bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental Sound Training in Cochlear Implant Users
Authors: Shafiro Valeriy , Sheft Stanley , Kuvadia Sejal , Gygi Brian 
Published: January 2015

Purpose
The study investigated the effect of a short computer-based environmental sound training regimen on the perception of environmental sounds and speech in experienced cochlear implant (CI) patients.

Method
Fourteen CI patients with the average of 5 years of CI experience participated. The protocol consisted of 2 pretests, 1 week apart, followed by 4 environmental sound training sessions conducted on separate days in 1 week, and concluded with 2 posttest sessions, separated by another week without training. Each testing session included an environmental sound test, which consisted of 40 familiar everyday sounds, each represented by 4 different tokens, as well as the Consonant Nucleus Consonant (CNC) word test, and Revised Speech Perception in Noise (SPIN-R) sentence test.

Results
Environmental sounds scores were lower than for either of the speech tests. Following training, there was a significant average improvement of 15.8 points in environmental sound perception, which persisted 1 week later after training was discontinued. No significant improvements were observed for either speech test.

Conclusions
The findings demonstrate that environmental sound perception, which remains problematic even for experienced CI patients, can be improved with a home-based computer training regimen. Such computer-based training may thus provide an effective low-cost approach to rehabilitation for CI users, and potentially, other hearing impaired populations.
Morphology and Syntax in Late Talkers at Age 5
Authors: Rescorla Leslie , Turner Hannah L. 
Published: January 2015

Purpose

This study reports age 5 morphology and syntax skills in late talkers identified at age 2 (
n
= 34) and typically developing comparison children (
n
= 20).

Results

The late talkers manifested significant morphological delays at ages 3 and 4 relative to comparison peers. Based on the 14 morphemes analyzed at age 5, the only significant group difference was on the third person regular –
s
inflection. This was also the only significant difference when we compared late talkers with continuing delay, late bloomers (who scored within 1 standard deviation of the comparison group in mean length of utterance), and typically developing peers. The late talker and comparison children differed greatly in mean total scores on the Index of Productive Syntax (Scarborough, 1990), a measure of syntactic complexity. The group with continuing delay scored significantly lower on the IPSyn than the late bloomer and typically developing groups, which did not differ from each other.

Conclusions
Findings are consistent with the higher order language group differences found through adolescence in these late talkers relative to comparison peers with similar socioeconomic status and similar nonverbal abilities, supporting the notion that late talkers have an ongoing weakness in language endowment that manifests differently over the course of development.
At the Intersection of Cognition and Grammar: Deficits Comprehending Counterfactuals in Turkish Children With Specific Language Impairment
Authors: Yarbay Duman Tuba , Blom Elma , Topbaş Seyhun 
Published: January 2015

Purpose
This study investigated the comprehension of counterfactual conditionals in monolingual Turkish children with specific language impairment (SLI) and typically developing (TD) children. Comprehending counterfactuals requires a well-developed cognitive system (Beck, Riggs, & Gorniak, 2009). Children with SLI have impaired cognitive functioning (Im-Bolter, Johnston, & Pascual-Leone, 2006), which affects their ability to comprehend counterfactuals.

Method

The sample consisted of 13 children (9 boys, 4 girls) with SLI who were matched in age and nonverbal intelligence with 13 TD children (8 boys, 5 girls; mean age 6;9 [years; months] for both groups). Each group completed a sentence comprehension and repetition task with 3 sentence conditions: nonconditional, factual, and counterfactual. Nonconditionals did not have
if
-embedding, whereas factual and counterfactual conditionals were morphosyntactically equivalent
if
-clauses, but only the latter was cognitively complex.

Results
Conditionals were more difficult to comprehend than nonconditionals for both groups. Counterfactuals were more difficult to comprehend than the morphosyntactically equivalent factual counterparts for the SLI group. There was no discrepancy between the groups for repetition of counterfactuals and factuals.

Conclusions

Children with SLI have difficulty processing counterfactuals due to morphosyntactic complexity (
if
-embedding) and the cognitive processes involved in comprehending counterfactuals. This indicates that cognitive complexity adds to sentence comprehension deficits in SLI.
Harmonic degree 1 maps are diffeomorphisms: Lewy’s theorem for curved metrics
Authors: Martin Gaven 
Published: January 2015

In 1936, H. Lewy showed that the Jacobian determinant of a harmonic homeomorphism between planar domains does not vanish and thus the map is a diffeomorphism. This built on the earlier existence results of Rado and Kneser. Schoen and Yau generalised this result to degree

1
1

harmonic mappings between closed Riemann surfaces. Here we give a new approach that establishes all these results in complete generality.
Latin American Agriculture in a World of Trade Agreements
Authors: Josling Tim , Paggi Mechel , Wainio John , Yamazaki Fumiko 
Published: January 2015

AbstractLatin American and Caribbean (LAC) countries are members of 29 distinct free trade agreements with other Latin American partners, and 44 such agreements exist between an LAC country and other countries. Among the LAC countries linked by an Free Trade Agreement (FTA), a large percentage of trade is already duty free though many trade barriers in agriculture persist. There is a significant difference in the trade patterns among the LAC countries. The Southern Cone countries, for example, have extensive agricultural exports to Asia and to the European Union (EU), and have few FTAs with regional countries. By contrast, countries in Central America and the Andean region have extensive trade agreements with each other, and have fewer exports outside the region. Meanwhile, other regions are negotiating ambitious mega‐agreements, particularly the Trans Pacific Partnership (TPP) and the Trans‐Atlantic Trade and Investment Partnership (T‐TIP). These could have significant impacts on the region, including trade diversion and preference erosion in major import markets. Several possible avenues exist for Latin American countries to accomplish the following: counter the impact of a TPP and T‐TIP on agricultural exports; strengthen existing bilateral trade agreements within the region; link existing multi‐country agreements such as Mercado Común del Sur (MERCOSUR) and the Pacific Alliance to North American Free Trade Agreement (NAFTA); consolidate the current trade agreements with the EU; or “sign on” to the TPP. This last option would be more attractive if China were to become a TPP participant. If China is not interested in joining the TPP, then for some countries a direct FTA with China could be contemplated.
Disease Beyond the Arch: A Systematic Review of Middle Aortic Syndrome in Childhood
Authors: Rumman Rawan K. , Nickel Cheri , Matsuda-Abedini Mina , Lorenzo Armando J. , Langlois Valerie , Radhakrishnan Seetha , Amaral Joao , Mertens Luc , Parekh Rulan S. 
Published: January 2015

BACKGROUND
Middle aortic syndrome (MAS) is a rare clinical entity in childhood, characterized by a severe narrowing of the distal thoracic and/or abdominal aorta, and associated with significant morbidity and mortality. MAS remains a relatively poorly defined disease. This paper systematically reviews the current knowledge on MAS with respect to etiology, clinical impact, and therapeutic options.

METHODS
A systematic search of 3 databases (Embase, MEDLINE, and Cochrane Central Register of Controlled Trials) yielded 1,252 abstracts that were screened based on eligibility criteria resulting in 184 full-text articles with 630 reported cases of childhood MAS. Data extracted included patient characteristics, clinical presentation, vascular phenotype, management, and outcomes.

RESULTS
Most cases of MAS are idiopathic (64%), 15% are associated with Mendelian disorders, and 17% are related to inflammatory diseases. Extra-aortic involvement including renal (70%), superior mesenteric (30%), and celiac (22%) arteries is common, especially among those with associated Mendelian disorders. Inferior mesenteric artery involvement is almost never reported. The majority of cases (72%) undergo endovascular or surgical management with residual hypertension reported in 34% of cases, requiring medication or reintervention. Clinical manifestations and extent of extra-aortic involvement are lacking.

CONCLUSIONS
MAS presents with significant involvement of visceral arteries with over two thirds of cases having renal artery stenosis, and one third with superior mesenteric artery stenosis. The extent of disease is worse among those with genetic and inflammatory conditions. Further studies are needed to better understand etiology, long-term effectiveness of treatment, and to determine the optimal management of this potentially devastating condition.
Deterministic identification of specific individuals from GWAS results
Authors: Cai Ruichu , Hao Zhifeng , Winslett Marianne , Xiao Xiaokui , Yang Yin , Zhang Zhenjie , Zhou Shuigeng 
Published: January 2015

Abstract
Motivation : Genome-wide association studies (GWASs) are commonly applied on human genomic data to understand the causal gene combinations statistically connected to certain diseases. Patients involved in these GWASs could be re-identified when the studies release statistical information on a large number of single-nucleotide polymorphisms. Subsequent work, however, found that such privacy attacks are theoretically possible but unsuccessful and unconvincing in real settings.
Results : We derive the first practical privacy attack that can successfully identify specific individuals from limited published associations from the Wellcome Trust Case Control Consortium (WTCCC) dataset. For GWAS results computed over 25 randomly selected loci, our algorithm always pinpoints at least one patient from the WTCCC dataset. Moreover, the number of re-identified patients grows rapidly with the number of published genotypes. Finally, we discuss prevention methods to disable the attack, thus providing a solution for enhancing patient privacy.
Availability and implementation : Proofs of the theorems and additional experimental results are available in the support online documents. The attack algorithm codes are publicly available at https://sites.google.com/site/zhangzhenjie/GWAS_attack.zip . The genomic dataset used in the experiments is available at http://www.wtccc.org.uk/ on request.
Contact : winslett@illinois.edu or zhenjie@adsc.com.sg
Supplementary information: Supplementary data are available from Bioinformatics online.
MetAmp: combining amplicon data from multiple markers for OTU analysis
Authors: Zhbannikov Ilya Y. , Foster James A. 
Published: January 2015

Abstract
Motivation: We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp works best with at least three markers, and is applicable to non-bacterial analyses and to non 16S markers. Our application and testing have been limited to 16S analysis of microbial communities.
Results: We clustered standard test sequences derived from the Human Microbiome Mock Community test sets and compared MetAmp and other tools with respect to their ability to recover OTUs for these benchmark bacterial communities. MetAmp compared favorably to QIIME, UPARSE and Mothur using amplicons from one, two, and three markers.
Availability and implementation: MetAmp is available at http://izhbannikov.github.io/MetAmp/
Contact: ilyaz@uidaho.edu , foster@uidaho.edu
Supplementary information : Supplementary data are available at Bioinformatics online.
Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection
Authors: Schmelcher Mathias , Shen Yang , Nelson Daniel C. , Eugster Marcel R. , Eichenseher Fritz , Hanke Daniela C. , Loessner Martin J. , Dong Shengli , Pritchard David G. , Lee Jean C. , Becker Stephen C. , Foster-Frey Juli , Donovan David M. 
Published: January 2015

Abstract

Objectives
In the light of increasing drug resistance in Staphylococcus aureus, bacteriophage endolysins [peptidoglycan hydrolases (PGHs)] have been suggested as promising antimicrobial agents. The aim of this study was to determine the antimicrobial activity of nine enzymes representing unique homology groups within a diverse class of staphylococcal PGHs.

Methods
PGHs were recombinantly expressed, purified and tested for staphylolytic activity in multiple in vitro assays (zymogram, turbidity reduction assay and plate lysis) and against a comprehensive set of strains (S. aureus and CoNS). PGH cut sites in the staphylococcal peptidoglycan were determined by biochemical assays (Park–Johnson and Ghuysen procedures) and MS analysis. The enzymes were tested for their ability to eradicate static S. aureus biofilms and compared for their efficacy against systemic MRSA infection in a mouse model.

Results
Despite similar modular architectures and unexpectedly conserved cleavage sites in the peptidoglycan (conferred by evolutionarily divergent catalytic domains), the enzymes displayed varying degrees of in vitro lytic activity against numerous staphylococcal strains, including cell surface mutants and drug-resistant strains, and proved effective against static biofilms. In a mouse model of systemic MRSA infection, six PGHs provided 100% protection from death, with animals being free of clinical signs at the end of the experiment.

Conclusions
Our results corroborate the high potential of PGHs for treatment of S. aureus infections and reveal unique antimicrobial and biochemical properties of the different enzymes, suggesting a high diversity of potential applications despite highly conserved peptidoglycan target sites.
OXY-2-15, a novel variant showing increased ceftazidime hydrolytic activity
Authors: Nijhuis R. H. T. , Oueslati S. , Zhou K. , Bosboom R. W. , Rossen J. W. A. , Naas T. 
Published: January 2015

Abstract

Objectives
Klebsiella oxytoca is a member of the family of Enterobacteriaceae and often contains the β-lactamase blaOXY gene. Although this β-lactamase does not naturally hydrolyse ceftazidime, this study describes possible in vivo selection of a clinical K. oxytoca isolate showing increased MICs of ceftazidime.

Methods
To reveal the molecular mechanism underlying this unusual resistance phenotype, WGS, cloning, overexpression, MIC and steady-state kinetic studies were performed.

Results
A patient was treated for a septic episode with ceftazidime (4 g/day). This therapy was based on earlier culture results in which, amongst others, a K. oxytoca (Velp-1) isolate was identified. After 11 days of treatment, K. oxytoca Velp-2 was isolated from a pus sample drained from the wound. The isolate showed increased resistance to ceftazidime (MIC ≥64 mg/L) compared with the original K. oxytoca isolate (Velp-1). WGS revealed the presence of a novel blaOXY-2 allele, designated blaOXY-2-15, with a two amino acid deletion at Ambler positions 168 and 169 compared with OXY-2-2. Cloning blaOXY-2-15 into Escherichia coli TOP10 resulted in increased MICs of ceftazidime, but reduced MICs of most other β-lactams compared with OXY-2-2. Steady-state kinetics confirmed the results of the MIC data, showing clearly significant ceftazidime hydrolysis.

Conclusions
This report shows the risk of in vivo selection of ceftazidime-resistant K. oxytoca isolates after prolonged ceftazidime treatment. Furthermore, it is the first known report of a K. oxytoca isolate conferring resistance to ceftazidime by a two amino acid deletion in the omega loop of OXY-2-2.
Treatment outcomes of surgery, antifungal therapy and immunotherapy in ocular and vascular human pythiosis: a retrospective study of 18 patients
Authors: Permpalung Nitipong , Worasilchai Navaporn , Plongla Rongpong , Upala Sikarin , Sanguankeo Anawin , Paitoonpong Leilani , Mendoza Leonel , Chindamporn Ariya 
Published: January 2015

Abstract

Objectives
Human pythiosis is a life-threatening disease for which no standard treatment protocols with proven efficacy exist. We present the results of our institutional pythiosis treatment protocol, composed of surgery, antifungal agents, iron chelator (only vascular cases) and immunotherapy.

Methods
We retrospectively analysed patients with proven vascular and ocular pythiosis in King Chulalongkorn Memorial Hospital from April 2003 to May 2013. Fisher's exact test and Wilcoxon's rank-sum test were used. The MICs of seven antifungal agents and combination drugs were investigated in eight clinical Pythium insidiosum strains.

Results
Eighteen patients were evaluated. Disease-free surgical margins were obtained in all surviving patients with vascular pythiosis (P = 0.08). Patients who underwent eye enucleation were significantly older than those who did not (P &lt; 0.05). Patients with vascular or ocular pythiosis did not differ significantly in the median time from disease onset to first surgery or in the relationship between the type of P. insidiosum antigen and treatment outcomes. In vitro susceptibility profiles of all isolates demonstrated that no single agent or combination treatment was substantially more effective than the others. The highest MIC was detected for amphotericin B, followed in order by voriconazole, fluconazole, anidulafungin, caspofungin, itraconazole and terbinafine. No synergistic effects of the combination drug treatments were found.

Conclusions
Surgery with adequate surgical margins is a crucial determinant of survival in patients with vascular pythiosis. Itraconazole and terbinafine do not have synergistic effects on Thai P. insidiosum strains. The role of immunotherapy remains inconclusive for both vascular and ocular pythiosis.
Self-Incompatibility-Induced Programmed Cell Death in Field Poppy Pollen Involves Dramatic Acidification of the Incompatible Pollen Tube Cytosol
Authors: Wilkins Katie A. , Bosch Maurice , Haque Tamanna , Teng Nianjun , Poulter Natalie S. , Franklin-Tong Vernonica E. 
Published: January 2015

Abstract
Self-incompatibility (SI) is an important genetically controlled mechanism to prevent inbreeding in higher plants. SI involves highly specific interactions during pollination, resulting in the rejection of incompatible (self) pollen. Programmed cell death (PCD) is an important mechanism for destroying cells in a precisely regulated manner. SI in field poppy (Papaver rhoeas) triggers PCD in incompatible pollen. During SI-induced PCD, we previously observed a major acidification of the pollen cytosol. Here, we present measurements of temporal alterations in cytosolic pH ([pH]cyt); they were surprisingly rapid, reaching pH 6.4 within 10 min of SI induction and stabilizing by 60 min at pH 5.5. By manipulating the [pH]cyt of the pollen tubes in vivo, we show that [pH]cyt acidification is an integral and essential event for SI-induced PCD. Here, we provide evidence showing the physiological relevance of the cytosolic acidification and identify key targets of this major physiological alteration. A small drop in [pH]cyt inhibits the activity of a soluble inorganic pyrophosphatase required for pollen tube growth. We also show that [pH]cyt acidification is necessary and sufficient for triggering several key hallmark features of the SI PCD signaling pathway, notably activation of a DEVDase/caspase-3-like activity and formation of SI-induced punctate actin foci. Importantly, the actin binding proteins Cyclase-Associated Protein and Actin-Depolymerizing Factor are identified as key downstream targets. Thus, we have shown the biological relevance of an extreme but physiologically relevant alteration in [pH]cyt and its effect on several components in the context of SI-induced events and PCD.
Reading experiences influencing the acceptance of e-book devices
Authors: Park Eunil , Sung Jungyeon , Cho Kwangsu 
Published: January 2015

Purpose
– This paper aims to explore users’ perception of, and then intention toward using, e-book devices as new reading devices, based upon an integrated technology acceptance model (TAM), reading engagement based upon flow theory and readability. The recent introduction of e-book devices has drastically changed the way people access and use reading content. However, few studies have explored the impact of reading experience on acceptance of e-book devices.

Design/methodology/approach
– A total of 219 participants participated in a survey after using e-book devices to analyze the research model.

Findings
– This study confirmed the crucial roles played by viewing experience, perceived mobility, perceived behavioral control, skill and readability. Also perceived usefulness and text satisfaction were found to have a positive and significant association with acceptance of e-book devices.

Research limitations/implications
– Implications and suggestions for researchers and manufacturers are also addressed in the present study.

Originality/value
– The current study focused on how actual reading experiences using e-book devices influences acceptance of e-book devices, through the triangular integrated model of TAM, reading engagement and readability features, and investigating users’ reading experience on the basis of responses to the characteristics of e-book devices.
Web content and design trends of Alabama academic libraries
Authors: Wilson Daniel Earl 
Published: January 2015

Purpose– This paper aims to evaluate the website content of Alabama academic libraries to examine their services, content and compliance with design and accessibility standards.Design/methodology/approach– A content analysis was conducted on 24 academic library websites discovered through Jeanne Burke’s Higher Education Directory and the Alabama Colleges directory website. All data were collected within a month.Findings– Study data revealed that while academic libraries are offering more online services, many continue to lack certain services or fail to implement basic web design and accessibility standards.Research limitations/implications– Inclusion into the study was limited to the independent library websites of Alabama institutions offering four-year degree courses and content data discoverable within three clicks of the home page. Future studies might identify why certain libraries lack reference chat services, social media accounts and/or certain accessibility accommodations. Additional research might evaluate multilingual websites and their methods for providing language options.Practical implications– The results of this study should assist in the evaluation of library websites and increase awareness of design and accessibility standards, enabling designers and policy makers to improve upon future website designs.Originality/value– This study presents a depth of evaluation and currency unseen in most web content analyses. The extent of this study should provide librarians, web designers, and library policy makers with a suitable comparison for website projects and evaluations.