bluuebunny/crossref_metadata_2025 huggingface dataset:
Conversational coordination: Collaboration for effective communication
Authors: Ricard Richard J.
Published: December 2008

This investigation focused on early school-aged children's ability to negotiate shared reference in a task-oriented communication game. Conversational partners worked together on initiating and refining mutually acceptable referential labels for a series of abstract figures. Each child participated as both a sender and a matcher. In Experiment 1, developmental trends in the use of conversational strategies such as utterance-contingent queries, acknowledgments, and negations were observed. However, communicative efficiency was disrupted when the children switched dyadic roles. They reintroduced figures with novel labels when switching to a speaking role from a previous matching role, and vice versa. In Experiment 2, communicative efficiency was again disrupted at the point of role switch, even when the children were given feedback designed to minimize cross-role inconsistency. Interestingly, in both experiments, communicative inefficiency did not reduce a dyad's overall communicative success. These results suggest that, while children are in the process of learning how best to coordinate the use of conversational strategies and procedural rules, they still manage effective communication, albeit with a little extra effort.
On the question of psalmody in the ancient synagogue
Authors: McKinnon James W.
Published: December 2008

Music historians are virtually unanimous in attributing the source of early Christian psalmody to the synagogue. In this they follow the vast majority of liturgical scholars, Protestant and Catholic alike. There is, after all, considerable plausibility to the view: nascent Christianity was a Jewish sect and its first liturgical gatherings shared with the synagogue its most revolutionary characteristic – the coming together of co-religionists in a meeting room rather than the witnessing of sacrifice in a temple court. Moreover, the liturgical practices of these gatherings resembled those of the synagogue; in particular the so-called ‘liturgy of the Word’ that preceded the Eucharist appears to have been modelled after the scripture-centred order of synagogue worship. And when one observes that the principal vehicle of early Christian chant was the Old Testament Book of Psalms it seems a natural assumption that the singing of those psalms was a practice borrowed from the synagogue. The present author shared this assumption until coming to question it when pursuing a related topic. The study that follows is a fulfilment of the intention stated then to explore the subject more thoroughly. In doing so it is necessary to begin with a general examination of Jewish liturgy in the time of Jesus, both the liturgy of the Temple and that of the synagogue.
Further thoughts on Gothicboka
Authors: Ebbinghaus E. A.
Published: December 2008

The article* shows that the Germanic-Gothic word forbookwas originally an athematic stem and that its etymology may lead to one or more of the Eurasian languages which were Indoeuropeanized and thus became Germanic.
Clinical evaluation of the effects of radiotherapy on oral mucosa and gingiva
Authors: Taheri M. , Sohrabi K. , Salehi M.H. , Najafi M.H.
Published: December 2008

Introduction:The use of radiotherapy, alone or in conjunction with surgical resection, is common in treating head and neck tumours. However, ionising radiation induces unavoidable changes in the surrounding normal tissues, causing severe complications. Therefore, we decided to study different effects of radiotherapy on gingiva and oral mucosa.

Methods and Materials:This prospective analytical study was performed on 30 patients with head and neck cancers referred to the radiotherapy department of Ghaem Hospital from March to October 2006. Data were collected by means of interviews, clinical examinations and patients’ medical file investigation. The impact of different dosages of radiation on gingiva and oral mucosa was investigated. Data analysis was performed using general linear model (GLM), Cochran and multivariate analysis of variance (MANOVA) tests via SPSS V. 11.5 software.

Results:A direct relationship between increase in radiation dosage, irritation of oral mucosa, ulcer development and mucositis was observed. But there was no significant relationship between NUG (necrotising ulcerative gingivitis) and perlèche and radiation dosage. Periodontal index (PI), gingival index (GI) and papillary bleeding index (PBI) were increased, but due to limited time of study (6–7 weeks), no change in gingival recession was observed. Plaque index (PLI) decreased during treatment process because of oral hygiene instructions.

Conclusion:The oral and periodontal health status of head and neck cancer patients before and during radiotherapy has been described in this article. The authors believe that prevention or reduction of side-effects of radiation should be an integral part of treatment as they may have tremendous effect on the patient's quality of life. This study supports the need for dental assessment and treatment planning before radiation therapy.
Peripheral blood lymphocyte counts during standard conformal radiotherapy and TomoTherapy/IMRT for prostate cancer
Authors: Elsworthy M. , Plowman P.N.
Published: December 2008

Lymphopaenia is the earliest and the most sensitive routinely assessed biological parameter of corporeal radiation exposure in clinical practice; bone marrow, lymph nodes and peripheral blood lymphocyte populations are also at risk. During radical prostate radiotherapy, in 28 patients, the mean peripheral lymphocyte count fell from 1.76 × 109/l (standard deviation (SD) 0.63, 95% confidence interval (conf.) 0.23) to 1.10 × 109/l (SD 0.38, conf. 0.14), (p < 0.05). The question was asked as to whether intensity-modulated radiation therapy (IMRT) by TomoTherapy would cause more lymphopaenia than three-field conformal radiotherapy, bearing in mind the ‘low dose bath’ effect of IMRT and the long ‘beam-on’ times. Thirteen patients receiving three-field conformal radiotherapy experienced a fall in peripheral lymphocyte counts from 2.02 (SD: 0.62. conf. 0.43) to 1.17 × 109/l (SD: 0.47, conf. 0.26) after 34–38 Gy, as compared to a fall from 1.6 × 109/l (SD: 0.6, conf. 0.35) to 1.04 × 109/l (SD: 0.3, conf. 0.15) for 15 TomoTherapy patients—non-significant differences. We conclude that for this (approximately) standard, small-volume pelvic radiotherapy and to the dose under scrutiny, we cannot detect differences between the two radiotherapy techniques in terms of the lymphopaenia accruing. Neutrophil counts were similarly non-significantly different.
Prospective cohort survey of patient satisfaction with on-treatment review by advanced practice urology radiographer
Authors: Treeby Jo
Published: December 2008

Radiographers are undertaking roles that are a development and extension of what has traditionally been seen as their remit. As with any development, it is important that such changes in practise have a positive rather than negative effect on patient care and patient experience. This article examines patient perception and level of patient satisfaction of an ‘on-treatment review’ conducted by a site-specific advanced practitioner radiographer instead of an oncology doctor. Overall, the results were positive suggesting that such reviews, when conducted by an appropriately trained individual, can enhance patient care and provide a satisfactory level of support during treatment.
An audit of a radiotherapy review clinic for breast cancer patients: a multi-disciplinary approach
Authors: Cameron J.L. , Blyth C.M. , Kirby A.S.
Published: December 2008

Purpose: With the advent of multi-disciplinary team working in Oncology practice, this audit was designed to assess patient satisfaction with this approach within an on-treatment review clinic for breast cancer patients. It also aimed to look at conformity of reporting of treatment side effects between different staff groups.

Patients and methods: A questionnaire was distributed to 230 radical breast cancer patients once a week after each review clinic. An oncologist and a radiographer or nurse reviewed the patients during weeks 1–4 of treatment. A review form was completed at each visit specifying any side effects noted.

Results: Patients appeared satisfied with their clinic visits to both the radiographer and nurse with 84 and 85% confidence and trust in the members of staff compared to 73% with the doctor. There was disparity in the recording of side effects between non-medical and medical staff groups.

Conclusion: This audit has provided good evidence to support the continuation of multi-disciplinary review clinics. A key benefit is the reduction in clinic waiting times for patients and a substantial time saving for the medics. It also supports role development for the radiographer and nurse involved.
Hyperprolaktinämie – in a man's world
Authors: Burri E. , Nüesch R. , Zulewski H.
Published: December 2008

Ein 60-jähriger Patient wurde wegen seit einigen Wochen bestehender, ziehender Schmerzen ohne Sekretausfluss in den Brustdrüsen vorstellig. Seit mehreren Jahren bestand eine erektile Dysfunktion und seit einiger Zeit auch ein Libidoverlust. Eine Sonographie der Brustdrüse zeigte Duktektasien ohne sicheren Nachweis einer Gynäkomastie, das Prolaktin im Serum war jedoch um das 5fache erhöht. Zusätzlich fanden sich in den Blutuntersuchungen ein erniedrigter Testosteron-Spiegel bei normalen LH- und FSH-Werten. Eine hypophysäre Raumforderung konnte in der Magnetresonanzuntersuchung (MRT) des Schädels nicht gefunden werden. Aufgrund der typischen Konstellation von Hyperprolaktinämie mit sekundärem Hypogonadismus in den Laboruntersuchungen und fehlendem Tumornachweis in der MRT der Hypophyse wurde nach Ausschluss einer sekundären Ursache die Diagnose einer idiopathischen Hyperprolaktinämie gestellt und eine medikamentöse Therapie mit einem Dopamin-Agonisten begonnen.
Formation and erosion of layered materials: Geologic and dust cycle history of eastern Arabia Terra, Mars
Authors: Fergason R. L. , Christensen P. R.
Published: December 2008

Eastern Arabia Terra is mantled in a layer of dust a few centimeters to a meter thick, yet contains morphologic features that suggest a history of multiple events of deposition and consolidation of fine‐grained material and a significant amount of erosion. Early in Martian history, this region was affected by volcanic and fluvial activity but has since been dominated by aeolian processes. Five craters in this region contain interior mound material that ranges in height from 1600 to 2100 m above the crater floor. The fluted erosional pattern and the thermal inertia are suggestive of a weakly indurated material, and the extensive layering implies that these mounds were formed by a repeated process or processes. Although these materials primarily occur within craters, there are materials outside craters that have similar erosional features and fine laminations, suggesting a more extensive deposit. The most likely process to form this material is the deposition and cementation of air fall dust and is potentially related to Martian obliquity changes. The significant amount of erosion of the intracrater mounds unit indicates a dramatic change from a depositional environment to an erosional regime over the past 106–108 years. Currently dust is accumulating in this region in years with planet‐encircling dust events, but global circulation model results indicate that dust devils may be removing slight amounts of dust from Arabia Terra. These observations suggest that the thickness of the dust mantle may not be currently increasing and may instead be in equilibrium.
On the impact of rainfall patterns on the hydrologic response
Authors: Nicótina L. , Alessi Celegon E. , Rinaldo A. , Marani M.
Published: December 2008

We study the influence exerted by space‐time rainfall patterns on the hydrologic response to determine the scales for which the spatial heterogeneity of rainfall may play a significant role in shaping the hydrographs generated in basins of varying characteristics. We perform numerical experiments using models based on the geomorphological theory of the hydrologic response, in which the spatial resolution of the input rainfall fields is coarse grained from 100 m to 50 km. The variation in the resulting hydrographs shows that rainfall spatial variability does not significantly influence the flood response for basin areas up to about 3500 km2in the cases considered, provided that the rainfall volume at each time interval is preserved. We then search for the physical interpretation of these results using the Jensen‐Shannon divergence measure to characterize differences in travel time distributions sampled by real and idealized disk‐shaped rainfall patterns of different size. Because the total residence time of a water parcel is often controlled by the travel time within hillslopes, we find that when typical hillslope size is smaller than the characteristic size of rainfall structures (say, a correlation length of rainfall intensity), the rainfall pattern effectively samples all possible residence times and the response of the catchment does not depend on the specific rainfall pattern. In larger basins (say, typically larger than 103km2) the travel time in the channels is expected to be an important part of the total residence time. In this case the response of a catchment will also be controlled by the specifics of the spatial distribution of rainfall.
Linking pulses of atmospheric deposition to DOC release in an upland peat‐covered catchment
Authors: Worrall F. , Burt T. P. , Adamson J. K.
Published: December 2008

Changes in atmospheric deposition have been proposed as one possible explanation of the widespread increase in DOC concentration observed in many Northern Hemisphere catchments. This study uses detailed, long‐term, monthly monitoring records of pH, conductivity SO4, and DOC in precipitation, soil water, and runoff chemistry from an upland peat‐covered catchment in northern England. By deriving impulse transfer functions this study explores whether changes in deposition lead to significant changes in the occurrence of each component in the soil and runoff water; especially significant changes in DOC. The study shows that (1) impulses in the deposition of acidity have no significant effect upon pH or DOC in soil water or runoff. (2) DOC in soil water and runoff is responsive to impulses in SO4 and conductivity, but only when those impulses are changes in soil water chemistry and not when they are in atmospheric deposition. (3) The effects of changes in SO4 and/or conductivity can easily be overemphasized if memory effects are not accounted for, and their effect is limited to only 1 or 2 months after a severe drought. This study can support the view that changes in ionic strength can result in changes in DOC concentration in soil water or runoff, but the system studied is unresponsive to changes in atmospheric deposition. Impulses in soil water SO4 do not lead to increases in DOC concentrations, and so this mechanism does not provide an explanation for DOC increases.
Individualization of textural and reactional microdomains in eclogites from the Bergen Arcs (Norway): Consequences for Rb/Sr and Ar/Ar radiochronometer behavior during polymetamorphism
Authors: Schneider Julie , Bosch Delphine , Monié Patrick
Published: December 2008

Rb/Sr, 40Ar/39Ar, and Sm/Nd isotopic data are reported in Caledonian eclogites from the Lindås Nappe, Bergen Arcs, Norway, in order to investigate processes controlling isotopic equilibrium at mineral scale in polymetamorphic rocks. The Bergen Arcs exposes Sveconorwegian ∼950–930 Ma granulites, partially overprinted by Caledonian eclogite‐facies metamorphism at ∼425 Ma and amphibolite‐facies metamorphism at ∼410 Ma. Geochemical and Rb‐Sr data from more than 10 phengite fractions separated from one sample reflect the composition of the microdomain (a few hundred microns in size) in which phengite crystallized. Phengite crystallized after garnet or plagioclase by dissolution‐precipitation processes yield apparent age between 700 and 600 Ma. At the time of their crystallization, these phengites inherited the isotopic composition of their precursor minerals, at a microdomain scale. Phengite from quartz veins, which crystallized from elements mobilized by the circulating fluid, yield an age closer to the eclogite‐facies metamorphic age. The closed system evolution of the eclogitizing fluid, the segregation of textural and reactional microdomains, the high Sr content of the studied phengite, and the short duration of the recrystallization processes (<1Ma) are interpreted as the main factors responsible for the lack of a Rb/Sr isotopic equilibrium, at the scale of hand samples. Such equilibrium is nevertheless reached in quartz veins where the crystallization of minerals implies that the fluid circulation acted as a factor of isotopic homogenization. The in situ single mineral Ar/Ar datings revealed that both eclogite‐ and amphibolite‐facies minerals are characterized by an excess of radiogenic argon (ages between 425 and 520 Ma). The excess of argon has been inherited from the previous granulite and has been only partially evacuated from the system by the circulating fluid. The apparent Sm/Nd ages from garnets inherited from the granulite‐facies metamorphism (c. 930 Ma) are in agreement with previous estimates. This result confirms that the diffusion of Nd in garnet does not occur at temperatures lower than 700°C. This study highlights the complexity of radiochronometer behavior during HP metamorphism and demonstrates that coupling different radiochronometers, such as Ar/Ar and Rb/Sr, does not always guarantee the validity of the geochronological results.
Seafloor alteration of basaltic glass: Textures, geochemistry, and endolithic microorganisms
Authors: Kruber Claudia , Thorseth Ingunn H. , Pedersen Rolf B.
Published: December 2008

The incipient low‐temperature alteration of glassy margins of recent seafloor lavas from the Mohns Ridge is characterized by scanning electron microscopy and bulk chemical analyses of major and trace elements. These investigations are designed to evaluate the endolithic microbial biomass, to identify relations between alteration textures and microorganisms, and to identify the chemical processes that take place during alteration. The basaltic glass along intersecting fractures and around vesicles is typically altered to concentrically zoned, yellow‐brown amorphous gel‐palagonite. In most fractures microorganisms are observed at the outer surfaces of palagonite rims, within porous zones of the rims, and frequently also at the glass‐palagonite interfaces. The cells act as nucleation sites for precipitation and become encrusted and embedded in palagonite with time. Zones of porous palagonite containing numerous hollow, fossilized cells alternate with zones of compact palagonite lacking distinct cell structures, which together indicate that the microbial growth is discontinuous. The palagonite has an average organic carbon content of 0.9 wt% (δ13Corg: −22‰), which derive from both living and fossilized biomass. The microbial growth and biomineralization are major controls on the porosity and texture of the palagonite and thus likely on the chemical exchange between glass and seawater. Pit marks in the glass in fractures both with and without microbes indicate that microbial as well as abiotic processes mediate pitting. Elemental and isotope data show that the transformation of glass to gel‐palagonite at seafloor conditions with high water/rock ratios results in near complete loss of Si and alkali elements to seawater; formation of Fe‐ and Al‐oxyhydroxides; complete exchange of alkaline earth elements like Sr with seawater; retention of V, Cu, Y, Pb, Th, U, and trivalent REEs, accompanied by a strong gain of these and other elements from seawater. Higher Fe/Ti ratios in the gel‐palagonite compared to the parental glass suggest that the palagonite represents a mixture of Fe‐Ti oxyhydroxides derived from both the glass and seawater.
High 3He emanations from the source regions of recent large earthquakes, central Japan
Authors: Umeda Koji , Ninomiya Atusi , McCrank Glen F.
Published: December 2008

Recently, two shallow MW 6.6 inland earthquakes, the 2004 mid‐Niigata prefecture earthquake and the 2007 Niigataken Chuetsu‐oki earthquake, occurred in the Niigata sedimentary basin near the boundary between the Eurasian and the North American Plates. In order to elucidate the geographic distribution of the 3He/4He ratios in and around the seismic source regions, new helium isotope data from hot spring gases and water samples from much denser sampling than in previous studies were determined. Although temporal changes in the 3He/4He ratios obtained from each well were unknown before and after the earthquakes, higher 3He/4He ratios were observed in the earthquake source regions compared to other regions. Geochemical evidence for the presence of hot spring gases and natural gases with anomalously high 3He/4He ratios (>3.8 RA) indicates infiltration of mantle fluids derived from the subcrustal lithosphere. A plausible source of mantle helium can be attributed to upward mobilization of aqueous fluids generated by dehydration of the subducting Pacific Plate slab, resulting in the acquisition of primordial helium from a mantle wedge as the fluids into the crust. In addition, aqueous fluids may raise the Earth's surface along permeable conduits leading to the reactivation of high‐angle inverted normal faults and the triggering of recent earthquakes.
Hurricane driven changes in land cover create biogeophysical climate feedbacks
Authors: Juárez Robinson I. Negrón , Chambers Jeffrey Q. , Zeng Hongcheng , Baker David B.
Published: December 2008

Hurricanes can devastate thousands of hectares of forested area producing changes beyond simply vegetation damage and biomass loss. This study reports changes in regional climate associated with Hurricane Rita which made landfall on the Gulf Coastal Plain on September 24th, 2005. Results demonstrate that over severely disturbed forested areas, biogeophysical effects produced by Rita created anomalous precipitation patterns, with a decrease in precipitation the following winter, and an increase during the subsequent summer season. The dominant biogeophysical effect was a change in albedo caused by ∼14,000 km2 of disturbed forested area (downed and dead, snapped and structurally damaged trees) from Rita, equivalent to a committed carbon release of 32 to 43% of the net annual U.S. sink in forest trees. As recent studies project a likely increase in hurricane intensity during the 21st century, understanding the potential impact of forest damage from hurricanes on regional climate is important.
Detection of in‐cloud lightning with VLF/LF and VHF networks for studies of the initial discharge phase
Authors: Betz H.‐D. , Marshall T. C. , Stolzenburg M. , Schmidt K. , Oettinger W. P. , Defer E. , Konarski J. , Laroche P. , Dombai F.
Published: December 2008

Lightning initiation and the associated in‐cloud parts of lightning flashes have been studied by comparing thunderstorm data from two independent networks, LINET and SAFIR‐type systems, operating in the VLF/LF and VHF regime, respectively. The two networks respond to radiation pulses with different length scales; an event detected by VLF/LF must be hundreds of meters long. In all 12 storms studied, up to half of the first in‐cloud events detected with the VHF networks were found to be closely time‐correlated with the first VLF/LF signal. Range‐normalized VLF/LF signal amplitudes of the time‐coincident events (TCEs) are comparable to amplitudes of weak cloud‐to‐ground strokes. Without measured preparatory VHF emission activity, initial breakdown in TCEs seems to start directly with a strong discharge step producing signatures in VLF/LF records. The TCE data are consistent with lightning initiation via a runaway breakdown mechanism that extended over hundreds of meters.
Atmospheric‐hydrodynamic coupling in the nearshore
Authors: Ortega‐Sánchez M. , Bramato S. , Quevedo E. , Mans C. , Losada M. A.
Published: December 2008

Natural beach shorelines commonly present morphological rhythmic or non‐rhythmic features of varying geometrical characteristics. Traditionally, their formation is believed to be due to wave‐induced processes, a line thoroughly investigated during the last few decades. However, these natural beach formations are frequently bounded by coastal cliffs (or capes) and are affected by intense winds, a fact not previously considered. This paper presents the results of a field survey, demonstrating the existence of atmospheric‐hydrodynamic coupling in the nearshore region outside of the breaking zone at Carchuna beach (Motril, Spain), where the atmospheric conditions are influenced by a lateral geographic obstacle (Cape Sacratif).
Collective behavior of earthquakes and faults: Continuum‐discrete transitions, progressive evolutionary changes, and different dynamic regimes
Authors: Ben‐Zion Yehuda
Published: December 2008

Crustal deformation patterns are affected by multiscale granulation and healing processes associated with phase transitions between continuum and discrete states of rocks. The ongoing continuum‐discrete transitions are accompanied by progressive evolution of disordered fault networks to dominant localized fault zones, development of bimaterial interfaces, and increasing dynamic weakening of fault surfaces. Results on individual fault zones point to three general dynamic regimes. The first is associated with broad range of heterogeneities, little dynamic weakening, power law frequency‐size statistics, temporal clustering of intermediate and large events, and accelerated seismic release before large earthquakes. The second is associated with relatively uniform localized structures, significant dynamic weakening, characteristic earthquake statistics, and quasi‐periodic temporal occurrence of large events without precursory accelerated release. For a range of conditions, the fault zone response can switch back and forth between the foregoing two dynamic regimes. Higher temperature, fluid content, and thickness of sedimentary cover reduce the seismic coupling in a region and change the properties of local earthquake sequences. Brittle regions with high seismic coupling have few foreshocks and long‐duration aftershock sequences with high event productivity, whereas more viscous regions with low seismic coupling have increased foreshocks activity and low‐productivity aftershock sequences or swarms. The results provide criteria for organizing data in classes associated with different evolutionary stages and different regional conditions. An ability to recognize the dynamic regime of a given fault zone or a region can increase the information content of the data and lead to improved strategies for seismic hazard assessment.
Heat as a tracer to determine streambed water exchanges
Authors: Constantz Jim
Published: December 2008

This work reviews the use of heat as a tracer of shallow groundwater movement and describes current temperature‐based approaches for estimating streambed water exchanges. Four common hydrologic conditions in stream channels are graphically depicted with the expected underlying streambed thermal responses, and techniques are discussed for installing and monitoring temperature and stage equipment for a range of hydrological environments. These techniques are divided into direct‐measurement techniques in streams and streambeds, groundwater techniques relying on traditional observation wells, and remote sensing and other large‐scale advanced temperature‐acquisition techniques. A review of relevant literature suggests researchers often graphically visualize temperature data to enhance conceptual models of heat and water flow in the near‐stream environment and to determine site‐specific approaches of data analysis. Common visualizations of stream and streambed temperature patterns include thermographs, temperature envelopes, and one‐, two‐, and three‐dimensional temperature contour plots. Heat and water transport governing equations are presented for the case of transport in streambeds, followed by methods of streambed data analysis, including simple heat‐pulse arrival time and heat‐loss procedures, analytical and time series solutions, and heat and water transport simulation models. A series of applications of these methods are presented for a variety of stream settings ranging from arid to continental climates. Progressive successes to quantify both streambed fluxes and the spatial extent of streambeds indicate heat‐tracing tools help define the streambed as a spatially distinct field (analogous to soil science), rather than simply the lower boundary in stream research or an amorphous zone beneath the stream channel.
Capillary bundle model of hydraulic conductivity for frozen soil
Authors: Watanabe Kunio , Flury Markus
Published: December 2008

We developed a capillary bundle model to describe water flow in frozen soil. We assume that the soil can be represented as a bundle of cylindrical capillaries. We consider that the freezing point in the capillaries is depressed according to the Gibbs‐Thomson effect and that when stable ice forms in a capillary, the ice forms in the center of the capillaries, leaving a circular annulus open for liquid water flow. We use the model to demonstrate how the hydraulic conductivity changes as a function of temperature for both saturated and unsaturated soils, using a sand and two silt loam soils as examples. As temperature decreases, more and more ice forms, and the water flux consequently decreases. In frozen soil near 0°C, water predominantly flows through ice‐free capillaries, so that the hydraulic conductivity of frozen soil is similar to that of an unfrozen soil with a water content equal to the unfrozen water content of the frozen soil. At low temperatures, however, ice forms in almost all capillaries, and the hydraulic conductivity of frozen soil is greater than that of unfrozen soil with the same water potential.
Urm1 at the crossroad of modifications
Authors: Pedrioli Patrick G A , Leidel Sebastian , Hofmann Kay
Published: December 2008

The ubiquitin‐like protein Urm1 can be covalently conjugated to other proteins, such as the yeast thioredoxin peroxidase protein Ahp1p, through a mechanism involving the ubiquitin E1‐like enzyme Uba4. Recent findings have revealed a second function of Urm1 as a sulphur carrier in the thiolation of eukaryotic cytoplasmic transfer RNAs (tRNAs). Interestingly, this new role of Urm1 is similar to the sulphur‐carrier activity of its prokaryotic counterparts, strengthening the hypothesis that Urm1 is a molecular fossil of the ubiquitin‐like protein family. Here, we discuss the function of Urm1 in light of its dual role in protein and RNA modification.
Neprilysin gene expression requires binding of the amyloid precursor protein intracellular domain to its promoter: implications for Alzheimer disease
Authors: Belyaev Nikolai D , Nalivaeva Natalia N , Makova Natalia Z , Turner Anthony J
Published: December 2008

Amyloid β‐peptide (Aβ) accumulation leads to neurodegeneration and Alzheimer disease; however, amyloid metabolism is a dynamic process and enzymic mechanisms exist for Aβ removal. Considerable controversy surrounds whether the intracellular domain of the amyloid precursor protein (AICD) regulates expression of the Aβ‐degrading metalloprotease, neprilysin (NEP). By comparing two neuroblastoma cell lines differing substantially in NEP expression, we show by chromatin immunoprecipitation (ChIP) that AICD is bound directly to the NEP promoter in high NEP‐expresser (NB7) cells but not in low‐expresser (SH‐SY5Y) cells. The methylation status of the NEP promoter does not regulate expression in these cells, whereas the histone deacetylase inhibitors trichostatin A and valproate partly restore NEP expression and activity in SH‐SY5Y cells. ChIP analysis also reveals AICD binding to the NEP promoter in rat primary neurons but not in HUVEC cells. Chromatin remodelling of crucial Alzheimer disease‐related genes by valproate could provide a new therapeutic strategy.
Open Source Drug Discovery
Authors: Yadav Jyoti , Consortium OSDD
Published: December 2008

Tuberculosis is a ravaging disease killing one person in every 1.5 minutes in India alone. Someone in the world is newly infected with TB bacilli every second. Overall, one-third of the world's population is currently infected with the TB bacillus. Left untreated, each person with active TB disease will infect on average between 10 and 15 people every year. 450 000 new MDR-TB cases are estimated to occur every year. Estimated 5% of TB patients are HIV infected. Although the complete genome sequence of the causative pathogen Mycobacterium tuberculosis was published about a decade ago and many years of painstaking efforts have been invested, we are still far from having a good, fast acting drug and vaccine which confers long lasting protection. Despite increasing investment, led by charities including the Gates Foundation, no novel drugs for TB have entered the market for many years.

Novel mechanisms for attracting funding, particularly private sector funding, into this research area are desperately needed. We wish to bring in the power of genomics, computational technologies and participation of young and brilliant talent from Universities and Industrial partners with a strong inclination to apply a concerted effort to address this important scourge. All researchers contribute data on tuberculosis drug targets and active molecules through a copyleft agreement; anyone who is prepared to keep to this may participate. All the data is Clickwrap protected and credit sharing will be based on a novel and flexible micro-attribution system. This system is aimed at providing due credit through an active process. Various levels of investigators shall have appropriate levels of rights, recognition and responsibilities.

Another valuable aspect is the partnerships of Industry with belief in Open Source systems and models. We name this concerted effort to tackle this dreaded disease as Open Source Drug Discovery for Tuberculosis.
Role of pravastatin in pulmonary hypertension in chronic obstructive pulmonary disease
Authors: Corte Tamera J. , Wort Stephen J.
Published: December 2008

COPD (chronic obstructive pulmonary disease) is a significant health concern as the fourth leading cause of morbidity and mortality in the U.S.A. Although the prevalence of PH (pulmonary hypertension) in COPD is unknown, its presence is a risk factor for mortality. In this comment, we consider the role of PH in COPD and its pathophysiology, with reference to ET-1 (endothelin-1) and cigarette smoke, as well as exercise and nocturnal hypoxia. We also explore potential mechanisms for the observed improvement in exercise tolerance following 6 months of pravastatin treatment in COPD patients with PH as reported by Lee and co-workers in the present issue of Clinical Science, including possible effects upon ET-1 and Rho kinase, or antioxidant effects, which may be particularly relevant in this group of mainly current smokers.
From photovoltaics to medical imaging: Applications of thin-film CdTe in x-ray detection
Authors: Kang J. , Parsai E. I. , Albin D. , Karpov V. G. , Shvydka Diana
Published: December 2008

Recent developments in photovoltaics created a commercially viable technology of large area uniform thin-film structures, potentially extendable to the field of medical imaging, where the capability of producing large area x-ray detectors is essential for the successful diagnosis and treatment of cancer. We propose a large area thin-film CdTe structure suitable for radiation detection and discuss its main characteristics under x-ray beams used in radiation therapy. While based on the same principle, the details of its operations are very dissimilar from that of photovoltaics.
Perceived Self-Tilt in Dynamic Visual Stimuli: Evidence for Suppression by Vestibulo-Tactile Inputs
Authors: Higashiyama Atsuki , Koga Kazuo
Published: December 2008

Perception of self-tilt is affected by shearing force acting on the otolith organs in the ears, by pressure acting on the tactile receptors in the skin, and by visual pattern falling on the retinae. We examined how the vestibular, somatosensory, and visual inputs interact in judging self-tilt in roll. Each of fourteen observers, sitting in a chair and gazing at a rotation pattern in the frontal plane, was tilted to various angles and verbally judged to what extent his/her body was tilted. The independent variables examined were body tilt (0° to ±108°), and the rate (7.5° s−1, 15° s−1, and 30° s−1) and direction (CW and CCW) of the visual rotating pattern. We found that (i) the sensory scale for self-tilt is represented by a third-order polynomial lacking the quadratic component, (ii) perceived self-tilt for the CW (or CCW) rotation of the visual pattern is displaced CCW (or CW), (iii) the linear and cubic components of the equation increase with an increase in the rate of rotation of the visual pattern, and (iv) if the body is tilted in concord with the direction of vection, the velocity of visual pattern is effective, but when the body is tilted in conflict with the direction of vection, it is less effective. These findings are interpreted in terms of vestibular and somatosensory suppressions exerted on the effects of vection.
Economics, cultural transmission, and the dynamics of the sex ratio at birth in China
Authors: Lipatov Mikhail , Li Shuzhuo , Feldman Marcus W.
Published: December 2008

In rural China, the ratio of newborn boys to newborn girls [sex ratio at birth (SRB)] has been rising for several decades, to values significantly above its biological norm. This trend has a number of alarming societal consequences, and has attracted the attention of scholars and politicians. The root of the problem lies in a 2,500-year-old culture of son preference. This culture is intricately linked with the economic reality of each couple's life, so that there are financial and psychological repercussions to parents who have no sons. To bring greater clarity and understanding to this issue, we present a quantitative framework that describes the interaction between economics and cultural transmission. We start with an explicit mechanism by which economic incentives can change cultural beliefs of a given individual, and go on to include a mechanism of cultural inheritance from generation to generation. We then show how economic conditions can affect the dynamics of cultural change in an entire society, and may lead to a decrease in the country's sex ratio at birth.
Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding
Authors: Frantz Christian , Barreiro Gabriela , Dominguez Laura , Chen Xiaoming , Eddy Robert , Condeelis John , Kelly Mark J.S. , Jacobson Matthew P. , Barber Diane L.
Published: December 2008

Newly generated actin free barbed ends at the front of motile cells provide sites for actin filament assembly driving membrane protrusion. Growth factors induce a rapid biphasic increase in actin free barbed ends, and we found both phases absent in fibroblasts lacking H+ efflux by the Na-H exchanger NHE1. The first phase is restored by expression of mutant cofilin-H133A but not unphosphorylated cofilin-S3A. Constant pH molecular dynamics simulations and nuclear magnetic resonance (NMR) reveal pH-sensitive structural changes in the cofilin C-terminal filamentous actin binding site dependent on His133. However, cofilin-H133A retains pH-sensitive changes in NMR spectra and severing activity in vitro, which suggests that it has a more complex behavior in cells. Cofilin activity is inhibited by phosphoinositide binding, and we found that phosphoinositide binding is pH-dependent for wild-type cofilin, with decreased binding at a higher pH. In contrast, phosphoinositide binding by cofilin-H133A is attenuated and pH insensitive. These data suggest a molecular mechanism whereby cofilin acts as a pH sensor to mediate a pH-dependent actin filament dynamics.
CaMKII locally encodes L-type channel activity to signal to nuclear CREB in excitation–transcription coupling
Authors: Wheeler Damian G. , Barrett Curtis F. , Groth Rachel D. , Safa Parsa , Tsien Richard W.
Published: December 2008

Communication between cell surface proteins and the nucleus is integral to many cellular adaptations. In the case of ion channels in excitable cells, the dynamics of signaling to the nucleus are particularly important because the natural stimulus, surface membrane depolarization, is rapidly pulsatile. To better understand excitation–transcription coupling we characterized the dependence of cAMP response element–binding protein phosphorylation, a critical step in neuronal plasticity, on the level and duration of membrane depolarization. We find that signaling strength is steeply dependent on depolarization, with sensitivity far greater than hitherto recognized. In contrast, graded blockade of the Ca2+ channel pore has a remarkably mild effect, although some Ca2+ entry is absolutely required. Our data indicate that Ca2+/CaM-dependent protein kinase II acting near the channel couples local Ca2+ rises to signal transduction, encoding the frequency of Ca2+ channel openings rather than integrated Ca2+ flux—a form of digital logic.
Schizosaccharomyces pombe Pak-related protein, Pak1p/Orb2p, phosphorylates myosin regulatory light chain to inhibit cytokinesis
Authors: Loo Tsui-Han , Balasubramanian Mohan
Published: December 2008

p21-activated kinases (Paks) have been identified in a variety of eukaryotic cells as key effectors of the Cdc42 family of guanosine triphosphatases. Pak kinases play important roles in regulating the filamentous actin cytoskeleton. In this study, we describe a function for the Schizosaccharomyces pombe Pak-related protein Pak1p/Orb2p in cytokinesis. Pak1p localizes to the actomyosin ring during mitosis and cytokinesis. Loss of Pak1p function leads to accelerated cytokinesis. Pak1p mediates phosphorylation of myosin II regulatory light chain Rlc1p at serine residues 35 and 36 in vivo. Interestingly, loss of Pak1p function or substitution of serine 35 and serine 36 of Rlc1p with alanines, thereby mimicking a dephosphorylated state of Rlc1p, leads to defective coordination of mitosis and cytokinesis. This study reveals a new mechanism involving Pak1p kinase that helps ensure the fidelity of cytokinesis.
FAM29A promotes microtubule amplification via recruitment of the NEDD1–γ-tubulin complex to the mitotic spindle
Authors: Zhu Hui , Coppinger Judith A. , Jang Chang-Young , Yates John R. , Fang Guowei
Published: December 2008

Microtubules (MTs) are nucleated from centrosomes and chromatin. In addition, MTs can be generated from preexiting MTs in a γ-tubulin–dependent manner in yeast, plant, and Drosophila cells, although the underlying mechanism remains unknown. Here we show the spindle-associated protein FAM29A promotes MT-dependent MT amplification and is required for efficient chromosome congression and segregation in mammalian cells. Depletion of FAM29A reduces spindle MT density. FAM29A is not involved in the nucleation of MTs from centrosomes and chromatin, but is required for a subsequent increase in MT mass in cells released from nocodazole. FAM29A interacts with the NEDD1–γ-tubulin complex and recruits this complex to the spindle, which, in turn, promotes MT polymerization. FAM29A preferentially associates with kinetochore MTs and knockdown of FAM29A reduces the number of MTs in a kinetochore fiber, activates the spindle checkpoint, and delays the mitotic progression. Our study provides a biochemical mechanism for MT-dependent MT amplification and for the maturation of kinetochore fibers in mammalian cells.
Synapses are regulated by the cytoplasmic tyrosine kinase Fer in a pathway mediated by p120catenin, Fer, SHP-2, and β-catenin
Authors: Lee Seung-Hye , Peng I.-Feng , Ng Yu Gie , Yanagisawa Masahiro , Bamji Shernaz X. , Elia Lisa P. , Balsamo Janne , Lilien Jack , Anastasiadis Panos Z. , Ullian Erik M. , Reichardt Louis F.
Published: December 2008

Localization of presynaptic components to synaptic sites is critical for hippocampal synapse formation. Cell adhesion–regulated signaling is important for synaptic development and function, but little is known about differentiation of the presynaptic compartment. In this study, we describe a pathway that promotes presynaptic development involving p120catenin (p120ctn), the cytoplasmic tyrosine kinase Fer, the protein phosphatase SHP-2, and β-catenin. Presynaptic Fer depletion prevents localization of active zone constituents and synaptic vesicles and inhibits excitatory synapse formation and synaptic transmission. Depletion of p120ctn or SHP-2 similarly disrupts synaptic vesicle localization with active SHP-2, restoring synapse formation in the absence of Fer. Fer or SHP-2 depletion results in elevated tyrosine phosphorylation of β-catenin. β-Catenin overexpression restores normal synaptic vesicle localization in the absence of Fer or SHP-2. Our results indicate that a presynaptic signaling pathway through p120ctn, Fer, SHP-2, and β-catenin promotes excitatory synapse development and function.
The Mad2 partial unfolding model: regulating mitosis through Mad2 conformational switching
Authors: Skinner John J. , Wood Stacey , Shorter James , Englander S. Walter , Black Ben E.
Published: December 2008

The metamorphic Mad2 protein acts as a molecular switch in the checkpoint mechanism that monitors proper chromosome attachment to spindle microtubules during cell division. The remarkably slow spontaneous rate of Mad2 switching between its checkpoint inactive and active forms is catalyzed onto a physiologically relevant time scale by a self–self interaction between its two forms, culminating in a large pool of active Mad2. Recent structural, biochemical, and cell biological advances suggest that the catalyzed conversion of Mad2 requires a major structural rearrangement that transits through a partially unfolded intermediate.
Parkin mitochondria in the autophagosome
Authors: McBride Heidi M.
Published: December 2008

Narendra et al. (see p. 795 of this issue) have made an exciting new discovery that links the fields of mitochondrial quality control and the genetics of Parkinson's disease (PD). Through an elegant series of high-resolution imaging experiments, they are the first to provide evidence that the PARK2 gene product Parkin is selectively recruited to damaged or uncoupled mitochondria. This recruitment leads to the clearance of the organelles through the autophagosome, demonstrating a primary function for Parkin in the regulation of mitochondrial turnover. This work significantly increases our understanding of PD and provides a new framework for the development of therapeutic interventions.
Integrated Management of Gummy Stem Blight of Watermelon by Green Manure and Melcast-scheduled Fungicides
Authors: Zhou Xin-Gen , Everts Kathryne L.
Published: December 2008

Watermelon gummy stem blight (GSB) management using a green manure cover crop, the weather-based disease forecasting program ‘Melcast,’ and bio- and reduced-risk fungicides was evaluated in Maryland. Soil incorporation of hairy vetch winter cover crop suppressed percent foliage affected by GSB in comparison to winter fallow in three of five trials conducted in 2004 and 2005. Programs of Reynoutria sachalinensis, Bacillus subtilis, or harpin protein applied in rotation with chlorothalonil provided control of GSB as effectively as did EBDC, boscalid, or cyprodinil plus fludioxonil. However, the bio-fungicide programs did not perform as well as chlorothalonil alternated with pyraclostrobin plus boscalid in 2005. Melcast-scheduled sprays of B. subtilis in rotation with chlorothalonil resulted in an average of 73% less synthetic fungicide applied to watermelon. However, GSB reduction in the B. subtilis program, although similar in 2005, was less that that obtained with chlorothalonil alone in 2004. These results suggest that the combined use of green manure with Melcast-scheduled fungicide applications could effectively manage GSB and reduce fungicide use. Biofungicides alternated with chlorothalonil also minimized use of synthetic fungicides and were effective under some conditions, but should be used with caution.

Accepted for publication 22 September 2008. Published 20 November 2008.