bluuebunny/crossref_metadata_2025_split huggingface dataset:
ARResT/Interrogate Immunoprofiling Platform: Concepts, Workflows, and Insights
Authors: Darzentas Nikos 
Published: May 2022

AbstractARResT/Interrogate was built within the EuroClonality-NGS working group to meet the challenge of developing and applying assays for the high-throughput sequence-based profiling of immunoglobulin (IG) and T-cell receptor (TR) repertoires. We herein present basic concepts, outline the main workflow, delve into EuroClonality-NGS-specific aspects, and share insights from our experiences with the platform.
cfDNA-Based NGS IG Analysis in Lymphoma
Authors: Pott Christiane , Kotrova Michaela , Darzentas Nikos , Brüggemann Monika , Khouja Mouhamad ,   on behalf of the EuroClonality-NGS Working Group
Published: May 2022

AbstractLiquid biopsy is a novel diagnostic approach at first developed to characterize the molecular profile of solid tumors by analyzing body fluids. For cancer patients, it represents a noninvasive way to monitor the status of the solid tumor with respect to representative biomarkers. There is growing interest in the utilization of circulating tumor DNA (ctDNA) analysis also in the diagnostic and prognostic fields of lymphomas. Clonal immunoglobulin (IG) gene rearrangements are fingerprints of the respective lymphoid malignancy and thus are highly suited as specific molecular targets for minimal residual disease (MRD) detection. Tracing of the clonal IG rearrangement patterns in ctDNA pool during treatment can be used for MRD assessment in B-cell lymphomas. Here, we describe a reproducible next-generation sequencing assay to identify and characterize clonal IG gene rearrangements for MRD detection in cell-free DNA.
Immunoglobulin/T Cell Receptor Capture Strategy for Comprehensive Immunogenetics
Authors: Stewart James Peter , Gazdova Jana , Srivastava Shambhavi , Revolta Julia , Harewood Louise , Maurya Manisha , Darzentas Nikos , Gonzalez David 
Published: May 2022

AbstractIn the era of genomic medicine, targeted next generation sequencing strategies (NGS) are becoming increasingly adopted by clinical molecular diagnostic laboratories to identify genetic diagnostic and prognostic biomarkers in hemato-oncology. We describe the EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay, which is designed to simultaneously detect B and T cell clonal rearrangements, translocations, copy number alterations, and sequence variants. The accompanying validated bioinformatics pipeline enables production of an integrated report. The combination of the laboratory protocol and bioinformatics pipeline in the EuroClonality-NDC minimizes the potential for human error, reduces economic costs compared to current molecular testing strategies, and should improve diagnostic outcomes.
Impact of big data analytics on supply chain performance: an analysis of influencing factors
Authors: Gopal P. R. C. , Rana Nripendra P. , Krishna Thota Vamsi , Ramkumar M. 
Published: May 2022

AbstractThis paper aims to understand the impact of big data analytics on the retail supply chain. For doing so, we set our context to select the best big data practices amongst the available alternatives based on retail supply chain performance. We have applied TODIM (an acronym in Portuguese for Interactive Multi-criteria Decision Making) for the selection of the best big data analytics tools among the identified nine practices (data science, neural networks, enterprise resource planning, cloud computing, machine learning, data mining, RFID, Blockchain and IoT and Business intelligence) based on seven supply chain performance criteria (supplier integration, customer integration, cost, capacity utilization, flexibility, demand management, and time and value). One of the intriguing understandings from this paper is that most of the retail firms are in a dilemma between customer loyalty and cost while implementing the big data practices in their organization. This study analyses the dominance of the big data practices at the retail supply chain level. This helps the newly emerging retail firms in evaluating the best big data practice based on the importance and dominance of supply chain performance measures.
cRel and Wnt5a/Frizzled 5 Receptor-Mediated Inflammatory Regulation Reveal Novel Neuroprotectin D1 Targets for Neuroprotection
Authors: Calandria Jorgelina M. , Do Khanh V. , Kala-Bhattacharjee Sayantani , Obenaus Andre , Belayev Ludmila , Bazan Nicolas G. 
Published: May 2022

Abstract
Wnt5a triggers inflammatory responses and damage via NFkB/p65 in retinal pigment epithelial (RPE) cells undergoing uncompensated oxidative stress (UOS) and in experimental ischemic stroke. We found that Wnt5a-Clathrin-mediated uptake leads to NFkB/p65 activation and that Wnt5a is secreted in an exosome-independent fashion. We uncovered that docosahexaenoic acid (DHA) and its derivative, Neuroprotectin D1 (NPD1), upregulate c-Rel expression that, as a result, blunts Wnt5a abundance by competing with NFkB/p65 on the Wnt5a promoter A. Wnt5a increases in ischemic stroke penumbra and blood, while DHA reduces Wnt5a abundance with concomitant neuroprotection. Peptide inhibitor of Wnt5a binding, Box5, is also neuroprotective. DHA-decreased Wnt5a expression is concurrent with a drop in NFkB-driven inflammatory cytokine expression, revealing mechanisms after stroke, as in RPE cells exposed to UOS. Limiting the Wnt5a activity via Box5 reduces stroke size, suggesting neuroprotection pertinent to onset and progression of retinal degenerations and stroke consequences.

Graphical Abstract
NPD1 disrupts Wnt5a feedback loop at two sites: (1) decreasing FZD5, thus Wnt5a internalization, and (2) by enhancing cREL activity, which competes with p65/NFkB downstream endocytosis. As a result, Wnt5a expression is reduced, and so is its inflammatory signaling in RPE cells and neurons in ischemic stroke.
Bone marrow-derived mesenchymal stem cells ameliorate severe acute pancreatitis by inhibiting oxidative stress in rats
Authors: Zhao Dongbo , Yu Weidi , Xie Wangcheng , Ma Zhilong , Hu Zhengyu , Song Zhenshun 
Published: May 2022

AbstractTo investigate whether bone marrow mesenchymal stem cells (BMSCs) attenuate pancreatic injury via mediating oxidative stress in severe acute pancreatitis (SAP). The SAP model was established in rats. Phosphate buffered saline (PBS) or BMSCs were injected into the rats by tail veins. ML385 was used to down-regulate Nrf2 expression in rats. Pancreatic pathological score was used to evaluated pancreatic injury. Inflammatory-associated cytokines, serum lipase and amylase, levels of myeloperoxidase, malondialdehyde, reactive oxygen species and superoxide dismutase, as well as catalase activity were measured for injury severity evaluation. ML385 aggravates oxidative stress in SAP + ML385 group, compared with SAP + PBS group. BMSCs transplantation alleviated pancreatic injury and enhance antioxidant tolerance in SAP + BMSCs group, while ML385 administration weakened this efficacy in SAP + BMSCs + ML385 group. In addition, BMSCs promoted Nrf2 nuclear translocation via PI3K/AKT signaling pathway. Besides, BMSCs reduced inflammatory response by inhibiting NF-κB signaling pathway in SAP. BMSCs can inhibit oxidative stress and reduce pancreatic injury via inducing Nrf2 nuclear translocation in SAP.
Prosodic sensitivity and phoneme awareness as predictors of reading fluency in German
Authors: Schmidt Barbara Maria , Breuer-Küppers Petra , Vahlhaus-Aretz Doris , Obergfell Anja Larissa , Schabmann Alfred 
Published: May 2022

AbstractThere are contradictory findings in the literature about prosodic sensitivity’s contribution to reading. In this study, we examined whether prosodic sensitivity makes a unique contribution to different reading outcomes in German after controlling for the effects of phonological awareness. Word reading, nonword reading and sentence reading as well as phonological awareness (PA), prosodic sensitivity (PS), and nonverbal IQ were assessed in a sample of N = 207 8- to 10-year-old German-speaking children in third grade. Results showed that after controlling for PA, PS was predictive of only sentence reading. A commonality analysis further showed that PS and PA share about 22% of the explained variance (R2 = .13) in sentence reading, while PS uniquely contributes 18% and PA 60% of this variance. The results indicate that PS is more strongly related to reading tasks with semantic demands.
Rapid triage for ischemic stroke: a machine learning-driven approach in the context of predictive, preventive and personalised medicine
Authors: Zheng Yulu , Guo Zheng , Zhang Yanbo , Shang Jianjing , Yu Leilei , Fu Ping , Liu Yizhi , Li Xingang , Wang Hao , Ren Ling , Zhang Wei , Hou Haifeng , Tan Xuerui , Wang Wei ,   on behalf of Global Health Epidemiology Reference Group (GHERG)
Published: May 2022

Abstract

Background
Recognising the early signs of ischemic stroke (IS) in emergency settings has been challenging. Machine learning (ML), a robust tool for predictive, preventive and personalised medicine (PPPM/3PM), presents a possible solution for this issue and produces accurate predictions for real-time data processing.

Methods
This investigation evaluated 4999 IS patients among a total of 10,476 adults included in the initial dataset, and 1076 IS subjects among 3935 participants in the external validation dataset. Six ML-based models for the prediction of IS were trained on the initial dataset of 10,476 participants (split participants into a training set [80%] and an internal validation set [20%]). Selected clinical laboratory features routinely assessed at admission were used to inform the models. Model performance was mainly evaluated by the area under the receiver operating characteristic (AUC) curve. Additional techniques—permutation feature importance (PFI), local interpretable model-agnostic explanations (LIME), and SHapley Additive exPlanations (SHAP)—were applied for explaining the black-box ML models.

Results
Fifteen routine haematological and biochemical features were selected to establish ML-based models for the prediction of IS. The XGBoost-based model achieved the highest predictive performance, reaching AUCs of 0.91 (0.90–0.92) and 0.92 (0.91–0.93) in the internal and external datasets respectively. PFI globally revealed that demographic feature age, routine haematological parameters, haemoglobin and neutrophil count, and biochemical analytes total protein and high-density lipoprotein cholesterol were more influential on the model’s prediction. LIME and SHAP showed similar local feature attribution explanations.

Conclusion
In the context of PPPM/3PM, we used the selected predictors obtained from the results of common blood tests to develop and validate ML-based models for the diagnosis of IS. The XGBoost-based model offers the most accurate prediction. By incorporating the individualised patient profile, this prediction tool is simple and quick to administer. This is promising to support subjective decision making in resource-limited settings or primary care, thereby shortening the time window for the treatment, and improving outcomes after IS.
Numerical simulation of proppant embedment in rough surfaces based on full reverse reconstruction
Authors: Lu Cong , Liu Jiaxing , Huang Fenglan , Wang Jin , Zhou Guangqing , Wang Jiandong , Meng Xianbo , Liu Yanhui , Wang Xiaoshan , Shan Xin , Liang Hao , Guo Jianchun 
Published: May 2022

AbstractIn the hydraulic fracturing process of shale reservoir, proppant will embed and deform under the action of high closure stress. Thus, it is necessary to analyze the mechanical process and influencing factors of proppant embedding in shale. This study reproduced rough fracture surface of real rock slabs based on the reverse reconstruction method and obtained the mechanical parameters of the rock slab and proppant. In this study, a numerical model for the elastoplastic deformation of the proppant embedding in the rough fracture surface, along with mechanical test experiments, is proposed. The reliability of the numerical model is verified by the proppant embedding simulation experiment. Based on this model, the process of proppant embedding in a rough fracture under the action of closing stress and the factors influencing the width of supporting fracture were analyzed. The results show that the embedment degree of the proppant is different in different areas of the rough fracture surface. Furthermore, a stress concentration effect is apparent. The proppant embedment becomes significant after the slab enters the plastic deformation stage under high closure stress. The slabs with high roughness and low Young's modulus or proppants with small particle sizes and high Young's moduli result in a smaller width of the propped fracture.
An Indigenous perspective on ecosystem accounting: Challenges and opportunities revealed by an Australian case study
Authors: Normyle Anna , Doran Bruce , Vardon Michael , Mathews Dean , Melbourne Julie , Althor Glenn 
Published: May 2022

AbstractThe System of Environmental-Economic Accounting Ecosystem Accounting (SEEA-EA) is widely promoted in environmental and economic policy and management. Unfortunately, the SEEA-EA has not substantively addressed the aspects of accounting that may be of interest to, or used by, Indigenous peoples. We investigate an Indigenous perspective on the potential of the SEEA-EA to support cultural and environmental management through collaborative workshops with managers of Nyamba Buru Yawuru, the Prescribed Body Corporate representing the Yawuru Traditional Owners in Western Australia. Our discussions highlight that while the SEEA-EA may be a valuable tool for empowering Indigenous people and supporting the management of their lands and seas, there are areas where the SEEA-EA needs to be broadened to better reflect cultural values, and the services to ecosystems provided by Indigenous peoples. Embedding Indigenous perspectives into the SEEA-EA would mean that it is of greater use to Indigenous peoples and their representative organisations and ensure that these values are better recognised in the policymaking of government.
Sexual Dysfunction in Infertile Men: A Systematic Review and Meta-Analysis
Authors: Liu Yang , Wang Yuning , Pu Zhuonan , Wang Yuchao , Zhang Yixin , Dong Chuankun , Zeng Yan , Zhou Shu 
Published: May 2022

Abstract

Background
According to previous studies of male infertility, we found that the association between sexual dysfunction and male infertility was reported rarely and controversially.

Aim
We carried out this 1meta-analysis to evaluate the prevalence of sexual dysfunction and the International Index of Erectile Function (IIEF) score in infertile men.

Methods
A systematic search of the target literature was conducted using PubMed, EMBASE, and Cochrane Library. Data were analyzed using Review Manager 5.4 software. Standardized mean differences (SMD) with the corresponding 95% confidence intervals (95% CIs) were implemented in 6 controlled studies as a measure of effect size to assess the relationship between sexual dysfunction and male infertility and Odds Ratio (OR) were performed for the morbidity between infertility group and fertility group.

Outcomes
Men in infertile group were found with higher prevalence of sexual dysfunction and lower IIEF values than in controls.

Results
A meta-analysis of morbidity was performed in 8 of 10 controlled studies. Meta-analysis of the 8 studies found remarkable higher prevalence of sexual dysfunction in men with infertility than in controls (OR = 2.66, 95% confidence interval = 1.69–4.19, P &lt; .0001; I² = 67%, P for heterogeneity = 0.004). Another meta-analysis of evidence suggested that IIEF in infertile men was lower than controls (SMD = −0.47, 95% confidence interval = −0.63 to −0.31, P &lt; .00001; I² = 64%, p for heterogeneity = 0.02).

Clinical Implications
We recommend further research based on the relevant criteria of region, sample size, rigorous statistical analysis, and research design.

Strengths & limitations
This systematic review is the first to evaluate the prevalence of sexual dysfunction and the score of sexual dysfunction in male infertility. Investigation on the topic is scarce, and only few studies used appropriate measures.

Conclusions
Male infertility was associated with an increase in the prevalence of sexual dysfunction. The areas most affected by sexual function were erectile function, orgasm and sexual desire.
Liu Y, Wang Y, Dong C, et al. Sexual Dysfunction in Infertile Men: A Systematic Review and Meta-Analysis. Sex Med 2022;10:100528.
‘Over to you’: considering the purpose of education through a student-centred sustainability project
Authors: Jackson Kirsty 
Published: May 2022

AbstractThe school strikes for climate action that began with Greta Thunberg in 2018 and spread worldwide in 2019, left many young people to ponder ‘what is the point of education if we have no future?’ In this investigation of a student-centred project on sustainability conducted with Year 4 students in Brisbane, the point of education was framed by Biesta’s three domains of purpose; Qualification, Socialisation and Subjectification. Sustainability education requires attention to each domain, that is, increasing children’s knowledge of sustainability (Qualification), facilitating their critical awareness of social practices related to sustainability (Socialisation), and expanding their capacity to act in response to the challenges of living sustainably (Subjectification). The project was designed using an action research model where children co-created the topic (reducing plastic usage) and then decided on how it would be investigated and reported. Interviews during and after the project, and episodes recorded in a research journal revealed changes in each of the three domains, with changes in the Subjectification domain being the focus of this study. The overall positive and multifaceted learning outcomes that occurred highlight what is possible when addressing issues of sustainability and the point of education in ways that matter to children.
A scale-wise analysis of intermittent momentum transport in dense canopy flows
Authors: Chowdhuri Subharthi , Ghannam Khaled , Banerjee Tirtha 
Published: May 2022

We investigate the intermittent dynamics of momentum transport and its underlying time scales in the near-wall region of the neutrally stratified atmospheric boundary layer in the presence of a vegetation canopy. This is achieved through an empirical analysis of the persistence time scales (periods between successive zero-crossings) of momentum flux events, and their connection to the ejection–sweep cycle. Using high-frequency measurements from the GoAmazon campaign, spanning multiple heights within and above a dense canopy, the analysis suggests that, when the persistence time scales (

$t_p$

) of momentum flux events from four different quadrants are separately normalized by

$\varGamma _{w}$

(integral time scale of the vertical velocity), their distributions

$P(t_p/\varGamma _{w})$

remain height-invariant. This result points to a persistent memory imposed by canopy-induced coherent structures, and to their role as an efficient momentum-transporting mechanism between the canopy airspace and the region immediately above. Moreover,

$P(t_p/\varGamma _{w})$

exhibits a power-law scaling at times

$t_{p}<\varGamma _{w}$

, with an exponential tail appearing for

$t_{p} \geq \varGamma _{w}$

. By separating the flux events based on

$t_p$

, we discover that around 80 % of the momentum is transported through the long-lived events (

$t_{p} \geq \varGamma _{w}$

) at heights immediately above the canopy, while the short-lived ones (

$t_{p} < \varGamma _{w}$

) only contribute marginally (

$\approx 20\,\%$

). To explain the role of instantaneous flux amplitudes in momentum transport, we compare the measurements with newly developed surrogate data and establish that the range of time scales involved with amplitude variations in the fluxes tends to increase as one transitions from within to above the canopy.
Barriers to an effective voucher programme for community-based aged care: a professional perspective
Authors: Kan Wing Shan 
Published: May 2022

AbstractLong-term care for older people is increasingly turning to consumer-directed approaches. As a case in point, the Hong Kong Government recently implemented a new voucher programme for community-based aged care based on a consumer-directed approach: the Community Care Service Voucher for the Elderly (CCSV). The objectives of this study were to explore the lived experience of professional workers vis-à-vis the new programme and to identify barriers to effective voucher use by older people in Hong Kong. In-depth individual interviews were conducted with 16 professionals who had primary responsibility for the voucher programme for community-based aged care. The interview guide covered five main areas: (a) professional's perception and experience on the voucher programme; (b) the decision-making process around the voucher programme; (c) personal capacities of older people; (d) family support and social networks; and (e) institutional support. Findings indicate several barriers to effective use of the CCSV including: lack of self-awareness of service needs, lower education level, poor health condition, lack of financial resources, lack of family support, inadequate family involvement in decision-making, lack of peer and professional support, lack of available services and poor service accessibility. Suggestions for strengthening the voucher programme include institution of a case management model and public education. Different factors or elements are required to facilitate older people to make sound and informed choices, and a case manager can assist in combining different resources and forms of support towards effective use of the CCSV.
COMPLEXITY, FUNCTION, AND RURALITY: PREHISTORIC MAYA COMMUNITIES OF NORTHWEST BELIZE
Authors: Valdez Fred , Trachman Rissa M. , Cortes-Rincon Marisol 
Published: May 2022

AbstractThe northwest region of Belize, known as the Rio Bravo Conservation and Management Area (RBCMA), is a research set-aside of interest for investigating hinterland communities of the prehistoric Maya. The hinterland or rural communities of the RBCMA are as diverse and complex as any across the Maya lowlands. The Programme for Belize Archaeological Project (PfBAP), of northwest Belize, provides various data for identifying and interpreting ancient Maya interactions in the region. With more than 25 seasons of Maya archaeological research in the region, PfBAP researchers are well placed to present aspects of nonurban life that helped make Maya civilization possible. The PfBAP utilizes survey and mapping strategies, material culture analyses, Light Detection and Ranging, and theoretical interests for evaluating ancient Maya life in the region's rural areas. There are four essential components herein contained for the PfBAP investigations of ancient Maya rural settlements in northwest Belize: (1) hinterland study strategies, (2) rural settlements, (3) rural diversity, and (4) nonurban life and rural elites. Sociopolitical systems (and/or interactions) are also posited for the prehistoric rural Maya. Where possible, suggested relationships between communities of varying size and complexity are discussed. The manifestations of production, identity, and equality are also defined as appropriate and integrated into the discussion of function(s) associated with rurality.