Digital Commons Network^™

De Novo Transcriptome Assembly Of The Green Alga Ankistrodesmus Falcatus, Rachel A. Schomaker, Jeffry L. Dudycha

Faculty Publications

Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic …

Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova Prof. Dr.

Faculty Publications

In this perspective, we feature recent advances in the field of actinide-containing metal–organic frameworks (An-MOFs) with a main focus on their electronic, catalytic, photophysical, and sorption properties. This discussion deviates from a strictly crystallographic analysis of An-MOFs, reported in several reviews, or synthesis of novel structural motifs, and instead delves into the remarkable potential of An-MOFs for evolving the nuclear waste administration sector. Currently, the An-MOF field is dominated by thorium- and uranium-containing structures, with only a few reports on transuranic frameworks. However, some of the reported properties in the field of An-MOFs foreshadow potential implementation of these materials and …

Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova

Faculty Publications

In this perspective, we feature recent advances in the field of actinide-containing metal-organic frameworks (An-MOFs) with a main focus on their electronic, catalytic, photophysical, and sorption properties. This discussion deviates from a strictly crystallographic analysis of An-MOFs, reported in several reviews, or synthesis of novel structural motifs, and instead delves into the remarkable potential of An-MOFs for evolving the nuclear waste administration sector. Currently, the An-MOF field is dominated by thorium- and uranium-containing structures, with only a few reports on transuranic frameworks. However, some of the reported properties in the field of An-MOFs foreshadow potential implementation of these materials and …

Modeled Changes In Source Contributions Of Particulate Matter During The Covid-19 Pandemic In The Yangtze River Delta, China, Jinlong Ma, Juanyong Shen, Peng Wang, Shengqiang Zhu, Yu Wang, Pengfei Wang, Gehui Wang, Jianmin Chen, Hongliang Zhang

Faculty Publications

Within a short time after the outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, Hubei, the Chinese government introduced a nationwide lockdown to prevent the spread of the pandemic. The quarantine measures have significantly decreased the anthropogenic activities, thus improving air quality. To study the impacts caused by the lockdown on specific source sectors and regions in the Yangtze River Delta (YRD), the Community Multiscale Air Quality (CMAQ) model was used to investigate the changes in source contributions to fine particulate matter (PM2.5) from 23 January to 28 February 2020, based on different emission control cases. Compared to case 1 …

Fungal Community Response To Long-Term Soil Warming With Potential Implications For Soil Carbon Dynamics, Gregory J. Pec, Linda T. A. Van Diepen, Melissa A. Knorr, A. Stuart Grandy, Jerry M. Melillo, Kristen M. Deangelis, Jeffrey L. Blanchard, Serita D. Frey

Faculty Publications

The direction and magnitude of climate warming effects on ecosystem processes such as carbon cycling remain uncertain. Soil fungi are central to these processes due to their roles as decomposers of soil organic matter, as mycorrhizal symbionts, and as determinants of plant diversity. Yet despite their importance to ecosystem functioning, we lack a clear understanding of the long-term response of soil fungal communities to warming. Toward this goal, we characterized soil fungal communities in two replicated soil warming experiments at the Harvard Forest (Petersham, Massachusetts, USA) which had experienced 5°C above ambient soil temperatures for 5 and 20 yr at …

Differences In Effectiveness And Use Of Laparoscopic Surgery In Locally Advanced Colon Cancer Patients, M. Schootman, Matthew Mutch, T. Loux, Jan M. Eberth Ph.D., N. O. Davidson

Faculty Publications

Patients with locally advanced colon cancer have worse outcomes. Guidelines of various organizations are conflicting about the use of laparoscopic colectomy (LC) in locally advanced colon cancer. We determined whether patient outcomes of LC and open colectomy (OC) for locally advanced (T4) colon cancer are comparable in all colon cancer patients, T4a versus T4b patients, obese versus non-obese patients, and tumors located in the ascending, descending, and transverse colon. We used data from the 2013–2015 American College of Surgeons’ National Surgical Quality Improvement Program. Patients were diagnosed with nonmetastatic pT4 colon cancer, with or without obstruction, and underwent LC (n …

Management Intensive Grazing On New England Dairy Farms Enhances Soil Nitrogen Stocks And Elevates Soil Nitrous Oxide Emissions Without Increasing Soil Carbon, Alexandra R. Contosta, Kyle A. Arndt, Eleanor E. Campbell, A. Stuart Grandy, Apryl L. Perry, Ruth K. Varner

Faculty Publications

Management intensive grazing (MIG), also known as rotational grazing or multi-paddock grazing, is purported to sequester carbon (C) in soils compared to other agricultural management systems. Prior research examining the potential for MIG to enhance soil C has been inconclusive, and past investigations have not addressed whether higher nitrous oxide (N2O) emissions may accompany increases in soil C stocks. Here we examined linkages among MIG, soil C accumulation, and N2O emissions in cool-season, organic pastures of the northeastern United States. We found that pastures under MIG increased soil C concentrations by 11% from 0–15 cm depth but that soil C …

Enhanced Atmospheric Oxidation Capacity And Associated Ozone Increases During Covid-19 Lockdown In The Yangtze River Delta, Yu Wang, Shengqiang Zhu, Jinlong Ma, Juanyong Shen, Pengfei Wang, Peng Wang, Hongliang Zhang

Faculty Publications

Aggressive air pollution control in China since 2013 has achieved sharp decreases in fine particulate matter (PM2.5), along with increased ozone (O-3) concentrations. Due to the pandemic of coronavirus disease 2019 (COVID-19), China imposed nationwide restriction, leading to large reductions in economic activities and associated emissions. In particular, large decreases were found in nitrogen oxides (NOx) emissions (>50%) from transportation. However, O-3 increased in the Yangtze River Delta (YRD), which cannot be fully explained by changes in NOx and volatile organic compound (VOCs) emissions. In this study, the Community Multi-scale Air Quality model was used to investigate O-3 increase …

Model For Quantifying The Quality Of Secure Service, Paul M. Simon, Scott R. Graham, Christopher Talbot, Micah J. Hayden

Faculty Publications

Although not common today, communications networks could adjust security postures based on changing mission security requirements, environmental conditions, or adversarial capability, through the coordinated use of multiple channels. This will require the ability to measure the security of communications networks in a meaningful way. To address this need, in this paper, we introduce the Quality of Secure Service (QoSS) model, a methodology to evaluate how well a system meets its security requirements. This construct enables a repeatable and quantifiable measure of security in a single- or multi-channel network under static configurations. In this approach, the quantification of security is based …

A Holistic Framework Integrating Plant-Microbe-Mineral Regulation Of Soil Bioavailable Nitrogen, Amanda B. Daly, Andrea Jilling, Timothy M. Bowles, Robert W. Buchowski, Serita D. Frey, Cynthia M. Kallenbach, Marco Keiluweit, Maria Mooshammer, Joshua P. Schimel, A. Stuart Grandy

Faculty Publications

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial …

Study Of The Reactions E + E - → 2 (Π + Π -) Π 0 Π 0 Π 0 And 2(Π + Π - ) Π 0 Π 0 Η At Center-Of-Mass Energies From Threshold To 4.5 Gev Using Initial-State Radiation, J.P. Lees, V. Poireau, V. Tisserand, E. Grauges, A. Palano, G. Eigen, D. N. Brown, Yu. G. Kolomensky, M. Fritsch, H. Koch, T. Schroeder, R. Cheaib, C. Hearty, T. S. Mattison, J. A. Mckenna, R. Y. So, V. E. Blinov, A. R. Buzykaev, V. P. Druzhinin, Milind Purohit, Et. Al.

Faculty Publications

We study the processes e⁺e⁻→ 2(π⁺π⁻)π⁰π⁰π⁰γ and 2(π⁺π⁻)π⁰π⁰ηγ in which an energetic photon is radiated from the initial state. The data were collected with the BABAR detector at SLAC. About 14 000 and 4700 events, respectively, are selected from a data sample corresponding to an integrated luminosity of 469 fb⁻¹. The invariant mass of the hadronic final state defines the effective e⁺e⁻ center-of-mass energy. The center-of-mass energies range from threshold to 4.5 GeV. …

The Effects Of Individual Differences, Non‐Stationarity, And The Importance Of Data Partitioning Decisions For Training And Testing Of Eeg Cross‐Participant Models, Alexander J. Kamrud, Brett J. Borghetti, Christine M. Schubert Kabban

Faculty Publications

EEG-based deep learning models have trended toward models that are designed to perform classification on any individual (cross-participant models). However, because EEG varies across participants due to non-stationarity and individual differences, certain guidelines must be followed for partitioning data into training, validation, and testing sets, in order for cross-participant models to avoid overestimation of model accuracy. Despite this necessity, the majority of EEG-based cross-participant models have not adopted such guidelines. Furthermore, some data repositories may unwittingly contribute to the problem by providing partitioned test and non-test datasets for reasons such as competition support. In this study, we demonstrate how improper …

Sodah: The Soils Data Harmonization Database, An Open-Source Synthesis Of Soil Data From Research Networks, Version 1.0, William R. Wieder, Derek Pierson, Stevan Earl, Kate Lajtha, Sara G. Baer, Ford Ballantyne, Asmeret Asefaw Berhe, Sharon A. Billings, Laurel M. Brigham, Stephany S. Chacon, Jennifer Fraterrigo, Serita D. Frey, Katerina Georgiou, Marie-Anne De Graaff, A. Stuart Grandy, Melannie D. Hartman, Sarah E. Hobbie, Chris Johnson, Jason Kaye, Emily Kyker-Snowman, Marcy E. Litvak, Michelle C. Mack, Avni Malhotra, Jessica A. M. Moore, Knute Nadelhoffer, Craig Rasmussen, Whendee L. Silver, Benjamin N. Sulman, Xanthe Walker, Samantha Weintraub

Faculty Publications

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information available for inquiry. Synthesizing these data is challenging, especially considering the legacy of soil data that have already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last access: 22 December 2020), a flexible database designed to harmonize diverse …

The Impact Of Aquaculture On The Genetics And Distribution Of The Onuphid Annelid Diopatra Biscayensis, Matthew P. Galaska, David S. Wethey, Andrés Arias, Stanislas F. Dubois, Kenneth M. Halanych, Sarah A. Woodin

Faculty Publications

Aim

Evolutionary history of natural populations can be confounded by human intervention such as the case of decorator worm species Diopatra (Onuphidae), which have a history of being transported through anthropogenic activities. Because they build tubes and act as ecosystem engineers, they can have a large impact on the overall ecosystem in which they occur. One conspicuous member, Diopatra biscayensis, which was only described in 2012, has a fragmented distribution that includes the Bay of Biscay and the Normanno-Breton Gulf in the English Channel. This study explores the origin of these worms in the Normanno-Breton region, which has been …

Complementation, Local Complementation, And Switching In Binary Matroids, James Oxley, Jagdeep Singh

Faculty Publications

In 2004, Ehrenfeucht, Harju, and Rozenberg showed that any graph on a vertex set V can be obtained from a complete graph on V via a sequence of the operations of complementation, switching edges and non-edges at a vertex, and local complementation. The last operation involves taking the complement in the neighbourhood of a vertex. In this paper, we consider natural generalizations of these operations for binary matroids and explore their behaviour. We characterize all binary matroids obtainable from the binary projective geometry of rank r under the operations of complementation and switching. Moreover, we show that not all binary …

Citations Versus Expert Opinions: Citation Analysis Of Featured Reviews Of The American Mathematical Society, Lawrence Smolinsky, Daniel S. Sage, Aaron J. Lercher, Aaron Cao

Faculty Publications

Peer review and citation metrics are two means of gauging the value of scientific research, but the lack of publicly available peer review data makes the comparison of these methods difficult. Mathematics can serve as a useful laboratory for considering these questions because as an exact science, there is a narrow range of reasons for citations. In mathematics, virtually all published articles are post-publication reviewed by mathematicians in Mathematical Reviews (MathSciNet) and so the data set was essentially the Web of Science mathematics publications from 1993 to 2004. For a decade, especially important articles were singled out in Mathematical Reviews …

Adaptive C0 Interior Penalty Methods For Hamilton–Jacobi–Bellman Equations With Cordes Coefficients, Susanne C. Brenner, Ellya L. Kawecki

Faculty Publications

In this paper we conduct a priori and a posteriori error analysis of the C interior penalty method for Hamilton–Jacobi–Bellman equations, with coefficients that satisfy the Cordes condition. These estimates show the quasi-optimality of the method, and provide one with an adaptive finite element method. In accordance with the proven regularity theory, we only assume that the solution of the Hamilton–Jacobi–Bellman equation belongs to H . 0 2

The Fermi-Gbm Gamma-Ray Burst Spectral Catalog: 10 Yr Of Data, S. Poolakkil, R. Preece, C. Fletcher, A. Goldstein, P. N. Bhat, E. Bissaldi, M. S. Briggs, E. Burns, W. H. Cleveland, M. M. Giles, C. M. Hui, D. Kocevski, S. Lesage, B. Mailyan, C. Malacaria, W. S. Paciesas, O. J. Roberts, P. Veres, A. Von Kienlin, C. A. Wilson-Hodge

Faculty Publications

We present the systematic spectral analyses of gamma-ray bursts (GRBs) detected by the Fermi Gamma-Ray Burst Monitor during its first ten years of operation. This catalog contains two types of spectra: time-integrated spectral fits and spectral fits at the brightest time bin, from 2297 GRBs, resulting in a compendium of over 18,000 spectra. The four different spectral models used for fitting the spectra were selected based on their empirical importance to the shape of many GRBs. We describe in detail our procedure and criteria for the analyses, and present the bulk results in the form of parameter distributions both in …

Polycyclic Aromatic Hydrocarbon-Dna Adducts In Gulf Of Mexico Sperm Whale Skin Biopsies Collected In 2012, Miriam C. Poirier, Letizia Marsili, Maria Cristina Fossi, Céline A.J. Godard-Codding, Elena E. Hernandez-Ramon, Nancy Si, Kathyayini V. Divi, Rao L. Divi, Iain Kerr, John Pierce Wise, John Pierce Wise, Catherine F. Wise, Sandra S. Wise, Abou El Makarim Aboueissa, James T.F. Wise

Faculty Publications

The northern Gulf of Mexico has a long history of polycyclic aromatic hydrocarbon (PAH) contamination from anthropogenic activities, natural oil seepages, and the 2010 Deepwater Horizon explosion and oil spill. The continental shelf of the same area is a known breeding ground for sperm whales (Physeter macrocephalus). To evaluate PAH-DNA damage, a biomarker for potential cancer risk, we compared skin biopsies collected from Gulf of Mexico sperm whales in 2012 with skin biopsies collected from sperm whales in areas of the Pacific Ocean in 1999-2001. All samples were obtained by crossbow and comprised both epidermis and subcutaneous blubber. To evaluate …

Circadian Rhythms In Legumes: What Do We Know And What Else Should We Explore?, Hazel Marie Kugan, Nur Ardiyana Rejab, Nurul Amylia Sahruzaini, Jennifer Ann Harikrishna, Niranjan Baisakh, Acga Cheng

Faculty Publications

The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24‐h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, …

On Graphic Arrangement Groups, Daniel C. Cohen, Michael J. Falk

Faculty Publications

A finite simple graph Γ determines a quotient PΓ of the pure braid group, called a graphic arrangement group. We analyze homomorphisms of these groups defined by deletion of sets of vertices, using methods developed in prior joint work with R. Randell. We show that, for a K4-free graph Γ, a product of deletion maps is injective, embedding PΓ in a product of free groups. Then PΓ is residually free, torsion-free, residually torsion-free nilpotent, and acts properly on a CAT(0) cube complex. We also show PΓ is of homological finiteness type Fm−1, but not Fm, where m is the number …