bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-CMV Guillain-Barré Syndrome with Anti-GM2 Antibodies: Two Cases and a Review of the Literature
Authors: Manaud Alice , Geraudie Amandine , Viguier Agnès , Mengelle Catherine , Fortenfant Françoise , Baudou Eloïse , Cheuret Emmanuel 
Published: June 2022

Abstract
Introduction Guillain-Barré syndrome (GBS) is an acute post-infectious inflammatory polyneuropathy of ubiquitous distribution. Cytomegalovirus (CMV) is the virus that is most frequently involved. All ages are affected but rare pediatric cases seem to show some distinctive features in terms of specificity and severity. Specific antibodies that target the peripheral nervous system have been identified in several forms of GBS in adults, such as anti-GM2 ganglioside antibodies in post-CMV GBS, which in most instances present as demyelinating polyneuropathies, with a more favorable progression and fewer complications.
Materials and Methods This is a retrospective report on two cases of post-CMV GBS with a demyelinating disorder and positive for anti-GM2 IgM. The review of the literature examines five other cases of children with post-CMV GBS with anti-GM2 IgM.
Results In terms of progression, our two cases of post-CMV GBS with a demyelinating disorder and anti-GM2 IgM are similar to the five other cases described in the literature. The CMV infection was asymptomatic or paucisymptomatic and involved girls (6/7), often presenting severe motor forms with frequent loss of the ability to walk (4/6), facial involvement (⅗), little respiratory involvement (⅙), and favorable progression with adapted treatment.
Conclusion Post-CMV GBS with anti-GM2 IgM is a specific clinical spectrum that seems to affect children as it affects adults with a predominance among females, demyelination, and severe motor involvement, but a good prognosis. On the other hand, unlike adults, the use of assisted ventilation does not seem to be more frequent.
The victimisation of farms in Ireland: fear of crime, social isolation and crime prevention
Authors: O’Brien Margueriete , Windle James 
Published: June 2022

AbstractThis paper explores farmer’s experiences of crime and their attitudes towards crime prevention in one rural hinterland. Farmer’s attitudes about safety and crime present a dichotomy: fear of victimisation was relatively high, yet few participants reported having been victimised, and there was a perception that agricultural crime was high in Ireland but low in their locality. Feelings of insecurity were partly influenced by the closure of rural Garda stations and uneven distribution of information technology. Participants were most concerned with theft of small machinery, violent coercion connected to fraudulent work, illegal dumping and trespassing, rather than thefts of expensive machinery and livestock. Participants reported being unable to afford some crime prevention measures and/or having insufficient time to implement them. The paper concludes by highlighting the relevance of Farrell and Tilley’s (2020) concept of elegant security to farm crime and discussing the role of community policing.
New surprises from tree vascular systems. A commentary on: ‘Seasonal patterns of increases in stem girth, vessel development and hydraulic function in deciduous tree species’
Authors: Groover Andrew 
Published: June 2022

This article comments on:Jessica Valdovinos-Ayala, Catherine Robles, Jaycie C. Fickle, Gonzalo Pérez-de-Lis, R. Brandon Pratt and Anna L. Jacobsen, Seasonal patterns of increases in stem girth, vessel development, and hydraulic function in deciduous tree species, Annals of Botany, Volume 130, Issue 3, 1 September 2022, Pages 355–365 https://doi.org/10.1093/aob/mcac032
Analytical Considerations in Deriving 99th Percentile Upper Reference Limits for High-Sensitivity Cardiac Troponin Assays: Educational Recommendations from the IFCC Committee on Clinical Application of Cardiac Bio-Markers
Authors: Aakre Kristin M , Saenger Amy K , Body Rick , Collinson Paul , Hammarsten Ola , Jaffe Allan S , Kavsak Pete , Omland Torbjørn , Ordonez-Lianos Jordi , Apple Fred S 
Published: June 2022

Abstract
The International Federation of Clinical Chemistry Committee on Clinical Application of Cardiac Bio-Markers provides evidence-based educational documents to facilitate uniform interpretation and utilization of cardiac biomarkers in clinical laboratories and practice. The committee’s goals are to improve the understanding of certain key analytical and clinical aspects of cardiac biomarkers and how these may interplay in clinical practice. Measurement of high-sensitivity cardiac troponin (hs-cTn) assays is a cornerstone in the clinical evaluation of patients with symptoms and/or signs of acute cardiac ischemia. To define myocardial infarction, the Universal Definition of Myocardial Infarction requires patients who manifest with features suggestive of acute myocardial ischemia to have at least one cTn concentration above the sex-specific 99th percentile upper reference limit (URL) for hs-cTn assays and a dynamic pattern of cTn concentrations to fulfill the diagnostic criteria for MI. This special report provides an overview of how hs-cTn 99th percentile URLs should be established, including recommendations about prescreening and the number of individuals required in the reference cohort, how statistical analysis should be conducted, optimal preanalytical and analytical protocols, and analytical/biological interferences or confounds that can affect accurate determination of the 99th percentile URLs. This document also provides guidance and solutions to many of the issues posed.
Recent Developments in Mutation Enrichment and Detection Technologies
Authors: Darbeheshti Farzaneh , Yu Fangyan , Ahmed Farzana , Adalsteinsson Viktor A , Makrigiorgos G Mike 
Published: June 2022

Abstract

Background
Presence of excess unaltered, wild-type DNA (wtDNA) providing information of little clinical value may often mask low-level mutations containing important diagnostic or therapeutic clues. This is a recurring hurdle in biotechnology and medicine, including cancer, prenatal diagnosis, infectious diseases, and organ transplantation. Mutation enrichment techniques that allow reduction of unwanted DNA to enable the detection of low-level mutations have emerged since the early 1990s. They are continuously being refined and updated with new technologies. The burgeoning interest in liquid biopsies for residual cancer monitoring, detection of resistance to therapy, and early cancer detection has driven an expanded interest in new and improved methodologies for practical and effective mutation enrichment and detection of low-level mutations of clinical relevance.

Content
Newly developed mutation enrichment technologies are described and grouped according to the main principle of operation, PCR-blocking technologies, enzymatic methods, and physicochemical approaches. Special emphasis is given to technologies enabling pre-PCR blockage of wtDNA to bypass PCR errors [nuclease-assisted minor-allele enrichment assay with overlapping probes (NaME-PrO) and UV-mediated cross-linking minor allele enrichment (UVME)] or providing high multiplexity followed by next-generation sequencing [Minor allele enriched sequencing through recognition oligonucleotides (MAESTRO)].

Summary
This review summarizes technological developments in rare mutation enrichment over the last 12 years, complementing pre-2010 reviews on this topic. The expanding field of liquid biopsy calls for improved limits of detection (LOD) and highly parallel applications, along with the traditional requirements for accuracy, speed, and cost-effectiveness. The current technologies are reviewed with regards to these new requirements.
Major adverse cardiovascular events after diagnosis of myocardial injury and types 1 and 2 myocardial infarction
Authors: Knott Jonathan D , Ola Olatunde , De Michieli Laura , Akula Ashok , Mehta Ramila A , Dworak Marshall , Crockford Erika , Lobo Ronstan , Rastas Nicholas , Karturi Swetha , Wohlrab Scott , Hodge David O , Grube Eric , Tak Tahir , Cagin Charles , Gulati Rajiv , Jaffe Allan S , Sandoval Yader 
Published: June 2022

Abstract

Aims
Limited US outcome data exist among patients with myocardial injury and types 1 and 2 myocardial infarction (MI) evaluated with high-sensitivity cardiac troponin (hs-cTn).

Methods and results
This is an observational US cohort study of emergency department (ED) patients undergoing hs-cTnT measurement. Cases with ≥1 hs-cTnT increase &gt;99th percentile were adjudicated following the Fourth Universal Definition of MI. Post-discharge major adverse cardiovascular events (MACE) included death, MI, heart failure (HF) hospitalization, stroke or transient ischaemic attack, and new-onset atrial fibrillation or flutter during 2 years follow-up. Among 2002 patients, 857 (43%) had ≥1 hs-cTnT &gt;99th percentile. Among these, 702 (81.9%) had myocardial injury, 64 (7.5%) had type 1 MI, and 91 (10.6%) had type 2 MI. Compared with patients without myocardial injury, type 2 MI [8.4 vs. 50%; adjusted hazard ratio (HR) 2.31, 95% confidence interval (CI) 1.49–3.58] and myocardial injury (8.4 vs. 47%; adjusted HR 3.13, 95% CI 2.39–4.09) had a higher risk of MACE, in large part because of death and HF hospitalizations. Compared with patients with type 1 MI, type 2 MI (23 vs. 50%; adjusted HR 2.24; 95% CI 1.23–4.10) and myocardial injury (23 vs. 47%; adjusted HR 2.02; 95% CI 1.20–3.40) also have a higher risk of MACE.

Conclusion
Among unselected US ED patients undergoing hs-cTnT measurement, most increases are due to myocardial injury, and type 2 MI is more frequent than type 1 MI. Patients with myocardial injury and type 2 MI have morbid outcomes, in large part due to death and HF.
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks
Authors: Johnson Connah G M , Fletcher Alexander G , Soyer Orkun S 
Published: June 2022

Abstract

Background
Spatial organization plays an important role in the function of many biological systems, from cell fate specification in animal development to multistep metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the in silico testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling.

Conclusions
Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chaste’s existing capabilities. In particular, ChemChaste enables (i) simulation of an arbitrary number of spatially diffusing chemicals, (ii) spatially heterogeneous chemical diffusion coefficients, and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chaste’s core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modeling bulk chemical reactions and their coupling with intracellular reactions.

Availability and implementation
ChemChaste version 1.0 is a free, open-source C++ library, available via GitHub at https://github.com/OSS-Lab/ChemChaste under the BSD license, on the Zenodo archive at zendodo doi, as well as on BioTools (biotools:chemchaste) and SciCrunch (RRID:SCR022208) databases.
Agricultural plant cataloging and establishment of a data framework from UAV-based crop images by computer vision
Authors: Günder Maurice , Ispizua Yamati Facundo R , Kierdorf Jana , Roscher Ribana , Mahlein Anne-Katrin , Bauckhage Christian 
Published: June 2022

Abstract

Background
Unmanned aerial vehicle (UAV)–based image retrieval in modern agriculture enables gathering large amounts of spatially referenced crop image data. In large-scale experiments, however, UAV images suffer from containing a multitudinous amount of crops in a complex canopy architecture. Especially for the observation of temporal effects, this complicates the recognition of individual plants over several images and the extraction of relevant information tremendously.

Results
In this work, we present a hands-on workflow for the automatized temporal and spatial identification and individualization of crop images from UAVs abbreviated as “cataloging” based on comprehensible computer vision methods. We evaluate the workflow on 2 real-world datasets. One dataset is recorded for observation of Cercospora leaf spot—a fungal disease—in sugar beet over an entire growing cycle. The other one deals with harvest prediction of cauliflower plants. The plant catalog is utilized for the extraction of single plant images seen over multiple time points. This gathers a large-scale spatiotemporal image dataset that in turn can be applied to train further machine learning models including various data layers.

Conclusion
The presented approach improves analysis and interpretation of UAV data in agriculture significantly. By validation with some reference data, our method shows an accuracy that is similar to more complex deep learning–based recognition techniques. Our workflow is able to automatize plant cataloging and training image extraction, especially for large datasets.
Interactions between demersal fish body condition and density during the regime shift of the Gulf of Lions
Authors: Bensebaini C M , Certain G , Billet N , Jadaud A , Gourguet S , Hattab T , Fromentin J M 
Published: June 2022

Abstract
Environmentally driven changes in small pelagic fish condition and size have been observed in the Gulf of Lions (GOL) since 2008, leading to a significant fishery crisis. However, the effect of changes in environment and/or in the small pelagic community on the demersal community remain unknown. For the first time, this study examines the body condition (bc) and population density of 22 demersal species since 1994, using dynamic factor analysis (DFA). Most (but not all) of demersal species have shown a common shift between 2006 and 2009, which is synchronous with that observed in small pelagic species and the environmental conditions in the GOL. It had been concluded that the environmentally driven changes detected in the pelagic fish community also affected the demersal fish community, but with less drastic and lasting consequences. As the DFA revealed that the bc displayed important variations for several species, notably hake (Merlucius merluccius), the interaction between the bc and population density was investigated using the Multivariate Autoregressive (MAR) model on hake population at three life stages (recruits, juveniles, and adults). Results showed that adult bc, while negatively affected by density, had a positive effect on recruitment. So hake bc could have affected population dynamics by promoting higher recruitment at low densities. Further work is needed to ascertain whether such effects exist in other demersal species.
Offshore wind farms affect the spatial distribution pattern of plaice Pleuronectes platessa at both the turbine and wind farm scale
Authors: Buyse Jolien , Hostens Kris , Degraer Steven , De Backer Annelies 
Published: June 2022

Abstract
We investigated how the distribution of plaice Pleuronectes platessa, a typical soft-sediment fish species, has been affected by the introduction of hard substrate [turbines and scour protection layer (SPL)] at both turbine and wind farm scale in two Belgian offshore wind farms (OWFs). Diving transects (40 m) at 11 monopiles revealed four times higher plaice abundances on the sandy patches of the SPL (average radius 16.5 m) compared to the surrounding sand. We suggest that the configuration of the SPL, i.e. an open rock field, offering increased food and shelter opportunities, with sandy patches in between, facilitating the natural burrowing behaviour of plaice, forms the basis for the increased plaice abundances at the turbine scale. At the wind farm scale, beam trawl catches in between the turbines and in reference zones revealed significantly increased plaice abundances in one OWF, which suggests that wind farms can act as refuge areas for plaice, at least under specific conditions. Differences in environmental conditions, turbine foundation type, and surrounding fishing pressure may explain the equivocal findings between both OWFs, whereas low statistical power could have hampered the detection of general refuge effects. Next to the integration of different spatial scales (turbine/wind farm) within one study, longer-term monitoring and including extra life history parameters (e.g. length and sex ratio) might enhance the detectability of potential refuge effects.
A Comparison of Lyme Serological Testing Platforms with a Panel of Clinically Characterized Samples from Various Stages of Lyme Disease
Authors: Pratt George W , Platt Mihae , Velez Ana , Rao Lokinendi V 
Published: June 2022

Abstract

Background
In 2019, the CDC updated serology testing guidelines for Lyme disease diagnosis to include alternative modified two-tiered testing that replaces the western blots of standard testing with an additional ELISA. Antibody-capture serological assays have also been used as an aid for Lyme diagnosis. A panel of clinically characterized samples from the CDC was tested to compare modified two-tiered testing to the standard two-tiered algorithm and an antibody capture immunoassay.

Methods
A CDC panel of 92 samples comprised a range of samples including early Lyme, Lyme neuroborreliosis, Lyme arthritis, infections by other pathogens, and healthy controls. The panel was tested on a standard two-tiered platform by the CDC, the ZEUS Borrelia Test System for modified two-tiered testing, and a lab-developed antibody-capture serological assay. Sensitivity and specificity results from each assay were compared to determine significance.

Results
The antibody-capture assay demonstrated increased sensitivity but decreased specificity compared to the modified and standard two-tiered platforms. There was no statistical difference found between the modified and standard two-tiered platforms.

Conclusions
Improved sensitivity of antibody-capture when testing early Lyme disease samples is offset by decreased specificity, especially with syphilis-positive samples. Modified two-tiered testing is similar to standard two-tiered methods while also being more scalable and simpler to interpret.
Loss of PROTEIN TARGETING TO STARCH 2 has variable effects on starch synthesis across organs and species
Authors: Watson-Lazowski Alexander , Raven Emma , Feike Doreen , Hill Lionel , Barclay J Elaine , Smith Alison M , Seung David 
Published: June 2022

Abstract
Recent work has identified several proteins involved in starch granule initiation, the first step of starch synthesis. However, the degree of conservation in the granule initiation process remains poorly understood, especially among grass species differing in patterns of carbohydrate turnover in leaves, and granule morphology in the endosperm. We therefore compared mutant phenotypes of Hordeum vulgare (barley), Triticum turgidum (durum wheat), and Brachypodium distachyon defective in PROTEIN TARGETING TO STARCH 2 (PTST2), a key granule initiation protein. We report striking differences across species and organs. Loss of PTST2 from leaves resulted in fewer, larger starch granules per chloroplast and normal starch content in wheat, fewer granules per chloroplast and lower starch content in barley, and almost complete loss of starch in Brachypodium. The loss of starch in Brachypodium leaves was accompanied by high levels of ADP-glucose and detrimental effects on growth and physiology. Additionally, we found that loss of PTST2 increased granule initiation in Brachypodium amyloplasts, resulting in abnormal compound granule formation throughout the seed. These findings suggest that the importance of PTST2 varies greatly with the genetic and developmental background and inform the extent to which the gene can be targeted to improve starch in crops.
Inconsistent Reporting of Adverse Life Events Is Predicted by Current Internalizing Distress Among Military Service Members
Authors: Martin-Wagar Caitlin A , Marquardt Craig A , Liu Yuchen , Arbisi Paul A , Erbes Christopher R , Polusny Melissa A 
Published: June 2022

ABSTRACT

Introduction
Accurate measurement of adverse life events is critical for understanding the effects of stressors on health outcomes. However, much of this research uses cross-sectional designs and self-report years after the events take place. The reliability of this retrospective reporting and the individual difference factors associated with inconsistent recall over time are not frequently addressed, especially among military service members.

Materials and Methods
A longitudinal cohort of National Guard service members (n = 801) completed the Deployment Risk and Resilience Inventory-2 Prior Stressors scale and several measures of general well-being, including anxious depressive symptomatology, personal functioning, perceived social support, and overall health at two time points (before and after completion of basic combat training; median 11-month interval).

Results
Consistency in reporting the life event items ranged from 69.5% to 99.7%, with an overall Cohen’s kappa coefficient of 0.215 for the scale, indicating minimal agreement. Lower well-being scores at Time 1 independently predicted yes-to-no changes in responding, whereas lower well-being scores at Time 2 independently predicted no-to-yes changes in responding. Follow-up mediations were conducted using study measures available only at Time 2. For all study measures, Time 2 well-being independently predicted changes from no-to-yes responding by way of indirect effects through self-reported non-specific internalizing distress and arousal.

Conclusions
These findings highlight the confounding effects of fluctuations in current emotional distress on past stressor recall. There is a need for additional caution regarding the use of retrospective self-report of adverse life events in research and clinical practice and greater consideration of current psychological distress at the time of measurement completion.
Unintended Consequences of Plant Domestication
Authors: Singh Jugpreet , van der Knaap Esther 
Published: June 2022

Abstract
Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.