Miracle-dz/UniFAR-FTUs huggingface dataset:
The Evolutionary Ebb and Flow of Genomic Nucleotide Content

Nucleotide content is one of the most obvious and most easily quantifiable features of a genome. Consequently, all reports of new genome sequences include a report on the nucleotide content, i.e., the frequencies of each of the four nucleotide bases in the genome sequence. Despite the ease with which nucleotide content can be measured, however, it has proved to be much more complicated to explain the evolution of the genomic nucleotide content. A number of different explanations have been proposed. These include the effects of biased mutational patterns (i.e. neutralist models) such as biased DNA repair during recombination, as well as the effect of natural selection on shaping the genomic nucleotide content (i.e. selectionist models). A well known example for the latter group of theories is the effect of temperature in selecting for higher GC content to enhance the thermostability of the DNA. However, many of these theories do not address the problem of variations in nucleotide content between different regions of a single genome, i.e., intragenomic compositional heterogeneity. In this study, I investigate the evolutionary behaviour of the genomic nucleotide content in a group of model organisms and show that the current state of the nucleotide content of a genome by itself cannot always explain the entire evolutionary history of that genome and, in fact, the sequence of events happening to a genome regarding its nucleotide content can be much more complicated than how it looks. For example I show that having an unbiased content doesn’t necessary mean a stationary nucleotide substitution model in an organism. In this study I show that the bias in nucleotide content of a genome can change its direction several times and this going back and forth can actually happen very fast; fast enough to trace the results of this ebb and flow within the same genus. I present an example of this evolutionary ebb and flow of genomic nucleotide content within genus Plasmodium. I also discuss that these exceptional behaviours of the nucleotide contents of the genomes can, indeed, affect other features of living organisms such as the substitution rates between different nucleotides as well as their protein content, and consequently they can interfere with phylogenetic studies. In order to explain the heterogeneities within a single genome, I investigate the relationship between gene length and the degree of nucleotide bias, and find that these two parameters show a significant negative correlation. This lead me to propose a mechanism that can explain heterogeneity in the nucleotide content of the genome, without having to invoke variations in mutational patterns between different parts of the same genome. My proposed model resembles Charlesworth’s “Background Selection” model. My findings shed light on the importance of the evolutionary behaviour of the genomic nucleotide content to be considered in studying different features of an organism as well as studying the evolutionary relationship between the organism of our interest and other related species.
Factors affecting patient’s satisfaction in outpatient clinics in Jordan: cross-sectional study

Background: Every healthcare institution aims to reach the highest quality of care. Quality of care comprises the structure, the process, and the outcome of the care. In this study, we will assess the structure and the process of healthcare system that can affect patient’s general satisfaction. Methods: In this cross-sectional study, we surveyed patients visiting outpatient’s clinics at Jordan University Hospital (JUH). We focused on aspects that are, according to previous studies, significantly affecting patient’s satisfaction, these include interaction with all healthcare providing personnel, time needed to complete different services, general cleanliness, and food services. Results: A total of 215 participants were included in this study, there were 77 (36%) men and 138 (64%) women. the mean score differences between those who rated their impression as “poor” and those who rated it as “excellent” were as following: interaction score, mean difference of 13.3 [95% confidence interval (CI): 6.4 to 20.19; P Conclusions: Focusing on all aspects affecting patient’s satisfaction can both improve the general impression about the facility and increase patient’s loyalty to it.
Effect of planting date, irrigation and weed-control method on yield and water-use efficiency of cumin (Cuminum cyminum)

A study was conducted during the winter season of 1996-97 and 1997-98 at the Agricultural Research Station, Mandor, Rajasthan to determine the effect of planting date, irrigation and weed-control measure on yield and water-use efficiency in cumin (Cuminum cyminum L.). Cumin planted on 15 November gave significantly higher seed yield (834 kg/ ha) than 30 November planting. Irrigation schedule of 4 irrigations resulted in significantly higher seed yield (889 kg/ha) of cumin over 3 irrigations under 15 November planting. However, under late-sown condition of 30 November, 3 irrigations gave seed yield statistically at par (748 kg/ha) with the schedule of 4 irrigations in cumin. Fluchloralin at 1.0 kg/ha as preplant incorporation resulted significantly higher seed yield (814 kg/ha) of cumin over weedy check and hand-weeding. However, the maximum seed yield (865 kg/ha) of cumin was obtained under weed-free treatment. Maximum water-use efficiency (5.83 kg/ha-mm) was recorded in 15 November planting and weed-free treatments (7.86 kg/ha-mm), followed by fluchloralin at 1.0 kg/ha. Marginally higher water-use efficiency was obtained under 3 irrigations over schedule of 4 irrigations during both years.
Effect of Intraventricular Hemorrhage on the Surgical Outcome of Ruptured Anterior Communicating Artery Aneurysm

Background: Several clinical conditions and factors have been proposed as the outcome predictors in patients with subarachnoid hemorrhage(SAH)followingrupturedintracranialaneurysms. Theimpactof theintraventricularhemorrhage(IVH),whichiscom-monly observed in the anterior communicating artery (ACoA) aneurysm, has not been discussed in detail. Objectives: The purpose of the study was to compare the outcome of early and delayed aneurysm surgery in patients with SAH regarding the presence of IVH. Methods: The study included consecutive ACoA aneurysm patients presenting with subarachnoid hemorrhage, who received microsurgical aneurysm clipping. The medical records of the patients were reviewed retrospectively. As the outcome, the Glasgow outcome score was compared between the two groups of the patients, regarding the presence or absence of the IVH. Results: 101patients(55males,46females)wereenrolledinthestudy. TheinitialCTscanrevealedthepresenceof IVHin49patients (mean age 52 ± 11.1 years). 52 patients (mean age 49 ± 10.7 years) had no sign of IVH. Regarding the time of surgery, 25, 44, and 32 patients underwent early (0 - 3 days), intermediate (4 - 14 days), and delayed (> 14 days) surgery from the ictus of SAH, respectively. Thefollow-upperiodwas27months(range0.5-76months). Thesurvivalratewas73.5% inthepresenceof IVHand94.2% inpatients without signs of IVH, which represented a signiﬁcant diﬀerence in the outcome between the two groups (P < 0.05). Conclusions: InpatientswithSAHhavinganeurysmslocatedintheACoAassociatedwiththethirdventricularhemorrhage,delayed surgery might be considered in achieving a better outcome.
Ankylosing Spondylitis Is Associated With Risk of New-Onset Obstructive Sleep Apnea: A Nationwide Population-Based Cohort Study

Objectives: Investigating the risk of obstructive sleep apnea(OSA) among ankylosing spondylitis (AS) patients based on administrative healthcare databases. Methods: We conducted a nationwide cohort study by using the Taiwan National Health Insurance Research Database with 1997-2013 claim records. The AS cohort included 2,210 patients who were newly diagnosed between 2003 and 2013. Randomly selected non-AS controls were matched at a 1:4 ratio. The endpoint was set as OSA occurrence or the end of 2013. Cumulative incidences, hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated after adjusting for age, gender, comorbidities, and co-medication. Multivariate analyses were performed using the Cox proportional hazards model. Due to the violation of the proportionality assumption, landmark analysis was conducted to explore the risk of OSA during specific follow-up periods. Results: The adjusted HR (aHR) of OSA in the AS group was 2.826 (95% C.I. = 1.727-4.625) compared to the control group. On landmark analysis, aHR was 7.919 (95% C.I. = 3.169-19.792) for the AS group 0-24 months from the index date and decreased to 1.816 (95% C.I. = 0.944-3.494) at ≥ 24 months from the index date. The increased risks of OSA in the AS group compared to the control group were found for both males and females (aHRs were 4.533 and 2.672). On age-stratified analysis, a significant risk only for the 40-59 age group with aHR of 3.913 (95% C.I. = 1.890-8.102). Conclusions: A higher risk of developing OSA was found among newly diagnosed AS cohort during the maximum 11-year follow-up period, especially within 2 years after newly diagnosed AS and in the 40-59 age group.
Mécanismes moléculaires de la graviperception chez le peuplier (Populus tremula x Populus alba)

Le redressement du peuplier suite a une stimulation gravitationnelle implique un processus de courbure locale lie a une elongation differentielle dans les zones en croissance primaire et un processus de courbure lie a la differenciation du bois de reaction dans les zones en croissance secondaire. Ces modifications morphogenetiques sont detectees au niveau de la region basale et apicale de la tige de peuplier inclinee. La region basale a developpe le bois de tension une semaine apres l'inclinaison, alors que la region apicale est reorientee 24 h apres l'inclinaison. Ceci implique que les tissus de la region basale et apicale de la tige repondent de facon differente a l'inclinaison. Une etude d'expression menee au niveau du transcriptome a ete realisee a partir des ARNm extraits de tiges ayant ete ou non inclinees pendant 45 min. En 45 min., la plante ne s'est pas redressee, mais a percu le signal. Cette approche a permis d'identifier des transcrits de genes impliques dans la graviperception. L'etude de la regulation du transcriptome a ete elargie par une analyse de la variation de l'accumulation des proteines extraites de tiges inclinees ou non. Les profils d'electrophorese bidimensionnelle des conditions non stressees et stressees de la region basale et apicale ont montre une variation dans l'accumulation des proteines. Une analyse par RT-PCR quantitative de certaines proteines differentielles dont l'activite est potentiellement regulee par la thioredoxine (Trx) montre une accumulation de transcrits variable entre la region apicale et basale et des changements d'expression rapides et transitoires. Une etude complementaire sur 2 thioredoxines (Trx) (western blot, immunolocalisation in situ) a permis de montrer d'une part l'expression de Trx h1 une semaine apres l'inclinaison et d'autre part la localisation de Trx h1 et Trx h2 au niveau des amyloplastes. L'ensemble de ces resultats a conduit a suggerer que les evenements moleculaires conduisant a la reorientation de la tige sont differents selon le tissu analyse. Probablement, chaque partie de la tige recoit et repond differemment au signal gravite.
Phenolic compounds of herbal infusions obtained from some species of the Lamiaceae family

Abstract The present investigation was to estimate the total phenolic content and composition of flavonoids and hydroxycinnamic acids in herbal infusions obtained from aerial parts of three Lamiaceae species (Dracocephalum moldavica, Ocimum americanum and Satureja hortensis). The total phenolic content of herbal infusions was determined using a spectrophotometric method, whereas the individual phenolics were assessed by high-performance liquid chromatography (HPLC). The HPLC method was developed and validated. The total phenolic content was measured by applying the Folin-Ciocalteu method with reference to gallic acid. Results were in the range from 29.39 to 65.38 mg estimated as gallic acid equivalents per gram of dry herb. The phenolic profile was, in turn, analysed by HPLC and consisted of gallic acid, hydroxycinnamic acids (caffeic, chlorogenic, ferulic, and rosmarinic) and flavonoids (rutin, hyperoside, quercitrin, quercetin, apigenin, apigenin-7-glucoside and catechin) in different concentrations. Rosmarinic acid was the predominant component among the hydroxycinnamic acids in herbal infusions of all three plants. This was found to be in the range of 3.64 to 5.28 mg per gram of dry herb. Apigenin-7-glucoside, quercitrin and hyperoside were the prevailing flavonoid components of the infusions.
Climatic influence on radial growth of Pinus wallichiana in Ziro Valley, Northeast Himalaya

Summary of principal component analysis for the common period 1859–2000 of five tree-ring site chronologies of P. wallichiana from Ziro Valley Principal component Site PC1 PC2 HAR 0.752* 0.178 HON 0.737* –0.168 MIC 0.695* 0.304 RAG –0.079 0.860* DOB 0.250 0.633* *Rotated principal component with the highest loading for each chro-nology. Figure 3. Dendrogram of P. wallichiana chronologies from hierar-chical cluster analysis. To evaluate the tree growth–climate relationship for a region, meteorological data (temperature and precipita-tion) from stations close to the sampling site are generally preferred, which could provide better understanding of climatic response to tree growth. These meteorological records are selected on the basis of their length, homoge-neity and completeness of data. In the Northeast Himala-yan region, stations having long climate records are not only limited in number, but most of them have high per-centage of missing values thereby restricting their utility in qualitative dendroclimatic analyses. The meteorological station, Ziro (93°42′E, 27°38′N, 1476 m asl), nearest to the sampling sites, has temperature and precipitation data extending from
Potentially Harmful Excipients in Neonatal Medications: An Observational and Cross-Regional Comparison of Japan and Europe

Objectives: We aimed to examine the administration of eight potentially harmful excipients of interest (EOI), including paraben, polysorbate 80, propylene glycol, benzoate, saccharin sodium, sorbitol, ethanol, and benzalkonium chloride, to hospitalized neonates in Japan and to compare the frequency of exposure to these excipients with previously reported European data. Methods: Data on all medicines administered to neonates during hospitalization between May 2014 and March 2018 along with patients’ demographic data were extracted from the patients’ medical records. Excipients were identified from the Summaries of Product Characteristics. Results: For parenteral medications, the records showed 178,858 prescriptions for 292 products administered to 1895 neonates. The EOI were found in 31,978 (17.9%) prescriptions for a relatively small number of products (n=29; 9.9%) and were administered to 1,454 (76.7%) neonates. In the parenteral prescriptions, benzyl alcohol, found in 20 (69.0%) products administered to 884 (46.6%) neonates, was the most common EOI. In enteral prescriptions, saccharin, found in nine (36.0%) products administered to 137 (13.7%) neonates, was the most common EOI. EOI administration was most frequent for the extremely preterm group of neonates. There was no difference in the number of EOI-containing prescription medications between Japan and Europe. However, a pan-European study reported a larger number of EOI-containing prescriptions and EOI-exposed neonates (OR: 2.5, 95%CI: 2.3 to 2.8, OR: 2.1, 95% CI: 1.8 to 2.5, respectively). Conclusions: Neonates admitted to our center received several potentially harmful pharmaceutical excipients as in the previously studied European centers, but the frequency of exposure was lower at our center. Administration of pharmaceutical products in powder form may have contributed to lowering EOI exposure at our center.
Reduction of total lymphocyte migration to the uterus during the first days of pregnancy and pseudopregnancy of the rabbit (Oryctolagus cuniculus)

THE INITIATION OF PREGNANCY IS A TRANSITIONAL PERIOD DURING WHICH VERY IMPORTANT CHANGES IN SEXUAL HORMONE LEVELS ARE REGISTERED. THESE CHANGES CAUSE MULTIPLE MORPHOLOGIC CHANGES IN THE ENDOMETRIUM THAT ARE QUITE NECESSARY FOR IMPLANTATION TO OCCUR. THE OBJECTIVE OF THE PRESENT STUDY WAS TO EVALUATE THE MIGRATION ACTIVITY OF TOTAL LYMPHOCYTES IN THE ENDOMETRIUM OF NEW ZEALAND BREED, FOUR MONTHS OLD, WHITE FEMALE RABBITS MAINTAINED IN INDIVIDUAL CAGES IN LABORATORY ANIMAL CONDITIONS WITH CYCLES OF 12 HOURS LIGHT AND 12 HOURS DARKNESS, WITH FEED AND WATER AD LIBITUM . WITH THESE ANIMALS THREE DIFFERENT GROUPS WERE FORMED: A) PREGNANT ANIMALS ON DAY 1, 2, 3, 4, 5 AND 8; B) ANIMALS IN A PSEUDO-PREGNANT STATE ON DAYS 1, 2, 3, 4, 5 AND 8 FOLLOWING THE ADMINISTRATION OF 100 IU OF HUMAN CHORIONIC GONADOTROPIN (HCG); AND C) NON PREGNANT ANIMALS (NP). THE RABBITS WERE SLAUGHTERED AT DIFFERENT TIMES ACCORDING TO THE EXPERIMENTAL PROTOCOL THROUGH A LETHAL SODIUM PENTOBARBITAL INTRACARDIAC INJECTION ONCE THE RABBIT WERE ANESTHETIZED. AFTER THE SLAUGHTER, FRAGMENTS OF BOTH UTERINE HORNS WERE EXCISED, AND FRAGMENTS OF UTERINE TISSUE WERE OBTAINED, FIXED AND PROCESSED BY PARAFFIN INCLUSION TO PERFORM HISTOLOGICAL CUTS THAT WERE STAINED WITH HEMATOXYLIN-EOSIN (H & E) AND GIEMSA. TOTAL LYMPHOCYTES PRESENT IN THE LUMINAL EPITHELIAL LAYER AND LAMINA PROPIA OF THE STROMA OF THE ENDOMETRIUM WERE COUNTED. THE NUMBER OF TOTAL LYMPHOCYTES PRESENT IN THE RABBIT ENDOMETRIUM DURING DAYS 1 TO 5 AND 8 OF GESTATION AND PSEUDO-GESTATION DECREASED (P
Molecular systematics of the armored neotropical catfish subfamily Neoplecostominae (Siluriformes: Loricariidae)

Morphological and molecular studies in the family Loricariidae have revealed that the relationships among its membersare not yet well resolved, and the present study was conducted with the main objective of improving our knowledge aboutthis highly diversified group of catfishes. Maximum parsimony and Bayesian analysis were conducted on a matrix of 53terminal taxa and 4676 characters with partial sequences of the genes COI, CytB, 16S rRNA, 12S rRNA and F-reticulon4. As outgroups, samples of the species Hemipsilichthys gobio and H. papillatus (subfamily Delturinae), Rineloricaria jaraguensis (subfamily Loricariinae), Hypostomus nigromaculatus (subfamily Hypostominae), Hypoptopoma inexpectatum (subfamily Hypoptopomatinae), and Corumbataia cuestae (subfamily Otothyrinae) were used. The resultsshowed that the subfamily Neoplecostominae is monophyletic, including Pseudotocinclus, and three clades wererecognized. The first one is composed of Pareiorhina rudolphi, P. cf. rudolphi and Pseudotocinclus. The second iscomposed of Isbrueckerichthys, Pareiorhaphis, Kronichthys and Neoplecostomus ribeirensis. The third is composed ofthe remaining species of the genera Neoplecostomus, except N. ribeirensis, Pareiorhina carrancas, P. cf. carrancas, Pareiorhina sp. 1 (possible new species) and an undescribed taxon referred to in this paper as new genus and species 2. In our analyses, Pareiorhina and Neoplecostomus are paraphyletic taxa.
Pathogenicity studies with Colletotrichum from different hosts on Sorghum and Sugar Cane.

At the United States Department of Agriculture Sugar Plant Investigations, Meridian, Mississippi, the author studied the pathogenicity to sugar-cane and sorghum of 593 isolates of Colletotrichum from 18 grass species, of which 563 were collected on sugar-cane, sorghum, Johnson grass [Sorghum halepense]. Sudan grass, broomcorn [S. bicolor var. technicus]. and Erianthus. Pathogenicity was judged by the capacity of the isolates to induce red rot in cut sugar-cane and sorghum stalks and leaf spot in sorghum following leaf whorl inoculations. The two methods, yielded comparable results. Three species of Colletotrichum have been described as occurring on different grasses, namely, C. falcatum [Physalospora tucumanensis [Glomerella tucumanensis]]. the agent of red rot of sugar-cane, C. lineola, and C. cereale, of which the two last-named were referred by G. W. Wilson (Phytopathology, 4, pp. 106-112, 1914) to a single species, C. graminicola. In these experiments the isolates fell into three groups on the basis of pathogenicity to sorghum and sugar-cane. Cultures isolated from sugar-cane formed a group which caused severe damage to the same host but rarely attacked sorghum, while those originating on sorghum, S. halepense, Sudan grass, S. bicolor var. technicus, and Erianthus were non-pathogenic to sugar-cane but mostly highly pathogenic to sorghum. Neither sorghum nor sugar-cane sustained any material damage from a third group of 28 isolates from 13 other grasses.
Detección de Mycobacterium avium subespecie paratuberculosis, por medio de PCR-anidada a partir de muestras de heces de ovinos: Detection of Mycobacterium avium subespecies paratuberculosis byb nested-PCR of ovine fecal samples

LA PARATUBERCULOSIS ES UNA ENTERITIS GRANULOMATOSA DE CURSO CRONICO OCASIONADA POR MYCOBACTERIUM AVIUM SUBESPECIE PARATUBERCULOSIS (MAP), AFECTA A RUMIANTES DOMESTICOS Y SILVESTRES. MAP ES EXCRETADA EN LAS HECES DE ANIMALES QUE DESARROLLAN LA ENFERMEDAD, Y LA TRANSMISION DE LA INFECCION SE DA MEDIANTE LA INGESTION DE ALIMENTOS Y AGUA CONTAMINADOS POR HECES DE ANIMALES INFECTADOS. CON EL OBJETIVO DE ESTABLECER EL DIAGNOSTICO DE PARATUBERCULOSIS EN OVINOS POR MEDIO DE LA PCR-ANIDADA A PARTIR DE MUESTRAS DE HECES, SE TRABAJARON 204 MUESTRAS DE HECES Y SUEROS DE OVINOS; LAS HECES SE EVALUARON POR PCR-ANIDADA Y CULTIVO BACTERIOLOGICO, LAS MUESTRAS DE SUEROS FUERON ANALIZADAS POR MEDIO DE INMUNODIFUSION EN AGAR GEL (LDGA). CON LA PCR-ANIDADA SE OBTUVO UN PRODUCTO DE AMPLIFICACION 210 PB QUE CORRESPONDE A LA IS900 DE MAP, EN 61 DE LAS 204 MUESTRAS. DE ESTAS, 43 ERAN DE ANIMALES POSITIVOS A IDGA Y 18 NEGATIVOS. MEDIANTE CULTIVO BACTERIOLOGICO SE AISLARON 17 CEPAS DE MAP; EN ESTE CONTEXTO, LA IDGA DETECTO A 91 ANIMALES COMO POSITIVOS. LA PCR-ANIDADA PERMITIO DETECTAR EN MENOR TIEMPO A MAYOR CANTIDAD DE ANIMALES QUE ESTABAN ELIMINANDO AL BACILO, AUN CUANDO HABIAN RESULTADO NEGATIVOS A LA PRUEBA SEROLOGICA; ESTE RESULTADO SE CONSIDERA IMPORTANTE, YA QUE GENERALMENTE ESTOS ANIMALES, AL PERMANECER DENTRO DE LA GRANJA, CONSTITUYEN LA PRINCIPAL FUENTE DE INFECCION PARA EL REBANO. SE DEBE CONSIDERAR A LA PCR-ANIDADA COMO ALTERNATIVA, CUANDO SE REQUIERA EL DIAGNOSTICO EN BREVE TIEMPO, PARA CONOCER EL ESTADO SANITARIO DEL REBANO CON RESPECTO A PARATUBERCULOSIS.
The roles of the preproghrelin-derived peptides - ghrelin, desacyl ghrelin and obestatin - in prostate cancer

iii TABLE OF CONTENTS viii LIST OF FIGURES xii LIST OF TABLES xv LIST OF ABBREVIATIONS xvi LIST OF PUBLICATIONS AND PRESENTATIONS xx STATEMENT OF ORIGINAL AUTHORSHIP xxii ACKNOWLEDGEMENTS xxiii Chapter 1: Introduction and Literature Review 1