Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ

The rod-shaped Gram-negative bacterium Escherichia coli multiplies by elongation followed by binary fission. Longitudinal growth of the cell envelope and synthesis of the new poles are organized by two protein complexes called elongasome and divisome, respectively. We have analyzed the spatio-temporal localization patterns of many of these morphogenetic proteins by immunolabeling the wild type strain MC4100 grown to steady state in minimal glucose medium at 28°C. This allowed the direct comparison of morphogenetic protein localization patterns as a function of cell age as imaged by phase contrast and fluorescence wide field microscopy. Under steady state conditions the age distribution of the cells is constant and is directly correlated to cell length. To quantify cell size and protein localization parameters in 1000s of labeled cells, we developed ‘Coli-Inspector,’ which is a project running under ImageJ with the plugin ‘ObjectJ. ’ ObjectJ organizes image-analysis tasks using an integrated approach with the flexibility to produce different output formats from existing markers such as intensity data and geometrical parameters. ObjectJ supports the combination of automatic and interactive methods giving the user complete control over the method of image analysis and data collection, with visual inspection tools for quick elimination of artifacts. Coli-inspector was used to sort the cells according to division cycle cell age and to analyze the spatio-temporal localization pattern of each protein. A unique dataset has been created on the concentration and position of the proteins during the cell cycle. We show for the first time that a subset of morphogenetic proteins have a constant cellular concentration during the cell division cycle whereas another set exhibits a cell division cycle dependent concentration variation. Using the number of proteins present at midcell, the stoichiometry of the divisome is discussed.
HIGH PREVALENCE OF HUMAN PAPILLOMAVIRUS (HPV) INFECTIONS AND HIGH FREQUENCY OF MULTIPLE HPV GENOTYPES IN HUMAN IMMUNODEFICIENCY VIRUS-INFECTED WOMEN IN INDIA

Groups of 208 human immunodeficiency virus (HIV)-infected women in India were studied for the presence of human papillomavirus with the general SPF10 PCR primer set. Virtually all (98%) women were found positive for human papillomavirus (HPV) DNA. Genotyping by the reverse hybridization line probe assay (HPV-LiPA) revealed a high prevalence of multiple genotypes (78.9% of the cases), with an average of 3.1 genotypes per patient (range, 1 to 10 genotypes). HPV 6 was the most prevalent genotype and was observed in 80 (39.2%) patients, followed by types 51 (31.9%), 11 (26.0%), 18 (24.0%), and 16 (22.5%). Of the genotypes detected, 40.9% were low-risk genotypes. Twenty-two (10.5%) patients showed normal (Pap I) cytology, 149 (71.6%) patients had inflammation (Pap II), and 28 patients (13.4%) had a Pap III score. The prevalence of high-risk genotypes increased with the cytological classification. There were no significant associations between the number of HPV genotypes detected and the cytological classification, HIV viral load, and CD4 count in these patients. In conclusion, the highly sensitive SPF10 LiPA system shows that very high proportions of HIV-infected women in Brazil is infected with HPV and often carry multiple HPV genotypes. Key-words: HIV, Human Papillomavirus, Genotypes, Women
Potential application of RAPD and RAHM markers in genome analysis of scombroid fishes

Total genomic DNA from 30 different specimens of Indian mackerel Rastrelliger kanagurta (Cuvier) and 5 king seer Scomberomorus commerson (Lacepede) was extracted by a simple modified phenolchloroform protocol. PCR amplification conditions using 10-mer arbitrary primers were optimized. Primers with the same nucleotide sequences produced varying Random amplified polymorphic DNA (RAPD) patterns and those with different sequences generated different banding patterns for the same template in the two commercially important scombroid fishes.
Does Obesity Cause Flat Foot

Objective: Obesity is becoming hype in the field of Nutrition and health. The Study aimed to determine the effects of obesity on foot structure and function, and the foot pain experienced by college students. Methods: Students from the department of health sciences and nursing were included in the study. The sampling was nonprobabilistic and based on the willingness of the students to respond. Height and weight were measured on the student with light clothes and without shoes using standard apparatus. The Body Mass Index was used as an Indicator of obesity. Each subject was classified by their BMI score and scored accordingly. Results: In this study, the overall prevalence of flat foot among obese subjects is 44%. The mean age of the participant was 20 years with S.D ± 3 and comparatively female students are high in number (62%). The variable weight and BMI are found to have significant statistical association (weight, p-value=0.00 and BMI, p-value=0.026). Conclusion: This study aimed to check whether the obesity can cause flat foot or not. As per our results, there has been a strong correlation between overweight or obese and flat foot presence, which indicates that there exists association. And gender, age have no association with the Flat foot, supporting the previous literature.
Monitoring and Evaluation of Cytomegalovirus Detection and Risk Factors in Pregnant Women from Egypt

Cytomegalovirus (CMV) is a β herpes virus with double-stranded DNA. Worldwide the current infective rate ranges between 40% and 100%. Fetal loss and abortion are responsible for significant emotional distress for couples desiring children. There are many documents which support the role of Cytomegalovirus (CMV) in spontaneous abortion. A total of one hundred and sixty-five (165) serum samples of pregnant women with anti-CMV IgG positive and with a definite diagnosis of previous abortion were determined. The detection of CMV was done using three methods, rapid chromatographic immunoassay, Enzyme-linked immunosorbent assays (ELISA), and real-time polymerase chain reaction (rt-PCR). The relation between age, time of the abortion, number of abortion, number of delivery, life style, blood transfusion, use of corticosteroids, gynecologic and medical history of abortion, residence and socioeconomic status, against CMV as risk factors of cases were studied. It was found that the best method for detection of CMV was rt-PCR (158/165) positive (96%), then ELISA was (132/165) positive (80%), and the last method rapid test was (99/165) positive (60%), All these methods useful in detection for treatment. Significant positive correlation between PCR, patients ages, number of abortion. While, the negative correlation between PCR and time of the abortion, number of delivery, use of corticosteroids, blood transfusion and life style were found.
Aphasia Types and Language Modality Disorder by Ischemic Stroke Patient

: This study focuses on analysing the types of aphasia caused by an ischemic stroke and their modality language disorder. The classification of aphasia syndromes employed in this research is based on Benson (1979). The subjects of the study were one male patient and two female patients with ischemic stroke in RSUD Subang. The data for this case study were collected and analyzed by using the TADIR test by Dharmaperwira-Prins (2000). Based on the analysis, it is concluded that there are two types of aphasia caused by the ischemic stroke, namely transcortical motor aphasia and broca’s aphasia. The participants with broca’s aphasia and transcortical motor aphasia had a disorder in spontaneous speech on personal information, such as listing, words and sentence naming, and not only verbally, but also in writing comprehension. The participant with broca aphasia had verbal paraphasia; however, the participant with transcortical motor aphasia only had literal paraphasia. Patients with broca’s Aphasia and transcortical motor aphasia produced fewer than 76 words per minute, which indicated that they suffered from a non-fluent type of aphasia. Disorder with reading aloud and repetition in broca’s aphasia were more severe than in those with a transcortical motor aphasia. The male transcortical motor participant was able to write, although suffering from literal paragraphia. On the contrary, the female participants were unable to write because they had the weakness on the right side of the body.
Self-administration and Reliability of Computerized Neurobehavioral Tests among Egyptian Pesticide Workers

Background: Behavioral Assessment and Research System (BARS) is a computerbased test system designed to assess neurobehavioral function and neurotoxicity in humans. This system is available in 5 languages including Arabic. Objectives: To assess the potential use of the Arabic version of computerized neurobehavioral system (BARS) and to compare performance of Egyptian pesticide workers to non-exposed populations using the same computerized battery. Participants and Methods: This study involved the administration of eight neurobehavioral tests from the Arabic computerized neurobehavioral test battery (BARS) to Egyptian workers occupationally exposed to pesticides (n= 25) as compared to non-exposed Egyptian workers (n= 25). One-week test-retest reliability of the computerized battery was measured among non-exposed participants. Results: Performance of pesticide non-exposed Egyptian workers did not show any significant differences between test and re-test (i.e., after one week). Performance of pesticide exposed workers was significantly lower in most of the administered computerized tests as compared to non-exposed Egyptian and US populations. Conclusions: The current findings demonstrate the potential utility of the Arabic computerized BARS in occupational epidemiological research especially in the short-term intervals. Stability of the administered Arabic BARS tests over the short-term interval makes it broadly applicable in assessing exposures at different workplaces and with different cultural and educational levels.
Thermofluor based high throughput stability optimisation of proteins for structural and functional studies

With the availability of many completely sequenced genomes, scientific research has shifted from genes to the products of the genes, the proteins. Structural genomics groups have been established worldwide, with the objective of determining protein structures on a genome-wide scale. New methods for protein production and structural determination have become necessary.Two methods for high throughput analysis of proteins are presented in the first part of this thesis. The first method is the thermofluor method, which presents a fast way to identify stabilizing conditions for a particular protein. It was shown that the addition of a stabilizing additive, identified with the thermofluor method, significantly increased the likelihood of growing protein crystals. The second method presented in this thesis provides a fast and robust way to detect metal containing proteins.The second part of this thesis describes the crystal structures of two RNA modifying enzymes, the pseudouridine synthase TruD and the RNA m5C methyltransferase YebU. The catalytic domain of TruD was shown to bear remarkable structural similarity to the other pseudouridine families despite a lack of sequence similarity. In addition to the catalytic domain, the structure of TruD also contained an insertion domain with a novel fold.YebU was also found have two structurally distinct domains. The N-terminal catalytic domain has a high structural similarity to other RNA m5C methyltransferases. The C-terminal domain was revealed to be a so-called PUA domain, which had not been predicted by previous sequence alignments.
Sedentary Behavior in Persons With Multiple Sclerosis: Is the Time Ripe for Targeting a New Health Behavior?

Sedentary behavior is prominent in persons with multiple sclerosis (MS) and may be associated with negative health consequences, yet our knowledge of sedentary behavior and its measurement, correlates, and consequences is in a stage of infancy—the focus on behavioral interventions might even be premature. This underscores the need for a research agenda focusing on sedentary behavior and its measurement, correlates, and consequences to inform the design of targeted interventions for persons with MS. Such research is important, as sedentary behavior represents a large opportunity for focal, theory-based behavioral interventions that could not only decrease sedentary behavior but also provide consequential life-changing benefits for persons with MS. The time is ripe for focal inquiry on sedentary behavior in MS and pursuing a new paradigm on health behavior change in this population.
The role of red-backed salamanders in ecosystems

Ecosystems provide a vast array of services that benefit human societies, which can be divided into provisioning, regulating, cultural, and supporting services. Amphibians provide provisioning services in the form of food and use in medical advances. As one of the major vertebrate groups, amphibians also play an important part in cultures throughout the world. Finally, amphibians can be extremely abundant and play important roles in ecosystem supporting services, including altering both physical structure and ecosystem functions. In aquatic systems, tadpoles can alter sedimentation, water clarity, and filamentous algae growth. Additionally, amphibians affect ecosystem functions, including nutrient cycling, decomposition, and primary production. Amphibians can alter the transfer of nutrients and energy between aquatic and terrestrial systems, but the net direction of flow varies temporally and depends on the amphibian community. After a review of these supporting services, I conducted two experiments to test the role of red-backed salamanders (Plethodon cinereus) in forested ecosystems. I examined the effects of salamanders on five 314-m2 plots with reduced salamanders and five reference plots. I found no evidence that salamanders affected litter or wood decomposition rates, nitrogen mineralization, nitrification, or acorn germination. Nor did salamanders affect the densities of predatory litter-dwelling macroinvertebrates. However, there was considerable variability in the density of salamanders among plots, even within treatments. Therefore, I conducted a second experiment where I manipulated the density of red-backed salamanders in enclosures (2 m2 x 1 m) and examined the effects on ecosystem functions. Despite the increased control and precision of this experiment, I did not observe effects of salamander density on decomposition, nitrogen cycling, acorn germination, or foliar insect damage. Since the timing of salamander activity could influence their role in ecosystem functions, I also examined the seasonal activity patterns of red-backed salamanders. I found that salamanders were most active in the spring and fall on warm, humid nights, following rain events. Salamander activity remained low through the summer even when conditions were favorable. Overall, red-backed salamanders had no measurable effects on the ecosystem functions I measured; however, future studies should examine the effects of salamanders in various forest types with different nutrient pools.
Phenotypic effects of opaque2 modifier genes in normal maize endosperm

The opaque2 modifier genes convert the soft, chalky endosperm, as found in maize opaque2 mutants, to a hard, vitreous phenotype. Modified opaque2 genotypes, also known as Quality Protein Maize (QPM), have increased levels of the essential amino acid lysine and a normal appearing kernel. The development of vitreous endosperm in QPM is associated with a two- to threefold increase in the γ-zein storage protein. To determine whether an increased concentration of γ-zein can influence hardness and the formation of vitreous endosperm in normal genotypes, we derived 13 modified normal inbreds from a cross of the normal line W64A with Pool 34 QPM. Analysis of protein content, kernel density and hardness revealed variation among the 13 inbreds. The modified normal inbreds show an increased content of γ-zein in the endosperm, similar to that of QPM. But the high level of γ-zein did not increase hardness and density above a threshold level. The modified normal inbreds did not have an increased lysine content, suggesting modifier genes, per se, do not improve the nutritional quality of maize endosperm
Étude de la matte sulfo-oxydante de la mangrove de Guadeloupe : caractérisation des micro-organismes principaux des familles Beggiatoaceae et Oscillatoriaceae

Les mattes de procaryotes constituent une niche ecologique diversifiee. peu etudie! <. en mangrove et jamais decrjte dans les Antilles. L'objectif de cette these est de decrire les procaryotes filamenteux reposant sur le sediment marin et de caracteriser les interactions entre la matte, milieu et entre les differents micro-organismes. Nous avons d'abord caracterise les micro-organismes majoritaires de la matte par le sequencage de l'ADNr 16S et des hybridations moleculaires (FISH). Il a ainsi ete possible de decrire deux nouvelles especes de Beggiatoaceae dont la structure a ete etudiee par microscopie electronique. De plus, afin de caracteriser l'environnement chimique de ces bacteries, des capteurs potentiometriques ont ete utilises. Ils ont permis de demontrer que les Beggiaotaceae oxydaient les sulfures en prelevant l'oxygene du milieu, tandis que des analyses de microscopie couplees a de l'EDX ont mis en evidence des reserves de soufre intracellulaires dans ces bacteries. Le sequencage de l'ADNr 16S des cyanobacteries filamenteuses a mis en evidence quatre nouvelles especes de l'ord~e des Oscillatoriales. Deux d'entre elles, du genre Planktothricoides ont revele une toxicite positive sur les Artemia sp:, les deux autres ont ete identifiees comme proches d'Oscillatoria spongeliae, une espece symbiotique d'eponge, bien que les coupes uItrafines d'une de ces souches aient montre une morphologie interne proche des Tychonema. L'analyse des donnees a permis d'etoffer les connaissances sur les communautes microbiennes de mangrove et constitue une base interessante de travail sur la contribution des micro-organismes au fonctionnement de l'ecosysteme mangrove dans son ensemble
ATP-Induced IL-1β Specific Secretion: True Under Stringent Conditions

Interleukin-1β is a potent proinflammatory cytokine, of which processing and secretion are tightly regulated. After exposure to various stimuli, mononuclear phagocytes synthesize the inactive precursor (pro-IL-1β), which is then cleaved intracellularly by caspase-1 and secreted. A widely used method for in vitro secretion of IL-1β employs LPS-primed human peripheral blood monocytes. Subsequently, adenosine triphosphate (ATP) is added to the cells in order to trigger the P2X7 receptor resulting in processing and secretion of mature IL-1β. However, it is often reported that secretion is due to cytotoxic effects of ATP with P2X7 receptor-activation-related cell death. We have challenged this concept and demonstrate IL-1β specific secretion, since there is no increase in cell death and IL-1α and IL-18 are not released in the same cultures. More importantly we show that these conclusions can only be drawn under stringent experimental conditions.
UvA-DARE (Digital Academic Repository) Revising the diagnosis of congenital amusia with the Montreal Battery of Evaluation of Amusia

This article presents a critical survey of the prevalent usage of the Montreal Battery of Evaluation of Amusia (MBEA; Peretz et al., 2003) to assess congenital amusia, a neuro-developmental disorder that has been claimed to be present in 4% of the population (Kalmus and Fry, 1980). It reviews and discusses the current usage of the MBEA in relation to cut-off scores, number of used subtests, manner of testing, and employed statistics, as these vary in the literature. Furthermore, data are presented from a large-scale experiment with 228 German undergraduate students who were assessed with the MBEA and a comprehensive questionnaire. This experiment tested the difference between scores that were obtained in a web-based study (at participants’ homes) and those obtained under laboratory conditions with a computerized version of the MBEA. In addition to traditional statistical procedures, the data were evaluated using Signal Detection Theory (SDT; Green and Swets, 1966), taking into consideration the individual’s ability to discriminate and their response bias. Results show that using SDT for scoring instead of proportion correct offers a bias-free and normally distributed measure of discrimination ability. It is also demonstrated that a diagnosis based on an average score leads to cases of misdiagnosis. The prevalence of congenital amusia is shown to depend highly on the statistical criterion that is applied as cut-off score and on the number of subtests that is considered for the diagnosis. In addition, three different subtypes of amusics were found in our sample. Lastly, signiﬁcant differences between the web-based and the laboratory group were found, giving rise to questions about the validity of web-based experimentation.