Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptation of Marrubium vulgare L Species to The Habitat Alteration in Disturbance Regime

MARRUBIUM VULGARE L (white horehound) is a perennial flowering species belongs to Labiatae (Lamiaceae). Marrubium genus is native to North Africa, Europe, and the Mediterranean basin. Worldwide, it represented by 30 species. In Egypt, there are two species only distributed in the northern coastal belt wherever calcareous or oolitic sand formation, especially in marginal lands and waste ground, the ruins of the old abandoned house and road sides. The main differences between the two species are life span (perennial and annual), number of calyx teeth (10 and 5) and the color of the corolla (white and pale pink) of M. vulgare and M. alysson, respectively. With the accelerated rate of climate change and urbanization and their destroyed effects on biodiversity loss and fragmentation of habitat. This study examines if some species could adapted to habitat disturbance. For this purposes we choose M. vulgare as a model species for habitat disturbance. Phenological aspects, distribution, density, size structure and reproductive efforts of M. vulgare were studied in four different locations in the western Mediterranean section. Locations are representing two different habitats: Road sides (wild habitats) and abandoned places (urban habitat). The study claimed that there are a significant difference between reproductive efforts, size index and density, whereas, no differences between the phenological aspects.
An improved metagenomic strategy reveals an unprecedentedly high level of intragenomic polymorphism of ribosomal DNA in three species of Camellia

The ribosomal DNA (rDNA) repeats of more and more species have been found to be polymorphic in the genome, and the understanding of this polymorphism is conducive not only to eliminating potential chaos in the metagenomic analysis (MGA), but also to providing rich information on rDNA evolution. In this study, the MGA previously used for the study of environmental microbial diversity was improved and extended to detect the intragenomic polymorphism (IGP) of rDNA in three species of Camellia L. The 3′‐end region of 26S rDNA of three individuals was amplified using degenerate primer pairs. Three annealing temperatures were applied to obtain as many ribotypes as possible, and equimolar amplicons from the three species were then pooled and sequenced using the Illumina MiSeq platform. An incredibly high level of IGP of rDNA was found in all three species. Nearly all of the ribotypes detected from this study were rDNA pseudogenes, and most of them have existed for a long time in the genome, with some generated from several rapid expansions. Our procedure provided an effective technique for detection of IGP of rDNA, and the particular evolutionary information of rDNAs in Camellia was also exploited.
The response of Arabidopsis to low potassium availability

The potassium ion (K+) is vital for plant growth and development, and K+ deficiency leads to reductions in crop yields. Given the significance of K+ deficiency in agriculture, it is important to understand the mechanisms by which K+ is taken into the plant and also how K+ deficiency impacts on the architecture of the root system, both of which will influence the ability of the crop to forage for K+ in the soil. The overall objective of the work described in this thesis is to uncover the mechanisms by which plant hormones control the root architectural responses to low K+ in the Arabidopsis accession Col-0. This question has been investigated using a combination of microscopy, genetics, chemical intervention, transcriptomics and analysis of the published literature. In response to low K+ Arabidopsis reduces its lateral root (LR) growth, and it was established that this reduction in growth is mediated through a reduction in cell division in the LR meristems. Analysis of RNA-Seq data allowed the identification of gene transcriptional changes in response to low K+. These data were then used to form hypotheses about the hormonal control of the reduction in LR growth. Data in this thesis allowed the identification of a role for the hormone gibberellin (GA) and for DELLA proteins in the modulation of LR growth in response to K+ starvation. These data were also used to identify the CBF1 transcription factor as a potential regulator of changes in cellular GA levels in response to low K+. The roles of reactive oxygen species (ROS), ethylene, auxin and abscisic acid (ABA) in the regulation of the root architectural responses to low K+ were investigated but no clear regulatory effects were identified. A role for ethylene and low K+ in the root gravitropic response was also identified. A model is proposed that describes the link between low K+ availability and root architectural changes mediated by altered GA signalling pathways.
SEMEN CHARACTERISTICS OF EXOTIC PIG BREEDS

A research was conducted to study the semen characteristics of Large White Yorkshire, Landrace and Duroc boar. The reaction time was 48.51 ± 3.02, 52.18 ± 5.61 and 31.84 ± 1.21 seconds and the ejaculation time was 462.93 ± 5.60, 399.24 ± 7.24 and 349.20 ± 7.40 seconds in Large White Yorkshire, Landrace and Duroc boars, respectively. Large White Yorkshire pigs had significantly (P<0.05) higher ejaculation time and semen volume compared to other two breeds. The sperm concentration was significantly (P<0.05) higher in Duroc breed (359.38 ± 2.94 million/ml) followed by Large White Yorkshire (319.66 ± 2.56) and Landrace (308.71 ± 3.27) breed. Breed had no significant influence on mass activity, progressive motility and abnormal sperm count. The live sperm per cent was significantly (P<0.05) higher in Landrace (90.73 ± 0.27) and Duroc (90.16 ± 0.43) compared to Large White Yorkshire (88.93 ± 0.26).
Associations of Meningioma Molecular Subgroup and Tumor Recurrence.

BACKGROUND We and others have identified mutually-exclusive molecular subgroups of meningiomas, however, the implications of this classification for clinical prognostication remain unclear. Integrated genomic and epigenomic analyses implicate unique oncogenic processes associated with each subgroup, suggesting the potential for divergent clinical courses. The aim of this study was to understand the associated clinical outcomes of each subgroup, as this could optimize treatment for patients. METHODS We analyzed outcome data for 469 meningiomas of known molecular subgroup, including extent-of-resection, post-operative radiation, surveillance imaging, and time to recurrence, when applicable. Statistical relationships between outcome variables and subgroup were assessed. Features previously associated with recurrence were further investigated after stratification by subgroup. We used Kaplan-Meier analyses to compare progression free survival, and identified factors significantly associated with recurrence using Cox proportional hazards modeling. RESULTS Meningioma molecular subgroups exhibited divergent clinical courses at two years of follow-up, with several aggressive subgroups (NF2, PI3K, HH, TRAF7) recurring at an average rate of 22x higher than others (KLF4, POLR2A, SMARCB1). PI3K-activated tumors recurred earlier than other subgroups, but had intermediate long-term outcome. Among low-grade tumors, HH and TRAF7 meningiomas exhibited elevated recurrence compared to other subgroups. Recurrence of NF2 tumors was associated with male gender, high-grade, and elevated Ki-67. Multi-variate analysis identified molecular subgroup as an independent predictor of recurrence, along with grade and previous recurrence. CONCLUSION We describe distinct clinical outcomes and recurrence rates associated with meningioma molecular subgroups. Our findings emphasize the importance of genomic characterization to guide post-operative management decisions for meningiomas.
Antibacterial Function of Fabrics Dyed with Extract from Chamaecyparis obtusa Leaves against Methicillin-resistant Staphylococcus aureus

Bacteria exist everywhere and continuously come into contact with daily surroundings and humans. Super bacterium methicillin-resistant Staphylococcus aureus, resistant to methicillin, has recently appeared. The morbidity and rate of death associated with super bacteria infection has increased. This study investigated the antibacterial activity of fabrics naturally dyed with Chamaecyparis obtusa leaves extract against methicillin-resistant Staphylococcus aureus. Fabrics were left for 15 min in a natural dyeing solution prepared by extraction from C. obtusa leaves using 11.3% (o.w.f) with a fixed liquor ratio of 1:22 at 40 o C. The dyeing process was conducted using three different mordants; subsequently, the K/S value of the dyed fabrics increased in the order of None < Cu < Fe < Al. The color fastness property of the fabrics to washing, dry-cleaning, and rubbing was found to be excellent and ranked in the 4-5 grade. The color fastness to light of natural dyeing is low in most cases and has the problem that the dye color soon becomes bleached. Yet, in most cases cloth dyed with retinispora leaves, the color fastnezz to light was good with a third to fourth grade. Non-mordant fabrics, aluminum mordants, and copper mordants also showed better antibacterial properties (99.9% reduction) against methicillin-resistant Staphylococcus aureus, compared to the control fabrics. The dyed fabrics showed the same antibacterial activity even after three washes. The results highlight the strong potential of fabrics naturally dyed with C. obtusa-extract as a medicinal material with excellent antibacterial function against methicillin-resistant Staphylococcus aureus.
Does Trimethoprim-Sulfamethoxazole prophylaxis induce myelosuppression in primary immune deficiency disease patients; A retrospective, 3 groups comparative study.

BACKGROUND The possible myelosuppression side effect of Trimethoprim-Sulfamethoxazole (TMP-SMX) on primary immune deficiency (PID) patients has not been established yet. OBJECTIVE Identify if the PID patients are at higher risk of developing myelosuppression secondary to the use of TMPSMX. METHODS Retrospective, three groups study, of PID patients (on and off TMP-SMX prophylaxis) and urinary tract infection (UTI) patients received prophylaxis TMP-SMX. Data about CBC results (WBC, ANC, Lymphocytes, RBC, Hemoglobin, and Platelet counts) at baseline, first, and maximum myelosuppression observed during the period of TMP-SMX administration were collected. RESULTS A total of 122 patients were included in this study (41 PID patients on TMP-SMX prophylaxis, 45 PID patients not on TMP-SMX prophylaxis, and 36 UTI patients on prophylaxis TMP-SMX). There are significant differences noticed in the percentage of patients who developed clinical myelosuppression (i.e. less than normal value for age) in ANC (39.0% vs. 8.9% vs. 16.7%, p = 0.002), RBC (36.6% vs. 13.3% vs. 13.9%, p = 0.014), WBC (41.5% vs. 13.3% vs. 13.9%, p = 0.003), and platelet (24.4% vs. 15.6% vs. 2.8%, p = 0.028) in group 1, 2, and 3, respectively. Significant difference in myelosuppression between the groups was most likely due to the combination of TMP-SMX effect on PID patients rather than the disease or the drug itself. CONCLUSIONS Primary immune deficiency (PID) patients are at higher risk of developing myelosuppression secondary to TMP-SMX prophylaxis (especially ANC) comparing to immune-competent patients or other PID patients who did not receive prophylactic TMP-SMX. Future larger prospective study is required to confirm this association.
Regulation of shoot branching in Arabidopsis by trehalose 6-phosphate.

-Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood. -We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds. -TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous trehalose-6-phosphate phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression of FLOWERING LOCUS T (FT) and up-regulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching in branched1 but not in ft mutant backgrounds. -These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT.
Primary Progressive Aphasia has a Unique Signature Distinct from Dementia of the Alzheimer's Type and Behavioral Variant Frontotemporal Dementia Regardless of Pathology.

Primary Progressive Aphasia has a Unique Signature Distinct from Dementia of the Alzheimer’s Type and Behavioral Variant Frontotemporal Dementia Regardless of Pathology Tamar Gefen, PhD, Qinwen Mao, MD, PhD, Missia Kohler, MD, Stacey Moeller, MS, Allegra Kawles, BA, Christina Coventry, MS, RN, Callen Spencer, BS, Jaclyn Lilek, BS, Kaouther Ajroud, PhD, Alex Feldman, MD, Margaret Flanagan, MD, Emily Rogalski, PhD, Sandra Weintraub, PhD, Alfred Rademaker, PhD, Changiz Geula, PhD, M. -Marsel Mesulam, MD, and Eileen Bigio, MD
Female adolescents and young women previously treated for pediatric malignancies: assessment of ovarian reserve and gonadotoxicity risk stratification for early identification of patients at increased infertility risk

Abstract Objectives Childhood and adolescent cancer survivors (CACSs) are at risk of adverse reproductive outcomes. Assessment of follicle-stimulating hormone (FSH) levels is the most common test used to diagnose premature ovarian insufficiency (POI) whereas anti-m|llerian hormone (AMH) and antral follicle count (AFC) have been proposed as ovarian reserve markers. We assessed the correlation between these markers and treatment gonadotoxicity risk (GR) in CACSs. Methods A total of 55 female CACSs were enrolled. GR was graded as low, medium, or high according to classifications based on disease and treatments and on cyclophosphamide equivalent dose score. FSH, AMH, and AFC were determined. POI was defined by amenorrhea and FSH>30 IU/L. For remaining patients, diminished ovarian reserve (DOR) was defined by AMH<5th centile. FSH and AFC cut-offs proposed in the literature as DOR markers were also considered (FSH>10 IU/L or >95th centile; AFC<8 or <5th centile). Results Ovarian reserve results to be compromised in 23 (41.8%) patients: 14 with DOR and 9 with an established POI. Results showed GR classifications to be a good predictor of ovarian reserve, with significantly lower AMH and AFC in the high-risk groups. AFC resulted to be directly correlated with AMH (r=0.75, p<0.001). Conclusions In CACSs, GR classifications correlate with post-treatment AMH and AFC. These are useful tools in the early identification of young patients with DOR, who may benefit from reproductive and fertility preservation counseling. Further studies are needed to determine the rate and time of progression from DOR to POI in this population.
Combining Ability Analysis: Morphological Traits for High Temperature Stress Tolerance in Indian Mustard [Brassica juncea (L.) Czern & Coss.]

Indian mustard (Brassica juncea) is a naturally autogamous species, yet in this crop frequent out-crossing occur which varies from 5 to 30% depending upon the environmental conditions and random variation of pollinating insects. Cytologically Indian mustard is an amphidiploid (2n=36), derived from interspecific cross of Brassica campestris (2n=20) and Brassica nigra (2n=16) followed by natural chromosome doubling. These relationships have been confirmed by the artificial synthesis of amphidiploids species by hybridizing basic diploid species and also by analysis of chloroplast and mitochondrial DNA restriction pattern of basic and amphidiploids International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 5 (2017) pp. 942-953 Journal homepage: http://www.ijcmas. com
An assessment of the mutation rate of human microsatellites

Microsatellites consist of 2-6 nucleotide repeats and are some of the most abundant variants in the human genome. Understanding their mutational patterns is of great interest in the field of population genetics. In this thesis the mutation rate of microsatellites in 1812 Icelandic trios is estimated. To achieve this, a matrix of data from deCODE’s popSTR genotyper was created and used to count deviations from Mendelian inheritance. The number of these deviations was then divided by the total mutational opportunities occurring in the data-matrix. The mutation rate for each parent was then estimated using the expectation-maximization (EM) method, providing separate estimates for the two sexes. Relationship with parental age was also assessed by modeling the parent’s age against the mutation rate measured with the Mendelian inheritance matrix. Furthermore, the mutation rate between motifs was estimated and the change in length was measured to see if longer motif were shortening and vice versa. Finally, correlation with slippage rate, calculated by popSTR’s algorithm, was estimated. All statistical methods were performed using the statistical software R and all code written in python programming language. The results are in good congruence with previous research, showing a relationship between the father’s age and mutation rate. Slippage rate estimated by popSTR has no correlation with mutation rate and the EM algorithm shows a higher mutation rate on the father’s side than on the mother’s side. Overall, this thesis creates a window into the mutational events of human microsatellites.
Phytochemical characteristics of Date Palm (Phoenix dactylifera L.) leaves extracts

Evaluation of the phytochemicals date palm leaves , . which have been shown the presence of many medical compound that are significant to the human health like tannins , alkaloids , trepenoids , carbohydrate , phenols, amino acids and flavonoids . So, the recent research activities are focused to assess natural sources date palm leaves antioxidants compounds . This is what explains the use of herbal drugs have gained importance in recent years which its efficacy and cost effectiveness few . Therefore, there is more growing trend in searching for antioxidants of natural origin.
Health-related quality of life of HIV-infected patients taking different antiretroviral regimens at a tertiary healthcare facility in northern Nigeria

Purpose: To evaluate the health-related quality of life (HRQoL) of patients taking different antiretroviral regimens. Methods: A cross-sectional descriptive design was used to evaluate HRQoL of patients on Highly Active Antiretroviral Therapy (HAART) at Usmanu Danfodiyo University Teaching Hospital (UDUTH), Sokoto, Nigeria. Data were collected using HIV/AIDS-Targeted Quality of Life instrument between May and November, 2015 from 872 adult outpatients who had been on their regimen for at least 6 months. Data were statistically analysed. Results: The overall HRQoL score of the patients was 59.40 ± 18.66. Among patients on the first-line regimens, those on TDF + FTC + EFZ (60.52 ± 19.17) and those on TDF + 3TC + EFZ (64.41 ± 18.04) reported the best HRQoL scores. The difference between the scores of patients on the two most utilised regimens; AZT + 3TC + NVP (58.14 ± 18.53) and TDF + 3TC + EFZ (64.41 ± 18.04) was significant (p < 0.05). Among patients on second-line regimens, those on TDF + FTC + LPVr (67.58 ± 14.80) reported the highest HRQoL score. Conclusion: Patients in this facility had a moderate HRQoL. TDF + 3TC + EFZ, TDF + FTC + EFZ and TDF + FTC + LPVr were the regimens with the best HRQoL outcomes. The use of these regimens should be encouraged for better patient well-being. Keywords: HIV, Health-related quality of life, Antiretroviral therapy, First-line antiretroviral regimen, Second-line antiretroviral regimen
Immunohistochemical expression of stem cell markers CD133 and Oct-4 in cases of endometrial hyperplasia and endometrial carcinoma

Background Endometrial cancer is the most common female genital tract cancer. According to the cancer stem cell (CSC) hypothesis, a tumor consists of more differentiated, highly proliferating cells, which constitute the tumor bulk and sustain tumor growth, besides undifferentiated slow-cycling cells with self-renewing capacity – the so-called CSCs. Establishment of reliable methods for the identification and effective isolation of CSCs might improve cancer therapy. Aim The aims of the present study were to evaluate the immunohistochemical expressions of stem cell markers CD133 and Oct-4 in cases of endometrial hyperplasia and endometrial carcinoma in comparison with normal endometrium and to correlate the results with the available clinicopathological data. Materials and methods A total of 90, archived, formalin-fixed, paraffin-embedded specimens were obtained, including 30 normal endometrium, 30 endometrial hyperplasia, and 30 endometrial carcinoma specimens during the period from 2010 to 2013. Results Increased expression of CD133 protein was detected in four (13.3%) normal endometrium specimens. In endometrial hyperplasia, the increased expression of CD133 protein was detected in five cases: two (22.2%), one (8.3%), and two (22.2%) cases of simple endometrial hyperplasia, atypical endometrial hyperplasia, and complex endometrial hyperplasia, respectively. On the other hand, in endometrial carcinoma cases, increased expressions of CD133 protein were found in three (11.1%) cases diagnosed as type 1 endometrial carcinoma, whereas type 2 endometrial carcinoma cases showed only low expression. However, increased expression of Oct4 protein in the normal endometrium was found in three (10.0%) cases. In endometrial hyperplasia, increased expression of Oct4 protein was detected in nine cases: two (22.2%), four (44.4%), and three (33.3%) cases of simple endometrial hyperplasia, atypical endometrial hyperplasia, and complex endometrial hyperplasia, respectively. Regarding the expression of Oct4 protein in endometrial carcinoma cases, the highest expression was found in 10 (37%) cases of type 1 carcinoma, whereas type 2 showed only low expression. A significant relationship was observed between CD133, Oct4, and tumor stage (P=0.00). Conclusion A positive correlation between the markers CD133 and Oct4 and the tumor stage was observed, indicating that CD133 and Oct4 may be used as significant prognostic markers. Further studies with larger sample sizes and follow-up data of longer intervals are recommended.
Phospho-regulation of the Hsp90 chaperone machinery

Hsp90 is a molecular chaperone modulating the activity of hundreds of client proteins. This activation process is regulated on several levels: by ATP hydrolysis, various specific Hsp90 co-chaperones and posttranslational modifications. In this context, phosphorylation of Hsp90 is of particular importance as there is a conserved phosphatase Ppt1, which specifically associates with Hsp90 and dephosphorylates it. This study allowed identifying in vivo phosphorylation sites of Hsp90 and determining a specific role of Ppt1. In general, phosphorylation down-regulates the Hsp90 machinery by different molecular mechanisms. Sites located in distant regions of Hsp90 affect the ATPase activity, conformational transitions in Hsp90 and co-chaperone binding.