Assessing the Vascular Deformability of Erythrocytes and Leukocytes: From Micropipettes to Microfluidics

Among the most crucial rheological characteristics of blood cells within the vasculature is their ability to undergo the shape change (i.e., deform). The significance of cellular deformability is readily apparent based solely on the disparate mean size of human erythrocytes (~8 μm) and leukocytes (10–25 μm) compared to the minimum luminal size of capillaries (4–5 μm) and splenic interendothelial clefts (0.5–1.0 μm) they must transit. Changes in the deformability of either cell will result in their premature mechanical clearance as well as an enhanced possibility of intravascular lysis. In this chapter, we will demonstrate how microfluidic devices can be used to examine the vascular deformability of erythrocytes and agranular leukocytes. Moreover, we will compare microfluidic assays with previous studies utilizing micropipettes, ektacytometry and micropore cell transit times. As will be discussed, microfluidics-based devices offer a low-cost, high throughput alternative to these previous, and now rather ancient, technologies

Capacitive displacement sensing for the Nanogate

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2004.Includes bibliographical references (p. 63-64).The Nanogate is a micro electro mechanical systems (MEMS) device that uses a cantilever structure to control the separation between two extremely flat surfaces. It has been proposed that the Nanogate be used as part of a nanoscale instrument for studying the behavior of fluids at the molecular scale. This thesis describes the development of an integrated capacitive displacement sensor which enables nanometer precision measurement of the separation of the surfaces of the Nanogate. The work in this thesis can be divided into two parts: fabrication of a new version of the Nanogate and the development of electronics for the capacitive sensor. The fabrication part involved redesigning the Nanogate package and fabrication process to integrate the capacitive sensing electrodes, as well as to improve the process yield. The development of capacitive sensing electronics for the Nanogate involved the design of an analog front-end to convert capacitance to voltage and a custom high precision data acquisition system to digitize the output. The measured capacitance is converted back to absolute displacement by calibration with a Michelson interferometer-based displacement sensor. The results show a resolution better than 0.1 nm and the long term drift error is less than 1 nm.by Hongshen Ma.S.M

ASTormer: An AST Structure-aware Transformer Decoder for Text-to-SQL

Text-to-SQL aims to generate an executable SQL program given the user utterance and the corresponding database schema. To ensure the well-formedness of output SQLs, one prominent approach adopts a grammar-based recurrent decoder to produce the equivalent SQL abstract syntax tree (AST). However, previous methods mainly utilize an RNN-series decoder, which 1) is time-consuming and inefficient and 2) introduces very few structure priors. In this work, we propose an AST structure-aware Transformer decoder (ASTormer) to replace traditional RNN cells. The structural knowledge, such as node types and positions in the tree, is seamlessly incorporated into the decoder via both absolute and relative position embeddings. Besides, the proposed framework is compatible with different traversing orders even considering adaptive node selection. Extensive experiments on five text-to-SQL benchmarks demonstrate the effectiveness and efficiency of our structured decoder compared to competitive baselines

Tissue factor pathway inhibitor-2 was repressed by CpG hypermethylation through inhibition of KLF6 binding in highly invasive breast cancer cells

<p>Abstract</p> <p>Background</p> <p>Tissue factor pathway inhibitor-2 (TFPI-2) is a matrix-associated Kunitz inhibitor that inhibits plasmin and trypsin-mediated activation of zymogen matrix metalloproteinases involved in tumor progression, invasion and metastasis. Here, we have investigated the mechanism of DNA methylation on the repression of TFPI-2 in breast cancer cell lines.</p> <p>Results</p> <p>We found that both protein and mRNA of TFPI-2 could not be detected in highly invasive breast cancer cell line MDA-MB-435. To further investigate the mechanism of TFPI-2 repression in breast cancer cells, 1.5 Kb TFPI-2 promoter was cloned, and several genetic variations were detected, but the promoter luciferase activities were not affected by the point mutation in the promoter region and the phenomena was further supported by deleted mutation. Scan mutation and informatics analysis identified a potential KLF6 binding site in TFPI-2 promoter. It was revealed, by bisulfite modified sequence, that the CpG island in TFPI-2 promoter region was hypermethylated in MDA-MB-435. Finally, using EMSA and ChIP assay, we demonstrated that the CpG methylation in the binding site of KLF-6 diminished the binding of KLF6 to TFPI-2 promoter.</p> <p>Conclusion</p> <p>In this study, we found that the CpG islands in TFPI-2 promoter was hypermethylated in highly invasive breast cancer cell line, and DNA methylation in the entire promoter region caused TFPI-2 repression by inducing inactive chromatin structure and decreasing KLF6 binding to its DNA binding sequence.</p

The protective role of DOT1L in UV-induced melanomagenesis

The DOT1L histone H3 lysine 79 (H3K79) methyltransferase plays an oncogenic role in MLL-rearranged leukemogenesis. Here, we demonstrate that, in contrast to MLL-rearranged leukemia, DOT1L plays a protective role in ultraviolet radiation (UVR)-induced melanoma development. Specifically, the DOT1L gene is located in a frequently deleted region and undergoes somatic mutation in human melanoma. Specific mutations functionally compromise DOT1L methyltransferase enzyme activity leading to reduced H3K79 methylation. Importantly, in the absence of DOT1L, UVR-induced DNA damage is inefficiently repaired, so that DOT1L loss promotes melanoma development in mice after exposure to UVR. Mechanistically, DOT1L facilitates DNA damage repair, with DOT1L-methylated H3K79 involvement in binding and recruiting XPC to the DNA damage site for nucleotide excision repair (NER). This study indicates that DOT1L plays a protective role in UVR-induced melanomagenesis

EIS using adjustable nanometer-gap electrodes

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 151-154).Electrochemical Impedance Spectroscopy (EIS) is a simple yet powerful chemical analysis technique for measuring the electrical permittivity and conductivity of liquids and gases. Presently, the limiting factor for using EIS as a portable chemical detection technology is the lack of absolute accuracy stemming from uncertainties in the geometrical factor used to convert measurable quantities of capacitance and conductance into the intrinsic parameters of permittivity and conductivity. The value of this geometrical conversion factor can be difficult to predict since it is easily affected by fringing electric fields, manufacturing variations, and surface chemistry. Existing impedance test cells typically address this problem using a calibration liquid with known permittivity and conductivity, however, this correction is not feasible in many applications since the calibration liquid may irreversibly contaminate the test electrodes. This thesis presents a technique for accurately measuring the permittivity and conductivity of liquids and gases without requiring the use of calibration liquids. This technique is made possible by precisely controlling the separation between two spherical electrodes to measure capacitance and conductance of the sample medium as a function of electrode separation. By leveraging the geometrical accuracy of the spherical electrodes and precise control of the electrode separation, the permittivity and conductivity of the sample can be determined without wet calibration. The electrode separation is adjusted using a flexure stage and a servomechanical actuator, which enables control the electrode separation with 0.25 nm resolution over a range of 50 gm. The nanometer smooth surfaces of the spherical electrodes also enable electrode gaps of less than 20 nm to be created.(cont.) The technique for measuring permittivity and conductivity presented in this thesis could eventually be adapted to make miniaturized disposable impedance test cells for chemical analysis. Such systems could take advantage of conductivity assays to determine the presence and concentration of specific substances. The adjustable nanometer electrode gap can also be used to study the properties of chemical and biological systems in highly confined states. These studies are fundamentally important for understanding biochemical processes in natural systems where reactions often take place inside confined structures such as cells, organelles, and the intercellular matrix.by Hongshen Ma.Ph.D

Calibration-free measurement of liquid permittivity and conductivity using electrochemical impedance test cell with servomechanically adjustable cell constant

This paper presents a technique and a device for measuring the permittivity and conductivity of liquids and gases that does not require prior calibration by a reference sample. The technique involves precisely controlling the separation between two closely spaced spherical electrodes to make electrical impedance measurements of the sample media as a function of electrode separation. By leveraging the geometrical accuracy of the spheres and precise control of the electrode separation, the permittivity and conductivity of the sample can be extracted using a simple geometrical model of the electrode. Calibration using a reference sample is replaced by mechanical calibration of the sphere diameter and separation control mechanism, which can be engineered simply and accurately using standard components and processes. The electrode separation is adjusted using a flexure stage and a servomechanical actuator, which enables control of the electrode separation with 0.25 nm resolution with a 50 mum range. Permittivity and conductivity measurements within 1% of established values have been demonstrated.National Science Foundation (Grant CCR-0122419