Miracle-dz/UniFAR-FTUs huggingface dataset:
Finishing The Euchromatic Sequence Of The Human Genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process.The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers {approx}99% of the euchromatic genome and is accurate to an error rate of {approx}1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number,birth and death. Notably, the human genome seems to encode only20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.
Structure of CARB-4 and AER-1 CarbenicillinHydrolyzing β-Lactamases

ABSTRACT We determined the nucleotide sequences ofblaCARB-4 encoding CARB-4 and deduced a polypeptide of 288 amino acids. The gene was characterized as a variant of group 2c carbenicillin-hydrolyzing β-lactamases such as PSE-4, PSE-1, and CARB-3. The level of DNA homology between thebla genes for these β-lactamases varied from 98.7 to 99.9%, while that between these genes andblaCARB-4 encoding CARB-4 was 86.3%. TheblaCARB-4 gene was acquired from some other source because it has a G+C content of 39.1%, compared to a G+C content of 67% for typical Pseudomonas aeruginosa genes. DNA sequencing revealed that blaAER-1 shared 60.8% DNA identity with blaPSE-3 encoding PSE-3. The deduced AER-1 β-lactamase peptide was compared to class A, B, C, and D enzymes and had 57.6% identity with PSE-3, including an STHK tetrad at the active site. For CARB-4 and AER-1, conserved canonical amino acid boxes typical of class A β-lactamases were identified in a multiple alignment. Analysis of the DNA sequences flankingblaCARB-4 and blaAER-1confirmed the importance of gene cassettes acquired via integrons inbla gene distribution.
Etude du système immunitaire d'un amphibien et analyse des effets de l'environnement sur sa réponse humorale

During my PhD, I have participated to the characterization of Pleurodeles waltl (urodele amphibian) antibody heavy chains and to the discovery of a new isotype that we named IgP. I have also demonstrated that each antibody heavy chain has its human counterpart. P. waltl IgM are the counterpart of human IgM. IgY are expressed in mucosa and are therefore the physiological counterpart of human IgA. Finally, IgP are predominantly expressed in larvae and are less diverse than IgM. These two characteristics are shared with antibodies produced by mammalian B1 cells. These studies allowed me to approach the effects of a long term spaceflight on the humoral immune response, i.e. the antibody mediated response, which up to now has been poorly studied. The Development and Immunogenetics team, JE 2537, has immunized adult P. waltl during their five month stay onboard the Mir space station and showed that heavy chain variable domains of specific IgM are encoded by genes belonging to the VHII and VHVI families. However, these families are used in different proportions in animals immunized onboard Mir by comparison to animals immunized on Earth. To better understand this difference, I have determined how these animals use their individual VHII and VHVI genes. My work revealed that only one VHII gene and four VHVI genes (A, B, C and D) are used by immunized animals. I observed an increase in the expression of IgM heavy chain mRNAs encoded by the VHII, VHVI.C and VHVI.D genes and a strong decrease in the expression of IgM heavy chain mRNAs encoded by the VHVI.A and VHVI.B genes in spaceflight animals, demonstrating that this environment affects the humoral response. These observations may be due to a change in B-cell selection under spaceflight conditions. Furthermore, I described for the first time the effects of spaceflight on somatic hypermutations. I isolated and characterized the P. waltl mRNA coding for the main effector of these mutations: the activation-induced cytidine deaminase (AID). I demonstrated that this protein is present and conserved in P. waltl. Then, I described somatic hypermutations in P. waltl. I mapped somatic hypermutations, studied their distribution and calculated their frequency in animals immunized on Earth and in animals immunized onboard the Mir space station. This work revealed a strong depression of somatic hypermutations in animals immunized onboard Mir. This observation does not result from a change in AID transcription. We believe that this may be the consequence of a lower B lymphocyte survival under spaceflight conditions.
Duel Effects of Ostracism at Work with Differing Regulatory Focus of Ostracized Workers: Affective Event Theory Application

The objective of the following paper is to examine the effects of ostracism at work on extra-role behavior, ingratiation and eudaimonia at work by taking mediating effect of sadness as well as moderating effects of employee regulatory focus. This phenomenon was examined through the lens of Affective event theory. The data was collected from 291 public sector employees of Pakistan. Data on variables of interest were collected through time lag and multi-rated survey which was divided into three parts. Data were analyzed through smart PLS software. Results indicated that sadness mediates the relationship between ostracism at work and extra-role behavior and between ostracism and ingratiation at work. The result indicated that promotion focus antagonistically moderate the relationship between sadness and extra-role and prevention focus failed to moderate the relationship between sadness and ingratiation at work. Furthermore, results also indicated that extra-role behavior positively related to eudaimonia and ingratiation at work negatively related to eudaimonia at work.
Constraints on post‐glacial boreal tree expansion out of far‐northern refugia

Aim To use a variety of data sources to infer how northern boreal trees recovered their range upon deglaciation and/or Holocene warming. Location Scandinavia, Alaska/north-west Canada (eastern Beringia). Methods Mapped fossil occurrences for Picea (spruce) were assessed against available palaeoenvironmental and phylogeographic information. Results For Scandinavia, Last Glacial Maximum (LGM) evidence of Picea is confined to one DNA record, but late-glacial and early-Holocene records include scattered macrofossils.Holocene pollen data show a clear east–west increase to high values.A haplotype unique to the Scandinavian Peninsula is recognized. For eastern Beringia pre- and post-LGM macrofossils occur, but the LGM fossil record comprises only scattered low pollen values. Early Holocene pollen values increase markedly c. 11 cal yr bp (north-west Canada) and c. 10 kcal yr bp (central Alaska). Also at this time three sites on the Bering Land Bridge indicate the presence of Picea where it is now absent. Several unique regional haplotypes were recorded; while most are rare one is common in some modern populations. Main conclusions Small Picea populations probably occurred in pre-Holocene Scandinavia, but pollen patterns argue against immediate expansion with the onset of warmer conditions. Despite relatively weak fossil evidence, refugial populations are also probable in eastern Beringia, particularly given the extent of unglaciated terrain. Post-glacial pollen patterns are more nuanced, suggesting two spatially and temporally distinct expansions, one possibly consistent with a unique central Alaskan haplotype, and subsequent westerly ‘filling-in’. The presence of macrofossils and/or neutral markers does not require that current northern populations are derived primarily from refugial ones, particularly where pollen patterns show delayed directional expansion of large populations though time. Refugial populations initially responded weakly to major post-glacial environmental change; if subject to genetic isolation and strong selection pressure they may have had little potential to do otherwise, instead being largely replaced by in-migrating populations with greater genetic diversity.
Simulation and statistical techniques to explore lymphoid tissue organogenesis

Secondary lymphoid organs have a key role in the initiation of adaptive immune responses to infection. Organogenesis occurs in foetal development, and the use of genetic tools, imaging technologies, and ex vivo culture systems has provided significant insights into the cellular components and associated signalling pathways that are involved. However such approaches tend to be reductionist and descriptive, focusing on the contribution of individual components, and cannot fully explain how lymphoid organs develop through interaction between biological components. In this study, a set of simulation and statistical tools have been developed that provide further insights into the molecular and biophysical mechanisms of lymphoid tissue organogenesis. Specifically, the formation of Peyer’s Patches, gut-associated secondary lymphoid organs, is examined. In collaboration with experimental immunologists, a structured process in the design and calibration of a computer simulation of the biological process has been conducted, leading to the development of a publicly accessible scientific tool where cell behaviour emerges that is statistically similar to that observed in ex vivo culture. Robust biological hypotheses can be generated through use of the tool to perform in silico experimentation that simulates different physiological conditions. A lack of available statistical tools to analyse in silico simulation results has been addressed through the development and release of the spartan toolkit, a set of techniques that can suggest the influence that pathways and components have on simulation behaviour, offering valuable biological insight into the system being explored. An analysis of simulation results using spartan suggests the influence of biological pathways on tissue formation changes during development, in contrast to hypotheses in the literature that suggest the process is chemokine driven. Data presented suggests the development period is biphasic, with cell adhesion the key factor early in development, and chemokine expression influential at later point. Through novel application of the statistical tools in spartan to perform a time-lapse analysis of cell behaviour, it is suggested this change in phase occurs between hours 24 and 36. Novel in silico experimentation performed has suggested the key biological factors in causing cell aggregation, and suggested a role for LTin cells in limiting size and number of Peyer’s Patches. A range of potential laboratory investigations have been suggested that could validate whether these simulation derived hypotheses are valid.
Modulators of Symbiotic Outcome in Sinorhizobium meliloti

Modulators of Symbiotic Outcome in Sinorhizobium meliloti Matthew Ben Crook, Jr. Department of Microbiology and Molecular Biology, BYU Doctor of Philosophy Microorganisms interact frequently with each other and with higher organisms. This contact and communication takes place at the molecular level. Microbial interactions with eukaryotes can be pathogenic or mutualistic. One of the best-studied symbioses is the complex interaction between nitrogen-fixing soil bacteria, termed rhizobia, and legumes. This symbiosis culminates in the elaboration of a new organ, the root nodule. Many of the molecular signals exchanged between the host plant and the invading rhizobia have been deduced, but there is still much that remains to be discovered. The molecular determinant of host range at the genus level of the plant host has been determined to be lipochitooligomers called Nod factors. The molecular determinants of host range at the species and cultivar level are less well-defined. Part of my work has been to identify and characterize accessory plasmids that disrupt the normal progression of symbiosis between legumes of the genus Medicago and their rhizobial symbiont, Sinorhizobium meliloti. A cre–loxP-based system capable of making large, defined deletions was developed for the analysis of these plasmids. This system is also being employed to cure the laboratory strain, S. meliloti Rm1021 of its two megaplasmids—a loss of nearly half of its genome. I have also done work to determine whether locally-collected sinorhizobia are native, invasive, or native with symbiosis genes acquired horizontally from invasive sinorhizobia. Finally, I have studied Sinorhizobium meliloti as a host by identifying an outer membrane porin that several bacteriophages use to adsorb to the S. meliloti cell surface.
Pengaruh Penggunaan Musik Terhadap Konsentrasi Belajar Anak Sekolah Dasar

Musik merupakan segala sesuatu yang menyenangkan, mendatangkan keceriaan, mempunyai irama ( ritme ), melody, timbre (tone colour ) tertentu untuk membantu tubuh dan pikiran saling bekerja sama. Musik telah lama dianggap memiliki pengaruh terhadap tubuh maupun jiwa manusia. Mendengarkan musik-musik ketika melaksanakan pembelajaran disamping menciptakan kenyamanan dalam belajar juga dapat meningkatkan konsentrasi anak dalam belajar. Beberpa musik-musik populer (misalnya Baroque String Conceert) sangat efektif untuk membaca dan meningkatkan konsentrasi, sedangkan musik klasik dan Baroque , apabila dirancang secara khusus dapat meningkatkan konsentrasi dan keinginan belajar.
Herbicide-Grazing Interactions in Cheat (Bromus secalinus)–Infested Winter Wheat (Triticum aestivum) 1

Field experiments were conducted to determine the interaction of grazing and herbicide treatments on cheat control and biomass, wheat biomass, wheat grain yield, and wheat yield components. Ethyl-metribuzin at 1120 g ai ha−1 and metribuzin at 420 g ai ha−1 reduced cheat biomass 91 to 99 and 97 to 98%, respectively. Grazing had no effect on herbicide efficacy. Grazing increased cheat biomass in the check by 24% at only one location but did not affect total wheat plus cheat biomass. With one exception, controlled cheat was replaced by wheat on a 1:1 biomass basis when herbicides caused no crop injury. All herbicide treatments increased grain yield, but grazing did not alter yield. At two locations, increased heads m−2 and spikelets/head accounted for most of the grain yield increases, but at one location seeds/spikelet and weight/seed were also increased. Harvest index was unaffected.
Molecular studies on the genus Muticaria Lindholm, 1925 (Pulmonata, Clausiliidae) from the Maltese Islands

Received 25.07. 2018; accepted 03.10. 2018; published online 28.12. 2019 Proceedings of the 4th International Congress on Biodiversity “Man, Natural Habitats and Euro-Mediterranean Biodiversity”, November, 17th-19th 2017 Malta The present study has been carried out with focus on Muticaria macrostoma group from the Maltese Islands to characterize and define, from a molecular standpoint, their identity and relationships with topotypical Sicilian Muticaria (i.e. M. syracusana, M. neuteboomi, M. cyclopica and M. brancatoi). Molecular study included amplification of 16S rDNA (ca. 300 bp) and COI (ca. 700 bp) gene partial sequences which were used for single and combined gene analysis by Bayesian Inference to achieve the phylogenetic reconstructions with the highest posterior probabilities. Obtained results showed that, within M. macrostoma group, the taxa mamotica and oscitans can be elevated to the specific rank, thus bringing to three the Maltese Muticaria species, i.e. M. macrostoma, M. mamotica, and M. oscitans; whereas scalaris may be considered a subspecies, or even a synonim. Present findings confirmed the validity of the Sicilian species M. syracusana, M. neuteboomi, M. cyclopica and M. brancatoi. Furthermore, the populations of the Sicilian and Maltese Muticaria seem to belong to two different levels of differentiation. Finally, we have also examined some Lampedusa populations but the position of this genus still remains to be clarified. In particular, it is confirmed that Lampedusa and Muticaria are different genera, but at present, the relations within the Lampedusa group need further studies to be analysed in details.
Developing an intervention to promote person-centred care to improve management of behaviours that challenge among people living with dementia

Background: This paper reports the development work conducted for a feasibility study (MEDREV) conducted in the UK evaluating: (i) a medication review to reduce the prescription of psychotropic medication for managing behaviours that challenge among people living with dementia: and (ii) a training intervention for care home staff designed to improve the management of behaviours that challenge without medication using person-centred care. This paper reports the development of (ii) the training intervention for care home staff.Methods: The intervention development was informed by the MRC guidelines for complex interventions and the phases of the Behaviour Change Wheel. We used an iterative approach responding to and consultations with stakeholders throughout the process. Results: The target behaviours of the intervention were: responding to challenging behaviour as an expression of unmet need; communicating with compassion. The intervention was required to educate about psychotropics and their side-effects, to help care staff relate to people with dementia as individuals with individual needs and wants, to reflect upon how one might deliver the values of person-centred care in care scenarios, and to promote good team communication and self-care. An interactive, brief, in-house training session was developed with a number of recommendations for systemic change. Conclusions: The intervention was developed in a systematic way taking into account the particularities of the care home context and the target population. These factors prompted many challenges as did the manner in which residential care home interventions are funded in the UK. An ideal intervention package would have incorporated environmental elements, more systemic support from the care home management, and more financial investment to offer a more detailed, longer lasting training intervention.
Exploratory study regarding the consumer motivations for purchasing local products and their generally accepted definition.

In Romania, there is no official definition for the local products and consumers often refer of their benefits thinking of organic products. In many studies, local products are associated with distance, time and farmers markets. In order to build adequate marketing strategies for local products is necessary to study the consumer and his personal motivations and perceptions regarding local products, because he represents the demand on the market. Given their importance for the community and its continuity, it is necessary to determine the consumer perception and significance within the consumers mind. The general opinion among researchers links the consumerâ€™s perception of local products with the starting point in building and implementing marketing strategies and studying the general demand.In order to obtain information for building the questionnaire, but also for identifying the consumer perception regarding their meaning and definition, two focus groups were organized in April 2013 and July 2013 with a group of 7 persons. The participants were selected according some criteria such as: being the decision-making factor in the buying process within the family, socio-professional status, age, education. Results show that people associate local products to smaller distances from producers to consumers, freshness, and reduced time from production until consumption. Participants mentioned some motivations for purchasing local products that could be grouped into four categories such as: environmental benefits, economy benefits, social and personal benefits. The focus group conducted offered important information both for building a questionnaire and for identifying intrinsic motivations for which people buy and appreciate local products. Â
The role of sympagic meiofauna in Arctic and Antarctic sea-ice food webs

Both Antarctic and Arctic sympagic meiofauna investigated in this study included taxa new to sea ice. Diversity, abundance and biomass of metazoan meiofauna were significantly higher in a perennially than in a seasonally ice-covered Antarctic region. Brackish meltponds on Arctic sea ice hosted various proto- and metazoans. Stable isotope and fatty acid analyses combined with grazing and predation experiments showed that most metazoan meiofauna prey on ciliates and some even on metazoans. Many of them supplement their diets with algae, bacteria and detritus. A few meiofauna taxa are mainly herbivorous, but can additionally prey on ciliates or nauplii. Ingestion rates were influenced by food density (functional response) and predator density (competition). Grazing rates and the derived grazing impact of the meiofauna community were generally low. Predation rates, in contrast, were very high in some taxa, and the derived predation impact of the meiofauna community was accordingly high.