bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Vestibular Dysfunction on the Development of Gross Motor Function in Children with Profound Hearing Loss
Authors: Inoue Aki , Iwasaki Shinichi , Ushio Munetaka , Chihara Yasuhiro , Fujimoto Chisato , Egami Naoya , Yamasoba Tatsuya
Published: February 2013

Objective: To evaluate the function of the superior and inferior vestibular nerve systems in children with profound sensorineural hearing loss, and to assess the influence of dysfunction of each vestibular nerve system on the development of gross motor function. Study Design: Retrospective study. Setting: A tertiary referral center. Methods: Eighty-nine children (age range: 20–97 months) with profound sensorineural hearing loss who were due to undergo cochlear implant surgery were recruited. Function of the superior vestibular nerve system was evaluated by the damped rotation test and the caloric test, whereas functions of the inferior vestibular nerve systems were evaluated by the vestibular evoked myogenic potential (VEMP) test. Gross motor development was assessed using the age of acquisition of head control and independent walking. Results: Among the children able to complete the vestibular function tests, abnormalities were found in 20% (16 of 84 children) in the damped rotation test, 41% (31 of 75 children) in the caloric test and 42% (26 of 62 children) in the VEMP test. Children who showed abnormal responses in the vestibular function tests showed significantly delayed acquisition of head control (p < 0.05) and independent walking (p < 0.05) in comparison with children with normal responses. The children who showed abnormal responses in all 3 vestibular tests showed the greatest delay in acquisition of gross motor function in comparison with the other groups. Conclusions: Children with profound hearing loss tend to have dysfunction in the superior as well as the inferior vestibular nerve systems. Both the superior and inferior vestibular nerve systems are important for the development of gross motor function in children.
COL2A1 Mutation in Spondylometaphyseal Dysplasia Algerian Type
Authors: Matsubayashi S. , Ikema M. , Ninomiya Y. , Yamaguchi K. , Ikegawa S. , Nishimura G.
Published: February 2013

Spondylometaphyseal dysplasia Algerian type (SMD-A) is an autosomal dominant disorder that was first reported in an Algerian family by Kozlowski et al. [Pediatr Radiol 1988;18:221-226]. Kozlowski's group reported a sporadic case in a 12-year-old Polish boy. They proposed SMD-A as a distinctive skeletal dysplasia and also suggested that a case of SMD reported by Schmidt et al. [J Pediatr 1963;63:106-112] might have had the same disorder. Afterwards, however, no additional report has emerged to date. In addition, the question whether SMD-A belongs to type II collagenopathy (a group of disorders due to a heterozygous mutation of -COL2A1) has been continuously under debate. Here we report a 7-year-old Japanese boy with a heterozygous missense mutation in COL2A1, 2582G>T (Gly861Val), whose phenotype matched that of SMD-A. Our observation supports the hypothesis that SMD-A is a variant of type II collagenopathy.
Aquagenic Palmar Wrinkling Induced by Combined Use of Salazopyrin and Indomethacin
Authors: Gündüz Özgür , Özsaraç KıvılcımÇınkır , Ercin Mustafa Emre
Published: February 2013

Aquagenic palmar wrinkling (APW) is an uncommon dermatological condition, which manifests as asymptomatic or tender palmar papules and may cause discomfort and manual functional limitations during its flares. Despite some studies implying a relationship between cystic fibrosis (CF) and APW, there are also reports of APW cases without an accompanying CF. In this report we describe a 19-year-old ankylosing spondylitis patient, who developed APW lesions after the start of combined salazopyrin and indomethacin treatment. His palmar lesions were resistant to topical corticosteroid and aluminium hydroxide therapy and disappeared only after stopping the anti-inflammatory drugs. With this report, we aim to highlight and address this underrecognized dermatological condition and possible role of aquaporins in its pathogenesis.
Genomic Heterogeneity in Acute Leukemia
Authors: Paulsson K.
Published: February 2013

Acquired genetic aberrations are the underlying cause of leukemogenesis in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). The karyotypes of AML and ALL cases are generally quite simple as seen by chromosome banding analysis, with few genetic changes and a limited number of subclones. However, investigations using fluorescence in situ hybridization, loss of heterozygosity analysis, single-nucleotide polymorphism arrays, and, most recently, massively parallel sequencing have challenged this view. In particular, comparison of diagnostic and relapse samples, modeling in transgenic mice, and whole-exome and whole-genome sequencing have indicated that widespread genomic heterogeneity, which is masked by a dominant clone, may be present in AML and ALL. In the present review, our current knowledge of genomic heterogeneity in acute leukemia is summarized.
Distant Metastasis from Benign Solitary Fibrous Tumor of the Kidney
Authors: Sasaki Hideo , Kurihara Tsuyoshi , Katsuoka Yuichi , Nakano Toru , Yoshioka Maki , Miyano Satetsu , Sato Yuichi , Uejima Iwao , Hoshikawa Masahiro , Takagi Masayuki , Chikaraishi Tatsuya
Published: February 2013

Solitary fibrous tumor (SFT) rarely occurs in the kidneys, and only one reported case of renal SFT has shown distant metastasis. We report the second case of renal SFT exhibiting distant metastasis. A 48-year-old man was referred to our hospital because of a right renal mass. An abdominal CT scan detected a large renal tumor, which was suspected to be a renal cell carcinoma. Right radical nephrectomy was performed, and the tumor was found to measure 28 × 18 × 10 cm. The pathological diagnosis was benign solitary fibrous tumor of the kidney. Eight years after the operation, lung and liver metastases developed. Pulmonary segmentectomy and partial hepatectomy were performed. The pathological diagnoses of these resected tissue specimens were compatible with benign SFT.
Multiple Pathologies in the Kidney Biopsy of a Recently Pregnant Woman
Authors: Kandukurti Kiran , Sun Jianlan , Venuto Rocco
Published: February 2013

We report a 42-year-old woman with underlying hypertension, mild renal dysfunction and proteinuria who presented as an obstetric emergency with uncontrolled hypertension and nephrotic syndrome. The rapid deterioration in her kidney function and worsening of her symptoms led to an urgent termination of her twin pregnancy. Although a clinical improvement was noticed within 10 days, the persistently elevated serum creatinine required further evaluation. A kidney biopsy showed changes consistent with acute tubular necrosis and resolving preeclampsia superimposed on focal segmental glomerulosclerosis and hypertensive kidney disease. The importance of a kidney biopsy in confirming clinical suspicions and determining patient prognosis is emphasized.
Implementation of a Silver Iodide Cloud-Seeding Parameterization in WRF. Part II: 3D Simulations of Actual Seeding Events and Sensitivity Tests
Authors: Xue Lulin , Tessendorf Sarah A. , Nelson Eric , Rasmussen Roy , Breed Daniel , Parkinson Shaun , Holbrook Pat , Blestrud Derek
Published: February 2013

Four cloud-seeding cases over southern Idaho during the 2010/11 winter season have been simulated by the Weather Research and Forecasting (WRF) model using the coupled silver iodide (AgI) cloud-seeding scheme that was described in Part I. The seeding effects of both ground-based and airborne seeding as well as the impacts of model physics, seeding rates, location, timing, and cloud properties on seeding effects have been investigated. The results were compared with those from Part I and showed the following: 1) For the four cases tested in this study, control simulations driven by the Real-Time Four Dimensional Data Assimilation (RTFDDA) WRF forecast data generated more realistic atmospheric conditions and precipitation patterns than those driven by the North America Regional Reanalysis data. Sensitivity experiments therefore used the RTFDDA data. 2) Glaciogenic cloud seeding increased orographic precipitation by less than 1% over the simulation domain, including the Snake River basin, and by up to 5% over the target areas. The local values of the relative precipitation enhancement by seeding were ~20%. Most of the enhancement came from vapor depletion. 3) The seeding effect was inversely related to the natural precipitation efficiency but was positively related to seeding rates. 4) Airborne seeding is generally more efficient than ground-based seeding in terms of targeting, but its efficiency depends on local meteorological conditions. 5) The normalized seeding effects ranged from 0.4 to 1.6 under various conditions for a certain seeding event.
Effects of Convective Gravity Wave Drag in the Southern Hemisphere Winter Stratosphere
Authors: Choi Hyun-Joo , Chun Hye-Yeong
Published: February 2013

The excessively strong polar jet and cold pole in the Southern Hemisphere winter stratosphere are systematic biases in most global climate models and are related to underestimated wave drag in the winter extratropical stratosphere—namely, missing gravity wave drag (GWD). Cumulus convection is strong in the winter extratropics in association with storm-track regions; thus, convective GWD could be one of the missing GWDs in models that do not adopt source-based nonorographic GWD parameterizations. In this study, the authors use the Whole Atmosphere Community Climate Model (WACCM) and show that the zonal-mean wind and temperature biases in the Southern Hemisphere winter stratosphere of the model are significantly alleviated by including convective GWD (GWDC) parameterizations. The reduction in the wind biases is due to enhanced wave drag in the winter extratropical stratosphere, which is caused directly by the additional GWDC and indirectly by the increased existing nonorographic GWD and resolved wave drag in response to the GWDC. The cold temperature biases are alleviated by increased downwelling in the winter polar stratosphere, which stems from an increased poleward motion due to enhanced wave drag in the winter extratropical stratosphere. A comparison between two simulations separately using the ray-based and columnar GWDC parameterizations shows that the polar night jet with a ray-based GWDC parameterization is much more realistic than that with a columnar GWDC parameterization.
The SST Gradient between the Southwestern Pacific and the Western Pacific Warm Pool: A New Factor Controlling the Northwestern Pacific Tropical Cyclone Genesis Frequency
Authors: Zhan Ruifen , Wang Yuqing , Wen Min
Published: February 2013

The sea surface temperature gradient (SSTG) between the southwestern Pacific Ocean (40°–20°S, 160°E–170°W) and the western Pacific warm pool (0°–16°N, 125°–165°E) in boreal spring has been identified as a new factor that controls the interannual variability of tropical cyclone (TC) frequency over the western North Pacific Ocean (WNP). This SSTG can explain 53% of the total variance of the WNP TC genesis frequency during the typhoon season for the period 1980–2011. The positive SSTG anomaly produces an anomalous cross-equatorial pressure gradient and thus anomalies in low-level southward cross-equatorial flow and tropical easterlies over the central-western Pacific. The anomalous easterlies further produce local equatorial upwelling and seasonal cooling in the central Pacific, which in turn maintains the easterly anomalies throughout the typhoon season. These dynamical/thermodynamical effects induced by the positive SSTG anomaly lead to a reduced low-level cyclonic shear, increased vertical wind shear, and weakened monsoon trough over the WNP, greatly suppressing WNP TC genesis during the typhoon season. This implies that the spring SSTG could be a good predictor for WNP TC genesis frequency.
The Case of Sharp Velocity Transitions in High Vertical Wind Shear When Measuring Doppler Velocities with Narrow Nyquist Intervals
Authors: Fabry Frédéric , Augros Clotilde , Bellon Aldo
Published: February 2013

An investigation was launched following unexpected observations of step-function transitions in Doppler velocities from scanning radars in regions of high vertical wind shear. It revealed that, if wind velocity transitions are sufficiently sharp and strong, then the measured velocity at each pulse repetition frequency undergoes an unusual smooth transition, from being in the right Nyquist interval to being in the wrong one. Hence, when these velocities are dealiased, a step function in velocity appears at the transition between where velocities were aliased and where they were not. The extent and the impacts of this data artifact are considered.
Achieving Seventh-Order Amplitude Accuracy in Leapfrog Integrations
Authors: Williams Paul D.
Published: February 2013

The leapfrog time-stepping scheme makes no amplitude errors when integrating linear oscillations. Unfortunately, the Robert–Asselin filter, which is used to damp the computational mode, introduces first-order amplitude errors. The Robert–Asselin–Williams (RAW) filter, which was recently proposed as an improvement, eliminates the first-order amplitude errors and yields third-order amplitude accuracy. However, it has not previously been shown how to further improve the accuracy by eliminating the third- and higher-order amplitude errors. Here, it is shown that leapfrogging over a suitably weighted blend of the filtered and unfiltered tendencies eliminates the third-order amplitude errors and yields fifth-order amplitude accuracy. It is further shown that the use of a more discriminating (1, −4, 6, −4, 1) filter instead of a (1, −2, 1) filter eliminates the fifth-order amplitude errors and yields seventh-order amplitude accuracy. Other related schemes are obtained by varying the values of the filter parameters, and it is found that several combinations offer an appealing compromise of stability and accuracy. The proposed new schemes are tested in numerical integrations of a simple nonlinear system. They appear to be attractive alternatives to the filtered leapfrog schemes currently used in many atmosphere and ocean models.
What Drives China's Growth?
Authors: Yueh Linda
Published: February 2013

This paper analyses the drivers and components of China's economic growth, showing that the structure of the economy is just as important as standard growth factors in determining its growth. The structural reforms that dismantled state-owned enterprises and shifted factors from agriculture to urban areas are key, as are technology transfers and know-how. Taking these factors into account, the paper shows that total factor productivity (TFP) not derived from those one-off reforms accounted for less than one-eighth of China's GDP growth during the first thirty years of the reform period. There are signs that efficiency is improving in the 2000s and productivity must continue to increase for the country to sustain its development.
Aberrant Development of the Suprachiasmatic Nucleus and Circadian Rhythms in Mice Lacking the Homeodomain Protein Six6
Authors: Clark Daniel D. , Gorman Michael R. , Hatori Megumi , Meadows Jason D. , Panda Satchidananda , Mellon Pamela L.
Published: February 2013

The suprachiasmatic nucleus (SCN) of the mammalian hypothalamus is the central pacemaker for peripheral and organismal circadian rhythms. The development of this hypothalamic structure depends on genetic programs throughout embryogenesis. We have investigated the role of the homeodomain transcription factor Six6 in the development of the SCN. We first showed that Six6 mRNA has circadian regulation in the mouse SCN. We then characterized the behavioral activity patterns of Six6-null mice under various photoperiod manipulations and stained their hypothalami using SCN-specific markers. Six6-null mice display abnormal patterns of circadian behavior indicative of SCN abnormalities. The ability of light exposure to reset rhythms correlates with the presence or absence of optic nerves, but all Six6-null mice show irregular rhythms. In contrast, wild-type mice with crushed optic nerves maintain regular rhythms regardless of light exposure. Using immunohistochemistry for arginine vasopressin (AVP), vasoactive intestinal polypeptide (VIP), and β-galactosidase, we demonstrated the lack of these SCN markers in all Six6-null mice regardless of the presence of optic nerve or partial circadian rhythms. Therefore, Six6 is required for the normal development of the SCN, and the Six6-null mouse can mount independent, although irregular, circadian rhythms despite the apparent absence of a histochemically defined SCN.
The effects of fluorouracil, epirubicin, and cyclophosphamide (FEC60) on the intestinal barrier function and gut peptides in breast cancer patients: an observational study
Authors: Russo Francesco , Linsalata Michele , Clemente Caterina , D’Attoma Benedetta , Orlando Antonella , Campanella Giovanna , Giotta Francesco , Riezzo Giuseppe
Published: February 2013

Background

Several GI peptides linked to intestinal barrier function could be involved in the modification of intestinal permeability and the onset of diarrhea during adjuvant chemotherapy. The aim of the study was to evaluate the circulating levels of zonulin, glucagon-like peptide-2 (GLP-2), epidermal growth factor (EGF) and ghrelin and their relationship with intestinal permeability and chemotherapy induced diarrhea (CTD).

Methods

Sixty breast cancer patients undergoing an FEC60 regimen were enrolled, 37 patients completed the study. CTD(+) patients were discriminated by appropriate questionnaire and criteria. During chemotherapy, intestinal permeability was assessed by lactulose/mannitol urinary test on day 0 and day 14. Zonulin, GLP-2, EGF and ghrelin circulating levels were evaluated by ELISA tests at five time-points (days 0, 3, 10, 14, and 21).

Results

During FEC60 administration, the lactulose/mannitol ratio was significantly higher on day 14 than at baseline. Zonulin levels were not affected by chemotherapy, whereas GLP-2 and EGF levels decreased significantly. GLP-2 levels on day 14 were significantly lower than those on day 0 and day 3, while EGF values were significantly lower on day 10 than at the baseline. In contrast, the total concentrations of ghrelin increased significantly at day 3 compared to days 0 and 21, respectively. Ten patients (27%) suffered from diarrhea. On day 14 of chemotherapy, a significant increase of the La/Ma ratio occurred in CTD(+) patients compared to CTD(−) patients. With regards to circulating gut peptides, the AUCg of GLP-2 and ghrelin were significantly lower and higher in CTD(+) patients than CTD(−) ones, respectively. Finally in CTD(+) patients a significant and inverse correlation between GLP-2 and La/Ma ratio was found on day 14.

Conclusions

Breast cancer patients undergoing FEC60 showed alterations in the intestinal permeability, which was associated with modifications in the levels of GLP-2, ghrelin and EGF. In CTD(+) patients, a different GI peptide profile and increased intestinal permeability was found in comparison to CTD(−) patients. This evidence deserves further studies for investigating the potentially different intestinal luminal and microbiota conditions.

Trial registration

Clinical trial NCT01382667
Redistributive effects of the National Health Insurance on physicians in Taiwan: a natural experiment time series study
Authors: Yang Chiang-Hsing , Huang Yu-Tung A , Hsueh Ya-Seng A
Published: February 2013

Background

Previous studies have evaluated the effects of various health manpower policies but did not include full consideration of the effect of universal health insurance on physician re-distribution. This study examines the effects of implementing National Health Insurance (NHI) on the problem of geographic mal-distribution of health providers in Taiwan.

Methods

Data on health providers and population between 1971 and 2001 are obtained from relevant governmental publications in Taiwan. Gini coefficients derived from the Lorenz curve are used under a spline regression model to examine the impact of the NHI on the geographic distribution of health providers.

Results

The geographic distribution equality of the three key health providers has improved significantly after the implementation of NHI program. After accounting for the influences of other confounding factors, Gini coefficients of the three key providers have a net reduction of 1.248% for dentists, 0.365% for western medicine physicians, and 0.311% for Chinese medicine physicians. Overall, the absolute values of the three key providers’ Gini coefficients also become close to one another.

Conclusions

This study found that NHI’s offering universal health coverage to all citizens and with proper financial incentives have resulted in more equal geographic distributions among the key health care providers in Taiwan.
Quantitation of cell-free DNA and RNA in plasma during tumor progression in rats
Authors: García-Olmo Dolores C , Picazo María G , Toboso Inmaculada , Asensio Ana I , García-Olmo Damián
Published: February 2013

Background

To clarify the implications of cell-free nucleic acids (cfNA) in the plasma in neoplastic disease, it is necessary to determine the kinetics of their release into the circulation.

Methods

To quantify non-tumor and tumor DNA and RNA in the plasma of tumor-bearing rats and to correlate such levels with tumor progression, we injected DHD/K12-PROb colon cancer cells subcutaneously into syngenic BD-IX rats. Rats were sacrificed and their plasma was analyzed from the first to the eleventh week after inoculation.

Results

The release of large amounts of non-tumor DNA into plasma was related to tumor development from its early stages. Tumor-specific DNA was detected in 33% of tumor-bearing rats, starting from the first week after inoculation and at an increasing frequency thereafter. Animals that were positive for tumor DNA in the plasma had larger tumors than those that were negative (p = 0.0006). However, the appearance of both mutated and non-mutated DNA fluctuated with time and levels of both were scattered among individuals in each group. The release of non-tumor mRNA was unaffected by tumor progression and we did not detect mutated RNA sequences in any animals.

Conclusions

The release of normal and tumor cfDNA into plasma appeared to be related to individual-specific factors. The contribution of tumor DNA to the elevated levels of plasma DNA was intermittent. The release of RNA into plasma during cancer progression appeared to be an even more selective and elusive phenomenon than that of DNA.
Epigenetic mechanisms in migraine: a promising avenue?
Authors: Eising Else , A Datson Nicole , van den Maagdenberg Arn MJM , Ferrari Michel D
Published: February 2013

Migraine is a disabling common brain disorder typically characterized by attacks of severe headache and associated with autonomic and neurological symptoms. Its etiology is far from resolved. This review will focus on evidence that epigenetic mechanisms play an important role in disease etiology. Epigenetics comprise both DNA methylation and post-translational modifications of the tails of histone proteins, affecting chromatin structure and gene expression. Besides playing a role in establishing cellular and developmental stage-specific regulation of gene expression, epigenetic processes are also important for programming lasting cellular responses to environmental signals. Epigenetic mechanisms may explain how non-genetic endogenous and exogenous factors such as female sex hormones, stress hormones and inflammation trigger may modulate attack frequency. Developing drugs that specifically target epigenetic mechanisms may open up exciting new avenues for the prophylactic treatment of migraine.
Hypothermia enhances induction of protective protein metallothionein under ischemia
Authors: Park Youn Hee , Lee Young Mi , Kim Dong Sun , Park Jaechan , Suk Kyoungho , Kim Jong Kun , Han Hyung Soo
Published: February 2013

Background

Hypothermic protection against ischemic stroke has been reported by many studies. Hypothermia is supposed to mitigate the effects of deleterious genes and proteins and promote the activity of protective genes and proteins in the ischemic brain. Metallothionein (MT)-1/2 is thought to be a crucial factor for metal homeostasis, immune function, and apoptosis. This protein was found to exert protective effects in models of brain injury as well. In the present study, we investigated the effect of hypothermia on MT expression and the underlying mechanisms.

Methods

Cultured bEnd.3 brain endothelial cells were exposed to oxygen glucose deprivation and reperfusion (OGD+R). Reverse transcription PCR and western blot analyses were performed to measure the expression of MT, transcription factors, and methylation regulating factors. Transcription factor binding assays were also performed. Methylation profiles of the promoter area were obtained with pyrosequencing.

Results

Hypothermia protected bEnd.3 cells from OGD+R. When the cells were exposed to OGD+R, MT expression was induced. Hypothermia augmented MT levels. While OGD+R-induced MT expression was mainly associated with metal regulatory transcription factor 1 (MTF-1), MT expression promoted by hypothermia was primarily mediated by the signal transducer and activator of transcription 3 (STAT3). Significantly increased STAT3 phosphorylation at Ser727 was observed with hypothermia, and JSI-124, a STAT-3 inhibitor, suppressed MT expression. The DNA demethylating drug 5-aza-2′-deoxycytidine (5-Aza) enhanced MT expression. Some of the CpG sites in the promoter MT=> it should be “the CpG sites in the MT promoter” showed different methylation profiles and some methylation regulating factors had different expressional profiles in the presence of OGD+R and hypothermia.

Conclusions

We demonstrated that hypothermia is a potent inducer of MT gene transcription in brain endothelial cells, and enhanced MT expression might contribute to protection against ischemia. MT gene expression is induced by hypothermia mainly through the STAT3 pathway. DNA methylation may contribute to MT gene regulation under ischemic or hypothermic conditions.
Large cell neuroendocrine carcinoma (LCNEC) of the urinary bladder: a case report
Authors: Colarossi Cristina , Pino Piero , Giuffrida Dario , Aiello Eleonora , Costanzo Rosario , Martinetti Daniela , Memeo Lorenzo
Published: February 2013

Neuroendocrine carcinoma of the urinary bladder is a rare entity, accounting less then 1% of urinary bladder malignancies. The vast majority of the neuroendocrine carcinoma of the urinary bladder is represented by small cell neuroendocrine carcinoma while just few cases of large cell neuroendocrine carcinoma (LCNEC) have been reported. In this cases report we describe a rare case of primary bladder LCNEC.

Virtual Slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2474700528951562
Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production
Authors: Chang Jui-Jen , Ho Feng-Ju , Ho Cheng-Yu , Wu Yueh-Chin , Hou Yu-Han , Huang Chieh-Chen , Shih Ming-Che , Li Wen-Hsiung
Published: February 2013

Background

Many microorganisms possess enzymes that can efficiently degrade lignocellulosic materials, but do not have the capability to produce a large amount of ethanol. Thus, attempts have been made to transform such enzymes into fermentative microbes to serve as hosts for ethanol production. However, an efficient host for a consolidated bioprocess (CBP) remains to be found. For this purpose, a synthetic biology technique that can transform multiple genes into a genome is instrumental. Moreover, a strategy to select cellulases that interact synergistically is needed.

Results

To engineer a yeast for CBP bio-ethanol production, a synthetic biology technique, called “promoter-based gene assembly and simultaneous overexpression” (PGASO), that can simultaneously transform and express multiple genes in a kefir yeast, Kluyveromyces marxianus KY3, was recently developed. To formulate an efficient cellulase cocktail, a filter-paper-activity assay for selecting heterologous cellulolytic enzymes was established in this study and used to select five cellulase genes, including two cellobiohydrolases, two endo-β-1,4-glucanases and one beta-glucosidase genes from different fungi. In addition, a fungal cellodextrin transporter gene was chosen to transport cellodextrin into the cytoplasm. These six genes plus a selection marker gene were one-step assembled into the KY3 genome using PGASO. Our experimental data showed that the recombinant strain KR7 could express the five heterologous cellulase genes and that KR7 could convert crystalline cellulose into ethanol.

Conclusion

Seven heterologous genes, including five cellulases, a cellodextrin transporter and a selection marker, were simultaneously transformed into the KY3 genome to derive a new strain, KR7, which could directly convert cellulose to ethanol. The present study demonstrates the potential of our strategy of combining a cocktail formulation protocol and a synthetic biology technique to develop a designer yeast host.
Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays
Authors: Fenart Stephane , Chabi Malika , Gallina Sophie , Huis Rudy , Neutelings Godfrey , Riviere Nathalie , Thomasset Brigitte , Hawkins Simon , Lucau-Danila Anca
Published: February 2013

Background

We performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles.

Results

Comparison of the hybridization quality, precision and accuracy of expression measurements, as well as an interpretation of differential gene expression in flax tissues were performed. Both array types yielded reproducible, accurate and comparable data that are coherent for expression measurements and identification of differentially expressed genes. 60-mers arrays gave higher hybridization efficiencies and therefore were more sensitive allowing the detection of a higher number of unigenes involved in the same biological process and/or belonging to the same multigene family.

Conclusion

The two flax arrays provide a good resolution of expressed functions; however the 60-mers arrays are more sensitive and provide a more in-depth coverage of candidate genes potentially involved in different biological processes.
Metagenomic profile of gut microbiota in children during cholera and recovery
Authors: Monira Shirajum , Nakamura Shota , Gotoh Kazuyoshi , Izutsu Kaori , Watanabe Haruo , Alam Nur Haque , Nakaya Takaaki , Horii Toshihiro , Ali Sk Imran , Iida Tetsuya , Alam Munirul
Published: February 2013

Background

The diverse bacterial communities colonizing the gut (gastrointestinal tract) of infants as commensal flora, which play an important role in nutrient absorption and determining the state of health, are known to alter due to diarrhea.

Method

Bacterial community dynamics in children suffering from cholera and during recovery period were examined in the present study by employing metagenomic tool, followed by DNA sequencing and analysis. For this, bacterial community DNA was extracted from fecal samples of nine clinically confirmed cholera children (age 2–3 years) at day 0 (acute cholera), day 2 (antibiotic therapy), day 7 and, and day 28, and the variable region of 16S rRNA genes were amplified by universal primer PCR.

Results

454 parallel sequencing of the amplified DNA followed by similarity search of the sequenced data against an rRNA database allowed us to identify V. cholerae, the cause of cholera, in all nine children at day 0, and as predominant species in six children, accounting for 35% of the total gut microbiota on an average in all the nine children. The relative abundance (mean ± sem %) of bacteria belonging to phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, was 55 ± 7, 18 ± 4, 13 ± 4, and 8 ± 4, respectively, at day 0, while these values were 12 ± 4, 43 ± 4, 33 ± 3, and 12 ± 2, respectively, at day 28. As antibiotic therapy began, V. cholerae count declined significantly (p< 0.001) and was found only in four children at day 2 and two children at day 7 with the relative abundance of 3.7% and 0.01%, respectively, which continued up to day 28 in the two children. Compared to acute cholera condition (day 0), the relative abundance of Escherichia coli, Enterococcus, and Veillonella increased at day 2 (antibiotic therapy) while Bifidobacterium, Bacteroides, and Ruminococcus decreased.

Conclusion

Cholera results expulsion of major commensal bacteria of phyla Bacteroidetes, Firmicutes, and Actinobacteria, and increase of harmful Proteobacteria to colonize the gut during acute and convalescence states. The observed microbiota disruption might explain the prevalent malnutrition in children of Bangladesh where diarrheal diseases are endemic.
The ototoxic effect of intratympanic terbinafine applied in the middle ear of rats
Authors: Sagit Mustafa , Somdas Mehmet Akıf , Korkmaz Ferhat , Akcadag Alper
Published: February 2013

Background

Otomycosis is defined as an infection of the external ear canal with fungal agents. The treatment of the disease is cleansing and drying of the external ear canal, identification and treatment of any predisposing factors and application of topical antifungal agents. Terbinafine is used as an antifungal agent to treat otomycosis. We proposed to investigate the probable ototoxic effect of terbinafine solution on auditory brain stem response (ABR) and distortion product otoacoustic emission (DPOAE) when applied intratympanically in the middle ear of rats.

Methods

The experiment was performed on 30 female Wistar albino rats. Thirty animals were divided into three groups of 10 animals each. 1% terbinafine solution was administered to the first group (group T). The second group (group G) was administered 40 mg/ml gentamicin solution (ototoxic control). The third group (group S) was administered saline solution (negative control). Baseline DPOAE measurements and ABR testing from the left ears were obtained from the animals in all groups under general anesthesia. Ear solutions were applied in the middle ear intratympanically with a dental needle. Treatment was initiated after baseline measurements and repeated once every two days for fifteen days.

Results

Pre and post-treatment DPOAE responses for all tested frequencies of group T and Group S showed no statistically significant difference. However, the group G demonstrated a significant change in ABR thresholds and DPOAE responses.

Conclusions

Terbinafine solution is a broad spectrum antifungal agent effective in the treatment of otomycosis. The present study demonstrated that its direct administration in the middle ear of rats does not affect inner ear function as measured by ABR and DPOAE responses.
Localized Ewing sarcoma of the tibia
Authors: Kashima Takeshi G , Gamage Nimali G , Dirksen Uta , Gibbons Christopher L M H , Ostlere Simon J , Athanasou Nicholas A
Published: February 2013

Ewing sarcoma (ES) is a high-grade malignant primary round cell tumour of bone in which there is commonly extension into extraosseous soft tissues at the time of diagnosis. This report details the clinical, radiological and pathological features of a case of ES of the tibia in which there was extensive osseous involvement but no infiltration beyond the periosteum into surrounding soft tissue. We also record the findings of one other ES case that exhibited similar behaviour. Both cases were male, involved the tibia and had the characteristic t (11;22) (q24;q12) translocation. No recurrence of tumour or metastasis has been seen in these two cases, both of which have had 6 years follow-up. Our findings indicate that there is heterogeneity in the behaviour of ES and show that localized ES is associated with a good prognosis.
Noninvasive biomarkers for the diagnosis of steatohepatitis and advanced fibrosis in NAFLD
Authors: Pearce Steven G , Thosani Nirav C , Pan Jen-Jung
Published: February 2013

Nonalcoholic fatty liver disease (NAFLD) is the most common cause of abnormal liver enzymes in both adults and children. NAFLD has a histologic spectrum ranging from simple steatosis to nonalcoholic steatohepatitis (NASH), advanced fibrosis, and cirrhosis. It is imperative to distinguish simple steatosis from NASH since the latter has a progressive disease course and can lead to end-stage liver disease. Liver biopsy has been considered as the gold standard for the diagnosis of NASH. However, liver biopsy is invasive, costly, and can rarely cause significant morbidity (risk of morbidity, 0.06-0.35%; risk of mortality, 0.1-0.01%). Imaging studies such as ultrasonography, computed tomography, and magnetic resonance imaging have limited sensitivity in detecting steatosis and cannot distinguish steatosis from NASH. Alanine aminotransferase (ALT) has been used as a surrogate marker for liver injuries. However, ALT is not an ideal marker for either diagnosis of NAFLD or distinguishing steatosis from NASH. Better noninvasive biomarkers or panels of biomarkers that are cheaper, reliable, and reproducible are urgently needed for patients with NASH to assist in establishing diagnosis, providing risk information, and monitoring disease progression and treatment response. In this article, we plan to concisely review the current advances in the use of biomarkers for the diagnosis of NASH.
New urinary biomarkers for diabetic kidney disease
Authors: Wang Cheng , Li CuiCui , Gong WenYu , Lou Tanqi
Published: February 2013

Diabetic kidney disease is the leading cause of end-stage renal disease in developed and developing countries. Microalbuminuria is the gold standard for detection and prediction of diabetic kidney disease and cardiovascular risk disease in clinical practice. However, microalbuminuria has several limitations, such as lower sensitive, larger variability. It is urgent to explore higher sensitivity and specificity for earlier detection of diabetic kidney disease and more accurate prediction of the progression to end stage renal disease. We reviewed some new and important urinary biomarkers, such as: transferrin, immunoglobulin G, immunoglobulin M, Cystanic C, podocytes, type IV collagen, 8-oxo-7, 8-dihydro-2'-deoxyguanosine, ceruloplasmin, monocyte chemoattractant protein-1 and so on. We need good quality, long-term, large longitudinal trials to validate published biomarkers and find new biomarkers, considering biomarkers reviewed here are from small cross-sectional studies.
Mapping groundwater salinization using transient electromagnetic and direct current resistivity methods in Azraq Basin, Jordan
Authors: Abu Rajab Jafar Sadi , El-Naqa Ali Ramadan
Published: February 2013

Hydrogeophysical characterization using the transient electromagnetic method (TEM) and the DC resistivity sounding (VES) method was implemented in the central part of Azraq Basin (Qa Basin), Jordan, to identify and map the spatial distribution of shallow fresh and saline groundwater in the upper aquifer systems. The alluvium (Al) and chert limestone (URC) shallow aquifers show different degrees of groundwater salinization. The range of groundwater resistivity varies from 0.06 to 10.8 ohm-m. Saline groundwater was detected at depths between 5 to 30 m where the aquifers have a wide spectrum of resistivity values from 0.14 to 120 ohm-m. The integrated geophysical and hydrogeologic models are significantly correlated in chloride concentration, groundwater resistivity, and aquifer resistivity. Using 1D inversion results from the TEM and VES soundings in addition to quasi-3D modeling (1D spatially constrained inversion) at selected TEM sites, groundwater resistivity variation was attributed to two different salinization mechanisms. First, the spatial distribution of the salt content in mud flat deposits had a significant effect on the groundwater salinity. Second, in situ dissolution of near-surface rock-forming salts occurred at areas away from the mud flat deposits. The proposed hydrogeophysical models revealed the potential effect of both mechanisms in the study area.
High-resolution gathers by inverse Q filtering in the wavelet domain
Authors: Braga Igor L. S , Moraes Fernando S.
Published: February 2013

We have developed and applied an inverse [Formula: see text] filter formulation using the continuous wavelet transform (CWT), which provides a natural domain for time-variant operations, such as compensation for propagation in attenuating and dispersive media. The well-known linear attenuation model, given as a function of time and frequency, was applied very efficiently over wavelet coefficients in the time-frequency domain to correct for amplitude and phase distortions, as necessary. The inverse CWT yields the recovered trace with a broader bandwidth. The process works on a trace-by-trace basis, making no distinction if the data is pre- or poststack. Our motivation was to develop gather conditioning tools to enhance prestack interpretation techniques such as amplitude variation with offset (AVO) analysis and inversion — a technique that is often compromised by tuning and other propagation related issues that degrade seismic resolution. Thus, we investigated the AVO fidelity of our filter and the sensitivity of the results to incorrect values of [Formula: see text], using real and synthetic data. Our synthetic data experiments clearly showed that AVO anomalies are recovered and preserved in a stable manner, even with values of [Formula: see text] off by 50% of its correct value. The application in time-migrated gathers shows a very natural increase in the vertical definition of the events, especially due to the partial elimination of the tuning effect. The benefits for imaging are also evidenced by comparing stacked sections before and after inverse [Formula: see text] filtering. The higher resolution of seismic sections leads to a better definition of smaller scale stratigraphic and structural features.
The marine controlled-source electromagnetic method in shallow water
Authors: Mittet Rune , Morten Jan Petter
Published: February 2013

We analyzed marine controlled-source electromagnetic (CSEM) acquisition in shallow water by analytic and numerical calculations. The problem at hand was the fact that the amplitude of the airwave due to a horizontal electric dipole becomes larger as the water depth is reduced. The amplitude of the scattered field from a buried thin resistor would be difficult to extract from the increased total field if the scattered-field amplitude were independent of water depth. However, we identified and explained a compensating effect where the amplitude of the scattered field increases with reduced water depth. This amplification effect makes marine CSEM surveys in shallow water feasible. We derived an approximate expression for the total field for a simple but realistic conductivity model. This expression explains why the amplitudes of the term that describes the background field contribution and the term that gives the scattered field from the thin resistor increase when the water depth is reduced. Our results and sensitivity analysis indicated that the sensitivity of marine CSEM data acquired in a water depth of 40 m is comparable to the sensitivity of marine CSEM data acquired in a water depth of 300 m.
Functional nucleic acids for detecting bacteria
Authors: Huang Po-Jung Jimmy , Liu Minchuan , Liu Juewen
Published: February 2013

Bacterial infection represents one of the leading causes of disease and death, and as such, bacterial detection is an important step in managing infectious diseases. The current protocol requires growing cell cultures, which can take several days. Fast detection of low copies of bacterial cells has thus posed an analytical challenge. Among the new strategies developed to achieve this goal, functional nucleic acids (FNAs) have emerged to be a promising platform. FNAs include DNAzymes, aptamers, and aptazymes, all of which can recognize analytes other than complementary nucleic acids. FNAs are obtained using a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). FNAs have been isolated against not only purified proteins and surface markers from bacterial cells but also whole cells. A diverse range of signaling mechanisms including fluorescence, color, and electrochemistry-based detection has been reported. Although the majority of current sensors cannot achieve single-cell sensitivity, with improved combinatorial selection techniques and the incorporation of nanomaterials to realize multivalent binding and signal amplification, FNAs represent a feasible solution for bacterial detection.
Crystal structure of (N,N'-bis-(salicylidene)-(1S,2S)-1,2-diphenyl-1,2- ethanediaminato)-nickel (II) hemihydrate, C112H93N8Ni4O12
Authors: Ding Shende
Published: February 2013

C112H93N8Ni4O12, monoclinic, C2 (no. 5), a = 17.27(1) Å, b = 18.82(1) Å, c = 7.873(5) Å, β = 95.76(1)°, V = 2546.4 Å3, Z = 1, Rgt(F) = 0.0647, wRref(F2) = 0.2077, T = 293 K
The crystal structure of the low-temperature phase of (NO)2SnCl6 and ordering of the NO+ ions
Authors: Henke Henning
Published: February 2013

At ambient conditions (NO)2SnCl6 is isostructural with the corresponding titanium and vanadium salts which all crystallize in space group P4/mnc (Z = 2) and display a fourfold disorder of the NO+ ions. Below T
c = 229 K the diffraction pattern splits into the components of a quadruplet twin, but unlike for (NO)2VCl6 remarkable discontinuities of the lattice parameters are not observed.

The transition from P4/mnc to space group P21/n (Z = 2) occurs in only one step which at T
c = 153 K, the temperature of the crystal structure determination, consists of an adaptive tilt (5.3°) of the SnCl6
2– octahedra leading to a reduction of the cationic disorder from four to merely two N—O alignments, which are differently populated. Despite of the continuously proceeding transition, the phase change from the high- to the low-temperature regime has to be classified as a 1st order process.
Steric control over C=O...C=O interactions in M(S2COR)2(dafone) compounds: M = Zn and Cd; R = Me, Et and iPr; dafone = 4,5-diazafluoren-9-one-N,N′
Authors: Câmpian Marius , Haiduc Ionel , Tiekink Edward R. T.
Published: February 2013

Crystallography shows that with the smaller xanthate-bound methyl groups in Zn(S2COMe)2(dafone) (1) and Cd(S2COMe)2(dafone) (3) anti-parallel C=O…C=O interactions link molecules into dimers. These are further associated via π—π interactions into a supramolecular chain, and in the case of 3 into a supramolecular two-dimensional array via C—H…S contacts. Increasing the size of the organic residue, i.e. to ethyl and isopropyl in Zn(S2COEt)2(dafone) (2), Cd(S2COEt)2(dafone) (4) and Cd(S2CO-iPr)2(dafone) (5), does not allow for the formation of this supramolecular architecture. Instead, supramolecular chains are sustained by C—H…S and C—H…π(chelate) interactions (the latter exclusively in the case of 5). The presence of recognisable/significant π—π and C—H…S and C—H…π(chelate) interactions is not consistent amongst the series yet only two crystal packing patterns are noted depending on the presence of the C=O…C=O interactions. This observation points to the importance of overall crystal packing considerations of binuclear species in 1 and 3, and mononuclear species in 2, 4 and 5.