VictorJuiz/thesis huggingface dataset:
Towards controlled nanostructure fabrication and characterization using combined scanning tunneling microscopy and atomic layer deposition [electronic resource]
Keywords: Physics.

Nanostructures play an increasingly important role in the design of a wide range of modern devices. Because of instrument limitations, major frontiers remain both in the systematic characterization of nanostructures and in the degree of control afforded in their fabrication. This thesis describes the design and realization of a new scientific instrument that combines a nanostructure fabrication technique - atomic layer deposition (ALD) - with a nanostructure characterization technique - scanning tunneling microscopy (STM) - in a single vacuum chamber. The instrument has the capability to monitor individual nanostructures in situ as they are grown with ALD, tracking changes in their physical and electronic structure as they develop. It can be used to monitor the natural growth of extremely thin ALD films with sub-nanometer resolution, providing information about materials which are candidates for thin film devices. In addition, the instrument is intended to be used to activate ALD growth locally through the influence of the STM tip, providing unprecedented control over the size, shape, and configuration of the created nanostructures and enabling their systematic study.
Towards internal wave resolving simulations of the ocean [electronic resource]
Keywords: Civil and Environmental Engineering.

Most ocean models solve the hydrostatic primitive equations. Small-scale processes such as nonlinear internal solitary waves, however, require computationally expensive nonhydrostatic simulations to be well-resolved because the balance of nonlinearity and dispersion is responsible for the wave's shape. The main goal of this dissertation is to inform the practice of nonhydrostatic ocean modeling. To this end, I have examined the accuracy and stability of poplar methods used in nonhydrostatic modeling. Most ocean models are second-order accurate, inducing numerical dispersion generated from odd-order terms in the truncation error. Numerical dispersion is problematic because it mimics physical dispersion due to nonhydrostasy. To ensure relative dominance of physical over numerical effects, simulations require the horizontal grid spacing ([Delta] x) to be less than the depth of the internal interface (h1). When this condition is not satisfied, numerical dispersion overwhelms physical dispersion, and modeled internal waves exist with a dynamical balance between nonlinearity and numerical dispersion. Satisfaction of this condition may be a significant additional resolution requirement beyond the current state-of-the-art in ocean modeling. To cope with this high horizontal resolution requirement, it becomes necessary to find other means of reducing resolution requirements and computational cost. To this end, I suggest a specific framework which has been implemented as a prototype for a next-generation ocean model. The new model is a nonhydrostatic, isopycnal-coordinate ocean model, which to my knowledge is the first of its kind. Isopycnal coordinates provide a natural representation of the problem physics which in turn reduces the number of vertical grid points and thus improves efficiency. Existing isopycnal-coordinate models are purely hydrostatic owing to the nearly hydrostatic scaling of most oceanic processes and the belief that nonhydrostatic effects are only associated with overturning motions which cannot be represented in isopycnal coordinates. However, processes such as nonlinear internal solitary waves are clearly nonhydrostatic and not associated with overturning motions. Thus a nonhydrostatic isopycnal coordinate model may be well-suited to simulating nonlinear internal solitary waves. Ideally, when the internal wave structure is predominantly mode-1, an isopycnal model with only two layers may suffice. I demonstrate that the new model is capable of simulating a variety of nonhydrostatic processes in idealized test cases with a reduced number of vertical layers.
Tracheal progenitor outgrowth from the niche during Drosophila melanogaster metamorphosis [electronic resource]
Keywords: Genetics.

While there has been great progress in identifying stem and progenitor cells and the signals that control their proliferation and differentiation, how stem/progenitor cells exit their niche and how they form new tissue is not well understood. Unlike in the embryo, tissue formation in an adult animal faces new challenges such as longer distances to migrate and a complex milieu of differentiated tissue to migrate around and/or coordinate with. To restore function to a tissue, stem/progenitor cells must also integrate into healthy tissue and coordinate growth with decaying tissue. In this thesis, I examine how tracheal progenitor cells exit their niche to form tracheal tissue during Drosophila melanogaster metamorphosis. Tracheal progenitors exit the niche in two waves. During the first wave, progenitors migrate onto the basal surface of larval tracheal branches destined for destruction, and track along the decaying branches. Progenitor outgrowth requires the embryonic tracheal branch inducer, Breathless FGFR, and surprisingly, the Branchless FGF ligand is expressed in larval branches along which progenitors crawl. In this way, outgrowth is coordinated with tissue decay. Progenitors that remain within the niche during the first wave exit later. However, instead of moving onto the basal surface of larval branches, progenitors exiting the niche during this second wave move along the apical surface, displacing larval cells, and repopulating the tracheal branch. This latter process does not resemble branching morphogenesis in the embryo and does not require Bnl/Btl FGF signaling, demonstrating that progenitor outgrowth does not always require embryonic guidance cues.
Trading volume reactions to earnings announcements and future firm performance [electronic resource]
Keywords: Business.

I investigate whether firms with higher abnormal trading volume (ATV) around earnings announcements (EAs) outperform those with lower ATV over the short and long terms following the EA. In addition, I address whether any positive relation between ATV around EAs and future firm performance is weaker for firms with a higher proportion of shares held by sophisticated investors. Consistent with theories that attribute ATV around public announcements primarily to differing investor interpretations of the news and that link differential interpretation to future returns, I find that, for several years after an EA, firms in the highest decile of ATV significantly outperform those in the lowest decile. Further, I find that ATV and earnings surprises explain future returns incremental to the three Fama and French (1993) and momentum risk-factors. Next, consistent with the proportion of ATV driven by lack of consensus regarding the price being lower when the presence of rational investors is higher, I document that the level of investor sophistication−a proxy for investor rationality−attenuates the positive relation between ATV and future returns. Taken together, my study lends support to and links two streams of theories from financial economics, and demonstrates that trading volume reactions to EAs provide information about future returns and firm financial performance that cannot be deduced from the price reactions or the magnitudes of earnings surprises. My study also documents that the positive relation between ATV and future firm performance is sensitive to the level of security holdings of sophisticated investors.
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines [electronic resource]
Keywords: Genetics

The human genome's nucleotide sequence contains a small amount of information relative to the complexity of the organism. The diversity of developmental programs and stimulus responses is instead enabled by a vast regulatory network of chemical modifications and protein interactions that determine the activity level of each genome element dynamically. Recent advances in molecular profiling techniques have led to the creation of large data sets that assay each regulatory interaction across the entire genome at once, with high sensitivity and precision. Here I introduce a new computational method, UniPeak, that synthesizes the output from any number of these experiments into a single straightforward analysis with rigorous quantitative measures. I then apply this method to the largest available data sets of genome regulation experiments, and integrate them with parallel experiments on genome activity. I discover and characterize novel regulatory interactions, and model how these interactions regulate the activity of genes.
Transformer array power combining and stacking for CMOS RF power amplifiers [electronic resource]
Keywords: Electrical Engineering

CMOS technology scaling has enabled the integration of RF transceivers on a single chip for various applications. However, as the feature sizes of the transistors scale, their breakdown voltages are reduced. Lower breakdown voltages lower the maximum voltage swings across the transistors and necessitate operation from a lower supply voltage. These factors, in turn, impose significant limitations on RF power amplifier design: (1) the low voltage swings limit the maximum power that can be delivered to the load, and (2) the DC-DC converter needed to generate a low supply voltage for the power amplifier from typical battery voltages increases the power consumption, size, and cost of the design. To address the first challenge, transistor stacking and transformer-based power combining are investigated as means of increasing the output power, while to address the second issue, transistor stacking and amplifier stacking are considered. Two CMOS RF power amplifier architectures serve as vehicles for exploring these concepts, each leading to the design and implementation of an experimental prototype. The first design is based on a stacked amplifier architecture with an off-chip matching network. Transistor stacking is used to increase the output power and supply voltage of the power amplifier, and a bias circuit is designed to enable operation of the power amplifier from a large supply voltage without exceeding the transistor breakdown limitations. The second design is an array RF PA architecture that employs (1) series-parallel transformers, (2) transistor stacking, and (3) amplifier stacking. This array RF PA uses series-parallel combinations of transformers to provide simultaneous impedance transformation and power combining. The proposed scalable transformer array architecture offers the possibility of designing a power amplifier to meet given specifications of output power and load impedance over a wide bandwidth. Stacking transistors in the array RF PA increases the output power provided by each of the unit PA stages comprising the array. In addition, the PA stages are themselves stacked. The two stacking methods increase the operating supply voltage. To demonstrate the proposed concept, a 2-by-4 amplifier array has been integrated in a 65-nm CMOS technology.
Two graph-based tests for high-dimensional inference [electronic resource]
Keywords: Statistics.

With modern science there is a growing emphasis on multivariate, complex data types. Some of these data are high dimensional. Others, such as survey preference, network, and tree data, cannot be characterized easily with standard models on Euclidean spaces. This dissertation details the investigation in this new setting of two classic statistical problems: change-point detection and two-sample comparison of categorical data. Change-point models are widely used in various fields for detecting lack of homogeneity in a sequence of observations. In many applications, the dimension of the observations in the sequence can be very high, even much larger than the length of the sequence. Testing the homogeneity of such sequences is a challenging but important problem. Existing approaches are limited in many ways. We proposed a new non-parametric approach that can be applied to data in high dimension, and even to non-Euclidean object data, as long as an informative similarity measure on the sample space can be defined. The approach is graph-based two-sample tests adapted to the scan-statistic setting. Graph-based two-sample tests are tests base on graphs connecting observations by similarity [Friedman and Rafsky, 1979, Rosenbaum, 2005]. We show that this new approach is powerful in high dimensions compared to parametric approaches. We also derive accurate analytic $-value approximations for very general situations, which lead to easy off-the-shelf homogeneity testing for large multivariate data sets. This approach has been applied on two data sets: The determination of authorship of a classic novel, and the detection of change in a social network over time. Two-sample comparison of categorical data is a classic problem in statistics. In many modern applications, the number of categories can be quite large, even comparable to the sample size, causing existing methods to have low power. When the number of categories is large, there is often underlying structure on the sample space that can be exploited. We propose a general non-parametric approach that makes use of similarity information on the space of categories in two-sample tests. Our approach addresses a shortcoming of existing graph-based two-sample tests by no longer requiring uniqueness of the underlying graph, thus allowing ties in the distance matrix defining the graph. We found two types of statistics that are both powerful and fast to compute. We show that their permutation null distributions are asymptotically normal and that their $-value approximations under typical settings are quite accurate, facilitating the application of this approach.
`Two souls, two thoughts', two self-schemas [electronic resource] : positive social and academic consequences of double consciousness in African-Americans
Keywords: Psychology.

African-Americans have long been theorized to experience double consciousness— a two-ness characterized by a sense of self as American and African-American. Six studies examined the hypothesis that this double consciousness, although forged and fueled by racism and inequality, can facilitate positive social and academic consequences for African-Americans. First, Studies 1-3 provided evidence that double consciousness can function as two self-schemas, two ways of thinking about the self that develop through elaborated engagement with two American cultures. Specifically, African-American participants were shown to shift their social behaviors (i.e., giving a speech, making cooperative decisions) in schema-relevant ways from more independent when primed with mainstream-American culture to more interdependent when primed with African-American culture. Study 3 showed that self-construal mediated this capacity to cultural frame-switch. Then, Studies 4 and 5 tested and supported the prediction that mainstream university settings that encourage frame-switching, through the inclusion of African-American ideas and practices, can enhance academic motivation and performance (i.e., persistence, verbal and creative problem solving) for African-Americans. Finally, using a national data set, Study 6A/B provides further evidence that educational settings which are inclusive of diverse cultural practices can promote achievement behaviors, as well as belongingness (positive interdependence), among African-American undergraduates. The discussion examines double consciousness as a basic psychological phenomenon that may arise with subordinate status (e.g., female or working class identities, situational positions of low power), and suggests the benefits of mainstream settings that promote frame-switching through the inclusion of non-dominant cultural ideas and practices.
Ultrasound induced neurostimulation [electronic resource]
Keywords: Bioengineering.

Ultrasound-induced neurostimulation has recently gained increasing attention. Developments in the use of ultrasound to stimulate and modulate neural activity have raised the possibility of using ultrasound as a new investigative and therapeutic tool in brain research. Little is known about the mechanisms by which it affects neural activity or about the range of acoustic parameters and stimulation protocols that elicit responses. In this thesis, conditions are established for transcranial stimulation of the nervous system in vivo, using the mouse somatomotor response. It is reported that (1) continuous-wave stimuli are as effective as or more effective than pulsed stimuli in eliciting responses, and responses are elicited with stimulus onset rather than stimulus offset; (2) stimulation success increases as a function of both acoustic intensity and acoustic duration; (3) interactions of intensity and duration suggest that successful stimulation results from the integration of stimulus amplitude over a time interval of 50 to 150 ms; (4) the motor response elicited appears to be an all-or-nothing phenomenon, meaning stronger stimulus intensities and durations increase the probability of a motor response without affecting the duration or strength of the response; and (5) motor responses, measured by normalized EMG signals in the neck and tail regions, change signifcantly when sonicating rostral and caudal regions of the mouse motor cortex. Taken together our findings present good evidence for being able to target selective parts of the motor cortex with ultrasound neurostimulation in the mouse, steps that should provide encouragement for the development of new applications in larger animal models, including humans.
Under the Microscope: Why US Intelligence Underestimated the Soviet Biological Weapons Program
Keywords: CISAC
Center for International Security and Cooperation
Stanford University
declassified documents
intelligence
security
United States
Soviet Union
bioweapons
Thesis

Through trend and detail analysis of declassified U.S. intelligence documents, this paper shows that ambiguity in dual-use biological research was the main underlying cause of the US Intelligence underestimation of the Soviet Bioweapons program. Although lack of prioritization of biowarfare issues and complacency due to mirror imaging also existed, such intelligence failures were a result of the uncertainty caused by the dual-use nature of biological research. General statements, lack of absolute certainty about the presence of a Soviet bioweapons program, and wavering attention given to intelligence collection on bioweapons in the Soviet Union were common trends amongst the documents. The nature of biological research and public health events do not lend themselves easily for differentiation between defensive, natural, and illicit. The inability to distinguish between legitimate research and biological research for offensive military purposes was a primary reason for the lack of certainty about the Soviet Union’s pursuits in biology. This unfortunately continues to be an issue as biological technology advances. But due to the clear ambiguity in purpose and potential of dual-use biological research, as well as to avoid infringement upon scientific research, intelligence communities must create stronger relationships with the scientific community, which in turn must develop strong community-responsibility and incentives to detract scientists from pursuing bioweapons under any capacity.
Understanding and tuning organic semiconductor packing during solution processing [electronic resource]
Keywords: Chemical Engineering.

Circuits based on organic semiconductors (OSCs) are being currently explored for flexible, transparent and low-cost electronic applications. However, to realize such applications, the charge transport performance of OSCs in thin film transistors (TFTs) must be improved. Using a solution processing method called solution shearing, we were able to create metastable polymorphs of various OSCs and improve the electronic performance. This is the first time industrially friendly coating processes have been utilized to change the molecular packing of OSCs. Changing the molecular packing to form metastable polymorphs through solution processing allows researchers to complement traditional synthetic methods to generate high performance OSCs. The first part of my research work details the use of solution shearing to increase the mobility of small molecular OSCs. The model OSC 6,13-bis(triisopropylsilylethynyl) pentacene (TPn) is used as the model compound for our study, and various metastable polymorph are created through solution processing. The highest mobility obtained for the metastable TFTs (4.6 cm2 V-1 s-1 ) is three times higher than the previous highest mobility found in literature. The lattice strain method to modify OSC charge transport was shown to be general to certain classes of small molecule and polymeric OSCs as well. In order to study crystallization of OSCs during solution shearing, my research extended to constructing a miniaturized solution shearing machine to be used in-situ at synchrotron facilities. We obtained high speed (100 frames/s), in-situ images of metastable crystal growth using a microbeam (20 [micrometer]) grazing incidence X-ray diffraction (GIXD) method. Using knowledge from these experiments, we were able to obtain design rules for creating lattice strain and polymorphism using other solution processing techniques. Finally, our research has brought the use of lattice strain closer industrial use through the use of selective deposition of OSCs. Industrial applications of lattice strained OFETs requires that the OFETS are patterned. We have developed a surface functionalization procedure that utilizes hydrophobic/hydrophilic interactions to isolate lattice strained OSCs. We show that charge carrier mobilities over 2 cm2/Vs are possible in the patterned OFETs of TIPS-pentacene, and that strained OFETs can exist at patterning sizes of 100 microns and lower. We show that the pattern size can have an effect on the lattice strain possible in the OSCs, and investigate methods that enable sub 10 micron scale patterning using solution shearing. In summary, we have shown that high performance, metastable polymorphs of various organic semiconductors can be fabricated through solution processing methods, and the underlying reasons for polymorphism is explained through the use of in-situ X-ray diffraction techniques.