Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of a Mutant of the Marine Bacterium Alcanivorax borkumensis SK2 Defective in Lipid Biosynthesis

ABSTRACT In many microorganisms, the key enzyme responsible for catalyzing the last step in triacylglycerol (TAG) and wax ester (WE) biosynthesis is an unspecific acyltransferase which is also referred to as wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT; AtfA). The importance and function of two AtfA homologues (AtfA1 and AtfA2) in the biosynthesis of TAGs and WEs in the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2 have been described recently. However, after the disruption of both the AtfA1 and AtfA2 genes, reduced but substantial accumulation of TAGs was still observed, indicating the existence of an alternative TAG biosynthesis pathway. In this study, transposon-induced mutagenesis was applied to an atfA1 atfA2 double mutant to screen for A. borkumensis mutants totally defective in biosynthesis of neutral lipids in order to identify additional enzymes involved in the biosynthesis of these lipids. At the same time, we have searched for a totally TAG-negative mutant in order to study the function of TAGs in A. borkumensis. Thirteen fluorescence-negative mutants were identified on Nile red ONR7a agar plates and analyzed for their abilities to synthesize lipids. Among these, mutant 2 M131 was no longer able to synthesize and accumulate TAGs if pyruvate was used as the sole carbon source. The transposon insertion was localized in a gene encoding a putative cytochrome c family protein (ABO_1185). Growth and TAG accumulation experiments showed that the disruption of this gene resulted in the absence of TAGs in 2 M131 but that growth was not affected. In cells of A. borkumensis SK2 grown on pyruvate as the sole carbon source, TAGs represented about 11% of the dry weight of the cells, while in the mutant 2 M131, TAGs were not detected by thin-layer and gas chromatography analyses. Starvation and lipid mobilization experiments revealed that the lipids play an important role in the survival of the cells. The function of neutral lipids in A. borkumensis SK2 is discussed.
Self-Organizing Neural Networks using Discontinuous Teacher Data for Incremental Category Learning

In this paper, we develop a neural model that forms categories of inputs for some practical applications such as pattern recognition, learning, image processing, and trend analysis. The developed model is based on natural mechanisms of biological behavior instead of artificial one such as clustering algorithms. The essential point of the model is to regard the teacher information as a first priority for an accurate learning. Then, the model can carry the accurate classification of complex and imbalanced categories by using discontinuous teacher data under an incremental learning environment. Simulation results demonstrate the usefulness and the weakness of the model on practical category formation tasks
A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment

The divergence of 16S rDNA sequences in marine sediment was investigated. Twenty unique partial sequences were found among 33 cloned following PCR. Thirteen shared 82 to 91% similarity with sequences of delta subclass sulfate-reducing bacteria. Three contained the target sequence for a sulfate-reducing bacterium-specific oligonucleotide probe designed from pure-culture studies.
Three Essays on Education Reform in the United States. PRGS Dissertation.

Government is increasingly allocating resources to measure the relative performance of providers of public goods, but the effect of this information on voting behavior is relatively unknown. In this paper, I study how voters react to performance information shocks in school board elections. I employ a difference-in-difference approach that compares incumbent reelection rates before and after the implementation of California’s Public Schools Accountability Act (PSAA) in districts discovered ex post to be high and low performing, relative to their apparent peers. Using detailed district election data between 1995 and 2006, I find support that in low-turnout years, voters tend to disregard new academic performance indicators in favor of other forms of information. However, in high turnout years, voters use the academic performance metrics to hold incumbents accountable, though I find little evidence that school board members can affect the performance metric. Finally, I show suggestive evidence that despite relatively uniform election coverage in the media, as time elapses and more information becomes available, the incumbent re-election effects strengthen. Taken together, my findings contribute a more nuanced understanding to the expressive and retrospective voting literature. Over the last decade, local, state, and federal governments have invested significant public dollars to create standardized metrics of comparison to aid policy-makers in their resource allocation and help constituents understand if providers of important public goods are working effectively and efficiently. Particularly since the passage of the federal law, No Child Left
Contamination and release of nanomaterials associated with the use of personal protective clothing.

INTRODUCTION We investigated nanomaterial release associated with the contamination of protective clothing during manipulation of clothing fabrics contaminated with nanoparticles. Nanomaterials, when released as airborne nanoparticles, can cause inhalation exposure which is the route of exposure of most concern to cause adverse health effects. Measurement of such nanoparticle re-suspension has not yet been conducted. Protective clothing can be contaminated with airborne nanoparticles during handling and operating processes, typically on the arms and front of the body. The contaminated clothing could release nanoparticles in the general room while performing other activities and manipulating the clothing after work. METHODS The exposures associated with three different fabric materials of contaminated laboratory coats (cotton, polyester, and Tyvek), including the magnitude of contamination and particle release, were investigated in this study by measuring the number concentration increase and the weight change on fabric pieces. This study simulated real life occupational exposure scenarios and was performed in both regular and clean room environments to investigate the effect of background aerosols on the measurements. Concentration were measured using particle spectrometers for diameters from 10nm to 10 µm. Collected aerosol particles and contaminated fabric surfaces were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and elemental composition analysis. RESULTS The magnitude of particle release from contaminated lab coat fabric was found to vary by the type of fabric material; cotton fabric showed the highest level of contamination and particle release, followed by Tyvek and polyester fabrics. The polyester lab coat material was found to have the lowest particle release to deposition (R/D) ratio. The particle release number concentrations were in a range of 768-119 particles cm(-3) and 586-187 particles cm(-3) in regular and clean rooms, respectively. Multiple peaks were observed in the number concentration distribution data, with particle diameters peaking at 40-50 and 100-300nm. CONCLUSIONS The SEM analysis of the contaminated fabric surface found test particles and other environmental particles. The elemental composition analysis presented detectable response to the studied alumina oxide particles. The laboratory coat primarily made of cotton woven material is not recommended for worker protection against nanoparticle exposure because of the highest particle contamination and release ability. In addition, the result demonstrated that a well-controlled (cleanroom) environment is critical to investigate the factors affecting nanoparticle interaction with protective clothing.
Stream : A Visualization Design Study

Text data, such as customer satisfaction reports, personal micro-blogs, or emails, is being produced like never before; but tools for visualizing this growing data source are lacking. Typical text visualizations, like word clouds and word trees, tend to leave out relevant context, remove dimensionality of the underlying data, and restrict access to source text. In this paper, we present the Sentiment Stream, a proposed form of text visualization. Sentiment Stream aggregates text documents by time and space bins, preserving temporal and spatial context, and finds the most emotional content in each bin using part of speech tagging and sentiment analysis. The most relevant word from each bin is displayed in a grid encoding time and space, sentiment is encoded using color, and objectivity is encoded using font weight. We demonstrate the application of Sentiment Stream on a dataset of 20 million Tweets following Hurricane Sandy in the week after landfall in October 2012 in New Jersey, USA. Because of the unique spatial, temporal, and emotional context provided by Sentiment Stream, we are able to make conclusions about the sentiment surrounding this natural disaster that would not have been possible using other text visualizations.
Hydrodynamics in bridging and aggregation of two colloidal particles in a near-critical binary mixture.

We investigate bridging and aggregation of two colloidal particles in a near-critical binary mixture when the fluid far from the particles is outside the coexistence (CX) curve and is rich in the component disfavored by the colloid surfaces. In such situations, the adsorption-induced interaction is enhanced, leading to bridging and aggregation of the particles. We realize bridging firstly by changing the temperature with a fixed interparticle separation and secondly by letting the two particles aggregate. The interparticle attractive force dramatically increases upon bridging. The dynamics is governed by hydrodynamic flow around the colloid surfaces. In aggregation, the adsorption layers move with the particles and squeezing occurs at narrow separation. These results suggest relevance of bridging in the reversible colloid aggregation observed so far. We use the local functional theory [J. Chem. Phys., 2012, 136, 114704] to take into account the renormalization effect and the simulation method [Phys. Rev. Lett. , 2000, 85, 1338] to calculate the hydrodynamic flow around the colloidal particles.
Asian-American variants of human papillomavirus 16 and risk for cervical cancer: a case-control study.

BACKGROUND Human papillomavirus 16 (HPV16) has a number of variants, each with a different geographic distribution and some that are associated more often with invasive neoplasias. We investigated whether the high incidence of cervical cancer in Mexico (50 cases per 100 000 women) may be associated with a high prevalence of oncogenic HPV16 variants. METHODS Cervical samples were collected from 181 case patients with cervical cancer and from 181 age-matched control subjects, all from Mexico City. HPV16 was detected with an E6/E7 gene-specific polymerase chain reaction, and variant HPV classes and subclasses were identified by sequencing regions of the E6 and L1/MY genes. Clinical data and data on tumor characteristics were also collected. All statistical tests were two-sided. RESULTS HPV16 was detected in cervical scrapes from 50.8% (92 of 181) of case patients and from 11% (20 of 181) of control subjects. All HPV16-positive samples, except one, contained European (E) or Asian-American (AA) variants. AA and E variants were found statistically significantly more often in case patients (AA = 23.2% [42 of 181]; E = 27.1% [49 of 181]) than in control subjects (AA = 1.1% [two of 181]; E = 10% [18 of 181]) (P<.001 for case versus control subjects for either E or AA variants, chi2 test). However, the frequency of AA variants was 21 times higher in cancer patients than in control subjects, whereas that ratio for E variants was only 2.7 (P =.006, chi2 test). The odds ratio (OR) for cervical cancer associated with AA variants (OR = 27.0; 95% confidence interval [CI] = 6.4 to 113.7) was higher than that associated with E variants (OR = 3.4; 95% CI = 1.9 to 6.0). AA-positive case patients (46.2 +/- 12.5 years [mean +/- standard deviation]) were 7.7 years younger than E-positive case patients (53.9 +/- 12.2 years) (P =.004, Student's t test). AA variants were associated with squamous cell carcinomas and adenocarcinomas, but E variants were associated with only squamous cell carcinomas (P =.014, Fisher's exact test). CONCLUSIONS The high frequency of HPV16 AA variants, which appear to be more oncogenic than E variants, might contribute to the high incidence of cervical cancer in Mexico.
Describing Natural Images Containing Novel Objects with Knowledge Guided Assitance

Images in the wild encapsulate rich knowledge about varied abstract concepts and cannot be sufficiently described with models built only using image-caption pairs containing selected objects. We propose to handle such a task with the guidance of a knowledge base that incorporate many abstract concepts. Our method is a two-step process where we first build a multi-entity-label image recognition model to predict abstract concepts as image labels and then leverage them in the second step as an external semantic attention and constrained inference in the caption generation model for describing images that depict unseen/novel objects. Evaluations show that our models outperform most of the prior work for out-of-domain captioning on MSCOCO and are useful for integration of knowledge and vision in general.
Calculation of age-specific fertility schedules from tabulations of parity in two censuses

The mathematics of stable populations recently has been generalized to cover populations with time-varying fertility and mortality by a modification incorporating the sum of age-varying growth rates in place of the fixed growth rate of a stable population. Equations that characterize nonstable populations apply to any cohort-like phenomenon with a measurable property that cumulates gains or losses through time. In particular, the equations fit the relation between a population’s average parity at a given age and age-specific fertility rates previously experienced at lower ages. Techniques devised to derive an intercensal life table from single-year age distributions in two censuses are adapted to estimate accurate intercensal fertility schedules from distributions of parity by age of woman in two censuses. Birth-order specific fertility schedules are also estimated.
Expression of Kv3.1 and Kv4.2 Genes in Developing Cerebellar Granule Cells

The expression of voltage-gated potassium channels plays an important role in the acquisition of membrane excitability in neurons. We examined the expression pattern of genes in developing cerebellar granule neurons in vivo and in vitro. In situ hybridization of Kv3.1 mRNA demonstrated that the gene was expressed at high levels in the external granule layer (EGL) as well as in the internal granule layer (IGL) at all postnatal stages (P) examined (from P3 to P10). In contrast, Kv4.2 mRNA was detected in the premigratory zone (PMZ) of the EGL, but not in the proliferative zone (PLZ), in addition to the IGL. This indicates that Kv4.2 gene expression initiates in the postmitotic migrating neurons. We also examined the expression of the channel genes in microexplant culture systems. Kv3.1 polypeptide was detected in parallel fibers of granule cells at 2 days in vitro, and the expression continued in later stages. The signal of Kv4.2 protein was very low at 2 days in vitro; however, the number of positive cells and the intensity of the signals were increased at 6 days in vitro. These in vitro observations matched those in vivo and our previous electrophysiological studies in which we demonstrated that delayed- rectifier-type current was predominant in the immature granule cells followed by the later appearance of A-type current. The patterns of K+ channel expression suggest that sequential expression of these channel genes primarily determines the membrane excitability.
CHILL‐COMA TOLERANCE, A MAJOR CLIMATIC ADAPTATION AMONG DROSOPHILA SPECIES

Abstract. — Most drosophilid species can be classified either as temperate or tropical. Adults of species were submitted to a cold treatment (0°C) and then brought back to ambient temperature. They generally exhibited a chill coma and the time needed to recover was measured. We found in a set of 26 temperate species that recovery was rapid (average 1.8 min, range 0.15–4.9). In contrast, a long recovery time (average 56 min, range 24–120) was observed for 48 tropical species. A few species, like Drosophila melanogaster, are cosmopolitan and can proliferate under temperate and tropical climates. In 9 of 10 such species, slight genetic differences were found: a shorter recovery in temperate than in tropical populations. Comparing physiological data to phylogeny suggests that chill‐coma tolerance has been a recurrent adaptation that is selected for in cold climates but tends to disappear under a permanently warm environment. This major climatic adaptation, evidenced in drosophilids, seems to occur in other insect groups also.
Dynamic Control of Session Input Rates in Communication Networks

We consider a distributed algorithm for dynamically adjusting the input rate of each session of a voice or data network so as to exercise flow control. The algorithm receives periodically information regarding the level of congestion along each session path and iteratively corrects the session input rate. In this paper we place emphasis on voice networks but the ideas involved can also be used for dynamic routing and flow control in data networks.
Genome‐wide association scans for secondary traits using case‐control samples

Genome‐wide association studies (GWAS) require considerable investment, so researchers often study multiple traits collected on the same set of subjects to maximize return. However, many GWAS have adopted a case‐control design; improperly accounting for case‐control ascertainment can lead to biased estimates of association between markers and secondary traits. We show that under the null hypothesis of no marker‐secondary trait association, naïve analyses that ignore ascertainment or stratify on case‐control status have proper Type I error rates except when both the marker and secondary trait are independently associated with disease risk. Under the alternative hypothesis, these methods are unbiased when the secondary trait is not associated with disease risk. We also show that inverse‐probability‐of‐sampling‐weighted (IPW) regression provides unbiased estimates of marker‐secondary trait association. We use simulation to quantify the Type I error, power and bias of naïve and IPW methods. IPW regression has appropriate Type I error in all situations we consider, but has lower power than naïve analyses. The bias for naïve analyses is small provided the marker is independent of disease risk. Considering the majority of tested markers in a GWAS are not associated with disease risk, naïve analyses provide valid tests of and nearly unbiased estimates of marker‐secondary trait association. Care must be taken when there is evidence that both the secondary trait and tested marker are associated with the primary disease, a situation we illustrate using an analysis of the relationship between a marker in FGFR2 and mammographic density in a breast cancer case‐control sample. Genet. Epidemiol. 33:717–728, 2009. © 2009 Wiley‐Liss, Inc.
Underivatized cyclic olefin copolymer as substrate material and stationary phase for capillary and microchip electrochromatography

We report, for the first time, the use of underivatized cyclic olefin copolymer (COC, more specifically: Topas) as the substrate material and the stationary phase for capillary and microchip electrochromatography (CEC), and demonstrate chromatographic separations without the need of coating procedures. Electroosmotic mobility measurements in a 25 μm id Topas capillary showed a significant cathodic EOF that is pH‐dependent. The magnitude of the electroosmotic mobility is comparable to that found in glass substrates and other polymeric materials. Open‐tubular CEC was employed to baseline‐separate three neutral compounds in an underivatized Topas capillary with plate heights ranging from 5.3 to 12.7 μm. The analytes were detected using UV absorbance at 254 nm, thus taking advantage of the optical transparency of Topas at short wavelengths. The fabrication of a Topas‐based electrochromatography microchip by nanoimprint lithography is also presented. The microchip has an array of pillars in the separation column to increase the surface area. The smallest features that were successfully imprinted were around 2 μm wide and 5 μm high. No plasma treatment was used during the bonding, thus keeping the surface properties of the native material. An RP microchip electrochromatography separation of three fluorescently labeled amines is demonstrated on the underivatized microchip with plate heights ranging from 3.4 to 22 μm.
The State and Parameter Estimation of an Li-Ion Battery Using a New OCV-SOC Concept

The open circuit voltage (OCV) is widely used to estimate the state of charge (SOC) in many SOC estimation algorithms. But the relationship between the OCV and SOC can not be exactly same for all batteries. Because the conventional OCV-SOC differs between batteries, there is a problem in that the OCV-SOC data should be measured to accurately estimate the SOC in different batteries. Therefore, the conventional OCV- SOC should be modified. In this paper, a new OCV-SOC that is independent of the battery conditions is proposed. Thus, problems resulting from the defects of the EKF can be avoided by preventing the OCV-SOC data from varying. In this paper, the SOC and battery capacity are estimated using the dual EKF with the proposed OCV-SOC.
Increased occurrence of pericardial effusion in patients with autosomal dominant polycystic kidney disease.

BACKGROUND AND OBJECTIVES Autosomal dominant polycystic kidney disease (ADPKD) is a common hereditary disease with prominent connective tissue manifestations. A frequent occurrence of asymptomatic pericardial effusion has been observed in patients with ADPKD. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Consecutive computed tomography scans from 60 patients with ADPKD (group 1), 100 patients without ADPKD and with serum creatinine concentration of > or = 1.1 mg/dl (group 2), and 100 potential kidney donors (group 3) were retrospectively examined. Pericardial effusion was graded from 0 to 4 on the basis of the distance between the parietal and visceral pericardia at mid, mid-low, and low levels of the heart on transaxial computed tomography scan sections. RESULTS Twenty-one (35%) of 60 patients in group 1 were found to have pericardial effusion, compared with 9 (9%) and 4 (4%) patients in groups 2 and 3, respectively. Ten of the 21 patients with pericardial effusion in group 1 but none of the patients in groups 2 and 3 had moderate to high effusion scores. The presence and severity of pericardial effusion were not associated with age, renal dysfunction, or hypertension. All pericardial effusions were asymptomatic. CONCLUSIONS Pericardial effusion occurs with an increased frequency in patients with ADPKD, possibly as a result of increased compliance of the parietal pericardium. Although frequently moderate to large, these effusions are generally well tolerated and clinically inconsequential.