Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Different Enteric Protozoa Parasites with Combination ofImmunological and Microscopic Methods, in Albania

Enteric protozoa are associated with diarrhoeal illnesses in humans, particularly in children, and represent a significant threat to public health that often was neglected. Several enteric protozoa cause severe morbidity and mortality in both humans and animals worldwide. Therefore, the study aims were to estimate the prevalence of enteric protozoa in children, comparison of the efficiency of microscopy and ELISA procedure in diagnose of protozoa, and in addition to shed light on risk behaviour for enteric protozoa. During September 2013-August 2014 we have examined 115 hospitalized patients in “Mother Theresa” hospital center in Tirana Albania, for Entamoeba histolytica; Cryptosporidium parvum and Giardia lamblia. Two methods, classic microscopy and ELISA were used for examination of enteric parasites in our study. The average year was 6.66 and the minimum age was 3 months old and maximum 15 years old. Based to the data 53.04% were female and 46.95% male. The prevalence of E histolytica; C parvum and G lamblia resulted 4.34%, 2.6% and 12.17% respectively by microscopy. By ELISA method the prevalence resulted 7.82%, 4.34% and 20.87% respectively. Also about 18; 44; 44 samples respectively are considered as equivocal by ELISA test. This high result of equivocal test to patients maybe were as result of the cross reaction between protozoa parasites. Depended of the methods that we have used the male were the most contaminated sex. In our study ELISA methods resulted to be more sensitive compared to classic microscopic, but other tests like PCR-based tests need to be used for understanding the actual prevalence and epidemiology of these protozoan parasites.
The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals

Inter-specific body mass allometries can evolve from the natural selection of mass, with ±1/4 and ±3/4 exponents following from the geometry of intra-specific interactions when density dependent foraging occurs in two spatial dimensions (2D, Witting, 1995). The corresponding values for three dimensional interactions (3D) are ±1/6 and ±5/6. But the allometric exponents in mobile organisms are more diverse than the prediction. The exponent for mass specific metabolism tends to cluster around −1/4 and −1/6 in terrestrial and pelagic vertebrates, but it is strongly positive in prokaryotes with an apparent value around 5/6 (DeLong et al., 2010). And a value around zero has been reported in protozoa, and on the macro evolutionary scale from prokaryotes over larger unicells to multicellular vertebrates (Makarieva et al., 2005, 2008). I show that mass specific metabolism can be selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, and that this selection of metabolism and mass is sufficient to explain metabolic exponents that decline from 5/6 over zero to −1/6 in 3D, and from 3/4 over zero to −1/4 in 2D. The decline follows from a decline in the importance of mass specific metabolism for the selection of mass, and it suggests i) that the body mass variation in prokaryotes is selected from primary variation in mass specific metabolism, ii) that the variation in multicellular animals are selected from primary variation in the handling and/or densities of the underlying resources, iii) that protozoa are selected as an intermediate lifeform between prokaryotes and multicellular animals, and iv) that macro evolution proceeds along an upper bound on mass specific metabolism.
Genes mirror migrations and cultures in prehistoric Europe – a population genomic perspective

Genomic information from ancient human remains is beginning to show its full potential for learning about human prehistory. We review the last few years' dramatic finds about European prehistory based on genomic data from humans that lived many millennia ago and relate it to modern-day patterns of genomic variation. The early times, the Upper Palaeolithic, appears to contain several population turn-overs followed by more stable populations after the Last Glacial Maximum and during the Mesolithic. Some 11,000 years ago the migrations driving the Neolithic transition start from around Anatolia and reach the north and the west of Europe millennia later followed by major migrations during the Bronze age. These findings show that culture and lifestyle were major determinants of genomic differentiation and similarity in pre-historic Europe rather than geography as is the case today.
Protective Effect of Ceratonia siliqua L. Against a Dextran Sulfate Sodium-Induced Alterations in Liver and Kidney in Rat.

Abstract The aim of the present study is to investigate the potential protective role of Ceratonia siliqua L. against dextran sodium sulfate (DSS)-induced oxidative damage and inflammation in liver and kidney of rats. The hepatotoxicity and nephrotoxicity were induced in rats by oral administration of synthetic DSS (5%) in the drinking water for over 7 days. However, carob pods aqueous extract (CPAE; 50 and 100 mg/kg body weight) was given by oral administration for 21 days. Myeloperoxidase (MPO) activity, malondialdehyde, H2O2 content, as well as the levels of antioxidant enzymes in organs were measured to observe the possible mechanisms. As a result, the CPAE counteracted DSS-induced increase of MPO activity, lipoperoxidation, and the activity of antioxidant enzymes, such as superoxide dismutase and catalase (CAT). DSS administration increased also in the organs hydrogen peroxide (H2O2) and free iron levels, whereas the CPAE pretreatment reversed all intracellular mediator perturbations. It was conclude.
EXPLOITING NEXT GENERATION SEQUENCING TO SOLVE THE HAPLOTYPING PUZZLE IN POLYPLOIDS: A SIMULATION STUDY

Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in Next Generation sequencing reads, by matching overlapping sNPs while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species. While a number of tools are available for haplotyping polyploids, the effects of the genomic makeup and the sequencing strategy followed on the accuracy of these methods have hitherto not been thoroughly evaluated. We developed the simulation pipeline haplosim to evaluate the performance of haplotype estimation algorithms for polyploids: HapCompass, HapTree and SDhaP, in settings varying in sequencing approach, ploidy levels and genomic diversity, using tetraploid potato as the model. Our results show that sequencing depth is the major determinant of haplotype estimation quality, that 1kb PacBio CCS reads and Illumina reads with large insert-sizes are competitive, and that all methods fail to produce good haplotypes when ploidy levels increase. Comparing the three methods, HapTree produces the most accurate estimates, but also consumes the most resources. There is clearly room for improvement in polyploid haplotyping algorithms.
Three improvements on KNN-NPR for traffic flow forecasting

Research has shown nonparametric regression to hold high potential to accurately forecast short-term traffic flows. However, many fundamental questions remain regarding the ability of KNN-NPR(K nearest neighbor nonparametric regression) to meet real-time system requirements and adequate accuracy requirements. So this paper puts forward three improvements which are: effective traffic state vector selection method based on self-association analysis and association analysis; improved variable K search method based on "dense degree"; and advanced data structures based on a dynamic cluster method and hash-function transformation. A field test fully proves that with three improvements, KNN-NPR can adequately meet real-time system requirements and accuracy requirements.
Computation and effect of field penetration through planes in multi-layered package power distribution networks for giga-processors

This paper discusses the field penetration through planes in package power distribution networks. A method is presented to efficiently compute the penetration of magnetic fields through an 'N' layer structure by solving Maxwell's equations. Several test cases have been simulated to compute the frequency and time domain response and their effect on the functioning of giga-processors. General rules have been proposed to suppress this phenomenon.
Determining the role of inflammation in the selection of JAK2 mutant cells in myeloproliferative neoplasms

Myeloproliferative neoplasm (MPN) is a hematologic malignancy characterized by the clonal outgrowth of hematopoietic cells with a somatically acquired mutation most commonly in JAK2 (JAK2V 617F). This mutation endows upon myeloid progenitors cytokine independent growth and consequently leads to excessive production of myeloid lineage cells. It has been previously suggested that inflammation may play a role in the clonal evolution of JAK2V 617F mutants. In particular, it is possible that one or more cellular kinetic parameters of hematopoietic stem cells (HSCs) are affected by inflammation, such as division or death rates of cells, and the probability of HSC differentiation. This suggests a mechanism that can steer the outcome of the cellular competition in favor of the mutants, initiating the disease. In this paper we create a number of mathematical evolutionary models, from very abstract to more concrete, that describe cellular competition in the context of inflammation. It is possible to build a model axiomatically, where only very general assumptions are imposed on the modeling components and no arbitrary (and generally unknown) functional forms are used, and still generate a set of testable predictions. In particular, we show that, if HSC death is negligible, the evolutionary advantage of mutant cells can only be conferred by an increase in differentiation probability of HSCs in the presence of inflammation, and if death plays a significant role in the dynamics, an additional mechanism may be an increase of HSC’s division-to-death ratio in the presence of inflammation. Further, we show that in the presence of inflammation, the wild type cell population is predicted to shrink under inflammation (even in the absence of mutants). Finally, it turns out that if only the differentiation probability is affected by the inflammation, then the resulting steady state population of wild type cells will contain a relatively smaller percentage of HSCs under inflammation. If the division-to-death rate is also affected, then the percentage of HSCs under inflammation can either decrease or increase, depending on other parameters.
MicroRNA expression profiles in prostate cancer cell lines

MicroRNAs (miRNAs), a group of small non-coding RNAs, can regulate gene expression by triggering translation repressing and/or RNA degradation. Recent studies proved that they were deeply involved in tumorigenesis. Here we show that, compared with the two normal prostate cell lines, eighteen miRNAs in the array were over-expressed and 18 showed lower levels of expression in at least 2 of 3 cancer cell lines using miRNA microarray. MiR-99a, miR-335, miR-375 and miR-625 were the most significantly over-expressed miRNAs, whereas miR-155, miR-205, miR-224, miR-422a, miR-422b, miR-452, and miR-452* (* refer to miR-452-3p) were among the most down-regulated miRNAs. Expressions of several of the most significantly differential expression miRNAs were confirmed by Northern blot analysis and real-time RT-PCR. In this study, the expression of miR-10a, miR-99a and miR-125b were also up-regulated in prostate cancer tissues compared with their own normal tissues. For miR-99a,its expression was up-modulated in prostate cancer in comparison with all three normal tissues. Whereas miR-27aand miR-205have lower level expression in cancer tissues than that in normal tissues. Some miRNAs are aberrantly expressed in human prostate cancer suggesting their involvement in the development and progression of this malignancies. Further studies of these deregulation miRNAs will help clarify their role in tumorigenesis and detect their potential clinical usefulness for early diagnosis, prognosis and therapy of prostate cancer.
Induced defenses alter the strength and direction of natural selection on reproductive traits in common milkweed

Evolutionary biologists have long sought to understand the ecological processes that generate plant reproductive diversity. Recent evidence indicates that constitutive antiherbivore defenses can alter natural selection on reproductive traits, but it is unclear whether induced defenses will have the same effect and whether reduced foliar damage in defended plants is the cause of this pattern. In a factorial field experiment using common milkweed, Asclepias syriaca, we induced plant defenses using jasmonic acid (JA) and imposed foliar damage using scissors. We found that JA-induced plants experienced selection for more inflorescences that were smaller in size (fewer flowers), while control plants only experienced a trend toward selection for larger inflorescences (more flowers); all effects were independent of foliar damage. Our results demonstrate that induced defenses can alter both the strength and direction of selection on reproductive traits, and suggest that antiherbivore defenses may promote the evolution of plant reproductive diversity.
Melendiz Çayı'nın (Aksaray-Ihlara) Epilitik Diyatome Florasının Mevsimsel Değişimi ve Su Akışının Toplam Organizmaya Etkisi

The seasonal variation of the composition and concentration of epilitic diatom flora was investigated at five chosen sampling stations in the Melendiz stream. In addition, temperature and pH were measured and the variation of total organism numbers was investigated in relation to speed of stream flow. The total organism numbers was high in May due to the speed of stream, while decrease speed of stream caused to increase in total organism number as do in June. In this study, Cocconeis placentula var. euglypta, Navicula cryptocephala, Navicula tripunctata, Cymbella ventricosa, Nitzschia amphibia and Nitzschia palea were dominant species in the flora of the stream Melendiz.
Arterial Travel Time Estimation Using SCATS Detectors

This paper introduces a model to estimate average link travel time of signalized arterials using data obtained from detectors in Sydney Co-Ordinated Adaptive Traffic System (SCATS). The proposed model makes use of detectors at the upstream stop line of a link to capture the arrival of vehicles, and use a platoon dispersion model to project the vehicle arrival times at the downstream stop line. Using the vehicle departure pattems obtained at detectors at the downstream stop line, the average link travel time is then estimated. The accuracy of the proposed model has been tested, by means of microscopic traffic simulations, for link lengths between 300 m to 800 m, and at different urban street level of service. Results indicate that the proposed link travel time estimation model has an average absolute error of 2.26 sec. INTRODUCTION With the development of Advanced Traveler Information Systems (ATIS), it has become more important to obtain accurate real-time travel time data that reflects the operating efficiency of a traffic network, for assessing the performance of traffic management strategies, and for provision of route-guidance information. Several researches have been conducted on arterial travel time or speed estimation despite the complexity caused by traffic signals at intersections. Most of these arterial travel time or speed estimation models rely on data gathered by loop detectors at a distance away from the stop line (Gault 1981, Sisiopiku and Rouphail 1994, Zhang 1999 and Xie et al. 2001). Relatively few efforts have been made for the case with detectors installed at the stop line, with the exception of Luk and Cahill (1986), because it is difficult to make use of stop-line detectors to measure the representative link speed, vehicle arrival rate and queue length at an intersection approach. In addition, conventional way of aggregating loop detector data at stop line at cyclic interval does not provide data of sufficient granularity. With the improvement and cost reduction in loop detector hardware, it is becoming possible to program new data processing logic into a detector's controller card, to record vehicle arrivals and departures over the detector at intervals of several seconds. It is with this in mind that a method of using stop-line detectors to estimate arterial travel time is developed and tested in this paper. The proposed arterial travel time estimation method makes use of the existing stop-line detectors of the traffic signal control system in Singapore named Green Link Determination, or GLIDE in short (Chin 1993). It is the local version of the wellknown Sydney Co-Ordinated Adaptive Traffic Systems (SCATS) (Sims and Assoc. Prof., Dept. of Civ. Engrg., Nat. Univ. of Singapore, 1 Engineering Dr. 2, Singapore 117576, Singapore (corresponding author). Email: cheu@nus.edu. sg. 2 Res. Scholar, Dept. of Civ. Engrg. , Nat. Univ. of Singapore. 3 Asst. Prof., Dept. of Civ. lEngrg. , Nat. Univ. of Singapore.
Gene fractionation and function in the ancient subgenomes of maize

The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. We also show that the two subgenomes of maize are distinct in epigenetic characteristics. Intriguingly, analysis of singleton genes reveals that these differences persist even after fractionation is complete.
Colonization and transmission of the gut microbiota of the burying beetle, Nicrophorus vespolloides, through development

Carrion beetles in the genus Nicrophorus rear their offspring on decomposing carcasses where larvae are exposed to a diverse microbiome of decomposer bacteria. Parents coat the carcass with antimicrobial secretions prior to egg hatch (defined as Pre-Hatch care) and also feed regurgitated food, and potentially bacteria, to larvae throughout development (defined as Full care). Here we partition the roles of pre- and post-hatch parental care in the transmission and persistence of culturable symbiotic bacteria to larvae. Using three treatment groups (Full-Care, Pre-Hatch care only, and No Care), we found that larvae receiving Full-Care are predominantly colonized by bacteria resident in the maternal gut, while larvae receiving No Care are colonized exclusively with bacteria from the carcass. More importantly, larvae receiving only Pre-Hatch care were also predominantly colonized by maternal bacteria; this result indicates that parental treatment of the carcass, including application of bacteria to the carcass surface, is sufficient to ensure symbiont transfer even in the absence of direct larval feeding. Later in development, we found striking evidence that pupae undergo a aposymbiotic stage, after which they are recolonized at eclosion with bacteria shed in the moulted larval cuticle and on the wall of the pupal chamber. Our results clarify the importance of pre-hatch parental care for symbiont transmission in Nicrophorus vespilloides, and suggest that these bacteria successfully outcompete decomposer bacteria during larval and pupal gut colonization. Importance Here we examine the origin and persistence of the culturable gut microbiota of larvae in the burying beetle Nicrophorus vespilloides. This insect is particularly interesting for this study because larvae are reared on decomposing vertebrate carcasses where they are exposed to high-densities of carrion-decomposing microbes. Larvae also receive extensive parental care in the form of carcass preservation and direct larval feeding. We find that parents transmit their gut bacteria to larvae both directly, through regurgitation, and indirectly via their effects on the carcass. In addition, we find that larvae become aposymbiotic during pupation, but are recolonized from bacteria shed onto the insect cuticle before adult eclosion. Our results highlight the diverse interactions between insect behavior and development on microbiota composition. They further indicate that strong competitive interactions mediate the bacterial composition of Nicrophorus larvae, suggesting that the bacterial communities of these insects may be highly coevolved with their host species.
Chlamydomonas reinhardtii UVS 11 gene is required for cell cycle arrest in response to DNA damage

Chlamydomonas reinhardtii repair-deficient mutant uvsll seems to be the first mutant in photoautotrophic eukaryotes with impaired DNA damage-dependent cell cycle control. The effect of DNA damage on the progression of algal cells through the cell cycle has been investigated. Cells were arrested with methyl benzimidazole-2-yl-carbamate (MBC) and treated with UV, X-ray and MMS, respectively, and the MBC block was maintained to simulate a G2 delay, a common response of eukaryotic cells with damaged DNA. Repair of DNA lesions was monitored by cell viability. Our results indicate that the UVS11 gene could play a role in checkpoint control, by blocking cell cycle progression if the DNA is damaged. This suggestion is supported with the fact that survival of damaged cells in uvsll is restored to nearly wild type level by imposing a G2 block with MBC.
Multiple-Locus Variable Number Tandem Repeat Analysis of Klebsiella pneumoniae: Comparison with Pulsed-Field Gel Electrophoresis.

AIM To assess whether multiple-locus variable-number tandem repeat analysis (MLVA) could replace pulsed-field gel electrophoresis (PFGE) for genotyping of Klebsiella pneumoniae, this study was conducted to compare the typeability, discriminatory power, and concordance of these methods. MATERIALS AND METHODS We used the nine variable number tandem repeat (VNTR) loci scheme to test its suitability for differentiating 114 ESBL-producing K. pneumoniae isolates collected from different clinical specimens in three hospitals of Tehran, Iran between April and December 2011. PFGE with XbaI was performed and the results were compared with those obtained by typing with MLVA. RESULTS MLVA and PFGE yielded 44 and 64 types, respectively. Simpson's Diversity Index of MLVA was 0.896 (a 95% confidence interval of 0.850-0.942) and of PFGE was 0.962 (a 95% confidence interval of 0.943-0.981). Congruence between PFGE and MLVA was low. The adjusted Wallace coefficient of PFGE to MLVA was 0.946; however, MLVA was less able to predict PFGE type (32.5%). A range of 2-12 alleles was identified at VNTR loci with Simpson's diversity values between 0.017 and 0.818. CONCLUSION MLVA is a PCR-based typing method and is much easier and more rapid in comparison to PFGE. These data indicate that the MLVA typing scheme used in this study is discriminative and reliable for typing of K. pneumoniae. However, optimization of the VNTR markers is required to improve the discriminatory power of the method.