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Nanoelectronic-Based Detection for Biology and Medicine 81.4 Nanopore Sensors for Characterization of Single DNA Molecules 1445

duced by controlling the electrolyte temperature, salt

concentration, viscosity, and the electrical bias voltage

across the nanopores [81.64]. The speed was reduced to

3bases/μs for 3kbp dsDNA through a 4–8 nm diam-

eter silicon nitride pore. This signiﬁcantly reduced the

bandwidth requirements on electronic sensing system.

However, slowing the DNA also slowed conducting

ions, which decreased the current blockage signal. In

another study, it was reported that most of the translo-

cation events followed a rule of constant event charge

deﬁcit. The experiments compared the distribution of

molecular event durations and blockade at various pH

values, conclusively demonstrating a large number of

long denatured ssDNA translocation in stretched-out

conformation [81.65]. The control of the translocation

speed and denaturation of dsDNA into ssDNA at high

pH is an elegant capability with synthetic nanopores,

which would bea challengewith α-HLbiological pores.

This work showed an ability to detect hybridization

from the translocation behavior.

To study pore formation after electron beam

deformation, electron energy-loss spectroscopy and

high-resolution electron microscopy studies were re-

ported [81.66]. The material composition was studied

extensively during pore shrinkage, pore expansion,

and pore closure, concluding that pore formation oc-

curred by removal of material at the entrance and

exit side of the electron beam. The pore formed had

wedge-like edges and contained Si, O, and N. Heng

et al. investigated the mechanical properties of DNA

using translocation of single molecules through the

nanopore [81.67]. They used pores with radii from

0.5to1.5nm in 10nm thick SiN membranes. They

also carried out molecular dynamics simulations to

explore the stretching and bending of DNA during

translocation through such small pores. They reported

a pore-dimension- and bias-dependent threshold for

translocation. Simulating a 1nm pore, they calculated

forces on DNA to be in the range of 1–300pN through

it and observed the threshold for dsDNA transloca-

tion conditioned by its mechanical properties. The

same authors also reported the permeation capabili-

ties through various sizes of nanopores by changing

the electric ﬁelds [81.68]. The electromechanical prop-

erties of DNA were studied to deﬁne threshold of

nanopore sizes that ssDNA or dsDNA could perme-

ate under various electric ﬁelds. Previously, the effect

of pH on such threshold was also investigated by

the same group [81.69, 70]. In the wake of the low-

salt current-enhancement studies reported by Bashir

and co-workers [81.58], Smeets et al. reported the ef-

fects of salt concentration on ion transport and DNA

translocation using 10nm diameter nanopores [81.59].

They changed the salt concentration by six orders

from 1 M to 1 μM, noting a three order of magni-

tude decrease in ionic conductance, deviating from

linear bulk behavior. They carried out 16.5μm long

dsDNA translocationexperiments for50mM to1M salt

concentrations, observing downward or upward translo-

cation pulses as a function of ion concentration. They,

like Bashir and co-workers had explained [81.58], de-

scribed a model attributing current decreases due to

partial blocking of the pore and current increases to

the motion of the counterions screening the charge of

the DNA backbone. They concluded a threshold KCl

concentration of 370±40mM where two competing

effects canceled out. Using the same nanopores, fab-

rication of point electrodes with radii 2 nm was also

reported [81.71]. The nanopores were ﬁlled with Au,

making conically shaped nanoelectrodes. Metal nano-

electrodes of such high temporal resolution can be

used for single-molecule detection and a variety of bio-

logical sensors for medical diagnostics. The fabrication

of nanopores has also been reported using conventional

ﬁeld-emission scanning electron microscope (FESEM)

instead of TEM [81.72

]. The irradiation from the elec-

tron source of the FESEM showed different shrinking

mechanism due to the effects of surface defects under

radiolysis and subsequent motion of silicon atoms to

the pore periphery. The process was reliable and re-

producible, opening the way to parallel fabrication of

nanopores in an array format. Another report inves-

tigated the ionic current ﬂuctuations associated with

the translocation of 1681bp long DNA as a function

of applied electric ﬁeld. The pulse direction (upward

or downward) was investigated to develop a model

of DNA counterion ionic current and dipole satura-

tion based on a remarkable work by Manning [81.73].

These experiments showed that, at low concentrations,

the electrophoretic bias can reverse the pulse directions

from upwards to downwards, indicating competition

between the mechanical blocking current and the cur-

rent arising from the condensed counterions on DNA

backbone, which saturated at high electric ﬁeld. The ex-

periments provided a direct way to explore the charge

polarization and dipolesaturation at the single-molecule

level.

Dekker and co-workers have also measured the

force on a single DNA while translocating through

a nanopore by using optical tweezers [81.74, 75], and

ionic transport in electrochemical reactions[81.76]. The

optical tweezers were used to slow down and arrest the

Part H 81.4

1446 Part H Automation in Medical and Healthcare Systems

Negative voltage

DNA

movement

≈ 1–2nm

≈ 16–18nm

SiO

Fig. 81.9 Schematic of the functionalized nanopore channels. The

chemical modiﬁcation and the probe hairpin-loop DNA reduced the

NPC diameter. Adapted by permission from Macmillan Publishers

Ltd: Nanotechnology [81.77], copyright (2007)

DNA midway through the pore and force measurements

were carried out. The study reported effective charge of

0.50±0.05 electrons per base pair, which is equivalent

to 25% of the bare DNA charge.

As explained earlier, it is important to slow down

DNA to gather more information with reasonable band-

width requirements on the electronic measurement

systems, while still maintaining high signal-to-noise

ratio. In a recent report, Iqbal et al. chemically func-

tionalized the nanopore channels (NPC) with hairpin-

loop DNA [81.77]. The functionalization with known

hairpin-loop probe ssDNA showed selective transport

behavior for target ssDNA that was complementary

to the probe. This chemical modiﬁcation of the sur-

face also restricted the movement of the target ssDNA.

The hairpin-loop conﬁguration imparted single-base-

mismatch sensitivity. Such a single base mismatch

between the probe and the target resulted in longer

translocation pulses and a signiﬁcantly reduced number

of translocation events. Figure 81.9 shows a schematic

of the functionalized NPC and the effective diameter

of the NPC after functionalization. They used short

ssDNA astarget molecules. The target ssDNA were stiff

polymers at the length used in this study, thus avoid-

ing the folding effect [81.78]. These single-molecule

measurements allowed separate measurements of the

molecular ﬂux and the pulse duration, providing a tool

to gain fundamental insight into the channel–molecule

interactions. They discovered that perfectly comple-

mentary ssDNA translocated faster and was transported

in higher numbers across the pores compared with a tar-

get that had even a single base mismatch with the probe

molecules. The experimental observations showed that

nanopores can be used as selective sensors for genes

of interest and that such selectivity could be electri-

cally measured by the translocation signatures at the

single-molecule level.

81.4.3 The Promise

of Low-Cost DNA Sequencing

The human genome project, completed in 2003, is

estimated to have cost US$2.7billion [81.79]. It

took more than 12 years to complete. With the ad-

vent of novel sequencing technologies and abundant

computation power the cost and time needed for se-

quencing a genome has reduced dramatically, now at

≈3 cents/base [81.80]. However, this is an enormous

amount for 3 billion bases to be sequenced. Nanopores,

in spite of their shortcomings and open challenges,

are a hope to achieve the US$1000/genome target as

set by the National Institutes of Health with more

than US$70 million in grant monies. The challenges

of nanopore technology are both material and electri-

cal. The reproducibility of the nanopore channels is

a concern where even an angstromical difference in

channel length changes the conductivity of the pore

and hence the baseline currents. Although the base-

line can be normalized, the noise varies from pore to

pore owing to the differences of physical and chem-

ical properties of the pore wall surfaces. There are

also issues of bandwidth; DNA passes way too fast

for the electronics readout to capture the full details

of translocation. The best optimal bandwidth of mea-

surements would still miss too many fast translocation

events, signiﬁcantly skewing the analysis of the pulse

behavior, while reducing the noises. The bandwidth is-

sue thus limits the speed of classiﬁcations that can be

made with nanopores. There are a number of noise

sources that are encountered in nanopore measure-

ments; especially 1/ f (ﬂicker) noise. Tackling such

diverse scientiﬁc challenges in the nanopore measure-

ments is an uphill task. However, the promise of cheap

and fast sequencing machines makes every effort worth

pursuing.

Part H 81.4

Nanoelectronic-Based Detection for Biology and Medicine References 1447

81.5 Conclusions and Outlook

This chapter summarized the state of the art in prob-

ing the electrical properties of molecules with special

emphasis on DNA conductivity. The various tech-

niques for DNA immobilization were discussed. The

biological ion channel pores extended to the idea of

solid-state nanopore, and the state of the art in nanopore

fabrication and its applications, were covered. Very re-

cently, two review articles have appeared [81.81, 82]

that cover the history and state of the art of the

nanopore research in more detail. For details of labo-

ratory protocols of setting up biological and synthetic

nanopores for DNA analysis, a laboratory manual ap-

peared in December 2007 [81.83]. It is the consensus

that nanopores have set some ambitious goals for the

research community, foremost being the sequencing

of the human genome for less than US$ 1000 dollar.

The conﬂuence of the sophisticated electronic sensing

and nanopore detection techniques has strong poten-

tial of achieving the US$ 1000 genome and much

more.

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Part H 81

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1451

Computer and

82. Computer and Robot-Assisted

Medical Intervention

Jocelyne Troccaz

Medical robotics includes assistive devices used by

the physician in order to make his/her diagnostic

or therapeutic practice easier and more efﬁcient.

This chapter focuses on such systems. It introduces

the general ﬁeld of computer-assisted medical

interventions, its aims, and its different compo-

nents, and describes the place of robots in this

context. The evolution in terms of general de-

sign and control paradigms in the development of

medical robots are presented and issues speciﬁc to

that application domain are discussed. A view of

existing systems, ongoing developments, and fu-

ture trends is given. A case study is detailed. Other

types of robotic help in the medical environment

exist (such as for assisting a handicapped person,

for rehabilitation of a patient or for replacement

of some damaged/suppressed limbs or organs) but

are outside the scope of this chapter.

82.1 Clinical Context and Objectives...............1451

82.2 Computer-Assisted Medical Intervention 1452

82.2.1 CAMI Major Components................1452

82.2.2 Added Value of a Robot ................1453

82.3 Main Periods

of Medical Robot Development ..............1454

82.3.1 The Era of Automation (1985–1995) 1454

82.3.2 The Era of Interactive Devices

(1990–2005) ................................1455

82.3.3 The Era of Small and Light

Dedicated Devices

(2000 to Present Day)....................1455

82.4 Evolution of Control Schemes.................1458

82.5 The Cyberknife System: A Case Study ......1459

82.6 Speciﬁc Issues in Medical Robotics .........1461

82.7 Systems Used in Clinical Practice ............1462

82.8 Conclusions and Emerging Trends ..........1463

82.9 Medical Glossary...................................1463

References ..................................................1464

82.1 Clinical Context and Objectives

Informatics and technology have dramatically trans-

formed clinical practice over the last decades. This

technically oriented evolution has run parallel to other

speciﬁc evolutions of medicine:

•

Diagnostic and therapy procedures tend to be less

and less invasive for the patient, aiming at reduc-

ing pain, postoperative complications, hospital stay,

and recovery time. Minimal invasiveness results in

smaller targets reached through narrow access (nat-

ural or not) with no direct sensing (vision, touch)

and limited degrees of freedom.

•

More and more data are handled for each patient

(e.g., images, signals) in order to prepare and mon-

itor the medical action, and these multimodal data

have to be shared by several participating actors.

•

As in many other domains, quality control gets

increasingly important and quantitative indicators

have to be made available.

•

Traceability becomes mandatory, especially regard-

ing the ever-increasing number of legal cases.

Traceability is also of primary importance in cost

management.

These evolutions make the medical action increasingly

complex for the clinician, at both the technical and

organizational levels. Computer-assisted medical inter-

vention may contribute a lot to those clinical objectives.

Part H 82

1452 Part H Automation in Medical and Healthcare Systems

They may provide quantitative and rational collabora-

tive access to patient information, fusion of multimodal

data, and their exploitation for planning and execution

of medical actions.

82.2 Computer-Assisted Medical Intervention

The development of this area from the early 1980s re-

sults from converging evolutions in medicine, physics,

materials, electronics, informatics, robotics, etc. This

ﬁeld and related subﬁelds are given several almost

synonymous names: computer-assisted medical in-

tervention (the most general), augmented surgery,

computer-assisted surgery, image-guided surgery, med-

ical robotics, surgical navigation, etc. We will use the

term computer-assisted medical intervention (CAMI)

herein for this domain.

We deﬁne CAMI as aiming to provide tools that

allow the clinician to use multimodal data in a ratio-

nal and quantitative way in order to plan, simulate,

and accuratelyand safelyexecutemini-invasivemedical

interventions. Medical interventions include both diag-

nostic and therapeutic actions. Therapy may involve

surgery, radiotherapy, local injection of drugs, interven-

tional radiology, etc. (Some of these medical terms are

explained in a glossary located at the end of this chap-

ter.)

82.2.1 CAMI Major Components

CAMI [82.1] may be described as a perception–

decision–action loop, as presented in Fig. 82.1. The

perception phase includes data acquisition and pro-

cessing, the development of speciﬁc sensors, and their

Virtual patient

Planning

Simulation

Perception

Action

Real world Virtual world

Decision

Guiding

systems

Biomechanical

models

Atlases

Statistical models

Fig. 82.1 CAMI methodology

calibration. Data may be acquired pre-, intra- or postop-

eratively. Images may provide anatomical information

or functional one; data provided by the sensors may be

one-dimensional (1-D), two-dimensional (2-D), three-

dimensional (3-D, sparse or dense) or four-dimensional

(4-D, i.e., varying with time). Each imaging sensor

brings its speciﬁc type of information and multimodal-

ity is in general necessary. The need to assist the

intervention in a quantitative and accurate way requires

the calibration of sensors enabling both the transforma-

tion from image coordinates to spatial coordinates and

the correction of possible image distortions. Speciﬁc

sensors such as position sensors (also called local-

izers) and surface sensors have been integrated into

CAMI components. Localizers give access to position

and orientation of objects (instruments, other sensors,

anatomical structures such as bones). Surface sensors

give access to the external surface of an object (an or-

gan, for instance). All those information are potentially

useful to plan and control the execution of a medical

action.

The main objective of the decision stage is to build

an integrated numerical model of the patient and, in

some cases, a model of the action. As mentioned pre-

viously, many types of information may be useful: data

provided by imaging sensors, for instance, but also

a priori medical knowledge (for instance, statistical

data about organ shapes or occurrence of pathologies,

biomechanical models of the limbs, etc.). One very im-

portant stage is data fusion, also called registration,

which corresponds to the action of representing all the

information in a single reference frame. Registration,

and in particular medical image registration [82.2], has

been a very active domain for three decades. From this

integrated model, the medical action can be planned;

for instance, one may have to determine the type, size,

position, and orientation of a knee prosthesis that pro-

vides the best alignment of hip, knee, and ankle joints;

or one may decide which number, shape, intensity, po-

sition, and orientation of radiation beams would allow

to radiate a tumor of a given shape, with a given dose,

whilst sparing organs at risks. Planning may involve

highly interactive tools where the clinician navigates

in the data and speciﬁes the selected strategy. It may

also include optimization tools when the medical goal

Part H 82.2

Computer and Robot-Assisted Medical Intervention 82.2 Computer-Assisted Medical Intervention 1453

can be speciﬁed as an optimization problem (radiother-

apy planning is an excellent example). In some cases,

planning may be very difﬁcult and simulators could pro-

vide help for the computation of the clinical outcome

of a selected action; for instance, when a bone frag-

ment has to be moved in the patient’s face, it may be

very useful for the surgeon to foresee the functional

and aesthetic consequences of this gesture on soft tis-

sues [82.3]. Registration and planning are included in

the decision stage.

Action requires accurate execution of the planned

intervention. Often, a registration stage is necessary

to transfer the planned action to the interventional

conditions; for instance, the action is planned from

preoperative data, e.g., magnetic resonance imaging

(MRI), and must be registered to the real patient in in-

traoperative conditions. Two main types of assistance

exist: navigational aids and robots. In the ﬁrst case, the

action is monitored using suitable sensors such as lo-

calizers; information is rendered to the clinician about

the planned and executed actions. The clinician makes

use of this information to control his/her action, such

systems are called passive. The ﬁrst surgical navigators

have been used for neurosurgery [82.4, 5]. The action

can also be performed more of less autonomously by

a robot. The ﬁrst application of a robot in CAMI took

place around 1985; the application ﬁeld was also neu-

rosurgery. The medical robot needs to be connected to

patient data and models in order to be able to transfer

the planned intervention to the robot coordinates; this

is the robot registration problem. The medical robot is

therefore always an image-guided robot.

Simulators may also be developed for training pur-

poses. The advantages are the abilities to provide

frequent and rare medical cases, to gain realistic ex-

perience with lower stress than with real patients, and

to quantitatively evaluate the practitioner. This may fa-

cilitate the acquisition of new medical skills, with new

techniques and/or tools. This can also be considered

a very valuable component of CAMI.

Based on numerical data, tracking of objects (in-

struments, sensors, and anatomical structures), and

positioning of tools with navigation or robotized aids,

those CAMI procedures are fully traceable.

82.2.2 Added Value of a Robot

Automation is generally not a primary goal of medical

robotics, where the interaction with a clinical opera-

tor has to be considered with a very special attention.

Indeed, most often medical robots are not intended to

replace the operator but rather to assist him/her where

his/her capabilities are limited. In general CAMI sys-

tems are considered only as sophisticated tools in the

hands of the clinician.

In medicine, like in many other application areas,

the advantages of the robot are its precision, ability to

repeat a task endlessly, potential connection to com-

puterized data and sensors, capability to operate in

hostile environments [biological or nuclear contamina-

tions, war or catastrophe areas, space (orbital station) or

undersea (submarine), etc.] where clinician presence or

abilities may be limited and humans may need medical

care.

Navigational aids have already demonstrated their

clinical added value in various specialties (neuro-

surgery, orthopaedics in particular) and their integration

in the clinical environment is generally easier than for

a robot. Safety issues are also more limited. Moreover

navigation systems are very often more cost effective.

These are the reasons why it is very important to use

a robot only for clinical applications where it can of-

fer functionalities that the navigation system cannot;

potential speciﬁc robot abilities are:

•

To realize complex geometric tasks (for instance, to

machine a 3-D bone cavity)

•

To handle heavy tools (e.g., radiation apparatus) or

sensors (e.g., an intraoperative surgical microscope)

•

To provide a third hand to the clinician

•

To be remotely controllable and to offer scaling ca-

pabilities in terms of transmitted motions or forces

•

To ﬁlter undesired movements (such as physiologi-

cal shaking in teleoperation)

•

To be force-controllable down to very small force

scales

•

To execute high-resolution high-accuracy motions

(for microsurgery)

•

To track moving organs and synchronize to external

events based on some signals

•

To be introduced into the patient for intrabody ac-

tions.

Another aspect that will be further discussed is the ab-

solute necessity to demonstrate the clinical added value

of the system, i. e., to prove that it brings a clear clin-

ical beneﬁt at some level (for the patient, hospital, or

healthcare system).

Part H 82.2

1454 Part H Automation in Medical and Healthcare Systems

82.3 Main Periods of Medical Robot Development

Early medical applications of robotics are characterized

by transferring to this domain accurate and automated

tool positioning capabilities of robots originally devel-

oped in industrial applications.

82.3.1 The Era of Automation (1985–1995)

As mentioned previously the ﬁrst surgical robots were

introduced in neurosurgery. Neurosurgery already had

a very long tradition of minimal invasiveness and use of

computerized 3-D imaging data; indeed, the ﬁrst com-

puted tomography (CT) scans in the early 1970s were

performed for brain imaging. Stereotactic neurosurgery

is a particular type of minimally invasive procedure

which consists of blindly introducing a linear tool

into the brain through a keyhole (3mm diameter) for

biopsies, removal of cysts or haematomas, placement

of stimulation (Parkinson disease) or measurement

(epilepsy) electrodes, etc. Conventionally, stereotactic

neurosurgery is performed with the help of a stereotac-

tic frame whose functions are to immobilize the patient

skull, register preoperative data to the intraoperative

situation (the frame is installed on the patient’s head be-

fore the preoperative examination), and ﬁnally to offer

mechanical guidance for tool insertion. Except for the

ﬁrst function, a robot can advantageously replace the

frame: it is easily connected to imaging data, is less in-

vasive, and may offer a larger range of trajectories for

tool positioning. Anthropomorphic robots associated

to stereotactic frames or robotized stereotactic frames

have been developed and clinically evaluated in the

early 1980s (for instance [82.6, 7]). Reference [82.7]

describes the accurate positioning of a guiding tool

with respect to preoperative data in a stereotactic neu-

a) b)

Fig. 82.2 (a) Grenoble robot for neurosurgery (TIMC laboratory and Grenoble University Hospital) and (b) the Neuro-

mate industrial version

rosurgery application using a Puma 260 robot. The

cited paper reports a series of 22 patients. While [82.8]

presents a CAMI system integrating a modiﬁed indus-

trial robot (reduced speed, nonbackdrivable joints) for

a similar application. The ﬁrst patient (Fig.82.2a) was

operated on with this system in 1989 and since then

hundreds of patients have been treated with this tech-

nology. This system was the academic precursor of the

Neuromate product (Fig.82.2b) with which thousands

of patients were treated. These systems are called semi-

active because the robot is only a guiding device and

the gesture (drilling the skull and inserting the needle)

is still performed by the surgeon through a mechanical

guide positioned by the robot.

Reference [82.9] proposed an automated view of

the whole process of stereotactic neurosurgery: a robot

equipped with different types of tools in a tool-feeder

effector was installed in a CT room; after imaging data

and planning, the robot performed the drilling of the

bone and the placement of the surgical tool. CT enabled

repeated image control. The robot was speciﬁcally de-

signed for this application. The ﬁrst two patients were

operated in 1993. Eight cases of biopsies are reported

in [82.9]. As far as we know, this system has not been

extensively used in clinical routine.

In orthopaedics, the placement of prostheses re-

quires the preparation of the bones; for instance a cavity

has to be drilled before inserting the femoral compo-

nent of a hip prosthesis; similarly, planar cuts have to

be realized on the tibia and femur extremities in order

to place knee prosthesis components. Thus, such stages

of the interventions are very close to machining a me-

chanical part: a 3-D shape has to be accurately realized

by sawing or milling with given position and orienta-

Part H 82.3