bluuebunny/crossref_metadata_2025 huggingface dataset:
Complex seasonal cycle of ecohydrology in the Southwest United States
Authors: Notaro Michael , Liu Zhengyu , Gallimore Robert G. , Williams John W. , Gutzler David S. , Collins Scott
Published: December 2010

This study investigates the causes for, and distribution of, unimodal versus bimodal seasonal cycle of vegetation greenness in the Southwest United States using extensive site observations, climate data, satellite data, and the Lund‐Potsdam‐Jena (LPJ) vegetation model. Peak vegetation greenness is achieved in a clockwise manner across the Southwest, beginning in spring in the Sonoran Desert following winter rains, then in Utah‐Colorado with snowmelt/summer rains, and finally in New Mexico–eastern Arizona with late summer monsoon rains. At high elevations, spring‐summer snowmelt is critical for supplying the necessary soil moisture to trigger vegetation growth. A bimodal seasonal cycle of vegetation greenness is evident in satellite data and LPJ simulations across eastern Arizona and western New Mexico, characterized by peaks during late spring–early summer and late summer–early autumn. This bimodal green‐up remains a pressing paradox for which many competing hypotheses exist. The mechanism for this seasonal pattern is demonstrated using LPJ and observational data and is found to deviate from the traditional pulse‐reserve paradigm. This paradigm states that rainfall events in arid lands produce nearly immediate pulses of vegetation growth and accumulation of reserves but does not consider cold dormancy, time‐lagged vegetation responses, or rainfall seasonality. The following soil moisture based mechanism for bimodal greening is proposed. The initial peak in vegetation greenness during late spring–early summer results from a break in cold dormancy and benefits from the gradual winter‐long accumulation of deep soil moisture from weak synoptic rain events and snowmelt in colder regions. Limited precipitation and ongoing transpiration, from the initial vegetation greening, trigger a midsummer drying of the soil and a consequential minimum in vegetation activity. Later, pulses of monsoon rainfall in late summer–early autumn support the secondary greening, although significant runoff of brief, intense rainstorms and substantial soil evaporation limit moisture to the upper soil layers.
Clinical Study and Molecular Genetic Analyses of Malaysian GEFS+ Patients
Authors: Tan Emmilia , Abdul Razak Salmi , Mohamed Yusoff Abdul Aziz , Abdullah Jafri Malin
Published: December 2010

Generalized epilepsy with febrile seizure plus (GEFS+) is a familial epilepsy syndrome characterized by phenotypic and genetic heterogeneity. Neuronal voltage gated sodium channel α-1 subunit gene, SCN1A is the most clinically relevant and associated with GEFS+. The objective was to study the clinical presentations of GEFS+ and analyze the SCN1A gene associated with Malaysian GEFS+ patients. Blood samples were collected from 30 unrelated GEFS+ patients and genomic DNA was obtained using the Qiagen DNA Blood Mini Kit following the manufacturer’s instructions. The 26 exons of SCN1A genes were analyzed by polymerase chain reaction (PCR) and denaturing high performance liquid chromatography (DHPLC). The aberrant profile peak from DHPLC analysis was confirmed by direct sequencing. The spectrum of phenotypes observed in Malaysian GEFS+ patients included febrile seizure (FS), febrile seizure plus (FS+) and afebrile generalized tonic clonic seizure (AGTCS). Direct sequencing of SCN1A revealed seven sequence variants including one novel SCN1A mutation that was associated with GEFS+. This suggests that mutation of the SCN1A gene is one of the prevalent causes of GEFS+ in Malaysia.
Effects of vegetation zones and climatic changes on fire-induced atmospheric carbon emissions: a model based on paleodata
Authors: Bremond Laurent , Carcaillet Christopher , Favier Charly , Ali Adam A. , Paitre Cédric , Bégin Yves , Bergeron Yves , Richard Pierre J. H.
Published: December 2010

An original method is proposed for estimating past carbon emissions from fires in order to understand long-term changes in the biomass burning that, together with vegetation cover, act on the global carbon cycle and climate. The past carbon release resulting from paleo-fires during the Holocene is examined using a simple linear model between measured carbon emissions from modern fires and sedimentary charcoal records of biomass burning within boreal and cold temperate forests in eastern Canada (Quebec, Ontario). Direct carbon emissions are estimated for each ecozone for the present period and the fire anomaly per kilo annum (ka) v. present day (0 ka) deduced from charcoal series of 46 lakes and peats. Over the postglacial, the Taiga Shield ecozone does not match the pattern of fire history and carbon release of Boreal Shield, Atlantic Maritime, and Mixedwood Plains ecozones. This feature results from different air mass influences and the timing of vegetation dynamics. Our estimations show, first, that the contribution of the Mixedwood Plains and the Atlantic Maritime ecozones on the total carbon emissions by fires remains negligible compared with the Boreal Shield. Second, the Taiga Shield plays a key role by maintaining important carbon emissions, given it is today a lower contributor.
Greenhouse warming and the 21st century hydroclimate of southwestern North America
Authors: Seager Richard , Vecchi Gabriel A.
Published: December 2010

Climate models robustly predict that the climate of southwestern North America, defined as the area from the western Great Plains to the Pacific Ocean and from the Oregon border to southern Mexico, will dry throughout the current century as a consequence of rising greenhouse gases. This regional drying is part of a general drying of the subtropics and poleward expansion of the subtropical dry zones. Through an analysis of 15 coupled climate models it is shown here that the drying is driven by a reduction of winter season precipitation associated with increased moisture divergence by the mean flow and reduced moisture convergence by transient eddies. Due to the presence of large amplitude decadal variations of presumed natural origin, observations to date cannot confirm that this transition to a drier climate is already underway, but it is anticipated that the anthropogenic drying will reach the amplitude of natural decadal variability by midcentury. In addition to this drop in total precipitation, warming is already causing a decline in mountain snow mass and an advance in the timing of spring snow melt disrupting the natural water storage systems that are part of the region’s water supply system. Uncertainties in how radiative forcing will impact the tropical Pacific climate system create uncertainties in the amplitude of drying in southwest North America with a La Niña-like response creating a worst case scenario of greater drying.
Roadmap for sustainable water resources in southwestern North America
Authors: Gleick Peter H.
Published: December 2010

The management of water resources in arid and semiarid areas has long been a challenge, from ancient Mesopotamia to the modern southwestern United States. As our understanding of the hydrological and climatological cycles has improved, and our ability to manipulate the hydrologic cycle has increased, so too have the challenges associated with managing a limited natural resource for a growing population. Modern civilization has made remarkable progress in water management in the past few centuries. Burgeoning cities now survive in desert regions, relying on a mix of simple and complex technologies and management systems to bring adequate water and remove wastewater. These systems have permitted agricultural production and urban concentrations to expand in regions previously thought to have inadequate moisture. However, evidence is also mounting that our current management and use of water is unsustainable. Physical, economic, and ecological limits constrain the development of new supplies and additional water withdrawals, even in regions not previously thought vulnerable to water constraints. New kinds of limits are forcing water managers and policy makers to rethink previous assumptions about population, technology, regional planning, and forms of development. In addition, new threats, especially the challenges posed by climatic changes, are now apparent. Sustainably managing and using water in arid and semiarid regions such as the southwestern United States will require new thinking about water in an interdisciplinary and integrated way. The good news is that a wide range of options suggest a roadmap for sustainable water management and use in the coming decades.
Relationship of farm salmon, sea lice, and wild salmon populations
Authors: Marty Gary D. , Saksida Sonja M. , Quinn Terrance J.
Published: December 2010

Increased farm salmon production has heightened concerns about the association between disease on farm and wild fish. The controversy is particularly evident in the Broughton Archipelago of Western Canada, where a high prevalence of sea lice (ectoparasitic copepods) was first reported on juvenile wild pink salmon (Oncorhynchus gorbuscha) in 2001. Exposure to sea lice from farmed Atlantic salmon (Salmo salar) was thought to be the cause of the 97% population decline before these fish returned to spawn in 2002, although no diagnostic investigation was done to rule out other causes of mortality. To address the concern that sea lice from fish farms would cause population extinction of wild salmon, we analyzed 10–20 y of fish farm data and 60 y of pink salmon data. We show that the number of pink salmon returning to spawn in the fall predicts the number of female sea lice on farm fish the next spring, which, in turn, accounts for 98% of the annual variability in the prevalence of sea lice on outmigrating wild juvenile salmon. However, productivity of wild salmon is not negatively associated with either farm lice numbers or farm fish production, and all published field and laboratory data support the conclusion that something other than sea lice caused the population decline in 2002. We conclude that separating farm salmon from wild salmon—proposed through coordinated fallowing or closed containment—will not increase wild salmon productivity and that medical analysis can improve our understanding of complex issues related to aquaculture sustainability.
Differential brain activity states during the perception and nonperception of illusory motion as revealed by magnetoencephalography
Authors: Crowe David A. , Leuthold Arthur C. , Georgopoulos Apostolos P.
Published: December 2010

We studied visual perception using an annular random-dot motion stimulus called the racetrack. We recorded neural activity using magnetoencephalography while subjects viewed variants of this stimulus that contained no inherent motion or various degrees of embedded motion. Subjects reported seeing rotary motion during viewing of all stimuli. We found that, in the absence of any motion signals, patterns of brain activity differed between states of motion perception and nonperception. Furthermore, when subjects perceived motion, activity states within the brain did not differ across stimuli of different amounts of embedded motion. In contrast, we found that during periods of nonperception brain-activity states varied with the amount of motion signal embedded in the stimulus. Taken together, these results suggest that during perception the brain may lock into a stable state in which lower-level signals are suppressed.
Regulation of global genome nucleotide excision repair by SIRT1 through xeroderma pigmentosum C
Authors: Ming Mei , Shea Christopher R. , Guo Xiumei , Li Xiaoling , Soltani Keyoumars , Han Weinong , He Yu-Ying
Published: December 2010

Disruption of the nucleotide excision repair (NER) pathway by mutations can cause xeroderma pigmentosum, a syndrome predisposing affected individuals to development of skin cancer. The xeroderma pigmentosum C (XPC) protein is essential for initiating global genome NER by recognizing the DNA lesion and recruiting downstream factors. Here we show that inhibition of the deacetylase and longevity factor SIRT1 impairs global genome NER through suppressing the transcription of XPC in a SIRT1 deacetylase-dependent manner. SIRT1 enhances XPC expression by reducing AKT-dependent nuclear localization of the transcription repressor of XPC. Finally, we show that SIRT1 levels are significantly reduced in human skin tumors from Caucasian patients, a population at highest risk. These findings suggest that SIRT1 acts as a tumor suppressor through its role in DNA repair.
T-cell cytokines differentially control human monocyte antimicrobial responses by regulating vitamin D metabolism
Authors: Edfeldt Kristina , Liu Philip T. , Chun Rene , Fabri Mario , Schenk Mirjam , Wheelwright Matthew , Keegan Caroline , Krutzik Stephan R. , Adams John S. , Hewison Martin , Modlin Robert L.
Published: December 2010

We investigated the mechanisms by which T-cell cytokines are able to influence the Toll-like receptor (TLR)-induced, vitamin D-dependent antimicrobial pathway in human monocytes. T-cell cytokines differentially influenced TLR2/1-induced expression of the antimicrobial peptides cathelicidin and DEFB4, being up-regulated by IFN-γ, down-regulated by IL-4, and unaffected by IL-17. The Th1 cytokine IFN-γ up-regulated TLR2/1 induction of 25-hydroxyvitamin D-1α-hydroxylase (i.e., CYP27B1), leading to enhanced bioconversion of 25-hydroxyvitamin D3(25D3) to its active metabolite 1,25D3. In contrast, the Th2 cytokine IL-4, by itself and in combination with the TLR2/1 ligand, induced catabolism of 25D3to the inactive metabolite 24,25D3, and was dependent on expression of vitamin D-24-hydroxylase (i.e., CYP24A1). Therefore, the ability of T-cell cytokines to differentially control monocyte vitamin D metabolism represents a mechanism by which cell-mediated immune responses can regulate innate immune mechanisms to defend against microbial pathogens.
Crystal structure of the Epstein-Barr virus (EBV) glycoprotein H/glycoprotein L (gH/gL) complex
Authors: Matsuura Hisae , Kirschner Austin N. , Longnecker Richard , Jardetzky Theodore S.
Published: December 2010

The Epstein-Barr virus (EBV) is a γ-herpesvirus that infects B cells and epithelial cells and that has been linked to malignancies in both cell types in vivo. EBV, like other herpesviruses, has three glycoproteins, glycoprotein B (gB), gH, and gL, that form the core membrane fusion machinery mediating viral penetration into the cell. The gH and gL proteins associate to form a heterodimeric complex, which is necessary for efficient membrane fusion and also implicated in direct binding to epithelial cell receptors required for viral entry. To gain insight into the mechanistic role of gH/gL, we determined the crystal structure of the EBV gH/gL complex. The structure is comprised of four domains organized along the longest axis of the molecule. Comparisons with homologous HSV-2 gH/gL and partial pseudorabies virus gH structures support the domain boundaries determined for the EBV gH/gL structure and illustrate significant differences in interdomain packing angles. The gL subunit and N-terminal residues of gH form a globular domain at one end of the structure, implicated in interactions with gB and activation of membrane fusion. The C-terminal domain of gH, proximal to the viral membrane, is also implicated in membrane fusion. The gH/gL structure locates an integrin binding motif, implicated in epithelial cell entry, on a prominent loop in the central region of the structure. Multiple regions of gH/gL, including its two extreme ends, are functionally important, consistent with the multiple roles of gH/gL in EBV entry.
DNA tandem repeat instability in the
Escherichia coli
chromosome is stimulated by mismatch repair at an adjacent CAG·CTG trinucleotide repeat
Authors: Blackwood John K. , Okely Ewa A. , Zahra Rabaab , Eykelenboom John K. , Leach David R. F.
Published: December 2010

Approximately half the human genome is composed of repetitive DNA sequences classified into microsatellites, minisatellites, tandem repeats, and dispersed repeats. These repetitive sequences have coevolved within the genome but little is known about their potential interactions. Trinucleotide repeats (TNRs) are a subclass of microsatellites that are implicated in human disease. Expansion of CAG·CTG TNRs is responsible for Huntington disease, myotonic dystrophy, and a number of spinocerebellar ataxias. In yeast DNA double-strand break (DSB) formation has been proposed to be associated with instability and chromosome fragility at these sites and replication fork reversal (RFR) to be involved either in promoting or in preventing instability. However, the molecular basis for chromosome fragility of repetitive DNA remains poorly understood. Here we show that a CAG·CTG TNR array stimulates instability at a 275-bp tandem repeat located 6.3 kb away on the
Escherichia coli
chromosome. Remarkably, this stimulation is independent of both DNA double-strand break repair (DSBR) and RFR but is dependent on a functional mismatch repair (MMR) system. Our results provide a demonstration, in a simple model system, that MMR at one type of repetitive DNA has the potential to influence the stability of another. Furthermore, the mechanism of this stimulation places a limit on the universality of DSBR or RFR models of instability and chromosome fragility at CAG·CTG TNR sequences. Instead, our data suggest that explanations of chromosome fragility should encompass the possibility of chromosome gaps formed during MMR.
Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower
Authors: Chanderbali André S. , Yoo Mi-Jeong , Zahn Laura M. , Brockington Samuel F. , Wall P. Kerr , Gitzendanner Matthew A. , Albert Victor A. , Leebens-Mack James , Altman Naomi S. , Ma Hong , dePamphilis Claude W. , Soltis Douglas E. , Soltis Pamela S.
Published: December 2010

The origin and rapid diversification of the angiosperms (Darwin's “Abominable Mystery”) has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and
Arabidopsis
) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and
Arabidopsis
. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.
KCNE1 alters the voltage sensor movements necessary to open the KCNQ1 channel gate
Authors: Osteen Jeremiah D. , Gonzalez Carlos , Sampson Kevin J. , Iyer Vivek , Rebolledo Santiago , Larsson H. Peter , Kass Robert S.
Published: December 2010

The delayed rectifier I
Ks
potassium channel, formed by coassembly of α- (KCNQ1) and β- (KCNE1) subunits, is essential for cardiac function. Although KCNE1 is necessary to reproduce the functional properties of the native I
Ks
channel, the mechanism(s) through which KCNE1 modulates KCNQ1 is unknown. Here we report measurements of voltage sensor movements in KCNQ1 and KCNQ1/KCNE1 channels using voltage clamp fluorometry. KCNQ1 channels exhibit indistinguishable voltage dependence of fluorescence and current signals, suggesting a one-to-one relationship between voltage sensor movement and channel opening. KCNE1 coexpression dramatically separates the voltage dependence of KCNQ1/KCNE1 current and fluorescence, suggesting an imposed requirement for movements of multiple voltage sensors before KCNQ1/KCNE1 channel opening. This work provides insight into the mechanism by which KCNE1 modulates the I
Ks
channel and presents a mechanism for distinct β-subunit regulation of ion channel proteins.
Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods
Authors: Liu Lei V. , Bell Caleb B. , Wong Shaun D. , Wilson Samuel A. , Kwak Yeonju , Chow Marina S. , Zhao Jiyong , Hodgson Keith O. , Hedman Britt , Solomon Edward I.
Published: December 2010

Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin Fe
III
peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4′ hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of Fe
III
BLM and ABLM as (BLM)Fe
III
─OH and (BLM)Fe
III
(
η
1
─OOH) species, respectively. The NRVS spectra of Fe
III
BLM and ABLM are strikingly different because in ABLM the δFe─O─O bending mode mixes with, and energetically splits, the doubly degenerate, intense O─Fe─N
ax
transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways.
Inactivation of p53 in breast cancers correlates with stem cell transcriptional signatures
Authors: Mizuno Hideaki , Spike Benjamin T. , Wahl Geoffrey M. , Levine Arnold J.
Published: December 2010

Breast cancer comprises a heterogeneous set of diseases distinguishable from one another by pathologic presentation and molecular signatures. However, each breast cancer subtype is also heterogeneous. Some of the heterogeneity may be attributable to genetic instability, but recent data emphasize that developmental plasticity may also contribute. The p53 tumor suppressor could constitute a nodal control point underlying both sources of heterogeneity because it is frequently inactivated during malignant progression and has recently been shown to function as a potent barrier preventing fully differentiated cells from reverting to pluripotent stem cells after expression of appropriate oncogenes. Using archival microarray datasets, we tested the hypothesis that a p53 mutation could allow cells within a tumor to acquire a stem cell-like state by looking for coordinate expression of stem cell identity genes. We show that breast and lung cancers with p53 mutations do exhibit stem cell-like transcriptional patterns. Such tumors were also depleted for differentiation genes regulated by the polycomb repressor complex 2. These data are consistent with a model in which loss of p53 function enables acquisition of stem cell properties, which are positively selected during tumor progression.
Report of the Committee on Irish Language A ttitudes Research
Authors: Edwards John
Published: December 2010

Regis forta emocio pri la oficiala politiko pri la irlanda. Irlandanoj ne volonte esprimis sian veran pensadon, sed la amase anglalingva etoso de la irlanda vivo bone indikas majoritatan sintenon al la revivigo de la irlanda - la oficiala nacia lingvo. La recenzata raporto, la unua grava irlanda lingvo-enketo, provas esti objektiva. Gi esploras la sintenojn al la irlanda, scipovon en gi kaj irlandan lingvouzon. Tamen oni enketis nur per intervjuo kaj memraporto, ne per observado au testado. Oni intervjuis cirkaǔ 2 500 personojn, el kiuj cirkaǔ 500 en la Gaeltacht (irlandlingvaj zonoj). Oni krome aparté atentis la edukadon kaj administradon, kie, gis antaǔ nelonge, la profesia progreso dependis de irlandlingvaj testoj.
Oni notis majoritate pozitivan sintenon al la lingvo kiel perilo de idento – sed tio ne implicas subtenon de la lingva politiko. Sed oni malalte taksis la lernejan instruadon de la irlanda. Regas generala pesimismo pri la estonteco de la lingvo, kiu estas taksata malnovmoda kaj neprestiga, ec ce enlogantoj de gaelaj zonoj. Tiuj kredas, ke la estonteco de la irlanda dependas de la pluvivo de la zonoj, kies registaran subtenon ciuj apogas.
Cirkaǔ 68 p.c. kredas, ke la irlanda devas resti deviga lernofako. Aparte la respond-antoj el la laborista klaso bedaǔris la preferan aljugon de registaraj postenoj al irland-lingvanoj. Oni ĝenerale deziras la pluvivon de la lingvo, sed ne la preferon al giaj parolantoj. Necesas distingi la simpation al lingvo kiel simbolon de idento kaj heredaĵo disde la apogo al komunikado per ĝi.
Pro la lerneja instruado, ĉiam pli da irlandanoj certagrade kompetentas en la irlanda. Sed la denaskaj parolantoj malpliigas kaj kun ili la konversacia kapablo. Pro la lerneja instruado kreskas la bazaj legokapablo kaj skribokapablo. Tutlande, nur 1,9 p.c. estas denaskuloj kaj 21 p.c. kompetentas pli ol iome. Nur unu persono el dudek uzas la lingvon intensive, 14 p.c. 'foje'. La angla kreskas eĉ en la Gaeltacht. Eĉ en laǔnome irlandlingvaj registaraj unuoj oni malofte au tute ne parolas irlande. Instruistoj de la irlanda instruas gin dum la leciono, sed ne apogas gin alie.
Tradicie oni lasis la revivigon de la lingvo al la lernejoj, sed pro la tutsocia ne-intereso pri la revivigo de la irlanda, la lernejoj ne sukcesis. Do kion faru la lernejoj? Kaj kian lingvopolitikon preferas la popolo? Malfelice oni ne rekte demandis tion.
Sume, oni apogas cefe la simbolan kaj kulturan rolojn de la irlanda; ne sajnas ke estontece pli da personoj parolos, au volos paroli, irlande. La lernejoj daǔre gravas, sed per si mem ne povos revivigi la lingvon. La raporto malfelice ne klare sumigas la laboron nek faras rekomendojn. Fakte, kaj por-gaela grupo kaj movado por libereco pri lingvoelekto bonvenigis la raporton, asertante, ke gi apogas iliajn starpunktojn. Domaĝe, ke la konkludoj estas tiel malfirmaj.
Meic Stephens, ed., The Welsh Language Today
Authors: Wood Richard E.
Published: December 2010

Dekkvin kontribuintoj analizas la historion kaj nuntempon de la kimra lingvo, nun parolata de 20 p.c. de la kimroj. La plejmulto parolas nur angle. Kvankam gi perdis sian kimran lingvon kaj kulturon pro ekonomia premo, tiu majoritato nun siavice ek-timas inversan ekonomian premon pro la revivigo de kimra nacia kultura movado. La libro ĉefe celas interpreti tiun movadon al la anglalingvaj kimroj.
Kontribuintoj diskutas interalie la rilaton inter la angla kaj kimra. Ĉe kelkaj parol-antoj okazas intermikso tiel, ke ne plu eblas distingi du lingvojn. La redaktoro, Stephens, mem estas denaska anglalingvano kiu elektis uzi la kimran sed en ĉi-tiu libro escepte uzas la anglan. Oni priskribas la nunajn dulingvan edukadon kaj mankon de uzo de la kimra en la scienco.
Por konkurenci kun la unueca angla necesas starigi normon de moderna parolata kimra. La skriba normo estas tro tradicia, kaj tro diferencas disde la parola, ofte dialekta, lingvaĵo.
Malforteco de la kimra estas en la ĵurnalismo. Eĉ la anglalingva kimra gazetaro ne parolas nome de la lando, tiel, ke la eǔropanoj kutime neniel konscias pri la nacia aparteco de Kimrujo.
Fine de la libro troviĝas politikaj ĉapitroj, interalie diskuto pri la aktivismaj, parte kontraǔleĝaj organizaĵoj. Iom romantika fina ĉapitro apelacias al kimra solidarigo kun la popoloj de la Tria Mondo. Pro siaj rezistemo kaj klarvido eble la nekonkerita kimra popolo jes regajnos sian lingvon, identon kaj antauan grandecon.
Per una prognosi circa la sopravvivenza del dialetto nel Cantone Ticino
Authors: Carlevaro Tazio
Published: December 2010

Pri prognozo koncerne la pluvivon de la dialekto en Kantono Ticino
Lastatempe du verkoj aperintaj en 1976 ('Il dialetto e l'italiano regionale nel Ticino', de Ottavio Lurati, kaj 'Censimento degli allievi delle scuole 1975-76', de Elio Venturelli kaj Nadia Bariffi) fajrigis grandajn diskutojn en periodajoj, radio kaj televido pri la hodiaŭa situacio de la tradicia lingvo parolata en la svisa kantono Ticino, la tipa lombarda dialekto (la itala lingvo estas la oficiala lingvo de la Kantono).
Oni rimarkis, ke iom post iom, pro socio-ekonomikaj sangigoj kaj internaj migroj, la dialekto limigas ĉiam pli al malfavorataj montregionoj kaj al malfavorataj enurbaj populacio-klasoj. Tio kondukas al malgrandigo de la prestigo de la dialekto, car gi estas stereotipe konsiderata la kaŭzo de la enlernejaj malfacilajoj de la lernantoj. La vera fakto estas, ke la dialekto estas rica esprimilo, kaj ke oni povus helpi la gelernantojn ne per kodo-sango (kiu ĝenerale estas mortiga por la dialekto - sed ankaŭ por la nova /itala/ kodo), sed per efika kompensa lingvo-instruado dulingva (itala kaj dialekto).
Dum la diskuto oni rimarkis vocojn de lingvodarvinistoj ("la dialekto devas malaperi, car gi estas la malpli forta"), de lingvaj tradiciistoj (kiuj deziras utiligi la dialekton kiel distingilon disde la italoj), kaj de moderuloj, kiuj proponas, ke oni gardu la dialekton en difinitaj intern-ticinaj roloj. Tiu lasta propono povos aktualigi nur se la uzo de la dialekto ne est os folklora kaj se gi estos unuiga kun la nord-italoj. Krome, en la lernejo, radio, televido, eldonado, la loko de la dialekto devos esti pli granda ol gi fakte estas. En la lernejo, krome, oni devos antauvidi kompensan lingvoedukadon kiu estu dulingva (kaj kontrastiga), por ke la dialekto ne igu sablono de la itala - kaj inverse.
Le Choc des langues au Québec 1760-1970, Guy Bouthillier et Jean Meynaud
Authors: Wood Richard E.
Published: December 2010

En originale konceptita kolekto, la kompilintoj represas dokumentojn, ofte nebone konatajn, ec de aùtoroj kies biografioj estas netroveblaj. Ne temas pri verkoj por fakuloj, aparté ne por lingvistoj. En la epoko de verkado, la lingvistiko kaj aparté la socilingvistiko kaj politika lingvistiko ne ekzistis.
La aùtoroj sekvas la lingvan problemon en Kebeko de 1760, post la brita venko, gis 1970, kiam la problemo daure restis nesolvita. La plimulto de la libro konsistas el la dokumentoj - eseoj, raportoj, oratorajoj, poemoj ktp., cefe de franc-kanadanoj sed foje de anglalingvanoj au francoj. Enkonduko kutime donas biografion. Entute la libro provizas kulturhistorion de Kebeko kun atento al la nacia, kultura kaj lingva idento.
Enkonduko diskutas la demandojn en socilingvistika kaj politik-lingvistika perspektivo. Gi parte diskutas la dokumentojn, sed parte générale esprimas la poiitikan filozofion de la verkintoj. La aùtoroj koncentrigas al Kebeko. La antaua espcro radii el Kebeko la francan civilizon kaj kulturon al la tuta Ameriko montrigis donkifiota, kaj la franclingvaj usonanoj nepre estos asimilitaj. Kebeko povos helpi la franclingvajn kanadanojn ekster Kebeko nur igante nacia hejmo de ciuj franc-kanadanoj (kp. la vortojn de la Balfour-deklaracio).
La lingva konduto igis temo de aktiva soci-scienca esploro nur lastatempe. Giajn cltrovojn oni raportas interalie en LMLP. Forpasis la epoko de sprita, engagita verkado pri kclkaj aspektoj de la temaro. Do ci tiu cefverko longe retenos sian dokumentan valoron.
Linguistic Denial and Linguistic Self-Denial
Authors: Sonntag Selma K. , Pool Jonathan
Published: December 2010

SUMARIO
La negatión y la auto-negación lingüística: Las ideologías del lenguaje en Estados Unidos
El norteamericano demuestra múltiples y altercantes percepciones, creencias, actitudes y marieras de razonar en cuanto a argumentas concernientes a la política del idioma. Sin embargo, las principales ideologías norteamericanas relativas al idioma son semejantes en cuanto a su negación de inigualdad lingüistica: su existencia, sus consecuencias y la posibilidad de sobrellevarla.
Aquellos que luchan por los derechos de las minorías lingüísticas aceptan algunas de las suposiciones principales de sus adversarios. Estas suposiciones incluyen el desunificante impacto politico de diversidad lingüistica dentro de la población, la validez de competencia lingüistica como un indice de lealtad nacional, la neutralidad étnica del idioma inglés común, la inferioridad intrínsica de los dialectos, la suficiencia de la fuerza de voluntad para dominar el idioma principal de la sociedad, la suficiencia de este dominio para progresar económicamente, y la exclusión por derecho del idioma en las categorías protegidas por ley contra la discriminación.
Estas generalizaciones surgen principalmente de debates políticos y opiniones judiciales acerca del reconocimiento oficial, en las elecciones y en las escuelas publicas, del idioma espaňol y del inglés empleado por la población negra.
RESUMO
Malagnoskoj pri malegaleco: La lingvaj opiniaroj en Usono
Inter usonanoj oni trovas diversajn kaj konfliktajn perceptojn, kredojn, emojn kaj rezonadojn pri la lingva politiko. La cefaj usonaj lingvaj ideologioj tamen similas pro tio, ke ili neas la lingvan malegalecon. Ili neas gian ekziston, giajn konsekvencojn kaj gian venkeblecon.
Batalantoj por la rajtoj de lingvaj malplimultoj akceptas iujncefajn supozojn de siaj kontraüuloj. Inter tiuj estas supozoj ke: lingva diverseco en la štatanaro kaüzas politikan malunuecon, lingvoscio valide indikas nacian lojalecon, la norma angla lingvo estas etne neütrala, dialektoj estas nature malindaj, oni povas mastri lacefan lingvon de sia socio se oni tion nur volas, tia mastreco suficas por ekonomia sukceso, oni juste ne aplikas al lingvaj grupoj la jurajn protektojn kontraú diskriminado. Tiujn generaligojn apogas cefe debatoj kaj jugistaj decidoj pri la oficialeco de la hispana kaj la nigrangla lingvoj ce la balotprocezo kaj en la publikaj lernejoj.
Some Reflections on South Africa and the Mother Tongue Principle
Authors: Knappert Jan
Published: December 2010

Kelkaj pensoj pri Sudafriko kaj la principo denaska lingvo
Timothy Reagan (en LPLP 10:1-13) pretendas, ke la Buroj de la Kaba Kolonio "ne estis angligitaj." Tio veras nur ce kamparaj blankuloj kaj urbaj neblankuloj. Koncerne la diskuton de Reagan pri klerigo en la denaska lingvo, la kazo de Ugando montras kiel tia politiko povas havi disigan efikon. La ekskluziva uzo de la angla lingvo en la lernejoj ankaǔ rezultigas problemojn pro la manko de instruistoj kaj aliaj rimedoj, kiel montras la ekzemploj de Kenjo kaj Tanzanio. En Sudafriko, la afrikaj gvidantoj deziras, ke iliaj infanoj lernu en la propra lingvo. La zulua verŝajne fine leviĝos kiel la perila lingvo.
Holmlund, Carin. Barns talspråk ur socialpedagogisk synvinkel
Authors: Jernudd Björn H.
Published: December 2010

La doktoriga tezo "Parola lingvo de infanoj el soci-pedagogia vidpunkto" bazigas sur la teorioj de B. Bernstein, anglo, pri klasaj diferencoj de sintaksa komplikeco de la lingvajo de infanoj, kaj provas identigi similajn diferencojn ce svedaj infanoj.
La esploristino elektis infanojn laü la okupo de la patro, la edukado, kaj la demando, cu la patrino laboras, au ne. Si kontrolis la lingvajon de la infanoj en kvar apartaj situacioj - prikomentante filmon, klangante ludon, enordigante bildojn, kaj ordon-ante samlernejanon pri arango de bildo.
Si asertas, ke eblas distingi inter la 'akademiaj' kaj la 'labor-klasaj' infanoj laü diversaj normoj kaj mezuriloj, krom en 'neformalaj' situacioj. Cu fakte eblas, estas malfacile au neeble jugi, pro neklara prezentado de la esplormaniero kaj rezultoj. La tuto estas malbone prezentita kaj ilustrita. La esploro formas parton de la studprojekto 'parola sintakso' ce la Universitato Lund.
Sahlman-Karlsson, Siiri. Specimens of American Finnish. A Field Study of Linguistic Behavior
Authors: Virtanen Reino
Published: December 2010

Jen unu el la malmultaj studoj pri la finna lingvo en Usono, verkita de aütorino kies unua studo pri la temo aperis jam en 1949. Si esploris la finnlingvajn komunumojn de la orienta kaj mez-okcidenta Usono dum tri jardekoj, kun interrompoj, kaj bedaürinde, sen sonbendaparato, manko kiu cefe sentigas en la fonologia parto. Do sia metodo ne estis tiel science rigora kiel tiu de la samfakulo Virtaranta, kies studoj tamen nur nun ekaperas.
La stilo estas neformala, verkita por europa leganto sen profunda scio pri Usono. La recenzanto trovas interesa la komparon inter la fresdata materialo kolektita de Sahlman-Karlsson, kaj la uson-finna lingvo de sia propra juneco, en nord-okcidenta Usono inter la du Mondmilitoj. Ekde tiam fortege kreskis la usona influo. Multaj nunaj formoj montras nivelon de angligo, kiu estus nepensebla en la antaümilitaj jaroj, cu kiel vortoj, cu kiel esprimoj au fonologiaj formoj. Oni povas kontrastigi ilin multnombre.
La fonologia capitro cefe pritraktas la finnan influon sur la angla, pli ol inverse. La intonacio persistas, kie la cetera finna influo velkas.
Dum Virtaranta taksas la uson-finnan esti variajo de la finna, Sahlman-Karlsson preskau nornas gin alia lingvo, 'finnangla' ('Finglish'), sed ne vere pruvas tian aserton. Si prave notas, ke la dua generacio regajnas la fieron pri sia finneco, kontraste kun la unua generacio de enmigrintoj. Tio estas tipa fenomeno ce la usonaj etnaj grupoj.
Si tamen ne bone konas la usonan edukadon, se si ne konscias ke, unuflanke, dum la Unua Mondmilito en kelkaj statoj oni perforte provis sufoki la fremdajn lingvojn, sed, aliflanke, hodiaü ekfloras stata dulingva edukado.
La uson-finna estas mortanta lingvo. La enmigrado ne helpos gin, car la novaj enmigrantoj jam iome lernis la anglan en la lernejo, kaj ne bezonas miksitan helplingvon. Pro tiu formorto, urge necesas pliaj sciencaj studoj, aparte pri tiuj aspektoj, ne traktitaj en la nuna studo, kiel la vortordo kaj la lingvaj sintenoj, ekzemple rilate lingvo-elekton en diversaj situacioj. Eble la autorino mem verkos tiajn.
Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina
Authors: Rapaka Rekha R. , Ricks David M. , Alcorn John F. , Chen Kong , Khader Shabaana A. , Zheng Mingquan , Plevy Scott , Bengtén Eva , Kolls Jay K.
Published: December 2010

Host defense against opportunistic fungi requires coordination between innate and adaptive immunity for resolution of infection. Antibodies generated in mice vaccinated with the fungus Pneumocystis prevent growth of Pneumocystis organisms within the lungs, but the mechanisms whereby antibodies enhance antifungal host defense are poorly defined. Nearly all species of fungi contain the conserved carbohydrates β-glucan and chitin within their cell walls, which may be targets of innate and adaptive immunity. In this study, we show that natural IgM antibodies targeting these fungal cell wall carbohydrates are conserved across many species, including fish and mammals. Natural antibodies bind fungal organisms and enhance host defense against Pneumocystis in early stages of infection. IgM antibodies influence recognition of fungal antigen by dendritic cells, increasing their migration to draining pulmonary lymph nodes. IgM antibodies are required for adaptive T helper type 2 (Th2) and Th17 cell differentiation and guide B cell isotype class-switch recombination during host defense against Pneumocystis. These experiments suggest a novel role for the IgM isotype in shaping the earliest steps in recognition and clearance of this fungus. We outline a mechanism whereby serum IgM, containing ancient specificities against conserved fungal antigens, bridges innate and adaptive immunity against fungal organisms.
PE-Assembler: de novo assembler using short paired-end reads
Authors: Ariyaratne Pramila Nuwantha , Sung Wing-Kin
Published: December 2010

Motivation: Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized.

Result: We present a method that eschews the traditional graph-based approach in favor of a simple 3′ extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods.

Availability: The software package can be found at http://www.comp.nus.edu.sg/~bioinfo/peasm/. Alternatively it is available from authors upon request.

Contact:  ksung@comp.nus.edu.sg; sungk@gis.a-star.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Scaffolding pre-assembled contigs using SSPACE
Authors: Boetzer Marten , Henkel Christiaan V. , Jansen Hans J. , Butler Derek , Pirovano Walter
Published: December 2010

Summary:  De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in finishing genomes, scaffolding algorithms are often built-in functions in de novo assembly tools and cannot be independently controlled. We here present a new tool, called SSPACE, which is a stand-alone scaffolder of pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%.

Availability:  www.baseclear.com/bioinformatics-tools/.

Contact:  walter.pirovano@baseclear.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
First Report of a Group 16SrII Phytoplasma Associated with Witches'-Broom of Eggplant in Oman
Authors: Al-Subhi A. M. , Al-Saady N. A. , Khan A. J. , Deadman M. L.
Published: December 2010

Eggplant (Solanum melongena L.) belongs to the family Solanaceae and is an important vegetable cash crop grown in most parts of Oman. In February 2010, plants showing phyllody symptoms and proliferation of shoots resembling those caused by phytoplasma infection were observed at Khasab, 500 km north of Muscat. Total genomic DNA was extracted from healthy and two symptomatic plants with a modified (CTAB) buffer method (2) and analyzed by direct and nested PCR with universal phytoplasma 16S rDNA primers P1/P7 and R16F2n/ R16R2, respectively. PCR amplifications from all infected plants yielded an expected product of 1.8 kb with P1/P7 primers and a 1.2-kb fragment with nested PCR, while no products were evident with DNA from healthy plants. Restriction fragment length polymorphism (RFLP) profiles of the 1.2-kb nested PCR products of two eggplant phyllody phytoplasma and five phytoplasma control strains belonging to different groups used as positive control were generated with the restriction endonucleases RsaI, AluI, Tru9I, T-HB8I, and HpaII. The eggplant phytoplasma DNA yielded patterns similar to alfalfa witches'-broom phytoplasma (GenBank Accession No. AF438413) belonging to subgroup 16SrII-D, which has been recorded in Oman (1). The DNA sequence of the 1.8-kb direct PCR product was deposited in GenBank (Accession No. HQ423156). Sequence homology results using BLAST revealed that the eggplant phyllody phytoplasma shared >99% sequence identity with Scaevola witches'-broom phytoplasma (Accession No. AB257291.1), eggplant phyllody phytoplasma (Accession No. FN257482.1), and alfalfa witches'-broom phytoplasma (Accession No. AY169323). The RFLP and BLAST results of 16S rRNA gene sequences confirm that eggplant phyllody phytoplasma is similar to the alfalfa phytoplasma belonging to subgroup 16SrII-D. To our knowledge, this is the first report of a phytoplasma of the 16SrII-D group causing witches'-broom disease on eggplant in Oman.

References: (1) A. J. Khan et al. Phytopathology 92:1038, 2002. (2) M. A. Saghai-Maroof et al. Proc. Natl. Acad. Sci. USA, 81:8014, 1984.
Leukemic T cells are specifically enriched in a unique CD3dimCD7low subpopulation of CD4+ T cells in acute‐type adult T‐cell leukemia
Authors: Tian Yamin , Kobayashi Seiichro , Ohno Nobuhiro , Isobe Masamichi , Tsuda Mayuko , Zaike Yuji , Watanabe Nobukazu , Tani Kenzaburo , Tojo Arinobu , Uchimaru Kaoru
Published: December 2010

The morphological discrimination of leukemic from non‐leukemic T cells is often difficult in adult T‐cell leukemia (ATL) as ATL cells show morphological diversity, with the exception of typical “flower cells.” Because defects in the expression of CD3 as well as CD7 are common in ATL cells, we applied multi‐color flow cytometry to detect a putative leukemia‐specific cell population in the peripheral blood from ATL patients. CD4+CD14− cells subjected to two‐color analysis based on a CD3 vs CD7 plot clearly demonstrated the presence of a CD3dimCD7low subpopulation in each of nine patients with acute‐type ATL. The majority of sorted cells from this fraction showed a flower cell‐like morphology and carried a high proviral load for the human T‐cell leukemia virus type 1 (HTLV‐I). Genomic integration site analysis (inverse long‐range PCR) and analysis of the T cell receptor Vβ repertoire by flow cytometry indicated that the majority of leukemia cells were included in the CD3dimCD7low subpopulation. These results suggest that leukemic T cells are specifically enriched in a unique CD3dimCD7low subpopulation of CD4+ T cells in acute‐type ATL. (Cancer Sci 2011; 102: 569–577)
Clinical usefulness of mitochondrial transcription factor A expression as a predictive marker in colorectal cancer patients treated with FOLFOX
Authors: Yoshida Yoichiro , Hasegawa Junichi , Nezu Riichiro , Kim Yong‐Kook , Hirota Masaki , Kawano Kiyoshi , Izumi Hiroto , Kohno Kimitoshi
Published: December 2010

We previously reported that mitochondrial transcription factor A (mtTFA) preferentially recognizes cisplatin‐damaged DNA via physical interaction with p53 and is upregulated by treatment with cisplatin and fluorouracil (5‐FU). The aim of the present study was to evaluate whether expression of mtTFA predicts the clinical outcome in patients with metastatic colorectal cancer treated with modified 5‐fluorouracil, leucovorin and oxaliplatin 6 (mFOLFOX6). Fifty‐nine patients with metastatic lesions from colorectal cancer treated with mFOLFOX6 were included in this study. The subjects consisted of 25 women and 34 men with a median age of 62 years. The patients were treated with oxaliplatin (85 mg/m2) plus leucovorin (200 mg/m2) as a 2‐h infusion on day 1, followed by 5‐FU (400 mg/m2) bolus and 46‐h continuous infusion of 2400 mg/m2. The expressions of mtTFA and p53 of resected primary tumors were examined by immunohistochemical analysis. Of the 59 patients, 33 (complete response 1, partial response 32) achieved a confirmed response to therapy. The positive cytoplasmic staining rate for mtTFA was 44.1% and that for p53 was 59.3%, respectively. Strong expression of mtTFA was detected in eight of 33 complete response/partial response (24.2%) and in 18 of 26 SD/PD (69.2%), indicating that mtTFA expression was significantly correlated with response to chemotherapy (P < 0.01). Median overall survival was significantly longer in patients without mtTFA expression (P = 0.0493). Multivariate analysis revealed that mtTFA expression significantly affected overall survival (hazard ratio 2.10, P = 0.036). Immunohistochemical study of mtTFA may be useful for predicting the clinical outcome of metastatic colorectal cancer patients treated with FOLFOX. (Cancer Sci 2011; 102: 578–582)