bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Introduction to theCallithrixGenus and Overview of Recent Advances in Marmoset Research
Authors: Malukiewicz Joanna , Boere Vanner , de Oliveira Maria Adélia Borstelmann , D’arc Mirela , Ferreira Jéssica V A , French Jeffrey , Housman Genevieve , de Souza Claudia Igayara , Jerusalinsky Leandro , R de Melo Fabiano , M Valença-Montenegro Mônica , Moreira Silvia Bahadian , de Oliveira e Silva Ita , Pacheco Felipe Santos , Rogers Jeffrey , Pissinatti Alcides , del Rosario Ricardo C H , Ross Corinna , Ruiz-Miranda Carlos R , Pereira Luiz C M , Schiel Nicola , de Fátima Rodrigues da Silva Fernanda , Souto Antonio , Šlipogor Vedrana , Tardif Suzette 
Published: July 2021

AbstractWe provide here a current overview of marmoset (Callithrix) evolution, hybridization, species biology, basic/biomedical research, and conservation initiatives. Composed of 2 subgroups, the aurita group (C aurita and C flaviceps) and the jacchus group (C geoffroyi, C jacchus, C kuhlii, and C penicillata), this relatively young primate radiation is endemic to the Brazilian Cerrado, Caatinga, and Atlantic Forest biomes. Significant impacts on Callithrix within these biomes resulting from anthropogenic activity include (1) population declines, particularly for the aurita group; (2) widespread geographic displacement, biological invasions, and range expansions of C jacchus and C penicillata; (3) anthropogenic hybridization; and (4) epizootic Yellow Fever and Zika viral outbreaks. A number of Brazilian legal and conservation initiatives are now in place to protect the threatened aurita group and increase research about them. Due to their small size and rapid life history, marmosets are prized biomedical models. As a result, there are increasingly sophisticated genomic Callithrix resources available and burgeoning marmoset functional, immuno-, and epigenomic research. In both the laboratory and the wild, marmosets have given us insight into cognition, social group dynamics, human disease, and pregnancy. Callithrix jacchus and C penicillata are emerging neotropical primate models for arbovirus disease, including Dengue and Zika. Wild marmoset populations are helping us understand sylvatic transmission and human spillover of Zika and Yellow Fever viruses. All of these factors are positioning marmosets as preeminent models to facilitate understanding of facets of evolution, hybridization, conservation, human disease, and emerging infectious diseases.
Infernal Affect: Christianity, Urbanization, and Economic Anxiety in China
Authors: Yuan Xiaobo 
Published: July 2021

AbstractThis article examines the making of uneasy relationships between Protestant Christianity, capitalist reform, and urbanization in China. Drawing on analysis of Chinese Christian media sources as well as ethnographic research conducted in the city of Nanjing, I demonstrate how religious communities become attuned to the excesses of urban life—specifically the anxiety, discontent, and mania surrounding housing ownership—and respond to tensions between spiritual feelings and economic activities. These tensions, I argue, in turn generate new vectors of desire and possibilities for collective life. In a heterogenous Chinese Christian landscape, I situate this affective reorientation in the emerging Reformed urban church movement, which has inspired a separatist ethos among underground “house churches.” In doing so, this article illuminates how religious groups work as affective communities in critically orienting to consumer culture and neoliberal individualism.
Persistent HBV replication and serological response during up to 15 years of tenofovir-based antiretroviral therapy in HIV/HBV-coinfected patients: a multicentre prospective cohort study
Authors: Dezanet Lorenza N C , Miailhes Patrick , Lascoux-Combe Caroline , Chas Julie , Maylin Sarah , Gabassi Audrey , Rougier Hayette , Delaugerre Constance , Lacombe Karine , Boyd Anders 
Published: July 2021

Abstract

Objectives
To determine the extent of hepatitis B virus (HBV) suppression and its association with seroclearance of hepatitis ‘e’ antigen (HBeAg) and hepatitis B surface antigen (HBsAg) in HIV/HBV-coinfected patients undergoing long-term tenofovir-based antiretroviral therapy (ART).

Methods
We prospectively followed 165 HIV/HBV-coinfected patients undergoing tenofovir-based ART. Serum HBV-DNA viral loads and HBeAg and HBsAg status were obtained at tenofovir initiation and every 6–12 months. We calculated the proportion achieving virological response (VR, &lt;60 IU/mL) during follow-up. We also calculated rates of HBeAg- and HBsAg-seroclearance, which were compared between those who achieved versus never achieved VR during follow-up using an Exact binomial test.

Results
During a median 8.1 years (IQR = 4.0–13.2) of tenofovir treatment, 152 (92.1%) patients were able to achieve VR and 13 (7.9%) never achieved VR (median HBV-DNA at the end of follow-up = 608 IU/mL, range = 67–52 400 000). The prevalence of individuals with detectable HBV-DNA (≥60 IU/mL) decreased during tenofovir treatment: 15.1% (n = 14/93) at 5 years, 3.2% (n = 2/62) at 10 years and, 3.2% (n = 1/31) at 15 years. 44/96 HBeAg-positive patients (6.15/100 person-years) had HBeAg-seroclearance and 13/165 patients overall (0.87/100 person-years) had HBsAg-seroclearance. No difference in HBeAg-seroclearance was observed between those who achieved versus never achieved VR (7.4 versus 3.7/100 person-years, P = 0.33), while HBsAg-seroclearance was only observed in those with VR (1.0 versus 0/100 person-years, P = 0.49; respectively). Individuals with VR also had a higher frequency of undetectable HIV-RNA during treatment (P &lt; 0.001).

Conclusions
During long-term tenofovir-based ART for HIV/HBV coinfection, persistent HBV viraemia is apparent, but becomes less frequent over time. HBsAg-seroclearance only occurred in those with full HBV and relatively high HIV suppression.
First Detections ofCuliseta longiareolata(Diptera: Culicidae) in Belgium and the Netherlands
Authors: Deblauwe Isra , Ibáñez-Justicia Adolfo , De Wolf Katrien , Smitz Nathalie , Schneider Anna , Stroo Arjan , Jacobs Frans , Vanslembrouck Adwine , Gombeer Sophie , Dekoninck Wouter , Müller Ruth , Van Bortel Wim 
Published: July 2021

AbstractCuliseta (Allotheobaldia) longiareolata (Macquart) (Diptera: Culicidae) is an ornithophilic mosquito species that occurs in the southern Palaearctic Region from the Azores to Central Asia, the Ethiopian Region, India, and Pakistan. Although it has a widespread distribution range, the species was only recently reported in Western and Central Europe. Between 2017 and 2020, larvae, pupae, and adults of Cs. longiareolata (n = 161) were found at 13 distinct locations in Belgium (n = 4) and The Netherlands (n = 9). Collected mosquitoes were morphologically identified and the identification was then validated by COI DNA barcoding. These are the first records of the species in the above-mentioned countries. The present results suggest that Cs. longiareolata could be increasing its distribution range in temperate regions, indicating a warming climate. As the species might be a potential vector of bird pathogens (e.g., West Nile virus), its spread in Western Europe is noteworthy.
Modes of a stellar system II: non-ergodic systems
Authors: Lau Jun Yan , Binney James 
Published: July 2021

ABSTRACT
An equation is derived for the energy of a small disturbance in a system that is generated by a distribution function (DF) of the form f(J) – most galaxies and star clusters can be closely approximated by such a DF. The theory of van Kampen modes is extended to such general systems. A bilinear form on the space of DFs is defined such that the energy of a disturbance is its norm under this form. It is shown that van Kampen modes which differ in frequency are then orthogonal, with the consequence that the energies of van Kampen modes are additive. Consequently, most of the insight into the dynamics of ergodic systems that was gained in a recent paper on the van Kampen modes of ergodic systems applies to real clusters and galaxies.
Stacked CMB lensing and ISW signals around superstructures in the DESI Legacy Survey
Authors: Hang Qianjun , Alam Shadab , Cai Yan-Chuan , Peacock John A 
Published: July 2021

ABSTRACTThe imprints of large-scale structures on the Cosmic Microwave Background (CMB) can be studied via the CMB lensing and Integrated Sachs–Wolfe (ISW) signals. In particular, the stacked ISW signal around supervoids has been claimed in several works to be anomalously high. In this study, we find cluster and void superstructures using four tomographic redshift bins with 0 &lt; z &lt; 0.8 from the DESI Legacy Survey and measure the stacked CMB lensing and ISW signals around them. To compare our measurements with ΛCDM model predictions, we construct a mock catalogue with matched galaxy number density and bias and apply the same photo-z uncertainty as the data. The consistency between the mock and the data is verified via the stacked galaxy density profiles around the superstructures and their quantity. The corresponding lensing convergence and ISW maps are then constructed and compared. The stacked lensing signal agrees with data well except at the highest redshift bin in density peaks, where the mock prediction is significantly higher, by approximately a factor of 1.3. The stacked ISW signal is generally consistent with the mock prediction. We do not obtain a significant signal from voids, AISW = −0.10 ± 0.69, and the signal from clusters, AISW = 1.52 ± 0.72, is at best weakly detected. However, these results are strongly inconsistent with previous claims of ISW signals at many times the level of the ΛCDM prediction. We discuss the comparison of our results with past work in this area and investigate possible explanations for this discrepancy.
Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions
Authors: Treaster Stephen , Daane Jacob M , Harris Matthew P 
Published: July 2021

AbstractThe quest to map the genetic foundations of phenotypes has been empowered by the modern diversity, quality, and availability of genomic resources. Despite these expanding resources, the abundance of variation within lineages makes it challenging to associate genetic change to specific phenotypes, without an a priori means of isolating the changes from background genomic variation. Evolution provides this means through convergence—that is, the shared variation that may result from replicate evolutionary experiments across independent trait occurrences. To leverage these opportunities, we developed TRACCER: Topologically Ranked Analysis of Convergence via Comparative Evolutionary Rates. Compared to current methods, this software empowers rate convergence analysis by factoring in topological relationships, because genetic variation between phylogenetically proximate trait changes is more likely to be facilitating the trait. Comparisons are performed not with singular branches, but with the complete paths to the most recent common ancestor for each pair of lineages. This ensures that comparisons represent a single context diverging over the same timeframe while obviating the problematic requirement of assigning ancestral states. We applied TRACCER to two case studies: mammalian transitions to marine environments, an unambiguous collection of traits that have independently evolved three times; and the evolution of mammalian longevity, a less delineated trait but with more instances to compare. By factoring in topology, TRACCER identifies highly significant, convergent genetic signals, with important incongruities and statistical resolution when compared to existing approaches. These improvements in sensitivity and specificity of convergence analysis generate refined targets for downstream validation and identification of genotype–phenotype relationships.
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
Authors: Chen Jielin , Cheng Mingpan , Salgado Gilmar F , Stadlbauer Petr , Zhang Xiaobo , Amrane Samir , Guédin Aurore , He Fangni , Šponer Jiří , Ju Huangxian , Mergny Jean-Louis , Zhou Jun 
Published: July 2021

Abstract
Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the ‘flanking effect’ in this work. This ‘flanking effect’ was more pronounced when nucleotides were added at the 5′-end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5′-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context.
Global detection of DNA repair outcomes induced by CRISPR–Cas9
Authors: Liu Mengzhu , Zhang Weiwei , Xin Changchang , Yin Jianhang , Shang Yafang , Ai Chen , Li Jiaxin , Meng Fei-Long , Hu Jiazhi 
Published: July 2021

AbstractCRISPR–Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing. The repair of DSBs leads to small insertions or deletions (indels) and other complex byproducts, including large deletions and chromosomal translocations. Indels are well understood to disrupt target genes, while the other deleterious byproducts remain elusive. We developed a new in silico analysis pipeline for the previously described primer-extension-mediated sequencing assay to comprehensively characterize CRISPR–Cas9-induced DSB repair outcomes in human or mouse cells. We identified tremendous deleterious DSB repair byproducts of CRISPR–Cas9 editing, including large deletions, vector integrations, and chromosomal translocations. We further elucidated the important roles of microhomology, chromosomal interaction, recurrent DSBs, and DSB repair pathways in the generation of these byproducts. Our findings provide an extra dimension for genome editing safety besides off-targets. And caution should be exercised to avoid not only off-target damages but also deleterious DSB repair byproducts during genome editing.
Diagnostic application of transcripts associated with antibody-mediated rejection in kidney transplant biopsies
Authors: Toulza Frederic , Dominy Kathy , Willicombe Michelle , Beadle Jack , Santos Eva , Cook H Terence , Szydlo Richard M , McLean Adam , Roufosse Candice 
Published: July 2021

ABSTRACT

Background
The diagnosis of antibody-mediated rejection (AMR) is reached using the Banff Classification for Allograft Pathology, which now includes gene expression analysis. In this study, we investigate the application of ‘increased expression of thoroughly validated gene transcripts/classifiers strongly associated with AMR’ as diagnostic criteria.

Method
We used quantitative real-time polymerase chain reaction for 10 genes associated with AMR in a retrospective cohort of 297 transplant biopsies, including biopsies that met the full diagnostic criteria for AMR, even without molecular data (AMR, n = 27), biopsies that showed features of AMR, but that would only meet criteria for AMR with increased transcripts [suspicious for AMR (AMRsusp), n = 49] and biopsies that would never meet criteria for AMR (No-AMR, n = 221).

Results
A 10-gene AMR score trained by a receiver-operating characteristic to identify AMR found 16 cases with a high score among the AMRsusp cases (AMRsusp-high) that had significantly worse graft survival than those with a low score (AMRsusp-low; n = 33). In both univariate and multivariate Cox regression analysis, the AMR 10-gene score was significantly associated with an increased hazard ratio (HR) for graft loss (GL) in the AMRsusp group (HR = 1.109, P = 0.004 and HR = 1.138, P = 0.012, respectively), but not in the whole cohort. Net reclassification index and integrated discrimination improvement analyses demonstrated improved risk classification and superior discrimination, respectively, for GL when considering the gene score in addition to histological and serological data, but only in the AMRsusp group, not the whole cohort.

Conclusions
This study provides evidence that a gene score strongly associated with AMR helps identify cases at higher risk of GL in biopsies that are suspicious for AMR but do not meet full criteria.
Data brokers co-opetition
Authors: Gu Yiquan , Madio Leonardo , Reggiani Carlo 
Published: July 2021

Abstract
Data brokers share consumer data with rivals and, at the same time, compete with them for selling. We propose a ‘co-opetition’ game of data brokers and characterize their optimal strategies. When data are ‘sub-additive’ with the merged value net of the merging cost being lower than the sum of the values of individual datasets, data brokers are more likely to share their data and sell them jointly. When data are ‘super-additive’, with the merged value being greater than the sum of the individual datasets, competition emerges more often. Finally, data sharing is more likely when data brokers are more efficient at merging datasets than data buyers.
Knockdown of Mitochondrial Uncoupling Proteins 1 and 2 (AtUCP1 and 2) in Arabidopsis thaliana Impacts Vegetative Development and Fertility
Authors: Arcuri Mariana de Lara Campos , Nunes-Laitz Alessandra Vasconcellos , Lima Rômulo Pedro Macêdo , Barreto Pedro , Marinho Andressa Nagatani , Arruda Paulo , Maia Ivan G 
Published: July 2021

ABSTRACT
Mitochondrial uncoupling proteins (UCPs) are mitochondrial inner membrane proteins that dissipate the proton electrochemical gradient generated by the respiratory chain complexes. In plants, these proteins are crucial for maintaining mitochondrial reactive oxygen species (ROS) homeostasis. In this study, single T-DNA insertion mutants for two (AtUCP1 and AtUCP2) out of the three UCP genes present in Arabidopsis thaliana were employed to elucidate their potential roles in planta. Our data revealed a significant increase in the Adenosine triphosphate (ATP)/Adenosine diphosphate (ADP) ratios of both mutants, indicating clear alterations in energy metabolism, and a reduced respiratory rate in atucp2. Phenotypic characterization revealed that atucp1 and atucp2 plants displayed reduced primary root growth under normal and stressed conditions. Moreover, a reduced fertility phenotype was observed in both mutants, which exhibited an increased number of sterile siliques and a lower seed yield compared with wild-type plants. Reciprocal crosses demonstrated that both male fertility and female fertility were compromised in atucp1, while such effect was exclusively observed in the male counterpart in atucp2. Most strikingly, a pronounced accumulation of hydrogen peroxide in the reproductive organs was observed in all mutant lines, indicating a disturbance in ROS homeostasis of mutant flowers. Accordingly, the atucp1 and atucp2 mutants exhibited higher levels of ROS in pollen grains. Further, alternative oxidase 1a was highly induced in mutant flowers, while the expression profiles of transcription factors implicated in gene regulation during female and male reproductive organ/tissue development were perturbed. Overall, these data support the important role for AtUCP1 and AtUCP2 in flower oxidative homeostasis and overall plant fertility.
The ubiquitin-interacting motif-type ubiquitin receptor HDR3 interacts with and stabilizes the histone acetyltransferase GW6a to control the grain size in rice
Authors: Gao Qiong , Zhang Ning , Wang Wei-Qing , Shen Shao-Yan , Bai Chen , Song Xian-Jun 
Published: July 2021

Abstract
For grain crops such as rice (Oryza sativa), grain size substantially affects yield. The histone acetyltransferase GRAIN WEIGHT 6a (GW6a) determines grain size and yield in rice. However, the gene regulatory network underlying GW6a-mediated regulation of grain size has remained elusive. In this study, we show that GW6a interacts with HOMOLOG OF DA1 ON RICE CHROMOSOME 3 (HDR3), a ubiquitin-interacting motif-containing ubiquitin receptor. Transgenic rice plants overexpressing HDR3 produced larger grains, whereas HDR3 knockout lines produce smaller grains compared to the control. Cytological data suggest that HDR3 modulates grain size in a similar manner to GW6a, by altering cell proliferation in spikelet hulls. Mechanistically, HDR3 physically interacts with and stabilizes GW6a in an ubiquitin-dependent manner, delaying protein degradation by the 26S proteasome. The delay in GW6a degradation results in dramatic enhancement of the local acetylation of H3 and H4 histones. Furthermore, RNA sequencing analysis and chromatin immunoprecipitation assays reveal that HDR3 and GW6a bind to the promoters of and modulate a common set of downstream genes. In addition, genetic analysis demonstrates that HDR3 functions in the same genetic pathway as GW6a to regulate the grain size. Therefore, we identified the grain size regulatory module HDR3–GW6a as a potential target for crop yield improvement.
Measuring Bias in Consumer Lending
Authors: Dobbie Will , Liberman Andres , Paravisini Daniel , Pathania Vikram 
Published: July 2021

AbstractThis article tests for bias in consumer lending using administrative data from a high-cost lender in the U.K. We motivate our analysis using a new principal-agent model of bias where loan examiners are incentivized to maximize a short-term outcome, not long-term profits, leading to bias against illiquid applicants at the margin of loan decisions. We identify the profitability of marginal applicants using the quasi-random assignment of loan examiners, finding significant bias against immigrant and older applicants when using the firm’s preferred measure of long-run profits but not when using the short-run measure used to evaluate examiner performance. In this case, market incentives based on characteristics that vary across groups lead to inefficient group-based bias.