bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adverse Effects of Trichothiodystrophy DNA Repair and Transcription Gene Abnormalities on Human Fetal Development
Authors: Moslehi Roxana , Signore Caroline , Troendle James , Dzutsev Amiran , Mills James 
Published: August 2009

AbstractThe effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair (NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24) with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18), accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational complications was noted in TTD-affected pregnancies. Gestational complications were noted in nearly all pregnancies resulting in TTD-affected offspring with XPD and TTDN1, but not TTD-A, gene mutations. Abnormal placental development may explain the constellation of observed complications; therefore, we hypothesize that some TTD genes play an important role in normal placental and fetal development. We investigated this hypothesis by analyzing the expression patterns of TTD genes. Expression of TTDA was strongly negatively correlated (r=-0.7,P<0.0001) with gestational age, while XPD, XPB and TTDN1 were consistently expressed from 14 to 40 weeks gestation. *Conclusion:* Our results indicate an important role for XPD, XPB and TTDN1 gene products during normal human placental and fetal development.
CXCL16 in HIV infection – a link between inflammation and viral replication
Authors: Landrø L. , Damås J. K. , Halvorsen B. , Fevang B. , Ueland T. , Otterdal K. , Heggelund L. , Frøland S. S. , Aukrust P. 
Published: August 2009

AbstractBackground  While some chemokines are thought to be protective in HIV‐infected individuals by their ability to block HIV entry into T cells and macrophages, chemokines could also have harmful effects in HIV infection through their ability to promote inflammation. Here, we examined the regulation and the effects of CXCL16, a newly discovered chemokine of the CXC family, in HIV‐infected patients.Materials and methods  We examined serum levels of CXCL16 in clinically well‐defined subgroups of HIV‐infected individuals both before (n = 62) and during HAART (n = 40) as well as in age‐ and sex‐matched healthy controls (n = 30). We also examined the effects of CXCL16 on inflammatory and anti‐inflammatory cytokines and HIV replication in peripheral blood mononuclear cells (PBMC).Results  Our main and novel findings were: (i) HIV‐infected patients had significant raised CXCL16 levels according to disease severity and progression. (ii) During HAART, the immunological improvement was accompanied by a modest increase in CXCL16 level. (iii) While soluble CXCL16 promoted an anti‐inflammatory response in PBMC from those on successful HAART, it induced an inflammatory response and enhanced HIV replication in PBMC from those with high viral load irrespectively of ongoing HAART. (iv) Recombinant HIV‐tat protein significantly increased CXCL16 release in THP‐1 macrophages.Conclusions  Our findings suggest a complex interaction between CXCL16 and HIV, promoting both inflammatory and anti‐inflammatory effects as well as HIV replication, partly dependent on accompanying HIV replication.
Global position analysis of the Pseudomonas aeruginosa quorum‐sensing transcription factor LasR
Authors: Gilbert Kerrigan B. , Kim Tae Hoon , Gupta Rashmi , Greenberg E. Peter , Schuster Martin 
Published: August 2009

SummaryIn Pseudomonas aeruginosa quorum sensing (QS), the transcriptional regulator LasR controls the expression of more than 300 genes. Several of these genes are activated indirectly via a second, subordinate QS regulator, RhlR. Conserved sequence elements upstream of individual other genes have been shown to bind LasR in vitro. To comprehensively identify all regions that are bound by LasR in vivo, we employed chromatin immunoprecipitation in conjunction with microarray analysis. We identified 35 putative promoter regions that direct the expression of up to 74 genes. In vitro DNA binding studies allowed us to distinguish between cooperative and non‐cooperative LasR binding sites, and allowed us to build consensus sequences according to the mode of binding. Five promoter regions were not previously recognized as QS‐controlled. Two of the associated transcript units encode proteins involved in the cold‐shock response and in Psl exopolysaccharide synthesis respectively. The LasR regulon includes seven genes encoding transcriptional regulators, while secreted factors and secretion machinery are the most over‐represented functional categories overall. This supports the notion that the core function of LasR is to co‐ordinate the production of extracellular factors, although many of its effects on global gene expression are likely mediated indirectly by regulatory genes under its control.
Haem‐delivery proteins in cytochrome c maturation System II
Authors: Ahuja Umesh , Kjelgaard Peter , Schulz Benjamin L. , Thöny‐Meyer Linda , Hederstedt Lars 
Published: August 2009

SummaryCytochromes of the c‐type function on the outer side of the cytoplasmic membrane in bacteria where they also are assembled from apo‐cytochrome polypeptide and haem. Two distinctly different systems for cytochrome c maturation are found in bacteria. System I present in Escherichia coli has eight to nine different Ccm proteins. System II is found in Bacillus subtilis and comprises four proteins: CcdA, ResA, ResB and ResC. ResB and ResC are poorly understood polytopic membrane proteins required for cytochrome c synthesis. We have analysed these two B. subtilis proteins produced in E. coli and in the native organism. ResB is shown to bind protohaem IX and haem is found covalently bound to residue Cys‐138. Results in B. subtilis suggest that also ResC can bind haem. Our results complement recent findings made with Helicobacter CcsBA supporting the hypothesis that ResBC as a complex translocates haem by attaching it to ResB on the cytoplasmic side of the membrane and then transferring it to an extra‐cytoplasmic location in ResC, from where it is made available to the apo‐cytochromes.
Cation/proton antiporter complements of bacteria: why so large and diverse?
Authors: Krulwich Terry A. , Hicks David B. , Ito Masahiro 
Published: August 2009

SummaryMost bacterial genomes have five to nine distinct genes predicted to encode transporters that exchange cytoplasmic Na+ and/or K+ for H+ from outside the cell, i.e. monovalent cation/proton antiporters. By contrast, pathogens that live primarily inside host cells usually possess zero to one such antiporter while other stress‐exposed bacteria exhibit even higher numbers. The monovalent cation/proton antiporters encoded by these diverse genes fall into at least eight different transporter protein families based on sequence similarity. They enable bacteria to meet challenges of high or fluctuating pH, salt, temperature or osmolarity, but we lack explanations for why so many antiporters are needed and for the value added by specific antiporter types in specific settings. In this issue of Molecular Microbiology, analyses of the pH dependence of cytoplasmic [Na+], [K+], pH and transmembrane electrical potential in the ‘poly extremophile’Natranaerobius thermophilus are the context for assessment of the catalytic properties of 12 predicted monovalent cation/proton antiporters in the genome of this thermophilic haloalkaliphile. The results provide a profile of adaptations of the poly extremophilic anaerobe, including a proposed role of cytoplasmic buffering capacity. They also provide new perspectives on two large monovalent cation/proton antiporter families, the NhaC and the cation/proton antiporter‐3 antiporter families.
Children with cerebral palsy: severity and trends over time
Authors: Surman Geraldine , Hemming Karla , Platt Mary J. , Parkes Jackie , Green Abbi , Hutton Jane , Kurinczuk Jennifer J. 
Published: August 2009

SummaryIncreasingly, more very‐low‐birthweight infants in the developed world are now expected to survive the neonatal period than was previously the case. There are concerns that there may be a related increase in the number of infants developing severe sensorimotor impairments. Pooled data from five registers contributing to the UK Network of Cerebral Palsy Registers, Surveys and Databases were used to identify patterns of motor impairment in relation to additional impairments and to birthweight, and to assess whether prevalence of cerebral palsy (CP) by birthweight and by severity of motor impairment had changed over time. Low‐birthweight infants are at greater risk of developing CP than larger‐birthweight babies.The CP rate amongst children with birthweights <2500 g was significantly higher at 16 per 1000 livebirths [95% confidence interval (CI) 14.9, 16.2] than 1.2 per 1000 livebirths [95% CI 11, 1.2] for normal‐birthweight children. Despite being at greater risk of developing CP, smaller‐birthweight babies are proportionately less likely to develop the most severe forms of motor impairment. Of those born weighing ≥2500 g, 23% compared with 15% weighing <1000 g (P < 0.001) were in the most severely motor impaired group. Severe motor impairment is associated with higher levels of additional impairments. CP rates for each motor impairment group in the 1990s were similar to those in the late 1970s. Rates of CP among infants born below normal birthweight are high but have decreased over time. The CP rate for infants weighing 1000–1499 g at birth decreased from around 180 per 1000 livebirths in 1979 to around 50 per 1000 livebirths from the early 1990s onwards.
Self‐selection and bias in a large prospective pregnancy cohort in Norway
Authors: Nilsen Roy M. , Vollset Stein Emil , Gjessing Håkon K. , Skjærven Rolv , Melve Kari K. , Schreuder Patricia , Alsaker Elin R. , Haug Kjell , Daltveit Anne Kjersti , Magnus Per 
Published: August 2009

SummarySelf‐selection in epidemiological studies may introduce selection bias and influence the validity of study results. To evaluate potential bias due to self‐selection in a large prospective pregnancy cohort in Norway, the authors studied differences in prevalence estimates and association measures between study participants and all women giving birth in Norway. Women who agreed to participate in the Norwegian Mother and Child Cohort Study (43.5% of invited; n = 73 579) were compared with all women giving birth in Norway (n = 398 849) using data from the population‐based Medical Birth Registry of Norway in 2000–2006. Bias in the prevalence of 23 exposure and outcome variables was measured as the ratio of relative frequencies, whereas bias in exposure‐outcome associations of eight relationships was measured as the ratio of odds ratios.Statistically significant relative differences in prevalence estimates between the cohort participants and the total population were found for all variables, except for maternal epilepsy, chronic hypertension and pre‐eclampsia. There was a strong under‐representation of the youngest women (<25 years), those living alone, mothers with more than two previous births and with previous stillbirths (relative deviation 30–45%). In addition, smokers, women with stillbirths and neonatal death were markedly under‐represented in the cohort (relative deviation 22–43%), while multivitamin and folic acid supplement users were over‐represented (relative deviation 31–43%). Despite this, no statistically relative differences in association measures were found between participants and the total population regarding the eight exposure‐outcome associations.Using data from the Medical Birth Registry of Norway, this study suggests that prevalence estimates of exposures and outcomes, but not estimates of exposure‐outcome associations are biased due to self‐selection in the Norwegian Mother and Child Cohort Study.
Trans‐Generational Influence of Human Disturbances in Japanese Quail: Egg Quality Influences Male Social and Sexual Behaviour
Authors: Bertin Aline , Hirschenhauser Katharina , Kotrschal Kurt 
Published: August 2009

AbstractIn many bird species prenatal exposure to yolk androgens of maternal origin has been found to influence offspring behavioural phenotype. In contrast to altricial birds, far less is known about maternal effects in precocial birds. In a previous experiment we found that female quail (Coturnix japonica) that were not previously habituated to humans (NH) produced eggs with less androgens (testosterone, androstenedione) and more progesterone when exposed to human disturbances than females habituated to humans (H). Here, we analysed social motivation and sexual behaviour of the male offspring of NH and H females. Classical behavioural test procedures were applied including separation, runway, partner choice and female encounter tests. As chicks, offspring of the NH females spent more time far from conspecifics than offspring of the H females. As adults, the same NH males showed less crowing and courtship behaviour (ritual preening) in female encounter tests than H males. Thus, maternal environment and egg quality may be key factors in the emergence of individual variability of appetitive behaviour, such as social proximity and courtship behaviour. Human disturbance of the mother seems to have triggered trans‐generational effects resulting in consistently reduced social and sexual motivation in offspring until adulthood.
Algorithm‐guided treatment versus treatment as usual for major depression
Authors: Yoshino Aihide , Sawamura Takehito , Kobayashi Nobuhisa , Kurauchi Sachi , Matsumoto Aki , Nomura Soichiro 
Published: August 2009

Aims:  The remission rates for patients with major depressive disorder (MDD) during algorithm‐guided treatment (AGT), which consisted of four treatment strategy steps were prospectively compared with treatment as usual (TAU).Methods:  The remission rates of patients with mild or moderate MDD during AGT (n = 83) were compared with TAU (n = 127).Results:  The remission rate in the AGT group (60.2%) was approximately 10% greater than that in the TAU group (49.7%). The median number of days to achieve remission in the AGT group (93 days) was half as long as that in the TAU group (191 days). The hazard ratio of remission was 1.5 (95% confidence interval: = 1.2–1.8). A higher rate of lithium augmentation in the AGT group (20.5%) compared to theTAU (4.7%) may have led to the greater remission rate. Most participants who did not achieve remission either during the initial or second treatment steps dropped out from AGT.Conclusions:  AGT may be superior to TAU for patients with mild or moderate MDD, based on the remission rates achieved. The later treatment steps in the AGT, however, were rarely utilized because participants who did not receive any benefit dropped out early.
Childhood emotional abuse and dissociation in patients with conversion symptoms
Authors: Sar Vedat , Islam Serkan , Öztürk Erdinç 
Published: August 2009

Aim:  The aim of the present study was to evaluate the relationship between reported childhood trauma and dissociation in patients who have a conversion symptom.Method:  Thirty‐two outpatients with a conversion symptom were evaluated using Dissociative Experiences Scale, Somatoform Dissociation Questionnaire, Childhood Trauma Questionnaire, Spielberger Trait Anxiety Inventory, Clinician‐Administered Dissociative State Scale, and Dissociative Disorders Interview Schedule.Results:  A DSM‐IV dissociative disorder was diagnosed in 46.9% of the patients. Conversion patients with a dissociative disorder had borderline personality disorder more frequently than those without a dissociative disorder. Among childhood trauma types, emotional abuse was the only significant predictor of dissociation in regression analysis. None of the childhood trauma types predicted borderline personality disorder criteria.Conclusions:  Borderline personality disorder, dissociation and reports of childhood emotional abuse refer to a subgroup among patients with conversion symptom. Dissociation seems to be a mediator between childhood trauma and borderline phenomena among these patients.
Differences in the structure, growth and survival of Parasenecio yatabei ramets with contrasting water relations on the slope of a stream bank
Authors: TOMIMATSU HAJIME , HOSODA JUN‐ICHI , HORI YOSHIMICHI 
Published: August 2009

Abstract Parasenecio yatabei (Asteraceae), a summer‐green perennial herb, is widely distributed on sloping mountain stream banks in cool‐temperate zone forests of Japan. We investigated the growth pattern, leaf longevity and leaf water relations of vegetatively independent plants (ramets) growing in two contrasting soil water conditions, that is, upper and lower stream banks (U ramets and L ramets, respectively). The objective of the present study was to clarify the physiological and morphological responses of the ramets to soil water conditions. Dry matter allocation to subterranean parts was higher in U ramets than in L ramets. The U ramet leaves survived for approximately 2 months longer than L ramet leaves. The ratio of subterranean part to aerial part dry matter was greater in U ramets than L ramets. Leaf mass per leaf area (LMA) tended to be greater in U ramets than L ramets throughout the growing season. The leaf bulk modulus of elasticity at full hydration was significantly higher in U ramets. Thus, ramet growth patterns and morphological traits varied with changing soil water conditions. The greater longevity of U ramet leaves may play a role in compensating for the reduced annual net carbon gain caused by lower photosynthetic activity. U ramets growing in environments with less water availability achieved high water‐use efficiency by a high passive water absorption capacity via a progressed root system and high productivity via longer leaf longevity with higher LMA and elasticity. Therefore, P. yatabei growing along mountain streams could have the ability to colonize the upper bank through higher survivorship based on these traits.
Seed germination of four Jordanian Stipa spp: differences in temperature regimes and seed provenances
Authors: HAMASHA HASSAN R. , HENSEN ISABELL 
Published: August 2009

Abstract Stipa steppes are considered to be an important model ecosystem in arid land ecology owing to their wide geographical distribution and their strong association with human activities. This paper presents data on the seed germination of four Jordanian Stipa species (Stipa capensis, Stipa parviflora, Stipa arabica and Stipa lagascae) that are widespread throughout various phytogeographical regions in Jordan. We studied variation in seed germination under laboratory conditions among populations and under various temperature regimes. There was significant variation in seed germination with temperature in all four species and seed provenance was significant for three out of the four species. The temperature levels that were most suitable for germination varied from low (8/4°C and 20/10°C) for S. lagascae to high (20/10°C and 32/20°C) for S. capensis; S. arabica and S. parviflora germinated equally well at all three temperature regimes. Variations among populations were species specific, but populations with the highest seed germination were always of arid and Saharan Mediterranean origin. Thus, seed germination was negatively correlated with annual precipitation. Such flexibility among temperatures and populations could be interpreted as an efficient survival strategy for species growing under unpredictable environmental conditions. Where artificial reseeding is necessary, differences among species and also among different seed provenances should be taken into account.
Fatigue‐relevant stress field parameters of welded lap joints: pointed slit tip compared with keyhole notch
Authors: LAZZARIN P. , BERTO F. , RADAJ D. 
Published: August 2009

ABSTRACTThe notch stress intensity factor (NSIF) based analytical frame is applied to the slit tips (or weld roots) of welded joints with inclusion of the T‐stress component. This T‐stress can be determined from FE models evaluating the ligament stresses close to the pointed slit tip. An alternative analytical frame is presented for the corresponding keyhole notches based on analytical solutions from the literature, which are applied to the ligament stresses.In the slit tip models, the mean local strain energy density (SED) with inclusion of the T‐stress effect is determined analytically and numerically in comparison, using two different fatigue‐relevant control radii, R0= 0.28 mm and R0= 0.15 mm, the former value well proven for thick‐sheet welded joints made of structural steel. The latter smaller value is tentatively proposed for thin‐sheet welded joints, in the direction suggested in the recent literature where a reduction of the microstructural support length for laser beam welds and resistance spot welds is recommended. The FEM‐based and analytical stress concentration factors (SCF) for the lap joint keyhole model and also the SED values for the corresponding pointed slit tips are found to be in good agreement. The J‐integral consisting of the first and second component (the latter containing the T‐stress) is compared with the corresponding SED values.
Global patterns in belowground communities
Authors: Fierer Noah , Strickland Michael S. , Liptzin Daniel , Bradford Mark A. , Cleveland Cory C. 
Published: August 2009

AbstractAlthough belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta‐analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome‐level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6–1.1% of soil organic carbon (r2 = 0.91) and 1–20% of total plant biomass carbon (r2 = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.