bluuebunny/crossref_metadata_2025_split huggingface dataset:
The finiteness threshold width of lattice polytopes
Authors: Blanco M. , Haase C. , Hofmann J. , Santos F. 
Published: April 2021

In each dimension

d
d

there is a constant

w
∞

(
d
)
∈

N

w^\infty (d)\in \mathbb {N}

such that for every

n
∈

N

n\in \mathbb {N}

all but finitely many lattice

d
d

-polytopes with

n
n

lattice points have lattice width at most

w
∞

(
d
)

w^\infty (d)

. We call

w
∞

(
d
)

w^\infty (d)

the finiteness threshold width in dimension

d
d

and show that

d
−
2
≤

w
∞

(
d
)
≤

O
∗

(

d

4

/

3

)

d-2 \le w^\infty (d)\le O^*\left ( d^{4/3}\right )

.

Blanco and Santos determined the value

w
∞

(
3
)
=
1

w^\infty (3)=1

. Here, we establish

w
∞

(
4
)
=
2

w^\infty (4)=2

. This implies, in particular, that there are only finitely many empty

4
4

-simplices of width larger than two. (This last statement was claimed by Barile et al. in [Proc. Am. Math. Soc. 139 (2011), pp. 4247–4253], but we have found a gap in their proof.)

Our main tool is the study of

d
d

-dimensional lifts of hollow

(
d
−
1
)

(d-1)

-polytopes.
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins
Authors: Sohrabi-Jahromi Salma , Söding Johannes 
Published: April 2021

AbstractMotivationUnderstanding how proteins recognize their RNA targets is essential to elucidate regulatory processes in the cell. Many RNA-binding proteins (RBPs) form complexes or have multiple domains that allow them to bind to RNA in a multivalent, cooperative manner. They can thereby achieve higher specificity and affinity than proteins with a single RNA-binding domain. However, current approaches to de novo discovery of RNA binding motifs do not take multivalent binding into account.ResultsWe present Bipartite Motif Finder (BMF), which is based on a thermodynamic model of RBPs with two cooperatively binding RNA-binding domains. We show that bivalent binding is a common strategy among RBPs, yielding higher affinity and sequence specificity. We furthermore illustrate that the spatial geometry between the binding sites can be learned from bound RNA sequences. These discovered bipartite motifs are consistent with previously known motifs and binding behaviors. Our results demonstrate the importance of multivalent binding for RNA-binding proteins and highlight the value of bipartite motif models in representing the multivalency of protein-RNA interactions.Availability and implementationBMF source code is available at https://github.com/soedinglab/bipartite_motif_finder under a GPL license. The BMF web server is accessible at https://bmf.soedinglab.org.Supplementary informationSupplementary data are available at Bioinformatics online.
Melatonin alleviates deoxynivalenol-induced apoptosis of human granulosa cells by reducing mutually accentuated FOXO1 and ER stress
Authors: Xue Rufeng , Li Shuhang , Zou Huijuan , Ji Dongmei , Lv Mingrong , Zhou Ping , Wei Zhaolian , Zhang Zhiguo , Cao Yunxia 
Published: April 2021

Abstract
Deoxynivalenol (DON) is one of the most prevalent Fusarium mycotoxins, which cause detrimental effects on human and animal reproductive systems by inducing oxidative stress. Increasing evidence has suggested the potential roles of melatonin in protecting granulosa cells from oxidative injury, but the underlying mechanisms remain largely elusive. Here, we demonstrated that suppression of FOXO1 and endoplasmic reticulum (ER) stress was engaged in melatonin-mediated protection against oxidative damage in human granulosa cells upon DON exposure in vitro. DON induced excess reactive oxygen species accumulation, cells viability loss, reduced estradiol-17β, and progesterone production in human granulosa cells, whereas melatonin ameliorated these phenotypes. Next, we found that the protective effect of melatonin against apoptosis was via reducing ER stress because the inhibition of ER stress displayed similar protective effects during DON treatment. Moreover, melatonin provided no additional protection when ER stress was inhibited. We further found that FOXO1 is a pivotal downstream effector of melatonin and ER stress in regulating DON-induced apoptosis in human granulosa cells. Blocking of FOXO1 reduced DON-induced cells death and FOXO1 activation could be suppressed by melatonin or ER stress inhibitor. However, melatonin failed to further restore cells viability in the presence of FOXO1 inhibitor. Collectively, our results reveal a new mechanism of melatonin in protecting against DON-induced apoptosis and dysfunction by suppressing ER stress and FOXO1 in human granulosa cells.
O15: DISRUPTION OF THE BLOOD-SPINAL CORD BARRIER PREDICTS PERMANENT PARAPLEGIA AFTER THORACOABDOMINAL AORTIC ANEURYSM REPAIR
Authors: Kelly J , Patel A , Onadim I , Abisi S , Bell R , Tyrrell M , Sallam M , Salih M , Mayr M , Bradbury E , Cho J , Gworzdz A , Booth T , Smith A , Modarai B 
Published: April 2021

Abstract

Introduction
Paraplegia post-thoracoabdominal aortic aneurysm (TAAA) repair remains both a devastating and poorly understood complication. We related temporal changes in cellular and protein composition of cerebrospinal fluid (CSF) to neurological outcomes after TAAA repair to gain mechanistic insights driving paraplegia.

Method
Patients undergoing TAAA repair (open or endovascular) with a CSF drain were prospectively recruited between 2016-2018. CSF was collected pre-operatively and 24-hourly until removal. Daily neurological examinations were performed by blinded neurologists to the study. CSF cell content was characterised by flow cytometry and proteome analysed by tandem-mass-tag proteomics. An in-vivo rat model was modified using 15 minutes of aortic occlusion to produce consistent paraplegia. Rats were analysed neuro-behaviourally and histologically.

Result
CSF was analysed from 52 patients (age: 70.27+/-11.4; 66% male; open (n=9), endovascular (n=43)). 12 developed paraplegia of whom 5 remained permanently-paraplegic. Demographics were comparable between paraplegics, those who recovered and without post-op neurology. Permanent paraplegia was associated with a significant infiltration of CSF CD45+ leucocytes (P&lt;0.0001). Levels of ADVS-1 was &gt;3-fold higher in permanent-paraplegics CSF versus those who recovered (P=0.0008). ADVS-1 &gt;15ng/ml predicted permanent paraplegia with 100% specificity. Pre-treatment with ADVS-1 inhibition significantly improved walking (&lt;0.001) and increased astrocytic staining in the lateral corticospinal, reticulospinal and rubrospinal tracts versus controls (P=0.03, 0.04, 0.04 respectively).

Conclusion
Permanent paraplegia is associated with shedding of ADVS-1 from parenchymal cord into CSF and blood/spinal-cord barrier disruption leading to cord oedema/leucocyte infiltration. Pre-treatment with ADVS-1 inhibition led to neurobehavioural and histological improvements offering translational hope for this devastating complication.

Take-home message
ADVS-1 is a novel biomarker of paraplegia where accurate biomarkers have proven challenging but more importantly it has proven a therapeutic target with genuine translational potential.
Robust and Dynamic Graph Convolutional Network For Multi-view Data Classification
Authors: Peng Liang , Kong Fei , Liu Chongzhi , Kuang Ping 
Published: April 2021

AbstractSince graph learning could preserve the structure information of the samples to improve the learning ability, it has been widely applied in both shallow learning and deep learning. However, the current graph learning methods still suffer from the issues such as outlier influence and model robustness. In this paper, we propose a new dynamic graph neural network (DGCN) method to conduct semi-supervised classification on multi-view data by jointly conducting the graph learning and the classification task in a unified framework. Specifically, our method investigates three strategies to improve the quality of the graph before feeding it into the GCN model: (i) employing robust statistics to consider the sample importance for reducing the outlier influence, i.e. assigning every sample with soft weights so that the important samples are with large weights and outliers are with small or even zero weights; (ii) learning the common representation across all views to improve the quality of the graph for every view; and (iii) learning the complementary information from all initial graphs on multi-view data to further improve the learning of the graph for every view. As a result, each of the strategies could improve the robustness of the DGCN model. Moreover, they are complementary for reducing outlier influence from different aspects, i.e. the sample importance reduces the weights of the outliers, both the common representation and the complementary information improve the quality of the graph for every view. Experimental result on real data sets demonstrates the effectiveness of our method, compared to the comparison methods, in terms of multi-class classification performance.
A Survey of Privacy Solutions using Blockchain for Recommender Systems: Current Status, Classification and Open Issues
Authors: Abduljabbar Tamara Abdulmunim , Tao Xiaohui , Zhang Ji , Zhou Xujuan , Li Lin , Cai Yi 
Published: April 2021

Abstract
Due to the rapid growth of Internet, E-commerce and Internet of Things, people use Web based services for most of their needs including buying items, reading books, watching online shows etc. Several companies are using recommender systems to influence people’s choices based on their likings, behaviours etc. Hence, people fear that their privacy is violated. Also, some of the online applications are not safe and secure. One way to overcome the privacy related issues is using secured solutions such as incorporating blockchain technologies for privacy-based applications. The decentralized nature of blockchain technologies have resolved several security, and authentication problems of Internet of Things systems. In this paper, we conduct a comprehensive survey on the privacy solutions for recommender systems emphasising current status, classification and open issues. We also discuss blockchain technology, including its structure as well as applications of blockchain technology for privacy solutions of recommender systems. Furthermore, we discuss the limitations and delve into future trends that blockchain technology can be adapted for privacy-base applications in the years to come.
Characterization of robustness and resilience in graphs: a mini-review
Authors: Schaeffer S E , Valdés V , Figols J , Bachmann I , Morales F , Bustos-Jiménez J 
Published: April 2021

Abstract
We briefly survey recent proposals that seek to capture in numerical terms the resilience and the robustness of a graph. After a brief introduction and the establishment of notation and terminology, we catalogue characterizations proposed in journal articles published within the last two decades. We then describe some of the numerous application areas for such characterizations. We experiment with implementations of numerous characteristics on several graph-generation models, after which we conclude with a discussion of open problems and future directions.
Thymomectomy plus total thymectomy versus simple thymomectomy for early-stage thymoma without myasthenia gravis: a European Society of Thoracic Surgeons Thymic Working Group Study
Authors: Guerrera Francesco , Falcoz Pierre Emmanuel , Moser Bernhard , van Raemdonck Dirk , Bille’ Andrea , Toker Alper , Spaggiari Lorenzo , Ampollini Luca , Filippini Claudia , Thomas Pascal Alexandre , Verdonck Bram , Mendogni Paolo , Aigner Clemens , Voltolini Luca , Novoa Nuria , Patella Miriam , Mantovani Sara , Bravio Ivan Gomes , Zisis Charalambos , Guirao Angela , Londero Francesco , Congregado Miguel , Rocco Gaetano , Du Pont Bert , Martucci Nicola , Esch Matthias , Brunelli Alessandro , Detterbeck Frank C , Venuta Federico , Weder Walter , Ruffini Enrico ,   the European Society of Thoracic Surgeons (ESTS) Thymic Working Group Participating Centers, Klepetko Walter , Olland Anne , Du Pont Bert , Nonaka Daisuke , Ozkan Berker , Lo Iacono Giorgio , Braggio Cesare , Filosso Pier Luigi , Brioude Geoffrey , van Schil Paul , Nosotti Mario , Valdivia Daniel , Bongiolatti Stefano , Inci Ilhan , Dimitra Rontogianni , Sànchez David , Grossi William , Moreno-Merino Sergio , Teschner Martin 
Published: April 2021

Abstract OBJECTIVESResection of thymic tumours including the removal of both the tumour and the thymus gland (thymothymectomy; TT) is the procedure of choice and is recommended in most relevant articles in the literature. Nevertheless, in recent years, some authors have suggested that resection of the tumour (simple thymomectomy; ST) may suffice from an oncological standpoint in patients with early-stage thymoma who do not have myasthenia gravis (MG) (non-MG). The goal of our study was to compare the short- and long-term outcomes of ST versus TT in non-MG early-stage thymomas using the European Society of Thoracic Surgeons thymic database.METHODSA total of 498 non-MG patients with pathological stage I thymoma were included in the study. TT was performed in 466 (93.6%) of 498 patients who had surgery with curative intent; ST was done in 32 (6.4%). The completeness of resection, the rate of complications, the 30-day mortality, the overall recurrence and the freedom from recurrence were compared. We performed crude and propensity score-adjusted comparisons by surgical approach (ST vs TT).RESULTSTT showed the same rate of postoperative complications, 30-day mortality and postoperative length of stay as ST. The 5-year overall survival rate was 89% in the TT group and 55% in the ST group. The 5-year freedom from recurrence was 96% in the TT group and 79% in the ST group.CONCLUSIONPatients with early-stage thymoma without MG who have a TT show significantly better freedom from recurrence than those who have an ST, without an increase in postoperative morbidity rate.
The influence of maize genotype on the rhizosphere eukaryotic community
Authors: Matus-Acuña Violeta , Caballero-Flores Gustavo , Martínez-Romero Esperanza 
Published: April 2021

ABSTRACTThe microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown in the same soil (common garden approach). This experimental design, coupled with 18S rDNA gene amplicon sequencing, allowed us to test the influence of maize and its genotype on the rhizosphere's eukaryotic community. We found that plant growth modified the eukaryotic community in soil, as diversity comparisons between maize rhizosphere and unplanted soil revealed significantly different eukaryotic composition. Various genera of nematodes and fungi, predominantly bacterial feeding nematodes and mycorrhizal fungi among other taxa, were increased in the rhizosphere samples. We also observed that maize genotype differentially shaped the relative abundance of the following fungal families in the rhizosphere: Acaulosporaceae, Aspergillaceae, Chaetomiaceae, Claroideoglomeraceae, Corticiaceae, Mortierellaceae, Trichocomaceae and Trichomeriaceae. Thus, plant genotype has a selective influence on establishing fungal communities in the rhizosphere. This study emphasizes the importance of an integrated consideration of plant genetics for future agricultural applications of microbes to crops.
Isolation of the Gene Encoding the Drosophila melanogaster Homolog of the Saccharomyces cerevisiae GCN2 eIF-2α Kinase
Authors: Olsen DeAnne S , Jordan Barbara , Chen Dreeny , Wek Ronald C , Cavener Douglas R 
Published: April 2021

AbstractGenomic and cDNA clones homologous to the yeast GCN2 eIF-2α kinase (yGCN2) were isolated from Drosophila melanogaster. The identity of the Drosophila GCN2 (dGCN2) gene is supported by the unique combination of sequence encoding a protein kinase catalytic domain and a domain homologous to histidyl-tRNA synthetase and by the ability of dGCN2 to complement a deletion mutant of the yeast GCN2 gene. Complementation of Δgcn2 in yeast by dGCN2 depends on the presence of the critical regulatory phosphorylation site (serine 51) of eIF-2α. dGCN2 is composed of 10 exons encoding a protein of 1589 amino acids. dGCN2 mRNA is expressed throughout Drosophila development and is particularly abundant at the earliest stages of embryogenesis. The dGCN2 gene was cytogenetically and physically mapped to the right arm of the third chromosome at 100C3 in STS Dm2514. The discovery of GCN2 in higher eukaryotes is somewhat unexpected given the marked differences between the amino acid biosynthetic pathways of yeast vs. Drosophila and other higher eukaryotes. Despite these differences, the presence of GCN2 in Drosophila suggests at least partial conservation from yeast to multicellular organisms of the mechanisms responding to amino acid deprivation.
Nonneutral Evolution and Differential Mutation Rate of Gender-Associated Mitochondrial DNA Lineages in the Marine Mussel Mytilus
Authors: Quesada Humberto , Warren Mary , Skibinski David O F 
Published: April 2021

Abstract
Mussels have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally, and the F type is transmitted maternally. To test hypotheses of the molecular evolution of both mtDNA genomes, 50 nucleotide sequences were obtained for 396 bp of the COIII gene of European populations of Mytilus edulis and the Atlantic and Mediterranean forms of M. galloprovincialis. Analysis based on the proportion of synonymous and nonsynonymous substitutions indicate that mtDNA is evolving in a non-neutral and complex fashion. Previous studies on American mussels demonstrated that the F genome experiences a higher purifying selection and that the M genome evolves faster. Here we show that these patterns also hold in European populations. However, in contrast to American populations, where an excess of replacement substitution between F and M lineages has been reported, a significant excess of replacement polymorphism within mtDNA lineages is observed in European populations of M. galloprovincialis.European populations also show an excess of replacement polymorphism within the F but not within the M genome with respect to American M. trossulus, as well as a consistent pattern of excess of rare variants in both F and M genomes. These results are consistent with a nearly neutral model of molecular evolution and a recent relaxation of selective constraints on European mtDNA. Levels of diversity are significantly higher for the M than F genome, and the M genome also accumulates synonymous and nonsynonymous substitutions at a higher rate, in contrast with earlier reports where no difference for the synonymous rate was observed. It is suggested that a subtle balance between relaxed selection and a higher mutation rate explains the faster evolutionary rate of the M lineage.
The Expected Number of Heterozygous Sites in a Subdivided Population
Authors: Nagylaki Thomas 
Published: April 2021

Abstract
A simple, exact formula is derived for the expected number of heterozygous sites per individual at equilibrium in a subdivided population. The model of infinitely many neutral sites is posited; the linkage map is arbitrary. The monoecious, diploid population is subdivided into a finite number of panmictic colonies that exchange gametes. The backward migration matrix is arbitrary, but time independent and ergodic (i.e., irreducible and aperiodic). With suitable weighting, the expected number of heterozygous sites is 4Neu, where Ne denotes the migration effective population number and u designates the total mutation rate per gene (or DNA sequence). For diploid migration, this formula is a good approximation if Ne ⪢ 1.
The Schizosaccharomyces pombe S-Phase Checkpoint Differentiates Between Different Types of DNA Damage
Authors: Rhind Nicholas , Russell Paul 
Published: April 2021

Abstract
We have identified an S-phase DNA damage checkpoint in Schizosaccharomyces pombe. This checkpoint is dependent on Rad3, the S. pombe homolog of the mammalian ATM/ATR checkpoint proteins, and Cds1. Cds1 had previously been believed to be involved only in the replication checkpoint. The requirement of Cds1 in the DNA damage checkpoint suggests that Cds1 may be a general target of S-phase checkpoints. Unlike other checkpoints, the S. pombe S-phase DNA damage checkpoint discriminates between different types of damage. UV-irradiation, which causes base modification that can be repaired during G1 and S-phase, invokes the checkpoint, while γ-irradiation, which causes double-stranded breaks that cannot be repaired by a haploid cell if induced before replication, does not invoke the checkpoint. Because the same genes are required to respond to UV- and γ-irradiation during G2, this discrimination may represent an active suppression of the γ response during S-phase.
Genetic Mechanisms Underlying Apimaysin and Maysin Synthesis and Corn Earworm Antibiosis in Maize (Zea mays L.)
Authors: Lee E A , Byrne P F , McMullen M D , Snook M E , Wiseman B R , Widstrom N W , Coe E H 
Published: April 2021

AbstractC-glycosyl flavones in maize silks confer resistance (i.e., antibiosis) to corn earworm (Helicoverpa zea [Boddie]) larvae and are distinguished by their B-ring substitutions, with maysin and apimaysin being the di- and monohydroxy B-ring forms, respectively. Herein, we examine the genetic mechanisms underlying the synthesis of maysin and apimaysin and the corresponding effects on corn earworm larval growth. Using an F2 population, we found a quantitative trait locus (QTL), rem1, which accounted for 55.3% of the phenotypic variance for maysin, and a QTL, pr1, which explained 64.7% of the phenotypic variance for apimaysin. The maysin QTL did not affect apimaysin synthesis, and the apimaysin QTL did not affect maysin synthesis, suggesting that the synthesis of these closely related compounds occurs independently. The two QTLs, rem1 and pr1, were involved in a significant epistatic interaction for total flavones, suggesting that a ceiling exists governing the total possible amount of C-glycosyl flavone. The maysin and apimaysin QTLs were significant QTLs for corn earworm antibiosis, accounting for 14.1% (rem1) and 14.7% (pr1) of the phenotypic variation. An additional QTL, represented by umc85 on the short arm of chromosome 6, affected antibiosis (R2 = 15.2%), but did not affect the synthesis of the C-glycosyl flavones.
A Bayesian Characterization of Hardy-Weinberg Disequilibrium
Authors: Shoemaker Jennifer , Painter Ian , Weir B S 
Published: April 2021

AbstractA Bayesian method for determining if there are large departures from independence between pairs of alleles at a locus, Hardy-Weinberg equilibrium (HWE), is presented. We endorse the view that a population will never be exactly in HWE and that there will be occasions when there is a need for an alternative to the usual hypothesis-testing setting. Bayesian methods provide such an alternative, and our approach differs from previous Bayesian treatments in using the disequilibrium and inbreeding coefficient parameterizations. These are easily interpretable but may be less mathematically tractable than other parameterizations. We examined the posterior distributions of our parameters for evidence that departures from HWE were large. For either parameterization, when a conjugate prior was used, the prior probability for small departures was itself small, i.e., the prior was weighted against small departures from independence. We could avoid this uneven weighting by using a step prior which gave equal weighting to both small and large departures from HWE. In most cases, the Bayesian methodology makes it clear that there are not enough data to draw a conclusion.