Automatic Cancer Tissue Detection Using Multispectral Photoacoustic Imaging

Convolutional neural networks (CNNs) have become increasingly popular in recent years because of their ability to tackle complex learning problems such as object detection, and object localization. They are being used for a variety of tasks, such as tissue abnormalities detection and localization, with an accuracy that comes close to the level of human predictive performance in medical imaging. The success is primarily due to the ability of CNNs to extract the discriminant features at multiple levels of abstraction. Photoacoustic (PA) imaging is a promising new modality that is gaining significant clinical potential. The availability of a large dataset of three dimensional PA images of ex-vivo human prostate and thyroid specimens has facilitated this current study aimed at evaluating the efficacy of CNN for cancer diagnosis. In PA imaging, a short pulse of near-infrared laser light is sent into the tissue, but the image is created by focusing the ultrasound waves that are photoacoustically generated due to the absorption of light, thereby mapping the optical absorption in the tissue. By choosing multiple wavelengths of laser light, multispectral photoacoustic (MPA) images of the same tissue specimen can be obtained. The objective of this thesis is to implement deep learning architecture for cancer detection using the MPA image dataset. In this study, we built and examined a fully automated deep learning framework that learns to detect and localize cancer regions in a given specimen entirely from its MPA image dataset. The dataset for this work consisted of samples with size ranging from 12 × 45 × 200 pixels to 64 × 64 × 200 pixels at five wavelengths namely, 760 nm, 800 nm, 850 nm, 930 nm, and 970 nm. The proposed algorithms first extract features using convolutional kernels and then detect cancer tissue using the softmax function, the last layer of the network. The AUC was calculated to evaluate the performance of the cancer tissue detector with a very promising result. To the best of our knowledge, this is one of the first examples of the application of deep 3D CNN to a large cancer MPA dataset for the prostate and thyroid cancer detection. While previous efforts using the same dataset involved decision making using mathematically extracted image features, this work demonstrates that this process can be automated without any significant loss in accuracy. Another major contribution of this work has been to demonstrate that both prostate and thyroid datasets can be combined to produce improved results for cancer diagnosis

Quality improvement in virtual classroom

Introductions: Online teaching method has shown to be equally effective as the traditional teaching method. An online teaching method, the virtual classroom (VCR) was developed for undergraduate medical students of Patan Academy of Health Sciences (PAHS). This study aims to present the outcome of complete audit cycle of VCR for quality improvement of the program. Methods: Feedbacks were collected from final year medical students who are posted in four different rural sites of PAHS. A validated google feedback form was used to collect the feedbacks from individual students after every VCR sessions. Students from 2017 were group one and students from 2018 were group two. Feedbacks were recorded in Likert scale of five. Ratings were done for quality of video, sound and power supply. Plan, do, study, and act (PDSA) cycle was used for quality improvement process. The necessary changes were done after analysis of data from group A. Same process was repeated for group B. Results: Fifty-six feedbacks were collected in first cycle. The complete PDSA audit cycle showed improvement in quality of VCR, with mean score on video of 3.0 and 4.1, audio 3.1 and 4.03, internet 3.6 and 4.03, power supply 4.0 and 3.98 in first cycle group A vs second cycle group B. Conclusions: Improvement was achieved by running quality feedback cycle and quality improvement cycle should be continued to maintain the quality achieved with this process. Keywords: audit cycle, PDSA cycle, virtual class roo

Mitigating the externality of diseases of poverty through health aid

Externality exists in healthcare when an individual benefits from others being healthy as it reduces the probability of getting sick from illness. Healthy workers are considered to be the more productive labourers leading to a country’s positive economic growth over time. Several research studies have modelled disease transmission and its economic impact on a single country in isolation. We developed a two-country diseaseeconomy model that explores disease transmission and crossborder infection of disease for its impacts. The model includes aspects of a worsening and rapid transmission of disease juxtaposed by positive impacts to the economy from tourism. We found that high friction affects the gross domestic product (GDP) of the lower-income country more than the higherincome country. Health aid from one country to another can substantially help grow the GDP of both countries due to the positive externality of disease reduction. Disease has less impact to both economies if the relative cost of treatment over an alternative (e.g. vaccination) is lower than the baseline value. Providing medical supplies to another country, adopting moderate friction between the countries, and finding treatments with lower costs result in the best scenario to preserve the GDP of both countries

Growth, Morphology, and Conductivity in Semimetallic/Metallic Films on Si(001)

This dissertation deals with the study of epitaxial growth of semimetallic (Bi) and metallic (Ag) films on Si(001) as well as in situ electrical transport study of those films via surface manipulation. The focus of the transport measurements is to study the influence of the surface morphology or structure on the resistance of the film. The most important challenge is the preparation of high quality films with well-defined morphology under ultra high vacuum conditions. In spite of the large lattice mismatch and different lattice geometry, it is possible to grow epitaxial Bi(111) films on Si(001) substrates, which are surprisingly smooth, relaxed and almost free of defects. Due to the two-fold symmetry of the substrates, the Bi(111) film is composed of crystallites rotated by 90 with respect to each other. Annealing of 6 nm film from 150 K to 450 K enables the formation of a periodic interfacial misfit dislocations, which accommodates a remaining lattice mismatch of 2.3 %. The surface/interface roughness and the bulk defect density of the film found to be extremely low, indicating the high crystalline quality of the film with atomically smooth surface and abrupt interface. Similar to the Bi films, Ag grows in a (111) orientation on Si(001) with two 90 rotated domains. The remaining strain of 2.2 % (tensile) is accommodated by the formation of an ordered network of dislocations. The Ag film exhibits atomically smooth surface. Those Bi films and Ag films were used as model systems to study the influence of the surface morphology on the electrical resistance. Surprisingly, all the Bi films (3 - 170 nm thicknesses) have shown an anomalous behavior of conductance with temperature and thickness. As in the case of doped semiconductor, the conductance increases exponentially from 150 K to 300 K and saturates at 350 K before finally decreasing with temperature. This behavior hints to the long predicted semimetal-to-semiconductor transition in the Bi films. However, the thickness dependent conductance behavior agrees with a previously observed metallic surface state, because the conductance does not change with thickness at 80 K. In situ measurements of the resistance during additional Bi deposition on the smooth Bi(111) films exhibit a square root dependent with coverage after a linear increase at very low coverage (1 % of a BL). Due to the extreme electronic properties of Bi, such as a large Fermi wavelength and a large electron mean free path, this behavior is not supported by the classical electron scattering model of Fuchs-Sondheimer. Since the Bi(111) surface state possesses two orders of magnitude higher number of carriers than in the bulk, the surface acts as a dominant channel of electron transport. During additional deposition of Bi, carriers are scattered at the adatoms and small islands, resulting in dramatic increase of surface resistance. Experimental results of nucleation and growth behavior at initial stages in Bi(111) homoepitaxy and the concept of 2D metallic surface states allow to explain the square root dependent of the resistance with coverage. Additionally, from the initial rise of resistance, a 2D surface state conductivity was determined, assuming that the surface states are completely destroyed after additional 0.5 BL Bi deposition. Applying the Boltzmann equation, the scattering mean free path at the 2D surface states was roughly estimated to be 15 nm. The situation becomes much simpler in the case of the resistance behavior during deposition of Ag on a smooth Ag(111) film. The Fuchs-Sondheimer model works quite well and qualitatively demonstrate the increase of film resistance due to the diffuse scattering caused by surface roughness. Furthermore, in a complex situation such as surface alloying via Au deposition on Ag films, the resistance increases dramatically even at room temperature, suggesting that the scattering efficiency in this case is even higher than the case of normal surface roughness.In dieser Dissertation wird das epitaktische Wachstum dünner halbmetallischer Wismut- bzw. metallischer Silberfilme auf Si(001) sowie der elektrische Transport durch diese Filme untersucht. Im Fokus der Transportmessungen steht die Untersuchung des Einflusses von Oberflächenmorphologie bzw. -struktur auf die Leitfähigkeit. Hierfür sind Filme mit hoher Kristallqualität unter Ultrahochvakuum-Bedingungen eine entscheidende Voraussetzung. Trotz des großen Unterschieds der beiden Gitterkonstanten und der verschiedenen Gittergeometrie ist es möglich, Bi(111) Filme auf Si(001) Substrate aufzuwachsen, die überraschend glatt, entspannt und praktisch frei von Defekten sind. Bedingt durch die 2-zählige Symmetrie des Substrates besteht der Bi(111) Film aus Mikrometer großen (111) Kristalliten, die jeweils um 90° gegeneinander verdreht sind. Eine verbleibende Gitterfehlanpassung von 2.3% wird durch die Ausbildung eines periodischen Netzwerks von Versetzungen an der Grenzfläche angepasst. Die Oberflächen- bzw. Grenzflächenrauhigkeit und die Volumendefektdichte des Films sind extrem gering, was die hohe Kristallgüte des Films mit einer atomar glatten Oberfläche und einer abrupten Grenzfläche widerspiegelt. Ähnlich wie für Wismut wachsen auch Silber-Filme mit einer (111) Orientierung und um jeweils 90° gedrehten Domänen auf Si(001). Auch hier passt ein Netzwerk von Versetzungen eine verbleibende Gitterfehlanpassung von 2.2% an. Auch hier ist der Silberfilm atomar glatt. Diese Silber- und Wismut-Filme wurden dann als Modellsystem für die Untersuchung des Einflusses der Oberflächenmorphologie auf den elektrischen Widerstand verwendet. Überraschenderweise zeigten alle Wismutfilme (3 - 170 nm Dicke) ein anomales Verhalten als Funktion der Schichtdicke und Temperatur. Wie im Fall eines dotierten Halbleiters stieg die Leitfähigkeit zwischen 150 und 300 K exponentiell an, zeigte ein Plateau bei 350 K bevor sie mit steigender Temperatur abfiel. Dieses Verhalten ließe sich mit dem lang vorhergesagten Halbleiter/Halbmetallübergang für dünne Bi-Filme erklären. Die zusätzlich beobachtete schichtdickenunabhängige Leitfähigkeit bei 80 K ist mit einem in der Literatur beschriebenen metallischen Oberflächenzustand zu erklären. Bei weiterem Bedampfen mit Wismut werden die Ladungsträger an den dabei entstehenden Wismutinseln gestreut und eine Erhöhung des Widerstands beobachtet, die nach einem linearen Anstieg eine wurzelförmige Abhängigkeit von der zusätzlichen Bedeckung aufweist. Auf Grund der besonderen elektronischen Eigenschaften von Wismut - wie eine große Fermiwellenlänge und eine große freie Weglänge der Elektronen - kann dieses Verhalten nicht durch ein klassisches Streumodell nach Fuchs-Sondheimer erklärt werden. Da jedoch der metallische Oberflächenzustand von Bi(111) bis zu zwei Größenordnungen mehr Ladungsträger aufweist wie das Filmvolumen stellt dieser den dominanten elektronischen Transportkanal dar. Bei weiterem Aufdampfen von Wismut bei 80 K werden die Elektronen an den isolierten Adatomen bzw. 2dim. Inseln gestreut, was einen deutlichen Anstieg des Widerstands bewirkt. Mit einer STM Analyse der Inseldichte und -größe in diesem Wachstumsbereich konnte der beobachtete wurzelförmige Anstieg des Oberflächenwiderstands erklärt werden. Unter der Annahme, dass der Oberflächenzustand nach Aufdampfen einer halben Atomlage Wismut vollständig zerstört ist, konnte die Leitfähigkeit im Oberflächenzustand auch quantitativ bestimmt werden. Die mittlere freie Streulänge für Transport im Oberflächenzustand konnte zu 15 nm bestimmt werden. Die Erklärung des Widerstandsanstiegs bei der Abscheidung weiteren Silbers auf ultradünne Silberfilme bei tiefen Temperaturen ist wesentlich einfacher. Die Beschreibung über Fuchs-Sondheimer erklärt den durch das Aufrauhen der Oberfläche bewirkten Widerstandsanstieg qualitativ sehr gut. Im Falle der Abscheidung von Gold auf die Silberfilme bewirkt die Oberflächenlegierung einen auch bei Zimmertemperatur deutlichen Anstieg des Widerstands. Offensichtlich ist die Streueffizienz in diesem Fall deutlich höher als für rauhe Oberflächen ist

Politics of Fear: Unitary Bias of a Federal Design in Nepal

This thesis explores the reasons that have led the framers of the constitution to centralize powers in the federal government of Nepal, despite claims for accommodation by its minority groups. It contends that the centralized model is chosen to neutralize the potential risk of secession. Taking discourse analysis as its methodological approach, the thesis examines this argument in two sections. First, it develops seven measures: the recognition of minorities, the demarcation of sub-unit boundaries, the distribution of powers, the constitutional amending formula, the appointment process of the Judges in the Supreme Court, the jurisdiction of the upper house in the federal parliament, and the constitutional (a)symmetries, and applies them in the constitution. Second, it assumes that the fear of disintegration existed in the polity due to i) Maoists’ interpretation of the ‘right to self-determination’ ii) utterances of secession threats by regional leaders and, iii) the foreign intervention in the domestic politics of Nepal. In its attempt to dampen the risk of disintegration, the current arrangement of the Nepali state fails to accommodate the demands for the ‘right to self-determination’ and autonomy, further augmenting the discontent among minorities. Despite the change in the structure, the thesis concludes that the present design has not lost the fundamental character of the previous unitary state that repressed diversity and claimed to maintain the territorial integrity. In order to reach this conclusion, official discourses such as the manifestos of political parties, their debates as recorded in the CA transcripts, and the official statements of the governments have been analyzed

Human Immunodeficiency Virus Related Knowledge, Risk Perception and Practices among Married Women of Reproductive Age: A Cross-sectional Study from Mid-western Development Region, Nepal

Background: Despite the implementation of anti.human immunodeficiency virus (HIV) interventions, it has continued to spread from high risk to the low risk population population with the devastating social, economic and health consequences. Aim: The aim of the following study is to identify HIV related knowledge, risk perceptions and practices among married women of reproductive age (MWRA) in Mid-Western Development Region, Nepal.Subjects and Methods: A community based, cross.sectional study was conducted during May-December 2010 among 618 MWRA in Mid-western Development Region, Nepal. Multistage random sampling was followed wherein four districts, representing each ecological zone were selected in the first stage. Nine Village Developments Committees with the total 81 clusters were selected in the second and third stages. Finally, 7/8  participants/cluster were selected randomly. Household interviews were conducted using pretested structured questionnaire. Data were analyzed by SPSS 16.0 (SPSS Inc. Chicago, IL, USA). Percentages, mean, Chi-square value and odds ratio were calculated. Results: Nearly three quarters (434/618) of all participants had heard about the HIV. Radio was the most common source of the information 73.3% (318/434) amongst all sources. Unsafe sex 55.3% (240/434), infected blood transfusion 33.2% (144/434), needle sharing 24.7% (107/434) and mother to child transmission 4.1% (18/434) were reported modes of HIV transmission. Condom use during extramarital sex 51.8% (225/434), use of sterilized syringes 24.2% (105/434), restricting sex within couple 22.6% (98/434) and blood safety 20.3% (88/434) were reported HIV preventive measures. Extramarital sex, needle sharing and sharing of the razors/blades were perceived to be the risk behaviors. About 4.9% (30/618) had extramarital sexual experience amongst all participants. Only a quarter (8/30) of those who had extramarital sex used condom regularly.Conclusions: Almost half of the MWRA had limited awareness on HIV transmission and preventive measures. There was poor HIV preventive practices; indicating knowledge-behavior gaps. Awareness raising and behavior change interventions are recommended.Keywords: Human immunodeficiency virus, Knowledge, Married women of reproductive age, Nepal, Practice, Risk perceptio

Counting crocodiles from the sky: Monitoring the critically endangered gharial (Gavialis gangeticus) population with an Unmanned Aerial Vehicle (UAV).

Technology is rapidly changing the methods in the field of wildlife monitoring. Unmanned aerial vehicle (UAV) is an example of a new technology that allows biologists to take to the air to monitor wildlife. Fixed Wing UAV was used to monitor critically endangered gharial population along 46 km of the Babai River in Bardia National Park. The UAV was flown at an altitude of 80 m along 12 pre-designed missions with a search effort of 2.72 hours of flight time acquired a total of 11,799 images covering an effective surface area of 8.2 km2 of river bank habitat. The images taken from the UAV could differentiate between gharial and muggers. A total count of 33 gharials and 31 muggers with observed density (per km2) of 4.64 and 4.0 for gharial and mugger respectively. Comparison of count data between one-time UAV and multiple conventional visual encounter rate surveys data showed no significant difference in the mean. Basking season and turbidity were important factors for monitoring crocodiles along the river bank habitat. Efficacy of monitoring crocodiles by UAV at the given altitude can be replicated in high priority areas with less operating cost and acquisition of high resolution data

SubFoveal Choroidal Imaging in High Myopic Nepalese Cohort

Current image captioning models produce fluent captions, but they rely on a one-size-fits-all approach that does not take into account the preferences of individual end-users. We present a method to generate descriptions with an adjustable amount of content that can be set at inference-time, thus providing a step toward a more user centered approach to image captioning