Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival and infectivity of Toxoplasma gondii and Cryptosporidium parvum oocysts bioaccumulated by Dreissena polymorpha

The study was aimed to understand the depuration process of Cryptosporidium parvum and Toxoplasma gondii oocysts by zebra mussel (Dreissena polymorpha), to consider the use of the zebra mussel as a bioremediation tool.
MOLECULAR AND GENOTYPIC STUDY OF SENV-D VIRUS COINFECTION IN Β-THALASSEMIC PATIENTS INFECTED WITH THE HEPATITIS C VIRUS IN IRAQ

Objective and Background: SEN virus has identified as a putative new hepatitis virus coinfected with hepatitis C in thalassemic patients. The study aimed to measure viremia with SEN virus among thalassemic patients infected and non-infected with hepatitis C virus (HCV). Further, to detect the genotype D and the genetic alterations in the internal transcribed spacer domains/regions of SENV-D genotypes. Patients and Methods: A total of 200 β-thalassemic patients were included. HCV-RNA and SEN-DNA are extracting automatically. Then, amplification for SEN-DNA by conventional polymerase chain reaction (PCR) was achieved. Furthermore, HCV-RNA was amplified using real-time PCR (RT-PCR). Sequencing analysis was also done for 14 samples of amplified SENV-D DNA. Results: Out of 100 positive ELISA-anti-HCV antibodies which were definite for RT-PCR, the mean viral load in these patients was 545806 ± 1,009,799 IU/ml (1,997,176 ±3,802,206) copies/ml. There was a significant increase in SENV-D in thalassemia patients without HCV infection (59%) than those in thalassemia patients with HCV infection (44%) and healthy subjects (7%). In a sequencing study, 11 samples were infected with D genotype only while three from thalassemia patients group were coinfected with D and H genotypes. Conclusions: The occurrence rate of SEN-V DNA in thalassemia patients is very high in Iraq. Further, SEN-V-D genotype is more prevalent, and the sequences of SEN-V-D nucleotides in persons with coinfection are the same sequences of persons that have an infection with SEN-V-D alone. The most countries which have similar sequences to Iraqi SENV-D genotype sequence are Iran followed by China, Japan, Brazil, and the United States of America.
An Immersive Multi-User Virtual Reality for Emergency Simulation Training: Usability Study

Background Virtual reality (VR) is increasingly used as simulation technology in emergency medicine education and training, in particular for training nontechnical skills. Experimental studies comparing teaching and learning in VR with traditional training media often demonstrate the equivalence or even superiority regarding particular variables of learning or training effectiveness. Objective In the EPICSAVE (Enhanced Paramedic Vocational Training with Serious Games and Virtual Environments) project, a highly immersive room-scaled multi-user 3-dimensional VR simulation environment was developed. In this feasibility study, we wanted to gain initial insights into the training effectiveness and media use factors influencing learning and training in VR. Methods The virtual emergency scenario was anaphylaxis grade III with shock, swelling of the upper and lower respiratory tract, as well as skin symptoms in a 5-year-old girl (virtual patient) visiting an indoor family amusement park with her grandfather (virtual agent). A cross-sectional, one-group pretest and posttest design was used to evaluate the training effectiveness and quality of the training execution. The sample included 18 active emergency physicians. Results The 18 participants rated the VR simulation training positive in terms of training effectiveness and quality of the training execution. A strong, significant correlation (r=.53, P=.01) between experiencing presence and assessing training effectiveness was observed. Perceived limitations in usability and a relatively high extraneous cognitive load reduced this positive effect. Conclusions The training within the virtual simulation environment was rated as an effective educational approach. Specific media use factors appear to modulate training effectiveness (ie, improvement through “experience of presence” or reduction through perceived limitations in usability). These factors should be specific targets in the further development of this VR simulation training.
PRESERVATION OF RED MEAT WITH NATURAL ANTIMICROBIAL PEPTIDES PRODUCED BY LACTIC ACID BACTERIA

Red meat has a limited shelf-life at refrigerated temperatures, where spoilage is mainly due to the proliferation of bacteria, yeast and moulds, acquired during the dressing process. In addition, almost a fifth of food-borne disease outbreaks, caused by microorganisms such as Escherichia coli 0157:H7, Listeria monocytogenes and Staphylococcus aureus are associated with red meat. To improve the microbiological quality of red meat, systems such as HACCP, GHP and GMP are currently practiced; however, these practices are not able to extend the shelf-life of these products. At present suitable food-grade preservatives are recommended, but the use of some of these preservatives is increasingly being questioned with regard to their impact on human health. Additionally, food service customers demand high quality products that have a relatively long shelf-life, but still prefer the appearance of minimally processed food. All these factors challenge the food manufacturing industry to consider more natural means of preservation. Antimicrobial metabolites of food grade bacteria, especially lactic acid bacteria, are attracting increasing attention as food preservatives. Bacteriocins are antimicrobial peptides (3 to 10 kDa) with variable activity spectra, mode of action, molecular weight, genetic origin and biochemical properties that are bacteriostatic or bactericidal to bacteria closely related and bacteria confined within the same ecological niche. Micro-organisms were isolated from beef, lamb and pork, obtained from four commercial retailers. The number of viable cells three days after the sell-by date at 4oC ranged from 80 cfu.g to 1.4 × 10 cfu.g. Fifty-three percent were Gram-negative bacteria, 35% Gram-positive and 12% yeast. The microbial population of the meat was greatly influenced by the origin, i.e. the retailer. Bacteriocins produced by Enterococcus faecalis BFE 1071, Lactobacillus curvatus DF 38, Lb. plantarum 423, Lb. casei LHS, Lb. salivarius 241 and Pediococcus pentosaceus ATCC 43201 were screened for activity against bacteria isolated from the different meat samples. Sixteen to 21% of the isolates, identified as members of Klebsiella, Shigella, Staphylococcus, Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Pediococcus, Streptococcus and Bacillus were sensitive to the bacteriocins. Curvacin DF 38, plantaricin 423 and caseicin LHS (2.35 to 3.4 kDa) had the broadest activity range and inhibited species of Lactobacillus, Pediococcus, Enterococcus, Listeria, Bacillus, Clostridium and Propionibacterium. The bacteriocins remained stable at 121oC for 20 min, in buffers with a pH ranging from 2 to 10 and in NaCl concentrations of between 0.1 and 10% (m/v). Like most peptides, they were
Pre-analytical and analytical variables that influence urinary volatile organic compound measurements

There has been rapidly accelerating interest in the utilization of volatile organic compounds (VOCs) as non-invasive methods for rapid point-of-care medical diagnostics. There is widespread variation in analytical methods and protocols, with little understanding of the effects of sample storage on VOC profiles. This study aimed to determine the effects on VOC profiles of different storage times, at room temperature, prior to freezing, of sealed urine samples from healthy individuals. Analysis using Field Asymmetric Ion Motility Spectrometry (FAIMS) determined the alterations in VOC and total ion count profiles as a result of increasing room temperature storage times. Results indicated that increasing exposure time to room temperature prior to freezing had a threefold effect. Firstly, increased urinary VOC profile variability, with a plateau phase between 12 and 48 hours, before further degradation. Secondly, an increase in total ion count with time exposed to room temperature. Finally, a deterioration in VOCs with each sample run during the analysis process. This provides new insight into the effect of storage of urine samples for VOC analysis using FAIMS technology. Results of this study provide a recommendation for a 12-hour maximum duration at room temperature prior to storage.
Sampling-based algorithms for motion planning with temporal logic specifications

Autonomous mobile robots are machines capable of performing tasks, operating without human intervention. Their presence has increased in applications such as personal assistance, manufacturing, etc. One of the main challenges of controlling a robot autonomously lies in the area of motion planning. This planning needs to consider elements such as system dynamics, uncertainties, dynamic environments, safety and reliability. These requirements have motivated the development of methods that combine control theory and model checking techniques to automatically compute plans that provably guarantee the execution of a given specification. Although model checking has been successfully used to verify discrete systems, its application in autonomous mobile systems presents certain challenges such as: (i) the problem of computing finite models from high-dimensional systems with infinite number of states; (ii) the computation of controllers for systems with kinematic and dynamic constraints; (iii) the computation of robust and reactive controllers to deal with uncertainties and dynamic environments; and (iv) the state explosion problem due to the total number of possible behaviour or states when multiple robots are considered. The challenges presented above are addressed in this thesis. Specifically, the proposed methods in this work are focused on the motion planning of mobile systems based on linear temporal logic and metric interval temporal logic specifications. They are based on sampling methods which are widely used in the point to point motion planning for high-dimensional systems with dynamic constraints. By using these methods and automata-based theory, the solutions in this thesis mitigate the state explosion problem presented in available methods. The main contributions of the thesis are summarised as follows. Chapter 4 develops a new algorithm to find optimal trajectories for deterministic systems with kinematic and differential constraints subject to co-safe temporal logic specifications. Systems with uncertainty in motion and sensing are considered in Chapters 5 and 6. In these chapters, two novel approaches to maximise the probability of completing temporal logic specifications are proposed. Finally, Chapter 7 presents a solution for multi-robot systems subject to cosafe linear temporal logic specifications. All the proposed algorithms are demonstrated with several numerical examples.
Translocating Adult Pacific Lamprey within the Columbia River Basin: State of the Science

ABSTRACT The Pacific lamprey (Entosphenus tridentatus) is in decline in the Columbia River Basin, and translocating adult lamprey to bypass difficult migration corridors has been implemented since 2000. We describe and report results from two current translocation programs, provide context for use of translocation, and discuss potential benefits, risks, and uncertainties. Both translocation programs appear to have increased the number of spawning adults and the presence of larvae and juveniles; however, any subsequent increase in naturally spawning adults will require at least one, and likely more, generations to be realized. It was seen that the number of adults entering the Umatilla River increased beginning four years after the first translocations. Potential benefits of translocation programs are increased pheromone production by ammocoetes to attract adults, increased lamprey distribution and abundance in target areas, increased marine-derived nutrients, and promotion of tribal culture. Potential ris.
FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps**

Abstract The geometry of reaction compartments can affect the local outcome of interface‐restricted reactions. Giant unilamellar vesicles (GUVs) are commonly used to generate cell‐sized, membrane‐bound reaction compartments, which are, however, always spherical. Herein, we report the development of a microfluidic chip to trap and reversibly deform GUVs into cigar‐like shapes. When trapping and elongating GUVs that contain the primary protein of the bacterial Z ring, FtsZ, we find that membrane‐bound FtsZ filaments align preferentially with the short GUV axis. When GUVs are released from this confinement and membrane tension is relaxed, FtsZ reorganizes reversibly from filaments into dynamic rings that stabilize membrane protrusions; a process that allows reversible GUV deformation. We conclude that microfluidic traps are useful for manipulating both geometry and tension of GUVs, and for investigating how both affect the outcome of spatially‐sensitive reactions inside them, such as that of protein self‐organization.
RCC1L (WBSCR16) isoforms coordinate mitochondrial ribosome assembly through their interaction with GTPases

Mitochondrial translation defects can be due to mutations affecting mitochondrial- or nuclear-encoded components. The number of known nuclear genes involved in mitochondrial translation has significantly increased in the past years. RCC1L (WBSCR16), a putative GDP/GTP exchange factor, has recently been described to interact with the mitochondrial large ribosomal subunit. In humans, three different RCC1L isoforms have been identified that originate from alternative splicing but share the same N-terminus, RCC1LV1, RCC1LV2 and RCC1LV3. All three isoforms were exclusively localized to mitochondria, interacted with its inner membrane and could associate with homopolymeric oligos to different extent. Mitochondrial immunoprecipitation experiments showed that RCC1LV1 and RCC1LV3 associated with the mitochondrial large and small ribosomal subunit, respectively, while no significant association was observed for RCC1LV2. Overexpression and silencing of RCC1LV1 or RCC1LV3 led to mitoribosome biogenesis defects that resulted in decreased translation. Indeed, significant changes in steady-state levels and distribution on isokinetic sucrose gradients were detected not only for mitoribosome proteins but also for GTPases, (GTPBP10, ERAL1 and C4orf14), and pseudouridylation proteins, (TRUB2, RPUSD3 and RPUSD4). All in all, our data suggest that RCC1L is essential for mitochondrial function and that the coordination of at least two isoforms is essential for proper ribosomal assembly.
Population structure of Atlantic cod (Gadus morhua) in the Newfoundland and Labrador area determined from genetic variation

The purpose of this study was to describe population structure and to determine the potential for genetic stock identification of Atlantic cod (Gadus morhua) in Newfoundland and Labrador using microsatellite loci, synaptophysin (SypI) locus, and a major histocompatibility complex (Mhc) locus. Variation at seven microsatellite loci (Gmo3, Gmo8, Gmo19, Gmo34, Gmo35, Gmo36, and Gmo37) and SypI was surveyed in approximately 5,050 cod from 19 putative populations. Variation at a class I Mhc locus was surveyed in 2,000 fish from the 19 populations. Ten populations were sampled over two or more years, and variation among populations was on average about 18 times greater than annual variation within populations. Regional structuring of the populations was apparent with inshore and offshore spawning populations forming distinct groups. The Flemish Cap population was the most distinctive of the offshore group, and the Gilbert’s Bay population in Labrador was the most distinctive of the inshore group. In Divisions 2J3KL, no significant genetic differentiation was observed among inshore cod sampling sites in Notre Dame Bay and Bonavista Bay. Some differentiation was observed between sites in Conception Bay and Trinity Bay, and also with other inshore sites, providing some evidence of distinct “bay” stocks of cod along the northeast coast of Newfoundland. All inshore cod samples were genetically distinct from all offshore samples of northern cod. The offshore samples were more heterogeneous, and there may be at least three distinct offshore spawning populations of northern cod. In Subdiv. 3Ps, genetic differentiation was observed between the inshore Placentia Bay and Fortune Bay samples, and the Placentia Bay sample was distinct from offshore samples of northern cod. Simulated mixed-stock fishery samples of northern cod suggested that variation at the seven microsatellite loci, the synaptophysin locus, and Mhc locus C should provide reasonably accurate estimates of stock composition (inshore vs. offshore) when the inshore component comprises at least 50% of the mixture. In Subdiv. 3Ps, bias of estimated stock compositions was marginal when offshore populations (Burgeo Bank, Halibut Channel) comprised the majority of the sample. However, bias in the estimated stock compositions increased when inshore populations comprised the majority of the sample. Increased baseline population sample sizes or additional discriminating markers are likely required to decrease the degree of bias in the estimated stock composition in this application.
The Rich Transcription 2004 NISTSPring Meeting Recognition Evaluation

This paper presents the design and results of the Rich Transcription Spring 2005 (RT-05S) Meeting Recognition Evaluation. This evaluation is the third in a series of community-wide evaluations of language technologies in the meeting domain. For 2005, four evaluation tasks were supported. These included a speech-to-text (STT) transcription task and three diarization tasks: " Who Spoke When " , " Speech Activity Detection " , and " Source Localization. " The latter two were first-time experimental proof-of-concept tasks and were treated as " dry runs ". For the STT task, the lowest word error rate for the multiple distant microphone condition was 30.0% which represented an impressive 33% relative reduction from the best result obtained in the last such evaluation-the Rich Transcription Spring 2004 Meeting Recognition Evaluation. For the diarization " Who Spoke When " task, the lowest diarization error rate was 18.56% which represented a 19% relative reduction from that of RT-04S.
Complementary DNA Cloning and Analysis of Gene Structure of Pyruvate Kinase from Drosophila melanogaster

structure of pyruvate kinase from Drosophila melanogaster. Zoological Studies 38(3): 322-332. Screening a λgt10 cDNA library of Drosophila melanogaster using a human pyruvate kinase (Pyk) cDNA clone (pCJ11) and a rat pituitary Pyk cDNA clone (pCJ22) as probes, we isolated 2 cDNA clones, cDMPK15 and cDMPK06. Complete nucleotide sequencing of the two cDNA clones (GenBank AF061507) revealed that they encompassed the coding region of pyruvate kinase cDNA (1602 bp; 533 amino acids + TAA) flanked by a 5' untranslated region of 240 bp and a 3' untranslated region of 253 bp. An alignment of the deduced amino acid sequence from the Pyk cDNA clones with those of PK from other organisms indicated that the amino acid residues constituting the active sites have been highly conserved. In addition, the overall positional identity between the sequence of the “Drosophila” enzyme and those from other sources was 42%-63%. Polymerase chain reaction was applied to amplify the genomic DNA fragments from the Pyk gene of D. melanogaster. These overlapping amplicons, which covered the complete coding region of Pyk, were further sequenced using cycle-sequencing with an ABI Prism 377 DNA sequencer. A total of 3447 bp of the nucleotide sequence (GenBank AF062478) was determined from these amplicons. By comparing these sequences with the sequence of Pyk cDNA clones isolated, 4 exons were identified of 282, 1390, 157, and 266 bp in length. The introns identified all contained the consensus 5'- and 3'-splicing sites (GT-AG). RT-PCR analysis was performed to determine the number of species of the Pyk transcript in adults of D. melanogaster. The observation that only a single amplicon appeared in each amplification suggests that a single Pyk transcript is expressed in adults of D. melanogaster, and might imply that there is only 1 Pyk gene in D. melanogaster.
The Effect of Mutation at Thr 295 of Saccharomyces cerevisiae eRF1 on Suppression of Nonsense Codons and eRF1 Structure

The termination of translation in Saccharomyces cerevisiae is controlled by two interacting polypeptide chain release factors, eRF1, and eRF3. Two regions in eRF1, at position 281-305 and 411-415, were proposed to be involved on the interaction to eRF3. In this study we have constructed and characterized eRF1 mutants at position 295 from threonine to alanine and serine residues resulting in eRF1(T295A) and eRF1(T295S) respectively. The mutations did not affect the viability or temperature sensitivity of the cells. The stop codons readthrough of the mutants were analyzed in vivo using PGK -stop codon- LACZ gene fusion and the results showed that the suppression of the mutants was increased in all of the codon terminations. The suppression of the UAG codon was the high for both mutants, with a 7-fold increased for eRF1(T295A) and a 9 fold increase for eRF1(T295S). The suppressor activity of eRF1(T295S) was higher compared to that of eRF1(T295A), suggesting that the accuracy of translational termination in eRF1(T295S) was lower than that of eRF1(T295A). Computer modeling analysis using Swiss-Prot and Amber version 9.0 programs revealed that the overall structure of eRF1 mutants has no significant difference with the wild type. However, substitution of threonine to serine on eRF1(T295S) triggered a secondary structure change on the other motif of the C-terminal domain of eRF1. This observation did not occur for on eRF1(T295A). This suggests that the high stop codon suppression on eRF1(T295S) is probably due to the slight modification of the structure of the C terminal motif.
Curcumin Mitigates Radiation-induced Lung Pneumonitis and Fibrosis in Rats

Radiation-induced lung injury is one of the most prominent factors that interfere with chest cancer radiotherapy, and poses a great threat to patients exposed to total body irradiation. Upregulation of pro-oxidant enzymes is one of the main mechanisms through which the late effects of ionizing radiation on lung injury can be exerted. Interleukin (IL)-4 and IL-13 are two important cytokines that have been proposed to be involved in this process. Through stimulation of dual oxidase 1 and 2 (DUOX 1 & 2), they induce chronic oxidative stress in irradiated tissues. In this study, we evaluated the effects of curcumin treatment on the regulation of IL-4 and IL-13, DUOX1 & 2 genes as well as the pathological changes developed by this treatment. Twenty male Wistar rats were divided into four groups: radiation only; curcumin only; radiation +curcumin; and control group with neither pharmacotherapy nor radiation. Curcumin was administered for 4 and 6 consecutive days before and after irradiation, respectively. Also, the chest area was irradiated with 15 Gy using a cobalt-60 gamma rays source. All rats were sacrificed 67 days after irradiation, followed by the assessment of the levels of IL-4 and IL-13; the expression of IL- 4 receptor-a1 (IL4Ra1), IL13Ra2, DUOX1 and DUOX2, and finally the histopathological changes were evaluated. Radiation led to the increased level of IL-4, while the level of IL-13 showed no change. QPCR results showed the upregulation of IL4Ra1, DUOX1 and DUOX2 following lung irradiation. Histopathological evaluation also showed a remarkable increase in pneumonitis and fibrosis. Treatment with curcumin downregulated the expression of IL-4, IL4Ra1, DUOX1 & 2. Furthermore, it could mitigate pneumonitis and fibrosis following lung irradiation. The late effects of radiation- induced lung injury may be due to the upregulation of DUOX1 & 2 genes. Curcumin, through modulation of these genes, may contribute to the protection against ionizing radiation.