bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface breaking cracks in resistance spot welds of dual phase steels with electrogalvanised and hot dip zinc coating
Authors: Tolf E , Hedegård J , Melander A
Published: February 2013

In normal production of resistance spot welded galvanised structures, it is difficult to completely avoid surface breaking cracks. Known key factors to cause cracking are zinc coating, electrode wear during subsequent welding and insufficient electrode cooling. In this report, an embrittlement mechanism was investigated that could be coupled to the galvanisation method for dual phase steels. With identical bulk material and weld parameters, the first 50 spot welds were crack free with electrogalvanised coating, while only 10 out of 50 were crack free with hot dip galvanised coating. Energy dispersive X-ray spectroscopy analysis of the worn electrode surfaces used for welding of the hot dip galvanised coating revealed areas of aluminium oxide. Since aluminium oxide is a very strong isolator, the electrical resistance will increase, which in turn is suggested to increase the surface temperature of the spot weld and thereby increase the probability for liquid metal embrittlement and surface cracks.
War Canoes or Social Units? Human Representation in Rock-Art Ships
Authors: Ling Johan
Published: February 2013

Scandinavian rock art may in general be regarded as idealized depictions of a social world, not a direct description of concrete social matters. Even so, rock art does convey important social information that calls for more thorough comment. This study concerns almost 1700 ship depictions from western Sweden that include human representations. The average ship is depicted with a crew of six to thirteen individuals and these craft may have represented prevailing ideals about the crewing of ships. The large ship images with numerous crews in clearly defined positions may be depictions of war canoes, staged for special maritime events. The study shows that the visual proportions of the rock-art ships are similar to those of the prehistoric war canoe from Hjortspring, Denmark. It is argued that the praxis of pecking ships into the rocks could have served to manifest the agency of the maritime social world and, to some extent, to make this ideology more dominant.
First Strontium Isotope Evidence of Mobility in the Neolithic of Southern France
Authors: Goude Gwenaélle , Castorina Francesca , Herrscher Estelle , Cabut Sandrine , Tafuri Mary Anne
Published: February 2013

This study presents the first87Sr/86Sr isotope results obtained on Neolithic humans from Southern France. These analyses aimed at exploring patterns of mobility in the Languedoc and Garonne areas, at sites dated to the Middle Neolithic (c. 4500–3500 cal BC). Strontium isotope analysis of tooth enamel and bone are a useful geochemical tracer to investigate the origin and residential mobility of ancient people. Strontium isotope ratios (87Sr/86Sr) of material from five sites located in two geographic areas were measured. Results obtained do not support our hypothesis of mobility for a number of individuals considered as outsiders in a previous study. On the other hand, the difference recorded between teeth and bone suggests mobility of other individuals between childhood and the last years of adult life. This preliminary study highlights the importance of combining multi-isotope analysis to discuss human subsistence economy and mobility.
Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis
Authors: Mylona Athina , Andrieu-Soler Charlotte , Thongjuea Supat , Martella Andrea , Soler Eric , Jorna Ruud , Hou Jun , Kockx Christel , van Ijcken Wilfred , Lenhard Boris , Grosveld Frank
Published: February 2013

Key Points

Lack of yolk-sac hematopoiesis in the Ldb1−/− mouse results from a decreased number of hemangioblasts and a differentiation block. Identification of genes and pathways regulated by Ldb1 in the hemangioblast reveals potential targets for early developmental manipulation.
M-pick, a modularity-based method for OTU picking of 16S rRNA sequences
Authors: Wang Xiaoyu , Yao Jin , Sun Yijun , Mai Volker
Published: February 2013

Background

Binning 16S rRNA sequences into operational taxonomic units (OTUs) is an initial crucial step in analyzing large sequence datasets generated to determine microbial community compositions in various environments including that of the human gut. Various methods have been developed, but most suffer from either inaccuracies or from being unable to handle millions of sequences generated in current studies. Furthermore, existing binning methods usually require a priori decisions regarding binning parameters such as a distance level for defining an OTU.

Results

We present a novel modularity-based approach (M-pick) to address the aforementioned problems. The new method utilizes ideas from community detection in graphs, where sequences are viewed as vertices on a weighted graph, each pair of sequences is connected by an imaginary edge, and the similarity of a pair of sequences represents the weight of the edge. M-pick first generates a graph based on pairwise sequence distances and then applies a modularity-based community detection technique on the graph to generate OTUs to capture the community structures in sequence data. To compare the performance of M-pick with that of existing methods, specifically CROP and ESPRIT-Tree, sequence data from different hypervariable regions of 16S rRNA were used and binning results were compared.

Conclusions

A new modularity-based clustering method for OTU picking of 16S rRNA sequences is developed in this study. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance levels to define OTUs. The source code is available at http://plaza.ufl.edu/xywang/Mpick.htm.
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information
Authors: Panwar Bharat , Gupta Sudheer , Raghava Gajendra P S
Published: February 2013

Background

The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure.

Results

In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL). It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i) vitamin interacting residues (VIRs), (ii) vitamin-A interacting residues (VAIRs), (iii) vitamin-B interacting residues (VBIRs) and (iv) pyridoxal-5-phosphate (vitamin B6) interacting residues (PLPIRs) have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM) features of protein sequences. Finally, we selected best performing SVM modules and obtained highest MCC of 0.53, 0.48, 0.61, 0.81 for VIRs, VAIRs, VBIRs, PLPIRs respectively, using PSSM-based evolutionary information. All the modules developed in this study have been trained and tested on non-redundant datasets and evaluated using five-fold cross-validation technique. The performances were also evaluated on the balanced and different independent datasets.

Conclusions

This study demonstrates that it is possible to predict VIRs, VAIRs, VBIRs and PLPIRs from evolutionary information of protein sequence. In order to provide service to the scientific community, we have developed web-server and standalone software VitaPred (http://crdd.osdd.net/raghava/vitapred/).
Does the essential oil of Lippia sidoidesCham. (pepper-rosmarin) affect its endophytic microbial community?
Authors: da Silva Thais Freitas , Vollú Renata Estebanez , Jurelevicius Diogo , Alviano Daniela Sales , Alviano Celuta Sales , Blank Arie Fitzgerald , Seldin Lucy
Published: February 2013

Background

Lippia sidoides Cham., also known as pepper-rosmarin, produces an essential oil in its leaves that is currently used by the pharmaceutical, perfumery and cosmetic industries for its antimicrobial and aromatic properties. Because of the antimicrobial compounds (mainly thymol and carvacrol) found in the essential oil, we believe that the endophytic microorganisms found in L. sidoides are selected to live in different parts of the plant.

Results

In this study, the endophytic microbial communities from the stems and leaves of four L. sidoides genotypes were determined using cultivation-dependent and cultivation-independent approaches. In total, 145 endophytic bacterial strains were isolated and further grouped using either ERIC-PCR or BOX-PCR, resulting in 76 groups composed of different genera predominantly belonging to the Gammaproteobacteria. The endophytic microbial diversity was also analyzed by PCR-DGGE using 16S rRNA-based universal and group-specific primers for total bacteria, Alphaproteobacteria, Betaproteobacteria and Actinobacteria and 18S rRNA-based primers for fungi. PCR-DGGE profile analysis and principal component analysis showed that the total bacteria, Alphaproteobacteria, Betaproteobacteria and fungi were influenced not only by the location within the plant (leaf vs. stem) but also by the presence of the main components of the L. sidoides essential oil (thymol and/or carvacrol) in the leaves. However, the same could not be observed within the Actinobacteria.

Conclusion

The data presented here are the first step to begin shedding light on the impact of the essential oil in the endophytic microorganisms in pepper-rosmarin.
Multiple tandem splicing silencer elements suppress aberrant splicing within the long exon 26 of the human Apolipoprotein B gene
Authors: Srirangalingam Umasuthan , Akker Scott A , Norman Dennis , Navaratnam Naveenan , Chew Shern L , Khoo Bernard
Published: February 2013

Background

Apolipoprotein B (APOB) is an integral component of the chylomicron and the atherogenic lipoproteins LDL and Lp(a). Exon 26 of the APOB pre-mRNA is unusually long at 7,572 nt and is constitutively spliced. It is also subject to RNA editing in the intestine, which generates a shortened isoform, APOB48, assembled exclusively into chylomicrons. Due to its length, exon 26 contains multiple pseudo splice sites which are not spliced, but which conform to the degenerate splice site consensus.

Results

We demonstrate that these pseudo splice sites are repressed by multiple, tandem splicing silencers distributed along the length of exon 26. The distribution of these elements appears to be heterogeneous, with a greater frequency in the middle 4,800 nt of the exon.

Conclusion

Repression of these splice sites is key to maintaining the integrity of exon 26 during RNA splicing and therefore the correct expression of both isoforms of APOB.
High mortality of pneumonia in cirrhotic patients with ascites
Authors: Hung Tsung-Hsing , Tseng Chih-Wei , Hsieh Yu-Hsi , Tseng Kuo-Chih , Tsai Chih-Chun , Tsai Chen-Chi
Published: February 2013

Background

Cirrhotic patients with ascites are prone to develop various infectious diseases. This study aimed to evaluate the occurrence and effect of major infectious diseases on the mortality of cirrhotic patients with ascites.

Methods

We reviewed de-identified patient data from the National Health Insurance Database, derived from the Taiwan National Health Insurance Program, to enroll 4,576 cirrhotic patients with ascites, who were discharged from Taiwan hospitals between January 1, 2004 and June 30, 2004. We collected patients’ demographic and clinical data, and reviewed diagnostic codes to determine infectious diseases and comorbid disorders of their hospitalizations. Patients were divided into an infection group and non-infection group and hazard ratios (HR) were determined for specific infectious diseases.

Results

Of the total 4,576 cirrhotic patients with ascites, 1,294 (28.2%) were diagnosed with infectious diseases during hospitalization. The major infectious diseases were spontaneous bacterial peritonitis (SBP) (645, 49.8%), urinary tract infection (151, 11.7%), and pneumonia (100, 7.7%). After adjusting for patients’ age, gender, and other comorbid disorders, the HRs of infectious diseases for 30-day and 90-day mortality of cirrhotic patients with ascites were 1.81 (1.54-2.11) and 1.60 (1.43-1.80) respectively, compared to those in the non-infection group. The adjusted HRs of pneumonia, urinary tract infection (UTI), spontaneous bacterial peritonitis (SBP), and sepsis without specific focus (SWSF) were 2.95 (2.05-4.25), 1.32 (0.86-2.05), 1.77 (1.45-2.17), and 2.19 (1.62-2.96) for 30-day mortality, and 2.57 (1.93-3.42), 1.36 (1.01-1.82), 1.51 (1.29-1.75), and 2.13 (1.70-2.66) for 90-day mortality, compared to those in the non-infection group.

Conclusion

Infectious diseases increased 30-day and 90-day mortality of cirrhotic patients with ascites. Among all infectious diseases identified, pneumonia carried the highest risk for mortality.
Patients’ perspectives on palliative chemotherapy of colorectal and non - colorectal cancer: a prospective study in a chemotherapy- experienced population
Authors: Mende Marika , Trautmann Karolin , Rentsch Anke , Hornemann Beate , Schuler Ulrich S , Ehninger Gerhard , Folprecht Gunnar
Published: February 2013

Background

A better understanding of patients’ views on the benefit and burden obtained from palliative chemotherapy would facilitate shared decision making. We evaluated palliative cancer patients’ reported outcomes (PROs) for toxicity and investigated the survival threshold for which they would repeat chemotherapy (CTx).

Methods

Patients who had received a minimum of three months of palliative CTx for advanced colorectal (CRC) or non-colorectal (non-CRC: upper gastrointestinal, lung and head-and-neck) cancer were assessed by questionnaire. Patients were questioned about PROs for toxicity, subjective burden from side effects, and were asked for the survival threshold necessary for them to repeat CTx. Expected survival (sum of indicated survival threshold and median survival time with best supportive care) was compared to the patients’ actual survival.

Results

One hundred and thirty-four patients (CRC: 58; non-CRC: 76) were surveyed. The most frequent PRO- grade 3/4 toxicities were acne (12.8%), fatigue (9.0%), and diarrhea (8.5%). The symptom causing the highest subjective burden was fatigue and was worse than expected in 29.9% of the patients. The median survival threshold for which patients would repeat CTx was significantly longer in CRC than in non-CRC patients (p=0.01). Median expected survival was significantly longer than actual median survival (CRC: 44.0 months [22.0-65.9] compared with 30.0 months of actual survival [20.9-39.1]; non-CRC: 22.0 months [15.3-28.6] compared with 19.0 months of actual survival [15.1-22.9], p=0.03).

Conclusion

Fatigue deserves more attention when toxicity of treatment and symptoms of disease are explained to patients. Patients’ survival expectations from palliative chemotherapy are higher than previously described, exceed the median survival time known from phase III trials, and are significantly longer than their actual survival.
Genetic engineering of Pyrococcus furiosus to use chitin as a carbon source
Authors: Kreuzer Martina , Schmutzler Karolin , Waege Ingrid , Thomm Michael , Hausner Winfried
Published: February 2013

Background

Bioinformatic analysis of the genes coding for the chitinase in Pyrococcus furiosus and Thermococcus kodakarensis revealed that most likely a one nucleotide insertion in Pyrococcus caused a frame shift in the chitinase gene. This splits the enzyme into two separate genes, PF1233 and PF1234, in comparison to Thermococcus kodakarensis. Furthermore, our attempts to grow the wild type strain of Pyrococcus furiosus on chitin were negative. From these data we assume that Pyrococcus furiosus is most likely unable to use chitin as a carbon source. The aim of this study was to analyze in vivo if the one nucleotide insertion is responsible for the inability to grow on chitin, using a recently described genetic system for Pyrococcus furiosus.

Results

A marker-less genetic system for Pyrococcus furiosus was developed using simvastatin for positive selection and 6-methylpurine for negative selection. Resistance against simvastatin was achieved by overexpression of the hydroxymethylglutaryl coenzyme A reductase gene. For the resistance to 6-methylpurine the hypoxanthine-guanine phosphoribosyltransferase gene was deleted. This system was used to delete the additional nucleotide at position 1006 in PF1234. The resulting chitinase in the mutant strain was a single subunit enzyme and aligns perfectly to the enzyme from Thermococcus kodakarensis. A detailed analysis of the wild type and the mutant using counted cell numbers as well as ATP and acetate production as growth indicators revealed that only the mutant is able to use chitin as a carbon source. An additional mutant strain containing a reduced chitinase version containing just one catalytic and one chitin-binding domain showed diminished growth on chitin in comparison to the mutant containing the single large enzyme.

Conclusions

Wild type Pyrococcus furiosus is most likely unable to grow on chitin in the natural biotope due to a nucleotide insertion which separates the chitinase gene into two ORFs, whereas a genetically engineered strain with the deleted nucleotide is able to grow on chitin. The overall high sequence identity of the two chitinases between P. furiosus and T. kodakarensis indicates that this mutation occurred very recently or there is still some kind of selection pressure for a functional enzyme using programmed +/−1 frameshifting.
Functional connectivity-based signatures of schizophrenia revealed by multiclass pattern analysis of resting-state fMRI from schizophrenic patients and their healthy siblings
Authors: Yu Yang , Shen Hui , Zhang Huiran , Zeng Ling-Li , Xue Zhimin , Hu Dewen
Published: February 2013

Background

Recently, a growing number of neuroimaging studies have begun to investigate the brains of schizophrenic patients and their healthy siblings to identify heritable biomarkers of this complex disorder. The objective of this study was to use multiclass pattern analysis to investigate the inheritable characters of schizophrenia at the individual level, by comparing whole-brain resting-state functional connectivity of patients with schizophrenia to their healthy siblings.

Methods

Twenty-four schizophrenic patients, twenty-five healthy siblings and twenty-two matched healthy controls underwent the resting-state functional Magnetic Resonance Imaging (rs-fMRI) scanning. A linear support vector machine along with principal component analysis was used to solve the multi-classification problem. By reconstructing the functional connectivities with high discriminative power, three types of functional connectivity-based signatures were identified: (i) state connectivity patterns, which characterize the nature of disruption in the brain network of patients with schizophrenia; (ii) trait connectivity patterns, reflecting shared connectivities of dysfunction in patients with schizophrenia and their healthy siblings, thereby providing a possible neuroendophenotype and revealing the genetic vulnerability to develop schizophrenia; and (iii) compensatory connectivity patterns, which underlie special brain connectivities by which healthy siblings might compensate for an increased genetic risk for developing schizophrenia.

Results

Our multiclass pattern analysis achieved 62.0% accuracy via leave-one-out cross-validation (p < 0.001). The identified state patterns related to the default mode network, the executive control network and the cerebellum. For the trait patterns, functional connectivities between the cerebellum and the prefrontal lobe, the middle temporal gyrus, the thalamus and the middle temporal poles were identified. Connectivities among the right precuneus, the left middle temporal gyrus, the left angular and the left rectus, as well as connectivities between the cingulate cortex and the left rectus showed higher discriminative power in the compensatory patterns.

Conclusions

Based on our experimental results, we saw some indication of differences in functional connectivity patterns in the healthy siblings of schizophrenic patients compared to other healthy individuals who have no relations with the patients. Our preliminary investigation suggested that the use of resting-state functional connectivities as classification features to discriminate among schizophrenic patients, their healthy siblings and healthy controls is meaningful.
Nimodipine, a calcium channel blocker, delays the spontaneous LH surge in women with regular menstrual cycles: a prospective pilot study
Authors: Nayot Dan , Klachook Shany , Casper Robert F
Published: February 2013

Background

Currently GnRH analogue injections are used to prevent premature LH surges in women undergoing assisted reproductive technology. This was a pilot study to determine the safety and effectiveness of nimodipine, an oral calcium channel blocker, to delay the mid-cycle spontaneous LH surge in women with regular menstrual cycles.

Methods

Eight women with regular menstrual cycles self-monitored three consecutive cycles for the day of an LH surge by daily urine assay. The first and third cycles were observatory. In the second cycle, subjects took nimodipine 60 mg by mouth three times daily for four days, starting two days prior to the expected LH surge day based on cycle one.

Results

The LH surge day in cycle 2 (nimodipine) was significantly delayed in comparison to both observatory cycle 1 (15.5+/−3.4 vs 14.0+/−2.8 days; p = 0.033) and cycle 3 (15.1+/−3.5 vs 13.1+/−2.4 days; p = 0.044). There was no difference in the LH surge day between the two observatory cycles (13.4+/−2.4 vs 13.1+/−2.4 days; p = 0.457). Three patients experienced a mild headache.

Conclusions

There was a statistically significant delay in the spontaneous LH surge day in the treatment cycle in comparison to both observatory cycles. Nimopidine should be further investigated as an oral alternative to delay a spontaneous LH surge.
Mortality in an Aboriginal Medical Service (Redfern) cohort
Authors: Morrell Stephen , Phillips Bronwen , Taylor Richard , Daniels John , Burgess Kate , Mayers Naomi
Published: February 2013

Background

Published estimates of Aboriginal mortality and life expectancy (LE) for the eastern Australian states are derived from demographic modelling techniques to estimate the population and extent of under-recording of Aboriginality in death registration. No reliable empirical information on Aboriginal mortality and LE exists for New South Wales (NSW), the most populous Australian state in which 29% of Aboriginal people reside.

This paper estimates mortality and LE in a large, mainly metropolitan cohort of Aboriginal clients from the Aboriginal Medical Service (AMS) Redfern, Sydney, NSW.

Methods

Identifying information from patient records accrued by the AMS Redfern since 1980 of definitely Aboriginal clients, without distinction between Aboriginal and Torres Strait Islander (n=24,035), was extracted and linked to the National Death Index (NDI) at the Australian Institute of Health and Welfare (AIHW). Age-specific mortality rates and LEs for each sex were estimated using the AMS patient population as the denominator, discounted for deaths. Directly age-standardised mortality and LEs were estimated for 1995–1999, 2000–2004 and 2005–2009, along with 95% confidence intervals. Comparisons were made with other estimates of Aboriginal mortality and LE and with the total Australian population.

Results

Mortality declined in the AMS Redfern cohort over 1995–2009, and the decline occurred mostly in the ≤44 year age range. Male LE at birth was estimated to be 64.4 years (95%CI:62.6-66.1) in 1995–1999, 65.6 years (95%CI:64.1-67.1) in 2000–2004, and 67.6 years (95%CI:65.9-69.2) for 2005–2009. In females, these LE estimates were 69.6 (95%CI:68.0-71.2), 71.1 (95%CI:69.9-72.4), and 71.4 (95%CI:70.0-72.8) years. LE in the AMS cohort was 11 years lower for males and 12 years lower for females than corresponding all-Australia LEs for the same periods. These were similar to estimates for Australian Aboriginal people overall for the same period by the Aboriginal Burden of Disease for 2009, using the General Growth Balance (GGB) model approach, and by the Australian Bureau of Statistics (ABS) for 2005–2007. LE in the AMS cohort was somewhat lower than these estimates for NSW Aboriginal people, and higher than ABS 2005–2007 estimates for Aboriginal people from Northern Territory, South Australia, and Western Australia.

Conclusions

The AMS Redfern cohort has provided the first empirically based estimates of mortality and LE trends in a large sample of Aboriginal people from NSW.
Microwave absorption properties of pyrolytic carbon nanofilm
Authors: Kuzhir Polina P , Paddubskaya Alesya G , Maksimenko Sergey A , Kaplas Tommi , Svirko Yuri
Published: February 2013

We analyzed the electromagnetic (EM) shielding effectiveness in the Ka band (26 to 37 GHz) of highly amorphous nanometrically thin pyrolytic carbon (PyC) films with lateral dimensions of 7.2 × 3.4 mm2, which consists of randomly oriented and intertwined graphene flakes with a typical size of a few nanometers. We discovered that the manufactured PyC films, whose thickness is thousand times less than the skin depth of conventional metals, provide a reasonably high EM attenuation. The latter is caused by absorption losses that can be as high as 38% to 20% in the microwave frequency range. Being semi-transparent in visible and infrared spectral ranges and highly conductive at room temperature, PyC films emerge as a promising material for manufacturing ultrathin microwave (e.g., K
a band) filters and shields.
Diatom attachment inhibition: limiting surface accessibility through air entrapment
Authors: Wu Alex H-F , Nakanishi Kenichi , Cho KL , Lamb Robert
Published: February 2013

Surfaces consisting of sub micron holes (0.420-0.765 μm) engineered into nanoparticle (12 nm) coatings were examined for marine antifouling behaviour that defines early stage settlement. Immersed surfaces were found to be resistant to a 5-hour attachment assay of Amphora coffeaeformis, a marine organism commonly found in abundance on fouled substrates such as foul-releasing paints and self-polishing coatings. Attachment inhibition was attributed to the accessibility of diatoms to the surface. This was governed by the size and morphology of trapped interfacial air pockets measured in-situ using synchrotron small angle x-ray scattering. Surfaces containing larger pores (0.765 μm) exhibited the highest resistance. Macroscopic wettability via contact angle measurements however remained at 160° and sliding angle of < 5° and was found to be independent of pore size and not indicative of early stage fouling behaviour. The balance of hierarchical nano/micro length scales was critical in defining the early stage stability of biofouling character of the interface.
On the existence of asymptotically almost periodic solutions for nonlinear systems
Authors: Song Juan , Cao Jianzhi , Li Xiong
Published: February 2013

In this paper, a nonlinear differential equation

x
′

=
A
(
t
,
x
)
+
f
(
t
)

is considered. Some new sufficient conditions for the existence of a bounded solution and an asymptotically almost periodic solution, which generalize and improve the previously known results, are established by using a dissipative-type condition for

A
(
t
,
x
)

. Finally, an example is presented to illustrate the feasibility and effectiveness of the new results.
Retrovirus infected cells contain viral microRNAs
Authors: Klase Zachary A , Sampey Gavin C , Kashanchi Fatah
Published: February 2013

The encoding of microRNAs in retroviral genomes has remained a controversial hypothesis despite significant supporting evidence in recent years. A recent publication demonstrating the production of functional miRNAs from the retrovirus bovine leukemia virus adds further credence to the fact that retroviruses do indeed encode their own miRNAs. Here we comment on the importance of this paper to the field, as well as examine the other known examples of miRNAs encoded by RNA viruses.
Evolutionary history of relict Congeria (Bivalvia: Dreissenidae): unearthing the subterranean biodiversity of the Dinaric Karst
Authors: Bilandžija Helena , Morton Brian , Podnar Martina , Ćetković Helena
Published: February 2013

Background

Patterns of biodiversity in the subterranean realm are typically different from those encountered on the Earth’s surface. The Dinaric karst of Croatia, Slovenia and Bosnia and Herzegovina is a global hotspot of subterranean biodiversity. How this was achieved and why this is so remain largely unresolved despite a long tradition of research. To obtain insights into the colonisation of the Dinaric Karst and the effects of the subterranean realm on its inhabitants, we studied the tertiary relictCongeria, a unique cave-dwelling bivalve (Dreissenidae), using a combination of biogeographical, molecular, morphological, and paleontological information.

Results

Phylogenetic and molecular clock analyses using both nuclear and mitochondrial markers have shown that the survivingCongerialineage has actually split into three distinct species, i.e.,C. kusceri, C. jalzicisp. nov. andC. mulaomerovicisp. nov., by vicariant processes in the late Miocene and Pliocene. Despite millions of years of independent evolution, analyses have demonstrated a great deal of shell similarity between modernCongeriaspecies, although slight differences in hinge plate structure have enabled the description of the two new species. Ancestral plesiomorphic shell forms seem to have been conserved during the processes of cave colonisation and subsequent lineage isolation. In contrast, shell morphology is divergent within one of the lineages, probably due to microhabitat differences.

Conclusions

Following the turbulent evolution of the Dreissenidae during the Tertiary and major radiations in Lake Pannon, species ofCongeriawent extinct. One lineage survived, however, by adopting a unique life history strategy that suited it to the underground environment. In light of our new data, an alternative scenario for its colonisation of the karst is proposed. The extantCongeriacomprises three sister species that, to date, have only been found to live in 15 caves in the Dinaric karst. Inter-specific morphological stasis and intra-specific ecophenotypic plasticity of the congerid shell demonstrate the contrasting ways in which evolution in the underground environments shapes its inhabitants.
Classification of chronic cough by systematic treatment cascade trial starting with beta agonist
Authors: Shimizu Hideyasu , Hayashi Masamichi , Saito Yuji , Mieno Yuki , Takeuchi Yasuo , Sasaki Fumihiko , Sakakibara Hiroki , Naito Kensei , Okazawa Mitsushi
Published: February 2013

Background

Chronic cough is one of the most challenging symptoms to diagnose and treat, not only because of the variety of underlying disorders but also its varying susceptibility to treatments. Etiological studies of chronic cough vary depending on the clinical settings and the particular interests of investigators.

Objectives

The purposes of this study were first to categorize the etiology of chronic cough by its response to systematic diagnostic treatments starting from the β2 agonist and second to sub-categorize β2 agonist responsive cough (BRC) by the airway hyperresponsiveness.

Methods

One hundred and eighty-four never-smokers received the maximal dose of procaterol to diagnose BRC. BRC was sub-categorized into two groups with or without airway hyperresponsiveness measured by the methacholine challenge test. Sinobronchial syndrome (SBS) was diagnosed by postnasal drip symptoms and by the response to clarythromycin and carbocysteine. Atopic cough (AC) was diagnosed by the evidence of atopy and the response to cetirizine hydrochloride. Gastroesophageal reflux disease (GERD) was diagnosed by the response to rabeprazole sodium. Since we did not investigate eosinophil counts in the tissue or in the induced sputum, no diagnosis of eosinophilic bronchitis was made.

Results

One hundred and nine patients had BRC. Twenty-three of them had bronchial asthma (BA), 53 had cough variant asthma (CVA) and 33 had non-hyperresponsive BRC (NHBRC). Thirty-one patients had GERD, 27 had AC and 14 had SBS. Twenty-five patients had more than one diagnosis in combination, while 6 had other miscellaneous diseases. Twelve patients were undiagnosed and 11 dropped out of the study.

Conclusions

The majority of chronic cough was BRC. NHBRC was a new chronic cough entity. GERD is a common cause of chronic cough in Japan, as in Western countries. AC and SBS are also causes of chronic cough in Japan.

Trial registration

University hospital medical information network (UMIN 000007483)
Upper extremity compartment syndrome after minor trauma: an imperative for increased vigilance for a rare, but limb-threatening complication
Authors: Seigerman Daniel A , Choi Daniel , Donegan Derek J , Yoon Richard S , Liporace Frank A
Published: February 2013

Background

Compartment syndrome of any extremity is a limb-threatening emergency requiring an emergent surgical management. Thus, ruling out compartment syndrome is often high on the list of priorities when treating high-energy injuries and fractures. However, even in the most seemingly benign injuries, this dangerous diagnosis must always remain on the differential and suspicion must remain high.

Case presentation

23-year-old factory worker presents after a low energy entrapment injury to his left forearm. Initial work-up and evaluation noted an isolated radial head dislocation with a normal physical motor and sensory exam. However, maintaining high suspicion for compartment syndrome despite serial normal physical exams, led objective compartment pressure measurement leading to definitive diagnosis. Emergent surgical intervention via compartment fasciotomies was performed, along with closed reduction and ligament repair. At 1 year follow-up, the patient was well-healed, back to work with full range of motion and not activity limitations.

Conclusion

Despite a seemingly benign injury pattern, and a relatively low energy mechanism, vigilant concern for compartment syndrome following any kind of entrapment injury should initiate serial examinations and compartment pressure measurements especially in circumstances with continued swelling and inability to perform an accurate clinical assessment due to an obtunded or medicated patient.
Three multiplex snapshot assays for SNP genotyping in candidate innate immune genes
Authors: Esteves Lisa M , Bulhões Sara M , Brilhante Maria J , Mota-Vieira Luisa
Published: February 2013

Background

Innate immune system is the first line of research when studying immune response to diverse infections and autoimmune/inflammatory diseases. This immune response has been reported to be genetically diverse, due to polymorphisms coded by different genes. For this reason, our purpose was to develop a multiplex assay that allows the genotyping of candidate single nucleotide polymorphisms (SNPs) in innate immune genes.

Findings

We developed three multiplex PCR panels coupled with the minisequencing (SNaPshot) technique (multiplex PCR, multiplex primer extension, and capillary electrophoresis). The panels were tested in a sample set composed of 100 anonymous DNAs from healthy blood donors living in São Miguel Island (Azores, Portugal). Sixteen relevant SNPs among nine genes of the innate immune system – IL1α, IL1β, IL6, IL10, IL12RB1, TLR2, TLR4, TLR9 and CD14 – were genotyped and validated by direct sequencing, with the exception of one that was undetected by minisequencing. We suggest that these panels can be used in future studies for detection of risk gene variants in several populations and/or diseases.

Conclusions

In summary, we propose a multiplex assay that is able to identify the most frequent candidate SNPs in innate immune genes, using a medium scale genotyping platform. The assays can be used to evaluate the risk gene variants in populations of various geographic origins.
Hybridization between two cestode species and its consequences for intermediate host range
Authors: Henrich Tina , Benesh Daniel P , Kalbe Martin
Published: February 2013

Background

Many parasites show an extraordinary degree of host specificity, even though a narrow range of host species reduces the likelihood of successful transmission. In this study, we evaluate the genetic basis of host specificity and transmission success of experimental F1 hybrids from two closely related tapeworm species (Schistocephalus solidus and S. pungitii), both highly specific to their respective vertebrate second intermediate hosts (three- and nine-spined sticklebacks, respectively).

Methods

We used an in vitro breeding system to hybridize Schistocephalus solidus and S. pungitii; hybridization rate was quantified using microsatellite markers. We measured several fitness relevant traits in pure lines of the parental parasite species as well as in their hybrids: hatching rates, infection rates in the copepod first host, and infection rates and growth in the two species of stickleback second hosts.

Results

We show that the parasites can hybridize in the in vitro system, although the proportion of self-fertilized offspring was higher in the heterospecific breeding pairs than in the control pure parental species. Hybrids have a lower hatching rate, but do not show any disadvantages in infection of copepods. In fish, hybrids were able to infect both stickleback species with equal frequency, whereas the pure lines were only able to infect their normal host species.

Conclusions

Although not yet documented in nature, our study shows that hybridization in Schistocephalus spp. is in principle possible and that, in respect to their expanded host range, the hybrids are fitter. Further studies are needed to find the reason for the maintenance of the species boundaries in wild populations.
Insulin and insulin-like growth factor signaling increases proliferation and hyperplasia of the ovarian surface epithelium and decreases follicular integrity through upregulation of the PI3-kinase pathway
Authors: King Shelby M , Modi Dimple A , Eddie Sharon L , Burdette Joanna E
Published: February 2013

Background

The ovarian surface epithelium responds to cytokines and hormonal cues to initiate proliferation and migration following ovulation. Although insulin and IGF are potent proliferative factors for the ovarian surface epithelium and IGF is required for follicle development, increased insulin and IGF activity are correlated with at least two gynecologic conditions: polycystic ovary syndrome and epithelial ovarian cancer. Although insulin and IGF are often components of in vitro culture media, little is known about the effects that these growth factors may have on the ovarian surface epithelium morphology or how signaling in the ovarian surface may affect follicular health and development.

Methods

Ovaries from CD1 mice were cultured in alginate hydrogels in the presence or absence of 5 μg/ml insulin or IGF-I, as well as small molecule inhibitors of IR/IGF1R, PI 3-kinase signaling, or MAPK signaling. Tissues were analyzed by immunohistochemistry for expression of cytokeratin 8 to mark the ovarian surface epithelium, Müllerian inhibiting substance to mark secondary follicles, and BrdU incorporation to assess proliferation. Changes in gene expression in the ovarian surface epithelium in response to insulin or IGF-I were analyzed by transcription array. Extracellular matrix organization was evaluated by expression and localization of collagen IV.

Results

Culture of ovarian organoids with insulin or IGF-I resulted in formation of hyperplastic OSE approximately 4–6 cell layers thick with a high rate of proliferation, as well as decreased MIS expression in secondary follicles. Inhibition of the MAPK pathway restored MIS expression reduced by insulin but only partially restored normal OSE growth and morphology. Inhibition of the PI 3-kinase pathway restored MIS expression reduced by IGF-I and restored OSE growth to a single cell layer. Insulin and IGF-I altered organization of collagen IV, which was restored by inhibition of PI 3-kinase signaling.

Conclusions

While insulin and IGF are often required for propagation of primary cells, these cytokines may act as potent mitogens to disrupt cell growth, resulting in formation of hyperplastic OSE and decreased follicular integrity as measured by MIS expression and collagen deposition. This may be due partly to altered collagen IV deposition and organization in the ovary in response to insulin and IGF signaling mediated by PI 3-kinase.
Massive edema of ovary with cytogenetic alteration of chromosome 12q13-15 in adolescent patient: a case report
Authors: De Cecio Rossella , Cantile Monica , Fortunato Nicola , De Chiara Annarosaria , Losito Nunzia Simona , Franco Renato , Botti Gerardo
Published: February 2013

Background

The massive edema of ovary, with or without fibromatosis, is a rare tumor-like entity characterized by an increase in volume of one or both ovaries for accumulation of edema fluid in the stroma that separates the follicular structures.

Case

We report a rare case, very peculiar also for its association with a massive stromal fibromatosis and for the presence, never described, of tumoral areas with CHOP gene translocation, on chromosome 12q13–15.
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Authors: Kawahara Yoshihiro , de la Bastide Melissa , Hamilton John P , Kanamori Hiroyuki , McCombie W Richard , Ouyang Shu , Schwartz David C , Tanaka Tsuyoshi , Wu Jianzhong , Zhou Shiguo , Childs Kevin L , Davidson Rebecca M , Lin Haining , Quesada-Ocampo Lina , Vaillancourt Brieanne , Sakai Hiroaki , Lee Sung Shin , Kim Jungsok , Numa Hisataka , Itoh Takeshi , Buell C Robin , Matsumoto Takashi
Published: February 2013

Background

Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group).

Results

The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community.

Conclusions

A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
Functional changes of the myocardium in survivors of high-voltage electrical injury
Authors: Park Kyoung-Ha , Han Sang Jin , Kim Hyun-Sook , Jo Sang Ho , Kim Sung-Ai , Choi Suk-Won , Kim Seong Hwan , Park Woo Jung
Published: February 2013

Introduction

There are limited long-term follow-up data on functional changes in the myocardium after high-voltage electrical injury (HVEI).

Methods

Twenty-three patients who had been exposed to HVEI (>20,000 volts) and preserved left ventricular ejection fraction (≥55%) were enrolled in the study. Echocardiographic parameters, including peak systolic strain (S) and strain rate (SR), were evaluated at baseline, six weeks and six months later. These data were compared with a healthy control group who were matched in terms of age, sex and body mass index.

Results

The systolic and diastolic blood pressure and the heart rate were significantly higher in the HVEI group compared with the control group at baseline and at six weeks, but not at the six-month follow-up. Conventional echocardiographic data showed no differences between the groups during the study period. In contrast to the S, the baseline and six weeks, SR was significantly increased in the HVEI group compared with the control group. However, at the six-month follow-up, there was no difference in the SR between the groups. Among the 23 patients with HVEI, 17 of the patients had vertical current injury, and 6 patients had horizontal current injury. There was no difference in terms of the conventional echocardiography, S and SR between the patients with vertical injury and those with horizontal injury at baseline and at the six-month follow-up.

Conclusions

The long-term contractile performance of the myocardium is preserved when patient do not experience left ventricular dysfunction in the early stages after HVEI.
Empirical mode decomposition for seismic time-frequency analysis
Authors: Han Jiajun , van der Baan Mirko
Published: February 2013

Time-frequency analysis plays a significant role in seismic data processing and interpretation. Complete ensemble empirical mode decomposition decomposes a seismic signal into a sum of oscillatory components, with guaranteed positive and smoothly varying instantaneous frequencies. Analysis on synthetic and real data demonstrates that this method promises higher spectral-spatial resolution than the short-time Fourier transform or wavelet transform. Application on field data thus offers the potential of highlighting subtle geologic structures that might otherwise escape unnoticed.