Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographic patterns of Plasmodium falciparum drug resistance distinguished by differential responses to amodiaquine and chloroquine

Chloroquine (CQ) resistance (CQR) in Plasmodium falciparum originated from at least six foci in South America, Asia, and Oceania. Malaria parasites from these locations exhibit contrasting resistance phenotypes that are distinguished by point mutations and microsatellite polymorphisms in and near the CQR transporter gene, pfcrt, and the multidrug resistance transporter gene, pfmdr1. Amodiaquine (AQ), a 4-aminoquinoline related to CQ, is recommended and often used successfully against CQ-resistant P. falciparum in Africa, but it is largely ineffective across large regions of South America. The relationship of different pfcrt and pfmdr1 combinations to these drug-resistant phenotypes has been unclear. In two P. falciparum genetic crosses, particular pfcrt and pfmdr1 alleles from South America interact to yield greater levels of resistance to monodesethylamodiaquine (MDAQ; the active metabolite of AQ) than to CQ, whereas a pfcrt allele from Southeast Asia and Africa is linked to greater CQ than MDAQ resistance with all partner pfmdr1 alleles. These results, together with (i) available haplotype data from other parasites; (ii) evidence for an emerging focus of AQ resistance in Tanzania; and (iii) the persistence of 4-aminoquinoline-resistant parasites in South America, where CQ and AQ use is largely discontinued, suggest that different histories of drug use on the two continents have driven the selection of distinct suites of pfcrt and pfmdr1 mutations. Increasing use of AQ in Africa poses the threat of a selective sweep of highly AQ-resistant, CQ-resistant parasites with pfcrt and pfmdr1 mutations that are as advantaged and persistent as in South America.
Expression , purification and characterization of a recombinant fusion protein based on the human papillomavirus-16 E 7 antigen

A fusion protein comprising a cell penetrating and immunostimulatory peptide corresponding to residues 32 to 51 of the Limulus polyphemus protein linked to human papillomavirus (HPV)-16 E7 antigen (LALF32-51-E7) was expressed in E. coli BL21 (DE3) cells. The recombinant protein in E. coli accounted for approximately 18% of the total cellular protein and purified with a single affinity chromatographic step. Yields of approximately 38 mg purified LALF32-51-E7 per liter of induced culture was obtained with an overall 52% recovery and constitutes a promising setting for the future production and scaling-up. Purified protein was characterized as soluble aggregates with molecular weight larger than 670 kDa, which is considered an important property to increase the immunogenicity of an antigen preparation. The recombinant fusion protein LALF32-51-E7 will be a promising vaccine candidate for the treatment of HPV-16 related malignancies.
Longitudinal development of secondary sexual characteristics in girls and boys between ages 91/2 and 151/2 years.

OBJECTIVES To identify ages when adolescents were in sexual maturity stages 2 through 5; to explain the relations between breast (girls), genital (boys), and pubic hair (girls and boys) development between ages 9(1/2) and 15(1/2) years; and to evaluate synchrony of pubertal development across characteristics. DESIGN Annual pubertal assessments. SETTING Ten locations in the United States. PARTICIPANTS A total of 859 adolescents (427 boys [49.7%] and 432 girls [50.3%]; 737 white [85.8%] and 122 black [14.2%]). MAIN OUTCOME MEASURES Changes in the 5 stages of breast, genital, and pubic hair development. RESULTS Girls were in breast maturity stages 2 and 3 earlier than comparable pubic hair stages. Although breast development in girls started earlier than pubic hair development, girls completed breast and pubic hair development at approximately the same age. Black girls were in all stages of breast and pubic hair development earlier than white girls. Boys were in stages 2, 3, 4, and 5 of genital development before the comparable pubic hair stage. In boys, genital development started earlier than pubic hair development, but pubic hair development was completed in less time. Black boys were in genital and pubic hair development about 7 months earlier than white boys. Black and white boys completed genital development in approximately 4(1/2) years, but black boys took approximately 6 months longer than white boys to complete pubic hair development. At stage 2, for 66.2% of girls, breast development preceded their pubic hair development; for 91.1% of boys, genital development preceded their pubic hair development. CONCLUSIONS The results of this study are useful in understanding normative variation in the timing and change in the development of secondary sexual characteristics at puberty. They will help identify adolescents with atypical changes in sexual maturation and unusual progression of sexual maturation and growth disorders.
Ageing, remembering, and executive function

This study was designed to investigate the relationship between executive functions and the age-related decline in episodic memory through the states-of-awareness approach. Following the presentation of a word list, a group of younger adults and a group of older adults undertook a recognition test in which they classified their responses according to the Remember-Know-Guess procedure (Gardiner & Richardson-Klavehn, 2000). In order to operationalise the executive function hypothesis, we investigated three specific executive functions (updating, shifting, and inhibition of a prepotent response) described in Miyake et al.'s (2000) theoretical model, and a complex executive task. The results revealed that fewer “R” responses were made during the recognition test by the older than the younger group, whereas there was no difference between the groups in the number of “K” responses. In addition, correlations indicated that remembering depended on executive function measures, whereas knowing did not. The hierarchical regression analyses showed that controlling for executive function, and particularly for the 2-back test, largely removed the age-related variance in remembering. These findings support the notion that executive dysfunction, and specifically updating decline, plays a central role in age-related memory loss.
CD4 Cell Response Before and After HAART Initiation According to Viral Load and Growth Indicators in HIV-1-Infected Children in Abidjan, Côte d'Ivoire

Objective:To analyze the determinants of CD4 change in children during 3 periods: before highly active antiretroviral therapy (HAART), during the first year after HAART initiation, and past 1 year after HAART initiation. Methods:One hundred seventy-seven children enrolled in a prospective cohort in Abidjan received HAART during a mean follow-up of 30 months. A linear mixed-effects model was used for the first period, a mixed-effects piecewise model for the second period, and an asymptotic mixed-effects model for long-term CD4 dynamics. Results:Before HAART initiation, CD4 percentage decreased along time [β = −0.59 (−0.92 to −0.26)] was positively associated with body mass index for age [β = 0.47 (0.22 to 0.72)] and negatively associated with viral load [β = −1.01 (−1.90 to −0.13)]. During the first year of treatment, the CD4 decrease reverted to a steep increase that was negatively associated with age at HAART initiation [β = −0.24 (−0.4 to −0.07)] and with the mean viral load under HAART [β = −1.51 (−2.21 to −0.81)]. The long-term CD4 percentage was also negatively associated with the mean viral load under HAART [β = −4.97 (−6.22 to −3.72)] and age at HAART initiation [β = −0.82 (−1.12 to −0.51)]. Conclusions:Before HAART initiation, the CD4 cell percentage was associated with growth indicators whereas, after HAART, an early increase and a long-term plateau were negatively associated with the viral load and age at HAART initiation.
Characteristics of wastes from electric and electronic equipment in Greece: results of a field survey

The lifespan of electric and electronic equipment is becoming shorter and the amount of related waste is increasing. This study aimed to contribute to the knowledge about qualitative and quantitative characteristics of such wastes in Greece. Specifically, results are presented from a field survey, which took place in the city of Thessaloniki, Greece, during the year 2002. The survey was conducted with suitable questionnaires in department stores and in households of various municipalities. Household appliances were grouped as follows: (A) large (refrigerator, freezer, washing machine, clothes dryer, electric cooker, microwave oven, electric heater), (B) small (vacuum cleaner, electric iron, hair dryer), (C) information technology and telecommunication equipment(PC, laptop, printer, phone) and (D) consumer equipment(radio, TV, video, DVD, console). The analysis indicated that the lifespan of all new goods is gradually reducing (apart from refrigerators, for which the lifespan was surprisingly found to be increasing) and provided linearized functions for predicting the lifespan, according to the year of manufacture, for certain large appliances.
Utilization of medium-chain triglycerides by neonatal piglets: I. Effects on milk consumption and body fuel utilization.

Two experiments were conducted utilizing neonatal piglets. In the first experiment, 18 piglets were used to determine the effect of an oral supplement of 0, 12 or 24 ml of a medium-chain triglyceride (MCT) product on subsequent milk consumption. Results from the weight-suckle-weight experiment showed that force-feeding 24 ml of the MCT decreased (P less than .05) milk intake but 12 ml did not. In the second experiment, two trials (each with 24 piglets) were used to investigate the effect of 12 ml of MCT or 12 ml of MCT plus . 6 mmol of L-carnitine on the concentration of blood glucose, ammonium N and urea N at 0, 12 or 24 h and liver and biceps femoris glycogen at 24 h post-treatment. Blood urea N decreased (P less than .05) in piglets receiving the MCT. Blood ammonium N and glucose concentrations were not different (P greater than .10) among treatments. In Trial 1, the predicted loss of liver glycogen was less (P less than .05) in pigs given the MCT treatment, but this response was not repeated in the second trial. In general, supplemental carnitine provided no added benefit over the MCT treatment alone. The results from this study indicate that MCT is utilized as a fuel by the newborn piglet and that its use may spare critical fuels, glycogen and protein, that were stored in the piglet prior to birth.
Gate Diffusion Input (GDI) logic in standard CMOS nanoscale process

In this paper CMOS compatible Gate Diffusion Input (GDI) design technique is proposed. The GDI method enables the implementation of a wide range of complex logic functions using only two transistors. This method is suitable for the design of low-power logic gates, with a much smaller area than Static CMOS and existing PTL techniques. As opposite to our originally proposed GDI logic, the modified GDI logic is fully compatible for implementation in a standard CMOS process. Simulations of basic GDI gates under process and temperature corners in 40nm CMOS process are shown and compared to similar CMOS gates. We show that while having the same delay, GDI gates achieve leakage and active power reduction of up to 70% and 50%, respectively.
P16 and Ki67 Immunostaining is a Useful Adjunct in the Assessment of Biopsies for HPV-Associated Anal Intraepithelial Neoplasia

P16 is a tumor suppressor gene product, shown to be overexpressed in most cervical carcinomas and dysplasias associated with high-risk human papilloma virus (HPV) infection. HPV is also associated with anal squamous dysplasias and carcinomas. Significant interobserver and intraobserver variation exists in the interpretation of biopsies for anal intraepithelial neoplasia (AIN). This study was undertaken to assess the potential role of p16 and Ki67 immunohistochemical expression in refining the diagnosis and grading of AIN.One-hundred and four anal biopsies from 74 patients were retrieved from the surgical pathology files of the department. After discrepancies were resolved and concurrence was achieved by at least 2 of 3 reviewing pathologists, the diagnoses were as follows: 37 negative, 12 condylomas without overt dysplasia, 14 AIN I, 25 AIN II, and 16 AIN III. p16 and Ki67 expression was evaluated by ABC immunoperoxidase staining whereas the presence of the high-risk subtypes of HPV virus was determined by in situ hybridization on a subset of the biopsies. Results were reviewed by 2 pathologists and positive and negative staining was correlated with H&E diagnoses. Nuclear and/or nuclear and cytoplasmic staining was considered as positive for p16 when present in >10% of squamous cells. Two patterns of positive p16 staining were observed: (1) “spotty” in which positive cells were scattered throughout the lesion and (2) “band” in which >90% of contiguous cells in the lesion stained positive. A band-like pattern of p16 immunoreactivity was seen in 21.4% AIN I, 80% AIN II, and 87.5% AIN III cases. None of the condylomas and only 1 of the negative cases showed a band of p16 positive staining. Spotty p16 immunoreactivity was observed in 8.1% negative, 8.3% condyloma, 14.3% AIN I, 12.0% AIN II, and 12.5% AIN III cases. More than 50% of nuclei stained positive for Ki67 in 28.6% AIN I, 48.0% AIN II, and 75.0% AIN III cases but in none of the negative or condyloma cases. On the basis of these results, a band-like pattern of p16 staining and Ki67 positivity in >50% of the squamous cell nuclei were strongly associated with high-grade AIN. Conversely, absence of a p16 band of positivity coupled with Ki67 positivity in <50% of nuclei was frequently associated with benign lesions. Band like p16 staining also correlated strongly with the presence of high-risk HPV. Most AIN I lesions stained similar to the nondysplastic cases. A small subset of biopsies studied did not conform to the pattern described above: 4 of 14 (28.6%) AIN I lesions showed a band-like pattern of p16 staining and/or >50% Ki67 positive nuclei. Two of these cases were positive for high-risk HPV DNA. 4 of 25 (16.0%) AIN II lesions comprising 9.8% of the 41 high-grade AINs (AIN II and III) showed spotty p16 positivity and <50% Ki67 positive nuclei. One was positive for high-risk HPV DNA. We conclude that when used together and evaluated in conjunction with H&E stained sections, p16 and Ki67 immunoexpression is a useful adjunct in the diagnosis and grading of AIN.
Food , drug , insect sting allergy , and anaphylaxis Anaphylaxis to cow ’ s milk formula containing short-chain galacto-oligosaccharide

Background: On the basis of the proven prebiotic effects of oligosaccharides in cow’s milk formula (CMF) in infants, CMFs are supplemented with oligosaccharides. Objective: We present a series of 5 cases of cow’s milk–tolerant but atopic patients with a history of respiratory allergies. All had anaphylaxis after the ingestion of CMF supplemented with short-chain galacto-oligosaccharide (scGOS). The allergen trigger was investigated. Methods: Clinical histories were collated. Skin prick tests (SPTs) and basophil activation tests (BATs) were carried out with the eliciting CMF that triggered anaphylaxis, with or without supplemented prebiotics (scGOS) and with scGOS fractions containing oligosaccharides of different chain lengths. Results: The median age of presentation was 6 years (range, 5-38 years). Anaphylaxis occurredwithin 30minutes of the first known exposure to CMF supplemented with prebiotics in all patients. Only 1 patient was subjected to oral challenge, which resulted in an anaphylactic reaction. All patients demonstrated IgE sensitization through SPTs and BATs to scGOS and fractions of scGOS containing 3 sugar units or greater but not to cow’smilk or long-chain fructo-oligosaccharide. Eight child control subjects tolerant to regular ingestion of scGOS-supplemented CMF and 1 adult volunteer were found to have negative results to scGOS through SPTs and BATs. In addition, in vitro BATs with donor basophils sensitized with sera from 2 of the 3 reported cases showed reactions to scGOS. The scGOS-induced basophil activation was inhibited in the presence of wortmannin, a phosphatidylinositol 3-kinase inhibitor.
Global Patterns of Diversification and Species Richness in Amphibians

Geographic patterns of species richness ultimately arise through the processes of speciation, extinction, and dispersal, but relatively few studies consider evolutionary and biogeographic processes in explaining these diversity patterns. One explanation for high tropical species richness is that many species‐rich clades originated in tropical regions and spread to temperate regions infrequently and more recently, leaving little time for species richness to accumulate there (assuming similar rates of diversification in temperate and tropical regions). However, the major clades of anurans (frogs) and salamanders may offer a compelling counterexample. Most salamander families are predominately temperate in distribution, but the one primarily tropical clade (Bolitoglossinae) contains nearly half of all salamander species. Similarly, most basal clades of anurans are predominately temperate, but one largely tropical clade (Neobatrachia) contains ∼96% of anurans. In this article, I examine patterns of diversification in frogs and salamanders and their relationship to large‐scale patterns of species richness in amphibians. I find that diversification rates in both frogs and salamanders increase significantly with decreasing latitude. These results may shed light on both the evolutionary causes of the latitudinal diversity gradient and the dramatic but poorly explained disparities in the diversity of living amphibian clades.
Open Reduction and Cerclage Wire Fixation for Long Oblique/Spiral Fractures of the Proximal Phalanx of the Fingers

Fifteen cases of long oblique/spiral fractures of the shaft of the proximal phalanx of the fingers treated by open reduction, cerclage wire fixation and immediate postoperative mobilisation were studied prospectively. Twelve patients presented early (within 24 hour of injury) and the remaining three cases were treated initially elsewhere by closed reduction and percutaneous oblique K-wire fixation with failure of the fixation. The latter three patients presented to our clinic late (10–14 days after injury). Following internal fixation with cerclage wires, no cases of infection, complex regional pain syndrome (CRPS) Type 1, fracture re-displacement, wire migration or extrusion were noted. One patient complained of a palpable wire which was removed 4 months after surgery. All fractures united and all patients returned to work at a mean of 8 (range 7–11) weeks after surgery. Twelve patients obtained a full range of motion (total active motion–TAM = 260°) and the remaining three patients had a mild (5–15°) flexion contracture of the proximal interphalangeal joint. Cerclage wire fixation is an acceptable technique of fixation for these fractures.
Modélisation simplifiée 3D de l'interaction sol-structure: application au génie parasismique.

Dans le domaine du genie parasismique, l'Interaction du Sol avec la Structure (ISS) est un phenomene important a considerer pour esperer rendre compte du comportement reel d'une structure et donc evaluer sa vulnerabilite. Ce travail presente la construction d'un element d'interface 3D modelisant une fondation superficielle de forme circulaire, rectangulaire ou filante reposant sur un massif de sol semi infini et permettant de prendre en compte l'ISS en considerant les non-linearites materielles (la plasticite du sol) et les non-linearites geometriques (le decollement de la fondation). Base sur la methode des macro-elements, cet element permet de travailler en variables globales (forces et deplacements) et comporte 5 degres de libertes. Tous les elements du torseur d'effort appliques a la fondation sont presents excepte le moment de torsion qui n'est pas pris en compte. Cette description globale permet ainsi de simplifier le modele en minimisant d'une part la preparation des donnees et du maillage et d'autre part les temps de calculs. Les nonlinearites sont traitees grâce aux theories classiques de plasticite et peuvent ainsi etre couplees de maniere simple selon la theorie des multi-mecanismes. Une description mathematique de chaque mecanisme est proposee. Le macro-element est implemente dans FedeasLab, un code element finis developpe dans Matlab. Des comparaisons avec des resultats experimentaux d'une fondation soumise a des chargements cycliques, ainsi que dynamiques mais aussi des simulations modelisant des ouvrages d'arts (bâtiment, pont.) montrent le bon fonctionnement du macro-element 3D d'ISS. Enfin, l'efficacite et la robustesse de ce genre d'outils permettent de faire des analyses parametriques faisant evoluer plusieurs parametres de sols qui seront presentees a l'issue de cette these.
From ideals towards practice: paradigmatic mismatches and drifts in method deployment

There is considerable debate in the information systems literature on how systems development methods (SDMs) are used in practice. On one side are those who take the position that these methods are not used at all. The other side posits that SDMs are used but not in the manner intended by the method developers. In practice, SDMs are adapted and modified to meet project exigencies, which results in unique methods‐in‐use in each project. We subscribe to the latter view and extend the argument by proposing that SDM modifications happen due to mismatches between the paradigmatic values inherent in the SDM, the method users and the organizational context. Further, planned modifications themselves result in shifts of paradigmatic values inherent in the SDM. To examine our contention, we conduct a case study in which we trace an SDM from its development to its deployment and use in an organization. We show where the mismatches occurred and provide explanations for the mismatches. Our results indicate that paradigm differences explain most of the mismatches, and different factors contribute to the paradigm drifts simultaneously, even towards diverging orientations. We conclude that the true value of an SDM, in addition to its tool and technique use, is a basis for examining and self‐reflecting about paradigmatic values. This is an essential part of learning to develop systems.
1 Introduction Understanding the Complexities of Child and Adolescent Psychopathology

A fundamental challenge inherent in the study of child and adolescent psychopathology is distinguishing normal from atypical behavior. There are several reasons why this decision-making process is so complex and why the task is so difficult. Determining “normal” from “abnormal” behavior requires an evaluation of the frequency of the behavior (e.g., does the behavior occur on a daily, hourly basis? ), the duration (is this a recent or ongoing problem), and whether the behavior is pervasive across all situations (or situation specific). With these factors in mind, we can now begin to probe whether the behavior is atypical within a developmental context. Ten of the most important questions that will need to be addressed are the following: