Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of regulatory phosphorylation sites on the human kinetochore

Ein grundlegendes Merkmal der Mitose ist die exakte Aufteilung des genetischen Materials auf die Tochterzellen. Ausschlaggebend fur diesen Prozess ist die Aufteilung der Schwesterchromatiden zu jeweils entgegengesetzten Zellpolen durch die Mitotische Spindel. Die Anheftung der Spindel-Mirotubuli erfolgt uber Kinetochore, proteinose Strukturen die sich an den Zentromeren der Chromosomesn befinden. Kinetochore sind dynamische Strukturen, die sensibel auf Mikrotubuli-Anheftung, Zugspannung sowie auf die Signalubertragung des „Spindle Assembly Checkpoint“ (SAC) reagieren, sie spielen daher eine auserordentlich wichtige Rolle bei der Ausbildung der Metaphase Spindeln sowie der Teilung der Schwester-Chromatiden in der Anaphase. Kinetochore bestehen aus vielen Proteinkomplexen, deren molekulare Charakterisierung gerade andauert. Zu den bereits naher charakterisierten Kinetochor-Proteinkomplexen gehoren unter anderem die Komplexe Mis12, Hec1 und RZZ, von denen man annimmt, dass sie die Generierung und Aufrechterhaltung der Zugspannung sowie die Rekrutierung von Spindel Checkpoint Komponenten an die Kinetochore regulieren. Weiterhin ist bekannt, dass sich viele Kinasen, wie Cdk1, Aurora B, Plk1, Mps1 und BubR1 an den Kinetochoren befinden, was darauf hinweist, dass Kinetochor-Proteine potentiell wichtige Substrate fur diese Kinasen darstellen. Mit dem Ziel, Komponenten und Phosphorylierungen dieser Proteinkomplexe in mitotischen humanen Zellen zu untersuchen, habe ich Antikorper gegen Kinetochor-Proteine hergestellt sowie HeLa Zellen generiert, die Kinetochor-Proteine mit Affinitats-tags expremieren. Ein Affinitats-tag erleichtert die Aufreinigung der Proteine und ermoglicht Massenspektrometrie Experimente durchzufuhren. Von funf generierten Antikorpern, zeigte sich einer (gegen die Mis12 Komponente DC8) als hoch spezifisch und effektiv fur die Immunprazipitation. Die Expression der getaggten Kinetochor-Komponenten war hingegen nicht ausreichend fur die angedachten Affinitats-Aufreinigungen. Mittels des generierten anti-DC8 Antikorpers, reinigte ich viele der bekannte Mis12 Komponenten, den kompletten Hec1 Komplex, weitere mitotische Spindel-Proteine (wie HP1-gamma, SPAG5 und dynein light chain) sowie einige neue Interaktionspartner (wie C15orf23, RABGAP1 und claspin) aus mitotischen sowie Interphase HeLa Zellextrakten auf. Durch weitere Analyse dieser aufgereinigten Proteinkomplexe identifizierte ich insgesamt 44 Phosphorylierungsstellen in sechs der Proteine, DC8, Q9H410, C15orf23, PFKFB2, RABGAP1 and SPAG5. Beim Vergleich der Phosphorylierungs-Muster dieser Proteine aus Interphase und Mitose, wurden 18 Mitose-spezifische Stellen gefunden. Die Identifizierung von Phosphorylierungsstellen leistet einen wichtigen Beitrag zum Verstandnis der dynamischen Steuerung der Kinetochore in der Mitose.
In v Itro antioxidant activity of methanol extract of AllIum scorodopr Asum

±1.03 mg) and ability to scavenge DPPH radical, as well as total phenolic (36.692 ± 4.475 µg G a/mg of dried bulb extract) and flavonoid content. Total phenolic and flavonoid content assay were correlated with ferric reducing power and “scavenging” radical capacity test, and correlation among them was significant. Our research showed that Allium scorodoprasum can be considered as plant with antioxidant compounds.
Effects of ultrasonic waves on eggshell strength and hatchability of layer-type breeder eggs

Two trials were conducted to investigate the effects of exposing layer-type breeder eggs before incubation to ultrasonic waves (ULT). Eggs were subjected to ULT of 117 volts at 40 kHz for up to 15 minutes. Eggshell breaking force (EBF), hatchability and chick hatching weight (CHW) of Balady breeder eggs (Trial 1), and egg weight loss, embryo weight, hatchability and CHW of Leghorn hen eggs (Trial 2) were measured. In Trial 1 the eggs were subjected to seven treatments: non-dipped (control), and dipped for 5, 10 and 15 minutes in a water bath (W5, W10 and W15) or a ULT bath (ULT5, ULT10 and ULT15). In Trial 2 the eggs were subjected to four treatments, a control (ULT0) and the ultrasonic treatments, ULT5, ULT10 and ULT15. In treatments ULT10 and ULT15 the EBF of Balady eggs was significantly reduced while the hatchability of the Balady and Leghorn eggs was significantly reduced by the ULT15 and W15 treatments, compared with the control. Orthogonal contrast (control vs. ULT) indicated that ULT exposure of eggs reduced their EBF significantly. Percentage egg weight loss, embryo weight and CHW was not affected by the treatments. It was concluded that exposure of eggs to ULT of 117 volts at 40 kHz for 15 minutes reduced EBF and hatchability of layer-type breeder eggs without altering egg weight loss, embryo weight or CHW.
Distribution and Some Properties of Cell Wall Polysaccharides in Rye Milling Fractions

Abstract A rye sample (cv. Voima) was fractionated by a laboratory scale roller mill into eight fractions: six flour fractions and bran and short fractions originating from the outer kernel layers. The extractabilities of dietary fibre and pentosan were clearly higher in the flour fractions than in the outer fractions. Pentosan and β-glucan were present throughout the kernel in different proportions, although in much higher amounts in the outer parts. The pentosan present in the outer layers was less branched (arabinose:xylose 0·63–0·75) than that in the flour fractions (arabinose:xylose 1·1–1·2). The outer fractions showed the highest water absorption capacities. When extracted with water the fractions yielded solutions with different viscosities, and the shorts extract had clearly the highest viscosity. Extract viscosity was shown to correlate with the content of water-extractable pentosan in the particular fraction. The molecular mass of the solubilised pentosans varied from 150 000 to 800 000 as revealed by size exclusion-HPLC with laser light-scattering detection. The pentosan with lower molecular mass was shown to be less branched than the larger polymers.
TAT-Mediated Delivery of p27 in Tumor Cell Lines as a Potential Therapeutic Peptide

TAT-fusion proteins (TAT-wt-p27, TAT-pt-p27, TAT-N'-p27) were introduced into the cells by protein transduction method. The mechanism by which transduced 27 influences on the regulation of cell cycle and apoptosis, were explored. TAT-p27-fusion proteins affected the proliferation of examined cell lines depending on type of the cells and protein. Transduced p27 induced accumulation of cyc D1 and D3, with slight differences among the form of protein. Expression of cyc D2 and E was mainly unchanged. Furthermore, TAT fusion proteins promoted apoptosis, which resulted in activation of cas 3, appearance of poly (ADP-ribose) polymerase and DNA fragments, as well as the activation of apoptosis-inducing factor. The results pointed that transduced p27 activates apoptosis through activation of different signal transduction pathways. Thus, the molecule of p27 could be appropriate for treatment of tumors with deregulated its function. Also, the protein transduction method could find the application in specifically targeted cancer therapy.
NUTRITIONAL VALUE OF YELLOW-POPLAR FLOWERS TO DEER IN THE SOUTHERN APPALACHIANS

Abstract Yellow-poplar (Liriodendron tulipifera) flowers have been reported to be an important component of the spring diets of white-tailed deer (Odocoileus virginianus) in the southern Appalachians. We quantified the nutritional contribution of yellow-poplar flowers by comparing flower nutrient content to published nutrient requirements for deer. Yellow-poplar flowers exceeded the calcium, phosphorus, crude protein, and digestible energy requirements (P < 0.001) for productive processes. However, sodium requirements for antler growth and digestible energy requirements for peak lactation for twin fawns were not met by yellow-poplar flowers. Similar to oak (Quercus spp.) mast in the fall months, yellow-poplar flowers are an important seasonal source of energy for deer.
Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods

Small intestinal bacterial overgrowth (SIBO) is a commonly diagnosed gastrointestinal disorder affecting millions of individuals throughout the United States. It refers to a condition in which there is an excess and imbalance of small intestinal bacteria. Despite its prevalence, it remains underdiagnosed due to the invasive nature of diagnostic testing. Symptoms observed in SIBO, including abdominal distension, bloating, diarrhea, and gas formation, are nonspecific and can overlap with other gastrointestinal disorders. Frequently cited predisposing factors include gastric acid suppression, dysmotility, gastric bypass, and opioids. The diagnostic gold standard remains small bowel aspirate and culture. However, due to its invasive nature, it remains an unpopular method among patients and clinicians alike. Glucose and lactulose breath testing have become the go-to diagnostic method in clinical practice due to its noninvasive nature and low cost. Treatment is guided towards the eradication of bacteria in the small bowel and usually consists of a prolonged course of oral antibiotics. Due to recent advances in our understanding of the human microbiome, we are surely poised for a transformation in our approach to diagnosing and treating this condition.
Occurrence of Cutaneous Melanoma in a Patient with Previous History of Uveal Melanoma. Same Embryology, Different Driver Mutation Landscape

Cutaneous and uveal melanomas originate from melanin-producing neural crest-derived cells. They differ from each other in their genetic background, ways of spreading and prognosis. Worldwide, malignant melanoma is a common skin tumor with poor prognosis and its prevalence is increasing rapidly in fair-skinned populations. Both cutaneous melanoma (CM) and ocular melanoma (OM) arise from melanocyte transformation and represent deadly forms of cancer. Early diagnosis and treatment increase the overall survival. We are reporting a case of a patient with previous history of uveal melanoma (UV) diagnosed with cutaneous melanoma, lentigo maligna type. The coexistence of both melanomas in the same patient is incredibly challenging due to the same embryonic origin; however, the pathogenesis and biological behaviors are quite different. BRAF and NRAS mutations dominate in lesions arising in an epithelial context such as conjunctival melanoma and CM. Histopathological examination remains the gold standard for the confirmation of the diagnosis.
Water Quality Assessment Using Water Quality Index and Principal Component Analysis: A Case Study of Historically Important Lakes of Guwahati City, North-East India

This study evaluates the water quality of ten ancient lakes of Guwahati city, located in North east India, using water quality index (WQI) and multivariate statistical methods.The surface water samples were subjected to comprehensive physico-chemical analysis involving important physical parameters (pH, EC, TDS, alkalinity, total hardness, DO, BOD, COD, turbidity); major cations (Ca2+, Mg2+, Na+, K+), and major anions (HCO3-, Cl-, SO42-, NO3-, F-, PO43). Principal component analysis (PCA) has been used to assess the factors which influence the quality of water. The results revealed that water quality variations are mostly affected by dissolved mineral salts along with anthropogenic activities in the areas contiguous to the lakes. The present study points out that pH, DO and BOD played a central role in affecting the WQI of these lakes. The WQI values range from 74.78 to 178.55, indicating that majority of the lakes fall in “very poor” and “unsuitable” category. It also reveals an alarming fact that none of the water tanks fall under good category. Hence, the water is not fit for drinking, and is also becoming toxic for the aquatic fauna. The analysis of hydro chemical facies of the pond water shows that most of the water samples belong to Ca-Mg-HCO3 type of water. These findings will be useful for decisions making regarding water quality management and can also be applied in water modelling for better environmental management and planning perspective.
How Colonization Time Influences Macroinvertebrate Community Measures on Artificial Substrates

ABSTRACT We examined how duration of sampling period affected macroinvertebrate community characteristics measured with artificial substrate samplers in a New Jersey stream. During spring 2001 sixty Hester-Dendy multiplate samplers were deployed in riffle and pool habitats at three locations along a stretch of Lower Merrill Creek. Duplicate samplers were recovered at each habitat weekly over two to six weeks. Abundance varied by an order of magnitude over the study but generally increased with time (20–250 invertebrates/sampler). Pooled taxonomic richness ranged from 8 to 25 taxa/sample. Simpson's Diversity (D) for riffles ranged from 0.58 to 0.91 (mean=0.81±0.06 SE), while pool diversity was less variable (0.83–0.95) and 10% higher (mean=0.88±0.01), Shannon Diversity was generally higher than D, more so in riffle habitats (12%) than in pool habitats (8.6%). While these artificial substrates present a more time- and energy-intensive means to assess macroinvertebrates than some other techniques (e.g., kick or dip nets), they can be used to generate quantitative and detailed stream community information. Based on our results, a five-week colonization period is optimal for using Hester-Dendy substrate samplers.
Contribution of the Symbiotic Plasmid to the Competitiveness of Rhizobium leguminosarum

Summary: Four different symbiotic plasmids from Rhizobium leguminosarum were introduced into three different recipient strains that lacked plasmid-linked symbiotic determinants. The twelve synthetic strains so constructed were each tested for competitiveness against a standard reference strain. The recipient strain and the introduced symbiotic plasmid contributed about equally to competitiveness in forming root nodules on pea plants: there was also significant interaction between strain and plasmid, although this was much less important than the main effects. Competitiveness for growth on the legume root surface (the rhizosphere) was attributable entirely to the recipient strain; the introduced plasmid had no significant effect.
Usare l’entropia come indice per evolvere una coppia di robot simulati in grado di esibire comportamenti auto-organizzati

This paper presents a method that allows measuring the level of self-organization of a collective robotic system. The paper also shows that the method can be used to produce a fitness index that allows using genetic algorithms to train robots to produce interesting navigation selforganising behaviours. The method is based on Boltzmann measure of entropy applied to the movement of the robots in space. The paper presents some results, obtained by using the index to evolve the neural-network controllers of a couple of simulated robot, that validate the method and show that it allows evolving robotic systems characterized by different levels of complexity.
Influence of Forest Canopy Gaps on Establishment of Mikania Micrantha Kunth, an Invasive Plant, in a Tropical Forest in Southern Western Ghats, India

Tropical forests are more resistant to plant invasion. However, reports of the occurrence of invasive alien plants within tropical forests have surged in recent years. The invasibility of the tropical forest ecosystem is enhanced with the disturbance mediated environmental fluctuations. The upwelling of natural light on the forest floor and associated resource fluctuation due to canopy gaps facilitate the establishment of light tolerant, invasive plants. Here the authors report the effect of the canopy gap on the establishment of M micrantha in a protected forest in Kerala, India. A significant direct relationship between the abundance of M micrantha with canopy openness and light intensity reveals how the forest canopy gap in the study area acts as a gateway to plant invasion.
Efficient Transaction Routing in a Widely Replicated Database

Large-scale environments such as P2P system provide tremendous of opportunities for storing shared data. They have very specific characteristics such as autonomy and heterogeneity of peers. However, having effective mechanisms for transactions routing, fast and consistent data access, is very challenging. To face this issue, we propose a transaction routing algorithm based on the availability and the process capacity of nodes. We have implemented our approach using FreePastry simulator. The results shows its feasibility and efficiency. RÉSUMÉ. Les environnements à large échelle comme les systèmes P2P ont montré depuis des années toute leur importance dans la gestion et le stockage des données. Ils possèdent des caractéristiques très particulières telles que l’autonomie des pairs et leurs hétérogénéités. Cependant, avoir des mécanismes efficaces pour le routage des transactions, l’accès rapide aux données constitue un challenge. Pour faire face à ce défi, nous proposons un algorithme de routage de transactions qui s’appuie sur la disponibilité des nœuds du système et qui prend en compte leur puissance de traitement et leur capacité de stockage. Nous avons mis en œuvre notre approche à l’aide du simulateur FreePastry. Les résultats obtenus montrent son adaptabilité et son efficacité.
The Challenge of Treating Oral Infections Caused by Biofilms

In natural systems, the harsh environments, nutrient/respiration needs, and sheer flow, make a community lifestyle preferable or inevitable for microorganisms. Furthermore, the bacteria take advantage of the communities’ organization to protect them from eradication by conventional antimicrobial therapy. A biofilm community is a microorganism aggregate characterized by cells that are attached to a substratum or interface or to each other; are embedded in a matrix of extracellular polymeric substances (EPS) that they have produced; and exhibit an altered phenotype with respect to growth rate and gene transcription [1]. The oral cavity is an example of a challenging environment for the long-term persistence of bacteria and fungi. Fluctuations in nutrient supply, temperature, pH, and the shear force of saliva flow have selected for a biofilm community adapted to high cell density, species diversity, and dynamic growth conditions [2, 3]. The microorganism production of EPS matrix is also very important for their interaction with the environment [4,5]. The EPS provides a physical barrier that inhibits attachment to macrophages and phagocytes, while the reduced microorganisms’ metabolic activity precludes the use of antibiotics that act on them during growth periods [6-9]. Those are some of the challenges encountered when there is a need to treat or eradicate a disease-causing biofilm. Beyond conventional treatments, which employ a variety of antimicrobial agents, the actual disruption of biofilms currently entails mechanical procedures such as scouring. In order to inactivate the encased microbial cells, antimicrobial molecules must diffuse throughout the biofilm matrix; but the EPS constituting this matrix present a diffusional barrier for these molecules by influencing either their rate of transport to the biofilm interior or by the reaction of the antimicrobial with the matrix material [1]. The viscoelastic properties of the polysaccharides in the EPS are also attributed to the difficulty in disrupting the mature biofilm [10]. Among well-documented
Resistance evaluation of African Manihot landraces gene-gun inoculated with African cassava mosaic virus-Cameroon

Cassava landraces of diverse origins on the African continent were evaluated to assess their resistance to African cassava mosaic Cameroon virus (ACMV-CM). A concentration of approximately 10 ng of the viral DNA was inoculated to each plant by the biolistic particle delivery system. Disease severity was scored on a scale of 1-5 in the greenhouse for eight weeks. The genotypes Mwibibi, TME 4, TME 14, TME 203 and TME 117 showed high susceptibilities with mean disease severity scores of more than 2. These were very closely comparable to the susceptibility of the control check TMS 60444. Comparatively, the genotypes TME 1, TME 2, TME 3, TME 5, TME 8, TME 12, TME 282, TME 127, TME 1671 and TME 1695 showed relatively higher resistance with mean severity scores of less than 2. These were lower than the susceptibility of the control except for TME 12. A southern blot hybridization analysis of the genotypes at weeks 2, 6 and 8 post-inoculation using a 794 bp fragment of ACMV-UG as DNA probe revealed three bands corresponding to the open circular (OC), linear (LN) and double-stranded (DS) forms of ACMV-CM. Therefore, landraces with relatively higher resistance levels held promise for use for further improvement in breeding programs to enhance the resistance against ACMV-CM as well as complement other desirable agronomic traits for higher productivity.
Explaining Black Box Models for Document Retrieval

In the evaluation of information retrieval models, ranking performance has long been considered the benchmark measure of model functionality. It has become apparent, however, that merely looking at accuracy and precision fails to capture the complexity of model behavior, allowing for the persistence of models that reinforce biases of unfair real-world data. It is often diﬃcult to apply standard fairness measures like statistical parity or to analyze a standard confusion matrix in ranking contexts. This study proposes an alternative method of analyzing the global behavior of ranking models through the aggregation of model agnostic local linear explanations. Using a LambdaMART model trained on a eighteen-feature dataset, we learned locally interpretable model explanations (LIME) for each data point in the held-out test set and used their aggregated weights to make judgements on the overall model’s decision making structure. From the LambdaMART model, we found that stream length, the summary statistics associated with term frequencies, and the summary statistics associated with TF ∗ IDF scores were the most consistently inﬂuential in the model’s decision making.
Effects of Flunixine Meglumine, Diclofenac Sodium, Metamizol Sodium and Carprofen on Oxidative Stress in Rats Subjected to Laparotomy

The aim of this study was to determine the effects of nonsteroid antiinflammatory drugs on oxidative stress in rats subjected to laparotomy. Rats (n=50) were divided into five equal groups. Control group (n=10, Group I) received physiological saline whereas Groups II-V (n=10 in each) received metamizole (50 mg/kg), flunixin meglumine (2.5 mg/kg), carprofen (2.5 mg/kg), or diclofenac (2.5 mg/kg) by intraperitoneal injection for 5 days following the operation. On postoperative day 6, blood samples were obtained; levels of malondialdehyde (MDA) and nitric oxide (NO) in serum, and erythrocyte glutathione (GSH), catalase levels were determined. NSAIDs caused a decrease in MDA, NO and GSH levels, whereas catalase levels increased with NSAID treatment. In conclusion, NSAIDs may have additional beneficial effects to their anti-inflammatory effects by diminishing the oxidative stress.
Using Code Review at School and at the Programming Club

Educational code review is an activity that not only helps prepare future programmers into practice, but also teaches students to work with code in a diﬀerent way. In the educational settings, activities focused on code review are mainly encountered at universities. In our research, we focused on lower levels of education and in our previous publications we presented the results of using code review at secondary school. Experimentally, we also tried to use the code review activities on the sessions at the leisure-time activities club. This paper provides a description of the research carried out. We compare the outcomes from the club with the results from the secondary school. We also give an overview of the beneﬁts, as well as the problems such activities can bring to the classroom.