bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Chemo-Dynamical History of the Milky Way as Revealed by SDSS/SEGUE
Authors: Beers Timothy C. 
Published: March 2010

AbstractAlthough originally conceived as primarily an extragalactic survey, the Sloan Digital Sky Survey (SDSS-I), and its extensions SDSS-II and SDSS-III, continue to have a major impact on our understanding of the formation and evolution of our host galaxy, the Milky Way. The sub-survey SEGUE: Sloan Extension for Galactic Exploration and Understanding, excuted as part of SDSS-II, obtained some 3500 square degrees of additional ugriz imaging, mostly at lower Galactic latitudes, in order to better sample the disk systems of the Galaxy. Most importantly, it obtained over 240,000 medium-resolution spectra for stars selected to sample Galactocentric distances from 0.5 to 100 kpc. In combination with stellar targets from SDSS-I, and the recently completed SEGUE-2 program, executed as part of SDSS-III, the total sample of SDSS spectroscopy for Galactic stars comprises some 500,000 objects.The development of the SEGUE Stellar Parameter Pipeline has enabled the determination of accurate atmospheric parameter estimates for a large fraction of these stars. Many of the stars in this data set within 5 kpc of the Sun have sufficiently well-measured proper motions to determine their full space motions, permitting examination of the nature of much more distant populations represented by members that are presently passing through the solar neighborhood. Ongoing analyses of these data are being used to draw a much clearer picture of the nature of our galaxy, and to supply targets for detailed high-resolution spectrscopic follow-up with the world's largest telescopes. Here we discuss a few highlights of recently completed and ongoing investigations with these data.
Using open access literature to guide full-text query formulation
Authors: Piwowar Heather , Chapman Wendy 
Published: March 2010

Abstract
Background
Much scientific knowledge is contained in the details of the full-text biomedical literature. Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume. Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar. However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users. We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched. We evaluated the feasibility of this approach by building a high-precision query for identifying studies that perform gene expression microarray experiments.*Methodology and Results*We built decision rules from unigram and bigram features of the open access literature. Minor syntax modifications were needed to translate the decision rules into the query languages of PubMed Central, Highwire Press, and Google Scholar. We mapped all retrieval results to PubMed identifiers and considered our query results as the union of retrieved articles across all portals. Compared to our reference standard, the derived full-text query found 56% (95% confidence interval, 52% to 61%) of intended studies, and 90% (86% to 93%) of studies identified by the full-text search met the reference standard criteria. Due to this relatively high precision, the derived query was better suited to the intended application than alternative baseline MeSH queries.*Significance*Using open access literature to develop queries for full-text portals is an open, flexible, and effective method for retrieval of biomedical literature articles based on article full-text. We hope our approach will raise awareness of the constraints and opportunities in mainstream full-text information retrieval and provide a useful tool for today’s researchers.
Ethics: A Model Curriculum for Teaching Professional Issues in University Speech-Language Pathology and Audiology Programs
Authors: Poole Mary Lou , Solomon Barbara 
Published: March 2010

Abstract
Educating graduate level speech-language pathology and audiology students has become a truly daunting task. As the American Speech-Language Hearing Association (ASHA's) Scope of Practice (ASHA, 2007) expanded over the last 15 years, so did demands and challenges placed on universities to offer a wide range of disorder classes and clinical experiences. With regards to the area of professional issues, many programs struggle with balancing and providing appropriate pedagogical learning and clinical experience. This article offers a Model Professional Issues Curriculum for educational programs in speech-language pathology and audiology that was developed by a consortium of representatives from several universities throughout the United States. The course content, which consists of 13 core topics, is presented using Bloom's Taxonomy as a guideline for teaching the learning outcomes addressed. Educators in clinical education will find this model useful for developing a course in Professional Issues or supplementing existing courses.
Fusion of biomimetic stealth probes into lipid bilayer cores
Authors: Almquist Benjamin D. , Melosh Nicholas A. 
Published: March 2010

Many biomaterials are designed to regulate the interactions between artificial and natural surfaces. However, when materials are inserted through the cell membrane itself the interface formed between the interior edge of the membrane and the material surface is not well understood and poorly controlled. Here we demonstrate that by replicating the nanometer-scale hydrophilic-hydrophobic-hydrophilic architecture of transmembrane proteins, artificial “stealth” probes spontaneously insert and anchor within the lipid bilayer core, forming a high-strength interface. These nanometer-scale hydrophobic bands are readily fabricated on metallic probes by functionalizing the exposed sidewall of an ultrathin evaporated Au metal layer rather than by lithography. Penetration and adhesion forces for butanethiol and dodecanethiol functionalized probes were directly measured using atomic force microscopy (AFM) on thick stacks of lipid bilayers to eliminate substrate effects. The penetration dynamics were starkly different for hydrophobic versus hydrophilic probes. Both 5- and 10 nm thick hydrophobically functionalized probes naturally resided within the lipid core, while hydrophilic probes remained in the aqueous region. Surprisingly, the barrier to probe penetration with short butanethiol chains (
E

o
,5 nm

= 21.8
k

b

T
,
E

o
,10 nm

= 15.3
k

b

T
) was dramatically higher than longer dodecanethiol chains (
E

o
,5 nm

= 14.0
k

b

T
,
E

o
,10 nm

= 10.9
k

b

T
), indicating that molecular mobility and orientation also play a role in addition to hydrophobicity in determining interface stability. These results highlight a new strategy for designing artificial cell interfaces that can nondestructively penetrate the lipid bilayer.
Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes
Authors: King Andrew J. , Cragg Simon M. , Li Yi , Dymond Jo , Guille Matthew J. , Bowles Dianna J. , Bruce Neil C. , Graham Ian A. , McQueen-Mason Simon J. 
Published: March 2010

The digestion of lignocellulose is attracting attention both in terms of basic research into its metabolism by microorganisms and animals, and also as a means of converting plant biomass into biofuels. Limnoriid wood borers are unusual because, unlike other wood-feeding animals, they do not rely on symbiotic microbes to help digest lignocellulose. The absence of microbes in the digestive tract suggests that limnoriid wood borers produce all the enzymes necessary for lignocellulose digestion themselves. In this study we report that analysis of ESTs from the digestive system of
Limnoria quadripunctata
reveals a transcriptome dominated by glycosyl hydrolase genes. Indeed, > 20% of all ESTs represent genes encoding putative cellulases, including glycosyl hydrolase family 7 (GH7) cellobiohydrolases. These have not previously been reported in animal genomes, but are key digestive enzymes produced by wood-degrading fungi and symbiotic protists in termite guts. We propose that limnoriid GH7 genes are important for the efficient digestion of lignocellulose in the absence of gut microbes. Hemocyanin transcripts were highly abundant in the hepatopancreas transcriptome. Based on recent studies indicating that these proteins may function as phenoloxidases in isopods, we discuss a possible role for hemocyanins in lignin decomposition.
Monomeric red fluorescent proteins with a large Stokes shift
Authors: Piatkevich Kiryl D. , Hulit James , Subach Oksana M. , Wu Bin , Abdulla Arian , Segall Jeffrey E. , Verkhusha Vladislav V. 
Published: March 2010

Two-photon microscopy has advanced fluorescence imaging of cellular processes in living animals. Fluorescent proteins in the blue-green wavelength range are widely used in two-photon microscopy; however, the use of red fluorescent proteins is limited by the low power output of Ti-Sapphire lasers above 1,000 nm. To overcome this limitation we have developed two red fluorescent proteins, LSS-mKate1 and LSS-mKate2, which possess large Stokes shifts with excitation/emission maxima at 463/624 and 460/605 nm, respectively. These LSS-mKates are characterized by high pH stability, photostability, rapid chromophore maturation, and monomeric behavior. They lack absorbance in the green region, providing an additional red color to the commonly used red fluorescent proteins. Substantial overlap between the two-photon excitation spectra of the LSS-mKates and blue-green fluorophores enables multicolor imaging using a single laser. We applied this approach to a mouse xenograft model of breast cancer to intravitally study the motility and Golgi-nucleus alignment of tumor cells as a function of their distance from blood vessels. Our data indicate that within 40 μm the breast cancer cells show significant polarization towards vessels in living mice.
Reducing the algorithmic variability in transcriptome-based inference
Authors: Tuna Salih , Niranjan Mahesan 
Published: March 2010

Abstract
Motivation: High-throughput measurements of mRNA abundances from microarrays involve several stages of preprocessing. At each stage, a user has access to a large number of algorithms with no universally agreed guidance on which of these to use. We show that binary representations of gene expressions, retaining only information on whether a gene is expressed or not, reduces the variability in results caused by algorithmic choice, while also improving the quality of inference drawn from microarray studies.
Results: Binary representation of transcriptome data has the desirable property of reducing the variability introduced at the preprocessing stages due to algorithmic choice. We compare the effect of the choice of algorithms on different problems and suggest that using binary representation of microarray data with Tanimoto kernel for support vector machine reduces the effect of the choice of algorithm and simultaneously improves the performance of classification of phenotypes.
Contact: mn@ecs.soton.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Susceptibility loci reported in genome‐wide association studies are associated with Crohn’s disease in Canadian children
Authors: AMRE D. K. , MACK D. R. , MORGAN K. , ISRAEL D. , DESLANDRES C. , SEIDMAN E. G. , LAMBRETTE P. , COSTEA I. , KRUPOVES A. , FEGURY H. , DONG J. , GRIMARD G. , LEVY E. 
Published: March 2010

Aliment Pharmacol Ther 31, 1186–1191SummaryBackground  Recent genome‐wide association studies based on adult and paediatric populations have implicated >30 genes/loci as susceptibility loci for Crohn’s disease (CD).Aims  To investigate whether reported genes/loci were also associated with CD in Canadian children.Design and Methods  A case‐control design was implemented at three paediatric gastroenterology clinics in Canada. Children ≤18 years of age with a confirmed diagnosis of CD were recruited along with controls. Single nucleotide polymorphisms (SNPs) in five genome‐wide association studies reported genes/loci were genotyped. Associations between individual SNPs and CD were examined.Results  A total of 406 cases and 415 controls were studied. The mean (±s.d.) age of the cases was 12.3 (±3.2) years. Most cases were male (56.6%), had ileo‐colonic disease (L3 ± L4, 52.0%) and inflammatory behaviour (B1 ± p, 86.9%) at diagnosis. Allelic association analysis (two‐tailed) showed that three of the five targeted SNPs were significantly associated with overall susceptibility for CD (ZNF365, r10995271, P = 0.001; PTPN2, rs1893217, P = 0.005; STAT3, rs744166, P = 0.01). Associations with SNP rs4613763 in the PTGER4 locus were marginally nonsignificant (P = 0.07). The ZNF365 and STAT3 SNPs were predominantly associated with ileal disease with or without colonic involvement.Conclusion  The identified susceptibility genes/loci for adult‐onset CD also confer risk for paediatric‐onset CD.
Mitochondrial D‐loop variations in paediatric acute myeloid leukaemia: a potential prognostic marker
Authors: Sharawat Surender K. , Bakhshi Radhika , Vishnubhatla Sreenivas , Bakhshi Sameer 
Published: March 2010

SummaryThe D‐Loop region of mitochondrial DNA (mtDNA) is the regulatory region for its replication and transcription. There are two hypervariable regions (HV‐I, HV‐II) and the rate of mutation in these regions is 100‐ to 200‐fold that of nuclear DNA. In the current study, the entire D‐loop region of mtDNA was amplified in two overlapping polymerase chain reaction fragments and variations were evaluated in 44 paediatric acute myeloid leukaemia (AML) patients by direct DNA sequencing methods. Median age of the patients was 8·5 years (1–18 years) and the male:female ratio was 3·8:1. A total of 222 variations were observed at 118 positions in the D‐Loop of 35/44 (79·5%) AML patients. The most common variations were T→C (24·6%) and C→T (21·4%) followed by A→G (15·8%). There was no significant difference in the event‐free survival (EFS) of patients with or without any variations (P = 0·40). Three variations in HV‐I, namely 16126T→C (P = 0·05), 16224T→C (P < 0·01) and 16311T→C (P < 0·001), were significantly associated with inferior EFS. In conclusion, this is the largest study to show a high frequency of mtDNA variations in paediatric AML and their potential relevance as a prognostic marker in this disease.
Screening sticky traps under low magnification for adult Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood) and Aleyrodes spp. (Hemiptera: Sternorrhyncha: Aleyrodidae)
Authors: Malumphy C. , Delaney M. A. , Pye D. , Quill J. 
Published: March 2010

Whiteflies are commonly transported in international plant trade, accounting for 25% of arthropods found in association with imported plant material in England and Wales between 1996 and 2006. Several species are of quarantine significance and rapid, accurate identifications are essential in order for phytosanitary services to decide upon appropriate action. Whitefly taxonomy is based on the puparium, but these are often difficult to detect when present at low densities. Adults are more conspicuous and are readily caught on yellow sticky traps. Screening traps under low magnification for adult Bemisia tabaci, Trialeurodes vaporariorum and Aleyrodes spp. using pigmentation characters was evaluated; 5151 adults were examined on 238 traps and their identity predicted. Twenty‐one percent of the adults were slide mounted and examined under high magnification to check their identity. The overall accuracy of the initial whitefly species prediction under low magnification was 98%. The speed and reliability of detecting adult B. tabaci on sticky traps was greatly improved and the number of adults requiring slide preparation reduced (by an average of 46% per trap) resulting in significant financial savings, compared to randomly selecting adults for slide mounting. Protocols are presented for removing adults from traps and making microscope‐slide preparations.
CREB expression in the brains of two closely related parasitic wasp species that differ in long‐term memory formation
Authors: Van Den Berg M. , Verbaarschot P. , Hontelez S. , Vet L. E. M. , Dicke M. , Smid H. M. 
Published: March 2010

AbstractThe cAMP/PKA signalling pathway and transcription factor cAMP response element‐binding protein (CREB) play key roles in long‐term memory (LTM) formation. We used two closely related parasitic wasp species, Cotesia glomerata and Cotesia rubecula, which were previously shown to be different in LTM formation, and sequenced at least nine different CREB transcripts in both wasp species. The splicing patterns, functional domains and amino acid sequences were similar to those found in the CREB genes of other organisms. The predicted amino acid sequences of the CREB isoforms were identical in both wasp species. Using real‐time quantitative PCR we found that two low abundant CREB transcripts are differentially expressed in the two wasps, whereas the expression levels of high abundant transcripts are similar.
Symptom clusters and experiences of patients with cancer
Authors: Karabulu Neziha , Erci Behice , Özer Nadiye , Özdemir Süreyya 
Published: March 2010

karabulu n., erci b., özer n. & özdemir s. (2010) Symptom clusters and experiences of patients with cancer. Journal of Advanced Nursing 66(5), 1011–1021.AbstractTitle.  Symptom clusters and experiences of patients with cancer. Aim.  This study is a report of a study to characterize the prevalence and severity of symptoms in patients with cancer and describing the clustering of symptoms.Background.  Patients with cancer experience multiple symptoms caused by multiple factors, including progression of the cancer, acute physiological changes associated with treatment, delayed side effects of treatment and long‐term consequences of the disease.Methods.  A convenience sample of 287 patients with cancer at a Turkish university hospital completed a structured questionnaire on demographical characteristics and a symptom inventory for patients with cancer. Cluster analysis, principal components and internal consistency reliability analyses were used to analyse the data. The study was conducted in 2007.Findings.  The most common symptoms experienced were fatigue, difficulty remembering, sadness, loss of appetite, lack of enjoyment of life, pain, distress, difficulty walking and dry mouth. The least experienced symptoms were shortness of breath and vomiting. Overall, 37·5% of the patients experienced moderate symptoms and 12·5% experienced severe symptoms. Among the severe symptoms were loss of appetite, fatigue, sadness, dry mouth and distress; however, 48% rated these as moderate or severe.Conclusions.  Symptom cluster research is still in its early years. Further work is needed to reach a standard definition of a symptom cluster and a consensus of its criteria. Additional studies are needed to examine symptom clusters in cancer survivors. As individuals are living longer with the disease, comprehensive understanding of the symptom clusters that may be unique to cancer survivors is critical.
Insecurity and shiftwork as characteristics of negative work environment: psychosocial and behavioural mediators
Authors: Elovainio Marko , Kuusio Hannamaria , Aalto Anna‐Mari , Sinervo Timo , Heponiemi Tarja 
Published: March 2010

elovainio m., kuusio h., aalto a.‐m., sinervo t. & heponiemi t. (2010) Insecurity and shiftwork as characteristics of negative work environment: psychosocial and behavioural mediators.Journal of Advanced Nursing 66(5), 1080–1091.AbstractTitle. Insecurity and shiftwork as characteristics of negative work environment: psychosocial and behavioural mediators.Aim. This paper is a report of an investigation into whether insecure work contract and shiftwork are associated with reduced wellbeing indicators, such as psychological distress, low job involvement and low work ability.Background. Insecure work contracts and shiftwork have repeatedly been found to contribute to the development and continuation of negative outcomes among healthcare professionals. In particular, nurses are generally considered as being at high risk of work‐related stress and reduced wellbeing.Methods. Cross‐sectional survey data from the Finnish Health Care Professional Study collected in 2006 were used. The random sample of Finnish Registered Nurses comprised 2100 women and men aged 22–65 years. Information on the work contract and shiftwork were self‐reported. The wellbeing indicators used were psychological distress (GHQ‐12), work ability and job involvement. Psychosocial work characteristics were measured using the Job Content Questionnaire and an organizational justice scale.Results. Variance and linear regression analyses showed that insecure work contract was associated with lower work ability and job involvement. Shiftwork was related to psychological distress, low job involvement and low work ability. Support for a mediating role of job demands and job control and a moderating role of relational justice was obtained.Conclusion. To reduce the negative effects of environmental stressors, such as insecure work contract and shiftwork, it may be better to focus on improving psychosocial work characteristics than on nurses’ health‐related behaviour.
Treatment development for systemicTetrahymenasp. infection in guppies,Poecilia reticulataPeters
Authors: Leibowitz M Pimenta , Chettri J Kumar , Ofir R , Zilberg D 
Published: March 2010

AbstractAntibacterial and antiparasitic agents and a cysteine protease inhibitor (E‐64) were tested againstTetrahymenainfection, a serious problem in guppy production worldwide. Chemicals were testedin vitroby a colorimetric assay forTetrahymenasurvival. The most effective were niclosamide, albendazole and chloroquine, with 23%, 35% and 60% survival, respectively, following 2‐h exposure to 100 ppm. Longer incubation periods resulted in greater reductions in survival. Niclosamide was further studiedin vivoat different dosages, administered orally toTetrahymena‐infected guppies. Mortality rates were significantly lower in all treatment groups; in trial I, 30% and 33% mortality in 5 and 40 mg kg−1niclosamide‐fed fishvs.59% mortality in controls; in trial II, 35%, 13% and 10% in 50, 100 and 200 mg kg−1niclosamide‐fed fishvs.64% in controls. The effect of the cysteine protease inhibitor E64 was tested in tissue culture, by measuring histolytic activity of the parasite (Tet‐NI) on a guppy‐fin cell line, based on cell depletion. Tet‐NI feeding activity was significantly reduced following pretreatment with E‐64 relative to non‐treated Tet‐NI. E‐64‐pretreated Tet‐NI was injected i.p. into guppies: recorded mortality rates were significantly lower (35%) than that in non‐treated Tet‐NI (60%), suggesting inhibition of the parasite’s cysteine protease as a possible therapeutic approach.