bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are place cells just memory cells? Memory compression leads to spatial tuning and history dependence
Authors: Benna Marcus K. , Fusi Stefano 
Published: May 2019

The observation of place cells has suggested that the hippocampus plays a special role in encoding spatial information. However, place cell responses are modulated by several non-spatial variables, and reported to be rather unstable. Here we propose a memory model of the hippocampus that provides a novel interpretation of place cells consistent with these observations. We hypothesize that the hippocampus is a memory device that takes advantage of the correlations between sensory experiences to generate compressed representations of the episodes that are stored in memory. A simple neural network model that can efficiently compress information naturally produces place cells that are similar to those observed in experiments. It predicts that the activity of these cells is variable and that the fluctuations of the place fields encode information about the recent history of sensory experiences. Place cells may simply be a consequence of a memory compression process implemented in the hippocampus.Significance StatementNumerous studies on humans revealed the importance of the hippocampus in memory formation. The rodent literature instead focused on the spatial representations that are observed in navigation experiments. Here we propose a simple model of the hippocampus that reconciles the main findings of the human and rodent studies. The model assumes that the hippocampus is a memory system that generates compressed representations of sensory experiences using previously acquired knowledge about the statistics of the world. These experiences can then be memorized more efficiently. The sensory experiences during the exploration of an environment, when compressed by the hippocampus, lead naturally to spatial representations similar to those observed in rodent studies and to the emergence of place cells.
Cell-to-cell Mathematical modeling of arrhythmia phenomena in excitable media
Authors: Garza Gabriel López 
Published: May 2019

AbstractIn this document are modeled arrhythmias with cellular automaton and ordinary differential equations systems. With an aperiodic, self-similar distribution of two-dimensional arrangement of cells, it is possible to simulate such phenomena as fibrillation, fluttering and a sequence of fibrillation-fluttering. The topology of the cytoarchitecture of a network of cells may determine the initiation and development of arrhythmias.
Still moving: The double-drift illusion survives smooth pursuit
Authors: Cavanagh Patrick , Tse Peter U. 
Published: May 2019

AbstractIf a gabor pattern drifts in one direction while its internal texture drifts in the orthogonal direction, observers see a remarkable shift in its perceived direction when it is viewed in the periphery. The reported direction of the double-drift stimulus (also known as the infinite regress and curveball illusions) is some combination of the actual external motion of the gabor envelope and the internal motion of its texture (Tse & Hsieh, 2006). Here we find that if the observers track a fixation point that moves in tandem with the gabor, the illusion is undiminished. The pursuit of the moving fixation spot keeps the gabor roughly fixed at one location on the retina, cancelling its external motion, leaving only the internal motion. The gabor is seen to move in the world at roughly its actual speed as the motion of the eye is discounted at some point to recover velocities in world coordinates (e.g. Wallach, 1959). Our finding indicates that the combination of internal and external motion that produces the double drift illusion must happen after the eye movement signals have been factored into stimulus motions. We also test the double drift effect at various path lengths, durations, and speeds, with both mid-grey and black backgrounds, all with a static fixation. These results confirm that a simple vector combination of the two speeds alone accounts for virtually all the direction shifts on the grey background. On the black background, the illusion is eliminated. These results place constraints on where perceived spatial coordinates arise in the visual processing hierarchy to locations at or beyond where compensation for pursuit eye movements arise, specifically V3A, V6, MSTd, and VIP (e.g., Nau et al, 2018).
Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation
Authors: Behring Jessica B , van der Post Sjoerd , Mooradian Arshag D , Egan Matthew J , Zimmerman Maxwell I , Clements Jenna L. , Bowman Gregory R , Held Jason M 
Published: May 2019

AbstractStimulation of receptor tyrosine kinases (RTK) such as EGF locally increase reactive oxygen species (ROS) levels at the plasma membrane that oxidize cysteines in proteins to enhance downstream signaling. Spatial confinement of ROS is an important regulatory mechanism to redox signaling, but it remains unknown why stimulation of different receptor tyrosine kinases (RTKs) at the plasma membrane target distinct sets of downstream proteins. To uncover additional mechanisms specifying which cysteines are redox regulated by EGF stimulation, we performed time-resolved quantification of the oxidation of 4,200 cysteine sites subsequent to EGF stimulation in A431 cells. EGF induces three distinct spatiotemporal patterns of cysteine oxidation in functionally organized protein networks, consistent with the spatial confinement model. Unexpectedly, protein crystal structure analysis and molecular dynamic simulation indicate widespread redox regulation of cryptic cysteines that are only solvent exposed upon changes in protein conformation. Phosphorylation and increased flux of nucleotide substrates serve as two distinct modes by which EGF specifies which cryptic cysteines become solvent exposed and redox regulated. Since proteins structurally regulated by different RTKs or cellular perturbations are largely unique, solvent exposure and redox regulation of cryptic cysteines is an important mechanism contextually delineating redox signaling networks.Significance StatementCellular redox processes are interconnected, but are not in equilibrium. Thus, understanding the redox biology of cells requires a systems-level, rather than reductionist, approach. Factors specifying which cysteines are redox regulated by a stimulus remain poorly characterized but are critical to understanding the fundamental properties of redox signaling networks. Here, we show that EGF stimulation induces oxidation of specific cysteines in 3 distinct spatiotemporal patterns. Redox regulated proteins include many proteins in the EGF pathway as well as many cysteines with known functional importance. Many redox regulated cysteines are cryptic and solvent exposed by changes in protein structure that were induced by EGF treatment. The novel finding that cryptic cysteines are redox regulated has important implications for how redox signaling networks are specified and regulated to minimize crosstalk. In addition, this time-resolved dataset of the redox kinetics of 4,200 cysteine sites is an important resource for others and is an important technological achievement towards systems-level understanding of cellular redox biology.
In vivoInteractions between Myosin XI, Vesicles, and Filamentous Actin Are Fast and Transient
Authors: Bibeau Jeffrey P. , Furt Fabienne , Mousavi S. Iman , Kingsley James L. , Levine Max F. , Tüzel Erkan , Vidali Luis 
Published: May 2019

AbstractThe apical actin cytoskeleton and active membrane trafficking machinery are essential in driving polarized cell growth. To better understand the interactions between myosin XI, vesicles, and actin filamentin vivo, we performed Fluorescence Recovery After Photobleaching (FRAP) and showed that the dynamics of myosin XIa at the tip are actin-dependent and that approximately half of myosin XI is bound to vesicles in the cell. To obtain single particle information, we used Variable Angle Epifluorescence Microscopy (VAEM) inPhyscomitrella patensprotoplasts to demonstrate that myosin XIa and VAMP72-labeled vesicles localize in time and space for periods lasting only a few seconds. Using tracking data with Hidden Markov Modeling (HMM), we showed that myosin XIa and VAMP72-labeled vesicles exhibit short runs of actin-dependent directed transport. We also found that the interaction of myosin XI with vesicles is short lived. Together, this bound fraction, fast off-rate, and short run lengths are expected to be critical for the dynamic oscillations observed at the cell apex, and may be vital for the regulation and recycling of the exocytosis machinery; while simultaneously promoting the vesicle focusing and secretion at the tip, necessary for cell wall expansion.
Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria
Authors: Charon Justine , Grigg Matthew J. , Eden John-Sebastian , Piera Kim A. , William Timothy , Rose Karrie , Davenport Miles P. , Anstey Nicholas M. , Holmes Edward C. 
Published: May 2019

AbstractParasites of the genus Plasmodium cause human malaria. Yet nothing is known about the viruses that infect these divergent eukaryotes. We investigated the Plasmodium virome by performing a meta-transcriptomic analysis of blood samples from malaria patients infected with P. vivax, P. falciparum or P. knowlesi. This revealed a novel bi-segmented narna-like RNA virus restricted to P. vivax and named Matryoshka RNA virus 1 (MaRNAV-1) to reflect its “Russian doll” nature: a virus, infecting a parasite, infecting an animal. MaRNAV-1 was abundant in geographically diverse P. vivax from humans and mosquitoes. Notably, a related virus (MaRNAV-2) was identified in Australian birds infected with a Leucocytozoon - eukaryotic parasites that group with Plasmodium in the Apicomplexa subclass hematozoa. This is the first report of a Plasmodium virus. As well as broadening our understanding of the eukaryotic virosphere, the restriction to P. vivax may help understand P. vivax-specific biology in humans and mosquitoes.
Staphylococcus aureususes the bacilliredoxin (BrxAB)/ bacillithiol disulfide reductase (YpdA) redox pathway to defend against oxidative stress under infections
Authors: Linzner Nico , Van Loi Vu , Fritsch Verena Nadin , Tung Quach Ngoc , Stenzel Saskia , Wirtz Markus , Hell Rüdiger , Hamilton Chris , Tedin Karsten , Fulde Marcus , Antelmann Haike 
Published: May 2019

ABSTRACTStaphylococcus aureusis a major human pathogen and has to cope with reactive oxygen and chlorine species (ROS, RCS) during infections. The low molecular weight thiol bacillithiol (BSH) is an important defense mechanism ofS. aureusfor detoxification of ROS and HOCl stress to maintain the reduced state of the cytoplasm. Under HOCl stress, BSH forms mixed disulfides with proteins, termed asS-bacillithiolations, which are reduced by bacilliredoxins (BrxA and BrxB). The NADPH-dependent flavin disulfide reductase YpdA is phylogenetically associated with the BSH synthesis and BrxA/B enzymes and was proposed to function as BSSB reductase. Here, we investigated the role of the bacilliredoxin BrxAB/BSH/YpdA pathway inS. aureusCOL under oxidative stress and macrophage infection conditionsin vivoand in biochemical assaysin vitro. Using HPLC thiol metabolomics, a strongly enhanced BSSB level and a decreased BSH/BSSB ratio were measured in theS. aureusCOLypdAdeletion mutant under control and NaOCl stress. Monitoring the BSH redox potential (EBSH) using the Brx-roGFP2 biosensor revealed that YpdA is required for regeneration of the reducedEBSHupon recovery from oxidative stress. In addition, theypdAmutant was impaired in H2O2detoxification as measured with the novel H2O2-specific Tpx-roGFP2 biosensor. Phenotype analyses further showed that BrxA and YpdA are required for survival under NaOCl and H2O2stressin vitroand inside murine J-774A.1 macrophages in infection assaysin vivo. Finally, NADPH-coupled electron transfer assays provide evidence for the function of YpdA in BSSB reduction, which depends on the conserved Cys14 residue. YpdA acts together with BrxA and BSH in de-bacillithiolation ofS-bacilithiolated GapDH. In conclusion, our results point to a major role of the BrxA/BSH/YpdA pathway in BSH redox homeostasis inS. aureusduring recovery from oxidative stress and under infections.
Ejaculate deterioration with male age, and its amelioration in Drosophila
Authors: Sepil Irem , Hopkins Ben R , Dean Rebecca , Bath Eleanor , Friedman Solomon , Swanson Ben , Ostridge Harrison J , Buehner Norene A , Wolfner Mariana F , Konietzny Rebecca , Thézénas Marie-Laëtitia , Sandham Elizabeth , Charles Philip D , Fischer Roman , Steinhauer Josefa , Kessler Benedikt M , Wigby Stuart 
Published: May 2019

AbstractDeclining ejaculate performance with male age is taxonomically widespread and has broad ramifications for fertility and fitness. However, we have a poor understanding of age-related changes to specific ejaculate components, how they cause reduced performance, and whether the decline is ameliorable. Here, we show that, in Drosophila, sperm production chronologically declines with age, invariant to mating activity, while repeated mating causes infertility via reduced sperm stores and viability. However, changes to sperm do not fully explain ejaculate deterioration: impacts on seminal fluid contribute to aspects of reduced ejaculate performance, associated with shifts in proteome abundance and quality. We show that ablation of insulin-like peptide-producing cells in males ameliorates aspects of ejaculate performance loss, suggesting that anti-ageing interventions can be coopted to benefit male reproductive health.One Sentence SummaryEjaculate performance declines with male age via mating-dependent sperm and seminal protein deterioration, but it can be ameliorated.
Multicenter Study of the Burden of Multidrug-Resistant Bacteria in the Etiology of Infected Diabetic Foot Ulcers
Authors: Adeyemo Adeyemi Temitayo , Kolawole Babatope A. , Rotimi Vincent Olubunmi , Aboderin Aaron Oladipo 
Published: May 2019

AbstractBackgroundInfected diabetic foot ulcer (IDFU) is a public health issue and a leading cause of non-traumatic limb amputation. Very few published data on IDFU is available in most West African countries. The objective of this study was to investigate the etiological agents of IDFU and the challenge of antibacterial drug resistance in the management of infections.MethodsThis was a prospective cross-sectional hospital-based study involving three tertiary healthcare facilities. Consecutive eligible patients presenting in the facilities were recruited. Tissue biopsies and/or aspirates were collected and cultured on a set of selective and non-selective media and incubated in appropriate atmospheric conditions for 24 to 72 hours. Isolates were identified by established standard methods. Antibiotic susceptibility testing was performed using modified Kirby-Bauer disc diffusion method. Specific resistance determinants were investigated by polymerase chain reaction-based protocols. Data analysis was done with SPSS version 20.ResultsNinety patients with clinical diagnosis of DFI were studied between July 2016 and April 2017. A total of 218 microorganisms were isolated, comprising 129 (59.2%) Gram-negative bacilli (GNB), 59 (27.1%) Gram-positive cocci (GPC) and 29 (13.2%) anaerobic bacteria. The top five facultative/aerobic bacteria encountered were: Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae and Citrobacter spp. representing 41 (18.8%), 23 (10.5%), 20 (9.2%), 19 (8.7%) and 19 (8.7%) isolates, in that order, respectively. The commonest anaerobes were Bacteroides spp., and Peptostreptococcus anaerobius which accounted for 7 (24.1%) and 6 (20.7%), respectively. Of the 93 IDFU cases, 74 (80%) were infected by multidrug-resistant (MDR) bacteria predominantly methicillin-resistant S. aureus, extended-spectrum β-lactamase-producing GNB, mainly of the CTX-M variety. Only 4 (3.1%) GNB were carbapenemase-producers encoded by blaVIM. Factors associated with presence of MDR bacteria were peripheral neuropathy (r= 4.05, P= 0.042) and duration of foot infection >1 month(r= 7.63, P= 0.015).ConclusionsMDR facultative/aerobic bacteria are overrepresented amongst agents causing IDFU. A relatively low proportion of the etiological agents were anaerobic bacteria. This finding should help formulate empirical therapeutic options for managing IDFU. Furthermore, drastic reduction in inappropriate use of cocktail of antibiotics for IDFUs is advocated to combat infection by MDR bacteria in these patients.
Comparison of the effects of running and badminton on executive function: a within-subjects design
Authors: Takahashi Shinji , Grove Philip M. 
Published: May 2019

AbstractMultiple cross-sectional studies have shown that regular complex exercises, which require cognitive demands (e.g., decision making) and various motions, are associated with greater positive effects on executive functions compared to simple exercises. However, the evidence of a single bout of complex exercises is mixed, and investigations on the acute effect of complex exercise using a well-controlled within-subjects research design are few. Therefore, we compared the acute effects of complex exercise on inhibitory functions with those of simple running. Twenty young adults performed three interventions, which were running, badminton, and seated rest as a control condition for 10 min each. During each intervention, oxygen consumption and heart rate were monitored. A Stroop test and a reverse-Stroop test were completed before and after each intervention. The intensities of the badminton and running were equivalent. Badminton significantly improved performance on the Stroop task compared to seated rest; however, running did not enhance performance on the Stroop task relative to seated rest. A single bout of complex exercise elicits a larger benefit to inhibitory function than a single bout of simple exercise. However, the benefit of complex exercise may vary depending on the type of cognitive control.
Significantly different expression levels of microRNAs associated with vascular invasion in hepatocellular carcinoma and their prognostic significance after surgical resection
Authors: Song Sung Kyu , Jung Woon Yong , Park Seung-Keun , Chung Chul-Woon , Park Yongkeun 
Published: May 2019

ABSTRACTBackgroundAlthough gross vascular invasion (VI) has prognostic significance in patients with hepatocellular carcinoma (HCC) who have undergone hepatic resection, few studies have investigated the relationship between gross VI and aberrant expression of microribonucleic acids (miRNAs and miRs). Thus, the objective of this study was to identify miRNAs selectively expressed in HCC with gross VI and investigate their prognostic significance.Materials and MethodsEligible two datasets (accession number: GSE20594 and GSE67140) were collected from the National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) database to compare miRNAs expression between HCC with and without gross VI. Differentially expressed miRNAs were externally validated using expression data from The Cancer Genome Atlas (TCGA) database. Prognostic significance and predicted functions of selected miRNAs for HCC were also investigated.ResultsThirty-five miRNAs were differentially expressed between HCC with and without gross VI in both datasets. Among them, four miRNAs were validated using TCGA database. miR-582 was upregulated to a greater extent while miR-99a, miR-100, and miR-148a were downregulated to a greater extent in patients with HCC and gross VI than in those with HCC but no VI. Receiver operating characteristic (ROC) curve analysis showed discriminatory power of these miRNAs in predicting gross VI. Multivariate survival analysis revealed that types of surgery, advanced tumor node metastasis (TNM) stage, and miR-100 underexpression were independently associated with tumor recurrence. It also revealed that types of surgery, advanced TNM stage, miR-100 underexpression, and miR-582 overexpression were independent risk factors for overall survival (OS) after hepatic resection for HCC. A text mining analysis revealed that these miRNAs were linked to multifaceted hallmarks of cancer, including “invasion and metastasis.”ConclusionsmiR-100 underexpression and miR-582 overexpression were associated with gross VI and poor survival of patients after hepatic resection for HCC.
Oregano powder reduces Streptococcus and increases SCFA concentration in a mixed bacterial culture assay of chicken
Authors: Bauer Benjamin W , Gangadoo Sheeana , Bajagai Yadav Sharma , Thu Hao Van Thi , Moore Robert J , Stanley Dragana 
Published: May 2019

AbstractFood borne illnesses have a world-wide economic impact and industries are continuously developing technologies to reduce the spread of disease caused by microorganisms. Antimicrobial growth promoters (AGPs) have been used to decrease microbiological infections in animals and their potential transfer to humans. In recent years there has been a global trend to remove AGPs from animal feed in an attempt to reduce the spread of antimicrobial resistant genes into the human population. Phytobiotics, such as oregano powder, are one of the potential replacements for AGPs due to their well-established antimicrobial components. 16S rRNA gene amplicons were used to determine the effect of oregano powder (1% w/v) on the microbiota of mixed bacterial cell cultures, which were obtained from the ceca of traditionally grown meat chickens (broilers). Oregano powder had a mild effect on the microbial cell cultures increasing Enterococcus faecium, rearranging ratios of members in the genus Lactobacillus and significantly reducing the genus Streptococcus (p=1.6e−3). Beneficial short chain fatty acids (SCFA), acetic and butyric acid, were also significantly increased in oregano powder supplemented cultures. These results suggest that oregano powder at a concentration of 1 % (w/v) may have beneficial influences on mixed microbial communities and SCFA production.
Heritage reporting by the Australian public sector
Authors: Woon Peir Peir , Chatterjee Bikram , Cordery Carolyn J. 
Published: May 2019

Purpose
The purpose of this paper is to contribute to the future development of heritage reporting in Australia. Public sector reporting of heritage has been a long-standing issue, due to shortcomings in (sector-neutral) for-profit-based financial reporting standards. Australia’s sector-neutral approach does not meet public sector users’ information needs. The authors develop a heritage reporting model to balance community and other stakeholders’ interests and address prior critiques.

Design/methodology/approach
The paper reviews heritage reporting requirements in Anglo-Western Countries, and analyses commentaries and research publications. It evaluates the existing reporting requirements in the context of new public management (which focusses on information and efficiency) and new public governance (NPG) (focussing on balancing interests and quality).

Findings
The paper proposes an NPG-based heritage reporting model which includes indicators of performance on the five UNESCO (1972) dimensions and operational guidelines issued by UNESCO (2015). These are identification, presentation, protection, conservation and transmission. The proposed model is consistent with the notion of US SFFAS 29 (the standard for Federal entities). Not all heritage must be capitalised and hence attachment of monetary value, but detailed disclosures are necessary.

Research limitations/implications
The authors expect the proposed heritage reporting model to better serve users of heritage information compared to the present Australian Accounting Standards Board 116: Property, Plant and Equipment.

Originality/value
The authors’ proposed model of heritage reporting attempts to answer Carnegie and Wolnizer’s (1995, 1999) six questions, addresses decades of concerns raised in previous literature and provides a new perspective to heritage reporting based on NPG that should better serve users’ needs.