bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Alternate Perspective on the Opening and Closing of the Intracratonic Purana Basins in Peninsular India
Authors: Basu Abhijit , Bickford M. E. 
Published: May 2015

Abstract
Purana basins in India are Proterozoic in age, filled with mostly marine, deltaic, and fluvial sediments, with some alluvial fan deposits in the basin margins. The basin fill is largely undeformed and unmetamorphosed, and the basins occur in many shallow (&lt;5 km), large and small depressions in the Archean-Paleoproterozoic cratons in peninsular India. An understanding of the reasons for the opening and closing of these intracratonic basins is elusive, far more so than that of the better-studied Phanerozoic intracratonic basins in the world. On the basis of meager, but robust new data, published in this century on the Purana basins and their host cratons’ lithostratigraphy, paleomagnetism, seismic images, geochronology, and paleontology, we propose a scenario of their opening and closing related to the assembly and disassembly of the supercontinents Kenorland, Columbia, and Rodinia.
The Marwar and the Bundelkhand cratons occur in the western and northern Indian blocks, respectively. The southern Indian Block consists of the Singhbhum, Bastar, Eastern Dharwar, and Western Dharwar cratons; these had amalgamated by ca. 2.5 Ga, but split and re-amalgamated along the western margin of the Bastar craton ca. 1.6 Ga. These three blocks, and East Antarctica, were assembled ca. 1000 Ma along the Aravalli-Delhi Fold Belt, Central Indian Tectonic Zone, and the Eastern Ghats Mobile Belt, as part of Rodinia.
There are three sets of Purana basins. The oldest set (Papaghni-Chitravati; Kaladgi-Badami; Lower Vindhyan; Gwalior-Bijawar-Sonrai) opened diachronously after 2.0 Ga and closed by 1.55 Ga. Others (Chhattisgarh; Indravati; Khariar; Ampani; Albaka; Mallampalli; Kurnool; Bhima; etc.) opened after the 1.6 Ga amalgamation event in the southern Indian block, and closed shortly after the 1000 Ma collision of East Antarctica with India. In the northern Indian block, the upper Vindhyan basin likely opened after 1.4 Ga. Sedimentation lingered in some of these basins for some time after 1000 Ma but ceased at the latest by 900 Ma. The Marwar basin in the western Indian block opened ca. 750 Ma, after the emplacement of the Malani Igneous Suite, and sedimentation ceased by 520 Ma, before the Cambrian Explosion.
We propose that the three crustal blocks were largely separate between ca. 2.0 and 1.0 Ga but may have collided with and separated from each other from time to time. Minor fracturing in the cratons, entirely within the crust, caused them to have uneven topography. The resulting depressions were filled with sediments as sea level rose; they sagged under the sediment load and as a result of far-field effects of packing and unpacking of large landmasses (Kenorland, Columbia, and Rodinia). Ensuing dynamic topography and sea level fluctuations gave rise to the opening and closing of the Purana basins and their sediment fills.
Mineral Magnetic Characterization of the Godavari River and Western Bay of Bengal Sediments: Implications to Source to Sink Relations
Authors: Kulkarni Y. R. , Sangode S.J. , Bloemendal J. , Meshram D. C. , Suresh N. 
Published: May 2015

Abstract
Godavari Drainage Basin (GDB) represents the largest Peninsular source of sediment flux into the Bay of Bengal. Mineral magnetic measurements are carried out on the GDB sediments along with the surface sediment cores from the adjoining western Bay of Bengal to explore the relationship between the two. The sediments from Godavari river transact shows varied floodplain to bed load composition with the former dominated by unimodal soft ferrimagnetic, Deccan basalt source. Whereas, the bed load show polymodal composition of mixed nature dominated by silici-clastic sediments derived from the Precambrian granites and Proterozoic sequences. The surface sediment cores (~100-300 cm) from the Bengal fan region off the Godavari delta broadly display an increasing trend in ferrimagnetic mineralogy towards top. Based on mineral magnetism the ferri- and para-magnetic susceptibilities are assigned to the basaltic and siliciclastic sources, respectively which also represents the low and high rain fall zones. The increasing upwards trend of the ferrimagnetic minerals in the western Bay of Bengal sediments, therefore, can be related to the predominance of basaltic source over the siliciclastic/cratonic source from the GDB. These controls of magnetic susceptibility in the Bengal fan sediments are assigned to the fluctuation of the two sources as a result of differential weathering in response to monsoonal variability.
Designing and evaluating Brain Powered Games for cognitive training and rehabilitation in at-risk African children
Authors: Giordani B. , Novak B. , Sikorskii A. , Bangirana P. , Nakasujja N. , Winn B. M. , Boivin M. J. 
Published: May 2015

Background.Valid, reliable, accessible, and cost-effective computer-training approaches can be important components in scaling up educational support across resource-poor settings, such as sub-Saharan Africa. The goal of the current study was to develop a computer-based training platform, the Michigan State University Games for Entertainment and Learning laboratory's Brain Powered Games (BPG) package that would be suitable for use with at-risk children within a rural Ugandan context and then complete an initial field trial of that package.Methods.After game development was completed with the use of local stimuli and sounds to match the context of the games as closely as possible to the rural Ugandan setting, an initial field study was completed with 33 children (mean age = 8.55 ± 2.29 years, range 6–12 years of age) with HIV in rural Uganda. The Test of Variables of Attention (TOVA), CogState computer battery, and the Non-Verbal Index from the Kaufman Assessment Battery for Children, 2nd edition (KABC-II) were chosen as the outcome measures for pre- and post-intervention testing. The children received approximately 45 min of BPG training several days per week for 2 months (24 sessions).Results.Although some improvements in test scores were evident prior to BPG training, following training, children demonstrated clinically significant changes (significant repeated-measures outcomes with moderate to large effect sizes) on specific TOVA and CogState measures reflecting processing speed, attention, visual-motor coordination, maze learning, and problem solving.Conclusions.Results provide preliminary support for the acceptability, feasibility, and neurocognitive benefit of BPG and its utility as a model platform for computerized cognitive training in cross-cultural low-resource settings.
Hodgepodge Historiography: Documents, Itineraries, and the Absence of Archives
Authors: White Luise 
Published: May 2015

AbstractAfrican historians frequently argue that it is almost impossible to research postcolonial history because of the absence or haphazard nature of African archives. I argue that this is not so much an obstacle to writing the history of Africa after 1960s as it is a complement to it: incomplete and chaotic archives and documents scattered around the globe reveal some of the sloppiness of governmentality and how hit-and-miss statecraft has been in the recent past.
Natural Language Processing for Real-Time Catheter-Associated Urinary Tract Infection Surveillance: Results of a Pilot Implementation Trial
Authors: Branch-Elliman Westyn , Strymish Judith , Kudesia Valmeek , Rosen Amy K. , Gupta Kalpana 
Published: May 2015

BACKGROUNDIncidence of catheter-associated urinary tract infection (CAUTI) is a quality benchmark. To streamline conventional detection methods, an electronic surveillance system augmented with natural language processing (NLP), which gathers data recorded in clinical notes without manual review, was implemented for real-time surveillance.OBJECTIVETo assess the utility of this algorithm for identifying indwelling urinary catheter days and CAUTI.SETTINGLarge, urban tertiary care Veterans Affairs hospital.METHODSAll patients admitted to the acute care units and the intensive care unit from March 1, 2013, through November 30, 2013, were included. Standard surveillance, which includes electronic and manual data extraction, was compared with the NLP-augmented algorithm.RESULTSThe NLP-augmented algorithm identified 27% more indwelling urinary catheter days in the acute care units and 28% fewer indwelling urinary catheter days in the intensive care unit. The algorithm flagged 24 CAUTI versus 20 CAUTI by standard surveillance methods; the CAUTI identified were overlapping but not the same. The overall positive predictive value was 54.2%, and overall sensitivity was 65% (90.9% in the acute care units but 33% in the intensive care unit). Dissimilarities in the operating characteristics of the algorithm between types of unit were due to differences in documentation practice. Development and implementation of the algorithm required substantial upfront effort of clinicians and programmers to determine current language patterns.CONCLUSIONSThe NLP algorithm was most useful for identifying simple clinical variables. Algorithm operating characteristics were specific to local documentation practices. The algorithm did not perform as well as standard surveillance methods.Infect. Control Hosp. Epidemiol. 2015;36(9):1004–1010
Simulating regional climate-adaptive field cropping with fuzzy logic management rules and genetic advance
Authors: PARKER P. , INGWERSEN J. , HÖGY P. , PRIESACK E. , AURBACHER J. 
Published: May 2015

SUMMARYAgriculture is a largely technical endeavour involving complicated managerial decision-making that affects crop performance. Farm-level modelling integrates crop models with agent behaviour to account for farmer decision-making and complete the representation of agricultural systems. To replicate an important part of agriculture in Central Europe a crop model was calibrated for a unique region's predominant crops: winter wheat, winter and spring barley, silage maize and winter rapeseed. Their cultivation was then simulated over multiple decades at daily resolution to test validity and stability, while adding the dimension of agent behaviour in relation to environmental and economic conditions. After validation against regional statistics, simulated future weather scenarios were used to forecast crop management and performance under anticipated global change. Farm management and crop genetics were treated as adaptive variables in the milieu of shifting climatic conditions to allow projections of agriculture in the study region into the coming decades.
Aortic dilatation in patients with Turner’s syndrome without structural cardiac anomaly
Authors: Alami Laroussi Nassiba , Dahdah Nagib , Dallaire Frédéric , Thérien Johanne , Fournier Anne 
Published: May 2015

AbstractIntroductionDilatation of the ascending aorta is described in Turner’s syndrome with variable prevalence (6.8–32%). Reported series typically include patients with associated cardiac anomalies.ObjectiveTo characterise the prevalence, age of onset, and the progress of dilatation of the ascending aorta in Turner’s syndrome patients free of structural cardiac anomalies. Potential risk factors such as karyotype and growth hormone therapy were analysed for correlation with aortic dilatation.MethodsWe carried out a retrospective study with data collected from medical records and echocardiography studies. Patients with Tuner’s syndrome followed-up between 1992 and 2010 with at least two echocardiography studies were eligible. Patients with previous cardiac surgery or under anti-hypertensive medication were excluded. Ascending aorta diameter measurements were adjusted for body surface area, and dilatation was defined as Z-score>2.ResultsThe study population consisted of 44 patients, aged 11.9±7.4 years at the first echocardiogram and 17.9±7.3 years at the last follow-up, with a follow-up duration of 6.0±3.7 years. A total of 13 (29.5%) patients exhibited aortic dilatation during follow-up, suggesting an actuarial estimate of the freedom from aortic dilatation dropping from 86 to 70% and then to 37% at 10, 20, and 30 years of age, respectively. There was no statistically significant impact of karyotype or growth hormone therapy on aortic Z-score progression.ConclusionThe prevalence of dilatation of the ascending aorta in Turner’s syndrome patients free of structural aortic anomalies is comparable with published data with associated lesions. Growth hormone therapy and karyotype had no significant impact; however, longitudinal follow-up is warranted.
Trends in overweight and obesity prevalence in Tuscan schoolchildren (2002–2012)
Authors: Lazzeri Giacomo , Panatto Donatella , Pammolli Andrea , Azzolini Elena , Simi Rita , Meoni Veronica , Giacchi Mariano V , Amicizia Daniela , Gasparini Roberto 
Published: May 2015

AbstractObjectiveThe aim of the present study was to examine the prevalence and time trends in childhood overweight including obesity and obesity among Tuscan children from 2002 to 2012.DesignCross-sectional study at five time points (Tuscan Nutritional Surveillance Surveys conducted in the years of 2002, 2006, 2008, 2010 and 2012). Trained personnel directly measured the height and weight of the subjects. BMI was assessed by means of the International Obesity Task Force (IOTF) and WHO cut-offs.SettingRepresentative sample of children in the Tuscany region (Italy).SubjectsChildren (n7183) aged between 7·5 and 9·5 years (3711 boys and 3472 girls).ResultsWith respect to the estimation of the absolute prevalence level of childhood overweight, a discrepancy was observed between the two criteria. In all surveys, more boys than girls were overweight (including obesity). Trend analysis showed a significant decrease in the prevalence of overweight including obesity and obesity in Tuscan children from 2002 to 2012 (32·0 %v. 25·8 %,P<0·001 on using IOTF criteria and 37·7 %v. 34·3 %,P<0·001 on using WHO criteria for overweight including obesity; and 10·0 %v. 6·7 %,P<0·001 on using IOTF criteria and 12·5 %v. 11·3 %,P=0·035 on using WHO criteria for obesity).ConclusionsThe present study is the first report from an Italian region showing a significant decrease in childhood obesity and overweight in the last 10 years. This reduction is probably a result of regional and local actions that have taken place in many sectors of society. However, efforts should be made to lower the prevalence of childhood obesity and overweight further.
Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism
Authors: Edlund Anna , Yang Youngik , Yooseph Shibu , Hall Adam P , Nguyen Don D , Dorrestein Pieter C , Nelson Karen E , He Xuesong , Lux Renate , Shi Wenyuan , McLean Jeffrey S 
Published: May 2015

Abstract
Dental caries, one of the most globally widespread infectious diseases, is intimately linked to pH dynamics. In supragingival plaque, after the addition of a carbohydrate source, bacterial metabolism decreases the pH which then subsequently recovers. Molecular mechanisms supporting this important homeostasis are poorly characterized in part due to the fact that there are hundreds of active species in dental plaque. Only a few mechanisms (for example, lactate fermentation, the arginine deiminase system) have been identified and studied in detail. Here, we conducted what is to our knowledge, the first full transcriptome and metabolome analysis of a diverse oral plaque community by using a functionally and taxonomically robust in vitro model system greater than 100 species. Differential gene expression analyses from the complete transcriptome of 14 key community members revealed highly varied regulation of both known and previously unassociated pH-neutralizing pathways as a response to the pH drop. Unique expression and metabolite signatures from 400 detected metabolites were found for each stage along the pH curve suggesting it may be possible to define healthy and diseased states of activity. Importantly, for the maintenance of healthy plaque pH, gene transcription activity of known and previously unrecognized pH-neutralizing pathways was associated with the genera Lactobacillus, Veillonella and Streptococcus during the pH recovery phase. Our in vitro study provides a baseline for defining healthy and disease-like states and highlights the power of moving beyond single and dual species applications to capture key players and their orchestrated metabolic activities within a complex human oral microbiome model.
Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants
Authors: Allum Fiona , Shao Xiaojian , Guénard Frédéric , Simon Marie-Michelle , Busche Stephan , Caron Maxime , Lambourne John , Lessard Julie , Tandre Karolina , Hedman Åsa K. , Kwan Tony , Ge Bing ,   The Multiple Tissue Human Expression Resource Consortium, Ahmadi Kourosh R. , Ainali Chrysanthi , Barrett Amy , Bataille Veronique , Bell Jordana T. , Buil Alfonso , Dermitzakis Emmanouil T. , Dimas Antigone S. , Durbin Richard , Glass Daniel , Hassanali Neelam , Ingle Catherine , Knowles David , Krestyaninova Maria , Lindgren Cecilia M. , Lowe Christopher E. , Meduri Eshwar , di Meglio Paola , Min Josine L. , Montgomery Stephen B. , Nestle Frank O. , Nica Alexandra C. , Nisbet James , O'Rahilly Stephen , Parts Leopold , Potter Simon , Sandling Johanna , Sekowska Magdalena , Shin So-Youn , Small Kerrin S. , Soranzo Nicole , Surdulescu Gabriela , Travers Mary E. , Tsaprouni Loukia , Tsoka Sophia , Wilk Alicja , Yang Tsun-Po , Zondervan Krina T. , Rönnblom Lars , McCarthy Mark I. , Deloukas Panos , Richmond Todd , Burgess Daniel , Spector Timothy D. , Tchernof André , Marceau Simon , Lathrop Mark , Vohl Marie-Claude , Pastinen Tomi , Grundberg Elin 
Published: May 2015

AbstractMost genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS.
Targeted mutagenesis in soybean using the CRISPR-Cas9 system
Authors: Sun Xianjun , Hu Zheng , Chen Rui , Jiang Qiyang , Song Guohua , Zhang Hui , Xi Yajun 
Published: May 2015

AbstractGenome editing is a valuable technique for gene function analysis and crop improvement. Over the past two years, the CRISPR-Cas9 system has emerged as a powerful tool for precisely targeted gene editing. In this study, we predicted 11 U6 genes in soybean (Glycine max L.). We then constructed two vectors (pCas9-GmU6-sgRNA and pCas9-AtU6-sgRNA) using the soybean U6-10 and Arabidopsis U6-26 promoters, respectively, to produce synthetic guide RNAs (sgRNAs) for targeted gene mutagenesis. Three genes, Glyma06g14180, Glyma08g02290 and Glyma12g37050, were selected as targets. Mutations of these three genes were detected in soybean protoplasts. The vectors were then transformed into soybean hairy roots by Agrobacterium rhizogenes infection, resulting in efficient target gene editing. Mutation efficiencies ranged from 3.2–9.7% using the pCas9-AtU6-sgRNA vector and 14.7–20.2% with the pCas9-GmU6-sgRNA vector. Biallelic mutations in Glyma06g14180 and Glyma08g02290 were detected in transgenic hairy roots. Off-target activities associated with Glyma06g14180 and Glyma12g37050 were also detected. Off-target activity would improve mutation efficiency for the construction of a saturated gene mutation library in soybean. Targeted mutagenesis using the CRISPR-Cas9 system should advance soybean functional genomic research, especially that of genes involved in the roots and nodules.
Shedding dynamics of Morogoro virus, an African arenavirus closely related to Lassa virus, in its natural reservoir host Mastomys natalensis
Authors: Borremans Benny , Vossen Raphaël , Becker-Ziaja Beate , Gryseels Sophie , Hughes Nelika , Van Gestel Mats , Van Houtte Natalie , Günther Stephan , Leirs Herwig 
Published: May 2015

AbstractArenaviruses can cause mild to severe hemorrhagic fevers. Humans mainly get infected through contact with infected rodents or their excretions, yet little is known about transmission dynamics within rodent populations. Morogoro virus (MORV) is an Old World arenavirus closely related to Lassa virus with which it shares the same host species Mastomys natalensis. We injected MORV in its host and sampled blood and excretions at frequent intervals. Infection in adults was acute; viral RNA disappeared from blood after 18 days post infection (dpi) and from excretions after 39 dpi. Antibodies were present from 7 dpi and never disappeared. Neonatally infected animals acquired a chronic infection with RNA and antibodies in blood for at least 3 months. The quantified excretion and antibody patterns can be used to inform mathematical transmission models and are essential for understanding and controlling transmission in the natural rodent host populations.
A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering
Authors: Roedig P. , Vartiainen I. , Duman R. , Panneerselvam S. , Stübe N. , Lorbeer O. , Warmer M. , Sutton G. , Stuart D. I. , Weckert E. , David C. , Wagner A. , Meents A. 
Published: May 2015

AbstractAt low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.