Zackary Whitlow - Academia.edu (original) (raw)

Uploads

Papers by Zackary Whitlow

Research paper thumbnail of Modeling of Axial Rotary Drilling Dynamics as a Step Towards Drilling Automation

Day 1 Tue, March 07, 2023

Analysis of low frequency axial drilling dynamics from block velocity input to surface weight on ... more Analysis of low frequency axial drilling dynamics from block velocity input to surface weight on bit (SWOB) or differential pressure outputs, shows significant regional variation. This range in dynamics poses a robustness challenge for automated drilling control systems. Many factors influence drilling dynamics such as pipe stiffness, mud properties, tortuosity, friction, bit design, and BHA geometry. A simple analytic model representing axial drilling dynamics is described and compared to a finite element drilling model and to drilling data. The analytic model shows that axial drilling dynamics may be represented by a first-order transfer function with a time constant dependent on axial stiffness and drillabillity.

Research paper thumbnail of New mRNAs Are Preferentially Translated during Vesicular Stomatitis Virus Infection

Journal of Virology, 2007

During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while syn... more During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while synthesis of viral proteins increases. VSV infection causes inhibition of host transcription and RNA transport. Therefore, most host mRNAs in the cytoplasm of infected cells were synthesized before infection. However, viral mRNAs are synthesized throughout infection and are newer than preexisting host mRNAs. To determine if the timing of appearance of mRNAs in the cytoplasm affected their translation during VSV infection, we transfected reporter mRNAs into cells at various times relative to the time of infection and measured their rate of translation in mock- and VSV-infected cells. We found that translation of mRNAs transfected during infection was not inhibited but that translation of mRNAs transfected prior to infection was inhibited during VSV infection. Based on these data, we conclude that the timing of viral mRNA appearance in the cytoplasm is responsible, at least in part, for the p...

Research paper thumbnail of Modeling and Control of Non-Laminated Active Magnetic Thrust Bearings

Non-laminated magnetic thrust bearings exhibit reduced dynamic performance, compared to laminated... more Non-laminated magnetic thrust bearings exhibit reduced dynamic performance, compared to laminated radial bearings, due to eddy current effects. Segmented thrust bearing stators have been introduced to increase actuator performance by disrupting eddy current paths in the same manner as laminations in radial magnetic bearings. However, due to manufacturing limitations, thrust bearing stators cannot be easily segmented to the extent that they would be considered fully laminated. Therefore, eddy currents continue to affect their dynamic performance significantly. This work aims to improve the performance of non-laminated thrust active magnetic bearings through improved modeling and control design. Currently, accurate modeling of segmented stator performance relies on finite element analysis, which is a time consuming process. In this work, an analytic model of cylindrical segmented electromagnetic actuators, including eddy currents effects, is developed. The model is an extension of the analytic model for C-type electromagnetic actuators developed by Zhu et al., [1, 2]. Zhu's work on cylindrical magnetic actuators, [3, 2] is also continued in order to develop an analytic model for cylindrical electromagnetic actuators with a center hole, i.e. non-laminated active magnetic thrust bearings. All analytic models developed in this work are verified via finite element analysis. Based on analytic and finite element modeling, it is found that thrust bearing stator segmentation results in dramatic improvements in dynamic performance. With six stator cuts, and depending on the specific geometry, bandwidth from current input to force output is typically improved by more than 2-fold. The potential for dynamic performance improvements for non-laminated magnetic thrust bearings by non-linear and dynamic compensation is also investigated. Simulations using a detailed non-linear model

Research paper thumbnail of Dynamic Performance of Segmented Active Magnetic Thrust Bearings

IEEE Transactions on Magnetics, 2016

Research paper thumbnail of Recruitment of the Transcriptional Coactivator HCF-1 to Viral Immediate-Early Promoters during Initiation of Reactivation from Latency of Herpes Simplex Virus Type 1

Journal of Virology, 2009

The transcriptional coactivator host cell factor 1 (HCF-1) is critical for the expression of imme... more The transcriptional coactivator host cell factor 1 (HCF-1) is critical for the expression of immediate-early (IE) genes of the alphaherpesviruses herpes simplex virus type 1 (HSV-1) and varicella-zoster virus. HCF-1 may also be involved in the reactivation of these viruses from latency as it is sequestered in the cytoplasm of sensory neurons but is rapidly relocalized to the nucleus upon stimulation that results in reactivation. Here, chromatin immunoprecipitation assays demonstrate that HCF-1 is recruited to IE promoters of viral genomes during the initiation of reactivation, correlating with RNA polymerase II occupancy and IE expression. The data support the model whereby HCF-1 plays a pivotal role in the reactivation of HSV-1 from latency.

Research paper thumbnail of Preferential Translation of Vesicular Stomatitis Virus mRNAs Is Conferred by Transcription from the Viral Genome

Journal of Virology, 2006

Host protein synthesis is inhibited in cells infected with vesicular stomatitis virus (VSV). It h... more Host protein synthesis is inhibited in cells infected with vesicular stomatitis virus (VSV). It has been proposed that viral mRNAs are subjected to the same inhibition but are predominantly translated because of their abundance. To compare translation efficiencies of viral and host mRNAs during infection, we used an enhanced green fluorescent protein (EGFP) reporter expressed from a recombinant virus or from the host nucleus in stably transfected cells. Translation efficiency of host-derived EGFP mRNA was reduced more than threefold at eight hours postinfection, while viral-derived mRNA was translated around sevenfold more efficiently than host-derived EGFP mRNA in VSV-infected cells. To test whether mRNAs transcribed in the cytoplasm are resistant to shutoff of translation during VSV infection, HeLa cells were infected with a recombinant simian virus 5 (rSV5) that expressed GFP. Cells were then superinfected with VSV or mock superinfected. GFP mRNA transcribed by rSV5 was not resis...

Research paper thumbnail of Glucocorticoid receptor upregulation during seawater adaptation in a euryhaline teleost, the tilapia (Oreochromis mossambicus)

General and Comparative Endocrinology, 2003

Cortisol is an important seawater (SW) osmoregulatory hormone in the Mozambique tilapia (Oreochro... more Cortisol is an important seawater (SW) osmoregulatory hormone in the Mozambique tilapia (Oreochromis mossambicus), a highly euryhaline cichlid able to live in environments ranging from fresh water (FW) to salinities well in excess of full-strength seawater. Previous studies indicate that cortisol may promote SW adaptation by increasing gill chloride cell differentiation, Na(+)/K(+)-ATPase activity and subsequent excretion of excess salt following seawater acclimation. Despite cortisol's widely accepted role as a SW-adapting hormone, cortisol receptor regulation during SW acclimation is not well understood. The purpose of these studies was to determine whether the intracellular glucocorticoid receptor (GR) might be regulated in a manner consistent with cortisol's actions in SW adaptation. Saturation radioligand binding assays were conducted on gill cytoplasm preparations from fish sampled 4 and 24h and 4 and 14 days after transfer from FW to 2/3 SW or FW (control). Affinity (K(d)) of the gill GR remained constant over the timecourse, while numbers of receptors (B(max)) in SW fish were significantly elevated compared with controls at 24h and 4 days after transfer. Plasma osmolality was higher in fish transferred to SW for 24h, 4 days, and 14 days compared with those animals moved to FW. Plasma cortisol levels and hepatic cortisol binding remained constant between SW and FW fish throughout the timecourse of the salinity challenge. These studies indicate that seawater acclimation is accompanied by a specific upregulation of intracellular GR numbers in gill tissue. The lack of increase in circulating cortisol following SW adaptation may reflect enhancement of clearance of the steroid. It appears that an increase in cortisol receptors, which is closely associated with the rise in blood osmotic pressure that accompanies SW exposure, is an important component of cortisol's ability to promote SW adaptation in the tilapia.

Research paper thumbnail of New mRNAs are preferentially translated during vesicular stomatitis virus infection

During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while syn... more During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while synthesis of viral proteins increases. VSV infection causes inhibition of host transcription and RNA transport. Therefore, most host mRNAs in the cytoplasm of infected cells were synthesized before infection. However, viral mRNAs are synthesized throughout infection and are newer than preexisting host mRNAs. To determine if the timing of appearance of mRNAs in the cytoplasm affected their translation during VSV infection, we transfected reporter mRNAs into cells at various times relative to the time of infection and measured their rate of translation in mock-and VSV-infected cells. We found that translation of mRNAs transfected during infection was not inhibited but that translation of mRNAs transfected prior to infection was inhibited during VSV infection. Based on these data, we conclude that the timing of viral mRNA appearance in the cytoplasm is responsible, at least in part, for the preferential translation of VSV mRNAs. A time course measuring translation efficiencies of viral and host mRNAs showed that the translation efficiencies of viral mRNAs increased between 4 and 8 h postinfection, while translation efficiencies of host mRNAs decreased. The increased translation efficiency of viral mRNAs occurred in cells infected with an M protein mutant virus that is defective in host shutoff, demonstrating that the enhanced translation of viral mRNA is genetically separable from inhibition of translation of host mRNA.

Research paper thumbnail of Modeling of Axial Rotary Drilling Dynamics as a Step Towards Drilling Automation

Day 1 Tue, March 07, 2023

Analysis of low frequency axial drilling dynamics from block velocity input to surface weight on ... more Analysis of low frequency axial drilling dynamics from block velocity input to surface weight on bit (SWOB) or differential pressure outputs, shows significant regional variation. This range in dynamics poses a robustness challenge for automated drilling control systems. Many factors influence drilling dynamics such as pipe stiffness, mud properties, tortuosity, friction, bit design, and BHA geometry. A simple analytic model representing axial drilling dynamics is described and compared to a finite element drilling model and to drilling data. The analytic model shows that axial drilling dynamics may be represented by a first-order transfer function with a time constant dependent on axial stiffness and drillabillity.

Research paper thumbnail of New mRNAs Are Preferentially Translated during Vesicular Stomatitis Virus Infection

Journal of Virology, 2007

During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while syn... more During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while synthesis of viral proteins increases. VSV infection causes inhibition of host transcription and RNA transport. Therefore, most host mRNAs in the cytoplasm of infected cells were synthesized before infection. However, viral mRNAs are synthesized throughout infection and are newer than preexisting host mRNAs. To determine if the timing of appearance of mRNAs in the cytoplasm affected their translation during VSV infection, we transfected reporter mRNAs into cells at various times relative to the time of infection and measured their rate of translation in mock- and VSV-infected cells. We found that translation of mRNAs transfected during infection was not inhibited but that translation of mRNAs transfected prior to infection was inhibited during VSV infection. Based on these data, we conclude that the timing of viral mRNA appearance in the cytoplasm is responsible, at least in part, for the p...

Research paper thumbnail of Modeling and Control of Non-Laminated Active Magnetic Thrust Bearings

Non-laminated magnetic thrust bearings exhibit reduced dynamic performance, compared to laminated... more Non-laminated magnetic thrust bearings exhibit reduced dynamic performance, compared to laminated radial bearings, due to eddy current effects. Segmented thrust bearing stators have been introduced to increase actuator performance by disrupting eddy current paths in the same manner as laminations in radial magnetic bearings. However, due to manufacturing limitations, thrust bearing stators cannot be easily segmented to the extent that they would be considered fully laminated. Therefore, eddy currents continue to affect their dynamic performance significantly. This work aims to improve the performance of non-laminated thrust active magnetic bearings through improved modeling and control design. Currently, accurate modeling of segmented stator performance relies on finite element analysis, which is a time consuming process. In this work, an analytic model of cylindrical segmented electromagnetic actuators, including eddy currents effects, is developed. The model is an extension of the analytic model for C-type electromagnetic actuators developed by Zhu et al., [1, 2]. Zhu's work on cylindrical magnetic actuators, [3, 2] is also continued in order to develop an analytic model for cylindrical electromagnetic actuators with a center hole, i.e. non-laminated active magnetic thrust bearings. All analytic models developed in this work are verified via finite element analysis. Based on analytic and finite element modeling, it is found that thrust bearing stator segmentation results in dramatic improvements in dynamic performance. With six stator cuts, and depending on the specific geometry, bandwidth from current input to force output is typically improved by more than 2-fold. The potential for dynamic performance improvements for non-laminated magnetic thrust bearings by non-linear and dynamic compensation is also investigated. Simulations using a detailed non-linear model

Research paper thumbnail of Dynamic Performance of Segmented Active Magnetic Thrust Bearings

IEEE Transactions on Magnetics, 2016

Research paper thumbnail of Recruitment of the Transcriptional Coactivator HCF-1 to Viral Immediate-Early Promoters during Initiation of Reactivation from Latency of Herpes Simplex Virus Type 1

Journal of Virology, 2009

The transcriptional coactivator host cell factor 1 (HCF-1) is critical for the expression of imme... more The transcriptional coactivator host cell factor 1 (HCF-1) is critical for the expression of immediate-early (IE) genes of the alphaherpesviruses herpes simplex virus type 1 (HSV-1) and varicella-zoster virus. HCF-1 may also be involved in the reactivation of these viruses from latency as it is sequestered in the cytoplasm of sensory neurons but is rapidly relocalized to the nucleus upon stimulation that results in reactivation. Here, chromatin immunoprecipitation assays demonstrate that HCF-1 is recruited to IE promoters of viral genomes during the initiation of reactivation, correlating with RNA polymerase II occupancy and IE expression. The data support the model whereby HCF-1 plays a pivotal role in the reactivation of HSV-1 from latency.

Research paper thumbnail of Preferential Translation of Vesicular Stomatitis Virus mRNAs Is Conferred by Transcription from the Viral Genome

Journal of Virology, 2006

Host protein synthesis is inhibited in cells infected with vesicular stomatitis virus (VSV). It h... more Host protein synthesis is inhibited in cells infected with vesicular stomatitis virus (VSV). It has been proposed that viral mRNAs are subjected to the same inhibition but are predominantly translated because of their abundance. To compare translation efficiencies of viral and host mRNAs during infection, we used an enhanced green fluorescent protein (EGFP) reporter expressed from a recombinant virus or from the host nucleus in stably transfected cells. Translation efficiency of host-derived EGFP mRNA was reduced more than threefold at eight hours postinfection, while viral-derived mRNA was translated around sevenfold more efficiently than host-derived EGFP mRNA in VSV-infected cells. To test whether mRNAs transcribed in the cytoplasm are resistant to shutoff of translation during VSV infection, HeLa cells were infected with a recombinant simian virus 5 (rSV5) that expressed GFP. Cells were then superinfected with VSV or mock superinfected. GFP mRNA transcribed by rSV5 was not resis...

Research paper thumbnail of Glucocorticoid receptor upregulation during seawater adaptation in a euryhaline teleost, the tilapia (Oreochromis mossambicus)

General and Comparative Endocrinology, 2003

Cortisol is an important seawater (SW) osmoregulatory hormone in the Mozambique tilapia (Oreochro... more Cortisol is an important seawater (SW) osmoregulatory hormone in the Mozambique tilapia (Oreochromis mossambicus), a highly euryhaline cichlid able to live in environments ranging from fresh water (FW) to salinities well in excess of full-strength seawater. Previous studies indicate that cortisol may promote SW adaptation by increasing gill chloride cell differentiation, Na(+)/K(+)-ATPase activity and subsequent excretion of excess salt following seawater acclimation. Despite cortisol's widely accepted role as a SW-adapting hormone, cortisol receptor regulation during SW acclimation is not well understood. The purpose of these studies was to determine whether the intracellular glucocorticoid receptor (GR) might be regulated in a manner consistent with cortisol's actions in SW adaptation. Saturation radioligand binding assays were conducted on gill cytoplasm preparations from fish sampled 4 and 24h and 4 and 14 days after transfer from FW to 2/3 SW or FW (control). Affinity (K(d)) of the gill GR remained constant over the timecourse, while numbers of receptors (B(max)) in SW fish were significantly elevated compared with controls at 24h and 4 days after transfer. Plasma osmolality was higher in fish transferred to SW for 24h, 4 days, and 14 days compared with those animals moved to FW. Plasma cortisol levels and hepatic cortisol binding remained constant between SW and FW fish throughout the timecourse of the salinity challenge. These studies indicate that seawater acclimation is accompanied by a specific upregulation of intracellular GR numbers in gill tissue. The lack of increase in circulating cortisol following SW adaptation may reflect enhancement of clearance of the steroid. It appears that an increase in cortisol receptors, which is closely associated with the rise in blood osmotic pressure that accompanies SW exposure, is an important component of cortisol's ability to promote SW adaptation in the tilapia.

Research paper thumbnail of New mRNAs are preferentially translated during vesicular stomatitis virus infection

During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while syn... more During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while synthesis of viral proteins increases. VSV infection causes inhibition of host transcription and RNA transport. Therefore, most host mRNAs in the cytoplasm of infected cells were synthesized before infection. However, viral mRNAs are synthesized throughout infection and are newer than preexisting host mRNAs. To determine if the timing of appearance of mRNAs in the cytoplasm affected their translation during VSV infection, we transfected reporter mRNAs into cells at various times relative to the time of infection and measured their rate of translation in mock-and VSV-infected cells. We found that translation of mRNAs transfected during infection was not inhibited but that translation of mRNAs transfected prior to infection was inhibited during VSV infection. Based on these data, we conclude that the timing of viral mRNA appearance in the cytoplasm is responsible, at least in part, for the preferential translation of VSV mRNAs. A time course measuring translation efficiencies of viral and host mRNAs showed that the translation efficiencies of viral mRNAs increased between 4 and 8 h postinfection, while translation efficiencies of host mRNAs decreased. The increased translation efficiency of viral mRNAs occurred in cells infected with an M protein mutant virus that is defective in host shutoff, demonstrating that the enhanced translation of viral mRNA is genetically separable from inhibition of translation of host mRNA.