Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics and population analysis Genome-wide genetic heterogeneity discovery with categorical covariates

Motivation: Genetic heterogeneity is the phenomenon that distinct genetic variants may give rise to the same phenotype. The recently introduced algorithm Fast Automatic Interval Search ( FAIS ) enables the genome-wide search of candidate regions for genetic heterogeneity in the form of any contiguous sequence of variants, and achieves high computational efﬁciency and statistical power. Although FAIS can test all possible genomic regions for association with a phenotype, a key limitation is its inability to correct for confounders such as gender or population structure, which may lead to numerous false-positive associations. Results: We propose FastCMH , a method that overcomes this problem by properly accounting for categorical confounders, while still retaining statistical power and computational efﬁciency. Experiments comparing FastCMH with FAIS and multiple kinds of burden tests on simulated data, as well as on human and Arabidopsis samples, demonstrate that FastCMH can drastically reduce genomic inﬂation and discover associations that are missed by standard burden tests. Availability and Implementation: An R package fastcmh is available on CRAN and the source code can be found at: https://www.bsse. ethz
Influence of ethylene on the incorporation of 3,4-[14C] methionine into polyamines in Daucus carota cells during somatic embryogenesis

The effects of ethylene on the formation of polyamines (spermidine, spermine) and on somatic embryogenesis were studied in carrot (Daucus carota) cell cultures. The flux of radioactivity from 3,4−[ 14 C] methionine into spermidine and spermine was examined and the activities of txo polyamine biosynthesis enzymes, arginine decarboxylase (ADC, EC 4.1.1.19) and S-adenosylmethionine decarboxylase (SAMDC, EC 4.1. 1.50° determined
COMPACT MICROSTRIP BANDPASS FILTER FARIDAH BINTI SAID

In microwave communication systems, the bandpass filter is an essential component, which is usually used in both transmitter and receiver. Parallel-coupled microstrip bandpass filter is one of the most popular filters in communication systems. However, this arrangement of parallel-coupled microstrip bandpass filter gives disadvantage in terms of size where the arrangement of this topology results in an electrically large in size of the filter. Therefore, this project focuses on designing a compact microstrip bandpass filter by using Sonnet Lite software software at centre frequency of 3.2GHz with the bandwidth of 400MHz. Besides, the design of the compact microstrip bandpass filter has achieved the objective when it successfully reduced the overall size to about 70% as compared to the size of conventional filter, which is parallel-coupled microstrip bandpass filter. Both filters give the same performance based on their frequency responses. The design also has successfully fabricated and measured by using network analyzer software to verify the simulated results obtained earlier. Although there is slightly mismatch between the simulated and measured frequency response due to some fabrication errors and variation of material properties, the design of filter is not affected since the results obtained from the designing process by using Sonnet Lite software are still valid and can be used in future improvement of the design. PTTA PERP UST AKA AN TUN KU T UN AMI NAH
Genetic variation in central and marginal populations of Quercus suber L.

Eighteen spontaneous populations of cork oak (Quercus suber) from Spain (14), Portugal (1), Morocco (1) and Italy (2), were surveyed at 14 loci from 12 enzyme systems. Percentage of polymorphic loci (64%), mean number of alleles (2.07), and mean expected heterozygosity (0.158) values were within the ranges described for the genus. Populations from the central range of the species and from peripheral areas were evaluated, and differences between these two kinds were assessed. Significant lower diversity (number of alleles and expected heterozygosity) was found for the most isolated and small size populations in contrast to central forests, showing the existence of mechanisms maintaining the levels of diversity even in some isolated stands. Interpopulation diversity (F st ) is 3.3 %, indicating extensive gene flows or recent postglacial expansion. A possible recent bottleneck is detected in two populations by comparing actual with expected heterozygosity from the number of detected alleles.
Changes in the macroalga taxa and zonation at the content keys, Florida

Macroalgal zonation on the exposed limestone reef of the Content Keys Florida was similar to that found between 1964 and 1968 with 65 of the 87 species in common. The number of macroalgae appears to have declined in the past 28 yrs with 38% Chlorophyta, 28% Phaeophyta, and 21% Rhodophyta being the same as those previously listed. Compared to the study of 28 yrs earlier, there was an upward shift in zones by 48% of the macroalgal species and a downward shift by 22% of the 65 species in common with both studies. Of the 17 species newly reported for the Content Keys, all are known from tropical to subtropical habitats. Ofthe newly reported species, two green and six red algae are also known from eutrophic habitats. It appears that macroalgal diversity has declined and is showing effects of nutrification similar to that reported elsewhere in the Florida Keys.
A Comparative Appraisal on Satellite Remote Sensing Data as a Utilitarian Tool in Forest Health and Fragmentation Analysis

The health of the forest vegetation is one of the driving factors and indicator of climate change impacts. Fragmentation of the forests on the other hand brings out the implications of the various stressing factors on the spatial extent of the forests especially the increasing population and industrialization, which has always impacted the forested regions in the form of deforestation for commercial purposes and conversion of forest land for cultivation. Hence there is a demand for spatial assessment and continuous monitoring of the forested regions. With a wide range of advancing technologies, remote sensing methods are increasingly being employed for monitoring a number of remotely measurable properties of different types of vegetation.This paper reviews the utilitarian application of remote sensing as a tool to assess the health of the forest regions. The various multispectral satellite image derived vegetation indices like Broadband and narrowband Greenness, leaf pigments, canopy water content and Light use efficiency can be used as a combined tool to generate a comprehensive health metrics for the forest canopy. These new indices may be useful in remote sensing plant physiology status as well. Various band ratio exist for above factors depending on the bands available in the selected dataset. A detailed discussion of the existing multispectral satellite sensors capable of studying the forest canopy is presented herewith, in addition to briefing on the potential of the latest microwave remote sensing technique for vegetation studies. The estimated vegetation indices can be used to generate the final health map of forest regions. Any change in the spatial extent of the forested areas and their pathway for future change can be assessed by the fragmentation analysis.The application of the discussed techniques in various environmental conditions are elaborated and the constraints in addition to the requirements for effective forest health monitoring is provided in this review.
Novel roles of actin binding proteins in Listeria monocytogenes actin-based motility revealed within a cellular context

Author(s): Buencamino, Raphael Hector | Advisor(s): Vale, Ronald D | Abstract: Novel Roles of Actin Binding Proteins in Listeria monocytogenes Actin-Based Motility Revealed Within a Cellular ContextBy Raphael H. Buencamino Actin-based motility is essential in many biological processes from fighting harmful organisms to the development of our bodies in the correct configuration. It has been dissected to its basic parts, finding the minimal set of actin binding proteins needed to produce movement. In contrast, actin-based motility in cells allows movement at a fast pace with a diverse set of activities and structures based on the cell's immediate function within the body. We dissected the mechanism of actin-based motility in vivo and found a set of proteins whose depletion drastically changes the character and efficiency of actin based movement. We accomplished this by using Listeria monocytogenes, a pathogen that expresses one bacterial protein, ActA, that allows Listeria to hijack the host proteins necessary to move within the cell using actin-based motility. To investigate the function and role of these host actin-binding proteins in actin-based motility, in vivo, we used a form of molecular "fractionation", a powerful technique only previously available for in vitro studies. RNAi interference in the Drosophila S2 cell line provided us this form of in vivo "fractionation" by allowing selective depletion of any protein whose cellular function we wished to examine. We first examined two proteins, profilin and ADF/cofilin, whose functions have been well documented through biochemical assays and in vitro systems. We also sought to dissect actin-based motility further and determine if other actin-binding proteins are involved in its mechanism. Our hypothesis is that with over 90 actin-binding proteins implicated in actin-based motility there are other key proteins that remain uncharacterized beyond the five in the current model. Our experiments identified that CAP is an essential protein for actin-based motility in vivo. Through our investigation we also discovered that fascin and other crosslinking proteins, though not essential for motility, might serve a new unique role in regulating the speed and dynamics of Listeria and its actin tail. Our observations have allowed us to identify and dissect the protein make-up of the actin-based motility machine.
Lamellodiscus (Plathelminthes, Monogenea, Diplectanidae) nouveaux parasites branchiaux des poissons marins du genre Pagrus (Teleostei, Sparidae)

Trois nouvelles especes de Lamellodiscus Johnston & Tiegs, 1922 ont ete recoltees sur les branchies de deux especes de Sparidae du genre Pagrus Cuvier, 1816: Lamellodiscus sarculus n. sp. et L. sigillatus n. sp. chez Pagrus coeruleostictus (Valenciennes, 1830) et L. rastellus n. sp. chez P. auriga (Valenciennes, 1843). Ces trois parasites appartiennent a l'ensemble des Lamellodiscus caracterises par des lamellodisques du groupe « ignoratus » a lamelles entieres et par un appareil copulateur du type en « lyre » compose de deux pieces, une simple et l'autre a deux branches. Dans cet ensemble les trois especes nouvelles se distinguent par la morphologie des pieces sclerifiees du hapteur et de l'appareil copulateur mâle. Elles ont ete observees chez leur hote respectif dans l'Atlantique (Senegal) et en Mediterranee (Tunisie). On assimile a un pseudospermatophore la masse de taille variable observee dans le vagin de nombreux Lamellodiscus possedant un appareil copulateur du type en « lyre ». La specificite des Lamellodiscus parasites des Sparidae du genre Pagrus parait oioxene.
Genetic Characterization of Genes Specific to Listeria monocytogenes Epidemic-Associated Serotype 4b Strains

CHENG, YING. Genetic Characterization of Genes Specific to Listeria monocytogenes Epidemic-Associated Serotype 4b Strains (Under the direction of Dr. Kathariou Sophia.) Listeria monocytogenes, a food-borne pathogen of humans and animals, can cause severe listeriosis with relatively high mortality. A cluster of closely related strains of L. monocytogenes (designated Epidemic Clone I) have been implicated in numerous outbreaks in Europe and North America, including the California outbreak of 1985. L. monocytogenes strains implicated in the 1998-1999 and the 2002 multistate outbreaks in the USA represent a unique epidemic-associated clonal group, designated Epidemic Clone II (ECII). Comparative genomic analyses across five genomes from different L. monocytogenes isolates and Listeria species identified a genomic region (region-18) in serotype 4b strains that may have been acquired by horizontal gene transfer. Region-18 is either absent or markedly divergent in ECII strains but conserved among other serotype 4b strains. Region-18 is flanked by a large gene encoding a putative cell-wall associated protein (wap) on one side and a well-known virulence gene internalin A (inlA) on the other side in serotype 4b strains. PCR primers and DNA probes derived from this ECII-specific region-18 can readily differentiate ECII strains from other serotype 4b strains. This facilitates the detection and monitoring of these strains belonging to ECII clonal group in foods, clinical samples, and the environment. Genetic characterization of wap by the construction of deletion mutants suggested that the ECII wap mutant but not the ECI wap mutant may be involved in specific environmental adaptations such as surface adherence and possibly biofilm formation in ECII strains. Mutational and functional analyses showed that the deletion mutant of region-18 in ECII had an enhanced death rate during post-stationary incubation at 42°C,suggesting that the ECII-specific region18 may be implicated in post-stationary stress responses. Two c72.44-negative variants of epidemic-associated L. monocytogenes serotype 4b strains were isolated from laboratory cultures. Naturally occurring c74.22-negative variants that exist under laboratory conditions without any noticeable phenotypic differences from their original forms may complicate the analysis of phage sensitivity and pathogenic characteristics. Genetic Characterization of Genes Specific to Listeria monocytogenes Epidemic-Associated Serotype 4b Strains
Palaebiology of the amiiform fishes from Early Cretaceous of Las Hoyas: An integrative multidisciplinary approach

The fossil record of the Early Cretaceous (Barremian) of Las Hoyas includes three taxa of amiiform fishes. These taxa, traditionally assigned to the species Caturus tarraconensis, Amiopsis woodwardi and Vidalamia catalunica, represent actually three new species. These species are the basis for a multidisciplinary study whose objective is to comprehend the palaeobiologý of these fishes in the context of a wetland ecosystem. From a phylogenetic point of view, one of the species represents a primitive lineage, with a mosaic combination of characters from both caturoids and amioids. The second species is classified as plesion Vidalamiinae, and the third oneas a member of this same subfamily. A palaeobiogeographic study of the order Amiiformes, including the three species from Las Hoyas, shows that the record of this group extends from at least the Early Jurassic to Recent times, reaching its maximum diversity during the Cretaceous. Its historical distribution is mainly explained by a series of vicariant events that originated from the Tethys Sea. The osseochronometric analysis of the growth cessation marks detected in the scales of the three species shows that they presented different growth profiles. Growth of amiiform fishes seems to have a phylogenetic component, and to be strongly influenced by environmental conditions, especially temperature. Actuotaphonomical experimentation of decay in extant fish carcasses confirms that a freshwater environment favors a total degradation of tissues. In consequence, the presence of a protection mechanism, such as microbial mats, is needed to justify the exceptional preservation of the fossil record from Las Hoyas. Additionally, this experimentation shows that carcasses suffer abrasion by transport even in very low energy systems. Absence of evidence of abrasion in the fossil fishes of Las Hoyas suggests that the association of this site is autochthonous in origin. Autochthony of the association allows to interpret the sample of each of the three species as representative of their original populations. An analysis of the population structure of these species shows that they presented habitat partitioning: juvenile and adult individuals did not inhabit the same environment. The ecological role played by the three species in the palaeowetland of Las Hoyas would be different both ontogenetically within each species and interspecifically.
Transplantation immunology 1957-1975.

: Knowledge of the transplantation immunity has increased rapidly in the past twenty years. The rejection of allograft is now known to involve the interaction of several subsets of lymphocytes, as well as humoral immunity. Efforts to suppress immunity to the allograft are effective but suppress other kinds of immunity also, thus rendering the recipient susceptible to opportunistic infections. Two approaches to modification of the immune response by impairing the ability of cells sensitized specifically against allograft antigen to kill such cells are described. These agents can and have been used therapeutically in humans for other reasons and have been shown in the laboratory to actually markedly prolong the life of renal allograft, without impairing the immune response to other antigens.
Detecção e tratamento de otite por Rhabditis blumi em bovinos da região Norte do Brasil

This study aimed to describe the occurrence of parasitic otitis caused by Rhabditis blumi in dairy cattle of the Gir race from a farm in northern Brazil. Forty-two samples were collected from cattle by swab washed from the external auditory canal (EAC). On clinical examination, in 71.4% (30/42) of the cattle the parasite was found in the cerumen of the ear canal, along with alopecia of head and hump caused by discomfort and itching of the auricular region. At microscopic analysis of material from the conjunctival sac the parasite was found in 90% (9/10) of the evaluated cattle. In addition, 9.5% (4/42) of the cattle showed nervous symptoms, such as mild to moderate rotation of the head, apathy, flaccid lips and unilateral ptosis, change in chewing and food accumulation in the oral cavity. Thirty cattle positive for Rhabditis spp. were randomly divided into three groups of 10 animals each: (G1) Cattle Control, (G2) Cattle treated with ivermectin 1% pour-on, and (G3) Cattle undergoing wash of the external auditory canal (EAC). Each treatment was repeated three times with intervals of seven days. In G1, 10 cattle remained infected throughout the study. In G2, 20% of the cattle were negative after the first two treatments, however were positive at the third evaluation. In G3, all cattle remained positive, but with decrease in parasite load. Identification by molecular analysis of amplified fragments through the expansion D2/D3 28S rDNA confirmed the presence of only Rhabditis blumi. Based on clinical, morphologic and molecular examination, it appears to be the first report of the occurrence of R. blumi infection in Gir cattle in the State of Para, due to the purchase of cattle from areas where parasitic otitis has been diagnosed, as from Minas Gerais, to produce crossbred animals (Gir x Holstein). This emphasizes the importance of prior clinical examination by the veterinary service in order to transfer only healthy animals to other properties or regions. This appears also to be the first report on R. blumi infection of the conjunctival sac in cattle. Treatment with ivermectin in G2 did not produce clinical improvement.
An Automated Chamber System for Measurements of Whole-vine Gas Exchange

The reported system interfaces a commercially available portable infrared gas analyzer with a measurement and control module for continuous and automated measurements of whole-canopy gas exchange. Readings were taken for several days, under mostly sunny or partly cloudy conditions, on two potted vines (total leaf area per vine of 1.3 m 2 ) enclosed in inflated polyethylene chambers. The air flow rate through the chambers was provided by a centrifugal blower and set at 5 L.s -1 by a butterfly valve. It prevented ΔCO 2 from dropping below -40 mL.L -1 . Switching of the two CO 2 analysis channels to the infrared gas analyzer (operated in a differential mode) was achieved by solenoid valves, whereas wet and dry-bulb temperatures at chambers' inlet and outlet were measured by low-cost, custom-made thermocouple psychrometers. Whole-vine assimilation rate (WVA) and whole-vine transpiration rate were calculated from the inlet-outlet differences in CO 2 and absolute humidity. When compared to assimilation measured on single leaves (SLA) under saturating light at equivalent times, the WVA reduction (area basis) was =50%, suggesting that whole-canopy photosynthetic efficiency based on SLA readings can be greatly overestimated.
Cloning of the Self-incompatibility SFB Gene from Chinese Apricot ‘Xiaobaixing’ and Construction of the SFB Expression Vectors

A BSTRACT . Three kinds of expression vectors of a pollen-S determinant were constructed to provide a reference for molecular breeding of self-compatible (SC) Prunus species. An S-haplotype-speciﬁc F-box (SFB) protein gene from the ‘Xiaobaixing’ apricot ( Prunus armeniaca ) was cloned by reverse transcription polymerase chain reaction (RT- PCR) and 3 # -rapid-ampliﬁcation of cDNA ends (3 # -RACE). A 1136-bp sequence complementary to the 3 # -end of the cDNA (GenBank accession number KP938528.2) with a 912-bp complete open reading frame (ORF) was obtained. The deduced amino acid sequence contained an F-box domain, two variable regions, and two hypervariable regions with structural characteristics similar to SFB in other Rosaceae plants. Sense, antisense, and RNA interference (RNAi) vectors for SFB were constructed by enzyme restriction. The target fragment was restricted using the corresponding restriction enzyme and then directionally inserted between the 35S cauliﬂower mosaic virus promoter and the nopaline synthase terminator (NOS-ter) of the expression vector pCAMBIA-35S-MCS-NOS- NPT II. The intron-containing hairpin RNA (ihpRNA) was obtained by fusion PCR. The constructed vectors were transferred into Agrobacterium tumefaciens strain LBA4404 by freezing/thawing. The RNAi vector of SFB was also transformed in tobacco ( Nicotiana tabacum ). The successful construction of these three expression vectors provides a basis for transforming ‘Xiaobaixing’ apricot and the breeding of SC Prunus cultivars.
Variation in selected morphological traits of Cfr. Salix viminalis from different experimental plots

Variation in selected morphological traits of Cfr. Salix viminalis from different experimental plots. Analyses were conducted on morphological traits (rod length, rod diameter in the butt end) were conducted on willow Cfr. Salix viminalis coming from experimental plots in Siemianice and in Zielonka. The percentage shares of the pith and bark were calculated. Rods from Siemianice were characterized by very high variation in length (from 26 cm to 154 cm). Rods form Zielonka had a very low percentage share of pith – below 1%.
The Adaptation of Field Collected Aedes aegypti (L.) and Aedes albopictus (Skuse) in Laboratory Condition

Aedes aegypti and Aedes albopictus has been incriminated in dengue transmission in Malaysia, and all available measures has been taken to reduce the dengue cases and mortality. However, statistical data showed increasing trend in dengue incident. The aim of this study is to evaluate the adaptability F1 offspring of field collected Aedes mosquitoes in a new environment (laboratory). Biological parameter of Aedes mosquito, such as the larval growth, survival and fecundity were scrutinized under laboratory condition. Data obtained from this study showed that both Aedes species were highly adaptable to laboratory condition. The finding of this study is essential for vector control. KeywordsAedes Albopictus; Aedes Aegypti; Larval Growth; Survival; Fecundity