bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral and lifetime resolution of fundus autofluorescence in advanced age‐related macular degeneration revealing different signal sources
Authors: Schultz Rowena , Hasan Somar , Curcio Christine A. , Smith Roland T. , Meller Daniel , Hammer Martin 
Published: July 2021

AbstractPurposeTo determine the fundus autofluorescence (FAF) lifetimes and spectral characteristics of individual drusen and hyperpigmentation independent of those with retinal pigment epithelium (RPE) in geographic atrophy (GA) areas in late‐stage age‐related macular degeneration (AMD).MethodsThree consecutive patients with complete RPE and outer retinal atrophy (cRORA) exhibiting drusen that were calcified or associated with hyperpigmentation were investigated with multimodal non‐invasive ophthalmic imaging including colour fundus photography (CFP), optical coherence tomography (OCT), near‐infrared reflectance (NIR), blue FAF and fluorescence lifetime imaging ophthalmoscopy (FLIO). Fluorescence lifetimes were measured in two spectral channels (short‐wavelength spectral channel (SSC): 500–560 nm and long‐wavelength spectral channel (LSC): 560–720 nm).ResultsDrusen lacking RPE coverage, as confirmed by CFP and OCT, had longer FAF lifetimes than surrounding cRORA by 127 ± 66 ps (SSC) and 113 ± 48 ps (LSC, both p = 0.008 in Wilcoxon test, N = 9) and by 209 ± 100 ps (SSC) and 121 ± 56 ps (LSC, p < 0.001, N = 14) in two patients. Hyperpigmentation in CFP in a third patient shows strong FAF with prolonged lifetimes. In the SSC, persistent FAF was found inside cRORA. A crescent‐shaped hyperfluorescence in an area of continuous RPE but lacking outer retina was seen in one eye with a history of anti‐VEGF treatment.ConclusionsShort‐wavelength fluorescence in cRORA points to fluorophores beyond RPE organelles. Fluorescence properties of drusen within cRORA differ from in vivo drusen covered by RPE. These limited findings from three patients give new insight into the sources of FAF that can be further elucidated in larger cohorts.
The impact of clonal diversity and mosaicism on haematopoietic function in Fanconi anaemia
Authors: Hughes Andrew D. , Kurre Peter 
Published: July 2021

SummaryRecent advances have facilitated studies of the clonal architecture of the aging haematopoietic system, and provided clues to the mechanisms underlying the origins of hematopoietic malignancy. Much less is known about the clonal composition of haematopoiesis and its impact in bone marrow failure (BMF) disorders, including Fanconi anaemia (FA). Understanding clonality in FA is likely to inform both the marked predisposition to cancer and the rapid erosion of regenerative reserve seen with this disease. This may also hold broader lessons for haematopoietic stem cell biology in other diseases with a clonal restriction. In this review, we focus on the conceptual basis and available tools to study clonality, and highlight insights in somatic mosaicism and malignant evolution in FA in the context of haematopoietic failure and gene therapy.
Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot
Authors: Goloboff Pablo A. , Catalano Santiago A. , Torres Ambrosio 
Published: July 2021

AbstractThis paper examines the implementation of parsimony methods in the programs PAUP*, MEGA and MPBoot, and compares them with TNT. PAUP* implements standard, well‐tested algorithms, and flexible search strategies and options for handling trees; its main drawback is the lack of advanced search algorithms, which makes it difficult to find most parsimonious trees for large and complex datasets. In addition, branch‐swapping can be much slower than in TNT for datasets with large numbers of taxa, although this is only occasionally a problem for phylogenomic datasets given that they typically have small numbers of taxa. The parsimony implementation of MEGA has major drawbacks. MEGA often fails to find parsimonious trees because it does not perform all possible branch swapping subtree pruning regrafting (SPR)/tree bisection‐reconnection (TBR) rearrangements. It furthermore fails to properly handle ambiguity or multiple equally parsimonious trees, and it uses the same addition sequence for all bootstrap replicates. The latter yields values of group support that depend on the order in which taxa are listed in the dataset. In addition, tree searches are very slow and do not facilitate the exploration of different starting points (as random seed is fixed). MPBoot searches for optimal trees using the ratchet, but it is based on SPR instead of TBR (and only evaluates by default a subset of the SPR rearrangements). MPBoot approximates bootstrap frequencies by first finding a sample of trees and then selecting from those trees for every replicate, without performing a tree‐search. The approximation is too rough in many cases, producing serious under‐ or overestimations of the correct support values and, for most kinds of datasets, slower estimations than can be obtained with TNT. In addition, bootstrapping with PAUP*, MEGA or MPBoot can attribute strong supports to groups that have no support at all under any meaningful concept of support, such as likelihood ratios or Bremer supports. In TNT, this problem is decreased by using the strict consensus tree to represent each replicate, or eliminated entirely by using different approximations of the Bremer support.
TRUST‐based features for detecting the intruders in the Internet of Things network using deep learning
Authors: Bhor Harsh Namdev , Kalla Mukesh 
Published: July 2021

AbstractInternet of Things (IoT) is a trending domain and has acquired much interest for various kinds of civilian applications. The purpose of IoT is to make objects accessible and interconnected via internet. Hence, security to IoT devices is a major issue because devices connected to the IoT network are resource‐constrained. In IoT, the nodes exchange information using insecure internet, which makes the network exposed to different attacks. This article proposes a new intrusion detection strategy, namely, Taylor‐spider monkey optimization‐based deep belief network (Taylor‐SMO‐based DBN). The KDD features and the trust factors are employed for intrusion detection. The KDD features are subjected to the classification, which is progressed using a newly devised optimization algorithm, namely, Taylor‐spider monkey optimization (Taylor‐SMO)‐based DBN. The proposed Taylor‐SMO algorithm is designed by integrating the Taylor series and spider monkey optimization (SMO) algorithm and is employed to train the deep belief network (DBN) to achieve accurate intrusion detection. The proposed Taylor‐SMO‐based DBN outperformed other methods with maximal accuracy of 90%, false alarm rate of10%, precision of 90%, and recall of 92%, respectively.
The risk of unintended deforestation from scaling sustainable livestock production systems
Authors: Castro‐Nunez Augusto , Buriticá Alexander , Gonzalez Carolina , Villarino Eliza , Holmann Federico , Perez Lisset , Del Río Martha , Sandoval Danny , Eufemia Luca , Löhr Katharina , Durango Sandra , Romero Miguel , Lana Marcos , Sotelo Steven , Rivera Ovidio , Loboguerrero Ana Maria , Quintero Marcela 
Published: July 2021

AbstractSilvopastoral systems (SPS)—production systems integrating trees, forages, and livestock within the same land area—are recognized as critical for reducing tropical deforestation and improving livelihoods, ecosystem services, and carbon sinks. Yet, research on how scaling SPS influences forest cover changes at large geographical scales is scant. Our study delves deeper into the interlinkages between scaling SPS and deforestation. In two surveys conducted among 144 Colombian Amazon livestock producers with traditional or SPS farms, we assessed changes in herd composition between 2016 and 2020. Results showed a change in herd composition, with fewer males and more cows/heifers, suggesting a shift toward specializing in milk production, which, with the appropriate environmental incentives and safeguards, would unlikely broaden deforestation. However, interlinkages between the dairy and beef value chains suggest that extra male cattle from SPS intensification would be moved for fattening as a source of beef to new pastures at the forest border. If SPS scaling interventions in the Colombian Amazon are to be truly deforestation‐free, they need to be designed based on a clear understanding of the interlinkages between food and land systems. Therefore, policies advancing the livestock and land‐use agenda must create mechanisms that support deforestation‐free livestock intensification, based on biophysical and socioeconomic evaluations.
Accelerating vaccine trial conduct in a pandemic with a hot spot‐based inclusion strategy using trial and epidemic simulation
Authors: van der Plas Johan L. , van Esdonk Michiel J. , Kamerling Ingrid M. C. , Cohen Adam F. 
Published: July 2021

AbstractClinical development of vaccines in a pandemic situation should be rigorous but expedited to tackle the pandemic threat as fast as possible. We explored the effects of a novel vaccine trial strategy that actively identifies and enrolls subjects in local areas with high infection rates. In addition, we assessed the practical requirements needed for such a strategy. Clinical trial simulations were used to assess the effects of utilizing these so‐called “hot spot strategy” compared to a traditional vaccine field trial. We used preset parameters of a pandemic outbreak and incorporated realistic aspects of conducting a trial in a pandemic setting. Our simulations demonstrated that incorporating a hot spot strategy shortened the duration of the vaccine trial considerably, even if only one hot spot was identified during the clinical trial. The active hot spot strategy described in this paper has clear advantages compared to a “wait‐and‐see” approach that is used in traditional vaccine efficacy trials. Completion of a clinical trial can be expedited by adapting to resurgences and outbreaks that will occur in a population during a pandemic. However, this approach requires a speed of response that is unusual for a traditional phase III clinical trial. Therefore, several recommendations are made to help accomplish rapid clinical trial setup in areas identified as local outbreaks. The described model and hot spot vaccination strategy can be adjusted to disease‐specific transmission characteristics and could therefore be applied to any future pandemic threat.
Melanoma mimicking atypical fibroxanthoma: Report of an unusual case
Authors: Wang Yanqing , Guo Ying 
Published: July 2021

AbstractMelanoma may mimic a variety of skin lesions clinically and histopathologically, and presents diagnostic challenges. In this article, we describe a case of melanoma in an 89‐year‐old man with a very rare histopathologic presentation, namely the presence of pleomorphic and multinucleated giant cells with abundant cytoplasm, highly resembling an atypical fibroxanthoma. The differential diagnoses in conjunction with the findings in immunohistochemical study are also discussed.
Effect of pre‐transplant JAK1/2 inhibitors and CD34 dose on transplant outcomes in myelofibrosis
Authors: Cyriac Sunu , Prem Shruti , Salas Maria Queralt , Chen Shiyi , Al‐Shaibani Zeyad , Lam Wilson , Law Arjun , Gupta Vikas , Michelis Fotios V. , Kim Dennis (Dong Hwan) , Lipton Jeffrey , Kumar Rajat , Mattsson Jonas , Viswabandya Auro 
Published: July 2021

AbstractAllogeneic hematopoeitic cell transplantation (allo‐HCT) is the only curative treatment for myelofibrosis (MF). We evaluate the impact of various factors on survival outcomes post‐transplant in MF. Data of 89 consecutive MF patients (primary 47%) who underwent allo‐HCT between 2005 and 2018 was evaluated. Fifty‐four percent patients had received JAK1/2 inhibitors (JAKi) pre‐HCT. The median CD34 count was 7.1x106 cells/kg. Graft failure was seen in 10% of the patients. Grade 3‐4 acute GVHD (aGVHD) and moderate/severe chronic graft versus host disease (cGVHD) occurred in 24% and 40% patients, respectively. Two‐year overall survival (OS) and relapse free survival (RFS) were 51% and 43%, respectively. Cumulative incidence of relapse (CIR) and non‐relapse mortality (NRM) at 2 years were 11% and 46%, respectively. Higher CD34 cell dose (≤5 × 106 cells/kg vs 5‐9 or ≥9 × 106 cells/kg) and lower pre‐HCT ferritin (</=1000 ng/ml) were associated with better OS, RFS and lower NRM. Grade 3‐4 aGVHD was associated with higher NRM. Use of pre‐transplant JAKi was associated with lower incidence of grade 3‐4 aGVHD. In summary, higher CD34 cell dose is associated with better allo‐HCT outcomes in MF and pre‐HCT JAKi use is associated with reduced risk of severe aGVHD. These two modifiable parameters should be considered during allo‐HCT for MF.
Interaction effects of environmental factors on soil nitrogen fractions based on a novel sequential extraction method
Authors: Wang Xinyue , Zhang Shirong , Zhong Qinmei , Li Ting , Wang Guiyin , Xu Xiaoxun , Pu Yulin 
Published: July 2021

AbstractSoil nitrogen (N) is controlled by several environmental factors. However, it is unclear how these factors and their interactions affect soil N fractions (SNFs) because of the lack of systematic N extraction methods. The Harbin–Dali belt, a transect more than 3,300 km long across China covering various climates, topographies, soil parent materials and vegetation types, was taken as the study area, and the interactive effects on SNFs in largely undisturbed woodlands and grasslands were explored using three SNFs: labile N, moderately stable N and stable N. The soil N fractions were obtained through a novel sequential extraction method that used distilled H2O, 0.5 M CaCl2, 1 M HCl, 6 M HCl, mixed acid (1 M HCl and 5 M HF; MA), concentrated HCl (cHCl) and concentrated H2SO4as extractive agents to successively separate H2O‐, CaCl2‐, 1 M HCl‐, 6 M HCl‐, MA‐, cHCl‐ and RES‐N fractions. The results showed that increasing mean annual temperature (MAT) directly decreased the concentrations of H2O‐, CaCl2‐ and 1 M HCl‐N, suggesting that warming may reduce available N. The interactions between MAT, parent material, aspect and aridity index also contributed to the three SNFs. Vegetation and its interactions with parent material primarily controlled 6 M HCl‐, cHCl‐ and RES‐N, and climate and topography had indirect effects during these processes. Particularly, more cHCl‐ and RES‐N were accumulated in areas with warm humid climates and rich vegetation species than in other environments. Moreover, soil labile N (H2O‐, CaCl2‐ and 1 M HCl‐N) and cHCl‐N exhibited potential as sensitive indicators for reflecting the changes in MAT and vegetation, respectively. Therefore, the various interactions between climate and other environmental factors controlled the changes in most SNFs. This novel sequential extraction method thus offers a reliable analytical approach to measuring SNFs.HighlightsSoil nitrogen fractions (SNFs) were fractionated via a novel sequential extraction method.Increasing MAT decreased the H2O‐, CaCl2‐ and 1 M HCl‐N concentrations.Interactions of climate, parent material and vegetation affected 6 M HCl‐, MA‐, cHCl‐ and RES‐N.H2O‐, CaCl2‐, 1 M HCl‐ and cHCl‐N are sensitive SNFs that reflect environmental changes.
Stress causes interspecific facilitation within a compost community
Authors: Hesse Elze , O'Brien Siobhan , Luján Adela M. , Sanders Dirk , Bayer Florian , van Veen Eleanor M. , Hodgson Dave J. , Buckling Angus 
Published: July 2021

AbstractEcological theory predicts interactions between species to become more positive under abiotic stress, while competition should prevail in more benign environments. However, experimental tests of this stress gradient hypothesis in natural microbial communities are lacking. We test this hypothesis by measuring interactions between 10 different members of a bacterial community inhabiting potting compost in the presence or absence of toxic copper stress. We found that copper stress caused significant net changes in species interaction signs, shifting the net balance towards more positive interactions. This pattern was at least in part driven by copper‐sensitive isolates – that produced relatively small amounts of metal‐detoxifying siderophores – benefitting from the presence of other species that produce extracellular detoxifying agents. As well as providing support for the stress gradient hypothesis, our results highlight the importance of community‐wide public goods in shaping microbial community composition.
Brain state‐dependent high‐frequency activity as a biomarker for abnormal neocortical networks in an epileptic spasms animal model
Authors: Lee Chih‐Hong , Le John T. , Swann John W. 
Published: July 2021

AbstractObjectiveEpileptic spasms are a hallmark of a severe epileptic state. A previous study showed neocortical up and down states defined by unit activity play a role in the generation of spasms. However, recording unit activity is challenging in clinical settings, and more accessible neurophysiological signals are needed for the analysis of these brain states.MethodsIn the tetrodotoxin model, we used 16‐channel microarrays to record electrophysiological activity in the neocortex during interictal periods and spasms. High‐frequency activity (HFA) in the frequency range of fast ripples (200–500 Hz) was analyzed, as were slow wave oscillations (1–8 Hz), and correlated with the neocortical up and down states defined by multiunit activity (MUA).ResultsHFA and MUA had high temporal correlation during interictal and ictal periods. Both increased strikingly during interictal up states and ictal events but were silenced during interictal down states and preictal pauses, and their distributions were clustered at the peak of slow oscillations in local field potential recordings. In addition, both HFA power and MUA firing rates were increased to a greater extent during spasms than interictal up states. During non‐rapid eye movement sleep, the HFA rhythmicity faithfully followed the MUA up and down states, but during rapid eye movement sleep when MUA up and down states disappeared the HFA rhythmicity was largely absent. We also observed an increase in the number of HFA down state minutes prior to ictal onset, consistent with the results from analyses of MUA down states.SignificanceThis study provides evidence that HFA may serve as a biomarker for the pathological up states of epileptic spasms. The availability of HFA recordings makes this a clinically practical technique. These findings will likely provide a novel approach for localizing and studying epileptogenic neocortical networks not only in spasms patients but also in other types of epilepsy.
Industry tournament incentives and corporate hedging policies
Authors: Lonare Gunratan , Nart Ahmet , Tuncez Ahmet M. 
Published: July 2021

AbstractThis paper examines how a tournament among CEOs to progress within the CEO labor market influences their corporate hedging policies. We employ a textual analysis of 10‐Ks to generate corporate hedging proxies, finding that the likelihood and intensity of hedging grow as the CEO labor market tournament prizes increase. We also explore the mitigating impact of corporate hedging on the adverse effects of risk‐inducing industry tournament incentives (ITIs) on the cost of debt and stock price crash risk, noting that these could be possible reasons behind the relation. Additionally, we observe that the relationship between ITIs and corporate hedging is less pronounced for firms that demonstrate more financial distress and for firms whose CEOs are the founders of the company or are of retirement age. We identify a causal relation between ITIs and corporate hedging using an instrumental variable approach and an exogenous shock sourced from changes in the enforceability of noncompetition agreements across states.
Planetary food regimes: Understanding the entanglement between human and planetary health in the Anthropocene
Authors: Beacham Jonathan 
Published: July 2021

AbstractFood regime theory provides a framework of continued and recurring interest to geographical perspectives in charting the contours connecting agri‐food and capitalist political economy. Drawing principally on Marxian regulation theory, the analytical framework of food regime theory outlines three periodised regimes from the starting point of 1870 to the present day. Yet there remains ongoing and unresolved debate as to how we characterise the contemporary third regime – and whether it is a regime on its own specific terms or merely an enduring hangover from the second. I argue that an underacknowledged dimension of attempts to characterise the third regime lies in the conjoined relationship between human and planetary health, which the diagnosis of the Anthropocene encourages us to recognise amid tumultuous global environmental change. Given food regime theory's evasive relationship with ecological dynamics within its explanatory framework, I suggest that a “planetary” retheorisation of its central contributions is increasingly prescient. In considering the growing tensions and contradictions afflicting the contemporary regime, and using soy as a working example, I work through three central arguments. First, that a planetary retheorisation serves to reveal the way in which planetary dynamics shape social life, enabling – albeit never wholly determining – food regimes. Second, that what and how people eat in their dietary practices are of planetary significance, which has been to some degree marginalised within the production‐centric analyses of food regime theory. Third, that the conceptual Anthropocene highlights how planetary and human health are intricately and inextricably connected, which food regime theory must better account for. I conclude by proposing that the explanatory potential of the contemporary third regime is being stretched, with contested trajectories and nascent contours raising questions around how we might understand quite what we are living through today.
Meet the victim: Police corruption, violence, and political mobilization
Authors: Ponce Aldo F. , Somuano Ma. Fernanda , Velázquez López Velarde Rodrigo 
Published: July 2021

AbstractRecent literature has analyzed the relationship between governmental corruption and political behavior, focusing on voting turnout (Stockemer, LaMontagne, & Scruggs, 2013). Fewer studies have examined the impact of corruption on nonelectoral political participation. This article fills this gap by examining how nonelectoral political participation is influenced by corruption within one of the most important institutions dealing with citizens' welfare and safety: the police. We focus our research on Mexico because the effects of police corruption have been increasingly felt in the country in recent decades. We find that experiences of police corruption raise the likelihood of taking the streets to protest. Interestingly, we also find that corruption experiences specifically with police bureaucracies lead to greater likelihood of nonelectoral participation through institutional channels. We also report that the combination of police corruption and violent crime alienates citizens from the political sphere.