Miracle-dz/UniFAR-FTUs huggingface dataset:
Toxoplasma In and Around Us

Toxoplasma infections are quite prevalent, with 1/4 to /2 of the adults in the U.S. and elsewhere asymptomatically infected. Toxoplasma was first discovered not in sick humans or livestock, but in laboratory animals! Not even in conventional rats and mice, but in gondis (Ctenodactylus gondi), small cricetid rodents from North Africa, which were used at the Pasteur Institute of Tunis for leishmaniasis research (Nicolle and Manceaux 1908). The gondis came from the foothills and mountains of southern Tunisia, and it was soon realized that they were not infected in nature, but that they became infected in the laboratory (Chatton and Blanc 1917). Ticks, chiggers, fleas, and black flies were examined as possible vectors, but inconclusively. Almost at the same time as in Tunisia, Toxoplasma was described from a laboratory rabbit from Sao Paulo, Brazil (Splendore, 1908), early suggesting its worldwide distribution. Little was discovered about the transmission of Toxoplasma, however, through the subsequent years until the late 1930's and 1940's when Toxoplasma was found in newborn babies in the U.S. by Wolf and Cowan (1937) and Sabin (1942). Although transplacental transmission was proven in man and animals, this mode of transmission turned out to be rare, at least in humans, although a number of epidemic outbreaks have been described from sheep (Watson and Beverley 1971). After the development of a sensitive serologic test by Sabin and Feldman (1948), Toxoplasma antibody was fond earthwide, especially in areas with moist and warm climates. Human Disease due to Toxoplasma
Moving species redundancy toward a more predictive framework

7 All authors contributed equally to this manuscript Abstract Human activities are driving rapid changes in species diversity in a wide range of habitats globally. These changes in species diversity raise questions about the ability of altered systems to continue to offer valuable ecosystem services. Maintenance of ecosystem services under changing biodiversity depends largely on the abil - ity of persisting species to fill the functional gaps left by species in decline, and thus on the ecological or func - tional redundancy of species. Previous work suggests that the concept of species redundancy holds little applied value because, among other reasons, this concept is highly context dependent. Our goal in this chapter is to demonstrate a conceptual framework in which the prevalence and importance of redundancy is examined across example environmental and biological gradients to determine conditions or situations in which redun - dancy should play a significant role. By exploring general conditions that should elevate the importance or prevalence of redundancy, we hope to demonstrate that this concept can be used predictively, despite its con - text-dependent nature.
New Species of Aphanius (Teleostei, Cyprinodontidae) from Isfahan Province of Iran and a Reanalysis of Other Iranian Species

Abstract A new killifish species, Aphanius isfahanensis, is described from the Isfahan basin of Iran. It is distinguished from the other Iranian species of Aphanius by adult color pattern, molecular character states of mitochondrial DNA sequence data, and in multivariate morphometric and meristic space. Based on the phylogenetic analysis of molecular sequence data, the new species is hypothesized to be sister taxon to A. sophiae plus A. persicus, which also occur in Iran.
MECHANISMS OF HEME-OXYGENASE-1 CYTOPROTECTION FOR GENE AND CELL BASED THERAPIES AGAINST CARDIOVASCULAR DISEASE

Establishing the cellular and molecular basis for cardiovascular disease and the application of tools to manipulate the cardiovascular system genetically provide potential for new forms of treatment against cardiovascular disease, including: atherosclerosis, myocardial ischemia, cardiac hypertrophy and heart failure. Heme oxygenase-1 (HO-1) is an enzyme that has potential for the treatment of cardiovascular diseases (CVD). Atherosclerotic plaques express high levels of HO-1. Advanced plaques are stabilized in part through the separation of plaque constituents from the blood by the fibrous cap made up of smooth muscle cells. Protection of smooth muscle cells from apoptosis in the fibrous cap may be a means of promoting plaque stability in patients. Here we show that expression of HO-1 in human vascular smooth muscle cells renders them resistant to apoptosis mediated by oxidative stress. The cytoprotective mechanism mediated by HO-1 is mediated in part through protein kinase B (Akt). Plaque rupture may lead to myocardial infarction. Tissue recovery after mycocardial infarction requires neovascularization for improved tissue perfusion. A novel cell type recently discovered in the circulation has been characterized as an endothelial progenitor cell (EPC) and appears capable of promoting neovascularization of post-infarct tissue, thereby enhancing tissue recovery and perfusion. Most EPCs transplanted into the infarct environment do not survive or are not retained to function in neovascularization. Here we show that expression of HO-1 and its cytoprotective partner Akt protect EPCs in an infarct environment and promote EPC function in an infarct environment. Oxidative stress can result in maladaptive cardiomyocyte hypertrophy. In a model of oxidative stress-induced myocyte hyperterophy we demonstrate the expression of HO-1 prevents cellular hypertrophy through antioxidant mechanisms and regulation of the transcription nuclear factor kappa B (NF-κB).
A Correction to the Perspective titled "TRAF2: A Double-Edged Sword?" by Xia and Chen

Page 1 In the PDF of the Perspective by Xia and Chen, the colors for Figure 1 were not showing and the URL at the bottom of each page of the PDF was incorrect. A color version of Figure 1, along with the correct URL, in a revised PDF (http://stke.sciencemag.org/cgi/reprint/sigtrans;2005/272/pe7) is available starting 1 March 2005. The original, uncorrected PDF can be accessed from http://stke. sciencemag.org/cgi/reprint/sigtrans;2005/273/er3.
The role of integrin-proximal complexes in cancer cell behavior and normal liver function

Cell-matrix and cell-cell adhesion proteins are of great significance for many fundamental cellular processes such as survival, differentiation, spreading, adhesion, migration as well as oncogenic transformation. In the present dissertation study, the role of different integrin-proximal protein complexes was investigated in vitro in cancer cells and in primary rat hepatocytes and in vivo in whole animals. First it was shown that migfilin, a newly identified cell-matrix adhesion protein, is also an important component of cell-cell junctions critical for the organization and strengthening of the adherens junctions. Next, Ras-Suppressor-1 (RSU-1), which interacts with the focal adhesion protein PINCH, was shown to regulate cell spreading and adhesion, although the exact mechanism is yet unclear. Furthermore, the role of Integrin-Linked Kinase (ILK) was investigated in vitro in the model system of matrix-induced hepatocyte differentiation. It was shown that ILK along with its binding partners PINCH and ƒN-parvin are dramatically down-regulated during the matrix-induced re-differentiation of hepatocytes. Thus, ILK and its binding partners likely play an important role in matrix-induced-hepatocyte differentiation.Finally, the role of ILK was examined in vivo by removing the protein from the whole animal or specifically from the liver. First ILK was removed from ILK-floxed mice following Cre-recombinase-adenoviral injections giving rise to animals with fulminant hepatitis characterized by massive apoptosis, abnormal mitoses, fatty change and necrosis in the liver. Then, ILK-floxed animals were crossbred with alpha-fetoprotein(AFP)-albumin, albumin, or Foxa3-Cre transgenic mice and thus ILK was genetically removed specifically from the liver. In all cases, the livers of the animals had disorganized liver architecture, absence of hepatocyte plates, increased fibrosis, absence of microvilli in the canaliculi, different degrees of malformations in the biliary system, apoptosis and compensatory proliferation. The present findings therefore, clearly show that ILK is critical for hepatocyte differentiation and survival and more importantly, this holds true in vivo where ILK is crucial for the maintainance of normal liver architecture and function.Thus, the present dissertation work highlights the importance of cell-matrix adhesion proteins in vitro and in vivo and enhances the scientific knowledge in the field of molecular, cellular, hepatocyte and liver biology.
A physiological and genetic analysis of growth characteristics in Hordeum spontaneum

The aim of this project was to determine to what extent physiological, morphological and chemical growth characteristics are genetically linked and/or caused by common factors. First, 84 accessions of H. spontaneum from different habitats in Israel were screened for their variation in growth traits. A cross was made between contrasting genotypes and the F3 offspring were grown under close to optimal conditions and analysed for their growth characteristics. A map was constructed using AFLP markers. On chromosome 1 two QTLs for relative growth rate and specific leaf area were found at the same location. On chromosome 4 two QTLs for photosynthesis per unit leaf area and stomatal conductance were found at the same position. These traits are probably genetically linked or controlled by a common factor.
Analysis of the Secretome and Identification of Novel Constituents From Culture Filtrate of Bacillus Calmette-Guerin Using High-resolution Mass Spectrometry

Tuberculosis (TB) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. Although its efficacy against TB has displayed a high degree of variability (0%–80%) in different trials, Mycobacterium bovis bacillus Calmette-Gue´rin (BCG) has been recognized as an important weapon for preventing TB worldwide for over 80 years. Because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacteria is considered to be an attractive reservoir of potential candidate antigens for the development of novel vaccines and diagnostic reagents. In this study, we performed a proteomic analysis of BCG culture filtrate proteins using SDS-PAGE and high-resolution Fourier transform mass spectrometry. In total, 239 proteins (1555 unique peptides) were identified, including 185 secreted proteins or lipoproteins. Furthermore, 17 novel protein products not annotated in the BCG database were detected and validated by means of RT-PCR at the transcriptional level. Addition-ally, the translational start sites of 52 proteins were confirmed, and 22 proteins were validated through extension of the translational start sites based on N-terminus-de-rived peptides. There are 103 secreted proteins that have not been reported in previous studies on the mycobacterial secretome and are unique to our study. The physico-chemical characteristics of the secreted proteins were determined. Major components from the culture supernatant, including low-molecular-weight antigens, lipoproteins, Pro-Glu and Pro-Pro-Glu family proteins, and Mce family proteins, are discussed; some components represent potential predominant antigens
Understandable Complexity

The field of systems biology has received considerable attention lately, but it is not easy to define or to enter. The book An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon greatly facilitates both. In particular, it combines fundamental concepts on biological networks with an introduction to their formal analysis, using a wide array of biological examples. The book’s intention is not to cover everything about systems biology—rather, it provides an original, pointed, and very intelligible essence of the field.
It’s not over yet: The impact of worry on emotional recovery

Emotional reactivity and recovery are crucial for maintaining well-being. It remains unknown, however, to what extent emotion modulates the time course of recovery assessed using a simple categorization task and how this varies based on individual differences in worry. To address these questions, 35 participants viewed emotional pictures, followed by abstract greeble targets, which were to be categorized. Greebles were presented between 100 ms and 4,000 ms after picture offset. Physiological measures including skin conductance level and the corrugator supercilii were recorded and served as indicators of responsivity to emotional pictures. Measures of reaction time (RT) and accuracy scores were taken as indicators of the impact of emotion on facilitation or interference to the greeble target. Effects of interference and facilitation were observed up to 4,000 ms after emotional pictures on RT and accuracy scores. High worry was associated with greater (1) corrugator supercilii and skin conductance level to negative versus positive and neutral pictures and (2) interference from emotional pictures on accuracy scores. Overall, these findings suggest that subsequent processing is still impacted up to 4,000 ms after the offset of emotional pictures, particularly for negative events in individuals with high worry.
Functional T Cell Responses to Tumor Antigens in Breast Cancer Patients Have a Distinct Phenotype and Cytokine Signature1

The overall prevalence with which endogenous tumor Ags induce host T cell responses is unclear. Even when such responses are detected, they do not usually result in spontaneous remission of the cancer. We hypothesized that this might be associated with a predominant phenotype and/or cytokine profile of tumor-specific responses that is different from protective T cell responses to other chronic Ags, such as CMV. We detected significant T cell responses to CEA, HER-2/neu, and/or MAGE-A3 in 17 of 21 breast cancer patients naive to immunotherapy. The pattern of T cell cytokines produced in response to tumor-associated Ags (TAAs) in breast cancer patients was significantly different from that produced in response to CMV or influenza in the same patients. Specifically, there was a higher proportion of IL-2-producing CD8+ T cells, and a lower proportion of IFN-γ-producing CD4+ and/or CD8+ T cells responding to TAAs compared with CMV or influenza Ags. Finally, the phenotype of TAA-responsive CD8+ T cells in breast cancer patients was almost completely CD28+CD45RA− (memory phenotype). CMV-responsive CD8+ T cells in the same patients were broadly distributed among phenotypes, and contained a high proportion of terminal effector cells (CD27−CD28−CD45RA+) that were absent in the TAA responses. Taken together, these results suggest that TAA-responsive T cells are induced in breast cancer patients, but those T cells are phenotypically and functionally different from CMV- or influenza-responsive T cells. Immunotherapies directed against TAAs may need to alter these T cell signatures to be effective.
Content of potentially anticarcinogenic flavonoids of 28 vegetables and 9 fruits commonly consumed in the Netherlands

The content of the potentially anticarcinogenic flavonoids quercetin, kaempferol, myricetin, apigenin, and luteolin of 28 vegetables and 9 fruits was determined by RP-HPLC with UVdetection. Fresh foods were purchased in a supermarket, a grocery, and a street market and combined to composites. Processed foods were purchased additionally. Sampling was carried out in spring, summer, winter, and spring of the following year
Effectiveness of 1, 2, AND 3 Human Papillomavirus Vaccine doses against HPV-16/18 positive High-grade Cervical Lesions.

Before 2016, human papillomavirus (HPV) vaccination was recommended in a three-dose schedule; however, many vaccine-eligible U.S. females received <3 doses, providing an opportunity to evaluate real-world vaccine effectiveness (VE) of 1, 2, and 3 doses. We analyzed data on cervical intraepithelial neoplasia grades 2-3 and adenocarcinoma in situ (CIN2+) from the HPV Vaccine Impact Monitoring Project (HPV-IMPACT), 2008-2014. Archived tissue from CIN2+ lesions was tested for 37 HPV types. Women were classified by number of doses received ≥24 months before CIN2+ detection. Using a test-negative design, VE was estimated as 1-adjusted odds ratio from a logistic regression model that compared vaccination history for women whose lesions tested positive for HPV-16/18 (vaccine-type cases) with all other CIN2+ (controls). Among 3,300 women with CIN2+, typing results, and vaccine history available, 1,561 (47%) were HPV-16/18 positive, 136 received (4%) 1 dose, 108 (3%) 2 doses, and 325 (10%) 3 doses. Adjusted odds ratios for vaccination with 1, 2, and 3 doses were 0.53 (95% confidence interval: 0.37, 0.76; VE=47%), 0.45 (95% confidence interval: 0.30, 0.69; VE=55%), and 0.26 (95% confidence interval 0.20, 0.35; VE=74%). We found significant VE against vaccine-type CIN2+ after 3 doses of HPV vaccine and lower but significant VE with 1 or 2 doses.
Biotransformation and DNA Repair in 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone-Induced Pulmonary Carcinogenesis

ii CO-AUTHORSHIP . iv ACKNOWLEDGEMENTS . v TABLE OF CONTENTS . vii LIST OF FIGURES . xi LIST OF TABLES . xiii LIST OF ABBREVIATIONS . xiv CHAPTER 1 GENERAL INTRODUCTION . 1 1.1 Statement of Research Problem . 1 1.2 Chemical Carcinogenesis . 3 1.2. 1 Lung Cancer . 5 1.2. 2 Molecular Alterations in Human Lung Cancer . 9 1.2. 3 Modelling Lung Cancer in the Mouse . 11 1.3 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) . 14 1.3. 1 Formation and Sources . 14 1.3. 2 Carcinogenicity of NNK in Experimental Animals . 16 1.3. 3 NNK and Linkage to Human Cancers . 18 1.4 Biotransformation of NNK . 20 1.4. 1 Metabolic Pathways . 20 1.4. 2 Cytochrome P450-Mediated NNK Biotransformation . 23 1.4. 3 Other NNK Biotransformation Enzymes . 28 1.4. 4 NNK Biotransformation in Experimental Animal Lung . 31 1.4. 5 NNK Biotransformation in Human Lung . 32 1.5 DNA Repair and NNK . 35 1.5. 1 DNA Repair Pathways . 35 1.5. 2 Nucleotide Excision Repair . 36 1.5. 3 NNK-DNA Adduct Formation. 44 1.5. 4 Repair of NNK-induced DNA Damage . 52 1.5. 5 Post DNA-Binding Events . 55 1.6 Research Hypotheses and Objectives . 58
DESCONTAMINACIÓN DE SUELOS CON PETRÓLEO CRUDO MEDIANTE MICROORGANISMOS AUTÓCTONOS Y PASTO ALEMÁN (Echinochloa polystachya (H.B.K.) Hitchc.) DECONTAMINATION OF SOILS POLLUTED WITH CRUDE PETROLEUM USING INDIGENOUS MICROORGANISMS AND ALEMÁN GRASS (Echinochloa polystachya (H.B.K.) Hitchc.)

The soils polluted with crude petroleum can be cleaned with different physical, chemical or biological technologies. The objective of the present study was to evaluate the cleaning of soils polluted with petroleum using aleman grass (Echinochloa polystachya) associated with rhizospheric native populations of bacteria and rhizospheric fungus. Thus, an experiment in a greenhouse was carried out with a 3×4×2 factorial completely randomized arrangement design with four replicates per treatment. Soil used had 98 mg kg − − − − −1 of total petroleum hydrocarbons (TPH) of basal origin; three petroleum concentrations (98 50 000 and 100 000 mg kg− −1 ), four inoculation types (without microorganisms, with bacteria, with fungi and with bacteria-fungi association), and two of plant (with rhizosphere and without rhizosphere of aleman grass), were evaluated. The Petri dishes counting method was used to determine bacteria and fungi. TPH degradation was determined by an infrared spectrophotometer with EPA 418.1 method, and the production of vegetable biomass by dry weight. Bacteria, fungi and the association bacteria-fungi had significant largest populations at 120 d (p=0.05) in the treatments with rhizosphere and aleman grass in soil with 50 000 mg kg−1 of TPH. The maximum populations were 16×107 colony former units (CFU) of bacteria per gram of dry soil and of 17×104 CFU of fungi. In the association the population of bacteria diminished by one exponential unit; however the fungi populations increased by three exponential units. Petroleum degradation was significantly higher (p=0.05) at 120 d in soils with 100 000 mg kg −1 with rhizosphere inoculated with bacteria-fungi association; the treatment removed 48% of TPH. The production of dry matter was significant in the control treatment (16.3 g) and the biggest decrease was 53% in the soil with 100 000 mg kg −1 of TPH inoculated with bacteria.
The Seychelles Paradise Flycatcher Terpsiphone corvina on La Digue: population size, habitat requirements and management options

Summary The conservation of the Seychelles Paradise Flycatcher on La Digue is reviewed and compared with an earlier investigation (1978). The status of the bird and its habitat on the western plateau, which holds nearly 80% of the world population, was investigated, as was the Special Reserve, notably the validity of the present boundary and the need for management initiatives. The population on the western plateau has changed little in 10 years, with one pair less but more individuals, and there has been a small (<5%) decline in preferred breeding habitat. The number of pairs using the reserve was unchanged from 1978. The carrying capacity is small (c.6 pairs). Only one significant trend was isolated in an investigation of 10 habitat variables, suggesting that more birds occurred where trees were larger. The reserve boundary should be redrawn to include a significant part of the main freshwater marsh: earlier study showed that highest densities were found in woodland close to wetland, and conservation of the marsh is vital. The reserve requires a non-interventionist woodland policy, creation of ponds to extend wetland, improved boundary marking, provision of interpretation facilities and development of educational use. Away from the reserve, statutory zonation of land on the plateau for woodland and sustainable timber production is needed as part of an overall land-use policy.
Comparison of Patient Experiences in Medicaid and Commercial Health Plans

Providing a good quality care for Medicaid patients has been a persistent challenge. To evaluate quality of care provided by Medicaid plans in comparison with that of commercial plans, this study used the CAHPS (Consumer Assessment of Health Plan Study) survey, which measured the experiences of patients using frequency report instead of traditional satisfaction measures that are more vulnerable to a response bias. This study found that Medicaid managed care services for children has not yet achieved the goals of providing access to and quality of care equivalent to that of commercial insurance. This study also confirmed potential problems in relying entirely on global ratings or satisfaction measures in assessing quality of care. While global ratings of Medicaid care were as good as and sometimes better than commercial counterparts, Medicaid patients reported worse access to necessary care. Based on the results, implications were drawn for future efforts in assessment and improvement of quality of care for Medicaid patients.
MOLECULAR CHARACTERIZATION OF ALPHA S1 CASEIN IRV ALLELE DISCOVERED IN ROMANIAN GREY STEPPE CATTLE AND IT'S FREQUENCY IN THIS BREED

U.S.A.M.V. Cluj-Napoca, Faculty of Animal Husbandry and Biotechnology, Regional Laboratory of Farm Animals Genotyping, Manastur Street, No. 3-5, 400372, Cluj-Napoca, Cluj County, Romania; U.S.A.M.V. Cluj-Napoca, Biotechnology Department; Research Station For Cattle Breeding Dancu (SCPCB Dancu), Iasi County, Romania; Corresponding author: Tel. :+40 264 596384; Fax: +40 264 593792, E-mail address: avbalteanu@yahoo.com (V. A. Balteanu).