Accelerating Genome Quantification in FPGA

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Description
The growth in speed and density of programmable logic devices, such as Field programmable gate arrays (FPGA), enables sophisticated designs to be created within a short time frame. The flexibility of a programmable device alleviates the difficulty of the integration

The growth in speed and density of programmable logic devices, such as Field programmable gate arrays (FPGA), enables sophisticated designs to be created within a short time frame. The flexibility of a programmable device alleviates the difficulty of the integration of a design with a wide range of components on a single chip. FPGAs bring both performance and power efficiency, especially for compute or data-intensive applications. Efficient and accurate mRNA quantification is an essential step for molecular signature identification, disease outcome prediction, and drug development, which is a typical compute- and data-intensive compute workload. In this work, I propose to accelerate mRNA quantification with FPGA implementation. I analyze the performance of mRNA Quantification with FPGA, which shows better or similar performance compared to that of CPU implementation.
Date Created
2022
Agent

Processing-in-Memory for Data-Intensive Applications, From Device to Algorithm

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Description
Over the past decades, the amount of data required to be processed and analyzed by computing systems has been increasing dramatically to exascale (10^18 bytes/s or ops). However, modern computing platforms' inability to deliver both energy-efficient and high-performance computing solutions

Over the past decades, the amount of data required to be processed and analyzed by computing systems has been increasing dramatically to exascale (10^18 bytes/s or ops). However, modern computing platforms' inability to deliver both energy-efficient and high-performance computing solutions leads to a gap between meets and needs, especially in resource-constraint Internet of Things (IoT) devices. Unfortunately, such a gap will keep widening mainly due to limitations in both devices and architectures. With this motivation, this dissertation's focus is on cross-layer (device/circuit/architecture/application) co-design of energy-efficient and high-performance Processing-in-Memory (PIM) platforms for implementing complex big data applications, i.e., deep learning, bioinformatics, graph processing tasks, and data encryption. The dissertation shows how to leverage innovations from device, circuit, and architecture to integrate memory and logic to break the existing memory and power walls and dramatically increase computing efficiency of today’s non-Von-Neumann computing systems.The proposed PIM platforms transform current volatile and non-volatile random access memory arrays to computational units capable of working as both memory and low-area-overhead, massively parallel, fast, reconfigurable in-memory logic. Instead of integrating complex logic units in cost-sensitive memory, the explored designs exploit hardware-friendly bit-line computing methods to implement complete Boolean logic functions between operands within a memory array in a reduced clock cycle, overcoming the multi-cycle logic issue in modern PIM platforms. Besides, new customized in-memory algorithms and mapping methods are developed to convert the crucial iteratively-used big data application's functions to bit-wise PIM-supported logic. To quantitatively analyze the performance of various PIM platforms running big data applications, a generic and comprehensive evaluation framework is presented. The overall system computing performance (throughput, latency, energy efficiency) for each application is explored through the developed framework. The device-to-algorithm co-simulation results on neural network acceleration demonstrate that the proposed platforms can obtain 36.8× higher energy-efficiency and 22× speed-up compared to state-of-the-art Graphics Processing Unit (GPU). In accelerating bioinformatics tasks such as biological sequence alignment, the presented PIM designs result in ~2×, 43.8×, 458× more throughput per Watt compared to state-of-the-art Application-Specific Integrated Circuit (ASIC), Field-Programmable Gate Array (FPGA), and GPU platforms, respectively.
Date Created
2021
Agent

Does a Chief Audit Executive Matter? Evidence from Corporate Disclosure of the Position

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Description
A Chief Audit Executive (CAE) is the leader of a company’s internal audit function. Because there is no mandated disclosure requirement for the internal audit structure, little is understood about the influence of a CAE on a company. Following the

A Chief Audit Executive (CAE) is the leader of a company’s internal audit function. Because there is no mandated disclosure requirement for the internal audit structure, little is understood about the influence of a CAE on a company. Following the logic that a CAE disclosed in SEC filings is more influential in a company’s oversight function, I identify an influential CAE using the disclosure of the role. I then examine the association between an influential CAE and monitoring outcomes. Using data hand collected from SEC filings for S&P 1500 companies from 2004 to 2015, I find companies that have an influential CAE are generally larger, older, and have a larger corporate board. More importantly, I find that an influential CAE in NYSE-listed companies is associated with higher internal control quality. This association is stronger for companies that reference a CAE’s direct interaction with the audit committee. This study provides an initial investigation into a common, but little understood position in corporate oversight.
Date Created
2019
Agent

Antigen 85B Peptidomic Analysis Allows Species-Specific Mycobacterial Identification

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Description

Background: Nontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined whether mass spectrometry analysis of an abundantly secreted mycobacterial

Background: Nontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined whether mass spectrometry analysis of an abundantly secreted mycobacterial antigen could identify specific NTM species.

Methods: We analyzed predicted tryptic peptides of the major mycobacterial antigen Ag85B for their capacity to distinguish Mycobacterium tuberculosis and three NTM species responsible for the majority of pulmonary infections caused by slow-growing mycobacterial species. Next, we analyzed trypsin-digested culture supernatants of these four mycobacterial species by liquid chromatography–tandem mass spectrometry (LC–MS/MS) to detect candidate species-specific Ag85B peptides, the identity of which were validated by LC–MS/MS performed in parallel reaction monitoring mode.

Results: Theoretical tryptic digests of the Ag85B proteins of four common mycobacterial species produced peptides with distinct sequences, including two peptides that could each identify the species origin of each Ag85B protein. LC–MS/MS analysis of trypsinized culture supernatants of these four species detected one of these species-specific signature peptides in each sample. Subsequent LC–MS/MS analyses confirmed these results by targeting these species-specific Ag85B peptides.

Conclusions: LC–MS/MS analysis of Ag85B peptides from trypsin-digested mycobacterial culture supernatants can rapidly detect and identify common mycobacteria responsible for most pulmonary infections caused by slow-growing mycobacteria, and has the potential to rapidly diagnose pulmonary infections caused by these mycobacteria through direct analysis of clinical specimens.

Date Created
2018-01-08
Agent

Time Domain Strain/Stress Reconstruction Based on Empirical Mode Decomposition: Numerical Study and Experimental Validation

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Description

Structural health monitoring has been studied by a number of researchers as well as various industries to keep up with the increasing demand for preventive maintenance routines. This work presents a novel method for reconstruct prompt, informed strain/stress responses at

Structural health monitoring has been studied by a number of researchers as well as various industries to keep up with the increasing demand for preventive maintenance routines. This work presents a novel method for reconstruct prompt, informed strain/stress responses at the hot spots of the structures based on strain measurements at remote locations. The structural responses measured from usage monitoring system at available locations are decomposed into modal responses using empirical mode decomposition. Transformation equations based on finite element modeling are derived to extrapolate the modal responses from the measured locations to critical locations where direct sensor measurements are not available. Then, two numerical examples (a two-span beam and a 19956-degree of freedom simplified airfoil) are used to demonstrate the overall reconstruction method. Finally, the present work investigates the effectiveness and accuracy of the method through a set of experiments conducted on an aluminium alloy cantilever beam commonly used in air vehicle and spacecraft. The experiments collect the vibration strain signals of the beam via optical fiber sensors. Reconstruction results are compared with theoretical solutions and a detailed error analysis is also provided.

Date Created
2016-08-16
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Effects of Carpal Tunnel Syndrome on Dexterous Manipulation Are Grip Type-Dependent

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Description

Carpal tunnel syndrome (CTS) impairs sensation of a subset of digits. Although the effects of CTS on manipulation performed with CTS-affected digits have been studied using precision grip tasks, the extent to which CTS affects multi-digit force coordination has only

Carpal tunnel syndrome (CTS) impairs sensation of a subset of digits. Although the effects of CTS on manipulation performed with CTS-affected digits have been studied using precision grip tasks, the extent to which CTS affects multi-digit force coordination has only recently been studied. Whole-hand manipulation studies have shown that CTS patients retain the ability to modulate multi-digit forces to object mass, mass distribution, and texture. However, CTS results in sensorimotor deficits relative to healthy controls, including significantly larger grip force and lower ability to balance the torques generated by the digits. Here we investigated the effects of CTS on multi-digit force modulation to object weight when manipulating an object with a variable number of fingers. We hypothesized that CTS patients would be able to modulate digit forces to object weight. However, as different grip types involve the exclusive use of CTS-affected digits (‘uniform’ grips) or a combination of CTS-affected and non-affected digits (‘mixed’ grips), we addressed the question of whether ‘mixed’ grips would reduce or worsen CTS-induced force coordination deficits. The former scenario would be due to adding digits with intact tactile feedback, whereas the latter scenario might occur due to a potentially greater challenge for the central nervous system of integrating ‘noisy’ and intact tactile feedback. CTS patients learned multi-digit force modulation to object weight regardless of grip type. Although controls exerted the same total grip force across all grip types, patients exerted significantly larger grip force than controls but only for manipulations with four and five digits. Importantly, this effect was due to CTS patients’ inability to change the finger force distribution when adding the ring and little fingers. These findings suggest that CTS primarily challenges sensorimotor integration processes for dexterous manipulation underlying the coordination of CTS-affected and non-affected digits.

Date Created
2013-01-10
Agent

Effects of Carpal Tunnel Syndrome on Adaptation of Multi-Digit Forces to Object Weight for Whole-Hand Manipulation

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Description

The delicate tuning of digit forces to object properties can be disrupted by a number of neurological and musculoskeletal diseases. One such condition is Carpal Tunnel Syndrome (CTS), a compression neuropathy of the median nerve that causes sensory and motor

The delicate tuning of digit forces to object properties can be disrupted by a number of neurological and musculoskeletal diseases. One such condition is Carpal Tunnel Syndrome (CTS), a compression neuropathy of the median nerve that causes sensory and motor deficits in a subset of digits in the hand. Whereas the effects of CTS on median nerve physiology are well understood, the extent to which it affects whole-hand manipulation remains to be addressed. CTS affects only the lateral three and a half digits, which raises the question of how the central nervous system integrates sensory feedback from affected and unaffected digits to plan and execute whole-hand object manipulation. We addressed this question by asking CTS patients and healthy controls to grasp, lift, and hold a grip device (445, 545, or 745 g) for several consecutive trials. We found that CTS patients were able to successfully adapt grip force to object weight. However, multi-digit force coordination in patients was characterized by lower discrimination of force modulation to lighter object weights, higher across-trial digit force variability, the consistent use of excessively large digit forces across consecutive trials, and a lower ability to minimize net moments on the object. Importantly, the mechanical requirement of attaining equilibrium of forces and torques caused CTS patients to exert excessive forces at both CTS-affected digits and digits with intact sensorimotor capabilities. These findings suggest that CTS-induced deficits in tactile sensitivity interfere with the formation of accurate sensorimotor memories of previous manipulations. Consequently, CTS patients use compensatory strategies to maximize grasp stability at the expense of exerting consistently larger multi-digit forces than controls. These behavioral deficits might be particularly detrimental for tasks that require fine regulation of fingertip forces for manipulating light or fragile objects.

Date Created
2011-11-16
Agent

Effects of Carpal Tunnel Syndrome on Adaptation of Multi-Digit Forces to Object Mass Distribution for Whole-Hand Manipulation

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Description

Background: Carpal tunnel syndrome (CTS) is a compression neuropathy of the median nerve that results in sensorimotor deficits in the hand. Until recently, the effects of CTS on hand function have been studied using mostly two-digit grip tasks. The purpose of

Background: Carpal tunnel syndrome (CTS) is a compression neuropathy of the median nerve that results in sensorimotor deficits in the hand. Until recently, the effects of CTS on hand function have been studied using mostly two-digit grip tasks. The purpose of this study was to investigate the coordination of multi-digit forces as a function of object center of mass (CM) during whole-hand grasping.

Methods: Fourteen CTS patients and age- and gender-matched controls were instructed to grasp, lift, hold, and release a grip device with five digits for seven consecutive lifts while maintaining its vertical orientation. The object CM was changed by adding a mass at different locations at the base of the object. We measured forces and torques exerted by each digit and object kinematics and analyzed modulation of these variables to object CM at object lift onset and during object hold. Our task requires a modulation of digit forces at and after object lift onset to generate a compensatory moment to counteract the external moment caused by the added mass and to minimize object tilt.

Results: We found that CTS patients learned to generate a compensatory moment and minimized object roll to the same extent as controls. However, controls fully exploited the available degrees of freedom (DoF) in coordinating their multi-digit forces to generate a compensatory moment, i.e., digit normal forces, tangential forces, and the net center of pressure on the finger side of the device at object lift onset and during object hold. In contrast, patients modulated only one of these DoFs (the net center of pressure) to object CM by modulating individual normal forces at object lift onset. During object hold, however, CTS patients were able to modulate digit tangential force distribution to object CM.

Conclusions: Our findings suggest that, although CTS did not affect patients’ ability to perform our manipulation task, it interfered with the modulation of specific grasp control variables. This phenomenon might be indicative of a lower degree of flexibility of the sensorimotor system in CTS to adapt to grasp task conditions.

Date Created
2012-11-21
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