A two-base encoded DNA sequence alignment problem in computational biology

The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics. The primary objective of the "sequence alignment" problem is to search for a new algorithm that facilitates the use of two-base encoded data for large-scale re-sequencing projects. This algorithm should be able to perform local sequence alignment as well as error detection and correction in a reliable and systematic manner, enabling the direct comparison of encoded DNA sequence reads to a candidate reference DNA sequence. We will first briefly review two well-known sequence alignment approaches and provide a rudimentary improvement for implementation on parallel systems. Then, we carefully examin a unique sequencing technique known as the SOLiDTM System that can be implemented, and follow by the results from the global and local sequence alignment. In this report, the team presents an explanation of the algorithms for color space sequence data from the high-throughput re-sequencing technology and a theoretical parallel approach to the dynamic programming method for global and local alignment. The combination of the di-base approach and dynamic programming provides a possible viewpoint for large-scale re-sequencing projects. We anticipate the use of distributed computing to be the next-generation engine for large-scale problems like such

Synchronized Artificial Natures: The Secret Life of Trees Connecting York, Delft and Alicante

This paper presents an experiment that explored teaching limits in architecture and computational arts. Three universities (York, Tu-Delft and Alicante) collaborated, commissioning and producing three Interactive scenographic spaces. These were formed by visitors, artificial trees as well as reactive technologies and emulated the way in which fungi communicate by connecting their roots underground. Over the four months of duration of the experiment, students learnt about programming resources in contemporary musical scenographic creation; graphic resources and digital manufacturing for 3D printing; component design; Arduino programming; and interfaces such as the “Game of Life” to explain the project in terms of cooperating particles. Theoretical backgrounds such as the architecture of contingency, readings such as “the secret life of the trees” by Wohlleben and performance practices such as “A-volve” by Mignonneau and Sommerer or “Hylozoic series” by Philip Beesley were approached in the workshop. The ultimate goals of this teaching practice described more explicitly in the paper include: understanding the ways in which communities cooperate; synchronous communication between scenic spaces as well as transparent design processes; and efforts to reduce excessive subject learning encapsulation in new Degrees based on the Bologna model

Natural immunity to SARS-CoV-2 and breakthrough infections in vaccinated and unvaccinated patients with cancer

Oncology; Public health; COVID-19Oncología; Salud pública; COVID-19Oncologia; Salut pública; COVID-19Background Consolidated evidence suggests spontaneous immunity from SARS-CoV-2 is not durable, leading to the risk of reinfection, especially in the context of newly emerging viral strains. In patients with cancer who survive COVID-19 prevalence and severity of SARS-CoV-2 reinfections are unknown. Methods We aimed to document natural history and outcome from SARS-CoV-2 reinfection in patients recruited to OnCovid (NCT04393974), an active European registry enrolling consecutive patients with a history of solid or haematologic malignancy diagnosed with COVID-19. Results As of December 2021, out of 3108 eligible participants, 1806 COVID-19 survivors were subsequently followed at participating institutions. Among them, 34 reinfections (1.9%) were reported after a median time of 152 days (range: 40–620) from the first COVID-19 diagnosis, and with a median observation period from the second infection of 115 days (95% CI: 27–196). Most of the first infections were diagnosed in 2020 (27, 79.4%), while most of reinfections in 2021 (25, 73.5%). Haematological malignancies were the most frequent primary tumour (12, 35%). Compared to first infections, second infections had lower prevalence of COVID-19 symptoms (52.9% vs 91.2%, P = 0.0008) and required less COVID-19-specific therapy (11.8% vs 50%, P = 0.0013). Overall, 11 patients (32.4%) and 3 (8.8%) were fully and partially vaccinated against SARS-CoV-2 before the second infection, respectively. The 14-day case fatality rate was 11.8%, with four death events, none of which among fully vaccinated patients. Conclusion This study shows that reinfections in COVID-19 survivors with cancer are possible and more common in patients with haematological malignancies. Reinfections carry a 11% risk of mortality, which rises to 15% among unvaccinated patients, highlighting the importance of universal vaccination of patients with cancer.OnCovid is sponsored by Imperial College London and received direct project funding and infrastructural support by the NIHR Imperial Biomedical Research Centre (BRC). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. Neither sponsor nor the funders of the study had any role in study design, data collection, data analysis, data interpretation, or writing of the report. All authors had access to all the data reported in the study

Latin America and the Caribbean: Fact Sheet on Leaders and Elections

This fact sheet tracks the current heads of government in Central and South America, Mexico, and the Caribbean. It provides the dates of the last and next elections for the head of government and the national independence date for each country

Small Bowel Ischemia in a Sickle Cell Patient

We report a case of small bowel ischemia secondary to sickle cell disease. Acute bowel ischemia is an uncommon presentation of patients with sickle cell disease. Historically, only a handful of cases have been reported. We also provide a summary of the literature relevant to sickle cell patients with acute bowel ischemia

XIV Men’s Volleyball Pan American Cup: Team mental toughness correlates perfectly with final placement

Mental toughness (MT) has been associated with competitive and non-competitive performance indicators in sport. On average, mentally tougher participants tend to be more successful. However, even in team-sport research, team MT is often disregarded over individual MT measurements. Results in team settings are trivial on whether team MT is related to athletic achievement/competitive performance. Volleyball is under-investigated in the applied MT literature. PURPOSE: To explore the relationship between team MT levels and competitive performance in volleyball. METHODS: Five national volleyball teams (i.e., Cuba, Mexico, Suriname, Dominican Republic, USA) were recruited during the XIV Men’s Pan American Cup (n=60; mage = 23.90, SD = 3.49). The Mental Toughness Index (MTI) was used for data collection in the beginning of the tournament. MTI consists of eight equally-weighted items with scores ranging from one (i.e., False, 100% of the time) to seven (i.e. True, 100% of the time). The maximum MTI score is 56. The average team MTI scores were calculated and then, compared against the tournament results in IBM SPSS statistics. RESULTS: The analysis concluded a perfect correlation between team MTI scores and tournament placement (r = -1, p \u3c 0.001). Therefore, the higher the team MTI scores, the higher the finishing place (e.g., the team with the highest team MTI score, MTICuba = 50.77, won the tournament). CONCLUSION: The results indicate a very strong relationship between team MT and competitive performance across American cultures. Practitioners may need to consider psychological skills training targeted to increase team MT as a means to increase competitive performance. The high level of skill, but also of difficulty to recruit, of these teams add on the significance of the findings. Our outcomes not only support larger-scale future research in similar and different settings (e.g., sport, continent, sex), but also interventional efforts. Limitations include self-report, cross-sectional design, and small sample size

Identification of chemicals that mimic transcriptional changes associated with autism, brain aging and neurodegeneration

Environmental factors, including pesticides, have been linked to autism and neurodegeneration risk using retrospective epidemiological studies. Here we sought to prospectively identify chemicals that share transcriptomic signatures with neurological disorders, by exposing mouse cortical neuron-enriched cultures to hundreds of chemicals commonly found in the environment and on food. We find that rotenone, a pesticide associated with Parkinson's disease risk, and certain fungicides, including pyraclostrobin, trifloxystrobin, famoxadone and fenamidone, produce transcriptional changes in vitro that are similar to those seen in brain samples from humans with autism, advanced age and neurodegeneration (Alzheimer's disease and Huntington's disease). These chemicals stimulate free radical production and disrupt microtubules in neurons, effects that can be reduced by pretreating with a microtubule stabilizer, an antioxidant, or with sulforaphane. Our study provides an approach to prospectively identify environmental chemicals that transcriptionally mimic autism and other brain disorders

Formation of octapod MnO nanoparticles with enhanced magnetic properties through kinetically-controlled thermal decomposition of polynuclear manganese complexes

Polynuclear manganese complexes are used as precursors for the synthesis of manganese oxide nanoparticles (MnO NPs). Altering the thermal decomposition conditions can shift the nanoparticle product from spherical, thermodynamically-driven NPs to unusual, kinetically-controlled octapod structures. The resulting increased surface area profoundly alters the NP's surface-dependent magnetism and may have applications in nanomedicine

Incidencia de la relación agua-cemento del mortero, en las propiedades mecánicas en pilas de ladrillos King Kong 18 huecos adicionado con puzolana de la cantera Raqchi, Cusco 2017.

La presente investigación está referida al estudio de las propiedades mecánicas en pilas de albañilería elaboradas con ladrillos adicionados con puzolana al 20% en peso, debido a su alta resistencia a compresión y otros parámetros como unidad mencionado en una tesis de referencia, con mortero de relaciones agua-cemento: 1.025, 1.050 y 1.075 y la comparación de estos especímenes con pilas tradicionales. La puzolana como material volcánico fue estudiada porque presenta mejores propiedades térmicas e incrementa la resistencia a la compresión en unidades elaboradas con este material. Para la elaboración de muestras, ensayos y análisis de los datos se emplearon normas técnicas peruana (NTP) referido al mortero, unidades y pilas de albañilería, normas ITINTEC que mencionan el procedimiento de elaboración de los ensayos, norma técnica mexicana (NMX) basada en el esfuerzo de adherencia de unidades por ensayo de corte. Las unidades de estudio fueron ladrillos King Kong 18 huecos añadidos con puzolana al 20% en peso, cuyas dimensiones fueron de 24 cm x 24 cm x 9 cm, el agregado utilizado en el diseño de mortero fueron de las canteras de Raqchi y Huacarpay en una dosificación de 50% de cada parte, fueron evaluados 81 especímenes de dados de mortero elaborados con relación agua-cemento de 1.025, 1.050 y 1.75, se fabricaron 48 pilas de albañilería de 3 unidades con juntas de 1.5 cm con diferentes relaciones agua cemento propuestas, se elaboración 48 pilas con desfase en 1 unidad para el ensayo de esfuerzo de adherencia con junta de 1.5 cm a diferentes relaciones agua-cemento planteadas. Observando los resultados obtenidos, se destaca la mayor resistencia a compresión axial de 78.95 kg/cm2, que fueron obtenidas de las pilas de albañilería elaborados con ladrillo añadidos con puzolana de relación agua-cemento 1.025, el cual incrementó en un 64.86% frente a una pila de albañilería con unidades típicas. El mayor resultado de adherencia en pilas fue de 3.76 kg/cm2, que fueron las pilas de albañilería desfasadas en 1 unidad elaboradas con ladrillos añadidos con puzolana en una relación agua cemento 1.050, el cual frente a un espécimen típico incrementa en un 31.93%. Se concluyó que las unidades puzolánicas son ladrillo tipo III, mejorando su resistencia a compresión y adherencia unidad-mortero.The present investigation is referred to the study of the mechanical properties in masonry piles made with bricks added with 20% pozzolan due to its high resistance to compression and other parameters as a unit mentioned in a reference thesis, with mortar of relationships water-cement: 1,025, 1,050 and 1,075 and the comparison of these specimens with traditional batteries. Pozzolan as a volcanic material was studied because it has better thermal properties and increases the resistance to compression in units made with this material. For the elaboration of samples, tests and analysis of the data, Peruvian technical standards (NTP) referring to mortar, masonry units and stacks were used, ITINTEC standards that mention the procedure for the preparation of the tests, Mexican technical standard (NMX) based on the adhesion effort of units per cutting test. The study units were King Kong bricks 18 holes added with 20% pozzolan in weight, whose dimensions were 24 cm x 24 cm x 9 cm, the aggregate used in the mortar design were from the quarries of Raqchi and Huacarpay in a dosage of 50% of each part, 81 specimens of mortar dice prepared with water-cement ratio of 1,025, 1,050 and 1.75 were evaluated, 48 masonry piles of 3 units were produced with 1.5 cm joints with different water-cement ratios proposed , 48 piles with phase shift in 1 unit were prepared for the adhesion stress test with joint of 1.5 cm at different watercement ratios. Observing the obtained results, it stands out the greater resistance to axial compression of 78.95 kg / cm2, which were obtained from the piles of masonry made with brick added with pozzolana of water-cement ratio 1.025, which increased by 64.86% compared to a masonry stack with typical units. The highest result of adhesion in piles was 3.76 kg / cm2, which were the piles of masonry phased out in 1 unit made with bricks added with pozzolan in a water-cement ratio 1.050, which in front of a typical specimen increases by 31.93%. It was concluded that the pozzolanic units are type III brick, improving its compressive strength and unit-mortar adhesion.Tesi

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Mock galaxy catalogues for the BOSS Final Data Release

We reproduce the galaxy clustering catalogue from the SDSS-III Baryon Oscillation Spectroscopic Survey Final Data Release (BOSS DR11 and DR12) with high fidelity on all relevant scales in order to allow a robust analysis of baryon acoustic oscillations and redshift space distortions. We have generated (6000) 12 288 MultiDark PATCHY BOSS (DR11) DR12 light cones corresponding to an effective volume of ~ 192 000 [h-1 Gpc]3 (the largest ever simulated volume), including cosmic evolution in the redshift range from 0.15 to 0.75. The mocks have been calibrated using a reference galaxy catalogue based on the halo abundance matching modelling of the BOSS DR11 and DR12 galaxy clustering data and on the data themselves. The production follows three steps. First, we apply the PATCHY code to generate a dark matter field and an object distribution including non-linear stochastic galaxy bias. Secondly, we run the halo/stellar distribution reconstruction HADRON code to assign masses to the various objects. This step uses the mass distribution as a function of local density and non-local indicators (i.e. tidal field tensor eigenvalues and relative halo exclusion separation for massive objects) from the reference simulation applied to the corresponding patchy dark matter and galaxy distribution. Finally, we apply the SUGAR code to build the light cones. The resulting MultiDarkPATCHY mock light cones reproduce the number density, selection function, survey geometry, and in general within 1s, for arbitrary stellar mass bins, the power spectrum up to k = 0.3 h Mpc-1, the two-point correlation functions down to a few Mpc scales, and the three-point statistics of the BOSS DR11 and DR12 galaxy samples.Fil: Kitaura, Francisco-Shu. Leibniz-Institut für Astrophysik Potsdam; AlemaniaFil: Rodriguez Torres, Sergio A.. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Chuang, Chia Hsun. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Zhao, Cheng. Tsinghua University; ChinaFil: Prada, Francisco. Consejo Superior de Investigaciones Científicas; España. Universidad Autónoma de Madrid; EspañaFil: Gil Marín, Héctor. University of Portsmouth; Reino UnidoFil: Guo, Hong. State University of Utah; Estados Unidos. Shanghai Astronomical Observatory; ChinaFil: Yepes, Gustavo. Universidad Autónoma de Madrid. Facultad de Ciencias; EspañaFil: Klypin, Anatoly. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; España. New Mexico State University; Estados UnidosFil: Scoccola, Claudia Graciela. Universidad Autónoma de Madrid; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Instituto de Astrof{isica de Canarias; España. Universidad de La Laguna; EspañaFil: Tinker, Jeremy. University of New York; Estados UnidosFil: McBride, Cameron. Harvard-Smithsonian Center for Astrophysics; Estados UnidosFil: Reid, Beth. Lawrence Berkeley National Laboratory; Estados Unidos. University of California at Berkeley; Estados UnidosFil: Sánchez, Ariel G.. Max Planck Institut für Extraterrestrische Physik; AlemaniaFil: Salazar Albornoz, Salvador. Max Planck Institut für Extraterrestrische Physik; Alemania. Ludwig Maximilians Universitat; AlemaniaFil: Grieb, Jan Niklas. Max Planck Institut für Extraterrestrische Physik; Alemania. Ludwig Maximilians Universitat; AlemaniaFil: Vargas Magana, Mariana. Universidad Nacional Autónoma de México; MéxicoFil: Cuesta, Antonio J.. Universidad de Barcelona; EspañaFil: Neyrinck, Mark. University Johns Hopkins; Estados UnidosFil: Beutler, Florian. Lawrence Berkeley National Laboratory; Estados UnidosFil: Comparat, Johan. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Percival, Will J.. University of Portsmouth; Reino UnidoFil: Ross, Ashley. Ohio State University; Estados Unidos. University of Portsmouth; Reino Unid