Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Variation in the Response to Vaccination

Vaccines are the most powerful means to prevent and diminish the burden of infectious disease. However, there are limitations to their use: vaccines are not yet available for all infectious diseases (including human immunodeficiency virus and respiratory syncytial virus), they sometimes lack efficacy, the response to vaccination is limited by maternal antibodies in very young infants, and the response to vaccination is variable or may even be absent in some individuals. This review focuses on genetic factors that determine the variable response to vaccination. The highly polymorphic human leukocyte antigen system, which is involved in antigen presentation, has been researched most in this aspect, and clearly affects the response to vaccination. Other, but less polymorphic pathways involved are the Toll-like receptor pathway, which is involved in antigen recognition and stimulation of the immune system, and the cytokine immunoregulatory network. The heritability, or the proportion of total variance that is due to additive genetic factors, appears to be particularly large for vaccine-induced antibody responses in young infants compared with cell-mediated responses and antibody responses in older, immunologically more mature individuals. Both antibody and cell-mediated responses are not only affected by loci within, but also strongly by loci outside the human leukocyte antigen system. Because most genes that are important in influencing immune responses to vaccination are still unknown, clearly more work is required. A better understanding of the factors that determine an effective response to vaccination may lead to the identification of specific genes and pathways as targets for the development of novel more uniformly effective vaccines.
Bioefficacy of Alpinia galanga (Zingiberaceae) Rhizome Extracts, (E) -p- Acetoxycinnamyl Alcohol, and (E) -p-Coumaryl Alcohol Ethyl Ether Against Bactrocera dorsalis (Diptera: Tephritidae) and the Impact on Detoxification Enzyme Activities

ABSTRACT The application of insecticides to control oriental fruit fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae), is a principal component of the current management of these fruit flies. However, we evaluated four extracts Alpinia galanga Wild Linn (Zingiberaceae) rhizomes against adult flies and found hexane and ethanol extracts to be most effective (LC50 = 4,866 and 6,337 ppm, respectively, after 24 h). This suggested that both nonpolar and polar compounds could be active in the candidate plant. Accordingly, the hexane extract was further processed to isolate nonpolar active compounds from this plant source. Two compounds, (E)-p-acetoxycinnamyl alcohol and (E) -p-coumaryl alcohol ethyl ether, were identified as active ingredients and found to be more active than total hexane extract (LC50 = 3,654 and 4,044 ppm, respectively, after 24 h). The data suggested that the compounds were not synergistic but may have some additive effect in a mixture. The activity of the hexane extract against detoxification enzymes, carboxylesterase (CE) and glutathione transferase (GST) also was determined in vitro. CE was inhibited by 70%, whereas GST was not significantly inhibited. Insect CEs mediate insecticide resistance via their induction; therefore, inhibition of these enzymes by plant allelochemicals could be a useful alternative approach for the management of the pest in the field.
HOM/HOX homeobox genes are present in hydra (Chlorohydra viridissima) and are differentially expressed during regeneration.

Hydra, a diblastic animal consisting of two cell layers, ectoderm and endoderm, is one of the most ancient animals displaying an anteroposterior axis with a head and a foot developing from an uncommitted gastric region. As such, hydra is an interesting model for studying the presence and function of homeobox genes in a phylogenetically old organism. By screening a Chlorohydra viridissima cDNA library with a ‘guessmer’ oligonucleotide, we have cloned several such cnidarian homeobox‐containing genes (cnox genes). Two of these, cnox1 and cnox2, display labial and Deformed type homeodomains respectively and could represent two ancestral genes of the HOM/HOX complexes; cnox3 exhibits some similarity to the BarH1 and the distal‐less type homeodomains and a fourth gene is highly related to the msh/Hox7 type of homeodomain. We used quantitative PCR to study levels of expression of these genes along the body axis and during head regeneration. In all cases, the expression in heads was stronger than that in the gastric region. cnox1 transcripts dramatically peaked within the first hours of head regeneration, whereas cnox2 and cnox3 reached their maximal levels 1 and 2 days after cutting respectively. This differential expression of homeobox genes at various stages of regeneration suggests that they play specific roles in regenerative processes.
Relationship Between Gastric Ulcer and Helicobacter pylori VacA Detected in Gastric Juice Using Bead‐ELISA Method

Background. VacA is an important pathogenetic factor produced by Helicobacter pylori. VacA has often been detected in supernatants of liquid cultures or lysates of whole bacterial cells. However, no studies have ever tried to assay VacA produced in the human stomach. We applied a very sensitive and simple method, bead‐ELISA, to detect VacA in gastric juice.
Posttransplant lymphoproliferative disorder in pediatric bone marrow transplant recipients: disseminated disease of donor origin demonstrated by fluorescence in situ hybridization.

BACKGROUND Posttransplant lymphoproliferative disorders in bone marrow transplantation are typically rapidly progressive and fatal B-cell lymphoid proliferations associated with Epstein-Barr virus, and are mostly of donor origin. We report three pediatric bone marrow transplant cases in which posttransplant lymphoproliferative disorder was diagnosed at postmortem examination. Epstein-Barr virus in these cases was identified by a combined in situ hybridization-immunoperoxidase technique and donor origin was identified by fluorescence in situ hybridization. METHODS Tissues obtained from postmortem examination were evaluated by light microscopy, immunohistochemistry, combined in situ hybridization-immunoperoxidase technique with Epstein-Barr virus-encoded RNA probe, and fluorescence in situ hybridization with X and Y centromeric probes. RESULTS Three pediatric patients underwent sex-mismatched, T-cell-depleted bone marrow transplants complicated by graft versus host disease, rapidly progressive multiple organ failure, and postmortem diagnosis of posttransplant lymphoproliferative disorder. Histologic examination and immunohistochemistry studies demonstrated immunoblastic lymphoma (one case) or polymorphic B-cell lymphoma (two cases). In all cases, Epstein-Barr virus-encoded RNA was detected by a combined in situ hybridization-immunoperoxidase technique. Fluorescence in situ hybridization for X and Y chromosomes in paraffin sections demonstrated donor origin in two cases (one case was indeterminate). CONCLUSION Fluorescence in situ hybridization was used to prove donor derivation of Epstein-Barr virus-associated posttransplant lymphoproliferative disorders in pediatric bone marrow transplant recipients. Many features of posttransplant lymphoproliferative disorders in pediatric bone marrow transplant recipients are very similar to adult cases, although a higher proportion of children appear to be diagnosed postmortem and have a fatal outcome.
Identification of algI and algJ in the Pseudomonas aeruginosa alginate biosynthetic gene cluster which are required for alginate O acetylation

Mucoid strains of Pseudomonas aeruginosa overproduce alginate, a linear exopolysaccharide Of D-mannuronate and variable amounts of L-guluronate. The mannuronate residues undergo modification by C-5 epimerization to form the L-guluronates and by the addition of acetyl groups at the 0-2 and 0-3 positions. Through genetic analysis, we previously identified algF, located upstream of algA in the 18-kb alginate biosynthetic operon, as a gene required for alginate acetylation. Here, we show the sequence of a 3.7-kb fragment containing the open reading frames termed algI, algJ, and algF. An algI::Tn5O1 mutant, which was defective in algIJFA because of the polar nature of the transposon insertion, produced alginate when algA was provided in trans. This indicated that the algIJF gene products were not required for polymer biosynthesis. To examine the potential role of these genes in alginate modification, mutants were constructed by gene replacement in which each gene (algI, algJ, or algF) was replaced by a polar gentamicin resistance cassette. Proton nuclear magnetic resonance spectroscopy showed that polymers produced by strains deficient in algIJF still contained a mixture of D-mannuronate and L-guluronate, indicating that C-5 epimerization was not affected. Alginate acetylation was evaluated by a colorimetric assay and Fourier transform-infrared spectroscopy, and this analysis showed that strains deficient in algIJF produced nonacetylated alginate. Plasmids that supplied the downstream gene products affected by the polar mutations were introduced into each mutant. The strain defective only in algF expression produced an alginate that was not acetylated, confirming previous results. Strains missing only algJ or algI also produced nonacetylated alginates. Providing the respective missing gene (algI, algJ, or algF) in trans restored alginate acetylation. Mutants defective in algI or algJ, obtained by chemical and transposon mutagenesis, were also defective in their ability to acetylate alginate. Therefore, algI and algJ represent newly identified genes that, in addition to algF, are required for alginate acetylation.
One Laptop per Child at Home: Short-Term Impacts from a Randomized Experiment in Peru†

This paper presents results from a randomized controlled trial whereby approximately 1,000 OLPC XO laptops were provided for home use to children attending primary schools in Lima, Peru. The intervention increased access and use of home computers, with some substitution away from computer use outside the home. Children randomized to receive laptops scored about 0.8 standard deviations higher in a test of XO proficiency but showed lower academic effort as reported by teachers. There were no impacts on academic achievement or cognitive skills as measured by the Raven's Progressive Matrices test. Finally, there was little evidence for spillovers within schools. (JEL I21, I28, J13, O15)
Corruption in Professional Sumo: An Update on Duggan and Levitt's Study

In the December 2002 issue of the American Economic Review, Mark Duggan and Steven D. Levitt published an article on corruption in professional sumo. In the present paper, we update Duggan and Levitt's study to take into account changes since January 2000. We find strong statistical evidence that corruption is reduced after January 2000 but reappears in the period from 2003 to 2006. In addition, we can show that the non-linearity in the incentive structure disappears from 2000 to 2003 and reappears after 2003. These results confirm the findings of Duggan and Levitt, who suggest that the structure of promotion in rankings gives incentives to the sumo wrestlers to rig matches.
Child maltreatment and the early onset of problem behaviors: Can a program of nurse home visitation break the link?

This study investigated the relationship between child maltreatment and the early onset of problem behaviors in the Elmira Nurse Home Visitation Program. Participants were predominantly low-income and unmarried mothers and their first-born children who were randomized either to receive over 2 years of home-visitation services by nurses or to be placed in a comparison group. Data were drawn from a follow-up study that took place when the children were 15 years of age. Results demonstrated that, in the comparison group, child maltreatment was associated with significant increases in the number of early onset problem behaviors reported by the youth. For the youth in the nurse-visited group there was no relationship between maltreatment and early onset problem behaviors. We suggest that this finding was due to the effects of the intervention in reducing the number as well as the developmental timing of the maltreatment incidents. Results suggest that prenatal and infancy home visiting by nurses can moderate the risk of child maltreatment as a predictor of conduct problems and antisocial behavior among children and youth born into at-risk families.
Four decades of scientific explanation

As Aristotle stated, scientific explanation is based on deductive argument - yet, Wesley C. Salmon points out, not all deductive arguments are qualified explanations. The validity of the explanation must itself be examined. "Four Decades of Scientific Explanation" provides a comprehensive account of the developments in scientific explanation that transpired in the last four decades of the twentieth century. It continues to stand as the most comprehensive treatment of the writings on the subject during these years. Building on the historic 1948 essay by Carl G. Hempel and Paul Oppenheim, "Studies in the Logic of Explanation," which introduced the deductive-nomological (D-N) model on which most work on scientific explanation was based for the following four decades, Salmon goes beyond this model's inherent basis of describing empirical knowledge to tells us "not only what, but also why. " Salmon examines the predominant models in chronological order and describes their development, refinement, and criticism or rejection. "Four Decades of Scientific Explanation" underscores the need for a consensus of approach and ongoing evaluations of methodology in scientific explanation, with the goal of providing a better understanding of natural phenomena.
Dynamics of natural infections of Rhabdias cf. hylae (Nematoda) in Bufo marinus (Amphibia) in Australia

Infrapopulation dynamics of the nematode Rhabdias cf. hylae within naturally-infected Bufo marinus in north Queensland, Australia, were detailed. Over 80% of 580 toads were infected with Rh. cf. hylae with a mean intensity of 16·1. Distribution of Rh. cf. hylae within the toad population was aggregated, with an increase in the variance-to-mean ratio with increasing toad size. Intensity of infection and length of nematode were both correlated with length of toad in the smaller size classes. Length of nematode was not related to intensity of infection at any time. Mean intensity of infection rose significantly in small toads following initial infection after metamorphosis. Over the same period, average length of nematode did not increase implying constant re-infection of the toads. Larger toads were not reinfected to the same extent, and the number of uninfected toads in the larger size class increased which indicated a natural loss of infections. Changes in parameters of Rh. cf. hylae infection within B. marinus were attributed to seasonal rainfall and its subsequent effect on the behaviour of the toad.
Evaluation of gold nanoparticles as the additive in real-time polymerase chain reaction with SYBR Green I dye

Gold nanoparticles (AuNPs) have been proven to be able to improve the specificity or increase the efficiency of a polymerase chain reaction (PCR) when a suitable amount of AuNPs was used. However, there is still a lack of systematic evaluation of AuNPs in real-time PCR. In this study, DNA degradation and the fluorescence quenching effect of AuNPs were first tested in real-time PCR. Then two different kinds of Taq DNA polymerase, native and recombinant Taq polymerase, were employed to evaluate the AuNPs’ effect on the threshold cycle (CT) values, standard curves and melting curves in real-time PCR. Different ratios of the amount of native Taq DNA polymerase to the amount of AuNPs were also tested. It was found that AuNPs could be applied in real-time PCR with correlation coefficient R2>0.989. The combination of 2.09 nM AuNPs with 3.75 U of native Taq DNA polymerase could make the amplification curves shift to the left and enhance the efficiency of the real-time PCR (0.628 39 without AuNPs compared with 0.717 89 with 2.09 nM AuNPs), thus enabling faster detection in comparison with those of control samples. However, no improvement ability of AuNPs was found in real-time PCR based on recombinant rTaq DNA polymerase. Besides, the results suggest that a complex interaction exists between AuNPs and native Taq DNA polymerase.
The β1-integrin-p-FAK-p130Cas-DOCK180-RhoA-vinculin is a novel regulatory protein complex at the apical ectoplasmic specialization in adult rat testes

During spermatogenesis, step 1 spermatids (round spermatids) derive from spermatocytes following meiosis I and II at stage XIV of the epithelial cycle begin a series of morphological transformation and differentiation via 19 steps in rats to form spermatozoa. This process is known as spermiogenesis, which is marked by condensation of the genetic material in the spermatid head, formation of the acrosome and elongation of the tail. Since developing spermatids are lacking the robust protein synthesis and transcriptional activity, the cellular, molecular and morphological changes associated with spermiogenesis rely on the Sertoli cell in the seminiferous epithelium via desmosome and gap junction between Sertoli cells and step 1-7 spermatids. Interestingly, a unique anchoring junction arises at the interface of step 8 spermatid and Sertoli cell known as apical ectoplasmic specialization (apical ES). Once it appears, apical ES is the only anchoring device restricted to the interface of step 8-19 spermatids and Sertoli cells to confer spermatid polarity, adhesion, signal communication, and structural support, and to provide nutritional support during spermiogenesis, replacing desmosome and gap junction. While the adhesion protein complexes that constitute the apical ES are known, the signaling protein complexes that regulate apical ES dynamics, however, remain largely unknown. Herein we report the presence of a FAK-p130Cas-DOCK180-RhoA-vinculin signaling protein complex at the apical ES, which is also an integrated component of the β1-integrin-based adhesion protein complex based on co-immunoprecipitation experiment. It was also shown that besides p-FAK-Tyr397 and p-FAK-Tyr576, β1-integrin, p130Cas, RhoA, and vinculin displayed stage-specific expression in the seminiferous epithelium during the epithelial cycle with predominant localization at the apical ES as demonstrated by immunohistochemistry. Based on these findings, functional studies can now be performed to assess the role of this b1-integrin-p-FAK-p130Cas-DOCK180-RhoA-vinculin protein complex in apical ES dynamics during spermiogenesis.
Prevalence and Correlates of Everyday Discrimination among U.S. Latinos.

OBJECTIVES: This study reports on the prevalence and correlates of perceived discrimination among a national sample of Latinos in the U.S. Understanding the prevalence and correlates of discrimination can help us better address disparities in the healthcare system. We define perceived discrimination as self-reported everyday experiences of unfair treatment. METHODS: Logistic regression analyses were used to assess rates of perceived discrimination among Latinos and identify correlates of discrimination. Data came from the National Latino and Asian American Study (NLAAS). RESULTS: The prevalence of perceived discrimination among Latinos was 30%. Cubans and Latinos with high ethnic identity were less likely to perceive discrimination compared to other Latino subgroups or Latinos with low ethnic identity. U.S.-born Latinos and Latinos arriving to the U.S. at younger ages were more likely to perceive discrimination compared to immigrants arriving at older ages. CONCLUSIONS: Perceived discrimination among Latinos is less prevalent than what has been reported for other minorities. Variations in perceived discrimination are related to sociodemographic and cultural differences across ethnic subgroups.
Human cytomegalovirus productively infects porcine endothelial cells in vitro.

BACKGROUND The possibility that human cytomegalovirus (HCMV) may infect porcine endothelial cells (ECs) was investigated. This may be relevant during xenotransplantation of porcine cells or organs into human recipients. METHODS HCMV was inoculated into low-passage porcine ECs. Replication of virus was detected by development of characteristic cytopathogenic effect. Appearance of immediate early, early, and late antigens was studied by immunocytochemical staining. Infectious virus was detected in human fibroblast cells. Presence of HCMV RNA was studied by Northern Blot and reverse transcriptase polymerase chain reaction. RESULTS All parameters indicated that a fresh clinical HCMV isolate productively infects porcine ECs. The same cells do not fully support replication of the laboratory strain Ad 169. CONCLUSION Our results may indicate the possibility of cross-species infectivity of HCMV to porcine cells.
A Multiband Slot Antenna for GPS/WiMAX/WLAN Systems

The design of a four-band slot antenna for the global positioning system (GPS), worldwide interoperability for microwave access (WiMAX), and wireless area network (WLAN) is presented. The antenna consists of a rectangular slot with an area of 0. 37λg × 0. 14λg = 48 × 18 mm2 (where λg is the guide wavelength), a T-shaped feed patch, an inverted T-shaped stub, and two E-shaped stubs to generate four frequency bands. The radiating portion and total size of the antenna are less than those of the tri-band antennas studied in literature. Parametric study on the parameters for setting the four frequency bands is presented and hence the methodology of using the design for other frequency bands is proposed. The multiband slot antenna is studied and designed using computer simulation. For verification of simulation results, the antenna is fabricated and measured. The simulated and measured return losses, radiation patterns, realized peak gains, and efficiencies of the antenna are presented. Measured results show that the antenna can be designed to cover the frequency bands from 1.575 to 1.665 GHz for the GPS system, 2.4-2.545 GHz for the IEEE 802.11b&g WLAN systems, 3.27- 3.97 GHz for the WiMAX system, and 5.17-5.93 GHz for the IEEE 802.11a WLAN system. The effects of the feeding cable used in measurement and of the cover are also investigated.
Fiber sizes and capillary to fiber ratios in skeletal muscle of exercised rats

Thirty male rats (Sprague‐Dawley), 25 days of age, were placed in exercise cages for seven days. They were matched into trios on the basis of the last four days total exercise and randomly placed in three groups: sedentary, spontaneous exercise and forced exercise. For the next 35 days, the sedentary group was permitted no exercise other than that allowed by their small individual cages. The spontaneous group remained in activity cages while the forced group in addition to being in activity cages, swam one 30‐minute period each day with weights equal to 20% of the body weight attached to their tails. At the end of the 35‐day activity period, the animals were sacrificed. The hind limbs were injected with India ink, embedded in gelatin and cut on the freezing microtome. The cross‐sectional area of red and white fibers from the gastrocnemius muscles were measured by using the polar planimeter. Ink‐filled capillaries were counted, in conjuction with fiber measurements.
Wiswesser Line Notation: Simplified Techniques for Converting Chemical Structures to WLN

Techniques have been developed for the generation of Wiswesser Line Notations (WLN), which require knowledge neither of rules for manual conversion of structures to line notations nor of computer programming. The desired WLN are obtained simply by drawing the structures of the compounds of interest on a tablet, which is linked to an appropriately programmned computer.