bluuebunny/crossref_metadata_2025_split huggingface dataset:
uORFlight: a vehicle towards uORF-mediated translational regulation mechanisms in eukaryotes
Authors: Niu Ruixia , Zhou Yulu , Mou Rui , Tang Zhijuan , Wang Zhao , Zhou Guilong , Guo Sibin , Yuan Meng , Xu Guoyong 
Published: July 2019

AbstractUpstream open reading frames (uORFs) are prevalent in eukaryotic mRNAs. They act as a translational control element for precisely tuning the expression of the downstream major open reading frame (mORF) with essential cellular functionalities. uORF variation has been clearly associated with several human diseases. In contrast, natural uORF variants in plants have not ever been identified or linked with any phenotypic changes. The paucity of such evidence encouraged us to generate this database-uORFlight (http://uorflight.whu.edu.cn). It facilitates the exploration of uORF variation among different splicing models of Arabidopsis and rice genes. Most importantly, users can evaluate uORF frequency among different accessions at the population scale and find out the causal single nucleotide polymorphism (SNP) or insertion/deletion (INDEL) which can be associated with phenotypic variation through database mining or simple experiments. Such information will help to make hypotheses of uORF function in plant development or adaption to changing environments on the basis of the cognate mORF function. This database also curates plant uORF relevant literature into distinct groups. To be broadly interesting, our database expands uORF annotation into more species of fungi (Botrytis cinerea), plant (Brassica napus, Glycine max, Gossypium raimondii, Medicago truncatula, Solanum lycopersicum, Solanum tuberosum, Triticum aestivum and Zea mays), metazoan (Caenorhabditis elegans and Drosophila melanogaster) and vertebrate (Homo sapiens, Mus musculus and Danio rerio). Therefore, uORFlight will light up the runway toward how uORF genetic variation determines phenotypic diversity and advance our understanding of translational control mechanisms.
Arbovirus Vectors of Epidemiological Concern in the Americas: A Scoping Review of Entomological Studies on Zika, Dengue and Chikungunya Virus Vectors
Authors: Jones Reilly , Kulkarni Manisha A. , Davidson Thomas M. V. ,   RADAM-LAC Research Team, Talbot Benoit 
Published: July 2019

AbstractBackgroundThree arthorpod-borne viruses (arboviruses) causing human disease have been the focus of a large number of studies in the Americas since 2013 due to their global spread and epidemiological impacts: Zika, dengue, and chikungunya viruses. A large proportion of infections by these viruses are asymptomatic. However, all three viruses are associated with moderate to severe health consequences in a small proportion of cases. Two mosquito species,Aedes aegyptiandAedes albopictus, are among the world’s most prominent arboviral vectors, and are known primary vectors for all three viruses in the Americas.ObjectivesThis review summarizes the state of the entomological literature surrounding the biology and ecology of vectors of Zika, dengue and chikungunya viruses and factors affecting virus transmission. The rationale of the review was to elucidate consensus and discord between studies, and guide future research based on identified knowledge gaps.ResultsA total of 196 studies were included in the scoping review after initial screening and subsequent exclusion of out-of-scope studies, secondary data publications, duplicate records, and studies unavailable in English language.Key findingsTemperature and humidity have the strongest impact on mosquito distribution and dynamics, development of immatures and arborviral infection rates. Low socioeconomic status and related factors, including poor infrastructure, inconsistent access to water, and high household resident density, have been consistently associated with arbovirus vector occurrence. Effects of interspecific competition on arboviral vector species is currently poorly understood. Vector competence for Zika virus is well established forAe. aegyptiandAe. albopictus. Information on Zika virus vector transmission dynamics is sparse in contrast to the wealth of research available for dengue and chikungunya viruses.ConclusionsBased on the internationally recognized urgency of Zika virus infection as a public health concern, further research on arbovirus vectors and transmission dynamics is of pressing need.
Foraging fidelity and individual specialisation in a temperate bat Myotis Nattereri
Authors: Mordue Simone , Mill Aileen , Shirley Mark , Aegerter James 
Published: July 2019

AbstractBat populations have declined globally over the last century largely due to anthropogenic change. Many temperate forest species of bat appear loyal to their foraging sites however, conservation of these sites rather than just habitat types is rarely considered and is essential to protect bat populations. It is not clear whether site fidelity in bats is species-specific or a more general trait or why it is exhibited but behaviour patterns could be important for conservation and management objectives. Foraging variation may occur due to ‘individual specialisation’, such that individuals differ significantly in their prey or habitat utilisation, independent of class-effects. If bats do exhibit individuality in their habitat choice, then protection of a mosaic of habitats rather than single preferred habitat per species may be critical to their conservation.The goal here was to determine whether Natterer’s bats show fidelity in their foraging choices and whether they show individual specialisation in their foraging habits.Thirty-four individual bats were tracked for at least one full night, from two different sites.Site fidelity in Natterer’s was consistent across a range of intervals (months and years) despite contrasting seasonal contexts. Individuals repeatedly exploited specific foraging locations and showed individual specialisation in their habitat use which is consistent with the behaviour of a territorial species.Studies designed to inform conservation and management of temperate bats should attempt to maximize the number of individuals from which movement data is sought, whilst ensuring that data represent a coherent and meaningful measure of behaviour such as a single full night. Bat conservation may need to shift from general descriptions of habitat preferences to considering individual specialisation in habitat use. Designing conservation strategies resilient to environmental change might then advocate protecting a mosaic of habitats to preserve the habitat specialisms of many individuals and enhance their productivity rather than advocating the preservation of a single preferred habitat only suited to a few individuals.
Perirhinal input to neocortical layer 1 controls learning
Authors: Doron Guy , Shin Jiyun N. , Takahashi Naoya , Bocklisch Christina , Skenderi Salina , Drüke Moritz , de Mont Lisa , Toumazo Maria , von Heimendahl Moritz , Brecht Michael , Naud Richard , Larkum Matthew E. 
Published: July 2019

AbstractSignals sent back to the neocortex from the hippocampus control the long-term storage of memories in the neocortex1,2, but the cellular mechanisms underlying this process remain elusive. Here, we show that learning is controlled by specific medial-temporal input to neocortical layer 1. To show this we used direct cortical microstimulation detection task that allowed the precise region of learning to be examined and manipulated. Chemogenetically suppressing the last stage of the medial temporal loop, i.e. perirhinal cortex input to neocortical layer 1, profoundly disrupted early memory formation but had no effect on behavior in trained animals. The learning involved the emergence of a small population of layer 5 pyramidal neurons (~10%) with significantly increased firing involving high-frequency bursts of action potentials that were also blocked by suppression of perirhinal input. Moreover, we found that dendritic excitability was correspondingly enhanced in a similarly-sized population of pyramidal neurons and suppression of dendritic activity via optogenetic activation of dendrite-targeting inhibitory neurons also suppressed learning. Finally, single-cell stimulation of cortical layer 5 pyramidal neurons showed that burst but not regular firing retrieved previously learned behavior. We conclude that the medial temporal input to the neocortex controls learning through a process in L1 that elevates dendritic calcium and promotes burst firing.
The Kinesin-5 Tail Domain Directly Modulates the Mechanochemical Cycle of the Motor for Anti-Parallel Microtubule Sliding
Authors: Bodrug Tatyana , Wilson-Kubalek Elizabeth , Nithianantham Stanley , Thompson Alex F. , Alfieri April , Gaska Ignas , Major Jennifer , Debs Garret , Inagaki Sayaka , Gutierrez Pedro , Gheber Larissa , McKenney Richard , Sindelar Charles , Milligan Ronald , Stumpff Jason , Rosenfeld Steven , Forth Scott T. , Al-Bassam Jawdat 
Published: July 2019

AbstractKinesin-5 motors organize mitotic spindles by sliding apart anti-parallel microtubules. They are homotetramers composed of two antiparallel dimers placing orthogonal motor and tail domains at opposite ends of a bipolar minifilament. Here, we describe a regulatory mechanism, involving direct binding of the tail to motor domain and reveal its fundamental role in microtubule sliding motility. Biochemical analyses reveal that the tail down-regulates microtubule-activated ATP hydrolysis by specifically engaging the motor in the nucleotide-free or ADP-bound states. Cryo-EM structures reveal that the tail stabilizes a unique conformation of the motor N-terminal subdomain opening its active site. Full-length kinesin-5 motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering along microtubules. The tail is critical for motors to zipper together two microtubules by generating substantial forces within sliding zones. The tail domain is essential for kinesin-5 mitotic spindle localization in vivo, which becomes severely reduced when the tail is deleted. Our studies suggest a revised microtubule-sliding model, in which tail domains directly engage motor domains at both ends of kinesin-5 homotetramers enhancing stability of the dual microtubule-bound states leading to slow motility yet high force production.
Celsr1a is essential for tissue homeostasis and onset of aging phenotypes in the zebrafish
Authors: Li Chunmei , Barton Carrie , Henke Katrin , Daane Jake , Caetano-Lopes Joana , Tanguay Robert , Harris Matthew P. 
Published: July 2019

SUMMARYThe use of experimental genetics has been invaluable in defining the complex mechanisms by which aging and longevity are regulated. Zebrafish, while a prominent model for understanding the genetic basis of vertebrate development, have not been used systematically to address questions of how and why we age. In a mutagenesis screen focusing on late developmental phenotypes, we identified a new mutant, fruehrentner, that displays typical signs of aging already at young adult stages. We find that the phenotype is due to loss-of-function in the non-classical cadherin EGF LAG seven-pass G-type receptor 1a (celsr1a). The premature aging phenotype is not associated with increased cellular senescence or decreased telomere length but is a result of a broad failure to maintain progenitor cell populations in tissues. Through the analysis of a knockin reporter line, we find that celsr1aGFP is expressed broadly in early development but becomes restricted during maturation. We show that celsr1a is essential for maintenance of stem cell progenitors and leads to shifts in cell fate determination. Although celsr1a has many signaling functions including establishment of polarity within tissues, we show that caloric restriction can ameliorate the effect of celsr1a on lifespan in part through compensatory upregulation of celsr1 paralogues. These data suggest that celsr1a function helps to mediate stem cell maintenance during maturation and homeostasis of tissues and thus regulates the onset or expressivity of aging phenotypes.
Signatures of relaxed selection in the CYP8B1 gene of birds and mammals
Authors: Shinde Sagar Sharad , Teekas Lokdeep , Sharma Sandhya , Vijay Nagarjun 
Published: July 2019

SummaryThe CYP8B1 gene is known to catalyse reactions that determine the ratio of primary bile salts and the loss of this gene has recently been linked to lack of cholic acid in the bile of naked-mole rats, elephants and manatees using forward genomics approaches. We screened the CYP8B1 gene sequence of more than 200 species and test for relaxation of selection along each terminal branch. The need for retaining a functional copy of the CYP8B1 gene is established by the presence of a conserved open reading frame across most species screened in this study. Interestingly, the dietary switch from bovid to cetacean species is accompanied by an exceptional ten amino-acid extension at the C-terminal end through a single base frame-shift deletion. We also verify that the coding frame disrupting mutations previously reported in the elephant are correct, are shared by extinct Elephantimorpha species and coincide with the dietary switch to herbivory. Relaxation of selection in the CYP8B1 gene of the wombat (Vombatus ursinus) also corresponds to drastic change in diet. In summary, our forward genomics based screen of bird and mammal species identifies recurrent changes in the selection landscape of the CYP8B1 gene concomitant with a change in dietary lipid content.
Chromosomal condensation leads to a preference for peripheral heterochromatin
Authors: MacPherson Quinn , Spakowitz Andrew J. 
Published: July 2019

ABSTRACTA layer of dense heterochromatin is found at the periphery of the nucleus. Because this peripheral heterochromatin functions as a repressive phase, mechanisms that relocate genes to the periphery play an important role in regulating transcription. Using Monte-Carlo simulations, we show that an interaction between chromatin and the nuclear boundary need not be specific to heterochromatin in order to preferentially locate heterochromatin to the nuclear periphery. This observation considerably broadens the class of possible interactions that result in peripheral positioning to include boundary interactions that either weakly attract all chromatin or strongly bind to a randomly chosen small subset of loci. The key distinguishing feature of heterochromatin is its high chromatin density with respect to euchromatin. In our model this densification is caused by HP1’s preferential binding to H3K9me3 marked histone tails. We conclude that factors that are themselves unrelated to the nuclear periphery can determine which genomic regions condense to form heterochromatin and thereby control which regions are relocated to the periphery.
Collagen-binding byDrosophilaSPARC is essential for survival and for collagen IV distribution and assembly into basement membranes
Authors: Duncan Sebastian , Delage Samuel , Chioran Alexa , Sirbu Olga , Brown Theodore J. , Ringuette Maurice J. 
Published: July 2019

AbstractThe assembly of basement membranes (BMs) into tissue-specific morphoregulatory structures requires non-core BM components. Work inDrosophilaindicates a principal role of collagen-binding matricellular glycoprotein SPARC (Secreted Protein, Acidic, Rich in Cysteine) in larval fat body BM assembly. We report that SPARC and collagen IV (Col(IV)) first colocalize in the trans-Golgi of hemocytes. Mutating the collagen-binding epitopes of SPARC leads to 2ndinstar larval lethality, indicating that SPARC binding to Col(IV) is essential for survival. Analysis of this mutant reveals increased Col(IV) puncta within adipocytes and intense perimeter Col(IV) staining surrounding the fat body as compared to wild-type larvae, reflecting a disruption in chaperone-like activity. In addition, Col(IV) in the wing imaginal disc was absent. Removal of the disulfide bridge in EF-hand2, which is known to enhance Col(IV) binding by SPARC, did not lead to larval lethality; however, a similar but less intense fat body phenotype was observed. Additionally, both SPARC mutants have altered fat body BM pore topography. Wing imaginal disc-derived SPARC did not localize within Col(IV)-rich matrices, indicating a distinct variant. Collectively, these data demonstrate the essential role of Col(IV) chaperone-like activity of SPARC toDrosophiladevelopment and indicate tissue-specific variants with differential functions.
The EO771 mammary cancer cell line displays a luminal B phenotype and it is sensitive to anti-estrogen treatments
Authors: Le Naour Augustin , Koffi Yvonne , Diab Mariane , Le Guennec Delphine , Rougé Stéphanie , Aldekwer Sahar , Goncalves-Mendes Nicolas , Talvas Jeremie , Farges Marie-Chantal , Caldefie-Chezet Florence , Vasson Marie-Paule , Rossary Adrien 
Published: July 2019

ABSTRACTDespite decades of therapeutic trials, detection, many drugs available and numerous studies on breast cancer, it remains the most deadly cancer in women. In order to choose the most appropriate treatment and to know the prognosis of the patients, the breast cancer is divided into different subtypes using a molecular classification. Thus, the need to discover new effective therapy is necessary, requiring to have models to test them. The EO771 (also named E0771 or EO 771) murine mammary cancer cell line is originally isolated from a spontaneous tumor in C57BL/6 mouse. Although frequently used, this cell line remains poorly characterized. Therefore, the EO771 phenotype was investigated. Transcriptomic and protein analysis allowed to classify the EO771 as luminal B subtype and more precisely estrogen receptor α negative, estrogen receptor β positive, progesterone receptor positive and ErbB2 positive. This phenotype was associated to a sensitivity to anti-estrogen treatments such as tamoxifen, 4-hydroxy-tamoxifen, endoxifen and fulvestrant.
A framework for tolerance design considering systematic and random uncertainties due to operating conditions
Authors: Khodaygan S. 
Published: July 2019

Purpose
The purpose of this paper is to present a novel Kriging meta-model assisted method for multi-objective optimal tolerance design of the mechanical assemblies based on the operating conditions under both systematic and random uncertainties.

Design/methodology/approach
In the proposed method, the performance, the quality loss and the manufacturing cost issues are formulated as the main criteria in terms of systematic and random uncertainties. To investigate the mechanical assembly under the operating conditions, the behavior of the assembly can be simulated based on the finite element analysis (FEA). The objective functions in terms of uncertainties at the operating conditions can be modeled through the Kriging-based metamodeling based on the obtained results from the FEA simulations. Then, the optimal tolerance allocation procedure is formulated as a multi-objective optimization framework. For solving the multi conflicting objectives optimization problem, the multi-objective particle swarm optimization method is used. Then, a Shannon’s entropy-based TOPSIS is used for selection of the best tolerances from the optimal Pareto solutions.

Findings
The proposed method can be used for optimal tolerance design of mechanical assemblies in the operating conditions with including both random and systematic uncertainties. To reach an accurate model of the design function at the operating conditions, the Kriging meta-modeling is used. The efficiency of the proposed method by considering a case study is illustrated and the method is verified by comparison to a conventional tolerance allocation method. The obtained results show that using the proposed method can lead to the product with a more robust efficiency in the performance and a higher quality in comparing to the conventional results.

Research limitations/implications
The proposed method is limited to the dimensional tolerances of components with the normal distribution.

Practical implications
The proposed method is practically easy to be automated for computer-aided tolerance design in industrial applications.

Originality/value
In conventional approaches, regardless of systematic and random uncertainties due to operating conditions, tolerances are allocated based on the assembly conditions. As uncertainties can significantly affect the system’s performance at operating conditions, tolerance allocation without including these effects may be inefficient. This paper aims to fill this gap in the literature by considering both systematic and random uncertainties for multi-objective optimal tolerance design of mechanical assemblies under operating conditions.
Multi-objective optimal design of double-sided switched reluctance linear generator for wave power generation
Authors: Zhao Shuyan , Chen Hao , Nie Rui , Liu Jinfu 
Published: July 2019

PurposeThis paper aims to propose a double-sided switched reluctance linxear generator (DSRLG) exclusively for wave power generation. The initial dimensions are given through design experience and principles. To ameliorate comprehensive performance of the DSRLG, the multi-objective optimization design is processed.Design/methodology/approachThe multi-objective optimization design of the DSRLG is processed by adopting a modified entropy technique for order of preference by similarity to ideal solution (TOPSIS) algorithm. First, sensitivity analyzes on geometric parameters of the DSRLG are conducted to determine several pivotal geometric parameters as optimization variables. Then, the multi-objective optimization is conducted on the basis of initial dimensions. After determination of synthetical evaluation value of each structure parameter, the best dimension scheme of the DSRLG is concluded.FindingsAfter verification by finite element method simulation and dynamic simulation, the final dimension scheme proves to perform better than the initial scheme. Finally, experiments are conducted to verify the accuracy of both the stable finite element DSRLG model and dynamic simulation system model so that the conclusion of this paper proves to be reliable and compelling.Originality/valueThis paper proposes an improved structure of the DSRLG, which is superior for wave power generation. Meanwhile, a novel modified entropy TOPSIS algorithm is applied to the field of electrical machine multi-objective optimal design for the first time.