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Book ; Online: Slide FFT on a homogeneous mesh in wafer-scale computing

van Putten, Maurice H. P. M. / Wilson, Leighton / Lavely, Adam W. / Hair, Mark

2024

Abstract: Searches for signals at low signal-to-noise ratios frequently involve the Fast Fourier Transform (FFT). For high-throughput searches, we here consider FFT on the homogeneous mesh of Processing Elements (PEs) of a wafer-scale engine (WSE). To minimize ... ...

Abstract	Searches for signals at low signal-to-noise ratios frequently involve the Fast Fourier Transform (FFT). For high-throughput searches, we here consider FFT on the homogeneous mesh of Processing Elements (PEs) of a wafer-scale engine (WSE). To minimize memory overhead in the inherently non-local FFT algorithm, we introduce a new synchronous slide operation ({\em Slide}) exploiting the fast interconnect between adjacent PEs. Feasibility of compute-limited performance is demonstrated in linear scaling of Slide execution times with varying array size in preliminary benchmarks on the CS-2 WSE. The proposed implementation appears opportune to accelerate and open the full discovery potential of FFT-based signal processing in multi-messenger astronomy. Comment: 7 pages, 6 figures
Keywords	Electrical Engineering and Systems Science - Signal Processing ; Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Data Structures and Algorithms
Subject code	004
Publishing date	2024-01-04
Publishing country	us
Document type	Book ; Online
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Article: A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.

Newman, Jonathan P / Zhang, Jie / Cuevas-López, Aarón / Miller, Nicholas J / Honda, Takato / van der Goes, Marie-Sophie H / Leighton, Alexandra H / Carvalho, Filipe / Lopes, Gonçalo / Lakunina, Anna / Siegle, Joshua H / Harnett, Mark T / Wilson, Matthew A / Voigts, Jakob

bioRxiv : the preprint server for biology

2023

Abstract: Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/ ... ...

Abstract	Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/sec) and low closed-loop latencies (<1ms) that uses a novel 0.3 mm thin tether to minimize behavioral impact. Head position and rotation are tracked in 3D and used to drive active commutation without torque measurements. ONIX can acquire from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, 3D-trackers, and other data sources. We used ONIX to perform uninterrupted, long (~7 hours) neural recordings in mice as they traversed complex 3-dimensional terrain. ONIX allowed exploration with similar mobility as non-implanted animals, in contrast to conventional tethered systems which restricted movement. By combining long recordings with full mobility, our technology will enable new progress on questions that require high-quality neural recordings during ethologically grounded behaviors.
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.30.554672
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Article ; Online: Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Daniel W. Kneller / Hui Li / Gwyndalyn Phillips / Kevin L. Weiss / Qiu Zhang / Mark A. Arnould / Colleen B. Jonsson / Surekha Surendranathan / Jyothi Parvathareddy / Matthew P. Blakeley / Leighton Coates / John M. Louis / Peter V. Bonnesen / Andrey Kovalevsky

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 11

Abstract: Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency. ...

Abstract	Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency.
Keywords	Science ; Q
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease.

Kneller, Daniel W / Li, Hui / Phillips, Gwyndalyn / Weiss, Kevin L / Zhang, Qiu / Arnould, Mark A / Jonsson, Colleen B / Surendranathan, Surekha / Parvathareddy, Jyothi / Blakeley, Matthew P / Coates, Leighton / Louis, John M / Bonnesen, Peter V / Kovalevsky, Andrey

Nature communications

2022 Volume 13, Issue 1, Page(s) 2268

Abstract: Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease ( ... ...

Abstract	Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (M
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; COVID-19 Vaccines ; Coronavirus 3C Proteases ; Cyclopropanes ; Humans ; Lactams ; Leucine/analogs & derivatives ; Nitriles ; Proline/analogs & derivatives ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; SARS-CoV-2 ; Sulfones ; Urea
Chemical Substances	Antiviral Agents ; COVID-19 Vaccines ; Cyclopropanes ; Lactams ; Nitriles ; Protease Inhibitors ; Sulfones ; narlaprevir (2857LA2O07) ; nirmatrelvir (7R9A5P7H32) ; N-(3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl)-3-(2-((((1,1-dimethylethyl)amino)carbonyl)amino)-3,3-dimethyl-1-oxobutyl)-6,6-dimethyl-3-azabicyclo(3.1.0)hexan-2-carboxamide (89BT58KELH) ; Urea (8W8T17847W) ; Proline (9DLQ4CIU6V) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Leucine (GMW67QNF9C)
Language	English
Publishing date	2022-04-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-29915-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book: The learning sciences in educational assessment

Leighton, Jacqueline P / Gierl, Mark J

the role of cognitive models

2011

Author's details	Jacqueline P. Leighton; Mark J. Gierl
Keywords	Cognition ; Educational psychology ; Educational tests and measurements
Language	English
Size	V, 270 S., Ill, 24 cm
Publisher	Cambridge Univ. Press
Publishing place	Cambridge u.a.
Document type	Book
Note	Includes bibliographical references and index
ISBN	0521122880 ; 0521194113 ; 9780521122887 ; 9780521194112
Database	Former special subject collection: coastal and deep sea fishing

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Article ; Online: Why Is This Auntminnie a Diagnostic Conundrum?: A Knowledge-Based Approach to Balo's Concentric Sclerosis From Reports of 3 Cases and Pooled Data From 68 Other Patients in the Literature.

Agarwal, Mohit / Ulmer, John L / Klein, Andrew P / Mark, Leighton P

Current problems in diagnostic radiology

2018 Volume 48, Issue 4, Page(s) 415–422

Abstract: Introduction: We came across 3 cases of Balo's concentric sclerosis (BCS). The first of these patients presented to an outside hospital and was transferred to our institution due to complications resulting from a biopsy. The other 2 patients, despite ... ...

Abstract	Introduction: We came across 3 cases of Balo's concentric sclerosis (BCS). The first of these patients presented to an outside hospital and was transferred to our institution due to complications resulting from a biopsy. The other 2 patients, despite having a characteristic imaging appearance and despite insistence on our part on the diagnosis of BCS, underwent a surgical procedure, which could have been prevented. This led us to review the available literature on BCS. Material and methods: A total of 68 patients diagnosed with BCS between 1995 and 2015 were studied and the data collected for the clinical presentation and course, imaging, spinal fluid analysis, treatment, and clinical and imaging outcome. Conclusions: A 25% surgery rate (biopsy or resection) was found in the study. We concluded that this relatively high surgery rate in this auntminnie nonsurgical disease is multifactorial; and includes factors like nonfamiliarity with the disease, anxiety on the part of patients and physicians, due to a sometimes rapidly deteriorating clinical picture; and resemblance of the disease with other entities such as tumor and infection. However, characteristic imaging appearance combined with acute or subacute presentation and dramatic improvement in clinical status after high-dose steroid chemotherapy; are highly suggestive of the disease, and can prevent unnecessary surgery.
MeSH term(s)	Adolescent ; Adrenal Cortex Hormones/therapeutic use ; Adult ; Biopsy, Needle ; Child ; Diffuse Cerebral Sclerosis of Schilder/diagnostic imaging ; Diffuse Cerebral Sclerosis of Schilder/therapy ; Female ; Hemiplegia/diagnosis ; Hemiplegia/etiology ; Humans ; Immunohistochemistry ; Magnetic Resonance Imaging/methods ; Male ; Middle Aged ; Neurosurgical Procedures/methods ; Prognosis ; Rare Diseases ; Risk Assessment ; Severity of Illness Index ; Survival Rate ; Treatment Outcome ; Young Adult
Chemical Substances	Adrenal Cortex Hormones
Language	English
Publishing date	2018-01-06
Publishing country	United States
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	198954-6
ISSN	1535-6302 ; 0363-0188
ISSN (online)	1535-6302
ISSN	0363-0188
DOI	10.1067/j.cpradiol.2017.12.008
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Book ; Online: The learning sciences in educational assessment

Leighton, Jacqueline P / Gierl, Mark J

the role of cognitive models

2011

Abstract: Identifies visual models of the knowledge and strategies students consider in the domains of reading, science and ... ...

Institution	ebrary, Inc
Author's details	Jacqueline P. Leighton, Mark J. Gierl
Abstract	Identifies visual models of the knowledge and strategies students consider in the domains of reading, science and mathematics
Keywords	Cognition ; Educational psychology ; Educational tests and measurements
Language	English
Size	Online-Ressource (v, 270 p), ill
Publisher	Cambridge University Press
Publishing place	Cambridge
Document type	Book ; Online
Note	Includes bibliographical references and index
ISBN	1283184281 ; 1283193302 ; 9780521122887 ; 9780521194112 ; 9781139092425 ; 9781283193306 ; 9781283184281 ; 0521122880 ; 0521194113 ; 1139092421
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: Prospective Cohort Study to Investigate the Safety of Preoperative Tumor Necrosis Factor Inhibitor Exposure in Patients With Inflammatory Bowel Disease Undergoing Intra-abdominal Surgery.

Gastroenterology

2022 Volume 163, Issue 1, Page(s) 204–221

Abstract: ... preoperative steroid use, and disease type), baseline variables significantly associated (P < .05 ... 2017. Current TNFi exposure was reported by 382 patients. Any infection (18.1% vs 20.2%, P = .469) and ... SSI (12.0% vs 12.6%, P = .889) rates were similar in patients currently exposed to TNFis and ...

Abstract	Background & aims: Whether preoperative treatment of inflammatory bowel disease (IBD) with tumor necrosis factor inhibitors (TNFis) increases the risk of postoperative infectious complications remains controversial. The primary aim of this study was to determine whether preoperative exposure to TNFis is an independent risk factor for postoperative infectious complications within 30 days of surgery. Methods: We conducted a multicenter prospective observational study of patients with IBD undergoing intra-abdominal surgery across 17 sites from the Crohn's & Colitis Foundation Clinical Research Alliance. Infectious complications were categorized as surgical site infections (SSIs) or non-SSIs. Current TNFi exposure was defined as use within 12 weeks of surgery, and serum was collected for drug-level analyses. Multivariable models for occurrence of the primary outcome, any infection, or SSI were adjusted by predefined covariates (age, sex, preoperative steroid use, and disease type), baseline variables significantly associated (P < .05) with any infection or SSI separately, and TNFi exposure status. Exploratory models used TNFi exposure based on serum drug concentration. Results: A total of 947 patients were enrolled from September 2014 through June 2017. Current TNFi exposure was reported by 382 patients. Any infection (18.1% vs 20.2%, P = .469) and SSI (12.0% vs 12.6%, P = .889) rates were similar in patients currently exposed to TNFis and those unexposed. In multivariable analysis, current TNFi exposure was not associated with any infection (odds ratio, 1.050; 95% confidence interval, 0.716-1.535) or SSI (odds ratio, 1.249; 95% confidence interval, 0.793-1.960). Detectable TNFi drug concentration was not associated with any infection or SSI. Conclusions: Preoperative TNFi exposure was not associated with postoperative infectious complications in a large prospective multicenter cohort.
MeSH term(s)	Cohort Studies ; Crohn Disease/complications ; Crohn Disease/drug therapy ; Crohn Disease/surgery ; Humans ; Inflammatory Bowel Diseases/complications ; Inflammatory Bowel Diseases/drug therapy ; Inflammatory Bowel Diseases/surgery ; Prospective Studies ; Retrospective Studies ; Surgical Wound Infection/epidemiology ; Surgical Wound Infection/etiology ; Tumor Necrosis Factor Inhibitors/adverse effects ; Tumor Necrosis Factor-alpha
Chemical Substances	Tumor Necrosis Factor Inhibitors ; Tumor Necrosis Factor-alpha
Language	English
Publishing date	2022-04-10
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	80112-4
ISSN	1528-0012 ; 0016-5085
ISSN (online)	1528-0012
ISSN	0016-5085
DOI	10.1053/j.gastro.2022.03.057
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Book ; Online: Identifying climate model structural inconsistencies allows for tight constraint of aerosol radiative forcing

Regayre, Leighton A. / Deaconu, Lucia / Grosvenor, Daniel P. / Sexton, David M. H. / Symonds, Christopher / Langton, Tom / Watson-Paris, Duncan / Mulcahy, Jane P. / Pringle, Kirsty J. / Richardson, Mark / Johnson, Jill S. / Rostron, John W. / Gordon, Hamish / Lister, Grenville / Stier, Philip / Carslaw, Ken S.

eISSN:

2023

Abstract: Aerosol radiative forcing uncertainty affects estimates of climate sensitivity and limits model skill at making climate projections. Efforts to improve the representations of physical processes in climate models, including extensive comparisons with ... ...

Abstract	Aerosol radiative forcing uncertainty affects estimates of climate sensitivity and limits model skill at making climate projections. Efforts to improve the representations of physical processes in climate models, including extensive comparisons with observations, have not significantly constrained the range of possible aerosol forcing values. A far stronger constraint, in particular for the lower (most-negative) bound, can be achieved using global mean energy-balance arguments based on observed changes in historical temperature. Here, we show that structural deficiencies in a climate model, revealed as inconsistencies among observationally constrained cloud properties in the model, limit the effectiveness of observational constraint of the uncertain physical processes. We sample uncertainty in 37 model parameters related to aerosols, clouds and radiation in a perturbed parameter ensemble of the UK Earth System Model and evaluate 1 million model variants (different parameter settings from Gaussian Process emulators) against satellite-derived observations over several cloudy regions. We show that it is possible to reduce the parametric uncertainty in global mean aerosol forcing by more than 50 %, constraining it to a range in close agreement with energy-balance constraints (around −1.3 to −0.1 W m −2 ). However, our analysis of a very large set of model variants exposes model internal inconsistencies that would not be apparent in a small set of model simulations. Incorporating observations associated with these inconsistencies weakens the forcing constraint because they require a wider range of parameter values to accommodate conflicting information. Our estimated aerosol forcing range is the maximum feasible constraint using our structurally imperfect model and the chosen observations. Structural model developments targeted at the identified inconsistencies would enable a larger set of observations to be used for constraint, which would then narrow the uncertainty further. Such an approach provides a rigorous ...
Subject code	551
Language	English
Publishing date	2023-02-16
Publishing country	de
Document type	Book ; Online
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Article ; Online: Cortical and Subcortical Substrates of Cranial Nerve Function.

Agarwal, Mohit / Ulmer, John L / Klein, Andrew P / Mark, Leighton P

Seminars in ultrasound, CT, and MR

2015 Volume 36, Issue 3, Page(s) 275–290

Abstract: The pivotal role of cranial nerves in a wholesome life experience cannot be overemphasized. Research has opened new avenues to understand cranial nerve function. Classical concept of strict bilateral cortical control of cranial nerves has given way to ... ...

Abstract	The pivotal role of cranial nerves in a wholesome life experience cannot be overemphasized. Research has opened new avenues to understand cranial nerve function. Classical concept of strict bilateral cortical control of cranial nerves has given way to concepts of hemispheric dominance and hemispheric lateralization. An astute Neuroradiologist should keep abreast of these concepts and help patients and referring physicians by applying this knowledge in reading images. This chapter provides an overview of cranial nerve function and latest concepts pertaining to their cortical and subcortical control.
MeSH term(s)	Brain/physiopathology ; Cranial Nerve Diseases/diagnosis ; Cranial Nerve Diseases/physiopathology ; Cranial Nerves/physiopathology ; Diagnostic Techniques, Neurological ; Functional Neuroimaging/methods ; Humans ; Magnetic Resonance Imaging/methods
Language	English
Publishing date	2015-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	1353113-x
ISSN	1558-5034 ; 0887-2171
ISSN (online)	1558-5034
ISSN	0887-2171
DOI	10.1053/j.sult.2015.05.008
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