bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Whole-Plant Monocot from the Early Cretaceous
Authors: Liu Zhong-Jian , Chen Li-Jun , Wang Xin 
Published: April 2018

AbstractThe Yixian Formation (the Lower Cretaceous) of China is world famous for its fossils of early angiosperms. Although these diverse angiosperms demonstrate an unexpectedly great diversity, few are preserved as whole plants (not mention of monocots), making our understanding of them incomplete. Here, we report a fossil angiosperm,Sinoherba ningchenensisgen. et sp. nov (Sinoherbaceae fam. nov.), from the Yixian Formation of China; this fossil has a physically connected underground stem with fibrous rootlets, a stem with branches and nodes, leaves with parallel-reticulate veins, and a panicle of female flowers with an ovary surrounded by perianth. Morphological and phylogenetic analyses revealed thatSinoherbais an herbaceous monocot taxon. This newly discovered fossil underscores the great diversity of angiosperms in the Lower Cretaceous Yixian Formation.
Representation of auditory motion directions and sound source locations in the human planum temporale
Authors: Battal Ceren , Rezk Mohamed , Mattioni Stefania , Vadlamudi Jyothirmayi , Collignon Olivier 
Published: April 2018

ABSTRACTThe ability to compute the location and direction of sounds is a crucial perceptual skill to efficiently interact with dynamic environments. How the human brain implements spatial hearing is however poorly understood. In our study, we used fMRI to characterize the brain activity of male and female humans listening to left, right, up and down moving as well as static sounds. Whole brain univariate results contrasting moving and static sounds varying in their location revealed a robust functional preference for auditory motion in bilateral human Planum Temporale (hPT). Using independently localized hPT, we show that this region contains information about auditory motion directions and, to a lesser extent, sound source locations. Moreover, hPT showed an axis of motion organization reminiscent of the functional organization of the middle-temporal cortex (hMT+/V5) for vision. Importantly, whereas motion direction and location rely on partially shared pattern geometries in hPT, as demonstrated by successful cross-condition decoding, the responses elicited by static and moving sounds were however significantly distinct. Altogether our results demonstrate that the hPT codes for auditory motion and location but that the underlying neural computation linked to motion processing is more reliable and partially distinct from the one supporting sound source location.SIGNIFICANCE STATEMENTIn comparison to what we know about visual motion, little is known about how the brain implements spatial hearing. Our study reveals that motion directions and sound source locations can be reliably decoded in the human Planum Temporale (hPT) and that they rely on partially shared pattern geometries. Our study therefore sheds important new lights on how computing the location or direction of sounds are implemented in the human auditory cortex by showing that those two computations rely on partially shared neural codes. Furthermore, our results show that the neural representation of moving sounds in hPT follows a “preferred axis of motion” organization, reminiscent of the coding mechanisms typically observed in the occipital hMT+/V5 region for computing visual motion.
A neural signature of pattern separation in the monkey hippocampus
Authors: Sakon John J. , Suzuki Wendy A. 
Published: April 2018

AbstractThe CA3 and dentate gyrus (DG) regions of the hippocampus are considered key for disambiguating sensory inputs from similar experiences in memory, a process termed pattern separation. The neural mechanisms underlying pattern separation, however, have been difficult to compare across species: rodents offer robust recording methods with less human-centric tasks while humans provide complex behavior with less recording potential. To overcome these limitations, we trained monkeys to perform a visual pattern separation task similar to those used in humans while recording activity from single CA3/DG neurons. We find that when animals discriminate recently seen novel images from similar (lure) images, behavior indicative of pattern separation, CA3/DG neurons respond to lure images more like novel than repeat images. Using a population of these neurons, we are able to classify novel, lure, and repeat images from each other using this pattern of firing rates. Notably, one subpopulation of these neurons is more responsible for distinguishing lures and repeats—the key discrimination indicative of pattern separation.
Low-frequency direct cortical stimulation of left superior frontal gyrus enhances working memory performance
Authors: Alagapan Sankaraleengam , Lustenberger Caroline , Hadar Eldad , Shin Hae Won , Fröhlich Flavio 
Published: April 2018

AbstractThe neural substrates of working memory are spread across prefrontal, parietal and cingulate cortices and are thought to be coordinated through low frequency cortical oscillations in the theta (3 – 8 Hz) and alpha (8 – 12 Hz) frequency bands. While the functional role of many subregions have been elucidated using neuroimaging studies, the role of superior frontal gyrus (SFG) is not yet clear. Here, we combined electrocorticography and direct cortical stimulation in three patients implanted with subdural electrodes to assess if superior frontal gyrus is indeed involved in working memory. We found left SFG exhibited task-related modulation of oscillations in the theta and alpha frequency bands specifically during the encoding epoch. Stimulation at the frequency matched to the endogenous oscillations resulted in reduced reaction times in all three participants. Our results support the causal role of SFG in working memory and suggest that SFG may coordinate working memory through low-frequency oscillations thus bolstering the feasibility of targeting oscillations for restoring cognitive function.
The impact of fibronection stripe patterns on the cellular and nuclear morphology of fibroblasts
Authors: Mamaghani Pooya , Donald Athene M. 
Published: April 2018

AbstractThe effect of biochemical environmental signals on cell mechanisms has been the subject of numerous studies for a long time. However, the in-vitro studies of biophysical cues on cells and tissues have recently become a popular focus of research. The development of micro-fabrication techniques has allowed the study of certain aspects of cell-substrate interactions in a more detailed form. Micro-topographical patterns on the cell substrates have been used to study many cell functions such as cell migration, adhesion, gene expression, cell division and differentiation. An understanding of cell-substrate interactions and the potential ability to control the interactions have very important applications in the field of tissue engineering and regenerative medicine. We have fabricated ridge-groove micro patterns on polydimethylsiloxane (PDMS) substrates with different ridge widths (8μm, 10μm, 12 μm, 25μm and 50μm) using standard photolithography technique. We used these patterns to print fibronectin stripes on PDMS substrates. NIH/3T3 fibroblast cells were cultured on these stripes and the dynamics of morphological changes were monitored in steady spreading phase (S-phase). Our data revealed that the thickness of the cell, measured by confocal microscopy, is considerably larger (approximately 40%) among the cells spreading on narrower stripes (8μm, 10μm and 12μm) compared to the cells expanding on wider (including control) patterns. The number of perinuclear actin stress fibers is significantly lower among narrower stripes which probably explains the cell thickness results. Confocal microscopy revealed that the cellular volume increases during cell adhesion processes and volume increase is positively correlated with the width of stripes. Nuclear volume also increases considerably during cell adhesion; however, confining cells on fibronectin stripes reduces nuclear volume enlargement independent from the of stripe size.
Discordant expression profile between RNA and protein for the genes involved in immune response network in adenovirus type 2 infected cells
Authors: Zhao Hongxing , Chen Maoshan , Valdés Alberto , Lind Sara Bergström , Pettersson Ulf 
Published: April 2018

AbstractAlternation of cellular genes expressions during Adenovirus type 2 (Ad2) infection in IMR-90 cells was studied using paired-end sequencing and stable isotope labeling of amino acids in cell culture mass spectrometric analysis (SILAC-MS). At transcriptional level, cellular genes involved in different pathways revealed distinct expression profiles. At early phase, the genes involved in regulation of cellular immune response, cellular signaling and cell growth control were among the most deregulated. Later follows, in an orderly fashion, genes involved in cell cycle control, DNA replication and further on genes engaged in RNA processing and protein translation. Comparison of cellular gene expression at transcriptional and posttranscriptional levels revealed low correlation. Here we highlight the genes which expose opposite expression profiles with an emphasis on key factors that play important roles in cellular immune pathways including NFκB, JAK/STAT, caspases and MAVS. Transcription of many of these genes was transiently induced early, but became down-regulated in the late phase. In contrast, their expressions at protein level were up-regulated early and so sustained until late phase of infection. Suppression at the transcriptional level and enhancement at the protein level of immune response genes most likely illustrate counteractions between Ad2 and its host cell.ImportanceOur paper comprises a state of the art quality transcriptomics data set unravelling the alterations in gene expression that take place during different phases of an adenovirus infection. The information allows us to draw conclusion about the cellular pathways that are perturbed by the virus. The data set also provides an important resource for scientists in general for future studies on mechanisms behind host/virus interactions in efforts to design tools for combatting virus infections.Moreover, our paper includes novel proteomics information unravelling an unexpected role of post transcriptional events in cellular gene expression, demonstrating that the current picture of the adenovirus replication cycle is simplified.
Hemispheric asymmetry of globus pallidus relates to alpha modulation in reward-related attentional tasks
Authors: Mazzetti C. , Staudigl T. , Marshall T. R. , Zumer J. M. , Fallon S. J. , Jensen O. 
Published: April 2018

AbstractWhile subcortical structures like the basal ganglia have been widely explored in relation to motor control, recent evidence suggests that their mechanisms extend to the domain of attentional switching. We here investigated the subcortical involvement in reward related top-down control of visual alpha-band oscillations (8 – 13 Hz), which have been consistently linked to mechanisms supporting the allocation of visuo-spatial attention. Given that items associated with contextual saliency (e.g. monetary reward or loss) attract attention, it is not surprising that the acquired salience of visual items further modulates. The executive networks controlling such reward-dependent modulations of oscillatory brain activity have yet to be fully elucidated. Although such networks have been explored in terms of cortico-cortical interactions, subcortical regions are likely to be involved. To uncover this, we combined MRI and MEG data from 17 male and 11 female participants, investigating whether derived measures of subcortical structural asymmetries predict interhemispheric modulation of alpha power during a spatial attention task. We show that volumetric hemispheric lateralization of globus pallidus (GP) and thalamus (Th) explains individual hemispheric biases in the ability to modulate posterior alpha power. Importantly, for the GP, this effect became stronger when the value-saliency parings in the task increased. Our findings suggest that the GP and Th in humans are part of a subcortical executive control network, differentially involved in modulating posterior alpha activity in the presence of saliency. Further investigation aimed at uncovering the interaction between subcortical and neocortical attentional networks would provide useful insight in future studies.Significance statementWhile the involvement of subcortical regions into higher level cognitive processing, such as attention and reward attribution, has been already indicated in previous studies, little is known about its relationship with the functional oscillatory underpinnings of said processes. In particular, interhemispheric modulation of alpha band (8-13Hz) oscillations, as recorded with magnetoencephalography (MEG), has been previously shown to vary as a function of salience (i.e. monetary reward/loss) in a spatial attention task. We here provide novel insights into the link between subcortical and cortical control of visual attention. Using the same reward-related spatial attention paradigm, we show that the volumetric lateralization of subcortical structures (specifically Globus Pallidus and Thalamus) explains individual biases in the modulation of visual alpha activity.
BioLogic, a parallel approach to cell-based logic gates
Authors: Millacura Felipe A. , Largey Brendan , French Christopher E. 
Published: April 2018

Abstract:In vivo logic gates have proven difficult to combine into larger devices. Our cell-based logic system, BioLogic, decomposes a large circuit into a collection of small subcircuits working in parallel, each subcircuit responding to a different combination of inputs. A final global output is then generated by a combination of the responses. Using BioLogic, for the first time a completely functional 3-bit full adder and full subtractor were generated using Escherichia coli cells; as well as a calculator-style display that shows a numeric result, from 0 to 7, when the proper 3 bit binary inputs are introduced into the system. BioLogic demonstrates the use of a parallel approach for the design of cell-based logic gates that facilitates the generation and analysis of complex processes, without the need for complex genetic engineering.
Holstein Friesian mid-lactation Milk Polar Metabolite Composition in relation to Dietary Fat Composition and Diacylglycerol O-acyltransferase 1 Genotype
Authors: te Pas Marinus F.W. , Vervoort Jacques , Kruijt Leo , Calus Mario P.L. , Smits Mari A. 
Published: April 2018

AbstractBackgroundThe metabolite composition of cow milk is dependent on a large variety of animal associated factors including diet, genotype and gut microbiome composition. The objective of this study was to investigate changes in cow milk polar metabolite composition resulting from dietary and DGAT1 (Diacylglycerol O-acyltransferase 1) genotype perturbations.Methods and ResultsCows were fed a standard diet and a diet supplemented with (poly)unsaturated fatty acids (experimental diet) for ten weeks. Metabolite profiles were determined using 1H NMR (1-Hydrogen Nuclear magnetic resonance) technology. The results showed that the diet affected the polar metabolite composition of milk via the metabolism of the cow and via the metabolism of the gut and rumen microbiota. The experimental diet reduced the metabolic rate, especially the energy metabolism and the amino-sugar and amino acid metabolism, of the cows.ConclusionOur results suggests the DGAT1 genotype affects both the diet related polar metabolite metabolism of the cow as well as that of the rumen microbiota. Milk metabolite levels in animals with more DGAT1 A-alleles were higher than milk metabolite levels in animals with more K-alleles.
Identification of a secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis
Authors: Cohen-Zontag Osnat , Lim Lisha Qiu Jin , Dahary Dvir , Olender Tsviya , Pilpel Yitzhak , Gerst Jeffrey E. 
Published: April 2018

AbstractEarlier dogma states that mRNAs encoding secreted and membrane protein (mSMPs) reach the ER in a translation-dependent manner through the signal recognition particle (SRP) pathway. In this pathway, the signal sequence of the translation product is recognized by SRP and the mRNA-ribosome-nascent-chain-SRP complex is recruited to the ER via the interaction with an endoplasmic reticulum (ER)-localized SRP receptor. This model suggests that the translation product dictates the delivery of mRNAs to the ER and that the mRNA is a passive passenger. However, new evidence challenges this model and implies the existence of both translation - and SRP-independent mRNA localization to the ER, raising the possibility that mRNAs have an active role in determining their localization to the ER.Besides serving as a template for protein translation, mRNAs carry information required for other regulatory processes such as mRNA processing, translation and transcription efficiency, degradation and localization. In yeast, mRNA localization governed by cis-acting sequence elements has been characterized for asymmetrically (e.g. bud) localized mRNAs that localize to, and are transported with, cortical ER. Now, we identify a cis motif in mSMPs that targets mRNAs mainly to the nuclear ER in yeast and increases both protein synthesis and secretion. Termed SECReTE, for secretion-enhancing cis regulatory targeting element, this motif was identified by computational analysis of genes encoding secretome proteins. SECReTE consists of ≥10 repetitive triplets enriched with pyrimidines (i.e. C’s and U’s) every third base (i.e. NNY, N - any nucleotide, Y - pyrimidine), and is found particularly in mRNAs coding for cell wall proteins. To study the physiological relevance of SECReTE, we introduced synonymous mutations that either elevate or decrease its overall score in genes coding for secreted proteins, without changing the protein sequence, and examined the physiological effects in yeast. An increase in the SECReTE score elevated the synthesis and secretion of endogenous proteins while, in contrast, a reduction led to less secretion and physiological defects. Importantly, the addition of SECReTE to the 3’UTR of an exogenous protein (e.g. SS-GFP) led to its increased secretion from yeast. SECReTE is present all through evolution and, thus, constitutes a novel RNA targeting motif found in both prokaryotes and eukaryotes.
Discovery of a two protease DNA damage checkpoint recovery mechanism
Authors: Burby Peter E. , Simmons Zackary W. , Schroedert Jeremy W. , Simmons Lyle A. 
Published: April 2018

AbstractThe DNA damage response is a signaling pathway found throughout biology. In many bacteria the DNA damage checkpoint is enforced by inducing expression of a small, membrane bound inhibitor that delays cell division providing time to repair damaged chromosomes. How cells sense successful DNA repair and promote checkpoint recovery is unknown. By using a high-throughput, forward genetic screen, we identified two unrelated proteases, YlbL and CtpA, that promote DNA damage checkpoint recovery inBacillus subtilis. Deletion of both proteases leads to accumulation of the checkpoint protein YneA. DNA damage sensitivity and increased cell elongation in protease mutants depends onyneA. Further, expression of YneA in protease mutants was sufficient to inhibit cell proliferation. Finally, we show that one of the two proteases, CtpA, directly cleaves YneAin vitro. With these results, we report the mechanism for DNA damage checkpoint recovery in bacteria that use membrane bound cell division inhibitors.
The impact of crop farmers’ decisions on future land use, land cover changes in Kintampo North Municipality of Ghana
Authors: Bessah Enoch , Bala Abdullahi , Agodzo Sampson Kweku , Okhimamhe Appollonia Aimiosino , Boakye Emmanuel Amoah , Ibrahim Saratu Usman 
Published: April 2018

Purpose
This paper aims to assess the rate and land category contributing to the changes in seven land-uses in the Kintampo North Municipality of Ghana and the effect of the decisions of land users on future landscapes.

Design/methodology/approach
LANDSAT images were classified to generate land use/cover maps to detect changes that had occurred between 1986 and 2014. In total, 120 farmers were also interviewed to determine their perceptions on land use changes. Interval, category and transition levels of changes were determined. Savanna woodland, settlement and forest were mostly converted to farmland in both intervals (1986-2001 and 2001-2014).

Findings
Results showed that rock outcrop, plantation, cropland and savanna woodland increased at an annual rate of 13.86, 1.57, 0.82 and 0.33 per cent, respectively, whilst forest, settlement and water body decreased at 4.90, 1.84 and 1.17 per cent annual rate of change, respectively. Approximately, 74 per cent of farmers will not change land use in the future, while 84.2 per cent plan to increase farm sizes.

Research limitations/implications
The study shows that more land cover will be targeted for conversion as farmers expand their farmlands. There is the need for strict implementation of appropriate land use/cover policies to sustain food production in the region in this era of changing climate and population increase.

Originality/value
This research assessed the land use changes in the Kintampo North Municipality and its impacts on agriculture and carbon stocks release via land use changes. It identified how the decisions of the local farmers on land management will affect future landscape.
From project risk to complexity analysis: a systematic classification
Authors: Hartono Budi 
Published: April 2018

Purpose
The purpose of this paper is to provide a systematic classification for frameworks, methods, and models of in-project quantitative risk analysis (IQRA) for the last 30 years.

Design/methodology/approach
An extensive literature review is conducted to identify pertinent IQRA works. Identified IQRA frameworks/methods/models are then classified on the basis of commonalities in key attributes and assumptions. Linkages between each category of IQRAs and dimensions of complexity are also observed.

Findings
Around 70 key publications on IQRAs are identified. Major attributes for each work are described. Five distinct categories of IQRAs emerge with unique linkages to complexity dimensions. An analytical framework in the form of a matrix is presented to illuminate evolution on modeling characteristics and to indicate a relationship between respective category and dimensions of project complexity.

Research limitations/implications
The research coverage is intended to be comprehensive but it is by no means exhaustive. This study highlights research opportunities in IQRAs and the possible extension toward in-project quantitative complexity analysis (IQCA).

Practical implications
The proposed matrix provides guidance to practitioners to select the appropriate category of IQRAs for a specific project complexity type in a contingency fashion. The study highlights lessons from development and utilization of IQRAs. Outstanding issues from IQRAs are discussed to avoid similar drawbacks for IQCAs.

Originality/value
This study provides an original framework/matrix to classify extant works in IQRAs. It also establishes an association between IQRAs and the emerging conceptual works of complexity.