bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating global trends (1988–2010) in harmonized multi‐satellite surface soil moisture
Authors: Dorigo Wouter , de Jeu Richard , Chung Daniel , Parinussa Robert , Liu Yi , Wagner Wolfgang , Fernández‐Prieto Diego 
Published: August 2012

Global trends in a new multi‐satellite surface soil moisture dataset were analyzed for the period 1988–2010. 27% of the area covered by the dataset showed significant trends (p = 0.05). Of these, 73% were negative and 27% positive. Subtle drying trends were found in the Southern US, central South America, central Eurasia, northern Africa and the Middle East, Mongolia and northeast China, northern Siberia, and Western Australia. The strongest wetting trends were found in southern Africa and the subarctic region. Intra‐annual analysis revealed that most trends are not uniform among seasons. The most prominent trend patterns in remotely sensed surface soil moisture were also found in GLDAS‐Noah and ERA Interim modeled surface soil moisture and GPCP precipitation, lending confidence to the obtained results. The relationship with trends in GIMMS‐NDVI appeared more complex. In areas of mutual disagreement more research is needed to identify potential deficiencies in models and/or remotely sensed products.
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents
Authors: Blaser Martin J , Dominguez-Bello Maria G , Contreras Monica , Magris Magda , Hidalgo Glida , Estrada Isidoro , Gao Zhan , Clemente Jose C , Costello Elizabeth K , Knight Rob 
Published: August 2012

Abstract
The human skin harbors complex bacterial communities. Prior studies showing high inter-individual variation focused on subjects from developed countries. We therefore compared cutaneous bacterial communities of Amerindians in the Venezuelan Amazon with subjects in the United States. Forearm skin specimens were studied from healthy Amerindians in Platanillal village in Amazonas State, and from healthy persons in New York and Colorado. All skin sampling used similar swab/buffer techniques. Multiplexed V2-targeted 16S rRNA gene pyrosequencing yielded high quality sequences from 112 samples. The results show 20 phyla, with three (Proteobacteria, Firmicutes, Actinobacteria) predominating. US residents and Venezuelan Amerindians had significantly different forearm skin bacterial community compositions, with United States dominated by Propionibacterium. Among the Amerindians, there was a deep split based on bacterial community membership, with 30 and 42 samples, respectively, falling into each of the two groups, not associated with age, gender, or body mass index. One Amerindian group had diversity similar to the United States, but was dominated by Staphylococcus rather than Propionibacterium. The other Amerindian group was significantly more diverse and even than the US or the other Amerindian group, and featured a broad range of Proteobacteria. The results provide evidence that ethnicity, lifestyle and/or geography are associated with the structure of human cutaneous bacterial communities.
Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis
Authors: Malmstrom Rex R , Rodrigue Sébastien , Huang Katherine H , Kelly Libusha , Kern Suzanne E , Thompson Anne , Roggensack Sara , Berube Paul M , Henn Matthew R , Chisholm Sallie W 
Published: August 2012

Abstract
Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world’s oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome—that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome.
Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient
Authors: Campbell Barbara J , Kirchman David L 
Published: August 2012

Abstract
Very little is known about growth rates of individual bacterial taxa and how they respond to environmental flux. Here, we characterized bacterial community diversity, structure and the relative abundance of 16S rRNA and 16S rRNA genes (rDNA) using pyrosequencing along the salinity gradient in the Delaware Bay. Indices of diversity, evenness, structure and growth rates of the surface bacterial community significantly varied along the transect, reflecting active mixing between the freshwater and marine ends of the estuary. There was no positive correlation between relative abundances of 16S rRNA and rDNA for the entire bacterial community, suggesting that abundance of bacteria does not necessarily reflect potential growth rate or activity. However, for almost half of the individual taxa, 16S rRNA positively correlated with rDNA, suggesting that activity did follow abundance in these cases. The positive relationship between 16S rRNA and rDNA was less in the whole water community than for free-living taxa, indicating that the two communities differed in activity. The 16S rRNA:rDNA ratios of some typically marine taxa reflected differences in light, nutrient concentrations and other environmental factors along the estuarine gradient. The ratios of individual freshwater taxa declined as salinity increased, whereas the 16S rRNA:rDNA ratios of only some typical marine bacteria increased as salinity increased. These data suggest that physical and other bottom-up factors differentially affect growth rates, but not necessarily abundance of individual taxa in this highly variable environment.
Yersinia pestis infection and laboratory conditions alter flea-associated bacterial communities
Authors: Jones Ryan T , Vetter Sara M , Montenieiri John , Holmes Jennifer , Bernhardt Scott A , Gage Kenneth L 
Published: August 2012

Abstract
We collected Oropsylla montana from rock squirrels, Spermophilus varigatus, and infected a subset of collected fleas with Yersinia pestis, the etiological agent of plague. We used bar-tagged DNA pyrosequencing to characterize bacterial communities of wild, uninfected controls and infected fleas. Bacterial communities within Y. pestis-infected fleas were substantially more similar to one another than communities within wild or control fleas, suggesting that infection alters the bacterial community in a directed manner such that specific bacterial lineages are severely reduced in abundance or entirely eliminated from the community. Laboratory conditions also significantly altered flea-associated bacterial communities relative to wild communities, but much less so than Y. pestis infection. The abundance of Firmicutes decreased considerably in infected fleas, and Bacteroidetes were almost completely eliminated from both the control and infected fleas. Bartonella and Wolbachia were unaffected or responded positively to Y. pestis infection.
A non-B DNA can replace heptamer of V(D)J recombination when present along with a nonamer: implications in chromosomal translocations and cancer
Authors: Nishana Mayilaadumveettil , Raghavan Sathees C. 
Published: August 2012

The RAG (recombination-activating gene) complex is responsible for the generation of antigen receptor diversity by acting as a sequence-specific nuclease. Recent studies have shown that it also acts as a structure-specific nuclease. However, little is known about the factors regulating this activity at the genomic level. We show in the present study that the proximity of a V(D)J nonamer to heteroduplex DNA significantly increases RAG cleavage and binding efficiencies at physiological concentrations of MgCl2. The position of the nonamer with respect to heteroduplex DNA was important, but not orientation. A spacer length of 18 bp between the nonamer and mismatch was optimal for RAG-mediated DNA cleavage. Mutations to the sequence of the nonamer and deletion of the nonamer-binding domain of RAG1 reinforced the role of the nonamer in the enhancement in RAG cleavage. Interestingly, partial mutation of the nonamer did not significantly reduce RAG cleavage on heteroduplex DNA, suggesting that even cryptic nonamers were sufficient to enhance RAG cleavage. More importantly, we show that the fragile region involved in chromosomal translocations associated with BCL2 (B-cell lymphoma 2) can be cleaved by RAGs following a nonamer-dependent mechanism. Hence our results from the present study suggest that a non-B DNA can replace the heptamer of RSS (recombination signal sequence) when present adjacent to nonamers, explaining the generation of certain chromosomal translocations in lymphoid malignancies.
Early Vocabulary Delay and Behavioral/Emotional Problems in Early Childhood: The Generation R Study
Authors: Henrichs Jens , Rescorla Leslie , Donkersloot Cootje , Schenk Jacqueline J. , Raat Hein , Jaddoe Vincent W. V. , Hofman Albert , Verhulst Frank C. , Tiemeier Henning 
Published: August 2012

PurposeThe authors tested associations between (a) parent-reported temporary vs. persistent vocabulary delay and (b) parent-reported behavioral/emotional problems in a sample of 5,497 young Dutch children participating in a prospective population-based study.MethodMothers completed the MacArthur Communicative Development Inventory—Netherlands (Zink & Lejaegere, 2003) at age 18 months and the Language Development Survey (Rescorla, 1989) at age 30 months, with expressive vocabulary delay defined as scores in the lowest 15th age- and gender-specific percentiles. The Child Behavior Checklist (Achenbach & Rescorla, 2000) was completed by mothers when their children were age 18 months and by both parents when their children were age 36 months, from which Internalizing Problems and Externalizing Problems scores were analyzed.ResultsAll analyses were adjusted for covariates. Expressive vocabulary delay at age 18 months was weakly related to Internalizing Problems scores at age 18 months as well as mother-reported Externalizing and Internalizing Problems scores at age 36 months (the latter for boys only). Expressive vocabulary delay at age 30 months was weakly associated with mother-reported Externalizing and Internalizing Problems scores (the latter for boys only) and father-reported Internalizing Problems scores. Persistent expressive vocabulary delay predicted the highest risk of mother-reported internalizing and externalizing problems at age 36 months.ConclusionThis population-based study showed modest associations between vocabulary delay and behavioral/emotional problems detectable from 18 months onward.
Enhancing Communication Through Gesture and Naming Therapy
Authors: Caute Anna , Pring Tim , Cocks Naomi , Cruice Madeline , Best Wendy , Marshall Jane 
Published: August 2012

Purpose
In this study, the authors investigated whether gesture, naming, and strategic treatment improved the communication skills of 14 people with severe aphasia.

Method
All participants received 15 hr of gesture and naming treatment (reported in a companion article [Marshall et al., 2012]). Half the group received a further 15 hr of strategic therapy, whereas the remaining 7 participants received no further input. The effects of therapy on communication were assessed with 2 novel measures. These measures required each participant to convey simple messages and narratives to his or her communication partner. In both assessments, a subset of the stimuli featured items that had been targets in gesture or naming treatment.

Results
Performance on the communication measures was stable over 2 baseline assessments but improved after gesture and naming treatment. Those participants who received additional strategic therapy made further gains on the message but not on the narrative task. Communication gains were not specific to the stimuli featuring trained items.

Conclusions
This study suggests that gesture and naming treatments can benefit interactive communication. The additional benefits of strategic therapy were less clear-cut but did have an impact on the transmission of simple messages. Gains seem to reflect the development of general communication skills rather than the use of trained gestures and/or words.
Word Learning Processes in Children With Cochlear Implants
Authors: Walker Elizabeth A. , McGregor Karla K. 
Published: August 2012

Purpose
To determine whether 3 aspects of the word learning process—fast mapping, retention, and extension—are problematic for children with cochlear implants (CIs).

Method
The authors compared responses of 24 children with CIs, 24 age-matched hearing children, and 23 vocabulary-matched hearing children to a novel object noun training episode. Comprehension and production were measured immediately following training (fast mapping) as well as 1 day later (retention). Extension was measured in terms of the ability of the participants to identify new (untrained) exemplars.

Results
Compared with their hearing age-mates, children with CIs performed marginally more poorly on fast mapping as measured by the comprehension probe and more poorly on retention as measured by comprehension and production probes. The age-mates improved over the retention interval, but the children with CIs did not. Most of the children with CIs performed similarly to their age-mates on extension, but 2 children underextended, and 5 children failed to understand the task. Compared with younger vocabulary-matched peers, children with CIs did not differ at fast mapping, retention, or extension.

Conclusions
Children with CIs demonstrated deficits in word learning, with retention being especially problematic. Their learning did not differ from that of younger children with similarly sized vocabularies.
Childhood Maltreatment and Communication Development
Authors: Hwa-Froelich Deborah 
Published: August 2012

Abstract
Purpose: Maltreatment of children is a common and international problem. The consequences of maltreatment often are misunderstood or unknown. In this article, I will define maltreatment and explore the communication development of children with a history of maltreatment.
I reviewed the literature on children experiencing maltreatment, including articles describing the communication development of children remaining in a maltreating environment, children who were recently removed from maltreatment, children in foster care, and children adopted from orphanages. In each study, I found evidence that children who experienced maltreatment demonstrated lower language performance or poorer social knowledge than children who had not experienced maltreatment.
Conclusion: Children who have experienced abuse and/or neglect are at risk of poorer receptive, expressive, and social language development. I will discuss the clinical implications of this finding.
Rate limit of protein elastic response is tether dependent
Authors: Berkovich Ronen , Hermans Rodolfo I. , Popa Ionel , Stirnemann Guillaume , Garcia-Manyes Sergi , Berne Bruce J. , Fernandez Julio M. 
Published: August 2012

The elastic restoring force of tissues must be able to operate over the very wide range of loading rates experienced by living organisms. It is surprising that even the fastest events involving animal muscle tissues do not surpass a few hundred hertz. We propose that this limit is set in part by the elastic dynamics of tethered proteins extending and relaxing under a changing load. Here we study the elastic dynamics of tethered proteins using a fast force spectrometer with sub-millisecond time resolution, combined with Brownian and Molecular Dynamics simulations. We show that the act of tethering a polypeptide to an object, an inseparable part of protein elasticity in vivo and in experimental setups, greatly reduces the attempt frequency with which the protein samples its free energy. Indeed, our data shows that a tethered polypeptide can traverse its free-energy landscape with a surprisingly low effective diffusion coefficient
D
eff
∼ 1,200 nm
2
/s. By contrast, our Molecular Dynamics simulations show that diffusion of an isolated protein under force occurs at
D
eff
∼ 10
8
nm
2
/s. This discrepancy is attributed to the drag force caused by the tethering object. From the physiological time scales of tissue elasticity, we calculate that tethered elastic proteins equilibrate in vivo with
D
eff
∼ 10
4
–10
6
nm
2
/s which is two to four orders magnitude smaller than the values measured for untethered proteins in bulk.
Parental Effect as a Primary Factor Limiting Egg‐to‐Fry Survival of Spring Chinook Salmon in the Upper Yakima River Basin
Authors: Johnson Christopher L. , Roni Philip , Pess George R. 
Published: August 2012

AbstractFew field estimates of egg‐to‐fry survival of Chinook salmon Oncorhynchus tshawytscha exist, although it is one of the major factors thought to limit freshwater production and recovery of Chinook salmon populations. This is likely due to the challenges of estimating survival at this life stage, which is further complicated by the variety of methods that have been employed. Our study objectives were to (1) develop a method by which spring Chinook salmon egg‐to‐fry survival could be estimated at a large spatial scale, and (2) investigate the primary factors affecting survival in the natural environment. We conducted a field experiment using 81 artificial redds to test our proposed method for evaluating egg‐to‐fry survival at a basin scale and to evaluate the effects of parentage (adult mating), river reach, and fine sediment infiltration on survival in the upper Yakima River basin, Washington. Egg‐to‐fry survival and preemergent Chinook salmon fry developmental stage were significantly different among matings, but were not detectably different among reaches. Fine sediment accumulation in egg boxes from artificial redds was largely below published threshold levels, explained less than 6% of the variation in survival, and was not correlated with developmental stage. In contrast, survival of individual matings in the natural environment and those same matings incubated under controlled hatchery conditions were highly correlated. Our study suggests that in years of low scour and potentially ideal incubation conditions, parental effects play an important role in determining in situ egg‐to‐fry survival, and that extensive replication and tracking of gamete viability is needed to separate parental effects from environmental factors affecting survival. We provide standardized methods for collecting egg‐to‐fry survival data and outline a number of potential biases that should be addressed in future research.
A Marteilia-Like Parasite in Blue Mussels Mytilus edulis in China
Authors: Wang Zhongwei , Lu Xin , Liang Yubo , Zheng Zheng 
Published: August 2012

Abstract
Species of the genus Marteilia (Phylum Paramyxea) are protozoan parasites of marine mollusks. Marteilia spp. have been detected in mollusks from different parts of the world, but the presence of these parasites in China has not been previously reported. Therefore, a survey was conducted to look for the presence of Marteilia spp. in blue mussels Mytilus edulis and Asian green mussels Perna viridis collected along China's coasts. Histological and PCR analyses revealed that 5 of 180 M. edulis (prevalence = 2.8%) were positive for infection with a Marteilia-like organism, whereas the parasite was not detected in any of the 80 P. viridis individuals tested. Total genomic DNA was extracted from the infected tissue sections for PCR amplification. The PCR amplification with Marteilia primers SS1 and SAS1 yielded the expected 641-bp product. Sequencing results showed that the 18S ribosomal RNA gene fragment from the protozoans found in M. edulis from China was 88% similar to that of Marteilia refringens, a species that was reported from M. edulis and European flat oysters Ostrea edulis collected in France. This is the first report of a Marteilia-like organism infecting M. edulis in China.
Received May 9, 2011; accepted March 4, 2012
Xanthogranulomatous Panniculitis of the Head of an Aquarium-Maintained California Moray
Authors: Erlacher-Reid Claire , Tuttle Allison D. , Frasca Salvatore 
Published: August 2012

Abstract
An aquarium-maintained male California moray Gymnothorax mordax had a symmetrical enlargement of the soft tissues of the head dorsal to the cranium for 2 years prior to its death. This individual was anesthetized for radiographic and ultrasonographic examination of the lesion, and blood was collected for plasma biochemical analytes and lipid profiles. Radiographs and ultrasound of the lesion demonstrated a symmetrical and homogeneous soft tissue density that was consistent with adipose tissue. Plasma cholesterol and triglyceride values appeared elevated; therefore, the animal's diet was amended to decrease fat consumption. Triglyceride values decreased after dietary changes were made; however, values for cholesterol, high-density lipoproteins, and low-density lipoproteins fluctuated but remained largely unchanged. Histopathological assessment of the lesion revealed localized xanthogranulomatous inflammation of hypodermal adipose tissue. The etiology of the lesion in this animal was never determined. This paper describes the first documented case of localized xanthogranulomatous panniculitis in a California moray and demonstrates the need for additional research on specific dietary requirements, species-specific physiological differences, and lesions involving the adipose tissue of morays in comparison with other teleost species.
Received September 16, 2011; accepted February 9, 2012
Effect of Trichlorfon on Hepatic Lipid Accumulation in Crucian Carp Carassius auratus gibelio
Authors: Xu WeiNa , Liu WenBin , Shao XianPing , Jiang GuangZhen , Li XianngFei 
Published: August 2012

Abstract
This study evaluated the toxic effects of the organophosphate pesticide trichlorfon on hepatic lipid accumulation in crucian carp Carassius auratus gibelio. Seventy-five fish were divided into five groups (each group in triplicate), and then exposed to 0, 0.5, 1.0, 2.0, and 4.0 mg/L of trichlorfon and fed with commercial feed for 30 d. At the end of the experiment, plasma and hepatic lipid metabolic biochemical status were analyzed. Triglyceride contents were significantly (P &lt; 0.05) increased in liver but decreased in plasma after 1.0, 2.0, and 4.0 mg/L trichlorfon treatments. Plasma insulin contents were markedly (P &lt; 0.05) increased when trichlorfon concentrations were 0.5, 1.0, and 4.0 mg/L. There were no significant differences in hepatic hormone-sensitive lipase contents between the trichlorfon-treated fish and the controls. Hepatic cyclic adenosine 3′, 5′-monophosphate, very-low-density lipoprotein, and apolipoprotein B100 contents were decreased in the fish when trichlorfon concentration was 2.0 mg/L. Furthermore, electron microscope observations showed rough endoplasmic reticulum dilatation and mitochondrial vacuolization in hepatocytes with trichlorfon exposure. On the basis of morphological and physiological evidence, trichlorfon influenced crucian carp hepatic pathways of lipid metabolism and hepatocellular ultrastructure, which resulted in lipid accumulation in the liver.
Received November 28, 2011; accepted February 16, 2012