bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Novel Spotted Fever Group Rickettsiae (Rickettsiales: Rickettsiaceae) in Ticks (Acari: Ixodidae) in Southwestern China
Authors: Wang Qian , Guo Wen-Bin , Pan Yu-Sheng , Jiang Bao-Gui , Du Chun-Hong , Que Teng-Cheng , Zhan Lin , Wu Jia-Hong , Yu Ming-Hui , Cui Xiao-Ming , Zhao Lin , Xu Da-Li , Xia Luo-Yuan , Ye Run-Ze , Li Jie , Li Lian-Feng , Wei Wei , Zhou Yu-Hao , Jiang Jia-Fu , Jia Na , Cao Wu-Chun 
Published: January 2021

Abstract
Spotted fever group rickettsiae, mainly maintained and transmitted by ticks, are important etiological agents of (re)emerging zoonotic diseases worldwide. It is of great significance to investigate spotted fever group rickettsiae in ticks in different areas for the prevention and control of rickettsioses. In this study, a total of 305 ticks were collected from wild and domestic animals in Chongqing, Guizhou, Yunnan, and Guangxi provinces of southwestern China during 2017–2019 and examined for the presence of spotted fever group rickettsiae by PCR with primers targeting the partial gltA, ompA, rrs, and htrA genes. Results showed that two spotted fever group rickettsiae species, including the pathogenic Candidatus Rickettsia jingxinensis (Rickettsiales: Rickettsiaceae) and a potential novel species Rickettsia sp. sw (Rickettsiales: Rickettsiaceae), were identified. The Ca. R. jingxinensis sequences were recovered from Rhipicephalus microplus (Ixodida: Ixodidae) and Haemaphysalis longicornis (Ixodida: Ixodidae) ticks and phylogenetically clustered with previous Ca. R. jingxinensis, Ca. R. longicornii (Rickettsiales: Rickettsiaceae), and Rickettsia sp. XY118 (Rickettsiales: Rickettsiaceae) strains. Rickettsia sp. sw was detected in Amblyomma geoemydae (Ixodida: Ixodidae) and Rh. microplus. Interestingly, as far as we know, this was the first report of Rickettsia (Rickettsiales: Rickettsiaceae) in A. geoemydae. Phylogenetic analyses indicated that this potential novel species was closely related to R. aeschlimannii (Rickettsiales: Rickettsiaceae) with gltA and ompA genes and grouped in a cluster composed of R. montanensis (Rickettsiales: Rickettsiaceae), R. raoultii (Rickettsiales: Rickettsiaceae), R. aeschlimannii, R. massiliae (Rickettsiales: Rickettsiaceae), and R. rhipicephali (Rickettsiales: Rickettsiaceae) with htrA, while formed a separate clade with rrs. The pathogenicity of Rickettsia sp. sw should be further confirmed. These results expand the knowledge of the geographical distribution and vector distribution of spotted fever group rickettsiae in China and are useful for assessing the potential public health risk.
EXPOSURE DOSE INDEX BASED ON NOISE FACTOR ANALYSIS IN DIGITAL MAMMOGRAPHY: VERIFICATION USING DIRECT-TYPE FLAT-PANEL DETECTOR SYSTEM
Authors: Maruyama Sho 
Published: January 2021

Abstract
In this study, the development of a reasonable index of optimized exposure dose is attempted. Using a direct-type flat-panel system, noise factors contained in the image are analyzed based on the relative standard deviation method, and it is verified that the proposed index conforms with the appropriate standards regarding minimum exposure dose. The findings indicate that Poisson noise is dominant in the general clinical dose range; this noise fraction formed 90% of the total noise in the system considered in this study. Considering the results of previous surveys, it is estimated that the point at which the content rate of the Poisson noise starts to decrease can be considered as the lower limit, below which the dose cannot be reduced further without compromising on image quality. As the ‘index’ obtained by this method can be easily measured, it is useful as a quantitative indicator for dose determination and optimization.
Is Music Therapy Effective in Cabin Fever Recovery?
Authors: Situmorang Dominikus David Biondi 
Published: January 2021

Objectives:
During the coronavirus disease (COVID-19) outbreak, there is an unhealthy psychological symptom in most people worldwide, namely cabin fever. Quite a few people in this world do not know the benefits of music therapy in helping to prevent and overcome cabin fever.

Methods:
Through this opinion “piece,” the author aims to discuss tips to prevent and overcome cabin fever through several studies with music therapy.

Conclusion:
The author proposes that everyone can use music therapy in preventing and overcoming cabin fever.
Dairy Fat Intake, Plasma Pentadecanoic Acid, and Plasma Iso‐heptadecanoic Acid Are Inversely Associated With Liver Fat in Children
Authors: Sawh Mary Catherine , Wallace Martina , Shapiro Emma , Goyal Nidhi P. , Newton Kimberly P. , Yu Elizabeth L. , Bross Craig , Durelle Janis , Knott Cynthia , Gangoiti Jon A. , Barshop Bruce A. , Gengatharan Jivani M. , Meurs Noah , Schlein Alexandra , Middleton Michael S. , Sirlin Claude B. , Metallo Christian M. , Schwimmer Jeffrey B. 
Published: January 2021

ABSTRACTObjectives:We sought to evaluate the relevance of pediatric dairy fat recommendations for children at risk for nonalcoholic fatty liver disease (NAFLD) by studying the association between dairy fat intake and the amount of liver fat. The effects of dairy fat may be mediated by odd chain fatty acids (OCFA), such as pentadecanoic acid (C15:0), and monomethyl branched chain fatty acids (BCFA), such as iso‐heptadecanoic acid (iso‐C17:0). Therefore, we also evaluated the association between plasma levels of OCFA and BCFA with the amount of liver fat.Methods:Observational, cross‐sectional, community‐based sample of 237 children ages 8 to 17. Dairy fat intake was assessed by 3 24‐hour dietary recalls. Plasma fatty acids were measured by gas chromatography‐mass spectrometry. Main outcome was hepatic steatosis measured by whole liver magnetic resonance imaging proton density fat fraction (MRI‐PDFF).Results:Median dairy fat intake was 10.6 grams/day (range 0.0‐‐44.5 g/day). Median liver MRI‐PDFF was 4.5% (range 0.9%–45.1%). Dairy fat intake was inversely correlated with liver MRI‐PDFF (r = −0.162; P = .012). In multivariable log linear regression, plasma C15:0 and iso‐C17:0 were inverse predictors of liver MRI‐PDFF (B = −0.247, P = 0.048; and B = −0.234, P = 0.009).Conclusions:Dairy fat intake, plasma C15:0, and plasma iso‐C17:0 were inversely correlated with hepatic steatosis in children. These hypothesis‐generating findings should be tested through clinical trials to better inform dietary guidelines.
AffordableCaenorhabditis eleganstracking system for classroom use
Authors: Leonard Nicholas , Vidal-Gadea Andrés G. 
Published: January 2021

AbstractFor decades the nematodeC. eleganshas served as an outstanding research organism owing to its unsurpassed experimental amenability. This advantage has also made this tiny worm an attractive vehicle for science instruction across higher learning institutions. However, the prohibitive cost associated with the automated behavioral assessment of these animals remains an obstacle preventing their full adoption in undergraduate and high school settings. To improve this situation, we developed an inexpensive worm tracking system for use by high school interns and undergraduate students. Over the past two years this tracker has been successfully used by undergraduate students in our introductory Cell and Molecular lab (BSC220) at Illinois State University. Here we describe and demonstrate the use of our inexpensive worm tracking system.
Optimizing vaccine allocation for COVID-19 vaccines: potential role of single-dose vaccination
Authors: Matrajt Laura , Eaton Julia , Leung Tiffany , Dimitrov Dobromir , Schiffer Joshua T. , Swan David A. , Janes Holly 
Published: January 2021

AbstractMost COVID-19 vaccines require two doses, however with limited vaccine supply, policymakers are considering single-dose vaccination as an alternative strategy. Using a mathematical model combined with optimization algorithms, we determined optimal allocation strategies with one and two doses of vaccine under various degrees of viral transmission. Under low transmission, we show that the optimal allocation of vaccine vitally depends on the single-dose efficacy (SDE). With high SDE, single-dose vaccination is optimal, preventing up to 22% more deaths than a strategy prioritizing two-dose vaccination for older adults. With low or moderate SDE, mixed vaccination campaigns with complete coverage of older adults are optimal. However, with modest or high transmission, vaccinating older adults first with two doses is best, preventing up to 41% more deaths than a singledose vaccination given across all adult populations. Our work suggests that it is imperative to determine the efficacy and durability of single-dose vaccines, as mixed or single-dose vaccination campaigns may have the potential to contain the pandemic much more quickly.
Optimizing testing for COVID-19 in India
Authors: Cherian Philip , Krishna Sandeep , Menon Gautam I. 
Published: January 2021

AbstractCOVID-19 testing across India uses a mix of two types of tests. Rapid Antigen Tests (RATs) are relatively inexpensive point-of-care lateral-flow-assay tests, but they are also less sensitive. The reverse-transcriptase polymerase-chain-reaction (RT-PCR) test has close to 100% sensitivity and specificity in a laboratory setting, but delays in returning results, as well as increased costs relative to RATs, may vitiate this advantage.India-wide, about 49% of COVID-19 tests are RATs, but some Indian states, including the large states of Uttar Pradesh (pop. 227.9 million) and Bihar (pop. 121.3 million) use a much higher proportion of such tests. Here we show, using simulations based on epidemiological network models, that the judicious use of RATs can yield epidemiological outcomes comparable to those obtained through RT-PCR-based testing and isolation of positives, provided a few conditions are met. These are (a) that RAT test sensitivity is not too low, (b) that a reasonably large fraction of the population, of order 0.5% per day, can be tested, (c) that those testing positive are isolated for a sufficient duration, and that (d) testing is accompanied by other non-pharmaceutical interventions for increased effectiveness. We assess optimal testing regimes, taking into account test sensitivity and specificity, background seroprevalence and current test pricing. We find, surprisingly, that even 100% RAT test regimes should be acceptable, from both an epidemiological as well as a economic standpoint, provided the conditions outlined above are met.Author summaryUsing network models, we study optimal ways of combining low sensitivity, relatively inexpensive point-of-care rapid antigen tests for COVID-19 with higher sensitivity but more expensive laboratory RT-PCR tests. We take into account background seroprevalence and current test pricing for such tests in India, finding that even purely rapid antigen test-based regimes can produce the same reduction in overall infections that pure RT-PCR tests are capable of. This is provided one can test at scale and isolate those testing positive effectively, that the sensitivity of the rapid test is not too low and that non-pharmaceutical interventions proceed in parallel for increased effectiveness.
COVID-19 immunization threshold(s): an analysis
Authors: Bautista Balbás Luis Alfredo , Conesa Mario Gil , Balbás Blanca Bautista , Jiménez Ainhoa Alcaide , Rodríguez Caravaca Gil 
Published: January 2021

2AbstractAs COVID-19 vaccine research efforts seem to be yielding the first tangible results, the proportion of individuals needed to reap the benefits of herd immunity is a key element from a Public Health programs perspective.This magnitude, termed the critical immunization threshold (q), can be obtained from the classical SIR model equilibrium equation, equaling (1 − 1/R0)/ ϵ, where R0 is the basic reproduction number and ϵ is the vaccine efficacy. When a significant proportion of the population is already immune, this becomes (n − 1/R0)/ ϵ, where n is the proportion of non-immune individuals. A similar equation can be obtained for short-term immunization thresholds(qt), which are dependent on Rt.qs for most countries are between 60-75% of the population. Current qt for most countries are between 20-40%.Therefore, the combination of gradual vaccination and other non-pharmaceutical interventions will mark the transition to the herd immunity, providing that the later turns out to be a feasible objective. Nevertheless, immunization through vaccination is a complex issue and many challenges might appear.
A transcriptionally distinct subpopulation of healthy acinar cells exhibit features of pancreatic progenitors and PDAC
Authors: Gopalan Vishaka , Singh Arashdeep , Rashidi Farid , Wang Li , Ruppin Eytan , Arda Efsun , Hannenhalli Sridhar 
Published: January 2021

AbstractPancreatic ductal adenocarcinoma (PDAC) tumors can originate either from acinar or ductal cells in the adult pancreas. We re-analyze multiple pancreas and PDAC single-cell RNA-seq datasets and find a subset of non-malignant acinar cells, which we refer to as acinar edge (AE) cells, whose transcriptomes highly diverge from a typical acinar cell in each dataset. Genes up-regulated among AE cells are enriched for transcriptomic signatures of pancreatic progenitors, acinar dedifferentiation, and several oncogenic programs. AE-upregulated genes are up-regulated in human PDAC tumors, and consistently, their promoters are hypo-methylated. High expression of these genes is associated with poor patient survival. The fraction of AE-like cells increases with age in healthy pancreatic tissue, which is not explained by clonal mutations, thus pointing to a non-genetic source of variation. We also find edge-like states in lung and liver tissues, suggesting that sub-populations of healthy cells across tissues can exist in pre-malignant states.
CcLBD25functions as a key regulator of haustorium development inCuscuta campestris
Authors: Jhu Min-Yao , Ichihashi Yasunori , Farhi Moran , Wong Caitlin , Sinha Neelima R. 
Published: January 2021

AbstractParasitic plants reduce yield of crops worldwide.Cuscuta campestrisis a stem parasite that attaches to its host, using haustoria to extract nutrients and water. We analyzed the transcriptome of sixC. campestristissues and identified a key gene,CcLBD25, as highly expressed in prehaustoria and haustoria. Our gene co-expression networks (GCN) from different tissue types and laser-capture microdissection (LCM) RNA-Seq data indicate thatCcLBD25could be essential for regulating cell wall loosening and organogenesis. We employed host-induced gene silencing (HIGS) by generating transgenic tomato hosts that express hairpin RNAs to target and down-regulateCcLBD25in the parasite. Our results showed thatC. campestrisgrowing onCcLBD25RNAi transgenic tomatoes transited to the flowering stage earlier and had less biomass compared withC. campestrisgrowing on wild type host. This suggests that the parasites growing on the transgenic plants were stressed due to insufficient nutrient acquisition. Anatomy ofC. campestrishaustoria growing onCcLBD25RNAi tomatoes showed reduced pectin digestion and lack of searching hyphae, which interfered with haustorium penetration and the formation of vascular connections. We developed anin vitrohaustorium (IVH) system to assay the number of prehaustoria produced on strands fromC. campestris. WhenC. campestriswas grown onCcLBD25RNAi tomatoes or wild type tomatoes, the former produce fewer prehaustoria than the latter, indicating that down-regulatingCcLBD25may affect haustorium initiation. The results of this study shed light on the role ofCcLBD25in haustorium development and might help to develop a parasite-resistant system in crops.One-sentence summaryCcLBD25plays a pivotal role in haustorium initiation, regulating pectin digestion, and searching hyphae development during the haustorium penetration process.
All-Flesh Tomato Regulated by Reduced Dosage ofAFFProvides New Insights into Berry Fruit Evolution
Authors: Liu Lei , Zhang Kang , Bai JinRui , Lu Jinghua , Lu Xiaoxiao , Hu Junling , Pan Chunyang , He Shumin , Yuan Jiale , Zhang Yiyue , Zhang Min , Guo Yanmei , Wang Xiaoxuan , Huang Zejun , Du Yongchen , Cheng Feng , Li Junming 
Published: January 2021

ABSTRACTThe formation of locule gel is not only an important developmental process in tomato but also a typical characteristic of berry fruit. In this study, we collected a tomato material that produces all-flesh fruits (AFF), whose locule tissue remains in a solid state during fruit development. We built genetic populations to fine map the causal gene of AFF trait, investigate the function ofAFFgene, and identified it as the causal locus conferring the locule gel formation. We determined the causal mutation as a 416-bp deletion that occurred in the promoter region ofAFF, which reduces the expression dosage ofAFF. The 416-bp deleted sequence has a high level of conservation among closely related Solanaceae species, as well as in the tomato population. The activity of the 416-bp deletion in down-regulating gene expression was further verified by the relative activity in a luciferase experiment. Furthermore, with the BC6 NIL materials, we reveal that the reduced expression dosage ofAFFdoes not impact the normal development of seeds, while produces non-liquefied locule tissue, which is distinct from that of the normal tomatoes in terms of metabolic components. Based on these findings, we propose that theAFFgene is the core node in locule tissue liquefaction, whose function cannot be compensated by its paralogsTAG1, TAGL1, orTAGL11. Our findings provide clues to investigate fruit type differentiation among Solanaceae crops, and also contributes to the breeding application of all flesh fruit tomatoes for the tomato processing industry.One Sentence SummaryThe sequence deletion that occurred in the cis-regulatory region ofAFF—the core node of locule tissue liquefaction determined here—reduced its expression dosage, and produced all flesh fruit tomato.
debar, a sequence-by-sequence denoiser for COI-5P DNA barcode data
Authors: Nugent Cameron M. , Elliott Tyler A. , Ratnasingham Sujeevan , Hebert Paul D. N. , Adamowicz Sarah J. 
Published: January 2021

AbstractDNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising —the separation of biological signal from instrument (technical) noise—of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochromecoxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.
Trial and error: a hierarchical modeling approach to test-retest assessment
Authors: Chen Gang , Pine Daniel S. , Brotman Melissa A. , Smith Ashley R. , Cox Robert W. , Haller Simone P. 
Published: January 2021

AbstractThe concept oftest-retest reliabilityindexes the consistency of a measurement across time. High reliability is critical for any scientific study, but specifically for the study of individual differences. Evidence of poor reliability of commonly used behavioral and functional neuroimaging tasks is mounting. Reports on low reliability of task-based fMRI have called into question the adequacy of using even the most common, well-characterized cognitive tasks with robust population-level effects, to measure individual differences. Here, we lay out a hierarchical framework that estimates reliability as a correlation divorced from trial-level variability, and show that reliability estimates tend to be higher compared to the conventional framework that adopts condition-level modeling and ignores across-trial variability. We examine how estimates from the two frameworks diverge and assess how different factors (e.g., trial and subject sample sizes, relative magnitude of cross-trial variability) impact reliability estimates. We also show that, under specific circumstances, the two statistical frameworks converge. Results from the two approaches are approximately equivalent if (a) the trial sample size is sufficiently large, or (b) cross-trial variability is in the same order of magnitude as, or less than, cross-subject variability. As empirical data indicate that cross-trial variability is large in most tasks, this work highlights that a large number of trials (e.g., greater than 100) may be required to achieve precise reliability estimates. We reference the toolsTRRand3dLMErfor the community to apply trial-level models to behavior and neuroimaging data and discuss how to make these new measurements most useful for current studies.
HIV modifies the m6A and m5C epitranscriptomic landscape of the host cell
Authors: Cristinelli Sara , Angelino Paolo , Janowczyk Andrew , Delorenzi Mauro , Ciuffi Angela 
Published: January 2021

AbstractThe study of RNA modifications, today known as epitranscriptomics, is of growing interest. The N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications are abundantly present on mRNA molecules, and impact RNA interactions with other proteins or molecules, thereby affecting cellular processes, such as RNA splicing, export, stability and translation. Recently m6A and m5C marks were found to be present on human immunodeficiency (HIV) transcripts as well and affect viral replication. Therefore, the discovery of RNA methylation provides a new layer of regulation of HIV expression and replication, and thus offers novel array of opportunities to inhibit replication. However, no study has been performed to date to investigate the impact of HIV replication on the transcript methylation level in the infected cell. We used a productive HIV infection model, consisting of the CD4+ SupT1 T cell line infected with a VSV-G pseudotyped HIVeGFP-based vector, to explore the temporal landscape of m6A and m5C epitranscriptomic marks upon HIV infection, and compare it to mock-treated cells. Cells were collected at 12, 24 and 36h post-infection for mRNA extraction and FACS analysis. M6A RNA modifications were investigated by methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-Seq). M5C RNA modifications were investigated using a bisulfite conversion approach followed by high-throughput sequencing (BS-Seq).Our data suggest that HIV Infection impacted the methylation landscape of HIV-infected cells, inducing mostly increased methylation of cellular transcripts upon infection. Indeed, differential methylation (DM) analysis identified 59 m6A hypermethylated and only 2 hypomethylated transcripts and 14 m5C hypermethylated transcripts and 7 hypomethylated ones. All data and analyses are also freely accessible on an interactive web resource (http://sib-pc17.unil.ch/HIVmain.html). Furthermore, both m6A and m5C methylations were detected on viral transcripts and viral particle RNA genomes, as previously described, but additional patterns were identified.This work used differential epitranscriptomic analysis to identify novel players involved in HIV life cycle, thereby providing innovative opportunities for HIV regulation.