Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein p7 In Vitro and In Vivo

ABSTRACT We developed and evaluated an immunoassay for the detection and quantification of human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein p7 using electrochemiluminescence technology. The assay had a dynamic range of 50 to 20,000 pg/ml and a lower detection limit equivalent to approximately 106.5 HIV-1 RNA copies/ml in culture supernatant. In vitro kinetic replication studies showed that the amount of p7 correlated strongly with the amount of p24 (R2 = 0.869; P < 0.0001) and viral RNA (R2 = 0.858; P = 0.0009). On the basis of the p7 and RNA concentrations, we calculated the median p7:RNA ratio to be approximately 1,400 p7 molecules per RNA molecule. HIV-1 p7 could be detected and quantified in culture supernatants of both group M subtype A to E viruses and group O viruses. The presence of p7 in vivo was evaluated in 81 serum samples collected from 62 HIV-1-infected individuals. Five samples were p7 positive, whereas 45 samples were HIV-1 p24 positive. Four of the five p7-positive samples were p24 positive as well. p7 could be detected only when serum HIV-1 RNA levels were greater than 106copies/ml. Anti-p7 antibodies were found in six samples, and all six were p7 negative. In contrast to the in vitro results, it appeared that HIV-1 p7 could not be used as a marker for viral quantification in vivo, since more than 90% of the serum samples were p7 negative. In combination with the low prevalence of anti-p7 antibodies, this may, in turn, be advantageous: the p7 assay may be a good alternative to the p24 assay as the readout system for determination of neutralizing activity against HIV-1 in serum or other fluids containing anti-p24 antibodies.
Pollination in the marine realm: microsatellites reveal high outcrossing rates and multiple paternity in eelgrass Zostera marina

The mating system was examined in two annual populations of eelgrass (Zostera marina), a marine angiosperm displaying subaqueous pollination. Multilocus genotyping using microsatellite DNA markers allowed the assessment of the pollen source based on single progeny as units of observation. Outcrossing was detectable by the presence of non-maternal alleles at one or more of the loci. In outcrossing cases, three microsatellite alleles were present in unripe seeds, consisting of both maternal alleles and the paternal allele composing the triploid primary endosperm. In ripe seeds, only the diploid embryonal genotype was amplifiable by PCR. Two intertidal populations situated in the German Wadden Sea were almost entirely outcrossing (t ± SE 0.96 ± 0.03, N=60 and 0.97 ± 0.029, N=37). Because of the high polymorphism displayed by the eight chosen microsatellites, representing a total of 69 and 76 alleles, the likelihood of erroneously inferring selfing was small (α=0.0026 and 0.0007). In order to study the correlation of paternity, the coefficient of relatedness was determined within sibships. Relatedness (r ± SE) was calculated as 0.357 ± 0.059 and 0.343 ± 0.037, indicating multiple paternities within inflorescences. Small amounts of tissue (≤0.1 mg) such as the developing seeds of recently fertilized ovules, were sufficient for PCR-amplification. Hence, PCR-based methods, such as multilocus microsatellite genotyping, allow the detection of pollen origin early in the development of progeny. They will be useful to distinguish postfertilization processes such as selective abortion and germination from other prefertilization determinants of plant mating systems.
Mislabelling of Donryu rats.

To theEditor: Between 1992 and 2000, 21papers1–21were published that used rats from inbred colonies in Melbourne and Tokyo thatwere believed to be of the Donryu (DRY) strain. These rats were thought tohave been the same strain as DRY used by Dr Tanase in early breedingexperiments in relation to blood pressure in spontaneously hypertensive rats(SHR). 22,23The original DRY strain had been held at the Sankyo Co, Ltd, in Japan. At sometime before 1991, however, it appears that in the company’s laboratoriesthere had been an unrecognised substitution of Fisher344 (F344) for DRY (see below) and that authentic DRY were culled and nolonger exist. In …
Integrating Statistics with a Microbiology Laboratory Activity

Statistics is an important tool for microbiologists but is virtually absent from undergraduate laboratory activities. The variables in a stringent protocol, the antibiotic disk diffusion assay described by the National Committee for Clinical Laboratory Standards, were examined by the authors as a means for introducing hypothesis testing and the application of elementary statistical tools. After several experiments, a lab activity was developed where students examine the effect of cell concentration on antibiotic activity and analyze data with the t test. They also collect data independently from the same samples and compare their measurements using analysis of variance (ANOVA). The outcome of the activity, including an assessment tool, indicated that students learned the appropriate use of the t test and ANOVA, gained an appreciation for standardized protocols, and enjoyed the experience.
Building an understanding of geological time: A cognitive synthesis of the “macro” and “micro” scales of time

Few discoveries in geology are more important than geological time. However, for most people it is impossible to grasp because of its massive scale. In this chapter we offer a solution to this problem based on our research in cognition and education. Our strategy involves the decoupling of geological time between the macro-scale of "deep time which includes the major features of earth history, and whose research we call event-based studies, and the micro-scale of relative time represented by strata, whose research we term logicbased studies. Our event-based study focuses on the problem of learning about macroevolution within the massive time scale of the fossil record. We approached this problem by creating a four-stage learning model in which the students manipulate a series of increasingly complex visual representations of evolution in time. Post program results indicate that students had a better understanding of macroevolution as seen in the fossil record; moreover, they appreciated that different events in absolute time required different scales of time to occur. Our logic-based studies used Montagnero’s diachronic thinking model as a basis for describing how students reconstruct geological systems in time. Using this model, we designed three specialized instruments to test a sample of middle and high school students. Our findings indicated that there were significant differences between grade 9–12 and grade 7–8 students in their ability to reconstruct geological systems. Moreover, grade 11-12 geology majors in Israel had a significant advantage over their non-geological counterparts in such reconstruction tasks.
Biological and molecular detection of HSVd - infecting peach and pear trees in Egypt.

Two isolates of Hop stunt viroid (HSVd) were characterized from naturally infected peach and pear trees during summer season (2007-2008) in Egypt. The two isolates of HSVd were biologically indexed using healthy peach and pear seedlings under insect proof greenhouse. Total RNAs were extracted from peach and pear leaves and used for reverse transcription-polymerase chain reaction (RT- PCR). About 300 bp DNA fragment was amplified from the samples by RT-PCR using HSVd (+) and HSVd (-) specific primers. Fifty-nine pear trees and forty-six peach samples showing stunting, yellowing and leaf blistering were analyzed for the presence of HSVd using tissue print hybridization. The reactivity of HSVd Dig-labeled probe varied from strongly positive, moderately positive and weekly positive reaction with infected samples. Magnified pictures of pear and peach tissue prints indicated that HSVd is phloem restricted as shown from the vascular tissues colored with purple hybridization signals. The percentages of positive infection was 93% in the total collected samples.
Narrator Point of View and Persuasion in Health Narratives: The Role of Protagonist–Reader Similarity, Identification, and Self-Referencing

Narratives are often used in messages about health threats. We posited that a 1st-person point of view (POV) narrative would have a greater effect than a 3rd-person POV on the mediators identification and self-referencing—an effect moderated by protagonist–reader similarity. Higher levels of identification and self-referencing were expected to elevate susceptibility and severity perceptions, leading to persuasion. Participants ages ≤30 years were recruited from a crowdsource website and randomly assigned to read one version of a faux magazine article about caffeine overdose. Article versions were defined by a 2 (1st- or 3rd-person POV) × 2 (similar or dissimilar protagonist) design. To manipulate similarity, we had respondents read an article in which the protagonist was also young (24 years of age) and of the same sex or much older (54 years of age) and of the opposite sex. Participants then completed a questionnaire measuring study variables. Contrary to expectations, POV did not affect identification or self-referencing. However, similarity directly impacted identification, which in turn influenced severity perceptions. Self-referencing was not affected by the experimental manipulations but had a direct effect on susceptibility and also mediated the identification → susceptibility relationship. Susceptibility and severity perceptions were associated with greater levels of persuasion. Implications for message design are discussed.
The Presence of Demodex Folliculorum in Various Obese Groups According to BMI Levels.

BACKGROUND This study aimed to detect the presence of the parasite Demodex folliculorum (DF) in various obese groups according to BMI Levels. MATERIALS AND METHODS A total of 182 patients (40.8 ± 14.8 years, min-max age 19 - 73 years) were enrolled in the study, of those 65 (35.7%) were female and 117 (64.3%) were male. They had previously applied to Mustafa Kemal University (Faculty of Medicine, Endocrine Outpatient Clinic) during 2012. A standardized skin surface biopsy method was used to research the existence of DF. Patients were classified into four main groups, including: obese (n = 89), overweight (n = 31), normal (n = 32), and underweight (n = 30). RESULTS There was no significant difference between groups in terms of age and sex. The total DF positivity was 19 (21.3%) in obese patients. Among those with positive DF, the mean BMI was 35.7 ± 12.1 kg/m(2), while those with negative DF had a mean BMI of 29.2 ± 9.2 kg/m(2). There was a significant difference between two groups (P = 0.002). Also, the underweight group has significantly higher DF positivity in comparison to the normal weight group. CONCLUSION The DF positivity was significantly higher in obese patients in accordance with the physiopathologic nature of the disease.
BIRTH SEASONALITY AS A RESPONSE TO A CHANGING RURAL ENVIRONMENT (KAYES REGION, MALI)

Summary Birth seasonality responds to a variety of environmental and socio-cultural factors. The present study was carried out to quantify the trends in seasonal variation in birth rate in seven districts in the Kayes region of Mali between 2007 and 2010 and to attempt to link climatic- and agricultural-cycle-dependent factors with birth seasonality. Lagged regression analysis based on time series analysis techniques was used to investigate seasonality of births registered in health facilities and its association with climate, labour migration, agriculture workload, malaria infection and food supply. There was a clear bimodal pattern in month-to-month institutional delivery rate variation, and this seasonal pattern repeated each year over the study period. The data showed that rates of health-facility-attended deliveries were high at the end of the dry season (April–June), fell rapidly in the first half of the rainy season, rose again during the later part of the rainy season (August–October) and fell to their lowest values after the rains. The first peak observed in spring (April–June) corresponded to conception nine months earlier during the rainy season (between July and September), while the second peak observed in the third quarter of the year (August–October) corresponded with conception at the beginning of the dry season right after the harvest period (between November and January). Between these peaks was an abrupt trough in July. The findings support a causal process through which climate change influences conception/birth seasonality in two direct and indirect pathways. On one side climate change influences conception/birth seasonality from the effects on fetal loss (changes in annual rainfall leading to changes in malaria incidence) and on the other side by affecting fecundability (changes in agricultural cycles leading to changes in food production, agricultural workload and socio-cultural events, which in turn influence energy balance and sexual behaviour). Labour migration, which is closely linked with the agricultural cycle, influences sexual intercourse and thus marital fertility. Finally, the model emphasizes an ecosystemic approach to the study of birth seasonality.
Intranuclear distribution, function and fate of glutathione and glutathione‐S‐conjugate in living rat hepatocytes studied by fluorescence microscopy

The availability of fluorescent probes to detect soluble and protein‐bound thiols has made it possible to investigate some aspects of reduced glutathione (GSH) metabolism and function in intact rat hepatocytes and in hepatocyte nuclei. Monochlorobimane (BmCl) has been employed to study the subcellular compartmentation of GSH and the formation and fate of the BmCl‐GSH conjugate. The occurrence of relatively high concentrations of GSH within the nuclear matrix has been inferred from fluorescence quantitation using image analysis. Concomitant biochemical studies have revealed the presence of a GSH‐stimulated ATP hydrolysis and of an ATP‐stimulated GSH accumulation in isolated nuclei, providing the molecular basis for nuclear glutathione compartmentation. The contemporary use of fluorescent probes to label nuclear free sulfhydryl groups, proteins and chromatin status led to the demonstration that intranuclear accumulation of glutathione may modulate the thiol/disulfide redox status of nuclear proteins and control chromatin compacting and decondensation. Microsc. Res. Tech. 36:243–252, 1997. © 1997 Wiley‐Liss, Inc.
Effect of the high molecular weight chitosan and sodium alginate on Candida albicans hydrophobicity and adhesion to cells.

UNLABELLED The aim of the present paper is to evaluate the effect of the high molecular weight chitosan (HMWC) and of sodium alginate (NaAL) on surface hydrophobicity of Candida albicans and on adhesion of the yeast to epithelial cells and fibroblasts of different proceeding. For this study, a collection strain and seven isolates of C. albicans from saliva (patients with denture stomatitis) were grown in Sabouraud glucose agar supplemented with HMWC or NaAL or in absence of them (control). Hydrophobicity was determined by adhesion to hydrocarbons method using two organic media (xylene and chloroform). For adhesion experiments, aqueous suspensions of yeasts were contacted with solutions of biopolymers and different cells (rat and human fibroblasts and epithelial cells Hep-2). The quantification of adhesion was made by optical microscopy. RESULTS A decrease in hydrophobicity was observed in the presence of HMWC (44%) and of NaAL (82%) when chloroform was employed as organic medium, meanwhile the decreases were of 30% with HMWC and 19% with NaAL in the presence of xylene. Adhesion of C. albicans to epithelial cells and human fibroblasts decreased significantly with both biopolymers. In the case of rat fibroblasts, a decrease was observed only with NaAL. None of experiments showed significant differences associated to fibroblast type. CONCLUSIONS Biopolymers showed effectiveness in reducing hydrophobicity and adhesion of C. albicans to cells, which are important virulence factors related to colonization of the soft tissues of host or acrylic surfaces present in the oral system.
Local Co-occurrence and Contrast Mapping for Document Image Binarization

Document Image Binarization refers to the task of transforming a scanned image of a handwritten or printed document into a bi-level representation containing only characters and background. Here, we address the historic document image binarization problem using a three-stage methodology. Firstly, we remove possible stains and noise from the document image by estimating the document background image. The remaining background and character pixels are separated using a Local Co-occurrence Mapping, local contrast and a two-state Gaussian Mixture Model. In the last stage, possible isolated misclassified blobs are removed by a morphology operator. The proposed scheme offers robust and fast performance, especially for handwritten documents.
Sensor Placement for Fault Diagnosis

An algorithm is developed for computing which sensors to add to meet a diagnosis requirement specification concerning fault detectability and fault isolability. The method is based only on the structural information in a model, which means that possibly large and nonlinear differential-algebraic models can be handled in an efficient manner. The approach is exemplified on a model of an industrial valve where the benefits and properties of the method are clearly shown.
Influence of viscosity and solubilization on dissolution rate.

Abstract The dissolution rate of benzoic acid in aqueous sucrose and methylcellulose solutions is inversely proportional to the viscosity of the dissolution medium. The total solubility of benzoic acid in aqueous solutions of polysorbate 80 increases linearly as the concentration of the surfactant is increased. As the concentration of polysorbate 80 is increased with a limited increase in viscosity of the micellar solution, the dissolution rate of benzoic acid is increased to a maximum rate and is related to the total solubility as depicted by the Noyes‐Whitney relation. At concentrations of polysorbate 80 exceeding the concentration corresponding to the maximum dissolution rate, the dissolution rate is decreased as the concentration of the surfactant is increased. Because the dissolution rate is inversely proportional to the viscosity, high concentrations of polysorbate 80 increase the viscosity of the micellar solutions to the extent that the dissolution rate is slowed although the total solubility is greatly increased. In micellar solutions maintained at a constant viscosity, the total solubility of benzoic acid increases linearly as the concentration of the surfactant is increased. The dissolution rate of benzoic acid in micellar solutions with a constant viscosity increases progressively without a maximum rate as the concentration of the surfactant is increased.
Pelvic floor muscle contractility: digital assessment vs transperineal ultrasound

A significant reduction in hiatal area and anteroposterior diameter can be induced by pelvic floor muscle contraction, and this has been demonstrated using three‐dimensional/four‐dimensional (3D/4D) transperineal ultrasound (TPS) in a small group of women. Our objective was to correlate pelvic floor muscle contractility using digital assessment with the change in TPS hiatus measurements during maximum pelvic floor muscle contraction.
Attention and primary visual cortex.

Evidence for attentional modulation of responses in primary visual cortex has been a matter of considerable debate. The classical notion concerning attention effects in visual cortex has held that the strongest effects are seen at the highest levels of the visual pathway, and that in primary visual cortex there is no effect of attention. The report by Somers et al. (1) of a functional MRI study indicating primary visual cortex (V1) modulation by instructions to attend illustrates the change that has taken place in recent years. This commentary expands on that theme by providing some of the history of work related to attention and V1 and by citing new studies of V1 modulation that use a variety of methods.
EVIDENCE FOR TEMPERATURE CHANGE AND OBLIQUE PULSATION FROM LIGHT CURVE FITS OF THE PULSATING WHITE DWARF GD 358

Convective driving, the mechanism originally proposed by Brickhill for pulsating white dwarf stars, has gained general acceptance as the generic linear instability mechanism in DAV and DBV white dwarfs. This physical mechanism naturally leads to a nonlinear formulation, reproducing the observed light curves of many pulsating white dwarfs. This numerical model can also provide information on the average depth of a star's convection zone and the inclination angle of its pulsation axis. In this paper, we give two sets of results of nonlinear light curve fits to data on the DBV GD 358. Our first fit is based on data gathered in 2006 by the Whole Earth Telescope; this data set was multiperiodic containing at least 12 individual modes. Our second fit utilizes data obtained in 1996, when GD 358 underwent a dramatic change in excited frequencies accompanied by a rapid increase in fractional amplitude; during this event it was essentially monoperiodic. We argue that GD 358's convection zone was much thinner in 1996 than in 2006, and we interpret this as a result of a short-lived increase in its surface temperature. In addition, we find strong evidence of oblique pulsation using two sets of evenly split triplets in the 2006 data. This marks the first time that oblique pulsation has been identified in a variable white dwarf star.
Nitric oxide is involved in control of Trypanosoma cruzi-induced parasitemia and directly kills the parasite in vitro

This study was carried out to determine the role of reactive nitrogen intermediates in Trypanosoma cruzi infection. In vitro, splenocytes obtained during the acute phase of infection produced elevated amounts of nitric oxide (NO) that were correlated with the resistance or susceptibility of the animals. In vivo, the levels of NO2- plus NO3- in plasma during the later phase of infection were higher in C57BL/6 mice than in BALBL/c mice. The treatment of infected C57BL/6 mice with inhibitors of NO synthase increased parasitemia and mortality. Finally, we found that the NO donor drug S-nitroso-acetyl-penicillamine is able to kill trypomastigotes in vitro in the absence of any other cells, suggesting a direct NO-mediated killing of T. cruzi.