Miracle-dz/UniFAR-FTUs huggingface dataset:
Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

ABSTRACT Obligatory anaerobic bacteria are major contributors to the overall metabolism of soil and the human gut. The metabolic pathways of these bacteria remain, however, poorly understood. Using isotope tracers, mass spectrometry, and quantitative flux modeling, here we directly map the metabolic pathways of Clostridium acetobutylicum, a soil bacterium whose major fermentation products include the biofuels butanol and hydrogen. While genome annotation suggests the absence of most tricarboxylic acid (TCA) cycle enzymes, our results demonstrate that this bacterium has a complete, albeit bifurcated, TCA cycle; oxaloacetate flows to succinate both through citrate/α-ketoglutarate and via malate/fumarate. Our investigations also yielded insights into the pathways utilized for glucose catabolism and amino acid biosynthesis and revealed that the organism's one-carbon metabolism is distinct from that of model microbes, involving reversible pyruvate decarboxylation and the use of pyruvate as the one-carbon donor for biosynthetic reactions. This study represents the first in vivo characterization of the TCA cycle and central metabolism of C. acetobutylicum. Our results establish a role for the full TCA cycle in an obligatory anaerobic organism and demonstrate the importance of complementing genome annotation with isotope tracer studies for determining the metabolic pathways of diverse microbes.
The MBOA-WiMedia specification for ultra wideband distributed networks

The WiMedia Alliance is undertaking the development of an UWB-based system specification with participation from more than 170 companies. UWB technology will provide data rates up to 480 Mb/s within a range of up to 10 m. High-rate UWB will enable fast download of content from one consumer electronic (CE) device to the next in seconds instead of minutes or longer. In addition, the low-power characteristic of UWB will make possible the ubiquitous use of this technology in portable and mobile CE devices, such as cameras, MP3 players, and CD players. The WiMedia Alliance is specifying the physical layer, the MAC sublayer, and convergence layers. The WiMedia PHY layer is based on multiband orthogonal frequency-division multiplexing. The WiMedia MAC is completely distributed, making it an excellent candidate not only for the aforementioned UWB applications, but also for the next-generation MAC protocols in the domain of cognitive radios as well as in cooperative communications
Image-Based Visual Servoing of a Quadrotor Using Virtual Camera Approach

In this paper, an image-based visual servoing control law is proposed for a quadrotor unmanned aerial vehicle using an on-board monocular camera and an inertial measurement unit sensor. Based on the perspective projection model, suitable image features are defined on a rotated image plane called virtual image plane, thus a decoupled image feature dynamics is achieved. Then, a translational velocity observer is presented using these image features. The image feature dynamics and quadrotor dynamics are combined to derive a nonlinear controller. The controller is based on backstepping technique to account for the underactuation of the quadrotor. The image-based visual servoing controller only needs three point features, which make it useable in general environment. The closed-loop system is proved globally asymptotic stable by means of Lyapunov analysis. Computer simulations that regulate a quadrotor to a desired position with respect to (w.r.t.) four points lying on a horizontal plane and three points lying on a full rotated slope are conducted separately. Smooth and efficient trajectories are obtained both in virtual image plane and Cartesian space. Finally, experimental tests including pushing and pulling the visual target are conducted to verify the validity and robustness of the proposed controller. The proposed control law regulates the quadrotor to a desired position, defined by desired image, from an unknown initial position, which can be used in monitoring, landing, and other applications.
Mixed Methods as Methodological Innovations: Problems and Prospects

One of the most recent methodological innovations has been in the area of what is now referred to as Mixed Methodology (hereafter MM). The most serious and comprehensive volume in this area is probably, The Handbook of Mixed Methods in Social and Behavioral Research (Tashakkori & Teddlie, 2003). The Handbook is a sophisticated compilation of various authors who explore the many dimensions of this emerging field. It is not my intention to review the volume, but rather to make the claim that MM still has a host of methodological issues that must be clarified before the potential development of this area can take their place as being relevant to the social and behavioural sciences. What I would like to do, then, is offer some ideas which can become the basis of further debate. The intent is to present an overview and summary of what I consider to be the major problems that still exist in the area of MM.
Automated multichannel fluorescent whole slide imaging and its application for cytometry

Slide‐based image cytometry (SBC) has several advantages over flow cytometry but it is not widely used because of its low throughput, complicated workflow, and high price. Fully automated microscopes became affordable with the advent of whole slide imaging (WSI) and they can be transformed into a cytometer. A MIRAX MIDI automated whole slide imager was used with metal‐halide and light emitting diode (LED)‐based fluorescent illumination, filter block changer, and a cooled monochrome charge coupled device camera. The MIRAX control software was further developed for fluorescent sample detection, autofocusing, multichannel digitization, and signal correction due to nonuniform illumination. Fluorescent calibration beads were used to verify the linearity of the system. The HistoQuant software package of the MIRAX viewer was used for image segmentation and quantitative analysis. The data was displayed by the histogram, scatter plot, and gallery functions of the same program. Fluorescent samples can be reliably detected, focused, and scanned. The measured integrated fluorescence showed linearity with exposure time and staining intensity. Automated fluorescent WSI with stable LED illumination and high‐quality homogeneous fluorescent slides can be used conveniently for SBC. © 2009 International Society for Advancement of Cytometry
Abiotic Surface Sensing and Biofilm-Dependent Regulation of Gene Expression in Escherichia coli

ABSTRACT To get further information on bacterial surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli K-12, random insertion mutagenesis with Mu dX, a mini-Mu carrying the promoterless lacZ gene, was performed with anompR234 adherent strain, and a simple screen was developed to assess changes in gene expression in biofilm cells versus planktonic cells. This screen revealed that major changes in the pattern of gene expression occur during biofilm development: the transcription of 38% of the genes was affected within biofilms. Different cell functions were more expressed in sessile bacteria: the OmpC porin, the high-affinity transport system of glycine betaine (encoded by theproU operon), the colanic acid exopolysaccharide (wca locus, formerly called cps), tripeptidase T (pepT), and the nickel high-affinity transport system (nikA). On the other hand, the syntheses of flagellin (fliC) and of a putative protein of 92 amino acids (f92) were both reduced in biofilms. Such a genetic reprogramming of gene expression in biofilms seems to result from changes in multiple environmental physicochemical conditions. In this work, we show that bacteria within biofilms encounter higher-osmolarity conditions, greater oxygen limitation, and higher cell density than in the liquid phase.
Induced smoothing for rank regression with censored survival times

Adaptions of weighted rank regression to the accelerated failure time model for censored survival data have been successful in yielding asymptotically normal estimates and flexible weighting schemes to increase statistical efficiencies. However, for only one simple weighting scheme, Gehan or Wilcoxon weights, are estimating equations guaranteed to be monotone in parameter components, and even in this case are step functions, requiring the equivalent of linear programming for computation. The lack of smoothness makes standard error or covariance matrix estimation even more difficult. An induced smoothing technique overcame these difficulties in various problems involving monotone but pure jump estimating equations, including conventional rank regression. The present paper applies induced smoothing to the Gehan–Wilcoxon weighted rank regression for the accelerated failure time model, for the more difficult case of survival time data subject to censoring, where the inapplicability of permutation arguments necessitates a new method of estimating null variance of estimating functions. Smooth monotone parameter estimation and rapid, reliable standard error or covariance matrix estimation is obtained. Copyright © 2006 John Wiley & Sons, Ltd.
An outer-rotor traction machine with halbach magnetized permanent magnets and concentrated fractional slot windings

A prototype outer-rotor traction machine with Halbach magnetized permanent magnet structure is introduced. Concentrated fractional slot windings are used to obtain a larger winding factor. The performance studies of the prototype are presented by using finite element analysis models. The flux distributions, torque capability and back emf are investigated. The experimental results match the analysis. The result shows that Halbach magnetized magnet and the fractional slot winding increase the back emf and torque capability of the machine.
A Genome-wide Association Analysis in Four Populations Reveals Strong Genetic Heterogeneity For Birth Weight

Low or high birth weight is one of the main causes for neonatal morbidity and mortality. They are also associated with adulthood chronic illness. Birth weight is a complex trait which is affected by baby’s genes, maternal environments as well as the complex interactions between them. To understand the genetic basis of birth weight, we reanalyzed a genome-wide association study data set which consists of four populations, namely Thai, Afro-Caribbean, European, and Hispanic population with regular linear models. In addition to fit the data with parametric linear models, we fitted the data with a nonparametric varying-coefficient model to identify variants that are nonlinearly modulated by mother’s condition to affect birth weight. For this purpose, we used baby’s cord glucose level as the mother’s environmental variable. At the 10-5 genome-wide threshold, we identified 33 SNP variants in the Thai population, 26 SNPs in the Afro-Caribbean population, 18 SNPs in the European population, and 7 SNPs in the Hispanic population. Some of the variants are significantly modulated by baby’s cord glucose level either linearly or nonlinearly, implying potential interactions between baby’s gene and mother’s glucose level to affect baby’s birth weight. There is no overlap between variants identified in the four populations, indicating strong genetic heterogeneity of birth weight between the four ethnic groups. The findings of this study provide insights into the genetic basis of birth weight and reveal its genetic heterogeneity.
Examination of contaminant-induced faults in connectors

This paper describes the results of an investigation into the effects of salt water exposure on cable connector impedances. A series of tests were performed to explore the shunting resistance across the pins of wiring harness connectors. The test results show that salt-induced corrosion and moisture may cause intermittent shunting resistances capable of affecting the normal operation of various systems. One important test result is that the induced shunting resistances are a nonlinear function of the applied voltage. This non-linear behavior can be important when evaluating the ESD or radiated RF susceptibility of products that may be exposed to a salt-water environment. An equivalent circuit based on measurements is developed to model the behavior of various salt-water/metal electrode interactions.
Expression of death‐associated protein kinase and recruitment to the tumor necrosis factor signaling pathway following brief seizures

Death‐associated protein (DAP) kinase is calcium‐regulated and known to function downstream of death receptors, prompting us to examine its role in the mechanism of seizure‐induced neuronal death. Brief seizures were focally evoked in rats, eliciting neuronal death within the CA3 subfield of the hippocampus, and to a lesser extent, cortex. Western blotting confirmed expression of DAP kinase within hippocampus and cortex at the predicted weight of ∼160 kDa. Immunohistochemistry revealed seizures triggered a significant increase in numbers of DAP kinase‐expressing cells within CA3 and cortex, without affecting cell counts within seizure‐resistant CA2 or the dentate gyrus. Numbers of DAP kinase‐expressing cells were increased in relation to specific patterns of injury‐causing seizure activity, electrographically defined. Seizures caused an early increase in DAP kinase binding to actin, and association with calmodulin. Co‐immunoprecipitation studies also revealed seizures triggered binding of DAP kinase to the tumor necrosis factor receptor 1 and the Fas‐associated death domain protein, commensurate with caspase‐8 proteolysis. In contrast, within surviving fields of the hippocampus, DAP kinase interacted with the molecular chaperone 14–3−3. These data suggest DAP kinase is involved in the molecular pathways activated during seizure‐induced neuronal death.
[Intrapartum and interval tubal sterilization].

BACKGROUND Brazil is a country with a high prevalence of tubal ligation, which is frequently performed at the time of delivery. In recent years, an increase in tubal reversal has been noticed, primarily among young women. OBJECTIVES To study characteristics correlated with the procedure, determine frequency of intrapartum tubal ligation, measure patient satisfaction rates and tubal sterilization regret, in a sample of post-tubal patients. METHODS Three hundred and thirty-five women underwent tubal ligation. The variables studied were related to the procedure: age at tubal ligation, whether ligation was performed intrapartum (vaginal or cesarean section) or after an interval (other than the intrapartum and puerperal period), health service performing the sterilization, medical expenses paid for the procedure, reason stated for choosing the method and causes related to satisfaction/regret: desire to become pregnant after sterilization, search for treatment and performance of tubal ligation reversal. The women were divided into two groups, a group undergoing ligation in the intrapartum period and a second group ligated after an interval, to evaluate the association between variables by using Fisher's exact test and chi-squared calculation with Yates' correction. The study was approved by the Ethics Committee of the institution. RESULTS There was a predominance of Caucasian women over 35 years of age, married, and with a low level of education of which 43.5% had undergone sterilization before 30 years of age. Two hundred and forty-five women underwent intrapartum tubal ligation, 91.2% of them had cesarean delivery and 44.6% vaginal delivery. In both groups undergoing intrapartum tubal ligation and ligation after an interval, 82.0% and 80.8% reported satisfaction with the method. Although 14.6% expressed a desire to become pregnant at some time after sterilization, consultation regarding sterility occurred in 3.4% and 2.3%, respectively, and one woman underwent tubal reversal. The most frequent reasons for choosing the method were satisfaction with the number of offspring (35.5% and 46.7%) and medical indication (41.6% and 32.2%), respectively. CONCLUSION The incidence of intrapartum tubal ligation was higher when the last delivery had been a cesarean section. No difference was detected among the groups regarding rates of satisfaction and regret after performance of the sterilization procedure.
A generalized cable equation for magnetic stimulation of axons

During magnetic stimulation, electric fields are induced both on the inside (intracellular region) and the outside (extracellular region) of nerve fibers. The induced electric fields in each region can be expressed as the sum of a primary and a secondary component. The primary component arises due to an applied time varying magnetic field and is the time derivative of a vector potential. The secondary component of the induced field arises due to charge separation in the volume conductor surrounding the nerve fiber and is the gradient of a scalar potential. The question, "What components of intracellular fields and extracellular induced electric fields contribute to excitation? " has, so far, not been clearly addressed. Here, the authors address this question while deriving a generalized cable equation for magnetic stimulation and explicitly identify the different components of applied fields that contribute to excitation. In the course of this derivation, the authors review several assumptions of the core-conductor cable model in the context of magnetic stimulation. It is shown that out of the possible 4 components, only the first spatial derivative of the intracellular primary component and the extracellular secondary component of the fields contribute to excitation of a nerve fiber. An earlier form of the cable equation for magnetic stimulation has been shown to result in solutions identical to three-dimensional (3D) volume-conductor model for the specific configuration of an isolated axon in a located in an infinite homogenous conducting medium. The authors extend and generalize this result by demonstrating that their generalized cable equation results in solutions identical to 3D volume conductor models even for complex geometries of volume conductors surrounding axons such as a nerve bundle of different conductivity surrounding axons. This equivalence in the solutions is valid for several representations of a nerve bundle such as anisotropic monodomain and bidomain models.
Processing of the Human Coronavirus 229E Replicase Polyproteins by the Virus-Encoded 3C-Like Proteinase: Identification of Proteolytic Products and Cleavage Sites Common to pp1a and pp1ab

ABSTRACT Replicase gene expression by the human coronavirus 229E involves the synthesis of two large polyproteins, pp1a and pp1ab. Experimental evidence suggests that these precursor molecules are subject to extensive proteolytic processing. In this study, we show that a chymotrypsin-like enzyme, the virus-encoded 3C-like proteinase (3CLpro), cleaves within a common region of pp1a and pp1ab (amino acids 3490 to 4068) at four sites. trans-cleavage assays revealed that polypeptides of 5, 23, 12, and 16 kDa are processed from pp1a/pp1ab by proteolysis of the peptide bonds Q3546/S3547, Q3629/S3630, Q3824/N3825, and Q3933/A3934. Relative rate constants for the 3CLpro-mediated cleavages Q2965/A2966, Q3267/S3268, Q3824/N3825, and Q3933/A3934 were derived by competition experiments using synthetic peptides and recombinant 3CLpro. The results indicate that coronavirus cleavage sites differ significantly with regard to their susceptibilities to proteolysis by 3CLpro. Finally, immunoprecipitation with specific rabbit antisera was used to detect the pp1a/pp1ab processing end products in virus-infected cells, and immunofluorescence data that suggest an association of these polypeptides with intracellular membranes were obtained.
ASCAT Surface State Flag (SSF): Extracting Information on Surface Freeze/Thaw Conditions From Backscatter Data Using an Empirical Threshold-Analysis Algorithm

Information on soil surface state is valuable for many applications such as climate studies and monitoring of permafrost regions. C-band scatterometer data indicate good potential to deliver information on surface freeze/thaw. Variation in state or amount of water contained in the soil causes significant alteration of dielectric properties of the soil which is markedly observable in scatterometer backscattered signal. A threshold-analysis method is developed to derive a set of parameters to be used in evaluating the normalized backscatter measurements through decision trees and anomaly detection modules for determination of freeze/thaw conditions. The model parameters are extracted from two years (2007-2008) backscatter data from ASCAT scatterometer onboard Metop satellite collocated with ECMWF ReAnalysis (ERA-Interim) soil temperature. Backscatter measurements are flagged as indicator of frozen/unfrozen surface, and snowmelt or existing water on the surface. The output product, so-called surface state flag (SSF), compares well with two modeled soil temperature data sets as well as the air temperature measurements from synoptic meteorological stations across the northern hemisphere. The SSF time series are also validated with soil temperature data available at four in situ observation sites in Siberian and Alaska regions showing the overall accuracy of about 80% to 90%.
Revisiting the Commodity Curse: A Financial Perspective

We study the response of a three-sector commodity-exporter small open economy to a commodity price boom. When the economy has access to international borrowing and lending, a temporary commodity price boom brings about the standard wealth effect that stimulates demand and has long-run implications on the sectoral allocation of labour. If dynamic productivity gains are concentrated in the traded goods sector, the commodity boom crowds out the traded sector and delays convergence to the world technology frontier. Financial openness by stimulating current demand, amplifies the crowding out effect and may even lead to a growth trap, in which no resources are allocated to the traded sector. From a normative point of view, our analysis suggests that capital account management policies could be welfare improving in those circumstances.
Women's empowerment and micro-finance programmes: strategies for increasing impact.

This study summarizes findings from a pilot project that distributed information and ran workshops in Ethiopia, Ghana, and India, on women's empowerment and microfinance. The project was funded by the British Small Enterprise Development Fund of the Department of International Development. Links between microfinance and women's empowerment are viewed as optimistic, limited by design, cost effective in eliminating poverty, and a misplaced diversion of resources. Microfinance programs range from small scale self-help groups to large poverty-targeted banks. One model may vary in delivery, group functions and structures, and complementary services. This project identified 3 contrasting approaches to microfinance and women's empowerment: the financial sustainability approach, the integrated community development approach, and the feminist empowerment approach. However, program evaluations revealed the need to question the assumptions underlying all 3 approaches. In most programs, women benefited to a limited degree. Many women did not control the loan use. Most women were engaged in low paid, traditionally female activities, and increases in income were small. Resources and time invested in economic activity were limited by responsibility for household consumption and unpaid domestic work. Microfinance programs sometimes created domestic tension between spouses and loss of spousal income and support. Group repayment pressures sometimes created pressures between women. Many women focused on personal rather than social objectives. The author proposes a gender strategy for microfinance and sets priorities for further research.