurements, resulting in larger datasets. The added spatial dimension and volume of measurements poses an analytics challenge that has, in the short-term, been addressed by adopting methods designed for the analysis of single-cell RNA-seq data. Though these methods work well in some cases, not all necessarily translate appropriately to spatial technologies. A common assumption is that total sequencing depth, also known as library size, represents technical variation in single-cell RNA-seq technologies, and this is often normalised out during analysis. Through analysis of several different spatial datasets, we noted that this assumption does not necessarily hold in spatial molecular data. To formally assess this, we explore the relationship between library size and independently annotated spatial regions, across 23 samples from 4 different spatial technologies with varying throughput and spatial resolution. We found that library size confounded biology across all technologies, regardless of the tissue being investigated. Statistical modelling of binned total transcripts shows that tissue region is strongly associated with library size across all technologies, even after accounting for cell density of the bins. Through a benchmarking experiment, we show that normalising out library size leads to sub-optimal spatial domain identification using common graph-based clustering algorithms. On average, better clustering was achieved when library size effects were not normalised out explicitly, especially with data from the newer sub-cellular localised technologies. Taking these results into consideration, we recommend that spatial data should not be specifically corrected for library size prior to analysis unless strongly motivated. We also emphasise that spatial data are different to single-cell RNA-seq and care should be taken when adopting algorithms designed for single cell data.
First Molecular Detection of Influenza D virus in Cattle from Commercial farm in Nigeria, Sub-Saharan Africa
Authors: Anjorin Abdul-Azeez A. , Moronkeji Gideon O. , Temenu Goodness O. , Maiyegun Omolade A. , Fakorede Christopher O. , Ajoseh Samuel O. , Salami Wasiu O. , Abegunrin Rebecca O. , Amisu Kehinde O. , Akinyemi Kabiru O. 
Published: March 2023

ABSTRACTInfluenza D virus (IDV) was first reported in pigs in the USA, and since then the virus has become a public health issue. In Nigeria, no work has been done on IDV despite the manifestation of influenza-like illness in cattle. This study aimed at molecular surveillance of IDV in cattle in Lagos. Prospective epidemiological investigation was initiated in a large commercial farm market where animals in open pens are reared, sold, and butchered under poor hygienic conditions without adequate biosecurity measures. A total of 80 nasopharyngeal swabs were collected between October and November 2021. The samples were extracted using an RNA purification kit (NIMR). RNA extracts were amplified following a two-step PCR using FIREScript RT cDNA synthesis kit (Solis Biodyne, Estonia), followed by PCR OneTaq Quick-load 2x master-mix (NEB, UK) in a Rotor-Gene thermocycler (Qiagen, Germany). Amplicons were detected using a 1.5% Gel electrophoresis. IDV was detected in 26/80 (32.5%) cattle. Sick animals showed 65% (17/26) almost double burden of IDV higher than 34.6% (9/26) in a healthy population, including 88.2% (15/17) Cattle with diarrhoea and 11.8% (2/17) with nausea having IDV. Bull recorded more than twice, 18/26 (69.2%) incidence by gender compared to Cow. Age prevalence showed 62.23% (18/26) highest detection in cattle of 4 years old, followed by 23.07% (6/26) in 5 years old, while the lowest 7.69% (2/26) was recorded in 3 years old. This study showed the first molecular detection of IDV in Nigeria and West Africa sub-region to the best of our knowledge. It underscores the need for continuous surveillance of IDV at the animal-human interface.
Assessing consumer preferences on halal service: the emergence of Sharia hospitals for Muslim consumer
Authors: Windasari Nila Armelia , Azhari Ni Putu Desinthya Ayu , Putra Ilham Fauzan 
Published: March 2023

Purpose
This study aims to examine customer preferences toward Sharia hospitals and to provide a new viewpoint by looking at consumers’ perspectives on choosing health-care services. Despite the growing demand for halal products, halal services, particularly hospital and Sharia-based health-care services, receive very little attention in the literature compared to other Sharia-type services such as Sharia banking, insurance or even hospitality. Previous research on health care discussed under the Sharia perspective mainly focused on service quality, directing discussions to the service providers’ perspectives.

Design/methodology/approach
This study uses choice-based conjoint analysis to examine customer preferences toward Sharia health-care service. There are five attributes with three levels each. To reduce respondent fatigue, the authors used SPSS Orthoplan to generate an orthogonal factorial design, which resulted in 21 choice cards. Cross-sectional data were collected from an online survey using a platform from Populix, an independent panel survey provider, to ensure no sample selection bias. A total of 270 responses were obtained to represent Muslim populations across Indonesia.

Findings
The results showed that the highest preference is highly rated to the familiarity and certification of the hospital brand that implies trust and guarantees to add value with the existence of halal certification for hospitals. In addition, this study revealed that Sharia services have higher positive signals over the physical infrastructure in determining preferences. On the other hand, add-on components that support the integration of other halal industries, such as halal culinary tourism, halal tourism and integration with transportation and halal accommodation, are still minor in the current preference.

Originality/value
Previous research on health care discussed under the Sharia perspective mainly focused on service quality, which directs the discussions to the service providers’ perspectives. This study provides a new point of view by looking at consumers’ perspectives about their preferences and decisions to choose a Sharia hospital.
Supply chain resilience and performance of manufacturing firms: role of supply chain disruption
Authors: Hamidu Zulaiha , Boachie-Mensah Francis O. , Issau Kassimu 
Published: March 2023

PurposeThe current study sought to investigate the moderating effect of supply chain disruptions (SCD) (supply chain – supply disruption, catastrophic disruption and infrastructure disruption) on the relationship between supply chain resilience (SCR) and supply chain performance (SCP) of manufacturing firms in Ghana.Design/methodology/approachThe quantitative research approach and explanatory research designs were utilised. A sample of 345 manufacturing firms were drawn from a population of 2,495 manufacturing firms in the Accra metropolis. The Partial Least Squares Structural Equation Modelling (PLS-SEM) was employed to accomplish the research objectives.FindingsFirst, the study revealed that SCR has a significant positive effect on SCP. Second, the authors found reasonable evidence to support that SCD have a significant positive moderating effect on the relationship between SCR and SCP, except for supply chain catastrophic disruption which had a negative impact. It can be concluded that the components of SCD have heterogeneous impact in the SCR and SCP nexus.Research limitations/implicationsThe study is limited to manufacturing firms in Ghana and does not make a distinction among resilience strategies.Practical implicationsIncreased SCR boost manufacturing companies' supply chains' performance and aid to lessen the adverse effects of SCD relating to infrastructure and supply. It implies that supply chain managers are able to reduce the effects of infrastructure and supply disruptions. Also, techniques that reduce the adverse impact of SCD relating to catastrophe would be beneficial for supply chain managers in Ghana and other countries with comparable economic environments.Originality/valueThe study provides a unique contribution on the moderating role of the dimensions of SCD (supply, infrastructure and catastrophic) on the nexus between SCR and SCP in a developing economy context in a dynamic changing environment. Policymakers would get better insights into instituting the required policies needed to revamp firms with weak supply chains as a result of supply chain disruption.
Perceived effectiveness of therapeutic community model as a rehabilitation approach for Sri Lankan individuals with substance use disorder
Authors: Dharmarathna Nishadi Darsha , Jayamaha Akila Randika , Ranadeva Nadeeka Dimuthu Kumari , Rajapakse Harshini , Gunasekara Chinthika , Fernando Neluka , Meegoda Lalitha 
Published: March 2023

Purpose
This study aims to evaluate the perceived effectiveness of residential treatment which follows the therapeutic community (TC) model for Sri Lankan individuals with substance use disorder (SUD).

Design/methodology/approach
A descriptive cross-sectional study was carried out in two selected residential treatment centers which follow the TC model as a rehabilitation approach. All the clients of the selected residential treatment centers were invited to take part in the study and data were collected from 75 consented male participants using an interviewer-administered questionnaire. The perceived effectiveness of the residential treatment was assessed using the Treatment Effectiveness Assessment instrument. Data were analyzed using descriptive statistics.

Findings
Most of the participants were Sinhalese (98.7%, n = 74) with a mean age of 27.0 ± 6.0 years. The average duration in which participants stayed at selected centers was 8.0 ± 4.0 months. Most of the participants reported that the encouragement during the program was sufficient (89.3%, n = 67), psychological support was satisfactory (89.3%, n = 67), freedom (69.5%, n = 52) and facilities were adequate (76.0%, n = 57) within the program. A higher proportion of participants said that the counselors and program guides were friendly (80.0%, n = 60), and participants were allowed to communicate with their family with restrictions (92.0%, n = 69). The mean perceived effectiveness score (score range 1–40) was 34.0 ± 7.0 and the four domain scores (score range 1–10) were substance use (9.0 ± 2.0), health (8.0 ± 2.0), lifestyle (9.0 ± 2.0) and community (9.0 ± 2.0). The majority (88.0%, n = 66) of the participants perceived a high level of treatment effectiveness.

Originality/value
There is a paucity of empirical evidence on effectiveness of TC model for individuals with SUD in South Asian countries including Sri Lanka. The findings of this study highlight that the participants perceived higher effectiveness of the residential treatment which follows the TC approach for Sri Lankan individuals with SUD.
Changes in trophic ecology of mobile predators in response to rainforest degradation
Authors: Kemp Victoria A. , Grey Jonathan , Hemprich‐Bennett David , Rossiter Stephen J. , Lewis Owen T. , Wilkinson Clare L. , Clare Elizabeth L. , Kratina Pavel 
Published: March 2023

Abstract

Accelerating loss and degradation of tropical forests has led to a pressing need to understand the conservation value of remaining forests. Whereas most studies focus on the responses in community composition and taxonomic richness, more sensitive responses to habitat degradation are likely to be apparent through changes in the trophic complexity of generalist predators. Food web theory predicts that both trophic position and niche breadth of predators decrease with habitat degradation, with consequences for biotic interactions and ecosystem functioning.

Using a stable isotope approach, we analysed trophic positions and niche breaths of an important guild of top predators: insectivorous bats, in the tropical forests of Sabah, Borneo. We aimed to determine the responses in their trophic ecology across an experimental gradient of forest degradation at different spatial scales.

At the landscape scale, trophic niche breadth contracted substantially (78%) in association with a narrow reduction (26%) in forest cover. However, food chains were longer in ecosystems with lower tree canopies, representative of localised habitat simplification. Marked differences in trophic niche breath of and trophic position between echolocation guilds provided further evidence for inter‐guild niche partitioning within bat assemblages. Overall, the functionally important shifts in trophic pathways discriminated among habitats of varying degrees of degradation more reliably than conventional community descriptors, such as diversity metrics.

Synthesis and applications. This study reveals that habitat quality thresholds—below which we see substantial changes to trophic complexity—are higher than previously considered. Our analysis suggests that patches of forest with cover above 90% should be prioritised for conservation over more highly degraded ecosystems. As these effects were detected after approximately 30 years post‐logging, they likely reflect relatively long‐term responses to forest degradation.
Effects of grazing on underground parts of marsh plants by wintering Middendorf's bean goose Anser fabalis middendorffii: Its role as a keystone species in plant communities
Authors: Ohkawara Kyohsuke , Tajiri Hironobu 
Published: March 2023

AbstractGeese are known to impact on the species composition and abundance of plant communities, with grazing pressure by flocks negatively affecting various aspects of vegetation and ecosystems. However, positive effects have also been highlighted, including grazing preventing competition among plants and helping to maintain a high level of biodiversity. The Middendorf's bean goose Anser fabalis middendorffii is one waterfowl that winters in the marsh lands of Japan. At the Katano‐kamoike pond, the species main wintering site in central Japan, the effects of goose grazing on the structure of marsh plant communities were investigated by using field observations and experiments. During observations of foraging behavior, A. fabalis middendorffii mainly foraged on underground parts of Zizania latifolia and Bolboschoenus fluviatilis, including rhizomes, roots, and tubers, at the marshlands of the pond. The field census showed the biomass of the underground parts was significantly reduced by A. fabalis middendorffii grazing during winter. Specifically, the biomass of rhizomes in Z. latifolia was drastically decreased. Data collected from exclosure experiments over 5 years suggested that grazing pressure regulated the overgrowth of B. fluviatilis and enhanced the abundance of Z. latifolia. Furthermore, a field census of marsh plants at the Shimofukuda reservoir, where there have been no A. fabalis middendorffii, confirmed that the absence of A. fabalis middendorffii was related to a decrease in the abundance and biodiversity of marsh plants. In the Katano‐kamoike pond, A. fabalis middendorffii may play a key role in maintaining plant diversity.
High‐protein rice flour in the development of gluten‐free pasta
Authors: Marana Ana I. Serrano , Morris Anita , Prinyawiwatkul Witoon , Xu Zhimin , King Joan M. 
Published: March 2023

AbstractCahokia Rice, a new biofortified high‐protein (10%–12%) variety of rice, was used to develop and analyze a gluten‐free pasta. Different pastas were made with high‐protein white rice flour (HPWRP), high‐protein brown rice flour (HPBRP), commercial white rice flour (CWRP), commercial brown rice flour (CBRP), and wheat flour (WP). Cooking quality of the pasta was evaluated by measuring pasting properties, cooking time, water absorption capacity, and cooking loss. Proximate analysis, color, and texture were done on dry and cooked pasta. Sensory testing was done to determine consumer acceptability and purchase intent of HPWRP and HPBRP in comparison to WP. HPWRP and HPBRP had higher pasting temperatures and lower peak viscosity than commercial rice flour pastas, which was related to the higher protein content. HPWRP and HPBRP had less cooking loss than CWRP and CBRP; all treatments had similar water absorption capacity (∼130%) except for WP that was higher (140%). White rice pastas along with WP took more time to cook than brown rice pastas. HPWRP and HPBRP had higher protein (around 7.5%) and fat content, creating a firmer cooked pasta (138.23 g HPBRP, 179.82 g HPWRP) than commercial rice pastas. Consumers’ overall liking of HPBRP (5.37), HPWRP (6.00), and WP (6.81) was acceptable. Color, firmness, and stickiness attributes negatively affected the overall liking of HPWRP and HPBRP. Cooked high‐protein rice flour pastas had improved firmness and cooking loss closer to wheat resulting in an acceptable product in overall liking. It is recommended to further improve the color, firmness, and stickiness of the pasta to reach higher sensory acceptability.Practical ApplicationThis research provides a possible use for a new high‐protein rice flour that can be used in gluten‐free products. This will help the rice industry by adding value to the product. Those persons who are Celiac or who desire more nutritional gluten‐free products will have a healthier gluten‐free pasta option.
Organic‐Inorganic Interaction Recorded by Polycyclic Aromatic Steranes in Continental Epithermal Ore Deposits
Authors: XU Huiyuan , LIU Quanyou , JIN Zhijun , ZHU Dongya , MENG Qingqiang , LI Pengpeng , ZHU Biqing 
Published: March 2023

AbstractContinental epithermal ore deposits are commonly associated with sedimentary organic matter, oils or solid bitumen. These organics embedded in mineral deposits can convey valuable information of the ore genesis. However, the extent to which the formation of ore minerals was recorded by organic compounds remains largely unknown, as also is how metal‐rich ores interfere with the molecular proxies in the temperature regime envisaged for hydrothermal activity. The molecular compositional changes of various polycyclic aromatic steranes and polycyclic aromatic hydrocarbons and compounds derived from the Jinding Pb/Zn deposit, SW China provide new data. Aliphatic regular steranes are present as traces. The transformation from polycyclic aromatic steranes to unsubstituted polycyclic aromatic hydrocarbons is observed to show an increased trend with increasing hydrothermal alteration levels; this is consistent with the transformation from unsubstituted polycyclic aromatic hydrocarbons to heterocyclic compounds. Dehydrocyclization (aromatization) of polycyclic biological compounds and hydrodecyclization (dearomatization) of polycyclic aromatic compounds are two important reaction pathways in hydrothermal systems with moderate temperature. This detailed investigation of organic‐inorganic interactions of two groups of polycyclic compounds with metal‐rich ores provides insights into the questions on how and to what extent the formation of Pb/Zn deposits can be recorded by organics. This work will improve our understanding of carbon reduction, oxidation or condensation in the deep Earth and the carbon exchange between the Earth's crust and mantle, and may shed light on the processes for ultra‐deep hydrocarbon exploration.
Carbon Enrichment in the Lithospheric Mantle: Evidence from the Melt Inclusions in Mantle Xenoliths from the Hainan Basalts
Authors: XU Xin , TIAN Wei , ZHANG Lifei , LI Huijuan 
Published: March 2023

AbstractIt is generally believed that the lithospheric mantle and the mantle transition zone are important carbon reservoirs. However, the location of carbon storage in Earth's interior and the reasons for carbon enrichment remain unclear. In this study, we report CO2‐rich olivine‐hosted melt inclusions in the mantle xenoliths of late Cenozoic basalts from the Penglai area, Hainan Province, which may shed some light on the carbon enrichment process in the lithospheric mantle. We also present a detailed petrological and geochemical investigation of the late Cenozoic basalts and mantle xenoliths from northern Hainan Island. The collected samples of late Cenozoic Hainan Island basalts belong to both alkaline and subalkaline series, showing fractionated REE patterns with high (La/Yb)Nvalues of 3.52–11.77, which are typical for OIB. Based on Al‐in‐olivine thermometry, the temperatures estimated for the mantle xenoliths can be divided into two groups. One group has temperatures of less than 1050°C, and the other group has temperature ranging from 1050°C to 1282°C. Clinopyroxene (La/Yb)N–Ti/Eu and clinopyroxene Ca/Al–Mg#diagrams indicate that the mantle peridotite experienced metasomatism from both silicate and carbonate melts. Melt inclusions in the olivine of mantle xenoliths include (1) CO2bubble–rich melt inclusions; (2) multiphase melt inclusions (glass + CO2bubble + daughter minerals); (3) pure glass melt inclusions. Magnesite is a daughter mineral in the olivine‐hosted melt inclusions, which could be interpreted as a secondary mineral formed by the interactions of CO2‐rich fluids with an olivine host, due to post‐entrapment effects. The glasses in olivine‐hosted melt inclusions have high SiO2contents (60.21–77.72 wt%). Our results suggest that a considerable amount of CO2‐rich melt inclusions are captured in the lithospheric mantle during metasomatism. The lithospheric mantle can therefore act as is a ‘carbon trap’, with much CO2being absorbed by the lithospheric mantle in this way.
Outcome following anaesthesia in infancy in the Nordic countries: Subgroup analysis of the NECTARINE study
Authors: Hansen Tom G. , Vieri Jenny , Børke Wenche Bakken , Castellheim Albert Gyllencreutz ,   Collaborators from the Nordic countries,   the NECTARINE Group Steering Committee
Published: March 2023

AbstractIntroductionThe neonate and children audit of anaesthesia practice in Europe (NECTARINE) prospective observational study reported an incidence of 35.2% of critical events requiring intervention during 6542 anaesthetics in 5609 infants up to 60 weeks postmenstrual age (PMA) from 165 centres in 31 European countries.MethodsSub‐analysis of the cohort from the Nordic countries (8% of the entire cohort) was conducted. Secondary aims were to describe the Nordic countries' anaesthetic practices and compare morbidity and mortality with the overall European cohort.ResultsEleven Nordic centres recruited 447 infants (66% males, 37.3% born preterm and 45% had congenital anomalies) undergoing anaesthesia for 530 surgical or non‐surgical procedures at 25–60 weeks PMA. Perioperative critical events triggered interventions in 228/530 (43%) cases. Hypotension (12.6%) or hypoxaemia (11.7%) were more common in younger patients and those with co‐morbidities. Hypo/hypercapnia occurred in 1.5%/4.7% of cases. More than two attempts for intubation were required in 13 (2.9%) infants (max three attempts). Distribution of ASA‐Physical Status Scores was similar to the total European cohort (40% was ASA > 2). A total of 236/530 (44.5%) patients were admitted to the postoperative intensive care unit. Thirty‐day morbidity (complications in 87/447 = 19.5%) and mortality (8/447, 1.8%) did not differ from the overall European cohort. Hospital re‐admissions were significant up to 90 days (98/447 = 21.9%).ConclusionsIn Nordic countries, anaesthesia in young infant children is resource‐demanding, and perioperative critical events and co‐morbidities are common. Thirty‐day morbidity and mortality data in the Nordic countries did not differ from the overall European cohort.