bluuebunny/crossref_metadata_2025_split huggingface dataset:
China in Copenhagen: Reconciling the “Beijing Climate Revolution” and the “Copenhagen Climate Obstinacy”
Authors: Conrad Björn 
Published: June 2012

AbstractThe contradiction between the astonishing dynamic of China's domestic climate policy agenda and its seemingly tenacious position in international climate negotiations presents a puzzle that, on closer inspection, reveals much about a nation at the crossroads, undecided which way to turn. The alterations in China's political interests connected to the issue of climate change are clearly evident in the domestic policy changes China introduced during previous years. However, China's leadership thus far has remained hesitant to translate this new set of interests fully into a coherent position in the international arena. China's mounting difficulties in reconciling its rapidly changing role on the international stage with its altered domestic situation, as well as its traditional foreign policy interests and principles, undermine its ability to pursue a consistent and effective strategy in international climate negotiations. China's reluctance to redefine its role in the international arena has led to a number of inconsistencies that particularly plagued its position during the Copenhagen conference, adding to the overall non-constructive dynamic of the proceedings that ultimately left China, as everyone else, with empty hands. The Copenhagen negotiations demonstrated that China's leadership will have to address these inconsistencies resolutely if it wants to realize the benefits that international climate cooperation offers.
Electrophysiological Indices of Phonological Impairments in Dyslexia
Authors: Desroches Amy S. , Newman Randy Lynn , Robertson Erin K. , Joanisse Marc F. 
Published: June 2012

Purpose
A range of studies have shown difficulties in perceiving acoustic and phonetic information in dyslexia; however, much less is known about how such difficulties relate to the perception of individual words. The authors present data from event-related potentials (ERPs) examining the hypothesis that children with dyslexia have difficulties with processing phonemic information within spoken words compared to age-matched readers with typical development.

Method

The authors monitored ERPs to auditory words during a simple picture-word matching task. The key manipulation was the inclusion of both matching stimuli and three types of mismatches (cohort, CONE-
comb
; rhyme, CONE-
bone
; and unrelated, CONE-
fox
).

Results
Children with dyslexia showed atypical N400 ERP waveforms to both types of phonological mismatches, but not to phonologically unrelated mismatches, reflecting a relative insensitivity to phonological overlap among auditory words.

Conclusion
The data suggest that children with dyslexia have impairments in integrating phonological information into word-level representations. The results suggest that speech perception difficulties in dyslexia might have consequences for processing auditory words.
What Do Children With Specific Language Impairment Do With Multiple Forms ofDO?
Authors: Rice Mabel L. , Blossom Megan 
Published: June 2012

PurposeThis study was designed to examine the early usage patterns of multiple grammatical functions ofDOin children with and without specific language impairment (SLI). Children’s use of this plurifunctional form is informative for evaluation of theoretical accounts of the deficit in SLI.MethodSpontaneous uses of multiple functions ofDOwere analyzed in language samples from 89 children: 37 children with SLI, ages 5;0–5;6 (years;months); 37 age-equivalent children; and 15 language-equivalent children, ages 2;8–4;10. Proportion correct and types of errors produced were analyzed for each function ofDO.ResultsChildren with SLI had significantly lower levels of proportion correct auxiliaryDOuse compared to both control groups, with omissions of theDOform as the primary error type. Children with SLI had near-ceiling performance on lexicalDOand ellipticalDO,similar to both control groups.ConclusionsPlurifunctionality is not problematic: Children acquire each function ofDOseparately. Grammatical properties of the function, rather than surface properties of the form, dictate whether children with SLI will have difficulty using the word. Overall, these results support the extended optional infinitive account of SLI and the use of auxiliaryDOomissions as part of a clinical marker for SLI.
Modifying Speech to Children Based on Their Perceived Phonetic Accuracy
Authors: Julien Hannah M. , Munson Benjamin 
Published: June 2012

Purpose
The authors examined the relationship between adults' perception of the accuracy of children’s speech and acoustic detail in their subsequent productions to children.

Method
Twenty-two adults participated in a task in which they rated the accuracy of 2- and 3-year-old children’s word-initial /s/ and /∫/ using a visual analog scale (VAS), then produced a token of the same word as if they were responding to the child whose speech they had just rated.

Result
The duration of adults' fricatives varied as a function of their perception of the accuracy of children’s speech: Longer fricatives were produced following productions that they rated as inaccurate. This tendency to modify duration in response to perceived inaccurate tokens was mediated by measures of self-reported experience interacting with children. However, speakers did not increase the spectral distinctiveness of their fricatives following the perception of inaccurate tokens.

Conclusion
These results suggest that adults modify temporal features of their speech in response to perceiving children’s inaccurate productions. These longer fricatives are potentially both enhanced input to children and an error-corrective signal.
Culture of Plains Topminnow in a Pond Constructed for Species Conservation
Authors: Schumann David A , Pasbrig Chelsey A , Koupal Keith D , Hoback W Wyatt 
Published: June 2012

Abstract
The plains topminnow Fundulus sciadicus appears to be experiencing reductions in geographic range and local abundance, which has led to regional protection throughout its native range. Conservation of this species may require introductions to reestablish populations at known historic locations. Therefore, a pond was constructed during September 2007 to house a refuge population of plains topminnow in Nebraska. A total of 123 plains topminnow were stocked into the pond in two stocking events during 2008. Plains topminnow populations were sampled throughout 2008 and mark–recapture population estimates were conducted after reproductive events during 2009 and 2010 resulting in estimates of 9,844 ± 1,698 (mean ± SD) and 3,974 ± 452 plains topminnow, respectively. Mean fish weight was used as an estimate of pond biomass, which was 28.4 kg/ha in 2009 and 44.9 kg/ha in 2010. Reproduction was first observed in 2008 and in each following year, and a strong year-class was produced in 2009, which suggested there were factors that limited reproduction in the other 2 years. Extensive culture may be an effective way to rear plains topminnow and related species. However, more research is needed to determine factors that affect year-class strength and production.
Evaluation of Plant and Animal Protein Sources as Partial or Total Replacement of Fish Meal in Diets for Nile Tilapia Fry and Juvenile Stages
Authors: Thompson Kenneth R , Velasquez Alejandro , Patterson Joshua T , Metts Linda S , Webster Carl D , Brady Yolanda J , Gannam Ann L , Twibell Ron G , Ostrand Susan L 
Published: June 2012

Abstract
Two feeding trials were conducted in a closed system with Nile tilapia Oreochromis niloticus fry (mean weight, 0.10 g; experiment 1) and juveniles (mean weight, 2.84 g; experiment 2) to examine the effects of total replacement of fish meal (FM), with and without supplementation of dl-methionine (Met) and l-lysine (Lys), by plant protein sources. In experiment 1, fry were fed nine isoenergetic (available energy [AE] = 4.0 kcal/g of diet) and isoproteic (40% protein as fed basis) practical diets containing protein primarily from soybean meal (SBM), with and without essential Met and Lys. After 5 weeks, final individual weight (FW; g/fish) and percent weight gain (PWG) of fry fed diet 1 (control with 20% FM) was significantly higher (P &lt; 0.05) compared with fry fed all other diets, while fry fed diet 9 containing 46% SBM and 22% feed-grade poultry by-product meal PBM) was significantly higher than all other diets (diets 2–8). Quantity of diet fed and percent survival did not differ significantly (P &gt; 0.05) among all diets. In experiment 2, juveniles were fed six isoenergetic (AE = 4.0 kcal/g of diet) and isoproteic (35% protein as fed basis) practical diets containing protein primarily from SBM, soybean protein concentrate (SPC), feed-grade PBM, or combinations of those. After 7 weeks, mean FW, PWG, and amount of diet fed for fish fed diets 1 (control with 20% FM) and 6 (with 20% SPC and 20% PBM) were significantly higher (P &lt; 0.05) compared with juveniles fed all other diets. Feed conversion ratio (FCR) was similar among treatments, but fish fed diet 5 (with 36% SPC and 0% FM) recorded the highest FCR value. Likewise, protein efficiency ratio (PER) was similar among treatments; however, PER in juveniles fed diets 3 (with 52% SBM and 0% FM) and 5 were significantly lower than in fish fed all other diets. Overall, no significant (P &gt; 0.05) difference was found in percent survival, which averaged 92.6% among all diets fed. These data suggest that Nile tilapia fry cannot utilize diets containing high levels (&gt;75%) of SBM when no animal protein ingredient is added, even with supplemental Met and Lys. However, a diet containing 20% SPC and 20% feed-grade PBM appears to be suitable for juvenile Nile tilapia, which may help reduce diet costs and allow for sustainable production.
Evaluation of Off-Flavor in Pond-Raised Channel Catfish following Partial Crop Harvest
Authors: Schrader Kevin K , Tucker Craig S 
Published: June 2012

Abstract
Ponds used to raise channel catfish Ictalurus punctatus in the southeastern United States often contain more food-sized catfish than processors can accept at one time. Fish remaining after initial harvest are returned to the pond and harvested again as soon as possible based upon processor demands. Some catfish farmers report that catfish crops initially declared “on-flavor” appear to develop off-flavors soon after the first harvest, which postpones harvest of the remaining population and delays subsequent production. We conducted a 9-month study on a commercial catfish farm in northwest Mississippi to determine whether fish systematically develop off-flavors after partial fish harvest and, if so, the type and origin of the flavor. Channel catfish and water samples were obtained from 12 ponds before initial harvest and then at intervals for 2 weeks after harvest. Water and catfish fillet samples were analyzed for geosmin and 2-methylisoborneol (MIB). Phytoplankton were identified and counted microscopically. Catfish fillets were also used in sensory analysis to determine quality and intensity of off-flavor. In most ponds, MIB levels decreased or remained unchanged in pond water after the first seining while geosmin levels remained very low (&lt;10 ng/L) in all ponds. Analysis indicated that mean MIB concentrations in catfish fillets either decreased or were unchanged after the initial harvest. Similar results were found for geosmin concentrations in catfish fillets. There was also no systematic change in fillet flavor quality as determined by sensory analysis. The MIB-producing cyanobacterium Planktothrix perornata was found in only three ponds, and the abundance of P. perornata decreased in two ponds after initial harvest and transiently increased in the third pond. Overall, we found no systematic changes in fish flavor quality after partial fish harvest and no indication that harvest activities changed ecological conditions that would cause an increase in odor-producing cyanobacteria.
GO-Elite: a flexible solution for pathway and ontology over-representation
Authors: Zambon Alexander C. , Gaj Stan , Ho Isaac , Hanspers Kristina , Vranizan Karen , Evelo Chris T. , Conklin Bruce R. , Pico Alexander R. , Salomonis Nathan 
Published: June 2012

Abstract
Summary: We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. The results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application.
Availability: http://www.genmapp.org/go_elite
Contact: nsalomonis@gladstone.ucsf.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
Authors: Habegger Lukas , Balasubramanian Suganthi , Chen David Z. , Khurana Ekta , Sboner Andrea , Harmanci Arif , Rozowsky Joel , Clarke Declan , Snyder Michael , Gerstein Mark 
Published: June 2012

Abstract
Summary: The functional annotation of variants obtained through sequencing projects is generally assumed to be a simple intersection of genomic coordinates with genomic features. However, complexities arise for several reasons, including the differential effects of a variant on alternatively spliced transcripts, as well as the difficulty in assessing the impact of small insertions/deletions and large structural variants. Taking these factors into consideration, we developed the Variant Annotation Tool (VAT) to functionally annotate variants from multiple personal genomes at the transcript level as well as obtain summary statistics across genes and individuals. VAT also allows visualization of the effects of different variants, integrates allele frequencies and genotype data from the underlying individuals and facilitates comparative analysis between different groups of individuals. VAT can either be run through a command-line interface or as a web application. Finally, in order to enable on-demand access and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment.
Availability and Implementation: VAT is implemented in C and PHP. The VAT web service, Amazon Machine Image, source code and detailed documentation are available at vat.gersteinlab.org.
Contact: lukas.habegger@yale.edu or mark.gerstein@yale.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
The Enduring Legacy of the Turing Machine
Authors: Fortnow Lance 
Published: June 2012

Abstract
The Church-Turing thesis has stood the test of time, capturing computation models Turing could not have conceived of, including digital computation, probabilistic, parallel and quantum computers and the Internet. The thesis has become accepted doctrine in computer science and the ACM has named its highest honor after Turing. Many now view computation as a fundamental part of nature, like atoms or the integers.
Forceps birth delivery, allergic sensitisation and asthma: a population‐based cohort study
Authors: Hancox R. J. , Landhuis C. E. , Sears M. R. 
Published: June 2012

SummaryBackgroundStudies indicate an increased risk of allergies among children born by caesarean section, possibly because immune development is altered by avoiding exposure to maternal vaginal flora. It is unknown if other obstetric interventions are associated with allergies.ObjectiveTo assess associations between delivery with forceps assistance and development of atopy and asthma.MethodsIn a population‐based cohort of 1037 individuals born in 1972/73, atopy was assessed by skin‐prick tests for common allergens at ages 13 and 32 years. A history of asthma was obtained at the same ages. Associations between birth with forceps assistance, atopy and asthma were assessed with adjustments for sex, head circumference at birth, parental atopy disease, birth order and socio‐economic status.ResultsChildren born using forceps were more likely to have atopy at ages 13 (53% vs. 44%) and 32 (68% vs 59%). They were also more likely to have asthma (21% vs. 11% and 23% vs. 16% at ages 13 and 32 respectively). Except for asthma at age 13, these associations were not statistically significant after adjustment for multiple confounding factors.Conclusions & Clinical RelevanceDelivery with forceps assistance is associated with an increased risk of atopy and asthma, but the associations were weaker after adjustment for confounding factors. The previously reported association between caesarean birth and atopic disease may be due to confounding rather than altered exposure to maternal flora, although other factors associated with a difficult labour cannot be ruled out.
Long‐term histopathology of allografts in sensitized kidney recipients
Authors: Miura Masayoshi , Harada Hiroshi , Fukasawa Yuichiro , Hotta Kiyohiko , Itoh Yosuke , Tamaki Tohru 
Published: June 2012

AbstractSuccessful desensitization therapy has brought satisfying short‐term outcomes in the recipients with anti‐donor antibody. We analyzed the long‐term pathology of the allografts in the sensitized kidney recipients. Eleven stable recipients after desensitization against positive flow cytometry T‐cell crossmatch (FTXM) were included. They were divided into two groups, based on the protocol biopsies findings at three to eight yr (group 1: subclinical glomerulitis and/or peritubular capillaritis, n = 5 and group 2: no rejection, n = 6). Estimated glomerular filtration rate (eGFR), presence of donor‐specific antibody (DSA), mean channel shift (MCS) of FTXM, urine protein levels, acute antibody‐mediated rejection (AAMR) episodes, and protocol biopsy findings were compared. Chronic transplant glomerulopathy was found in final biopsy of all group 1 cases. DSA was positive in 60% but C4d was positive in 20% case of the group 1. The history of AAMR was only found in the group 1. There was no difference in eGFR decline or proteinuria. The MCS of FTXM was higher in the group 1. The recipients with AAMR history, high MCS in FTXM, and subclinical microvascular inflammation in the early protocol biopsies have risk for developing chronic rejection in long term.
A case of de novo focal segmental glomerulosclerosis occurred one and half years after kidney transplantation supposed to be caused by calcineurin inhibitor
Authors: Ikeda Yoichiro , Nangaku Masaomi , Ishibashi Yoshitaka , Hirohama Daigoro , Uozaki Hiroshi , Tojo Akihiro , Ishikawa Akira , Fujita Toshiro 
Published: June 2012

AbstractA 64‐yr‐old man with end‐stage kidney disease caused by hypertensive nephrosclerosis underwent living‐unrelated ABO‐identical kidney transplantation (KTx) at the age of 60 yr from his 60‐yr‐old wife. Maintenance trough concentration of cyclosporine A (CsA) was 100 ± 30 ng/mL. Five months after KTx, proteinuria gradually increased to around 1 g/d. TRBx at eight months after KTx revealed the new‐onset alteration of mild arteriolosclerosis with intimal hyalinosis, which might reflect calcineurin inhibitor (CNI)–associated arteriopathy (CAA). Nearly one and half years after KTx, urinary protein excretion became nearly 2 g/d. TRBx revealed the advanced CAA and findings of focal segmental glomerulosclerosis (FSGS). Then, CNI was switched from CsA to tacrolimus (TAC). TRBx at two and half years after KTx revealed progressed arteriolar transmural thickening and striped fibrosis, which were supposed to be induced by an increase in serum TAC concentration because of acute enterocolitis. Then, TAC dose was reduced to serum trough concentration 5–8 ng/mL, but urinary protein excretion was increased up to 10 g/d. Reduction of TAC to trough concentration 2.0 ± 0.5 ng/mL reduced urinary protein excretion. Attempts to elevate TAC trough concentration within normal range (4–8 ng/mL) reproducibly induced the recurrence of an increase in sCr or urinary protein excretion. All these findings supported the etiology of graft dysfunction, and proteinuria of this case was FSGS.
Granulomatous tubulointerstitial nephritis in a renal allograft: three cases report and review of literature
Authors: Hotta Kiyohiko , Fukasawa Yuichiro , Sasaki Hajime , Seki Toshimori , Togashi Masaki , Harada Hiroshi 
Published: June 2012

AbstractGranulomatous interstitial nephritis (GIN) is a rare histologic diagnosis in renal allografts. We report three cases with GIN. Case 1: a 37‐yr‐old woman received a kidney from her mother. On follow‐up 15 months later, serum creatinine was increased and a graft biopsy showed epithelioid granuloma in the center of massive mononuclear cell infiltration. She had presented with refractory urinary tract infection treated with antibiotics before biopsy. The case was presumed to be GIN associated with UTI or hypersensitivity to medication. Case 2: a 47‐yr‐old woman received a second graft from a non‐heart‐beating donor. A protocol graft biopsy was performed six months after transplantation and showed several granulomatous nodules. She was followed closely without therapy. Case 3: a 27‐yr‐old woman received an ABO‐incompatible kidney from her father. A protocol graft biopsy was performed three months after transplantation and showed granulomatous reaction with severe mononuclear cell infiltration. She received steroid pulse therapy. The two latter patients had no obvious factor contributing to GIN. Therefore, they were presumed to have idiopathic GIN. Infection is considered to be the main causative factor of GIN in renal allografts. This paper describes rare cases of GIN that had no infectious episode in the renal allografts.
A case of BK virus nephropathy and cytomegalovirus infection concurrent with plasma cell–rich acute rejection
Authors: Mafune Aki , Tanno Yudo , Yamamoto Hiroyasu , Kobayashi Akimitsu , Saigawa Hajime , Yokoo Takashi , Hayakawa Hiroshi , Miyazaki Youichi , Yokoyama Keitaro , Yamaguchi Yutaka , Hosoya Tatsuo 
Published: June 2012

AbstractThe BK virus is a double‐stranded DNA virus to which 90% of adults have been exposed. BK virus infections typically result in an oral or respiratory infection; however, BK virus reactivation is an infectious disease of concern in kidney transplant recipients. The prevalence of BK virus nephropathy (BKN) in kidney transplant recipients is approximately 5%, and most cases occur within one yr after kidney transplantation. Graft survival of BKN is reported to be 30–60%, and the standard treatment strategy for BKN is reducing immunosuppressive therapy and close monitoring for rejection. Viral infection is most common in the early post‐transplantation phase, and BKN or acute rejection is one of the major factors involved in graft loss. However, in this report, we describe the successful management of BKN and cytomegalovirus infection concurrent with plasma cell–rich acute rejection.