Miracle-dz/UniFAR-FTUs huggingface dataset:
SECONDARY STRUCTURE IN RIBONUCLEIC ACIDS.

of magnesium and aluminum; this should greatly extend the range of experimental work that can be done in this laboratory. The lack of target materials of high atomic number is a most serious problem. We have a program in progress in the United States for the production of milligram amounts of berkelium and californium and microgram amounts of einsteinium. According to present plans, about one milligram of Cf252 should be obtained in about 1968. In order to prepare these elements on a more reasonable time scale, new, expensive, high-flux reactors producing 1015 to 1016 neutrons per square centimeter per second are needed. In conclusion, it appears that the addition of new transuranium elements to the periodic table can be expected and that their study will add much to our knowledge of atomic and nuclear structure.
Correlated Switch Binding and Signaling in Bacterial Chemotaxis*

In Escherichia coli, swimming behavior is mediated by the phosphorylation state of the response regulator CheY. In its active, phosphorylated form, CheY exhibits enhanced binding to a switch component, FliM, at the flagellar motor, which induces a change from counterclockwise to clockwise flagellar rotation. When Ile95 of CheY is replaced by a valine, increased clockwise rotation correlates with enhanced binding to FliM. A possible explanation for the hyperactivity of this mutant is that residue 95 affects the conformation of nearby residues that potentially interact with FliM. In order to assess this possibility directly, the crystal structure of CheY95IV was determined. We found that CheY95IV is structurally almost indistinguishable from wild-type CheY. Several other mutants with substitutions at position 95 were characterized to establish the structural requirements for switch binding and clockwise signaling at this position and to investigate a general relationship between the two properties. The various rotational phenotypes of these mutants can be explained solely by the amount of phosphorylated CheY bound to the switch, which was inferred from the phosphorylation properties of the mutant CheY proteins and their binding affinities to FliM. Combined genetic, biochemical, and crystallographic results suggest that residue 95 itself is critical in mediating the surface complementarity between CheY and FliM.
Measurement in vivo of proliferation rates of slow turnover cells by 2H2O labeling of the deoxyribose moiety of DNA

We describe here a method for measuring DNA replication and, thus, cell proliferation in slow turnover cells that is suitable for use in humans. The technique is based on the incorporation of 2H2O into the deoxyribose (dR) moiety of purine deoxyribonucleotides in dividing cells. For initial validation, rodents were administered 4% 2H2O in drinking water. The proliferation rate of mammary epithelial cells in mice was 2.9% per day and increased 5-fold during pregnancy. Administration of estradiol pellets (0–200 μg) to ovariectomized rats increased mammary epithelial cell proliferation, according to a dose–response relationship up to the 100 μg dose. Similarly, proliferation of colon epithelial cells was stimulated in a dose–response manner by dietary cholic acid in rats. Bromodeoxyuridine labeling correlated with the 2H2O results. Proliferation of slow turnover cells was then measured. Vascular smooth muscle cells isolated from mouse aorta divided with a half-life in the range of 270–400 days and die-away values after 2H2O wash-out confirmed these slow turnover rates. The proliferation rate of an adipocyte-enriched fraction from mouse adipose tissue depots was 1–1.5% new cells per day, whereas obese ad libitum-fed ob/ob mice exhibited markedly higher fractional and absolute proliferation rates. In humans, stable long-term 2H2O enrichments in body water were achieved by daily 2H2O intake, without toxicities. Labeled dR from fully turned-over blood cells (monocytes or granulocytes) exhibited a consistent amplification factor relative to body 2H2O enrichment (≈3.5-fold). The fraction of newly divided naive-phenotype T cells after 9 weeks of labeling with 2H2O was 0.056 (CD4+) and 0.043 (CD8+) (replacement rate <0.1% per day). In summary, 2H2O labeling of dR in DNA allows safe, convenient, reproducible, and inexpensive measurement of cell proliferation in humans and experimental animals and is well suited for slow turnover cells.
Evidence for regulated expression of Telomeric Repeat-containing RNAs (TERRA) in parasitic trypanosomatids

The Telomeric Repeat-containing RNAs (TERRA) participate in the homeostasis of telomeres in higher eukaryotes. Here, we investigated the expression of TERRA in Leishmania spp. and Trypanosoma brucei and found evidences for its expression as a specific RNA class. The trypanosomatid TERRA are heterogeneous in size and partially polyadenylated. The levels of TERRA transcripts appear to be modulated through the life cycle in both trypanosomatids investigated, suggesting that TERRA play a stage-specific role in the life cycle of these early-branching eukaryotes.
Integration of a Solid Freeform Fabrication Process into a Feature-Based CAD System Environment

The design and implementation of a feature-based software system for the Solid Freeform Fabrication (SFF) process is discussed. For the SFF process to be an effective design tool in a manufacturing system, the tight integration of the process into a feature-based CAD system is desired. A feature set for determining the optimal part orientation is identified, and the procedure is described.
Embedded Implicit Stand‐Ins for Animated Meshes: A Case of Hybrid Modelling

In this paper, we address shape modelling problems, encountered in computer animation and computer games development that are difficult to solve just using polygonal meshes. Our approach is based on a hybrid‐modelling concept that combines polygonal meshes with implicit surfaces. A hybrid model consists of an animated polygonal mesh and an approximation of this mesh by a convolution surface stand‐in that is embedded within it or is attached to it. The motions of both objects are synchronised using a rigging skeleton. We model the interaction between an animated mesh object and a viscoelastic substance, which is normally represented in an implicit form. Our approach is aimed at achieving verisimilitude rather than physically based simulation. The adhesive behaviour of the viscous object is modelled using geometric blending operations on the corresponding implicit surfaces. Another application of this approach is the creation of metamorphosing implicit surface parts that are attached to an animated mesh. A prototype implementation of the proposed approach and several examples of modelling and animation with near real‐time preview times are presented.
A GFP-based assay to quantify the impact of effectors on the ex planta development of the slowly growing barley pathogen Rhynchosporium commune

A growth assay was established for the barley pathogen Rhynchosporium commune with EGFP-tagged fungal mutants. This assay was used to study the effect of four antibiotics (hygromycin B, nourseothricin, kanamycin, phleomycin) and a herbicide (phosphinothricin) on fungal development. Fitting the growth curves to the modified Gompertz model allowed calculating growth parameters, such as lag periods of fungal colony formation and mycelial growth rates as well as EC50 values. Except kanamycin all compounds were efficient inhibitors so that the corresponding resistance-conferring genes can be used as markers for selection of fungal transformation-based mutants. In addition the assay was used to quantify the inhibitory activity of a barley secondary metabolite, the indole alkaloid gramine.
Amygdalae Calcifications Associated with Disease Duration in Lipoid Proteinosis

Objectives. To describe imaging findings of central nervous system involvement in patients with lipoid proteinosis. Methods. Patients with lipoid proteinosis followed in the dermatology and neurology departments of the State University of Campinas between 2002 and 2004 were evaluated using high‐resolution MRI and computerized tomography (CT). Results. We reviewed the charts of three patients (two women) with lipoid proteinosis with, ages ranging from 5 to 44 years. Symptomatic disease duration ranged from 2 to 39 years. MRI scans showed hypointense signal in FLAIR and T2 images in the amygdalae in two of three patients. Brain CT scans from two patients showed that MRI findings were calcifications. The calcification was more evident in patients with longer disease duration. Epilepsy was identified in one patient with longer disease duration. No other epileptogenic lesion was identified on MRI in this patient. Conclusion. Lipoid proteinosis is associated with bilateral amygdalae calcification. These findings were more evident in patients with longer disease duration. Epilepsy, when present, may be related to these calcifications. Patients with lipoid proteinosis should be followed with MRI/CT in order to identify these abnormalities.
Analysis of Protein Lysine Acetylation In Vitro and In Vivo

Protein lysine acetylation, referring to acetylation of the ɛ‐amino group of a lysine residue, has recently emerged as an important post‐translational modification for regulating protein functions in various organisms. Like phosphorylation, lysine acetylation is a rapidly reversible and precisely controlled covalent modification that serves as a simple on/off switch or participates in a codified manner with other post‐translational modifications to regulate protein functions in different cellular and developmental processes. This unit describes and discusses methods used for in vitro and in vivo determination of lysine acetylation. Curr. Protoc. Protein Sci. 54:14.11. 1‐14.11. 17. © 2008 by John Wiley & Sons, Inc.
Correction: MDA-5 Recognition of a Murine Norovirus

The fifth author's name is displayed incorrectly in the by-line and in the article citation. The author's correct attribution is Herbert W. Virgin. The correct citation is: McCartney SA, Thackray LB, Gitlin L, Gilfillan S, Virgin HW, et al. (2008) MDA-5 Recognition of a Murine Norovirus. PLoS Pathog 4(7): e1000108. doi:10.1371/journal.ppat. 1000108
Modulation of serum parathyroid hormone and ionized calcium concentrations during reproduction in rats fed a low calcium diet

Moderate dietary restriction of calcium (0.1% Ca) was used to accentuate the changes in serum immunoreactive parathyroid hormone (iPTH) that had been reported earlier in lactating rats fed 0.4% Ca diet. In addition, the effects of this low‐Ca diet on serum total and ionized Ca and iPTH during pregnancy, extended lactation, and weaning were examined. The positive correlation between serum total and ionized Ca was highly significant (r = 0.88, p < 0.001, n = 120). Serum iPTH was significantly higher (36%) in pregnant rats on the day of parturition compared to nonmated controls, and there was a concomitant decrease in both total and ionized serum Ca. Within 1 day after parturition, however, serum Ca had risen to the control level. Serum iPTH remained significantly elevated during the first 2 weeks of lactation, and increased further during the third week of lactation to a level more than twice that of nonlactating controls. Serum Ca fell gradually during the second week of lactation. The high serum iPTH levels were maintained for another 2 weeks when lactation was extended with foster litters. Within 6 hr of removal of the suckling pups on day 16 of lactation, maternal serum ionized and total Ca had risen and serum iPTH had fallen; all three parameters were at levels similar to those of nonmated controls by 24–48 hr after weaning. The data suggest that serum ionized Ca is a major factor contributing to the hyperparathyroid state during lactation in rats fed a low‐Ca diet.
Oculocutaneous albinism type IV: A boy of Moroccan descent with a novel mutation in SLC45A2

Oculocutaneous albinism type IV (OCA4 [MIM606574]) caused by mutations of the SLC45A2 gene is an autosomal recessive disorder of pigmentation characterized by reduced biosynthesis of melanin pigment in the skin, hair, and eye. We had the opportunity to examine a Belgian boy of Moroccan descent with clinically severe OCA and screened the mutation in his SLC45A2 gene. Sequencing of exon 1, of which the PCR product showed aberrant patterns in the SSCP gel, revealed that the patient was a homozygote for p.H38R mutation. We demonstrated that the p.H38R‐mutant protein was functionally incapable of melanin synthesis using melanocyte cultures (under white cells; uw) established from a mouse model of OCA4. This is the second report of the occurrence of OCA4 in a member of an African ethnic group. © 2009 Wiley‐Liss, Inc.
Driver lane changing behavior analysis based on parallel Bayesian networks

Driver behavior model is one of the key technologies for the driver assistance and safety system which can provide useful priori knowledge for detecting the abnormal behaviors effectively. The paper introduces the Driver behavior model which is established by the parallel Bayesian networks with steering angles and their difference and the final status of driver behavior is decided by the largest probability of the each status during the time of lane changing. In addition, the transition time of the status is automatic tagged by the multi-variable Gaussian model of steering angles and their difference. Finally, the parallel Bayesian network model is compared with the Gaussian Bayesian Network of the steering angles. The state transition diagram of driver behavior and the analysis of experiment results are given.
DC and RF characterization of RF MOSFET embedding structure

It is not so easy to correlate DC Kelvin measurement data of an RF transistor and its non-Kelvin RF measurement data, because the actual bias voltages in the latter are not known precisely. Knowing the bias voltages requires accurate characterization of its embedding structure. This paper reports on an attempt at correlating DC and RF measurements of parasitic resistances associated with a MOSFET test structure, including a transmission line, on a CMOS chip.
Photosynthetic picoplankton in Argentina lakes

Fil: Izaguirre, Irina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Instituto de Ecologia, Genetica y Evolucion de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecologia, Genetica y Evolucion de Buenos Aires; Argentina
A Survey On Automated Dynamic Malware Analysis Evasion and Counter-Evasion: PC, Mobile, and Web

Automated dynamic malware analysis systems are important in combating the proliferation of modern malware. Unfortunately, malware can often easily detect and evade these systems. Competition between malware authors and analysis system developers has pushed each to continually evolve their tactics for countering the other. In this paper we systematically review i) "fingerprint"-based evasion techniques against automated dynamic malware analysis systems for PC, mobile, and web, ii) evasion detection, iii) evasion mitigation, and iv) offensive and defensive evasion case studies. We also discuss difficulties in experimental evaluation, highlight future directions in offensive and defensive research, and briefly survey related topics in anti-analysis.
Evaluation of HBT device linearity using advanced measurement techniques

With this work we address the linearity of HBT devices when operated at their optimum bias and matching conditions at baseband, fundamental and second harmonic. Using active harmonic load pull and pulsed I-V / s-parameter device characterization, the intrinsic linearity properties of SiGe and III-V based HBT devices are evaluated and compared. From this exercise the bias dependent Cbc behavior is identified as key differentiator for the linearity of the different technologies.
Air pollution modeling over Shanghai and Guangzhou

As one of the most prominent pollutants that threaten human health over big cities, fine particle matter (PM2.5) has largely attracted public and researches’ attention. Critical challenges are unresolved regarding how to effectively predict atmospheric PM2.5 concentrations. Here, our team aimed to capture the PM2.5 high-frequency dynamics over Shanghai and Guangzhou using advanced machine learning technique. Our results showed that PM2.5 concentration could be forecasted with historical PM2.5 record and meteorology forcings including temperature, humidity, precipitation, pressure, wind speed, and due point temperature. Our sensitivity analyses further revealed that the perdition was robust against critical model parameters across cities. The underlying sink processes could be different despite of their similar temporal features.
Pharmacotherapy of iron overload in thalassaemic patients

The recommended treatment for thalassaemia major is regular blood transfusions, although these lead to the harmful accumulation of iron in the body. If untreated, iron overload is responsible for heart, liver and endocrine diseases. The only two iron chelating agents available for the treatment of iron overload are deferoxamine and deferiprone. The standard iron chelation therapy is based on the use of deferoxamine. Although this drug was introduced in the 1970s, it still remains the treatment of choice. Recently, another iron chelator, deferiprone, became available for clinical use in the European Community. Deferiprone is indicated as second-line treatment in patients with thalassaemia major, for whom deferoxamine therapy is contraindicated or in patients who present with serious toxicity to deferoxamine therapy. This paper examines this chelating agent and compares it with deferoxamine in order to ascertain the current and potential contribution of deferiprone to the treatment of thalassaemic patients.
Do Thank-You Calls Increase Charitable Giving? Expert Forecasts and Field Experimental Evidence

Calling to thank donors is considered a key fundraising strategy in the charitable giving industry. Yet the effectiveness of thank-you calls remains untested. We conduct field experiments with public television stations and a national nonprofit in which 500,000 new donors were randomized to receive a thank-you call or not. Fundraising professionals predicted that the calls—which followed standard practices in the industry—would increase donor retention by 80 percent. In stark contrast, we found a precisely estimated null effect of calls on donor retention. (JEL C83, C93, D64, D91, L31, L82)
New Algorithms for Evaluating the Log-Likelihood Function Derivatives in the AI-REML Method

In this study, we propose several improvements of the Average Information Restricted Maximum Likelihood algorithms for estimating the variance components for genetic mapping of quantitative traits. The improved methods are applicable when two variance components are to be estimated. The improvements are related to the algebraic part of the methods and utilize the properties of the underlying matrix structures. In contrast to previously developed algorithms, the explicit computation of a matrix inverse is replaced by the solution of a linear system of equations with multiple right-hand sides, based on a particular matrix decomposition. The computational costs of the proposed algorithms are analyzed and compared.
A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls.

The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity.
Dicyclohexylcarbodiimide-binding proteins related to the short circuit of the proton-pumping activity of photosystem II. Identified as light-harvesting chlorophyll-a/b-binding proteins.

In photosynthesis of higher plants, photosystem II drives electron transfer from the water-oxidizing manganese centre at the lumenal side to bound plastoquinone at the stromal side of the thylakoid membrane. Proton release into the lumen and proton uptake from the stroma, i.e. net proton pumping, follows as consequence of vectoral electron transport. The proton pumping activity can be short circuited by covalent modification with N,N'-dicyclohexylcarbodiimide (cHxN)2C of certain proteins in the 20-28-kDa range. After modification, protons from water oxidation are no longer released into the thylakoid lumen, but instead transferred through the photosystem complex to protonate the photoreduced bound quinone at the other side of the membrane [Jahns, P., Polle, A. & Junge, W. (1988) EMBO J. 7, 589-594]. Here we identify the pertinent (cHxN)2C-binding proteins by amino acid sequence analysis and localize (cHxN)2C-binding sites within their primary structure. The proteins that are associated with the proton short circuit are light-harvesting chlorophyll-a/b-binding proteins. Our results imply that in addition to acting as antennae they may serve another function: the funneling into the thylakoid lumen of protons, which are liberated in the water-oxidizing Mn centre.