bluuebunny/crossref_metadata_2025_split huggingface dataset:
First mass spectrometric report of cryptocyanin, a moulting protein from the mud crab Scylla serrata (Forskål, 1775) (Decapoda: Brachyura: Portunidae) in India
Authors: Asthana Manu , Ahamed Maqusood , Shanthi Chittibabu 
Published: November 2020

Abstract
The mud crab Scylla serrata (Forskål, 1775) is a highly abundant and economically important species throughout coastal India. Cryptocyanin plays an important role during the moult cycle of brachyuran crabs, and the presence of cryptocyanin and haemocyanin in oocytes, embryos, and zoeas of various species suggests that cryptocyanin is available from the very early stage of cuticle formation in development. Cryptocyanin is highly similar to haemocyanin in structure, but it is a copper-free enzyme that lacks an oxygen-binding capacity. Cryptocyanin has furthermore been reported as an important factor in immunity in crustaceans. The precise molecular weight of the cryptocyanin protein from gill tissues of S. serrata (79.11 kDa) is reported with the help of the matrix-assisted laser desorption/ionization mass spectrophotometry (MALDI-MS) technique.
Yield Response of Determinate Chipping Potato to Artificial Defoliation
Authors: Hoback W Wyatt , Hayashida Rafael , Ziems Jesse , Zechmann Ben , de Freitas Bueno Adeney , Higley Leon G 
Published: November 2020

Abstract
The relationship between canopy defoliation by insects and yield loss in potato (Solanum tuberosum L.) has been extensively researched. However, detailed analysis of varieties with different properties and examination of methods of defoliation are still lacking. Absence of research results has led many producers to use a very conservative economic threshold (ET) of 10% defoliation in the management of insect defoliators. A series of leaf removal experiments was conducted on a determinate chipping variety of potato at different plant stages. In 2002, the highest levels of defoliation induced upon the plant canopy were 50, 30, and 75% for tuber initiation, full bloom, and plant maturity stages, respectively. In 2003, defoliation levels were increased to 70, 80, and 90% for tuber initiation, full bloom, and plant maturity, respectively. Total yield was unaffected, and no significant changes in market sized yield, or number of marketable tubers were observed at any growth stage in either year. Because the determinate variety showed remarkable ability to recover from substantial defoliation, two different methods of defoliation: hand cut (cutting the edge of leaves with scissors while avoiding the midrib) and hole punching (hole-punching leaf tissue [15.08-mm diameter] while avoiding midrib) were tested. Although total yield was unaffected, marketable yield and small potato yield were reduced, Thus, although defoliation methods must be considered, a 10% defoliation ET is exceedingly conservative and an ET of 60% for all stages of determinate chipping potato could be adopted by growers.
Surface Movement of Billbugs (Coleoptera: Curculionidae) in Harvested and Nonharvested Sod
Authors: Gireesh Midhula , Joseph Shimat V 
Published: November 2020

Abstract
The billbug complex, Sphenophorus spp. (Coleoptera: Curculionidae), is an important pest on the sod farms of Georgia. The feeding damage of larvae within stolons and on roots delays the sod harvest and makes it difficult to conduct machine harvests. To develop an effective management strategy, the timing of insecticide applications is critical. The activity of billbugs, especially soon after sod harvest, has not been documented, as newly emerging adults could reinfest the harvested area or adjacent nonharvested sod fields. In 2019 and 2020, adult billbugs were sampled from harvested and nonharvested areas of sod farms by using linear pitfall traps. Although a significantly greater number of billbug adults were captured from the nonharvested sod, the data showed that adults were present in the harvested sod area. To understand the direction of billbug movement in harvested and nonharvested sod, a square area was selected, and the sod inside the square was removed. Linear pitfall traps were deployed along the perimeter of square areas to collect adults from outside and inside the square. In 2020, a significantly greater number of billbug adults were collected in the traps from the nonharvested areas outside the square than from harvested area inside the square, whereas in 2019, adult captures were similar from both areas. The data documented the activity of billbugs in the areas where sod was harvested, posing a risk of infestation for both strips of nonharvested grass in the harvested area and the adjacent, nonharvested sod fields that were near harvest.
Update From the Advisory Committee on Immunization Practices
Authors: O′Leary Sean T , Maldonado Yvonne A , Kimberlin David W 
Published: November 2020

Abstract
The Advisory Committee on Immunization Practices (ACIP), a group of medical and public health experts, normally meets 3 times per year to develop recommendations for vaccine use in the United States. Because of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) pandemic, there are several SARS-CoV-2 vaccines currently in late-stage clinical trials, so the ACIP is now meeting monthly for single day meetings, with plans to continue standard 2- to 3-day meetings as per usual (February, June, and October). Emergency meetings of ACIP may occur if a vaccine candidate receives an Emergency Use Authorization from the food and drug administration (FDA). This Update provides a combined summary of the August 26 and September 22, 2020, meetings, both of which focused completely on Coronavirus disease 2019 (COVID-19) vaccines. The representatives from the American Academy of Pediatrics (Y. A. M. and D. W. K.) and the Pediatric Infectious Diseases Society (S. T. O.) are present as liaisons to the ACIP.
β-Catenin/Lin28/let-7 regulatory network determines type II alveolar epithelial stem cell differentiation phenotypes following thoracic irradiation
Authors: Liu Xiaozhuan , Zhang Tingting , Zhou Jianwei , Xiao Ziting , Li Yanjun , Zhang Yuwei , Yue Haodi , Li Zhitao , Tian Jian 
Published: November 2020

Abstract
The contribution of type II alveolar epithelial stem cells (AEC II) to radiation-induced lung fibrosis (RILF) is largely unknown. Cell differentiation phenotypes are determined by the balance between Lin28 and lethal-7 microRNA (let-7 miRNA). Lin28 is activated by β-catenin. The aim of this study was to track AEC II phenotypes at different phases of injury following thoracic irradiation and examine the expression of β-catenin, Lin28 and let-7 to identify their role in AEC II differentiation. Results showed that coexpression of prosurfactant protein C (proSP-C, an AEC II biomarker) and HOPX (homeobox only protein X, an AEC I biomarker) or vimentin (a differentiation marker) was detected in AEC II post-irradiation. The protein expression levels of HOPX and proSP-C were significantly downregulated, but vimentin was significantly upregulated following irradiation. The expression of E-cadherin, which prevents β-catenin from translocating to the nucleus, was downregulated, and the expression of β-catenin and Lin28 was upregulated after irradiation (P &lt; 0.05 to P &lt; 0.001). Four let-7 miRNA members (a, b, c and d) were upregulated in irradiated lungs (P &lt; 0.05 to P &lt; 0.001), but let-7d was significantly downregulated at 5 and 6 months (P &lt; 0.001). The ratios of Lin28 to four let-7 members were low during the early phase of injury and were slightly higher after 2 months. Intriguingly, the Lin28/let-7d ratio was strikingly increased after 4 months. We concluded that β-catenin contributed to RILF by promoting Lin28 expression, which increased the number of AEC II and the transcription of profibrotic molecules. In this study, the downregulation of let-7d miRNA by Lin28 resulted in the inability of AEC II to differentiate into type I alveolar epithelial cells (AEC I).
Every cloud has a silver lining: how abiotic stresses affect gene expression in plant-pathogen interactions
Authors: Zarattini Marco , Farjad Mahsa , Launay Alban , Cannella David , Soulié Marie-Christine , Bernacchia Giovanni , Fagard Mathilde 
Published: November 2020

AbstractCurrent environmental and climate changes are having a pronounced influence on the outcome of plant–pathogen interactions, further highlighting the fact that abiotic stresses strongly affect biotic interactions at various levels. For instance, physiological parameters such as plant architecture and tissue organization together with primary and specialized metabolism are affected by environmental constraints, and these combine to make an individual plant either a more or less suitable host for a given pathogen. In addition, abiotic stresses can affect the timely expression of plant defense and pathogen virulence. Indeed, several studies have shown that variations in temperature, and in water and mineral nutrient availability affect the expression of plant defense genes. The expression of virulence genes, known to be crucial for disease outbreak, is also affected by environmental conditions, potentially modifying existing pathosystems and paving the way for emerging pathogens. In this review, we summarize our current knowledge on the impact of abiotic stress on biotic interactions at the transcriptional level in both the plant and the pathogen side of the interaction. We also perform a metadata analysis of four different combinations of abiotic and biotic stresses, which identifies 197 common modulated genes with strong enrichment in Gene Ontology terms related to defense . We also describe the multistress-specific responses of selected defense-related genes.
TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis
Authors: Herrera-Vásquez Ariel , Fonseca Alejandro , Ugalde José Manuel , Lamig Liliana , Seguel Aldo , Moyano Tomás C , Gutiérrez Rodrigo A , Salinas Paula , Vidal Elena A , Holuigue Loreto 
Published: November 2020

Abstract
Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription–PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.
Strategies for Sustainability of University-Based Medical Laboratory Sciences Programs
Authors: Behan Kristina Jackson 
Published: November 2020

Abstract
The COVID-19 pandemic has taken a major toll on the economy and funding for public education. For that reason, the pandemic has a worrisome effect on the sustainability of university/college based Medical Laboratory Sciences MLS training programs. Stakeholders of university-based MLS programs include university administrators, students, clinical affiliates and faculty. Each group has specific goals and challenges that affect the sustainability of the program. This report details strategies that can be used to satisfy the goals specific to key stakeholders that lead to sustainability. These strategies apply in pandemic times and in the back-to-normal future.
Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes
Authors: Tennessen Jacob A , Duraisingh Manoj T 
Published: November 2020

Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host–parasite coevolutionary dynamics.
Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly
Authors: Cipullo Miriam , Pearce Sarah F , Lopez Sanchez Isabel G , Gopalakrishna Shreekara , Krüger Annika , Rosenberger Florian A , Busch Jakob D , Li Xinping , Wredenberg Anna , Atanassov Ilian , Rorbach Joanna 
Published: November 2020

Abstract
Human mitoribosomes are macromolecular complexes essential for translation of 11 mitochondrial mRNAs. The large and the small mitoribosomal subunits undergo a multistep maturation process that requires the involvement of several factors. Among these factors, GTP-binding proteins (GTPBPs) play an important role as GTP hydrolysis can provide energy throughout the assembly stages. In bacteria, many GTPBPs are needed for the maturation of ribosome subunits and, of particular interest for this study, ObgE has been shown to assist in the 50S subunit assembly. Here, we characterize the role of a related human Obg-family member, GTPBP5. We show that GTPBP5 interacts specifically with the large mitoribosomal subunit (mt-LSU) proteins and several late-stage mitoribosome assembly factors, including MTERF4:NSUN4 complex, MRM2 methyltransferase, MALSU1 and MTG1. Interestingly, we find that interaction of GTPBP5 with the mt-LSU is compromised in the presence of a non-hydrolysable analogue of GTP, implying a different mechanism of action of this protein in contrast to that of other Obg-family GTPBPs. GTPBP5 ablation leads to severe impairment in the oxidative phosphorylation system, concurrent with a decrease in mitochondrial translation and reduced monosome formation. Overall, our data indicate an important role of GTPBP5 in mitochondrial function and suggest its involvement in the late-stage of mt-LSU maturation.
Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems
Authors: Mestre Mario Rodríguez , González-Delgado Alejandro , Gutiérrez-Rus Luis I , Martínez-Abarca Francisco , Toro Nicolás 
Published: November 2020

AbstractBacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.
Genome-wide integration site detection using Cas9 enriched amplification-free long-range sequencing
Authors: van Haasteren Joost , Munis Altar M , Gill Deborah R , Hyde Stephen C 
Published: November 2020

Abstract
The gene and cell therapy fields are advancing rapidly, with a potential to treat and cure a wide range of diseases, and lentivirus-based gene transfer agents are the vector of choice for many investigators. Early cases of insertional mutagenesis caused by gammaretroviral vectors highlighted that integration site (IS) analysis was a major safety and quality control checkpoint for lentiviral applications. The methods established to detect lentiviral integrations using next-generation sequencing (NGS) are limited by short read length, inadvertent PCR bias, low yield, or lengthy protocols. Here, we describe a new method to sequence IS using Amplification-free Integration Site sequencing (AFIS-Seq). AFIS-Seq is based on amplification-free, Cas9-mediated enrichment of high-molecular-weight chromosomal DNA suitable for long-range Nanopore MinION sequencing. This accessible and low-cost approach generates long reads enabling IS mapping with high certainty within a single day. We demonstrate proof-of-concept by mapping IS of lentiviral vectors in a variety of cell models and report up to 1600-fold enrichment of the signal. This method can be further extended to sequencing of Cas9-mediated integration of genes and to in vivo analysis of IS. AFIS-Seq uses long-read sequencing to facilitate safety evaluation of preclinical lentiviral vector gene therapies by providing IS analysis with improved confidence.
Histones participate in base excision repair of 8-oxodGuo by transiently cross-linking with active repair intermediates in nucleosome core particles
Authors: Ren Mengtian , Shang Mengdi , Wang Huawei , Xi Zhen , Zhou Chuanzheng 
Published: November 2020

Abstract8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) is a biomarker of oxidative DNA damage and can be repaired by hOGG1 and APE1 via the base excision repair (BER) pathway. In this work, we studied coordinated BER of 8-oxodGuo by hOGG1 and APE1 in nucleosome core particles and found that histones transiently formed DNA-protein cross-links (DPCs) with active repair intermediates such as 3′-phospho-α,β-unsaturated aldehyde (PUA) and 5′-deoxyribosephosphate (dRP). The effects of histone participation could be beneficial or deleterious to the BER process, depending on the circumstances. In the absence of APE1, histones enhanced the AP lyase activity of hOGG1 by cross-linking with 3′-PUA. However, the formed histone-PUA DPCs hampered the subsequent repair process. In the presence of APE1, both the AP lyase activity of hOGG1 and the formation of histone-PUA DPCs were suppressed. In this case, histones could catalyse removal of the 5′-dRP by transiently cross-linking with the active intermediate. That is, histones promoted the repair by acting as 5′-dRP lyases. Our findings demonstrate that histones participate in multiple steps of 8-oxodGuo repair in nucleosome core particles, highlighting the diverse roles that histones may play during DNA repair in eukaryotic cells.
Length of Stay Beyond Medical Readiness in a Neurosurgical Patient Population and Associated Healthcare Costs
Authors: Linzey Joseph R , Foshee Rachel , Moriguchi Francine , Adapa Arjun R , Koduri Sravanthi , Kahn Elyne N , Williamson Craig A , Sheehan Kyle , Rajajee Venkatakrishna , Thompson B Gregory , Muraszko Karin M , Pandey Aditya S 
Published: November 2020

Abstract

BACKGROUND
Length of stay beyond medical readiness (LOS-BMR) leads to increased expenses and higher morbidity related to hospital-acquired conditions.

OBJECTIVE
To determine the proportion of admitted neurosurgical patients who have LOS-BMR and associated risk factors and costs.

METHODS
We performed a prospective, cohort analysis of all neurosurgical patients admitted to our institution over 5 mo. LOS-BMR was assessed daily by the attending neurosurgeon and neuro-intensivist with a standardized criterion. Univariate and multivariate logistic regressions were performed.

RESULTS
Of the 884 patients admitted, 229 (25.9%) had a LOS-BMR. The average LOS-BMR was 2.7 ± 3.1 d at an average daily cost of $9 148.28 ± $12 983.10, which resulted in a total cost of $2 076 659.32 over the 5-mo period. Patients with LOS-BMR were significantly more likely to be older and to have hemiplegia, dementia, liver disease, renal disease, and diabetes mellitus. Patients with a LOS-BMR were significantly more likely to be discharged to a subacute rehabilitation/skilled nursing facility (40.2% vs 4.1%) or an acute/inpatient rehabilitation facility (22.7% vs 1.7%, P < .0001). Patients with Medicare insurance were more likely to have a LOS-BMR, whereas patients with private insurance were less likely (P = .048).

CONCLUSION
The most common reason for LOS-BMR was inefficient discharge of patients to rehabilitation and nursing facilities secondary to unavailability of beds at discharge locations, insurance clearance delays, and family-related issues.