bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agriculture and land use implications of early climate change mitigation efforts without reliance on net-negative emissions
Authors: Hasegawa Tomoko , Fujimori Shinichiro , Frank Stefan , Humpenöder Florian , Bertram Christoph , Després Jacques , Drouet Laurent , Emmerling Johannes , Gusti Mykola , Harmsen Mathijs , Keramidas Kimon , Oshiro Ken , Rochedo Pedro , Ruijven Bastiaan van , Cabardos Anique-Marie , Deppermann Andre , Fosse Florian , Havlík Petr , Krey Volker , Popp Alexander , Schaeffer Roberto , Vuuren Detlef van , Riahi Keywan 
Published: July 2022

Abstract
Allowing delayed climate mitigation actions and overshoot of temperature targets requires large scale negative carbon emissions that may induce adverse side-effects on land, food and ecosystems in the second half of this century. Meanwhile, meeting climate goals without net negative emissions inevitably needs the implementation of early and quick emissions reduction measures, which also brings challenges in the near-term. Here we identify the implications of scenarios without a dependence on net-negative carbon emissions on land-use and food systems. We find that early climate actions without the reliance on net-negative carbon emissions have multiple benefits and trade-offs in land-use and food systems, and avoid the need for drastic (mitigation-induced) shifts in land-use in the long term. Further long-term benefits are lower food prices, a reduced risk of hunger and lower water scarcity. At the same time, however, near-term mitigation pressure in the AFOLU sectors and the required land area for energy crops increases, resulting in additional agricultural intensification.
Identification of a cuproptosis related chromatin regulators signature for lung adenocarcinoma
Authors: Wei Lu , Wu Yueyue , Xie Yi , Yang Yichen , Yan Xinghu , Wei Zhihao , Huang Liqun 
Published: July 2022

Abstract
Background: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related mortality worldwide, displaying dismal prognosis. Growing evidence now links cuproptosis related genes (CRGs) and chromatin regulators (CRs) to cancer progression. However, the relationship between CRGs and CRs is not yet fully understood. Therefore, we aimed to reveal the connection and prognostic value of these two factors in LUAD patients. Methods: Cuproptosis related genes (CRGs) and chromatin regulators (CRs) were retrieved from previous top studies. For TCGA analysis, mRNA expression andclinical information for LUAD were downloaded via R package. Functional enrichment was analyzed through the ClusterProfler package. Cox regression analysis and LASSO regression analysis were utilized to train models for predicting outcome in LUAD. The Kaplan-Meier curve analyses was used to assess the prognosis for cases categorized as High-risk and Low-risk groups. DsigDB dataset was performed to screen the potential drugs for LUAD treatment. Results: We visualized an protein-protein interaction (PPI) network between CRGs and CRs. Functional analysis suggested that CRs were mainly enriched in chromatin modification and cell cycle pathways. The prognosis prediction model was successfully constructed and validated for the patients with LUAD. Moreover, we also showed 11-CRs-based model was an independent prognostic factor for LUAD patients. This CR-based model was associated with immune cells infiltration as well as immune checkpoint. Seven prospective drugs was detected for the treatment of LUAD patients. Conclusion: In conclusion, our findings provide unique information not available in previous studies, casting novel insights about the correlation between CRGs and CRs in LUAD. We also identified several prognostic biomarkers for the survival of patients with LUAD.
Seed bank dynamics of the annual halophyte Salicornia ramosissima: towards a sustainable exploitation of its wild populations
Authors: Polo Alejandro , Fragoso Alba , Infante-Izquierdo María D. , Nieva Francisco J.J. , Muñoz-Rodríguez Adolfo F. , Castillo Jesús M. 
Published: July 2022

Abstract
Halophytes are able to survive in the high salted areas of the world, and have been recognized as sources of bioactive metabolites. There is a need to design sustainable strategies for the use of wild populations of halophytic species in order to avoid irrational gathering. Seed banks are essential for resilience and regeneration in salty ecosystems. We sampled annual seed production, aerial and soil seed banks and seed dynamics for a year in four wild populations of the annual halophyte Salicornia ramosissima growing in saltpans, in order to develop sustainable management practices for the use of its populations. The seed production of S. ramosissima depended mainly on plant density rather than on the number of seeds produced by each individual plant. In three of the four study populations, most of the annual seed production was exported out of the saltpans (> 79%) and only between 14–20% was accumulated in the initial aerial and soil seed banks. These initial seed banks were highly depleted during the year until the next fruiting period, when they accumulated less than 1% of the annual seed production (from 19 to 15302 seed m− 2). Salicornia ramosissima established a persistent soil seed bank in two of the four locations. Annual seed production would be key for the preservation of those S. ramosissima populations that do not establish persistent soil seed banks. In view of our results, each population of S. ramosissima should be studied independently to design population-specific management plans.
Assessing preventability of postmenopausal breast cancer by lifestyle risk factors: influence by method, data source, and timing of exposure measurement
Authors: Wu You , Kim Hanseul , Wang Kai , Song Mingyang , Wang Molin , Tamimi Rulla , Eliassen Heather , Smith-Warner Stephanie , Willett Walter , Giovannucci Edward 
Published: July 2022

Abstract
Background
Population attributable risk (PAR%) reflects the preventable fraction of disease. However, PAR% estimates of cancer have shown large variation across populations, methods, and data sources.
Methods
We evaluated variations in PAR% of postmenopausal breast cancer by obesity, alcohol, fruit and vegetable intake, and physical activity in the Nurses’ Health Study (NHS). For the low-risk method, the age-standardized incidence rate in the low-risk group was compared with the overall rate. The partial PAR% method estimated the PAR% by the risk factors while adjusting for other covariates. The conventional method estimated the PAR% based on the exposure distribution and relative risks in the NHS, or from US national surveys and meta-analyses. For each model, we compared the results obtained using baseline or repeated measurements.
Results
When considering the risk factors simultaneously, within the NHS, the low-risk method yielded overall PAR% for the baseline, simple update, and cumulative average models of 17.4%, 25.2%, 29.3%; the partial PAR% method yielded estimates at 13.7%, 28.0%, 31.2%. When considering each risk factor individually and then combined, the estimates by the partial PAR% were 12.5%, 20.7%, 18.9%; while the conventional method gave corresponding PAR% of 13.8%, 21.1%, 18.6%. The estimated PAR% based on meta-analyses and US national surveys was 25.6%.
Conclusions
The three methods provided similar PAR% based on the same data source, timing of measurements, and target populations. However, sizable increases in the PAR% were observed for repeated measures over a single measure and for calculations based on achieving all recommendations jointly rather than individually.
Drivers and coping mechanisms to floods: experiences of residents in urban Kumasi, Ghana
Authors: Antwi-Agyei Philip , Baffour-Ata Frank , Koomson Sarah , Kyeretwie Nana Kwame , Nti Nana Barimah , Owusu Afia Oforiwaa , Abdul Fukaiha Razak 
Published: July 2022

Abstract
Over the last few years, the recurrence and severity of floods in urban Kumasi have increased considerably with devastating consequences for both lives and properties. Yet, the perspectives of residents who have experienced these floods have often been ignored in policy developments. This study used a mixed-methods approach including household surveys and key informant interviews to determine the drivers and coping mechanisms to floods in three selected communities in urban Kumasi, Ghana. Results showed that the study respondents perceived changes in rainfall and floods through increasing amounts of rainfall, increasing duration of rainy season and increased incidences of floods. A multiplicity of causes were reported by the study respondents including poor design of drains, choked drains and inadequate drain infrastructure. Destruction of properties, decreased economic productivity and soil erosion were reported as the major effects of floods. The respondents implemented various coping mechanisms including temporary migration and relying on family and friends to manage the adverse effects of floods. Findings indicated that access to weather and climate information, access to household communication gadgets, age of respondents and period of staying in the community were significant coping mechanisms employed by the respondents. Barriers impeding the implementation of these coping mechanisms reported by study respondents included financial constraints, inadequate support from government and non-governmental institutions and lack of understanding on early warning systems. Accessibility to timely weather and climate information should be prioritized to help people improve their information sharing and decision-making processes in managing floods in urban Kumasi.
Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon
Authors: Kakoulidis Panos , Vlachos Ioannis , Thanos Dimitris , Emiris Ioannis , Anastasiadou Ema 
Published: July 2022

Abstract
Using protein structure to predict function, interactions, and evolutionary history is still an open challenge, with existing approaches relying extensively on protein homology and families. Here, we present Machaon, a new data-driven method combining orientation invariant metrics on phi-psi angles, inter-residue contacts and surface complexity. It can be readily applied on whole structures or segments—such as domains and binding sites. Machaon was applied on SARS-CoV-2 Spike monomers of native, Delta and Omicron variants and identified correlations with a wide range of viral proteins from close to distant taxonomy ranks, as well as host receptors, such as ACE2. The associated whole structures have: 32.7% and 38.5% sequence identities on protein secondary structure and gene coding region, 86% chemical and 22.1% protein tertiary structure similarities (median values, native Spike). Machaon’s meta-analysis revealed Spike’s relationships with biological processes such as ubiquitination and angiogenesis and highlighted different patterns in virus attachment among the studied variants. Available at: https://github.com/anastasiadoulab/machaon .
Pre-research on enhanced heat transfer method for special vehicles at high altitude based on machine learning
Authors: Li Chunming , Sun Xiaoxia , Gao Hongyang , Zhang Yu 
Published: July 2022

Abstract
The performance of the thermal management system has a great influence on the stability of the special purpose vehicles, and it is of great significance to enhance heat transfer of the radiator. Common research methods for radiators include fluid mechanics numerical simulation and experimental measurements, both of which are time-consuming and expensive. Applying the surrogate model to the analysis of flow and heat transfer in louver fin can effectively reduce the computational cost and obtain more data. A simplified louver fin heat transfer unit is established, and computational fluid dynamics (CFD) simulations is used to obtain the flow and heat transfer characteristics of this geometry structure. A three-factor and six-level orthogonal design is carried out with three structural parameters, the angle θ, the length a and the spacing Lp of the louver fins. The results of the orthogonal design are subjected to range analysis, and the effects of the three parameters θ, a and Lp on the j, f and JF factors are obtained. On this basis, a proxy model of the heat transfer performance for louver fins was established based on the artificial neural network algorithm, and the model was trained with the data obtained by the orthogonal design, and finally the fin structure with the largest JF factor was found. Compared with the original model, the optimized model improves the heat transfer factor j by 2.87%, the friction factor f decreases by 30.4% and the comprehensive factor JF increases by 15.7%.
Minor microbial alterations after faecal diversion do not affect the healing process of anus-near pressure ulcers in patients with spinal cord injury - results of a matched case-control study.
Authors: Brechmann Thorsten , Lichtenthäler Luisa , Pussin Andreas , Aach Mirko , Grasmücke Dennis , Schildhauer Thomas , Schmiegel Wolff 
Published: July 2022

Abstract
Background: Pressure ulcers are a common complication in patients with spinal cord injury. The role of faecal diversion to support anus-near ulcer healing is under debate and its impact on the microbial colonisation pattern is unclear. The aim was to evaluate the primary microbial colonisation and secondary infection depending on the presence of a pre-existing diverting stoma and investigate the effect on the wound healing.

Methods: A total of 120 spinal cord injured patients who had undergone surgery of an anus-near decubitus stage 3 or 4 were included in a retrospective matched-pair cohort study. Matching was realised according to age, gender, body mass index and general condition.

Results: The most common species in both groups was Staphylococcus aureus (45.0 %). The only significantly different primary colonisation affected Escherichia coli, that was found in the stoma patients less often (18.3 and 43.3 %, p < 0.01). A secondary microbial colonisation occurred in 15.8 % and was equally distributed, except for Enterococcus spp. that was present only in the stoma group (6.7 %, p < 0.05). The time to complete cure took longer in the stoma group (78.5 versus 57.0 days, p < 0.05) and was associated with a larger ulcer size (25 versus 16 cm2, p < 0.01). After correction for the ulcers’ size, there was no association to outcome parameters such as overall success, healing time or adverse events.

Conclusion: The presence of a diverting stoma alters the microbial flora of an anus-near decubitus slightly without impact on the healing process.
Nylon Cable-Tie Assisted Forearm Fasciotomy Wound Closure
Authors: Hsieh Chiung Hui , Ho Chun Yee , Chang Che Wei 
Published: July 2022

Abstract
Background: Closure of forearm fasciotomy wounds is challenging. Traditional methods for reconstruction are skin grafts or flaps. A skin graft or flap leaves an unpleasant appearance and requires a donor site. Initially, there is no skin defect or only limited defect. Presented here is a method utilizing looped cable ties for delayed primary closure of forearm fasciotomy wounds.Methods:Patients who underwent fasciotomy of forearms for compartment syndrome and cable tie assisted closure from 2017 to 2020 in Far Eastern memorial Hospital were included. Follow-up observations of all patients were conducted until December 2020. We retrospectively reviewed the cause of forearm compartment syndrome, the initial maximum width of the fasciotomy wounds, and the time for primary closure of the wounds.Results: There were seven patients eligible for inclusion. Four patients suffered from compartment syndrome of the forearm caused by iatrogenic vascular rupture after the procedures. The other reasons for the compartment syndrome included open-type fracture and fasciitis. Emergency fasciotomy was arranged for all the patients, and cable ties were applied for delayed primary wound closure. Six of them, with the median initial maximum width of a wound of 5.15 cm [3.8 - 6.3cm], achieved successful wound closure by cable ties without skin grafts or flaps on median day 12 [ day 6 - 19]. One patient who had distal and proximal radius fracture received skin graft reconstruction after the application of cable ties for 14 days.Conclusion: Cable ties--inexpensive and readily available materials--can be adjusted according to the different tension along the wound edges. They provide a simple, effective, and safe way to close difficult forearm fasciotomy wounds.
A Study of Individualized Diagnosis and Treatment for Depression with Atypical Features (iDoT-AFD): study protocol for a randomized clinical trial
Authors: Zhou Rubai , Zhang Huifeng , He Shen , Li Yi , Xu Guiyun , Huang Jinsong , Wang Huaning , Wang Qian , Li Biao , Wang Xuemei , Chen Ningning , Li Fang , Li Xiaosa , Liu Mengjun , Peng Daihui 
Published: July 2022

Abstract
Background Major depressive disorder (MDD) with atypical features, namely depression with atypical features (AFD), is one of the most common clinical specifiers of MDD, characterized by high risk of converting to bipolar disorder (BD). However, there is still lack of clinical guidelines for the diagnosis, treatment, and prognosis of AFD. Our study mainly focuses on three issues about what’s the objective endophenotype of AFD, how to select appropriate personalized treatment for AFD, what’s the predictive biomarkers of conversion to BD.Methods The Study of Individualized Diagnosis and Treatment for Depression with Atypical Features (iDoT-AFD) is a multicenter, prospective study consisting of a 12-week randomized-intervention trial followed by a real-world follow-up until 4 years or reaching the study endpoint. It is enrolling 480 patients with AFD (120 per treatment arm), 100 patients with BD, and 100 healthy controls (HC). Multivariate-dimension information is collected including clinical features, cognitive function, kynurenine pathway metabolomics, and multimodal magnetic resonance imaging (MRI) data. The iDoT-AFD study can be classified into three parts including the cross-sectional part and the prospective part. Firstly, multivariate informatics analyzes are performed to recognize patients with AFD from participants including the first-episode and recurrent atypical depression, patients with BD and HC. Secondly, patients with atypical depression are randomly allocated to one of the four treatment groups including ‘single application of selective serotonin reuptake inhibitor (SSRI) or serotonin-noradrenaline reuptake inhibitor (SNRI)’, ‘SSRI/SNRI combined with mood stabilizer’, ‘SSRI/SNRI combined with quetiapine (≥ 150mg/d)’, or ‘treatment as usual (TAU)’, and then followed up 12 weeks to find out the optimized treatment strategies. Thirdly, patients with atypical depression are followed up in the real world until 4 years or switching to BD to explore risk factors of conversion from atypical depression to BD and build the conversion risk early-warning model eventually.Discussion First enrolment was in August 2019, and the recruitment is ongoing. The iDoT-AFD study explores clinical and biological markers for the diagnosis, treatment, and prognosis of AFD, and further provide evidence for clinical guidelines of this depressive specifier which has high risk switching to BD.Trial registration Clinical Trials.gov ID: NCT04209166. Registered on December 19, 2019.
Simulation of dam break due to overpass flow and study of its effects on downstream areas (Case study: Shahrchay Dam)
Authors: farahmand ghasem , Golmohammadi Hassan , Ashrafi Mohammad , Samet Komil , Patel Nilanchal 
Published: July 2022

Abstract
Shahrchay Dam is one of the dams that, due to its geological and climatic conditions, there exists a considerable possibility of overflow and consequently its break. The Dam is considered an imminent threat to Urmia city due to its proximity to the downstream residential areas. Therefore, this study aims to investigate the dam break modeling and, finally, the resulting flood zonation in the downstream areas of the Dam. To achieve this goal, we developed two hydraulic models, viz. BREACH-GUI, OpenFOAM of dam break based on (physical parameters of the Dam and downstream geographical features) and then using HEC-RAS, Arc-GIS software vulnerable areas against floods marked by a 100-year return period. The results show that the two hydraulic models in question have yielded similar dam break results. More precisely, the BREACH-GUI model has calculated the maximum output velocity at the bottom of the Dam at a distance of 1 km at about 13 meters per second with a height of 12 meters. In contrast, the OpenFOAM model has calculated the maximum velocity at a distance of 900 meters at an altitude of 11 meters at 20 meters. Flood zoning due to dam break shows about 18% of the area of Urmia city, 73% of Band village, 68% of Noshan Sofla village, and 76% of Noshan Olya village due to rising water flow caused by dam break with a population of 136,000 people directly affected.
A numerical approach for preventing the dispersion of infectious disease in a meeting room
Authors: Ahmadzadeh Mahdi , Shams Mehrzad 
Published: July 2022

Abstract
Airborne transmission of respiratory aerosols carrying infectious viruses has generated many concerns about cross-contamination risks, particularly in indoor environments. The study addresses the emitted viral particles during coughing from the infected person and their transport dynamics inside the safe social distance meeting room. CFD based on coupled Eulerian-Lagrangian techniques is used to explore the characteristics of the airflow field in the domain. The main objective of this study is to investigate the effects of the number of open and closed windows, exhaust layouts, and location of the air conditioner systems on the dispersion of the particles. The results show that opening adjacent windows of the emission source has a better performance against the exit of particles from the environment than opening the window(s) that is farthest from that. Moreover, the results demonstrated reducing the distance between the ventilation systems installed location and the ceiling can decrease the fraction of the suspended particles by over 35%, and at-risk individuals from 6 to 2 people. As well, changing the location of inputs from the back of the infected person to the front of that can raise the shelf time of the particles and their concentration rises from 4.125 to 5%, respectively.
Structure-based discovery of a non-canonical prototype long-chain monoacylglycerol lipase through an endogenous catalysis intermediate complex
Authors: Pinotsis Nikos , Krüger Anna , Tomas Nicolas , Chatziefthymiou Spyros , Litz Claudia , Mortensen Simon , Daffé Mamadou , Marrakchi Hedia , Antranikian Garabed , Wilmanns Matthias 
Published: July 2022

Abstract
The identification and characterization of enzyme function is largely lacking behind the rapidly increasing availability of large numbers of sequences and associated high-resolution structures. This is often hampered by lack of knowledge on in vivo relevant substrates. Here, we present a case study of a high-resolution structure of an unusual orphan lipase in complex with an endogenous C18 monoacyl catalysis intermediate from the expression host, which is insoluble under aqueous conditions and thus not accessible for studies in solution. The data allowed its functional characterization as a prototypic long-chain monacylglycerol lipase, which uses a minimal lid domain to position the substrate through a hydrophobic tunnel directly to the enzyme’s active site. Knowledge about the molecular details of the substrate binding site allowed us to boost the enzymatic activity by adjusting protein/substrate interactions, demonstrating the potential of our findings for future biotechnology applications.