bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel hierarchical porous carbon prepared by a one-step template route for electric double layer capacitors and Li–Se battery devices
Authors: Lei Youyi , Liang Xinmiao , Yang Li , Jiang Ping , Lei Zhenyu , Wu Shuaishuai , Feng Jiwen
Published: February 2020

Low-cost hierarchical porous carbon materials with a controllable structure for supercapacitors and lithium selenium batteries.
Functional DNA-based hydrogel intelligent materials for biomedical applications
Authors: Zhou Liping , Jiao Xiangyu , Liu Songyang , Hao Mingda , Cheng Siyang , Zhang Peixun , Wen Yongqiang
Published: February 2020

Multifunctional intelligent DNA hydrogels have been reviewed for many biomedical applications.
Tailoring synaptic plasticity in a perovskite QD-based asymmetric memristor
Authors: Gong Yue , Wang Yan , Li Ronghua , Yang Jia-Qin , Lv Ziyu , Xing Xuechao , Liao Qiufan , Wang Junjie , Chen Jinrui , Zhou Ye , Han Su-Ting
Published: February 2020

Dual direction current modulation has been enabled in an asymmetric electrode configuration, which has been mediated by optoelectronic signals to emulate the important synaptic plasticity.
Interfacial strain driven magnetoelectric coupling in (111)-oriented self-assembled BiFeO3–CoFe2O4 thin films
Authors: Wang Lei , Bian Jihong , Lu Lu , Liang Zhongshuai , Zhang Dawei , Yang Bian , Li Linglong , Lu Guanghao , Yang Yaodong
Published: February 2020

The piezoelectric amplitude drops by 44.7% and meanwhile the out-of-plane tensile strain rises by 11.0% under reverse magnetic fields in (1–3)-type BFO–CFO thin films.
Polarity Inversion Catalysis by the 1,4-Addition of N-Heterocyclic Carbenes
Authors: Nguyen Xuan B. , Nakano Yuji , Lupton David W.
Published: February 2020

Polarity inversion is the hallmark of N-heterocyclic carbene (NHC) organocatalysis, with the generation and reaction of acyl anion equivalents known for more than 70 years. In contrast, polarity inversion through 1,4-addition of NHCs to conjugate acceptors was first applied in a catalytic reaction in 2006. This sub-field of NHC-organocatalysis has developed steadily over the subsequent years, enabling novel coupling reactions, enantioselective cycloisomerizations, polymerizations, and other reactions. In this review, this emerging area of NHC-organocatalysis is discussed with comprehensive coverage. In addition, notes regarding the use of other Lewis base catalysts for related reactions, and comments regarding NHC selection for this type of catalysis, are provided.
Large-scale stage-specific regulation of gene expression during host–pathogen interactions in CSP44 bread wheat carrying APR gene Lr48
Authors: Jain Neelu , Rani Sushma , Sharma Chanchal , Sinha Nivedita , Singh Anupam , Sharma Jai Bhagwan , Prasad Pramod , Saripalli Gautam , Sharma Pradeep Kumar , Balyan Harindra Singh , Gupta Pushpendra Kumar , Prabhu Kumble Vinod
Published: February 2020

Genome-wide transcriptome analysis was undertaken in a leaf-rust resistant bread wheat line CSP44 (selected from Australian cv. Condor) carrying the adult plant resistance (APR) gene Lr48. Two pre-adult plant (P-AP) susceptible stages (S48 and S96) and two adult plant (AP) resistant stages (R48 and R96) were used for RNA-seq. At the susceptible P-AP stage (during S48 to S96), expression increased in 2062 genes, and declined in 130 genes; 1775 of 2062 differentially expressed genes (DEGs) also exhibited high expression during early incompatible stage R48. Comparison of S96 with R96 showed that the expression of 80 genes was enhanced and that of 208 genes declined at the AP stage. At the resistant AP stage (during R48 to R96), expression of mere 25 genes increased and that of 126 genes declined. Apparently, the resistance during late adult stage (R96) is caused by regulation of the expression of relatively fewer genes, although at pre-adult stage (S48 to S96), expression of large number of genes increased; expression of majority of these genes kept on increasing during adult stage at R48 also. These and other results of the present study suggest that APR may mimic some kind of systemic acquired resistance (SAR). The host-specific DEGs belonged to 10 different classes including genes involved in defence, transport, epigenetics, photosynthesis, genes encoding some transcription factors etc. The pathogen (Puccinia triticina) specific DEGs (including three genes encoding known biotrophic effectors) seem to help the pathogen in infection/growth through large-scale stage-specific enhanced expression of host’s genes. A putative candidate gene for Lr48 containing protein kinase domain (its ortholog in rice encoding OsWAK8) was also identified.
Arabidopsis cysteine-rich trans-membrane module (CYSTM) small proteins play a protective role mainly against heat and UV stresses
Authors: Joshi Janak Raj , Singh Vikram , Friedman Haya
Published: February 2020

The genomes of Arabidopsis and other plants contain cysteine-rich small protein of unknown function, harbouring a transmembrane module (CYSTM proteins). In this work we show that the transcript of one gene (At1g05340) encoding a CYSTM protein is induced mainly by heat and to a lesser extent by UV, but less by NaCl or sorbitol. A functional analysis of At1g05340 and its paralog At2g32210 using T-DNA insertional mutants revealed a decrease in seedlings root length, and a lower PSII efficiency in mature plant, due to heat stress and to a lesser extent due to UV stress, in comparison to the effect on wild-type plants. The sensitivity of these mutants to salt or osmotic stresses did not differ from wild type response, indicating a specific function for these genes in heat and UV. Heat and UV increased reactive oxygen species levels in wild type; however, the levels were higher in the mutant line than in wild type due to heat treatment, but was similar in the mutant lines and wild type due to UV stress. Taken together, our results suggest that these small cysteine-rich proteins are necessary for thermotolerance and protection from UV exposure. The proteins encoded by these genes most likely, act in heat stress by reducing reactive oxygen species level by yet unknown mechanism.
Are endourological procedures for nephrolithiasis treatment associated with renal injury? A review of potential mechanisms and novel diagnostic indexes
Authors: Mykoniatis Ioannis , Sarafidis Pantelis , Memmos Dimitrios , Anastasiadis Anastasios , Dimitriadis Georgios , Hatzichristou Dimitrios
Published: February 2020

Nephrolithiasis is one of the most common urological conditions with a huge socio-economic impact. About 50% of recurrent stone-formers have just one lifetime recurrence and >10% of patients present with a high recurrent disease requiring subsequent and sometimes multiple surgical interventions. The advent of new technology has made endourological procedures the pinnacle of stone treatment, including procedures like percutaneous nephrolithotomy (PCNL), retrograde intrarenal surgery and miniaturized PCNL procedures. Researchers have primarily focused on comparisons with respect to stone-free rates, procedure parameters and post-operative complications. However, the effect of these three procedures on renal function or indexes of renal injury has not been sufficiently examined. This was only reported in a few studies as a secondary objective with the use of common and not the appropriate and detailed renal parameters. This review presents current literature regarding the use of novel and highly predictive biomarkers for diagnosing acute kidney injury, discusses potential mechanisms through which endourological procedures for renal stone treatment may affect renal function and proposes areas with open questions where future research efforts in the field should focus.
Spatiotemporal trends and prognosis of end-stage renal disease patients with biopsy-proven immunoglobulin A nephropathy in France from 2010 to 2014
Authors: Robert Thomas , Jantzen Rodolphe , Cambier Alexandra , Jamme Matthieu , Couchoud Cecile , Brunet Philippe , Gentile Stéphanie , Rondeau Eric , Mesnard Laurent , Lapidus Nathanael ,   the REIN registry
Published: February 2020

Background

Although end-stage renal disease (ESRD) is frequently used as an outcome marker for primary immunoglobulin A nephropathy (IgAN), the clinical course after reaching ESRD is not well documented. This study examined patients’ characteristics and survival in ESRD-related biopsy-proven IgAN in France.

Methods

French Renal Epidemiology and Information Network Registry data from 2010 to 2014 were used to analyse patients’ survival and outcome in incident ESRD patients >16 years of age with biopsy-proven primary IgAN, in comparison with other primary and secondary glomerulonephritis (GN), adult polycystic kidney disease (ADPKD) or diabetes. Multivariable survival analysis was adjusted for age, sex, time on dialysis and comorbidities.

Results

Among 17 138 incident dialysis patients with ESRD, IgAN (242.8/10 000 dialysis initiation) represents the most common GN related to ESRD during 2010. IgAN patients were the youngest, and had the fewest comorbidities and the highest use of peritoneal dialysis (PD) (17%). In comparison with the haemodialysis group, hazard ratios for death were not different in the preemptive transplantation group [0.46, 95% confidence interval (CI) 0.17–1.28] and in the PD group (0.77, 95% CI 0.44–1.33). Mortality rates in IgAN patients with preemptive transplantation and in those receiving dialysis waiting for transplantation were 2.9% (95% CI 0.0–5.6) and 6.7% (95% CI 0.9–12.3). Mortality rates of ADPKD patients receiving dialysis waiting for transplantation were higher (18%, 95% CI 3.1–30.6).

Conclusion

IgAN has the best prognosis among primary and secondary GN. IgAN patients receiving dialysis waiting transplantation seem to have a more favourable prognosis than ADPKD patients, who usually comprise the reference population. The underlying reasons for the difference in access treatment modalities should be investigated to improve survival with respect to renal disease.
Bridge to recovery with Berlin Heart EXCOR in children <10 kg with dilated cardiomyopathy: a histological analysis
Authors: Tominaga Yuji , Ueno Takayoshi , Kido Takashi , Kanaya Tomomitsu , Narita Jun , Ishida Hidekazu , Toda Koichi , Kuratani Toru , Sawa Yoshiki
Published: February 2020

OBJECTIVES

This study aimed to identify the histological characteristics associated with bridge to recovery using Berlin Heart EXCOR® (BHE) in paediatric patients <10 kg with dilated cardiomyopathy.

METHODS

Of the 10 consecutive patients <10 kg with dilated cardiomyopathy who underwent BHE implantation between 2013 and 2018, 4 patients showed improvement in left ventricular (LV) function, resulting in successful BHE explantation (recovery group). The remaining 6 patients showed persistent LV dysfunction and underwent heart transplantation (non-recovery group). The following variables were compared between the 2 groups: (i) histological findings in LV myocardium obtained at BHE implantation and (ii) LV function after BHE implantation assessed with echocardiography and cardiac catheterization.

RESULTS

The degree of myocardial fibrosis was significantly lower, and the capillary vascular density was significantly higher in the recovery group than in the non-recovery group [16% (standard deviation 5.9%) vs 28% (5.9%), P = 0.021, and 65 (11) vs 43 (18) units/high-power field, P = 0.037, respectively]. The changes during 3 months after BHE implantation in LV diastolic dimension (z-score) and ejection fraction were significantly greater in the recovery group than in the non-recovery group [−9.6 (3.5) vs −3.6 (4.5), P = 0.045, and 36% (13%) vs 13% (13%), P = 0.032, respectively].

CONCLUSIONS

In paediatric patients <10 kg with dilated cardiomyopathy, bridge to recovery with BHE implantation was achieved in patients with less injured LV myocardial histology at BHE implantation.
Performance of Rapid Polymyxin™ NP and Rapid Polymyxin™ Acinetobacter for the detection of polymyxin resistance in carbapenem-resistant Acinetobacter baumannii and Enterobacterales
Authors: Kon Hadas , Abramov Shirin , Amar Ben Dalak Maayan , Elmaliach Noy , Schwartz David , Carmeli Yehuda , Lellouche Jonathan
Published: February 2020

Background

The global spread of carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii (CRAB) has prompted the reintroduction of colistin as a last-resort treatment. Although the recommended method for colistin susceptibility testing is broth microdilution (BMD), methods that are more rapid and easy to use are needed.

Objectives

To evaluate the performance of two commercial kits for colistin susceptibility testing: Rapid Polymyxin™ NP (RP-NP) for CRE and Rapid Polymyxin™ Acinetobacter (RP-AB) for CRAB.

Methods

A total of 76 CRE and 87 CRAB isolates were collected from hospitalized patients in Europe and Israel. The isolates were subcultured twice on 5% sheep blood in tryptic soy agar. We tested colistin susceptibility using the RP-NP and RP-AB kits and compared the results with those from BMD.

Results

Of the CRE isolates, 25% (19/76) were resistant to colistin using BMD. Categorical agreement between RP-NP and BMD was 93.4% (71/76), major errors 1.8% (1/57) and very major errors 21.1% (4/19). Sensitivity was 78.9% and specificity was 98.2%. Of the CRAB isolates, 58.6% (51/87) were resistant to colistin by BMD. Categorical agreement between RP-AB and BMD was 59.8% (52/87), major errors 13.9% (5/36) and very major errors 58.8% (30/51). Sensitivity of RP-AB was 41.2% and specificity was 86.1%.

Conclusions

In many of the tested isolates, weak or inconclusive colour changes in the test wells caused difficulty in interpretation, resulting in an unacceptable rate of very major errors.
Mycobacterium abscessus infection of a new tattoo in an Australian traveller returning from Bali, Indonesia
Authors: Kerkemeyer Karolina L , Darby Jonathan D , Green Jack
Published: February 2020

Skin infection with atypical mycobacteria can occur following inoculation by tattooing. It may be seen in clinical practice with increasing frequency due to the popularity of tattooing among travellers. Diagnosis requires fresh tissue biopsy requested for mycobacterial culture, and treatment involves prolonged combination antimicrobial therapy guided by sensitivities.
Molecular and functional characterization of the SBP-box transcription factor SPL-CNR in tomato fruit ripening and cell death
Authors: Lai Tongfei , Wang Xiaohong , Ye Bishun , Jin Mingfei , Chen Weiwei , Wang Ying , Zhou Yingying , Blanks Andrew M , Gu Mei , Zhang Pengcheng , Zhang Xinlian , Li Chunyang , Wang Huizhong , Liu Yule , Gallusci Philippe , Tör Mahmut , Hong Yiguo
Published: February 2020

SlSPL-CNR, an SBP-box transcription factor (TF) gene residing at the epimutant Colourless non-ripening (Cnr) locus, is involved in tomato ripening. This epimutant provides a unique model to investigate the (epi)genetic basis of fruit ripening. Here we report that SlSPL-CNR is a nucleus-localized protein with a distinct monopartite nuclear localization signal (NLS). It consists of four consecutive residues ‘ 30KRKR33’ at the N-terminus of the protein. Mutation of the NLS abolishes SlSPL-CNR’s ability to localize in the nucleus. SlSPL-CNR comprises two zinc-finger motifs (ZFMs) within the C-terminal SBP-box domain. Both ZFMs contribute to zinc-binding activity. SlSPL-CNR can induce cell death in tomato and tobacco, dependent on its nuclear localization. However, the two ZFMs have differential impacts on SlSPL-CNR’s induction of severe necrosis or mild necrotic ringspot. NLS and ZFM mutants cannot complement Cnr fruits to ripen. SlSPL-CNR interacts with SlSnRK1. Virus-induced SlSnRK1 silencing leads to reduction in expression of ripening-related genes and inhibits ripening in tomato. We conclude that SlSPL-CNR is a multifunctional protein that consists of a distinct monopartite NLS, binds to zinc, and interacts with SlSnRK1 to affect cell death and tomato fruit ripening.
Towards automated detection of psychosocial risk factors with text mining
Authors: Uronen L , Moen H , Teperi S , Martimo K-P , Hartiala J , Salanterä S
Published: February 2020

Background

Psychosocial risk factors influence early retirement and absence from work. Health checks by occupational health nurses (OHNs) may prevent deterioration of work ability. Health checks are documented electronically mostly as free text, and therefore the effect of psychological risk factors on working capacity is difficult to detect.

Aims

To evaluate the potential of text mining for automated early detection of psychosocial risk factors by examining health check free-text documentation, which may indicate medical statements recommending early retirement, prolonged sick leave or rehabilitation. Psychosocial risk factors were extracted from OHN documentation in a nationwide occupational health care registry.

Methods

Analysis of health check documentation and medical statements regarding pension, sick leave and rehabilitation. Annotations of 13 psychosocial factors based on the Prima-EF standard (PAS 1010) were used with a combination of unsupervised machine learning, a document search engine and manual filtering.

Results

Health check documentation was analysed for 7078 employees. In 83% of their health checks, psychosocial risk factors were mentioned. All of these occurred more frequently in the group that received medical statements for pension, rehabilitation or sick leave than the group that did not receive medical statement. Documentation of career development and work control indicated future loss of work ability.

Conclusions

This study showed that it was possible to detect risk factors for sick leave, rehabilitation and pension from free-text documentation of health checks. It is suggested to develop a text mining tool to automate the detection of psychosocial risk factors at an early stage.
Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA
Authors: Madru Clément , Raia Pierre , Hugonneau-Beaufet Inès , Pehau-Arnaudet Gérard , England Patrick , Lindahl Erik , Delarue Marc , Carroni Marta , Sauguet Ludovic
Published: February 2020

Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD-PCNA complex fromPyrococcus abyssiat 3.77Å. Using an integrative structural biology approach - combining cryo-EM, X-ray crystallography and protein-protein interaction measurements - we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA with an unprecedented level of detail. PolD recruits PCNAviaa complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polα replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation phase and a processive phase during replication.
Semi-supervised segmentation and genome annotation
Authors: Chan Rachel C.W. , McNeil Matthew , Roberts Eric G. , Mendez Mickaël , Libbrecht Maxwell W. , Hoffman Michael M.
Published: February 2020

Segmentation and genome annotation methods automatically discover joint signal patterns in whole genome datasets. Previously, researchers trained these algorithms in a fully unsupervised way, with no prior knowledge of the functions of particular regions. Adding information provided by expert-created annotations to supervise training could improve the annotations created by these methods. We implemented semi-supervised learning using virtual evidence in the annotation method Segway. Additionally, we defined a positionally tolerant precision and recall metric for scoring genome annotations based on the proximity of each annotation feature to the truth set. We demonstrate semi-supervised Segway’s ability to learn patterns corresponding to provided transcription start sites on a specified supervision label, and subsequently recover other transcription start sites in unseen data on the same supervision label.
Early dynamics of transmission and control of COVID-19: a mathematical modelling study
Authors: Kucharski Adam J , Russell Timothy W , Diamond Charlie , Liu Yang ,   CMMID nCoV working group, Edmunds John , Funk Sebastian , Eggo Rosalind M
Published: February 2020

Background

An outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.

Methods

We combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.

Findings

We estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.

Interpretation

Our results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.

Funding

Wellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)
Phase separation of toxic dipeptide repeat proteins related to C9orf72 ALS/FTD
Authors: Jafarinia Hamidreza , van der Giessen Erik , Onck Patrick R.
Published: February 2020

The expansion mutation in the C9orf72 gene is the most common known genetic cause for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). This mutation can produce five dipeptide repeat proteins (DPRs), of which three are known to be toxic: poly-PR, poly-GR, and poly-GA. The toxicity of poly-GA is attributed to its aggregation in the cytoplasm, while for poly-PR and poly-GR several toxicity pathways have been proposed. The toxicity of the DPRs has been shown to depend on their length, but the underlying molecular mechanism of this length dependence is not well understood. To address this, a one-bead-per-amino-acid (1BPA) coarse-grained molecular dynamics model is used to study the single-molecule and phase separation properties of the DPRs. We find a strong dependence of the phase separation behavior on both DPR length and concentration, with longer DPRs having a higher propensity to phase separate and form condensed phases with higher concentrations. The critical lengths required for phase separation (25 for poly-PR and 50 for poly-GA) are comparable to the toxicity threshold limit of 30 repeats found for the expansion mutation in patient cells, suggesting that phase separation could play an important role in DPR toxicity.
Artificial-Cell-Type Aware Cell Type Classification in CITE-seq
Authors: Lian Qiuyu , Xin Hongyi , Ma Jianzhu , Konnikova Liza , Chen Wei , Gu Jin , Chen Kong
Published: February 2020

Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), couples the measurement of surface marker proteins with simultaneous sequencing of mRNA at single cell level, which brings accurate cell surface phenotyping to single cell transcriptomics. Unfortunately, multiplets in CITE-seq datasets create artificial cell types and complicates the automation of cell surface phenotyping. We propose CITE-sort, an artificial-cell-type aware surface marker clustering method for CITE-seq. CITE-sort is aware of and is robust to multiplet-induced artificial cell types. We benchmarked CITE-sort with real and simulated CITE-seq datasets and compared CITE-sort against canonical clustering methods. We show that CITE-sort produces the best clustering performance across the board. CITE-sort not only accurately identifies real biological cell types but also consistently and reliably separates multiplet-induced artificial-cell-type droplet clusters from real biological-cell-type droplet clusters. In addition, CITE-sort organizes its clustering process with a binary tree, which facilitates easy interpretation and verification of its clustering result and simplifies cell type annotation with domain knowledge in CITE-seq.
Osh6 requires Ist2 for localization to the ER-PM contacts and efficient phosphatidylserine transport
Authors: Martín D’Ambrosio Juan , Albanèse Véronique , Lipp Nicolas-Frédéric , Fleuriot Lucile , Debayle Delphine , Drin Guillaume , Čopič Alenka
Published: February 2020

Osh6 and Osh7 are lipid transfer proteins (LTPs) that move phosphatidylserine (PS) from the endoplasmic reticulum (ER) to the plasma membrane (PM). High PS level at the PM is key for many cellular functions. Intriguingly, Osh6/7 localize to ER-PM contact sites, although they lack membrane-targeting motifs, in contrast to multidomain LTPs that both bridge membranes and convey lipids. We show that Osh6 localization to contact sites depends on its interaction with the cytosolic tail of the ER-PM tether Ist2, a homologue of TMEM16 proteins. We identify a motif in the Ist2 tail, conserved in yeasts, as the Osh6-binding region, and we map an Ist2-binding surface on Osh6. Mutations in the Ist2 tail phenocopyosh6Δ osh7Δdeletion: they decrease cellular PS levels, and block PS transport to the PM. Our study unveils an unexpected partnership between a TMEM16-like protein and a soluble LTP, which together mediate lipid transport at contact sites.
Anterior thalamic function is required for spatial coding in the subiculum and is necessary for spatial memory
Authors: Frost Bethany E. , Martin Sean K. , Cafalchio Matheus , Islam Md Nurul , Aggleton John P. , O’Mara Shane M.
Published: February 2020

Hippocampal function relies on the anterior thalamic nuclei, but the reasons remain poorly understood. While anterior thalamic lesions disrupt parahippocampal spatial signalling, their impact on the subiculum is unknown, despite the importance of this area for hippocampal networks. We recorded subicular cells in rats with either permanent (N-methyl-D-aspartic acid) or reversible (muscimol) anterior thalamic lesions. Bayesian and other statistical analyses underscored the notable absence of the diverse spatial signals normally found in the subiculum, including place cells, following permanent anterior thalamic lesions. Likewise, there was marked disruption of these diverse spatial signals during transient lesions. By contrast, permanent anterior thalamic lesions had no discernible impact on CA1 place fields. Anterior thalamic lesions reduced spatial alternation performance (permanently or reversibly) to chance, while leaving a non-spatial recognition memory task unaffected. These findings, which help explain why anterior thalamic damage is so deleterious for spatial memory, cast a new spotlight on the importance of subiculum function and reveal its dependence on anterior thalamic signalling.

Graphical Abstract
In vitroandin vivodevelopment of the human intestinal niche at single cell resolution
Authors: Czerwinski Michael , Holloway Emily M. , Tsai Yu-Hwai , Wu Angeline , Yu Qianhui , Wu Josh , Walton Katherine D. , Sweet Caden , Childs Charlie , Glass Ian , Treutlein Barbara , Camp J. Gray , Spence Jason R.
Published: February 2020

The human intestinal stem cell (ISC) niche supports ISC self-renewal and epithelial function, yet little is known about the development of the human ISC niche. We used single-cell mRNA sequencing (scRNA-seq) to interrogate the human intestine across 7-21 weeks of gestation. Using these data coupled with marker validationin situ, molecular identities and spatial locations were assigned to several cell populations that comprise the epithelial niche, and the cellular origins of many niche factors were determined. The major source of WNT and RSPONDIN ligands were ACTA2+ cells of the muscularis mucosa. EGFwas predominantly expressed in the villus epithelium and the EGF-family memberNEUREGULIN1(NRG1) was expressed by subepithelial mesenchymal cells. Functional data from enteroid cultures showed that NRG1 improved cellular diversity, enhanced the stem cell gene signature, and increased enteroid forming efficiency, whereas EGF supported a secretory gene expression profile and stimulated rapid proliferation. This work highlights unappreciated complexities of intestinal EGF/ERBB signaling and identifies NRG1 as a stem cell niche factor.
VSS: Variance-stabilized signals for sequencing-based genomic signals
Authors: Bayat Faezeh , Libbrecht Maxwell
Published: February 2020

Motivation

A sequencing-based genomic assay such as ChIP-seq outputs a real-valued signal for each position in the genome that measures the strength of activity at that position. Most genomic signals lack the property of variance stabilization. That is, a difference between 100 and 200 reads usually has a very different statistical importance from a difference between 1,100 and 1,200 reads. A statistical model such as a negative binomial distribution can account for this pattern, but learning these models is computationally challenging. Therefore, many applications—including imputation and segmentation and genome annotation (SAGA)—instead use Gaussian models and use a transformation such as log or inverse hyperbolic sine (asinh) to stabilize variance.

Results

We show here that existing transformations do not fully stabilize variance in genomic data sets. To solve this issue, we propose VSS, a method that produces variance-stabilized signals for sequencingbased genomic signals. VSS learns the empirical relationship between the mean and variance of a given signal data set and produces transformed signals that normalize for this dependence. We show that VSS successfully stabilizes variance and that doing so improves downstream applications such as SAGA. VSS will eliminate the need for downstream methods to implement complex mean-variance relationship models, and will enable genomic signals to be easily understood by eye.

Contact

maxwl@sfu.ca.

Availability

https://github.com/faezeh-bayat/Variance-stabilized-units-for-sequencing-based-genomic-signals.
DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening
Authors: Fine Jonathan , Muhoberac Matthew , Fraux Guillaume , Chopra Gaurav
Published: February 2020

Benchmarking is a crucial step in evaluating virtual screening methods for drug discovery. One major issue that arises among benchmarking datasets is a lack of a standardized format for representing the protein and ligand structures used to benchmark the virtual screening method. To address this, we introduce the Directory of Useful Benchmarking Sets (DUBS) framework, as a simple and flexible tool to rapidly created benchmarking sets using the protein databank. DUBS uses a simple input text based format along with the Lemon data mining framework to efficiently access and organize data to protein databank and output commonly used inputs for virtual screening software. The simple input format used by DUBS allows users to define their own benchmarking datasets and access the corresponding information directly from the software package. Currently, it only takes DUBS less than 2 minutes to create a benchmark using this format. Since DUBS uses a simple python script, users can easily modify to create more complex benchmarks. We hope that DUBS will be a useful community resource to provide a standardized representation for benchmarking datasets in virtual screening.
rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments
Authors: Chow Eugene Yui-Ching , Lyu Kaixin , Kwok Chun Kit , Chan Ting-Fung
Published: February 2020

We recently developed the rG4-seq method to detect and map in vitro RNA G-quadruplex (rG4s) structures on a transcriptome-wide scale. rG4-seq of purified human HeLa RNA has revealed many non-canonical rG4s and the effects adjacent sequences have on rG4 formation. In this study, we aimed to improve the outcomes and false-positive discrimination in rG4-seq experiments using a bioinformatic approach. By establishing connections between rG4-seq library preparation chemistry and the underlying properties of sequencing data, we identified how to mitigate indigenous sampling errors and background noise in rG4-seq. We applied these findings to develop a novel bioinformatics pipeline named rG4-seeker(https://github.com/TF-Chan-Lab/rG4-seeker), which uses tailored noise models to autonomously assess and optimize rG4 detections in a replicate-independent manner. Compared with previous methods, rG4-seeker exhibited better false-positive discrimination and improved sensitivity for non-canonical rG4s. Using rG4-seeker, we identified novel features in rG4 formation that were missed previously. rG4-seeker provides a reliable and sensitive approach for rG4-seq investigations, laying the foundations for further elucidation of rG4 biology.
The Changing Landscape of Sport Concussion
Authors: Guskiewicz Kevin M. , Walton Samuel R.
Published: February 2020

It was not too long ago that many people referred to concussion as a “hidden injury” and a “complex injury for which we still had much to learn.” We still have a lot to learn about these injuries, but because of the advancement of concussion research we are better informed today than we were just a decade ago. Much of this work began in the early to mid-1990s with studies aimed at equipping clinicians with better concussion-assessment tools. We needed to remove the guesswork, so more systematic and objective concussion-assessment batteries (sideline and clinic) that included symptom checklists, cognitive tests, and balance assessments were developed and validated. As a result, it became easier to detect and/or rule out concussions and to track recovery for several days postinjury. From 2009 through 2014, all 50 states and the District of Columbia passed concussion legislation requiring concussion education for high school and youth athletes, among other things. This was a critical period in which more emphasis was placed on concussion prevention, ultimately leading to increased reporting of these injuries and a reduction in the number of unreported and undiagnosed concussions. More recently, the corpus of science has evolved to identify potential blood and neuroimaging biomarkers to complement the traditional-clinical assessment tools, and newer studies are focused on treatment after concussion—challenging the notions that “rest is best” and that the effects of concussion are permanent and immutable. The research is ongoing, and several large multisite studies will yield important findings to help guide clinical decision making in the next few years.
Investigation of the mechanism of action of a potent pateamine A analog, des-methyl, des-amino pateamine A (DMDAPatA)
Authors: Kommaraju Sai Shilpa , Aulicino Julieta , Gobbooru Shruthi , Li Jing , Zhu Mingzhao , Romo Daniel , Low Woon-Kai
Published: February 2020

The natural product pateamineA (PatA) is a highly potent antiproliferative agent. PatA and the simplified analog desmethyl, desamino pateamineA (DMDAPatA) have exhibited cytotoxicity selective for rapidly proliferating cells, and have been shown to inhibit cap-dependent translation initiation through binding to eIF4A (eukaryotic initiation factor 4A) of the eIF4F complex. PatA and DMDAPatA are both known to stimulate the RNA-dependent ATPase, and ATP-dependent RNA helicase activities of eIF4A. The impact of other eIF4F components, eIF4E and eIF4G, on DMDAPatA action were investigated in vitro and in cultured mammalian cells. The perturbation of the eIF4A–eIF4G association was found to be eIF4E- and mRNA cap-dependent. An inhibitory effect on helicase activity of eIF4A was observed when it was part of a complex that mimicked the eIF4F complex. We propose a model of action for DMDAPatA (and by supposition PatA) where the cellular activity of the compound is dependent on an “active” eIF4F complex.
Malignant Insulinoma with Multiple Liver Metastases and Hypercalcitoninemia in a Patient with Type 2 Diabetes Mellitus Presenting as Recurrent Episodes of Diaphoresis due to Severe Hypoglycemia
Authors: Ciacciarelli Marco , Caruso Gianluca , Rengo Marco , Maceroni Piero , Misurale Carmen , D’Armiento Eleonora , Polidoro Alessandro , Napoli Cristina , Lombardini Alberto , Ceratti Umberto , Colunga Biancatelli Ruben Manuel Luciano , Calvosa Leonardo , Milanese Romina , Ferri Sonia , Massaro Teresa , Lorusso Andrea , Sorrentino Veronica , Petrozza Vincenzo , Iuliano Luigi
Published: February 2020

Insulinoma is an insulin-producing pancreatic neuroendocrine tumor that can be malignant in about 10% of cases. Locoregional invasion, lymph node metastases, or remote metastases are the main criteria of malignant insulinoma. Its incidence in patients with pre-existing diabetes mellitus (DM) is exceptionally rare. In this report, we describe a 66-year-old man with long-standing type 2 DM who presented with recurrent episodes of diaphoresis due to severe hypoglycemia despite the withdrawal of insulin therapy, hypercalcitoninemia, and biochemical and radiological findings suggestive of metastatic malignant insulinoma. Unfortunately, after few days of diazoxide treatment, edema, hypotension, oliguria, and water retention were observed, patient’s clinical status deteriorated rapidly, and he died in our department from acute renal failure.
Notes on mating behaviour and a possible new host plant for Megacyllene angulata (Fabricius, 1775) (Cerambycidae, Coleoptera)
Authors: Nascimento Francisco  Eriberto De Lima , Mendes Diego Matheus De Mello , Silva Neto Alberto Moreira da
Published: February 2020

The mating behavior of M. angulata (Fabricius, 1775) is described, illustrated and discussed. Additionally, we also comment on the possible new host plant of this species based on two plants (Luehea cymulosa Spruce ex Benth. (Malvaceae) and Doliocarpus dentatus (Aubl.) Standl (Dilleniaceae) on which copulation occurs.
Do Morphological Similarities and human-induced dispersal explain the non-native occurrence of Serpulidae (Annelida) in Southwest Atlantic? Taxonomic detailing is the key
Authors: Rodrigues Andrielle Raposo , Skinner Luís Felipe , Brasil Ana Claudia Dos Santos
Published: February 2020

Species of Serpulidae are common on benthic and biofouling communities, occurring attached on both natural and artificial substrates. In this paper, Serpulids were collected from intertidal to subtidal areas, on rocky shore and suspended artificial plates in port areas. Herein we report three new records of serpulid species to the coast of Rio de Janeiro, Brazil. We also discuss the misidentification of Spirobranchus tetraceros, which was previously reported to the north of Rio de Janeiro.
Neotropical Acanthoderini (Coleoptera, Cerambycidae, Lamiinae): Synonymies and new status in some genera, new species, transferences and new distributional records
Authors: Santos-Silva Antonio , Botero Juan Pablo , Wappes James E.
Published: February 2020

Taxonomic notes are provided in some Acanthoderini genera. Three new species are described: Scythropopsis intricata Santos-Silva, Botero and Wappes from Mexico, Aegomorphus robustus Santos-Silva, Botero and Wappes and Eupromerella boliviana Santos-Silva, Botero and Wappes from Bolivia. The following synonymies are proposed: Psapharochrus Thomson, 1864 as synonym of Aegomorphus Haldeman, 1847; Acanthoderes (Psapharochrus) albomaculatus Fuchs, 1963 and Acanthoderes griseomaculata Zajciw, 1971 as synonyms of Symperasmus alboniger (Bates, 1861); Pteridotelus contaminatus Thomson, 1865 as synonym of Scythropopsis melanostictica (White, 1855); Psapharochrus jameswappesi Tavakilian, 2018 as synonym of Aegomorphus wappesi (Galileo, Martins & Santos-Silva, 2015); and Psapharochrus histrio Casey, 1913 and Psapharochrus guatemalensis Casey, 1913 as synonyms of Aegomorphus circumflexus (Jacquelin du Val, 1857). Acanthoderus circumflexus Jacquelin DuVal, 1857 is proposed as nomen protectum and Acanthocinus rusticus Klug, 1829 as nomen oblitum. Aegomorphus contaminatus (Thomson, 1965) is revalidated. Scythropopsis Thomson, 1864 and Symperasmus Thomson, 1864 are herein elevated to genus rank. The geographical distribution of ten species is expanded and a key to differentiate Acanthoderes, Aegomorphus, Scythropopsis, and Symperasmus is provided.
Clinical signs associated with a case of iatrogenic poisoning by a turpentine-based commercial product in a 3-day-old foal
Authors: Briceño Abelardo Morales , Al Mahrouqi Hilal , Al Kayyoomi Abdallah , Oliva Harmon , Brewer Kimberly , Tobin Thomas
Published: February 2020

The aim of this study is to report a case of iatrogenic poisoning by a turpentine-based commercial product in a 3-day-old foal and the successful treatment of this condition. A 3-day-old male foal presented with acute cardio-respiratory collapse, anaphylactic shock, severe respiratory distress, dyspnea and pulmonary edema. The animal’s history included previous administration of a commercial veterinary product (UNITIPAN). Clinical examination revealed: temperature: (39.9 °C), pulse: 135 bpm, respiration: 51 bpm, mucous membranes: moist and congested, capillary refill time: 3 sec or less. The foal was treated with emergency hydration, duphalyte, steroidal anti-inflammatory, atropine sulphate and antibiotic. After 6 h of treatment, the foal was stabilized and vital signs were normalized 8 h after treatment start.
O alegre canto da perdiz, de Paulina Chiziane, e o reconhecimento de alguns aspectos histórico-culturais moçambicanos
Authors: Ricardo Mariany Teresinha
Published: February 2020

Este artigo se dedica à abordagem que o romance O alegre canto da perdiz, escrito por Paulina Chiziane, confere à temática racial em Moçambique. Para tanto, a escrita do romance será situada dentro do contexto moçambicano, para, então, observamos os impactos que o contato racial tem na formação identitária dos personagens. Esses impactos, por sua vez, estão relacionados aos processos de racialização e de diferenciação negativa que marcam, até hoje, o mundo em que vivemos.
Lee-Li Yang: a radicalização do fingimento poetico
Authors: Leal Luciana Brandão
Published: February 2020

Este artigo apresenta uma leitura de poesias escritas por Lee-Li Yang, heterônimo feminino do poeta moçambicano Virgílio de Lemos. Para tanto, consideram-se os aspectos semióticos que caracterizam a dicção feminina, bem como o erotismo e a melancolia presentes nos poemas de Lee-Li Yang. A partir da leitura dos poemas selecionados, evidencia-se que há, realmente, características literárias que são predominantemente do universo feminino. Pretende-se, também, avaliar em que medida o poeta Virgílio de Lemos simula, na escrita de Lee-Li Yang, a “experiência corporal, interior, social e cultural” (JORGE, 1995, p. 23) inerente ao universo das mulheres.
ílio de Lemos. Para tanto, consideram-se os aspectos semióticos que caracterizam a dicção feminina, bem como o erotismo e a melancolia presentes nos poemas de Lee-Li Yang. A partir da leitura dos poemas selecionados, evidencia-se que há, realmente, características literárias que são predominantemente do universo feminino. Pretende-se, também, avaliar em que medida o poeta Virgílio de Lemos simula, na escrita de Lee-Li Yang, a “experiência corporal, interior, social e cultural” (JORGE, 1995, p. 23) inerente ao universo das mulheres.
“Como é possível perder-te sem nunca ter te achado”: Narrativa e Absolvição em O amor dos homens avulsos, de Victor Heringer
Authors: Silva Samuel Lima da
Published: February 2020

Neste artigo o espaço analítico é destinado à averiguação do tema da absolvição no romance O amor dos homens avulsos (2016), de autoria de Victor Heringer, percebendo o modo como o homoerotismo se encontra presentificado na narrativa em questão. Há, aqui, uma narrativa memorialística em que o protagonista encontra-se encarcerado em si mesmo, em um estado de desolação. As análises que serão empreendidas no presente estudo percebem, no romance, uma estética da absolvição que presentifica o desejo homoerótico e a memória afetiva, ambas sendo descortinadas ao longo da obra.
Corpo-prostituto
Authors: Nascimento Dorinaldo Dos Santos
Published: February 2020

Para este trabalho, elegemos dez narrativas de expressão homoerótica (contos e romances), de autores e períodos díspares, com o propósito de analisarmos numa perspectiva diacrônica/panorâmica e pela interlocução teórico-crítica entre estudos literários e culturais (questões de gênero e sexualidades), produções literárias nacionais que plasmam em seus enredos o corpo masculino mercantilizável de sujeitos prostitutos e as inter-relações e desdobramentos com personagens clientes no negócio do sexo.
Entrevista com Amara Moira
Authors: Costa Caio Jade Puosso C. G. , DeLuca Naná
Published: February 2020

Entrevista realizada com a escritora Amara Moira, por e-mail, em 20 de setembro de 2019, em São Paulo.
Rainhas Gingas de José Eduardo Agualusa
Authors: Maia Helder Thiago , Silva Mariana Alves da
Published: February 2020

Neste trabalho, analisamos a construção da personagem Rainha Ginga em três romances de José Eduardo Agualusa: Nação Crioula: A correspondência secreta de Fradique Mendes (1997), O ano em que Zumbi tomou o rio (2002) e O vendedor de passados (2004), buscando compreender como a versão literária desta figura histórica permite refletir sobre memória, passado, identidade nacional e questões de gênero.
A noite das mulheres cantoras: luz e sombra
Authors: Franzin Adilson Fernando
Published: February 2020

A noite das mulheres cantoras é o décimo romance publicado por Lídia Jorge, uma das mais importantes escritoras portuguesas da atualidade. Na trama romanesca, num jogo de luz e sombra, à medida em que a narrativa caminha para o desfecho, revelações de cariz sexual irão abalar a relação de João de Lucena e Solange de Matos, as quais poderão ser compreendidas neste artigo sob a luz dos estudos de gênero.
Atear fogo é queimar a si
Authors: Pimentel Renata
Published: February 2020

Trata-se de breve investigação sobre Orgia (2011), do argentino Tulio Carella, obra que relata a experiência durante os anos que viveu em Recife, na década de 1960. Sob a denominação de Diários, os eventos relatados tematizam o choque cultural do estrangeiro no nordeste do Brasil, a dificuldade de inserção no meio social, intelectual e artístico e seu refúgio nas aventuras sexuais, sobretudo com homens, negros, pobres e marginais, pela região central da cidade ou pelo cais recifense. Carella foi preso e deportado em circunstâncias políticas aludidas no livro, mas melhor esclarecidas em obras como a de Hermilo BORBA FILHO (1972). Aqui se questiona o enquadramento pacífico do texto como gênero confessional, colocando-o sob investigação em paralelo com o conjunto da produção deste autor, desconhecida no Brasil, para revelar o quanto a escrita de Carella denuncia conscientemente a estrutura colonial, falso moralista e burguesa da cultura recifense e põe em xeque a masculinidade heteronormativa. Como referencial usamos FISCHER (2009), ZAMBRANO (1995), SILVA (2015), ZUMTHOR (2007), para contribuir com um olhar diverso à fortuna crítica sobre Carella e Orgia e revelar uma obra densa, repleta de camadas.
Editorial Dossiê n.24: Dissidências de gênero e sexualidade nas Literaturas de Língua Portuguesa
Authors: Lopes Aline Da Silva , Silva Esdras Soares da , Mariano José Victor Da Silva , Nery Pereira Edson Salviano , Bento Oluwa Seyi Salles , Maia Helder Thiago
Published: February 2020

Editorial do dossiê n.24 "Dissidências de gênero e sexualidade nas literaturas de língua portuguesa".