bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
Authors: Brown Christopher T , Sharon Itai , Thomas Brian C , Castelle Cindy J , Morowitz Michael J , Banfield Jillian F 
Published: December 2013

Abstract

Background
The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored.

Results
To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community.
We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation.
During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences related to respiratory metabolism and motility.

Conclusions
Genome-based analysis provided direct insight into strain-specific potential for anaerobic respiration and yielded the first genome for the genus Varibaculum. Importantly, comparison of these de novo assembled genomes with closely related isolate genomes supported the accuracy of the metagenomic methodology. Over a one-week period, the early gut microbial community transitioned to a community with a higher representation of obligate anaerobes, emphasizing both taxonomic and metabolic instability during colonization.
RETRACTED ARTICLE: Progesterone receptor assembly of a transcriptional complex along with activator protein 1, signal transducer and activator of transcription 3 and ErbB-2 governs breast cancer growth and predicts response to endocrine therapy
Authors: Díaz Flaqué María C , Galigniana Natalia M , Béguelin Wendy , Vicario Rocío , Proietti Cecilia J , Russo Rosalía Cordo , Rivas Martín A , Tkach Mercedes , Guzmán Pablo , Roa Juan C , Maronna Esteban , Pineda Viviana , Muñoz Sergio , Mercogliano María Florencia , Charreau Eduardo H , Yankilevich Patricio , Schillaci Roxana , Elizalde Patricia V 
Published: December 2013

Abstract
Introduction
The role of the progesterone receptor (PR) in breast cancer remains a major clinical challenge. Although PR induces mammary tumor growth, its presence in breast tumors is a marker of good prognosis. We investigated coordinated PR rapid and nonclassical transcriptional effects governing breast cancer growth and endocrine therapy resistance.

Methods
We used breast cancer cell lines expressing wild-type and mutant PRs, cells sensitive and resistant to endocrine therapy, a variety of molecular and cellular biology approaches, in vitro proliferation studies and preclinical models to explore PR regulation of cyclin D1 expression, tumor growth, and response to endocrine therapy. We investigated the clinical significance of activator protein 1 (AP-1) and PR interaction in a cohort of 99 PR-positive breast tumors by an immunofluorescence protocol we developed. The prognostic value of AP-1/PR nuclear colocalization in overall survival (OS) was evaluated using Kaplan-Meier method, and Cox model was used to explore said colocalization as an independent prognostic factor for OS.

Results
We demonstrated that at the cyclin D1 promoter and through coordinated rapid and transcriptional effects, progestin induces the assembly of a transcriptional complex among AP-1, Stat3, PR, and ErbB-2 which functions as an enhanceosome to drive breast cancer growth. Our studies in a cohort of human breast tumors identified PR and AP-1 nuclear interaction as a marker of good prognosis and better OS in patients treated with tamoxifen (Tam), an anti-estrogen receptor therapy. Rationale for this finding was provided by our demonstration that Tam inhibits rapid and genomic PR effects, rendering breast cancer cells sensitive to its antiproliferative effects.

Conclusions
We here provided novel insight into the paradox of PR action as well as new tools to identify the subgroup of ER+/PR + patients unlikely to respond to ER-targeted therapies.
Simple diagnosis ofSTAT1gain-of-function alleles in patients with chronic mucocutaneous candidiasis
Authors: Mizoguchi Yoko , Tsumura Miyuki , Okada Satoshi , Hirata Osamu , Minegishi Shizuko , Imai Kohsuke , Hyakuna Nobuyuki , Muramatsu Hideki , Kojima Seiji , Ozaki Yusuke , Imai Takehide , Takeda Sachiyo , Okazaki Tetsuya , Ito Tsuyoshi , Yasunaga Shin'ichiro , Takihara Yoshihiro , Bryant Vanessa L , Kong Xiao-Fei , Cypowyj Sophie , Boisson-Dupuis Stéphanie , Puel Anne , Casanova Jean-Laurent , Morio Tomohiro , Kobayashi Masao 
Published: December 2013

AbstractCMCD is a rare congenital disorder characterized by persistent or recurrent skin, nail, and mucosal membrane infections caused by Candida albicans. Heterozygous GOF STAT1 mutations have been shown to confer AD CMCD as a result of impaired dephosphorylation of STAT1. We aimed to identify and characterize STAT1 mutations in CMCD patients and to develop a simple diagnostic assay of CMCD. Genetic analysis of STAT1 was performed in patients and their relatives. The mutations identified were characterized by immunoblot and reporter assay using transient gene expression experiments. Patients' leukocytes are investigated by flow cytometry and immunoblot. Six GOF mutations were identified, three of which are reported for the first time, that affect the CCD and DBD of STAT1 in two sporadic and four multiplex cases in 10 CMCD patients from Japan. Two of the 10 patients presented with clinical symptoms atypical to CMCD, including other fungal and viral infections, and three patients developed bronchiectasis. Immunoblot analyses of patients' leukocytes showed abnormally high levels of pSTAT1 following IFN-γ stimulation. Based on this finding, we performed a flow cytometry-based functional analysis of STAT1 GOF alleles using IFN-γ stimulation and the tyrosine kinase inhibitor, staurosporine. The higher levels of pSTAT1 observed in primary CD14+ cells from patients compared with control cells persisted and were amplified by the presence of staurosporine. We developed a flow cytometry-based STAT1 functional screening method that would greatly facilitate the diagnosis of CMCD patients with GOF STAT1 mutations.
Electronic Self-Report Assessment for Cancer and Self-Care Support: Results of a Multicenter Randomized Trial
Authors: Berry Donna L. , Hong Fangxin , Halpenny Barbara , Partridge Ann H. , Fann Jesse R. , Wolpin Seth , Lober William B. , Bush Nigel E. , Parvathaneni Upendra , Back Anthony L. , Amtmann Dagmar , Ford Rosemary 
Published: December 2013

Purpose The purpose of this trial was to evaluate the effect of a Web-based, self-report assessment and educational intervention on symptom distress during cancer therapy. Patients and Methods A total of 752 ambulatory adult participants were randomly assigned to symptom/quality-of-life (SxQOL) screening at four time points (control) versus screening, targeted education, communication coaching, and the opportunity to track/graph SxQOL over time (intervention). A summary of the participant-reported data was delivered to clinicians at each time point in both groups. All participants used the assessment before a new therapeutic regimen, at 3 to 6 weeks and 6 to 8 weeks later, completing the final assessment at the end of therapy. Change in Symptom Distress Scale–15 (SDS-15) score from pretreatment to end of study was compared using analysis of covariance and regression analysis adjusting for selected variables. Results We detected a significant difference between study groups in mean SDS-15 score change from baseline to end of study: 1.27 (standard deviation [SD], 6.7) in the control group (higher distress) versus −0.04 (SD, 5.8) in the intervention group (lower distress). SDS-15 score was reduced by an estimated 1.21 (95% CI, 0.23 to 2.20; P = .02) in the intervention group. Baseline SDS-15 score (P < .001) and clinical service (P = .01) were predictive. Multivariable analyses suggested an interaction between age and study group (P = .06); in subset analysis, the benefit of intervention was strongest in those age > 50 years (P = .002). Conclusion Web-based self-care support and communication coaching added to SxQOL screening reduced symptom distress in a multicenter sample of participants with various diagnoses during and after active cancer treatment. Participants age > 50 years, in particular, may have benefited from the intervention.
Serum 2-Hydroxyglutarate Production in IDH1- and IDH2-Mutated De Novo Acute Myeloid Leukemia: A Study by the Acute Leukemia French Association Group
Authors: Janin Maxime , Mylonas Elena , Saada Véronique , Micol Jean-Baptiste , Renneville Aline , Quivoron Cyril , Koscielny Serge , Scourzic Laurianne , Forget Sébastien , Pautas Cécile , Caillot Denis , Preudhomme Claude , Dombret Hervé , Berthon Céline , Barouki Robert , Rabier Daniel , Auger Nathalie , Griscelli Frank , Chachaty Elisabeth , Leclercq Edwige , Courtier Marie-Hélène , Bennaceur-Griscelli Annelise , Solary Eric , Bernard Olivier Adrien , Penard-Lacronique Virginie , Ottolenghi Chris , de Botton Stéphane 
Published: December 2013

Purpose Mutated isocitrate dehydrogenases (IDHs) 1 and 2 produce high levels of 2-hydroxyglutarate (2-HG). We investigated whether, in acute myeloid leukemia (AML), serum 2-HG would predict the presence of IDH1/2 mutations at diagnosis and provide a marker of minimal residual disease (MRD). Patients and Methods Serum samples from 82 patients at diagnosis of de novo AML (IDH1/2 mutated, n = 53) and 68 patients without AML were analyzed for total 2-HG and its ratio of D to L stereoisomers by mass spectrometry. We measured 2-HG levels and molecular markers of MRD (WT1 and NPM1) in serial samples of 36 patients with IDH1/2 mutations after induction therapy. Results In patients with AML with IDH1/2 mutations, 2-HG serum levels were significantly higher than in patients with IDH1/2 wild type (P < .001). Area under the receiver operating characteristic curve was 99%. The optimum diagnostic cutoff between IDH1/2 mutated and normal was 2 μmol/L (sensitivity, 100%; specificity, 79%). Quantification of the D/L stereoisomers increased specificity (100%; 95% CI, 83% to 100%) compared with total 2-HG (P = .031). In patients with IDH2 R172 mutations, 2-HG levels were higher relative to those with other IDH1/2 mutations (P < .05). During follow-up, serum 2-HG levels showed strong positive correlation with WT1 and NPM1 (P < .001). After induction therapy, total 2-HG serum levels < 2 μmol/L were associated with better overall (P = .008) and disease-free survival (P = .005). Conclusion Serum 2-HG is a predictor of the presence of IDH1/2 mutations and outcome in these patients. Discrimination between D/L stereoisomers improved specificity.
Formation and growth of shelterbelt plantings of Voronezh region
Authors: Михин  , Mikhin Dmitriy , Трегубов  , Tregubov Oleg 
Published: December 2013

Shelterbelt plantings in the Voronezh region occupy an area of approximately 60 thousand
hectares. They were created at different times with tree species: poplars, silver birch,
English oak, common and green ash , locust, elm, English field maple and Bosnian maple,
little-leaved linden; bushes – Elaeagnus angustifolia,
yellow acacia, Tatarian honeysuckle, fly honeysuckle, alder buckthorn and other
pure and mixed in composition. Width of the bands, row spacing, and planting density
determine their growth and condition. It was found that in artificial linear stands with the main species of silver birch with an increase of double width, there is average decrease of the growth parameters to 12 %. Mixed cultures of birch are more productive and in them by the age of 25 years conservation, average diameter, height is greater for 4,
8…16, 3 % as compared to pure composition
forest belts. Silver birch is in a dominant
position in the stands with green ash, locust,
Norway maple and forest apple trees.
European ash has higher inventory indices in
co-cultivation with English oak and Norway
maple than with elm and silver birch. Similar
laws are identified also for green ash. For all
the considered species active growth period in
height and diameter up to the age of 10…15
years is observed. At the same time at middleaged
stands on the main soil types, there are
differences in the growth of marginal tree belt
and central belts. During this period of growth
convex transverse profile is usually formed.
L2 development around tests: Learner response processes and dynamic assessment
Authors: Poehner Matthew E. , van Compernolle Rémi A. 
Published: December 2013

Abstract
This paper examines learner response processes during a Dynamic Assessment (DA) of L2 reading comprehension. We present a detailed case analysis of an L2 French learner whose success in responding to a comprehension item obscures her understanding of the text and the challenges it poses. This aligns with research indicating that learners may orient to such assessments as problem-solving rather than comprehension activities (Rupp, Fern, and Choi 2006). In DA, learner response processes are externalized through dialogue with the assessor, or mediator, who does not simply document these processes but intervenes. We trace how the mediator regulates learner orientation to the task, pursues reasons behind learner choices, and cooperates with the learner to create opportunities for learning during the assessment.
Language choices in L2 English sentence production: Why speakers could have used modal perfect but didn’t
Authors: Conroy Mark A. , Cupples Linda 
Published: December 2013

Abstract
This study compared production of modal perfect sentences by native English speakers and advanced non-native English speakers from Asian L1 backgrounds in discourse and discourse-free contexts. In experiment 1, native and non-native speakers reconstructed modal perfect sentences from sentential anagrams under time pressure. Both speaker groups were faster to construct modal perfect sentences than closely matched control sentences. In experiment 2, native and non-native speakers read and responded orally to stories designed to elicit modal perfect. The results revealed that non-native speakers produced significantly fewer modal perfect sentences than native speakers. Taken together, the findings suggest that although non-native speakers from Asian L1 backgrounds have the syntactic capability to produce modal perfect under constrained conditions in a sentential anagram task, they are less likely than native speakers to produce such constructions in particular discourse contexts, perhaps as a result of differences in cultural background. Implications for English language instruction are discussed.
Antenatal and Postnatal Growth and 5-Year Cognitive Outcome in Very Preterm Infants
Authors: Leppänen Marika , Lapinleimu Helena , Lind Annika , Matomäki Jaakko , Lehtonen Liisa , Haataja Leena , Rautava Päivi 
Published: December 2013

OBJECTIVES:
To study how antenatal growth affects cognitive outcome in very preterm infants and to determine whether there is an association between growth in any particular time period between birth and 5 years of age and cognitive outcome. Small for gestational age (SGA) and non-SGA infants were analyzed separately, because antenatal growth may affect postnatal growth.

METHODS:
Very low birth weight (&lt;1501 g) infants born between 2001 and 2006 and infants born at &lt;32 gestational weeks between 2004 and 2006 who were treated at Turku University Hospital (n = 181) were followed. Weight, length, and head circumference (HC) of the infants were measured at 9 time points between birth and 5 years. The growth was determined as a z score change between measurement points. Cognitive development was assessed at 5 years of age with the Wechsler Preschool and Primary Scales of Intelligence–Revised. The association between growth and full-scale IQ (FSIQ) was studied.

RESULTS:
Growth in length and height was not associated with 5-year cognitive outcome. However, weight (r = 0.18, P = .04) and HC growth (r = 0.25, P = .01) between birth and 2 years of corrected age correlated to FSIQ in non-SGA children. In SGA children, HC growth (r = 0.33, P = .03) around term age correlated to FSIQ.

CONCLUSIONS:
Cognitive outcome was similar in SGA and non-SGA very preterm infants. Growth affected cognition positively in both subgroups, but the critical time period was different.
Accuracy of Pulse Oximetry in Children
Authors: Ross Patrick A. , Newth Christopher J.L. , Khemani Robinder G. 
Published: December 2013

OBJECTIVE:
For children with cyanotic congenital heart disease or acute hypoxemic respiratory failure, providers frequently make decisions based on pulse oximetry, in the absence of an arterial blood gas. The study objective was to measure the accuracy of pulse oximetry in the saturations from pulse oximetry (SpO2) range of 65% to 97%.

METHODS:
This institutional review board–approved prospective, multicenter observational study in 5 PICUs included 225 mechanically ventilated children with an arterial catheter. With each arterial blood gas sample, SpO2 from pulse oximetry and arterial oxygen saturations from CO-oximetry (SaO2) were simultaneously obtained if the SpO2 was ≤97%.

RESULTS:
The lowest SpO2 obtained in the study was 65%. In the range of SpO2 65% to 97%, 1980 simultaneous values for SpO2 and SaO2 were obtained. The bias (SpO2 – SaO2) varied through the range of SpO2 values. The bias was greatest in the SpO2 range 81% to 85% (336 samples, median 6%, mean 6.6%, accuracy root mean squared 9.1%). SpO2 measurements were close to SaO2 in the SpO2 range 91% to 97% (901 samples, median 1%, mean 1.5%, accuracy root mean squared 4.2%).

CONCLUSIONS:
Previous studies on pulse oximeter accuracy in children present a single number for bias. This study identified that the accuracy of pulse oximetry varies significantly as a function of the SpO2 range. Saturations measured by pulse oximetry on average overestimate SaO2 from CO-oximetry in the SpO2 range of 76% to 90%. Better pulse oximetry algorithms are needed for accurate assessment of children with saturations in the hypoxemic range.
Hand Pulling Following Mowing and Herbicide Treatments Increases Control of Spotted Knapweed (Centaurea stoebe)
Authors: MacDonald Neil W. , Martin Laurelin M. , Kapolka Corey K. , Botting Timothy F. , Brown Tami E. 
Published: December 2013

AbstractExtensive areas in the upper Midwest have been invaded by spotted knapweed, and effective management strategies are required to reestablish native plant communities. We examined effects of mowing, mowing plus clopyralid, or mowing plus glyphosate in factorial combination with hand pulling and burning on knapweed abundances on a knapweed-infested site in western Michigan. We applied mowing and herbicide treatments in summer 2008, and seeded all plots with native grasses and forbs in spring 2009. We conducted the knapweed pulling treatment from 2009 to 2012 in July. The prescribed burn was conducted in April 2012. By 2012, hand pulling reduced adult knapweed densities to 0.57 ± 0.12 m−2(0.053 ± 0.011 ft−2) (mean ± SE), which was 5.8% of nonpulled treatments, juvenile densities to 0.29 ± 0.07 m−2(2.1% of nonpulled treatments), and seedling densities to 0.07 ± 0.06 m−2(2.6% of nonpulled treatments). After 3 yr, hand pulling reduced seed bank densities to 68 ± 26 m−2as compared to 524 ± 254 m−2in nonpulled treatments and 369 ± 66 m−2in adjacent untreated areas of the study site. Without hand pulling, effects of mowing or mowing plus glyphosate were short-lived and allowed knapweed to rapidly resurge. In comparison, although a single mowing plus clopyralid treatment maintained significantly reduced densities of knapweed for 4 yr, by 2012 knapweed biomass in the nonpulled clopyralid treatment was approximately 60% of that in the other nonpulled treatments. Burning had minimal impacts on knapweed densities regardless of treatment combination, probably as a result of low fire intensity. Results demonstrated that persistent hand pulling used as a follow-up to single mowing or mowing plus herbicide treatments can be an effective practice for treating isolated spotted knapweed infestations or for removing small numbers of knapweed that survive herbicide applications.
Modeling Potential Range Expansion of the Invasive Shrub Leucaena leucocephala in the Hengchun Peninsula, Taiwan
Authors: Chiou Chyi-Rong , Wang Hsiao-Hsuan , Chen Yen-Jui , Grant William E. , Lu Ming-Lun 
Published: December 2013

AbstractPrediction of invasive species distributions from survey data is widely recognized as a significant component of forest management and conservation planning. Leucaena leucocephala is the most aggressive invasive shrub and tree in the Hengchun peninsula in southern Taiwan. We analyzed geo-referenced data to identify potential variables of invasion and to predict likelihood of further invasion using boosted regression trees. Our results, which classified 92% of the cells correctly with regard to species presence and absence, indicated probability of invasion is correlated with climatic conditions (temperature and precipitation), landscape features (altitude; slope ratio and aspect; percentages of natural or secondary forest, agriculture land, developed area, and water bodies; and distances to the nearest forest edge and river), and anthropogenic factors (length of forest edge, and distances to the nearest road and agriculture land). The most influential variables are average annual temperature, altitude, precipitation, and slope. Continued range expansion by L. leucocephala is most likely to proceed (1) from the eastern and western portions toward the central portion of Hengchun township and (2) throughout the southern and toward the eastern portions of Manjhou township. Our model should provide useful information to aid forest managers in the development of long term monitoring and control strategies for L. leucocephala, in the early detection and eradication of newly established invasions, and also a framework for the integration and analysis of new presence and absence field data as they become available.