Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Investigations of the Fungal Lytic Polysaccharide Monooxygenase Reaction Mechanism using X-ray and Neutron Protein Crystallography.

O’DELL, WILLIAM BRADLEY. Structural Investigations of the Fungal Lytic Polysaccharide Monooxygenase Reaction Mechanism using X-ray and Neutron Protein Crystallography. (Under the direction of Dr. Flora Meilleur). Industrial production of biofuels and other value-added products derived from cellulosic feedstocks relies on enzymatic hydrolysis of cellulose to convert biomass to soluble sugars. The overall conversion efficiency and the cost of final products are influenced greatly by the efficiency of hydrolases which is diminished by cellulose recalcitrance arising from high degrees of polymerization, crystallinity and intra-/intermolecular hydrogen bonding. Efforts over the last 20 years to discover more efficient hydrolases have instead identified oxidative enzymes that boost the efficiency of cellulose conversion. These lytic polysaccharide monooxygenases (LPMOs) break cellulose chains by oxidizing carbon atoms involved in glycosidic bonds. LPMOs do not directly release soluble sugars but instead function as an important adjuvant to hydrolase function that increases industrial conversion efficiency by one or more orders of magnitude. LPMOs are mononuclear copper metalloenzymes dependent upon an input of reducing equivalents that activate molecular O2 for the net insertion of an oxygen atom into a carbon– hydrogen bond. Herein are described important new structural characterizations of this reactivity derived from crystallographic studies of the enzyme Neurospora crassa LPMO9D in resting and O2-activated states. High resolution X-ray cryocrystallography has revealed that fungal LPMOs activate O2 as an equatorial ligand of the active site Cu(I/II) ion. Molecular O2 activation likely follows an initial “pre-binding” step in which molecular O2 occupies a polar binding site adjacent to the active site ion. Analysis of the first reported LPMO structure determined by neutron protein crystallography provided new details of protonation states and hydrogen bonding around the active site and indicated a role of a conserved histidine in stabilizing “pre-bound” O2. This role has been confirmed with quantum calculations. The impacts of this research for current mechanistic understanding and future experiments are also discussed. © Copyright 2017 William Bradley O’Dell All Rights Reserved Structural Investigations of the Fungal Lytic Polysaccharide Monooxygenase Reaction Mechanism using X-ray and Neutron Protein Crystallography by William Bradley O’Dell A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy
Identification of hub genes in gastric cancer by integrated bioinformatics analysis

Background Gastric cancer (GC) is one of the most common cancer worldwide. With the high rates of metastasis and recurrence, its overall survival remains poor at the present time. Hence, seeking new potential therapeutic targets of GC is important and urgent. Methods We retrieved the gene expression profiles and clinical data from The Cancer Genome Atlas (TCGA) datasets. After screening differentially expressed genes (DEGs), we carried out the survival analysis for overall survival to pick out robust DEGs. To explore the role of these robust DEGs, we conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Subsequently, protein interactions network was constructed utilizing the Search Tool for the Retrieval of Interacting Genes (STRING) database. We then presented the module analysis and filtered out hub genes by the Cytoscape software. Finally, Kaplan-Meier analysis was utilized to demonstrate the prognostic role of these hub genes. Results According to the gene expression profiles of TCGA and the survival analysis, 238 robust DEGs were filtered out, consisting of 140 up-regulated and 98 down-regulated genes. The up-regulated DEGs were mainly enriched in systemic lupus erythematosus, cytokine activity, and alcoholism, while down-regulated DEGs were mainly enriched in steroid hormone receptor activity, immune response, and metabolism. Through the construction of the protein-protein interaction (PPI) network, eight hub genes were finally screened out, including CCR8, HIST1H3B, HIST1H2AH, HIST1H2AJ, NPY, HIST2H2BF, GNG7, and CCL25. Conclusions Our study picked out eight hub genes, which might be potential prognostic biomarkers for GC and even be treatment targets for clinical implication in the future.
Exploration of the data space via trans-dimensional sampling: the case study of seismic double difference data

Abstract. Double differences (DD) seismic data are widely used to define elasticity distribution in the Earth's interior, and its variation in time. DD data are often pre-processed from earthquakes recordings through expert-opinion, where couples of earthquakes are selected based on some user-defined criteria, and DD data are computed from the selected couples. We develop a novel methodology for preparing DD seismic data based on a trans-dimensional algorithm, without imposing pre-defined criteria on the selection of couples of events. We apply it to a seismic database recorded on the flank of Katla volcano (Iceland), where elasticity variations in time has been indicated. Our approach quantitatively defines the presence of changepoints that separate the seismic events in time-windows. Within each time-window, the DD data are consistent with the hypothesis of time-invariant elasticity in the subsurface, and DD data can be safely used in subsequent analysis. Due to the parsimonious behavior of the trans-dimensional algorithm, only changepoints supported by the data are retrieved. Our results indicate that: (a) retrieved changepoints are consistent with first-order variations in the data (i.e. most striking changes in the DD data are correctly reproduced in the changepoint distribution in time); (b) changepoint locations in time do correlate neither with changes in seismicity rate, nor with changes in waveforms similarity (measured through the cross-correlation coefficients); and (c) noteworthy, the changepoint distribution in time seems to be insensitive to variations in the seismic network geometry during the experiment. Our results proofs that trans-dimensional algorithms can be positively applied to pre-processing of geophysical data before the application of standard routines (i.e. before using them to solve standard geophysical inverse problems) in the so called exploration of the data space.
Validation of a Scale to Measure the Perception of SARS-CoV-2 Vaccines Acceptance: The VAC-COVID-19 Scale

Introduction: Since the announcement of the start of SARS-CoV-2 vaccines development, many myths and vaccine opponents have come to the fore. Therefore, in this scenario, it is imperative to have an instrument to assess the population perception of this subject matter. Objective: To validate a scale to measure the perception of SARS-CoV-2 vaccines acceptance. Methods: This is an instrumental and multicentre study, through which a list of possible reasons for whether or not people would be vaccinated was generated. After submitting them to 15 experts, a pilot survey was conducted virtually in a population of almost 3000 participants in the 24 regions of Peru. Descriptive statistics and the exploratory factor analysis (EFA) were conducted using the FACTOR program. Results: The Kaiser-Meyer-Olkin (KMO) coefficient (KMO = 0.917) and the Bartlett’s test of sphericity (3343.3;gl = 136;p <0.001) were conducted. According to EFA results, two factors were found to explain 58.17% of the total variance. The fit indices show that the proposed model is adequate (χ2 = 826.321;df = 43;p = 0.001;RMR = 0.054;GFI = 0.952;AGFI = 0.927;CFI = 0.946;TLI = 0.931;and RMSEA = 0.078). Finally, Cronbach’s α was found to be very satisfactory for the generated scale (α = 0.831;95% CI = 0.82 – 0.84). Conclusion: A simple and efficient scale was validated to assess positive and negative perceptions of SARS-CoV-2 vaccines (the VAC-COVID-19 scale), with a Cronbach’s coefficient of 0.831. © 2021 by Author/s and Licensed by Modestum.
Higher education students’ aspirations for their post-university lives: evidence from six European nations

ABSTRACT While there is now a relatively large literature on young people's aspirations with respect to their transitions from compulsory schooling, the body of work on the aspirations of those within higher education is rather less well-developed. This article draws on data from undergraduate students in six European countries to explore their hopes for their post-university lives. It demonstrates that although aspirations for employment were discussed most frequently, non-economic plans and desires were also important. Moreover, despite significant commonalities across the six nations, aspirations were also differentiated, to some extent at least, by national context, institutional setting and subject of study.
German views on US nuclear weapons in Europe: public and elite perspectives

ABSTRACT Stationing of US nuclear weapons in Europe is a pillar of NATO deterrence. Despite their growing contestation, scholarly research on contemporary attitudes of both voters and political elites to the continued stationing of these weapons on their soil is lacking. We conducted original surveys of 2020 Germans and of 101 Bundestag members. Our results show scepticism about the military utility of US nuclear weapons in Germany, and aversion towards their use. At the same time, the results show a sizable support among both politicians and citizens for their removal from German territory as part of new nuclear arms control initiatives.
Church’s response to migrants’ quest for identity formation

Migration has received diverse responses from the dominant powers in the political, social and religious spheres. Assimilation, domination and cohesion are some of the responses to the integration of people who cross regional and national borders and reside within their new locations for a considerable period of time. These responses include both positives, which are largely short-term solutions, with a lot of losses and trauma for the migrants. The reasons for these kinds of responses lie in the factors that cause and influence migration. Political and religious conflict, economics, societal factors such as language and culture, health issues such HIV or AIDS and other pandemics and environmental factors are some of the causes of migration. Contribution: This research will contribute to determining the relationship between the church and migration for identity formation. The question I wish to explore is how the church can respond to the quest for identity which shapes the social welfare and cultural co-existence of the South African society and migrants in post-apartheid South Africa. Because of the complexity of identity and the effect that migration has (had) on shaping identity, I will first provide a description of migration and identity. The article will then address the factors that cause migration and the possible ways in which migration can shape identity. A brief discussion of a theology of migration will be introduced. This will be followed by a critical discussion of how the church as a pilgrim community can contribute to identity formation and the peaceful co-existence of differentiated people.
Unique Mechanisms for the Availability of Declarative Memory Elements and the Strengthening of Cognitive Operations

The purpose of this study was to investigate the role of memory for prior cognitive operations and availability of declarative memory elements in long-term semantic priming. The impetus for this investigation was the role of working memory (WM) in complex cognitive processing. Empirical estimates of WM are too limited to explain complex cognitive processes. Therefore, contemporary models of WM propose access to long-term memory (LTM) to expand these limits. The priming literature provides one theoretical mechanism for access to LTM: long-term semantic priming. However, explanations for long-term semantic priming include both increased availability of LTM elements and the facilitation of prior cognitive operations. Our goal was to examine if the facilitation of prior cognitive operations is dependent on the availability of previously encountered LTM elements. A task used in previous research proposed to capture the facilitation of cognitive operations coupled with a directed forgetting manipulation was used to examine this relationship. Three experiments were conducted to that end. All experiments resulted in facilitation of the procedure of categorization. Experiments 1 and 2 additionally found relatively poor recognition for items that participants were told to forget despite the fact that categorization was facilitated for related items. Experiment 3 resulted in similarly poor recognition for category names that participants were told to forget. Taken together, the experiments in this investigation demonstrate a clear separation between the cognitive operations and declarative elements of the categorization task. Namely, the continued availability of declarative elements is not necessary for the subsequent facilitation of categorization operations.
An Evaluation Framework on Additive Manufacturing for Hydraulic Systems in Wind Turbines Focused on System Simplification

The wind energy industry showed rapid growth in the past decade, pushing designs to the physical limits. In the last few years, the exponential growth of the wind turbine sizes capped, and the performance upgrades are reached with optimization processes. The first wave was on major parts, but with time advancing the “cost out” strategies are pushed to minor components. A major problem is service costs and the continuous search for missing spare parts in the market. The main aim of this study is to identify when is the best entry point for the additive manufacturing (AM) technology by the hydraulic manufacturer wind turbine companies. From the commercial application for expensive prototypes, it has evolved to economical home use applications. The newly available machines allow printing parts with competing precision to machining equivalents. The material selections range from plastics to metals with mechanical properties equally good or better. This project aims to provide a comprehensive review of the implementation of AM for hydraulic systems in wind turbines. Application screening was done by desk research and on AM technologies. Scientific research has been found on the topic for benchmarking, viability, and cost models. It has been found that there are still missing data for the mechanical properties of the available materials. The result of the decision-weighted matrix shows that the business could gain a competitive advantage by the AM implementation in terms of resources savings and productivity. Although from the technological and market perspective it is justified to initiate before further action the business should review its organization viability.
Use of multispectral satellite data to assess impacts of land management practices on wetlands in the Limpopo Transfrontier River Basin, South Africa

ABSTRACT The study sought to assess the impacts of land use and land cover (LULC) changes on two wetland systems (Makuleke and Nylsvley Nature Reserve) in the Limpopo Transfrontier River Basin (LTRB) in South Africa between 2014 and 2018. To fulfil this objective, multi-date Landsat images were used. Furthermore, the maximum likelihood classification algorithm was used to identify various LULC classes within delineated wetlands. The LULC changes were mapped from the two wetlands, with high overall accuracies, ranging from 80% to 89% for both study areas. The spatial extent of the Makuleke wetland declined by 2% between 2014 and 2018, whereas the Nylsvley wetland decreased by 3%. Built-up areas have increased slightly over the 2014 and 2018 period because of population growth and infrastructure development, which occupy a portion of the wetland. In Nylsvley wetland, it was evident that during the 5-year monitoring period, croplands increased steadily in the Nylsvley catchment. Overall, the results demonstrated a steady decline in natural vegetation cover in both wetlands. This information can aid in enforcing wetland legislations and LULC management practices that can help protect them from further encroachment and degradation.
The Value of Complete Blood Count For The Prognosis Analysis of Esophageal Squamous Cell Carcinoma

Objective To investigate the value of complete blood count in predicting the survival rate of patients with esophageal squamous cell carcinoma. Methods A total of 3587 patients with esophageal squamous cell carcinoma who were initially admitted to the Affiliated Cancer Hospital of Xinjiang Medical University from January 2010 to December 2017 were collected by retrospective study. The relevant clinical data were collected by the medical record system, and the patients were followed up by the hospital medical record follow-up system. The follow-up outcome was death. The survival time of all patients was obtained. The survival curve was established using the cut-off value of each index obtained by ROC curve. The Cox proportional hazards regression analysis model and nomogram were established to predict the survival prognosis of esophageal squamous cell carcinoma. The role of each index in the prognosis of patients with esophageal squamous cell carcinoma was studied Results The cut-off values of NLR, NMR, LMR, RDW and PDW in blood routine were 3.52, 10.22, 2.25, 13.85% and 12.05%, respectively. Survival curve analysis showed that patients aged < 60 years and NLR < 3.52 had survival. All indicators were divided into high and low groups according to ROC curve. Univariate Cox regression analysis model showed that RDW (≥ 13.85) and NLR (≥ 3.52) groups were risk factors for the prognosis of ESCC, with HR values of 1.099 (1.015–1.191; p = 0.020) and 1.340 (1.231–1.458; p < 0.001) compared with RDW (< 13.85) and NLR (< 3.52), respectively; multivariate Cox regression analysis model showed that NLR was significantly associated with the prognosis of ESCC, with HR of 1.342 (1.232–1.461; p < 0.001) for NLR (≥ 3.52) NLR (< 3.52). Conclusion NLR results in blood count can be used to predict the survival of patients with esophageal squamous cell carcinoma.
Flash flood impacts nowcasting within the PICS project (2018-2022):  End-users involvement and first results

Flash-flood events can have catastrophic socio-economic consequences. To reduce their impacts, it is of crucial importance to set up efficient warning systems. Although first operational flash-flood warning systems have recently been implemented, some limitations are clearly identified by end-users: non-exhaustive geographic coverage, limited lead times, warnings based on hazard assessment instead of risk. However, the desirable improvements raise real scientific challenges in various domains. In this context, the PICS (Prevision immediate des impacts des crues soudaines – Flash-flood events impacts nowcasting - 2018-2022) project gathers French scientific teams with varied skills (meteorologists, hydrologists, hydraulicians, economists, social geographers) and operational stakeholders (civil security, local authorities, insurance companies, managers of hydroelectric facilities and transport network). Funded by the French national research agency (ANR), it aims to develop and evaluate pre-operational forecasting chains able to estimate the potential impacts of flash floods with short anticipation lead times (up to 6 hours). These modelling chains include different components. Distributed hydrological models transform the observed and forecasted rainfall into runoff. Hydraulic models translate this runoff into potential flooded areas. Impact models incorporate these results to evaluate the potential for social and economic impacts. The research and operational partners selected four case studies based on various criteria, including the occurrence of human impacts and damages, the availability of validation data. Validation data include discharges recorded at gauging stations, but also more original information collected after each event, such as peak discharges and maximum water levels estimated from flood marks, insurance claims, damages observed on infrastructure (roads, railway…), victims interviews, casualties,etc. This presentation focuses on the methodology used for the involvement of representative potential end-users, leading to fruitfull dialogues and informative outcomes. Some of the first results of the project are also presented.
Resurvey of vascular plants and soil arthropods on the summit of Mount Corazón (Andes of Ecuador) after 140 years

ABSTRACT Opportunities to track environmental changes over more than a century are rare in tropical mountains. Edward Whymper’s survey of flora and fauna on the summit of Mt. Corazón (Ecuador, 4788 m a.s.l.) in 1880 provides a unique opportunity to compare historical observations with the current composition of plant and insect communities on a tropical alpine mountain top. We studied Whymper’s archives and historic specimens in London and Paris, and performed a resurvey of vascular plants and ground beetles (Coleoptera Carabidae) in January 2020. Currently, a large part of the summit area of Corazón is heavily damaged by trampling and stone removal due to mountain tourism, and no vascular plants are present in the deteriorated area on the top of the ridge. However, more species were collected in 2020 than in 1880: 22 of vascular plants vs. 7, and 4 of ground beetles vs. 1. Upslope shifts over 140 years may partly explain this increase in species richness, although the low numbers of Whymper’s sampling may also be due to less skilled collectors and to the presence of permanent snow beds on the summit. The current faunistic and floristic data presented in this contribution can be used as a baseline for future resurveys of Corazón, in order to monitor changes in the species distribution and community composition of its summit area. Owing to the very small area of its superpáramo and to the soil deterioration by trampling along the summit ridge, Corazón is especially exposed to the effects of climate change and to the risk of extirpation of endemic cold-adapted specialists.
Can edible oils, as practical phase change materials, be used for body cooling after physical work in a hot–humid environment?

This study investigated whether wearing phase change material (PCM) packs made of edible oils, such as coconut oil (CO) and palm oil (PO), after engaging in physical activities can alleviate heat strain in a hot and humid environment. Eleven healthy young males performed a treadmill exercise for 30 min. After the physical activity, the participants underwent resting recovery for 30 min with or without a cooling vest made of either CO‐ or PO‐based PCM packs. Results showed that wearing PCM packs made of edible oils as a personal cooling device significantly reduced tympanic temperature, mean skin temperature, and heart rate during the recovery period. The CO‐ and PO‐based PCM packs also improved perceptual thermal strain during recovery. Hence, PCMs made of edible oils can be used as a cooling device to reduce heat strain and improve comfort after physical work in a hot and humid environment. From the aspects of ergonomics and human factors, the use of CO‐ and PO‐based PCM packs for personal cooling is a viable option for preventing heat‐related disorders and maintaining productivity and workers' well‐being.