bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of healthcare claims to validate the Prevention of Arrhythmia Device Infection Trial cardiac implantable electronic device infection risk score
Authors: Ahmed Fozia Z , Blomström-Lundqvist Carina , Bloom Heather , Cooper Christopher , Ellis Christopher , Goette Andreas , Greenspon Arnold J , Love Charles J , Johansen Jens Brock , Philippon Francois , Tarakji Khaldoun G , Holbrook Reece , Sherfesee Lou , Xia Ying , Seshadri Swathi , Lexcen Daniel R , Krahn Andrew D 
Published: January 2021

Abstract

Aim
The Prevention of Arrhythmia Device Infection Trial (PADIT) infection risk score, developed based on a large prospectively collected data set, identified five independent predictors of cardiac implantable electronic device (CIED) infection. We performed an independent validation of the risk score in a data set extracted from U.S. healthcare claims.

Methods and results
Retrospective identification of index CIED procedures among patients aged ≥18 years with at least one record of a CIED procedure between January 2011 and September 2014 in a U.S health claims database. PADIT risk factors and major CIED infections (with system removal, invasive procedure without system removal, or infection-attributable death) were identified through diagnosis and procedure codes. The data set was randomized by PADIT score into Data Set A (60%) and Data Set B (40%). A frailty model allowing multiple procedures per patient was fit using Data Set A, with PADIT score as the only predictor, excluding patients with prior CIED infection. A data set of 54 042 index procedures among 51 623 patients with 574 infections was extracted. Among patients with no history of prior CIED infection, a 1 unit increase in the PADIT score was associated with a relative 28% increase in infection risk. Prior CIED infection was associated with significant incremental predictive value (HR 5.66, P &lt; 0.0001) after adjusting for PADIT score. A Harrell’s C-statistic for the PADIT score and history of prior CIED infection was 0.76.

Conclusion
The PADIT risk score predicts increased CIED infection risk, identifying higher risk patients that could potentially benefit from targeted interventions to reduce the risk of CIED infection. Prior CIED infection confers incremental predictive value to the PADIT score.
The microbial dimension of submarine groundwater discharge: current challenges and future directions
Authors: Ruiz-González Clara , Rodellas Valentí , Garcia-Orellana Jordi 
Published: January 2021

ABSTRACT
Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.
Accumulation ofcis- andtrans-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species
Authors: Lupo Offir , Krieger Gat , Jonas Felix , Barkai Naama 
Published: January 2021

AbstractGene regulatory variations accumulate during evolution and alter gene expression. While the importance of expression variation in phenotypic evolution is well established, the molecular basis remains largely unknown. Here, we examine two closely related yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus, which show phenotypical differences in morphology and cell cycle progression when grown in the same environment. By profiling the cell cycle transcriptome and binding of key transcription factors (TFs) in the two species and their hybrid, we show that changes in expression levels and dynamics of oscillating genes are dominated by upstream trans-variations. We find that multiple cell cycle regulators show both cis- and trans-regulatory variations, which alters their expression in favor of the different cell cycle phenotypes. Moreover, we show that variations in the cell cycle TFs, Fkh1, and Fkh2 affect both the expression of target genes, and the binding specificity of an interacting TF, Ace2. Our study reveals how multiple variations accumulate and propagate through the gene regulatory network, alter TFs binding, contributing to phenotypic changes in cell cycle progression.
Hox genes are essential for the development of eyespots inBicyclus anynanabutterflies
Authors: Matsuoka Yuji , Monteiro Antónia 
Published: January 2021

AbstractThe eyespot patterns found on the wings of nymphalid butterflies are novel traits that originated first in hindwings and subsequently in forewings, suggesting that eyespot development might be dependent on Hox genes. Hindwings differ from forewings in the expression of Ultrabithorax (Ubx), but the function of this Hox gene in eyespot development as well as that of another Hox gene Antennapedia (Antp), expressed specifically in eyespots centers on both wings, are still unclear. We used CRISPR-Cas9 to target both genes in Bicyclus anynana butterflies. We show that Antp is essential for eyespot development on the forewings and for the differentiation of white centers and larger eyespots on hindwings, whereas Ubx is essential not only for the development of at least some hindwing eyespots but also for repressing the size of other eyespots. Additionally, Antp is essential for the development of silver scales in male wings. In summary, Antp and Ubx, in addition to their conserved roles in modifying serially homologous segments along the anterior–posterior axis of insects, have acquired a novel role in promoting the development of a new set of serial homologs, the eyespot patterns, in both forewings (Antp) and hindwings (Antp and Ubx) of B. anynana butterflies. We propose that the peculiar pattern of eyespot origins on hindwings first, followed by forewings, could be due to an initial co-option of Ubx into eyespot development followed by a later, partially redundant, co-option of Antp into the same network.
Sperm fate is promoted by the mir-44 microRNA family in the Caenorhabditis elegans hermaphrodite germline
Authors: Maniates Katherine A , Olson Benjamin S , Abbott Allison L 
Published: January 2021

Abstract
Posttranscriptional regulation of gene expression, typically effected by RNA-binding proteins, microRNAs (miRNAs), and translation initiation factors, is essential for normal germ cell function. Numerous miRNAs have been detected in the germline; however, the functions of specific miRNAs remain largely unknown. Functions of miRNAs have been difficult to determine as miRNAs often modestly repress target mRNAs and are suggested to sculpt or fine tune gene expression to allow for the robust expression of cell fates. In Caenorhabditis elegans hermaphrodites, cell fate decisions are made for germline sex determination during larval development when sperm are generated in a short window before the switch to oocyte production. Here, analysis of newly generated mir-44 family mutants has identified a family of miRNAs that modulate the germline sex determination pathway in C. elegans. Mutants with the loss of mir-44 and mir-45 produce fewer sperm, showing both a delay in the specification and formation of sperm as well as an early termination of sperm specification accompanied by a premature switch to oocyte production. mir-44 and mir-45 are necessary for the normal period of fog-1 expression in larval development. Through genetic analysis, we find that mir-44 and mir-45 may act upstream of fbf-1 and fem-3 to promote sperm specification. Our research indicates that the mir-44 family promotes sperm cell fate specification during larval development and identifies an additional posttranscriptional regulator of the germline sex determination pathway.
Differential metabolic sensitivity of insulin-like-response- and TORC1-dependent overgrowth inDrosophilafat cells
Authors: Devilliers Maelle , Garrido Damien , Poidevin Mickael , Rubin Thomas , Le Rouzic Arnaud , Montagne Jacques 
Published: January 2021

AbstractGlycolysis and fatty acid (FA) synthesis directs the production of energy-carrying molecules and building blocks necessary to support cell growth, although the absolute requirement of these metabolic pathways must be deeply investigated. Here, we used Drosophila genetics and focus on the TOR (Target of Rapamycin) signaling network that controls cell growth and homeostasis. In mammals, mTOR (mechanistic-TOR) is present in two distinct complexes, mTORC1 and mTORC2; the former directly responds to amino acids and energy levels, whereas the latter sustains insulin-like-peptide (Ilp) response. The TORC1 and Ilp signaling branches can be independently modulated in most Drosophila tissues. We show that TORC1 and Ilp-dependent overgrowth can operate independently in fat cells and that ubiquitous over-activation of TORC1 or Ilp signaling affects basal metabolism, supporting the use of Drosophila as a powerful model to study the link between growth and metabolism. We show that cell-autonomous restriction of glycolysis or FA synthesis in fat cells retrains overgrowth dependent on Ilp signaling but not TORC1 signaling. Additionally, the mutation of FASN (Fatty acid synthase) results in a drop in TORC1 but not Ilp signaling, whereas, at the cell-autonomous level, this mutation affects none of these signals in fat cells. These findings thus reveal differential metabolic sensitivity of TORC1- and Ilp-dependent growth and suggest that cell-autonomous metabolic defects might elicit local compensatory pathways. Conversely, enzyme knockdown in the whole organism results in animal death. Importantly, our study weakens the use of single inhibitors to fight mTOR-related diseases and strengthens the use of drug combination and selective tissue-targeting.
Cotton Fiber Development Requires the Pentatricopeptide Repeat Protein GhIm for Splicing of Mitochondrial nad7 mRNA
Authors: Zhang Dayong , Chen Chuan , Wang Haitang , Niu Erli , Zhao Peiyue , Fang Shuai , Zhu Guozhong , Shang Xiaoguang , Guo Wangzhen 
Published: January 2021

Abstract
Pentatricopeptide repeat (PPR) proteins encoded by nuclear genomes can bind to organellar RNA and are involved in the regulation of RNA metabolism. However, the functions of many PPR proteins remain unknown in plants, especially in polyploidy crops. Here, through a map-based cloning strategy and Clustered regularly interspaced short palindromic repeats/cas9 (CRISPR/cas9) gene editing technology, we cloned and verified an allotetraploid cotton immature fiber (im) mutant gene (GhImA) encoding a PPR protein in chromosome A03, that is associated with the non-fluffy fiber phenotype. GhImA protein targeted mitochondrion and could bind to mitochondrial nad7 mRNA, which encodes the NAD7 subunit of Complex I. GhImA and its homolog GhImD had the same function and were dosage-dependent. GhImA in the im mutant was a null allele with a 22 bp deletion in the coding region. Null GhImA resulted in the insufficient GhIm dosage, affected mitochondrial nad7 pre-mRNA splicing, produced less mature nad7 transcripts, and eventually reduced Complex I activities, up-regulated alternative oxidase metabolism, caused reactive oxygen species (ROS) burst and activation of stress or hormone response processes. This study indicates that the GhIm protein participates in mitochondrial nad7 splicing, affects respiratory metabolism, and further regulates cotton fiber development via ATP supply and ROS balance.
Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila
Authors: Tian Yuan , Smith-Bolton Rachel K 
Published: January 2021

Abstract
To regenerate, damaged tissue must heal the wound, regrow to the proper size, replace the correct cell types, and return to the normal gene-expression program. However, the mechanisms that temporally and spatially control the activation or repression of important genes during regeneration are not fully understood. To determine the role that chromatin modifiers play in regulating gene expression after tissue damage, we induced ablation in Drosophila melanogaster imaginal wing discs, and screened for chromatin regulators that are required for epithelial tissue regeneration. Here, we show that many of these genes are indeed important for promoting or constraining regeneration. Specifically, the two SWI/SNF chromatin-remodeling complexes play distinct roles in regulating different aspects of regeneration. The PBAP complex regulates regenerative growth and developmental timing, and is required for the expression of JNK signaling targets and the growth promoter Myc. By contrast, the BAP complex ensures correct patterning and cell fate by stabilizing the expression of the posterior gene engrailed. Thus, both SWI/SNF complexes are essential for proper gene expression during tissue regeneration, but they play distinct roles in regulating growth and cell fate.
Proper CycE–Cdk2 activity in endocycling tissues requires regulation of the cyclin-dependent kinase inhibitor Dacapo by dE2F1b in Drosophila
Authors: Kim Minhee , Delos Santos Keemo , Moon Nam-Sung 
Published: January 2021

Abstract
Polyploidy is an integral part of development and is associated with cellular stress, aging, and pathological conditions. The endocycle, comprised of successive rounds of G and S phases without mitosis, is widely employed to produce polyploid cells in plants and animals. In Drosophila, maintenance of the endocycle is dependent on E2F-governed oscillations of Cyclin E (CycE)–Cdk2 activity, which is known to be largely regulated at the level of transcription. In this study, we report an additional level of E2F-dependent control of CycE–Cdk2 activity during the endocycle. Genetic experiments revealed that an alternative isoform of Drosophila de2f1, dE2F1b, regulates the expression of the p27CIP/KIP-like Cdk inhibitor Dacapo (Dap). We provide evidence showing that dE2F1b-dependent Dap expression in endocycling tissues is necessary for setting proper CycE–Cdk2 activity. Furthermore, we demonstrate that dE2F1b is required for proliferating cell nuclear antigen expression that establishes a negative feedback loop in S phase. Overall, our study reveals previously unappreciated E2F-dependent regulatory networks that are critical for the periodic transition between G and S phases during the endocycle.
The conserved regulator of autophagy and innate immunity hlh-30/TFEB mediates tolerance of enterohemorrhagic Escherichia coli in Caenorhabditis elegans
Authors: Tsai Chia-En , Yang Fang-Jung , Lee Ching-Han , Hsueh Yen-Ping , Kuo Cheng-Ju , Chen Chang-Shi 
Published: January 2021

Abstract
Infection with antibiotic-resistant bacteria is an emerging life-threatening issue worldwide. Enterohemorrhagic Escherichia coli O157: H7 (EHEC) causes hemorrhagic colitis and hemolytic uremic syndrome via contaminated food. Treatment of EHEC infection with antibiotics is contraindicated because of the risk of worsening the syndrome through the secreted toxins. Identifying the host factors involved in bacterial infection provides information about how to combat this pathogen. In our previous study, we showed that EHEC colonizes in the intestine of Caenorhabditis elegans. However, the host factors involved in EHEC colonization remain elusive. Thus, in this study, we aimed to identify the host factors involved in EHEC colonization. We conducted forward genetic screens to isolate mutants that enhanced EHEC colonization and named this phenotype enhanced intestinal colonization (Inc). Intriguingly, four mutants with the Inc phenotype showed significantly increased EHEC-resistant survival, which contrasts with our current knowledge. Genetic mapping and whole-genome sequencing (WGS) revealed that these mutants have loss-of-function mutations in unc-89. Furthermore, we showed that the tolerance of unc-89(wf132) to EHEC relied on HLH-30/TFEB activation. These findings suggest that hlh-30 plays a key role in pathogen tolerance in C. elegans.
A microbial gene catalog of anaerobic digestion from full-scale biogas plants
Authors: Ma Shichun , Jiang Fan , Huang Yan , Zhang Yan , Wang Sen , Fan Hui , Liu Bo , Li Qiang , Yin Lijuan , Wang Hengchao , Liu Hangwei , Ren Yuwei , Li Shuqu , Cheng Lei , Fan Wei , Deng Yu 
Published: January 2021

Abstract

Background
Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood.

Findings
In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination.

Conclusions
This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.
Detection and source parametrization of small-energy fireball events in Western Alps with ground-based infrasonic arrays
Authors: Belli Giacomo , Pace Emanuele , Marchetti Emanuele 
Published: January 2021

SUMMARY
We present infrasound signals generated by four fireball events occurred in Western Alps between 2016 and 2019 and that were recorded by small aperture arrays at source-to-receiver distances &lt;300 km. Signals consist in a series of short-lived infrasonic arrivals that are closely spaced in time. Each arrival is identified as a cluster of detections with constant wave parameters (backazimuth and apparent velocity), that change however from cluster to cluster. These arrivals are likely generated by multiple infrasonic sources (fragmentations or hypersonic flow) along the entry trajectory. We developed a method, based on 2-D ray tracing and on the independent optically determined time of the event, to locate the source position of the multiple arrivals from a single infrasonic array data and to reconstruct the 3-D trajectory of a meteoroid in the Earth's atmosphere. The trajectories derived from infrasound array analysis are in excellent agreement with trajectories reconstructed from eyewitnesses reports for the four fireballs. Results suggest that the trajectory reconstruction is possible for meteoroid entries located up to ∼300 km from the array, with an accuracy that depends on the source-to-receiver distance and on the signal-to-noise level. We also estimate the energy of the four fireballs using three different empirical laws, based both on period and amplitude of recorded infrasonic signals, and discuss their applicability for the energy estimation of small energy fireball events ($\le 1{\rm{kt\,\,TNT\,\,equivalent}}$).
Compressive learning with privacy guarantees
Authors: Chatalic A , Schellekens V , Houssiau F , de Montjoye Y A , Jacques L , Gribonval R 
Published: January 2021

AbstractThis work addresses the problem of learning from large collections of data with privacy guarantees. The compressive learning framework proposes to deal with the large scale of datasets by compressing them into a single vector of generalized random moments, called a sketch vector, from which the learning task is then performed. We provide sharp bounds on the so-called sensitivity of this sketching mechanism. This allows us to leverage standard techniques to ensure differential privacy—a well-established formalism for defining and quantifying the privacy of a random mechanism—by adding Laplace of Gaussian noise to the sketch. We combine these standard mechanisms with a new feature subsampling mechanism, which reduces the computational cost without damaging privacy. The overall framework is applied to the tasks of Gaussian modeling, k-means clustering and principal component analysis, for which sharp privacy bounds are derived. Empirically, the quality (for subsequent learning) of the compressed representation produced by our mechanism is strongly related with the induced noise level, for which we give analytical expressions.
Sober in Mecca, Drunk in Byzantium: Antinomian Space in the Poetry of ʿAṭṭār
Authors: Zargar Cyrus Ali 
Published: January 2021

AbstractThis paper investigates premodern conceptions of spaces of otherness, particularly within the context of Persian Sufi poetry. Abbasid-era travel literature describing monasteries, as well as real hostilities between Muslims and Christians, gave symbolic dimensions to spaces of antinomian activity in thirteenth-century eastern Iran. Making use of Edward Soja’s thirdspace, as well as Jorge Luis Borges’s the Aleph, this paper pays particular attention to the pseudo-hagiographical narrative of the “Shaykh of Ṣanʿān” in the poem Manṭiq al-Ṭayr (Speech of the Birds). In this account by the Persian poet Farīd al-Dīn ʿAṭṭār (d. 1221), Byzantium contrasts with the Kaʿba in Mecca, just as the wine-house, the Christian church, and the ruins contrast with normative spaces wherein expectations of decorum can lead to ostentatious and insincere modes of worship. By creating magical spaces of infidelity, spaces devoid of piety, ʿAṭṭār conveys themes of losing oneself to a carnal and ultimately divine Other.