bluuebunny/crossref_metadata_2025 huggingface dataset:
Prosecutors and Sentencing
Authors: Demleitner Nora V.
Published: April 2021

Prosecutorial decisions play an important, and sometimes a decisive, role in a defendant’s ultimate sentence. They begin with the selection of charges and may end with a recommendation on clemency or expungement of a criminal conviction. The influence of prosecutors over the sentence, therefore, is far more extensive than that of any other official. The charging decision sets the starting point for the sentence range. The prosecution tends to control entry into diversion programs that may spare an offender a criminal record after complying with a set of requirements. Plea bargains, which have become more frequent even in Europe’s civil law countries, usually focus on the type and scope of the criminal justice sentence. Mandatory minimum sentences, mandatory aggravators, and stacked charges provide prosecutors with overwhelming bargaining power, causing many defendants to waive their right to a trial. Judges tend to follow the parties’ agreements and impose the recommended sentence. In many states prosecutors routinely weigh in on parole decisions and determine whether to proceed against defendants for supervision violations. Even in clemency decisions, they frequently submit a recommendation.
Transnational Climate Law
Authors: Affolder Natasha
Published: April 2021

Climate change shatters the idea that jurisdictional borders and doctrinal debates about the scope of the “legal” are the sole tensions with which a concept of transnational law must contend. Climate change exposes a further fault line underlying legal thought and practice—the ultimate frailty of a model of human/nature interactions premised on the background assumption of an inexhaustible planet of infinite resources. Newly minted climate laws and climate lawsuits are emerging not against a blank slate but rather in a context where the concept of nature as a resource to be exploited for human use is deeply embedded in and through law. This chapter reaches beyond the most visible manifestations of climate law—legislation and lawsuits that appear already bearing the climate law label—to explore the ways in which a transnational law lens illuminates the rather larger subject areas of unenvironmental law and unclean energy law.
Transnational Legal Orders and Global Health
Authors: Ahmed Aziza
Published: April 2021

In studying how public health laws operate, many scholars and practitioners frequently put the the state in the center. This chapter argues that we must look beyond the state. By utilizing a transnational law frame, scholars and practitioners are able to see the many international, regional, and domestic actors that shape national lawmaking on health. A transnational legal analysis allows for the assessment of the factors, including the broader sociopolitical and economic forces that inform lawmaking and domestic actors as they are subject to intersecting layers of governance emanating from national, international, and transnational governance.
Ontogenetic Origins of Infant Pointing
Authors: Liszkowski Ulf , Rüther Johanna Nuria
Published: April 2021

Human pointing is foundational to language acquisition and sociality. The current chapter explores the ontogenetic origins of the human pointing gesture in infancy. First, the authors define infant pointing in terms of function, cognition, motivation, and morphology. Then, the authors review current evidence for predictors of infant pointing on child and caregiver levels, because any predictors provide insights into the basic developmental factors. From this review, the authors introduce and discuss a number of pertinent accounts on the emergence of pointing: social shaping accounts (pointing-from-reaching; pointing-from-non-communicative pointing) and social cognition accounts (pointing-from-imitation; pointing-from-gaze-following). The authors end by presenting a synthesis, which holds that child-level cognitive factors, specifically directedness and social motivation, interact with caregiver-level social factors, specifically responsiveness and assisting actions relevant to infants’ directed activity. The interaction of these factors creates social goals and formats that scale up to pointing acts expressing triadic relations between infant, caregiver, and entities at a distance in the context of joint activity and experience.
Dante’s Other Worlds
Authors: Hawkins Peter S.
Published: April 2021

When Dante chose to situate his Commedia in the three realms of the Catholic afterlife, he had many sources to draw upon: Aeneid VI, the legacy of Scripture, medieval dream visions, theologians like Augustine and Aquinas, iconography, and perhaps even Mohammed’s Night Journey. What he borrowed, however, he invariably made his own. His hell brings order and psychological depth to the traditional welter of infernal retribution. His purgatory spirals above ground along the radiant slopes of an antipodean mountain, while paradise moves from one light show to another before blossoming into a white rose. The cities and landmarks of the world he knew also become ways to conjure the imagined other world, forging a lively connection between the two. Each afterlife realm, moreover, explores a spiritual disposition articulated through landscape, dialogue, and imagery: the claustrophobic egotism of Inferno, the dynamic of transformation in Purgatorio, and the luminous intersubjectivity of Paradiso.
Conversion, Palinody, Traces
Authors: Rushworth Jennifer
Published: April 2021

Taking three terms which represent different ways of relating to experience, time, and narration, this chapter proposes attention to what remains, in the form traces, against the pressure of conversion which requires, instead, a complete break with the past. Traces are here understood as vestiges or footprints, with literal and metaphorical implications inspired by Sigmund Freud’s reading of Gradiva’s footsteps in his essay on Jensen’s novel, and followed back to Beatrice’s footsteps in Vita Nova and Inferno. Just as Freud understands Pompeii as a symbol of a force which is at once destructive and preservative—in other words, repression—, so this chapter shows that palinody in Dante is a mechanism that conserves as well as hides. The resultant understanding of Dante’s works is volcanic as well as non-linear.
Queering Dante
Authors: Cestaro Gary
Published: April 2021

This chapter investigates the queer in Dante. By queer we understand a critical practice that resists both heteronormative assumptions about desire and fixed binary notions of gender. The essay explores where and how Dante’s texts engage difference around sexuality/gender, especially sodomy and same-sex desire. It also surveys professional academic reactions to queer moments in Dante’s poem, particularly the sodomy cantos (Inf. XV–XVI, Purg. XXVI), where we detect a distinct strain of homophobic defensiveness. Finally, the essay begins to recount the fascinating history of Dante reception by queer readers—armchair enthusiasts and activists, scholars, poets, writers, and filmmakers.
Chattel Slaveries in Classical Greece
Authors: Figueira Thomas J. , Jensen Sean R.
Published: April 2021

Greek chattel or commercial slavery developed from general growth and sophistication of economic activity in emerging city-state culture. At Athens and elsewhere, non-commercial forms of slavery evanesced. As the supply of Greek slaves lessened for economic and ideological reasons, Greeks began to acquire slaves almost exclusively from non-Greek peoples. Slaves were considered private property but, as Aristotle argued, they were also considered ‘animate tools’, a category marking distinction from other animal property. Athenian slaves could enjoy a measure of behavioural latitude, some protection from arbitrary violence, and in some ways participated in the wider polis. However, exploitation was normal (sometimes with abuse) and constituted the essence of the slave system. Slave labour was prominent in the classical Greek economy, as slaves were numerous. Finally, although manumission was possible and perhaps frequent, complete integration into wider society was limited at Athens.
Introduction
Authors: Dietze Carola
Published: April 2021

This chapter analyzes the most important trends in the writing of the history of terrorism since the beginning of terrorism research in the late nineteenth century up to today. It presents the origins of terrorism studies in Western social sciences and international relations, and it contextualizes the standard narrative of the history of terrorism put forward by the political scientists David C. Rapoport and Walter Laqueur. The chapter traces major developments in the history of terrorism in professional historiography in the Soviet Union or Russia as well as Europe and the United States during and after the Cold War, and especially since the attacks on September 11, 2001, and it outlines the results and effects of that historiography. On the basis of the evaluation of the scholarship available to date, the article maps out the rationale and the contours of the new global history of terrorism pursued in The Oxford Handbook of the History of Terrorism.
Development, deployment and in-field demonstration of mobile coronavirus SARS-CoV-2 Nucleic acid amplification test
Authors: Paton Teagan F. , Marr Ian , O’Keefe Zoe , Inglis Timothy J. J.
Published: April 2021

Introduction. The evolving SARS-CoV-2 coronavirus pandemic presents a series of challenges to clinical diagnostic services. Many proprietary PCR platforms deployed outside centralised laboratories have limited capacity to upscale when public health demands increase. We set out to develop and validate an open-platform mobile laboratory for remote area COVID-19 diagnosis, with a subsequent field trial.

Gap Statement. In regional Western Australia, molecular diagnostic support is limited to near point-of-care devices. We therefore aimed to demonstrate open-platform capability in a rapidly deployable format within the context of the COVID-19 pandemic.

Methodology. We compared, selected and validated components of a SARS-CoV-2 RT-PCR assay in order to establish a portable molecular diagnostics laboratory. The optimal combination of PCR assay equipment, reagents and consumables required for operation to national standards in regional laboratories was identified. This comprised RNA extraction and purification (QuickGene-480, Kurabo, Japan), a duplex RT-PCR assay (Logix Smart COVID-19, Co-Diagnostics, USA), a Myra liquid handling robot (Biomolecular Systems, Australia) and a magnetic induction thermal cycler (MIC, Biomolecular Systems).

Results The 95 and 99% limits of detection were 1.01 copies μl−1 (5.05 copies per reaction) and 2.80 copies μl−1 (14.00 copies per reaction) respectively. The Co-Diagnostics assay amplified both SARS-CoV-1 and −2 RNA but showed no other cross reactivity. Qualitative results aligned with the reference laboratory SARS-CoV-2 assay (sensitivity 100% [95 % CI 96.48–100%], specificity 100% [95% CI 96.52–100%]). In field trials, the laboratory was operational within an hour of arrival on-site, can process up to 36 samples simultaneously, produces results in two and a half hours from specimen reception, and performed well during six consecutive runs during a 1 week deployment.

Conclusion. Our mobile laboratory enables an adaptive response to increased test demand, and unlike many proprietary point-of-care PCR systems, rapid substitution with an alternative assay if gene targets change or reagent supply chains fail. We envisage operation of this RT-PCR assay as a standby capability to meet varying regional test demands under public health emergency operations guidance.
Kidney function and long-term treatment with lithium salts for bipolar disorder Determinants of mGFR and accuracy of kidney microcysts detection in the diagnosis of CKD
Authors: Tabibzadeh Nahid , Faucon Anne-Laure , Vidal-Petiot Emmanuelle , Serrano Fidéline , Males Lisa , Fernandez Pedro , Khalil Antoine , Rouzet François , Tardivon Coralie , Mazer Nicolas , Dubertret Caroline , Delavest Marine , Marlinge Emeline , Etain Bruno , Bellivier Frank , Vrtovsnik François , Flamant Martin
Published: April 2021

Background and objectives

Kidney damage during early stages of lithium treatment in bipolar disorder is still hypothetical. We aimed at identifying the determinants of a decreased measured glomerular filtration rate (mGFR) and the accuracy of kidney MRI imaging in its detection.

Design, setting, participants and measurements

Cross sectional cohort study. Systematic evaluation including mGFR of 217 consecutive adult patients treated with lithium carbonate. Kidney MRI imaging in 99 patients with half-Fourier turbo spinecho and Single-shot with long echo time sequences.

Results

Median age was 51 [27-62] years, and median lithium treatment duration was 5 [2-14] years. 52% of patients had a stage 2 CKD. In multivariable analysis, the determinants of a lower mGFR were a longer lithium treatment duration (β −0.8 [-1; - 0.6] ml/min/1.73m2GFR decrease for each year of treatment), a higher age (β −0.4 [-0.6; −0.3] ml/min/1.73m2for each year of age, p<0.001), albuminuria (β −3.97 [-6.6;-1.3], p=0.003), hypertension (β −6.85 [-12.6;-1.1], p=0.02) and hypothyroidism (β −7.1 [-11.7;-2.5], p=0.003). Serum lithium concentration was not associated with mGFR. Patients with mGFR<60 ml/min/1.73m2(22%) had a higher prevalence and number of renal microcysts. Renal MRI displayed renal microcyst(s) in 51% of patients, detected as early as one year after lithium treatment initiation. mGFR and lithium treatment duration were strongly correlated in patients with microcyst(s) (r=-0.64, p<0.001), but not in patients with no microcysts (r=-0.24, p=0.09). The presence of microcysts was associated with the detection of an mGFR <45 ml/min/1.73m2(AUC 0.893, p<0.001, sensitivity 80%, specificity 81% for a cut-off value of 5 microcysts).

Conclusions

Besides usual risk factors of GFR decrease, lithium treatment duration strongly impacted mGFR independently of age, especially in patients with microcysts. Hypothyroidism was also negatively associated with kidney function in these patients. MRI might help detect early lithium-induced kidney damage and inform preventive strategies.
An Ecological Study to Investigate Links Between Atmospheric Pollutants From Farming and SARS-CoV-2 Mortality
Authors: Contiero Paolo , Borgini Alessandro , Bertoldi Martina , Abita Anna , Cuffari Giuseppe , Tomao Paola , D’Ovidio Maria Concetta , Reale Stefano , Scibetta Silvia , Tagliabue Giovanna , Boffi Roberto , Krogh Vittorio , Tramuto Fabio , Maida Carmelo Massimo , Mazzucco Walter ,   “SARS-CoV-2 and Environment Working Group”
Published: April 2021

Exposure to atmospheric particulate matter and nitrogen dioxide has been linked to SARS-CoV-2 infection and death. We hypothesized that an interaction between SARS-CoV-2 infection and exposure to farming-related atmospheric pollutants worsens the effect of SARS-CoV-2 on mortality. Our objective was investigate this hypothesis by performing an ecological study in five Italian Regions (Piedmont, Lombardy, Veneto, Emilia-Romagna and Sicily) linking all-cause mortality, by province (administrative entities within regions), to atmospheric particulate matter (PM2.5and PM10) nitrous oxide (N2O), ammonia (NH3) and methane (CH4) mainly produced by agricultural activities. Study outcome was change in all-cause mortality during March-April 2020, compared to March-April 2015-2019 (period) as assessed by mortality rate ratios (MRRs) estimated using multivariate negative binomial regression models that adjusted for air temperature, humidity and population density. The MRR for the interaction of period with NH3exposure, considering all pollutants together was 1.133, equivalent to a 13.3% increase in mortality over and above that due to period (proxy for COVID-19 mortality) for each ton/km2increase in NH3emissions. Although the study was ecological, and did not provide evidence of a causal link between SARS-CoV-2 and farming-related pollutants, in accord with the precautionary principle we recommend application of measures to limit NH3exposure particularly while the COVID-19 pandemic continues.
Distorted TCR repertoires define multisystem inflammatory syndrome in children
Authors: Malik Amna , Tóth Eszter N. , Teng Michelle S. , Hurst Jacob , Watt Eleanor , Wise Lauren , Kent Natalie , Bartram Jack , Grandjean Louis , Dominguez-Villar Margarita , Adams Stuart , Cooper Nichola
Published: April 2021

While the majority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) display mild or no symptoms, rare individuals develop severe disease presenting with multisystem inflammatory syndrome (MIS-C). The reason for variable clinical manifestations is not understood. Here, we carried out TCR sequencing and conducted comparative analyses of TCR repertoires between children with severe (n=12) or mild (n=8) COVID-19. We compared these repertoires with unexposed individuals (samples collected pre-COVID-19 pandemic: n=8) and with the Adaptive Biotechnologies MIRA dataset, which includes over 135,000 high-confidence SARS-CoV-2-specific TCRs. We show that the repertoires of severely ill children are characterised by the expansion of TRBV11-2 chains with high junctional and CDR3 diversity. Moreover, the CDR3 sequences of TRBV11-2 clones shift away from SARS-CoV-2 specific T cell clones, resulting in distorted TCR repertoires. In conclusion, our study reports that CDR3-independent expansion of TRBV11-2+ cells, lacking SARS-CoV-2 specificity, defines severity of disease in children.
Making Words Count with Computerised Identification of Hypertrophic Cardiomyopathy Patients
Authors: Slater Luke T , Bradlow William , Desai Trupti , Aziz Amir , Evison Felicity , Ball Simon , Gkoutos Georgios V.
Published: April 2021

Background

The traditional outpatient model in hypertrophic cardiomyopathy (HCM) is under pressure. Population health management based on an accurate patient record provides an efficient, cost-effective alternative.

Methods

To improve the accuracy of the HCM patient list in a single hospital, we developed a rule-based information extraction natural language processing (NLP) framework. The framework employed ontological expansion of vocabulary and exclusion-first annotation, and received training by an ‘expert in the loop’. The output stratified patients with atrial fibrillation (AF) and heart failure (HF), those without active cardiology care and likely screened individuals.

Results

The algorithm was validated against multiple data sources, including manual validation, for HCM, AF and HF and family history of the disease. Overall precision and recall were 0.854 and 0.865 respectively. The pipeline found 25,356 documents featuring HCM-related terms belonging to 11,083 patients. Excluding scanned documents resulted in 17,178 letters from 3,120 patients. Subsequent categorisation identified 1,753 real cases, of whom 357 had AF and 205 had HF. There were 696 likely screened individuals. Adjusting for 304 false-negative patients, the total HCM cohort was 2,045 patients. 214 were not under a cardiologist. NLP uncovered 709 patients who were absent in the registry or hospital disease codes.

Conclusion

This novel NLP framework generated a hospital-wide record of patients with HCM and defined various cohorts, including the small set of HCM patients lacking current cardiology input. Existing data sources inadequately described this population, spotlighting NLP’s essential role for clinical teams planning to move to a population health management model of care.
Creation of X-linked Alport Syndrome Rat Model withCol4a5Deficiency
Authors: Namba Masumi , Kobayashi Tomoe , Kohno Mayumi , Koyano Takayuki , Hirose Takuo , Fukushima Masaki , Matsuyama Makoto
Published: April 2021

Alport syndrome is an inherited chronic human kidney disease, characterized by glomerular basement membrane abnormalities. This disease is caused by mutations inCOL4A3, COL4A4, orCOL4A5gene. The knockout mice forCol4α3, Col4α4, andCol4α5are developed and well characterized for the study of Alport syndrome. However, disease progression and effects of pharmacological therapy depend on the genetic variability. This model is reliable only to mice. Therefore in this study, we created a novel Alport syndrome rat model utilizing rGONAD technology.Col4α5deficient rats showed hematuria, proteinuria, high levels of BUN, Cre, and then died at 18 to 28 weeks of age (Hemizygous mutant males). Histological and ultrastructural analyses displayed the abnormalities including parietal cell hyperplasia, mesangial sclerosis, and interstitial fibrosis. Then, we demonstrated that α3/α4/α5 (IV) and α5/α5/α6 (IV) chains of type IV collagen disrupted in theCol4α5deficient rats. Moreover, immunofluorescence analyses revealed that some glomeruli ofCol4α5mutant rats were found to be disrupted from postnatal day 0. Thus,Col4α5mutant rat is a reliable candidate for Alport syndrome model for underlying the mechanism of renal diseases and further identifying potential therapeutic targets for human renal diseases.
Genome-wide comprehensive analysis of miRNAs and their target genes expressed in resistant and susceptibleCapsicum annuumlandrace duringPhytophthora capsiciinfection
Authors: Rabuma Tilahun , Gupta Om Prakash , Chhokar Vinod
Published: April 2021

MiRNAs regulate plants responses to fungal infection and immunity by modulating the gene expression. Despite extensive works on miRNA’s role during plant-fungus interaction, work inCapsicum annuum-Phytophthora capsicipathosystem is limited. Therefore, in the current study, genome-wide known and novel miRNAs were identified in two contrasting chilli pepper landraces,i.e.GojamMecha_9086 (resistant) and Dabat_80045 (susceptible) duringP. capsiciinfection. The small RNA deep sequencing resulted in 79 known miRNAs corresponding to 24 miRNAs families and 477 novel miRNAs along with 22,895 potential targets, including 30 defence-related genes againstP. capsiciinfection. The expression analysis of ∼29 known & 157 novel miRNAs in resistant and 30 known and 176 novel miRNAs in susceptible landrace revealed differential accumulation pattern. RT-qPCR of a set of 8 defence related miRNAs representing 4 novel (Pz-novel-miR428-1, Pz-novel-miR160-1, Pz-novel-miR1028-1, Pz-novel-miR204-1) and 4 known (Pz-known-miR803-1, Pz-known-miR2059-1, Pz-known-miR2560-1, Pz-known-miR1872-1) revealed differential accumulation pattern in both resistant and susceptible landrace. Additionally, validation of 8 target genes of corresponding miRNAs using RA-PCR, which as good as 5’ RLM-RACE, revealed an inverse relation with their corresponding miRNAs suggesting their key role during disease response. This study provides comprehensive genome-wide information about the repertoire of miRNAs and their target genes expressed in resistant and susceptible chilli pepper landrace, which can serve as a valuable resource for better understanding the post-transcriptional regulatory mechanism duringC. annuum-P. capsicipathosystem.
CRTC2 regulates plasma cell metabolism and survival
Authors: Hong Jason S , Ahsan Fasih M , Montecino-Rodriguez Encarnacion , Pioli Peter D , Lee Min-sub , Nguyen Thang L , Brooks David G , Golovato Justin , Niazi Kayvan R , Dorshkind Kenneth , Teitell Michael A
Published: April 2021

Antibody secreting cell (ASC) function and longevity determines the strength and durability of a humoral immune response. Previously, we identified the inactivation of the CREB-regulated transcriptional coactivator-2 (CRTC2) in anin vitroB cell differentiation assay that produced functional ASCs. However, the requirement for CRTC2 inactivation in ASC physiologyin vivoremains unknown. Using transgenic (TG) mice that express a constitutively active form of CRTC2 (Crtc2-AA) as an experimental tool, we demonstrate thatCrtc2repression in plasma cells (PCs) is an intrinsic requirement for ASC metabolic fitness. Sustained CRTC2 activity shortens the survival of splenic and bone marrow PCs, resulting in reduced numbers of long-lived PCs and antibody deficits against T cell dependent and independent antigens, and an acute viral infection. TG PCs resemble short-lived PCs with reductions in glycolysis, oxidative metabolism, spare respiratory capacity, and antibody secretion. Mechanistically,Crtc2repression is necessary for the fidelity of PC gene expression and mRNA alternative-splicing programs. Combined,Crtc2repression in PCs must occur to support PC metabolism and extend ASC survival during a humoral immune response.
ARickettsiellaendosymbiont is a potential source of essential B-vitamins for the poultry red mite,Dermanyssus gallinae
Authors: Price Daniel R. G. , Bartley Kathryn , Blake Damer P. , Karp-Tatham Eleanor , Nunn Francesca , Burgess Stewart T. G. , Nisbet Alasdair J.
Published: April 2021

Obligate blood-sucking arthropods rely on symbiotic bacteria to provision essential B vitamins that are either missing or at sub-optimal amounts in their nutritionally challenging blood diet. The poultry red miteDermanyssus gallinae, an obligate blood-feeding ectoparasite, is primarily associated with poultry and a serious threat to the hen egg industry. Thus far, the identity and biological role of nutrient provisioning bacterial mutualists fromD. gallinaeare little understood. Here, we demonstrate that aRickettsiellaGammaproteobacteria in maternally transmitted inD. gallinaeand universally present inD. gallinaemites collected at different sites throughout Europe. In addition, we report the genome sequence of uncultivable endosymbiont “CandidatusRickettsiella rubrum” fromD. gallinaeeggs. The endosymbiont has a circular 1. 89 Mbp genome that encodes 1973 protein. Phylogenetic analysis confirms the placementR. rubrumwithin theRickettsiellagenus, closely related to a facultative endosymbiont from the pea aphid andCoxiella-like endosymbionts from blood feeding ticks. Analysis of theR. rubrumgenome reveals many protein-coding sequences are either pseudogenized or lost, butR. rubrumhas retained several B vitamin biosynthesis pathways, confirming the importance of these pathways in evolution of its nutritional symbiosis withD. gallinae. In silicometabolic pathway reconstruction revealed thatR. rubrumis unable to synthesise protein amino acids and therefore these nutrients are likely provisioned by the host. In contrastR. rubrumretains biosynthetic pathways for B vitamins: thiamine (vitamin B1) via the salvage pathway; riboflavin (vitamin B2) and pyridoxine (vitamin B6) and the cofactors: flavin adenine dinucleotide (FAD) and coenzyme A (CoA) that likely provision these nutrients to the host. We propose that bacterial symbionts which are essential to blood-feeding arthropod survival provide attractive targets for the development of novel control methods.
Transcriptomic analysis of quinoa reveals a group of germin-like proteins induced byTrichoderma
Authors: Rollano-Peñaloza Oscar M. , Mollinedo Patricia A. , Widell Susanne , Rasmusson Allan G.
Published: April 2021

Symbiotic strains of fungi in the genusTrichodermaaffect growth and pathogen resistance of many plant species, but the interaction is not known in molecular detail. Here we describe the transcriptomic response of two cultivars of the cropChenopodium quinoato axenic co-cultivation withTrichoderma harzianumBOL-12 andTrichoderma afroharzianumT22. The response ofC. quinoaroots to BOL-12 and T22 in the early phases of interaction was studied by RNA sequencing and RT-qPCR verification. Interaction with the two fungal strains induced partially overlapping gene expression responses. Comparing the two plant genotypes, a broad spectrum of putative quinoa defense genes were found activated in the cultivar Kurmi but not in the Real cultivar. In cultivar Kurmi, relatively small effects were observed for classical pathogen response pathways but instead aC. quinoa-specific clade of germin-like genes were activated. Germin-like genes were found to be more rapidly induced in cultivar Kurmi as compared to Real. The same germin-like genes were found to also be upregulated systemically in the leaves. No strong correlation was observed between any of the known hormone-mediated defense response pathways and any of the quinoa-Trichodermainteractions. The differences in responses are relevant for the capabilities of applyingTrichodermaagents for crop protection of different cultivars ofC. quinoa.
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae
Authors: Schön Max E. , Zlatogursky Vasily V. , Singh Rohan P. , Poirier Camille , Wilken Susanne , Mathur Varsha , Strassert Jürgen F. H. , Pinhassi Jarone , Worden Alexandra Z. , Keeling Patrick J. , Ettema Thijs J. G. , Wideman Jeremy G. , Burki Fabien
Published: April 2021

The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we used single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.
A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis
Authors: Alvelos Maria Inês , Szymczak Florian , Castela Ângela , Marín-Cañas Sandra , de Souza Bianca Marmontel , Gkantounas Ioannis , Colli Maikel , Fantuzzi Federica , Cosentino Cristina , Igoillo-Esteve Mariana , Marselli Lorella , Marchetti Piero , Cnop Miriam , Eizirik Décio L.
Published: April 2021

Exposure of human pancreatic beta cells to pro-inflammatory cytokines or metabolic stressors is used to model events related to type 1 and type 2 diabetes, respectively. Quantitative real-time PCR is commonly used to quantify changes in gene expression. The selection of the most adequate reference gene(s) for gene expression normalization is an important pre-requisite to obtain accurate and reliable results. There are no universally applicable reference genes, and the human beta cell expression of commonly used reference genes can be altered by different stressors. Here we aimed to identify the most stably expressed genes in human beta cells to normalize quantitative real-time PCR gene expression.

We used comprehensive RNA-sequencing data from the human pancreatic beta cell line EndoC-βH1, human islets exposed to cytokines or the free fatty acid palmitate in order to identify the most stably expressed genes. Genes were filtered based on their level of significance (adjusted P-value >0.05), fold-change (|fold-change| <1.5) and a coefficient of variation <10%. Candidate reference genes were validated by quantitative real-time PCR in independent samples.

We identified a total of 264 genes stably expressed in EndoC-βH1 cells and human islets following cytokine- or palmitate-induced stress, displaying a low coefficient of variation. Validation by quantitative real-time PCR of the top five genesARF1,CWC15,RAB7A,SIAH1andVAPAcorroborated their expression stability under most of the tested conditions. Further validation in independent samples indicated that the geometric mean ofACTBandVAPAexpression can be used as a reliable normalizing factor in human beta cells.
Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer
Authors: Ankill Jørgen , Aure Miriam Ragle , Bjørklund Sunniva , Langberg Severin ,   Oslo Breast Cancer Research Consortium (OSBREAC), Kristensen Vessela N. , Vitelli Valeria , Tekpli Xavier , Fleischer Thomas
Published: April 2021

Breast cancer is a highly heterogeneous disease driven by multiple factors including genetic and epigenetic alterations. DNA methylation patterns have been shown to be altered on a genome-wide scale and previous studies have highlighted the critical role of aberrant DNA methylation on gene expression and breast cancer pathogenesis. Here, we perform genome-wide expression-methylation Quantitative Trait Loci (emQTL), a method for integration of CpG methylation and gene expression to identify disease-driving genes under epigenetic control. By grouping these emQTLs by biclustering we identify associations representing important biological processes associated with breast cancer pathogenesis such as proliferation and tumor infiltrating fibroblasts. We report hypomethylation at enhancers carrying transcription factor binding sites of key proliferation-driving transcription factors such as CEBP-β, FOSL1, and FOSL2, with concomitant high expression of cell cycle- and proliferation-related genes in aggressive breast tumors. The identified CpGs and genes were found to be connected through chromatin loops, together indicating that proliferation in aggressive breast tumors is under epigenetic regulation by DNA methylation. Interestingly, there was a significant correlation between proliferation-related DNA methylation and gene expression also within subtypes of breast cancer, thereby showing that varying proliferation may be explained by epigenetic profiles across breast cancer subtypes. Indeed, the identified proliferation gene signature was prognostic both in the Luminal A and Luminal B subtypes. Taken together, we show that proliferation in breast cancer is linked to hypomethylation at specific enhancers and transcription factor binding mediated through chromatin loops.
DENTATE GRANULE CELLS ARE HYPEREXCITABLE IN THE TGF344-AD RAT MODEL OF ALZHEIMER’S DISEASE
Authors: Smith Lindsey A. , Goodman Anthoni M. , McMahon Lori L.
Published: April 2021

The dentate gyrus is both a critical gatekeeper for hippocampal signal processing and one of the first regions to dysfunction in Alzheimer’s disease (AD). Accordingly, the appropriate balance of excitation and inhibition through the dentate is a compelling target for mechanistic investigation and therapeutic intervention of early AD. Previously, we reported increased LTP magnitude at medial perforant path-dentate granule cell (MPP-DGC) synapses in slices from TgF344-AD rats compared to Wt as early as 6 months. We next determined that the enhanced LTP magnitude was due to heightened function of β-ARs leading us to ask if dentate granule cells (DGCs) also have modified passive or active membrane properties which may also contribute to hyperexcitability or aberrant hippocampal processing. Although there was no detectable difference in spine density and presynaptic release probability, dentate granule cells (DGCs) themselves might have increased electrical response to synaptic input during LTP induction, which was measured as a significant increase in charge transfer during high-frequency stimulation. In this study, we found passive membrane properties and active membrane properties are altered, leading to increased TgF344-AD DGC excitability. Specifically, TgF344-AD DGCs have an increased input resistance and decreased rheobase, decreased sag, and increased action potential (AP) spike accommodation. Importantly, we find that the voltage response increased in DGCs from TgF344-AD compared to Wt accompanied by decreased delay to fire the first AP, indicating that for the same amount of depolarizing current injection TgF344-AD DGCs membranes are more excitable. Taken together, DGCs of TgF344-AD rats are more excitable, but due to heightened accommodation, may be unable to discharge at high frequency for longer durations of time, compared to their Wt littermates.
Thiophenesulfonamides are specific inhibitors of quorum sensing in pathogenic Vibrios
Authors: Newman Jane D. , Shah Priyanka , Chopra Jay , Shi Eda , McFadden Molly E. , Horness Rachel E. , Brown Laura C. , van Kessel Julia C.
Published: April 2021

Vibriobacteria are pathogens of fish, shellfish, coral, and humans due to contaminated seafood consumption.Vibriovirulence factors are controlled by the cell-to-cell communication called quorum sensing, thus this signaling system is a promising target for therapeutic design. We screened a compound library and identified nine compounds, including several 2-thiophenesulfonamides, that inhibit the master quorum sensing transcription factor LuxR inVibrio campbelliibut do not affect cell growth. We synthesized a panel of 50 thiophenesulfonamide compounds to examine the structure-activity relationship effects on quorum sensingin vivo.The most potent molecule identified, PTSP (3-phenyl-1-(thiophen-2-ylsulfonyl)-1H-pyrazole), specifically inhibits LuxR homologs in multiple strains ofVibrio vulnificus,Vibrio parahaemolyticus, andV. campbelliiwith sub-micromolar concentrations. PTSP efficacy is driven by amino acid conservation in the binding pocket, which is accurately predicted usingin silicomodeling of inhibitors. Our results underscore the potential for developing thiophenesulfonamides as specific quorum sensing-directed treatments forVibrioinfections.
Recurrent connectivity underlies lateralized temporal processing differences in Auditory Cortex
Authors: Neophytou Demetrios , Arribas Diego , Levy Robert B. , Park Memming , Oviedo Hysell V.
Published: April 2021

Brain asymmetry in the sensitivity to spectrotemporal modulation is an established functional feature that underlies the perception of speech and music. Recent studies in humans suggest separable neural mechanisms must underlie these cognitively complex functions. The left Auditory Cortex (ACx) is believed to specialize in processing fast temporal components of speech sounds, and the right ACx slower components. However, the circuit features and neural computations behind these lateralized spectrotemporal processes are poorly understood. To answer these mechanistic questions we use mice, an animal model that captures some relevant features of human communication systems. In this study, we screened for circuit features that could subserve temporal integration differences between the left and right ACx. We mapped excitatory input to principal neurons in all cortical layers and found significantly stronger recurrent connections in the superficial layers of the right ACx compared to the left. We hypothesized that the underlying recurrent neural dynamics would exhibit differential characteristic timescales corresponding to their hemispheric specialization. To investigate, we recorded spike trains from awake mice and estimated the network time constants using a quasi-Bayesian method to combine evidence from multiple weak signal-to-noise ratio neurons. We found longer temporal integration windows in the right ACx compared to the left as predicted by stronger recurrent excitation. Our study shows direct evidence that stronger recurrent synaptic connections lead to longer network time scales. These findings support speech processing theories that purport asymmetric integration time constants is a crucial feature of lateralization in auditory processing.
The Instability of Functional Connectomes Across the First Year of Life
Authors: Dufford Alexander J. , Noble Stephanie , Gao Siyuan , Scheinost Dustin
Published: April 2021

The uniqueness and stability of the adolescent and adult functional connectome has been demonstrated to be high (80–95% identification) using connectome-based identification (ID) or “fingerprinting”. However, it is unclear to what extent individuals exhibit similar distinctiveness and stability in infancy, a developmental period of rapid and unparalleled brain development. In this study, we examined connectome-based ID rates within and across the first year of life using a longitudinal infant dataset at 1 month and 9 months of age. We also calculated the test–retest reliability of individual connections across the first year of life using the intraclass correlation coefficient (ICC). Overall, we found substantially lower infant ID rates than have been reported in adult and adolescent populations. Within-session ID rates were moderate and significant (ID = 48.94–70.83%). Between-session ID rates were very low and not significant, with task-to-task connectomes resulting in the highest between-session ID rate (ID = 26.6%). Similarly, average edge-level test-retest reliability was higher within-session than between-session (mean within-session ICC = 0.17, mean between-session ICC = 0.10). These findings suggest a lack of uniqueness and stability in functional connectomes across the first year of life consistent with the unparalleled changes in brain functional organization during this critical period.
Transcriptome profiling reveals CD73 and age-driven changes in neutrophil responses againstStreptococcus pneumoniae
Authors: Bhalla Manmeet , Heinzinger Lauren R. , Morenikeji Olanrewaju B. , Marzullo Brandon , Thomas Bolaji N. , Bou Ghanem Elsa N.
Published: April 2021

Neutrophils are required for host resistance againstStreptococcus pneumoniaebut their function declines with age. We previously found that CD73, an enzyme required for antimicrobial activity, is down-regulated in neutrophils from aged mice. This study explored transcriptional changes in neutrophils induced byS. pneumoniaeto identify pathways controlled by CD73 and dysregulated with age. Ultrapure bone marrow-derived neutrophils isolated from wild type (WT) young, old, and CD73KO young mice were mock-challenged or infected withS. pneumoniae ex vivo. RNA sequencing was performed to identify differentially expressed genes (DEGs). We found that infection triggered distinct global transcriptional changes across hosts, that were strongest in CD73KO neutrophils. Surprisingly, there were more down-regulated than up-regulated genes in all groups upon infection. Down-regulated DEGs indicated a dampening of immune responses in old and CD73KO hosts. Further analysis revealed that CD73KO neutrophils expressed higher numbers of long non-coding RNAs (lncRNAs) compared to WT controls. Predicted network analysis indicated that CD73KO specific lncRNAs control several signaling pathways. We found that genes in the JNK-MAPK-pathway were up-regulated upon infection in CD73KO and WT old but not in young mice. This corresponded to functional differences, as phosphorylation of the downstream AP-1 transcription factor component c-Jun was significantly higher in infected CD73KO and old mice neutrophils. Importantly, inhibiting JNK/AP-1 rescued the ability of these neutrophils to killS. pneumoniae. Altogether, our findings revealed that neutrophils modify their gene expression to better adapt to bacterial infection and that this capacity declines with age and is regulated by CD73.
BRAF inhibitor resistance confers increased sensitivity to mitotic inhibitors
Authors: Misek SA , Dexheimer TS , Akram M , Conrad SE , Schmidt JC , Neubig RR , Gallo KA
Published: April 2021

Single agent and combination therapy with BRAFV600E/Kand MEK inhibitors have remarkable efficacy against melanoma tumors with activating BRAF mutations, but in most cases resistance eventually develops. The purpose of this study is to uncover pharmacological vulnerabilities of BRAFi-resistant melanoma cells, with the goal of identifying new therapeutic options for patients whose tumors have developed resistance to BRAFi/MEKi therapy. We screened a well-annotated compound library against a panel of isogenic pairs of parental and BRAFi-resistant melanoma cell lines to identify classes of compounds that selectively target BRAFi-resistant cells over their BRAFi-sensitive counterparts. Two distinct patterns of increased sensitivity to classes of pharmacological inhibitors emerged. In two cell line pairs, BRAFi resistance conferred increased sensitivity to compounds that share the property of cell cycle arrest at M-phase, including inhibitors of aurora kinase (AURK), polo-like kinase (PLK), tubulin, and kinesin. Live cell microscopy used to track mitosis in real time revealed that parental, but not BRAFi-resistant, melanoma cells were able to exit from compound-induced mitotic arrest through mitotic slippage, thus escaping death. Consistent with the key role of Cyclin B1 levels in regulating mitosis at the spindle checkpoint, in arrested cells we found higher Cyclin B1 levels in parental over BRAFi-resistant melanoma cells, suggesting that altered Cyclin B1 expression levels may explain why these BRAFi resistant cells have gained increased vulnerability to mitotic inhibitors. Another BRAFi-resistant cell line showed increased sensitivity to Chk1/2 inhibitors, possibly due to an accumulation of DNA damage, resulting in mitotic failure. This study shows that BRAFi-resistance in melanoma cells confers vulnerability to pharmacological disruption of mitosis and suggests a targeted synthetic lethal approach to treat BRAF-mutant melanomas that have become resistant to BRAF/MEK-directed therapies.
Microbiota depletion promotes human rotavirus replication in an adult mouse model
Authors: Gozalbo-Rovira Roberto , Santiso-Bellón Cristina , Buesa Javier , del Campo Antonio Rubio , Vila-Vicent Susana , Muñoz Carlos , Yebra María J. , Monedero Vicente , Rodríguez-Díaz Jesús
Published: April 2021

The study of human rotavirus (RV) infectivityin vivohas been limited by the lack of small animal models able to efficiently replicate the principal human RV genotypes. In recent years, intestinal microbiota-virus-host interaction has emerged as a key factor in mediating enteric virus pathogenicity. With the aim of developing an adult mouse infection model for RV we performed faecal microbiota transplant (FMT) with healthy infants as donors in antibiotic-treated mice. Contrarily to control mice, in the FMT group, but also in antibiotic-treated mice without FMT, challenge with the human RV G1P[8] genotype, Wa strain (RVwa), resulted in viral shedding in the faeces for 6 days. RV titres in faeces were also significantly higher in antibiotic-treated animals with or without FMT. This excluded the hypothesis that donor’s microbiota promoted infection. Antibiotic treatment followed by self-FMT resulted in incomplete re-establishment of mouse microbiota which partially restored suppression of RVwainfection. Microbial composition analysis revealed profound changes in the intestinal microbiota of antibiotic-treated animals, whereas some bacterial groups, including members ofLactobacillus, Bilophila, MucispirillumandOscillospira, reappeared after self-FMT. In antibiotic-treated and FMT animals, differences were observed in gene expression of immune mediators such as IL10, TNF-α and IFNγ and the fucosyltransferase FUT2, responsible for H-type antigen synthesis in the small intestine. Collectively, our results suggest that antibiotic-induced microbiota depletion eradicates the microbial taxa that restrict human RV infectivity in mice. Viral permissiveness could involve changes in the innate immune system at the small intestine and alterations in the bacteria population that potentially interact with RV, creating a favourable environment for human RV replication in mice.
Brazilian Land Registry Impacts on Land Use Conversion
Authors: Jung Suhyun , Dyngeland Cecilie , Rausch Lisa , Rasmussen Laura Vang
Published: April 2021

Voluntary land registries can affect land use by facilitating both the public's ability to monitor land use and farmers' access to credit. We estimate the impacts of participation in a land registry on the conversion of natural vegetation to agricultural land use by examining the impacts of the rural environmental registry (CAR) in Brazil, using a dynamic land use model. We show that although participation in the CAR does not significantly affect crop area, it does influence pasture expansion, with variation by farm size and environmental compliance level. Our results provide insights for agricultural land‐use policies by illuminating how the intended environmental objectives of land registry programs might be undermined by credit policies.