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  1. Article ; Online: The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations.

    Jones, Jeremy / Clark, Robert D / Lawless, Michael S / Miller, David W / Waldman, Marvin

    Journal of computer-aided molecular design

    2024  Volume 38, Issue 1, Page(s) 14

    Abstract: Computer-aided drug design has advanced rapidly in recent years, and multiple instances of in silico designed molecules advancing to the clinic have demonstrated the contribution of this field to medicine. Properly designed and implemented platforms can ... ...

    Abstract Computer-aided drug design has advanced rapidly in recent years, and multiple instances of in silico designed molecules advancing to the clinic have demonstrated the contribution of this field to medicine. Properly designed and implemented platforms can drastically reduce drug development timelines and costs. While such efforts were initially focused primarily on target affinity/activity, it is now appreciated that other parameters are equally important in the successful development of a drug and its progression to the clinic, including pharmacokinetic properties as well as absorption, distribution, metabolic, excretion and toxicological (ADMET) properties. In the last decade, several programs have been developed that incorporate these properties into the drug design and optimization process and to varying degrees, allowing for multi-parameter optimization. Here, we introduce the Artificial Intelligence-driven Drug Design (AIDD) platform, which automates the drug design process by integrating high-throughput physiologically-based pharmacokinetic simulations (powered by GastroPlus) and ADMET predictions (powered by ADMET Predictor) with an advanced evolutionary algorithm that is quite different than current generative models. AIDD uses these and other estimates in iteratively performing multi-objective optimizations to produce novel molecules that are active and lead-like. Here we describe the AIDD workflow and details of the methodologies involved therein. We use a dataset of triazolopyrimidine inhibitors of the dihydroorotate dehydrogenase from Plasmodium falciparum to illustrate how AIDD generates novel sets of molecules.
    MeSH term(s) Artificial Intelligence ; Drug Design ; Algorithms ; Evolution, Molecular
    Language English
    Publishing date 2024-03-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-024-00552-6
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  2. Article ; Online: Mind-Body Interventions for Youth with Chronic Medical Conditions: A Scoping Review of the Literature.

    Srinivasan, Roshini / McVoy, Molly / Neudecker, Mandy / Divan, Mina Kumari / Wu, Amy / Cascio, Michelle E / Dusek, Jeffery A / Miller, David W

    Journal of integrative and complementary medicine

    2024  

    Abstract: Background and purpose: ...

    Abstract Background and purpose:
    Language English
    Publishing date 2024-03-18
    Publishing country United States
    Document type Journal Article
    ISSN 2768-3613
    ISSN (online) 2768-3613
    DOI 10.1089/jicm.2023.0427
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  3. Book ; Online: Innovations in trigger and data acquisition systems for next-generation physics facilities

    Bartoldus, Rainer / Bernius, Catrin / Miller, David W.

    2022  

    Abstract: Data-intensive physics facilities are increasingly reliant on heterogeneous and large-scale data processing and computational systems in order to collect, distribute, process, filter, and analyze the ever increasing huge volumes of data being collected. ... ...

    Abstract Data-intensive physics facilities are increasingly reliant on heterogeneous and large-scale data processing and computational systems in order to collect, distribute, process, filter, and analyze the ever increasing huge volumes of data being collected. Moreover, these tasks are often performed in hard real-time or quasi real-time processing pipelines that place extreme constraints on various parameters and design choices for those systems. Consequently, a large number and variety of challenges are faced to design, construct, and operate such facilities. This is especially true at the energy and intensity frontiers of particle physics where bandwidths of raw data can exceed 100 Tb/s of heterogeneous, high-dimensional data sourced from >300M individual sensors. Data filtering and compression algorithms deployed at these facilities often operate at the level of 1 part in $10^5$, and once executed, these algorithms drive the data curation process, further highlighting the critical roles that these systems have in the physics impact of those endeavors. This White Paper aims to highlight the challenges that these facilities face in the design of the trigger and data acquisition instrumentation and systems, as well as in their installation, commissioning, integration and operation, and in building the domain knowledge and technical expertise required to do so.

    Comment: Contribution to Snowmass 2021
    Keywords High Energy Physics - Experiment ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Systems and Control ; Physics - Instrumentation and Detectors
    Subject code 306
    Publishing date 2022-03-14
    Publishing country us
    Document type Book ; Online
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  4. Book ; Online: PELICAN

    Bogatskiy, Alexander / Hoffman, Timothy / Miller, David W. / Offermann, Jan T.

    Permutation Equivariant and Lorentz Invariant or Covariant Aggregator Network for Particle Physics

    2022  

    Abstract: Many current approaches to machine learning in particle physics use generic architectures that require large numbers of parameters and disregard underlying physics principles, limiting their applicability as scientific modeling tools. In this work, we ... ...

    Abstract Many current approaches to machine learning in particle physics use generic architectures that require large numbers of parameters and disregard underlying physics principles, limiting their applicability as scientific modeling tools. In this work, we present a machine learning architecture that uses a set of inputs maximally reduced with respect to the full 6-dimensional Lorentz symmetry, and is fully permutation-equivariant throughout. We study the application of this network architecture to the standard task of top quark tagging and show that the resulting network outperforms all existing competitors despite much lower model complexity. In addition, we present a Lorentz-covariant variant of the same network applied to a 4-momentum regression task.
    Keywords High Energy Physics - Phenomenology ; Computer Science - Machine Learning ; High Energy Physics - Experiment
    Publishing date 2022-11-01
    Publishing country us
    Document type Book ; Online
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  5. Article: Dietary gamma-aminobutyric acid supplementation does not mitigate stress responses in weaner pigs given adrenocorticotropic hormone and experimentally infected with enterotoxigenic Escherichia coli

    Sterndale, Samantha O / Miller, David W / Mansfield, Josephine P / Kim, Jae Cheol / Pluske, John R

    Livestock science. 2022 Feb., v. 256

    2022  

    Abstract: Gamma-aminobutyric acid (GABA) is a non-protein amino acid, a major inhibitory neurotransmitter in the central nervous system that stimulates feed intake and inhibits the hypothalamic-pituitary-adrenal (HPA) axis. We hypothesised that: (1) GABA ... ...

    Abstract Gamma-aminobutyric acid (GABA) is a non-protein amino acid, a major inhibitory neurotransmitter in the central nervous system that stimulates feed intake and inhibits the hypothalamic-pituitary-adrenal (HPA) axis. We hypothesised that: (1) GABA supplementation in the diet would reduce markers of the stress response in weaned pigs injected with adrenocorticotropic hormone (ACTH) and inoculated with enterotoxigenic Escherichia coli (ETEC); and (2) this reduction in stress responses would improve performance after weaning. A total of 96 newly-weaned male pigs (Large White x Landrace) were stratified into a two by four factorial arrangement with respective factors being (i) with/without ACTH injection and ETEC infection (challenge versus non-challenge) and (ii) four dietary GABA levels (0, 60, 80, 100 mg/kg). On days 8 and 9 after weaning, piglets were orally inoculated with ETEC (0.8 ml via two gelatinized capsules; serotype O149; F4) as well as being given 5 IU ACTH intramuscularly (IM), which occurred an hour before ETEC inoculation. Pigs in the non-challenged group were given IM 0.2 mL of sterile saline and sham infected with two capsules of PBS. Faecal consistency scores were recorded daily, pigs and feed were weighed weekly to determine performance and blood samples were collected at days 6, 9 and 14. GABA supplementation did not reduce plasma cortisol. However challenged pigs had higher levels compared to the non-challenge group at day 9 (P = 0.001). Performance was not influenced by GABA supplementation (P > 0.05). Between days 8–14, 54.3% of pigs in the challenge group developed diarrhoea compared to 5.6% in the non-challenged group (P = 0.001). These data indicate that eliciting both an ETEC infection challenge and an acute stress response after weaning initiated an endocrine stress response. The use of GABA in feed did not reduce this stress response, reduce diarrhoea or improve production performance.
    Keywords Large White ; central nervous system ; corticotropin ; cortisol ; diarrhea ; dietary supplements ; enterotoxigenic Escherichia coli ; feed intake ; gamma-aminobutyric acid ; gelatinization ; landraces ; males ; neurotransmitters ; serotypes ; stress response ; weanlings
    Language English
    Dates of publication 2022-02
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2226176-X
    ISSN 1878-0490 ; 1871-1413
    ISSN (online) 1878-0490
    ISSN 1871-1413
    DOI 10.1016/j.livsci.2021.104818
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  6. Article: The use of dexamethasone to attenuate stress responses of post-weaned pigs exposed to a mixing challenge

    Sterndale, Samantha O / Miller, David W / Mansfield, Josephine P / Kim, Jae Cheol / Pluske, John R

    Livestock science. 2022 Jan., v. 255

    2022  

    Abstract: Weaning piglets usually involves mixing of non-littermate pigs into a new environment that causes social and physical stress due to the vigorous fighting and contributes to the post-weaning growth check. Dexamethasone (DEX) is a synthetic corticosteroid ... ...

    Abstract Weaning piglets usually involves mixing of non-littermate pigs into a new environment that causes social and physical stress due to the vigorous fighting and contributes to the post-weaning growth check. Dexamethasone (DEX) is a synthetic corticosteroid shown to attenuate stress responses via negative feedback on the hypothalamic-pituitary-adrenal (HPA) axis. The hypothesis tested in this study was that DEX given before the imposition of a stressful challenge, namely mixing non-littermate pigs, would ameliorate the stress response, sustain gastrointestinal tract (GIT) function, and increase growth performance. At weaning (d0), 96 male piglets (6.5 ± 0.9 kg) were allocated into pens with their littermates (4/pen) and allowed to acclimate for 14 days, at which point they were allocated to a 2 × 2 factorial arrangement of treatments from d14 to d28 with the respective factors being (i) treatment (administration of DEX or saline; DEX v SAL) and (ii) group type (mixing of non-littermate pigs or pigs kept as littermates; MIXED v NonMIXED). The study finished on d28 after weaning. On d12 and 13, pigs in the DEX treatment were given intramuscular injections of 0.2 mg/kg DEX at 0600 h and 1800 h (total 4 doses/pig; 0.8 mg/kg), while pigs in the control treatment were given the same volume of SAL. On d14 at 0800 h, 48 pigs were mixed with non-littermates and 48 pigs remained with their littermates. Individual body weights were measured weekly, and blood was collected at 1200 h on d11, d14 (4 h after mixing), and d16. On d14 and 16, four pigs per treatment group (n = 16) were given an intra-gastric dose of a solution containing 2.5 mL/kg 20% mannitol and 0.036 g/kg Co-EDTA to test gastrointestinal permeability. Plasma cortisol was greater (P = 0.001) in MIXED pigs at both 4 h after mixing (d14) and 2d after mixing (d16). Pigs given DEX tended (P = 0.100) to have a reduced cortisol concentration at day 14 regardless of the mixing treatment. The concentration of d-mannitol in plasma was reduced (P = 0.024) in pigs dosed with DEX compared to control pigs two days after mixing (d16). Growth performance was not improved by DEX treatment during the study. These results suggest that DEX has the ability to reduce some plasma stress markers and reduced intestinal permeability, possibly due to its anti-inflammatory properties, although DEX treatment did not improve performance.
    Keywords cortisol ; dexamethasone ; digestive tract ; growth performance ; intestines ; males ; mannitol ; permeability ; stress response
    Language English
    Dates of publication 2022-01
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2226176-X
    ISSN 1878-0490 ; 1871-1413
    ISSN (online) 1878-0490
    ISSN 1871-1413
    DOI 10.1016/j.livsci.2021.104785
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  7. Book ; Online: Explainable Equivariant Neural Networks for Particle Physics

    Bogatskiy, Alexander / Hoffman, Timothy / Miller, David W. / Offermann, Jan T. / Liu, Xiaoyang

    PELICAN

    2023  

    Abstract: PELICAN is a novel permutation equivariant and Lorentz invariant or covariant aggregator network designed to overcome common limitations found in architectures applied to particle physics problems. Compared to many approaches that use non-specialized ... ...

    Abstract PELICAN is a novel permutation equivariant and Lorentz invariant or covariant aggregator network designed to overcome common limitations found in architectures applied to particle physics problems. Compared to many approaches that use non-specialized architectures that neglect underlying physics principles and require very large numbers of parameters, PELICAN employs a fundamentally symmetry group-based architecture that demonstrates benefits in terms of reduced complexity, increased interpretability, and raw performance. We present a comprehensive study of the PELICAN algorithm architecture in the context of both tagging (classification) and reconstructing (regression) Lorentz-boosted top quarks, including the difficult task of specifically identifying and measuring the $W$-boson inside the dense environment of the Lorentz-boosted top-quark hadronic final state. We also extend the application of PELICAN to the tasks of identifying quark-initiated vs.~gluon-initiated jets, and a multi-class identification across five separate target categories of jets. When tested on the standard task of Lorentz-boosted top-quark tagging, PELICAN outperforms existing competitors with much lower model complexity and high sample efficiency. On the less common and more complex task of 4-momentum regression, PELICAN also outperforms hand-crafted, non-machine learning algorithms. We discuss the implications of symmetry-restricted architectures for the wider field of machine learning for physics.

    Comment: 50 pages, 34 figures, 12 tables
    Keywords High Energy Physics - Phenomenology ; Computer Science - Machine Learning ; High Energy Physics - Experiment
    Subject code 004
    Publishing date 2023-07-31
    Publishing country us
    Document type Book ; Online
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  8. Article: Ability of different assay platforms to measure renal biomarker concentrations during ischaemia-reperfusion acute kidney injury in dogs

    Davis, Jennifer / Rossi, Gabriele / Miller, David W / Cianciolo, Rachel E / Raisis, Anthea L

    Research in veterinary science. 2021 Mar., v. 135

    2021  

    Abstract: Several protein biomarkers have been shown to be useful for the early diagnosis of acute kidney injury (AKI) in animals and people. Multiplex assays for measurement of a panel of renal biomarkers in canine samples have recently become available. This ... ...

    Abstract Several protein biomarkers have been shown to be useful for the early diagnosis of acute kidney injury (AKI) in animals and people. Multiplex assays for measurement of a panel of renal biomarkers in canine samples have recently become available. This study compared the use of two such assays, versus previously validated ELISAs, to measure five biomarkers in canine samples during ischaemia-reperfusion (IR) AKI. Blood and urine was collected from six male anaesthetised greyhounds that underwent 1-h of renal ischaemia (severe hypotension induced by acute haemorrhage) and 2-h of reperfusion (intravenous fluid resuscitation). Histology confirmed presence of acute tubular injury at 2 h of reperfusion. Concentrations of clusterin, cystatin C, kidney-injury molecule 1 (KIM-1), monocyte chemoattractant protein 1, and neutrophil gelatinase-associated lipocalin (NGAL) at baseline and following IR, measured by two different multiplex assays and previously-validated single analyte immunoassays, were compared. Only NGAL was significantly elevated following IR with all assays investigated. Whether concentrations of the other four biomarkers were significantly increased following IR depended on the assay used. Concentrations of cystatin C and KIM-1 measured with the multiplex assays were of a vast magnitude lower than those measured with the corresponding single analyte ELISAs. We conclude that further validation is required before these assays can reliably be used to measure AKI biomarkers in canine samples.
    Keywords acute kidney injury ; biomarkers ; chemokine CCL2 ; dogs ; early diagnosis ; hemorrhage ; histology ; hypotension ; intravenous injection ; ischemia ; males ; neutrophils ; research ; urine ; veterinary medicine
    Language English
    Dates of publication 2021-03
    Size p. 547-554.
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 840961-4
    ISSN 1532-2661 ; 0034-5288
    ISSN (online) 1532-2661
    ISSN 0034-5288
    DOI 10.1016/j.rvsc.2020.11.005
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  9. Article: Analytical validation and reference intervals for a commercial multiplex assay to measure five novel biomarkers for acute kidney injury in canine urine

    Davis, Jennifer / Raisis, Anthea L. / Miller, David W. / Hosgood, Giselle L. / Rossi, Gabriele

    Research in veterinary science. 2021 Oct., v. 139

    2021  

    Abstract: Novel urinary biomarkers are increasingly utilized for the diagnosis of acute kidney injury (AKI) in dogs. Magnetic-bead based immunoassays for the simultaneous measurement of multiple biomarkers represent a potentially efficient and cost effective tool ... ...

    Abstract Novel urinary biomarkers are increasingly utilized for the diagnosis of acute kidney injury (AKI) in dogs. Magnetic-bead based immunoassays for the simultaneous measurement of multiple biomarkers represent a potentially efficient and cost effective tool for investigators; however there is limited data to support their reliable use in dogs. Analytical validation of a commercial multiplex assay for the measurement of five AKI biomarkers: clusterin, cystatin C, kidney-injury molecule 1 (KIM-1), monocyte chemoattractant protein 1 and neutrophil gelatinase-associated lipocalin (NGAL) in canine urine was performed. The effect of pre-analytical factors including potential interfering substances and sample storage methods were investigated. Urine from 110 healthy dogs was used to determine reference intervals for each biomarker measured, according to American Society of Veterinary Clinical Pathology guidelines. Additionally, urine from 21 dogs with pyuria was used to evaluate the impact of pyuria on biomarker concentration.The assay performed with acceptable accuracy and precision for the measurement of NGAL only. Clinically relevant urine concentrations of bilirubin, haemoglobin, and synthetic colloid solutions led to interference (mean percentage difference > +/− 15% compared to control) with measurement of all or some of the biomarkers. All biomarkers were stable in urine stored at 20–22 °C for 2 h, 4 °C for 12 h, or -20 °C for 6 months. Reference intervals could not be established for KIM-1 due to unacceptable measurement imprecision (intra- and inter assay coefficient of variation 45% and 20% respectively). Urine NGAL concentration was significantly elevated in pyuria (P < 0.001).
    Keywords acute kidney injury ; bilirubin ; biomarkers ; chemokine CCL2 ; cost effectiveness ; dogs ; hemoglobin ; neutrophils ; research ; urine ; veterinary medicine
    Language English
    Dates of publication 2021-10
    Size p. 78-86.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 840961-4
    ISSN 1532-2661 ; 0034-5288
    ISSN (online) 1532-2661
    ISSN 0034-5288
    DOI 10.1016/j.rvsc.2021.07.009
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  10. Article ; Online: Validation of a commercial magnetic bead-based multiplex assay for 5 novel biomarkers of acute kidney injury in canine serum.

    Davis, Jennifer / Raisis, Anthea L / Miller, David W / Rossi, Gabriele

    Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc

    2020  Volume 32, Issue 5, Page(s) 656–663

    Abstract: Interest is growing in measurement of novel biomarkers for the diagnosis of acute kidney injury. Multiplex assays may provide a rapid and cost-effective way of measurement; however, sparse information is published regarding their use in dogs. We aimed to ...

    Abstract Interest is growing in measurement of novel biomarkers for the diagnosis of acute kidney injury. Multiplex assays may provide a rapid and cost-effective way of measurement; however, sparse information is published regarding their use in dogs. We aimed to validate a commercial magnetic bead-based assay for 5 biomarkers: clusterin (Clus), cystatin C (CysC), kidney injury molecule 1 (KIM-1), monocyte chemoattractant protein 1 (MCP-1), and neutrophil gelatinase-associated lipocalin (NGAL). Intra- and inter-assay imprecision, linearity under dilution (LUD), spike recovery (S-R), and hemoglobin interference were evaluated using serum from healthy and diseased dogs. Additionally, the effect of sample type (serum vs. plasma) was investigated. All values for Clus and MCP-1 were outside the assay's measurable range. Intra- and inter-assay precision were acceptable for NGAL (CVs 8.8% and 13.2%, respectively). Regression analysis of LUD and S-R indicated good linearity for CysC and NGAL. Hemolysis did not affect measurement of any biomarker. Measured concentrations of CysC (
    MeSH term(s) Acute Kidney Injury/diagnosis ; Acute Kidney Injury/veterinary ; Animals ; Biomarkers/blood ; Dog Diseases/diagnosis ; Dogs ; Female ; Immunoassay/methods ; Immunoassay/veterinary ; Male
    Chemical Substances Biomarkers
    Language English
    Publishing date 2020-07-05
    Publishing country United States
    Document type Journal Article ; Validation Study
    ZDB-ID 287603-6
    ISSN 1943-4936 ; 1040-6387
    ISSN (online) 1943-4936
    ISSN 1040-6387
    DOI 10.1177/1040638720939520
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