Miracle-dz/UniFAR-FTUs huggingface dataset:
Photomask-based integration process of low-defect suspended carbon nanotubes into SOI MEMS

A fully-developed photomask-based integration process is reported. The process can integrate suspended carbon nanotubes (CNTs) into micro-structures on silicon-on-insulator chips. The process features batch-compatible fabrication and post-growth metallization of suspended CNTs, which has never been demonstrated by any other processes. The post-growth metallization avoids deterioration of the metals at the elevated CNT growth temperature and enables mechanically robust double-clamped configuration. Two key steps ensure a significant reduction of the risk for damage or contamination of the CNTs during post-growth processing. SiO2 bridges were fabricated to physically support CNTs during the wet processing, and a protective Al2O3 layer (∼40 nm) was deposited to prevent resist contamination during lithography. The combination of these two steps enables the removal of the unprotected suspended segments of unwanted CNTs by oxygen plasma ashing, improving device yield by a factor of six. The electrically interfaced suspended CNT device possessed high CNT quality (D/G+ intensity ratio of 1/224 in Raman spectroscopy) and good electrical properties, such as low device resistances as low as 105 kΩ and reduced gate hysteresis as low as 65 mV in ambient air. Measurements of eights devices indicate that the release step did not have a systematic influence on the device resistances.
Applied Dynamic Factor Modeling in Finance

In this dissertation, I study model misspecification in applications of dynamic factor models to finance. In Chapter 1, my co-author Jacob Warren and I examine factors for volatility of equities. Historical literature on the subject decomposes volatility into a factor component and an idiosyncratic remainder. Recent work has suggested that idiosyncratic volatility of US equities data has a factor structure, with the factor highly correlated with, and possibly precisely the market volatility. In this paper we attempt to characterize the underlying factor and find that it can be decomposed into a statistical (PCA) and structural (market volatility) factor. We also show that this feature is not unique to equities, appearing in diverse sets of financial data. Lastly, we find that this dual-factor approach is slightly dominated in forecasting environments by a single statistical factor, suggesting that accurate measurement of the factors provides a direction for future work. In Chapter 2, I explore the use of dynamic factor models in yield curve forecasting and an exploration of the spanning hypothesis – that is, whether all information necessary for forecasting yields is contained in the current yield curve. Only linear tests of the spanning hypothesis are typically conducted in the literature, and the results are subject to substantial disagreement. In this paper, I explore a key modern nonlinearity, namely the zero lower bound (ZLB). I first demonstrate in simulation that only very small nonlinearities in the measurement equation are necessary to break down the assumed linear spanning relationship. Because bond yields are determined by forward-looking behavior of investors, the effect of the ZLB affects spanning results as early as 1995. New nonlinear spanning tests are found to behave appropriately. Using the full set of yields instead of truncating to a small number of principal components is quantitatively important but does not eliminate the omitted nonlinearity effect. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Economics First Advisor Francis X. Diebold
Facultative role for T cells in extrafollicular Toll-like receptor-dependent autoreactive B-cell responses in vivo

Extrafollicular (EF) B-cell responses are increasingly being recognized as an alternative pathway of B-cell activation, particularly in autoimmunity. Critical cellular interactions required for the EF B-cell response are unclear. A key question in autoimmunity, in which Toll-like receptor (TLR) signals are costimulatory and could be sufficient for B-cell activation, is whether T cells are required for the response. This is pivotal, because autoreactive B cells are considered antigen-presenting cells for autoreactive T cells, but where such interactions occur has not been identified. Here, using AM14 site-directed transgenic rheumatoid factor (RF) mice, we report that B cells can be activated, differentiate, and isotype-switch independent of antigen-specific T-cell help, αβ T cells, CD40L signaling, and IL-21 signaling to B cells. However, T cells do dramatically enhance the response, and this occurs via CD40L and IL-21 signals. Surprisingly, the response is completely inducible T-cell costimulator ligand independent. These results establish that, although not required, T cells substantially amplify EF autoantibody production and thereby implicate T-independent autoreactive B cells as a potential vector for breaking T-cell tolerance. We suggest that these findings explain why autoreactivity first focuses on self-components for which B cells carry TLR ligands, because these will uniquely be able to activate B cells independently of T cells, with subsequent T–B interactions activating autoreactive T cells, resulting in chronic autoimmunity.
A modified micrometeorological gradient method for estimating O 3 dry depositions over a forest canopy

Abstract. Small pollutant concentration gradients between levels above a plant canopy result in large uncertainties in estimated air–surface exchange fluxes when using existing micrometeorological gradient methods, including the aerodynamic gradient method (AGM) and the modified Bowen ratio method (MBR). A modified micrometeorological gradient method (MGM) is proposed in this study for estimating O3 dry deposition fluxes over a forest canopy using concentration gradients between a level above and a level below the canopy top, taking advantage of relatively large gradients between these levels due to significant pollutant uptake in the top layers of the canopy. The new method is compared with the AGM and MBR methods and is also evaluated using eddy-covariance (EC) flux measurements collected at the Harvard Forest Environmental Measurement Site, Massachusetts, during 1993–2000. All three gradient methods (AGM, MBR, and MGM) produced similar diurnal cycles of O3 dry deposition velocity (Vd(O3)) to the EC measurements, with the MGM method being the closest in magnitude to the EC measurements. The multi-year average Vd(O3) differed significantly between these methods, with the AGM, MBR, and MGM method being 2.28, 1.45, and 1.18 times that of the EC, respectively. Sensitivity experiments identified several input parameters for the MGM method as first-order parameters that affect the estimated Vd(O3). A 10% uncertainty in the wind speed attenuation coefficient or canopy displacement height can cause about 10% uncertainty in the estimated Vd(O3). An unrealistic leaf area density vertical profile can cause an uncertainty of a factor of 2.0 in the estimated Vd(O3). Other input parameters or formulas for stability functions only caused an uncertainly of a few percent. The new method provides an alternative approach to monitoring/estimating long-term deposition fluxes of similar pollutants over tall canopies.
High-Frequency Modeling of Power Transformers for Use in Frequency Response Analysis (FRA)

This paper presents an advanced model of the frequency response of a three-phase power transformer for use in conjunction with diagnostic measurements by the method of frequency response analysis (FRA). The model includes high- frequency behavior of the laminated core and the insulation through taking into account the frequency dependencies of the complex permittivity of insulation materials (paper, pressboard, and oil) and of the anisotropic complex permeability of magnetic core and conductors. A lumped parameter circuit model is used to simulate the frequency response of open-circuit impedance, short-circuit impedance, and impedance between primary and secondary windings, in which the characteristics of circuit elements are calculated by means of the finite-element method. The effect of correct representation of each circuit element on the FRA response is analyzed and discussed in comparison to measurement results on a real transformer.
Statistical Approach for Selecting Elite Ants

Applications of ACO algorithms to obtain better solutions for combinatorial optimization problems have become very popular in recent years. In ACO algorithms, group of agents repeatedly perform well defined actions and collaborate with other ants in order to accomplish the defined task. In this paper, we introduce new mechanisms for selecting the Elite ants dynamically based on simple statistical tools. We also investigate the performance of newly proposed mechanisms.
An Integrated Glucose‐Insulin Model to Describe Oral Glucose Tolerance Test Data in Healthy Volunteers

The extension of the previously developed integrated models for glucose and insulin (IGI) to include the oral glucose tolerance test (OGTT) in healthy volunteers could be valuable to better understand the differences between healthy individuals and those with type 2 diabetes mellitus (T2DM). Data from an OGTT in 23 healthy volunteers were used. Analysis was based on the previously developed intravenous model with extensions for glucose absorption and incretin effect on insulin secretion. The need for additional structural components was evaluated. The model was evaluated by simulation and a bootstrap. Multiple glucose and insulin concentration peaks were observed in most individuals as well as hypoglycemic episodes in the second half of the experiment. The OGTT data were successfully described by the extended basic model. An additional control mechanism of insulin on glucose production improved the description of the data. The model showed good predictive properties, and parameters were estimated with good precision. In conclusion, a previously presented integrated model has been extended to describe glucose and insulin concentrations in healthy volunteers following an OGTT. The characterization of the differences between the healthy and diabetic stages in the IGI model could potentially be used to extrapolate drug effect from healthy volunteers to T2DM.
Drivers of expenditure growth in outpatient care services.

OBJECTIVE To identify and analyze drivers of costs for healthcare services delivered in outpatient settings. STUDY DESIGN We estimated 2 regression models of state-level annual outpatient expenditures. The first model uses data on operating costs for hospital outpatient services from hospital cost reports. The second model uses outpatient claims data from a large, national, group health insurer, and covers all varieties of outpatient providers for a specific insured population. RESULTS Several different cost drivers affected the growth of outpatient costs in the late 1990s. Foremost among the drivers is the change associated with demographics and general economic conditions, and economy-wide inflation, which together accounted for 60% of the growth in outpatient costs. Characteristics directly related to the healthcare sector had a smaller, but still significant role in cost growth. The supply of physicians and specialists accounted for 10% of cost growth, whereas supply and structure of outpatient facilities were responsible for an additional 5% of outpatient cost increase. The health status of the population was associated with 8% of expenditure growth; technology and treatment practices accounted for 7% of growth; and provider operating costs, such as wage levels, were linked to 9% of the growth. CONCLUSIONS Some level of growth in outpatient care spending may be cost effective, because outpatient services can substitute for more expensive care in other settings. Strategies for limiting growth in the costs of outpatient care will be more effective if focused on enhancing cooperation between payers, providers, and other stakeholders in assuring an appropriate and cost-effective supply of outpatient care resources.
Learning from the experiences of people with HIV using general practitioner services in London: a qualitative study

Aim To explore the experiences of people with HIV (PWHIV) using general practitioner (GP) services in order to identify barriers to use. Background Traditionally, GPs have little involvement in the care of PWHIV. However, as HIV becomes a chronic condition and the population of PWHIV ages, there is a need to increase this involvement. Despite high levels of GP registration, the majority of PWHIV in London report that their GP is not involved in their HIV care. Methods This paper presents qualitative findings from a mixed method study of PWHIV’s experiences of clinical services. Survey respondents were purposively sampled to recruit 51 PWHIV who took part in eight focus groups. Participants were asked about their experience of using GP services. Findings Three factors emerged which mediated experiences of GP care. Competence: respondents were concerned about the potential for misdiagnosis of symptoms, lack of awareness of the health needs of PWHIV and experiences of prescribing, which could lead to drug interactions. Continuity: not being able to get appointments quickly enough, not being able to see the same doctor twice and not being able to keep the same GP when one changed address were experienced as impediments to use. Communication: lack of communication between GPs and HIV specialists led to what participants called ‘patient ping-pong’ where they found themselves acting as a go-between for different clinical specialists trying to make sense of their care. Conclusion Meaningful contact between HIV specialists and GPs is likely to allay concerns about competency as treatment and care decisions can be taken collaboratively between the GP, HIV specialist and patient. A key component of acceptable GP care for PWHIV is likely to be the application of long-term condition management approaches, which includes empowered patient self-management.
Immediate‐early gene regulation by interplay between different post‐translational modifications on human histone H3

In mammalian cells, induction of immediate‐early (IE) gene transcription occurs concomitantly with histone H3 phosphorylation on Ser 10 and is catalyzed by mitogen‐activated protein kinases (MAPKs). Histone H3 is an evolutionarily conserved protein located in the core of the nucleosome, along with histones H2A, H2B, and H4. The N‐terminal tails of histones protrude outside the chromatin structure and are accessible to various enzymes for post‐translational modifications (PTM). Phosphorylation, O‐GlcNAc modification, and their interplay often induce functional changes, but it is very difficult to monitor dynamic structural and functional changes in vivo. To get started in this complex task, computer‐assisted studies are useful to predict the range in which those dynamic structural and functional changes may occur. As an illustration, we propose blocking of phosphorylation by O‐GlcNAc modification on Ser 10, which may result in gene silencing in the presence of methylated Lys 9. Thus, alternate phosphorylation and O‐GlcNAc modification on Ser 10 in the histone H3 protein may provide an on/off switch to regulate expression of IE genes. J. Cell. Biochem. 103: 835–851, 2008. © 2007 Wiley‐Liss, Inc.
Prescribing Thiamine to Inpatients With Alcohol Use Disorders: How Well Are We Doing?

Objectives:Thiamine deficiency is a potentially dangerous sequela of alcohol use disorders (AUDs). European and British guidelines recommend administering high-dose parenteral thiamine 3 times daily to avoid consequences of thiamine deficiency such as Wernicke-Korsakoff syndrome (WKS), and suggest that traditional thiamine dosages are likely inadequate. Research into thiamine and WKS has lagged in the United States, and to date, no study has examined how thiamine is prescribed to inpatients with AUD in an American hospital. Methods:Thiamine prescribing data (amount, route, and frequency schedule) were collected for inpatients at a large, American, teaching hospital, who were referred to the addiction psychiatry service for AUD. Data were analyzed using Statistical Product and Service Solutions. Results:A total of 217 inpatients with AUD were included. A substantial percentage of them were not prescribed thiamine. Of those who were prescribed thiamine, nearly all were prescribed oral thiamine at traditional dosages, including high-risk patients. Conclusions:This is the first study to report on the prescribing of thiamine to inpatients with AUD at an American teaching hospital. It serves to confirm what many already suspected: that more education is needed to improve the diagnostic challenges of WKS, the detection of risk factors for WKS, and the adequate dosing of thiamine for prevention and treatment of WKS.
The resolution and regeneration of a cointegrate plasmid reveals a model for plasmid evolution mediated by conjugation and oriT site-specific recombination.

Cointegrate plasmids are useful models for the study of plasmid evolution if their evolutionary processes can be replicated under laboratory conditions. pBMB0228, a 17 706 bp native plasmid originally isolated from Bacillus thuringiensis strain YBT-1518, carries two nematicidal crystal protein genes, cry6Aa and cry55Aa. In this study, we show that pBMB0228 is in fact a cointegrate of two plasmids and contains two functional replication regions and two functional mobilization regions. Upon introduction into B. thuringiensis strain BMB171, pBMB0228 spontaneously resolves into two constituent plasmids via recombination at its oriT1 and oriT2 sites. The resolution does not require conjugation but can be promoted by conjugation. We further confirm that the resolution is mediated by oriT site-specific recombination requiring Mob02281 or Mob02282. Additionally, the two constituent plasmids of pBMB0228 are mobilizable, and can fuse back via oriT site-specific integration after entering into the same cell by conjugation. Our study confirms that native plasmid can reversibly interconvert between a cointegrate structure and its constituent plasmids. This study provides insight into the evolution of cointegrate plasmids, linking plasmid evolution with conjugation and the oriT site-specific recombination function of relaxase.
El efecto de la innovación en el desarrollo y crecimiento de México: una aproximación usando las patentes

En este artículo se presenta un modelo empírico basado en datos generadosa lo largo de una década de análisis, y cuyo propósito es explicar el impacto de la propiedad intelectual utilizando los registros de patentes como un indicador. Elmodelo correlaciona aún más la actividad de patentar con el desarrollo económico y el crecimiento en México. Se presenta un patrón de actividad positiva entre una mayor inversión de recursos en investigación y desarrollo (I+D) por un lado, y el desarrollo económico y el crecimiento por el otro, observado a través de aumentos en el volumen de solicitudes de patentes nacionales. La creación e implementación de políticas públicas orientadas a aumentar el capital intelectual y la innovación podrían beneficiar a una economía emergente como la de México de innumerables maneras.
Description of movement quality in patients with low back pain: A qualitative study as a first step to a practical definition

ABSTRACT Purpose: As a first step to formulate a practical definition for movement quality (MQ), this study aims to explore how Dutch allied health care professionals (AHCPs) describe MQ of daily life activities in patients with low back pain (LBP). Methods: In this qualitative cross-sectional digital survey study, Dutch AHCPs (n = 91) described MQ in open text (n = 91) and with three keywords (n = 90). After exploratory qualitative content analysis, the ICF linking rules (International Classification of Functioning, Disability and Health) were applied to classify MQ descriptions and keywords. Findings: The identified meaningful concepts (MCs) of the descriptions (274) and keywords (239) were linked to ICF codes (87.5% and 80.3%, respectively), Personal factors (5.8% and 5.9%, respectively), and supplementary codes (6.6% and 13.8%, respectively). The MCs were linked to a total of 31 ICF codes, especially to b760 ‘control of voluntary movement functions’, b7602 ‘coordination of voluntary movements’, d4 ‘Mobility’, and d230 ‘carry out daily routine’. Negative and positive formulated descriptions elucidated different MQ interpretations. Conclusions: Descriptions of MQ given by Dutch AHCPs in patients with LBP cover all ICF components. Coordination and functional movements are seen as the most elementary concepts of MQ. Variation in MQ descriptions and interpretations hinders defining MQ and indicates the necessity of additional steps.
PCR in the diagnosis of cutaneous tuberculosis

Visando melhorar o diagnostico laboratorial da Tuberculose Cutânea, foi realizado o estudo da aplicacao da tecnica de PCR em amostras de tecidos cutâneos macerados, descontaminados (com H2SO4 4% para eliminacao da microbiota normal), neutralizados (com NaOH 4%) e armazenadas a -20oC. Das 37 amostras submetidas ao estudo, 16,22% apresentavam baciloscopias positivas para bacilos alcool-acidos resistentes (metodo concentrado) e em 43,24% houve o isolamento do Mycobacterium tuberculosis em meio de cultivo Lowenstein-Jensen. Utilizando-se de primers para a regiao 16S rDNA do M. tuberculosis, o DNA micobacteriano foi detectado em 24,32% das biopsias. A sensibilidade e especificidade da PCR foram 43,7% e 90,4%, respectivamente. Devido a baixa sensibilidade e resultados divergentes entre as tecnicas bacteriologicas e PCR (para a sequencia 16S rDNA), as amostras foram repetidas em um novo PCR com primers para a regiao IS6110. Tanto a sensibilidade como a especificidade da PCR com primers para IS6110 alcancaram 100% em relacao ao cultivo. Os resultados confirmam a eficacia da PCR utilizando primers para a sequencia IS6110 e oferecem a possibilidade da tecnica ser aplicada em amostras congeladas enviadas por servicos que nao identificam o M. tuberculosis por tecnicas de biologia molecular.
The impact of reference-day risk on beta estimation and a proposed solution

ABSTRACT The ability to accurately estimate systematic risk (or beta) when reference-day risk is considered, is an ineluctable requirement for all applications of the capital asset pricing model (CAPM). This research documents evidence of reference-day risk for shares on the Johannesburg All Share Index. In response to the need for greater accuracy when estimating systematic risk, this paper contributes a volume-weighted-average-price (VWAP) method for estimating beta which may be employed when reference-day risk is considered. Furthermore, this research applies a graphical time-series approach to test the underlying risk-reward tenet postulated by the CAPM. Using beta as a measure of systematic risk, this research finds that the CAPM appears to imperfectly specify the risk-reward trade-off.