Browsing by Subject "Science & Technology"

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Open Access
(0,2) hybrid models
(Journal of High Energy Physics, 2018-09-01) Bertolini, M; Plesser, MR
© 2018, The Author(s). We introduce a class of (0,2) superconformal field theories based on hybrid geometries, generalizing various known constructions. We develop techniques for the computation of the complete massless spectrum when the theory can be interpreted as determining a perturbative heterotic string compactification. We provide evidence for surprising properties regarding RG flows and IR accidental symmetries in (0,2) hybrid CFTs. We also study the conditions for embedding a hybrid theory in a particular class of gauged linear sigma models. This perspective suggests that our construction generates models which cannot be realized or analyzed by previously known methods.
Open Access
(1,1) L-space knots
(COMPOSITIO MATHEMATICA, 2018-05-01) Greene, JE; Lewallen, S; Vafaee, F
We characterize the (1, 1) knots in the three-sphere and lens spaces that admit non-trivial L-space surgeries. As a corollary, 1-bridge braids in these manifolds admit non- trivial L-space surgeries. We also recover a characterization of the Berge manifold amongst 1-bridge braid exteriors.
Open Access
A baseline paleoecological study for the Santa Cruz Formation (late–early Miocene) at the Atlantic coast of Patagonia, Argentina
(Palaeogeography, Palaeoclimatology, Palaeoecology, 2010-06) Vizcaíno, SF; Bargo, MS; Kay, RF; Fariña, RA; Di Giacomo, M; Perry, JMG; Prevosti, FJ; Toledo, N; Cassini, GH; Fernicola, JC
Coastal exposures of the Santa Cruz Formation (late-early Miocene, southern Patagonia, Argentina) between the Coyle and Gallegos rivers have been a fertile ground for recovery of Miocene vertebrates for more than 100 years. The formation contains an exceptionally rich mammal fauna, which documents a vertebrate assemblage very different from any living community, even at the ordinal level. Intensive fieldwork performed since 2003 (nearly 1200 specimens have been collected, including marsupials, xenarthrans, notoungulates, litopterns astrapotheres, rodents, and primates) document this assertion. The goal of this study is to attempt to reconstruct the trophic structure of the Santacrucian mammalian community with precise stratigraphic control. Particularly, we evaluate the depauperate carnivoran paleoguild and identify new working hypotheses about this community. A database has been built from about 390 specimens from two localities: Campo Barranca (CB) and Puesto Estancia La Costa (PLC). All species have been classified as herbivore or carnivore, their body masses estimated, and the following parameters estimated: population density, on-crop biomass, metabolic rates, and the primary and secondary productivity. According to our results, this model predicts an imbalance in both CB and PLC faunas which can be seen by comparing the secondary productivity of the ecosystem and the energetic requirements of the carnivores in it. While in CB, the difference between carnivores and herbivores is six-fold, in PLC this difference is smaller, the secondary productivity is still around three times that of the carnivore to herbivore ratio seen today. If both localities are combined, the difference rises to around four-fold in favour of secondary productivity. Finally, several working hypotheses about the Santacrucian mammalian community and the main lineages of herbivores and carnivores are offered. © 2010 Elsevier B.V. All rights reserved.
Open Access
A basic systems account of trauma memories in PTSD: is more needed?
(2015-01-01) Rubin, DC
Open Access
A Brain to Spine Interface for Transferring Artificial Sensory Information.
(Scientific reports, 2020-01-21) Yadav, Amol P; Li, Daniel; Nicolelis, Miguel AL
Lack of sensory feedback is a major obstacle in the rapid absorption of prosthetic devices by the brain. While electrical stimulation of cortical and subcortical structures provides unique means to deliver sensory information to higher brain structures, these approaches require highly invasive surgery and are dependent on accurate targeting of brain structures. Here, we propose a semi-invasive method, Dorsal Column Stimulation (DCS) as a tool for transferring sensory information to the brain. Using this new approach, we show that rats can learn to discriminate artificial sensations generated by DCS and that DCS-induced learning results in corticostriatal plasticity. We also demonstrate a proof of concept brain-to-spine interface (BTSI), whereby tactile and artificial sensory information are decoded from the brain of an "encoder" rat, transformed into DCS pulses, and delivered to the spinal cord of a second "decoder" rat while the latter performs an analog-to-digital conversion during a sensory discrimination task. These results suggest that DCS can be used as an effective sensory channel to transmit prosthetic information to the brain or between brains, and could be developed as a novel platform for delivering tactile and proprioceptive feedback in clinical applications of brain-machine interfaces.
Open Access
A classical proof that the algebraic homotopy class of a rational function is the residue pairing
(Linear Algebra and Its Applications, 2020-06-15) Kass, JL; Wickelgren, K
© 2020 Elsevier Inc. Cazanave has identified the algebraic homotopy class of a rational function of 1 variable with an explicit nondegenerate symmetric bilinear form. Here we show that Hurwitz's proof of a classical result about real rational functions essentially gives an alternative proof of the stable part of Cazanave's result. We also explain how this result can be interpreted in terms of the residue pairing and that this interpretation relates the result to the signature theorem of Eisenbud, Khimshiashvili, and Levine, showing that Cazanave's result answers a question posed by Eisenbud for polynomial functions in 1 variable. Finally, we announce results answering this question for functions in an arbitrary number of variables.
Open Access
A classification for extant ferns
(Taxon, 2006-01-01) Smith, AR; Pryer, KM; Schuettpelz, E; Korall, P; Schneider, H; Wolf, PG
We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.
Open Access
A comparative analysis of EGFR-targeting antibodies for gold nanoparticle CT imaging of lung cancer.
(PloS one, 2018-01) Ashton, Jeffrey R; Gottlin, Elizabeth B; Patz, Edward F; West, Jennifer L; Badea, Cristian T
Computed tomography (CT) is the standard imaging test used for the screening and assessment of suspected lung cancer, but distinguishing malignant from benign nodules by CT is an ongoing challenge. Consequently, a large number of avoidable invasive procedures are performed on patients with benign nodules in order to exclude malignancy. Improving cancer discrimination by non-invasive imaging could reduce the need for invasive diagnostics. In this work we focus on developing a gold nanoparticle contrast agent that targets the epidermal growth factor receptor (EGFR), which is expressed on the cell surface of most lung adenocarcinomas. Three different contrast agents were compared for their tumor targeting effectiveness: non-targeted nanoparticles, nanoparticles conjugated with full-sized anti-EGFR antibodies (cetuximab), and nanoparticles conjugated with a single-domain llama-derived anti-EGFR antibody, which is smaller than the cetuximab, but has a lower binding affinity. Nanoparticle targeting effectiveness was evaluated in vitro by EGFR-binding assays and in cell culture with A431 cells, which highly express EGFR. In vivo CT imaging performance was evaluated in both C57BL/6 mice and in nude mice with A431 subcutaneous tumors. The cetuximab nanoparticles had a significantly shorter blood residence time than either the non-targeted or the single-domain antibody nanoparticles. All of the nanoparticle contrast agents demonstrated tumor accumulation; however, the cetuximab-targeted group had significantly higher tumor gold accumulation than the other two groups, which were statistically indistinguishable from one another. In this study we found that the relative binding affinity of the targeting ligands had more of an effect on tumor accumulation than the circulation half life of the nanoparticles. This study provides useful insight into targeted nanoparticle design and demonstrates that nanoparticle contrast agents can be used to detect tumor receptor overexpression. Combining receptor status data with traditional imaging characteristics has the potential for better differentiation of malignant lung tumors from benign lesions.
Open Access
A comprehensive assessment of patient reported symptom burden, medical comorbidities, and functional well being in patients initiating direct acting antiviral therapy for chronic hepatitis C: Results from a large US multi-center observational study.
(PloS one, 2018-01) Evon, Donna M; Stewart, Paul W; Amador, Jipcy; Serper, Marina; Lok, Anna S; Sterling, Richard K; Sarkar, Souvik; Golin, Carol E; Reeve, Bryce B; Nelson, David R; Reau, Nancy; Lim, Joseph K; Reddy, K Rajender; Di Bisceglie, Adrian M; Fried, Michael W
Symptom burden, medical comorbidities, and functional well-being of patients with chronic hepatitis C virus (HCV) initiating direct acting antiviral (DAA) therapy in real-world clinical settings are not known. We characterized these patient-reported outcomes (PROs) among HCV-infected patients and explored associations with sociodemographic, liver disease, and psychiatric/substance abuse variables.PROP UP is a large US multicenter observational study that enrolled 1,600 patients with chronic HCV in 2016-2017. Data collected prior to initiating DAA therapy assessed the following PROs: number of medical comorbidities; neuropsychiatric, somatic, gastrointestinal symptoms (PROMIS surveys); overall symptom burden (Memorial Symptom Assessment Scale); and functional well-being (HCV-PRO). Candidate predictors included liver disease markers and patient-reported sociodemographic, psychiatric, and alcohol/drug use features. Predictive models were explored using a random selection of 700 participants; models were then validated with data from the remaining 900 participants. The cohort was 55% male, 39% non-white, 48% had cirrhosis (12% with advanced cirrhosis); 52% were disabled or unemployed; 63% were on public health insurance or uninsured; and over 40% had markers of psychiatric illness. The median number of medical comorbidities was 4 (range: 0-15), with sleep disorders, chronic pain, diabetes, joint pain and muscle aches being present in 20-50%. Fatigue, sleep disturbance, pain and neuropsychiatric symptoms were present in over 60% and gastrointestinal symptoms in 40-50%. In multivariable validation models, the strongest and most frequent predictors of worse PROs were disability, unemployment, and use of psychiatric medications, while liver markers generally were not.This large multi-center cohort study provides a comprehensive and contemporary assessment of the symptom burden and comorbid medical conditions in patients with HCV treated in real world settings. Pain, fatigue, and sleep disturbance were common and often severe. Sociodemographic and psychiatric markers were the most robust predictors of PROs. Future research that includes a rapidly changing population of HCV-infected individuals needs to evaluate how DAA therapy affects PROs and elucidate which symptoms resolve with viral eradication.(Clinicaltrial.gov: NCT02601820).
Open Access
A diploids-first approach to species delimitation and interpreting polyploid evolution in the fern genus astrolepis (pteridaceae)
(Systematic Botany, 2010-04-01) Beck, James B; Windham, Michael D; Yatskievych, George; Pryer, Kathleen M
Polyploidy presents a challenge to those wishing to delimit the species within a group and reconstruct the phylogenetic relationships among these taxa. A clear understanding of the tree-like relationships among the diploid species can provide a framework upon which to reconstruct the reticulate events that gave rise to the polyploid lineages. In this study we apply this "diploids-first" strategy to the fern genus Astrolepis (Pteridaceae). Diploids are identified using the number of spores per sporangium and spore size. Analyses of plastid and low-copy nuclear sequence data provide well-supported estimates of phylogenetic relationships, including strong evidence for two morphologically distinctive diploid lineages not recognized in recent treatments. One of these corresponds to the type of Notholaena deltoidea, a species that has not been recognized in any modern treatment of Astrolepis. This species is resurrected here as the new combination Astrolepis deltoidea . The second novel lineage is that of a diploid initially hypothesized to exist by molecular and morphological characteristics of several established Astrolepis allopolyploids. This previously missing diploid species is described here as Astrolepis obscura. © Copyright 2010 by the American Society of Plant Taxonomists.
Open Access
A formal Anthropocene is compatible with but distinct from its diachronous anthropogenic counterparts: a response to W.F. Ruddiman’s ‘three flaws in defining a formal Anthropocene’
(Progress in Physical Geography, 2019-06-01) Zalasiewicz, J; Waters, CN; Head, MJ; Poirier, C; Summerhayes, CP; Leinfelder, R; Grinevald, J; Steffen, W; Syvitski, J; Haff, P; McNeill, JR; Wagreich, M; Fairchild, IJ; Richter, DD; Vidas, D; Williams, M; Barnosky, AD; Cearreta, A
© The Author(s) 2019. We analyse the ‘three flaws’ to potentially defining a formal Anthropocene geological time unit as advanced by Ruddiman (2018). (1) We recognize a long record of pre-industrial human impacts, but note that these increased in relative magnitude slowly and were strongly time-transgressive by comparison with the extraordinarily rapid, novel and near-globally synchronous changes of post-industrial time. (2) The rules of stratigraphic nomenclature do not ‘reject’ pre-industrial anthropogenic signals – these have long been a key characteristic and distinguishing feature of the Holocene. (3) In contrast to the contention that classical chronostratigraphy is now widely ignored by scientists, it remains vital and widely used in unambiguously defining geological time units and is an indispensable part of the Earth sciences. A mounting body of evidence indicates that the Anthropocene, considered as a precisely defined geological time unit that begins in the mid-20th century, is sharply distinct from the Holocene.
Open Access
A host gene expression approach for identifying triggers of asthma exacerbations.
(PloS one, 2019-01) Lydon, Emily C; Bullard, Charles; Aydin, Mert; Better, Olga M; Mazur, Anna; Nicholson, Bradly P; Ko, Emily R; McClain, Micah T; Ginsburg, Geoffrey S; Woods, Chris W; Burke, Thomas W; Henao, Ricardo; Tsalik, Ephraim L
RATIONALE:Asthma exacerbations often occur due to infectious triggers, but determining whether infection is present and whether it is bacterial or viral remains clinically challenging. A diagnostic strategy that clarifies these uncertainties could enable personalized asthma treatment and mitigate antibiotic overuse. OBJECTIVES:To explore the performance of validated peripheral blood gene expression signatures in discriminating bacterial, viral, and noninfectious triggers in subjects with asthma exacerbations. METHODS:Subjects with suspected asthma exacerbations of various etiologies were retrospectively selected for peripheral blood gene expression analysis from a pool of subjects previously enrolled in emergency departments with acute respiratory illness. RT-PCR quantified 87 gene targets, selected from microarray-based studies, followed by logistic regression modeling to define bacterial, viral, or noninfectious class. The model-predicted class was compared to clinical adjudication and procalcitonin. RESULTS:Of 46 subjects enrolled, 7 were clinically adjudicated as bacterial, 18 as viral, and 21 as noninfectious. Model prediction was congruent with clinical adjudication in 15/18 viral and 13/21 noninfectious cases, but only 1/7 bacterial cases. None of the adjudicated bacterial cases had confirmatory microbiology; the precise etiology in this group was uncertain. Procalcitonin classified only one subject in the cohort as bacterial. 47.8% of subjects received antibiotics. CONCLUSIONS:Our model classified asthma exacerbations by the underlying bacterial, viral, and noninfectious host response. Compared to clinical adjudication, the majority of discordances occurred in the bacterial group, due to either imperfect adjudication or model misclassification. Bacterial infection was identified infrequently by all classification schemes, but nearly half of subjects were prescribed antibiotics. A gene expression-based approach may offer useful diagnostic information in this population and guide appropriate antibiotic use.
Open Access
A hybrid ion-atom trap with integrated high resolution mass spectrometer
(Review of Scientific Instruments, 2019-10-01) Jyothi, S; Egodapitiya, KN; Bondurant, B; Jia, Z; Pretzsch, E; Chiappina, P; Shu, G; Brown, KR
© 2019 Author(s). In this article, we describe the design, construction, and implementation of our ion-atom hybrid system incorporating a high resolution time of flight mass spectrometer (TOFMS). Potassium atoms (39K) in a magneto optical trap and laser cooled calcium ions (40Ca+) in a linear Paul trap are spatially overlapped, and the combined trap is integrated with a TOFMS for radial extraction and detection of reaction products. We also present some experimental results showing interactions between 39K+ and 39K, 40Ca+ and 39K+, as well as 40Ca+ and 39K pairs. Finally, we discuss prospects for cooling CaH+ molecular ions in the hybrid ion-atom system.
Open Access
A microscopic model of the Stokes-Einstein relation in arbitrary dimension.
(The Journal of chemical physics, 2018-06) Charbonneau, Benoit; Charbonneau, Patrick; Szamel, Grzegorz
The Stokes-Einstein relation (SER) is one of the most robust and widely employed results from the theory of liquids. Yet sizable deviations can be observed for self-solvation, which cannot be explained by the standard hydrodynamic derivation. Here, we revisit the work of Masters and Madden [J. Chem. Phys. 74, 2450-2459 (1981)], who first solved a statistical mechanics model of the SER using the projection operator formalism. By generalizing their analysis to all spatial dimensions and to partially structured solvents, we identify a potential microscopic origin of some of these deviations. We also reproduce the SER-like result from the exact dynamics of infinite-dimensional fluids.
Open Access
A Modular Multilevel Series/Parallel Converter for a Wide Frequency Range Operation
(IEEE Transactions on Power Electronics, 2019-10-01) Li, Z; Ricardo Lizana, F; Yu, Z; Sha, S; Peterchev, AV; Goetz, SM
When providing ac output, modular multilevel converters (MMCs) experience power fluctuation in the phase arms. The power fluctuation causes voltage ripple on the module capacitors, which grows with the output power and inversely to the output frequency. Thus, low-frequency operations of MMCs, e.g., for motor drives, require injecting common-mode voltages and circulating currents, and strict dc voltage output relative to ground is impossible. To address this problem, this paper introduces a novel module topology that allows parallel module connectivity in addition to the series and bypass states. The parallel state directly transfers power across the modules and arms to cancel the power fluctuations and hence suppresses the capacitor voltage ripple. The proposed series/parallel converter can operate at a wide frequency range down to dc without common-mode voltages or circulating currents; it also allows sensorless operation and full utilization of the components at higher output frequencies. We present detailed simulation and experiment results to characterize the advantages and limitations of the proposed solution.
Open Access
A molecular phylogeny of scaly tree ferns (Cyatheaceae).
(American journal of botany, 2007-05) Korall, P; Conant, DS; Metzgar, JS; Schneider, H; Pryer, KM
Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (∼500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised.
Open Access
A new look at an old disease: Is Pompe disease a neuromuscular disorder with CNS involvement?
(Molecular Genetics and Metabolism, 2020-02) Korlimarla, Aditi; Chen, Steven; Austin, Stephanie L; Provenzale, James M; Kishnani, Priya S
Open Access
A new non-enzymatic method for isolating human intervertebral disc cells preserves the phenotype of nucleus pulposus cells.
(Cytotechnology, 2014-12) Tang, Xinyan; Richardson, William J; Fitch, Robert D; Brown, Christopher R; Isaacs, Robert E; Chen, Jun
Cells isolated from intervertebral disc (IVD) tissues of human surgical samples are one of potential sources for the IVD cellular therapy. The purpose of this study was to develop a new non-enzymatic method, "tissue incubation", for isolating human IVD cells. The IVD tissues of annulus fibrosus (AF) and nucleus pulposus (NP) were incubated separately in tissue culture flasks with culture medium. After 7-10 days incubation, cells were able to migrate out of IVD tissues and proliferate in vitro. After 3-4 weeks culture, expanded cells were harvested by trypsinization, and the remaining tissues were transferred to a new flask for another round of incubation. The molecular phenotype of IVD cells from juvenile and adult human samples was evaluated by both flow cytometry analysis and immunocytochemical staining for the expression of protein markers of NP cells (CD24, CD54, CD239, integrin α6 and laminin α5). Flow cytometry confirmed that both AF and NP cells of all ages positively expressed CD54 and integrin α6, with higher expression levels in NP cells than in AF cells for the juvenile group sample. However, CD24 expression was only found in juvenile NP cells, and not in AF or older disc cells. Similar expression patterns for NP markers were also confirmed by immunocytochemistry. In summary, this new non-enzymatic tissue incubation method for cell isolation preserves molecular phenotypic markers of NP cells and may provide a valuable cell source for the study of NP regeneration strategies.
Open Access
A novel approach to assess livestock management effects on biodiversity of drylands
(Ecological Indicators, 2015-01-01) Chillo, V; Ojeda, RA; Anand, M; Reynolds, JF
In drylands livestock grazing is the main production activity, but overgrazing due to mismanagement is a major cause of biodiversity loss. Continuous grazing around water sources generates a radial gradient of grazing intensity called the piosphere. The ecological sustainability of this system is questionable and alternative management needs to be evaluated. We apply simple indicators of species response to grazing gradients, and we propose a novel methodological approach to compare community response to grazing gradients (double reciprocal analysis). We assessed degradation gradients of biodiversity under different management strategies in semiarid rangelands of the Monte desert (Argentina) by analyzing changes in vegetation, ants and small mammal richness and diversity, and variation due to seasonality. At the species level, we determined the trend in abundance of each species along the gradient, and the potential cross-taxa surrogacy. At the community level, the new methodological consists of assessing the magnitude of biodiversity degradation along different piospheres by comparing the slopes of linear functions obtained by the double reciprocal analysis. We found that most species showed a decreasing trend along the gradient under continuous grazing; while under rotational grazing fewer species showed a decreasing trend, and a neutral trend (no change in the abundance along the gradient of grazing intensity) was the most common. We found that vegetation cannot be used as a surrogacy taxon of animal response. Moreover, weak cross-taxa surrogacy was found only for animal assemblages during the wet season. The double reciprocal analysis allowed for comparison of multi-taxa response under different seasons and management types. By its application, we found that constrains in precipitation interacted with disturbance by increasing the negative effect of grazing on vegetation, but not on animal assemblages. Continuous grazing causes biodiversity loss in all situations. Rotational grazing prevents the occurrence of vegetation degradation and maintains higher levels of animal diversity, acting as an opportunity for biodiversity conservation under current scenarios of land use extensification. Our approach highlights the importance of considering multi-taxa and intrinsic variability in the analysis, and should be of value to managers concerned with biodiversity conservation.
Open Access
A numerical analysis of chromatographic profiles in North American taxa of the fern genus Gymnocarpium
(Canadian Journal of Botany, 1983-10-01) Pryer, Kathleen M; Britton, Donald M; McNeill, John
As part of a systematic investigation of the genus Gymnocarpium in North America, a survey of chromatographic profiles in species and hybrids of the genus was initiated. It was established through cluster analysis and ordination of the phenolic data that morphologically distinguishable taxa of Gymnocarpium can be recognized by their chromatographic profiles alone. These data provide supportive evidence for the recognition of G. robertianum and G. jessoense ssp. parvulum as distinct taxa and for the hybrid status of G. × intermedium. They also suggest that, as currently circumscribed, G. jessoense ssp. jessoense is a heterogeneous taxon.

Browsing by Subject "Science & Technology"

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