Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability

Protein functional annotation relies on the identification of accurate relationships, sequence divergence being a key factor. This is especially evident when distant protein relationships are demonstrated only with three-dimensional structures. To address this challenge, we describe a computational approach to purposefully bridge gaps between related protein families through directed design of protein-like ``linker'' sequences. For this, we represented SCOP domain families, integrated with sequence homologues, as multiple profiles and performed HMM-HMM alignments between related domain families. Where convincing alignments were achieved, we applied a roulette wheel-based method to design 3,611,010 protein-like sequences corresponding to 374 SCOP folds. To analyze their ability to link proteins in homology searches, we used 3024 queries to search two databases, one containing only natural sequences and another one additionally containing designed sequences. Our results showed that augmented database searches showed up to 30% improvement in fold coverage for over 74% of the folds, with 52 folds achieving all theoretically possible connections. Although sequences could not be designed between some families, the availability of designed sequences between other families within the fold established the sequence continuum to demonstrate 373 difficult relationships. Ultimately, as a practical and realistic extension, we demonstrate that such protein-like sequences can be ``plugged-into'' routine and generic sequence database searches to empower not only remote homology detection but also fold recognition. Our richly statistically supported findings show that complementary searches in both databases will increase the effectiveness of sequence-based searches in recognizing all homologues sharing a common fold. (C) 2013 Elsevier Ltd. All rights reserved.

An elastoplastic constitutive relation of whisker-reinforced composite for meso damage: Part I - formulation

An elastoplastic constitutive relation is developed for meso damage of whisker-reinforced composites. A model is constructed that includes orientation distribution of whiskers and slip systems as well as interface and crystal sliding. Evolution of damage will be addressed. Given in Part I is the formulation while examples will be illustrated in Part II.

Utilización de "microorganismos efectivos" en el manejo de insectos-plagas del cultivo del tomate (Lycopersicum esculentum Mill) variedad UC-82 en el Valle de Sébaco, Matagalpa

El trabajo se realizó de Octubre de 1996 a Marzo de 1997, en la Estación Experimental "Raúl González" del valle de Sébaco, Matagalpa. Se evaluó la utilización de "Microorganismos Efectivos" en el manejo de insectos-plagas y enfermedades en el cultivo del tomate (Lycopersicum esculentum Mili), variedad UC-82. Los tratamientos utilizados fueron: Tratamiento 1, Productos Químicos; Tratamiento 2, Neem (Azadirachta indica); Tratamiento 3, EM-5B (extracto de hierbas y microorganismos); Tratamiento 4, EM-5 (microorganismos); Tratamiento 5, Testigo absoluto (sin ningún tipo de aplicación). En la etapa de semillero los tratamientos EM-5 y EM-5B mostraron un efecto reductor sobre las poblaciones de mosca blanca (Bemisia tabaci Genn). Después del trasplante la mayor densidad de mosca blanca se observó en el tratamiento a base de productos químicos. El mayor porcentaje de poblaciones de Lyriomiza spp. lo obtuvieron los tratamientos químicos y EM-5. En cuanto al porcentaje de población de Diabrotica spp. no se presentaron diferencias significativas a lo largo del experimento. Referente al daño causado por Heliothis spp. se observó a los 77 DDT (días después del trasplante), los tratamientos en los que menos daños se presentaron fueron neem y químico. Sin embargo estos mismos tratamientos mostraron mayor incidencia de virosis a los 42 DDT, asi mismo no se observó diferencias estadísticas. La mayor altura la presentó el tratamiento EM-5B y el mayor número de hijos lo obtuvo el tratamiento químico y EM-5. También se presentaron resultados positivos entre los caracteres grosor del mesocarpio y diámetro polar y ecuatorial obteniendo los mejores resultados EM- 5 y EM-5B. En cuanto al rendimiento comercial de producción el tratamiento que dio valores más aceptables fue el de Neem con 26,974 Kg/Ha de frutos comercializables con rendimiento total 27,979 Kg/Ha; haciendo la salvedad que este tratamiento fue fertilizado con el biofertilizante EM-Bokashi

Efecto de densidad poblacional de plantas y fertilización nitrogenada sobre el crecimiento y rendimiento de cultivo de ajonjolí (Sesamun indicum L.) variedad INTA Aj-2000

El presente trabajo se planificó con el propósito de determinar la influencia de diferentes densidades de siembra (99,630, 120,979 y 142, 328 plantas / ha) y dosis de fertilizante nitrogenado (29.62, 59.24 y 88.86 kg / ha de nitrógeno) sobre el crecimiento y rendimiento del cultivo del ajonjolí (Sesamum indicun L), variedad INTA Aj-2000 y análisis económico de los tratamientos en estudio, bajo las condiciones ecológicas del Centro Experimental de Occidente, Posoltega, Chinandega. El ensayo se estableció en la época de Postrera del 2001 (30 de Agosto al 20 de Diciembre del 2001), utilizándose un diseño de bloques completos al azar con arreglos en parcelas divididas y estableciéndose cuatro repeticiones. De las variables evaluadas, solamente la altura de planta (cm), el número de cápsulas por planta, el número de plantas acamadas y el rendimiento mostraron un efecto significativo ante los niveles del Factor A (densidades de siembra), del Factor B (dosis de nitrógeno) y la interacción densidad por nitrógeno. Para el rendimiento de grano, el nivel a 3 (142,328 plantas / ha) del Factor A, el nivel b 2 (59.24 kg de N /ha) del Factor B y las interacciones a 3 b 2 y a 2 b 2 indujeron obtener los mayores rendimiento de grano y cuando se aplicó la densidad de siembra de 120,979 plantas / ha y se aplicó 59.24 kg/ha de nitrógeno (a 2 b 2 ) se obtuvo el tratamiento mas rentable económicamente (1,195 kg / ha), con una tasa de retorno marginal del 663.90 por ciento

Aquaculture Asia, Vol.14, No.2, pp.1-40, April-June 2009

Sustainable aquaculture GLOBALG.A.P. standard in Thai shrimp farms: Mission (im)possible? p.4 Leepaisomboon, T., Chuchird, N., Limsuwan, C., Steenbruggen, E.R., and Mungkung, R. The Victorian trout industry & the bushfires p.6 Mosig, J. Small-scale aquaculture in the Ayeyarwady Delta, Myanmar p.10 Edwards, P. The history, status, and future prospects of monosex tilapia culture in Thailand p.18 Belton, B., Turongruang, D., Bhujel, R. and Little, D.C. Mangroves of Nakhon Si Thammarat Province in southern Thailand: Species diversity, community structure and current status p.20 By Amarasinghe, M.D., Dulyapurk, V., Taparhudee, W., Yoonpundh, R. and Jumnongsong, S. Research and farming techniques Induced breeding of pacu (Piaractus brachypomus) in captivity with pituitary extract p.23 Chattarjee, N.R. and Mazumdar, B. Aquatic animal health Fumonisins - mycotoxins of increasing importance in fish! p. 24 Griessler, K. and Encarnação, P. Genetics and biodiversity Microsatellite DNA markers, a fisheries perspective. Part 1: The nature of microsatellites p.27 Sekar, M., Suresh, E., Kumar, N.S., Nayak, S.K., Balakrishna, C. Asia-Pacific Marine Finfi sh Aquaculture Magazine Formulated feed for tiger grouper grow-out p.30 Rachmansyah, Usman, Palinggi, N.N. and Williams, K. NACA Newsletter 36

Frame survey of Kainji Lake, northern Nigeria, 1996

Since 1993, annual frame surveys have been conducted by the Nigerian-German Kainji Lake Fisheries Promotion Project to determine the distribution and number of fishing localities, fishing canoes and fishing gears around Kainji Lake, Nigeria. The total number of fishing localities has increased from 221 in 1993 to 286 in 1996. The fishing localities included 245 permanent fishing villages, 29 permanent fishing camps, 8 temporary fishing camps (with fishermen from Kainji Lake) and 4 temporary fishing camps (with fishermen from outside Kainji Lake area). There was an increase in the total number of fishing entrepreneurs, fishing assistants and fishing canoes over the years. A total number of 5,499 fishing entrepreneurs, 12,449 fishing assistants and 9,278 fishing canoes were recorded during the 1996 frame survey. From 1995 there was a decrease in the number of shoreline fisherfolk and a decrease in the number of transport canoes, the number of engines remained the same. During the 1996 survey, a total number of 18,655 gill nets, 1,560 drift nets, 753 beach seines, 5,548 cast nets, 7,400 longlines and 36,979 traps were recorded. The concentration of the gears (number per km shoreline) was highest in substrata 06 and 08. The total number of gill nets increased from 17,680 in 1995 to 18,655 in 1996. For the remaining 5 gear types a decrease in number was observed. Despite increasing numbers of gears on the lake, of concern is the decline recorded in all the fishing methods of the number of gears owned by individual entrepreneurs. This was most notable in the gill net and longline fisheries. These two fisheries have the lowest daily catch values and coupled with the problem of gear theft on the lake, ownership in future, may be expected to fall further. The number of larger fishing units also declined as did the number of gears new entrants enter the fishery with. The decline is particularly worrying for the beach seine fishery where diversification into other fishing methods would be beneficial in light of the present ban on seines. The group of not active fishing entrepreneurs (those who do not themselves participate in fishing activities) had the highest ownership of gears whilst the new entrants into the fishery had the lowest. There was evidence that these new entrants into the fishery were using cast nets which is worrying given the trend of using smaller mesh size of this gearSince 1993, annual frame surveys have been conducted by the Nigerian-German Kainji Lake Fisheries Promotion Project to determine the distribution and number of fishing localities, fishing canoes and fishing gears around Kainji Lake, Nigeria. The total number of fishing localities has increased from 221 in 1993 to 286 in 1996. The fishing localities included 245 permanent fishing villages, 29 permanent fishing camps, 8 temporary fishing camps (with fishermen from Kainji Lake) and 4 temporary fishing camps (with fishermen from outside Kainji Lake area). There was an increase in the total number of fishing entrepreneurs, fishing assistants and fishing canoes over the years. A total number of 5,499 fishing entrepreneurs, 12,449 fishing assistants and 9,278 fishing canoes were recorded during the 1996 frame survey. From 1995 there was a decrease in the number of shoreline fisherfolk and a decrease in the number of transport canoes, the number of engines remained the same. During the 1996 survey, a total number of 18,655 gill nets, 1,560 drift nets, 753 beach seines, 5,548 cast nets, 7,400 longlines and 36,979 traps were recorded. The concentration of the gears (number per km shoreline) was highest in substrata 06 and 08. The total number of gill nets increased from 17,680 in 1995 to 18,655 in 1996. For the remaining 5 gear types a decrease in number was observed. Despite increasing numbers of gears on the lake, of concern is the decline recorded in all the fishing methods of the number of gears owned by individual entrepreneurs. This was most notable in the gill net and longline fisheries. These two fisheries have the lowest daily catch values and coupled with the problem of gear theft on the lake, ownership in future, may be expected to fall further. The number of larger fishing units also declined as did the number of gears new entrants enter the fishery with. The decline is particularly worrying for the beach seine fishery where diversification into other fishing methods would be beneficial in light of the present ban on seines. The group of not active fishing entrepreneurs (those who do not themselves participate in fishing activities) had the highest ownership of gears whilst the new entrants into the fishery had the lowest. There was evidence that these new entrants into the fishery were using cast nets which is worrying given the trend of using smaller mesh size of this gear. (PDF contains 44 pages)

星间激光通信光束微弧度跟瞄性能检测装置的设计原理

基于矢量折射定理，研究了透射光束通过双棱镜实现微弧度量级偏转的设计原理，解决了星间激光通信精跟瞄检测的难题。推导了正交双棱镜实现光束偏转的精确公式，提出以水平张角和垂直张角表达光束视场，并说明了单棱镜实现光束偏转的一般情况。根据设计指标和计算结果确定了棱镜的主要参量，进而对光束的偏转结果进行了数值模拟。最后的实验结果与模拟结果基本一致。结果表明：取棱镜棱角α为4°时，棱镜每旋转1’，透射光束变化约1μrad；分别控制双棱镜在其最小偏向角一侧小角度偏转，可以实现光束在水平方向和垂直方向500μ范围内的精确扫

Double-line-density gratings structure for compression and generation of double femtosecond laser pulses

Grating pairs are widely used for pulse compression and stretching. Normally, the two gratings are identical. We propose a very simple structure with double-line-density reflective gratings for pulse compression and generation of double pulses, which has the advantages of no material dispersion, compact in volume, simple in structure, etc. The use of reflective Dammann gratings fully demonstrated the principle of this structure. The output pulses are well verified by a standard frequency-resolved optical gating apparatus. This structure will be highly interesting in ultrashort pulse compression and other more practical applications of femtosecond laser pulses. (c) 2007 Optical Society of America.

Derechos humanos y educación : retos de una nueva sociedad

[EU]Hitzaurrea (X. Etxague eta A. Lareki). - Giza Eskubideak eta gaitasunak derrigorrezko hezkuntzan: zeharkakotasunetik lantzeko proposamena (E. Cruz). - Giza Eskubideak eta adimen urritasuna duten pertsonak: Ordiziako Garaguneko esperientzia bat (J. F. Amiama). - Begirada bat Euskal Herriko haurrentzako eta gazteentzako aisia hezigarriari. Etengabe eraikitzen ari den eskubidea (J. Jiménez). - Informazioa eskuratzeko eskubidea landako eskoletan eta eskola unitarioetan (A. Fernández). - Gazteak sare sozialen bidez gizalegez sozializatzeko teoria politikoa helburu (E. Fernández eta J. M. Gutiérrez). - Komunikatzeko eskubidea eta pribatutasun eskubidea sarean: binomio kezkagarria 14 urtetik beherako seme alabak dituzten familientzat (J. Altuna). - Arimaren sufrimendua lausatzeko bertsoak (P. Pérez).

Effects of Yb concentration on the fluorescence spectra of Yb-doped YAlO3 single crystals

0.5 at.% Yb:YAlO3(YAP), 5 at.% Yb:YAP and 15 at.% Yb:YAP were grown using the Czochralski method. Their absorption and fluorescence spectra were measured at room temperature and their emission line shape was calculated using the method of reciprocity. It was observed that the fluorescence spectra changed appreciably with the increasing of Yb concentration. For 0.5 at.% Yb:YAP, the line shape of fluorescence is very similar with the calculated emission line shape; with the increasing of Yb doping concentration, the line shape of fluorescence is very different from the calculated emission line shape. These phenomena are caused by the strong self-absorption at 979 and 999 nm for Yb:YAP. (c) 2005 Elsevier B.V. All rights reserved.