Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytotoxicity of 1-deoxysphingolipid unraveled by genome-wide genetic screens and lipidomics in Saccharomyces cerevisiae

Hereditary Sensory and Autonomic Neuropathy (HSAN) type IA and IC are caused by elevated levels of an atypical class of lipid named 1-deoxysphingolipid (DoxSL). How elevated levels of DoxSL perturb the physiology of the cell and how the perturbations lead to HSAN IA/C are largely unknown. In this study, we show that C26-1-deoxydihydroceramide (C26-DoxDHCer) is highly toxic to the cell, while C16- and C18-DoxDHCer are less toxic. Genome-wide genetic screens and lipidomics revealed the dynamics of DoxSL accumulation and DoxSL species responsible for the toxicity over the course of DoxSL accumulation. Furthermore, we show that disruption of F-actin organization, alteration of mitochondrial shape, and accumulation of hydrophobic bodies by DoxSL are not sufficient to cause complete cellular failure. However, combined with collapsed ER membrane, these perturbations cause cell death. Thus, we have unraveled key principles of DoxSL cytotoxicity that help to explain the clinical features of HSAN IA/C.
The evolution of the bacterial chemotaxis network

Advances in biomolecular technology allow us to sequence entire genomes, but how genes and molecular networks influence the emergence and evolution of phenotypic traits is still unclear. Different fields in biology and medicine are working hard to unravel the relationship between the genome and phenotypes. In this thesis, a new (mechanistic) approach combining systems biology and evolutionary biology is explored to tackle the genotype-phenotype problem. The chemotaxis network of Escherichia coli is used as a model system for its relatively simple network configuration associated with a complex trait such as chemotactic performance. A mathematical model was developed and in silico evolutionary experiments were performed with different environmental conditions. The results show that due to the complexity of the genomic architecture, most individual gene loci have an inconsistent relationship with fitness. In other words, direct relationships between genes and phenotypes are far more complex than just a linear correlation. The reconstruction of the fitness landscape shows that its structure is highly heterogeneous and there are cases in which mutations have unpredictable and inconsistent effects. Another result shows that contrary to static environments, fluctuating environments facilitate the exploration of the fitness landscape. The results in this thesis show the potential of the evolutionary-systems-biology approach, which could help to understand how complex diseases (e.g. cancer or diabetes) develop or how bacteria evolve to become drug resistant.
Does indication matter in the functional outcome of reverse shoulder arthroplasty? - A comparative retrospective study

Reverse Shoulder Arthroplasty is done for Cuff Tear Arthropathy (CTA) and other indications. We hypothesize that CTA patients and patients with other indications will have differing functional outcome following RSA. We retrospectively studied 23 patients treated in our center between 2014 and 2017. The patients who were aged 60 and above with normal Deltoid function, normal cognition and a minimum follow-up of 12 months were included. Of the 23 patients, 16 had CTA and 7 had either a complex fracture dislocation, arthritis with malunion, excision arthroplasty or a chronic dislocation. We compared the functional outcome using Constant Shoulder Score at a mean follow up of 24.6 months. The post-operative scores were significantly higher in the CTA group, but the magnitude of functional improvement from preoperative status following RSA was either comparable (absolute change) or even better (percentage change) in non-CTA patients compared to CTA patients. There were no significant differences in the complication rates between the two groups. We conclude that one should not be discouraged by the lower values of functional scores in RSA done for non-CTA indications and be aware that the functional improvement following RSA in such complex cases is encouragingly better than that following RSA in CTA.
Techniques for hardware-accelerated parsing for network and bioinformatic applications

Since the development of the first parsers, parsing has generally been considered a software problem. Software parsers have been developed for many different uses including compiling software, rendering web pages, and even translating languages. However, as new technologies and discoveries emerge, traditional software techniques for parsing data are either not fast enough to keep up with data rates, or simply take too long to produce results in a reasonable period of time. This dissertation discusses techniques and architectures for accelerating parsing in two different domains. One requires parsing of high-speed streaming data. The other requires parsing of very large data sets with a computationally complex parsing algorithm. The first part of this dissertation focuses on architectures for accelerated parsing of network data. As network rates continue to increase and the volume of data transferred across networks escalates, it will become progressively more difficult for software packet examination techniques to maintain the required throughput. Couple this with the development of new networking technologies, such as content-based routing and publish/subscribe networks, and it is clear that high-speed architectures for parsing packet payloads are required. New architectures for both pattern-matching and parsing are presented and compared to existing architectures. Additionally, two example applications are presented. The first is a simple content-based router. The second is an email parser capable of delineating and extracting user-specified portions of email messages. The second part of this dissertation examines another parsing problem where high throughput is desired, but for which many parses are possible for each input, and all such parses must be considered. The difficulty of the problem is amplified by the large volumes of data that must be parsed. More specifically, this work investigates techniques and architectures suitable for accelerating the complex parsing algorithm used for discovering new RNA molecules in genome databases. Two different hardware architectures are presented and evaluated against a well-known software suite.
Female preference for artificial courtship songs in 'Drosophila melanogaster' and 'D. simulans'

Fertilisation between species may be prevented by differences in their mating systems, if a mating signal of one species is not recognised as such by another species. Closely related species are often most differentiated in their mating systems. Speciation may come about as a consequence of divergence of mating signals and preferences of species. Reinforcement of differences in mating systems may be a consequence of sympatry of sibling species. Understanding mating systems, particularly in terms of how they contribute to reproductive isolation, is therefore central to the study of speciation and animal diversity. Visual, chemical and auditory stimuli are required for mate-recognition in the Drosophila melanogaster complex. Among these stimuli is a species-specific male auditory signal, pulse song. Female preference for conspecific mean interpulse-interval (IPI) and IPI rhythm may contribute towards reproductive isolation of species, and divergence in this aspect of the mating system may be an important cause or effect of speciation of fruit flies. The two chapters of this thesis examine different aspects of female preference for pulse song. The first chapter considers the contribution made by female preference for conspecific pulse song towards the sexual isolation of the sibling species Drosophila melanogaster and D. simulans. Synthetic pulse songs are shown to be most effective in stimulating females when they are of conspecific mean IPI and IPI cycle length. Preferences for conspecific signals are found to be broad. In the second chapter, it is asked which element of IPI periodicity accounts for its property as a sexual stimulant in D. melanogaster. The most likely explanation, increased variation in IPI, is eliminated: female receptivity is not increased by playback of a novel synthetic song which varies to the same degree as rhythmic song but does not oscillate. In an appendix, some differences between D. sechellia and D. simulans in microsatellite loci are reported. General Introduction. 1 Chapter One: The role of female preference for pulse song in the reproductive isolation of Drosophila melanogaster and D. simulans 1.
A gall-forming insect manipulates hostplant phytohormone synthesis, concentrations, and signaling

Insect galls are highly specialized plant organs formed by an intimate biochemical interaction between the plant and a gall-inducing insect. Galls provide the insect enhanced nutrition and protection against natural enemies and environmental stresses. Because galls are plant organs, their development is likely to be governed by native phytohormones that function in organogenesis. We characterized concentrations of both growth and stress phytohormones in ungalled leaves and the leaf galls of Daktulosphaira vitifoliae on wild grape Vitis riparia at 4 different developmental stages. We found clear evidence of hormone manipulation by phylloxera during gall initiation and development. Phylloxera suppressed accumulation of of gibberellins, auxin, and jasmonates during the first two gall stages while absiscic acid concentrations were suppressed throughout development. Concentrations of 3 cytokinins and salicylate were greatly elevated during the earliest gall stage and declined sharply thereafter. We found no evidence of expression of cytokinin biosynthesis genes during the first gall stage, which strongly suggests that phylloxera supplied those phytohormones. High salicylate concentrations could have been caused by cytokinins, a response to microbes, or both. Our results suggest a central role for cytokinins in gall initiation and indicate the importance of the insect’s ability to manipulate other hormones.
The use of methoxyflurane (Penthrox®) for procedural analgesia in the emergency department and pre-hospital environment

Background Methoxyflurane is an inhaled analgesic agent licensed in the United Kingdom for the relief of moderate to severe pain in conscious patients with trauma. Methoxyflurane has been widely used by Australian ambulance services since the 1970s. Aims Primary aim: To assess the efficacy of methoxyflurane for procedural analgesia in the emergency department and pre-hospital environment. Secondary aims: to assess the efficacy of methoxyflurane for analgesia in the emergency department and pre-hospital environment; to assess the safety of methoxyflurane as an analgesic. Method A literature search of Medline, EMBASE, CINAHL and Cochrane databases was performed. A total of 59 articles were reviewed. Results One study using methoxyflurane for procedural analgesia in the emergency department was found. Multiple studies demonstrate the use of methoxyflurane for procedural analgesia for painful procedures outside the emergency department. Compared to other analgesics, methoxyflurane provides adequate analgesia. Overall, methoxyflurane is inferior to fentanyl or morphine, but it provides quicker onset analgesia compared to fentanyl and tramadol. It provides similar analgesia to nitrous oxide. Nephrotoxicity is dose dependent. Used in the analgesic doses, the risk of clinically significant kidney injury is negligible. Rare cases of unpredictable, severe hepatitis are reported. Discussion The efficacy of methoxyflurane and its acceptability to patients and clinicians has been shown in a number of studies. As would be expected in any procedural analgesic choice, patient and clinician factors and the procedure planned are all important considerations. Compared to other analgesic agents, methoxyflurane performs favourably with a low chance of adverse events. Conclusion Methoxyflurane is an efficacious analgesic agent in the emergency department and pre-hospital environment. It is easily portable and has a rapid onset. Methoxyflurane is suitable for use in procedural analgesia and as a bridging analgesic agent. Risks to the patient from renal or hepatic injury, cardiorespiratory depression or malignant hyperthermia are low.
Growth and Mortality Rates of Cornu aspersum: Organic Snail Culture System, Black Sea Region

The study was aimed to examine a snail organic culture system and describe the cultivation properties of Cornu aspersum. The environmental parameters of the culture system and their effects on the growth and mortality rates of C. aspersum were determined between November 2014-October 2015. Snails were fed Spinacia sp. (spinach), Urtica sp. (nettles), Brassica oleracea sp (cabbage) and formulated diet. The feeding and growth rates increased with increasing temperature. Shell height growth rate was the highest in spring while the live weight growth rate was the highest in summer. Mortality rate of the baby snail was higher between November 2014 and May 2015 due to stress conditions such as handling and varying temperatures during their first stages of life. High mortality observed in adults could be associated with the spawning activity of the matured snails that caused physiological exhaustion. The result showed that the best culture cycle for C. aspersum was from spring to autumn in Black Sea region and in order to prevent postreproductive mortality, snails reached to marketable size should be harvested.
Automatic Pavement Crack Detection Using Texture and Shape Descriptors

Abstract Pavement distress detection and analysis is the most important part of automated pavement inspection systems. Due to the circumstances such as complex texture, uneven illumination, and nonuniform background, pavement distress detection is not a simply edge detection process. Over the past 30 years, lots of methods were proposed to detect pavement distresses, especially cracks. In this letter, a novel automatic pavement crack detection approach based on texture analysis and shape descriptors is proposed. Pavement surface is seen as a texture surface, and distresses are defined as inhomogeneities occurring in the texture surface. Six texture features and two translation-invariant shape descriptors were used here as discriminate features against irregular texture and uneven illumination. By using a SVM classifier, all sub-images are classified as crack or non-crack. Final results were obtained after post-processing, which includes segmentation, fake-crack eliminating, and crack-measuring methods. Compared with a traditional edge detector such as a Canny operator, experimental results demonstrated that all cracks are correctly detected by the proposed method, even in a strong texture background or in the surface with uneven illumination.
From Simulation to Imitation

Background We contend that a conceptual conflation of simulation and imitation persists at the heart of claims for the power of game-based simulations for learning. Recent changes in controller-technologies and gaming systems, we argue, make this conflation of concepts more readily apparent, and its significant educational implications more evident. Aim This article examines the evolution in controller technologies of imitation that support players’ embodied competence, rather than players’ ability to simulate such competence. Digital gameplay undergoes an epistemological shift when player and game interactions are no longer restricted to simulations of actions on a screen, but instead support embodied imitation as a central element of gameplay. We interrogate the distinctive meanings and affordances of simulation and imitation and offer a critical conceptual strategy for refining, and indeed redefining, what counts as learning in and from digital games. Method We draw upon actor-network theory to identify what is educationally significant about the digitally mediated learning ecologies enabled by imitation-based gaming consoles and controllers. Actor-network theory helps us discern relations between human actors and technical artifacts, illuminating the complex inter-dependencies and inter-actions of the socio-technical support networks too long overlooked in androcentric theories of human action and cognitive psychology. Conclusion By articulating distinctions between simulation and imitation, we show how imitative practices afforded by mimetic game controllers and next-generation motion-capture technologies offer a different picture of learning through playing digital games, and suggest novel and productive avenues for research and educational practice.
TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism

Modern supercomputers have very powerful multi-core CPUs. The programming model on these supercomputer is switching from pure MPI to MPI for inter-node communication, and shared memory and threads for intra-node communication. Consequently the bottleneck in most systems is no longer computation but communication between nodes. In this paper, we present a new compositing algorithm for hybrid MPI parallelism that focuses on communication avoidance and overlapping communication with computation at the expense of evenly balancing the workload. The algorithm has three stages: a direct send stage where nodes are arranged in groups and exchange regions of an image, followed by a tree compositing stage and a gather stage. We compare our algorithm with radix-k and binary-swap from the IceT library in a hybrid OpenMP/MPI setting, show strong scaling results and explain how we generally achieve better performance than these two algorithms.
POPULATION GENETIC STRUCTURE OF SPINY LOBSTERS, Panulirus homarus AND Panulirus ornatus, IN THE INDIAN OCEAN, CORAL TRIANGLE, AND SOUTH CHINA SEA

Populations of spiny lobsters worldwide are threatened by overfishing, while its supply from aquaculture is currently insufficient to meet the market demand. This current study investigated the genetic structure of two economically important spiny lobsters, P. homarus and P. ornatus sourced from the Indian Ocean and South China Sea. Fragments of the cytochrome oxidase subunit-I (COI) gene of the mitochondrial DNA of 71 P. homarus and 42 P. ornatus collected from 6 and 5 fish landing sites in Indonesia, respectively, were sequenced. Homologous sequences from the Indian Ocean and South China Sea available at GenBank were included in the analysis. No genetic differences were observed in P. ornatus populations from the two geographic regions (xST = -0.005) while a diminutive difference was found in the populations of P. homarus (xST = -0.002 and 0.009). These results, combined with a negative Tajima’s D estimates, points to a deficit of nucleotide variation relative to the expectations from the mutation/drift equilibrium. Reconstruction of the phylogeny of P. homarus demonstrates that all Indonesian samples of P. homarus are grouped in one cluster and share the common cluster with GenBank data originated from Taiwan, Vietnam, India, Sri Lanka, Oman, and Iran. The phylogeny of P. ornatus indicates that there are two separated lineages existing in Indonesia.
Present insight on achalasia – from diagnosis to treatment

Introduction. Achalasia is a most frequent primary motility disorder of the oesophagus with the prevalence of 10/100,000 individuals, with no gender predominance. Due to its rare occurrence, at the early stages may be erroneously diagnosed, leading to progression of disease and delayed treatment. Objectives. The main aim of the review is to depict current data about achalasia, including pathogenesis, diagnosis, and possible treatment modalities, particularly the latest, minimally invasive technique: per-oral endoscopic myotomy (POEM). State of knowledge. The ethology of achalasia remains unknown, although autoimmune, viral or neurodegenerative causes may be considered triggers of the disease. In some cases, achalasia may be secondary to other conditions (e.g. malignancy, Chagas disease). Typical symptoms of achalasia are dysphagia (for both liquids and solids), regurgitations, heartburn and weight loss. The diagnosis is based on endoscopy, oesophageal high-resolution manometry (HRM) and X-ray with barium swallow. Therapies used in the treatment of achalasia focus on improving food passage by reducing LES pressure. These procedures include pharmacologic treatment, pneumatic balloon dilation, Heller myotomy and endoscopic myotomy. POEM was first introduced in humans by Inoue in 2008. Recent studies have revealed excellent short-term outcome of POEM with no serious complications. Conclusion. Achalasia is an incurable disease; however, available therapies can effectively reduce patients̀ symptoms. Further evaluation may lead to the establishment of tailored-topatient treatment, and it is believed that POEM will become a gold standard for treatment of achalasia.
Sexual Dysfunction in Males with Alcohol Dependence Syndrome

Introduction: Sexual dysfunction leads to distress and poor interpersonal relationships in alcohol dependent males with an active sexual life. If not addressed, it may precipitate relapse. Aims: Aim of the study is to assess the prevalence and type of sexual dysfunction in alcohol dependent males and its relation to duration and quantity of alcohol consumed. Material and Methods: One hundred male subjects admitted to a de-addiction center, attached to a tertiary care rural teaching hospital meeting the diagnosis of alcohol dependence syndrome [F10.2] were assessed for sexual dysfunction using Arizona Sexual Experience Scale (ASEX), International Index for Erectile Dysfunction questionnaire (IIEF) and Sexual dysfunction checklist (SDCL). Results: Sixty one percent had one or more sexual dysfunctions. The most common being decreased sexual desire, premature ejaculation, frequency dissatisfaction and erectile disorder. The amount of alcohol consumed and the duration of alcohol dependence appeared to be significantly associated with sexual dysfunction. Conclusion: Sexual dysfunction is common in subjects with alcohol dependence syndrome. Long term dependence and heavy drinking had a positive linear relationship with sexual dysfunction. Psychiatrists should routinely evaluate and treat the sexual dysfunction to prevent relapse and improve interpersonal relations. Keywords: Alcohol dependence syndrome, Sexual dysfunction, Male.
Demographic and causal pattern of acute uppergastrointestinal bleeding in Mosul

Objectives: To assess the age and sex distribution of 200 patients presented with acute upper gastrointestinal bleeding (AUGIB) in Al-Salam General Hospital in Mosul, and to identify the causes of bleeding through endoscopic examination. Patients and methods: This is a case series study of 200 patients with (AUGIB) at the endoscopy unit in Al-Salam general hospital in Mosul, during the period from April 1999 to January 2009. The endoscopic findings, causes of bleeding and the patients' age and gender were recorded, analysed and the results were compared with other similar studies. Results: The mean age of the patients was 43.68 ± 19.11 years; those aged 60 years and above constituted 25.5% (51/200). Male:female ratio was ~ 2:1 (135 male, 65 female). Gastroduodenitis with erosions and duodenal ulcer (DU) were the main causes of (AUGIB) constituting 42.5% and 30.5% respectively. Actively bleeding (DU) constituted 36.1% (22/61) while actively bleeding erosions constituted 16.5% (14/85) which is a significant difference (p=0.008). Non-steroidal anti-inflammatory drugs (NSAIDs) were associated with bleeding in 9% of the cases (18/200). Conclusions: In this sample from Mosul city, (AUGIB) afflicted a relatively younger age group compared with western studies, while male: female ratio was nearly similar (2:1). Gastroduodenitis with erosions dominated the causes of bleeding and (DU) came next in frequency, while (DU) is the main cause in most western studies. The results of this study coincide more with the results from some developing countries.