Miracle-dz/UniFAR-FTUs huggingface dataset:
Histidine-Rich Protein II: a Novel Approach to Malaria Drug Sensitivity Testing

ABSTRACT The production of histidine-rich protein II (HRP2), a histidine- and alanine-rich protein produced by Plasmodium falciparum, is closely associated with the development and proliferation of the parasite and therefore is perfectly suited to reflect growth inhibition as a measure of drug susceptibility. It was the aim of the present study to develop a malaria drug sensitivity assay based on the measurement of HRP2 in a simple enzyme-linked immunosorbent assay (ELISA). The new test proved to be as reliable as traditional in vitro assays, while it was considerably easier to establish and perform. Parasites are incubated at an initial level of parasitemia of 0.01 to 0.1% on microculture plates predosed with ascending concentrations of antimalarial drugs. After incubation for 48 to 72 h, the samples are freeze-thawed and transferred to ELISA plates. The complete ELISA takes about 2.5 h to perform, may be carried out with commercially available test kits, and requires relatively little technical equipment. In correlation analysis, the results closely paralleled those obtained by the isotopic assay (R = 0.892; P < 0.0001) and World Health Organization schizont maturation tests (R = 0.959; P < 0.0001). The novel HRP2 drug susceptibility assay proved to be very sensitive, simple to establish, and highly reproducible. It can be used for a wide range of applications, from epidemiological studies to the screening of new drugs, and may have the potential to replace traditional in vitro techniques. Standard operating procedures, updated information, and analytical software are available from http://malaria.farch. net .
Cigarette smoking and rheumatoid arthritis severity

OBJECTIVES Cigarette smoking may influence rheumatoid arthritis (RA) disease incidence and may have direct biological effects on the lungs and systemically. This study sought to determine if cigarette smoking is associated with RA disease severity. METHODS Clinical evaluations of patients seen in the University of Iowa rheumatology and orthopaedic ambulatory clinics were conducted. A letter of interest was mailed to 1701 patients who were first assigned an ICD-9-CM diagnostic code for RA in one of these clinics. A total of 857 patients expressed interest and were offered a clinical examination and 395 were evaluated over an 18 month period. Of these, 336 satisfied examiner criteria for prevalent RA and were included in the analysis. The disease characteristics and arthritis care utilisation of these patients seemed representative of prevalent cases in the general community. RA disease severity was assessed by radiographic bone erosions (graded as either present/absent and using the Larsen system), rheumatoid factor seropositivity, and presence of subcutaneous rheumatoid nodules. RESULTS Pack years of cigarette smoking was significantly associated with rheumatoid factor seropositivity (p = 0.0001), radiographic erosions (p = 0.024), and nodules (p = 0.051). After adjustment for potential confounders, smokers with ≥25 pack years were 3.1 times more likely to be rheumatoid factor positive (95% CI 1.7, 5.6) and 2.4 times more likely to show radiographic erosions (95% CI 1.2, 4.5) than never smokers. Less severe radiographic disease seemed to be more strongly associated with cigarette smoking than more severe disease. CONCLUSION Cigarette smoking may adversely influence the severity of RA in a potentially dose dependent fashion.
Optotype and grating visual acuity in preschool children.

PURPOSE To investigate the contribution of stimulus and response differences to the different developmental courses of grating and optotype visual acuity at the preschool age range. METHODS Binocular visual acuity at 228 cm was assessed in 205 children in 7 age groups between 2.5 and 6 years and in 12 adults. Acuities were obtained in three tasks: detection of a grating in one of two positions, discrimination of the orientation of a single grating, and discrimination of the orientation of the gap in an uncrowded Landolt-C optotype. The three paradigms were as similar as possible in stimulus contrast, luminance, presentation mode, and psychophysical procedure. RESULTS Mean grating and optotype acuities were lower than adult acuities at all ages. Optotype acuity was overall higher and increased faster with age than grating acuities. Grating orientation acuity was slightly but not significantly lower than grating detection acuity in all but one age group. The grating detection task was successful at earlier ages (100% at 3.5 years) than both the optotype acuity task (100% at 4.5 years) and the grating orientation task (100% at 5.75 years). CONCLUSIONS Optotype and grating acuities follow a different developmental course in children between 3 and 6 years of age, with optotype acuity growing superior to grating acuity in that age range. The similarity of grating orientation to grating detection acuities and the difference between grating and optotype acuities suggest that superior optotype acuity is due to stimulus characteristics rather than to the complexity of the response required.
A generic hybrid model for bulk elastodynamics, with application to ultrasonic nondestructive evaluation

Practical ultrasonic inspection requires modeling tools that enable rapid and accurate visualization; because of the increasing sophistication of practical inspection, it is becoming increasingly difficult to use a single modeling method to represent an entire inspection process. Hybrid models that utilize different or interacting numerical schemes in different regions, to use their relative advantages to maximal effect, are attractive in this context, but are usually custom-made for specific applications or sets of modeling methods. The limitation of hybrid schemes to particular modeling techniques is shown here to be related to their fundamental formulation. As a result, it becomes clear that a formalism to generalize hybrid schemes can be developed: an example of the construction of a generic hybrid modeling interface is given for the abstraction of bulk ultrasonic wave phenomena, common in practical inspection problems. This interface is then adapted to work within a prototype hybrid model consisting of two smaller finite element model-domains, and explicitly demonstrated for bulk ultrasonic wave propagation and scattering examples. Sources of error and ways to improve the accuracy of the interface are also discussed.
Reduction in apolipoprotein-mediated removal of cellular lipids by immortalization of human fibroblasts and its reversion by cAMP: lack of effect with Tangier disease cells.

High density lipoprotein (HDL) phospholipids and apolipoproteins remove cellular lipids by two distinct mechanisms, but their relative contribution to reverse cholesterol transport is unknown. Whereas phospholipid-mediated cholesterol efflux from cultured cells reflects the activity of the HDL receptor SR-BI, apolipoprotein-mediated lipid removal is regulated in response to changes in cellular cholesterol content (positive) and cell proliferation rates (negative). Here we show that immortalization of human skin fibroblast lines with the papillomavirus E6/E7 oncogenes increased their proliferation rates and selectively reduced the activity of the apolipoprotein-mediated lipid removal pathway. This reduction was accompanied by a decrease in cellular cAMP levels and was reversed by treatment with a cAMP analog. The stimulatory effect of cAMP was independent of changes in cellular phenotype or activities of cholesteryl ester cycle enzymes. The severely impaired apolipoprotein-mediated lipid removal pathway in Tangier disease fibroblasts, which persisted after immortalization, was not improved by treatment with a cAMP analog, implying that the cellular defect in Tangier disease is upstream from this cAMP-dependent signaling pathway.These results indicate that papillomavirus-induced immortalization of fibroblasts selectively reduces the activity of the apolipoprotein-mediated lipid removal pathway by a cAMP-dependent process, perhaps to prevent loss of cellular lipids needed for continual membrane synthesis.
Simplified Procedure for Estimating Earthquake-Induced Deviatoric Slope Displacements

A simplified semiempirical predictive relationship for estimating permanent displacements due to earthquake-induced deviatoric deformations is presented. It utilizes a nonlinear fully coupled stick-slip sliding block model to capture the dynamic performance of an earth dam, natural slope, compacted earth fill, or municipal solid-waste landfill. The primary source of uncertainty in assessing the likely performance of an earth/waste system during an earthquake is the input ground motion. Hence, a comprehensive database containing 688 recorded ground motions is used to compute seismic displacements. A seismic displacement model is developed that captures the primary influence of the system’s yield coefficient ( ky ) , its initial fundamental period ( Ts ) , and the ground motion’s spectral acceleration at a degraded period equal to 1.5 Ts . The model separates the probability of “zero” displacement (i.e., ⩽1 cm ) occurring from the distribution of “nonzero” displacement, so that very low values of calculated.
DoS-resilient virtual networks through multipath embedding and opportunistic recovery

Network virtualization can potentially limit the impact of attacks by isolating traffic from different networks. However, routers and links are still vulnerable to attacks on the underlying network. Specifically, should a physical link be compromised, all embedded virtual links will be affected. Previous work protects virtual networks by setting aside backup resources. Although effective, this solution tends to be expensive as backup resources usually remain idle. In this paper, we present a novel virtual network allocation approach which explores the trade-off between resilience to attacks and efficiency in resource utilization. Our approach is composed of two complementary strategies, one preventive and the other reactive. The former embeds virtual links into multiple substrate paths, while the latter attempts to reallocate any capacity affected by an underlying DoS attack. Both strategies are modeled as optimization problems. Numerical results show the level of resilience to attacks and the low cost demanded by our approach.
Using Subspace Pursuit Algorithm to Improve Performance of the Distributed Compressive Wide-Band Spectrum Sensing

This paper applies a compressed algorithm to improve the spectrum sensing performance of cognitive radio technology. At the fusion center, the recovery error in the analog to information converter (AIC) when reconstructing the transmit signal from the received time-discrete signal causes degradation of the detection performance. Therefore, we propose a subspace pursuit (SP) algorithm to reduce the recovery error and thereby enhance the detection performance. In this study, we employ a wide-band, low SNR, distributed compressed sensing regime to analyze and evaluate the proposed approach. Simulations are provided to demonstrate the performance of the proposed algorithm.
Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin.

We demonstrate that interspecific sequence conservation can provide a systematic guide to the identification of functional cis-regulatory elements within a large expanse of genomic DNA. The test was carried out on the otx gene of Strongylocentrotus purpuratus. This gene plays a major role in the gene regulatory network that underlies endomesoderm specification in the embryo. The cis-regulatory organization of the otx gene is expected to be complex, because the gene has three different start sites (X. Li, C.-K. Chuang, C.-A. Mao, L. M. Angerer, and W. H. Klein, 1997, Dev. Biol. 187, 253-266), and it is expressed in many different spatial domains of the embryo. BAC recombinants containing the otx gene were isolated from Strongylocentrotus purpuratus and Lytechinus variegatus libraries, and the ordered sequence of these BACs was obtained and annotated. Sixty kilobases of DNA flanking the gene, and included in the BAC sequence from both species, were scanned computationally for short conserved sequence elements. For this purpose, we used a newly constructed software package assembled in our laboratory, "FamilyRelations. " This tool allows detection of sequence similarities above a chosen criterion within sliding windows set at 20-50 bp. Seventeen partially conserved regions, most a few hundred base pairs long, were amplified from the S. purpuratus BAC DNA by PCR, inserted in an expression vector driving a CAT reporter, and tested for cis-regulatory activity by injection into fertilized S. purpuratus eggs. The regulatory activity of these constructs was assessed by whole-mount in situ hybridization (WMISH) using a probe against CAT mRNA. Of the 17 constructs, 11 constructs displayed spatially restricted regulatory activity, and 6 were inactive in this test. The domains within which the cis-regulatory constructs were expressed are approximately consistent with results from a WMISH study on otx expression in the embryo, in which we used probes specific for the mRNAs generated from each of the three transcription start sites. Four separate cis-regulatory elements that specifically produce endomesodermal expression were identified, as well as ubiquitously active elements, and ectoderm-specific elements. We confirm predictions from other work with respect to target sites for specific transcription factors within the elements that express in the endoderm.
The Implicit Life Satisfaction Measure

The Implicit Association Test, developed by Greenwald and colleagues in 1998, was adapted to measure satisfaction with life by assessing the strength of automatic associations of My life with Good- versus Bad-related words. A series of studies explored some psychometric as well as methodological properties of the Implicit Life Satisfaction measure (ILS). The ILS demonstrated good internal consistency and moderate temporal stability. Studies revealed that: (i) the type of stimuli used for target and attribute categories influences the magnitude of the ILS effect; (ii) participants could voluntarily suppress their satisfaction with life on the ILS, but not enhance it; and (iii) handedness of categories did not affect the participants’ performance on the ILS. Overall, the ILS measures are: (i) independent of traditional life satisfaction self-report measures; and (ii) positive for most people.
Activation of Chromosomal DNA Replication inSaccharomyces cerevisiae by Acidic Transcriptional Activation Domains

ABSTRACT A large body of evidence from viral systems has established that transcription factors play an important and direct role in activating viral DNA replication. Among the transcriptional activation domains that can stimulate viral DNA replication are acidic domains such as those derived from herpes simplex virus VP16 and the tumor suppressor p53. Here we show that acidic activation domains can also activate a cellular origin of replication in a chromosomal context. When tethered to the yeast ARS1 (autonomously replicating sequence 1) origin of replication, both VP16 and p53 activation domains can enhance origin function. In addition, the C-terminal acidic region of the yeast transcription factor ABF1, which normally activates the ARS1 origin, is sufficient for activating ARS1 function when tethered to the origin. Mutations at residues Trp-53 and Phe-54 of a 20-residue (41 to 60) activation region of p53 abolish the activation of both replication and transcription, suggesting that the same structural determinants may be employed to activate both processes in yeast. Furthermore, using a two-dimensional gel electrophoresis method, we demonstrate that the GAL4-p53 chimeric activator can activate initiation of chromosomal replication from an origin inserted at the native ARS1 locus. These findings strongly suggest functional conservation of the mechanisms used by the acidic activation domains to activate viral DNA replication in mammalian cells and chromosomal replication in yeast.
Ruse and Representations: On Children's Ability to Conceal Information.

This study reports a marked development between the ages of 3 and 5 years in children's ability to conceal information. In a situation of high-affect involvement, 3-year-olds did not know to misinform or withhold information from a competitor who always chose the object for which they themselves had previously stated a preference. Although only 29% of 3-year-olds knew to influence the competitor's mental state, 87% knew to physically exclude the competitor. There was no difference between children's performance when trying to obtain the object for themselves or predicting what a story character would do. The success of the older children in concealing information indicated their new representational understanding that to influence another's behavior, one must influence that person's mental state. Jeremy (aged 3): Mommy, go out of the kitchen. Mother: Why, Jeremy? Jeremy: Because I want to take a cookie. Recent research on children's understanding of mental representations suggests that until 4 to 5 years of age, children do not understand that someone's action is dependent on his or her epistemic state (Flavell, 1988; Gopnik & Astington, 1988; Hartl & Wimmer, 1989; Perner, 1988a). If children cannot represent the beliefs of another person, they cannot use these representational states to predict the behavior of that person. Consequently, when they do come to recognize that a person's behavior is mediated by the person's beliefs, whether those beliefs are true or false, they should begin to recognize that an important means of changing that behavior is to change the other's beliefs. The choice to inform, to conceal information, or to misinform presupposes an understanding that if someone is ignorant of the true state of affairs or holds a false belief, his or her response will differ from someone who has the appropriate knowledge. This may be a key cognitive underpinning of new behaviors such as children's ability to conceal information. Now one can make sense of the above anecdote. What this 3-year-old seems to know is that mother's physical presence is an inhibiting factor. He must ensure that mother is out of the kitchen. What the young child does not realize, however, is that it is the mother's informational state that will prevent the taking of the cookie. At 3 years of age, providing or depriving mother of knowledge is seen as irrelevant to the mother's actions.
Identification and characterization of an endogenous chemotactic ligand specific for FPRL2

Chemotaxis of dendritic cells (DCs) and monocytes is a key step in the initiation of an adequate immune response. Formyl peptide receptor (FPR) and FPR-like receptor (FPRL)1, two G protein–coupled receptors belonging to the FPR family, play an essential role in host defense mechanisms against bacterial infection and in the regulation of inflammatory reactions. FPRL2, the third member of this structural family of chemoattractant receptors, is characterized by its specific expression on monocytes and DCs. Here, we present the isolation from a spleen extract and the functional characterization of F2L, a novel chemoattractant peptide acting specifically through FPRL2. F2L is an acetylated amino-terminal peptide derived from the cleavage of the human heme-binding protein, an intracellular tetrapyrolle-binding protein. The peptide binds and activates FPRL2 in the low nanomolar range, which triggers intracellular calcium release, inhibition of cAMP accumulation, and phosphorylation of extracellular signal–regulated kinase 1/2 mitogen-activated protein kinases through the Gi class of heterotrimeric G proteins. When tested on monocytes and monocyte-derived DCs, F2L promotes calcium mobilization and chemotaxis. Therefore, F2L appears as a new natural chemoattractant peptide for DCs and monocytes, and the first potent and specific agonist of FPRL2.
Link Prediction Across Time via Cross-Temporal Locality Preserving Projections

SUMMARY Link prediction is the task of inferring the existence or absence of certain relationships among data objects such as identity, interaction, and collaboration. Link prediction is found in various applications in the ﬁelds of information integration, recommender systems, bioinformatics, and social network analysis. The increasing interest in dynamically changing networks has led to growing interest in a more general link prediction problem called temporal link prediction in the data mining and machine learning communities. However, only links among nodes at the same time point are considered in temporal link prediction. We propose a new link prediction problem called cross-temporal link prediction in which the links among nodes at di ﬀ erent time points are inferred. A typical example of cross-temporal link prediction is cross-temporal entity resolution to determine the identity of real entities represented by data objects observed in di ﬀ erent time periods. In dynamic environments, the features of data change over time, making it di ﬃ cult to identify cross-temporal links by directly comparing observed data. Other examples of cross-temporal links are asynchronous communications in social networks such as Face-book and Twitter, where a message is posted in reply to a previous message. We adopt a dimension reduction approach to cross-temporal link prediction; that is, data objects in di ﬀ erent time frames are mapped into a common low-dimensional latent feature space, and the links are identi-ﬁed on the basis of the distance between the data objects. The proposed method uses di ﬀ erent low-dimensional feature projections in di ﬀ erent time frames, enabling it to adapt to changes in the latent features over time. Using multi-task learning, it jointly learns a set of feature projection matrices from the training data, given the assumption of temporal smoothness of the projections. The optimal solutions are obtained by solving a single generalized eigenvalue problem. Experiments using a real-world set of bibliographic data for cross-temporal entity resolution and a real-world set of emails for unobserved asynchronous communication inference showed that introducing time-dependent feature projections improved the accuracy of link prediction.
Board Determinants in Banking Industry. An International Perspective: BOARD DETERMINANTS IN BANKING INDUSTRY

We identify the factors influencing the board composition of an international sample of commercial banks over the period 1996–2006. After considering the dual role of the board as monitor and advisor, our analysis shows that no one board composition is optimal for the banking industry and that any such recommendation could harm bank governance. Our results suggest that more complex banks that have a low ownership concentration and are headquartered in a civil law country should have larger and more independent boards. JEL Classification: G21; G34