bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decision Support Tools to Inform the Rehabilitation and Management of High Graded Forests
Authors: Curtze Alexander C , Muth Allyson B , Larkin Jeffery L , Leites Laura P 
Published: February 2022

Abstract
Numerous forests in the eastern United States have been degraded due to past exploitative timber harvesting known as high grading. High graded forest stands may not improve without active rehabilitation and may require targeted silvicultural treatments. This study focuses on high graded mixed-oak (mixed-Quercus spp.) stands and aims to develop a model that can identify past high grading and to determine modifications that may improve forest management recommendations provided by the prominent decision support tool, SILVAH. We present a model that uses standard forest inventory measurements and does not require knowledge of preharvest stand conditions to predict with moderate to high accuracy whether a stand was high graded, which could be particularly useful for nonindustrial private forests. Results indicate that modifications to SILVAH may be necessary to improve its utility for prescribing silvicultural treatments in high graded stands.
Assessing the Absorption and Economic Impact of Suppression and Repair Spending of the 2017 Eagle Creek Fire, Oregon
Authors: Politoski Danny , Dittrich Ruth , Nielsen-Pincus Max 
Published: February 2022

Abstract
The frequency of large wildfires in the US has increased over the past few decades, and more communities will need to prepare for the inevitability of wildfire in the future. In this article, we examine the local and regional economic impact of fire suppression and postfire repair spending for the 2017 Oregon Eagle Creek fire. The Eagle Creek fire is unique in that it occurred close to a large metropolitan area, Portland, and along an important transportation corridor, Interstate 84. We found that the proportion of repair spending absorbed by local and regional counties was 85%, whereas 26% of suppression spending was absorbed by local and regional counties. We quantified the wider economic impact of this spending using the input-output model, IMPLAN. Suppression spending created a total economic output of $4 million (initial input $2.4 million) while repair spending created an economic output of $14 million per year over two years (initial input $14.5 million).
Three faces of recursion axioms: the case of constructive dynamic logic of relation changers
Authors: Hatano Ryo , Sano Katsuhiko 
Published: February 2022

Abstract
This paper proposes an intuitionistic generalization of van Benthem and Liu’s dynamic logic of relation changers, where relation changers are dynamic operators that rewrite each agent’s accessibility relation. We employ Nishimura’s Kripke semantics for a constructive propositional dynamic logic to define the semantics of relation changers. Strong completeness results of Hilbert-style axiomatizations for constructive dynamic logic of relation changers are established by two types of rewriting strategies via recursion axioms: inside-out and outside-in strategies. To establish the semantic completeness by outside-in strategy, we propose the notion of composition of relation changers and an appropriately defined notion of length of a formula. Moreover, we reveal that recursion axioms have additional two faces: semantic and proof-theoretic ones. As for the semantic face, we introduce an alternative semantics for dynamic logic of relation changers to specify the semantic meaning of recursion axioms used in the inside-out strategy. This leads us to a semantic completeness proof of the axiomatization for the original semantics, which does not require a rewriting strategy based on recursion axioms. As for the proof-theoretic face, we transform each of recursion axioms required in the outside-in strategy into two (left and right) inference rules to provide a sequent calculus for dynamic logic of relation changers. Since the resulting sequent calculus is cut-free but semi-analytic, it still enjoys the Craig interpolation theorem by Maehara’s method.
Room-temperature third-order nonlinear Hall effect in Weyl semimetal TaIrTe4
Authors: Wang Cong , Xiao Rui-Chun , Liu Huiying , Zhang Zhaowei , Lai Shen , Zhu Chao , Cai Hongbing , Wang Naizhou , Chen Shengyao , Deng Ya , Liu Zheng , Yang Shengyuan A , Gao Wei-Bo 
Published: February 2022

AbstractThe second-order nonlinear Hall effect observed in the time-reversal symmetric system has not only shown abundant physical content, but also exhibited potential application prospects. Recently, a third-order nonlinear Hall effect has been observed in MoTe2 and WTe2. However, few-layer MoTe2 and WTe2 are usually unstable in air and the observed third-order nonlinear Hall effect can be measured only at low temperature, which hinders further investigation as well as potential application. Thus, exploring new air-stable material systems with a sizable third-order nonlinear Hall effect at room temperature is an urgent task. Here, in type-II Weyl semimetal TaIrTe4, we observed a pronounced third-order nonlinear Hall effect, which can exist at room temperature and remain stable for months. The third-order nonlinear Hall effect is connected to the Berry-connection polarizability tensor instead of the Berry curvature. The possible mechanism of the observation of the third-order nonlinear Hall effect in TaIrTe4 at room temperature has been discussed. Our findings will open an avenue towards exploring room-temperature nonlinear devices in new quantum materials.
A Review of Hemophagocytic Lymphohistiocytosis in Patients With HIV
Authors: Tabaja Hussam , Kanj Amjad , El Zein Said , Comba Isin Yagmur , Chehab Omar , Mahmood Maryam 
Published: February 2022

AbstractWe provide an elaborate review of cases published between January 2005 and April 2021 on hemophagocytic lymphohistiocytosis (HLH) in HIV patients. Seventy articles describing 81 adult patients (age ≥19 years) were included. The median age was 40 years, and 78% were males. Only 65% were known to have HIV before presentation. CD4 count was ≥200 cells/mm3 in 23%, and HIV viral load was &lt;200 copies/mL in 41%. The lack of meticulous reporting of ≥5 of 8 criteria for HLH diagnosis was evident in a third of cases. At least 1 infectious agent—other than HIV—was believed to trigger HLH in 78% of patients. The most common were Epstein-Barr virus (26%), human herpesvirus 8 (21%), and Histoplasma capsulatum (17%). Sixty percent survived. Among those, 93% received treatment for identified secondary trigger(s), while 51% received HLH-directed therapy. There was significant heterogeneity in the treatment regimens used for HLH.
Lung Transplant Candidates With Pretransplant Gastroesophageal Reflux and Antibodies to Lung Self-antigens Have Shorter CLAD-free Survival After Transplant
Authors: Razia Deepika , Mittal Sumeet K. , Bansal Sandhya , Ravichandran Ranjithkumar , Smith Michael A. , Walia Rajat , Bremner Ross M. , Mohanakumar Thalachallour , Tokman Sofya 
Published: February 2022

Background.
Pre–lung transplant (LTx) gastroesophageal reflux (GER) and circulating antibodies against the lung self-antigens (SAbs) collagen V and K-alpha-1 tubulin may predispose recipients to chronic lung allograft dysfunction (CLAD). We aimed to study the association of pre-LTx GER or pre-LTx SAbs with CLAD.

Methods.
In this retrospective analysis of patients who underwent LTx between 2015 and 2019, pre-LTx GER and SAbs were dichotomously defined as present or absent. The study group comprised recipients with either GER‚ SAbs, or both, and the control group comprised recipients without GER or SAbs. Endpoints included CLAD and survival.

Results.
Ninety-five LTx recipients were divided into a study group (n = 71; 75%) and a control group (n = 24; 25%). Pretransplant GER was associated with pre-LTx SAbs (odds ratio [95% confidence intervals], 5.022 [1.419-17.770]; P = 0.012). In addition, the study group (either GER‚ SAbs, or both) had a higher risk of CLAD (hazard ratio [95% confidence intervals], 8.787 [1.694-45.567]; P = 0.010) and lower CLAD-free survival after LTx than the control group (P = 0.007); however, overall survival was similar between the 2 groups (P = 0.618).

Conclusions.
GER was associated with elevated SAbs in LTx candidates, and either GER, SAbs, or both were associated with CLAD in LTx recipients. This association suggests that GER may cause an immune response to normally sequestered lung-associated self-antigens that drives ongoing lung injury.
Inducible Nitric Oxide Synthase deficiency leads to early demyelination by altering the balance between pro- and anti-inflammatory responses against Murine-β-Coronavirus
Authors: Kamble Mithila , Saadi Fareeha , Kumar Saurav , Saha Bhaskar , Sarma Jayasri Das 
Published: February 2022

AbstractThe neurological disease Multiple sclerosis (MS) is characterized by neuroinflammation and demyelination orchestrated by the activated glial cells, the CNS infiltrating leukocytes, and their reciprocal interaction through inflammatory signals. Inducible nitric oxide synthase (iNOS), an enzyme that catalyzes sustained nitric oxide production in response to an inflammatory stimulus, is a pro-inflammatory marker expressed particularly by the microglia/macrophages (MG/Mφ) during neuroinflammation. In MS, iNOS has been reportedly associated with the disease pathology; however, studies dissecting its role in the underlying mechanisms, specifically demyelination, are limited. Therefore, we studied the role of iNOS in a recombinant beta-coronavirus-MHV-RSA59-induced neuroinflammation, which is a prototypic animal model used to investigate the pathological hallmarks of MS, neuroinflammatory demyelination, and axonal degeneration. During the acute phase of infection with RSA59, wildtype C57BL/6 (WT) mice had significantly upregulated iNOS expression in macrophages, natural killer cells, and natural killer T cells suggesting a role for iNOS in RSA59-induced neuroinflammation. Studies comparing RSA59-infected WT and iNOS-deficient mice revealed that iNOS deficiency aggravated the disease with increased CNS infiltration of macrophages and neutrophils and enhanced mortality. As early as 9-10 days after the infection, the CNS of iNOS-deficient mice had substantially higher demyelination marked with morphologically defined MG/Mφ in the demyelinating regions. Transcript analysis confirmed the significant upregulation of type2 macrophage (M2) markers-Arginase 1, CD206, and TREM2-in the CNS of iNOS-deficient mice. Corroborating to the phenotype, the iNOS-deficient mice showed a significantly higher expression of TGFβ-an anti-inflammatory cytokine- and increased T regulatory (Treg) cell infiltration, indicating an anti-inflammatory milieu established early after the infection. These observations highlight a protective role of iNOS in virus-induced neuroinflammation whereas its absence leads to MG/Mφ polarization towards a phenotype that may be involved in the exacerbated demyelination pathology.Author summaryContrary to the reported pathogenic role of inducible nitric oxide synthase (iNOS) in multiple sclerosis and related autoimmune animal models, we show that the mice deficient in iNOS show an exacerbated disease with accelerated demyelination accompanied by heightened production of an anti-inflammatory and phagocytic markers and more numbers of Tregs in a mouse model of a recombinant mouse hepatitis virus RSA59 infection. Therefore, iNOS may play protective and regulatory roles in this beta-coronavirus infection.
Visual Acuity alterations in heavily impaired Congenital Zika Syndrome (CZS) children
Authors: Baran Luiz C. P. , Lima Diego da S. , Silva Leonardo A. , Tabares Heydi S. , Dias Sarah L. , Zin Andrea Araújo , Moreira Maria Elisabeth Lopes , Costa Marcelo F. , Ventura Dora F. 
Published: February 2022

AbstractWe aim to assess visual acuity (VA) in Congenital Zika Syndrome (CZS)-children to evaluate visual loss. To that end we evaluated 41 CZS- children, from Rio de Janeiro using Teller Acuity Cards. They had Zika virus-infection confirmed by reverse transcription–polymerase chain reaction (RT-PCR) or clinical evaluation. VA below normative values was present in 39/41 (95%). In 10 cases, VA was only marginally below normal; in the remaining 29 cases, VA was more than 0.15 logMAR below the lower limit. There was no relationship between VA and cognitive domain tasks, although there was a relationship between VA and motor domain tasks. Thirty-seven children performed at least one task in the cognitive set, 14 children did not perform any task in the motor set. Children with VA above the lower limit performed better in the cognitive and motor tasks. We concluded that ZIKV- infected children with CSZ were highly VA impaired which correlated with motor performance, but not with cognitive performance. Part of the children had VA within the normal limits and displayed better performance in the cognitive and motor set. Therefore, even if heavily impaired, most children had some degree of visual acuity and visual function and may benefit from visual rehabilitation.
Pilot Plant-Based Lifestyle Medicine Program in an Urban Public Healthcare System: Evaluating Demand and Implementation
Authors: Albert Stephanie L. , Massar Rachel , Kwok Lorraine , Correa Lily , Polito-Moller Krisann , Joshi Shivam , Shah Sapana , McMacken Michelle 
Published: February 2022

ABSTRACTBackgroundLifestyle interventions that optimize nutrition, physical activity, sleep health, social connections, and stress management, and address substance use can reduce cardiometabolic risk. Despite substantial evidence that healthful plant-based diets are beneficial for long-term cardiometabolic health and longevity, uncertainty lies in how to implement plant-based lifestyle programs in traditional clinical settings, especially in safety-net contexts with finite resources.MethodsIn this mixed-methods implementation evaluation of the Plant-Based Lifestyle Medicine Program piloted in a large public healthcare system, we surveyed participants and conducted qualitative interviews and focus groups with stakeholders to assess program demand in the eligible population, and feasibility of implementation within the safety-net setting.FindingsProgram demand was high and exceeded capacity. Participants’ main motivations for joining the program included gaining more control over life, reducing medication, and losing weight. The program team, approach, and resources were successful facilitators. However, the program faced administrative and payor-related challenges within the safety-net setting, and participants reported barriers to access.ConclusionsStakeholders found the program to be valuable, despite challenges in program delivery and access. Findings provide guidance for replication. Future research should focus on randomized controlled trials to assess clinical outcomes as a result of program participation.
HiDiver: A Suite of Methods to Merge Magnetic Resonance Histology, Light Sheet Microscopy, and Complete Brain Delineations
Authors: Johnson G. Allan , Tian Yuqi , Cofer Gary P. , Cook James C. , Gee James C. , Hall Adam , Hornburg Kathryn , Qi Yi , Yeh Fang-Cheng , Wang Nian , White Leonard E. , Williams Robert W. 
Published: February 2022

ABSTRACTWe have developed new imaging and computational workflows to produce accurately aligned multimodal 3D images of the mouse brain that exploit high resolution magnetic resonance histology (MRH) and light sheet microscopy (LSM) with fully rendered 3D reference delineations of brain structures. The suite of methods starts with the acquisition of geometrically accurate (in-skull) brain MRIs using multi-gradient echo (MGRE) and new diffusion tensor imaging (DTI) at an isotropic spatial resolution of 15 μm. Whole brain connectomes are generated using over 100 diffusion weighted images acquired with gradients at uniformly spaced angles. Track density images are generated at a super-resolution of 5 μm. Brains are dissected from the cranium, cleared with SHIELD, stained by immunohistochemistry, and imaged by LSM at 1.8 μm/pixel. LSM channels are registered into the reference MRH space along with the Allen Brain Atlas (ABA) Common Coordinate Framework version 3 (CCFv3). The result is a high-dimensional integrated volume with registration (HiDiver) that has a global alignment accuracy of 10–50 μm. HiDiver enables 3D quantitative and global analyses of cells, circuits, connectomes, and CNS regions of interest (ROIs). Throughput is sufficiently high that HiDiver is now being used in comprehensive quantitative studies of the impact of gene variants and aging on rodent brain cytoarchitecture.
Plant phenotypic plasticity changes pollinator-mediated selection
Authors: Dorey Thomas , Schiestl Florian P. 
Published: February 2022

AbstractMany organisms change their phenotype in response to the environment, a phenomenon called phenotypic plasticity. Yet we hardly understand how such plasticity can affect biotic interactions and the resulting phenotypic selection. Here we use fast cycling Brassica rapa plants in a proof-of-concept experiment in the greenhouse to study the link between plasticity and selection. We detected strong plasticity in morphology, nectar, and floral scent in response to different soil types and aphid herbivory. We found positive selection on nectar and several morphological traits. Bumblebee-mediated selection on a principle component representing plant height, flower number, and flowering time (mPC3) differed depending on soil type and herbivory. For plants growing in richer soil, selection was stronger in the absence of herbivores, whereas for plants growing in poorer soil selection was stronger with herbivory. We showed that bumblebees visited tall plants with many flowers over-proportionally when they were rare (i.e. in plants in poor soil with herbivory), thus causing stronger positive selection on this trait-combination. We suggest that with strong plasticity under most stressful conditions, a shift in pollinator behavior may speed up adaptation to local environmental factors.
NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions
Authors: Vayena Evangelia , Chiappino-Pepe Anush , MohammadiPeyhani Homa , Francioli Yannick , Hadadi Noushin , Ataman Meriç , Hafner Jasmin , Pavlou Stavros , Hatzimanikatis Vassily 
Published: February 2022

AbstractAdvances in medicine and biotechnology rely on the further understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant biochemical knowledge gaps remain uncharacterized. Several approaches have been developed during the past years to identify missing metabolic annotations in genome-scale. However, these approaches suggest missing metabolic reactions within a limited set of already characterized metabolic capabilities. In this study, we introduce NICEgame (Network Integrated Computational Explorer for Gap Annotation of Metabolism), a workflow to characterize missing metabolic capabilities in genome-scale metabolic models using the ATLAS of Biochemistry. NICEgame suggests alternative sets of known and hypothetical reactions to resolve gaps in metabolic networks, assesses their thermodynamic feasibility, and suggests candidate genes and proteins to catalyze the introduced reactions. We use gene essentiality data use to identify metabolic gaps in the latest genome-scale model of Escherichia coli, iML1515. We apply our gap-filling approach and further enhance its genome annotation, by suggesting reactions and putative genes to resolve 46 % of the false negative gene essentiality predictions.
Mechanism of RNA Polymerase I selection by transcription factor UAF
Authors: Baudin Florence , Murciano Brice , Fung Herman K.H. , Fromm Simon A. , Mattei Simone , Mahamid Julia , Müller Christoph W. 
Published: February 2022

SummaryPre-ribosomal RNA is selectively transcribed by RNA Polymerase (Pol) I in eukaryotes. The yeast transcription factor Upstream Activating Factor (UAF) represses Pol II transcription and mediates Pol I preinitiation complex (PIC) formation during the early stages of transcription initiation at the 35S ribosomal RNA gene. To unravel the DNA recognition and Pol I selection mechanisms of UAF, we determined the structure of UAF bound to native promoter DNA and transcription factor TBP. We found that UAF recognizes DNA using a hexameric histone-like scaffold with markedly different interactions than the nucleosome and the histone-fold-rich TFIID. UAF strategically sequesters TBP from DNA and Pol II/III-specific factors, and positions it for Core Factor binding, supporting Pol I recruitment. Our findings therefore reveal the molecular basis of Pol I selection for ribosome biogenesis. As well, they reveal an unexpected potential within the histone fold as a motif for specific protein-DNA interactions inside the cell.
SARS-CoV-2 Nsp1 N-terminal and linker regions as a platform for host translational shutoff
Authors: Graziadei Andrea , Schildhauer Fabian , Spahn Christian , Kraushar Matthew , Rappsilber Juri 
Published: February 2022

AbstractIn the early stages of SARS-CoV-2 infection, non-structural protein 1 (Nsp1) inhibits the innate immune response by inserting its C-terminal helices into the mRNA entry channel of the ribosome and promoting mRNA degradation. Nevertheless, the mechanism by which Nsp1 achieves host translational shutoff while allowing for viral protein synthesis remains elusive. We set out to characterize the interactome of full-length Nsp1 and its topology by crosslinking mass spectrometry in order to investigate the role of the N-terminal domain and linker regions in host translational shutoff. We find that these regions are in contact with 40S proteins lining the mRNA entry channel and detect a novel interaction with the G subunit of the eIF3 complex. The crosslink-derived distance restraints allowed us to derive an integrative model of full-length Nsp1 on the 40S subunit, reporting on the dynamic interface between Nsp1, the ribosome and the eIF3 complex. The significance of the Nsp1-eIF3G interaction is supported by further evidence that Nsp1 predominantly binds to 40-43S complexes. Our results point towards a mechanism by which Nsp1 is preferentially recruited to canonical initiation complexes, leading to subsequent mRNA degradation.
Mechanism of commitment to a mating partner in Saccharomyces cerevisiae
Authors: Jacobs Katherine C. , Gorman Olivia , Lew Daniel J. 
Published: February 2022

AbstractMany cells detect and follow gradients of chemical signals to perform their functions. Yeast cells use gradients of extracellular pheromones to locate mating partners, providing a tractable model to understand how cells decode the spatial information in gradients. To mate, yeast cells must orient polarity toward the mating partner. Polarity sites are mobile, exploring the cell cortex until they reach the proper position, where they stop moving and “commit” to the partner. A simple model to explain commitment posits that a high concentration of pheromone is only detected upon alignment of partner cells’ polarity sites, and causes polarity site movement to stop. Here we explore how yeast cells respond to partners that make different amounts of pheromone. Commitment was surprisingly robust to varying pheromone levels, ruling out the simple model. We also tested whether adaptive pathways were responsible for the robustness of commitment, but our results show that cells lacking those pathways were still able to accommodate changes in pheromone. To explain this robustness, we suggest that the steep pheromone gradients near each mating partner’s polarity site trap the polarity site in place. This mechanism has evolutionary implications because it enables sexual selection for cells making more pheromone.