bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for the Solar Radiation Influence on Downward Longwave Irradiance Measurements by Pyrgeometers
Authors: Meloni Daniela , Di Biagio Claudia , di Sarra Alcide , Monteleone Francesco , Pace Giandomenico , Sferlazzo Damiano Massimiliano 
Published: July 2012

Abstract
Measurements of broadband downward longwave (LW) irradiance are carried out at Lampedusa, Italy, in the Mediterranean, jointly with solar irradiance, since 2004 using shaded and unshaded Eppley Precision Infrared Radiometers (PIRs) and Kipp & Zonen CGR4 pyrgeometers. The calibrations of the different pyrgeometers are traceable to the Physikalisch-Meteorologisches Observatorium Davos World Radiation Center (PMOD/WRC). Nighttime measurements from intercalibrated pyrgeometers agree within ±2 W m−2. The performance of the pyrgeometers when operated unshaded has been analyzed by comparison with shaded instruments. For the PIR, the nonhomogeneous dome temperature in cloud-free conditions produces differences in LW irradiance within ±4 W m−2, depending on the time of the day and the season. The effect of the LW fraction of solar radiation reaching the sensor and a possible shortwave leakage of the dome interference filter produces differences between shaded and unshaded pyrgeometers during daytime. In cloud-free conditions, the unshaded PIR overestimates the LW irradiance measured by a shaded PIR by up to 10 W m−2, and by up to 12 W m−2 compared to a shaded CGR4. Conversely, the unshaded CGR4 LW irradiances agree with those of a shaded PIR within the measurements’ uncertainties. An empirical formula to correct the solar effect of the PIR has been derived. Applying this correction, the average LW irradiance overestimate for cloud-free conditions decreases from 3.8 ± 1.8 to 0.0 ± 1.3 W m−2 in spring, and from 3.2 ± 1.7 to 0.0 ± 1.3 W m−2 in summer. Thus, LW irradiance from an unshaded PIR can be derived within about ±2 W m−2 of a shaded PIR.
A Methodology for the Characterization of Periodicities in Nonsteady Time Series: Application to Tropospheric Ozone Recharging Cycles in the Western Mediterranean Basin
Authors: Palau Jose Luis , Rovira Francisco 
Published: July 2012

Abstract
Environmental measurements often show unsteady variability and background red noise (stochastic component) superimposed on persistent trivial daily, seasonal, and annual variability. In addition to this, environmental time series often present gaps due to a myriad of possible factors, such as malfunction of the sensors, connection loss, etc. As a result, interpreting and identifying periodicities in this type of time series by means of spectral analysis tools, like the Fourier transform, are difficult and lack precision. To overcome these difficulties, a methodology is proposed in the first part of this paper that integrates statistical tools (iterative Student’s t test), parametric reconstruction, and spectral analysis (Lomb periodogram and wavelets). In the second part of the paper, this methodology is tested (i) in the high-frequency part of the spectrum of two (well known) synthetic time series and (ii) to identify nontrivial (e.g., daily cycles) high-frequency periodicities (linked to some mesometeorological processes) in three tropospheric ozone time series recorded by the Valencia regional air quality monitoring network (on the Mediterranean side of Spain) during a 14-yr period. This methodology can determine statistically significant, seasonally dependent recurrences in the high-frequency variability (&lt;15 days) observed in ozone time series measured in a Mediterranean region of Spain under high noise-to-signal ratios.
Coded Statutory Data Sets for Evaluation of Public Health Law
Authors: Costich Julia Field 
Published: July 2012

Background and objectives: The evaluation of public health law requires reliable accounts of underlying statutes and regulations. States often enact public health-related statutes with nonuniform provisions, and variation in the structure of state legal codes can foster inaccuracy in evaluating the impact of specific categories of law. The optimal format for empirical analysis is a machine-readable 50-state coded data set. This study provides a comprehensive assessment of these resources and related materials with a focus on statutory data sets. Research design: An exhaustive literature search was followed by a “pearling” or “snowball” approach to assure the most complete inventory of this very diverse and diffuse information. We also interviewed three leading investigators to identify barriers to wider use and availability of coded legal data sets. Results: We identified relatively few accessible coded statutory data sets, and others that are not available for use outside the group or individual that compiled them. The Robert Wood Johnson Foundation-funded Public Health Law Research Program has made funding available for the development and dissemination of additional data sets, as well as extensive guidance regarding their use in the evaluation of public health law. Investigators reported serious obstacles to these activities in the past. Conclusions: Compilation of coded statutory data sets requires a focused investment of resources that has only recently become available. Funders should require grantees to make their work accessible to other investigators so as to assure development of public health law research and evaluation.
HIF-1 expression is associated with CCL2 chemokine expression in airway inflammatory cells: implications in allergic airway inflammation
Authors: Baay-Guzman Guillermina J , Bebenek Ilona G , Zeidler Michelle , Hernandez-Pando Rogelio , Vega Mario I , Garcia-Zepeda Eduardo A , Antonio-Andres Gabriela , Bonavida Benjamin , Riedl Marc , Kleerup Eric , Tashkin Donald P , Hankinson Oliver , Huerta-Yepez Sara 
Published: July 2012

AbstractBackgroundThe pathogenesis of allergic airway inflammation in asthmatic patients is complex and characterized by cellular infiltrates and activity of many cytokines and chemokines. Both the transcription factor hypoxia inducible factor-1 (HIF-1) and chemokine CCL2 have been shown to play pivotal roles in allergic airway inflammation. The interrelationship between these two factors is not known. We hypothesized that the expression of HIF-1 and CCL2 may be correlated and that the expression of CCL2 may be under the regulation of HIF-1. Several lines of evidence are presented to support this hypothesis.MethodsThe effects of treating wild-type OVA (ovalbumin)-sensitized/challenged mice with ethyl-3,4-dihydroxybenzoate (EDHB), which upregulate HIF, on CCL2 expression, were determined. Mice conditionally knocked out for HIF-1β was examined for their ability to mount an allergic inflammatory response and CCL2 expression in the lung after intratracheal exposure to ovalbumin. The association of HIF-1α and CCL2 levels was also measured in endobronchial biopsies and bronchial fluid of asthma patients after challenge.ResultsWe show that both HIF-1α and CCL2 were upregulated during an OVA (ovalbumin)-induced allergic response in mice. The levels of HIF-1α and CCL2 were significantly increased following treatment with a pharmacological agent which upregulates HIF-1α, ethyl-3,4-dihydroxybenzoate (EDHB). In contrast, the expression levels of HIF-1α and CCL2 were decreased in the lungs of mice that have been conditionally knocked out for ARNT (HIF-1β) following sensitization with OVA when compared to levels in wild type mice. In asthma patients, the levels of HIF-1α and CCL2 increased after challenge with the allergen.ConclusionsThese data suggest that CCL2 expression is regulated, in part, by HIF-1 in the lung. These findings also demonstrate that both CCL2 and HIF-1 are implicated in the pathogenesis of allergic airway inflammation.
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer
Authors: Johansson Maria U , Zoete Vincent , Michielin Olivier , Guex Nicolas 
Published: July 2012

Abstract

Background
Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software.

Results
In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function.

Conclusions
The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike.
Characterization of the small RNA component of leaves and fruits from four different cucurbit species
Authors: Jagadeeswaran Guru , Nimmakayala Padma , Zheng Yun , Gowdu Kanchana , Reddy Umesh K , Sunkar Ramanjulu 
Published: July 2012

Abstract

Background
MicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants. The Cucurbitaceae or cucurbit family represents some of economically important species, particularly those with edible and medicinal fruits. Genomic tools for the molecular analysis of members of this family are just emerging. Partial draft genome sequence became available recently for cucumber and watermelon facilitating investigation of the small RNA component of the transcriptomes in cucurbits.

Results
We generated four small RNA libraries from bottle gourd (Lagenaria siceraria), Cucurbita moschata, Cucurbita pepo, and, watermelon (Citrullus lanatus var. lanatus) in order to identify conserved and novel lineage specific miRNAs in these cucurbits. Deep sequencing of small RNA libraries from these species resulted in 1,597,263, 532,948, 601,388, and 493,384 unique sRNA reads from bottle gourd, moschata, pepo and watermelon, respectively. Sequence analysis of these four libraries resulted in identification of 21 miRNA families that are highly conserved and 8 miRNA families that are moderately conserved in diverse dicots. We also identified 4 putative novel miRNAs in these plant species. Furthermore, the tasiRNAs were identified and their biogenesis was determined in these cucurbits. Small RNA blot analysis or q-PCR analyses of leaf and fruit tissues of these cucurbits showed differential expression of several conserved miRNAs. Interestingly, the abundance of several miRNAs in leaves and fruits of closely related C. moschata and C. pepo was also distinctly different. Target genes for the most conserved miRNAs are also predicted.

Conclusion
High-throughput sequencing of small RNA libraries from four cucurbit species has provided a glimpse of small RNA component in their transcriptomes. The analysis also showed considerable variation within four cucurbit species with regards to expression of individual miRNAs.
Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress
Authors: Yang Shihui , Giannone Richard J , Dice Lezlee , Yang Zamin K , Engle Nancy L , Tschaplinski Timothy J , Hettich Robert L , Brown Steven D 
Published: July 2012

Abstract

Background

Clostridium thermocellum is a candidate consolidated bioprocessing biocatalyst, which is a microorganism that expresses enzymes for both cellulose hydrolysis and its fermentation to produce fuels such as lignocellulosic ethanol. However, C. thermocellum is relatively sensitive to ethanol compared to ethanologenic microorganisms such as yeast and Zymomonas mobilis that are used in industrial fermentations but do not possess native enzymes for industrial cellulose hydrolysis.

Results
In this study, C. thermocellum was grown to mid-exponential phase and then treated with ethanol to a final concentration of 3.9 g/L to investigate its physiological and regulatory responses to ethanol stress. Samples were taken pre-shock and 2, 12, 30, 60, 120, and 240 min post-shock, and from untreated control fermentations for systems biology analyses. Cell growth was arrested by ethanol supplementation with intracellular accumulation of carbon sources such as cellobiose, and sugar phosphates, including fructose-6-phosphate and glucose-6-phosphate. The largest response of C. thermocellum to ethanol shock treatment was in genes and proteins related to nitrogen uptake and metabolism, which is likely important for redirecting the cells physiology to overcome inhibition and allow growth to resume.

Conclusion
This study suggests possible avenues for metabolic engineering and provides comprehensive, integrated systems biology datasets that will be useful for future metabolic modeling and strain development endeavors.
Characterization of a putative grapevine Zn transporter, VvZIP3, suggests its involvement in early reproductive development in Vitis vinifera L
Authors: Gainza-Cortés Felipe , Pérez-Dïaz Ricardo , Pérez-Castro Ramón , Tapia Jaime , Casaretto José A , González Sebastián , Peña-Cortés Hugo , Ruiz-Lara Simón , González Enrique 
Published: July 2012

AbstractBackgroundZinc (Zn) deficiency is one of the most widespread mineral nutritional problems that affect normal development in plants. Because Zn cannot passively diffuse across cell membranes, it must be transported into intracellular compartments for all biological processes where Zn is required. Several members of the Zinc-regulated transporters, Iron-regulated transporter-like Protein (ZIP) gene family have been characterized in plants, and have shown to be involved in metal uptake and transport. This study describes the first putative Zn transporter in grapevine. Unravelling its function may explain an important symptom of Zn deficiency in grapevines, which is the production of clusters with fewer and usually smaller berries than normal.ResultsWe identified and characterized a putative Zn transporter from berries ofVitis vinifera L., named VvZIP3. Compared to other members of the ZIP family identified in theVitis vinifera L.genome,VvZIP3is mainly expressed in reproductive tissue - specifically in developing flowers - which correlates with the high Zn accumulation in these organs. Contrary to this, the low expression ofVvZIP3in parthenocarpic berries shows a relationship with the lower Zn accumulation in this tissue than in normal seeded berries where its expression is induced by Zn. The predicted protein sequence indicates strong similarity with several members of the ZIP family from Arabidopsis thaliana and other species. Moreover, VvZIP3 complemented the growth defect of a yeast Zn-uptake mutant, ZHY3, and is localized in the plasma membrane of plant cells, suggesting that VvZIP3 has the function of a Zn uptake transporter.ConclusionsOur results suggest that VvZIP3 encodes a putative plasma membrane Zn transporter protein member of the ZIP gene family that might play a role in Zn uptake and distribution during the early reproductive development inVitis vinifera L., indicating that the availability of this micronutrient may be relevant for reproductive development.
Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses
Authors: Brenner Wolfram G , Schmülling Thomas 
Published: July 2012

AbstractBackgroundThe plant hormone cytokinin regulates growth and development of roots and shoots in opposite ways. In shoots it is a positive growth regulator whereas it inhibits growth in roots. It may be assumed that organ-specific regulation of gene expression is involved in these differential activities, but little is known about it. To get more insight into the transcriptional events triggered by cytokinin in roots and shoots, we studied genome-wide gene expression in cytokinin-treated and cytokinin-deficient roots and shoots.ResultsIt was found by principal component analysis of the transcriptomic data that the immediate-early response to a cytokinin stimulus differs from the later response, and that the transcriptome of cytokinin-deficient plants is different from both the early and the late cytokinin induction response. A higher cytokinin status in the roots activated the expression of numerous genes normally expressed predominantly in the shoot, while a lower cytokinin status in the shoot reduced the expression of genes normally more active in the shoot to a more root-like level. This shift predominantly affected nuclear genes encoding plastid proteins. An organ-specific regulation was assigned to a number of genes previously known to react to a cytokinin signal, including root-specificity for the cytokinin hydroxylase geneCYP735A2and shoot specificity for the cell cycle regulator geneCDKA;1. Numerous cytokinin-regulated genes were newly discovered or confirmed, including the meristem regulator genesSHEPHERDandCLAVATA1, auxin-related genes (IAA7,IAA13,AXR1, PIN2, PID), several genes involved in brassinosteroid (CYP710A1,CYP710A2,DIM/DWF) and flavonol (MYB12,CHS,FLS1) synthesis, various transporter genes (e.g.HKT1), numerous members of the AP2/ERF transcription factor gene family, genes involved in light signalling (PhyA,COP1,SPA1), and more than 80 ribosomal genes. However, contrasting with the fundamental difference of the growth response of roots and shoots to the hormone, the vast majority of the cytokinin-regulated transcriptome showed similar response patterns in roots and shoots.ConclusionsThe shift of the root and shoot transcriptomes towards the respective other organ depending on the cytokinin status indicated that the hormone determines part of the organ-specific transcriptome pattern independent of morphological organ identity. Numerous novel cytokinin-regulated genes were discovered which had escaped earlier discovery, most probably due to unspecific sampling. These offer novel insights into the diverse activities of cytokinin, including crosstalk with other hormones and different environmental cues, identify the AP2/ERF class of transcriptions factors as particularly cytokinin sensitive, and also suggest translational control of cytokinin-induced changes.
Correlation of anterior segment optical coherence tomography measurements with graft trephine diameter following descemet stripping automated endothelial keratoplasty
Authors: Tan Gavin S , He Mingguang , Tan Donald T , Mehta Jodhbir S 
Published: July 2012

Abstract

Background
To assess repeatability of the Zhongshan Assessment Program (ZAP) software measurement of Anterior Segment Optical Coherence Tomography (ASOCT) images and correlate with graft trephine diameter following Descemet Stripping Automated Endothelial Keratoplasty (DSAEK)

Methods
Retrospectively evaluated interventional case series. 121 consecutive eyes undergoing DSAEK over a 26 month period underwent ASOCT imaging 1month after their surgery. ASOCT images were processed using ZAP software which measured the graft and cornea parameters including anterior and posterior graft arc length and cord length, posterior cornea arc length (PCAL) and anterior chamber width.

Results
The graft measurements showed good repeatability on ASOCT using ZAP with high intra class coefficient and small variation in the coefficient of variation. On ASOCT, the mean recipient PCAL was 12.99+/−0.69mm and the anterior chamber width was 11.16+/−0.57mm. The mean Graft anterior arc length was 9.69+/−0.66mm and the mean Graft anterior cord length was 8.92+/−2.94mm. The mean graft posterior arc length was 9.24+/−0.75mm and the mean graft posterior cord length was 8.15+/−0.57mm. Graft posterior arc length (rho=0.788, p< 0.001) correlated best with intra-operative graft trephine diameter. The mean ratio of posterior graft arc length to PCAL was 0.712 +/− 0.056.

Conclusions
We have validated the repeatability of the ZAP software for DSAEK graft measurements from ASOCT images and shown that the graft arc length parameters calculated from the ASOCT images correlate well with the intra-operative graft trephine diameter. This software may help surgeons determine the optimal DSAEK graft size based on pre-operative ASOCT measurements of the recipient eye.
A population-based study of Kurdish breast cancer in northern Iraq: Hormone receptor and HER2 status. A comparison with Arabic women and United States SEER data
Authors: Majid Runnak A , Mohammed Hazha A , Hassan Hemin A , Abdulmahdi Wasan A , Rashid Rekawt M , Hughson Michael D 
Published: July 2012

AbstractBackgroundHormone receptor (HR) and HER2 expression predict the therapeutic response and prognosis of breast cancer. In the Middle-East, breast cancer is diagnosed at a young age, and Arabic women are reported to have a low frequency of HR positive tumors. This study investigates HR and HER2 expression among Kurdish and Arabic women.MethodsDuring 2008–2010, the Sulaimaniyah Directorate of Health records identified 514 Sulaimaniyah Kurdish women, 227 Kurdish women of other Governates, and 83 Arabic women with a first diagnosis of breast cancer. The breast cancers of 432 women had immunohistochemistry (IHC) performed for estrogen and progesterone receptors (ER and PR) and HER2. Age specific and age standardized incidence rates were calculated for Sulaimaniyah Kurds. Results were compared with Egypt and with United States (US) SEER data.ResultsThe median patient age was 46 years and 60.4% were < 50 years old. Tumors of 65.2% of women were ER+/HER2- with the rate increasing to 78.3% in patients ≥ 60 years old in proportions similar to US whites. The total annual age standardized incidence for breast cancer among Sulaimaniyah Kurds was 40.5/100,000 women, a rate similar to Egypt but much lower than the US. By HR/HER2 subtype, the highest age specific incidence rates were 16.4 and 45.4/100,000 for ER+/PR+/HER2- tumors in women < 50 or ≥ 50 years old, respectively (US whites: 37.7 and 226.1/100,000). Tumors of 20.4% of Sulaimaniyah women were HER2+ with annual incidence rates for ER-/PR-/HER2+ tumors of women <50 or ≥ 50 years old being 4.0 and 6.3/100,000 (US whites: 3.2 and 14.4/100,000). No significant differences in ER or HER2 status were found between Kurdish and Arabic patients.ConclusionsCompared to the US, low age standardized and age specific breast cancer incidence rates were found in Kurdish women; nevertheless, the proportional expression of HR and HER2 for both Kurds and Arabs was comparable to that of US white women. The great majority of the breast cancer was ER+/HER2- and should respond to anti-estrogen therapy.