bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract
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.
On the existence of asymptotically almost periodic solutions for nonlinear systems
Authors: Song Juan , Cao Jianzhi , Li Xiong 
Published: February 2013

Abstract
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

Abstract
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

AbstractBackgroundPatterns 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.ResultsPhylogenetic 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.ConclusionsFollowing 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

Abstract

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)