bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute
Authors: Chakhonkaen Sriprapai , Pitnjam Keasinee , Saisuk Wachira , Ukoskit Kittipat , Muangprom Amorntip 
Published: July 2012

Abstract

Background
Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.

Results
From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.

Conclusions
Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.
Ventilatory support in critically ill hematology patients with respiratory failure
Authors: Molina Rosario , Bernal Teresa , Borges Marcio , Zaragoza Rafael , Bonastre Juan , Granada Rosa María , Rodriguez-Borregán Juan Carlos , Núñez Karla , Seijas Iratxe , Ayestaran Ignacio , Albaiceta Guillermo M ,   the EMEHU study investigators
Published: July 2012

Abstract
Introduction
Hematology patients admitted to the ICU frequently experience respiratory failure and require mechanical ventilation. Noninvasive mechanical ventilation (NIMV) may decrease the risk of intubation, but NIMV failure poses its own risks.

Methods
To establish the impact of ventilatory management and NIMV failure on outcome, data from a prospective, multicenter, observational study were analyzed. All hematology patients admitted to one of the 34 participating ICUs in a 17-month period were followed up. Data on demographics, diagnosis, severity, organ failure, and supportive therapies were recorded. A logistic regression analysis was done to evaluate the risk factors associated with death and NIVM failure.

Results
Of 450 patients, 300 required ventilatory support. A diagnosis of congestive heart failure and the initial use of NIMV significantly improved survival, whereas APACHE II score, allogeneic transplantation, and NIMV failure increased the risk of death. The risk factors associated with NIMV success were age, congestive heart failure, and bacteremia. Patients with NIMV failure experienced a more severe respiratory impairment than did those electively intubated.

Conclusions
NIMV improves the outcome of hematology patients with respiratory insufficiency, but NIMV failure may have the opposite effect. A careful selection of patients with rapidly reversible causes of respiratory failure may increase NIMV success.
Metformin attenuates ventilator-induced lung injury
Authors: Tsaknis George , Siempos Ilias I , Kopterides Petros , Maniatis Nikolaos A , Magkou Christina , Kardara Matina , Panoutsou Stefania , Kotanidou Anastasia , Roussos Charis , Armaganidis Apostolos 
Published: July 2012

Abstract
Introduction
Diabetic patients may develop acute lung injury less often than non-diabetics; a fact that could be partially ascribed to the usage of antidiabetic drugs, including metformin. Metformin exhibits pleiotropic properties which make it potentially beneficial against lung injury. We hypothesized that pretreatment with metformin preserves alveolar capillary permeability and, thus, prevents ventilator-induced lung injury.

Methods
Twenty-four rabbits were randomly assigned to pretreatment with metformin (250 mg/Kg body weight/day per os) or no medication for two days. Explanted lungs were perfused at constant flow rate (300 mL/min) and ventilated with injurious (peak airway pressure 23 cmH2O, tidal volume ≈17 mL/Kg) or protective (peak airway pressure 11 cmH2O, tidal volume ≈7 mL/Kg) settings for 1 hour. Alveolar capillary permeability was assessed by ultrafiltration coefficient, total protein concentration in bronchoalveolar lavage fluid (BALF) and angiotensin-converting enzyme (ACE) activity in BALF.

Results
High-pressure ventilation of the ex-vivo lung preparation resulted in increased microvascular permeability, edema formation and microhemorrhage compared to protective ventilation. Compared to no medication, pretreatment with metformin was associated with a 2.9-fold reduction in ultrafiltration coefficient, a 2.5-fold reduction in pulmonary edema formation, lower protein concentration in BALF, lower ACE activity in BALF, and fewer histological lesions upon challenge of the lung preparation with injurious ventilation. In contrast, no differences regarding pulmonary artery pressure and BALF total cell number were noted. Administration of metformin did not impact on outcomes of lungs subjected to protective ventilation.

Conclusions
Pretreatment with metformin preserves alveolar capillary permeability and, thus, decreases the severity of ventilator-induced lung injury in this model.
Toward almost closed genomes with GapFiller
Authors: Boetzer Marten , Pirovano Walter 
Published: July 2012

AbstractDe novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
Risk of Colorectal Cancer After Detection and Removal of Adenomas at Colonoscopy: Population-Based Case-Control Study
Authors: Brenner Hermann , Chang-Claude Jenny , Rickert Alexander , Seiler Christoph M. , Hoffmeister Michael 
Published: July 2012

Purpose Empirical evidence for recommendations of surveillance intervals after detection and removal of adenomas at colonoscopy is still sparse and mostly based on observations of adenoma recurrence. We aimed to assess risk of colorectal cancer (CRC) according to time since polypectomy and factors that might be relevant for risk stratification. Methods In a population-based case-control study conducted in Germany, detailed history and results of previous large-bowel endoscopies were obtained by interview and from medical records. Risk of CRC among participants with detection of at least one adenoma at a preceding colonoscopy compared with participants without previous large-bowel endoscopy was assessed according to time since polypectomy among 2,582 cases with CRC and 1,798 matched controls. Results Adjusted odds ratios (95% CIs) of CRC for participants with polypectomy less than 3, 3 to 5, and 6 to 10 years ago (using participants without previous endoscopy as reference group) were 0.2 (0.2 to 0.3), 0.4 (0.3 to 0.6), and 0.9 (0.5 to 1.5), respectively. Strong, significant risk reduction within 5 years was consistently seen for women and men, younger and older participants, patients with and without high-risk polyps (three or more polyps, at least one polyp ≥ 1 cm, at least one polyp with villous components), and those with and without polypectomy in the right colon. With adjusted odds ratios of 0.1 (0.1 to 0.2), 0.3 (0.2 to 0.5) and 0.4 (0.2 to 0.8) for patients with polypectomy less than 3, 3 to 5, and 6 to 10 years ago, risk reduction was particularly strong for left-sided CRC. Conclusion Extension of surveillance intervals to 5 years should be considered, even after detection and removal of high-risk polyps.
Combining general practice with international work: online survey of experiences of UK GPs
Authors: Smith Chris , Pettigrew Luisa M , Seo Ha-Neul , Dorward Jienchi 
Published: July 2012

Objectives To conduct an exploratory study to learn about the experiences of GPs who have undertaken international work. Design Cross-sectional survey Setting Online survey of UK-based GPs. Members of all UK RCGP faculties were invited to participate by email and the survey was publicised on the RCGP website Participants All UK-based GPs Main outcome measures Types of UK and international work undertaken, barriers, competencies gained, influence on career and future plans. Results The study identified 439 respondents, in a variety of GP roles at all career stages, who had undertaken international work in their role as a doctor. GPs are undertaking international work in both high and low/middle-income countries, engaging in a wide range of clinical and non-clinical activities. Respondents reported gaining a range of competencies from international work, which could be transferred back to the UK setting to a variable degree. Commonly cited barriers to international work were having to leave friends and family, and concerns regarding future employment and pension. Most reported that engaging in international work had influenced the direction of their career, with the largest proportion stating that they wish to work predominantly in the UK, with some international work in the future. Conclusion The study highlights the variety of ways in which UK GPs are combining UK general practice and international work, competencies gained with such work, and ability to transfer these back to the UK setting. Historical barriers to international work still exist and future research could further examine the value of such work.
Risk Factors for In-Hospital Mortality Among Children With Tuberculosis: The 25-Year Experience in Peru
Authors: Drobac Peter C. , Shin Sonya S. , Huamani Pedro , Atwood Sidney , Furin Jennifer , Franke Molly F. , Lastimoso Charmaine , del Castillo Hernan 
Published: July 2012

OBJECTIVE:
We examined factors associated with in-hospital death among children with tuberculosis (TB). We hypothesized that a negative response to tuberculin skin testing (TST) would predict decreased survival.

METHODS:
This retrospective cohort comprised 2392 children ages 0 to 14 years hospitalized with TB at a Peruvian referral hospital over the 25-year study period. Detailed chart abstraction captured clinical history including TB contacts, physical examination findings, diagnostic data, treatment regimen, and hospitalization outcome. We used Cox proportional hazards regression analyses to determine risk factors for mortality.

RESULTS:
Of 2392 children, 2 (0.1%) were known to be HIV-positive, 5 (0.2%) had documented multidrug-resistant TB, and 266 (11%) died. The median time from hospitalization to death was 16 days (interquartile range: 4–44 days). Reaction of &lt;5 mm induration on TST predicted death in a multivariable analysis (hazard ratio [HR]: 3.01; 95% confidence interval [CI]: 2.15–4.21; P &lt; .0001). Younger age, period of admission, alteration of mental status (HR: 3.25; 95% CI: 2.48–4.27; P &lt; .0001), respiratory distress (HR: 1.40; 95% CI: 1.07–1.83; P = .01), peripheral edema (HR: 1.97; 95% CI: 1.42–2.73; P &lt; .0001), and hemoptysis (HR: 0.57; 95% CI: 0.32–1.00; P = .05) were associated with mortality. Treatment regimens that contained rifampicin (HR: 0.47; 95% CI: 0.33–0.68; P &lt; .0001) were associated with improved survival.

CONCLUSIONS:
Negative reaction to TST is highly predictive of death among children with active TB. In children with clinical and radiographic findings suggestive of TB, a negative TST should not preclude or delay anti-TB therapy.
Misclassification of Newborns Due to Systematic Error in Plotting Birth Weight Percentile Values
Authors: Rochow Niels , Raja Preeya , Straube Sebastian , Voigt Manfred 
Published: July 2012

OBJECTIVES:
Higher than expected small for gestational age (SGA) rates and lower than expected large for gestational age (LGA) rates have been observed. A possible explanation is a leftward shift of percentile curves for birth weight due to a systematic error in plotting birth weight values in charts (ie, plotting weekly mean birth weight data at the beginning of the weeks). Our objectives were to assess how common this plotting error is and to analyze the effect of this error on SGA and LGA classification based on data from the German perinatal survey.

METHODS:
First, a systematic literature search for birth weight charts was performed, and the charts were analyzed for the plotting error. Second, percentile values (10th, 50th, and 90th) for 25 to 42 completed weeks of gestation were calculated from the data of 1 181 200 male singleton newborns (German perinatal survey, 1995–2000). Birth weight percentile curves were calculated with and without the plotting error, and the resulting SGA and LGA rates were analyzed.

RESULTS:
Fourteen of the 16 identified publications contained the systematic error in plotting. Using our calculated percentile curves, a leftward shift caused by the plotting error led to an SGA rate of 12.5% and an LGA rate of 7.7%; ∼5% of newborns were misclassified.

CONCLUSIONS:
Percentile charts should be examined for the described systematic error and, if necessary, corrected.
The Experience of Families With Children With Trisomy 13 and 18 in Social Networks
Authors: Janvier Annie , Farlow Barbara , Wilfond Benjamin S. 
Published: July 2012

BACKGROUND:
Children with trisomy 13 and trisomy 18 (T13-18) have low survival rates and survivors have significant disabilities. For these reasons, interventions are generally not recommended by providers. After a diagnosis, parents may turn to support groups for additional information.

METHODS:
We surveyed parents of children with T13-18 who belong to support groups to describe their experiences and perspectives.

RESULTS:
A total of 503 invitations to participate were sent and 332 questionnaires were completed (87% response rate based on site visits, 67% on invitations sent) by parents about 272 children. Parents reported being told that their child was incompatible with life (87%), would live a life of suffering (57%), would be a vegetable (50%), or would ruin their family (23%). They were also told by some providers that their child might have a short meaningful life (60%), however. Thirty percent of parents requested “full” intervention as a plan of treatment. Seventy-nine of these children with full T13-18 are still living, with a median age of 4 years. Half reported that taking care of a disabled child is/was harder than they expected. Despite their severe disabilities, 97% of parents described their child as a happy child. Parents reported these children enriched their family and their couple irrespective of the length of their lives.

CONCLUSIONS:
Parents who engage with parental support groups may discover an alternative positive description about children with T13-18. Disagreements about interventions may be the result of different interpretations between families and providers about the experiences of disabled children and their quality of life.
Prevalence and Correlates of Low Fundamental Movement Skill Competency in Children
Authors: Hardy Louise L. , Reinten-Reynolds Tracie , Espinel Paola , Zask Avigdor , Okely Anthony D. 
Published: July 2012

OBJECTIVE:
To describe the demographic and health-related characteristics of school-aged children with low competency in fundamental movement skills (FMS).

METHODS:
Cross-sectional representative school-based survey of Australian elementary and high school students (n = 6917) conducted in 2010. Trained field staff measured students’ height, weight, and assessed FMS and cardiorespiratory endurance (fitness). Information on students’ demographics and physical activity was collected by questionnaire.

RESULTS:
Overall, the prevalence of students with low motor skill competency was high. Girls with low socioeconomic status (SES) were twice as likely to be less competent in locomotor skills compared with high SES peers. Among boys, there was a strong association between low competency in FMS and the likelihood of being from non–English-speaking cultural backgrounds. There was a clear and consistent association between low competency in FMS and inadequate cardiorespiratory fitness. For boys, there was a clear association between low competency in object-control skills and not meeting physical activity recommendations. Conversely, the odds of being inactive were double among girls who had low competency in locomotor skills.

CONCLUSIONS:
Low competency in FMS is strongly associated with lower cardiorespiratory fitness and physical activity levels in children and adolescents. The characteristics of students with competency in FMS differ by gender and skills types and show that interventions need to target girls from low SES backgrounds and boys from non–English-speaking cultural backgrounds. The high prevalence of low competency in FMS among Grade 4 students indicates that FMS interventions need to start during the preschool and early school years.
Surface Plasmon Resonance based optical temperature sensor using ZnO:N thin film
Authors: Jindal Kajal , Tomar Monika , Gupta Vinay 
Published: July 2012

ABSTRACTTemperature dependent optical properties of RF-sputtered c-axis oriented ZnO:N thin film have been investigated. Surface Plasmon modes are excited at the metal-dielectric interface in the Kretschmann-Reather configuration using prism coupling technique. Effect of ZnO:N thin film deposited over Prism-Au structure on the SPR reflectance is studied over a wide range of temperature from 300–500 K at 633 nm wavelength. The value of dielectric constant of ZnO:N film obtained by fitting the experimentally obtained data with the theoretically generated SPR curve at the optical frequency is found to increase linearly with temperature. The increase in dielectric constant (4.03 to 4.11) with increase in temperature from 300 K to 500 K indicates a promising application of the system as an efficient low-cost temperature sensor.
Synthesis of embedded Si nano-particles using swift heavy ions and its optical properties
Authors: Sahoo P. K. , Mahapatra D. P. , Kanjilal D. 
Published: July 2012

ABSTRACTEmbedded Si nano-particles of average size around 5nm were synthesized in an amorphous Si matrix by two stage ion implantation processes. It has been observed that amorphous Si (a-Si) layers were recrystallized using 50 MeV Au ions with enhanced regrowth rate with activation energy in the range of 0.29 eV. During the crystallization process Si nanocrystals were formed in the a-Si layers due to sudden quenching of the molten tracks created by MeV Au ions. The recrystalizations were confirmed by Rutherford backscattering spectrometry-Channeling (RBSC) technique. The structural modification and nanocluster creation that emerged during recrystallization process was observed in high-resolution transmission electron microscopy and photoluminescence (PL) spectroscopy. The PL emission was observed over a broad band of 2.8 – 3.4 eV and centered at 3.25 eV. The Si nano-crystal formation can be explain by a mechanism combining the melting within the ion tracks by thermal spike process and the subsequent recrystallization nucleated from the crystalline sides at the interface.
Nanotextured Material for Applications in CSF Sample Screening and Characterization
Authors: Vattipalli Krishna , Brandigampala Savindra , McGraw Claire , Chatterjee Gaurav , Kasturirangan Srinath , Schulz Philip , Sierks Michael , Prasad Shalini 
Published: July 2012

ABSTRACTNeurodegenerative disease is primarily characterized by protein misfolding and the resultant protein aggregation. Presence of soluble oligomeric aggregates of proteins including various Aβ and α-syn aggregate species can be correlated to the onset and progression of many neurodegenerative diseases. The ability to detect protein misfolding requires the design of a diagnostics assay the will enable molecular level probing. The use of nanoporous ceramic templates enables size based immobilization of the target proteins and by leveraging the principle of “macromolecular crowding” protein association can be mapped with a high degree of resolution. By tailoring the surface functionalization within nanoporous ceramic templates, macromolecular immobilization can be selectively controlled, which in turn significantly enhances the perturbation to the electrical double layer/. The changes to the electrical double layer are measured with a high degree of sensitivity through impedance spectroscopy.Pre symptomatic diagnosis and distinction between Alzheimer’s and Parkinson’s diseases can be achieved by the specific detection and quantification of levels of each of these different toxic protein species in cerebrospinal fluid (CSF). Detection using highly selective morphology specific reagents in conjunction with the ultrasensitive nanoporous electronic biosensor showed the presence of different protein morphologies in human CSF samples. Detection is primarily achieved by identifying the specific association of the protein with its receptor using electrochemical impedance spectroscopy. Furthermore, we show that these morphology specific reagents can readily classify between post-mortem CSF samples from AD, PD and cognitively normal sources. These studies suggest that detection of specific oligomeric aggregate species holds great promise as sensitive biomarkers for neurodegenerative disease.