bluuebunny/crossref_metadata_2025_split huggingface dataset:
MULTIMODAL IMAGING ADDS NEW INSIGHTS INTO ACUTE SYPHILITIC POSTERIOR PLACOID CHORIORETINITIS
Authors: Tsui Edmund , Gal-Or Orly , Ghadiali Quraish , Freund K. Bailey 
Published: October 2017

Purpose:
Acute syphilitic posterior placoid chorioretinitis (ASPPC) is an uncommon manifestation of ocular syphilis with distinct clinical features. We describe new multimodal imaging findings in a patient with ASPPC.

Methods:
Observational case report with multimodal imaging.

Results:
A 44-year-old woman presented with 5 days of decreased vision in her right eye. Visual acuity was counting fingers in her right eye and 20/20 in her left eye. Funduscopic examination of the right eye showed a yellow placoid macular lesion with extension beyond the equator, which was encircled by an annular ring of outer retinal whitening. Ultra-widefield fundus autofluorescence demonstrated hyperautofluorescence corresponding to the placoid lesion. Examination of the left eye appeared unremarkable, but ultra-widefield fundus autofluorescence showed an area of hyperautofluorescence located superonasal to the optic nerve. Optical coherence tomography of the right eye demonstrated subretinal fluid and overlying disruption of the ellipsoid zone. Fluorescein angiography demonstrated early hypofluorescent and hyperfluorescent spots and late staining within the placoid lesion. Optical coherence tomography angiography showed several areas of decreased flow signal within the placoid lesion at the level of the choriocapillaris. Laboratory testing revealed a rapid plasma reagin titer of 1:1,024. Two months after treatment with intravenous penicillin G, visual acuity had improved to 20/25 in her right eye, and optical coherence tomography showed partial restoration of the ellipsoid zone. The annular ring resolved with near normalization of fundus autofluorescence and optical coherence tomography angiography demonstrated resolution of flow.

Conclusion:
Multimodal imaging provides further insight into the pathogenesis of ASPPC. Ultra-widefield fundus autofluorescence may show evidence of ellipsoid zone disruption in areas that clinically appear normal. Flow voids within the choriocapillaris in ASPPC appear to resolve with appropriate treatment, a finding that suggests a transient disruption of choriocapillaris flow in ASPPC.
A Research of Pyogenic Granuloma Genesis Factor With Immunohistochemical Analysis
Authors: Park Si Hyun , Lee Jun Ho , Tak Min Sung , Lee Hyun Ju , Choi Hwan Jun 
Published: October 2017

Abstract
Pyogenic granuloma (PG) is a type of vascular tumor for which the growth mechanism is poorly understood. Estrogen and progesterone may influence vascular malformations by increasing neovascularization in the lesions. Pregnancy tumor is a term for PG that occurs on the gingival mucosa of pregnant women in response to local irritation or injury. The etiology and pathogenesis of this phenomenon are not fully understood. Hormonal imbalance has been hypothesized to be responsible for the development of gingival hyper-reactive inflammatory responses. Moreover, it has been shown in vitro that the female sex hormone is a potential regulator of the production of several growth factors, such as vascular endothelial growth factor (VEGF), basic fibroblast growth factor, and nerve growth factor, in various cell types. Epidermal growth factor receptor (EGFR) is also involved in a signaling cascade that influences proliferation and other tumor-promoting activities, as well as the responsiveness to chemotherapy. The aim of this study was to examine the relationship between PG pathogenesis and hormone imbalance in 21 patients. All specimens were analyzed by immunohistochemical staining with hematoxylin and eosin for the following hormones: estrogen receptor, progesterone receptor, VEGF, and EGFR. The analysis of the specimens showed that estrogen receptor and EGFR were not associated with PG, while VEGF was statistically related to PG. In addition, there was no significantly difference between sex, tumor location, or pregnancy. There are few studies about correlation between the pathogenesis of PG and sex hormones or growth factors demonstrated via immunohistochemical analysis. The results of this study indicate that estrogen and progesterone do not influence the pathogenesis of PG; however, VEGF may be associated with the pathogenesis of PG.
Ribosome flow model with extended objects
Authors: Zarai Yoram , Margaliot Michael , Tuller Tamir 
Published: October 2017

We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called theribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including non-homogeneous transition rates along mRNA, the fact that every ribosome covers several codons, and the fact that ribosomes cannot overtake one another. The RFMEO is a mean-field approximation of an important model from statistical mechanics called thetotally asymmetric simple exclusion process with extended objects(TASEPEO). We demonstrate that the RFMEO describes biophysical aspects of translation better than previous mean-field approximations, and that its predictions correlate well with those of TASEPEO. However, unlike TASEPEO, the RFMEO is amenable to rigorous analysis using tools from systems and control theory. We show that the ribosome density profile along the mRNA in the RFMEO converges to a unique steady-state density that depends on the length of the mRNA, the transition rates along it, and the number of codons covered by every ribosome, but not on the initial density of ribosomes along the mRNA. In particular, the protein production rate also converges to a unique steady state. Furthermore, if the transition rates along the mRNA are periodic with a common period Tthen the ribosome density along the mRNA and the protein production rate converge to a unique periodic pattern with period T, that is, the model entrains to periodic excitations in the transition rates. Analysis and simulations of the RFMEO demonstrate several counterintuitive results. For example, increasing the ribosome footprint may sometimes lead to an increase in the production rate. Also, for large values of the footprint the steady-state density along the mRNA may be quite complex (e.g. with quasi-periodic patterns) even for relatively simple (and non-periodic) transition rates along the mRNA. This implies that inferring the transition rates from the ribosome density may be non-trivial. We believe that the RFMEO could be useful for modelling, understanding and re-engineering translation as well as other important biological processes.
Antifungal activity of water-stable copper-containing metal-organic frameworks
Authors: Bouson Supaporn , Krittayavathananon Atiweena , Phattharasupakun Nutthaphon , Siwayaprahm Patcharaporn , Sawangphruk Montree 
Published: October 2017

Although metal-organic frameworks (MOFs) or porous coordination polymers have been widely studied, their antimicrobial activities have not yet been fully investigated. In this work, antifungal activity of copper-based benzene-tricarboxylate MOF (Cu-BTC MOF), which is water stable and industrially interesting, is investigated against
Candida albicans
,
Aspergillus niger
,
Aspergillus oryzae
and
Fusarium oxysporum
. The Cu-BTC MOF can effectively inhibit the growth rate of
C. albicans
and remarkably inhibit the spore growth of
A. niger
,
A. oryzae
and
F. oxysporum
. This finding shows the potential of using Cu-BTC MOF as a strong biocidal material against representative yeasts and moulds that are commonly found in the food and agricultural industries.
The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham Cycle
Authors: Ebenhöh Oliver , Spelberg Stephanie 
Published: October 2017

AbstractThe photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham Cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle’s structure was fuelled by the findings of Gibbs and Kandler in 1956 and 1957, when they observed that radioactive14CO2was dynamically incorporated in hexoses in a very atypical and asymmetrical way, a phenomenon later termed the ‘photosynthetic Gibbs effect’. Now, it is widely accepted that the photosynthetic Gibbs effect is not in contradiction to the reaction scheme proposed by Calvin, Benson and Bassham, but the arguments given have been largely qualitative and hand-waving. To fully appreciate the controversy and to understand the difficulties in interpreting the Gibbs effect, it is illustrative to illuminate the history of the discovery of the Calvin-Benson-Bassham Cycle. We here give an account of central scientific advances and discoveries, which were essential prerequisites for the elucidation of the cycle. Placing the historic discoveries in the context of the modern textbook pathway scheme illustrates the complexity of the cycle and demonstrates why especially dynamic labelling experiments are far from easy to interpret. We conclude by arguing that only mathematical models based on a sound theory are capable of resolving conflicting interpretations and providing a consistent quantitative explanation.
Adult Neurogenesis Conserves Hippocampal Learning Capacity
Authors: Alam Md Jahangir , Kitamura Takashi , Saitoh Yoshito , Ohkawa Noriaki , Kondo Takashi , Inokuchi Kaoru 
Published: October 2017

AbstractMemory coding strengthens synaptic efficacy in the hippocampus via a long-term potentiation (LTP)-like mechanism. Given that animals are able to store memories of everyday experiences, hippocampal circuits should be able to avoid saturation of overall synaptic weight to preserve learning capacity. However, the underlying mechanism for this is still poorly understood. Here, we show that adult neurogenesis in rats plays a crucial role in the maintenance of the hippocampal learning capacity for learning. Artificial saturation with hippocampal LTP impaired learning capacity in contextual fear conditioning, which then completely recovered after 14 days, when LTP had decayed to the basal level. Ablation of neurogenesis by X-ray irradiation delayed the recovery of learning capacity, while enhancement of neurogenesis using running wheel sped up the recovery. Thus, one benefit of ongoing adult neurogenesis is the maintenance of hippocampal learning capacity through homeostatic renewing of hippocampal memory circuits. Decreased neurogenesis in aged animals may underlie declines in cognitive function with aging.
Aqueous ethanol permeation across Sterlitech flat sheet aquaporin membranes
Authors: Lewis Jeremy , Alshami Ali 
Published: October 2017

AbstractAquaporin (Aqp) embedded membranes have become a topic of recent research due to the superior selectivity of Aqp to water and its acceptable flux. Most researchers have utilized Aqp membranes for water purification purposes such as reverse and forward osmosis desalination of sea and brackish water and wastewater treatment. This paper investigated the permeation of aqueous ethanol across commercial aquaporin membranes for possible applications in ethanol dehydration in the process and biofuel refining industries. The study revealed that rather than being selectively rejected, ethanol was able to diffuse through the membrane with minimal changes in composition from feed to permeate, even at low feed concentrations of ethanol. The total flux across the membranes were shown to average 3.86 liters/m2h (LMH). The presence of ethanol increased the relative rate of water transport across the membrane. When comparing total flux of pure water to aqueous ethanol solutions, the flux was higher for solutions containing any ethanol.
Whole genome sequence and comparative analysis ofBorrelia burgdorferiMM1
Authors: Jabbari Neda , Glusman Gustavo , Joesch-Cohen Lena M. , Reddy Panga Jaipal , Moritz Robert L. , Hood Leroy , Lausted Christopher G. 
Published: October 2017

AbstractLyme disease is caused by spirochaetes of theBorrelia burgdorferisensu lato genospecies. Complete genome assemblies are available for fewer than ten strains ofBorrelia burgdorferisensu stricto, the primary cause of Lyme disease in North America. MM1 is a sensu stricto strain originally isolated in the midwestern United States. Aside from a small number of genes, the complete genome sequence of this strain has not been reported. Here we present the complete genome sequence of MM1 in relation to other sensu stricto strains and in terms of its Multi Locus Sequence Typing. Our results indicate that MM1 is a new sequence type which contains a conserved main chromosome and 15 plasmids. Our results include the first contiguous 28.5 kb assembly of lp28-8, a linear plasmid carrying thevlsantigenic variation system, from aBorrelia burgdorferisensu stricto strain.
Genomic divergence footprints in the bracovirus ofCotesia sesamiaeidentified by targeted re-sequencing approach
Authors: Gauthier Jérémy , Gayral Philippe , Le Ru Bruno Pierre , Jancek Séverine , Dupas Stéphane , Kaiser Laure , Gyapay Gabor , Herniou Elisabeth A. 
Published: October 2017

AbstractThe African parasitoid waspCotesia sesamiaeis structured in contrasted populations showing differences in host range and the recent discovery of a specialist related species,C. typhae, provide a good framework to study the mechanisms that link the parasitoid and their host range. To investigate the genomic bases of divergence between these populations, we used a targeted sequencing approach on 24 samples. We targeted a specific genomic region encoding the bracovirus, which is deeply involved in the interaction with the host. High sequencing coverage was obtained for all samples allowing the study of genetic variations between wasp populations and species. Combining population genetic estimations, the diversity (π), the relative differentiation (FST) and the absolute differentiation (dxy), and branch-site dN/dS measures, we identified six divergent genes impacted by positive selection belonging to different gene families. These genes are potentially involved in host adaptation and in the specialization process. Fine scale analyses of the genetic variations also revealed deleterious mutations and large deletions on certain genes inducing pseudogenization and loss of function. These results highlight the crucial role of the bracovirus in the molecular interactions between the wasp and its hosts and in the evolutionary processes of specialization.
Neural signatures of dynamic emotion constructs in the human brain
Authors: Grootswagers Tijl , Kennedy Briana L. , Most Steven B. , Carlson Thomas A. 
Published: October 2017

AbstractHow is emotion represented in the brain: is it categorical or along dimensions? In the present study, we applied multivariate pattern analysis (MVPA) to magnetoencephalography (MEG) to study the brain’s temporally unfolding representations of different emotion constructs. First, participants rated 525 images on the dimensions of valence and arousal and by intensity of discrete emotion categories (happiness, sadness, fear, disgust, and sadness). Thirteen new participants then viewed subsets of these images within an MEG scanner. We used Representational Similarity Analysis (RSA) to compare behavioral ratings to the unfolding neural representation of the stimuli in the brain. Ratings of valence and arousal explained significant proportions of the MEG data, even after corrections for low-level image properties. Additionally, behavioral ratings of the discrete emotions fear, disgust, and happiness significantly predicted early neural representations, whereas rating models of anger and sadness did not. Different emotion constructs also showed unique temporal signatures. Fear and disgust – both highly arousing and negative – were rapidly discriminated by the brain, but disgust was represented for an extended period of time relative to fear. Overall, our findings suggest that 1) dimensions of valence and arousal are quickly represented by the brain, as are some discrete emotions, and 2) different emotion constructs exhibit unique temporal dynamics. We discuss implications of these findings for theoretical understanding of emotion and for the interplay of discrete and dimensional aspects of emotional experience.
Tree-ensemble analysis tests for presence of multifurcations in single cell data
Authors: Macnair Will , Roditi Laura De Vargas , Ganscha Stefan , Claassen Manfred 
Published: October 2017

AbstractWe introduce TreeTop, an algorithm for single-cell data analysis to identify and assess statistical significance of branch points in biological processes with possibly multi-level branching hierarchies. We demonstrate branch point identification for processes with varying topologies, including T cell maturation, B cell differentiation and hematopoiesis. Our analyses are consistent with recent experimental studies suggesting a shallow hierarchy of differentiation events in hematopoiesis, rather than the classical multi-level hierarchy.
Neocortical microdissection at columnar and laminar resolution for molecular interrogation
Authors: Kole Koen , Celikel Tansu 
Published: October 2017

AbstractThe heterogeneous organization of the mammalian neocortex poses a challenge to elucidate the molecular mechanisms underlying its physiological processes. Although high-throughput molecular methods are increasingly deployed in neuroscience, their anatomical specificity is often lacking. Here we introduce a targeted microdissection technique that enables extraction of high-quality RNA and proteins at high anatomical resolution from acutely prepared brain slices. We exemplify its utility by isolating single cortical columns and laminae from the mouse primary somatosensory (barrel) cortex. Tissues can be isolated from living slices in minutes, and the extracted RNA and protein are of sufficient quantity and quality to be used for RNA-sequencing and mass spectrometry. This technique will help to increase the anatomical specificity of molecular studies of the neocortex, and the brain in general as it is applicable to any brain structure that can be identified using optical landmarks in living slices.
Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank
Authors: Tikkanen Emmi , Gustafsson Stefan , Amar David , Shcherbina Anna , Waggott Daryl , Ashley Euan A. , Ingelsson Erik 
Published: October 2017

AbstractBackgroundHand grip strength, a simple indicator of muscular strength, has been associated with a range of health conditions, including fractures, disability, cardiovascular disease and premature death risk. Twin studies have suggested a high (50-60%) heritability, but genetic determinants are largely unknown.AimsIn this study, our aim was to study genetic variation associated with muscular strength in a large sample of 334,925 individuals of European descent from the UK Biobank, and to evaluate shared genetic aetiology with and causal effects of grip strength on physical and cognitive health.Methods and ResultsIn our discovery analysis of 223,315 individuals, we identified 101 loci associated with grip strength at genome-wide significance (P<5×10−8). Of these, 64 were associated (P<0.01 and consistent direction) also in the replication dataset (N=111,610). Many of the lead SNPs were located in or near genes known to have a function in developmental disorders (FTO, SLC39A8, TFAP2B, TGFA, CELF1, TCF4, BDNF, FOXP1, KIF1B, ANTXR2), and one of the most significant genes based on a gene-based analysis (ATP2A1) encodes SERCA1, the critical enzyme in calcium uptake to the sarcoplasmic reticulum, which plays a major role in muscle contraction and relaxation. Further, we demonstrated a significant enrichment of gene expression in brain-related transcripts among grip strength associations. Finally, we observed inverse genetic correlations of grip strength with cardiometabolic traits, and positive correlation with parents’ age of death and education; and showed that grip strength was causally related to fitness, physical activity and other indicators of frailty, including cognitive performance scores.ConclusionsIn our study of over 330,000 individuals from the general population, the genetic findings for hand grip strength suggest an important role of the central nervous system in strength performance. Further, our results indicate that maintaining good muscular strength is important for physical and cognitive performance and healthy aging.
Simple nanofluidic devices for high-throughput, non-equilibrium studies at the single-molecule level
Authors: Fijen Carel , Fontana Mattia , Lemay Serge G. , Mathwig Klaus , Hohlbein Johannes 
Published: October 2017

ABSTRACTSingle-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. Probing chemical and biological interactions and reactions with high throughput and time resolution, however, remains challenging and often requires surface-immobilized entities. Here, utilizing camera-based fluorescence microscopy, we present glass-made nanofluidic devices in which fluorescently labelled molecules flow through nanochannels that confine their diffusional movement. The first design features an array of parallel nanochannels for high-throughput analysis of molecular species under equilibrium conditions allowing us to record 200.000 individual localization events in just 10 minutes. Using these localizations for single particle tracking, we were able to obtain accurate flow profiles including flow speeds and diffusion coefficients inside the channels.A second design featuring a T-shaped nanochannel enables precise mixing of two different species as well as the continuous observation of chemical reactions. We utilized the design to visualize enzymatically driven DNA synthesis in real time and at the single-molecule level. Based on our results, we are convinced that the versatility and performance of the nanofluidic devices will enable numerous applications in the life sciences.
Origins of fractional control in regulated cell death
Authors: Santos Luís C. , Vogel Robert , Chipuk Jerry E. , Birtwistle Marc R. , Stolovitzky Gustavo , Meyer Pablo 
Published: October 2017

AbstractIndividual cells in clonal populations often respond differently to environmental changes; for binary phenotypes, such as cell death, this can be measured as a fractional response. These types of responses have been attributed to cell-intrinsic stochastic processes and variable abundances of biochemical constituents, such as proteins, but the influence of organelles has yet to be determined. We use the response to TNF-related apoptosis inducing ligand (TRAIL) and a new statistical framework for determining parameter influence on cell-to-cell variability through the inference of variance explained, DEPICTIVE, to demonstrate that variable mitochondria abundance correlates with cell survival and determines the fractional cell death response. By quantitative data analysis and modeling we attribute this effect to variable effective concentrations at the mitochondria surface of the pro-apoptotic protein Bax. Further, we demonstrate that inhibitors of antiapoptotic Bcl-2 family proteins, used in cancer treatment, may increase the diversity of cellular responses, enhancing resistance to treatment.