997 research outputs found
open-AIMS/ADRIA.jl: v0.7.0-dev.1
No full textWhat's Changed
Update use of functions due to new import approach by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/334
Migrate from SnoopPrecompile to PrecompileTools by @timholy in https://github.com/open-AIMS/ADRIA.jl/pull/335
Add planning horizon factor by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/336
Replace use of area attribute/field with call to function site_area() to ensure correct values by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/337
Remove reference to defunct fields when making factors constant by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/338
Make use of planning horizon in sims by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/340
Changes to support running ADRIA with external model (ReefMod Engine) data by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/341
CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/343
CompatHelper: add new compat entry for OrderedCollections at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/344
CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/345
Split ADRIA-mod domain definition by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/346
Add GBR zones by priority by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/347
Exit with error if given path is not a directory by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/350
Make Aviz into an extension package by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/349
CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/351
CompatHelper: add new compat entry for ImageMagick at version 1, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/352
Update bleaching mortality model to align with published paper by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/354
Add option to use JMcDM functions in ADRIA site selection by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/348
Address mismatched number of elements under certain conditions by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/358
Remove Copras method due to erroring by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/359
CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/363
CompatHelper: add new compat entry for JMcDM at version 0.7, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/362
Update documentation by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/361
Scenario discovery docs by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/364
Fix: Metric errors when applied to a single simulation by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/365
Address ranking errors in mcda outputs by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/367
Add temporal clustering by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/370
Fix incorrect type check by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/371
CompatHelper: add new compat entry for Clustering at version 0.15, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/372
CompatHelper: bump compat for Zarr to 0.9, (keep existing compat) by @github-actions in https://github.com/open-AIMS/ADRIA.jl/pull/373
Update time series clustering and add visualization functionality by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/374
Update scenario viz by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/355
Refactor run_scenarios to improve when running multiple rcps by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/376
Bump version number and add new author by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/378
Update docstrings for growth function by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/375
Add map visualization - displays k-area by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/356
Consider near-term conditions with greater weight than far-future conditions by @ConnectedSystems in https://github.com/open-AIMS/ADRIA.jl/pull/387
Changes to number of species in ADRIA by @Rosejoycrocker in https://github.com/open-AIMS/ADRIA.jl/pull/380
Temporal clustering for spatial data by @Zapiano in https://github.com/open-AIMS/ADRIA.jl/pull/382
New Contributors
@timholy made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/335
@Zapiano made their first contribution in https://github.com/open-AIMS/ADRIA.jl/pull/370
Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.5.0...v0.7.0-dev.
Towards a human rights approach to water in Lebanon: Implementation beyond 'reform'
No full textThis paper examines what it means for Lebanon to adopt a human rights approach to water. Experts agree that there is a crisis in the water sector, with the poor suffering disproportionately in terms of access to, availability and quality of water. The paper details the gap between Lebanon's political acceptance of water as a human right, and its implementation. It suggests that the civil war, Israeli occupation and mismanagement reduced Lebanon's capacity to ensure an adequate water and sanitation services to its citizens. A lack of political will due to clientalist and sectarian considerations in public policy, ineffective public participation and tension over transboundary water resources have further intensified this problem and has led to the continued dominance of traditional security considerations in water policy. The paper asserts that the main goals set by the current reform process of the water sector address important capacity issues, such as efficiency gains and cost recovery, but do not signal a political shift towards a human rights-based approach.ALHAJJAR Z, 1997, MIYAH LUBNANIYA SALA; AMERY HA, 1992, BEIRUT REV, P3; Bluemel EB, 2004, ECOL LAW QUART, V31, P957; *CDR, 2005, CDR 15 YEAR MAST PLA; *CDR, 2005, PROGR REP JUL 2005; COMAIR F, 2005, MIYAH LUBNAN BAYN DI; CORM G, 1998, MONDE DIPLOMATIQUE; DARWISH A, 2004, 11 HEINR BOLL FDN; ELFADEL M, 2000, WATER RESOURCES DEV, V16, P615; ELFADEL M, 2003, WATER RESOURCES DEV, V18, P315; *ERM WORLD BANK, 1995, LEB NAT ENV STRAT AS; *ESCWA, 2003, ASS ROL PRIV SECT DE; *ESCWA UNDP, 2002, WAT TAR AN LEB; FISK R, 2002, INDEPENDENT 0926; GASPER T, 2004, KHAYARAT LUBNAN, P123; Gleick Peter H., 1998, WATER POLICY, V1, P487; Hamzeh Nizar, 2001, MIDDLE E STUDIES, V37, P167; HARIRI R, BALANCED DEV PROTECT; JABER B, 2002, WATER DEMAND MANAGEM; KHAWLI M, 2000, LUBNAN THARWA; KILGORE A, 2006, WASHINGTON REPORT MI, P20; Kingston Paul, 2001, ARAB STUDIES Q, V23, P55; Klawitter S, 2005, INT J WATER RESOUR D, V21, P253, DOI 10.1080-07900620500036414; KUBURSI A, 1999, ARAB STUDIES Q, V21, P69; KUNIG E, 1999, 27 U LOND SCH OR AFR; *LEB REP, 2002, POS REP SERV AR HASB; *LEB REP, 2006, LEB ROAD REC REC; MAJZOUB T, 2001, AHAD YASHRAB MASHARI; Makdisi S., 2004, LESSONS LEBANON EC W, DOI 10.1080-14753680500064067; Makhoul Jihad, 2004, ARAB STUDIES Q, V26, P25; MALLAT H, 1995, WATER MIDDLE E LEGAL; *METAP, WAT QUAL MAN; *MEW, 1999, ACT PLAN MIN EN WAT; MEY J, 1992, WAQ MIYAH LUBN C P B; MEY J, 2002, ENVIRON MONIT ASSESS, V77, P11; *MOE, 2001, LEB STAT ENV REP; *MOE, 2005, DRAFT NAT ENV ACT PL; *MOSA, 1998, MAPP LIV COND LEB AN; Naff T., 1984, WATER MIDDLE E CONFL; Ofeish S.A., 1999, ARAB STUDIES Q, V21, P97; SAAB N, 2005, KHAYARAT LUBNAN, P253; Seaver BM, 2000, POLIT SCI QUART, V115, P247, DOI 10.2307-2657902; Stork Joe, 1983, MERIP REPORTS, V116, P19; *UN, 2006, CONS APP PROC LEB CR; *UN, 2006, RIGHT WAT; *UNDP, 2003, MILL DEV GOALS LEB R; *UNDP, 2006, HUM DEV REP 2006 WAT; *UNDP ESCWA, 2003, WORKSH GROUNDW LEG R; *UNHCHR, 2005, 2 DRAFT COUNTR PROF; *UNOCHA, 2006, 36 OCHO; *UNRWA, LEB CAMP REF PROF; *WORLD BANK, 2005, 34462 WORLD BANK; *WORLD BANK ERM, STAT ENV; *WORLD WAT FOR, 2006, RIGHT WAT RIGHT ALL; Yamout G, 2007, WATER RESOUR MANAG, V21, P611, DOI 10.1007-s11269-006-9033-322
A tracer study of Lebanese upper secondary school students
No full textThis paper presents data arising from a tracer study of 90 terminating Beirut upper secondary school students. Nearly all the students intended to transit to university, about half of them to science and technology programmes, and subsequently did so. Median anticipated earnings upon graduation were realistic, but a lack of information or guidance about higher education and career options was noted by a considerable proportion. The results of the study are discussed with reference to the as yet poorly elucidated dynamics of schooling with regard to attrition and transition to higher education and employment in Lebanon. © 2006 Elsevier Ltd. All rights reserved.ALSAMARRAI S, 2005, 31 PRUS; Boyd S., 2001, SCH FINAL YEAR SCH S; *CENTR INT AG, 2006, CIA FACTB; *CTR ED RES DEV, 2005, STAT REP AC YEAR 200; Daehlen M., 2005, J ED WORK, V18, P385; GOUVIAS D, 2005, J ED WORK, V18, P421, DOI 10.1080-13639080500327790; *GOV MALT, 2006, GUID COUNS SERV; HAJJ M, 2002, J DEV EC POLICIES, V4, P43; HASHEM ME, 2002, WORLD ED ENCY SURVEY; Humphrey M, 2004, ARAB STUDIES Q, V26, P31; International Labour Organisation, 1987, INT STAND CLASS OCC; KABBANI B, 2005, 0234 WORLD BANK; Lloyd CB, 2003, COMP EDUC REV, V47, P444, DOI 10.1086-378247; SOLIMAN AM, 1991, INT J ADV COUNS, V14, P3, DOI 10.1007-BF00116712; THEODORY GC, 1982, INT J ADV COUNS, V5, P121, DOI 10.1007-BF00119093; *UN, 2003, RES GLOB SKILL FORM; Vlaardingerbroek B, 2001, INT J EDUC DEV, V21, P315, DOI 10.1016-S0738-0593(00)00006-744
Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels
No full textMitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion
Regulation of stem cell identity by miR-200a during spinal cord regeneration
No full text© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walker, S. E., Sabin, K. Z., Gearhart, M. D., Yamamoto, K., & Echeverri, K. Regulation of stem cell identity by miR-200a during spinal cord regeneration. Development, 149(3), (2022): dev200033, https://doi.org/10.1242/dev.200033.Axolotls are an important model organism for multiple types of regeneration, including functional spinal cord regeneration. Remarkably, axolotls can repair their spinal cord after a small lesion injury and can also regenerate their entire tail following amputation. Several classical signaling pathways that are used during development are reactivated during regeneration, but how this is regulated remains a mystery. We have previously identified miR-200a as a key factor that promotes successful spinal cord regeneration. Here, using RNA-seq analysis, we discovered that the inhibition of miR-200a results in an upregulation of the classical mesodermal marker brachyury in spinal cord cells after injury. However, these cells still express the neural stem cell marker sox2. In vivo cell tracking allowed us to determine that these cells can give rise to cells of both the neural and mesoderm lineage. Additionally, we found that miR-200a can directly regulate brachyury via a seed sequence in the 3′UTR of the gene. Our data indicate that miR-200a represses mesodermal cell fate after a small lesion injury in the spinal cord when only glial cells and neurons need to be replaced.K.Z.S. was supported by a National Institutes of Health grant (T32 GM113846). K.E. is supported by a grant from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01 HD092451), by start-up funds from the Marine Biological Laboratory and by funding from the Owens Family Foundation. Open Access funding provided by the Marine Biological Laboratory. Deposited in PMC for immediate release
Transformation of mucocartilage to a definitive cartilage during metamorphosis in the sea lamprey, Petromyzon-marinus
No full textPT: J; CR: ARCHER CW, 1982, CELL DIFFER, V11, P245 BROWDER LW, 1980, DEV BIOL, P577 CAPLAN AI, 1973, J EMBRYOL EXP MORPH, V29, P571 DAMAS H, 1935, ARCH BIOL, V46, P171 DARNELL J, 1986, MOL CELL BIOL EDE DA, 1983, CARTILAGE, V2, P143 EIKENBERRY EF, 1984, J MOL BIOL, V176, P261 FOX H, 1975, J EMBRYOL EXP MORPH, V34, P191 FUKUDA Y, 1984, AM J ANAT, V170, P597 GODMAN GC, 1960, J BIOPHYS BIOCHEM CY, V8, P719 GOEL SC, 1970, J EMBRYOL EXPTL MORP, V23, P169 GOSS RJ, 1972, AM ZOOL, V12, P151 GOULD RP, 1972, EXP CELL RES, V72, P325 HALL BK, 1978, DEV CELLULAR SKELETA, P86 HAM AW, 1979, HISTOLOGY HARDISTY MW, 1971, BIOL LAMPREYS, V1, P127 HARDISTY MW, 1971, BIOL LAMPREYS, V1, P85 HARDISTY MW, 1981, BIOL LAMPREYS, V3, P333 HASTY KA, 1981, DEV BIOL, V86, P198 HASTY KA, 1983, J HISTOCHEM CYTOCHEM, V31, P1367 HEASMAN J, 1978, J EMBRYOL EXP MORPH, V46, P119 HORNBRUCH A, 1970, NATURE, V226, P764 HUNZIKER EB, 1982, J ULTRASTRUCT RES, V81, P1 JANNERS MY, 1970, DEV BIOL, V23, P136 JOHNELS A, 1948, ACTA ZOOL-STOCKHOLM, V29, P139 JURAND A, 1965, P ROY SOC B, V162, P387 KIMURA S, 1982, COMP BIOCH PHYSL, V73, P335 KOSHER RA, 1980, J EMBRYOL EXP MORPH, V56, P91 KOSHER RA, 1983, CARTILAGE, V1, P59 LASH JW, 1978, DEV BIOL, V66, P151 LINSENMAYER TF, 1981, CELL BIOL EXTRACELLU, P5 MANGIA F, 1970, ARCH ANAT MICROSC MO, V59, P283 MARTIN GR, 1985, TRENDS BIOCHEM SCI, V10, P285 MILLER EJ, 1969, P NATL ACAD SCI USA, V64, P1264 NATHANSON MA, 1980, DEV BIOL, V78, P301 OLSON M, 1971, AM J ANAT, V131, P197 POTTER IC, 1978, CAN J ZOOL, V56, P561 SCHMIDT AJ, 1968, CELLULAR BIOL VERTEB SCHNEIDER A, 1879, ANATOMIE ENTWICKELUN, P85 SEARLS RL, 1972, DEV BIOL, V28, P123 SHEEHAN DC, 1980, THEORY PRACTICE HIST SHELDON H, 1983, CARTILAGE, V1, P87 SHEREN SB, 1986, COMP BIOCHEM PHYS B, V85, P5 SHORE RC, 1981, J ANAT, V133, P67 STOCKWELL RA, 1979, BIOL CARTILAGE CELLS STUDNICKA FK, 1897, ARCH MIKROSK ANAT, V48, P606 SUMMERBELL D, 1973, NATURE, V244, P492 THOROGOOD PV, 1975, J EMBRYOL EXP MORPH, V33, P581 VONDERMARK K, 1979, CLIN ORTHOP RELAT R, V139, P185 WATENABE K, 1974, CELL TISS RES, V155, P321 WRIGHT GM, 1982, AM J ANAT, V165, P39 WRIGHT GM, 1983, AM J ANAT, V167, P59 WRIGHT GM, 1983, EXPERIENTIA, V39, P495 WRIGHT GM, 1984, CAN J ZOOL, V62, P2445 YOUSON JH, 1979, CAN J ZOOL, V57, P1808 YOUSON JH, 1982, J MORPHOL, V171, P89; NR: 56; TC: 10; J9: J MORPHOL; PG: 21; GA: K6234Source type: Electronic(1
The effect of rearing in a shelved environment on behavioral and physiological markers of welfare in rats (Rattus norvegicus)
No full textEarly-life experiences are critical modifiers of development. An important component of early-life experience is the nature of maternal interactions, which can be modified by stress. During rearing, mothers are typically allocated to single-level cages where they are readily accessible to pups, a potentially stressful scenario not reflective of nature. Accordingly, mothers regularly removed from the rearing environment interact differently with their offspring, leading to long-term changes in offspring physiology and behavior. Such changes commonly include modifications within the hypothalamic-pituitary-adrenal axis, of which corticosterone is a major component. Modifications in the hypothalamic-pituitary-adrenal axis may also be manifested through changes in affective behavior and assessed via tests such as the open field and elevated plus maze as well as via ultrasonic vocalization (USV) analysis. As a means of assessing the impact of rearing in a shelved environment, we allocated mothers to standard single-level cages or cages with an integrated shelf, which allowed the mother to temporarily escape pups. While there were no differences in fecal corticosterone, behavior in the elevated plus maze, or USVs, male rats reared in standard cages weighed more, and all standard single-level housed rats spent more time in the center of the open field. The observed differences indicate that allocating nursing mothers to shelved environments throughout the postnatal period has long-lasting effects on offspring behavior that must be considered when establishing dam enrichment protocols
Retinitis Pigmentosa GTPase Regulator (RPGR) protein isoforms in mammalian retina:insights into X-linked Retinitis Pigmentosa and associated ciliopathies
No full textMutations in the cilia-centrosomal protein Retinitis Pigmentosa GTPase Regulator (RPGR) are a frequent cause of retinal degeneration. The RPGR gene undergoes complex alternative splicing and encodes multiple protein isoforms. To elucidate the function of major RPGR isoforms (RPGR 1-19 and RPGR ORF15), we have generated isoform-specific antibodies and examined their expression and localization in the retina. Using sucrose-gradient centrifugation, immunofluorescence and co-immunoprecipitation methods, we show that RPGR isoforms localize to distinct sub-cellular compartments in mammalian photoreceptors and associate with a number of cilia-centrosomal proteins. The RCC1-like domain of RPGR, which is present in all major RPGR isoforms, is sufficient to target it to the cilia and centrosomes in cultured cells. Our findings indicate that multiple isotypes of RPGR may perform overlapping yet somewhat distinct transport-related functions in photoreceptors
The effect of rearing in a shelved environment on behavioral and physiological markers of welfare in rats (Rattus norvegicus)
No full textEarly-life experiences are critical modifiers of development. An important component of early-life experience is the nature of maternal interactions, which can be modified by stress. During rearing, mothers are typically allocated to single-level cages where they are readily accessible to pups, a potentially stressful scenario not reflective of nature. Accordingly, mothers regularly removed from the rearing environment interact differently with their offspring, leading to long-term changes in offspring physiology and behavior. Such changes commonly include modifications within the hypothalamic-pituitary-adrenal axis, of which corticosterone is a major component. Modifications in the hypothalamic-pituitary-adrenal axis may also be manifested through changes in affective behavior and assessed via tests such as the open field and elevated plus maze as well as via ultrasonic vocalization (USV) analysis. As a means of assessing the impact of rearing in a shelved environment, we allocated mothers to standard single-level cages or cages with an integrated shelf, which allowed the mother to temporarily escape pups. While there were no differences in fecal corticosterone, behavior in the elevated plus maze, or USVs, male rats reared in standard cages weighed more, and all standard single-level housed rats spent more time in the center of the open field. The observed differences indicate that allocating nursing mothers to shelved environments throughout the postnatal period has long-lasting effects on offspring behavior that must be considered when establishing dam enrichment protocols.Sir James Dunn Animal Welfare CentreAtlantic Veterinary College, University of Prince Edward Islan
A role for SUMO modification in transcriptional repression and activation
No full textSince the discovery of the SUMO (small ubiquitin-related modifier) family of proteins just over a decade ago, a plethora of substrates have been uncovered including many regulators of transcription. Conjugation of SUMO to target proteins has generally been considered as a repressive modification. However, there are now a growing number of examples where SUMOylation has been shown to activate transcription. Here, we discuss whether there is something intrinsically repressive about SUMOylation, or if the outcome of this modification in the context of transcription will prove to be largely substrate-dependent. We highlight some of the technical challenges that will be faced by attempting to answer this question
- …
