Miracle-dz/UniFAR-FTUs huggingface dataset:
Condensin aids sister chromatid decatenation by topoisomerase II

The condensin complex is a key determinant of mitotic chromosome architecture. In addition, condensin promotes resolution of sister chromatids during anaphase, a function that is conserved from prokaryotes to human. Anaphase bridges observed in cells lacking condensin are reminiscent of chromosome segregation failure after inactivation of topoisomerase II (topo II), the enzyme that removes catenanes persisting between sister chromatids following DNA replication. Circumstantial evidence has linked condensin to sister chromatid decatenation but, because of the difficulty of observing chromosome catenation, this link has remained indirect. Alternative models for how condensin facilitates chromosome resolution have been put forward. Here, we follow the catenation status of circular minichromosomes of three sizes during the Saccharomyeces cerevisiae cell cycle. Catenanes are produced during DNA replication and are for the most part swiftly resolved during and following S-phase, aided by sister chromatid separation. Complete resolution, however, requires the condensin complex, a dependency that becomes more pronounced with increasing chromosome size. Our results provide evidence that condensin prevents deleterious anaphase bridges during chromosome segregation by promoting sister chromatid decatenation.
Role of Organic Acids in the Manganese-Independent Biobleaching System of Bjerkandera sp. Strain BOS55

ABSTRACT Bjerkandera sp. strain BOS55 is a white rot fungus that can bleach EDTA-extracted eucalyptus oxygen-delignified kraft pulp (OKP) without any requirement for manganese. Under manganese-free conditions, additions of simple physiological organic acids (e.g., glycolate, glyoxylate, oxalate, and others) at 1 to 5 mM stimulated brightness gains and pulp delignification two- to threefold compared to results for control cultures not receiving acids. The role of the organic acids in improving the manganese-independent biobleaching was shown not to be due to pH-buffering effects. Instead, the stimulation was attributed to enhanced production of manganese peroxidase (MnP) and lignin peroxidase (LiP) as well as increased physiological concentrations of veratryl alcohol and oxalate. These factors contributed to greatly improved production of superoxide anion radicals, which may have accounted for the more extensive biobleaching. Optimum biobleaching corresponded most to the production of MnP. These results suggest that MnP from Bjerkandera is purposefully produced in the absence of manganese and can possibly function independently of manganese in OKP delignification. LiP probably also contributed to OKP delignification when it was present.
An Efficient Finite Tree Automata Library

Numerous computer systems use dynamic control and data structures of unbounded size. These data structures have often the character of trees or they can be encoded as trees with some additional pointers. This is exploited by some currently intensively studied techniques of formal verification that represent an infinite number of states using a finite tree automaton. However, currently there is no tree automata library implementation that would provide an efficient and flexible support for such methods. Thus the aim of this Master's Thesis is to provide such a library. The present paper first describes the theoretical background of finite tree automata and regular tree languages. Then it surveys the current implementations of tree automata libraries and studies various verification techniques, outlining requirements for the library. Representation of a finite tree automaton and algorithms that perform standard language operations on this representation are proposed in the next part, which is followed by description of library implementation. Through a series of experiments it is shown that the library can compete with other available tree automata libraries, in certain areas being even significantly superior to them.
Color face recognition under various learning scenarios

In this paper, the usage of the YCbCr transformation in the input stage of a Face Recognition (FR) system is examined. Chromatic sampling ratios used in MPEG standards have been applied on the input face images to examine a possible integration of video and FR systems. Experiments were conducted in a number of learning scenarios and imaging conditions, and it was observed that almost all the YCbCr inputs lead to good FR systems. In addition, the conditions in which color inputs enhance the FR performance over gray scale were evaluated both for supervised and unsupervised FR systems since the computational time and storage space involved in color FR systems is high.
Doxorubicin dose for congestive heart failure modeling and the use of general ultrasound equipment for evaluation in rats. Longitudinal in vivo study.

INTRODUCTION For the evaluation of the congestive heart failure (CHF) in rat models, the use of special equipment for echocardiography for dynamic evaluation is suggested. The optimal doxorubicin dose for CHF induction has still not been established. AIMS The aims of our study was to find a reliable doxorubicin CHF rat model using a general ultrasound (US) equipment for in vivo ultrasound examination of the systemic circulation, to establish the optimal doxorubicin dose, and to assess the feasibility of US guided administration of the drug. MATERIAL AND METHODS Sixty Wistar rats, weighing 180-200 g were assigned to 3 groups (n=20 in each): group A - 4 time intraperitoneal doxorubicin "Sigma"administration, cumulative dose 2.49 mg/animal or 12.45 mg/kg; group B and 5 time doxorubicin administration, cumulative dose 3.03 mg/animal or 15.15 mg/kg; and group C- controls (injected same volume of saline). Dynamic US using linear 12 MHz transducer was used to establish the CHF modifications. Two rats with CHF were injected under US guidance in the pleural cavity with 0.06 ml cardiotropic drug levosimendan and two rats in the pericardial cavity. RESULTS We established the optimal cumulative doxorubicin dose for CHF induction at 12.45 mg/kg. At a higher dose, more than 40% of animals died. A lower dose did not induce significant clinical and US CHF criteria. Congestion (followed by weight gain) led to lower animal mortality. Preliminary results indicate a similar positive cardioprotective effect of drug injection into pericardial and pleural cavities under US guidance, demonstrating that this technique is useful for drug administration. CONCLUSIONS US is an effective modality for in vivo monitoring of the rat organs for the study of cardiovascular function or for drug administration under US guidance. Suggested model (optimal dose of doxorubicin for simulation of CHF of 2.5 mg/animal, a cumulative dose of 12.45 mg/kg in 4 injections every 3 days) can be used for research purposes.
Influences of triploidy, parentage and genetic diversity on growth of the Pacific oyster Crassostrea gigas reared in contrasting natural environments

An increasing number of hypotheses are being proposed to explain the faster growth potential of triploids in molluscs, including their partial sterility or their higher heterozygosity compared to diploids. Triploid advantage however, remains controversial for poorer sites, because of a potential trade‐off with survival. These questions were addressed in Crassostrea gigas by deploying meiosis II triploids and their diploid siblings from a single mass spawning of three males and seven females, in two contrasting locations for their trophic resources. One hundred and fifty individuals were sampled at each site after nine months, measured for weight and biochemical composition, and genotyped using three microsatellite and seven allozyme loci. Higher performance was observed at the fast‐growing site for all traits except shell weight, and triploids had greater weights and biochemical contents than diploids at harvest. Triploids also grew faster at the poorer site, and showed similar survival rates to diploids at both sites. Triploids had significantly higher average allozyme and microsatellite diversity. However, they performed better for a wide range of individual heterozygosity values, arguing for an advantage of the triploid state per se, that could be due to positive effects on growth of both sterility of triploids with subsequent resource re‐allocation and possible faster transcription with three copies of each gene. Despite evidence of very low or no inbreeding in the diploid sample, positive associations between individual allozyme diversity and growth were detected, which explained little but significant amounts of phenotypic variation. These associations were interpreted as direct effects of allozymes, either alone or including epistatic interactions with other loci. In addition, measures of individual distance (mean‐d2) specific to microsatellites, were negatively correlated with growth in diploids, indicating possible effects of outbreeding depression between more distant genomes of parents from distinct populations.
Content hole search in community-type content

In community-type content such as blogs and SNSs, we call the user's unawareness of information as a "content hole" and the search for this information as a "content hole search. " A content hole search differs from similarity searching and has a variety of types. In this paper, we propose different types of content holes and define each type. We also propose an analysis of dialogue related to community-type content and introduce content hole search by using Wikipedia as an example.
Teachers Perceptions of Real and Virtual Field Work in Environmental Education

Various researchers declared that according to environmental education’s aims, teaching must consist of three bases: about the nature, in the nature and for the nature. Nowadays it is especially difficult to overcome the problems regarding the fieldwork. The linear regression exposed financial issues, lack of time, responsibility of teachers and oversized groups of students. The purpose of the study was to expose the main obstacles of 202 Slovenian teachers (emphasis on Biology, Science teachers) and to analyse the conditions regarding the environmental education. As one of solutions for overcoming those obstacles, virtual trips were presented. Results have shown that teachers are generally more in favour of the virtual fieldwork than students, but not all of them are equally favourable to the new technology. The nonparametric analyses showed the statistical significant differences for teachers’ subject, their teaching experiences and their digital competence. Keywords: Biology, ecology, environmental education, fieldwork, virtual field trips;
PET-CT in oncology: making the most of CT

Abstract Combined positron emission tomography–computed tomography (PET-CT) has made a significant impact on cancer imaging. The use of CT to map tissue attenuation for correction of PET images and the ability to co-register the functional information provided by PET with the anatomical data afforded by CT, has resulted in demonstrable improvements in diagnostic accuracy. However, attenuation correction and anatomical localisation may not represent the full benefits of integrating CT with PET. The use of CT acquisition techniques for patient positioning and the use of contrast media can improve diagnostic performance, and incorporation of CT image processing techniques such as perfusion CT, 3D imaging and computer-assisted diagnosis offers new applications. The interpretation of PET-CT images can be improved by fully integrating the morphological appearances on CT into image analysis. Better utilisation of the CT component of PET-CT could further enhance the benefits of PET-CT in oncology but will have implications for manufacturers and purchasers of PET-CT equipment and analysis software. Furthermore, specialists working in PET-CT will need CT competencies beyond knowledge of cross-sectional anatomy. CT continues to exhibit rapid evolution and these advances will inevitably impact on the practice of PET-CT.
JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE‐HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL

Violation of the molecular clock has been amply documented, and is now routinely taken into account by molecular dating methods. Comparative analyses have revealed a systematic component in rate variation, relating it to the evolution of life‐history traits, such as body size or generation time. Life‐history evolution can be reconstructed using Brownian models. However, the resulting estimates are typically uncertain, and potentially sensitive to the underlying assumptions. As a way of obtaining more accurate ancestral trait and divergence time reconstructions, correlations between life‐history traits and substitution rates could be used as an additional source of information. In this direction, a Bayesian framework for jointly reconstructing rates, traits, and dates was previously introduced. Here, we apply this model to a 17 protein‐coding gene alignment for 73 placental taxa. Our analysis indicates that the coupling between molecules and life history can lead to a reevaluation of ancestral life‐history profiles, in particular for groups displaying convergent evolution in body size. However, reconstructions are sensitive to fossil calibrations and to the Brownian assumption. Altogether, our analysis suggests that further integrating inference of rates and traits might be particularly useful for neontological macroevolutionary comparative studies.
Progress towards a strontium optical lattice clock at NPL

The 1S0 - 3P0 transition at 698 nm in neutral strontium has the potential to be an extremely precise optical frequency standard [1] and is one of several candidates for a future redefinition of the second. Recent measurements of this transition at three national laboratories around the world have fractional frequency uncertainties in the 1015 range and agree to within a hertz [2,3,4]. To realise fully the potential accuracy of this frequency standard, in depth studies of systematic effects need to be performed in order to characterise them at the level necessary for a redefinition of the second. At the National Physical Laboratory we are developing a compact, diode laser based optical lattice clock. We intend to study the clock transition in both 88Sr and 87Sr with focus on the uncertainties in the frequency shifts due to blackbody radiation. The setup incorporates a novel permanent magnet based Zeeman slower [5].
Combining supervised learning with color correlograms for content-based image retrieval

The paper addresses how relevance feedback can be used to improve the performance of content-based image retrieval. We present two supervised learning methods: learning the query and learning the metric. We combine the learning methods with the recently proposed color correlograms for image indexing/retrieval. Our results on a large image database of over 20; 000 images suggest that these learning methods are quite effective for content-based image retrieval.
Cyclophosphamide plus tumor necrosis factor‐α chemoimmunotherapy cured mice: Life‐long immunity and rejection of re‐implanted primary lymphoma

Changes in functionally and phenotypically definable spleno‐cyte subsets in aging mice which had been rendered tumor‐free in early life by immunochemotherapy (cyclophosphamide plus tumor necrosis factor‐α) were studied in the syngeneic EL4 lymphoma‐C57BL/6 murine model. Treatment‐induced long‐term survivors (LTS) surviving rechallenge are termed “immune‐LTS”. On day 120 (day 0, initial tumor inoculation), splenocytes from day 60 rechallenged immune‐LTS developed significantly greater specific anti‐EL4 cytolytic activity in an ex vitro assay than those from non‐rechallenged LTS. Splenocytes from combination‐treated groups developed significantly higher activity than those from cyclophosphamide‐induced immune‐LTS. The splenic effector precursor was a CD8+ T cell. The specific anti‐EL4 effector cell from the cyclophosphamide‐induced immune‐LTS was CD4− CD8+; however, approximately 50% of those from combination‐treated immune‐LTS appeared to be CD4+CD8+. On day 520 immune‐LTS were randomized into 2 groups. One group was re‐implanted with EL4 tumor; all mice survived. The other group was killed and, even though their splenocytes developed considerable anti‐EL4 activity, their allogeneic responsiveness was as reduced as that of age* matched controls. Phenotypic analysis, compared with splenocytes from young and age‐matched controls, revealed changes in the makeup of each T‐cell subset, except the CD4+CD8+, and all subsets, except the CD4− CD8−, had increases in CD44 positivity. On day 625, the age of these mice was equivalent to the median life‐span of C57BL/6 mice; nevertheless, their splenocytes developed high anti‐EL4 activity. Phenotypic analysis indicated that, compared to day 520, there was a major decrease in CD4− CD8+ splenocytes; we suggest that these cells had migrated to the site of tumor eradication.
Accuracy of homeless adults' self-reports.

Clinical researchers often rely on personal interviews with the subjects of their studies to document their individual health services experiences. Unfortunately, the accuracy of the recall of the respondents may be a large source of error for which it is difficult to compensate. The potential for inaccurate recall may be magnified by problems that are particularly endemic to the homeless population, such as chronic medical illness, overwhelming social problems, substance abuse, or mental health problems.1-3 If we are attempting to study the homeless population through personal interviews, we must be able to quantify the potential errors introduced by inaccurate recall. This article will discuss the previous literature concerning the accuracy of self-reports of homeless respondents. We report the results of our own study that specifically addresses the issue of the accuracy of homeless adults'reporting of ambulatory medical visits and compare these findings with those based on studies of the general public. Finally, we will offer suggestions on methods to improve the accuracy of recall of homeless respondents. Five previous studies elucidate the accuracy of interview responses of homeless
Inhibition of synaptic transmission and G protein modulation by synthetic CaV2.2 Ca2+ channel peptides

Non‐technical summary Nerve cells (neurones) in the body communicate with each other by releasing chemicals (neurotransmitters) which act on proteins called receptors. An important group of receptors (called G protein coupled receptors, GPCRs) regulate the release of neurotransmitters by an action on the ion channels that let calcium into the cell. Here, we show for the first time that small peptides based on specific regions of calcium ion channels involved in GPCR signalling can themselves inhibit nerve cell communication. We show that these peptides act directly on calcium channels to make them more difficult to open and thus reduce calcium influx into native neurones. These peptides also reduce GPCR‐mediated signalling. This work is important in increasing our knowledge about modulation of the calcium ion channel protein; such knowledge may help in the development of drugs to prevent signalling in pathways such as those involved in pain perception.
Simulated Testing of an Adaptive Multimedia Information Retrieval System

The Semantic Gap is considered to be a bottleneck in image and video retrieval. One way to increase the communication between user and system is to take advantage of the user's action with a system, e.g. to infer the relevance or otherwise of a video shot viewed by the user. In this paper we introduce a novel video retrieval system and propose a model of implicit information for interpreting the user's actions with the interface. The assumptions on which this model was created are then analysed in an experiment using simulated users based on relevance judgements to compare results of explicit and implicit retrieval cycles. Our model seems to enhance retrieval results. Results are presented and discussed in the final section.
Assessment of ventricular function in adults with repaired Tetralogy of Fallot using myocardial deformation imaging.

AIMS Many patients with repaired Tetralogy of Fallot (ToF) have right ventricular (RV) volume overload due to pulmonary regurgitation (PR). We studied the effect of volume overload on global and regional RV and left ventricular (LV) deformation, and their relationships with conventional diagnostic parameters. METHODS AND RESULTS In this cross-sectional study, 94 prospectively recruited ToF patients (61% male, age 32.8 ± 9.5 years, age at repair 1.9 [0.8-5.7] years, 39% pulmonary homograft) and 85 healthy controls of similar age and sex underwent echocardiography and electrocardiography. In a subset of patients, cardiac magnetic resonance imaging, bicycle ergometry, and NT-proBNP measurement were performed within the same day. With speckle-tracking echocardiography, we analysed peak systolic global longitudinal strain (GLS), segmental longitudinal strain and strain rate of the RV free wall, LV lateral wall, and septum. Patients had a lower RV free wall strain than controls (-18.1 ± 4.5 vs. -26.5 ± 4.5%, P < 0.001), especially at the apical segment (-15.9 ± 7.4 vs. -28.2 ± 7.7%, P < 0.001), and lower RV strain rate. LV GLS was also lower (-17.4 ± 2.5 vs. -19.6 ± 1.9%, P < 0.001), mainly due to the interventricular septum. Patients with PR >25% had higher LV GLS and RV free wall strain than patients with PR ≤25% (P = 0.004, P = 0.039, respectively). No relationships were found with NT-proBNP or exercise capacity. CONCLUSION RV free wall strain and strain rate are decreased in adults late after ToF repair, especially at the apical segment suggesting that apical function is most affected in these RVs. Regarding the LV, septal strain is decreased indicating that RV dysfunction adversely affects LV function, probably by mechanical coupling of the ventricles.