Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius

The “baby machine” provides a means of generating synchronized cultures of minimally perturbed cells. We describe the use of this technique to establish the key cell-cycle parameters of hyperthermophilic archaea of the genus Sulfolobus. The 3 DNA replication origins of Sulfolobus acidocaldarius were mapped by 2D gel analysis to near 0 (oriC2), 579 (oriC1), and 1,197 kb (oriC3) on the 2,226-kb circular genome, and we present a direct demonstration of their activity within the first few minutes of a synchronous cell cycle. We also detected X-shaped DNA molecules at the origins in log-phase cells, but these were not directly associated with replication initiation or ongoing chromosome replication in synchronized cells. Whole-genome marker frequency analyses of both synchronous and log-phase cultures showed that origin utilization was close to 100% for all 3 origins per round of replication. However, oriC2 was activated slightly later on average compared with oriC1 and oriC3. The DNA replication forks moved bidirectionally away from each origin at ≈88 bp per second in synchronous culture. Analysis of the 3 Orc1/Cdc6 initiator proteins showed a uniformity of cellular abundance and origin binding throughout the cell cycle. In contrast, although levels of the MCM helicase were constant across the cell cycle, its origin localization was regulated, because it was strongly enriched at all 3 origins in early S phase.
Free-form motion processing

Motion is the center of attention in many applications of computer graphics. Skeletal motion for articulated characters can be processed and altered in a variety of ways to increase the versatility of each motion clip. However, analogous techniques have not yet been developed for free-form deforming surfaces like cloth and faces. Given the time-consuming nature of producing each free-form motion clip, the ability to alter and reuse free-form motion would be very desirable. We present a novel method for processing free-form motion that opens up a broad range of possible motion alterations including motion blending, keyframe insertion, and temporal signal processing. Our method is based on a simple yet powerful differential surface representation that is invariant under rotation and translation and which is well suited for surface editing in both space and time.
Depth Super Resolution by Rigid Body Self-Similarity in 3D

We tackle the problem of jointly increasing the spatial resolution and apparent measurement accuracy of an input low-resolution, noisy, and perhaps heavily quantized depth map. In stark contrast to earlier work, we make no use of ancillary data like a color image at the target resolution, multiple aligned depth maps, or a database of high-resolution depth exemplars. Instead, we proceed by identifying and merging patch correspondences within the input depth map itself, exploiting patch wise scene self-similarity across depth such as repetition of geometric primitives or object symmetry. While the notion of 'single-image' super resolution has successfully been applied in the context of color and intensity images, we are to our knowledge the first to present a tailored analogue for depth images. Rather than reason in terms of patches of 2D pixels as others have before us, our key contribution is to proceed by reasoning in terms of patches of 3D points, with matched patch pairs related by a respective 6 DoF rigid body motion in 3D. In support of obtaining a dense correspondence field in reasonable time, we introduce a new 3D variant of Patch Match. A third contribution is a simple, yet effective patch up scaling and merging technique, which predicts sharp object boundaries at the target resolution. We show that our results are highly competitive with those of alternative techniques leveraging even a color image at the target resolution or a database of high-resolution depth exemplars.
The moderating effects of prosocial behaviour, friendship quality and social problem solving in the relationship between risk factors and peer victimization in Colombian early adolescents.

The current series of three studies was designed to use the “buffering hypothesis” model to assess the relative buffering effectiveness of positive peer experiences and personal characteristics in the association between risk factors and peer victimization in a sample of 623 Colombian early adolescents. These longitudinal studies assessed the extent to which changes in victimization varied as a function of the interaction between risk factors and positive peer and personal experiences. Using structural equation modeling techniques, the results provide evidence that reveals the specificities of the protective effects of each of the moderators. Results from Study 1 supported previous findings by revealing a significant change on children’s victimization scores across the school year. More specifically, it was found that students experienced a decline on their victimization scores over the school year, and that this decline was especially strong for the students who had the highest levels of victimization at the beginning of the year. Similarly, results from Study 1 showed that both aggression and avoidance were predictive of initial scores on peer victimization, however, only avoidance was found to predict the ways in which children change over the school year. The buffering effectiveness of prosocial behaviour was also tested in this study. It was found that prosociality acts as a buffer only for highly relationally aggressive children at the beginning of the school year, and for highly avoidant children across the school year. Study 2 examined the moderating effect of positive provisions of friendship in the association between aggression, avoidance and peer victimization over time. Contrary to our expectations, results showed that for relationally aggressive students, having a high quality friendship predicted an increase on their victimization scores over time. In contrast, for highly avoidant children friendships were protective against risk of peer victimization. Finally, Study 3 examined how social problem solving skills impacted the relationship between risk factors and peer victimization over time. Only a main effect of this variable was found at the beginning of the year; no moderating effects emerged in the analyses. Results from all studies supported the buffering hypothesis model by providing evidence that the protective effect of positive peer experiences and personal characteristics is especially effective for children who are considered to be at-risk.
Intrathecal synthesis of IgG, IgA, IgM and IgD in untreated multiple sclerosis and controls

ABSTRACT— The intrathecal production (ITP) of the immunoglobulins (Ig) G, A, M and D was examined in untreated patients with multiple sclerosis (MS) and controls. Sensitive sandwich enzyme‐linked immunosorbent assay systems were applied to the determination of IgA, IgM and IgD levels in the cerebrospinal fluid and plasma from a group of 61 consecutive MS patients (41 relapsing‐remitting and 20 secondary chronic progressive MS). Age‐related reference limits for all Ig variables were defined in a group of 57 patients with tension headache. ITP of IgG was demonstrated in 85% of the MS patients, ITP of IgA in 41%, of IgM in 44% and of IgD in 18%. Among 9 MS patients with normal IgG index, 3 displayed ITP of IgA, 3 of IgM and 1 of IgD. Plasma IgA was elevated in 20% and plasma IgM in 24% of the MS cases. No significant variation of Ig ITP was demonstrated in a different group of 27 untreated MS patients examined during exacerbation and remission. Among control patients with other inflammatory nervous system diseases, ITP of IgA, IgM and IgD was found more frequently, and of IgG in a smaller percentage compared with MS patients.
Immunity to pertussis 5 years after booster immunization during adolescence.

BACKGROUND We conducted a 5-year follow-up study on the persistence of pertussis-specific antibody and cell-mediated immunity after booster immunization of adolescents aged 11-13 years with a tricomponent acellular pertussis vaccine (Boostrix; trials diphtheria-tetanus-acellular pertussis [Tdap]-004/030). METHODS Cellular and humoral immunity to pertussis toxin (PT), filamentous hemagglutinin, and pertactin were measured in adolescents (age, 16 years) 5 years after booster immunization. Similar investigations were performed for control adolescents who had received only diphtheria and tetanus booster vaccination. RESULTS Five years after pertussis booster vaccination, the geometric mean concentrations of immunoglobulin G (IgG) elicited by each of the 3 pertussis vaccine antigens decreased from 1-month and 3-year postvaccination levels, but with the exception of PT IgG, were still higher than the prevaccination levels. PT IgG levels were undetectable in 28% of the subjects, but 44% of those subjects still tested positive for cell-mediated immunity to PT. Filamentous hemagglutinin IgG and pertactin IgG levels were significantly higher in Tdap-boosted adolescents than in the control subjects. Antibody concentrations at 1 month after vaccination strongly predicted antibody persistence. Cell-mediated immunity levels to PT, filamentous hemagglutinin, and pertactin persisted above the prebooster levels measured 5 years earlier. CONCLUSIONS The results of the present study of adolescents indicate that the interval between acellular pertussis booster immunizations might be extended beyond 5 years.
Diaspora entrepreneurship : a study of Nigerian entrepreneurs in London

The dynamic evolution of Diaspora Entrepreneurship reflects broad range of vistas; profoundly tensing up ‘conventional wisdom’, pressing knowledge boundaries and simultaneously exposing fundamental paradoxes in the characterisation of ethnic-minority groups in the context of their entrepreneurship. Prior efforts at researching and advancing knowledge in this sphere have been hugely complicated, not less by the ‘problematic of subjectivity’. Against this background, this thesis explores inter-subjective discourses and situated practices with a view to unravelling the temporal and spatial dimensions of entrepreneurship among Nigerians, the most populous Black-Africans in the UK. Thus, from contextual lenses of Nigerian entrepreneurs in London, the thesis unpacks the dialectics of diaspora entrepreneurship to allow the formulation and stabilisation of a diagnostic schema. Leaning on the philosophical axioms of interpretive discourse analysis, data are extracted from first-generation Nigerian entrepreneurs principally through the use of narrative interviews. The study finds taxonomical fluidity in the schematisation of contemporary ethnic entrepreneurship as well as its trajectories of growth. Whilst increasingly enmeshed in the evolving phenomenon of diaspora entrepreneurship, ‘home’/‘host’ country dualisms are revealed and found to impact entrepreneurial values and identities. Essentially, the duality of entrepreneurial spaces reveals ambivalent positions, constraining the representation of ethnic entrepreneurship whilst at the same time pointing to new subject position. In both spaces, the study recognises unique trends, opportunity structures and spatial arrangements impacting business development and strategies. The study demonstrates that ethnic entrepreneurship is a plethora of competing and negotiated value systems and meaning structures from which it is possible to assert that diaspora entrepreneurship is a product of persistent interface between multitude of social forces, attributes, states of being, actions, networks, attitudes, emotions, values, and beliefs. Therefore, by revealing entrepreneurship encounters as acts of empowerment, resistance and expression for newly immigrant ethnic groups in Britain, new sites of knowledge are evidenced.
Monte Carlo estimation of value-at-risk, conditional value-at-risk and their sensitivities

Value-at-risk and conditional value at risk are two widely used risk measures, employed in the financial industry for risk management purposes. This tutorial discusses Monte Carlo methods for estimating value-at-risk, conditional value-at-risk and their sensitivities. By relating the mathematical representation of value-at-risk to that of conditional value-at-risk, it provides a unified view of simulation methodologies for both risk measures and their sensitivities.
S-Band Dual-Polarization Radar Observations of Winter Storms

AbstractThis study is based on analyses of dual-polarization radar observations made by the 11-cm-wavelength Colorado State University–University of Chicago–Illinois State Water Survey (CSU–CHILL) system during four significant winter storms in northeastern Colorado. It was found that values of specific differential phase KDP often reached local maxima of ∼0.15°–0.4° km−1 in an elevated layer near the −15°C environmental temperature isotherm. The passage of these elevated positive KDP areas is shown to be linked to increased surface precipitation rates. Calculations using a microwave scattering model indicate that populations of highly oblate ice particles with moderate bulk densities and diameters in the ∼0.8–1.2-mm range can generate KDP (and differential reflectivity ZDR) values that are consistent with the radar observations. The persistent correlation between the enhanced KDP level and the −15°C temperature regime suggests that rapidly growing dendrites likely played a significant role in the product.
How Ricin Damages the Ribosome

Ricin belongs to the group of ribosome-inactivating proteins (RIPs), i.e., toxins that have evolved to provide particular species with an advantage over other competitors in nature. Ricin possesses RNA N-glycosidase activity enabling the toxin to eliminate a single adenine base from the sarcin-ricin RNA loop (SRL), which is a highly conserved structure present on the large ribosomal subunit in all species from the three domains of life. The SRL belongs to the GTPase associated center (GAC), i.e., a ribosomal element involved in conferring unidirectional trajectory for the translational apparatus at the expense of GTP hydrolysis by translational GTPases (trGTPases). The SRL represents a critical element in the GAC, being the main triggering factor of GTP hydrolysis by trGTPases. Enzymatic removal of a single adenine base at the tip of SRL by ricin blocks GTP hydrolysis and, at the same time, impedes functioning of the translational machinery. Here, we discuss the consequences of SRL depurination by ricin for ribosomal performance, with emphasis on the mechanistic model overview of the SRL modus operandi.
Understanding the Evolution of Mammalian Brain Structures; the Need for a (New) Cerebrotype Approach

The mammalian brain varies in size by a factor of 100,000 and is composed of anatomically and functionally distinct structures. Theoretically, the manner in which brain composition can evolve is limited, ranging from highly modular (“mosaic evolution”) to coordinated changes in brain structure size (“concerted evolution”) or anything between these two extremes. There is a debate about the relative importance of these distinct evolutionary trends. It is shown here that the presence of taxa-specific allometric relationships between brain structures makes a taxa-specific approach obligatory. In some taxa, the evolution of the size of brain structures follows a unique, coordinated pattern, which, in addition to other characteristics at different anatomical levels, defines what has been called here a “taxon cerebrotype”. In other taxa, no clear pattern is found, reflecting heterogeneity of the species’ lifestyles. These results suggest that the evolution of brain size and composition depends on the complex interplay between selection pressures and constraints that have changed constantly during mammalian evolution. Therefore the variability in brain composition between species should not be considered as deviations from the normal, concerted mammalian trend, but in taxa and species-specific versions of the mammalian brain. Because it forms homogenous groups of species within this complex “space” of constraints and selection pressures, the cerebrotype approach developed here could constitute an adequate level of analysis for evo-devo studies, and by extension, for a wide range of disciplines related to brain evolution.
Generating a Knockdown Transgene against Drosophila Heterochromatic Tim17b Gene Encoding Mitochondrial Translocase Subunit

Heterochromatic regions of eukaryotic genomes contain multiple functional elements involved in chromosomal dynamics, as well as multiple housekeeping genes. Cytological and molecular peculiarities of heterochromatic loci complicate genetic studies based on standard approaches developed using euchromatic genes. Here, we report the development of an RNAi-based knockdown transgenic construct and red fluorescent reporter transgene for a small gene, Tim17b, which localizes in constitutive heterochromatin of Drosophila melanogaster third chromosome and encodes a mitochondrial translocase subunit. We demonstrate that Tim17b protein is required strictly for protein delivery to mitochondrial matrix. Knockdown of Tim17b completely disrupts functions of the mitochondrial translocase complex. Using fluorescent recovery after photobleaching assay, we show that Tim17b protein has a very stable localization in the membranes of the mitochondrial network and that its exchange rate is close to zero when compared with soluble proteins of mitochondrial matrix. These results confirm that we have developed comprehensive tools to study functions of heterochromatic Tim17b gene.
Bidirectional LSTM for Named Entity Recognition in Twitter Messages

In this paper, we present our approach for named entity recognition in Twitter messages that we used in our participation in the Named Entity Recognition in Twitter shared task at the COLING 2016 Workshop on Noisy User-generated text (WNUT). The main challenge that we aim to tackle in our participation is the short, noisy and colloquial nature of tweets, which makes named entity recognition in Twitter message a challenging task. In particular, we investigate an approach for dealing with this problem by enabling bidirectional long short-term memory (LSTM) to automatically learn orthographic features without requiring feature engineering. In comparison with other systems participating in the shared task, our system achieved the most effective performance on both the ‘segmentation and categorisation’ and the ‘segmentation only’ sub-tasks.
The DnaA homolog of the hyperthermophilic eubacterium Thermotoga maritima forms an open complex with a minimal 149‐bp origin region in an ATP‐dependent manner

In Escherichia coli, ATP‐DnaA, but not ADP‐DnaA, forms an initiation complex that undergoes site‐specific duplex DNA unwinding, open complex formation. However, it remains unclear how highly the ATP‐dependent activation of the initiation factor is conserved in evolution. The hyperthermophile Thermotoga maritima is one of the most ancient eubacteria in evolution. Here, we show that the DnaA homolog (tmaDnaA) of this bacterium forms open complexes with the predicted origin region (tma‐oriC) in vitro. TmaDnaA has a strong and specific affinity for ATP/ADP as well as for 12‐mer repeating sequences within the tma‐oriC. Unlike ADP‐tmaDnaA, ATP‐tmaDnaA is highly cooperative in DNA binding and forms open complexes in a manner that depends on temperature and the superhelical tension of the tma‐oriC‐bearing plasmid. The minimal tma‐oriC required for unwinding is a 149‐bp region containing five repeats of the 12‐mer sequence and two AT‐rich 9‐mer repeats. TmaDnaA‐binding to the 12‐mer motif provokes DNA bending. The 9‐mer region is the duplex‐unwinding site. The tmaDnaA‐binding and unwinding motifs of tma‐oriC share sequence homology with corresponding archaeal and eukaryotic sequences. These findings suggest that the ATP‐dependent molecular switch of the initiator and the mechanisms in the replication initiation complex are highly conserved in eubacterial evolution.
Tnt1 Retrotransposon Mutagenesis: A Tool for Soybean Functional Genomics1[W][OA]

Insertional mutagenesis is a powerful tool for determining gene function in both model and crop plant species. Tnt1, the transposable element of tobacco (Nicotiana tabacum) cell type 1, is a retrotransposon that replicates via an RNA copy that is reverse transcribed and integrated elsewhere in the plant genome. Based on studies in a variety of plants, Tnt1 appears to be inactive in normal plant tissue but can be reactivated by tissue culture. Our goal was to evaluate the utility of the Tnt1 retrotransposon as a mutagenesis strategy in soybean (Glycine max). Experiments showed that the Tnt1 element was stably transformed into soybean plants by Agrobacterium tumefaciens-mediated transformation. Twenty-seven independent transgenic lines carrying Tnt1 insertions were generated. Southern-blot analysis revealed that the copy number of transposed Tnt1 elements ranged from four to 19 insertions, with an average of approximately eight copies per line. These insertions showed Mendelian segregation and did not transpose under normal growth conditions. Analysis of 99 Tnt1 flanking sequences revealed insertions into 62 (62%) annotated genes, indicating that the element preferentially inserts into protein-coding regions. Tnt1 insertions were found in all 20 soybean chromosomes, indicating that Tnt1 transposed throughout the soybean genome. Furthermore, fluorescence in situ hybridization experiments validated that Tnt1 inserted into multiple chromosomes. Passage of transgenic lines through two different tissue culture treatments resulted in Tnt1 transposition, significantly increasing the number of insertions per line. Thus, our data demonstrate the Tnt1 retrotransposon to be a powerful system that can be used for effective large-scale insertional mutagenesis in soybean.
ON THE GEOMETRY OF GOURSAT STRUCTURES

A Goursat structure on a manifold of dimension n is a rank two distribution Ɗ such that dim Ɗ (i) = i + 2, for 0 ≤ i ≤ n -2, where Ɗ (i) denote the elements of the derived flag of Ɗ , defined by Ɗ (0) = Ɗ and Ɗ (i+1) = Ɗ (i) + [Ɗ (i) ,Ɗ (i) ] . Goursat structures appeared first in the work of von Weber and Cartan, who have shown that on an open and dense subset they can be converted into the so-called Goursat normal form. Later, Goursat structures have been studied by Kumpera and Ruiz. In the paper, we introduce a new local invariant for Goursat structures, called the singularity type, and prove that the growth vector and the abnormal curves of all elements of the derived flag are determined by this invariant. We provide a detailed analysis of all abnormal and rigid curves of Goursat structures. We show that neither abnormal curves, if n ≥ 6, nor abnormal curves of all elements of the derived flag, if n ≥ 9, determine the local equivalence class of a Goursat structure. The latter observation is deduced from a generalized version of Backlund's theorem. We also propose a new proof of a classical theorem of Kumpera and Ruiz. All results are illustrated by the n -trailer system, which, as we show, turns out to be a universal model for all local Goursat structures.