Miracle-dz/UniFAR-FTUs huggingface dataset:
Nested-PCR multiplex test with increased sensitivity for detection of allogeneic cells transplanted from male to female mice

Cell therapy has shown encouraging perspectives for human and veterinary medicine. Experimentally, genetic manipulation allows to mark and locate allogeneic cells. However, this makes their genotype/phenotype different from non-marked cells used clinically. Alternatively, the presence of the Y-chromosome enables male donor cells detection in female organisms. However, the concentration of engrafted cells may be minimal in tissues, due to systemic distribution. In this study, a nested-PCR multiplex test was developed, aiming to increase the sensitivity of the presence/absence diagnosis of male mice adipose-derived (ADSC-Y) and bone marrow mononuclear (BMNC-Y) cells in samples of blood and lungs from females, after endovenous transplantation. Four females received placebos; four females received ADSC-Y from two males; and four females received BMNC-Y from two males. The PCR first-step included two primer sets (multiplex): one for amplification of a Y-chromosome fragment (SRYout; 300bp); the other for amplification of an X-chromosome (DXNds3 gene) fragment. In the PCR second-step, one primer set (SRYinn) was used for amplification of a 110bp fragment, restrained in the SRYout amplification product. The PCR internal control (DXNds3 gene) was detected in all DNA samples, whereas the SRY gene external fragment (300bp) was detected exclusively in ADSC-Y and BMNC-Y pure DNA samples. The SRY gene internal fragment (110bp) was detected in 100% of the blood and lung samples from the ADSC-Y and BMNC-Y female recipients. The nested-PCR technique increased sensitivity and reliability for molecular diagnostic of presence or absence of male mice cells in body fluids and tissues of female recipients after endovenous transplantation.
Caspase-7 loop conformations as a means of allosteric control

The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2$) from the other half of the dimer to bind substrate. In an inactive form, the two L2$ loops form a cross-dimer hydrogen-bond network over the dimer interface. Although the L2$ loop has been implicated as playing a central role in the formation of the active-site loop bundle, its precise role in catalysis has not been shown. A detailed understanding of the active and inactive conformations is essential to control the caspase function. We have interrogated the contributions of the residues in the L2$ loop to catalytic function and enzyme stability. In wild-type and all mutants, active-site binding results in substantial stabilization of the complex. One mutation, P214A, is significantly destabilized in the ligand-free conformation, but is as stable as wild type when bound to substrate, indicating that caspase-7 rests in different conformations in the absence and presence of substrate. Residues K212 and I213 in the L2$ loop are shown to be essential for substrate-binding and thus proper catalytic function of the caspase. In the crystal structure of the I213A mutant, the void created by side-chain deletion is compensated for by rearrangement of tyrosine 211 to fill the void, suggesting that the requirements of substrate-binding are sufficiently strong to induce the active
Seed Development and Quality in Maize Cultivars

In order to evaluate seed development and quality of maize (Zea mays) cultivars (DC-370, SC-500, OSSK-602 and SC-604), a split plot experiment (using R.C.B. design) with three replicates was conducted in 2009 at the Research Farm of the Faculty of Agriculture, University of Tabriz, Iran. Seeds were harvested at five day intervals in eight stages. Subsequently, the quality of seed samples was determined in the laboratory. Germination percentage and seedling dry weight were enhanced, but electrical conductivity of seed leachates was reduced with increasing seed weight on mother plant. Maximum seed quality of maize cultivars was attained at the end of seed filling phase. Seed quality at earlier harvests was low, because of immaturity. Differences in maximum seedling dry weight of maize cultivars were attributed to variation in genetic constitution. It was concluded that in maize cultivars, maximum seed quality could be achieved at physiological maturity.
Amyloid β42 Activates a G-Protein-Coupled Chemoattractant Receptor, FPR-Like-1

Amyloid b (Ab) is a major contributor to the pathogenesis of Alzheimer’s disease (AD). Although Ab has been reported to be directly neurotoxic, it also causes indirect neuronal damage by activating mononuclear phagocytes (microglia) that accumulate in and around senile plaques. In this study, we show that the 42 amino acid form of b amyloid peptide, Ab42, is a chemotactic agonist for a seven-transmembrane, G-protein-coupled receptor named FPR-Like-1 (FPRL1), which is expressed on human mononuclear phagocytes. Moreover, FPRL1 is expressed at high levels by inflammatory cells infiltrating senile plaques in brain tissues from AD patients. Thus, FPRL1 may mediate inflammation seen in AD and is a potential target for developing therapeutic agents.
Interspecific territoriality and competitive interactions between American Black Ducks Anas rubripes and Mallard A. platyrhynchos

Interactions between pairs of American Black Ducks and Mallards were studied at six sites in northeastern Nova Scotia during territory establishment. Interspecific territoriality was well developed and most frequently resulted in competitive superiority by resident pairs, regardless of species. Also, intruding pairs sometimes remained on territories already occupied by the other species. Exclusion of Black Duck pairs by Mallards occurred twice.
The role of Kinesin-3 in regulating synaptic development in Drosophila

III I hereby declare that I have produced the work entitled: " the role of Kinesin‐3 in regulating synaptic development in Drosophila " , submitted for the award of a doctorate, on my own (without external help), have used only the sources and aids indicated and have marked passages included from other works, whether verbatim or in content, as such. I swear upon oath that these statements are true and that I have not concealed anything. I am aware that making a false declaration under oath is punishable by a term of imprisonment of up to three years or by a fine. Tübingen, ___________________________ ________________________________ Date Signature IV V As the universe's evolvement is ever vigorous, a man should constantly strive for self-perfection. As the earth's condition is receptive devotion, a man should cultivate virtue to hold the outer world. Acknowledgements Foremost I would like express my gratitude to my thesis committee members, Dr. Aaron Diantonio for their comments on my projects and providing reagents. with whom I have been collaborating. I also thank Baran Koç for helping with data analysis. Thanks to Junyi Zhu and Vrinda SKumar for transferring my flies and thanks to Jeannine Kern for watering my plants when I am not in the lab. Special thanks to Vrinda and her father for helping me buy medicines from India for my father's illness. Thanks to Dr. for being great colleagues. We have spent a lot of nice time together. I wish you all best of luck for the future. I believe there must still be people that I forget to mention here, but thank all of you who have helped me during my stay in Tübingen for my PhD. I can never use enough words to express my gratitude to my family. If it were not for my father's insistence on supporting us to enjoy the best possible education, I could not have been who I am now. If it were not for my mother's unconditional love, I would not have got the strength to conquer so many obstacles and complete my study. My elder sister Hui is always my defender, teacher and friend. I feel so lucky to have an excellent sister. I also want to thank my brother-in-law who is tolerant and supports the family. And I thank my niece, who brings new hope for the family. I love you all so much. I am …
Chromatin Flavors: Chromatin composition and domain organization in Drosophila melanogaster

Chromatin was originally identified by W. Flemming in 1882 as not much more than the stainable substance of the cell nucleus. Flemming named this substance according to the Greek word “chroma”, meaning color. In 1911 chromatin was characterized as proteins, named histones, that were attached to nucleic acid (DNA). In the following years it became clear that chromatin formed the structural basis of genetic information. Not until more than 30 years later the DNA, and not the histone proteins as was widely expected, was identified as the carrier of the genetic information. In 1952 the role of DNA in inheritance was confirmed and not much later Watson and Crick discovered the double-helical structure of DNA based on the DNA crystal analyses of Franklin, Gosling and Wilkins.
Estimación de la superficie quemada en los incendios forestales de Canarias en 2007 utilizando sinérgicamente imágenes MODIS y anomalías térmicas

El presente trabajo plantea una metodologia rapida, precisa y economica para la estimacion del area quemada en los incendios forestales utilizando tecnicas de teledeteccion. El algoritmo utilizado se basa en la determinacion o establecimiento de umbrales a partir de la banda del infrarrojo cercano. Se han utilizados los productos de reflectancia MODIS y las series temporales de anomalias termicas proporcionadas por la NASA. Dicho umbral que separa area quemada de no quemada se ha basado en la busqueda de la maxima coincidencia entre area quemada definida por la banda del infrarrojo cercano y zona de influencia de las anomalias termicas. Los resultados muestran la utilidad de la metodologia propuesta para la estimacion de areas quemadas y su importancia a la hora de localizar de una forma rapida las zonas de intervencion prioritaria, asi como para la planificacion de futuros trabajos de restauracion de la zona afectada.
In situ analysis of nitrifying bacteria in sewage treatment plants

Autotrophic microbial nitrification is the key process in the removal of ammonia from wastewater. To avoid the limitations of traditional microbiological methods an in situ identification technique for ammonia- and nitrite-oxidizing bacteria was developed. Based on comparative sequence analyses we designed a collection of 16S ribosomal RNA-targeted oligonucleotide probes for all validly described members of the genus Nitrobacter . Whole cell hybridizations of target and reference cells with fluorescent probe derivatives were used to determine the optimal hybridization stringency for each of the probes. These probes were applied together with a recently developed probe for important members of the genus Nitrosomonas for simultaneous identification of ammonia- and nitrite-oxidizing bacteria in natural and engineered systems. Ammonia-oxidizing bacteria were identified in situ in river water, epiphytic biofilms from eutrophic wetlands, oligotrophic biofilms, a nitrifying trickling filter biofilm as well as in all analyzed nitrifying activated sludge samples. In none of these samples could Nitrobacter cells be detected in situ . However, all hitherto described Nitrobacter species and a strain of Nitrobacter sp. isolated from one of the analyzed nitrifying activated sludge samples showed bright hybridization signals with all Nitrobacter specific probes. Possible reasons for the absence of in situ detectable Nitrobacter cells are discussed.
Race and Computer Vision

-- Forthcoming in Andreas Sudmann (ed.) The Democratization of AI. Berlin, Germany: Transcript. -- This article examines how attempts to make computer vision systems accessible to users with darker skin tones has led to either the hypervisibility of phenotypic racial traits, particularly morphological features like hair texture and lip size, or the invisibility of race. Drawing on critical race theory and the problematic history of racial representation in photographic media, he demonstrates how racial biases are prevalent in the visual datasets that many contemporary computer vision algorithms are trained on, essentially hardcoding these biases into our computer vision technologies, like Google Photos. The most frequent industry reaction to these hardcoded racial biases is to render race invisible in the system, as was done with Google Photos. He further shows how the invisibility of race in computer vision leads to the familiar problems of ‘color blindness,’ only expressed in new media. The author argues that these constitute fundamental problems for the potential democratization of AI and outlines some concrete steps that we might take to more strongly demand egalitarian computer vision systems.
Measure for Measure: Politics of Quantifying Individuals to Govern Them

»Maß für Maß: Die Politik, Individuen zu quantifizieren, um sie zu regieren«. This article compares a variety of modes of quantifying individuals to govern them. The analytical grid issues from a former research program on the Politics of Statistics that focused on one of these modes of governing by numbers, the statistical nation state, which is here included in an array of more recently developed governing numbers based on benchmarking, digital tracking, or self-quantifying. Three main operations differentiate modes of governing by numbers: measuring individuals for quantification, taking political measures accordingly to guide their behaviors, and an intermediate operation that is often less visible although situated between the two previous ones and needed to link them: evaluating the situation through a measured judgment that justifies the monitoring based on numbers. This analysis breaks down data into the sequential steps of the transformations chain of information formats needed to pass from an individual person to a governing figure. The plurality of modes of evaluation, and its reduction by quantification, is given high significance, as well as the way each mode of governing affects individuals, their identity and their possibility to critically reflect and question.
Two new species of Raillietina (Cestoda : Davaineidae) from Columbiformes of Beppu City, Japan

Six and twelve cestode specimens were obtained from the small intestine of the pigeons, Columba livia domestica captured at Beppu City, on January 10 and 24, 1992. The former and the latter cestodes were identified as R. (R.) kyushuensis n. sp. and R. (R.) japonensis n. sp. , respectively. Thirty six species of the subgenus Raillietina of the genus Raillietina have been reported from the pigeon. The former new species closely resembles Raillietina (Raillietina) flaminata Meggitt, 1931, but it differs from that by the smaller size of scolex, the larger size of rostellar hooks, the larger number of testes, the location of cirrus pouch and the larger number of egg capsules
A primer of population genetics

Part 1 Genetic variation: genetic and molecular essentials types of polymorphisms organization of genetic variation inbreeding. Part 2 The causes of evolution: mutation migration natural selection random genetic drift. Part 3 Molecular population genetics: molecular polymorphisms patterns of change in nucleotide and amino acid sequences polymorphism and divergence molecular phylogenetics transposable elements. Part 4 The genetic architecture of complex traits: types of complex traits phenotypic variation genetics and environment artificial selection correlation between relatives quantitative genetics of natural populations complex traits with discrete expression quantitative trait loci (QTLs).
Ecological Versatility and Community Ecology

Preface 1. An introduction to ecological versatility 2. Defining and measuring versatility 3. Studies of versatility in natural populations 4. The influence of interspecific interactions on versatility 5. The influence of population structure on versatility 6. Ecological versatility and population dynamics 7. Versatility and interspecific competition 8. Ubiquity or habitat diversity 9. Recapitulation and commentary Glossary of terms Appendices References.
Possibilities and Deliminations In Vivo Determination of Egg Composition

The aim of these experiments was to examine the applicability of two different methods (TOBEC and CT) for the in vivo prediction of egg composition. In the first experiment the electrical conductivity of 46 hen's eggs was measur ed by means of the TOBEC (Total Body Electrical Conductivity) method and correlations were calculat ed between the measured values and different egg components (dry matter, protein, fat). In the secon d experiment 120 hen's eggs were scanned by CT (computer tomography), in order to develop the CT measurement protocol and to determine correlations between the information content of the CT images and yolk content of the eggs. In the case of the TOBEC measurements it was established that the dry matter and fat content of the eggs could be measured with medium accuracy (R≤=0.472 and R≤=0.486, respectively), when the electrical conductivity (E-value) and the weight of the eggs a re used as independent variables in the linear regression model. In the second experiment it was o bserved that the separation of egg yolk and albumen is not possible based on the X-ray density values of the pixels (CT picture elements) because of the overlapping values of yolk and albumen. The determination of the surface of egg yolk on the CT pictures gave fairly good results, but this type of the evaluation is very time consuming. Therefor e further development of the new egg-separation and s egmentation software is needed, which can be used to determine the whole volume of the yolk, alb umen and shell automatically.
Top 10 of the most dangerous weed species in maize stands in the Slovak Republic in the years 2000-2010.

In the years 2000 – 2011 (12 years) was conducted weed survey on the farms in conventional farming system. The goal was to detect the most harmful weeds, as important biotic, environmental stress factor, on the farms in the canopies of maize for grain in maize, sugar beet and potato production regions of the Slovak Republic. The fields were selected in all production regions of Slovakia. An actual weed infestation was evaluated before preemergence application of herbicides. Screening of each field was made on 1 m area with four replications. The four randomly established sample quadrants were situated minimally 20 m from field margin and apart from each other, respectively. The level of infestation was evaluated according to average density of weeds per square meter. Obtained data from farms was statistically analyzed by correlation analysis in Statistica 7.0. According to the obtained data and results of weed survey the most troublesome weeds with the heaviest weed infestation level of maize for grain stands were in maize production region Chenopodium spp. , Amaranthus spp. and Echinochloa crus galli (L.)P. Beauv. ; in sugar beet production region Persicaria spp. , Atriplex spp. and Echinochloa crus galli (L.)P. Beauv. ; in potato production region Atriplex spp. , Chenopodium spp. and Elytrigia repens (L.) P. Beauv. An actual weed infestation depends on production region. After herbicides control the significant changes in weed flora were noted in term of abundance and share of some weed species on total weed community. The dynamics of actual weed infestation depend on climate conditions of maize, sugar beet and potato production region, forecrop and canopy health condition. Weeds are always a problem in maize for grain stands. They can rapidly reduced the yield of maize, but management and control may be considered necessary to safeguard crop quality and yield. The originality of result is in mapping the weed species and its actual weed infestation in cultural crops (maize for grain stands).
Mediadores da via intrínseca da morte celular programada relacionados à infecção in vitro pelo herpesvirus bovino tipo 5

Bovine herpesvirus 5 (BoHV-5) is α-herpesvirus responsible for neurological disease in young cattle and also occasionally incriminated in reproductive disorders. In spite of many studies describing the apoptotic pathways induced by viruses belonging to the family Herpesviridae, scare information about intrinsic programmed cell death pathway in host-BoHV-5 interactions is currently available. BoHV-5 was able to replicate and to produce cytopathology characterized by cellular swelling and cell fusion on both mesenchymal and epithelial cell lines. Viral antigens were detected in infected cells by immunofluorescence assay at 48 to 96 h post-infection (p.i.). According to sequential p.i observation, at 48 to 72 h p.i. higher fluorescent signals were visible for anti-apoptotic BCl-2 antigens in comparison to Bax, considered a proapoptotic protein. Infected cells revealed an increase of BCl-2 phenotype population from 48 to 96 h p.i. by flow cytometric analysis. At 48 to 96 h p.i. Bax mRNA was not expressed among of any infected cell monolayers. In contrast, BCl-2 mRNA was quantified Log10 1,6 x 10 cDNA copies at all p.i. for both cells. BoHV-5 replication seems to modulate BCl-2 expression and respective gene transcription in order to enhance production of progeny virus.
Deriving Daily Discharges from Satellite Radar Altimetry and Ensemble Learning Regression in Poorly Gauged River Basins

to estimate river discharge (Q). However, most studies have used a rating curve based on a single hydraulic variable or the Manning equation (multiplicative method). Kim et al. (2019) have applied the ensemble learning regression method for estimating river discharge (ELQ), which provided more accurate results than the previous methods based on a single rating curve (depth-discharge relationship). However, ELQ has been tested only over the Congo River and obtained Q at sparsely distributed dates (35-day interval of Envisat altimetry data). In this study, we aimed at estimating daily Q from 2003 to 2005 (3-year) using ELQ and linearly interpolated altimetry-derived water levels over the lower Mekong River as a case study. Donghwan Kim1, Hyongki Lee1, Faisal Hossain, Susantha Jaysinghe2, Senaka Basnayake2, Farrukh Chishtie2, Duong Du Bui3 Deriving Daily Discharges from Satellite Radar Altimetry and Ensemble Learning Regression in Poorly Gauged River Basins
Production of nucleic acid-related substances by fermentative processes. XVII. Inosine accumulation by mutants of Brevibacterium ammoniagenes strain improvement and culture conditions.

Improvements were found in the inosine productivity of Brevibacterium ammoniagenes KY 13714, which is an adenine leaky and 6-mercaptoguanine resistant mutant. A highly productive mutant, KY 13761, was selected after the addition of 6-methyIthiopurine resistance and guanine requiring character to KY 13714 and after repeating single colony isolation.Culture conditions for the practical production of inosine were investigated using KY 13761. It was found that the concentrations of phosphate, magnesium, and adenine were important. Carbon sources and natural nutrients also showed profound effects on inosine accumulation. Especially, effective was the feeding of inverted molasses and urea for production of inosine. Under optimal conditions, 31 mg of inosine per ml was accumulated after 42 hr cultivation in a 5 liter jar fermenter at 32°C. A growth-associated type of accumulation was confirmed in inosine production with KY 13761.