Miracle-dz/UniFAR-FTUs huggingface dataset:
Advanced Methods in Comparative Politics: Modeling Without Conditional Independence

OF THE DISSERTATION Advanced Methods in Comparative Politics: Modeling Without Conditional Independence by David George Carlson Doctor of Philosophy in Political Science Washington University in St. Louis, 2018 Professor Jacob M. Montgomery, Chair One of the most significant assumptions we invoke when making quantitative inferences is the conditional independence between observations. There are, however, many situations when we may doubt this independence. For instance, two seemingly distinct data-generating processes may in fact share unobserved relations. Time-series and cross-sectional studies are also plagued by a lack of independence. If we ignore this common violation of our fundamental modeling assumptions we may draw improper conclusions from our data. This dissertation introduces two methods to the political science literature: a zero-inflated multivariate ordered probit and Gaussian process regression for time-series cross-sectional analyses. This latter model is then applied to demonstrate that executives in Latin America enjoy increased public support following ideological moderation, but executives are less willing to moderate during election years. These effects, however, are conditional on the extremity of the executive. The dissertation as a whole contributes both methodologically and theoretically to the field.
Relationship between ERCC1 polymorphisms, disease progression, and survival in the Gynecologic Oncology Group Phase III Trial of intraperitoneal versus intravenous cisplatin and paclitaxel for stage III epithelial ovarian cancer.

PURPOSE We hypothesized that common polymorphisms in excision repair cross-complementation group 1 (ERCC1), involved in nucleotide excision repair of platinum-induced damage, would be associated with progression-free survival (PFS) and overall survival (OS) in women with optimally resected, stage III epithelial ovarian cancer (EOC) treated with cisplatin and paclitaxel (C+P). PATIENTS AND METHODS Single nucleotide polymorphism analysis was carried out by direct pyrosequencing at two sites (codon 118 and C8092A) in ERCC1 in leukocyte DNA from women who participated in the Gynecologic Oncology Group (GOG) phase III protocol-172 and were randomly assigned to intraperitoneal or intravenous C+P. RESULTS ERCC1 genotyping was performed in 233 of the 429 women who participated in GOG-172. The genotype distribution at codon 118 was 17% with C/C, 43% with C/T, and 40% with T/T, and the genotype distribution at C8092A was 56% with C/C, 37% with C/A, and 7% with A/A. Adjusted Cox regression analysis revealed that the codon 118 polymorphism in ERCC1 was not significantly associated with disease progression or death. Women with the C8092A C/A or A/A genotypes compared with the C/C genotype had an increased risk of disease progression (hazard ratio [HR] = 1.44; 95% CI, 1.06 to 1.94; P = .018) and death (HR = 1.50; 95% CI, 1.07 to 2.09; P = .018). Median PFS and OS were 6 and 17 months shorter for women with the C8092A C/A or A/A genotypes versus the C/C genotype, respectively. CONCLUSION Although the ERCC1 codon 118 polymorphism does not seem to be associated with clinical outcome, the C8092A polymorphism was an independent predictor of PFS and OS in women with optimally resected EOC.
hMre11 and hRad50 nuclear foci are induced during the normal cellular response to DNA double-strand breaks

We previously identified a conserved multiprotein complex that includes hMre11 and hRad50. In this study, we used immunofluorescence to investigate the role of this complex in DNA double-strand break (DSB) repair. hMre11 and hRad50 form discrete nuclear foci in response to treatment with DSB-inducing agents but not in response to UV irradiation. hMre11 and hRad50 foci colocalize after treatment with ionizing radiation and are distinct from those of the DSB repair protein, hRad51. Our data indicate that an irradiated cell is competent to form either hMre11-hRad50 foci or hRad51 foci, but not both. The multiplicity of hMre11 and hRad50 foci is much higher in the DSB repair-deficient cell line 180BR than in repair-proficient cells. hMre11-hRad50 focus formation is markedly reduced in cells derived from ataxia-telangiectasia patients, whereas hRad51 focus formation is markedly increased. These experiments support genetic evidence from Saccharomyces cerevisiae indicating that Mre11-Rad50 have roles distinct from that of Rad51 in DSB repair. Further, these data indicate that hMre11-hRad50 foci form in response to DNA DSBs and are dependent upon a DNA damage-induced signaling pathway.
Rehabilitation in the context of HIV: an interprofessional multi-stakeholder process for curriculum development.

UNLABELLED With longer survival, individuals living with human immunodeficiency virus (HIV) infection are facing a multitude of health-related challenges due to HIV, its associated concurrent health conditions, and treatments. Despite the need for rehabilitation, few rehabilitation professionals work with people living with HIV, with many feeling they lack adequate knowledge and skills to assess and treat this population. PURPOSE We describe a national multi-stakeholder consultation used to inform the development of an interprofessional curriculum for rehabilitation professionals on HIV/AIDS. METHODS We conducted a series of focus groups and key informant interviews (either in person or by telephone) with people living with HIV, rehabilitation professionals, physicians, curriculum experts, and other HIV stakeholders. Participants were asked to describe their perceived learning needs of rehabilitation professionals and to identify relevant content and delivery methods for a future interprofessional HIV/AIDS curriculum. RESULTS Seven focus groups and 31 interviews with a total of 74 key informants were conducted, resulting in recommendations for content to include in HIV rehabilitation professional curricula and ways to deliver these curricula effectively. CONCLUSIONS A national multi-stakeholder environmental scan was a useful preliminary step to inform the development of an interprofessional curriculum for rehabilitation professionals on HIV/AIDS. Recommendations serve as scaffold from which to build content and delivery of future curricula.
SQT1, which encodes an essential WD domain protein of Saccharomyces cerevisiae, suppresses dominant-negative mutations of the ribosomal protein gene QSR1

QSR1 is an essential Saccharomyces cerevisiae gene, which encodes a 60S ribosomal subunit protein required for joining of 40S and 60S subunits. Truncations of QSR1 predicted to encode C-terminally truncated forms of Qsr1p do not substitute for QSR1 but do act as dominant negative mutations, inhibiting the growth of yeast when expressed from an inducible promoter. The dominant negative mutants exhibit a polysome profile characterized by 'half-mer' polysomes, indicative of a subunit joining defect like that seen in other qsr1 mutants (D. P. Eisinger, F. A. Dick, and B. L. Trumpower, Mol. Cell. Biol. 17:5136-5145, 1997.) By screening a high-copy yeast genomic library, we isolated several clones containing overlapping inserts of a novel gene that rescues the slow-growth phenotype of the dominant negative qsr1 truncations. The suppressor of qsr1 truncation mutants, SQT1, is an essential gene, which encodes a 47.1-kDa protein containing multiple WD repeats and which interacts strongly with Qsr1p in a yeast two-hybrid system. SQT1 restores growth and the "half-mer" polysome profile of the dominant negative qsr1 mutants to normal, but it does not rescue temperature-sensitive qsr1 mutants or the original qsr1-1 missense allele. In yeast cell lysates, Sqt1p fractionates as part of an oligomeric protein complex that is loosely associated with ribosomes but is distinct from known eukaryotic initiation factor complexes. Loss of SQT1 function by down regulation from an inducible promoter results in formation of half-mer polyribosomes and decreased Qsr1p levels on free 60S subunits. Sqt1p thus appears to be involved in a late step of 60S subunit assembly or modification in the cytoplasm.
Suppression of citrus leafminer, Phyllocnistis citrella, with an attract‐and‐kill formulation

The citrus leafminer, Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae), is a worldwide pest of citrus crops and is responsible for proliferation of citrus bacterial canker, Xanthomonas axonopodis (Hasse) pv. citri (Gamma Proteobacteria: Xanthomonadaceae). We developed and evaluated an attracticide formulation, termed MalEx, for control of P. citrella. MalEx is a viscous paste with UV‐protective properties that is dispensed as 50‐μl droplets using custom‐made calibrated pumps. A formulation containing 0.016%P. citrella pheromone [3:1 blend of (Z,Z,E)‐7,11,13‐hexadecatrienal and (Z,Z)‐7,11‐hexadecadienal] and 6% permethrin was found to suppress male response to pheromone in the field better than formulations containing 10× less pheromone. Although formulations without permethrin showed some suppression of male activity because of mating disruption, addition of 6% permethrin to the formulation was required for optimal efficacy. When MalEx, containing 0.016% pheromone and 6% permethrin, was applied at 3 000 point sources ha−1, the application height did not influence efficacy of male P. citrella suppression within mature 4‐m tall citrus trees. Decreasing the rate of MalEx from 3 000 to 1 500 droplets ha−1 reduced efficacy as measured by both male P. citrella activity and larval infestation. Although 4 500 droplets ha−1 did not result in statistically better efficacy than 3 000 droplets ha−1, there was a noticeable trend for higher efficacy as droplet density increased. Continuous treatment of 0.5‐ha blocks of citrus with MalEx over the course of 112 days reduced larval infestation of new flush, as compared with those in untreated control plots, by 3.6–7.2× depending on droplet application density. In laboratory behavioral bioassays, the attractiveness of MalEx droplets to male P. citrella was drastically reduced after 21 days of field aging. However, our laboratory investigation confirmed that 100% of males contacting MalEx droplets, aged up to 35 days in the field, were killed within 24 h. Direct observation of male P. citrella behavior in the field confirmed that attracted males made contact with droplets. Control of P. citrella with MalEx should reduce the number of required broad spectrum sprays for leafminer management in both field and citrus nursery settings.
Detection and classification of emergent behaviors using multi-agent simulation framework (WIP)

In recent years the concept of emergence has captured significant attention in the field of complex systems. However, the inability to predict and control emergent phenomena prevents us from exploring its full potential. The research effort in this paper focuses on exploring emergent behaviors by proposing a framework for analysis of systems that exhibit such behaviors. The framework provides a platform for simulating and analyzing behaviors in multi-agent system, including detection and classification of emergence into different types. In this paper, we follow the classification of emergent behaviors according to Fromm's taxonomy. In addition, the paper presents a scenario implementation using swarms of Unmanned Aerial Vehicles (UAVs) to demonstrate the applicability of the proposed approach. Since this is a part of on-going research, future direction is also discussed.
[Imaging and quantitative measurement of brain extracellular space using MRI Gd-DTPA tracer method].

OBJECTIVE To observe the diffusion of Gd-DTPA in brain extracellular space (ECS) by magnetic resonance imaging(MRI) and investigate the feasibility of ECS measurement by using MRI tracer method in vivo. METHODS 2 microL Gd-DTPA was introduced into ECS by caudate nucleus according to stereotaxic atlas in 8 Sprague Dawley(SD) rats (male, 280-320 g). The MRI scans were performed at 1 h, 3 h, 6 h, 9 h and 12 h respectively after administration. MRI appearances of Gd-DTPA diffusion and distribution was observed and compared. The MRI signal enhancement was measured at each time point. The neuroethology assessment was performed after MRI scanning at 12 h. RESULTS The injection was accurate at the center of the caudate nucleus in 6 rats, while, at the capsula externa in other 2 rats. Gd-DTPA diffused isotropically after it was introduced into caudate nucleus, which spread into lateral cortex at 3 h. The MRI signal enhancement distributed mainly in the middle cerebral artery territory. A significant difference was found between the signal enhancement ratio at 1 h and that at 3 h in the original point of caudate nucleus (t=95.63, P<0.01), and the signal enhancement attenuated following the exponential power function y=1.7886x(-0.1776) (R2=0.94). In 2 rats with the injection point at capsula externa, Gd-DTPA diffused anisotropically along the fiber track of white matter during 1 h to 3 h, and spread into the lateral cortex at 6 h. CONCLUSION The diffusion and clearance of Gd-DTPA in brain ECS could be monitored and measured quantitatively in vivo by MRI tracer method.
Routing and Spectrum Allocation in OFDM-Based Optical Networks with Elastic Bandwidth Allocation

Orthogonal Frequency Division Multiplexing (OFDM) has been recently proposed as a modulation technique for optical networks, due to its good spectral efficiency and impairment tolerance. Optical OFDM is much more flexible compared to traditional WDM systems, enabling elastic bandwidth transmissions. We consider the planning problem of an OFDM-based optical network where we are given a traffic matrix that includes the requested transmission rates of the connections to be served. Connections are provisioned for their requested rate by elastically allocating spectrum using a variable number of OFDM subcarriers. We introduce the Routing and Spectrum Allocation (RSA) problem, as opposed to the typical Routing and Wavelength Assignment (RWA) problem of traditional WDM networks, and present various algorithms to solve the RSA. We start by presenting an optimal ILP RSA algorithm that minimizes the spectrum used to serve the traffic matrix, and also present a decomposition method that breaks RSA into two substituent subproblems, namely, (i) routing and (ii) spectrum allocation (R+SA) and solves them sequentially. We also propose a heuristic algorithm that serves connections one-by-one and use it to solve the planning problem by sequentially serving all traffic matrix connections. To feed the sequential algorithm, two ordering policies are proposed; a simulated annealing meta-heuristic is also used to obtain even better orderings. Our results indicate that the proposed sequential heuristic with appropriate ordering yields close to optimal solutions in low running times.
Load power estimation based secondary control for microgrids

The well-known active power-frequency and reactive power-voltage amplitude droop control is widely used in the coordinative control of parallel inverters in microgrids. However, this conventional droop method may cause frequency and voltage deviation, which affects the accuracy of power supply. This paper proposes a novel secondary control strategy to compensate this deviation. This strategy mimics the Master-Slave control but requires no communication lines among the parallel inverters. The master inverter adopts conventional droop method (using power to control frequency and voltage amplitude) and is controlled as a voltage source while the slave inverters adopt reversed droop method (using frequency and voltage amplitude to control power) and are controlled as current sources. The droop characteristic bias of slave inverters is designed online based on the estimation of load power demand. Through this method, frequency and voltage deviation can be eliminated and power sharing can be realized among all the slave inverters. Simulation and experimental results are provided to prove the effectiveness of the proposed control strategy.
Racial/Ethnic Transition and Hierarchy Among Ascending Neighborhoods

This article examines the racial/ethnic population dynamics of ascending neighborhoods—those experiencing socioeconomic growth. Drawing on Census and American Community Survey data from 1990 to 2010, we first explore whether changes in racial/ethnic composition occur alongside ascent. We find that, while most neighborhoods’ racial/ethnic composition does not dramatically change during this period, neighborhoods that experienced ascent are much more likely to transition from majority-minority to mixed race or predominantly White than nonascending neighborhoods. Then, we use microdata to analyze whether two potential drivers of ascent, the in-migration of higher-socioeconomic status (SES) households and changes in the fortunes of long-term residents, are racially/ethnically stratified. We argue that the process of neighborhood socioeconomic ascent perpetuates neighborhood racial/ethnic hierarchy. While most Black and Hispanic neighborhoods remain majority-minority, those that ascend are more likely to experience a succession of high-SES White residents replacing minority residents.
A Critical Comparison of Alternative Distribution Configurations in Omni-Channel Retailing in Terms of Cost and Greenhouse Gas Emissions

New opportunities and challenges forced by the ever-increasing importance of the online channel have arisen for retailers. The retailing industry is moving to a new phase, in which the distinctions between traditional and online channels disappear, namely omni-channel (OC) retailing. At the same time, the awareness of environmentally sustainable processes has been enhanced around the world and the environmental impact that results from the online order fulfilment process is becoming a key issue for logistics managers. The new challenge is to understand how multiple channels can be synergistically managed to provide a seamless customer experience, taking an economic and environmental perspective simultaneously. Retailers need to define the distribution configuration for serving the online demand, making decisions on the integration level between online and traditional channels. In this paper, we developed an assessment model of the operational costs and greenhouse gas emissions for three distribution configurations in OC retailing. The model was also applied to a real case operating in the consumer electronics industry. Results highlighted that the search for synergies between online and traditional flows in both warehouse and transport activities is a key factor for the economic and environmental sustainability of OC systems.
Does the adolescent patellar tendon respond to 5 days of cumulative load during a volleyball tournament?

Patellar tendinopathy (jumper's knee) has a high prevalence in jumping athletes. Excessive load on the patellar tendon through high volumes of training and competition is an important risk factor. Structural changes in the tendon are related to a higher risk of developing patellar tendinopathy. The critical tendon load that affects tendon structure is unknown. The aim of this study was to investigate patellar tendon structure on each day of a 5‐day volleyball tournament in an adolescent population (16–18 years). The right patellar tendon of 41 players in the Australian Volleyball Schools Cup was scanned with ultrasound tissue characterization (UTC) on every day of the tournament (Monday to Friday). UTC can quantify structure of a tendon into four echo types based on the stability of the echo pattern. Generalized estimating equations (GEE) were used to test for change of echo type I and II over the tournament days. Participants played between eight and nine matches during the tournament. GEE analysis showed no significant change of echo type percentages of echo type I (Wald chi‐square = 4.603, d.f. = 4, P = 0.331) and echo type II (Wald chi‐square = 6.070, d.f. = 4, P = 0.194) over time. This study shows that patellar tendon structure of 16–18‐year‐old volleyball players is not affected during 5 days of cumulative loading during a volleyball tournament.
Collaboratively modeling buildings from large-scale street-side and remote sensing images

This paper proposed an approach to rapidly generate 3D models for street-side buildings from street-side images, remote sensing images, and GPS information. Traditional modeling methods usually require a single user to fulfill all processes of 3D modeling, and lack efficient management on massive data. Thus, they are unsuitable for large-scale modeling. In order to overcome those drawbacks, we employ the pipeline idea. The modeling processes are divided into several steps, which are further assembled to form a pipeline elaborately. We allocate computing resources into each step according to their requirements; on the other side, human resources are deployed into the pipeline to achieve team-work modeling. To demonstrate the effectiveness of our approach, we developed a distributed prototype system for rapid large-scale urban 3D modeling. This system was tested to build an urban scene with more than 500, 000 street-side images. The results show great improvement on modeling efficiency compared with traditional methods, and it reveals a great prospect in applications.
Evolution of Different Y Chromosomes in Two Medaka Species, Oryzias dancena and O. latipes

Although the sex-determining gene DMY has been identified on the Y chromosome in the medaka (Oryzias latipes), this gene is absent in most Oryzias species, suggesting that closely related species have different sex-determining genes. Here, we investigated the sex-determination mechanism in O. dancena, which does not possess the DMY gene. Since heteromorphic sex chromosomes have not been reported in this species, a progeny test of sex-reversed individuals produced by hormone treatment was performed. Sex-reversed males yielded all-female progeny, indicating that O. dancena has an XX/XY sex-determination system. To uncover the cryptic sex chromosomes, sex-linked DNA markers were screened using expressed sequence tags (ESTs) established in O. latipes. Linkage analysis of isolated sex-linked ESTs showed a conserved synteny between the sex chromosomes in O. dancena and an autosome in O. latipes. Fluorescence in situ hybridization (FISH) analysis of these markers confirmed that sex chromosomes of these species are not homologous. These findings strongly suggest an independent origin of sex chromosomes in O. dancena and O. latipes. Further analysis of the sex-determining region in O. dancena should provide crucial insights into the evolution of sex-determination mechanisms in vertebrates.