bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactivating vocabularies in the elderly
Authors: Cordi M.J. , Schreiner T. , Rasch B. 
Published: November 2017

AbstractQuality of memory and sleep decline with age, but the mechanistic interactions underlying the memory function of sleep in older adults are still unknown. It is widely assumed that the beneficial effect of sleep on memory relies on reactivation during Non-rapid eye movement (NREM) sleep, and targeting these reactivations by cue re-exposure reliably improves memory in younger participants. Here we tested whether the reactivation mechanism during sleep is still functional in old age by applying targeted memory reactivation (TMR) during NREM sleep in healthy adults over 60 years. In contrast to previous studies in young participants, older adults’ memories do not generally benefit from TMR during NREM sleep. On an individual level, a subgroup of older adults still profited from cueing during sleep. These improvers tended to have a better sleep efficiency than non-improvers. In addition, the oscillatory results resembled those obtained in younger participants, involving increases in theta (~6Hz) and spindle (~13 Hz) power for remembered and gained words in a later time windows. In contrast, non-improvers showed no increases in theta activity and even strongly reduced spindle power for later gained vs. lost words. Our results suggest that reactivations during sleep might lose their functionality for memory in some older adults, while this mechanism is still intact in a subgroup of participants. Further studies need to examine more closely the determinants of preserving the memory function of sleep during healthy aging.Grant informationThe study was supported by grant of the Swiss National Science Foundation (SNSF) No. 100014_162388. T.S. is supported by a grant of the Swiss National Science Foundation (SNSF) No. P2ZHP1_164994.AbbreviationsN1 and N2Stage 1 and 2 sleepSWSSlow-wave sleepSWAslow-wave activityREMRapid eye movement sleepTSTTotal sleep timeTMRtargeted memory reactivation
Mouse lemurs’ and degraded habitat
Authors: Knoop Simon , Chikhi Lounès , Salmona Jordi 
Published: November 2017

AbstractMadagascar is known for its unique biodiversity including its endemic primates, the lemurs. This biodiversity is threatened by deforestation, forest degradation and anthropogenic disturbances. Several mouse lemurs (genus Microcebus) have been shown to cope with habitat disturbances and degradation. However, there are 24 recognized mouse lemur species living in very different habitats, and it is not clear whether all these species respond similarly to forest degradation. Here, we review the literature on mouse lemur use of degraded habitat. We further question whether mouse lemurs show variation in degraded habitat use, with respect to forest type, conservation status and distribution range. We show that data on degraded forest (DF) use is available for 14 species and geographically aggregated in a few locations. However, data are scarce for most species, and lacking for almost half of the currently recognized species. Our results however confirm that most mouse lemur species are able to cope with, but do not necessarily respond positively to habitat degradation. We found no variation in degraded habitat use, with respect to forest type, conservation status and distribution range. However, we identified food resources availability, understory structure, predation, and tree hole availability to be the most frequently invoked factors potentially influencing DF use. The relative frequency of these four factors vary among forest types suggesting that differences may exist but still require research efforts for ecological and environmental differences among regions to be fully understood.RESEARCH HIGHLIGHTSLittle differences in the use of degraded forest (DF) between forest types, distribution ranges or conservation status.Varying factors potentially affecting DF use, such as food resources, forest structure, tree hole availability and predation.
Influence ofOenococcus oeniandBrettanomyces bruxellensison Aged Wine Microbial Taxonomic and Functional Profiles
Authors: Zepeda-Mendoza Marie Lisandra , Edwards Nathalia Kruse , Madsen Mikkel Gulmann , Abel-Kistrup Martin , Puetz Lara , Sicheritz-Ponten Thomas , Swiegers Jan H. 
Published: November 2017

AbstractIn the wine making process, the interactions between lactic acid bacteria (LAB), yeast and other wine microflora have an impact on the wine quality. In this study, we investigate the influence of the LABOenococcus oeniand the spoilage yeastBrettanomyces bruxellensison the microbial community of a Cabernet Sauvignon wine. We generated metagenomic datasets from inoculations of three strains ofB. bruxellensis, in combination with twoO. oenistrains, one with and one without cinnamoyl esterase activity. This esterase activity releases hydroxycinnamic acids (HCAs) that can subsequently be processed by someB. bruxellensisstrains able to generate off-flavor compounds. We evaluated the influence of theO. oeniandB. bruxellensison the microbial taxonomic and functional potential profile, particularly regarding off-flavor formation due to HCAs. We found that the effect on the microbial profiles depends oni) theO. oeniandB. bruxellensisstrains being combined andii) the abundance they reach in the final wine, which depends on certain unidentified conditions. We confirmed that the potential ofB. bruxellensisto produce off-flavor compounds from HCAs depends on the strain. Interestingly, the samples without microbial inoculants also had this potential, suggesting that native grape microbiota could also influence the levels of HCA. We also found that the presence ofB. bruxellensisdoes not interfere with the malolactic fermentation of the evaluatedO. oenistrains, which leads to a less acidic taste. We show that metagenomic approaches can help uncover the complex wine microbial community traits, such as flavor, impacted by the simultaneous presence ofO. oeniandB. bruxellensis.
Could cyanobacteria have made the salinity transition during the late Archean?
Authors: Herrmann A. , Gehringer M.M. 
Published: November 2017

AbstractModern molecular evolutionary studies suggest the freshwater origin of cyanobacteria during the late Archean, about 2.7 Ga ago, with an even earlier evolution of oxidative photosynthesis. The large amount of oxygen required to oxygenate the Earth’s atmosphere during the Great Oxygenation Event (GOE) ~2.4 Ga is thought to have been produced by large cyanobacterial blooms in the open ocean. This then poses the question as to whether ancient lineages of cyanobacteria would have survived the salinity transition. This study investigates the effect of increasing salinity on the photosynthetic efficiency of two modern day descendants of ancient cyanobacteria, Chroococidiopsis thermalis PCC7203 and the root species, Gloeobacter violaceus PCC7421. Organisms were cultured in fresh, brackish or sea water analogous media under a present atmospheric level (PAL) atmosphere or an atmosphere with reduced O2 and elevated CO2 (rO2eCO2). The net photosynthesis (NP) rates were determined in liquid cultures, while the O2 and redox profiles were determined in pseudomats. While C. thermalis PCC7203 was able to grow under increasing salinities under both atmospheres tested, G. violaceus PCC7421 could not make the salinity change to sea water. NP rates were reduced for C. thermalis under increasing salinities, as were the levels of dissolved O2 in the media. A gene screen indicated that C. thermalis genome carries genes for both sucrose and trehalose synthesis, whereas G. violaceus has only the later genetic component, suggesting a mechanism for their differing salt tolerances. This study supports the hypothesis of Cyanobacterial evolution in freshwater environments and their transition into increasingly salty environments during the late Archaean, prior to the GOE.
Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization
Authors: Collins Kieran D. , Hu Shuai , Grasberger Helmut , Kao John Y. , Ottemann Karen M. 
Published: November 2017

AbstractThe epithelial layer of the gastrointestinal tract contains invaginations, called glands or crypts, which are colonized by symbiotic and pathogenic microorganisms and may function as designated niches for certain species. Factors that control gland colonization are poorly understood, but bacterial chemotaxis aids occupation of these sites. We report here that a Helicobacter pylori cytoplasmic chemoreceptor, TlpD, is required for gland colonization in the stomach. tlpD mutants demonstrate gland colonization defects characterized by a reduction in the percent of glands colonized, but not in number of bacteria per gland. Consistent with TlpD’s reported role in reactive oxygen species (ROS) avoidance, tlpD mutants showed hallmarks of exposure to large amounts of ROS. To assess the role of host-generated ROS in TlpD-dependent gland colonization, we utilized mice that lack either the ability to generate epithelial hydrogen peroxide or immune cell superoxide. tlpD gland colonization defects were rescued to wild-type H. pylori levels in both of these mutants. These results suggest that multiple types of innate immune generated ROS production limit gland colonization and that bacteria have evolved specific mechanisms to migrate through this gauntlet to establish in the glands.Classification: Biological sciences; microbiologySignificance statementMicrobial colonization of the gastrointestinal tract occurs at distinct sites within the tissue including glandular structures found in the stomach and intestine. Multiple lines of evidence suggest that glands supply niches that promote chronic microbial colonization, a process that is critical for symbiotic and pathogenic bacteria to maintain themselves. In this report, we show that host-produced reactive oxygen species (ROS) constrain gland colonization by the gastric pathogen Helicobacter pylori. A bacterial cytoplasmic chemoreceptor, TlpD, allows H. pylori to avoid ROS and enhances H. pylori’s ability to colonize a broad swath of glands. We propose that hosts limit gland access and spread by producing ROS, and bacteria counter with chemotactic responses that allow navigation through this gauntlet.
Three dimensional cross-modal image inference: label-free methods for subcellular structure prediction
Authors: Ounkomol Chek , Fernandes Daniel A. , Seshamani Sharmishtaa , Maleckar Mary M. , Collman Forrest , Johnson Gregory R. 
Published: November 2017

AbstractFluorescence microscopy has enabled imaging of key subcellular structures in living cells; however, the use of fluorescent dyes and proteins is often expensive, time-consuming, and damaging to cells. Here, we present a tool for the prediction of fluorescently labeled structures in live cells solely from 3D brightfield microscopy images. We show the utility of this approach in predicting several structures of interest from the same static 3D brightfield image, and show that the same tool can prospectively be used to predict the spatiotemporal position of these structures from a bright-field time series. This approach could also be useful in a variety of application areas, such as cross-modal image registration, quantification of live cell imaging, and determination of cell state changes.
Pyk2 suppresses contextual fear memory in a kinase-independent manner
Authors: Suo Lun , Zheng Jin , Zhou Yuxiao , Jia Liling , Kuang Yanping , Wu Qiang 
Published: November 2017

AbstractPost-traumatic stress disorder (PTSD) is a psychological illness characterized by recalling a feeling of distress when re-experiencing the original trauma-related cues. This associative fear response plays an important role in some psychiatric disorders and elucidation of the underlying mechanisms is of great importance. Here, we constructed Pyk2 null mice and found that these mutant mice showed enhancement in contextual-fear memory, but no changes in auditory-cued and spatial-referenced learning and memory. Moreover, using kinase mutant mice, we observed that Pyk2 suppressed contextual fear memory in a kinase-independent pathway. Using high-throughput RNA sequencing, we found that immediate early genes (IEGs), such as Npas4, cFos, Zif268/Egr1, Arc, and Nr4a1, were enhanced in Pyk2 null mice. We further demonstrated that Pyk2 disruption affected pyramidal neuronal complexity and spine dynamics. Thus, we demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2 null mice provides a model for understanding fear-related disorders.
Dynamics and interactions of highly resolved marine plankton via automated high frequency sampling
Authors: Needham David M. , Fichot Erin B. , Wang Ellice , Berdjeb Lyria , Cram Jacob A. , Fichot Cedric G. , Fuhrman Jed A. 
Published: November 2017

AbstractShort time-scale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA molecules (rRNA) ofBacteria,Archaea, andEukaryotaonce to twice-daily between March 2014 and May 2014 from the surface ocean off Catalina Island, California. TypicallyOstreococcus, Braarudosphaera, Teleaulax, and Synechococcusdominated phytoplankton sequences (including chloroplasts) while SAR11,Sulfitobacter, andFluviicoladominated non-phytoplanktonBacteriaandArchaea. We observed short-lived increases of diatoms, mostlyPseudo-nitzschiaandChaetoceros, with quickly respondingBacteriaandArchaeaincludingFlavobacteriaceae(Polaribacter&Formosa),Roseovarius, andEuryarchaeota(MGII), notably the exact amplicon sequence variants we observed responding similarly to another diatom bloom nearby, three years prior. We observed correlations representing known interactions among abundant phytoplankton rRNA sequences, demonstrating the biogeochemical and ecological relevance of such interactions: 1) The kleptochloroplastidic ciliateMesodinium18S rRNA gene sequences and a singleTeleaulaxtaxon (via 16S rRNA gene sequences) were correlated (Spearmanr=0.83) yet uncorrelated to aTeleaulax18S rRNA gene OTU, or any other taxon (consistent with a kleptochloroplastidic or karyoklepty relationship) and 2) the photosynthetic prymnesiophyteBraarudosphaera bigelowiiand two strains of diazotrophic cyanobacterium UCYN-A were correlated and each taxon was also correlated to other taxa, includingB. bigelowiito a verrucomicrobium and a dictyochophyte phytoplankter (allr> 0.8). We also report strong correlations (r> 0.7) between various ciliates, bacteria, and phytoplankton, suggesting interactions via currently unknown mechanisms. These data reiterate the utility of high-frequency time-series to show rapid microbial reactions to stimuli, and provide new information aboutin-situdynamics of previously recognized and hypothesized interactions.
The Neutrophil-to-Lymphocyte Ratio as a Prognostic Indicator in Head and Neck Cancer: A Systematic Review and Meta-Analysis
Authors: Tham Tristan , Bardash Yonatan , Herman Saori Wendy , Costantino Peter D. 
Published: November 2017

AbstractBackgroundThe aim of this systematic review and meta-analysis was to investigate the relationship between the Neutrophil-to-Lymphocyte Ratio (NLR) and prognosis in HNC.MethodsStudies were identified from Pubmed, Embase, Scopus, and the Cochrane Library. A systematic review and meta-analysis were performed to generate the pooled hazard ratios (HR) for overall survival (OS), disease free survival (DFS), and progression free survival (PFS).ResultsOur analysis combined the results of over 6770 patients in 26 cohorts (25 studies). The pooled data demonstrated that an elevated NLR significantly predicted poorer OS, DFS, and PFS. Heterogeneity was found for OS, PFS, and marginally for DFS. Subgroup analysis in OS demonstrated that elevated NLR remained an indicator of poor prognosis.ConclusionsElevated pretreatment NLR is a prognostic marker for HNC. It represents a simple and easily obtained marker that could be used to stratify groups of high-risk patients that might benefit from adjuvant therapy.
Venous Thromboembolism Risk in Head and Neck Cancer: Significance of the Preoperative Platelet-to-Lymphocyte Ratio
Authors: Tham Tristan , Rahman Lauren , Persaud Christina , Costantino Peter 
Published: November 2017

Abstract (250 limit)ObjectiveWe aimed to investigate the association between the preoperative platelet-to-lymphocyte ratio (PLR) and venous thromboembolism (VTE) in head and neck cancer (HNC) patients undergoing major surgery.Study DesignRetrospective cohort studySettingAcademic tertiary hospital from 2011 to 2017Subjects and MethodsPatients with confirmed HNC undergoing major surgery were included in this study. The preoperative PLR was recorded for all patients. Known VTE risk factors, including age, sex, smoking, BMI, prior VTE, and anticoagulation were also recorded. Risk factors were screened in univariate analysis using Wilcoxon’s rank sum test and χ2 test (Bonferroni corrected). Significant covariates were subsequently included in a multivariate regression model. Bootstrap techniques were used to obtain credible confidence intervals (CI).ResultsThere were 306 patients enrolled with 7 cases of VTE (6 DVTs and 1 PE). On univariate analysis, length of stay (p = 0.0026), length of surgery (p = 0.0029), and PLR (p = 0.0002) were founded to have significant associations with VTE. A Receiver Operator Characteristic (ROC) curve was constructed, that yielded an AUROC of 0.905 (95% CI: 0.82 - 0.98). Using an optimized cutoff, the multivariate model showed that length of surgery (β 95% CI: 0.0001 - 0.0006; p = 0.0056), and PLR (β 95% CI: 5.3256 - 5.3868; p < 0.0001) were significant independent predictors of VTE.ConclusionThis exploratory pilot study has shown that PLR offers a potentially accurate risk stratification measure as an adjunct to current tools in VTE risk prediction, without additional cost to health systems.Oral PresentationThis data was presented as an oral presentation at the Annual American Academy of Otolaryngology – Head and Neck Surgery (AAO-HNSF) Meeting, 13th September 2017
Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture
Authors: Wakabayashi Ken , Schmidt Ryan W. , Gakuhari Takashi , Koganebuchi Kae , Ogawa Motoyuki , Karsten Jordan K. , Sokhatsky Mykhailo , Oota Hiroki 
Published: November 2017

AbstractBackgroundThe Eneolithic (~ 5,500 yrBP) site of Verteba Cave in Western Ukraine contains the largest collection of human skeletal remains associated with the archaeological Cucuteni-Tripolye Culture. Their subsistence economy is based largely on agro-pastoralism and had some of the largest and most dense settlement sites during the Middle Neolithic in all of Europe. To help understand the evolutionary history of the Tripolye people, we performed mtDNA analyses on ancient human remains excavated from several chambers within the cave.ResultsBurials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics. Nucleotide diversity (π) is low among all sequence types and our network analysis indicates highly similar mtDNA sequence types for samples in chamber G3. Using different sample sizes due to the uncertainly in number of individuals (11, 28, or 15), we found Tajima’s D statistic to vary. When all sequence types are included (11 or 28), we do not find a trend for demographic expansion (negative but not significantly different from zero); however, when only samples from Site 7 (peak occupation) are included, we find a significantly negative value, indicative of demographic expansion.ConclusionsOur results suggest individuals buried at Verteba Cave had overall low mtDNA diversity, most likely due to increased conflict among sedentary farmers and nomadic pastoralists to the East and North. Early Farmers tend to show demographic expansion. We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.
Tn5Prime, a Tn5 based 5’ Capture Method for Single Cell RNA-seq
Authors: Cole Charles , Byrne Ashley , Beaudin Anna E. , Forsberg E. Camilla , Vollmers Christopher 
Published: November 2017

AbstractRNA-seq is a powerful technique to investigate and quantify entire transcriptomes. Recent advances in the field have made it possible to explore the transcriptomes of single cells. However, most widely used RNA-seq protocols fail to provide crucial information regarding transcription start sites. Here we present a protocol, Tn5Prime, that takes advantage of the Tn5 transposase based Smartseq2 protocol to create RNA-seq libraries that capture the 5’ end of transcripts. The Tn5Prime method dramatically streamlines the 5’ capture process and is both cost effective and reliable. By applying Tn5Prime to bulk RNA and single cell samples we were able to define transcription start sites as well as quantify transcriptomes at high accuracy and reproducibility. Additionally, similar to 3’ end based high-throughput methods like Drop-Seq and 10X Genomics Chromium, the 5’ capture Tn5Prime method allows the introduction of cellular identifiers during reverse transcription, simplifying the analysis of large numbers of single cells. In contrast to 3’ end based methods, Tn5Prime also enables the assembly of the variable 5’ ends of antibody sequences present in single B-cell data. Therefore, Tn5Prime presents a robust tool for both basic and applied research into the adaptive immune system and beyond.
SgTiler: a fast method to design tiling sgRNAs for CRISPR/Cas9 mediated screening
Authors: Ahmed Musaddeque , He Housheng Hansen 
Published: November 2017

AbstractSummaryScreening of genomic regions of interest using CRISPR/Cas9 is getting increasingly popular. The system requires designing of single guide RNAs (sgRNAs) that can efficiently guide the Cas9 endonuclease to the targeted region with minimal off-target effects. Tiling sgRNAs is the most effective way to perturb regulatory regions, such as promoters and enhancers. sgTiler is the first tool that provides a fast method for designing tiling sgRNAs.Availability and ImplementationsgTiler is a command line tool that requires only one command to execute. Its source code is freely available on the web at https://github.com/HansenHeLab/sgTiler. sgTiler is implemented in Python and supported on any platform with Python and Bowtie.