Publications by authors named "Ana M Sanchez"

153 Publications

Quantum Transport of the 2D Surface State in a Nonsymmorphic Semimetal.

Nano Lett 2021 Apr 9. Epub 2021 Apr 9.

Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, United States.

In a topological semimetal with Dirac or Weyl points, the bulk-boundary correspondence principle predicts a gapless edge mode if the essential symmetry is still preserved at the surface. The detection of such topological surface state has been considered as the fingerprint prove for crystals with nontrivial topological bulk band. On the contrary, it has been proposed that even with symmetry broken at the surface, a new surface band can emerge in nonsymmorphic topological semimetals. The symmetry reduction at the surface lifts the bulk band degeneracies and produces an unusual "floating" surface band with trivial topology. Here, we first report quantum transport probing to ZrSiSe thin flakes and directly reveal transport signatures of this new surface state. Remarkably, though topologically trivial, such a surface band exhibits substantial two-dimensional Shubnikov-de Haas quantum oscillations with high mobility, which signifies a new protection mechanism and may open applications for quantum computing and spintronic devices.
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http://dx.doi.org/10.1021/acs.nanolett.0c04946DOI Listing
April 2021

Structure-function analysis of fission yeast cleavage and polyadenylation factor (CPF) subunit Ppn1 and its interactions with Dis2 and Swd22.

PLoS Genet 2021 Mar 12;17(3):e1009452. Epub 2021 Mar 12.

Molecular Biology Program, Sloan-Kettering Institute, New York, New York, United States of America.

Fission yeast Cleavage and Polyadenylation Factor (CPF), a 13-subunit complex, executes the cotranscriptional 3' processing of RNA polymerase II (Pol2) transcripts that precedes transcription termination. The three-subunit DPS sub-complex of CPF, consisting of a PP1-type phosphoprotein phosphatase Dis2, a WD-repeat protein Swd22, and a putative phosphatase regulatory factor Ppn1, associates with the CPF core to form the holo-CPF assembly. Here we probed the functional, physical, and genetic interactions of DPS by focusing on the Ppn1 subunit, which mediates association of DPS with the core. Transcriptional profiling by RNA-seq defined limited but highly concordant sets of protein-coding genes that were dysregulated in ppn1Δ, swd22Δ and dis2Δ cells, which included the DPSΔ down-regulated phosphate homeostasis genes pho1 and pho84 that are controlled by lncRNA-mediated transcriptional interference. Essential and inessential modules of the 710-aa Ppn1 protein were defined by testing the effects of Ppn1 truncations in multiple genetic backgrounds in which Ppn1 is required for growth. An N-terminal 172-aa disordered region was dispensable and its deletion alleviated hypomorphic phenotypes caused by deleting C-terminal aa 640-710. A TFIIS-like domain (aa 173-330) was not required for viability but was important for Ppn1 activity in phosphate homeostasis. Distinct sites within Ppn1 for binding to Dis2 (spanning Ppn1 aa 506 to 532) and Swd22 (from Ppn1 aa 533 to 578) were demarcated by yeast two-hybrid assays. Dis2 interaction-defective missense mutants of full-length Ppn1 (that retained Swd22 interaction) were employed to show that binding to Dis2 (or its paralog Sds21) was necessary for Ppn1 biological activity. Ppn1 function was severely compromised by missense mutations that selectively affected its binding to Swd22.
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http://dx.doi.org/10.1371/journal.pgen.1009452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7990198PMC
March 2021

Transcriptional profiling of fission yeast RNA polymerase II CTD mutants.

RNA 2021 Feb 12. Epub 2021 Feb 12.

Sloan Kettering Institute;

The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol2) consists of tandem repeats of a consensus heptapeptide Y S P T S P S The CTD recruits numerous proteins that drive or regulate gene expression. The trafficking of CTD-interacting proteins is orchestrated by remodeling CTD primary structure via Ser/Thr/Tyr phosphorylation and proline isomerization, which collectively inscribe a CTD code. The fission yeast CTD consists of 29 heptad repeats. To decipher the output of the fission yeast CTD code, we genetically manipulated CTD length and amino acid content and then gauged the effects of these changes on gene expression. Whereas deleting 11 consensus heptads has no obvious effect on fission yeast growth, RNA-seq revealed that 25% of the protein-coding transcripts were dysregulated by CTD truncation. We profiled the transcriptomes of full-length CTD mutants, in which: all Tyr1 residues were replaced by Phe; all Ser2, Thr4, or Ser7 positions were changed to Ala; and half of the essential CTD code "letters" Pro3, Ser5, and Pro6 were mutated to Ala. Overlapping RNA-seq profiles suggested that a quarter of the complement of up-regulated mRNAs and half of the down-regulated mRNAs seen in full-length CTD mutants might be attributable to a decrement in wild-type CTD heptad number. Concordant mutant-specific transcriptional profiles were observed for , , and cells, and for and cells, suggesting that Tyr1-Ser2-Thr4 and Ser5-Pro6 comprise distinct "words" in the fission yeast CTD code. The phosphate regulon, which is repressed by lncRNA-mediated transcription interference, is de-repressed by CTD mutations P6•P6A and S5•S5A. De-repression of pho1 in P6•P6A and S5•S5A cells depends on cleavage and polyadenylation factor subunits Swd22 and Ppn1 and transcription termination factor Rhn1, signifying that Pro6 and Ser5 mutations elicit precocious lncRNA 3'-processing/termination.
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http://dx.doi.org/10.1261/rna.078682.121DOI Listing
February 2021

Demographic effects of interacting species: exploring stable coexistence under increased climatic variability in a semiarid shrub community.

Sci Rep 2021 Feb 4;11(1):3099. Epub 2021 Feb 4.

iuFOR-EiFAB, University of Valladolid, Campus Duques de Soria, 42004, Soria, Spain.

Population persistence is strongly determined by climatic variability. Changes in the patterns of climatic events linked to global warming may alter population dynamics, but their effects may be strongly modulated by biotic interactions. Plant populations interact with each other in such a way that responses to climate of a single population may impact the dynamics of the whole community. In this study, we assess how climate variability affects persistence and coexistence of two dominant plant species in a semiarid shrub community on gypsum soils. We use 9 years of demographic data to parameterize demographic models and to simulate population dynamics under different climatic and ecological scenarios. We observe that populations of both coexisting species may respond to common climatic fluctuations both similarly and in idiosyncratic ways, depending on the yearly combination of climatic factors. Biotic interactions (both within and among species) modulate some of their vital rates, but their effects on population dynamics highly depend on climatic fluctuations. Our results indicate that increased levels of climatic variability may alter interspecific relationships. These alterations might potentially affect species coexistence, disrupting competitive hierarchies and ultimately leading to abrupt changes in community composition.
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http://dx.doi.org/10.1038/s41598-021-82571-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7862631PMC
February 2021

Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing.

mSphere 2020 10 14;5(5). Epub 2020 Oct 14.

Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA

High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3'-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).
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http://dx.doi.org/10.1128/mSphere.00551-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565892PMC
October 2020

Preferred growth direction of III-V nanowires on differently oriented Si substrates.

Nanotechnology 2020 Nov;31(47):475708

Department of Electronic and Electrical Engineering, University College London, London WC1E 7JE, United Kingdom.

One of the nanowire (NW) characteristics is its preferred elongation direction. Here, we investigated the impact of Si substrate crystal orientation on the growth direction of GaAs NWs. We first studied the self-catalyzed GaAs NW growth on Si (111) and Si (001) substrates. SEM observations show GaAs NWs on Si (001) are grown along four <111> directions without preference on one or some of them. This non-preferential NW growth on Si (001) is morphologically in contrast to the extensively reported vertical <111> preferred GaAs NW growth on Si (111) substrates. We propose a model based on the initial condition of an ideal Ga droplet formation on Si substrates and the surface free energy calculation which takes into account the dangling bond surface density for different facets. This model provides further understanding of the different preferences in the growth of GaAs NWs along selected <111> directions depending on the Si substrate orientation. To verify the prevalence of the model, NWs were grown on Si (311) substrates. The results are in good agreement with the three-dimensional mapping of surface free energy by our model. This general model can also be applied to predictions of NW preferred growth directions by the vapor-liquid-solid growth mode on other group IV and III-V substrates.
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http://dx.doi.org/10.1088/1361-6528/abafd7DOI Listing
November 2020

Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms.

Sci Rep 2020 08 6;10(1):13214. Epub 2020 Aug 6.

Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.

The critical role of the regulatory elements at the 5' end of the HIV-1 genome in controlling the life cycle of HIV-1 indicates that this region significantly influences virus fitness and its biological properties. In this study, we performed a detailed characterization of strain-specific variability of sequences from the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation sequencing (NGS) techniques. Overall, we found that this region of the HIV-1 genome displayed a low degree of intra-strain variability. On the other hand, inter-strain variability was found to be as high as that reported for gag and env genes (13-17%). We observed strain-specific single point and clustered mutations in the U5, PBS, and gag leader sequences (GLS), generating potential strain-specific transcription factor binding sites (TFBS). Using an infrared gel shift assay, we demonstrated the presence of potential TFBS such as E-box in CRF22_01A, and Stat 6 in subtypes A and G, as well as in their related CRFs. The strain-specific variation found in the sequence corresponding at the RNA level to functional domains of the 5' UTR, could also potentially impact the secondary/tertiary structural rearrangement of this region. Thus, the variability observed in this 5' end of the genomic region of divergent HIV-1 strains strongly suggests that functions of this region might be affected in a strain-specific manner. Our findings provide new insights into DNA-protein interactions that regulate HIV-1 replication and the influence of strain characterization on the biology of HIV-1 infection.
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http://dx.doi.org/10.1038/s41598-020-70083-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7411029PMC
August 2020

Checked patterned elemental distribution in AlGaAs nanowire branches via vapor-liquid-solid growth.

Nanoscale 2020 Aug 16;12(29):15711-15720. Epub 2020 Jul 16.

Department of Electronic and Electrical Engineering, University College London, London WC1E 7JE, UK.

Morphology, crystal defects and crystal phase can significantly affect the elemental distribution of ternary nanowires (NWs). Here, we report the synergic impact of the structure and crystal phase on the composition of branched self-catalyzed AlGaAs NWs. Branching events were confirmed to increase with Al incorporation rising, while twinning and polytypism were observed to extend from the trunk to the branches, confirming the epitaxial nature of the latter. The growth mechanism of these structures has been ascribed to Ga accumulation at the concave sites on the rough shell. This is in agreement with the ab initio calculations which reveal Ga atoms tend to segregate at the trunk/branch interface. Notably, uncommon, intricate compositional variations are exposed in these branched NWs, where Ga-rich stripes parallel to the growth direction of the branches intersect with another set of periodic arrangements of Ga-rich stripes which are perpendicular to them, leading to the realization of an elemental checked pattern. The periodic variations perpendicular to the growth direction of the branches are caused by the constant rotation of the sample during growth whilst Ga-rich stripes along the growth direction of the branches are understood to be driven by the different nucleation energies and polarities on facets of different crystal phase at the interface between the catalyst droplets and the branched NW tip. These results lead to further comprehension of phase segregation and could assist in the compositional engineering in ternary NWs via harnessing this interesting phenomenon.
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http://dx.doi.org/10.1039/d0nr02577aDOI Listing
August 2020

Emergent Antipolar Phase in BiFeO-LaSrMnO Superlattice.

Nano Lett 2020 Aug 9;20(8):6045-6050. Epub 2020 Jul 9.

Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.

Ferroelectric-paraelectric superlattices show emerging new states, such as polar vortices, through the interplay and different energy scales of various thermodynamic constraints. By introducing magnetic coupling at BiFeO-LaSrMnO interfaces epitaxially grown on SrTiO substrate, we find, for the first time in thin films, a sub-nanometer thick lamella-like BiFeO. The emergent phase is characterized by an arrangement of a two unit cell thick lamella-like structure featuring antiparallel polarization, resulting an antiferroelectric-like structure typically associated with a morphotropic phase transition. The antipolar phase is embedded within a nominal 3 structure and is independent of the BiFeO thickness (4-30 unit cells). Moreover, the superlattice structure with the morphotropic phase demonstrates azimuth-independent second harmonic generation responses, indicating a change of overall symmetry mediated by a delicate spatial distribution of the emergent phase. This work enriches the understanding of a metastable state manipulated by thermodynamic constraints by lattice strain and magnetic coupling.
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http://dx.doi.org/10.1021/acs.nanolett.0c02063DOI Listing
August 2020

The role of root community attributes in predicting soil fungal and bacterial community patterns.

New Phytol 2020 11 24;228(3):1070-1082. Epub 2020 Jul 24.

Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain.

Roots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading of plant canopies and root systems. Thus, soil microbe-plant links are not completely understood. Using a combination of DNA metabarcoding and spatially explicit sampling at the plant neighbourhood scale, we assessed the influence of the plant root community on soil bacterial and fungal diversity (species richness, composition and β-diversity) in a dry Mediterranean scrubland. We found that root composition and biomass, but not richness, predict unique fractions of variation in microbial richness and composition. Moreover, bacterial β-diversity was related to root β-diversity, while fungal β-diversity was related to aboveground plant β-diversity, suggesting that plants differently influence both microbial groups. Our study highlights the role of plant distribution both belowground and aboveground, soil properties and other spatially structured factors in explaining the heterogeneity in soil microbial diversity. These results also show that incorporating data on both plant community compartments will further our understanding of the relationships between soil microbial and plant communities.
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http://dx.doi.org/10.1111/nph.16754DOI Listing
November 2020

Inactivation of fission yeast Erh1 de-represses expression: evidence that Erh1 is a negative regulator of lncRNA termination.

RNA 2020 10 16;26(10):1334-1344. Epub 2020 Jun 16.

Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA.

Fission yeast Erh1 exists in a complex with RNA-binding protein Mmi1. Deletion of up-regulates the phosphate homeostasis gene , which is normally repressed by transcription in of a 5' flanking lncRNA. Here we present evidence that de-repression of by eΔ is achieved through precocious 3'-processing/termination of lncRNA synthesis, to wit: (i) Δ does not affect the activity of the or promoters per se; (ii) de-repression by Δ depends on CPF (cleavage and polyadenylation factor) subunits Ctf1, Dis2, Ssu72, Swd22, and Ppn1 and on termination factor Rhn1; (iii) de-repression requires synthesis by the Asp1 IPP kinase of inositol 1-pyrophosphates (1-IPPs); (iv) de-repression is effaced by mutating Thr4 of the RNA polymerase II CTD to alanine; and (v) Δ exerts an additive effect on de-repression in combination with mutating CTD Ser7 to alanine and with deletion of the IPP pyrophosphatase Aps1. These findings point to Erh1 as an antagonist of lncRNA termination in the axis. In contrast, in Δ cells there is a reduction in mRNA and increase in the formation of a read-through transcript, consistent with Mmi1 being an agonist of termination. We envision that Erh1 acts as a brake on Mmi1's ability to promote CPF-dependent termination during lncRNA synthesis. Consistent with this idea, Δ de-repression of was eliminated by mutating the Mmi1-binding sites in the lncRNA.
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http://dx.doi.org/10.1261/rna.076463.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7491324PMC
October 2020

Enhanced Superconductivity in Few-Layer TaS due to Healing by Oxygenation.

Nano Lett 2020 May 1;20(5):3808-3818. Epub 2020 May 1.

National Graphene Institute, University of Manchester, Oxford Road, Manchester, United Kingdom M13 9PL.

When approaching the atomically thin limit, defects and disorder play an increasingly important role in the properties of two-dimensional (2D) materials. While defects are generally thought to negatively affect superconductivity in 2D materials, here we demonstrate the contrary in the case of oxygenation of ultrathin tantalum disulfide (TaS). Our first-principles calculations show that incorporation of oxygen into the TaS crystal lattice is energetically favorable and effectively heals sulfur vacancies typically present in these crystals, thus restoring the electronic band structure and the carrier density to the intrinsic characteristics of TaS. Strikingly, this leads to a strong enhancement of the electron-phonon coupling, by up to 80% in the highly oxygenated limit. Using transport measurements on fresh and aged (oxygenated) few-layer TaS, we found a marked increase of the superconducting critical temperature () upon aging, in agreement with our theory, while concurrent electron microscopy and electron-energy loss spectroscopy confirmed the presence of sulfur vacancies in freshly prepared TaS and incorporation of oxygen into the crystal lattice with time. Our work thus reveals the mechanism by which certain atomic-scale defects can be beneficial to superconductivity and opens a new route to engineer in ultrathin materials.
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http://dx.doi.org/10.1021/acs.nanolett.0c00871DOI Listing
May 2020

Genetic interactions and transcriptomics implicate fission yeast CTD prolyl isomerase Pin1 as an agent of RNA 3' processing and transcription termination that functions via its effects on CTD phosphatase Ssu72.

Nucleic Acids Res 2020 05;48(9):4811-4826

Dept. of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.

The phosphorylation pattern of Pol2 CTD Y1S2P3T4S5P6S7 repeats comprises an informational code coordinating transcription and RNA processing. cis-trans isomerization of CTD prolines expands the scope of the code in ways that are not well understood. Here we address this issue via analysis of fission yeast peptidyl-prolyl isomerase Pin1. A pin1Δ allele that does not affect growth per se is lethal in the absence of cleavage-polyadenylation factor (CPF) subunits Ppn1 and Swd22 and elicits growth defects absent CPF subunits Ctf1 and Dis2 and termination factor Rhn1. Whereas CTD S2A, T4A, and S7A mutants thrive in combination with pin1Δ, a Y1F mutant does not, nor do CTD mutants in which half the Pro3 or Pro6 residues are replaced by alanine. Phosphate-acquisition genes pho1, pho84 and tgp1 are repressed by upstream lncRNAs and are sensitive to changes in lncRNA 3' processing/termination. pin1Δ hyper-represses PHO gene expression and erases the de-repressive effect of CTD-S7A. Transcriptional profiling delineated sets of 56 and 22 protein-coding genes that are down-regulated and up-regulated in pin1Δ cells, respectively, 77% and 100% of which are downregulated/upregulated when the cis-proline-dependent Ssu72 CTD phosphatase is inactivated. Our results implicate Pin1 as a positive effector of 3' processing/termination that acts via Ssu72.
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http://dx.doi.org/10.1093/nar/gkaa212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229847PMC
May 2020

Heterostructure and -factor engineering for low-threshold and persistent nanowire lasing.

Light Sci Appl 2020 17;9:43. Epub 2020 Mar 17.

1Department of Physics and Astronomy and The Photon Science Institute, The University of Manchester, Manchester, M13 9PL UK.

Continuous room temperature nanowire lasing from silicon-integrated optoelectronic elements requires careful optimisation of both the lasing cavity -factor and population inversion conditions. We apply time-gated optical interferometry to the lasing emission from high-quality GaAsP/GaAs quantum well nanowire laser structures, revealing high -factors of 1250 ± 90 corresponding to end-facet reflectivities of  = 0.73 ± 0.02. By using optimised direct-indirect band alignment in the active region, we demonstrate a well-refilling mechanism providing a quasi-four-level system leading to multi-nanosecond lasing and record low room temperature lasing thresholds (~6 μJ cm pulse) for III-V nanowire lasers. Our findings demonstrate a highly promising new route towards continuously operating silicon-integrated nanolaser elements.
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http://dx.doi.org/10.1038/s41377-020-0279-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078256PMC
March 2020

A Case of Complex and Abnormal Behaviors at Night: The Role of the Epilepsy Monitoring Unit in Diagnosis.

Case Rep Neurol 2020 Jan-Apr;12(1):18-23. Epub 2020 Jan 15.

Department of Neurology, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA.

Complex nocturnal behaviors associated with sleep have many potential causes, including parasomnias and epilepsy. Although the type of event and description can frequently lead to a diagnosis, sometimes it is challenging clinically to determine the cause of the behaviors, requiring a more in-depth investigation. We report the case of a 29-year-old woman with a long history of complex abnormal behaviors and visual hallucinations at night. An extensive clinical evaluation failed to reveal a definitive cause of these episodes, prompting a 3-day epilepsy monitoring unit admission. During the stay, several events were captured on video electroencephalography, leading to a conclusive final diagnosis. This case highlights the challenging task of finding a definitive diagnosis in cases of complex nocturnal behaviors and the potential role of an admission to an epilepsy monitoring unit to help diagnose the cause of these behaviors.
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http://dx.doi.org/10.1159/000505230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011724PMC
January 2020

Polarization Screening Mechanisms at LaSrMnO-PbTiO Interfaces.

ACS Appl Mater Interfaces 2020 Mar 24;12(9):10657-10663. Epub 2020 Feb 24.

Department of Physics, University of Warwick, Coventry CV4 7AL, U.K.

The structural, electronic, and magnetic properties of interfaces between epitaxial LaSrMnO and PbTiO have been explored via atomic resolution transmission electron microscopy of a functional multiferroic tunnel junction. Measurements of the polar displacements and octahedral tilting show the competition between the two distortions at the interface and demonstrate strong dependence on the polarization orientation. The density functional theory provides information on the electronic and magnetic properties, where the interface termination plays a crucial role in the screening mechanisms.
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http://dx.doi.org/10.1021/acsami.9b21619DOI Listing
March 2020

Does Endometriosis Influence the Embryo Quality and/or Development? Insights from a Large Retrospective Matched Cohort Study.

Diagnostics (Basel) 2020 Feb 3;10(2). Epub 2020 Feb 3.

Reproductive Sciences Laboratory, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy.

In vitro fertilization can be an effective tool to manage the endometriosis-associated infertility, which accounts for 10% of the strategy indications. Nevertheless, a negative effect of endometriosis on IVF outcomes has been suggested. The aim of this study was to evaluate the potential effect of endometriosis in the development of embryos at cleavege stage in assisted reproduction treatment cycles. A total of 429 cycles from women previously operated for moderate/severe endometriosis were compared with 851 cycles from non-affected women. Patients were matched by age, number of oocyte retrieved and study period. A total of 3818 embryos in cleavage stage have been analyzed retrospectively. Overall, no difference was found between women with and without endometriosis regarding the number of cleavage stage embryos obtained as well as the percentage of good/fair quality embryos. Excluding cycles in which no transfers were performed or where embryos were frozen in day three, no difference was observed for blastulation rate or the percentage of good/fair blastocysts obtained. Despite similar fertilization rate and number/quality of embryos, a reduction in ongoing pregnancy rate was observed in patients affected, possibly due to an altered endometrial receptivity or to the limited value of the conventional morphological evaluation of the embryo.
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http://dx.doi.org/10.3390/diagnostics10020083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168899PMC
February 2020

Engineering the Side Facets of Vertical [100] Oriented InP Nanowires for Novel Radial Heterostructures.

Nanoscale Res Lett 2019 Dec 30;14(1):399. Epub 2019 Dec 30.

Department of Electronic Materials Engineering, Research School of Physics and Engineering, The Australian National University, Canberra, ACT 2601, Australia.

In addition to being grown on industry-standard orientation, vertical [100] oriented nanowires present novel families of facets and related cross-sectional shapes. These nanowires are engineered to achieve a number of facet combinations and cross-sectional shapes, by varying their growth parameters within ranges that facilitate vertical growth. In situ post-growth annealing technique is used to realise other combinations that are unattainable solely using growth parameters. Two examples of possible novel radial heterostructures grown on these vertical [100] oriented nanowire facets are presented, demonstrating their potential in future applications.
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http://dx.doi.org/10.1186/s11671-019-3177-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937364PMC
December 2019

Alpine vegetation dataset from three contrasting mountain ranges differing in climate and evolutionary history.

Data Brief 2019 Dec 15;27:104816. Epub 2019 Nov 15.

Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnológicas, Universidad Rey Juan Carlos, Móstoles, Spain.

Vegetation above treeline constitutes one of the most vulnerable ecosystems to climate warming and other drivers of Global Change. Given the panorama of such an uncertain future facing these plant communities, it is critical to know how they respond to environmental changes and improve the knowledge on the potential impacts of climate change on their distribution. Recently, with the impressive development of trait-based approaches, relevant progress has been made to better understand the relationships between environmental conditions and plant communities. In this data paper, we describe data on abundances of 327 alpine plant species across 430 subplots of 2.4 m × 2.4 m in three mountain ranges (Sierra de Guadarrama and Pyrenees in Spain, and the Central Andes in Chile). We provide data on different environmental variables that represent variation in abiotic conditions and operate at different spatial scales (e.g., climatic, topographic and soil conditions). Data on six plant functional traits are also shown, which were measured on ten individuals of each species, following standard protocols. We provided the dataset as tables in the supplementary material. This information could be used to analyse the relationship between the alpine vegetation and changes in environmental conditions, and ultimately, to understand ecosystem functioning and guide conservation strategies of theses threatened and valuable ecosystems.
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http://dx.doi.org/10.1016/j.dib.2019.104816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880020PMC
December 2019

Impacts of climate, soil and biotic interactions on the interplay of the different facets of alpine plant diversity.

Sci Total Environ 2020 Jan 28;698:133960. Epub 2019 Aug 28.

Departamento de Biología, Geología, Física y Química inorgánica, Universidad Rey Juan Carlos, Madrid, Spain.

Disentangling the processes that drive plant community assembly is critical for understanding the patterns of plant diversity. We studied how different abiotic and biotic factors shape the interplay between the facets of alpine plant diversity, functional (FD), phylogenetic (PD) and taxonomic diversity (TD), in three different mountain ranges with contrasting evolutionary histories and climate conditions (Pyrenees and Mediterranean-type mountains in central Spain and Chilean Andes). We hypothesized that the causal links vary in strength and sign across regions. We used species inventories, functional trait data, and a phylogeny from 84 plant communities spread throughout three high-mountain alpine grasslands. Structural equation models were used to test our causal hypotheses on the relationships observed between the three diversity facets, and the abiotic (elevation, potential solar radiation and soil total nitrogen) and biotic factors (C-score). Despite our causal model presented a high variability in each mountain range, TD always decreased with increasing elevation (sum of direct and indirect effects). We also found some patterns suggesting that assembly processes could be climatically/biogeographically structured such as the negative relationship between FD and elevation found in Mediterranean mountains and the negative relationship between FD and TD found in both Spanish mountain ranges (independently of their different climates). A remarkable finding of this study is that ecological factors such as soil total nitrogen and elevation indirectly alter the relationships between the diversity facets. Our results suggest that diversity facets are simultaneously affected by different ecological and biogeographical/evolutionary processes, resulting in some general trends but also in parallel idiosyncratic patterns. Our findings highlight that although FD stand out by its explanatory power of community processes, TD and PD provide a complementary and necessary view that should not be disregarded in the attempt to globally explain community assembly processes.
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http://dx.doi.org/10.1016/j.scitotenv.2019.133960DOI Listing
January 2020

Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination.

Nucleic Acids Res 2019 09;47(16):8452-8469

Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.

Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here, we show that phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3'-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of the Asp1 and Aps1 IPP pyrophosphatases is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1Δ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3'-processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.
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http://dx.doi.org/10.1093/nar/gkz567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895273PMC
September 2019

Strain-gradient mediated local conduction in strained bismuth ferrite films.

Nat Commun 2019 Jun 26;10(1):2791. Epub 2019 Jun 26.

Department of Physics, The University of Warwick, Coventry, CV4 7AL, UK.

It has been recently shown that the strain gradient is able to separate the light-excited electron-hole pairs in semiconductors, but how it affects the photoelectric properties of the photo-active materials remains an open question. Here, we demonstrate the critical role of the strain gradient in mediating local photoelectric properties in the strained BiFeO thin films by systematically characterizing the local conduction with nanometre lateral resolution in both dark and illuminated conditions. Due to the giant strain gradient manifested at the morphotropic phase boundaries, the associated flexo-photovoltaic effect induces on one side an enhanced photoconduction in the R-phase, and on the other side a negative photoconductivity in the morphotropic [Formula: see text]-phase. This work offers insight and implication of the strain gradient on the electronic properties in both optoelectronic and photovoltaic devices.
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http://dx.doi.org/10.1038/s41467-019-10664-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594973PMC
June 2019

Estimating belowground plant abundance with DNA metabarcoding.

Mol Ecol Resour 2019 Sep 20;19(5):1265-1277. Epub 2019 Jul 20.

Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Spain.

Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R  = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.
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http://dx.doi.org/10.1111/1755-0998.13049DOI Listing
September 2019

Defect Dynamics in Self-Catalyzed III-V Semiconductor Nanowires.

Nano Lett 2019 Jul 20;19(7):4574-4580. Epub 2019 Jun 20.

Department of Physics , University of Warwick , Coventry CV4 7AL , United Kingdom.

The droplet consumption step in self-catalyzed III-V semiconductor nanowires can produce material that contains a high density of line defects. Interestingly, these defects are often associated with twin boundaries and have null Burgers vector, i.e., no long-range strain field. Here, we analyze their stability by considering the forces that act on them and use in situ aberration corrected scanning transmission electron microscopy (STEM) to observe their behavior in GaAsP nanowires (NWs) using short annealing cycles. Their movement appears to be consistent with the thermally activated single- or double-kink mechanisms of dislocation glide, with velocities that do not exceed 1 nm s. We find that motion of individual defects depends on their size, position, and surrounding environment and set an upper limit to activation energy around 2 eV. The majority of defects (>70%) are removed by our postgrowth annealing for several seconds at temperatures in excess of 640 °C, suggesting that in situ annealing during growth at lower temperatures would significantly improve material quality. The remaining defects do not move at all and are thermodynamically stable in the nanowire.
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http://dx.doi.org/10.1021/acs.nanolett.9b01508DOI Listing
July 2019

Flexible Memristors Based on Single-Crystalline Ferroelectric Tunnel Junctions.

ACS Appl Mater Interfaces 2019 Jul 20;11(26):23313-23319. Epub 2019 Jun 20.

Department of Physics , University of Warwick , CV4 7AL , Coventry , United Kingdom.

Ferroelectric tunnel junction (FTJ) based memristors exhibiting continuous electric field controllable resistance states have been considered promising candidates for future high-density memories and advanced neuromorphic computational architectures. However, the use of rigid single crystal substrate and high temperature growth of the epitaxial FTJ thin films constitutes the main obstacles to using this kind of heterostructure in flexible computing devices. Here, we report the integration of centimeter-scale single crystalline FTJs on flexible plastic substrates, by water-etching based epitaxial oxide membrane lift-off and the following transfer. The resulting highly flexible FTJ membranes retain the single-crystalline structure along with stable and switchable ferroelectric polarization as the grown-on single crystal substrate state. We show that the obtained flexible memristors, i.e., FTJs on plastic substrates, present high speed and low voltage mediated memristive behaviors with resistance changes over 500% and are stable against shape change. This work is an essential step toward the realization of epitaxial ultrathin ferroelectric oxide film-based electronics on large-area, flexible, and affordable substrates.
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http://dx.doi.org/10.1021/acsami.9b04738DOI Listing
July 2019

Implementation of a responsible conduct of research education program at Duke University School of Medicine.

Account Res 2019 07 2;26(5):288-310. Epub 2019 Jun 2.

c Office of Scientific Integrity , Duke University , Durham , NC , USA.

Academic medical centers rarely require of their research faculty and staff to participate in educational programs on the responsible conduct of research (RCR). There is also little published evidence of RCR programs addressing high-profile, internal cases of misconduct as a way of promoting deliberation and learning. In the wake of major research misconduct, Duke University School of Medicine (DUSoM) expanded its RCR education activities to include all DUSoM faculty and staff engaged in research. The program included formal deliberation of the Translational Omics misconduct case, which occurred at Duke. Over 5,000 DUSoM faculty and staff participated in the first phase of this new program, with a 100% completion rate. The article reports on the program's development, challenges and successes, and future directions. This experience at Duke University illustrates that, although challenging and resource intensive, engagement with RCR activities can be integrated into programs for all research faculty and staff. Formal, participatory deliberation of recent cases of internal misconduct can add a novel dimension of reflection and openness to RCR educational activities.
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http://dx.doi.org/10.1080/08989621.2019.1621755DOI Listing
July 2019

Self-Formed Quantum Wires and Dots in GaAsP-GaAsP Core-Shell Nanowires.

Nano Lett 2019 06 31;19(6):4158-4165. Epub 2019 May 31.

Department of Physics , University of Warwick , Coventry CV4 7AL , United Kingdom.

Quantum structures designed using nanowires as a basis are excellent candidates to achieve novel design architectures. Here, triplets of quantum wires (QWRs) that form at the core-shell interface of GaAsP-GaAsP nanowires are reported. Their formation, on only three of the six vertices of the hexagonal nanowire, is governed by the three-fold symmetry of the cubic crystal on the (111) plane. In twinned nanowires, the QWRs are segmented, to alternating vertices, forming quantum dots (QDs). Simulations confirm the possibility of QWR and QD-like behavior from the respective regions. Optical measurements confirm the presence of two different types of quantum emitters in the twinned individual nanowires. The possibility to control the relative formation of QWRs or QDs, and resulting emission wavelengths of the QDs, by controlling the twinning of the nanowire core, opens up new possibilities for designing nanowire devices.
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http://dx.doi.org/10.1021/acs.nanolett.9b01673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007271PMC
June 2019

Highly Strained III-V-V Coaxial Nanowire Quantum Wells with Strong Carrier Confinement.

ACS Nano 2019 May 9;13(5):5931-5938. Epub 2019 May 9.

Department of Electronic and Electrical Engineering , University College London , London WC1E 7JE , United Kingdom.

Coaxial quantum wells (QWs) are ideal candidates for nanowire (NW) lasers, providing strong carrier confinement and allowing close matching of the cavity mode and gain medium. We report a detailed structural and optical study and the observation of lasing for a mixed group-V GaAsP NW with GaAs QWs. This system offers a number of potential advantages in comparison to previously studied common group-V structures ( e. g., AlGaAs/GaAs) including highly strained binary GaAs QWs, the absence of a lower band gap core region, and deep carrier potential wells. Despite the large lattice mismatch (∼1.7%), it is possible to grow defect-free GaAs coaxial QWs with high optical quality. The large band gap difference results in strong carrier confinement, and the ability to apply a high degree of compressive strain to the GaAs QWs is also expected to be beneficial for laser performance. For a non-fully optimized structure containing three QWs, we achieve low-temperature lasing with a low external (internal) threshold of 20 (0.9) μJ/cm/pulse. In addition, a very narrow lasing line width of ∼0.15 nm is observed. These results extend the NW laser structure to coaxial III-V-V QWs, which are highly suitable as the platform for NW emitters.
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http://dx.doi.org/10.1021/acsnano.9b01775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007272PMC
May 2019

Structure of Fission Yeast Transcription Factor Pho7 Bound to Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis.

Mol Cell Biol 2019 07 13;39(13). Epub 2019 Jun 13.

Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA

Pho7 is the fission yeast ZnCys transcriptional factor that drives a response to phosphate starvation in which phosphate acquisition genes are upregulated. Here we report a crystal structure at 1.6-Å resolution of the Pho7 DNA-binding domain (DBD) bound at its target site 2 in the promoter (5'-TCGGAAATTAAAAA). Comparison to the previously reported structure of Pho7 DBD in complex with its binding site in the promoter (5'-TCGGACATTCAAAT) reveals shared determinants of target site specificity as well as variations in the protein-DNA interface that accommodate different promoter DNA sequences. Mutagenesis of Pho7 amino acids at the DNA interface identified nucleobase contacts at the periphery of the footprint that are essential for the induction of expression in response to phosphate starvation and for Pho7 binding to site 1 in the promoter.
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http://dx.doi.org/10.1128/MCB.00132-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580706PMC
July 2019

Kinetics of polyphenol content of dry flowers and floral bio-residues of saffron at different temperatures and relative humidity conditions.

Food Chem 2019 Aug 25;290:87-94. Epub 2019 Mar 25.

Cátedra de Química Agrícola, ETSI Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071 Albacete, Spain. Electronic address:

The cultivation of Crocus sativus L. is valued for its dried stigmas, but the rest of the parts of its flowers are increasingly important. Saffron flowers (SF) are natural sources of antioxidant compounds. Kaempferols and anthocyanins are the main compounds of the high-phenolic content of SF. This work studies the evolution of flavonols and anthocyanins of dry SF and floral bio-residues of saffron (FBR) and their kinetics at different temperatures and relative humidity (RH) conditions. There was a degradation process of anthocyanins that fitted a second-order kinetic model and kaempferols showed better fit in a first-order kinetics model. The best storage conditions for anthocyanins studied in SF and FBR was 25 °C and 23% RH. The main kaempferol (Kaempferol 3-O-sophoroside) was no deteriorated in FBR. These results could contribute to the using SF and FBR as food and active ingredients in cosmetic industry, as well as development of new food products.
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http://dx.doi.org/10.1016/j.foodchem.2019.03.129DOI Listing
August 2019