bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs
Authors: Michel Elisa , Masson Estelle , Bubbendorf Sandrine , Lapicque Léocadie , Nidelet Thibault , Segond Diego , Guézenec Stéphane , Marlin Thérèse , Devillers Hugo , Rué Olivier , Onno Bernard , Legrand Judith , Sicard Delphine ,   the participating bakers
Published: June 2019

AbstractPreserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast,Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to theKazachstaniagenus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence ofKazachstania humilisin sourdoughs made with artisanal-like practices and the occurrence ofKazachstania bulderiin sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and nonsourdough strains were found forK. humilisbut not forK. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities.
Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling
Authors: Perkins Melinda Liu , Benzinger Dirk , Arcak Murat , Khammash Mustafa 
Published: June 2019

1AbstractDesigning and implementing synthetic biological pattern formation remains a challenge due to underlying theoretical complexity as well as the difficulty of engineering multicellular networks bio-chemically. Here, we introduce a “cell-in-the-loop” approach where living cells interact through in silico signaling, establishing a new testbed to interrogate theoretical principles when internal cell dynamics are incorporated rather than modeled. We present a theory that offers an easy-to-use test to predict the emergence of contrasting patterns in gene expression among laterally inhibiting cells. Guided by the theory, we experimentally demonstrated spontaneous checkerboard patterning in an optogenetic setup where cell-to-cell signaling was emulated with light inputs calculated in silico from real-time gene expression measurements. The scheme successfully produced spontaneous, persistent checkerboard patterns for systems of sixteen patches, in quantitative agreement with theoretical predictions. Our research highlights how tools from dynamical systems theory may inform our understanding of patterning, and illustrates the potential of cell-in-the-loop for engineering synthetic multicellular systems.
Spinal V3 interneurons and left-right coordination in mammalian locomotion
Authors: Danner Simon M. , Zhang Han , Shevtsova Natalia A. , Borowska Joanna , Rybak Ilya A. , Zhang Ying 
Published: June 2019

AbstractCommissural interneurons (CINs) mediate interactions between rhythm-generating locomotor circuits located on each side of the spinal cord and are necessary for left-right limb coordination during locomotion. While glutamatergic V3 CINs have been implicated in left-right coordination, their functional connectivity remains elusive. Here, we addressed this issue by combining experimental and modeling approaches. We employed Sim1Cre/+; Ai32 mice, in which light-activated Channelrhodopsin-2 was selectively expressed in V3 interneurons. Fictive locomotor activity was evoked by NMDA and 5-HT in the isolated neonatal lumbar spinal cord. Flexor and extensor activities were recorded from left and right L2 and L5 ventral roots, respectively. Bilateral photoactivation of V3 interneurons increased the duration of extensor bursts resulting in a slowed down on-going rhythm. At high light intensities, extensor activity could become sustained. When light stimulation was shifted toward one side of the cord, the duration of extensor bursts still increased on both sides, but these changes were more pronounced on the contralateral side than on the ipsilateral side. Additional bursts appeared on the ipsilateral side not seen on the contralateral side. Further increase of the stimulation could suppress the contralateral oscillations by switching to a sustained extensor activity, while the ipsilateral rhythmic activity remained. To delineate the function of V3 interneurons and their connectivity, we developed a computational model of the spinal circuits consisting of two (left and right) rhythm generators (RGs) interacting via V0V, V0D and V3 CINs. Both types of V0 CINs provided mutual inhibition between the left and right flexor RG centers and promoted left-right alternation. V3 CINs mediated mutual excitation between the left and right extensor RG centers. These interactions allowed the model to reproduce our current experimental data, while being consistent with previous data concerning the role of V0V and V0D CINs in securing left-right alternation and the changes in left-right coordination following their selective removal. We suggest that V3 CINs provide mutual excitation between the spinal neurons involved in the control of left and right extensor activity, which may promote left-right synchronization during locomotion.
NMRdock: Lightweight and Modular NMR Processing
Authors: East Kyle W. , Leith Andrew , Ragavendran Ashok , Delaglio Frank , Lisi George P. 
Published: June 2019

ABSTRACTNMR is a widely employed tool in chemistry, biology, and physics for the study of molecular structure and dynamics. Advances in computation have produced scores of software programs necessary for the processing and analysis of NMR data. However, the production of NMR software has been largely overseen by academic labs, each with their own preferred OS, environment, and dependencies. This lack of broader standardization and the complexity of installing and maintaining NMR-related software creates a barrier of entry into the field. To further complicate matters, as computation evolves, many aging software packages become deprecated. To reduce the barrier for newcomers and to prevent deprecation of aging software, we have created the NMRdock container. NMRdock utilizes containerization to package NMR processing and analysis programs into a single, easy-to-install Docker image that can be run on any modern OS. The current image contains two bedrock NMR data processing programs (NMRPipe and NMRFAM Sparky). However, future development of NMRdock aims to add modules for additional analysis programs to build a library of tools in a standardized and easy-to-implement manner. NMRdock is open source and free to download at https://compbiocore.github.io/nmrdock/.
The temporal transcription factor E93 controls dynamic enhancer activity and chromatin accessibility during development
Authors: Nystrom Spencer L. , Niederhuber Matthew J. , McKay Daniel J. 
Published: June 2019

ABSTRACTHow temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that theDrosophilatranscription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that provision of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings become responsive after a developmental transition, suggesting that parallel temporal pathways work alongside E93. These findings support a model wherein E93 expression functions as an instructive cue that defines a broad window of developmental time through control of chromatin accessibility.
Reaction mechanisms of Pol IV, RDR2 and DCL3 drive RNA channeling in the siRNA-directed DNA methylation pathway
Authors: Singh Jasleen , Mishra Vibhor , Wang Feng , Huang Hsiao-Yun , Pikaard Craig S. 
Published: June 2019

SummaryIn eukaryotes with multiple small RNA pathways the mechanisms that channel RNAs within specific pathways are unclear. Here, we reveal the reactions that account for channeling in the siRNA biogenesis phase of the Arabidopsis RNA-directed DNA methylation pathway. The process begins with template DNA transcription by NUCLEAR RNA POLYMERASE IV (Pol IV) whose atypical termination mechanism, induced by nontemplate DNA basepairing, channels transcripts to the associated RNA-dependent RNA polymerase, RDR2. RDR2 converts Pol IV transcripts into double-stranded RNAs then typically adds an extra untemplated 3’ terminal nucleotide to the second strands. The dicer endonuclease, DCL3 cuts resulting duplexes to generate 24 and 23nt siRNAs. The 23nt RNAs bear the untemplated terminal nucleotide of the RDR2 strand and are underrepresented among ARGONAUTE4-associated siRNAs. Collectively, our results provide mechanistic insights into Pol IV termination, Pol IV-RDR2 coupling and RNA channeling from template DNA transcription to siRNA guide strand/passenger strand discrimination.
Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging
Authors: Oaks Jamie R. , L’Bahy Nadia , Cobb Kerry A. 
Published: June 2019

AbstractFactors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show previous estimates of co-expansion among five Alaskan populations of threespine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.
Regular Architecture (RegArch): A standard expression language for describing protein architectures
Authors: Ortega Davi R. , Jensen Grant J. 
Published: June 2019

AbstractDomain architecture – the arrangement of features in a protein – exhibits syntactic patterns similar to the grammar of a language. This feature enables pattern mining for protein function prediction, comparative genomics, and studies of molecular evolution and complexity. To facilitate such work, here we propose Regular Architecture (RegArch), an expression language to describe syntactic patterns in protein architectures. Like the well-known Regular Expressions for text, RegArchs codify positional and non-positional patterns of elements into nested JSON objects. We describe the standard and provide a reference implementation in JavaScript to parse RegArchs and match annotated proteins.
Bactericidal efficiency and mechanism of specifically targeted antimicrobial peptides optimized based on structural and functional relationships
Authors: Tan Peng , Lai Zhenheng , Zhu Yongjie , Shao Changxuan , Akhtar Muhammad Usman , Li Weifen , Zheng Xin , Shan Anshan 
Published: June 2019

AbstractIn contrast to traditional broad-spectrum antibiotics, it is difficult for bacteria to develop resistance to most specifically targeted antimicrobial peptides (STAMPs), moreover, they can maintain a normal ecological balance and provide long-term protection for the body. However, therapeutic applications of STAMPS are hindered by their weak activity, and imperfect specificity as well as lack of knowledge to understand their structure-activity relationships. To further investigate the effects of different parameters on the biological activities of STAMPs, a peptide sequence, WKKIWKDPGIKKWIK, was truncated, extended, and provided with an increased charge and altered amphipathicity. In addition, a novel template modification method was introduced, in which a phage-displayed peptide that recognized and bound to E. coli cells was attached at the end of the sequence. Compared with the traditional template modification method, peptide 11, which contained a phage-displayed peptide at the C-terminus, exhibited superior narrow-spectrum antibacterial activity against E. coli compared to that of parental peptide 2, and the activity and specificity of 11 were increased by 5.0 and 2.4 times, respectively. Additionally, 11 showed low cell toxicity and relatively desirable salt, serum, acid and alkaline stability. In this study, 11 specifically killed E. coli by causing cytoplasmic membrane rupture and cytosol leakage. In summary, these findings are useful for improving the activity and specificity of STAMPs and show that peptide 11 is better able to combat the growing threat of E. coli infections.
Numerically quantifying energy loss caused by squirt flow
Authors: Quintal Beatriz , Caspari Eva , Holliger Klaus , Steeb Holger 
Published: June 2019

ABSTRACTIn interconnected microcracks, or in microcracks connected to spherical pores, the deformation associated with the passage of mechanical waves can induce fluid flow parallel to the crack walls, which is known as squirt flow. This phenomenon can also occur at larger scales in hydraulically interconnected mesoscopic cracks or fractures. The associated viscous friction causes the waves to experience attenuation and velocity dispersion. We present a simple hydromechanical numerical scheme, based on the interface‐coupled Lamé–Navier and Navier–Stokes equations, to simulate squirt flow in the frequency domain. The linearized, quasi‐static Navier–Stokes equations describe the laminar flow of a compressible viscous fluid in conduits embedded in a linear elastic solid background described by the quasi‐static Lamé–Navier equations. Assuming that the heterogeneous model behaves effectively like a homogeneous viscoelastic medium at a larger spatial scale, the resulting attenuation and stiffness modulus dispersion are computed from spatial averages of the complex‐valued, frequency‐dependent stress and strain fields. An energy‐based approach is implemented to calculate the local contributions to attenuation that, when integrated over the entire model, yield results that are identical to those based on the viscoelastic assumption. In addition to thus validating this assumption, the energy‐based approach allows for analyses of the spatial dissipation patterns in squirt flow models. We perform simulations for a series of numerical models to illustrate the viability and versatility of the proposed method. For a 3D model consisting of a spherical crack embedded in a solid background, the characteristic frequency of the resulting P‐wave attenuation agrees with that of a corresponding analytical solution, indicating that the dissipative viscous flow problem is appropriately handled in our numerical solution of the linearized, quasi‐static Navier–Stokes equations. For 2D models containing either interconnected cracks or cracks connected to a circular pore, the results are compared with those based on Biot's poroelastic equations of consolidation, which are solved through an equivalent approach. Overall, our numerical simulations and the associated analyses demonstrate the suitability of the coupled Lamé–Navier and Navier–Stokes equations and of Biot's equations for quantifying attenuation and dispersion for a range of squirt flow scenarios. These analyses also allow for delineating numerical and physical limitations associated with each set of equations.
Nested intrashelf platform clinoforms—Evidence of shelf platform growth exemplified by Lower Cretaceous strata in the Barents Sea
Authors: Midtkandal Ivar , Faleide Thea Sveva , Faleide Jan Inge , Planke Sverre , Anell Ingrid , Nystuen Johan Petter 
Published: June 2019

AbstractTwo nested clinoform set types of different scales and steepness are mapped and analysed from high‐resolution seismic data. Restoration of post‐depositional faulting reveals a persistent pattern of small‐scale, high‐angle clinoforms contained within platform‐scale, low‐angle clinothems, showing a combined overall progradational depositional system. The large clinoforms lack a well‐defined platform edge, and show a gradual increase in dip from topset to foreset. A consistent recurring stratal pattern is evident from the architecture, and is considered a result of interplay between relative sea‐level change and autocyclic switching of sediment delivery focal points that brought sediment to the platform edge. This un‐interrupted succession records how intra‐shelf platforms prograde. Quantitative clinoform analysis may assist in determining the most influential depositional factors. Post‐depositional uplift and erosion requires restoration with re‐burial to maximum burial depth. Backstripping, decompaction and isostatic correction was performed assuming a range of lithologic compositions, as no wells test the lithology. Nearby wells penetrate strata basinward of the clinoforms, proving mudstone content above 50%, which in turn guide restoration values. Typical restored platform heights are 250–300 m, with correspondingly sized platform‐scale clinoform heights. Typical large‐scale clinoform foreset dip values are 1.3°–2.4°. Small‐scale clinothems are typically 100 m thick, with restored foreset dip angles at 4.4° ‐ > 10°. The results suggest that intrashelf platform growth occurs in pulses interrupted by draping of strata over its clinoform profile. The resultant architecture comprises small‐scale clinoforms nested within platform‐scale clinothems.
Mammalian target of rapamycin (mTOR) inhibitors and skin cancer risk in nonrenal solid organ transplant recipients: systematic review and meta‐analysis
Authors: Phan Kevin , Moloney Fergal J. , Hogarty Daniel T. , Lenane Patsy , McColl Douglas , Yazdabadi Anousha 
Published: June 2019

AbstractBackgroundSolid organ transplant recipients have an increased risk of malignancy compared with the general population. Mammalian target of rapamycin (mTOR) inhibitors have been used as immunosuppressants in transplant recipients. There remains a lack of evidence of this treatment in nonrenal solid organ transplantation. We aimed to perform a systematic review and meta‐analysis to assess the effects of mTOR inhibitors on secondary nonmelanoma skin cancer (NMSC) malignancies in nonrenal transplant recipients.MethodsA systematic review and meta‐analysis was performed according to Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines. Eligible studies for the present systematic review and meta‐analysis included those in which patient cohorts underwent heart, liver, lung, and pancreas (i.e. nonrenal solid organ) transplantation, with treatment group being those treated with an mTOR inhibitor such as sirolimus or everolimus, and control group being placebo, or alternative non‐mTOR inhibitor treatment such as calcineurin inhibitors or as per standard treatment protocol.ResultsFrom the six included studies, we found no significant difference in the odds of either primary or secondary NMSC (OR 0.73, 95% CI 0.41–1.29, P = 0.28). Pooled analysis of patients with secondary NMSC demonstrated a trend toward significant benefit with mTOR inhibitor treatment (OR 0.61, 95% CI 0.37–1.02, P = 0.06) but no protective effect for primary NMSC (OR 0.53, 95% CI 0.03–9.96, P = 0.67).ConclusionsOur results suggest that in nonrenal transplant recipients, mTOR inhibitors may have a protective effect against secondary NMSC but not primary NMSC posttransplantation. Extrapolating the findings of reduced NMSC in renal transplant populations to nonrenal transplant cases should be cautioned.
Interoception, conditioning, and fear: The panic threesome
Authors: Van Diest Ilse 
Published: June 2019

AbstractThe present article aims to illustrate and review evidence on how associative learning involving interoceptive stimuli (interoceptive conditioning) can lead to changes in physiological, emotional, and perceptual outcomes. We first outline a functional perspective on Pavlovian conditioning and provide a general introduction and historical background on interoceptive conditioning as a special instance of Pavlovian conditioning. Next, biological and learning accounts of panic disorder are discussed, followed by an analysis of which stimuli and responses may be most promising to model learning that is relevant to panic disorder. Finally, studies on interoceptive fear conditioning with respiratory stimuli are reviewed and discussed, and future directions are outlined.