Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro biosynthesis of diphthamide, studied with mutant Chinese hamster ovary cells resistant to diphtheria toxin

Diphthamide, a unique amino acid, is a post-translational derivative of histidine that exists in protein synthesis elongation factor 2 at the site of diphtheria toxin-catalyzed ADP-ribosylation of elongation factor 2. We investigated steps in the biosynthesis of diphthamide with mutants of Chinese hamster ovary cells that were altered in different steps of this complex post-translational modification. Biochemical evidence indicates that this modification requires a minimum of three steps, two of which we accomplished in vitro. We identified a methyltransferase activity that transfers methyl groups from S-adenosyl methionine to an unmethylated form of diphthine (the deamidated form of diphthamide), and we tentatively identified an ATP-dependent synthetase activity involved in the biosynthesis of diphthamide from diphthine. Our results are in accord with the proposed structure of diphthamide (B. G. VanNess, et al., J. Biol. Chem. 255:10710-10716, 1980).
Distribution of Alzheimer‐type pathologic changes in nondemented elderly individuals matches the pattern in Alzheimer's disease

We studied the topographic distribution of Alzheimer's disease (AD)-type pathologic changes in the brains of 25 presumed nondemented elderly individuals. Neurofibrillary tangles (NFT) and senile plaques (SP) were evaluated quantitatively in nine to 20 cytoarchitectural fields using thioflavine S, Alz-50, and anti-β/A4 amyloid immunohistochemistry. Our observations suggest that (1) most individuals over the age of 55 have at least a few NFT and SP; (2) the topographic distribution of NFT and SP in nondemented elderly individuals follows a consistent pattern of vulnerability in different cytoarchitectural areas; (3) NFT occur most frequently in the entorhinal and perirhinal cortices and the CA1/subiculum field of the hippocampus, while neocortical areas are less frequently affected; (4) immunohistochemically defined subtypes of SP have distinct patterns of distribution. β/A4 immunoreactive SP are present in neocortical areas > limbic areas. Alz-50 immunoreactive SP are infrequent and limited to those areas that contain Alz-50-positive neurons and NFT. These patterns closely match the hierarchical topographic distribution of NFT and SP observed in AD, suggesting a commonality in the pathologic processes that lead to NFT and SP in both aging and AD.
Development of nanocapsules bearing doxorubicin for macrophage targeting through the phosphatidylserine ligand: a system for intervention in visceral leishmaniasis.

OBJECTIVES The purpose of this study was to explore the applicability, targeting potential and drug delivery to specialized phagocytes via phosphatidylserine (PS)-specific ligand-anchored nanocapsules (NCs) bearing doxorubicin. METHODS The layer-by-layer method was utilized to prepare NCs having a nanoemulsion core loaded with doxorubicin (NCs-DOX), which was further grafted with PS. PS-coated NCs (PS-NCs-DOX) were compared with NCs-DOX for in vitro targeting ability by studying uptake by macrophages, intracellular localization, in vivo pharmacokinetics and organ distribution studies. The in vivo antileishmanial activity of free doxorubicin, NCs-DOX and PS-NCs-DOX was tested against visceral leishmaniasis in Leishmania donovani-infected hamsters. RESULTS Flow cytometric data revealed 1.75-fold enhanced uptake of PS-NCs-DOX in J774A.1 macrophage cell lines compared with NCs-DOX. In vivo organ distribution studies in Wistar rats demonstrated a significantly higher extent of accumulation of PS-NCs-DOX compared with NCs-DOX in macrophage-rich organs, particularly in liver and spleen. Highly significant antileishmanial activity (P < 0.05 compared with NCs) was observed with PS-NCs-DOX, causing 85.23% ± 4.49% inhibition of splenic parasitic burden. NCs-DOX and free doxorubicin caused only 72.88% ± 3.87% and 42.85% ± 2.11% parasite inhibition, respectively, in Leishmania-infected hamsters (P < 0.01 for PS-NCs-DOX versus free doxorubicin and NCs-DOX versus free doxorubicin). CONCLUSIONS We conclude that the PS targeting moiety can provide a new insight for efficient drug delivery to specialized macrophages and thus may be developed for effective use in macrophage-specific delivery systems, especially for leishmaniasis.
Lessons learned from the deployment of a multihop IEEE 802.11g testbed using COTS devices

A lot of attention has been given to multihop wireless networks lately, but further research is needed. This attention has motivated an increase in the number of 802.11-based deployments, both indoor and outdoor. These testbeds are used to run measurements in order to analyze and understand the limitation and differences between analytical or simulation-based figures and the results from real-life experimentation. In this paper we describe the lessons learned from the deployment of a wireless multihop testbed under the false floor of a laboratory in our Computer Science building. We assess the radio shielding provided by the false floor panels, and run exhaustive and controlled experiments to analyze the performance limits of commercial off-the-shelf hardware. The results obtained confirm that experimental measurements can severely deviate from the expected theoretical values.
Detection, Isolation, and Identification of Vibrio cholerae from the Environment

Recent molecular advances in microbiology have greatly improved the detection of bacterial pathogens in the environment. These improvements and a downward trend in the cost of molecular detection methods have contributed to increased frequency of detection of pathogenic microorganisms where traditional culture‐based detection methods have failed. Culture methods also have been greatly improved, and the confluence of the two suites of methods provides a powerful tool for detection, isolation, and characterization of pathogens. While molecular detection provides data on the presence and type of pathogens, culturing methods allow a researcher to preserve the organism of interest for “‐omics” studies, such as genomic, metabolomic, secretomic, and transcriptomic analysis, which are rapidly becoming more affordable. This has yielded a clearer understanding of the ecology and epidemiology of microorganisms that cause disease. In this unit, we present commonly accepted methods for isolation, detection, and characterization of V. cholerae, providing more extensive knowledge of the ecology and epidemiology of this organism. This unit has been fully revised and updated from the earlier version with the latest knowledge and additional information not previously included. Curr. Protoc. Microbiol. 26:6A.5. 1‐6A.5. 51. © 2012 by John Wiley & Sons, Inc.
Controllable Ink-Jet Printing Technique on Various Channel Width Designs toward Zinc Oxide-Based Thin Film Transistor

Ink-jet printed (IJP) thin-film transistor (TFT) electronics employing solution processed materials is considered to be the key technique to achieve mask-less, low-cost, large-area, and low temperature fabrication systems. We propose an approach for a direct printing highly transparent conducting oxide material of zinc oxide (ZnO) which the use of semiconductor layer with different transistor channel widths without any photolithography process defined. In this work, we describe the ink-jet printing ZnO TFT with three-types channel widths, and electrical characteristics with low voltage operation, high performance of switch on/off state and low temperature fabrication (200~300°C). These printed TFT thus represent an uniquely attractive path for realizing high flexibility printed electronics.
Parents' perceptions of pediatric primary care quality: effects of race/ethnicity, language, and access.

OBJECTIVE To examine the effects of race/ethnicity, language, and potential access on parents' reports of pediatric primary care experiences. DATA SOURCES/STUDY SETTING Primary survey data were collected (67 percent response rate) from 3,406 parents of students in kindergarten through sixth grade in a large urban school district in California during the 1999-2000 school year. DATA COLLECTION The data were collected by mail, telephone, and in person. Surveys were administered in English, Spanish, Vietnamese, and Tagalog. STUDY DESIGN Data were analyzed using multiple regression models. The dependent variable was parents' reports of primary care quality, assessed via the previously validated Parents' Perceptions of Primary Care measure (P3C). The independent variables were race/ethnicity, language, and potential access to care (insurance status, presence of a regular provider of care), controlling for child age, gender, and chronic health condition status, and mother's education. PRINCIPAL FINDINGS Parents' reports of primary care quality varied according to race/ethnicity, with Asian and Latino parents reporting lower P3C scores than African Americans and whites. In multivariate analyses, both language and potential access exerted strong independent effects on primary care quality, reducing the effect of race/ethnicity such that the coefficient for Latinos was no longer significant, and the coefficient for Asians was much smaller, though still statistically significant. CONCLUSIONS To reduce racial/ethnic disparities in primary care, attention should be paid both to policies aimed at improving potential access and to providing linguistically appropriate services.
A Systematic Approach to DC-Bus Control Design in Single-Phase Grid-Connected Renewable Converters

This paper presents a method for design and control of dc-bus capacitance and transients in a renewable single-phase grid-connected converter. Conventionally, a proportional (P) or proportional-integrating (PI) controller is commonly used and the design stage is performed using trial-error or using a simplified analysis that does not take the dynamics of the current control loop into consideration. This paper proposes 1) a systematic and efficient method for design of dc-bus PI controller gains; and 2) an accurate method for the design of the dc-bus controller gains without neglecting the dynamics of the current control loop. Two main objectives are to have control over the amount of output current harmonics and over the level of bus fluctuations caused by random input power swings. The proposed method is transparent and it provides a convenient and rigorous insight for the designer to properly select the size of dc-bus component and to determine the controller gains.
Clonality analysis of multiple hepatocellular carcinomas by loss of heterozygosity pattern determined by chromosomes 16q and 13q

Background and Aim: Loss of heterozygosity (LOH) on chromosomes 16q and 13q, associated with tumor development, is frequently found in hepatocellular carcinoma (HCC). In light of this, an attempt was made to use the LOH pattern determined by microsatellite markers on 16q and 13q to discriminate clonality.
The Effect of office‐based flexible endoscopic surgery on hemodynamic stability 1 2 3

Because of technological advances in endoscopy equipment, office‐based flexible endoscopic surgery (OBFES) is becoming more widespread and common in practice. In our experience, we have noticed that patients often have marked rises in heart rate (HR) and blood pressure (BP). However, to our knowledge, changes in hemodynamic stability during these procedures have never been studied. The primary aim of this study was to investigate changes in BP, HR, and oxygen (O2) saturation in patients undergoing unsedated laryngeal surgery.
Study of the optimum level of electrode placement for the evaluation of absolute lung resistivity with the Mk3.5 EIT system

Inter-subject variability has caused the majority of previous electrical impedance tomography (EIT) techniques to focus on the derivation of relative or difference measures of in vivo tissue resistivity. Implicit in these techniques is the requirement for a reference or previously defined data set. This study assesses the accuracy and optimum electrode placement strategy for a recently developed method which estimates an absolute value of organ resistivity without recourse to a reference data set. Since this measurement of tissue resistivity is absolute, in Ohm metres, it should be possible to use EIT measurements for the objective diagnosis of lung diseases such as pulmonary oedema and emphysema. However, the stability and reproducibility of the method have not yet been investigated fully. To investigate these problems, this study used a Sheffield Mk3.5 system which was configured to operate with eight measurement electrodes. As a result of this study, the absolute resistivity measurement was found to be insensitive to the electrode level between 4 and 5 cm above the xiphoid process. The level of the electrode plane was varied between 2 cm and 7 cm above the xiphoid process. Absolute lung resistivity in 18 normal subjects (age 22.6 ± 4.9, height 169.1 ± 5.7 cm, weight 60.6 ± 4.5 kg, body mass index 21.2 ± 1.6: mean ± standard deviation) was measured during both normal and deep breathing for 1 min. Three sets of measurements were made over a period of several days on each of nine of the normal male subjects. No significant differences in absolute lung resistivity were found, either during normal tidal breathing between the electrode levels of 4 and 5 cm (9.3 ± 2.4 Ω m, 9.6 ± 1.9 Ω m at 4 and 5 cm, respectively: mean ± standard deviation) or during deep breathing between the electrode levels of 4 and 5 cm (10.9 ± 2.9 Ω m and 11.1 ± 2.3 Ω m, respectively: mean ± standard deviation). However, the differences in absolute lung resistivity between normal and deep tidal breathing at the same electrode level are significant. No significant difference was found in the coefficient of variation between the electrode levels of 4 and 5 cm (9.5 ± 3.6%, 8.5 ± 3.2% at 4 and 5 cm, respectively: mean ± standard deviation in individual subjects). Therefore, the electrode levels of 4 and 5 cm above the xiphoid process showed reasonable reliability in the measurement of absolute lung resistivity both among individuals and over time.
Functional Activation during the Rapid Visual Information Processing Task in a Middle Aged Cohort: An fMRI Study

The Rapid Visual Information Processing (RVIP) task, a serial discrimination task where task performance believed to reflect sustained attention capabilities, is widely used in behavioural research and increasingly in neuroimaging studies. To date, functional neuroimaging research into the RVIP has been undertaken using block analyses, reflecting the sustained processing involved in the task, but not necessarily the transient processes associated with individual trial performance. Furthermore, this research has been limited to young cohorts. This study assessed the behavioural and functional magnetic resonance imaging (fMRI) outcomes of the RVIP task using both block and event-related analyses in a healthy middle aged cohort (mean age = 53.56 years, n = 16). The results show that the version of the RVIP used here is sensitive to changes in attentional demand processes with participants achieving a 43% accuracy hit rate in the experimental task compared with 96% accuracy in the control task. As shown by previous research, the block analysis revealed an increase in activation in a network of frontal, parietal, occipital and cerebellar regions. The event related analysis showed a similar network of activation, seemingly omitting regions involved in the processing of the task (as shown in the block analysis), such as occipital areas and the thalamus, providing an indication of a network of regions involved in correct trial performance. Frontal (superior and inferior frontal gryi), parietal (precuenus, inferior parietal lobe) and cerebellar regions were shown to be active in both the block and event-related analyses, suggesting their importance in sustained attention/vigilance. These networks and the differences between them are discussed in detail, as well as implications for future research in middle aged cohorts.
Improved Immunogenicity of Recombinant Mycobacterium bovis Bacillus Calmette‐Guérin Strains Expressing Fusion Protein Ag85A‐ESAT‐6 of Mycobacterium tuberculosis

Early secretory antigen target 6 (ESAT‐6) is a dominant target for cell‐mediated immunity in the early phase of tuberculosis (TB) in patients with TB, causing T‐cell proliferation and gamma interferon (IFN‐γ) production, which has been considered to be a protective antigen that can be used for future vaccine development. Ag85A is the most essential component for bacterial survival within macrophages and has been used in numerous vaccine preparations, which can induce strong cellular immune responses. In this study, we constructed a new recombinant bacilli Calmette‐Guérin (BCG) strain (rBCG‐AE) that could express fusion protein Ag85A‐ESAT‐6 of Mycobacterium tuberculosis and evaluated its immunogenicity in BALB/c mice. There was no evidence for increased virulence of this rBCG. Our experiments illustrated that the rBCG‐AE was able to induce higher titer of antibody and elicit more long‐lasting and stronger Th1 type cellular immune responses than the parental BCG strain, or rBCG‐A (expressing Ag85A) strain, or rBCG‐E (expressing ESAT‐6) strain, which are characterized by the strong antibody response, the proliferation rate of splenocytes, the ratio of CD4+ T and CD8+ T cells stimulated by tuberculin‐purified protein derivative and elevated levels of IFN‐γ in antigen‐stimulated splenocyte cultures. The results show that rBCG‐AE is an improved TB vaccine for further study.
Lifetime direct costs of stroke for indigenous patients adjusted for comorbidities

Objective: To estimate the lifetime health costs of stroke by comorbidity and indigenous status in Australia's Northern Territory (NT), where a large indigenous population resides. Methods: Incidence-based cohort study using linked hospital, primary care, and Pharmaceutical Benefits Scheme data to estimate lifetime direct costs for hemorrhagic stroke (HS), ischemic stroke (IS) and undetermined stroke (UND). Inverse probability-weighted survival analysis was adapted to adjust for loss to follow-up. Log-linear modeling was used to analyze the net stroke costs and marginal comorbidity costs by indigenous status. Results: Between 1992 and 2013, there were 3,733 patients admitted with stroke in the NT (74% were incident strokes, 38% indigenous, 56% male, 56% IS). In 2012/2013 Australian dollars, the estimated lifetime cost for an incident stroke in NT was $302,538 AUD ($207,218 USD) per patient. The net lifetime cost per non-indigenous female HS patient aged <45 years without comorbidity (reference category) was $72,773 AUD ($49,844 USD); IS cost 54% and UND 9% more than HS (p < 0.01). Stroke cost was greater for indigenous patients (∆ 44%) and patients with renal disease (∆ 71%), coronary heart disease (∆ 44%), hypertension (∆ 30%), and diabetes (∆ 28%) in comparison with the reference category (all p < 0.01). Chronic obstructive pulmonary disease, atrial fibrillation, depression, and cancer were negatively associated with lifetime stroke costs. Conclusions: The costs of stroke for indigenous people and patients with different comorbidities are substantial and an integrated prevention strategy is needed.
Moving Teenagers Out of High-Risk Neighborhoods: How Girls Fare Better than Boys

Moving to Opportunity (MTO) offered public housing residents the opportunity to move to low-poverty neighborhoods. Several years later, boys in the experimental group fared no better on measures of risk behavior than their control group counterparts, whereas girls in the experimental group engaged in lower-risk behavior than control group girls. The authors explore these differences by analyzing data from in-depth interviews conducted with 86 teens in Baltimore and Chicago. They find that daily routines, fitting in with neighborhood norms, neighborhood navigation strategies, interactions with peers, friendship making, and distance from father figures may contribute to how girls who moved via MTO benefited more than boys.
Changes in blood B cell phenotypes and Epstein-Barr virus load in chronically human immunodeficiency virus–infected patients before and after antiretroviral therapy.

BACKGROUND Switched and nonswitched memory B cells, which usually constitute the main reservoirs of Epstein‐Barr virus (EBV), are rapidly depleted in patients with chronic human immunodeficiency virus (HIV) infection. Because the EBV load is frequently increased in these patients, other B cell reservoirs might participate in EBV persistence. METHODS We examined the combined expression of CD27, SIgD/G/M, CD38, CD10, CD5, CXCR5, CD62L, CD44, and CXCR3 on B cells from healthy donors (n = 30) and from HIV type 1-infected patients (n = 23) at diagnosis and after highly active antiretroviral therapy. The plasma HIV load and the DNA EBV load in peripheral blood mononuclear cells were assessed. RESULTS Increased frequencies of CD38+SIgD+CD10+ B cells were found in patients with an EBV load >10(3)copies per 10(6)peripheral blood mononuclear cells and a strong depletion of memory B cells. This phenotype resembles that of transitional B cell subsets. Elevated percentages of these B cells were still found in 2 patients showing no decrease in EBV load after highly active antiretroviral therapy. CONCLUSIONS Because transitional-like B cells persist concomitantly with high EBV load after highly active antiretroviral therapy, we suggest that this population might be an alternative EBV reservoir in patients with chronic HIV infection who have strongly reduced numbers of memory B cells. The consequences of EBV infection of immature B cells are discussed with regard to B cell maturation and a higher prevalence of B cell lymphoma in HIV‐infected patients.
Exploring group theory and topology for analyzing the structure of biological hierarchies

The concepts of population and species play a fundamental role in biology. The existence and precise definition of higher-order hierarchies, such as division into species, is open to debate among biologists. We seek to show a fractal structure of species by utilizing group theory, topology, and a set of zeta functions. First, we present a new metric, small $s$, that uses data from the natural environment to measure extents that are beyond the range of neutral (harmonic) logarithmic populations and are specific to a given species. We define this metric by modifying the Price equation, utilizing a Dirichlet series and an operator based on number theory. As expected, the box dimension of our model is $\dim_BA = 2$ and 2 is a critical line for the appearance of the fractal structure of species, which is confirmed by observation. Prime $p$ numbers can be calculated from corresponding $\Im(s)$ values of non-trivial zero points of the Riemann zeta function. Integrating all methods, we are able to define a species as a $p$-Sylow subgroup of a particular community in a single niche, confirmed by topological analysis. Calculation of the norm of prime closed geodesics $|N(p)|$ shows that noninteracting adaptive species are in the mode $|N(p)| = 2/3$, while interacting neutral populations are in the mode $|N(p)| = 1$. The border between fluctuating populations and ordered species is $\Re(s) = 2$, as expected by various sets of fractal zeta functions. The mod 4 of primes corresponding to $\Im(s)$, the zero points of the Riemann zeta function and the Hurwitz zeta function, reveal adaptive and disadaptive situations among individuals. We thus posit a metric that is useful for discrimination between population data and species data. In our patch with zeta dominance (PzDom) model, calculations only require knowledge of the density of individuals over time.