bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localized patterns and semi-strong interaction, a unifying framework for reaction–diffusion systems
Authors: Al Saadi Fahad , Champneys Alan , Verschueren Nicolas 
Published: August 2021

AbstractSystems of activator–inhibitor reaction–diffusion equations posed on an infinite line are studied using a variety of analytical and numerical methods. A canonical form is considered, which contains all known models with simple cubic autocatalytic nonlinearity and arbitrary constant and linear kinetics. Restricting attention to models that have a unique homogeneous equilibrium, this class includes the classical Schnakenberg and Brusselator models, as well as other systems proposed in the literature to model morphogenesis. Such models are known to feature Turing instability, when activator diffuses more slowly than inhibitor, leading to stable spatially periodic patterns. Conversely in the limit of small feed rates, semi-strong interaction asymptotic analysis shows existence of isolated spike-like patterns. This paper describes the broad bifurcation structures that connect these two regimes. A certain universal two-parameter state diagram is revealed in which the Turing bifurcation becomes sub-critical, leading to the onset of homoclinic snaking. This regime then morphs into the spike regime, with the outer-fold being predicted by the semi-strong asymptotics. A rescaling of parameters and field concentrations shows how this state diagram can be studied independently of the diffusion rates. Temporal dynamics is found to strongly depend on the diffusion ratio though. A Hopf bifurcation occurs along the branch of stable spikes, which is subcritical for small diffusion ratio, leading to collapse to the homogeneous state. As the diffusion ratio increases, this bifurcation typically becomes supercritical and interacts with the homoclinic snaking and also with a supercritical homogeneous Hopf bifurcation, leading to complex spatio-temporal dynamics. The details are worked out for a number of different models that fit the theory using a mixture of weakly nonlinear analysis, semi-strong asymptotics and different numerical continuation algorithms.
SOCS: negative regulators of cytokine signaling for immune tolerance
Authors: Yoshimura Akihiko , Ito Minako , Mise-Omata Setsuko , Ando Makoto 
Published: August 2021

Abstract
Cytokines are important intercellular communication tools for immunity. Many cytokines promote gene transcription and proliferation through the JAK/STAT (Janus kinase/signal transducers and activators of transcription) and the Ras/ERK (GDP/GTP-binding rat sarcoma protein/extracellular signal-regulated kinase) pathways, and these signaling pathways are tightly regulated. The SOCS (suppressor of cytokine signaling) family members are representative negative regulators of JAK/STAT-mediated cytokine signaling and regulate the differentiation and function of T cells, thus being involved in immune tolerance. Human genetic analysis has shown that SOCS family members are strongly associated with autoimmune diseases, allergy and tumorigenesis. SOCS family proteins also function as immune-checkpoint molecules that contribute to the unresponsiveness of T cells to cytokines.
Osteoimmunology as an intrinsic part of immunology
Authors: Takayanagi Hiroshi 
Published: August 2021

Abstract
Osteoimmunology has emerged as a field linking immunology and bone biology, but it has yet to be recognized as belonging to mainstream immunology. However, the extent of the research fields immunology actually covers has been enormously widened, and it is now ready to include such an interdisciplinary subject. One of the most obvious examples of an interaction between the immune and bone systems is the pathogenesis of rheumatoid arthritis, where bone resorption is increased by the autoimmune response. Moreover, the regulation of the immune system by bone cells has been clearly demonstrated by the finding that osteoprogenitor cells contribute to hematopoietic stem cell maintenance as well as the suppression of hematopoietic malignancy. Thus, the bidirectional dialogue has been established and inevitably will lead to the union of bone and immunity. Here, I summarize the history and concept of osteoimmunology, providing a perspective on the future of immunology.
Express check-in: developing a personal health record for patients admitted to hospital with medical emergencies: a mixed-method feasibility study
Authors: Subbe Christian P , Tomos Hawys , Jones Gwenlli Mai , Barach Paul 
Published: August 2021

AbstractBackgroundPatient participation is increasingly recognized as a key component in the redesign of healthcare processes and is advocated as a means to improve patient safety.ObjectiveTo explore the usage of participatory engagement in patient-created and co-designed medical records for emergency admission to the hospital.Methodsdesign: prospective iterative development and feasibility testing of personal health records; setting: an acute medical unit in a university-affiliated hospital; participants: patients admitted to hospital for medical emergencies; interventions: we used a design-led development of personal health record prototypes and feasibility testing of records completed by patients during the process of emergency admission. ‘Express-check-in’ records contained items of social history, screening questions for sepsis and acute kidney injury in addition to the patients’ ideas, concerns and expectations; main outcome measures: the outcome metrics focused on feasibility and a selection of quality domains, namely effectiveness of recording relevant history, time efficiency of the documentation process, patient-centredness of resulting records and staff and patient feedback. The incidence of sepsis and acute kidney injury were used as surrogate measures for assessing the safety impact.ResultsThe medical record prototypes were developed in an iterative fashion and tested with 100 patients, in which 39 patients were 70 or older and 25 patients were classified as clinically frail. Ninety-six per cent of the data items were completed by patients with no or minimal help from healthcare professionals. The completeness of these patient records was superior to that of the corresponding medical records in that they contained deeply held beliefs and fears, whereas concerns and expectations recorded by patients were only mirrored in a small proportion of the formal clinical records. The sepsis self-screening tool identified 68% of patients requiring treatment with antibiotics. The intervention was feasible, independent of the level of formal education and effective in frail and elderly patients with support from family and staff. The prototyped records were well received and felt to be practical by patients and staff. The staff indicated that reading the patients’ documentation led to significant changes in their clinical management.ConclusionsMedical record accessibility to patients during hospital care contributes to the co-management of personal healthcare and might add critical information over and above the records compiled by healthcare professionals.
Novel tigecycline resistance gene cluster tnfxB3-tmexCD3-toprJ1b in Proteus spp. and Pseudomonas aeruginosa, co-existing with tet(X6) on an SXT/R391 integrative and conjugative element
Authors: Wang Cheng-Zhen , Gao Xun , Lv Lu-Chao , Cai Zhong-Peng , Yang Jun , Liu Jian-Hua 
Published: August 2021

Abstract

Objectives
To characterize a novel MDR efflux pump gene cluster tnfxB3-tmexCD3-toprJ1b carried by Proteus spp. and Pseudomonas aeruginosa strains from chickens.

Methods
Antimicrobial susceptibility testing, conjugation and WGS were performed to characterize tnfxB3-tmexCD3-toprJ1b-positive isolates. Cloning and reverse transcription-quantitative PCR were performed to investigate the function of tnfxB3-tmexCD3-toprJ1b.

Results
The WGS data revealed that a novel efflux pump gene cluster, tnfxB3-tmexCD3-toprJ1b, was identified on the chromosome of the Proteus cibarius strain SDQ8C180-2T, where an SXT/R391-family integrative and conjugative element (ICE) was found to co-carry tet(X6) and tnfxB3-tmexCD3-toprJ1b. Further retrospective analysis found two other tnfxB3-tmexCD3-toprJ1b variants in a Proteus mirabilis isolate and a P. aeruginosa isolate, respectively. tmexCD3-toprJ1b and its variants increased the MICs of tigecycline (8-fold) and other antibiotics (2–8-fold) in Escherichia coli host strains. The TNfxB3 protein down-regulated the expression of the tmexCD3-toprJ1b operon. Moreover, genetic-context analyses showed that tnfxB3-tmexCD3-toprJ1b together with adjacent integrase genes appeared to compose a transferable module ‘int1-like+int2-like+hp1+hp2+ISCfr1+tnfxB3-tmexCD3-toprJ1b’, which was inserted into the umuC-like gene of this ICE. Further analysis of the tnfxB3-tmexCD3-toprJ1b-harbouring sequences deposited in GenBank revealed similar transferable modules inserted into umuC-like genes in plasmids or chromosomes of Klebsiella pneumoniae, Pseudomonas spp. and Aeromonas spp., implying that these modules could be transferred across different bacterial species.

Conclusions
To the best of our knowledge, this is the first identification of a novel tigecycline gene cluster, tmexCD3-toprJ1b, which co-exists with tet(X6) within an ICE. More attention should be paid to the co-transfer of these two tigecycline resistance determinants via an ICE to other Gram-negative bacteria.
Retrospective Evaluation of the Antibody Prevalence in Epilepsy and Encephalopathy (APE2) Score
Authors: Poore Brad , Hamilton Robert , Kelliher Michael T , Mahmood Sundis , Mindiola-Romero Andres E , Richards Ryland , Motanagh Samaneh , Cervinski Mark A , Nerenz Robert D 
Published: August 2021

Abstract

Background
Autoimmune encephalitis (AE) is a rare collection of disorders that present with a diverse and often nebulous set of clinical symptoms. Indiscriminate use of multi-antibody panels decreases their overall utility and predictive value. Application of a standardized scoring system may help reduce the number of specimens that generate misleading or uninformative results.

Methods
The results of autoimmune encephalopathy, epilepsy, or dementia autoantibody panels performed on serum (n = 251) or cerebrospinal fluid (CSF) (n = 235) specimens from October 9th, 2016 to October 11th, 2019 were collected. Retrospective chart review was performed to calculate the Antibody Prevalence in Epilepsy and Encephalopathy (APE2) score for patients with an antibody above the assay-specific reference interval and to classify results as true or false positive.

Results
Of the 486 specimens, 60 (12.3%) generated positive results for any AE antibody (6 CSF and 54 serum). After removing 2 duplicate specimens collected from a single patient, 10 of the remaining 58 were determined to be true positives and 8 contained neural-specific antibodies. Application of the APE2 score revealed that 89% of all true positives and 86% of specimens with neural-specific antibodies had a score ≥4. In contrast, 76% of false positives, 74% of clinically nonspecific antibodies, and 85% of the negative specimens had an APE2 score &lt;4.

Conclusion
The APE2 score can improve the diagnostic utility of autoimmune encephalopathy evaluation panels.
Achievement of the minimal clinically important difference following open proximal hamstring repair
Authors: Lawton Cort D , Sullivan Spencer W , Hancock Kyle J , Burger Joost A , Nawabi Danyal H , Kelly Bryan T , Ranawat Anil S , Nwachukwu Benedict U 
Published: August 2021

ABSTRACT
There is a paucity of literature on patient-reported outcome measures (PROMs) following proximal hamstring repair beyond return to play, patient satisfaction and pain improvement. The minimal clinically important difference (MCID) defines the minimum degree of quantifiable improvement that a patient can perceive, but the MCID and predictors of this measure have not been defined for this patient population. This study aimed to define the MCID and determine the efficacy of open proximal hamstring repair through achievement of MCID and identify characteristics predictive of achieving MCID. A retrospective cohort review of an institutional hip registry was conducted, analyzing the modified Harris Hip Score (mHHS) and International Hip Outcome Tool (iHOT-33). MCID was calculated using a distribution-based method. Demographic and clinical variables predictive of achieving MCID were analyzed using univariable and multivariate logistic regression analyses. Thirty-nine patients who underwent open proximal hamstring repair were included. The mean patient age was 48.5 ± 12.4 years, with a mean follow-up of 37.1 ± 28 months. The MCID was determined for each PROM (mHHS—11.8; iHOT-33—12.6). A high percentage of patients achieved MCID for both PROMs (mHHS—85.7%; iHOT-33—91.4%). Univariate logistical regression demonstrated increased age (P = 0.163), increased body mass index (BMI; P = 0.072), requirement for inpatient admission (P = 0.088) and pre-operative iHOT-33 (P = 0.104) trended towards clinically significant predictors of not achieving MCID. A high percentage of patients achieved MCID while age, BMI, inpatient admission and pre-operative iHOT-33 appear to influence the achievement of clinically significant outcome in patients undergoing open proximal hamstring repair.
Spatio-temporal modelling of the effect of selected environmental and land-use factors on acid grassland vegetation
Authors: Damgaard Christian 
Published: August 2021

AbstractAcid grasslands are threatened both by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to understand and quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of acid grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. The important sources of measurement and sampling uncertainties have been included using a hierarchical model structure. Furthermore, uncertainties associated with the measurement and sampling are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. Generally, increasing atmospheric nitrogen deposition led to more grass-dominated acid grassland habitats at the expense of the cover of forbs. Sandy soils were relatively more acidic, and the effects of soil type on the vegetation include both direct effects of soil type and indirect effects mediated by the effect of soil type on soil pH. Both soil type and soil pH affected the vegetation of acid grasslands. Even though only a relatively small proportion of the temporal variation in cover was explained by the model, it would still be useful to quantify the uncertainties when using the model for generating local ecological predictions and adaptive management plans.
UAVs as remote sensing platforms in plant ecology: review of applications and challenges
Authors: Sun Zhongyu , Wang Xiaonian , Wang Zhihui , Yang Long , Xie Yichun , Huang Yuhui 
Published: August 2021

AbstractAimsUnmanned aerial vehicles (UAVs), i.e. drones, have recently emerged as cost-effective and flexible tools for acquiring remote sensing data with fine spatial and temporal resolution. It provides a new method and opportunity for plant ecologists to study issues from individual to regional scales. However, as a new method, UAVs remote sensing applications in plant ecology are still challenged. The needs of plant ecology research and the application development of UAVs remote sensing should be better integrated.MethodsThis report provides a comprehensive review of UAV-based remote sensing applications in plant ecology to synthesize prospects of applying drones to advance plant ecology research.Important FindingsOf the 400 references, 59% were published in remote sensing journals rather than in plant ecology journals, reflecting a substantial gap between the interests of remote sensing experts and plant ecologists. Most of the studies focused on UAV remote sensing’s technical aspects, such as data processing and remote sensing inversion, with little attention on answering ecological questions. There were 61% of studies involved community-scale research. RGB and multispectral cameras were the most used sensors (75%). More ecologically meaningful parameters can be extracted from UAV data to better understand the canopy surface irregularity and community heterogeneity, identify geometrical characteristics of canopy gaps and construct canopy chemical assemblies from living vegetation volumes. More cooperation between plant ecologists and remote sensing experts is needed to promote UAV remote sensing in advancing plant ecology research.
COVID-19 Vaccine Distribution: Bolstering the Air Force Immunizations Model
Authors: Adams Karla E , Smith Derek , White Kevin 
Published: August 2021

ABSTRACT
From its emergence and declaration as a worldwide pandemic, coronavirus disease-2019 (COVID-19) has been associated with significant medical and logistical challenges. Initial obstacles ranged from the need to develop testing platforms to the determination of effective treatments to decrease the significant morbidity and mortality associated with the disease. Due to significant scientific breakthroughs, the most recent pressing challenge has been the distribution of vaccines against severe acute respiratory syndrome coronavirus 2 to prevent the spread of the infection across the world. Historically, the U.S. Military has been involved in immunizations delivery to prevent disease among its troops. This experience has led to the establishment of programs designed to distribute safe vaccinations to service members and beneficiaries. It is upon this infrastructure that the Air Force (AF) medical community was thrust to devise and execute COVID-19 vaccine delivery implementation across all military treatment facilities. In the AF, specialty trained allergist and immunologists provide the technical expertise for the establishment and execution of the AF immunizations program. These medical professionals have the proficiency, knowledge, and experience to run efficient mass immunization events in order to provide vaccines in a safe and rapid environment. Despite this, significant challenges attributable to the variable and novel nature of COVID-19 vaccine logistical requirements have led to unanswered questions and debate that needed resolution before and during the launch of this program. Here we describe the process for establishing a mass vaccination program for COVID-19 vaccine delivery and our experience-based problem solving approach at a large AF military treatment facility.
Eumops floridanus (Chiroptera: Molossidae)
Authors: Vannatta Jessica M , Gore Jeffery A , Mathis Verity L , Carver Brian D 
Published: August 2021

Abstract
Eumops floridanus (Allen, 1932) is a molossid commonly called the Florida bonneted bat or the Florida mastiff bat. Eumops floridanus is the largest species of bat in Florida and is one of 16 species in the genus Eumops. With one of the smallest distributions of any bat in the United States, it is endemic to southern peninsular Florida where it roosts in cavities of live and dead trees and man-made structures. Eumops floridanus was formerly classified as a subspecies of E. glaucinus but has been elevated to species level based on morphology. Due primarily to its restricted distribution, small population size, and the continued loss of habitat, E. floridanus is federally listed as “Endangered” (EN) by the United States Fish and Wildlife Service.
Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption
Authors: Abrahams Liam , Savisaar Rosina , Mordstein Christine , Young Bethan , Kudla Grzegorz , Hurst Laurence D 
Published: August 2021

AbstractTranscripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5–30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8–20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.
Unveiling mRNP composition by fluorescence correlation and cross-correlation spectroscopy using cell lysates
Authors: Mateu-Regué Àngels , Christiansen Jan , Bagger Frederik Otzen , Hellriegel Christian , Nielsen Finn Cilius 
Published: August 2021

Abstract
Understanding the mRNA life cycle requires information about the dynamics and macromolecular composition and stoichiometry of mRNPs. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are appealing technologies to study these macromolecular structures because they have single molecule sensitivity and readily provide information about their molecular composition and dynamics. Here, we demonstrate how FCS can be exploited to study cytoplasmic mRNPs with high accuracy and reproducibility in cell lysates. Cellular lysates not only recapitulate data from live cells but provide improved readings and allow investigation of single mRNP analysis under particular conditions or following enzymatic treatments. Moreover, FCCS employing minute amounts of cells closely corroborated previously reported RNA dependent interactions and provided estimates of the relative overlap between factors in the mRNPs, thus depicting their heterogeneity. The described lysate-based FCS and FCCS analysis may not only complement current biochemical approaches but also provide novel opportunities for the quantitative analysis of the molecular composition and dynamics of single mRNPs.
NgAgo possesses guided DNA nicking activity
Authors: Lee Kok Zhi , Mechikoff Michael A , Kikla Archana , Liu Arren , Pandolfi Paula , Fitzgerald Kevin , Gimble Frederick S , Solomon Kevin V 
Published: August 2021

Abstract
Prokaryotic Argonautes (pAgos) have been proposed as more flexible tools for gene-editing as they do not require sequence motifs adjacent to their targets for function, unlike popular CRISPR/Cas systems. One promising pAgo candidate, from the halophilic archaeon Natronobacterium gregoryi (NgAgo), has been the subject of debate regarding its potential in eukaryotic systems. Here, we revisit this enzyme and characterize its function in prokaryotes. NgAgo expresses poorly in non-halophilic hosts with most of the protein being insoluble and inactive even after refolding. However, we report that the soluble fraction does indeed act as a nicking DNA endonuclease. NgAgo shares canonical domains with other catalytically active pAgos but also contains a previously unrecognized single-stranded DNA binding domain (repA). Both repA and the canonical PIWI domains participate in DNA cleavage activities of NgAgo. NgAgo can be programmed with guides to nick targeted DNA in Escherichia coli and in vitro 1 nt outside the 3′ end of the guide sequence. We also found that these endonuclease activities are essential for enhanced NgAgo-guided homologous recombination, or gene-editing, in E. coli. Collectively, our results demonstrate the potential of NgAgo for gene-editing and provide new insight into seemingly contradictory reports.