Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning About Missing Data Mechanisms in Electronic Health Records-based Research: A Survey-based Approach

Background: Bias due to missing data is a major concern in electronic health record (EHR)-based research. As part of an ongoing EHR-based study of weight change among patients treated for depression, we conducted a survey to investigate determinants of missingness in the available weight information and to evaluate the missing-at-random assumption. Methods: We identified 8,345 individuals enrolled in a large EHR-based health care system who had monotherapy treatment for depression from April 2008 to March 2010. A stratified sample of 1,153 individuals completed a detailed survey. Logistic regression was used to investigate determinants of whether a patient (1) had an opportunity to be weighed at treatment initiation (baseline), and (2) had a weight measurement recorded. Parallel analyses were conducted to investigate missingness during follow-up. Throughout, inverse-probability weighting was used to adjust for the design and survey nonresponse. Analyses were also conducted to investigate potential recall bias. Results: Missingness at baseline and during follow-up was associated with numerous factors not routinely collected in the EHR including whether or not the patient had ever chosen not to be weighed, external weight control activities, and self-reported baseline weight. Patient attitudes about their weight and perceptions regarding the potential impact of their depression treatment on weight were not related to missingness. Conclusion: Adopting a comprehensive strategy to investigate missingness early in the research process gives researchers information necessary to evaluate key assumptions. While the survey presented focuses on outcome data, the overarching strategy can be applied to any and all data elements subject to missingness.
Making Space for Intuition in Decision Making: The case of project prioritization

Researchers and practitioners advocate strongly for the use of quantitative data and calculations of costs and benefits as the basis for organizational decision making. We investigate decision making in the form of project prioritization. We use a rich empirical dataset built from a longitudinal study of the prioritization of information technology projects in a large financial institution. Our findings indicate that during project prioritization meetings, senior decision makers apply a set of techniques to make space for the use of intuition in the decision process. We also describe how intuition is manifested during the meetings. Our empirical study provides evidence on the central role of intuition when solving loosely structured problems such as the ones encounter during information technology projects prioritization.
Preoperative staging of gastric cancer: comparison of endoscopic US and dynamic CT.

Fifty consecutive patients with gastric adenocarcinoma proved by means of biopsy underwent preoperative staging with endoscopic ultrasonography (US). Dynamic computed tomography (CT) of the chest and abdomen was performed before surgery in 33 of the patients. In all 50 patients, the TNM classification of the American Joint Committee on Cancer was used to compare the imaging findings with pathologic findings in specimens resected at surgery. When the depth of tumor penetration was evaluated, the findings at endoscopic US and those at pathologic examination were concordant in 46 of 50 patients (92%), and the findings at dynamic CT and those at pathologic examination, in 14 of 33 patients (42%) (P less than .00042). Evaluation of regional lymph node metastases showed a concordance of 78% with endoscopic US and 48% with dynamic CT (P less than .038). Overall determination of stage with both dynamic CT and endoscopic US showed a concordance of 73%, compared with a concordance of 45% for dynamic CT alone (P less than .028).
From Form to Function: Detecting the Affordance of Tool Parts using Geometric Features and Material Cues

Title of dissertation: From Form to Function: Detecting the Affordance of Tool Parts using Geometric Features and Material Cues Austin O. Myers, Doctor of Philosophy, 2016 Dissertation directed by: Professor Yiannis Aloimonos Department of Computer Science With recent advances in robotics, general purpose robots like Baxter are quickly becoming a reality. As robots begin to collaborate with humans in everyday workspaces, they will need to understand the functions of objects and their parts. To cut an apple or hammer a nail, robots need to not just know a tool’s name, but they must find its parts and identify their potential functions, or affordances. As Gibson remarked, “If you know what can be done with a[n] object, what it can be used for, you can call it whatever you please. ” We hypothesize that the geometry of a part is closely related to its affordance, since its geometric properties govern the possible physical interactions with the environment. In the first part of this thesis, we investigate how the affordances of tool parts can be predicted using geometric features from RGB-D sensors like Kinect. We develop several approaches to learn affordance from geometric features: using superpixel based hierarchical sparse coding, structured random forests, and convolutional neural networks. To evaluate the proposed methods, we construct a large RGB-D dataset where parts are labeled with multiple affordances. Experiments over sequences containing clutter, occlusions, and viewpoint changes show that the approaches provide precise predictions that can be used in robotics applications. In addition to geometry, the material properties of a part also determine its potential functions. In the second part of this thesis, we investigate how material cues can be integrated into a deep learning framework for affordance prediction. We propose a modular approach for combining high-level material information, or other mid-level cues, in order to improve affordance predictions. We present experiments which demonstrate the efficacy of our approach on an expanded RGB-D dataset, which includes data from non-tool objects and multiple depth sensors. The work presented in this thesis lays a foundation for the development of robots which can predict the potential functions of tool parts, and provides a basis for higher level reasoning about affordance. From Form to Function: Detecting the Affordance of Tool Parts using Geometric Features and Material Cues
von Willebrand Factor without the A2 Domain Is Resistant to Proteolysis

Summary von Willebrand factor (vWF) is a complex multimeric plasma glycoprotein, that plays a critical role in the mediation of platelet adhesion to the damaged vascular wall, and functions as a carrier protein for factor VIII. vWF has a domain structure consisting of repeated A, B, C, and D domains. The A1 domain is involved in binding to the platelet receptor glycoprotein (GP) lb, and the A3 domain has a binding site for collagen. A function of the A2 domain has not been described, although point mutations identified in von Willebrand disease (vWD) type 2A patients are localized in this domain. To study the role of the A2 domain a deletion mutant was constructed which lacked the A2 domain, ΔA2- vWF. Previous studies have shown that this approach is a powerful tool to study the function of a domain in a protein since it does not affect the activity of other domains. After expression in baby hamster kidney (BHK) cells, ΔA2-vWF was compared to wild-type (WT) vWF, and to ΔAl-vWF (Lankhof et al., Blood 86: 1035,1995). Ristocetin induced platelet binding was slightly increased but botrocetin induced platelet binding was normal as was binding to heparin and collagen type III. Adhesion studies to surface coated purified ΔA2-vWF or to ΔA2-vWF preincubated on collagen under flow conditions showed no abnormalities. Incubation with normal human plasma showed that ΔA2-vWF like WT-vWF was not sensitive to proteolysis. After addition of urea, WT-vWF becomes sensitive to the protease, indicating that unfolding of the molecule is necessary for exposure of the cleavage site. ΔA2- vWF tested under the same conditions was resistant, indicating that the protease sensitive site is located in the A2 domain.
Current-clamped, modified series resonant DC-link power converter for a general purpose induction motor drive

A new AC/AC power converter topology, in which all the switches operate in a resonant fashion to reduce switching losses, is proposed. The topology enables conduction-period control of individual current pulses, whereby pulse-width modulation (PWM) could be achieved to a fair degree of accuracy with the associated controller. The scheme implements current peak (resonant) limiting by a simple diode clamp. Improved switch utilization (voltage /spl times/ current) and reduced part-count could be cited as the merits of the circuit over the previous soft-switched current-sourced AC/AC configurations. It is experimentally verified that the output PWM controller could be used to implement constant V/F operation, and the results are presented. In-depth design criteria for the topology that gives optimized voltage stresses are presented. A charge-based, line current feed-forward, mode-controller is introduced at the input and digitally verified. Feasibility of the simultaneous control over both input power-factor and smooth input-output line currents are studied and the digital verification is presented.
Hand gesture recognition in mobile devices: Enhancing the musical experience

Mobile devices typically include a built-in camera that allows high deﬁnition video recording. This, combined with last generation mobile processors, makes possible real-time computer vision that can potentially enhance the interaction with various mobile applications. We propose a system that makes use of the built-in camera to recognize and detect diﬀerent hand gestures that could be ultimately mapped to any application. As an example, we show how the system can control real-time music synthesis parameters, and to better capture its eﬀectiveness we provide links to video demos. We then show how our method is easily extendible to other applications. We conclude the paper with qualitative usage observations and a discussion of future plans.
MorA Defines a New Class of Regulators Affecting Flagellar Development and Biofilm Formation in Diverse Pseudomonas Species

ABSTRACT Assembly of bacterial flagella is developmentally important during both planktonic cell growth and biofilm formation. Flagellar biogenesis is complex, requiring coordinated expression of over 40 genes, and normally commences during the log-to-stationary transition phase. We describe here a novel membrane-localized regulator, MorA, that controls the timing of flagellar development and affects motility, chemotaxis, and biofilm formation in Pseudomonas putida. MorA is conserved among diverse Pseudomonas species, and homologues are present in all Pseudomonas genomes sequenced thus far. In P. putida, the absence of MorA derepresses flagellar development, which leads to constitutive formation of flagella in the mutant cells in all growth phases. In Pseudomonas aeruginosa, the absence of MorA led to a reduction in biofilm formation. However, unlike the motility of P. putida, the motility of the P. aeruginosa mutants was unaffected. Our data illustrate a novel developmentally regulated sensory and signaling pathway for several properties required for virulence and ecological fitness of Pseudomonas species.
Isolation of NDM-producing Providencia rettgeri in Brazil.

Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, RJ, Brazil; Departamento de Bioquı́mica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS IPB-LACEN-RS), Porto Alegre, RS, Brazil; Hospital Nossa Senhora da Conceição, Porto Alegre, RS, Brazil
Oxidative DNA Damage Defense Systems in Avoidance of Stationary-Phase Mutagenesis in Pseudomonas putida

ABSTRACT Oxidative damage of DNA is a source of mutation in living cells. Although all organisms have evolved mechanisms of defense against oxidative damage, little is known about these mechanisms in nonenteric bacteria, including pseudomonads. Here we have studied the involvement of oxidized guanine (GO) repair enzymes and DNA-protecting enzyme Dps in the avoidance of mutations in starving Pseudomonas putida. Additionally, we examined possible connections between the oxidative damage of DNA and involvement of the error-prone DNA polymerase (Pol)V homologue RulAB in stationary-phase mutagenesis in P. putida. Our results demonstrated that the GO repair enzymes MutY, MutM, and MutT are involved in the prevention of base substitution mutations in carbon-starved P. putida. Interestingly, the antimutator effect of MutT was dependent on the growth phase of bacteria. Although the lack of MutT caused a strong mutator phenotype under carbon starvation conditions for bacteria, only a twofold increased effect on the frequency of mutations was observed for growing bacteria. This indicates that MutT has a backup system which efficiently complements the absence of this enzyme in actively growing cells. The knockout of MutM affected only the spectrum of mutations but did not change mutation frequency. Dps is known to protect DNA from oxidative damage. We found that dps-defective P. putida cells were more sensitive to sudden exposure to hydrogen peroxide than wild-type cells. At the same time, the absence of Dps did not affect the accumulation of mutations in populations of starved bacteria. Thus, it is possible that the protective role of Dps becomes essential for genome integrity only when bacteria are exposed to exogenous agents that lead to oxidative DNA damage but not under physiological conditions. Introduction of the Y family DNA polymerase PolV homologue rulAB into P. putida increased the proportion of A-to-C and A-to-G base substitutions among mutations, which occurred under starvation conditions. Since PolV is known to perform translesion synthesis past damaged bases in DNA (e.g., some oxidized forms of adenine), our results may imply that adenine oxidation products are also an important source of mutation in starving bacteria.
Treg cells in thrombotic thrombocytopenic purpura associated with systemic lupus erythematosus patients

Abstract Aim: Treg cells are of critical importance for maintenance of tolerance. The purpose of the this study was to observe the number of Treg cells in the patients with thrombotic thrombocytopenic purpura (TTP) associated with systemic lupus erythematosus (SLE), and to study pathogenesis of TTP with SLE. Methods: Seven patients with TTP associated with SLE and seven healthy volunteers were studied. The Treg cells were examined by flow cytometry. Clinical and laboratory data, such as urinary protein, serum creatinine, endothelial markers and immunologic serologics, were obtained from each patient and healthy volunteer. Glomerular injury was assessed by histopathology. Serum IL-2, IL-4, IL-6 and anti-endothelial cell antibody were analyzed by ELISA and anti-ADAMTS13 antibody were detected by Western blotting. Results: Treg cells significantly decreased in TTP with SLE patients compared with controls (p < 0.05). Treg cells are negatively correlated with blood urea nitrogen, serum uric acid, supernatant IL-4, and proteinuria, and positively with estimated glomerular filtration rate (eGFR) in TTP with SLE patients. Treg cells gradually decreased as the severity of renal histology increased. Serum IL-2, IL-6, supernatant IL-4, anti-endothelial cell antibody, and anti-ADAMTS13 antibody significantly increased in TTP with SLE patients compared to those of the control groups (all p < 0.05). In contrast, serum levels of C3 were significantly decreased in TTP with SLE patients compared to those of the control groups (p < 0.05). Conclusions: Treg cells are not only lower in TTP with SLE patients, but also are correlated with disease severity in TTP with SLE patients. Treg cells may play an important role in the pathogenesis of TTP with SLE.
Common randomness in information theory and cryptography - I: Secret sharing

As the first part of a study of problems involving common randomness at distance locations, information-theoretic models of secret sharing (generating a common random key at two terminals, without letting an eavesdropper obtain information about this key) are considered. The concept of key-capacity is defined. Single-letter formulas of key-capacity are obtained for several models, and bounds to key-capacity are derived for other models. >
Are the Bio‐ and Chemiluminescence States of the Firefly Oxyluciferin the Same as the Fluorescence State?

A usual strategy in both experimental and theoretical studies on bio‐ and chemiluminescence is to analyze the fluorescent properties of the bio‐ and chemiluminescence reaction product. Recent findings in a coelenteramide and Cypridina oxyluciferin model raise a concern on the validity of this procedure, showing that the light emitters in each of these luminescent processes might differ. Here, the thermal decomposition path of the firefly dioxetanone and the light emission states of the Firefly oxyluciferin responsible for the bio‐, chemiluminescence, and fluorescence of the molecule are characterized using ab initio quantum chemistry and hybrid quantum chemistry/molecular mechanics methods to determine if the scenario found in the coelenteramide and Cypridina oxyluciferin study does also apply to the Firefly bioluminescent systems. The results point out to a unique emission state in the bio‐, chemiluminescence, and fluorescence phenomena of the Firefly oxyluciferin and, therefore, using fluorescence properties of this system is reasonable.
Immunization completeness of children under two years of age in Nova Scotia, Canada.

OBJECTIVES Canada's progress in establishing a national immunization registry and coordinated immunization schedule across provinces has been slow. The absence of a centralized registry means there are only limited data available on childhood immunization coverage in Canada. The aim of this study was to estimate the completeness and timeliness of immunization for two year-old children in Nova Scotia. METHODS The study included 8,245 babies born in Nova Scotia during 2006. Immunization data were derived from three sources: Provincial Medical Insurance Physician Billing data, public health records, and self-report by parents. Immunization uptake rates for vaccines included in the Nova Scotia immunization schedule were calculated at ages 12, 18 and 24 months. Logistic regression was used to analyze vaccine uptake in relation to socio-economic factors. A telephone survey of a sample of parents of study children was completed. RESULTS The overall immunization completeness rate was 49% at 12 months, 40% at 18 months and 58% at 24 months of age. Immunization completeness was significantly higher in more socially disadvantaged communities. CONCLUSIONS Nova Scotia spends many millions of dollars on vaccine purchase and administration, but, as with numerous Canadian jurisdictions, there is no accurate system for monitoring or evaluating the program. The timeliness and completeness of immunization administration to pre-school children in Nova Scotia is inadequate. Further work should elucidate the barriers and enablers to immunization to ensure that public health education targets those most likely to be under-immunized. A provincial vaccination database should be established to monitor and evaluate the system.
Fatigue in cystic fibrosis

Fatigue is a debilitating symptom in patients with cystic fibrosis (CF). Although fatigue is commonly reported in these patients, an effective treatment for this symptom has not been found. The factors associated with fatigue in CF have not been investigated. We conducted a prospective, case–control study in adult patients with CF. All the patients were chronically infected with Pseudomonas aeruginosa and were enrolled in the study during disease stability. A gender and age-matched control group was also recruited. Subjective assessment included three questionnaires: the Chalder fatigue questionnaire, St Mary’s Hospital sleep questionnaire (SQ), and the scaled general health and Hillier questionnaire (GHQ). For patients with CF, spirometry, body mass index (BMI), haemoglobin level, C-reactive protein, and the burden of pulmonary exacerbations (PExs) were assessed. The control group completed all the three questionnaires, and their BMI was measured. A total of 78 participants were enrolled in the study (44 patients with CF and 34 control). Female patients with CF received antibiotics for more days than male patients with CF. The fatigue score did not differ between female and male participants in either the patients with CF or the control group; however, the fatigue score was greater for both the sexes in the patients with CF compared with the control group: p = 0.038 for female and p = 0.048 for male. The scores for the SQ and the GHQ did not differ between the two study groups. The fatigue score correlated with the total score for SQ (p < 0.0001) in patients with CF, but not in control participants. In patients with CF and the individuals in the control group, a close correlation was found between the fatigue score and the GHQ domain-specific scores and with the total score; p < 0.0001 for patients with CF and p = 0.001 for control. No correlations were found between the fatigue score and any of the objective parameters studied.
Bangladeshi Migrant Workers in Malaysia's Construction Sector

The 1980s and 1990s were characterized by an absorption of foreign labour into the Malaysian economy that was unprecedented in terms of numbers and rapidity. From approximately 500,000 foreign workers in 1984 (Ministry of Human Resources, 1991) their numbers shot up beyond 1.2 million in 1991 (Pillai, 1992) and 2.4 million in early 1998 (Utusan Malaysia, 1998). Labour voids manifested particularly during the high-growth period of 1988-1997 were the main inducing agent. Construction was among the sectors which came to rely heavily on foreign workers owing to a confluence
Differential Use, Differential Effects: Investigating the Roles of Different Modes of News Use in Promoting Political Participation

The present study clarifies the role of the informational use of media in facilitating citizens' political participation by focusing on three distinctive modes of news experience i.e., news reading, posting, and endorsing within the context of online social networking sites SNSs. The findings show that news posting contributes to greater participation in politics by positively mediating the relationship between the use of SNSs and participatory activities. In contrast, news reading and endorsing were not significantly associated with political participation. In addition, the study found that the indirect effects of SNS use on participation via news posting are highest among those with a high degree of network political expertise and lower among those with an average level of such expertise.
Conceptual Design of Vertical Passenger Seat for Standing Cabin in Commercial Transport Aircraft

The competition between airlines today is changed towards the affordability of their air transportation service. The airlines are competing to lower their offered flight ticket prices as to capture high demands from leisure and business travelers, who are also price-sensitive customers. Theoretically, by having more passengers onboard the aircraft, the flight ticket price can be lowered since the imposed operational costs can be shared by more passengers per flight. The standing cabin concept has been proposed where the passengers are transported in a cabin of an aircraft in an upright position, similar to standing on buses and trains. This paper explores the conceptual design of vertical seat for the passengers to be applied in such standing cabin concept. 