Physical Sciences and Mathematics Commons^™

Integrating Multiple Modalities Into Deep Learning Network, Patrick Mcneil

Patrick McNeil

Deep learning networks in the literature traditionally only used a single input modality (or data stream). Integrating multiple modalities into deep learning networks with the goal of correlating extracted features was a major issue. Traditional methods involved treating each modality separately and then writing custom code to combine the extracted features. Current solutions for small numbers of modalities (three or less) showed there are multiple architectures for modality integration. With an increase in the number of modalities, the “curse of dimensionality” affects the performance of the system. The research showed current methods for larger scale integrations required separate, custom created …

Acid And Base Stress And Transcriptomic Responses In Bacillus Subtilis., Brian Jones, Jessica C. Wilks, Ryan D. Kitko, Sarah H. Cleeton, Grace E. Lee, Chinagozi S. Ugwu, Sandra S. Bondurant, Joan L. Slonczewski

Brian Jones

Acid and base environmental stress responses were investigated in Bacillus subtilis. B. subtilis AG174 cultures in buffered potassium-modified Luria broth were switched from pH 8.5 to pH 6.0 and recovered growth rapidly, whereas cultures switched from pH 6.0 to pH 8.5 showed a long lag time. Log-phase cultures at pH 6.0 survived 60 to 100% at pH 4.5, whereas cells grown at pH 7.0 survived <15%. Cells grown at pH 9.0 survived 40 to 100% at pH 10, whereas cells grown at pH 7.0 survived <5%. Thus, growth in a moderate acid or base induced adaptation to a more extreme acid or base, respectively. Expression indices from Affymetrix chip hybridization were obtained for 4,095 protein-encoding open reading frames of B. subtilis grown at external pH 6, pH 7, and pH 9. Growth at pH 6 upregulated acetoin production (alsDS), dehydrogenases (adhA, ald, fdhD, and gabD), and decarboxylases (psd and speA). Acid upregulated malate metabolism (maeN), metal export (czcDO and cadA), oxidative stress (catalase katA; OYE family namA), and the SigX extracytoplasmic stress regulon. Growth at pH 9 upregulated arginine catabolism (roc), which generates organic acids, glutamate synthase (gltAB), polyamine acetylation and transport (blt), the K(+)/H(+) antiporter (yhaTU), and cytochrome oxidoreductases (cyd, ctaACE, and qcrC). The SigH, SigL, and SigW regulons were upregulated at high pH. Overall, greater genetic adaptation was seen at pH 9 than at pH 6, which may explain the lag time required for growth shift to high pH. Low external pH favored dehydrogenases and decarboxylases that may consume acids and generate basic amines, whereas high external pH favored catabolism-generating acids.

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Predicting Economic Optimal Nitrogen Rate With The Anaerobic Potentially Mineralizable Nitrogen Test, Jason D. Clark, Fabián G. Fernández, Kristen S. Veum, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A. M. Laboski, Emerson D. Nafziger, Carl J. Rosen, John E. Sawyer, John F. Shanahan

John E. Sawyer

Estimates of mineralizable N with the anaerobic potentially mineralizable N (PMN_an) test could improve predictions of corn (Zea mays L.) economic optimal N rate (EONR). A study across eight US midwestern states was conducted to quantify the predictability of EONR for single and split N applications by PMN_an. Treatment factors included different soil sample timings (pre-plant and V5 development stage), planting N rates (0 and 180 kg N ha⁻¹), and incubation lengths (7, 14, and 28 d) with and without initial soil NH₄–N included with PMN_an. Soil was sampled …

United States Midwest Soil And Weather Conditions Influence Anaerobic Potentially Mineralizable Nitrogen, Jason D. Clark, Kristen S. Veum, Fabián G. Fernández, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A. M. Laboski, Emerson D. Nafziger, Carl J. Rosen, John E. Sawyer, John F. Shanahan

John E. Sawyer

Nitrogen provided to crops through mineralization is an important factor in N management guidelines. Understanding of the interactive effects of soil and weather conditions on N mineralization needs to be improved. Relationships between anaerobic potentially mineralizable N (PMN_an) and soil and weather conditions were evaluated under the contrasting climates of eight US Midwestern states. Soil was sampled (0–30 cm) for PMN_an analysis before pre-plant N application (PP_0N) and at the V5 development stage from the pre-plant 0 (V5_0N) and 180 kg N ha⁻¹ (V5_180N) rates and incubated for 7, 14, …

Reverse Mathematics And Uniformity In Proofs Without Excluded Middle, Jeffry L. Hirst, Carl Mummert

Carl Mummert

We show that when certain statements are provable in subsystems of constructive analysis using intuitionistic predicate calculus, related sequential statements are provable in weak classical subsystems. In particular, if a \Pi^1_2 sentence of a certain form is provable using E-HA^ω along with the axiom of choice and an independence of premise principle, the sequential form of the statement is provable in the classical system RCA. We obtain this and similar results using applications of modified realizability and the Dialectica interpretation. These results allow us to use techniques of classical reverse mathematics to demonstrate the unprovability of several mathematical principles …

Reverse Mathematics And Properties Of Finite Character, Damir D. Dzhafarov, Carl Mummert

Carl Mummert

We study the reverse mathematics of the principle stating that,for every property of finite character, every set has a maximal subset satisfying the property. In the context of set theory, this variant of Tukey’s lemma is equivalent to the axiom of choice. We study its behavior in the context of second-order arithmetic, where it applies to sets of natural numbers only, and give a full characterization of its strength in terms of the quantifier structure of the formula defining the property. We then study the interaction between properties of finite character and finitary closure operators, and the interaction between these …

Order Statistics On The Spacings Between Order Statistics, Iosif Pinelis

Iosif Pinelis

No abstract provided.

The Analysis Of Protein-Bound Thiocyanate In Plasma Of Smokers And Non-Smokers As A Marker Of Cyanide Exposure, Stephanie L. Youso, Gary A. Rockwood, Brian A. Logue

Brian Logue

When cyanide is introduced into the body, it quickly transforms through a variety of chemical reactions, normally involving sulfur donors, to form more stable chemical species. Depending on the nature of the sulfur donor, cyanide may be transformed into free thiocyanate, the major metabolite of cyanide transformation, 2-amino-2-thiazoline-4-carboxylic acid or protein-bound thiocyanate (PB-SCN) adducts. Because protein adducts are generally stable in biological systems, it has been suggested that PB-SCN may have distinct advantages as a marker of cyanide exposure. In this study, plasma was analyzed from 25 smokers (chronic low-level cyanide exposure group) and 25 non-smokers for PB-SCN. The amount …

The Analysis Of Cyanide And Its Breakdown Products In Biological Samples, Brian A. Logue, Diane M. Hinkens, Steven I. Baskin, Gary A. Rockwood

Brian Logue

Cyanide is a toxic chemical that may be introduced into living organisms as a result of natural processes and/or anthropogenic uses (legal or illicit). Exposure to cyanide can be verified by analysis of cyanide or one of its breakdown products from biological samples. This verification may be important for medical, law-enforcement, military, forensic, research, or veterinary purposes. This review will discuss current bioanalytical techniques used for the verification of cyanide exposure, identify common problems associated with the analysis of cyanide and its biological breakdown products, and briefly address the metabolism and toxicokinetics of cyanide and its breakdown products in biological …

Simultaneous High-Performance Liquid Chromatography-Tandem Mass Spectrometry (Hplc-Ms-Ms) Analysis Of Cyanide And Thiocyanate From Swine Plasma, Raj K. Bhandari, Erica Manandhar, Robert P. Oda, Gary A. Rockwood, Brian A. Logue

Brian Logue

An analytical procedure for the simultaneous determination of cyanide and thiocyanate in swine plasma was developed and validated. Cyanide and thiocyanate were simultaneously analyzed by high-performance liquid chromatography tandem mass spectrometry in negative ionization mode after rapid and simple sample preparation. Isotopically labeled internal standards, Na¹³C¹⁵N and NaS¹³C¹⁵N, were mixed with swine plasma (spiked and nonspiked), proteins were precipitated with acetone, the samples were centrifuged, and the supernatant was removed and dried. The dried samples were reconstituted in 10 mM ammonium formate. Cyanide was reacted with naphthalene-2,3-dicarboxaldehyde and taurine to form N-substituted …

The Analysis Of 2-Amino-2-Thiazoline-4-Carboxylic Acid In The Plasma Of Smokers And Non-Smokers, Brian A. Logue, Wendy K. Maserek, Gary A. Rockwood, Michael W. Keebaugh, Steven I. Baskin

Brian Logue

ATCA (2-amino-2-thiazoline-4-carboxylic acid) is a promising marker to assess cyanide exposure because of several advantages of ATCA analysis over direct determination of cyanide and alternative cyanide biomarkers (i.e. stability in biological matrices, consistent recovery, and relatively small endogenous concentrations). Concentrations of ATCA in the plasma of smoking and non-smoking human volunteers were analyzed using gaschromatography mass-spectrometry to establish the feasibility of using ATCA as a marker for cyanide exposure. The levels of ATCA in plasma of smoking volunteers, 17.2 ng/ml, were found to be significantly (p < 0.001) higher than that of non-smoking volunteers, 11.8 ng/ml. Comparison of ATCA concentrations of smokers relative to nonsmokers in both urine and plasma yielded relatively similar results. The concentration ratio of ATCA for smokers versus non-smokers in plasma and urine was compared to similar literature studies of cyanide and thiocyanate, and correlations are discussed. This study supports previous evidence that ATCA can be used to determine past cyanide exposure and indicates that further studies should be pursued to validate the use of ATCA as a marker of cyanide exposure.

Organ-Distribution Of The Metabolite 2-Aminothiazoline-4-Carboxylic Acid In A Rat Model Following Cyanide Exposure, Ilona Petrikovics, David E. Thompson, Gary A. Rockwood, Brian A. Logue

Brian Logue

The reaction of cyanide (CN⁻) with cystine to produce 2-aminothiazoline-4-carboxylic acid (ATCA) is one of the independent detoxification pathways of cyanide in biological systems. In this report, in vivo production of ATCA and its distributions in plasma and organs were studied after a subcutaneous sublethal dose of 4 mg/kg body weight potassium cyanide (KCN) administration to rats. At this sublethal dose of KCN, ATCA concentration was not significantly increased in the plasma samples, however, it was found significantly increased in liver samples. These results suggested that ATCA might not be a good diagnostic biomarker in plasma for sublethal …

Determination Of The Cyanide Metabolite 2-Aminothiazoline-4-Carboxylic Acid In Urine And Plasma By Gas Chromatography–Mass Spectrometry, Brian A. Logue, Nicholas P. Kirschten, Ilona Petrikovics, Matthew A, Moser, Gary A. Rockwood, Steven I. Baskin

Brian Logue

The cyanide metabolite 2-aminothiazoline-4-carboxylic acid (ATCA) is a promising biomarker for cyanide exposure because of its stability and the limitations of direct determination of cyanide and more abundant cyanide metabolites. A simple, sensitive, and specific method based on derivatization and subsequent gas chromatography–mass spectrometry (GC–MS) analysis was developed for the identification and quantification of ATCA in synthetic urine and swine plasma. The urine and plasma samples were spiked with an internal standard (ATCA-d2), diluted, and acidified. The resulting solution was subjected to solid phase extraction on a mixed-mode cation exchange column. After elution and evaporation of the solvent, a silylating …

Determination Of Dimethyl Trisulfide In Rabbit Blood Using Stir Bar Sorptive Extraction Gas Chromatography-Mass Spectrometry, Erica Mananadhar, Nujud Maslamani, Ilona Petrikovics, Gary A. Rockwood, Brian A. Logue

Brian Logue

Cyanide poisoning by accidental or intentional exposure poses a severe health risk. The current Food and Drug Administration approved antidotes for cyanide poisoning can be effective, but each suffers from specific major limitations concerning large effective dosage, delayed onset of action, or dependence on enzymes generally confined to specific organs. Dimethyl trisulfide (DMTS), a sulfur donor that detoxifies cyanide by converting it into thiocyanate (a relatively nontoxic cyanide metabolite), is a promising next generation cyanide antidote. Although a validated analytical method to analyze DMTS from any matrix is not currently available, one will be vital for the approval of DMTS …

Determination Of Cyanide Exposure By Gas Chromatography–Mass Spectrometry Analysis Of Cyanide-Exposed Plasma Proteins, Stephanie L. Youso, Gary A. Rockwood, John A. Lee, Brian A. Logue

Brian Logue

Exposure to cyanide can occur in a variety of ways, including exposure to smoke from cigarettes or fires, accidental exposure during industrial processes, and exposure from the use of cyanide as a poison or chemical warfare agent. Confirmation of cyanide exposure is difficult because, in vivo, cyanide quickly breaks down by a number of pathways, including the formation of both free and protein-bound thiocyanate. A simple method was developed to confirm cyanide exposure by extraction of protein-bound thiocyanate moieties from cyanide-exposed plasma proteins. Thiocyanate was successfully extracted and subsequently derivatized with pentafluorobenzyl bromide for GC–MS analysis. Thiocyanate levels as low …

Cyanide Toxicokinetics: The Behavior Of Cyanide, Thiocyanate And 2-Amino-2-Thiazoline-4-Carboxylic Acid In Multiple Animal Models, Raj K. Bhandari, Robert P. Oda, Ilona Petrikovics, David E. Thompson, Matthew Brenner, Sari B. Mahon, Vikhyat S. Bebarta, Gary A. Rockwood, Brian A. Logue

Brian Logue

Cyanide causes toxic effects by inhibiting cytochrome c oxidase, resulting in cellular hypoxia and cytotoxic anoxia, and can eventually lead to death. Cyanide exposure can be verified by direct analysis of cyanide concentrations or analyzing its metabolites, including thiocyanate (SCN⁻) and 2-amino-2-thiazoline-4-carboxylic acid (ATCA) in blood. To determine the behavior of these markers following cyanide exposure, a toxicokinetics study was performed in three animal models: (i) rats (250–300 g), (ii) rabbits (3.5–4.2 kg) and (iii) swine (47–54 kg). Cyanide reached a maximum in blood and declined rapidly in each animal model as it was absorbed, distributed, metabolized and …

Wildlife Conservation, Zoos And Animal Protection: A Strategic Analysis, Andrew N. Rowan

Andrew N. Rowan, DPhil

The publication consists of the proceedings of a workshop, sponsored by the Gilman Foundation, and held in April of 1994 at the White Oak Conservation Center in Florida. About thirty participants were invited from zoos, animal protection groups and academic institutions to discuss concepts such as wild, captive and tame; animal well-being in the wild and in zoos; and protecting individuals versus conserving populations. In order to maximize the time engaged in discussion, several individuals were identified to prepare target articles which were distributed to all participants before the meeting. These articles form the main chapters in this book. Other …

The Relationship Of Animal Protection Interests To Animal Damage Management: Historic Paths, Contemporary Concerns And The Uncertain Future, John Hadidian

John Hadidian, PhD

More than a decade ago Schmidt (1989) called for consideration of animal welfare to become a "firstorder" decision rule in wildlife management concerns, including animal damage control. Although there has been movement in that direction, this clearly has not yet come to pass. This paper takes a brief look at the interests we call animal damage management, animal welfare and protection, animal rights, and environmentalism in order to speculate about their shared concerns and the uncertain future before them. Since animal damage and the management of that damage cannot be abstracted from the environmental context in which they occur, this …

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Persistent Dopants And Phase Segregation In Organolead Mixed-Halide Perovskites, Bryan A. Rosales, Long Men, Sarah D. Cady, Michael P. Hanrahan, Aaron J. Rossini, Javier Vela

Sarah Cady

Organolead mixed-halide perovskites such as CH3NH3PbX3–aX′a (X, X′ = I, Br, Cl) are interesting semiconductors because of their low cost, high photovoltaic power conversion efficiencies, enhanced moisture stability, and band gap tunability. Using a combination of optical absorption spectroscopy, powder X-ray diffraction (XRD), and, for the first time, 207Pb solid state nuclear magnetic resonance (ssNMR), we probe the extent of alloying and phase segregation in these materials. Because 207Pb ssNMR chemical shifts are highly sensitive to local coordination and electronic structure, and vary linearly with halogen electronegativity and band gap, this technique can provide the true chemical speciation and composition …

Cu2znsns4 Nanorods Doped With Tetrahedral, High Spin Transition Metal Ions: Mn2+, Co2+, And Ni2+, Michelle J. Thompson, Kyle J. Blakeney, Sarah D. Cady, Malinda D. Reichert, Joselyn Del Pilar-Albaladejo, Seth T. White, Javier Vela

Sarah Cady

Because of its useful optoelectronic properties and the relative abundance of its elements, the quaternary semiconductor Cu2ZnSnS4 (CZTS) has garnered considerable interest in recent years. In this work, we dope divalent, high spin transition metal ions (M2+ = Mn2+, Co2+, Ni2+) into the tetrahedral Zn2+ sites of wurtzite CZTS nanorods. The resulting Cu2MxZn1–xSnS4 (CMTS) nanocrystals retain the hexagonal crystalline structure, elongated morphology, and broad visible light absorption profile of the undoped CZTS nanorods. Electron paramagnetic resonance (EPR), X-ray photoelectron spectroscopy (XPS), and infrared (IR) spectroscopy help corroborate the composition and local ion environment of the doped …

Pre-Methylation Of Lignin To Improve Storage Stability Of Oil Produced By Solvent Liquefaction, Jae-Young Kim, Parinaz Hafezi-Sefat, Sarah D. Cady, Ryan G. Smith, Robert C. Brown

Sarah Cady

In this study, we methylated hydroxyl groups (phenolic hydroxyl: Phe-OH and aliphatic hydroxyl: Aliph-OH) in soda lignin (SL) prior to solvent liquefaction to improve storage stability of the resulting oil. We investigated two methylating reagents, dimethyl sulfate (DMS) and dimethyl carbonate (DMC), for selective Phe-OH and total hydroxyl group (Phe-OH and Aliph-OH) blocking. Samples of SL, DMS-SL, and DMC-SL were depolymerized into oils under supercritical ethanol (350 °C). Both methylated lignins produced higher amounts of oils and smaller amounts of char compared to untreated SL due to suppressed charring reactions. Oil produced from SL had relatively higher functional group contents …

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The Multilinear Structure Of Relu Networks, Thomas Laurent

Thomas Laurent

We study the loss surface of neural networks equipped with a hinge loss criterion and ReLU or leaky ReLU nonlinearities. Any such network defines a piecewise multilinear form in parameter space. By appealing to harmonic analysis we show that all local minima of such network are non-differentiable, except for those minima that occur in a region of parameter space where the loss surface is perfectly flat. Non-differentiable minima are therefore not technicalities or pathologies; they are heart of the problem when investigating the loss of ReLU networks. As a consequence, we must employ techniques from nonsmooth analysis to study these …

Deep Linear Networks With Arbitrary Loss: All Local Minima Are Global, Thomas Laurent

Thomas Laurent

We consider deep linear networks with arbitrary convex differentiable loss. We provide a short and elementary proof of the fact that all local minima are global minima if the hidden layers are either 1) at least as wide as the input layer, or 2) at least as wide as the output layer. This result is the strongest possible in the following sense: If the loss is convex and Lipschitz but not differentiable then deep linear networks can have sub-optimal local minima.

“Everyday” Knowledge And A New Paradigm Of Animal Research, David Fraser, Jeffrey M. Spooner, Catherine A. Schuppli

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A Geomorphic Enthalpy Method: Description And Application To The Evolution Of Fluvial-Deltas Under Sea-Level Cycles, William Anderson, Jorge Lorenzo Trueba, Vaughan Voller

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