title: In Vivo computation - Where computing meets nanosystem for smart tumor biosensing

authors: Ali, Muhammad

subjects: thesis with publication

abstract: According to World Health Organization, 13.1 million people will die in the world just because of cancer by 2030. Early tumor detection is very crucial to saving the world from this alarming mortality rate. However, it is an insurmountable challenge for the existing medical imaging techniques with limited imaging resolution to detect microscopic tumors. Hence, the need of the hour is to explore novel cross-disciplinary strategies to solve this problem. The rise of nanotechnologies provides a strong belief to solve complex medical problems such as early tumor detection. Nanoparticles with sizes ranging between 1-100 nanometers can be used as contrast agents. Their small sizes enable them to leak out of blood vessels and accumulate within tumors. Moreover, their chemical, optical, magnetic and electronic properties also change at nanoscale, which make them an ideal probing agent to spatially highlight the tumor site. Though, using nanoparticles to target malignant tumors is a promising concept, only 0.7% of the injected nanoparticles reach the tumor according to the statistical results of last 10 years.

In PhD work, we proposed novel in vivo computational frameworks for fast, accurate and robust nanobiosensing. Specifically, the peritumoral region corresponds to the “objective function”; the tumor is the “global optimum”; the region of interest is the “domain” of the objective function; and the nanoswimmers are the “computational agents” (i.e., guesses or optimization variables). First, in externally manipulable in vivo computation, nanoswimmers are used as contrast agents to probe the region of interest. The observable characteristics of these nanoswimmers, under the influence of tumor-induced biological gradients, are utilized by the external tracking system to steer nanoswimmers towards the possible tumor direction. To take it one step ahead, we provide solutions to the real-life constraints of in vivo natural computation such as uniformity of the external steering force and finite life span of the nanoswimmers. To overcome these challenges, we propose a multi-estimate-fusion strategy to obtain a common steering direction for the swarm of nanoswimmers and an iterative memory-driven gradient descent optimization strategy for faster tumor sensitization.

Next, we proposed a parallel framework called autonomous in vivo computation, where the tumor sensitization is highly scalable and tracking-free. We demonstrate that the tumor-triggered biophysical gradients can be leveraged by nanoparticles to collectively move toward the potential tumor hypoxic regions without the aid of any external intervention. Although individual nanoparticles have no target-directed locomotion ability due to limited communication and computation capability, we showed that once passive collaboration is achieved, they can successfully avoid obstacles and detect the tumor.

Finally, to address the respective limitations of externally manipulable and autonomous settings such as constant monitoring and slow detection, we proposed a semi-autonomous in vivo computational framework. We showed that the spot sampling strategy for an autonomous swarm of nanoswimmers can achieve faster tumor sensitization in complex environments. This approach makes the swarm highly scalable along with giving it the freedom from constant monitoring.

The performance of the aforementioned tumor sensitization frameworks is evaluated through comprehensive in silico experiments that mimic the realistic targeting processes in externally manipulable, self-regulatable and semi-autonomous settings. The efficacies of the proposed frameworks are demonstrated through numerical simulations that incorporate various physical constraints with respect to controlling and steering of computational agents, their motion in discretized vascular networks and their motion under the influence of disturbance and noise.

text: In Vivo computation - Where computing meets nanosystem for smart tumor biosensing According to World Health Organization, 13.1 million people will die in the world just because of cancer by 2030. Early tumor detection is very crucial to saving the world from this alarming mortality rate. However, it is an insurmountable challenge for the existing medical imaging techniques with limited imaging resolution to detect microscopic tumors. Hence, the need of the hour is to explore novel cross-disciplinary strategies to solve this problem. The rise of nanotechnologies provides a strong belief to solve complex medical problems such as early tumor detection. Nanoparticles with sizes ranging between 1-100 nanometers can be used as contrast agents. Their small sizes enable them to leak out of blood vessels and accumulate within tumors. Moreover, their chemical, optical, magnetic and electronic properties also change at nanoscale, which make them an ideal probing agent to spatially highlight the tumor site. Though, using nanoparticles to target malignant tumors is a promising concept, only 0.7% of the injected nanoparticles reach the tumor according to the statistical results of last 10 years.

In PhD work, we proposed novel in vivo computational frameworks for fast, accurate and robust nanobiosensing. Specifically, the peritumoral region corresponds to the “objective function”; the tumor is the “global optimum”; the region of interest is the “domain” of the objective function; and the nanoswimmers are the “computational agents” (i.e., guesses or optimization variables). First, in externally manipulable in vivo computation, nanoswimmers are used as contrast agents to probe the region of interest. The observable characteristics of these nanoswimmers, under the influence of tumor-induced biological gradients, are utilized by the external tracking system to steer nanoswimmers towards the possible tumor direction. To take it one step ahead, we provide solutions to the real-life constraints of in vivo natural computation such as uniformity of the external steering force and finite life span of the nanoswimmers. To overcome these challenges, we propose a multi-estimate-fusion strategy to obtain a common steering direction for the swarm of nanoswimmers and an iterative memory-driven gradient descent optimization strategy for faster tumor sensitization.

Next, we proposed a parallel framework called autonomous in vivo computation, where the tumor sensitization is highly scalable and tracking-free. We demonstrate that the tumor-triggered biophysical gradients can be leveraged by nanoparticles to collectively move toward the potential tumor hypoxic regions without the aid of any external intervention. Although individual nanoparticles have no target-directed locomotion ability due to limited communication and computation capability, we showed that once passive collaboration is achieved, they can successfully avoid obstacles and detect the tumor.

Finally, to address the respective limitations of externally manipulable and autonomous settings such as constant monitoring and slow detection, we proposed a semi-autonomous in vivo computational framework. We showed that the spot sampling strategy for an autonomous swarm of nanoswimmers can achieve faster tumor sensitization in complex environments. This approach makes the swarm highly scalable along with giving it the freedom from constant monitoring.

The performance of the aforementioned tumor sensitization frameworks is evaluated through comprehensive in silico experiments that mimic the realistic targeting processes in externally manipulable, self-regulatable and semi-autonomous settings. The efficacies of the proposed frameworks are demonstrated through numerical simulations that incorporate various physical constraints with respect to controlling and steering of computational agents, their motion in discretized vascular networks and their motion under the influence of disturbance and noise.

year: 2023

title: Abundance and Function of Multiple Haemoglobin Isomorphs from Rainbow Trout (Oncorhynchus mykiss)

authors: Tempero, Grant Wayne

subjects: Hemoglobin

abstract: Haemoglobins perform the vital physiological function of transporting oxygen from the external environment to the tissues. Poikilothermic rainbow trout (Oncorhynchus mykiss = Salmo gairdneri = S. irideus) produce multiple forms of haemoglobin that respond differently to varying environmental and physiological conditions. However, the timescale and physiology of these changes are not known. Changes in isomorph abundance may potentially originate from the production of new isomorphs in already circulating erythrocytes. Alternatively, new isomorphs may be produced through the reassembly of extant haemoglobin subunits. The final hypothesis is that changes in isomorph abundance occur through the production of new erythrocytes with red blood cells ‘pre-programmed’ to produce a particular set of haemoglobins. Changes originating from production of new erythrocytes would require longer periods of time before being detectable; weeks to months depending on the temperature regime. To test this, paired groups of rainbow trout were subjected to either 10ºC or 20ºC for 5, 7, 14, 21 and 28 days. A total of 14 isomorphs were observed after the haemolysate was separated using cellulose acetate electrophoresis. However, no detectable differences in isomorph abundance were found between treatment groups. In a follow-up experiment, anaemia was induced in rainbow trout to stimulate the production of new erythrocytes. The trout were then held at either 10ºC or 20ºC for 21 days. This resulted in relative increases in the abundance of anodal haemoglobin isomorphs in the 20ºC acclimated group and a corresponding decrease in cathodal haemoglobin isomorphs. To further confirm that changes in abundance were occurring through the production of new erythrocytes, separation of erythrocytes into age classes was undertaken to compare the isomorphs present in mature erythrocytes with those from erythrocytes produced under amended temperature regimes. Using Percoll density gradients, red blood cells from anaemia-induced trout acclimated to either 10ºC or 20ºC were enriched into mature and young erythrocyte fractions. Further significant differences in abundance were found between both anodal and cathodal isomorphs when compared between treatment groups. From these results it was concluded that changes in haemoglobin isomorph abundance originated from the production of new erythrocytes. Cellulose acetate gel electrophoresis was carried out on seven haemoglobin fractions that had undergone prior separation from whole haemolysate by Fast Protein Liquid Chromatography. Each haemoglobin fraction was found to be composed of two isomorphs for a total of 14 haemoglobin isomorphs. The oxygen binding properties of each fraction was examined under varying conditions of temperature, pH, ATP and chloride concentrations. Cathodal functional groups HbI to HbIII were found to be insensitive to temperature, pH, chloride and the organic phosphate ATP. In contrast, the anodal fractions (HbIV to HbVII) all responded to pH and temperature changes, while HbVI and HbVII responded to ATP. However, no fraction responded to increased chloride concentrations. These results suggest that different varieties of rainbow trout may produce different forms of haemoglobin as part of an adaptive response to local environmental conditions, leading to variation in the functional properties of some of the less abundant functional groups such as HbIII. Despite the theory that cathodal haemoglobins function as emergency back-up supplies of oxygen being proposed more than thirty years ago, no published information can be found for it being tested in the laboratory. Two groups of anaemia-induced rainbow trout were placed in a divided annular flume for 24 days. The high activity group was subjected to a forced swimming speed of 2.5 body lengths (B.L.) s-1 for 6 h d-1. When not undergoing forced exercise the treatment group were maintained at the same speed as the low activity group of 0.5 B.L. s-1. Significant differences in haemoglobin isomorph abundance were present between the initial samples taken at the time of anaemia induction and high and low activity groups. However, only the C4 isomorph demonstrated a significant difference between high and low activity groups. When total anodal and cathodal isomorphs were compared between initial state, high activity and low activity groups, no differences were present. These data suggest that the induction of anaemia had an effect on the composition of the isomorphs but no physiological effect on oxygen delivery. In addition, the swimming velocity of 2.5 B.L. s-1 employed for the high activity group may have been an insufficient stimulus to induce changes in isomorph abundance. It is concluded that changes in haemoglobin isomorph abundance occur in response to chronic changes in the environment. Increases in the abundance of anodal isoforms in response to increasing temperature allows for increased delivery of oxygen to tissues undergoing increases in metabolic activity associated with higher temperatures. The multiple haemoglobin isomorphs of rainbow trout provide an increased efficiency in delivery of oxygen to tissues under varying metabolic conditions of pH, temperature and oxygen saturation. The cathodal and anodal haemoglobin functional groups of rainbow trout exhibit different oxygen affinities in response to temperature, pH and ATP concentration but not to physiologically realistic chloride concentrations. The oxygen binding properties of the isomorphs within the cathodal and anodal functional groups are broadly similar. However, differences in responses by the anodal functional groups to NTPs may exist. An examination of the hypothesis that cathodal haemoglobins act as reserve oxygen delivery sources under prolonged activity produced no significant results. However, this hypothesis still remains viable and needs to be tested under different experimental conditions. This work provides a basis for further research into the adaptive abilities of rainbow trout. The selection of rainbow trout which better adapt to wide ranges of environmental conditions would allow for targeted introduction by fisheries managers to aquatic systems previously not considered optimal for trout growth thereby expanding the fishery.

text: Abundance and Function of Multiple Haemoglobin Isomorphs from Rainbow Trout (Oncorhynchus mykiss) Haemoglobins perform the vital physiological function of transporting oxygen from the external environment to the tissues. Poikilothermic rainbow trout (Oncorhynchus mykiss = Salmo gairdneri = S. irideus) produce multiple forms of haemoglobin that respond differently to varying environmental and physiological conditions. However, the timescale and physiology of these changes are not known. Changes in isomorph abundance may potentially originate from the production of new isomorphs in already circulating erythrocytes. Alternatively, new isomorphs may be produced through the reassembly of extant haemoglobin subunits. The final hypothesis is that changes in isomorph abundance occur through the production of new erythrocytes with red blood cells ‘pre-programmed’ to produce a particular set of haemoglobins. Changes originating from production of new erythrocytes would require longer periods of time before being detectable; weeks to months depending on the temperature regime. To test this, paired groups of rainbow trout were subjected to either 10ºC or 20ºC for 5, 7, 14, 21 and 28 days. A total of 14 isomorphs were observed after the haemolysate was separated using cellulose acetate electrophoresis. However, no detectable differences in isomorph abundance were found between treatment groups. In a follow-up experiment, anaemia was induced in rainbow trout to stimulate the production of new erythrocytes. The trout were then held at either 10ºC or 20ºC for 21 days. This resulted in relative increases in the abundance of anodal haemoglobin isomorphs in the 20ºC acclimated group and a corresponding decrease in cathodal haemoglobin isomorphs. To further confirm that changes in abundance were occurring through the production of new erythrocytes, separation of erythrocytes into age classes was undertaken to compare the isomorphs present in mature erythrocytes with those from erythrocytes produced under amended temperature regimes. Using Percoll density gradients, red blood cells from anaemia-induced trout acclimated to either 10ºC or 20ºC were enriched into mature and young erythrocyte fractions. Further significant differences in abundance were found between both anodal and cathodal isomorphs when compared between treatment groups. From these results it was concluded that changes in haemoglobin isomorph abundance originated from the production of new erythrocytes. Cellulose acetate gel electrophoresis was carried out on seven haemoglobin fractions that had undergone prior separation from whole haemolysate by Fast Protein Liquid Chromatography. Each haemoglobin fraction was found to be composed of two isomorphs for a total of 14 haemoglobin isomorphs. The oxygen binding properties of each fraction was examined under varying conditions of temperature, pH, ATP and chloride concentrations. Cathodal functional groups HbI to HbIII were found to be insensitive to temperature, pH, chloride and the organic phosphate ATP. In contrast, the anodal fractions (HbIV to HbVII) all responded to pH and temperature changes, while HbVI and HbVII responded to ATP. However, no fraction responded to increased chloride concentrations. These results suggest that different varieties of rainbow trout may produce different forms of haemoglobin as part of an adaptive response to local environmental conditions, leading to variation in the functional properties of some of the less abundant functional groups such as HbIII. Despite the theory that cathodal haemoglobins function as emergency back-up supplies of oxygen being proposed more than thirty years ago, no published information can be found for it being tested in the laboratory. Two groups of anaemia-induced rainbow trout were placed in a divided annular flume for 24 days. The high activity group was subjected to a forced swimming speed of 2.5 body lengths (B.L.) s-1 for 6 h d-1. When not undergoing forced exercise the treatment group were maintained at the same speed as the low activity group of 0.5 B.L. s-1. Significant differences in haemoglobin isomorph abundance were present between the initial samples taken at the time of anaemia induction and high and low activity groups. However, only the C4 isomorph demonstrated a significant difference between high and low activity groups. When total anodal and cathodal isomorphs were compared between initial state, high activity and low activity groups, no differences were present. These data suggest that the induction of anaemia had an effect on the composition of the isomorphs but no physiological effect on oxygen delivery. In addition, the swimming velocity of 2.5 B.L. s-1 employed for the high activity group may have been an insufficient stimulus to induce changes in isomorph abundance. It is concluded that changes in haemoglobin isomorph abundance occur in response to chronic changes in the environment. Increases in the abundance of anodal isoforms in response to increasing temperature allows for increased delivery of oxygen to tissues undergoing increases in metabolic activity associated with higher temperatures. The multiple haemoglobin isomorphs of rainbow trout provide an increased efficiency in delivery of oxygen to tissues under varying metabolic conditions of pH, temperature and oxygen saturation. The cathodal and anodal haemoglobin functional groups of rainbow trout exhibit different oxygen affinities in response to temperature, pH and ATP concentration but not to physiologically realistic chloride concentrations. The oxygen binding properties of the isomorphs within the cathodal and anodal functional groups are broadly similar. However, differences in responses by the anodal functional groups to NTPs may exist. An examination of the hypothesis that cathodal haemoglobins act as reserve oxygen delivery sources under prolonged activity produced no significant results. However, this hypothesis still remains viable and needs to be tested under different experimental conditions. This work provides a basis for further research into the adaptive abilities of rainbow trout. The selection of rainbow trout which better adapt to wide ranges of environmental conditions would allow for targeted introduction by fisheries managers to aquatic systems previously not considered optimal for trout growth thereby expanding the fishery.

year: 2011

title: Lifting barriers: Leadership, tactical, and strategic issues from, and for, indigenous community development

authors: Murthy, Vikram

subjects: indigenous communities

abstract: This paper uses learnings from a project with indigenous youth to engage with a recurring challenge in indigenous community organisation (ICO) development initiatives: The unwitting detraction from outcome efficacy by charismatic and influential indigenous leadership leading with an out-of-date repertoire. Using material from recent literature in the fields of non-profit management, new leadership, and social enterprise, the paper suggests guides to improved practice for meeting this challenge. It also sets out to effectiveness, will better underwrite sensitivity in entrepreneurial environments with complex cultural and social beliefs and practices. Such a repertoire will energise intraorganisational communal and consensual processes, which would resonate culturally with the ICO's normative behaviours and values, and would thus help the organisation marshall its collective will to frame futures that best capture their stakeholders' hopes and aspirations. Finally, it recommends that future research examine interfaces between these fields and the spiritual frameworks of indigenous world-views.

text: Lifting barriers: Leadership, tactical, and strategic issues from, and for, indigenous community development This paper uses learnings from a project with indigenous youth to engage with a recurring challenge in indigenous community organisation (ICO) development initiatives: The unwitting detraction from outcome efficacy by charismatic and influential indigenous leadership leading with an out-of-date repertoire. Using material from recent literature in the fields of non-profit management, new leadership, and social enterprise, the paper suggests guides to improved practice for meeting this challenge. It also sets out to effectiveness, will better underwrite sensitivity in entrepreneurial environments with complex cultural and social beliefs and practices. Such a repertoire will energise intraorganisational communal and consensual processes, which would resonate culturally with the ICO's normative behaviours and values, and would thus help the organisation marshall its collective will to frame futures that best capture their stakeholders' hopes and aspirations. Finally, it recommends that future research examine interfaces between these fields and the spiritual frameworks of indigenous world-views.

year: 2006