bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Polyatomic Tomography over Abelian Groups: Some Remarks on Consistency, Tree Packings and Complexity
Authors: Gritzmann Peter , Langfeld Barbara 
Published: February 2020

AbstractThe paper deals with an inverse problem of reconstructing matrices from their marginal sums. More precisely, we are interested in the existence of $$r\times s$$

r
×
s

matrices for which only the following information is available: The entries belong to known subsets of c distinguishable abelian groups, and the row and column sums of all entries from each group are given. This generalizes Ryser’s classical problem of characterizing the set of all 0–1-matrices with given row and column sums and is a basic problem in (polyatomic) discrete tomography. We show that the problem is closely related to packings of trees in bipartite graphs, prove consistency results, give algorithms and determine its complexity. In particular, we find a somewhat unusual complexity behavior: the problem is hard for “small” but easy for “large” matrices.
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

Abstract
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 &gt;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

Abstract

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 &gt;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 &lt;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

Abstract

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

METHODS
Of the 10 consecutive patients &lt;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 &lt;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

AbstractBackgroundThe 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.ObjectivesTo 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.MethodsA 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.ResultsOf 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%.ConclusionsIn 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.
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

Abstract
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

Abstract

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

SummaryReplicative 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

AbstractSegmentation 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

AbstractBackgroundAn 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.MethodsWe 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.FindingsWe 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.InterpretationOur 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.FundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)
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

AbstractCellular 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

AbstractOsh6 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

SummaryHippocampal 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

SUMMARYThe 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

AbstractMotivationA 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.ResultsWe 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.Contactmaxwl@sfu.ca.Availabilityhttps://github.com/faezeh-bayat/Variance-stabilized-units-for-sequencing-based-genomic-signals.