Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Sperm chromatin Staining Techniques as a Predictive Diagnostic Tool for Male Infertility

Background: It is a scientific fact today that routine seminal analysis is only a poor predictor of male reproductive potentiality, so that there is an increased need for finding out new functional tests in the assessment of male infertility. Objective: The aim of the present study was to investigate the predictive value of sperm chromatin integrity assays as a complementary tool to assist in diagnosis of infertility. Methodology: This study was carried out between January 2013 and November 2013 including one hundred (100)selected infertile men who attended to fertility Center in Al-Sadr Medical City. The study also included twenty (20) healthy fertile volunteers as a control. Aniline blue (AB) staining was used to differentiate between normal condensed chromatin (unstained) and abnormal decondensed chromatin (blue), while toluidine blue (TB) was use to differentiate between normal intact sperm DNA (blue) and abnormal damaged sperm DNA (purple), this is the first study in Iraq that employed (TB) to assess sperm DNA fragmentation. Results: The results showed that there was a high significant difference (p<0.01) in sperm chromatin decondensation and sperm DNA damage between infertile and fertile men. The study also revealed a significantdifference (p<0.05) in sperm DNA damage between normozoospermic and fertile men, but no significant difference (p>0.05) was found in the sperm chromatin condensation. Both sperm chromatin condensation and sperm DNA damage showed a significant positive correlation with sperm morphology, and a significant negative correlation with sperm concentration, motility and progressive motility. Conclusions: The study concluded that sperm DNA fragmentation (by TB staining) has good predictive value in discriminating infertile and fertile men over seminal fluid analysis. Recommendations: TB and AB staining of sperm chromatin can be used in the course of infertility diagnosis. However, more investigations may be needed to confirm the discriminating power of sperm chromatin condensation assays (by AB staining) to be ready to use in the routine workup in the fertility clinics.
Chromobacterium Violaceum Strains Growth Conditions Impacting N- Acyl Homoserine Lactones AHL Production

Chromobacterium violaceum is a Gram-negative bacillus that is a facultative anaerobic, oxidase positive, glucose fermenting, and non-lactose fermenting. C. violaceum is free living which can be found in the soil and water. C. violaceum produces a possible antioxidant called violacein a purple pigment that is considered to be one of the significant characteristics of C.violaceum. Chromobacterium violaceum one of the Gram negative bacteria which use Quorum Sensing (QS) occurs within a single bacterial species, and regulates a lot of different processes ,essentially serving as a simple communication network so that QS is the accumulation of signaling molecule that enable a single cell to sense the communication from other cells . The density and bioluminescence through quorum sensing is manipulated via the signaling molecule N-acyl-homoserine (AHLs) that is produced by C. violaceum. The major objective in this work is to determine the reason why 14N1 cannot produce the pigment on LB media in cultures using heavy cell inoculum and high concentration of AHL on all the C. violaceum strains. C. violaceum 14N23 and 14N1 were isolated from copper basin, Tennessee and (ATCC) 12472 and (ATCC) 31532 obtained from American Type Culture Collection (ATCC), and CV026. 14N1 produces a pigment after 24 hours by using high inoculation 20% which is 10 ml overnight culture of 14N1 to 40 ml LB broth media with different shaker's speed started from (in static culture , 150,175,225). On the AHLs 14N1 did not produce a pigment and that the same with 14N23. However, 12472 did produce a pigment after 24 hours, and the positive control (ATCC) 31532 produced and the negative control CV026 did not.
Evaluation of Phytochemical Constituents and In vitro Antioxidant Activities of Plumbago indica Root Extracts

Plumbago indica (Plumbaginaceae) is a perennial herb, commonly cultivated in India for its therapeutic value. The goal of current study was to evaluate the phytochemical constituents and to explore the in vitro antioxidant properties of methanolic extracts of P. indica. Preliminary phytochemical evaluations revealed the presence of steroids, tannins, glycosides, phenols, flavonoids and saponins in the root methanolic extracts. Determinations of their in vitro antioxidant activity were carried out by using 2,2-diphenyl-1-picrylhydrazyl in an assay based on the method of Oyaizu. Hydroxyl radical scavenging activity was also measured in the same extracts. Results from this research project indicated that P. indica roots are indeed rich in phytochemicals and had substantial antioxidant activities, implying that P. indica roots can be used as a potential source of natural
Tissue expression of CD10 and CD15 proteins in gastric lesions: correlation with clinicopathological features

Background Gastric cancer represents the third fundamental cause of cancer mortality worldwide. The stroma assumes a noteworthy part in the growth and progression of gastric carcinoma regardless of its epithelial nature. This research was conducted to analyze the expression of CD10 and CD15 in cancer cells, stromal cells, and inflammatory cells, with a view toward gastric carcinoma development, and contrast them with clinicopathological parameters. Materials and methods A total of 78 examined cases of gastric lesions, i.e., eight non-neoplastic biopsies, 10 dysplastic carcinoma, and 60 gastric carcinoma, were analyzed immunohistochemically for CD10 and CD15 expression. Results CD10 was expressed in 58% of tumor cells (tCD10), 67% of stromal cells (sCD10), and 57% of infiltrating inflammatory cells (iCD10), and CD15 was expressed in 55% of tumor cells (tCD15) and 47% of infiltrating inflammatory cells (iCD15). Their expressions increased progressively throughout the growth and advancement of gastric carcinoma. The outflow of CD10 by stromal cells and CD15 by inflammatory cells was fundamentally higher in gastric carcinomas than in normal and dysplastic mucosa. A significant correlation between stromal CD10 expression and tumor grade, depth of invasion (T stage), lymph node metastasis, distant metastasis, and stage was discovered. Likewise, tCD15 was significantly associated with T category, lymphoid node metastasis (N category), distant metastasis (M category), and tumor stage. Conclusion CD10 and CD15 could be optimistic targets incorporated in the assessment of the enhancement rate of growth, invasion, and metastasis of gastric carcinoma.
System-level optimal yield: increased value, less risk, improved stability, and better fisheries

The discipline and practice of fisheries science and management have had an useful, successful, and interesting history. The discipline has developed over the past century and a half into a very reductionist, highly quantitative, socially impactful endeavor. Yet given our collective successes in this field, some notable challenges remain. To address these challenges, many have proposed ecosystem-based fisheries management that takes a more systematic approach to the management of these living marine resources. Here I describe systems theory and associated constructs underlying system dynamics, elucidate how aggregate properties of systems can and have been used, contextualize these aggregate features relative to optimal yield, and note how this approach can produce useful estimates and outcomes for fisheries management. I explore two contrasting examples where this approach has and has not been considered, highlighting the benefits of applying such an approach. I conclude by discussing ways in which we mi.
EFFECT OF GROWTH REGULATORS ON ROOTING OF CUTTINGS IN PLUM CV. KALA AMRITSARI

1200 cuttings made from the trees of Plum cv. Kala Amritsariwere planted in 60 beds of size 1×1m. , with 20 cuttings on each bed. Uniform sized 40 cuttings per replication were treated with ten treatments of IBA and PHB growth regulators by slow dip (24 hours) and quick dip (2 minutes) method before planting along with control.Results showed that IBA@2000ppm quick dip was found to be significant in improving the shoot and root characters in cuttings with maximum shoot length (16.87cm), average shoot girth (0.46cm), shoot number (4.22), fresh weight of shoots (6.82), dry weight of shoots (1.43g), leaf number (154.28), average leaf area (305.79 cm 2 ), root number (44.90), average root length (10.88cm), length of longest root (13.5cm), fresh weight of roots (1.52g), dry weight of roots (1.09). While the cuttings treated with slow dip of IBA 150 ppm exhibited significant survival percentage (81.00%), percentage of rooted cuttings (74.33%) and sprouting percent (75.17%).
Phytochemical Investigation of the Medicinal Plant Taxodium distichum and Library Screening of Thalictrum Alkaloids for New Antileishmanial Drug Leads

ii DEDICATION . iv ACKNOWLEDGMENTS . v VITA . x TABLE OF CONTENTS . xiii LIST OF TABLES . xx LIST OF FIGURES . xxii LIST OF SCHEMES. xxx LIST OF ABBREVIATIONS . xxxi CHAPTER 1. OVERVIEW OF LEISHMANIASIS . 1 A. Background on and Significance of Leishmaniasis . 1 1. Morphology, transmission, and life cycle . 2 2. Classification and geographical distribution . 7 2.1 Cutaneous leishmaniasis . 8 2.2 Visceral leishmaniasis . 10
Molecular control of gene expression by Brucella BaaR, an IclR-family repressor

The Brucella abortus general stress response sigma factor, σE1, directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection. Characterizing the functions of σE1 regulated genes therefore contributes to understanding of B. abortus physiology and infection biology. Transcription of the IclR family regulator, Bab2_0215, is indirectly activated by σE1 but its function remains undefined. We present a structural and functional characterization of Bab2_0215, which we have named Brucella adipic acid activated regulator (BaaR). BaaR adopts a classic IclR-family fold and directly regulates the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase (acaD2), and represses transcription. We identified three carboxylic acids (adipic acid tetradecanedioic acid, ε-aminocaproic acid) and a lactone (ε-caprolactone) that enhance transcription from the baaR and acaD2 promoters. However, neither the activating acids nor caprolactone enhance transcription by binding directly to BaaR. Induction of baaR transcription by adipic acid requires the gene bab2_0213, which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a set of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program regulated downstream of σE1.
Biological Pathways Based Approaches to Model and Control Gene Regulatory Networks

The aim of effective cancer treatment is to prolong the patients’ life while offering a reasonable quality of life during and after treatment. The treatments must carry their actions/effects in a manner such that a very large percentage of tumor cells die or shift into a state where they stop proliferating. The fundamental issue in systems biology is to model gene interaction via gene regulatory networks (GRN) and hence provide an informatics environment to study the effects of gene mutation as well as derive newer and effective intervention (via drugs) strategies to alter the cancerous state of the network, thereby eradicating the tumor. In this dissertation, we present two approaches to model gene regulatory networks. These approach are different, albeit having a common structure to them. We develop the GRN under a Boolean formalism with deterministic and stochastic framework. The knowledge used to model these networks are derived from biological pathways, which are partial and incomplete. This work is an attempt towards understanding the dynamics of a proliferating cell and to control this system. Initial part (deterministic) of this work focuses on formulating a deterministic model by assuming the pathway regulations to be complete and accurate. Using these models algorithms were developed to pin-point faults (mutations) in the network and design personalized combination therapy depending on the expression signature of specific output genes. To introduce stochastic nature onto the model due to incompleteness in the prior biological knowledge, an uncertainty class of models was defined over the biological network. Two such uncertainty class of models are modeledone over the state transitions and the other over the node transitions in the system. This knowledge is transferred to priors, and the existing Bayesian theory is used to update and converge to a good model. The Bayesian control theory for Markovian processes is applied to the problem of interven-
Occurrence of diamondback moths Plutella xylostella and their parasitoid wasps Cotesia vestalis in mizuna greenhouses and their surrounding areas

Pest insects invade commercial greenhouses from the surrounding areas. We aimed to clarify whether (1) the seasonal population dynamics of local pest insects affects their greenhouse invasions and (2) carnivorous natural enemies of the pests mirror this invasion. We compared the occurrence of diamondback moth [DBM: Plutella xylostella (Lepidoptera: Plutellidae)] larvae and their native parasitoid wasps Cotesia vestalis (Hymenoptera: Braconidae) on mizuna plants [Brassica rapa var. laciniifolia (Brassicales: Brassicaceae)] in commercial greenhouses, with their population dynamics on a wild cruciferous weed Rorippa indica (Brassicales: Brassicaceae) in satoyama in Kyoto, Japan. C. vestalis followed the occurrence of DBM larvae on both mizuna and R. indica; no C. vestalis were recorded in greenhouses free from DBM larvae. C. vestalis females were more attracted to volatiles emitted from DBM-infested than from uninfested mizuna. However, the presence of DBM in greenhouses could not always be explained by its seasonal population dynamics in the surroundings.
Structural Analysis of Leukemia Related Gene Network

Genome forms gene networks in the complicated interactive ways and further study on the cancer-related gene networks can help to understand and predict many unknown biological functions of cancer-related genome, and then obtain the useful informations about molecular mechanism of the formation of cancer. In this research, using the method of mutual information, we construct gene networks corresponding to normal control group and diseased experimental group of acute lymphoblastic leukemia (abbreviated as ALL). Through contrasting the structure difference of two kinds of networks, we find 23 structural key genes of ALL with significant degree-difference, where 21 genes are confirmed to be closely related to the formation of ALL. The match ratio between the prediction by model and literature is up to 91.3%. According to the effectiveness of the method in this work, we can predict that the remaining two genes CXCL1 and TACSTD2 are closely related to ALL. The significant differences of the network structures between control and experimental groups will enlighten the biomedical scientists that the reason of normal organism suffering from leukemia maybe is the great changes of some genes in vivo. The finding of structural key genes of ALL will help the biomedical scientist to further research the pathogenesis of ALL.
Grazing and Orthoptera: a review

Orthoptera are an important biological component of grasslands as a crucial link in the food chain. Grazing, either by wild animals or livestock for human food production, exerts considerable influence on the Orthoptera of grasslands. For example, grazing prevents succession of open grasslands to scrub and forest, creates heterogeneity in sward height, and provides patches of bare earth through the action of livestock hooves breaking the vegetative cover. Grazing may also interact with other forms of grassland management such as burning to produce quite complex interactions which vary greatly between regions and Orthoptera species. Threats to grassland Orthoptera include overgrazing; conversely, abandonment of grazing can lead to the loss of open habitats vital to many species. It is important to have ungrazed areas to provide refuges for species negatively affected by grazing. Rotational management – moving domestic livestock between different pastures – will also allow a range of sward structures to develop over a landscape. The over-arching principle for grazing management should be to establish a heterogeneous sward with a range of sward heights and bare earth for oviposition/basking. In more extensive systems, patches of scrub can form habitat of woody vegetation for species such as bush crickets. The greatest diversity of habitats should provide the highest species richness.
Effects of anti-poaching patrols on the distribution of large mammals in Taï National Park, Côte d'Ivoire

Abstract The effectiveness of protected area management is a major concern. In Taï National Park, Côte d'Ivoire, recurrent human pressure challenges the ability of law enforcement authorities to protect wildlife. During 2010–2015 we studied the implementation of law enforcement in the Park to determine (1) the potential for improvement of the protection of large mammals and (2) the minimum patrolling effort needed to obtain increases in their populations. We recorded presence of large mammals and illegal activities in two areas within the Park, the research area (210 km2) and the rest of the Park (5,150 km2), and compiled data about patrolling efforts from the Park authorities. Using a generalized linear mixed model we identified a relationship between increased patrolling effort and the relative abundance of large mammals, especially for monkey groups, pygmy hippopotamuses Choeropsis liberiensis and duikers. At low patrolling efforts duiker encounter rates remained stable, whereas rates of encounter with monkey groups and pygmy hippopotamuses decreased. Chimpanzee Pan troglodytes verus encounter rates were slower to respond and remained stable at higher patrolling effort, but decreased at low patrolling effort. Our findings suggest that a minimum of 1.32 patrol days per km2 over 2 years is required for chimpanzee and monkey populations to increase, whereas a patrolling effort of 0.48 days per km2 over 2 years would lead to an increase in duiker and pygmy hippopotamus populations. We maintain that the patrolling effort required to ensure an increase in wildlife can be estimated relatively precisely from multi-year biomonitoring programmes.
The Second Known Tetraploid Species of Parthenogenetic Tetrapod (Reptilia: Squamata: Teiidae): Description, Reproduction, Comparisons With Ancestral Taxa, And Origins Of Multiple Clones

Abstract We describe the second known tetraploid amniote that reproduces by parthenogenetic cloning. This all-female species of whiptail lizard originated in the laboratory from hybridization between Aspidoscelis uniparens (triploid parthenogen) and Aspidoscelis inornatus (diploid bisexual species). Similar clonal lineages of tetraploids arose from at least 44 F1 hybrid females. These were produced by at least 15 A. uniparens that mated with several different males of A. inornatus from both New Mexico and Arizona stock. Inheritance of alleles at eight microsatellite deoxyribonucleic acid (msDNA) loci in the tetraploid species confirms its parentage, whereas DNA quantification and behavior of chromosomes in meiosis demonstrate that tetraploidy and heterozygosity are maintained generation after generation. We compared univariate and multivariate variation in scalation between the tetraploids, their parental taxa, and four museum specimens from New Mexico that were reported as putative hybrids. Two of the putative hybrids are confirmed as such, but the other two are A. inornatus. The similarities of A. uniparens and the tetraploids suggest that tetraploid females may exist in old samples misidentified as A. uniparens. Clones of the tetraploid species are so similar to each other in morphology and msDNA that we have been unable to distinguish most individuals or separate lineages from the P1 through multiple generations (up to F7) on the basis of the 12 msDNA loci analyzed in this study. We discuss taxonomic aspects of the multiple hybrid origins of similar clones and apply one specific name. For some systematists, depending on the species concept preferred, these lizards represent a complex of multiple cryptic species that cannot be reliably identified or diagnosed (one species for each F1 hybrid female that cloned a lineage). These specimens of known parentage provide valuable insights for taxonomic treatment of natural parthenogenetic clones. In addition, we show that the degree of morphological variation in clonal parthenogens and bisexual A. inornatus can be similar to each other.
Novel roles of the circadian clock protein neuronal PAS domain protein 2 (NPAS2) in the response to oxidative and heat stress

Human NPAS2 is a basic-helix-loop-helix (BHLH) transcription factor with two N-terminal PAS domains that forms a hetero-dimeric complex with BMAL1/ARNTL to regulate the transcription of key circadian clock genes like Period and Cryptochrome. NPAS2 is unique in higher eukaryotic cells as both PAS domains contain one heme group each, which bind carbon monoxide. Although NPAS2 has been linked to cancer and neurological disorders, very little is known about its cellular roles. The results obtained in this study support a model in which NPAS2 responds to oxidative and heat stress in distinct manners. While oxidative stress results in the post-translational modification of NPAS2 and the formation of high molecular weight complexes, heat stress reduces the protein levels of NPAS2. These differences are also reflected in the changes to the NPAS2 mRNA levels. While oxidative stress increases expression of NPAS2, heat stress causes a drop in mRNA levels. The responses are cell line specific as, for example, the drop in NPAS2 protein levels after a heat shock was observed in MCF-7 breast cancer cells and HeLa cervical cancer cells, but not in non-malignant HEK-293 cells which may be of neuronal origin. Since both stress types are known to affect the peripheral clocks in human tissues in a manner which may be regulated by the MAP kinase p38β, it is proposed that NPAS2 is a novel target of this kinase. Why NPAS2 is regulated differently depending on the type of stress, could be linked with the different ways the p38 MAP kinase pathway responds to heat and oxidative stress. While heat activation is dependent on upstream kinases, heat activation may be dependent on the heat-induced increase in carbon monoxide in human cells. The works shows also that NPAS2 mRNA levels drop in the response to serum starvation and that the neuroblastoma KELLY cell line does not, or only at a very reduced level, express NPAS2 although an analysis of a large panel of human tissues shows high NPAS2 expression in the brain. A bioinformatical analysis of missense single nucleotide polymorphisms (SNPs) located the N-terminal domain of NPAS2 identifies two SNPs (S204P, rs750277651 and T252N, rs555063320) which may affect a p38 (S202) and EYRK1A (T252) kinase modification site, respectively. This is of interest as p38β may regulate NPAS2 and the dual-specific DYRK1A kinase is known to regulate the protein turnover of Cryptochrome. In summary, the work makes a strong case for NPAS2 as a novel target of the p38β MAP kinase pathway in the cellular response to oxidative and heat stress.