bluuebunny/crossref_metadata_2025_split huggingface dataset:
CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation
Authors: Martin Galen T , Seymour Danelle K , Gaut Brandon S 
Published: June 2021

Abstract
Methylated CHH (mCHH) islands are peaks of CHH methylation that occur primarily upstream to genes. These regions are actively targeted by the methylation machinery, occur at boundaries between heterochromatin and euchromatin, and tend to be near highly expressed genes. Here we took an evolutionary perspective by studying upstream mCHH islands across a sample of eight grass species. Using a statistical approach to define mCHH islands as regions that differ from genome-wide background CHH methylation levels, we demonstrated that mCHH islands are common and associate with 39% of genes, on average. We hypothesized that islands should be more frequent in genomes of large size, because they have more heterochromatin and hence more need for defined boundaries. We found, however, that smaller genomes tended to have a higher proportion of genes associated with 5′ mCHH islands. Consistent with previous work suggesting that islands reflect the silencing of the edge of transposable elements (TEs), genes with nearby TEs were more likely to have mCHH islands. However, the presence of mCHH islands was not a function solely of TEs, both because the underlying sequences of islands were often not homologous to TEs and because genic properties also predicted the presence of 5′ mCHH islands. These genic properties included length and gene-body methylation (gbM); in fact, in three of eight species, the absence of gbM was a stronger predictor of a 5′ mCHH island than TE proximity. In contrast, gene expression level was a positive but weak predictor of the presence of an island. Finally, we assessed whether mCHH islands were evolutionarily conserved by focusing on a set of 2,720 orthologs across the eight species. They were generally not conserved across evolutionary time. Overall, our data establish additional genic properties that are associated with mCHH islands and suggest that they are not just a consequence of the TE silencing machinery.
Mitochondrial perturbation reduces susceptibility to xenobiotics through altered efflux in Candida albicans
Authors: Hossain Saif , Veri Amanda O , Liu Zhongle , Iyer Kali R , O’Meara Teresa R , Robbins Nicole , Cowen Leah E 
Published: June 2021

Abstract
Candida albicans is a leading human fungal pathogen, which can cause superficial infections or life-threatening systemic disease in immunocompromised individuals. The ability to transition between yeast and filamentous forms is a major virulence trait of C. albicans, and a key regulator of this morphogenetic transition is the molecular chaperone Hsp90. To explore the mechanisms governing C. albicans morphogenesis in response to Hsp90 inhibition, we performed a functional genomic screen using the gene replacement and conditional expression collection to identify mutants that are defective in filamentation in response to the Hsp90 inhibitor, geldanamycin. We found that transcriptional repression of genes involved in mitochondrial function blocked filamentous growth in response to the concentration of the Hsp90 inhibitor used in the screen, and this was attributable to increased resistance to the compound. Further exploration revealed that perturbation of mitochondrial function reduced susceptibility to two structurally distinct Hsp90 inhibitors, geldanamycin and radicicol, such that filamentous growth was restored in the mitochondrial mutants by increasing the compound concentration. Deletion of two representative mitochondrial genes, MSU1 and SHY1, enhanced cellular efflux and reduced susceptibility to diverse intracellularly acting compounds. Additionally, screening a C. albicans efflux pump gene deletion library implicated Yor1 in the efflux of geldanamycin and Cdr1, in the efflux of radicicol. Deletion of these transporter genes restored sensitivity to Hsp90 inhibitors in MSU1 and SHY1 homozygous deletion mutants, thereby enabling filamentation. Taken together, our findings suggest that mitochondrial dysregulation elevates cellular efflux and consequently reduces susceptibility to xenobiotics in C. albicans.
Multi-stage malaria parasite recognition by deep learning
Authors: Li Sen , Du Zeyu , Meng Xiangjie , Zhang Yang 
Published: June 2021

Abstract

Motivation
Malaria, a mosquito-borne infectious disease affecting humans and other animals, is widespread in tropical and subtropical regions. Microscopy is the most common method for diagnosing the malaria parasite from stained blood smear samples. However, this technique is time consuming and must be performed by a well-trained professional, yet it remains prone to errors. Distinguishing the multiple growth stages of parasites remains an especially challenging task.

Results
In this article, we develop a novel deep learning approach for the recognition of malaria parasites of various stages in blood smear images using a deep transfer graph convolutional network (DTGCN). To our knowledge, this is the first application of graph convolutional network (GCN) on multi-stage malaria parasite recognition in such images. The proposed DTGCN model is based on unsupervised learning by transferring knowledge learnt from source images that contain the discriminative morphology characteristics of multi-stage malaria parasites. This transferred information guarantees the effectiveness of the target parasite recognition. This approach first learns the identical representations from the source to establish topological correlations between source class groups and the unlabelled target samples. At this stage, the GCN is implemented to extract graph feature representations for multi-stage malaria parasite recognition. The proposed method showed higher accuracy and effectiveness in publicly available microscopic images of multi-stage malaria parasites compared to a wide range of state-of-the-art approaches. Furthermore, this method is also evaluated on a large-scale dataset of unseen malaria parasites and the Babesia dataset.

Availability
Code and dataset are available at https://github.com/senli2018/DTGCN_2021 under a MIT license.
Physical activity advice in the UK bowel cancer screening setting: qualitative healthcare professional perspectives
Authors: Semper Kelly , Hernon James , Wynter Trevor , Baker Katherine , Saxton John M 
Published: June 2021

Summary
Providing physical activity advice in the bowel cancer screening setting could help to reduce the risk of cancer and cardiometabolic disease in older adults. This study investigated the views of healthcare professionals (HCPs) regarding the provision of physical activity advice as part of the UK Bowel Cancer Screening Programme. A purposive sample of HCPs (aged 22–63 years, with 1–26 years of experience) from four bowel cancer screening disciplines (four endoscopists, four colorectal surgeons, four staff nurses and four specialist screening practitioners) were recruited from a large National Health Service gastroenterology unit. Data collection used individual interviews and focus groups, with topics being guided by an a priori topic guide. All interviews and focus groups were audio-recorded and transcribed verbatim. Three key themes, which contextualize the views and perceptions of HCPs recruited to the study, emerged from the framework analysis: (i) appraisal of the concept; (ii) perceived barriers to implementation; (iii) steps to implementation. While the general concept was viewed positively, there were differences of opinion and a range of perceived barriers were revealed. Ideas for effective implementation were also presented, taking into consideration the need for time efficiencies and importance of optimizing effectiveness. This qualitative study provided important insights into the perceptions of HCPs regarding the provision of physical activity advice in the bowel cancer screening setting, and yielded novel ideas for effective implementation.
Ten-eleven translocation 2 modulates allergic inflammation by 5-hydroxymethylcytosine remodeling of immunologic pathways
Authors: Meng Cuida , Gu Lei , Li Yujing , Li Ronghua , Cao Yiqu , Li Ziyi , Allen Emily G , Zhu Dongdong , Jin Peng 
Published: June 2021

Abstract
Allergic rhinitis (AR) is an allergen-specific immunoglobulin E-mediated inflammatory disease. Both genetic and environmental factors could play a role in the pathophysiology of AR. 5-methylcytosine (5mC) can be converted to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (Tet) family of proteins as part of active deoxyribonucleic acid (DNA) demethylation pathway. 5hmC plays an important role in the regulation of gene expression and differentiation in immune cells. Here, we show that loss of Tet protein 2 (Tet2) could impact the severity of AR in the ovalbumin-induced mouse model. Genome-wide 5hmC profiling of both wild-type and Tet2 KO mice in response to AR revealed that the loss of Tet2 could lead to 5hmC alteration at specific immune response genes. Both partial loss and complete loss of Tet2 alters the 5hmC dynamic remodeling for the adaptive immune pathway as well as cytokines. Thus, our results reveal a new role of Tet2 in immunology, and Tet2 may serve as a promising target in regulating the level of immune response.
Macrolide-associated ototoxicity: a cross-sectional and longitudinal study to assess the association of macrolide use with tinnitus and hearing loss
Authors: Vanoverschelde Anna , Oosterloo Berthe C , Ly Nelly F , Ikram M Arfan , Goedegebure André , Stricker Bruno H , Lahousse Lies 
Published: June 2021

Abstract

Background
Macrolides are widely prescribed antibiotics for many different indications. However, there are concerns about adverse effects such as ototoxicity.

Objectives
To investigate whether macrolide use is associated with tinnitus and hearing loss in the general population.

Methods
Cross-sectional (n = 4286) and longitudinal (n = 636) analyses were performed within the population-based Rotterdam Study. We investigated with multivariable logistic regression models the association between macrolides and tinnitus, and with multivariable linear regression models the association between macrolides and two different hearing thresholds (both ears, averaged over 0.25, 0.5, 1, 2, 4 and 8 kHz and 2, 4 and 8 kHz). Both regression models were adjusted for age, sex, systolic blood pressure, alcohol, smoking, BMI, diabetes, education level, estimated glomerular filtration rate and other ototoxic or tinnitus-generating drugs. Cumulative exposure to macrolides was categorized according to the number of dispensed DDDs and duration of action.

Results
In the fully adjusted model, ever use of macrolides was associated with a 25% higher likelihood of prevalent tinnitus (OR = 1.25; 95% CI 1.07–1.46). This association was more prominent in participants with a cumulative dose of more than 14 DDDs and among users of intermediate- or long-acting macrolides. Macrolide use in between both assessments was associated with more than a 2-fold increased risk on incident tinnitus. No general association between macrolides and hearing loss was observed. A borderline significant higher hearing threshold in very recent users (≤3 weeks) was found.

Conclusions
Macrolide use was significantly associated with both prevalent and incident tinnitus. Macrolide-associated tinnitus was likely cumulative dose-dependent.
Rise of the Machines: Artificial Intelligence and the Clinical Laboratory
Authors: Haymond Shannon , McCudden Christopher 
Published: June 2021

Abstract

Background
Artificial intelligence (AI) is rapidly being developed and implemented to augment and automate decision-making across healthcare systems. Being an essential part of these systems, laboratories will see significant growth in AI applications for the foreseeable future.

Content
In laboratory medicine, AI can be used for operational decision-making and automating or augmenting human-based workflows. Specific applications include instrument automation, error detection, forecasting, result interpretation, test utilization, genomics, and image analysis. If not doing so today, clinical laboratories will be using AI routinely in the future, therefore, laboratory experts should understand their potential role in this new area and the opportunities for AI technologies. The roles of laboratorians range from passive provision of data to fuel algorithms to developing entirely new algorithms, with subject matter expertise as a perfect fit in the middle. The technical development of algorithms is only a part of the overall picture, where the type, availability, and quality of data are at least as important. Implementation of AI algorithms also offers technical and usability challenges that need to be understood to be successful. Finally, as AI algorithms continue to become available, it is important to understand how to evaluate their validity and utility in the real world.

Summary
This review provides an overview of what AI is, examples of how it is currently being used in laboratory medicine, different ways for laboratorians to get involved in algorithm development, and key considerations for AI algorithm implementation and critical evaluation.
Transgender data collection in the electronic health record: Current concepts and issues
Authors: Kronk Clair A , Everhart Avery R , Ashley Florence , Thompson Hale M , Schall Theodore E , Goetz Teddy G , Hiatt Laurel , Derrick Zackary , Queen Roz , Ram A , Guthman E Mae , Danforth Olivia M , Lett Elle , Potter Emery , Sun Simón(e) D , Marshall Zack , Karnoski Ryan 
Published: June 2021

AbstractThere are over 1 million transgender people living in the United States, and 33% report negative experiences with a healthcare provider, many of which are connected to data representation in electronic health records (EHRs). We present recommendations and common pitfalls involving sex- and gender-related data collection in EHRs. Our recommendations leverage the needs of patients, medical providers, and researchers to optimize both individual patient experiences and the efficacy and reproducibility of EHR population-based studies. We also briefly discuss adequate additions to the EHR considering name and pronoun usage. We add the disclaimer that these questions are more complex than commonly assumed. We conclude that collaborations between local transgender and gender-diverse persons and medical providers as well as open inclusion of transgender and gender-diverse individuals on terminology and standards boards is crucial to shifting the paradigm in transgender and gender-diverse health.
Effect of Subcutaneous Topical Ozone Therapy on Second-Degree Burn Wounds in Rats: An Experimental Study
Authors: Karakaya Emre , Akdur Aydincan , Ayvazoğlu Soy Ebru , Araz Coşkun , Ok Atilgan Alev , Özturan Özer Eda , Şençelikel Tuğçe , Haberal Mehmet 
Published: June 2021

Abstract
Burns are one of the most severe traumas, causing coagulative destruction of the skin. The use of various products that accelerate wound healing in patients with burns may affect rates of patient survival and reduce complications. We studied the effects of subcutaneous ozone injection on second-degree burn wounds in an animal model. For this study, 72 Sprague–Dawley male rats were divided randomly into the following three groups: control group, silver sulfadiazine group, and ozone group; each group was then divided randomly into two subgroups (day 7 or day 14 examination and euthanized). Superficial partial-thickness burns were created on the lower back. In the control group, subcutaneous 0.9% serum saline was injected daily into the burn area. In the silver sulfadiazine group, burns were dressed daily with silver sulfadiazine. In the ozone group, subcutaneous ozone was injected daily into the burn area. We performed tissue hydroxyproline level measurements and histopathological evaluations. When groups were compared in terms of weight change, no significant difference was found between day 7 and day 14. With regard to tissue hydroxyproline levels, the ozone group had significantly higher levels on both days 7 and 14 (P &lt; .001). In histopathological evaluations, we determined that wound healing in the ozone group was significantly higher than in the other groups. We found that subcutaneous ozone therapy was more effective than silver sulfadiazine in the healing process of second-degree burn wounds and could be safely used in the treatment of burn wounds.
Needs Assessment for Corn Insect Pest Management in Iowa
Authors: Dean Ashley N , Hodgson Erin W , Rieck-Hinz Angela , Anderson Meaghan 
Published: June 2021

AbstractCorn, Zea mays L. (Cyperales: Poaceae), production is essential to Iowa’s economy and provides food, feed, and fuel beyond the state. Farmers face a number of challenges in corn production, including insect pests, and understanding farmers’ perceptions and concerns is critical for extension personnel to provide adequate and relevant programming. The Iowa State University Agriculture and Natural Resources Crops Team conducted a survey of Iowa farmers and agribusiness professionals during the 2019–2020 extension season. The goal was to understand farmer perceptions of corn pests and whether farmers experienced challenges with resistance to Bt traits or insecticides. Additionally, we aimed to realize farmers’ confidence in developing resistance management plans and discussing those needs with their input suppliers and advisors. Our survey revealed that northern corn rootworm, Diabrotica barberi Smith & Lawrence (Coleoptera: Chrysomelidae), was the pest of greatest concern across the state. People were generally more concerned about belowground Bt trait performance than aboveground traits, though only 12% of respondents reported Bt trait failure for corn rootworms. In general, people were not concerned about the performance of seed treatments or soil- or foliar-applied insecticides. Farmers generally felt very confident in developing a resistance management plan and discussing their needs with their advisors. The results of this survey will be used to target extension programming throughout the state and increase confidence for farmers and agribusiness employees to discuss resistance management plans together.
The emergence of systematic argument distinctions in artificial sign languages
Authors: Motamedi Yasamin , Smith Kenny , Schouwstra Marieke , Culbertson Jennifer , Kirby Simon 
Published: June 2021

AbstractWord order is a key property by which languages indicate the relationship between a predicate and its arguments. However, sign languages use a number of other modality-specific tools in addition to word order such as spatial agreement, which has been likened to verbal agreement in spoken languages, and role shift, where the signer takes on characteristics of propositional agents. In particular, data from emerging sign languages suggest that, though some use of a conventional word order can appear within a few generations, systematic spatial modulation as a grammatical feature takes time to develop. We experimentally examine the emergence of systematic argument marking beyond word order, investigating how artificial gestural systems evolve over generations of participants in the lab. We find that participants converge on different strategies to disambiguate clause arguments, which become more consistent through the use and transmission of gestures; in some cases, this leads to conventionalized iconic spatial contrasts, comparable to those found in natural sign languages. We discuss how our results connect with theoretical issues surrounding the analysis of spatial agreement and role shift in established and newly emerging sign languages, and the possible mechanisms behind its evolution.
Aboveground net primary productivity and soil respiration display different responses to precipitation changes in desert grassland
Authors: Zhang Lihua , Wang Junfeng , Zhao Ruifeng , Guo Yafei , Hao Lianyi 
Published: June 2021

AbstractPrecipitation (PPT) changes affect both aboveground vegetation dynamics and belowground carbon cycling processes, particularly in arid and semiarid regions. However, it remains unclear how extreme PPT variation can affect soil carbon sequestration potential. A 3-year PPT manipulation experiment with five levels (±40%, ±20% and ambient PPT) was conducted in a desert grassland of western Loess Plateau. Aboveground net primary productivity (ANPP) and soil respiration (Rs) were measured to examine whether the responses of ANPP and Rs to PPT changes displayed a double asymmetry model. The ANPP was more sensitive to extreme drought than extreme wet treatments in wet and dry years, which displayed a negative asymmetric model. The change in ANPP was mainly due to the direct effect of PPT change, and plant density variation also exerted some influence in the dry year. In contrast, Rs displayed a positive asymmetry response to PPT change in dry year. This may be ascribed to enhanced autotrophic respiration due to the enhanced positive responses of plant growth and ANPP to wet treatments as well as stronger birch effect of rainfall events on heterotrophic respiration. The saturating response of Rs to extreme drought (−40% PPT treatment) was also found in the dry year. Nevertheless, the response of Rs to PPT change displayed a negative asymmetry model in wet years. The contrasting models for ANPP and Rs in response to altered PPT regime suggest that extreme wet or dry treatments may increase soil C pools effluxes toward debt in this desert grassland.
Males With Traumatic Lower Limb Loss Differ in Body Fat Distribution Compared to Those Without Limb Loss
Authors: Spain David R , Andrews Anne M , Crews Sara A , Khan Joetta M 
Published: June 2021

ABSTRACTObjectivesThe primary objective was to examine body fat composition in males with traumatic lower limb loss and a comparison group without limb loss. A secondary objective was to determine if there are differences in body fat composition by traumatic limb loss level.Research Methods and ProceduresCross-sectional analyses of baseline in-person intake data was completed at a large military medical center. Data were collected from 2011 to 2020, and analysis was conducted in 2020. Participants (n = 89) included males who sustained traumatic lower limb loss (n = 50) and an age-matched comparison group without limb loss (n = 39). Mean age of participants was 36.0 ± 13.2 years. Main outcomes measured included age, height, body mass index, weight, body fat mass and percent, android fat mass and percent, gynoid fat mass and percent, and android/gynoid percent fat ratio. Differences between groups were assessed using t-tests or Mann–Whitney U tests. Differences between limb loss levels were assessed using one-way ANOVA or Wilcoxon signed-rank test.ResultsBody fat percent (P = .001), gynoid fat percent (P = .010), android fat mass (P = .01), and percent (P = .02) were higher in the group with limb loss. There were no differences in body fat composition between limb loss levels (P &gt; .05).ConclusionMales with traumatic lower limb loss had a higher body fat percent compared to those without limb loss. Given higher body fat composition in individuals with limb loss and the relationship between body fat composition and cardiovascular disease risk, including body composition analysis with clinical screening could identify changes and allow for early intervention.