bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time is vision: functional preservation and enhanced capacity for recovery in subacute occipital stroke
Authors: Saionz Elizabeth L. , Tadin Duje , Melnick Michael D. , Huxlin Krystel R. 
Published: November 2019

AbstractStroke damage to the primary visual cortex (V1) causes a loss of vision known as hemianopia or cortically-induced blindness (CB). While early, spontaneous, perimetric improvements can occur, by 6 months post-stroke, the deficit is considered chronic and permanent. Despite evidence from sensorimotor stroke showing that early injury responses heighten neuroplastic potential, to date, rehabilitation research has focused only on chronic CB patients. Consequently, little is known about the functional properties of subacute, post-stroke visual systems, and whether they can be harnessed to enhance visual recovery. Here, for the first time, we show that conscious visual discrimination abilities are partially preserved inside subacute, perimetrically-defined blind fields, disappearing by 6 months post-stroke. Complementing this discovery, we show that global motion discrimination training initiated subacutely leads to comparable magnitude of recovery as that initiated in chronic CB. However, it does so 6 times faster, generalizes to deeper, untrained regions of the blind field, and to other [untrained] aspects of motion perception, preventing their degradation upon reaching the chronic period. Untrained subacutes exhibited only spontaneous improvements in perimetry - spontaneous recovery of motion discriminations was never observed. Thus, in CB, the early post-stroke period appears characterized by gradual - rather than sudden - loss of visual processing. Subacute training stops this degradation, and is dramatically more efficient at eliciting recovery than identical training in the chronic period. Finally, spontaneous improvements in subacutes appear restricted to luminance detection, whereas recovering discrimination abilities requires deliberate training. Simply stated, after an occipital stroke, “time is VISION”.One Sentence SummaryThe first 3 months after an occipital stroke are characterized by a gradual - not sudden - loss of visual perceptual abilities and increased rehabilitative potential if visual discrimination training is administered in the blind field.
Endogenous responses in brain pH andPO2in a rodent model of birth asphyxia
Authors: Pospelov Alexey S. , Puskarjov Martin , Kaila Kai , Voipio Juha 
Published: November 2019

ABSTRACTAimTo study brain-sparing physiological responses in a rodent model of birth asphyxia which reproduces the asphyxia-defining systemic hypoxia and hypercapnia.MethodsSteady or intermittent asphyxia was induced for 15-45 min in anesthetized 6 and 11 days old rats and neonatal guinea pigs using gases containing 5% or 9% O2plus 20% CO2(in N2). Hypoxia and hypercapnia were induced with low O2and high CO2, respectively. Oxygen partial pressure (PO2) and pH were measured with microsensors within the brain and subcutaneous (“body”) tissue. Blood lactate was measured after asphyxia.ResultsBrain and bodyPO2fell to apparent zero with little recovery during 5% O2asphyxia and 5% or 9% O2hypoxia, and increased more than twofold during 20% CO2hypercapnia. Unlike bodyPO2, brainPO2recovered rapidly to control after a transient fall (rat), or was slightly higher than control (guinea pig) during 9% O2asphyxia. Asphyxia (5% O2) induced a respiratory acidosis paralleled by a progressive metabolic (lact)acidosis that was much smaller within than outside the brain. Hypoxia (5% O2) produced brain-confined alkalosis. Hypercapnia outlasting asphyxia suppressed pH recovery and prolonged the post-asphyxiaPO2overshoot. All pH changes were accompanied by consistent shifts in the blood-brain barrier potential.ConclusionRegardless of brain maturation stage, hypercapnia can restore brainPO2and protect the brain against metabolic acidosis despite compromised oxygen availability during asphyxia. This effect extends to recovery phase if normocapnia is restored slowly, and it is absent during hypoxia, demonstrating that exposure to hypoxia does not mimic asphyxia.
RNA-guided Retargeting of Sleeping Beauty Transposition in Human Cells
Authors: Kovač Adrian , Miskey Csaba , Menzel Michael , Grueso Esther , Gogol-Döring Andreas , Ivics Zoltán 
Published: November 2019

ABSTRACTTwo different approaches of genomic modification are currently used for genome engineering and gene therapy: integrating vectors, which can efficiently integrate large transgenes but are unspecific with respect to their integration sites, and nuclease-based approaches, which are highly specific but not efficient at integrating large genetic cargoes. Here we demonstrate biased genome-wide integration of the Sleeping Beauty (SB) transposon by combining it with components of the CRISPR/Cas9 system. We provide proof-of-concept that it is possible to influence the target site selection of SB by fusing it to a catalytically inactive Cas9 (dCas9) and by providing a single guide RNA (sgRNA) against the human Alu retrotransposon. Enrichment of transposon integrations was dependent on the sgRNA, occurred in a relatively narrow, ∼200 bp window around the targeted sites and displayed an asymmetric pattern with a bias towards sites that are downstream of the sgRNA targets. Our data indicate that the targeting mechanism specified by CRISPR/Cas9 forces integration into genomic regions that are otherwise poor targets for SB transposition. Future modifications of this technology may allow the development of methods for efficient and specific gene insertion for precision genetic engineering.
Unspecific expression in limited excitatory cell populations in interneuron-targeting Cre-driver lines can have large functional effects
Authors: Müller-Komorowska Daniel , Opitz Thoralf , Elzoheiry Shehabeldin , Schweizer Michaela , Beck Heinz 
Published: November 2019

1AbstractTransgenic Cre-recombinase expressing mouse lines are widely used to express fluorescent proteins and opto-/chemogenetic actuators, making them a cornerstone of modern neuroscience. Particularly, the investigation of interneurons has benefitted from the ability to target genetic constructs to defined cell types. However, the cell type specificity of some mouse lines has been called into questions. Here we show for the first time the functional consequences of unspecific expression in a somatostatin-Cre (SST-Cre) mouse line. We find large optogenetically evoked excitatory currents originating from unspecifically targeted CA3 pyramidal cells. We also used public Allen Brain Institute data to estimate expression specificity in other Cre lines. Another SST-Cre mouse lines shows comparable unspecificity, whereas a Parvalbumin-Cre mouse line shows much less unspecific expression. Finally, we make suggestions to ensure that the results from in-vivo use of Cre mouse lines are interpretable.
Rhomboid protease RHBDL4 promotes retrotranslocation of aggregation-prone proteins for degradation
Authors: Bock Josephine , Kühnle Nathalie , Knopf Julia D. , Landscheidt Nina , Lee Jin-Gu , Ye Yihong , Lemberg Marius K. 
Published: November 2019

AbstractProtein degradation is fundamentally important to ensure cell homeostasis. In the endoplasmic reticulum (ER), the ER-associated degradation (ERAD) pathway targets incorrectly folded and unassembled proteins into the cytoplasm for turnover by the proteasome. In contrast, lysosomal degradation serves as a failsafe mechanism for removing proteins that resist ERAD by forming aggregates. Previously, we showed that the ER- resident rhomboid protease RHBDL4, together with p97, mediates membrane protein degradation. However, whether RHBDL4 acts in concert with additional ERAD components is unclear, and its full substrate spectrum remains to be defined. Here, we show that besides membrane proteins, RHBDL4 cleaves aggregation-prone luminal ERAD substrates. Because RHBDL4 with mutations in the rhomboid domain leads to stabilization of substrates at the cytoplasmic side, we hypothesize that analogue to the homologue ERAD factor derlin, RHBDL4 is directly involved in substrate retrotranslocation. RHBDL4’s interaction with the erlin ERAD complex and reciprocal interaction of rhomboid substrates with erlins suggest that RHBDL4 and erlins form a complex that clips substrates and thereby rescues aggregation-prone peptides in the ER lumen from terminal aggregation.
Semaphorin 3A induces cytoskeletal paralysis in tumor-specific CD8+ T cells
Authors: Barnkob Mike B , Michaels Yale S , André Violaine , Macklin Philip S , Gileadi Uzi , Valvo Salvatore , Rei Margarida , Kulicke Corinna , Chen Ji-Li , Jain Vitul , Woodcock Victoria , Colin-York Huw , Hadjinicolaou Andreas V , Kong Youxin , Mayya Viveka , Bull Joshua A , Rijal Pramila , Pugh Christopher W , Townsend Alain R , Olsen Lars R , Fritzsche Marco , Fulga Tudor A , Dustin Michael L , Jones E Yvonne , Cerundolo Vincenzo 
Published: November 2019

ABSTRACTSemaphorin-3A (Sema3A) regulates tumor angiogenesis, but its role in modulating anti-tumor immunity is unclear. We demonstrate that Sema3A secreted within the tumor microenvironment (TME) suppresses tumor-specific CD8+ T cell function via Neuropilin-1 (NRP1), a receptor that is upregulated upon activation with T cells’ cognate antigen. Sema3A inhibits T cell migration, assembly of the immunological synapse, and tumor killing. It achieves these functional effects through hyper-activating the acto-myosin system in T cells leading to cellular paralysis. Finally, using a clear cell renal cell carcinoma patient cohort, we demonstrate that human tumor-specific CD8+ T cells express NRP1 and are trapped in Sema3A rich regions of tumors. Our study establishes Sema3A as a potent inhibitor of anti-tumor immunity.
A cell fate switch in theC. elegansseam cell lineage occurs through modulation of the Wnt asymmetry pathway in response to temperature increase
Authors: Hintze Mark , Koneru Sneha L. , Gilbert Sophie P.R. , Katsanos Dimitris , Barkoulas Michalis 
Published: November 2019

AbstractPopulations often display consistent developmental phenotypes across individuals despite the inevitable biological stochasticity. Nevertheless, developmental robustness has limits and systems can fail upon change in the environment or the genetic background. We use here the seam cells, a population of epidermal stem cells inCaenorhabditis elegans, to study the influence of temperature change and genetic variation on cell fate. Seam cell development has mostly been studied so far in the lab reference strain (N2), grown at 20° temperature. We demonstrate that an increase in culture temperature to 25°, introduces variability in the wild-type seam cell lineage with a proportion of animals showing an increase in seam cell number. We map this increase to lineage-specific symmetrisation events of normally asymmetric cell divisions at the final larval stage, leading to the retention of seam cell fate in both daughter cells. Using genetics and single molecule imaging, we demonstrate that this symmetrisation occurs via changes in the Wnt asymmetry pathway, leading to aberrant Wnt target activation in anterior cell daughters. We find that intrinsic differences in the Wnt asymmetry pathway already exist between seam cells at 20° and this may sensitise cells towards a cell fate switch at increased temperature. Finally, we demonstrate that wild isolates ofC. elegansdisplay variation in seam cell sensitivity to increased culture temperature, although seam cell numbers are comparable when raised at 20°. Our results highlight how temperature can modulate cell fate decisions in an invertebrate model of stem cell patterning.
A machine learning strategy that leverages large datasets to boost statistical power in small-scale experiments
Authors: Fondrie William E. , Noble William S. 
Published: November 2019

AbstractMachine learning methods have proven invaluable for increasing the sensitivity of peptide detection in proteomics experiments. Most modern tools, such as Percolator and PeptideProphet, use semi-supervised algorithms to learn models directly from the datasets that they analyze. Although these methods are effective for many proteomics experiments, we suspected that they may be suboptimal for experiments of smaller scale. In this work, we found that the power and consistency of Percolator results was reduced as the size of the experiment was decreased. As an alternative, we propose a different operating mode for Percolator: learn a model with Per-colator from a large dataset and use the learned model to evaluate the small-scale experiment. We call this a “static modeling” approach, in contrast to Percolator’s usual “dynamic model” that is trained anew for each dataset. We applied this static modeling approach to two settings: small, gel-based experiments and single-cell proteomics. In both cases, static models increased the yield of detected peptides and eliminated the model-induced variability of the standard dynamic approach. These results suggest that static models are a powerful tool for bringing the full benefits of Percolator and other semi-supervised algorithms to small-scale experiments.Abstract Figure
Profilin 1 Controls the Assembly, Organization, and Dynamics of Leading Edge Actin Structures Through Internetwork Competition and Collaboration
Authors: Skruber Kristen , Warp Peyton V. , Shklyarov Rachael , Thomas James D. , Swanson Maurice S. , Henty-Ridilla Jessica L. , Read Tracy-Ann , Vitriol Eric A. 
Published: November 2019

AbstractHow actin monomers are distributed to different networks remains poorly understood. One emerging concept is that the monomer pool is limited and heterogenous, causing biased assembly and internetwork competition. However, most knowledge regarding monomer distribution comes from studies where competing networks are discrete. In metazoans, many actin-based structures are complex, containing competing networks that overlap and are functionally interdependent. Addressing how monomers control the assembly and organization of these complex structures is critical to understanding how actin functions in cells. Here, we identify the monomer-binding protein profilin 1 (PFN1) as a major determinant of actin assembly, organization, and network homeostasis in mammalian cells. At the leading edge, PFN1 controls the localization and activity of the assembly factors Arp2/3 and Mena/VASP, with discrete stages of internetwork competition and collaboration occurring at different PFN1 concentrations. This causes substantial changes to leading edge actin architecture and the types of structures that form there.
Generation of novel diagnostic and therapeutic exosomes to detect and deplete pro-tumorigenic M2-macrophages
Authors: Rashid Mohammad Harun , Borin Thaiz F. , Ara Roxan , Alptekin Ahmet , Liu Yutao , Arbab Ali S. 
Published: November 2019

AbstractGiven their pro-tumorigenic function and prevalence in most malignant tumors with lower survival, early detection and intervention of CD206-positive M2-macrophages may boost the clinical outcome. To determinein vivodistribution of M2-macrophages, we adopted111In-oxine-based radiolabeling of the targeted exosomes. When injected these radiolabeled targeted exosomes into breast tumor-bearing mice, exosomes accumulated at the periphery of the primary tumor, metastatic foci in the lungs, spleen, and liver.Ex vivoquantification of radioactivity also showed similar distribution. Injected DiI dye-labeled exosomes into the same mice showed adherence of exosomes to the CD206-positive M2-macrophages onex vivofluorescent microscopy imaging. In addition, we utilized these engineered exosomes to carry the Fc portion of IgG2b with the intention of augmenting antibody-dependent cell-mediated cytotoxicity. We have auspiciously demonstrated that M2-macrophage targeting therapeutic exosomes deplete M2-macrophages bothin vitroandin vivo, and reduce tumor burden increasing survival in a metastatic breast cancer model.
Redox signaling modulates Rho activity and tissue contractility in theC. elegansspermatheca
Authors: Kelley Charlotte A. , De Henau Sasha , Bell Liam , Dansen Tobias B. , Cram Erin J. 
Published: November 2019

AbstractActomyosin based contractility in smooth muscle and non-muscle cells is regulated by signaling through the small GTPase Rho and by calcium-activated pathways. We use the myoepithelial cells of theCaenorhabditis elegansspermatheca to study the mechanisms of coordinated myosin activationin vivo. Here, we demonstrate that redox signaling regulates RHO-1/Rho activity in this contractile tissue. Exogenous hydrogen peroxide treatment decreases spermathecal contractility by inhibiting RHO-1, which is mediated through a conserved cysteine in its active site (C20). Further, we identify a gradient of oxidation across the spermathecal tissue, which is regulated by the cytosolic superoxide dismutase, SOD-1. SOD-1 functions in the Rho pathway to inhibit RHO-1 through oxidation of C20. Our results suggest that SOD-1 functions to regulate the redox environment and to fine-tune Rho activity across the spermatheca.
A two-lane mechanism for selective biological ammonium transport
Authors: Williamson Gordon , Tamburrino Giulia , Mirandela Gaëtan Dias , Boeckstaens Mélanie , Bage Marcus , Pisliakov Andrei , Ives Callum M. , Terras Eilidh , Bizior Adriana , Hoskisson Paul A. , Marini Anna Maria , Zachariae Ulrich , Javelle Arnaud 
Published: November 2019

AbstractThe transport of charged molecules across biological membranes faces the dual problem of accommodating charges in a highly hydrophobic environment while maintaining selective substrate translocation. A particular controversy has existed around the mechanism of ammonium exchange by the ubiquitous Amt/Mep/Rh transporter family, an essential process in all kingdoms of life. Here, using a combination of electrophysiology, yeast functional complementation and extended molecular dynamics simulations, we reveal a unique two-lane pathway for electrogenic NH4+ transport in two archetypal members of the family. The pathway underpins a mechanism by which charged H+ and neutral NH3 are carried separately across the membrane after NH4+ deprotonation. This mechanism defines a new principle of achieving transport selectivity against competing ions in a biological transport process.
Structure and activation mechanism of the BBSome membrane-protein trafficking complex
Authors: Singh Sandeep , Gui Miao , Koh Fujiet , Yip Matthew C.J. , Brown Alan 
Published: November 2019

AbstractBardet-Biedl syndrome (BBS) is an incurable ciliopathy caused by the failure to correctly establish or maintain cilia-dependent signaling pathways. Eight proteins associated with BBS assemble into the BBSome, a master regulator of the ciliary membrane proteome. We report the electron cryomicroscopy (cryo-EM) structures of the native bovine BBSome in inactive and active states at 3.1 and 3.5 Å resolution, respectively. In the active state, the BBSome is bound to an Arf-family GTPase (ARL6/BBS3) that recruits the BBSome to ciliary membranes. ARL6 recognizes a composite binding site formed by BBS1 and BBS7 that is occluded in the inactive state. Activation requires an unexpected swiveling of the β-propeller domain of BBS1, the key subunit implicated in substrate recognition, which widens a central cavity of the BBSome. Structural mapping of disease-causing mutations suggests that pathogenesis predominantly results from disruption of autoinhibition and activation.
SpaB, an atypically adhesive basal pilin from the lactobacillar SpaCBA pilus: crystallization and X-ray diffraction analysis
Authors: Kumar Megta Abhin , Palva Airi , von Ossowski Ingemar , Krishnan Vengadesan 
Published: November 2019

The SpaB pilin is recognized as the basal subunit of the sortase-dependent SpaCBA pilus, which is known to be produced by the Gram-positive Lactobacillus rhamnosus GG, a gut-adapted commensal advocated to have health benefits. Despite seeming to function as an archetypal basal pilin by serving as the terminal subunit in pilus assembly, SpaB also assumes an atypical role as a mucoadhesive protein. To shed light on the structural factors that contribute to this dual functional behaviour, a recombinant form of the L. rhamnosus GG SpaB pilin was produced and purified for crystallization and X-ray diffraction experiments. The crystallization of SpaB remained particularly challenging until the implementation of a three-pronged crystallization approach involving C-terminal tail truncation, surface lysine methylation and magnesium additives. Ultimately, hexagonal crystals of SpaB were produced and were able to diffract to a resolution of 2.4 Å. This crystal form belonged to space group P6522 or P6122, with unit-cell parameters a = b = 51.53, c = 408.22 Å, α = β = 90.0, γ = 120.0°. Obtaining an interpretable electron-density map via single-wavelength anomalous diffraction (SAD) using iodide-derivative data sets did not succeed owing to the weak anomalous signal. As an alternative, attempts to provide phases by molecular replacement using the iodide-SAD data from SpaB and a collection of distant homology models (<28% sequence identity) are in progress.
Managing customer relationships in emerging markets
Authors: Gaur Sanjaya Singh , Kingshott Russel P.J. , Sharma Piyush 
Published: November 2019

Purpose
The purpose of this paper is to study the impact of relationship comfort and relationship proneness on the ability of service firms to build and maintain customer relationships in emerging markets (EMs).

Design/methodology/approach
A field-survey was conducted with retail-banking customers in India (n=300) using a structured self-administered questionnaire with well-established scales.

Findings
Relationship comfort positively affects key relationship marketing (RM) constructs (e.g. customer satisfaction, trust, commitment and loyalty) and relationship proneness positively moderates (strengthens) the impact of relationship comfort on customer commitment and loyalty.

Research limitations/implications
The findings may not be generalizable to all customer types using bank services as well as other types of services and in other EMs.

Practical implications
Service firms in EMs can build and maintain robust customer relationships by using relationship comfort and relationship proneness to strengthen key RM constructs, such as customer satisfaction, trust, commitment and loyalty.

Originality/value
The paper highlights the importance of maintaining RM as a tool to build valuable customer relationships but also reveals the importance of relationship comfort and relationship proneness in building trust-based customer relationships in the EMs.
The impact of surveillance and procedurally just behavior on civilian affect and responses in hypothetical interactions with police officers
Authors: Roche Sean Patrick 
Published: November 2019

Purpose
The purpose of this paper is to investigate the impact of surveillance from civilian smartphones and police body-worn cameras (BWCs), procedurally just tactics, and legal culpability on individuals’ emotional reactions and willingness to comply during police interactions.

Design/methodology/approach
Data are used from two randomized factorial survey vignette experiments conducted with a national sample of Americans (n=962).

Findings
The presence of BWCs reduces reported fear in both vignettes, and also reduces reported anger in one vignette. In contrast, the presence of a smartphone is not significantly related to anger or fear. In both vignettes, non-procedurally just treatment increases reported fear and anger, and decreases intent to comply, with reported anger mediating the relationship between non-procedurally just treatment and compliance.

Originality/value
These findings suggest different forms of surveillance may have distinct effects on citizens’ reported emotional states and behavioral intentions. Further, the results corroborate research on the relationship between procedural justice and affect, and provide evidence procedurally just strategies may decrease crime directly by preemptively dampening non-compliance.