bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secular variations in seawater chemistry controlling dolomitization in shallow reflux systems: insights from reactive transport modelling
Authors: Gabellone Tatyana , Whitaker Fiona 
Published: December 2015

AbstractDolomitization often plays a critical role in the pore network development of platform carbonates, with implications for reservoir quality distribution. Understanding both the hydrological system driving dolomitization and the chemistry of the fluids involved is fundamental to constrain predictions of the geometry and the petrophysical properties of dolomite bodies. Here, the role of secular variations in seawater Mg/Ca as a control on dolomitization and early porosity modification was evaluated using one‐dimensional reactive transport models and fluids based on modern (aragonite sea), Mississippian and Aptian (calcite sea) seawaters. The sensitivity of dolomitization to a range of extrinsic controls (brine salinity, temperature, fluid flow rate and pCO2) and to intrinsic reactivity of the sediments (effective reactive surface area) was also explored. Simulations suggest faster calcite replacement by dolomite for seawaters with higher Mg/Ca, indicating that dolomitization potential is determined more by Mg/Ca rather than saturation index. Increasing evaporative concentration enhances reaction rate independent of the effect of enhanced density‐driven fluid flux. In addition to brine composition, effective surface area of precursor sediments and temperature exert a critical control on replacement rate, while secular variations of pH and carbonate alkalinity associated with changes in pCO2 are only secondary controls. Above flow rates of 0·01 m yr−1 replacive dolomitization is reaction‐limited rather than flux limited, favouring alteration of fine‐grained carbonates and suggesting that preferential alteration of grainstone units is rare unless head gradients are low. Post‐replacement dolomite cementation is flux dependent, and thus favoured in areas of high head gradient and high permeability sediments and, contrary to replacement, supersaturation is a more important driver than Mg/Ca. While uncertainties remain regarding low‐temperature dolomitization kinetics, the capability of numerical simulations to decouple individual controls provides new insights which can be used, in conjunction with traditional comparative sedimentology, to generate more rigorous conceptual models for individual reservoir settings.
Pre‐Cenomanian vs. Cenozoic folding in the High Atlas revealed by palaeomagnetic data
Authors: Torres‐López Sara , Casas Antonio M. , Villalaín Juan José , El Ouardi Hamidou , Moussaid Bennacer 
Published: December 2015

AbstractPalaeomagnetic data, and specifically remagnetizations, are used to constrain the geometric reconstruction at 100 Ma of three anticlines cored by gabbroic intrusions and Triassic shales in the Central High Atlas, Morocco. Previous palaeomagnetic results have revealed that the Mesozoic sediments of this region acquired a pervasive remagnetization at the end of the Early Cretaceous. The restoration of palaeomagnetic vectors to the remagnetization stage (100 Ma) allows us to determine the dip of the beds during this period and, thereby, to reconstruct structures during that time and determine the relative contributions of Mesozoic magmatic/diapiric uplift vs. Cenozoic compression to the present‐day dip. Our results indicate that three major anticlines in the Central High Atlas (Tasraft, Tassent and Tissila) were initiated to different degrees before the Late Cretaceous and were reactivated during Cenozoic compression to acquire their present‐day geometry. We also discuss the origin of these structures.
A versatile Multisite Gateway‐compatible promoter and transgenic line collection for cell type‐specific functional genomics in Arabidopsis
Authors: Marquès‐Bueno Maria Mar , Morao Ana K. , Cayrel Anne , Platre Matthieu P. , Barberon Marie , Caillieux Erwann , Colot Vincent , Jaillais Yvon , Roudier François , Vert Grégory 
Published: December 2015

SummaryMulticellular organisms are composed of many cell types that acquire their specific fate through a precisely controlled pattern of gene expression in time and space dictated in part by cell type‐specific promoter activity. Understanding the contribution of highly specialized cell types in the development of a whole organism requires the ability to isolate or analyze different cell types separately. We have characterized and validated a large collection of root cell type‐specific promoters and have generated cell type‐specific marker lines. These benchmarked promoters can be readily used to evaluate cell type‐specific complementation of mutant phenotypes, or to knockdown gene expression using targeted expression of artificial miRNA. We also generated vectors and characterized transgenic lines for cell type‐specific induction of gene expression and cell type‐specific isolation of nuclei for RNA and chromatin profiling. Vectors and seeds from transgenic Arabidopsis plants will be freely available, and will promote rapid progress in cell type‐specific functional genomics. We demonstrate the power of this promoter set for analysis of complex biological processes by investigating the contribution of root cell types in the IRT1‐dependent root iron uptake. Our findings revealed the complex spatial expression pattern of IRT1 in both root epidermis and phloem companion cells and the requirement for IRT1 to be expressed in both cell types for proper iron homeostasis.
Engraftment for CD34 selected stem cell products is not compromised by cryopreservation
Authors: Reich‐Slotky Ronit , Bachegowda Lohith S. , Ancharski Michael , Gergis Usama , van Besien Koen , Cushing Melissa M. 
Published: December 2015

BACKGROUNDThe coinfusion of haploidentical CD34+ selected peripheral blood stem cell products with umbilical cord blood (UCB) provides early neutrophil recovery, long‐term UCB engraftment, and a lower incidence of graft‐versus‐host disease; however, this complex transplant presents a scheduling challenge for both the cellular therapy laboratory and the clinical team. Cryopreservation of the haploidentical product can facilitate scheduling, but has been previously shown to be associated with infusion reactions and delayed platelet (PLT) engraftment in allogeneic hematopoietic progenitor cell transplant.STUDY DESIGN AND METHODSTo test whether cryopreservation of the CD34+ selected product compromises the graft, we compared neutrophil and PLT engraftment kinetics for patients receiving freshly infused or cryopreserved products. Seventy‐two products collected from haploidentical related donors were CD34+ selected and infused in a combined transplant with UCB: 32 were cryopreserved before infusion and 40 were infused fresh.RESULTSNo adverse infusion events were reported in either group and there was no difference in neutrophil and PLT engraftment time between fresh and cryopreserved products.CONCLUSIONCryopreservation of a CD34+‐selected product can be safely used in a combined transplant with UCB and does not affect engraftment time.
SCLERACTINIAN CORAL RECRUITMENT DENSITY IN COASTAL WATER OF BALOK, PAHANG, MALAYSIA
Authors: Rani Mohd Husaini , Saad Shahbudin , Akmal Khodzari Mohd Fikri , Ramli Rafindde , Yusof Muhamad Hamizan 
Published: December 2015

Study on scleractinian coral recruitment is important in understanding the mechanisms that regulate their population and the resilience of coral reef communities to disturbance. This study aims to investigate temporal recruitment density of scleractinian coral at selected remote area in Balok, Pahang. Two types of settlement plates, which are terra-cotta tiles and artificial reef, were deployed at three stations to determine the recruitment density. The retrieval of the settlement plate was done at every three months interval started from March to September 2014. A total of 159 coral recruits were counted with mean recruitment densities on both terracotta tiles was 1.52 ± 0.65 and artificial reef plate was 4.37 ± 1.84 respectively. Recruitment was dominated by Platygyra (36%) followed by Porites (32%), Fungia (17%), Turbinaria (7%), Acropora (2%), Stylopora (2%), Montipora (1%), Leptoria (1%), Favites (1%) and Echinophyllia (1%). Kruskal - Wallis ANOVA test shown that recruitment densities varied significantly with plate’s orientation (p < 0.05), but not with sampling stations, type of substrates and month retrieval. Artificial reef plate has better recruitment densities compared to terra-cotta tiles. Coral spat settlement and recruitment patterns were consistent with adult coral distributions. The percentage cover of adult coral varied within the three stations. A total of 33 coral genera from 13 families were recorded during coral video transect survey with Station 3 showed the highest H’ (2.35). Meanwhile, Station 2 showed higher EH’ indexes with 0.82. Therefore, results of this study is important because coral recruitment pattern reflect its adult coral population, and if it closely monitored and harvested sustainably, the survival of parent population could be increased for successful breeding.
ISOLATION OF THERMOTOLERANT BACTERIA PRODUCING FIBRINOLYTIC ENZYME
Authors: Ab. Shukor Nurul Aqilah , Amid Azura , Ismail Mohamed , Abd Samad Nadiah Syuhada 
Published: December 2015

Fibrinolytic enzymes were widely used in the treatment of cardiovascular diseases. However, the efficiency of the commercial enzymes are still lack of perfection because there are many side effects as well as not tolerant to downstream processing such as heat sensitive during spray drying process. Therefore, this study presents newly isolated thermophiles bacteria producing fibrinolytic enzyme. Sample was collected from Hot Spring Selayang at Selayang Selangor. Spread plate agar containing skim milk powder growth at pH 7, 53 for 24 hours was utilized to isolate thermotolerant bacteria producing protease. Further isolation on bacteria producing fibrinolytic enzyme was carried out using fibrin plate. 16S rDNA gene sequence analysis was used to identify the genotype of the isolates. 27 colonies of thermotolerant bacteria were isolated, however, only 19 of them showing proteolytic activity. All of the 19 isolates are motile and cocci in shapes, with 4 types of arrangement, which are single, diplo (pair), strepto (chain) and staphylo (cluster). HSP04 and HSP11 are gram positive bacteria and others are gram negative. From 19 isolates only 6 were chosen for further analysis. HSP23 showed the highest fibrinolytic activity compared with others. HSP23 was identified as Bacillus licheniformis with 98 % similarity to Bacillus licheniformis DCM 13 and Bacillus licheniformis strain ATCC 14580.
Pulse-Dose Radiofrequency in Athletic Pubalgia: Preliminary Results
Authors: Masala Salvatore , Fiori Roberto , Raguso Mario , Ojango Christine , Morini Marco , Cuzzolino Alessandro , Calabria Eros , Simonetti Giovanni 
Published: December 2015

Context:Chronic pubalgia affects around 10% of athletes.Objective:To determine the role of pulse-dose radiofrequency (PDRF) in athletes with chronic pubalgia and investigate the causes with imaging.Design:Prospective nonrandomized single-group study.Patients:PDRF was performed on 32 patients with a chronic pain that had been refractory to conservative therapies during the last 3 mo.Intervention:The genital branches of the genitofemoral, ilioinguinal, and iliohypogastric nerves and the obturator nerve were the goals of treatment. A 10-cm, 20-gauge cannula was inserted with a percutaneous access on the upper and lower edges of the iliopubic branch. After the spindle was removed, a radiofrequency needle with a 10-mm “active tip” was inserted. The radiofrequency technique was performed with 1200 pulses at 45 V and 20-ms duration, followed by a 480-ms silent phase.Main Outcome Measures:The follow-up with a clinical examination was performed at 1, 3, 6, and 9 mo after the procedure. During the follow-up visits, the patients were asked to rate their pain on a 0–10 VAS scale.Results:All of the enrolled patients completed the study. Mean VAS score before the treatment was 8.4 ± 0.6. Twenty-four patients had a reduction of pain VAS scores more than 50% during all follow-up visits and started training and physiotherapy in the days after the radiofrequency procedure. Six patients, each treated 2 times, had a reduction more than 50% of VAS scores and could start training and physiotherapy only after the 2nd procedure. One patient had no pain relief with 2 treatments. Pain intensity decreased up to 9 mo in 31 patients (mean VAS scores 3.4 ± 0.5 at 6 mo and 3.8 ± 0.9 at 9 mo). No complications were observed.Conclusions:PDRF is an effective and safe technique in management of chronic pubalgia in athletes.
Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs
Authors: Jimenez-Infante Francy , Ngugi David Kamanda , Vinu Manikandan , Alam Intikhab , Kamau Allan Anthony , Blom Jochen , Bajic Vladimir B. , Stingl Ulrich 
Published: December 2015

ABSTRACT

The OM43 clade within the family
Methylophilaceae
of
Betaproteobacteria
represents a group of methylotrophs that play important roles in the metabolism of C
1
compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.
Multiple Posttranslational Modifications of Leptospira biflexa Proteins as Revealed by Proteomic Analysis
Authors: Stewart Philip E. , Carroll James A. , Olano L. Rennee , Sturdevant Daniel E. , Rosa Patricia A. 
Published: December 2015

ABSTRACT

The saprophyte
Leptospira biflexa
is an excellent model for studying the physiology of the medically important
Leptospira
genus, the pathogenic members of which are more recalcitrant to genetic manipulation and have significantly slower
in vitro
growth. However, relatively little is known regarding the proteome of
L. biflexa
, limiting its utility as a model for some studies. Therefore, we have generated a proteomic map of both soluble and membrane-associated proteins of
L. biflexa
during exponential growth and in stationary phase. Using these data, we identified abundantly produced proteins in each cellular fraction and quantified the transcript levels from a subset of these genes using quantitative reverse transcription-PCR (RT-PCR). These proteins should prove useful as cellular markers and as controls for gene expression studies. We also observed a significant number of
L. biflexa
membrane-associated proteins with multiple isoforms, each having unique isoelectric focusing points.
L. biflexa
cell lysates were examined for several posttranslational modifications suggested by the protein patterns. Methylation and acetylation of lysine residues were predominately observed in the proteins of the membrane-associated fraction, while phosphorylation was detected mainly among soluble proteins. These three posttranslational modification systems appear to be conserved between the free-living species
L. biflexa
and the pathogenic species
Leptospira interrogans
, suggesting an important physiological advantage despite the varied life cycles of the different species.
Enhancement of Swimming Speed Leads to a More-Efficient Chemotactic Response to Repellent
Authors: Karmakar Richa , Uday Bhaskar R. V. S. , Jesudasan Rajesh E. , Tirumkudulu Mahesh S. , Venkatesh K. V. 
Published: December 2015

ABSTRACT

Negative chemotaxis refers to the motion of microorganisms away from regions with high concentrations of chemorepellents. In this study, we set controlled gradients of NiCl
2
, a chemorepellent, in microchannels to quantify the motion of
Escherichia coli
over a broad range of concentrations. The experimental technique measured the motion of the bacteria in space and time and further related the motion to the local concentration profile of the repellent. Results show that the swimming speed of bacteria increases with an increasing concentration of repellent, which in turn enhances the drift velocity. The contribution of the increased swimming speed to the total drift velocity was in the range of 20 to 40%, with the remaining contribution coming from the modulation of the tumble frequency. A simple model that incorporates receptor dynamics, including adaptation, intracellular signaling, and swimming speed variation, was able to qualitatively capture the observed trend in drift velocity.
Markerless Gene Deletion with Cytosine Deaminase in Thermus thermophilus Strain HB27
Authors: Wang Lei , Hoffmann Jana , Watzlawick Hildegard , Altenbuchner Josef 
Published: December 2015

ABSTRACT

We developed a counterselectable deletion system for
Thermus thermophilus
HB27 based on cytosine deaminase (encoded by
codA
) from
Thermaerobacter marianensis
DSM 12885 and the sensitivity of
T. thermophilus
HB27 to the antimetabolite 5-fluorocytosine (5-FC). The deletion vector comprises the pUC18 origin of replication, a thermostable kanamycin resistance marker functional in
T. thermophilus
HB27, and
codA
under the control of a constitutive putative trehalose promoter from
T. thermophilus
HB27. The functionality of the system was demonstrated by deletion of the
bglT
gene, encoding a β-glycosidase, and three carotenoid biosynthesis genes,
CYP175A1
,
crtY
, and
crtI
, from the genome of
T. thermophilus
HB27.
Meta-analysis of the effectiveness of traditional Chinese herbal formula Zhen Wu Decoction for the treatment of hypertension
Authors: Xiong Xingjiang , Wang Pengqian , Li Shengjie 
Published: December 2015

ObjectivesZhen Wu Decoction (ZWD), a famous classic herbal formula documented in traditional Chinese medicine (TCM), is widely available in China for treating hypertensive patients with kidneyyangdeficiency and fluid retention syndrome. This systematic review aims to evaluate the effectiveness and safety of ZWD for hypertension.MethodsCochrane Central Register of Controlled Trials, PubMed, Embase, the Chinese National Knowledge Infrastructure, the Chinese Scientific Journal Database, the Chinese Biomedical Literature Database, and the Wanfang Database were searched from their inception to November 2014. Randomised controlled trials of ZWD used alone or in combination with antihypertensive drugs against placebo, no intervention or antihypertensive drugs in hypertensive patients were identified. Two assessors independently reviewed each trial. The Cochrane risk of bias assessment tool was used for quality assessment.ResultsSeven trials involving 472 hypertensive patients were identified. Compared with antihypertensive drugs, ZWD showed no significant effects in lowering blood pressure (BP) (n=177; risk ratio (RR) 1.06; 95% CI 0.87 to 1.28; p=0.58); however, ZWD plus antihypertensive drugs (ZPAD) significantly lowered systolic BP (n=80; weighted mean difference (WMD) −14.00 mm Hg, 95% CI −18.84 to −9.16 mm Hg; p<0.00001), diastolic BP (n=80; WMD −8.00 mm Hg, 95% CI −11.35 to −4.65 mm Hg; p<0.00001), and BP (n=215; RR 1.21, 95% CI 1.08 to 1.37; p=0.001). TCM symptoms and syndromes were significantly improved by either ZWD (n=177; RR 1.58, 95% CI 1.28 to 1.95; p<0.0001) or ZPAD (n=215; RR 1.30, 95% CI 1.14 to 1.49; p=0.0001). Adverse effects were not reported.ConclusionsThis systematic review revealed no definite conclusion about the application of ZWD for hypertension due to the poor methodological quality, high risk of bias, and inadequate reporting on clinical data. More rigorously designed trials, especially addressing continuous BP and adverse effects, are warranted.
Alcohol consumption and mortality in patients with mild Alzheimer's disease: a prospective cohort study
Authors: Berntsen Sine , Kragstrup Jakob , Siersma Volkert , Waldemar Gunhild , Waldorff Frans Boch 
Published: December 2015

ObjectiveTo investigate the association between alcohol consumption and mortality in patients recently diagnosed with mild Alzheimer's disease (AD).DesignA post hoc analysis study based on a clinical trial population.SettingThe data reported were collected as part of the Danish Alzheimer's Intervention Study (DAISY), a longitudinal multicentre randomised controlled study on the efficacy of psychosocial intervention in patients with mild AD across five county districts in Denmark.Participants321 patients with mild AD (Mini-Mental State Examination ≥20) were included. Data regarding current daily alcohol consumption were obtained from the patient's primary caregivers at inclusion.Main outcomeAll-cause mortality retrieved from The Danish Civil Registration System over a period of 36 months after baseline.ResultsInformation about alcohol consumption was obtained from all 321 study participants: 8% were abstinent, 71% only had alcohol occasionally (1 or <1 unit/day), 17% had 2–3 units/day and 4% had more than 3 units/day. An analysis adjusted for a range of potential confounders demonstrated a reduced mortality for patients with moderate alcohol consumption (2–3 units/day): HR 0.23 (95% CI (0.08 to 0.69)) compared with patients who had 1 or <1 unit/day. Mortality was not significantly different in abstinent patients or in patients with an alcohol consumption of more than 3 units/day, compared with patients drinking 1 or <1 unit/day.ConclusionsIn this cohort of patients with mild AD, moderate alcohol consumption (2–3 units/day) was associated with a significantly lower mortality over a period of 36 months. Further studies are needed in this area. These may especially focus on the association between alcohol consumption and cognitive decline in patients with AD.