bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deligne Categories and the Limit of Categories Rep(GL(m|n))
Authors: Entova-Aizenbud Inna , Hinich Vladimir , Serganova Vera 
Published: June 2018

Abstract
For each integer $t$ a tensor category $\mathcal{V}_t$ is constructed, such that exact tensor functors $\mathcal{V}_t\rightarrow \mathcal{C}$ classify dualizable $t$-dimensional objects in $\mathcal{C}$ not annihilated by any Schur functor. This means that $\mathcal{V}_t$ is the “abelian envelope” of the Deligne category $\mathcal{D}_t=\operatorname{Rep}(GL_t)$. Any tensor functor $\operatorname{Rep}(GL_t)\longrightarrow \mathcal{C}$ is proved to factor either through $\mathcal{V}_t$ or through one of the classical categories $\operatorname{Rep}(GL(m|n))$ with $m-n=t$. The universal property of $\mathcal{V}_t$ implies that it is equivalent to the categories $\operatorname{Rep}_{\mathcal{D}_{t_1}\otimes \mathcal{D}_{t_2}}(GL(X),\epsilon )$, ($t=t_1+t_2$, $t_1$ not an integer) suggested by Deligne as candidates for the role of abelian envelope.
First constraints on the stellar mass function of star-forming clumps at the peak of cosmic star formation
Authors: Dessauges-Zavadsky Miroslava , Adamo Angela 
Published: June 2018

Abstract
Star-forming clumps dominate the rest-frame ultraviolet morphology of galaxies at the peak of cosmic star formation. If turbulence driven fragmentation is the mechanism responsible for their formation, we expect their stellar mass function to follow a power law of slope close to −2. We test this hypothesis performing the first analysis of the stellar mass function of clumps hosted in galaxies at $z$ ∼ 1–3.5. The clump sample is gathered from the literature with similar detection thresholds and stellar masses determined in a homogeneous way. To overcome the small number statistics per galaxy (each galaxy hosts up to a few tens of clumps only), we combine all high-redshift clumps. The resulting clump mass function follows a power law of slope ∼−1.7 and flattens at masses below $2\times 10^7\, \mathrm{M}_{\odot }$. By means of randomly sampled clump populations, drawn out of a power-law mass function of slope −2, we test the effect of combining small clump populations, detection limits of the surveys, and blending on the mass function. Our numerical exercise reproduces all the features observed in the real clump mass function confirming that it is consistent with a power law of slope ≃ − 2. This result supports the high-redshift clump formation through fragmentation in a similar fashion as in local galaxies, but under different gas conditions.
Optical Principles of Fluorescence-Guided Brain Tumor Surgery: A Practical Primer for the Neurosurgeon
Authors: Zhang Daniel Y , Singhal Sunil , Lee John Y K 
Published: June 2018

Abstract
Fluorescence-guided surgery is a rapidly growing field that has produced some of the most important innovations in surgical oncology in the past decade. These intraoperative imaging technologies provide information distinguishing tumor tissue from normal tissue in real time as the surgery proceeds and without disruption of the workflow. Many of these fluorescent tracers target unique molecular or cellular features of tumors, which offers the opportunity for identifying pathology with high precision to help surgeons achieve their primary objective of a maximal safe resection. As novel fluorophores and fluorescent probes emerge from preclinical development, a practical understanding of the principles of fluorescence remains critical for evaluating the clinical utility of these agents and identifying opportunities for further innovation. In this review, we provide an “in-text glossary” of the fundamental principles of fluorescence with examples of direct applications to fluorescence-guided brain surgery. We offer a detailed discussion of the various advantages and limitations of the most commonly used intraoperative imaging agents, including 5-aminolevulinic acid, indocyanine green, and fluorescein, with a particular focus on the photophysical properties of these specific agents as they provide a framework through which to understand the new agents that are entering clinical trials. To this end, we conclude with a survey of the fluorescent properties of novel agents that are currently undergoing or will soon enter clinical trials for the intraoperative imaging of brain tumors.
Endoscopic Resection of Hemorrhaged Third Ventricle Cavernous Malformation: 2-Dimensional Operative Video
Authors: Palandri Giorgio , Sorenson Thomas , Zucchelli Mino , Acciarri Nicola , Mantovani Paolo , Sturiale Carmelo 
Published: June 2018

Abstract
Cavernous malformations of the third ventricle are uncommon vascular lesions. Evidence suggests that cavernous malformations in this location might have a more aggressive natural history due to their risk of intraventricular hemorrhage and hydrocephalus.
1
The gold standard of treatment is considered to be microsurgical gross total resection of the lesion. However, with progressive improvement in endoscopic capabilities, several authors have recently advocated for the role of minimally-invasive neuroendoscopy for resecting intraventricular cavernous malformations.
2-4
In this timely intraoperative video, we demonstrate the gross total resection of a third ventricle cavernous malformation that presented with hemorrhage via a right-sided trans-frontal neuroendoscopic approach.
GPCR kinase 2–interacting protein‐1 protects against ischemia‐reperfusion injury of the spinal cord by modulating ASK1/JNK/p38 signaling
Authors: Chen Jian , Wang Qian , Zhou Wei , Zhou Zheng , Tang Peng‐Yu , Xu Tao , Liu Wei , Li Lin‐Wei , Cheng Lin , Zhou Zhi‐Min , Fan Jin , Yin Guo‐Yong 
Published: June 2018

ABSTRACTGPCR kinase 2–interacting protein‐1 (GIT1) is a scaffold protein that plays an important role in cell adaptation, proliferation, migration, and differentiation; however, the role of GIT1 in the regulation of neuronal death after spinal cord injury remains obscure. Here, we demonstrate that GIT1 deficiency remarkably increased neuronal apoptosis and enhanced JNK/p38 signaling, which resulted in stronger motor deficits by ischemia‐reperfusion in vivo, consistent with the finding of oxygen‐glucose deprivation/reoxygenation–induced neuronal injury in vitro. After treatment with JNK and p38 inhibitors, abnormally necroptotic cell death caused by GIT1 knockdown could be partially rescued, with the recovery of neuronal viability, which was still poorer than that in control neurons. Meanwhile, overactivation of JNK/p38 after GIT1 depletion was concomitant with excessive activity of apoptosis signal‐regulating kinase‐1 (ASK1) that could be abolished by ASK1 silencing in HEK293T cells. Finally, GIT1 could disrupt the oligomerization of ASK1 via interaction between the synaptic localization domain that contains the coiled‐coil (CC)‐2 domain of GIT1 and the C‐terminal CC domain of ASK1. It suppressed the autophosphorylation of ASK1 and led to decreasing activity of the ASK1/JNK/p38 pathway. These data reveal a protective role for GIT1 in neuronal damage by modulating ASK1/JNK/p38 signaling.—Chen, J., Wang, Q., Zhou, W., Zhou, Z., Tang, P.‐Y., Xu, T., Liu, W., Li, L.‐W., Cheng, L., Zhou, Z.‐M., Fan, J., Yin, G.‐Y. GPCR kinase 2‐interacting protein‐1 protects against ischemia‐reperfusion injury of the spinal cord by modulating ASK1/JNK/p38 signaling. FASEB J. 32, 6833–6847 (2018). www.fasebj.org
Olfactory language and abstraction across cultures
Authors: Majid Asifa , Burenhult Niclas , Stensmyr Marcus , de Valk Josje , Hansson Bill S. 
Published: June 2018

Olfaction presents a particularly interesting arena to explore abstraction in language. Like other abstract domains, such as time, odours can be difficult to conceptualize. An odour cannot be seen or held, it can be difficult to locate in space, and for most people odours are difficult to verbalize. On the other hand, odours give rise to primary sensory experiences. Every time we inhale we are using olfaction to make sense of our environment. We present new experimental data from 30 Jahai hunter-gatherers from the Malay Peninsula and 30 matched Dutch participants from the Netherlands in an odour naming experiment. Participants smelled monomolecular odorants and named odours while reaction times, odour descriptors and facial expressions were measured. We show that while Dutch speakers relied on concrete descriptors, i.e. they referred to odour sources (e.g.smells like lemon), the Jahai used abstract vocabulary to name the same odours (e.g.musty). Despite this differential linguistic categorization, analysis of facial expressions showed that the two groups, nevertheless, had the same initial emotional reactions to odours. Critically, these cross-cultural data present a challenge for how to think about abstraction in language.This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Learning abstract words and concepts: insights from developmental language disorder
Authors: Ponari Marta , Norbury Courtenay Frazier , Rotaru Armand , Lenci Alessandro , Vigliocco Gabriella 
Published: June 2018

Some explanations of abstract word learning suggest that these words are learnt primarily from the linguistic input, using statistical co-occurrences of words in language, whereas concrete words can also rely on non-linguistic, experiential information. According to this hypothesis, we expect that, if the learner is not able to fully exploit the information in the linguistic input, abstract words should be affected more than concrete ones. Embodied approaches instead argue that both abstract and concrete words can rely on experiential information and, therefore, there might not be any linguistic primacy. Here, we test the role of linguistic input in the development of abstract knowledge with children with developmental language disorder (DLD) and typically developing children aged 8–13. We show that DLD children, who by definition have impoverished language, do not show a disproportionate impairment for abstract words in lexical decision and definition tasks. These results indicate that linguistic information does not have a primary role in the learning of abstract concepts and words; rather, it would play a significant role in semantic development across all domains of knowledge.This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
NFAT5 participates in Inducible Nitric Oxide Synthase activation by hypoxia in MEF cells
Authors: Serman Yair , Fuentealba Rodrigo A. , Pasten Consuelo , Rocco Jocelyn , Ko Ben C. B. , Carrión Flavio , Irarrázabal Carlos E. 
Published: June 2018

AbstractWe previously described the protective role of NFAT5 during hypoxia, in an independent way of HIF-1α. Alternatively, inducible NO synthase (iNOS) is also induced by hypoxia. The aim of this study was to establish the NFAT5 target gene in mouse embryonic fibroblasts (MEF) cell stimulated by hypoxia. NFAT5, iNOS, NO level, aquaporin 1 (AQP1) and urea transporter 1 (UTA1) were induced by low oxygen levels in MEF cells. Additionally, NFAT5 and UTA1 were induced in reoxygenation (after 24hrs of hypoxia). NFAT5 transactivation domain (TAD) was induced during hypoxia and hypoxia/reoxygenation. Two MEF cells line independently produced for altered NFAT5 (Knockout and DBD-mutant) lost the iNOS and AQP1 induction by low oxygen. The iNOS induction was recovered in NFAT5-KO MEF cells, when recombinant NFAT5 protein expression was reconstituted, but not for NFAT5 DBD-mutant MEF cells, explained by its dominant negative effect. Finally, we found a negative feedback loop of iNOS effect over NFAT5 protein abundance. This work provides a relevant information about signaling pathway of NFAT5 during adaptive responses to oxygen depletion.
Cell type specific control of basolateral amygdala plasticity via feedforward inhibition
Authors: Guthman E. Mae , Ma Ming , Chu Philip , Baca Serapio M. , Restrepo Diego , Huntsman Molly M. 
Published: June 2018

AbstractThe basolateral amygdala (BLA) plays a vital role in associating specific sensory stimuli with salient valence information. Excitatory principal neurons (PNs) undergo plastic changes to encode this integrated sensory-valence information; however, local BLA inhibitory interneurons (INs) gate the plasticity of the PNs via feed forward inhibition (FFI). Despite extensive literature implicating parvalbumin expressing (PV+) INs in FFI in cortex and hippocampus, prior anatomical experiments in BLA implicate somatostatin expressing (Sst+) INs in BLA. In the present study, we combined patch clamp electrophysiology with chemogenetics, unsupervised cluster analysis, and predictive modeling and found that a previously unreported subpopulation of fast-spiking Sst+ INs mediate BLA FFI and gate plasticity.
Hyperparameter-free optimizer of stochastic gradient descent that incorporates unit correction and moment estimation
Authors: Yamada Kazunori D 
Published: June 2018

ABSTRACTIn the deep learning era, stochastic gradient descent is the most common method used for optimizing neural network parameters. Among the various mathematical optimization methods, the gradient descent method is the most naive. Adjustment of learning rate is necessary for quick convergence, which is normally done manually with gradient descent. Many optimizers have been developed to control the learning rate and increase convergence speed. Generally, these optimizers adjust the learning rate automatically in response to learning status. These optimizers were gradually improved by incorporating the effective aspects of earlier methods. In this study, we developed a new optimizer: YamAdam. Our optimizer is based on Adam, which utilizes the first and second moments of previous gradients. In addition to the moment estimation system, we incorporated an advantageous part of AdaDelta, namely a unit correction system, into YamAdam. According to benchmark tests on some common datasets, our optimizer showed similar or faster convergent performance compared to the existing methods. YamAdam is an option as an alternative optimizer for deep learning.
The immune checkpoint kick start: Optimization of neoadjuvant combination therapy using game theory
Authors: West Jeffrey , Robertson-Tessi Mark , Luddy Kimberly , Park Derek S. , Williamson Drew F.K. , Harmon Cathal , Khong Hung T. , Brown Joel , Anderson Alexander R.A. 
Published: June 2018

AbstractAn upcoming clinical trial at the Moffitt Cancer Center for women with stage 2/3 ER+breast cancer combines an aromatase inhibitor and a PD-L1 checkpoint inhibitor, and aims to lower a preoperative endocrine prognostic index (PEPI) that correlates with relapse-free survival. PEPI is fundamentally a static index, measured at the end of neoadjuvant therapy before surgery. We develop a mathematical model of the essential components of the PEPI score in order to identify successful combination therapy regimens that minimize both tumor burden and metastatic potential, based on time-dependent trade-offs in the system. We consider two molecular traits, CCR7 and PD-L1 which correlate with treatment response and increased metastatic risk. We use a matrix game model with the four phenotypic strategies to examine the frequency-dependent interactions of cancer cells. This game was embedded into an ecological model of tumor population growth dynamics. The resulting model predicts both evolutionary and ecological dynamics that track with changes in the PEPI score. We consider various treatment regimens based on combinations of the two therapies with drug holidays. By considering the trade off between tumor burden and metastatic potential, the optimal therapy plan was found to be a 1 month kick start of the immune checkpoint inhibitor followed by five months of continuous combination therapy. Relative to a protocol with both therapeutics given together from the start, this delayed regimen results in transient sub-optimal tumor regression while maintaining a phenotypic constitution that is more amenable to fast tumor regression for the final five months of therapy. The mathematical model provides a useful abstraction of clinical intuition, enabling hypothesis generation and testing of clinical assumptions.
LADL: Light-activated dynamic looping for endogenous gene expression control
Authors: Rege Mayuri , Kim Ji Hun , Valeri Jacqueline , Dunagin Margaret C. , Metzger Aryeh , Gong Wanfeng , Beagan Jonathan A. , Raj Arjun , Phillips-Cremins Jennifer E. 
Published: June 2018

AbstractMammalian genomes are folded into tens of thousands of long-range looping interactions1,2. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which chromatin loops are dynamic on short time scales remains a fundamental unanswered question. Currently available strategies for loop engineering involve synthetic transcription factors tethered to dCas93,4 or zinc fingers5,6, which are constitutively expressed5,6 or induced on long time scales by the presence of a small molecule3. Here we report a new class of 3-D optoepigenetic tools for the directed rearrangement of 3-D chromatin looping on short time scales using blue light. We create synthetic architectural proteins by fusing the CIBN protein subunit from Arabidopsis thaliana with enzymatically dead Cas9 (dCas9). We target our light-activated dynamic looping system (LADL) to two genomic anchors with CRISPR guide RNAs and engineer their spatial co-localization via light-induced heterodimerization of the cryptochrome 2 (CRY2) protein with dCas9-CIBN. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Looping changes occur as early as four hours after light induction. Using single molecule RNA FISH, we observe a LADL-induced increase in the total nascent Zfp462 transcripts and the number of Zfp462 alleles expressing simultaneously per cell. Moreover, LADL also increased synchronous Sox2 expression after reinforcement of a known Sox2-SE looping interaction. LADL facilitates loop synchronization across a large population of cells without exogenous chemical cofactors and can enable future efforts to engineer reversible and oscillatory looping on short time scales.
Multiobjective Strain Design: A Framework for Modular Cell Engineering
Authors: Garcia Sergio , Trinh Cong T. 
Published: June 2018

ABSTRACTDiversity of cellular metabolism can be harnessed to produce a large space of molecules. However, development of optimal strains with high product titers, rates, and yields required for industrial production is laborious and expensive. To accelerate the strain engineering process, we have recently introduced a modular cell design concept that enables rapid generation of optimal production strains by systematically assembling a modular cell with an exchangeable production module(s) to produce target molecules efficiently. In this study, we formulated the modular cell design concept as a general multiobjective optimization problem with flexible design objectives derived from mass action. We developed algorithms and an associated software package, named ModCell2 to implement the design. We demonstrated that ModCell2 can systematically identify genetic modifications to design modular cells that can couple with a variety of production modules and exhibit a minimal tradeoff among modularity, performance, and robustness. Analysis of the modular cell designs revealed both intuitive and complex metabolic architectures enabling modular production of these molecules. We envision ModCell2 provides a powerful tool to guide modular cell engineering and sheds light on modular design principles of biological systems.
Parameter inference with analytical propagators for stochastic models of autoregulated gene expression
Authors: Veerman Frits , Popović Nikola , Marr Carsten 
Published: June 2018

ABSTRACTStochastic gene expression in regulatory networks is conventionally modelled via the Chemical Master Equation (CME). As explicit solutions to the CME, in the form of so-called propagators, are oftentimes not readily available, various approximations have been proposed. A recently developed analytical method is based on a separation of scales that assumes significant differences in the lifetimes of mRNA and protein in the network, allowing for the efficient approximation of propagators from asymptotic expansions for the corresponding generating functions. Here, we showcase the applicability of that method to simulated data from a ‘telegraph’ model for gene expression that is extended with an autoregulatory mechanism. We demonstrate that the resulting approximate propagators can be applied successfully for Bayesian parameter inference in the non-regulated model; moreover, we show that, in the extended autoregulated model, autoactivation or autorepression may be refuted under certain assumptions on the model parameters. Our results indicate that the method showcased here may allow for successful parameter inference and model identification from longitudinal single cell data.
Accurate in vivo population sequencing uncovers drivers of within-host genetic diversity in viruses
Authors: Gelbart Maoz , Harari Sheri , Ben-Ari Ya’ara , Kustin Talia , Wolf Dana , Mandelboim Michal , Mor Orna , Pennings Pleuni , Stern Adi 
Published: June 2018

ABSTRACTMutations fuel evolution and facilitate adaptation to novel environments. However, characterizing the spectrum of mutations in a population is obscured by high error rates of next generation sequencing. Here, we present AccuNGS, a novel in vivo sequencing approach that detects variants as rare as 1:10,000. Applying it to 46 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV, revealed large differences in within-host genetic diversity among virus populations. Haplotype reconstruction revealed that increased diversity was mostly driven by multiple transmitted/founder viruses in HIV and CMV samples. Conversely, we detected an abundance of defective virus genomes (DVGs) in RSV samples, including hyper-edited genomes, nonsense mutations and single point deletions. Higher proportions of DVGs correlated with increased viral loads, suggesting increased cellular co-infection rates, which enable DVG persistence. AccuNGS establishes a general platform that allows detecting DVGs, and in general, rare variants that drive evolution.
High-sensitivity c-reactive protein and total and saturated fat intake in adolescent students: a longitudinal study
Authors: Cândida de Lima Martins Camila , Emília Leite de Lima Ferreira Flávia , Cavalcanti de Almeida Aléssio Tony 
Published: June 2018

AbstractObjectiveThe present study aimed to assess the relationship between hs-CRP concentrations and total and saturated fat intake in adolescents after a year of follow-up.MethodsA longitudinal study carried out in the years 2014 and 2015 evaluated 408 adolescents from the municipal and state public schools of João Pessoa, Paraíba, between 10 and 14 years of age, who participated in the Longitudinal Study on Sedentary Behavior, Physical Activity, Eating Habits and Adolescent Health (LONCAAFS). Data were obtained on sociodemographic data, anthropometric nutritional status, physical activity and hs-CRP concentration. The consumption of total and saturated fats was evaluated from the 24 hour recall.ResultsThe associations between concentrations of hs-CRP and total and saturated fat intake were performed by linear regression considering panel data, individual fixed effect, balanced bank, stratified by sex and BMI. The mean values of the hs-CRP variable were significantly different between the analyzed years (p = 0.024). The percentage of total and saturated fat consumption is within the recommended level in both years, with no significant difference (p> 0.05). No statistically significant associations were found between hs-CRP and total fat consumption (β = −0.19p = 0.582) and saturated fat (β = 0.20, p = 0.282).ConclusionThe study did not present significant evidence on the relationship between the concentrations of hs-CRP and the consumption of total and saturated fats, as one year of follow-up may not have promoted evident changes in the levels of hs-CRP in adolescents.