bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Exonuclease V–qPCR Assay to Analyze the State of the Human Papillomavirus 16 Genome in Cell Lines and Tissues
Authors: Myers Julia E. , Zwolinska Katarzyna , Sapp Martin J. , Scott Rona S. 
Published: October 2020

AbstractIntegration of the human papillomavirus (HPV) genome into host cell chromosomes has been observed in a majority of HPV‐positive cervical cancers and a subset of oral HPV‐associated cancers. HPV integration also occurs in long‐term cell culture. Screening for HPV integration can be labor intensive and yield results that are difficult to interpret. Here we describe an assay based on exonuclease V (ExoV/RecBCD) and quantitative polymerase chain reaction (qPCR) to determine if samples from cell lines and tissues contain episomal or integrated HPV. This assay can be applied to screen other small DNA viruses with episomal/linear genome configurations in their viral lifecycle and has the potential to be used in clinical settings to define viral genomic conformations associated with disease. © 2020 Wiley Periodicals LLC.Basic Protocol: Exonuclease V genomic DNA digestion and qPCR for detection of HPV16 genome configuration in cellsSupport Protocol: Exonuclease V analysis of HPV16 genome configuration in tissuesAlternate Protocol: Determining HPV integration type or integrity of HPV episome
Inverse correlation between serum complement component C1q levels and whole blood type‐1 interferon signature in active tuberculosis and QuantiFERON‐positive uveitis: implications for diagnosis
Authors: Schrijver Benjamin , Dijkstra Douwe J , Borggreven Nicole V , La Distia Nora Rina , Huijser Erika , Versnel Marjan A , van Hagen P Martin , Joosten Simone A , Trouw Leendert A , Dik Willem A 
Published: October 2020

AbstractObjectivesTo examine the relation between serum C1q levels and blood type‐1 interferon signature (type‐1 IFN signature) in active pulmonary tuberculosis (APTB) and to determine whether combined measurement of serum C1q and type‐1 IFN signature may add to the diagnosis of QuantiFERON‐positive (QFT+) patients with uveitis of unknown cause.MethodsC1q was determined (ELISA) in serum from two distinct Indonesian cohorts, and in total, APTB (n = 72), QFT+ uveitis of unknown aetiology (n = 58), QFT− uveitis (n = 51) patients and healthy controls (HC; n = 73) were included. The type‐1 IFN signature scores were previously determined.ResultsSerum C1q was higher in APTB than HC (P < 0.001). APTB patients with uveitis had higher serum C1q than APTB patients without uveitis (P = 0.0207). Serum C1q correlated inversely with type‐1 IFN signature scores in APTB (P = 0.0036, r2 = 0.3526), revealing that these biomarkers for active TB disease can be mutually exclusive. Stratification of QFT+ patients with uveitis of unknown cause, by serum C1q and type‐1 IFN signature, yielded four groups with different likelihood of suffering from active TB uveitis.ConclusionSerum C1q is elevated in APTB, especially in those cases with uveitis. We propose that combined measurement of blood type‐1 IFN signature and serum C1q may provide added value in the diagnosis of active TB disease. Combined measurement of type‐1 IFN signature and serum C1q in QFT+ patients without signs of active TB disease, but suffering from uveitis of unknown cause, may be of help to identify cases with low or high likelihood of having active TB uveitis, which may facilitate clinical management decisions.
Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course
Authors: Garcia‐Vedrenne Ana E. , Orland Chloé , Ballare Kimberly M. , Shapiro Beth , Wayne Robert K. 
Published: October 2020

AbstractTransitioning from in‐person to remote learning can present challenges for both the instructional team and the students. Here, we use our course “Biodiversity in the Age of Humans” to describe how we adapted tools and strategies designed for a flipped classroom to a remote learning format. Using anonymous survey data collected from students who attended the course either in‐person (2019) or remotely (2020), we quantify student expectations and experiences and compare these between years. We summarize our experience and provide ten “tips” or recommendations for a transition to remote learning, which we divide into three categories: (a) precourse instructor preparation; (b) outside of class use of online materials; and (c) during class student engagement. The survey results indicated no negative impact on student learning during the remote course compared to in‐person instruction. We found that communicating with students and assessing specific needs, such as access to technology, and being flexible with the structure of the course, simplified the transition to remote instruction. We also found that short, pre‐recorded videos that introduce subject materials were among the most valuable elements for student learning. We hope that instructors of undergraduate ecology and evolution courses can use these recommendations to help establish inclusive online learning communities that empower students to acquire conceptual knowledge and develop scientific inquiry and literacy skills.
What do you mean “functional” in ecology? Patterns versus processes
Authors: Volaire Florence , Gleason Sean M. , Delzon Sylvain 
Published: October 2020

AbstractUse of the term “functional" trait has increased exponentially in ecology. Although accounting for numerous ecological questions, this concept raises several issues. We propose that the term “functional” could be misleading because (1) no rigorous criteria exist to identify “functional” traits and (2) it suggests that only some traits (“functional” ones) can inform our understanding of species functioning, whatever the scale or discipline. Hence, the concept of "functional" trait in ecology is starting to be challenged and it remains unclear why some traits should be considered functional, whereas other traits should not.We argue that the most used “functional” traits are meaningful because they reflect important differences between populations or species, based on synchronic comparisons, that is, irrespective of time (hereafter “pattern” traits). Hence, they are useful for identifying trade‐offs and strategies across large numbers of observations, usually at rather coarse scales, and are most often used in analyses of “big data.” However, given that many ecological processes occur across short time scales and narrow gradients of climate and resource availability, the efficacy of these traits to inform us about these ecological processes appears questionable. We show that trait measurements that take time explicitly into account (hereafter “process” traits) differ from pattern traits because they quantify the flows of material and energy within a given environment across a defined period of time. Although pattern traits and process traits are both functional, it is important to understand the differences between the approaches. Moreover, better accounting of ontogeny, life form, plasticity, and genetic variability is required to enhance the convergence between pattern and process approaches. This revised framework allows more explicit connections between trait ecology and other biological sciences. It should enhance the study of processes at all scales in order to investigate efficiently the adaptive responses of biological organisms to climate change.
Contrasting vulnerability of monospecific and species‐diverse forests to wind and bark beetle disturbance: The role of management
Authors: Dobor Laura , Hlásny Tomáš , Zimová Soňa 
Published: October 2020

Abstract

Wind and bark beetle disturbances have increased in recent decades, affecting Europe's coniferous forests with particular severity. Management fostering forest diversity and resilience is deemed to effectively mitigate disturbance impacts, yet its efficiency and interaction with other disturbance management measures remain unclear.

We focused on Central Europe, which has become one of the hotspots of recent disturbance changes. We used the iLand ecosystem model to understand the interplay between species composition of the forest, forest disturbance dynamics affected by climate change, and disturbance management. The tested measures included (a) active transformation of tree species composition toward site‐matching species; (b) intensive removal of windfelled trees, which can support the buildup of bark beetle populations; and (c) reduction of mature and vulnerable trees on the landscape via modified harvesting regimes.

We found that management systems aiming to sustain the dominance of Norway spruce in the forest are failing under climate change, and none of the measures applied could mitigate the disturbance impacts. Conversely, management systems fostering forest diversity substantially reduced the level of disturbance. Significant disturbance reduction has been achieved even without salvaging and rotation length reduction, which is beneficial for ecosystem recovery, carbon, and biodiversity.

Synthesis and applications: We conclude that climate change amplifies the contrast in vulnerability of monospecific and species‐diverse forests to wind and bark beetle disturbance. Whereas forests dominated by Norway spruce are not likely to be sustained in Central Europe under climate change, different management strategies can be applied in species‐diverse forests to reach the desired control over the disturbance dynamic. Our findings justify some unrealistic expectations about the options to control disturbance dynamics under climate change and highlight the importance of management that fosters forest diversity.
On the importance of predictor choice, modelling technique, and number of pseudo‐absences for bioclimatic envelope model performance
Authors: Čengić Mirza , Rost Jasmijn , Remenska Daniela , Janse Jan H. , Huijbregts Mark A. J. , Schipper Aafke M. 
Published: October 2020

AbstractBioclimatic envelope models are commonly used to assess the influence of climate change on species' distributions and biodiversity patterns. Understanding how methodological choices influence these models is critical for a comprehensive evaluation of the estimated impacts. Here we systematically assess the performance of bioclimatic envelope models in relation to the selection of predictors, modeling technique, and pseudo‐absences. We considered (a) five different predictor sets, (b) seven commonly used modeling techniques and an ensemble model, and (c) three sets of pseudo‐absences (1,000 pseudo‐absences, 10,000 pseudo‐absences, and the same as the number of presences). For each combination of predictor set, modeling technique, and pseudo‐absence set, we fitted bioclimatic envelope models for 300 species of mammals, amphibians, and freshwater fish, and evaluated the predictive performance of the models using the true skill statistic (TSS), based on a spatially independent test set as well as cross‐validation. On average across the species, model performance was mostly influenced by the choice of predictor set, followed by the choice of modeling technique. The number of the pseudo‐absences did not have a strong effect on the model performance. Based on spatially independent testing, ensemble models based on species‐specific nonredundant predictor sets revealed the highest predictive performance. In contrast, the Random Forest technique yielded the highest model performance in cross‐validation but had the largest decrease in model performance when transferred to a different spatial context, thus highlighting the need for spatially independent model evaluation. We recommend building bioclimatic envelope models according to an ensemble modeling approach based on a nonredundant set of bioclimatic predictors, preferably selected for each modeled species.
Long‐term nutrient enrichment, mowing, and ditch drainage interact in the dynamics of a wetland plant community
Authors: Goodwillie Carol , McCoy Michael W. , Peralta Ariane L. 
Published: October 2020

AbstractFertilization studies have elucidated basic principles of the role of nutrients in shaping plant communities and demonstrated the potential effects of anthropogenic nutrient deposition. Yet less is known about how these effects are mediated by interacting ecological factors, particularly in nutrient‐poor wetland habitats. In a long‐term experiment in a coastal plain wetland, we examined how fertilization and mowing affected the diversity and composition of a plant community as it reestablished after major disturbance. A drainage ditch in proximity to the experimental plots allowed us also to consider the influence of hydrology and its interactions with nutrient addition. Fertilization decreased species richness, with wetland specialist species showing especially great losses, and several lines of evidence suggest that the effect was mediated by competition for light. Altered hydrology via ditch drainage had effects that were similar to fertilization, with more rapidly draining plots showing lower diversity and decreased abundance of wetland species. Plant community diversity and dynamics were influenced by complex interactions between fertilization, disturbance, and hydrology. The negative effect of fertilization on species richness was initially mitigated by mowing, but in later years was more evident in mowed than in unmowed plots. In the absence of disturbance, nutrient addition increased the rate of transition to primarily woody communities. Similarly, drained plots experienced increased rates of succession compared to wetter plots. Our results suggest that these interactions need to be considered to understand the potential effects of anthropogenic nutrient addition and hydrologic alterations to wetland ecosystems.
Influence of decompensated heart failure on cardiac acoustic biomarkers: impact on early readmissions
Authors: Erath Julia W. , Wanczura Piotr , Wranicz Jerzy , Linke Axel , Rohrer Ursula , Scherr Daniel 
Published: October 2020

AbstractAimsPreventing hospitalization by detecting early evidence of heart failure (HF) decompensation in an outpatient setting can improve patient's quality of life and reduce costs of care. The purpose of this study was to assess the value of cardiac acoustic biomarkers (CABs), a combination of cardiohaemic vibrations synchronized with ECG signals, and heart rate (HR) for detecting HF decompensation during first 3 months after hospital discharge for HF.Methods and resultsPatients with an ejection fraction ≤35% (HFrEF) and hospitalized for decompensated HF were enrolled in a prospective observational study. All subjects wore a wearable cardioverter‐defibrillator (ZOLL LifeVest®, Pittsburgh, PA, USA) that is capable of recording CABs and HR. The primary endpoint of the study was the first HF event, defined as HF readmission or HF emergency room visit. From June 2017 through August 2019, 671 patients with HFrEF were enrolled. Eighty‐one patients (12.1%) had a total of 112 HF events. The algorithm detected HF events with a median of 32 days (interquartile range = 11‐45) in advance of the first HF event. The algorithm had a sensitivity of 69%, specificity of 60%, positive predictive value of 19%, and a negative predictive value of 94%. Of note, the baseline (first 7 days post‐enrolment) algorithm using CABs and HR was superior to New York Heart Association classification in detecting patients more likely to have HF decompensation (sensitivity and specificity of 61% and 68% vs. 46% and 55%, respectively).ConclusionsThis prospective international registry showed that an algorithm incorporating CABs and HR data detected HF events 30 days in advance of the event in patients with HFrEF during first 3 months after hospital discharge. Therefore, integrating CAB technology into clinical practice may prevent HF rehospitalizations.
‘Nur'turing tumor T cell tolerance and exhaustion: novel function for Nuclear Receptor Nur77 in immunity
Authors: Lith Sanne C. , van Os Bram W. , Seijkens Tom T.P. , de Vries Carlie J.M. 
Published: October 2020

AbstractThe nuclear receptor Nur77 is expressed in a multitude of tissues, regulating cell differentiation and homeostasis. Dysregulation of Nur77 signaling is associated with cancer, cardiovascular disease, and disorders of the CNS. The role of Nur77 in T cells has been studied for almost 30 years now. There is a clear appreciation that Nur77 is crucial for apoptosis of self‐reactive T cells. However, the regulation and function of Nur77 in mature T cells remains largely unclear. In an exciting development, Nur77 has been recently demonstrated to impinge on cancer immunotherapy involving chimeric antigen receptor (CAR) T cells and tumor infiltrating lymphocytes (TILs). These studies indicated that Nur77 deficiency reduced T cell tolerance and exhaustion, thus raising the effectiveness of immune therapy in mice. Based on these novel insights, it may be proposed that regulation of Nur77 activity holds promise for innovative drug development in the field of cellular immunotherapy in cancer. In this review, we therefore summarize the role of Nur77 in T cell selection and maturation; and further develop the idea of targeting its activity in these cells as a potential strategy to augment current cancer immunotherapy treatments.
Polymorphisms of the μ‐opioid receptor gene influence cerebral pain processing in fibromyalgia
Authors: Ellerbrock Isabel , Sandström Angelica , Tour Jeanette , Kadetoff Diana , Schalling Martin , Jensen Karin B. , Kosek Eva 
Published: October 2020

AbstractBackgroundDysregulation of the μ‐opioid receptor has been reported in fibromyalgia (FM) and was linked to pain severity. Here, we investigated the effect of the functional genetic polymorphism of the μ‐opioid receptor gene (OPRM1) (rs1799971) on symptom severity, pain sensitivity and cerebral pain processing in FM subjects and healthy controls (HC).MethodsSymptom severity and pressure pain sensitivity was assessed in FM subjects (n = 70) and HC (n = 35). Cerebral pain‐related activation was assessed by functional magnetic resonance imaging during individually calibrated painful pressure stimuli.ResultsFibromyalgia subjects were more pain sensitive but no significant differences in pain sensitivity or pain ratings were observed between OPRM1 genotypes. A significant difference was found in cerebral pain processing, with carriers of at least one G‐allele showing increased activation in posterior cingulate cortex (PCC) extending to precentral gyrus, compared to AA homozygotes. This effect was significant in FM subjects but not in healthy participants, however, between‐group comparisons did not yield significant results. Seed‐based functional connectivity analysis was performed with the seed based on differences in PCC/precentral gyrus activation between OPRM1 genotypes during evoked pain across groups. G‐allele carriers displayed decreased functional connectivity between PCC/precentral gyrus and prefrontal cortex.ConclusionsG‐allele carriers showed increased activation in PCC/precentral gyrus but decreased functional connectivity with the frontal control network during pressure stimulation, suggesting different pain modulatory processes between OPRM1 genotypes involving altered fronto‐parietal network involvement. Furthermore, our results suggest that the overall effects of the OPRM1 G‐allele may be driven by FM subjects.SignificanceWe show that the functional polymorphism of the μ‐opioid receptor gene OPRM1 was associated with alterations in the fronto‐parietal network as well as with increased activation of posterior cingulum during evoked pain in FM. Thus, the OPRM1 polymorphism affects cerebral processing in brain regions implicated in salience, attention, and the default mode network. This finding is discussed in the light of pain and the opioid system, providing further evidence for a functional role of OPRM1 in cerebral pain processing.
FogWise: On the limits of the coexistence of heterogeneous applications on Fog computing and Internet of Vehicles
Authors: de Mendonça Junior Francisco Ferreira , Lopes Dias Kelvin , d'Orey Pedro M. , Kokkinogenis Zafeiris 
Published: October 2020

AbstractMobile devices, Internet of Things applications, and connected vehicles in the Internet of Vehicles (IoV) are proliferating. Recently, vehicles have emerged as a possibility to become communication and processing infrastructures called vehicular Fog computing (VFC). Thus, science and industry forecast increasing demand for communication and cloud infrastructures to deal with data traffic, processing, and storage. Still, they do not evaluate that properly. This work investigates how heterogeneity affects the ability of IoV and VFC to meet application requirements. We leverage Fog computing, which extends Edge and Cloud computing and complements them, especially to meet str applications with strict latency requirements. We built a simulation model that evaluates how vehicles behave in such an environment. We argue that vehicles need to follow request‐processing‐response‐actuation programming model based on distributed auction protocol to match clients and servers and still meet latency requirements. We extend and propose requirements that both applications and architectures should meet. Preliminary results indicate thresholds in terms of vehicle density, request rate, request size, client‐server ratio, and auction method in which VFC can operate to meet application requirements under mobility.
The effect of redox agents on conformation and structure characterization of gluten protein: An extensive review
Authors: Abedi Elahe , Pourmohammadi Kiana 
Published: October 2020

AbstractGluten protein as one of the plant resources is affected by redox agent. Chemical modifications by redox agent have myriad advantages mainly short reaction times, no requirement for specialized equipment, low cost, and highly clear modification impacts. The gluten network properties could be influenced through redox agents (oxidative and reducing agents) which are able to alter the strength of dough via different mechanisms for various purposes. The present review examined the impact of different redox compounds on gluten and its subunits based on their effects on their bonds and conformations and thus with their impacts on the physico‐chemical, morphological, and rheological properties of gluten and their subunits. This allows for the use of gluten for different of purposes in the food and nonfood industry.
Instrument development of health providers' Knowledge, Attitude and Practice of Hospice Care Scale in China
Authors: Shu Zhiqun , Wang Yiting , Li Tiantian , Jing Limei , Sun Xiaoming 
Published: October 2020

AbstractObjectiveTo match the reform of hospice development in China, this study aimed to construct an indigenized health providers' Knowledge, Attitude and Practice of Hospice Care (KAPHC) Scale in China with good validity and reliability.MethodsWe used three steps to develop the scale, establishing items‐pool firstly based on literature review and expert consultation, followed by forming a draft‐scale design through synthetically consideration, and finally modifying the draft by conducting a self‐administrative survey in sampled institution and testing the reliability and validity by statistical analysis.ResultsThe KAPHC Scale was comprised of 15 knowledge items, 24 attitude items and 22 practice items. In the part of knowledge, the Cronbach's α coefficient was 0.686, the average difficulty was 0.62 and average discrimination was 0.46. The attitude items were divided into four domains (KMO = 0.770), with Cronbach's α coefficient of 0.868. The practice items included confidence of practices and self‐reported behaviors (KMO = 0.732), with Cronbach's α coefficient of 0.958.ConclusionThe KAPHC Scale demonstrated good validity and reliability. As an effective tool, the scale may contribute to assessing health providers' KAP status of hospice care and exploring their future education needs in mainland China.