Miracle-dz/UniFAR-FTUs huggingface dataset:
A review Historical evolution of preformistic versus neoformistic (epigenetic) thinking in embryology

In the classical embryology there exist two main concepts to explain the rising of a living being. At one hand there exists the theory of preformation i.e. all the parts of the future embryo would already exist preformed during the preembryonic or early embryonic period. On the other hand there is the epigenetic view in which it is propounded that all parts arise by neoforma- tion from interacting (induction) previously existing, apparently simpler structures. We found evidence that initially a kind of pre- formation (or pre-existence), disposed in concentric circular layers, exists in the full grown oocyte and early germ. After normal development these circular layers will settle successively, from the centrum to the periphery, into the central nervous system, the notochord, somites, lateral plates (coelom) definitive endoderm. Under influence of mechanical and gravitational forces an early epigenetic development starts by unequal oblique uptake (unidirectional chaos) and segregation of ooplasmic determinants in the germ. So an epigenetic cascade of early general body plan formation occurs in the vertebrate embryo. Recently, we demonstrated by hemi-sectioning of avian unincubated blastoderms that both a kind of preformational (mosaicism) as epigenetic (regulation) behaviour depends on the spatial, ooplasmic distribution of Rauber's sickle material, homologous to the also sickle-shaped Wnt expressing gene region in ascidians. This clearly brings preformation and epigenesis much closer together since there is a common influencing ooplasmic factor. An ooplasmic continuity bridging the premature oocyte ooplasm to the embryonic primordial germ cells of the following generation is demonstrated. Both nuclear and ooplasmic continuity in the oocytes, present in the ovary of birds and mammals, is shown by radioactive premeiotic DNA labelling.
A PHYLOGENY OF BEJARIA (ERICACEAE: ERICOIDEAE) BASED ON MOLECULAR DATA

Phylogenetic relationships of ten of the fifteen recognized species of Bejaria were examined using molecular ( ndhF 5', mat K; chloroplast and waxy ; nuclear) data. Parsimony analyses were performed in PAUP for each gene, combined chloroplast data and total combined data. Bayesian analyses were performed in MrBayes for the waxy, combined chloroplast and total combined data sets. Bejarieae (Bejaria, Bryanthus and Ledothamnus) is not monophyletic in any analysis. The sampled members of Bejaria are monophyletic in all analyses with strong support. Bejaria racemosa, the only species from North America, is strongly supported as sister to all other Bejaria members.
Untargeted metabolomics as a novel tool in coffee research

Plant Research International, Wageningen-UR, Wageningen, The Netherlands Departamento de Engenharia, Universidade Federal de Lavras, Lavras, 37.200-000, Minas Gerais, Brasil Department of Plant Physiology, Wageningen-UR, Wageningen, The Netherlands Corresponding author: Ric de Vos, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands E-mail: ric.devos@wur.nl; tel: +31-317-476983; fax: +31-317-418094
Septoria epambrosiae sp. nov. on Ambrosia artemisiifolia (common ragweed).

Farr, D. F. & L. A. Castelbury (2001). Septoria epambrosiae sp. nov. on Ambrosia artemisiifolia (common ragweed). Sydowia 53(1): 81-92. Recently an unidentified Septoria was reported to be pathogenic on Ambrosia artemisiifolia L. (common ragweed) in Hungary and may have potential as a biocontrol agent for this noxious weed. After reviewing the two previously known species of Septoria on Ambrosia (Asteraceae), the Septoria from Hungary is described as a new species, Septoria epambrosiae. A synopsis of the three species of Septoria on Ambrosia is provided. Based on a molecular analyses of the nSSU and complete ITS region of the rDNA, the taxonomic relationships of S. epambrosiae are determined. Septoria epambrosiae clusters with members of the Dothideales with the teleomorph most likely a species of Mycosphaerella.
Influencia de la producción integrada del olivar sobre la calidad del aceite de oliva virgen

A study has been conducted to determine the influence of integrated olive production on the quality of extra virgin olive oil. On two different dates, samples from three different holdings were taken in integrated production (I) parcels, and in conventional production (C) parcels, both adjacent. The analytical determinations were free acidity, peroxide value, K 232 and K 270 , fatty acid composition, esterols, phenolic compounds, tocopherols, stability to oxidation and sensory analysis. Most interesting among the results obtained were total contents of esterols and tocopherols, higher in olive oils of integrated production.
The application and challenges of RNA-sequencing to the study of circadian rhythms

The circadian clock drives daily rhythms in behavior and physiology, often in anticipation of the coming dusk or dawn. Almost all organisms possess an internal time-keeper, as it represents an adaptation to one of the most ancient selective pressures; the day-night cycle. Mounting evidence suggests the clock plays important roles in critical metabolic and signalling pathways, the sleep/wake cycle, immune function, as well as learning and memory. Perhaps more importantly, misregulation of the clock is associated with metabolic disorders, neurodegeneration, and incidence of cancer. In an effort to unlock the connections between the circadian clock and these downstream effects, researchers have searched for genes with rhytmic transcription driven by the clock. These so-called clock-controlled genes (CCGs) mediate these observed rhythms in important biological pathways. Over the past decade, researchers have searched for these CCGs using microarrays. However, with the growing popularity of high-throughput sequencing, and revelations about both the number and importance of non-coding RNAs (ncRNAs), investigators have begun to use RNA-seq for their circadian profiles. While RNA-seq has led to important findings about the circadian regulation of RNA editing, small RNAs, and epigenetic modifications, there is still much about its biases and limitations that we are still discovering. To this end, this thesis seeks to build upon this foundation and examine the use of RNA-seq for studying circadian transcription. I applied a hybrid RNA-seq, microarray approach to assay the circading transcriptome in liver, and eleven other mouse tissues. Notably, I saw that 1/3rd of ncRNAs conserved between human and mouse show rhythmic transcription. These rhythmic transcripts are strong candidates for future functional validation, and include important miRNA and snoRNA precursors. Additionaly, I found hundreds novel ncRNAs with rhythmic expression, which may provide novel CCGs. Lastly, I developped and applied a method for identifying the sources of bias in RNA-seq protocols. Taken together, this work extends our understanding of the circadian transcriptome, and the challenges associated with interpreting RNA-seq data. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Genomics & Computational Biology First Advisor John B. Hogenesch
Temperature affects plant development, flowering and tuber dormancy in calla lily (Zantedeschia)

Summary The effects of temperature on plant growth, flowering and tuber dormancy of coloured calla lily were investigated in the two cultivars Calla Gold (CG, hybrid of Z. rehmannii) and Black Magic (BM, hybrid of Z. albomaculata). Four experiments were performed in controlled conditions in a phytotron, under shade (50% of solar radiation) and 16 h daylength. Effects of temperature on plant development and tuber size were studied in Exp. 1 at constant temperature regimes of 17/12, 22/17, 27/22 and 32/27°C (day/night temperature). Dormancy and flowering potential of the tubers produced under these conditions were subsequently determined at the same temperatures in Exp. 2. Effects of temperature shifts during the growth-cycle were studied in Exp. 3 and 4 by transferring plants between low (22/16 or 23/15°C) and high (28/22 or 29/21°C) temperature, and compared with controls grown at constant temperature. After plant senescence and tuber harvest, time-course of bud sprouting and elongation were followed during storage at 20°C, as a measure of tuber dormancy relaxation. CG sprouted and flowered earlier, produced flowers over a wider range of temperatures and had smaller tubers than BM, but the responses of the two cultivars to temperature were generally similar. Leaf production was faster, and flowering and senescence were generally earlier with increasing temperature in the range 17/12 to 32/27°C. In contrast, the proportion of flowering plants was highest at 22/17°C, and tubers were larger at 22/17°C (CG) and at 22/17 – 27/22°C (BM). Plants flowered if the tubers had previously grown at 17/12°C or 22/17°C, while 27/22°C and 32/27°C were inhibitory. Length of the growth-cycle (from tuber planting to plant senescence) was relatively constant in the range 22/16 to 29/21°C, spanning 6–7 months in both cultivars. Temperature during the growth-cycle affected tuber size and its dormancy. Smaller and more dormant tubers were produced the longer the period of the growth-cycle that the plants spent at high (28/22 or 29/21°C) compared with low temperature (22/16 or 23/15°C). Tuber dormancy (time to onset of bud sprouting) was negatively correlated with rate of bud elongation during storage. Sprouting in storage was generally earlier, and bud elongation faster, when tubers were grown at low than at high temperature.
Development Of Kinase Catalyzed Biotinylation To Study Phosphoproteomics

DEVELOPMENT OF KINASE CATALYZED BIOTINYLATION TO STUDY PHOSPHOPROTEOMICS by KONA ARACHCHILAGE CHAMARA SENEVIRATHNE AUGUST 2013 Advisor: Prof. Mary Kay Pflum Major: Chemistry (Organic) Degree: Doctor of Philosophy Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to identify phosphoproteins in normal and diseased states is critical to fully characterize cell biology. Our lab recently discovered kinase-catalyzed biotinylation, where ATP-biotin is utilized by kinases to label phosphopeptides or phosphoproteins with a biotin tag. To explore kinase-catalyzed biotinylation, kinetic measurements were obtained with various kinases and the data indicated that kinase-catalyzed biotinylation occurs with catalytic efficiency appropriate for phosphoproteomics application. Next, the susceptibility of the biotin tag to phosphatases was characterized and found that the phosphorylbiotin group was relatively insensitive to protein phosphatases. Importantly, robust kinase-catalyzed biotinylation occurs without the need for phosphatase inhibitor treatment. The results suggest that kinase-catalyzed biotinylation is well suited for phosphoproteomics studies, with particular utility towards monitoring low abundance phosphoproteins. Finally, we report application of kinase-catalyzed biotinylation to the enrichment of the phosphopeptides in cell lysates for mass spectrometrybased phosphoproteomics analysis. Significantly, the biotinylation strategy was used to enrich full-length phosphoprotein, which is challenging using metal ion purification. With the utility of
The influence of gene polymorphisms, modifiable lifestyle factors, and toxicants on the protective effects of the paraoxonase genes

PON1 is an important esterase and antioxidant that circulates through the blood bound to HDL. Its ability to hydrolyze synthetic organophosphates (OPs), a component of many pesticides, makes this a potentially important enzyme in agricultural communities. Its dramatic individual variation within communities due to common polymorphic variants and influence by lifestyle, heath parameters, and exposures makes this an intricate mechanism of internal protection. Significant contradiction remains in the literature regarding the activity of this enzyme during aging, but no study thus far has examined intraindividual variation in adults over time. This study attempts to determine what factors affect individual PON1 activity over a 15-year time span in an agricultural population by examining 337 individuals from the Keokuk County Rural Health Study through the Great Plains Center for Agricultural Health at The University of Iowa. These individuals underwent medical screenings and questionnaires roughly every five years from 1994-2011. Serum was analyzed for PON1 activity using a non-toxic two-substrate spectrophotometric assay with phenyl acetate (PA, arylesterase activity) and 4(chloromethyl)phenyl acetate (CMPA, CMPAse activity). Four polymorphisms, Q192R, L55M, T-108C, in PON1 and PON2S311C, were also genotyped for each individual, with Q192R and PON2S311C showing the strongest correlations with both CMPA and PA levels. This population averaged 50 years of age at the study onset and was pre-hypertensive and overweight throughout. Mean serum PA levels over the three rounds were 82.05 units/mL, 85.62 units/mL, and 81.3 units/mL, respectively. Using CMPA as the substrate, mean serum PON1 levels were 21.73 units/mL, 24.10 units/mL, and 22.80 units/mL, respectively. Male smokers had significantly lower PA activity for all three rounds.
Differential gene expression in the heart of hypoxic chicken fetuses (Gallus gallus)

Evidence has shown that hypoxic hearts have greater heart/fetus mass ratio. However, it is still unclear if either hyperplasia or hypertrophy causes the relatively increased heart mass. Furthermore, the genes that might be involved in the process have not yet been identified. In the present study, the cardiac transcriptome was analyzed to identify differentially expressed genes related to hypoxia. Eggs were incubated for 15 and 19 days in two different environments, normoxic and hypoxic. Normalized microarray results were analyzed to isolate differentially expressed probes using the Affymetrix chip. Total RNA was also isolated from another set of fetuses incubated in the same conditions and used to perform a qPCR in order to confirm the microarray results. In the four groups (15N, 15H, 19N, 19H), some probes were differentially expressed. From the eggs incubated for 15 days, the microarray revealed five probes that were differentially expressed according to the criteria (p 2) in the two programs (PLIER & RMA) used to normalize the data. From the eggs incubated up to 19 days, eight probes were differentially expressed in both programs. No further tests were performed on the 19 days fetuses since there was no significant difference in that group after incubation for the heart/fetus mass ratio. Apolipoprotein-A1, p22, similar to ENS-1 and b2 adrenergic receptor were further tested in qPCR (15 days sample). The differently expressed genes are linked to cell division and should be further studied to identify their function, especially the similar to ENS-1.
Simulation of experimental force-displacement curves by a Finite Element elimination technique

A recently developed Finite Element (FE) elimination technique to simulate automatic crack propagation was used to predict experimentally measured force-displacement curves for chevron-notched three-point bending specimens with side-grooves. Numerical predictions (2D, plane strain) and experimental measurements (3D) are compared for this special notch geometry by using a calculated 'effective width'. The FE elimination algorithm is applied to ductile failure of Al(6061)-(20vol%)SiC metal matrix composites. Macroscopic crack appearance and corresponding force-displacement curves have been successfully simulated by using a combination of critical stress and strain values as failure criterion.
UNstoppable

In 2016, December 1st—already an occasion to highlight the importance of health and human rights as World AIDS Day—took on new significance as a landmark in one of the highest-profile health and human rights cases of the twenty-first century. This was the day that United Nations (UN) Secretary-General Ban Ki-moon finally issued an apology on behalf of the organization for its role in causing the Haitian cholera epidemic that has claimed close to 10,000 lives and made another 800,000 fall ill.1 This simple apology is something that victims of the epidemic have been waiting to hear for years, ever since cholera-infected feces from a United Nations Stabilization Mission in Haiti (MINUSTAH) peacekeeping base were allowed to enter the river system relied on by tens of thousands of Haitians back in October 2010. That the apology took this long to receive highlights the struggles that advocates continue to face in getting the UN to make things right for victims of the epidemic. Haitians devastated by cholera—through their own illness or the deaths of breadwinners and loved ones—first petitioned the UN for remedies in November 2011, a year after the epidemic began. The obligation to provide remedies for “personal injury, illness or death arising from or directly attributed to MINUSTAH” is explicitly contemplated in the Status of Forces Agreement between the UN and the government of Haiti, itself rooted in the Convention on Privileges and Immunities of the United Nations (CPIUN), which makes the mandatory settlement of claims a reciprocal duty in exchange for broad immunity from suit in court.2 Nonetheless, the UN did not dignify the request with a response until 15 months had gone by, at which point the request was tersely dismissed on the grounds that it was “not receivable” since “consideration of these claims would necessarily include a review of political and policy matters. ”3 No explanation was given as to how negligent sanitation was a political or policy matter, or how the injuries suffered by Haitians differed from others the UN has compensated as a matter of course in the past. The victims of the epidemic did not back down, however; instead, they took further steps to assert their fundamental rights, from the right to health to the right to due legal process. At the heart of the advocacy movement was a pair of organizations, the Haiti-based Bureau des Avocats Internationaux (BAI) and its American-based partner, the Institute for Justice and Democracy in Haiti (IJDH). Tiny organizations with limited resources, they faced Herculean odds taking on the world’s largest intergovernmental organization. Nevertheless, seeking justice for their clients, BAI and IJDH launched a lawsuit against the UN in the fall
Using Word Embeddings in Linked Data Search Poster description

In the last decade, a vast number of linked data (LD) datasets have been created. One of the main challenges in the consumption of linked data is to create visual and natural language interfaces for common users – interfaces which hide the complexity of underlying schemata and the need to write queries in languages such as SPARQL [1]. Ontodia is an open-source library for simple OWL and RDF diagramming and visual exploration. Additionally to the graphical representation, Ontodia provides natural language input fields for example to search for specific entities or within the properties of an entity. Currently, only exact matches to a user query in the labels of properties and entities are found and returned. Giving an example, if a user searches in the Wikidata dataset for the “successes” of entity Roger Federer, no exact matches in property labels exist, and therefore no result can be displayed. Using pre-trained word embedding models, which were extended with representations of the Wikidata properties (see below for system details), the improved system ranks the entity properties by similarity to the input query. Figure 1 provides a screenshot of the result for the described scenario.
Myxopapillary Ependymoma with Drop Metastasis in a Young Child

Background : Myxopapillary ependymoma (MPE) is a rare variant of ependymoma. It has an indolent course in adults but in children it is aggressive. Because of its rarity there are no guidelines for management of metastatic MPE. Hence we report this case of MPE with drop metastasis treated with cranio-spinal irradiation (CSI) after subtotal resection (STR). Case Report : A 9 year old girl was evaluated elsewhere for low backache. MRI whole spine showed intra-dural mass compressing the conus and another lesion in the sacral spinal canal. She underwent STR. Post-operative histopathological examination was consistent with myxopapillary ependymoma. She was treated with CSI. Conclusion : Cranio spinal irradiation is essential for the treatment of metastatic MPE in pediatric population.
One Case of Suspected Angiostenosis Revealed by MRA Following Carotid Endarterectomy Due to a Rare Cause

We herein report on a case in which magnetic resonance angiography (MRA) following carotid endarterectomy revealed the appearance of angiostenosis due to an artifact of metallic powder, which was thought to have come from an old surgical instrument. The patient was a 77-year-old male. Carotid endarterectomy (CEA) was performed for stenosis in the internal carotid artery of his left neck (82%). Upon observing a decline in renal function following CEA surgery, a postoperative cervical MRA revealed the appearance of high-grade stenosis at the common carotid artery on which surgery was performed. No stenosis was revealed upon carotid ultrasonography and angiography. In the original MRA image, an orbicular low intensity area was observed in concordance with the narrow segment. 3D computed tomography (3D-CT) revealed a metallic finding, suggesting it was an artifact caused by metal powder. Close inspection of the metal surgical instruments used during surgery revealed slight damage to a suture snare which had been used for 30 years. Going forward, it is necessary to pay attention to old surgical instruments, introduce a system by which the number of years and the frequency of use of each surgical instrument can be learned, and replace them with new equipment as necessary.
Layering Learning for Work-Readiness in a Science Programme

In order to prepare our students for a challenging workplace, the Department of Viticulture and Oenology at Stellenbosch University in South Africa have ‘layered’ Engaged Learning strategies throughout the four-year undergraduate degree in an approach that is innovative in a science-based programme. In this research project, we assessed the effects of service-learning (SL) and a six-month internship on student employability by analysing reflections that were collected over a number of years. We also asked industry members whether they felt students had improved in key areas after the final year internship. The student submissions for SL showed evidence of personal growth and transformation, and those for the internship reflected industry requirements for professional skills in a complex and technically demanding milieu. It was found that these engaged experiences provided sound preparation for working life, as well as giving students opportunities for self-questioning and personal growth, which is unusual in the natural sciences learning environment.