Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain Tissue Matters in the Study of FKBP5 Gene Expression Activities in Schizophrenia – A Meta-Analysis

Background: Gene FKBP5 has been linked to stress and cognition symptoms of schizophrenia (SCZ). However, few studies have reported changes in direct expression of FKBP5 in the brain of SCZ patients. Method: Here we performed a systematic review and a meta-analysis to explore gene expression activity of FKBP5 in brain tissue in the SCZ. Ten RNA expression datasets were acquired from Gene Expression Omnibus, including 543 samples (269 SCZ cases and 274 controls). Both fixed-effect and random-effects models were employed for meta-analysis. Multiple linear regression (MLR) was employed to study the impact of three factors (Case Control Ratio, Female Male Ratio of Cases, Tissue and Country) on SCZ. Results: FKBP5 presented no significant log fold change (LFC) in SCZ (LFC = 0.064; p-value = 0.30). MLR models showed that Case Control Ratio, Female Male Ratio of Cases and Country were not significant factors for the expression fold change of FKBP5 (p-values > 0.39) in regards to SCZ and that tissue was a wake impact factor (p-value < 0.11). Literature based pathway analysis showed that tissues from this study were not linked to stress or cognition related functions. Conclusion: Gene expression levels of FKBP5 vary within different brain regions, and this needs to be take into consideration when studied in relation to SCZ.
Basal Stem Rot of Oil Palm : Incidence, Etiology and Control

Basal stem rot (BSR) caused by Ganoderma spp. is a disease of economic importance in oil palm in Malaysia. Although much is known on the occurrence of this devastating disease, fundamental studies on it and its pathogen are rather limited. At present, there appears to be ambiguity in the identity of the causal organisms: there is difficulty in getting oil palms to be artificially infected and that control measures advocated are largely inadequate to contain the disease. Present studies are thus focused on answering these issues. An assessment of the BSR situation on selected estates was also carried out to assist in the understanding of the disease. The assessment carried out showed that serious incidence of the disease was "confined to coastal and riverine estates. However, the disease can now be seen to occur in a few in land estates albeit sporadically and at very low incidence. It was demonstrated that previous crops did not necessarily dict ate significant incidence of BSR. The underplanting technique and certain soil types can predispose plantings to much higher BSR incidence.
Spatial analysis of brassinosteroid signaling in the stem cell niche of Arabidopsis primary root = Caracterització molecular de la funció de BRI1 en les cèl•lules mare de lʼarrel dʼArabidopsis

The present PhD thesis work reports the molecular and genetic dissection for the role of plant steroid hormones Brassinosteroids (BRs) in root growth and development of Arabidopsis thaliana (Arabidopsis). A genetic, physiological and cellular analysis of existing BR mutants, together with the discovery of a novel pathway for the control of BR mediated stem cell divisions. The results presented here provide experimental evidence for a role of BRs in stem cell homeostasis in the primary root of Arabidopsis. Specifically, BRs promote columella stem cell differentiation and the division of a set of low mitotic cells called quiescent center (QC) that maintain the surrounding stem cells. Using a microgenomic approach, a novel BR signaling component, BRAVO (Brassinosteroids at Vascular and Organizing Centre) has been identified that is specifically expressed in the stem cells. BRAVO encodes a R2-R3 MYB transcription factor (MYB56) that acts as a negative regulator of BR-mediated QC divisions. This study uncovers a fine example of negative regulation model; BRAVO is directly repressed and interacts with BES1 creating a molecular switch that controls QC divisions. The work carried out during this PhD thesis shed light to a new function of brassinosteroids in the regulation of stem cells. BRAVO provides plasticity to the stem cells to response to DNA damage, and at the same time robustness to ensure QC function upon damage. The control of plant stem cell homeostasis is pivotal to understand plant adaptation to environmental changing conditions and provides a new mechanism to understand plants life span.
PHYLOGENETIC DIVERSITY OF BACTERIAL POPULATION IN RUMEN

In order to investigate the microbial diversity in rumen, bacterial 16S rRNA genes were amplified from total microbial DNA isolated from rumen fluid. The amplificated genes were incorporated into pBluescript SK II vector and electroporated into E.coli JM109 cells. The transformants, recognized in hybridization experiments (colony blot) by oligonucleotide DNA probe specific for the Cytophaga-Flavobacterium subgroup of the Cytophaga-Flexibacter-Bacteroides phylum and Prevotella-Bacteroides specific probe, were subjected to the RFLP analysis. On the basis of the RFLP profiles the Jaccard’s similarity coefficients were calculated and the dendrograms were created using the UPGMA method. The representative clones were chosen from the established groups of clones and the 16S rDNA was partially sequenced, compared to already known rRNA sequences in data banks and analysed using Clustal and Phylip phylogenetic packages. A large genetic variability of the rumen bacteria belonging to the Cytophaga-Flexibacter-Bacteroides phylum was established.
Genetic Background Influences Behavior and Responses to Epigenetic Changes Induced by a Methyl-Donor Diet

With recent strides in epigenetics, mainstream media informs the public that we can “beat our genes” by, for instance, changing our diet. Genetics, however, still plays a role in phenotype. Folate and other methyl-donor pathway components are widely supplemented due to their ability to prevent neural tube defects during prenatal development. In addition to vitamins, these compounds are also added to commercial flour, energy drinks, and other supplements. Several lines of evidence suggest that these supplements act through epigenetic mechanisms, including altering DNA methylation. Increasing evidence suggests potential deleterious effects of excessive folate. Given the benefits of these compounds, risk statements must be made with caution.
Oestrus expression and timing of ovulation in pigs.

: Oestrus is the period around ovulation in which sows show a standing response for boars, thus allowing the boars to mate with the sows. The duration of oestrus may vary between sows from 24 h up to 96 h, which is not related to systemic oestrogen concentrations. The moment of ovulation after onset of oestrus may vary from 10 h to 85 h. Consequently, onset of oestrus is not a good predictor for the time of ovulation. A reliable prediction of ovulation time would be worthwhile, since fertilization results are highly dependent on the moment of insemination relative to the moment of ovulation. However, at present, the duration of oestrus is the best 'predictor' of ovulation time and is independent of the duration of oestrus; ovulation takes place on average 70% of the way through oestrus. The following factors have been found to influence the duration of oestrus (and consequently the optimal time for insemination): boar-stimuli, stress, interval from weaning to oestrus, season and parity. Further study is needed to determine the causes of the variability in oestrus expression between sows, including the regulation of oestrus behaviour at the level of the brain.
AB0363 Rheumatoid arthritis and sickle cell disease: clinical, biological, radiological and therapeutics specific aspects. a retrospective observational study

Background Thanks to medical advances in sickle cell disease (SCD) treatments, practitioners have to be aware of new comorbidities, as rheumatoid arthritis (RA). Methods We conducted a retrospective, observational and monocentric study about clinical, biological and radiological specific aspects of RA in SCD patients and studied the impact of anti-rheumatic drugs, comparing the number of SCD flares occuring six months before/after their introduction, using medical files and phone inquiry. Results Twenty-three patients were included in this study. Data about RA treatments and SCD flares could be collected for 15 patients. Middle age at RA diagnostic was 32.9 years-old, sexe ratio was 4.75F/1M. 74% of the patients were RF positive, 65% were ACPA positive. 74% of the patients had articular damages. Among them, 100% had severe carpite which appears to be the major radiological expression of RA in SCD patients, occuring sometimes without finger bone erosion. 100% received at least one specific drug for RA, 35% a biotherapy. There was no significant difference in the number of crisis before and after methotrexate introduction (p=1) or anti TNF alpha drugs (p=0.35 IC95% [−1.26;0.51]. Methotrexate had to be stopped for 3 patients because of acute chest syndrome, which did not occur with anti TNF. No infection was noticed. Conclusions In conclusion, in SCD, RA occurs sooner in life course and to be more severe with a particular pattern: carpite and tarsite without finger bone erosion. The use of biotherapy appears to be safe, with a close monitoring. Disclosure of Interest None declared
Malaria prevalence and risk analysis among pregnant women in Bungoma county, Kenya

Malaria during pregnancy has adverse consequences on the mother and fetus. Information describing the prevalence, Plasmodium species types and the influence of socio-economic risk factors of malaria in pregnancy is scarce. In order to determine the distribution of malaria parasite species and risk factors among pregnant women in Bungoma County, a cross sectional hospital based study was carried out between March 2016 and January 2017 among 750 consented expectant mothers seeking antenatal services at the Bungoma County hospital. Malaria positivity and species identification were determined microscopically using Giemsa stain technique. Socio economic risk factors were collected using a structured pre-tested questionnaire. Data was analysed using STATA version 12. Descriptive analysis was used to determine malaria prevalence. Chi-square (X2) and regression analyses were used to determine the association between malaria and risk factors with P-
Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD

Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility of de novo protein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generate de novo proteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that these de novo peptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development. One Sentence Summary Loss of TDP-43 function results in the expression of de novo proteins from mis-spliced mRNA transcripts.
Effects of algal sedimentation and Monoporeia affinis on nutrient fluxes, pore water profiles and denitrification in sediment microcosms

A flow-through experiment was conducted to study the effects of a simulated algal sedimentation (8.0 g C m -2 ) and the amphipod Monoporeia affinis (5000 ind. m -2 ) using well-oxidised sediment from the Gulf of Bothnia. Pore water nutrient profiles, nutrient fluxes, sediment denitrification and O 2 consumption as well as NH 4 + excretion of M. affinis were followed for 7 days. After the algal enrichment, the NO 3 - concentration fell to near zero in the pore water and a decrease in the denitrification rate was observed. This occurred since the concentration of NO 3 - in the flow-through water was low and coupled nitrification-denitrification formed the main denitrification pathway. The share of denitrification compared to other loss processes of N from the sediment reduced from 37% in the control cores to 0.7% in the algae treated cores. The efflux of NH 4 + from the sediment formed 99% of the total loss of N in the algae treated cores. A massive efflux of NH 4 + and PO 4 3- was observed after the algal enrichment. The amphipods did not increase denitrification.
Sublethal Effects of Chlorinated Phenols and Resin Acids on Rainbow Trout (Salmo gairdneri)

The aim of this work was to study the effects of toxic compounds in pulp and paper mill effluents on fish and fish physiology. This was done by studying the accumulation of 2,4-dichlorophenol, 2,4,6-trichlorophenol and dehydroabietic acid in fish and the physiological responses of fish to this accumulation. Tests were performed at two concentrations, 5 µg/l and 50 µg/l, and during the exposure period mainly hematological parameters were measured in the fish. The toxicants tested affected most of the parameters analysed (blood hematocrit, leucocrit, hemoglobin, mean cellular hemoglobin count; plasma glucose, lactate; liver glycogen). Significant changes were also found in enzyme concentrations of UDP-glucuronyl transferase activity in the liver. Chlorinated phenols seem to increase the activity of this enzyme while the resin acids seem to decrease the activity. The accumulation of the toxicants tested is most significant at the beginning of the exposure period and the toxicants are concentrated in the liver. After 20 days of exposure the concentrations in the liver decrease and this shows the ability of fish to eliminate the substances tested or to change them to an excretable form. The accumulation of the toxicants seems to correlate with the physiological responses of the fish.
Unintentional retinal artery amputation during macular peeling

Objective: To report a case of unintentional retina artery amputation during macular peeling. Methods: Observational case report Results: A 73-year-old female underwent surgery to treat epiretinal membrane (ERM) associated with severe staphyloma in her left eye. While the ERM/posterior hyaloid membrane visually enhanced with triamcinolone (TA) was peeled, a movement of the forceps unintentionally involved the inferior temporal branch artery near the inner edge of the staphyloma. The artery was avulsed and amputated. Oozing from the retinal cleft that had once enfolded the artery and microscopic bleeding from the amputation stump were observed. The vitreous hemorrhage obscured a view of the fundus more than 4 weeks after the surgery. After 8 weeks, postoperative visual acuity was improved; however, the superior nasal visual field was lost, and the patient was aware of the broken vessel as a floater in her vision. Conclusions: Macular peeling is technically challenging, so meticulous attention must be paid to avoid any damage on vessels. The retina tissue was stretched in a staphyloma and vessels were bulged into the vitreous space especially at the inner edge of the staphyloma. High levels of TA dye here buried the texture of the retina. Excessive TA should be removed prior to macular peeling.
Sustained pupil constriction following brief light exposure: relation to retinal health

The pupillary light reflex (PLR) is an indispensable clinical measure of visual, neurological and autonomic function which, until recently, was thought to be driven by only rods and cones. In 2000, a novel subset of retinal ganglion cells (RGCs) was discovered that express melanopsin and are intrinsically photosensitive (ipRGC). These ipRGCs contribute to the PLR and are responsible for the sustained pupilloconstriction observed following light offset (the post-illumination pupil response (PIPR)). The primary goal of this project was to examine the PIPR in a broad sample of the general human population. Using a newly-developed, wide-field optical system, we demonstrate that all normal subjects display a post-illumination pupil response in response to a 10-second, 470nm light stimulus. We demonstrated that this PIPR was not correlated with subject characteristics such as age, race and gender, and that the only factor affecting the magnitude of the PIPR was the baseline pupil diameter. In most normal individuals, the PIPR was substantial (mean = 1.4 mm), and this test therefore has the potential to be utilized as a tool in evaluating subjects with either retinal or melanopsin-related disorders. Glaucoma is a group of diseases of the optic nerve that causes optic neuropathy (GON) associated with visual field loss. The second goal of the project was to test the PIPR in a group of patients with GON and compare the results with normal subjects and visual fields. Our results indicate that there was a significant difference between the GON patients and age-matched controls (p<0.05). We also demonstrated that the loss of PIPR correlated with the severity of visual field loss (as evidenced by the mean deviation (MD) loss). In conclusion, using a newly-developed, wide-field optical system, we have demonstrated that all normal subjects display a post-illumination pupil response which is reduced in patients with GON. Thus, testing for PIPR has the potential to be utilized as a clinical tool in evaluating and following patients with GON or melanopsin-related disorders. %%%%1 online resource (xi, 89 p. : ill., digital, PDF file)%%%%%%%%Vision Science;%%%%Optometry;%%%%ipRGC glaucoma optic neuropathy pupillary light reflex%%%%UNRESTRICTED
Genetic and phenotypic analysis of dominant Enhancers of torpedo on the second and third chromosomes of Drosophila melanogaster

The torpedo tyrosine lunase gene of Drosophila rnelamgmter encodes the homologue of the vertebrate Epidermal Growth Factor receptor (Pnce etal., 1989; Schej ter and Shilo, 1989). The activity of the torpedo gene product is required for embryogenesis, oogenesis, pupal viability, the development of certain imaginal discs and for the patterning of specific imaginal disc derivatives (Schupbach, 1987; Clifford and Schupbach, 1989). To identify genes which interact with the torpedo locus, genetic screens designed to generate mutations which dominantly enhance phenotypes associated with mutations in torpedo were conducted. A total of 25 such mutations, called Enhancers of torpedo, or E(top)s, were recovered. Twenty mutations were mapped to the second chromosome; five were mapped to the third chromosome. In Section I, both the genetic and phenotypic characterization of the 20 E(top)s which were mapped to the second chromosome is presented. The precise number of genes represented by these 20 mutations is currently unknown. However, preliminary results indicate that at least one locus distinct from torpedo has been identified. In Section 11, the characterization of the five E(top)s located on the third chromosome is presented. Complementation tests and phenotypic data are consistent with the idea that each of these mutations identifies a gene. Three of these mutations, E(top) 2-21, E(top) Dl 05 and E(top) K24 (which has been renamed Bare nakedfly), also behave as dominant enhancers of a gene called Hairless. Genetic map positions have been determined for these three mutations. The E(top) 2-21 mutation was localized to a position of 15.9 map units, the E(top) Dl05 locus was assigned to a position of 87.1 map units, and the Bare nakedfly mutation was mapped to a position of 64.2 map units.
The Influence of Romantic Relationships on Substance Use in Emerging Adulthood

The current work built on prior research showing aspects of romantic relationships, including relationship quality and partner substance use, influence individual risk for substance use during emerging adulthood. Analyses were based on a sample of males from the Pathways to Desistance Project (PDP) data. Romantic relationships were quantified with an aggregate measure of relationship quality and specific measures of relationship satisfaction, monitoring, and partner antisocial behavior. With a focus on emerging adulthood, the current work was centered on Waves 8 and 9 of the PDP data. Regression models tested the association between the relationship measures and alcohol intoxication, marijuana use, and hard drug use in the past year. Models considered both contemporaneous and longitudinal effects. Across the aspects of romantic relationships, monitoring and partner antisocial behavior had the most consistent association with substance use. The association between monitoring and substance use was strongest when longitudinal effects were tested among those in a relationship at both Waves 8 and 9. Peer antisocial behavior and prior substance use were also associated with substance use. Results show that romantic relationships have an important influence on substance use within a criminal justice involved sample.
Molecular characterization of the eye-specific Om(2D) mutation in Drosophila ananassae

2 IN"TRODUCTION . 4 Chapter I. Molecular cloning and characterization of the Drosophila ornithine aminotransferase gene . 14 IN"TRODUCTION . 15 MATERIALS AND METHODS . 18 RESULTS . 25 DISCUSSION . 41 Chapter II. Retrotransposon-induced ectopic expression of the Om (2D) gene causes the eye-specific Om (2D) phenotype in Drosophila ananassae . 44 IN"TRODUCTION . 45 MATERIALS AND METHODS . 47 RESULTS . 53 DISCUSSION . 70 Chapter ID. Characterization of the Om (2D) gene of Drosophila ananassae . 74 IN"TRODUCTION . '. 75 MATERIALS AND METHODS . 77 RESULTS . 79 DISCUSSION . 88 GENERAL DISCUSSION . 90 REFERENCES . 96
Factors associated with patient satisfaction in a private health care setting in India: A cross-sectional analysis

The present study was conducted to assess patient satisfaction and factors associated with it in a tertiary care hospital in India; and to evaluate the delay in discharge process and its association with satisfaction. It is a cross-sectional analysis of secondary data abstracted from patient satisfaction forms of 1,054 individuals. We analysed factors associated with rating of hospital services and overall hospital experience. We also evaluated the delay in discharge process and its association with overall satisfaction of these patients. We used regression models to assess factor associated with satisfaction scores and “good hospital experience”. About 91% of individuals reported that their experience in the hospital was good. The mean satisfaction scores were significantly lower in patients with delays in discharge due to insurance problems (-0.14, 95% CI: -0.27, -0.02). An increase in one unit in doctor’s score was significantly associated with “good rating” of hospital services (OR: 1.37, 95% CI: 1.19, 1.58). Similarly, one unit increase in the housekeeping score (OR: 1.34, 95% CI: 1.18, 1.52) and billing score (OR: 1.83, 95% CI: 1.56, 2.16) were significantly associated with an overall “good” rating. Thus, problems faced by patients and relatives during completion of billing procedures are important factors that determine overall satisfaction with health care settings. Improving the interpersonal and communication skills of doctors will be an important intervention for better hospital experience.