bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular cloning of doublesex genes of four cladocera (water flea) species
Authors: Toyota Kenji , Kato Yasuhiko , Sato Masaru , Sugiura Naomi , Miyagawa Shinichi , Miyakawa Hitoshi , Watanabe Hajime , Oda Shigeto , Ogino Yukiko , Hiruta Chizue , Mizutani Takeshi , Tatarazako Norihisa , Paland Susanne , Jackson Craig , Colbourne John K , Iguchi Taisen
Published: April 2013

Background

The gene doublesex (dsx) is known as a key factor regulating genetic sex determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and DapmaDsx2) from a freshwater branchiopod crustacean, Daphnia magna, which are expressed in males but not in females. D. magna produces males by parthenogenesis in response to environmental cues (environmental sex determination) and we showed that DapmaDsx1 expression during embryonic stages is responsible for the male trait development. The D. magna dsx genes are thought to have arisen by a cladoceran-specific duplication; therefore, to investigate evolutionary conservation of sex specific expression of dsx genes and to further assess their functions in the environmental sex determination, we searched for dsx homologs in four closely related cladoceran species.

Results

We identified homologs of both dsx genes from, D. pulex, D. galeata, and Ceriodaphnia dubia, yet only a single dsx gene was found from Moina macrocopa. The deduced amino acid sequences of all 9 dsx homologs contained the DM and oligomerization domains, which are characteristic for all arthropod DSX family members. Molecular phylogenetic analysis suggested that the dsx gene duplication likely occurred prior to the divergence of these cladoceran species, because that of the giant tiger prawn Penaeus monodon is rooted ancestrally to both DSX1 and DSX2 of cladocerans. Therefore, this result also suggested that M. macrocopa lost dsx2 gene secondarily. Furthermore, all dsx genes identified in this study showed male-biased expression levels, yet only half of the putative 5’ upstream regulatory elements are preserved in D. magna and D. pulex.

Conclusions

The all dsx genes of five cladoceran species examined had similar amino acid structure containing highly conserved DM and oligomerization domains, and exhibited sexually dimorphic expression patterns, suggesting that these genes may have similar functions for environmental sex determination in cladocerans.
Serum γ-glutamyltransferase and uric acid levels are associated with impaired fasting glucose in adults from Inner Mongolia, China
Authors: Wu Jie , Qiu Ling , Yan Wen-hua , Cheng Xin-qi , Wu Wei , Guo Xiu-zhi , Ding Hai-tao , Han Hui-juan , Han Shao-mei , Zhu Guang-jin
Published: April 2013

Background

Serum γ-glutamyltransferase (GGT) and uric acid (UA) levels are elevated in patients with diabetes or cardiovascular disease. Prediabetes, characterized by impaired glucose tolerance, is an important risk factor for overt diabetes as well as cardiovascular disease. Therefore, the aim of this study was to explore the relationship between GGT, UA and prediabetes in a Chinese population, and provide a scientific basis for the early prevention and treatment of diabetes.

Methods

We performed a cross-sectional population-based study in a cohort of 2694 subjects (1211 men and 1483 women, aged 35–86 years). Questionnaires and physical examinations were performed using standardized procedures. Fasting blood was collected to measure glucose and other biochemical parameters. The subjects were divided into two groups with either normal fasting glucose (NFG) or impaired fasting glucose (IFG), according to international diagnostic criteria. Logistic regression analysis was performed to estimate odds ratios (OR) and 95% confidence intervals.

Results

Compared with the NFG group, the IFG group had significantly higher blood pressure but lower high-density lipoprotein–cholesterol in women. Body mass index, waist circumference, triglyceride, glucose, GGT, and UA levels were significantly higher in males and females in the IFG group than those in the NFG group. Logistic regression analysis revealed that the OR for prediabetes increased with increasing serum GGT quartiles and UA quartiles. GGT and UA were positively associated with prediabetes in men and women, independent of age, ethnicity, smoking, alcohol consumption, blood pressure, physical labor, and other confounders.

Conclusions

We found that serum GGT and UA levels were positively associated with prediabetes in men and women living in areas inhabited by Chinese ethnic minorities. As elevated GGT and UA levels were associated with significantly increased risk of prediabetes, they may be used as sensitive biological markers of prediabetes.
Increasing trends in central obesity among Chinese adults with normal body mass index, 1993–2009
Authors: Du Tingting , Sun Xingxing , Yin Ping , Huo Rui , Ni Chaochao , Yu Xuefeng
Published: April 2013

Background

Central obesity is thought to be more pathogenic than overall obesity and studies have shown that the association between waist circumference (WC) and mortality was strongest in those with a normal body mass index (BMI). The objective of our study was to determine secular trends in the prevalence of central obesity (WC ≥ 90 cm for men and ≥ 80 cm for women) among Chinese adults with normal BMI from 1993 to 2009 and to examine the impact of performance of combined BMI and WC on the prevalence of obesity in Chinese adults.

Methods

We used data from the China Health and Nutrition Survey (CHNS) conducted from 1993 to 2009. From which we included a total of 52023 participants aged ≥ 18 years.

Results

The age-standardized prevalence of central obesity among Chinese adults with BMI < 25 kg/m2 increased from 11.9% in 1993 to 21.1% in 2009 (P for linear trend <0.001). The upward trends were noted in both genders, all ages, rural/urban settings, and education groups (all P for linear trend <0.001), with greater increments in men, participants aged 18–64 years, and rural residents (P for interaction terms survey × sex, survey × age, and survey × rural/urban settings were 0.042, 0.003, and < 0.001, respectively). Trends in the prevalence of central obesity were similar when a more stringent BMI < 23 kg/m2 cut point (Asian cut point) was applied. Central obesity is associated with a higher risk of incident hypertension within normal BMI category. More than 65% individuals with obesity would be missed if solely BMI was measured.

Conclusions

We observed an upward trend in the prevalence of central obesity among participants with normal BMI irrespective of sex, age, rural/urban settings, and education level. Central obesity is associated with a higher risk of incident hypertension within normal BMI category. Approximately two thirds of the individuals with obesity would be missed if WC was not measured. It is, therefore, urgent to emphasize the importance of WC as a measure to monitor the prevalence of obesity.
Response to microtubule-interacting agents in primary epithelial ovarian cancer cells
Authors: Pellicciotta Ilenia , Yang Chia-Ping Huang , Venditti Charis A , Goldberg Gary L , Shahabi Shohreh
Published: April 2013

Background

Ovarian cancer constitutes nearly 4% of all cancers among women and is the leading cause of death from gynecologic malignancies in the Western world. Standard first line adjuvant chemotherapy treatments include Paclitaxel (Taxol) and platinum-based agents. Taxol, epothilone B (EpoB) and discodermolide belong to a family of anti-neoplastic agents that specifically interferes with microtubules and arrests cells in the G2/M phase of the cell cycle. Despite initial success with chemotherapy treatment, many patients relapse due to chemotherapy resistance. In vitro establishment of primary ovarian cancer cells provides a powerful tool for better understanding the mechanisms of ovarian cancer resistance. We describe the generation and characterization of primary ovarian cancer cells derived from ascites fluids of patients with epithelial ovarian cancer.

Methods

Chemosensitivity of these cell lines to Taxol, EpoB and discodermolide was tested, and cell cycle analysis was compared to that of immortalized ovarian cancer cell lines SKOV3 and Hey. The relationship between drug resistance and αβ-tubulin and p53 status was also investigated.

Results

All newly generated primary cancer cells were highly sensitive to the drugs. αβ-tubulin mutation was not found in any primary cell lines tested. However, one cell line that harbors p53 mutation at residue 72 (Arg to Pro) exhibits altered cell cycle profile in response to all drug treatments. Immortalized ovarian cancer cells respond differently to EpoB treatment when compared to primary ovarian cancer cells, and p53 polymorphism suggests clinical significance in the anti-tumor response in patients.

Conclusions

The isolation and characterization of primary ovarian cancer cells from ovarian cancer patients’ specimens contribute to further understanding the nature of drug resistance to microtubule interacting agents (MIAs) currently used in clinical settings.
Gaining a better understanding of respiratory health inequalities among cities: An ecological case study on elderly males in the larger French cities
Authors: Aschan-Leygonie Christina , Baudet-Michel Sophie , Mathian Hélène , Sanders Lena
Published: April 2013

Background

In recent years, there have been a growing number of studies on spatial inequalities in health covering a variety of scales, from small areas to metropolitan areas or regions, and for various health outcomes. However, few investigations have compared health status between cities with a view to gaining a better understanding of the relationships between such inequalities and the social, economic and physical characteristics. This paper focuses on disparities in respiratory health among the 55 largest French cities. The aim is to explore the relationships between inter-urban health patterns, city characteristics and regional context, and to determine how far a city’s health status relates to the features observed on different geographical scales.

Methods

We used health data describing hospitalizations for Chronic Obstructive Pulmonary Disease (COPD) as a proxy for respiratory health, and the total number of hospitalizations (overall) as a proxy for general health. This last indicator was used as a benchmark. A large set of indicators relating to socioeconomic, physical and amenity aspects of the cities (urban units) was also constructed. Data were analyzed using linear correlations and multiple linear regression models.

Results

The results suggest that socioeconomic characteristics are major discriminators for inequalities in respiratory health status among urban units. Indeed, once combined to socioeconomic characteristics, only a climate indicator remained significant among the physical indicators. It appeared that the pollution indicators which were significantly correlated with COPD hospitalization rates loosed significance when associated to the socio-economic indicators in a multiple regression. The analysis showed that among the socio-economic indicators, an employment indicator derived at the regional scale, and two indicators reflecting the unequal intra-urban spatial distribution of population according to their education, were the most efficient to describe differences in the respiratory health status of urban units.

Conclusion

In order to design effective urban policies, it is essential to gain a better understanding of the differences among cities in their entirety, rather than solely differences across small urban areas or individuals.
The impact of Cysteine-Rich Intestinal Protein 1 (CRIP1) in human breast cancer
Authors: Ludyga Natalie , Englert Sonja , Pflieger Kerstin , Rauser Sandra , Braselmann Herbert , Walch Axel , Auer Gert , Höfler Heinz , Aubele Michaela
Published: April 2013

Background

CRIP1 (cysteine-rich intestinal protein 1) has been found in several tumor types, its prognostic impact and its role in cellular processes, particularly in breast cancer, are still unclear.

Methods

To elucidate the prognostic impact of CRIP1, we analyzed tissues from 113 primary invasive ductal breast carcinomas using immunohistochemistry. For the functional characterization of CRIP1, its endogenous expression was transiently downregulated in T47D and BT474 breast cancer cells and the effects analyzed by immunoblotting, WST-1 proliferation assay and invasion assay.

Results

We found a significant correlation between CRIP1 and HER2 (human epidermal growth factor receptor 2) expression levels (p = 0.016) in tumor tissues. In Kaplan Meier analyses, CRIP1 expression was significantly associated with the distant metastases-free survival of patients, revealing a better prognosis for high CRIP1 expression (p = 0.039). Moreover, in multivariate survival analyses, the expression of CRIP1 was an independent negative prognostic factor, along with the positive prognosticators nodal status and tumor size (p = 0.029). CRIP1 knockdown in the T47D and BT474 breast cancer cell lines led to the increased phosphorylation of MAPK and Akt, to the reduced phosphorylation of cdc2, and to a significantly elevated cell proliferation in vitro (p < 0.001). These results indicate that reduced CRIP1 levels may increase cell proliferation and activate cell growth. In addition, CRIP1 knockdown increased cell invasion in vitro.

Conclusions

Because the lack of CRIP1 expression in breast cancer tissue is significantly associated with a worse prognosis for patients and low endogenous CRIP1 levels in vitro increased the malignant potential of breast cancer cells, we hypothesize that CRIP1 may act as a tumor suppressor in proliferation and invasion processes. Therefore, CRIP1 may be an independent prognostic marker with significant predictive power for use in breast cancer therapy.
Cardiometabolic risk factors among HIV patients on antiretroviral therapy
Authors: Kiage James N , Heimburger Douglas C , Nyirenda Christopher K , Wellons Melissa F , Bagchi Shashwatee , Chi Benjamin H , Koethe John R , Arnett Donna K , Kabagambe Edmond K
Published: April 2013

Background

HIV and combination antiretroviral therapy (cART) may increase cardiovascular disease (CVD) risk. We assessed the early effects of cART on CVD risk markers in a population with presumed low CVD risk.

Methods

Adult patients (n=118) in Lusaka, Zambia were recruited at the time of initiation of cART for HIV/AIDS. Cardiometabolic risk factors were measured before and 90 days after starting cART. Participants were grouped according to cART regimens: Zidovudine + Lamivudine + Nevirapine (n=58); Stavudine + Lamivudine + Nevirapine (n=43); and ‘other’ (Zidovudine + Lamivudine + Efavirenz, Stavudine + Lamivudine + Efavirenz, Tenofovir + Emtricitabine + Efavirenz or Tenofovir + Emtricitabine + Nevirapine, n=17). ANOVA was used to test whether changes in cardiometabolic risk markers varied by cART regimen.

Results

From baseline to 90 days after initiation of cART, the prevalence of low levels of high-density lipoprotein cholesterol (<1.04 mmol/L for men and <1.30 mmol/L for women) significantly decreased (78.8% vs. 34.8%, P<0.001) while elevated total cholesterol (TC ≥5.18 mmol/L, 5.1% vs. 11.9%, P=0.03) and the homeostasis model assessment of insulin resistance ≥3.0 (1.7% vs. 17.0%, P<0.001) significantly increased. The prevalence of TC:HDL-c ratio ≥5.0 significantly decreased (44.9% vs. 6.8%, P<0.001). These changes in cardiometabolic risk markers were independent of the cART regimen.

Conclusion

Our results suggest that short-term cART is associated with a cardioprotective lipid profile in Zambia and a tendency towards insulin resistance regardless of the cART regimen.
Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria
Authors: Moolman M Charl , Huang Zhuangxiong , Krishnan Sriram Tiruvadi , Kerssemakers Jacob WJ , Dekker Nynke H
Published: April 2013

Background

Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this approach to other species of bacteria, many of whom have dimensions in the sub-micron range, or to a larger range of growth conditions, a readily-fabricated device containing sub-micron features is required.

Results

Here we detail the fabrication of a versatile device with growth channels whose widths range from 0.3 μ m to 0.8 μ m. The device is fabricated using electron beam lithography, which provides excellent control over the shape and size of different growth channels and facilitates the rapid-prototyping of new designs. Features are successfully transferred first into silicon, and subsequently into the polydimethylsiloxane that forms the basis of the working microfluidic device. We demonstrate that the growth of sub-micron scale bacteria such as Lactococcus lactis or Escherichia coli cultured in minimal medium can be followed in such a device over several generations.

Conclusions

We have presented a detailed protocol based on electron beam fabrication together with specific dry etching procedures for the fabrication of a microfluidic device suited to study submicron-sized bacteria. We have demonstrated that both Gram-positive and Gram-negative bacteria can be successfully loaded and imaged over a number of generations in this device. Similar devices could potentially be used to study other submicron-sized organisms under conditions in which the height and shape of the growth channels are crucial to the experimental design.
Daily cytokine fluctuations, driven by leptin, are associated with fatigue severity in chronic fatigue syndrome: evidence of inflammatory pathology
Authors: Stringer Elizabeth Ann , Baker Katharine Susanne , Carroll Ian R , Montoya Jose G , Chu Lily , Maecker Holden T , Younger Jarred W
Published: April 2013

Background

Chronic fatigue syndrome (CFS) is a debilitating disorder characterized by persistent fatigue that is not alleviated by rest. The lack of a clearly identified underlying mechanism has hindered the development of effective treatments. Studies have demonstrated elevated levels of inflammatory factors in patients with CFS, but findings are contradictory across studies and no biomarkers have been consistently supported. Single time-point approaches potentially overlook important features of CFS, such as fluctuations in fatigue severity. We have observed that individuals with CFS demonstrate significant day-to-day variability in their fatigue severity.

Methods

Therefore, to complement previous studies, we implemented a novel longitudinal study design to investigate the role of cytokines in CFS pathophysiology. Ten women meeting the Fukuda diagnostic criteria for CFS and ten healthy age- and body mass index (BMI)-matched women underwent 25 consecutive days of blood draws and self-reporting of symptom severity. A 51-plex cytokine panel via Luminex was performed for each of the 500 serum samples collected. Our primary hypothesis was that daily fatigue severity would be significantly correlated with the inflammatory adipokine leptin, in the women with CFS and not in the healthy control women. As a post-hoc analysis, a machine learning algorithm using all 51 cytokines was implemented to determine whether immune factors could distinguish high from low fatigue days.

Results

Self-reported fatigue severity was significantly correlated with leptin levels in six of the participants with CFS and one healthy control, supporting our primary hypothesis. The machine learning algorithm distinguished high from low fatigue days in the CFS group with 78.3% accuracy.

Conclusions

Our results support the role of cytokines in the pathophysiology of CFS.
Optimization of reaction parameters in hydrothermal synthesis: a strategy towards the formation of CuS hexagonal plates
Authors: Auyoong Yow Loo , Yap Pei Lay , Huang Xing , Abd Hamid Sharifah Bee
Published: April 2013

Background

For decades, copper sulphide has been renowned as the superior optical and semiconductor materials. Its potential applications can be ranged from solar cells, lithium-ion batteries, sensors, and catalyst systems. The synthesis methodologies of copper sulphide with different controlled morphology have been widely explored in the literature. Nevertheless, the understanding on the formation chemistry of CuS is still limited. The ultimate approach undertaking in this article is to investigate the formation of CuS hexagonal plates via the optimization of reaction parameters in hydrothermal reaction between copper (II) nitrate and sodium thiosulphate without appending any assistant agent.

Results

Covellite (CuS) hexagonal plates were formed at copper ion: thiosulphate ion (

Cu

2
+

:

S

2

O
3

2
−

) mole ratio of 1:2 under hydrothermal treatment of 155°C for 12 hours. For synthesis conducted at reaction temperature lower than 155°C, copper sulphate (CuSO4), krohnite (NaCu2(SO4)(H2O)2] and cyclooctasulphur (S8) were present as main impurities with covellite (CuS). When

Cu

2
+

:

S

2

O
3

2
−

mole ratio was varied to 1: 1 and 1: 1.5, phase pure plate-like natrochalcite [NaCu2(SO4)(H2O)] and digenite (Cu9S5) were produced respectively. Meanwhile, mixed phases of covellite (CuS) and cyclooctasulphur (S8) were both identified when

Cu

2
+

:

S

2

O
3

2
−

mole ratio was varied to 1: 2.5, 1: 3 and 1: 5 as well as when reaction time was shortened to 1 hour.

Conclusions

CuS hexagonal plates with a mean edge length of 1 μm, thickness of 100 nm and average crystallite size of approximately (45 ± 2) nm (Scherrer estimation) were successfully synthesized via assisting agent- free hydrothermal method. Under a suitable

Cu

2
+

:

S

2

O
3

2
−

mole ratio, we evidenced that the formation of covellite (CuS) is feasible regardless of the reaction temperature applied. However, a series of impurities were attested with CuS if reaction temperature was not elevated high enough for the additional crystallite phase decomposition. It was also identified that

Cu

2
+

:

S

2

O
3

2
−

mole ratio plays a vital role in controlling the amount of cyclooctasulphur (S8) in the final powder obtained. Finally, reaction time was recognized as an important parameter in impurity decomposition as well as increasing the crystallite size and crystallinity of the CuS hexagonal plates formed.
Production and partial characterization of extracellular amylase enzyme from Bacillus amyloliquefaciens P-001
Authors: Deb Promita , Talukdar Saimon Ahmad , Mohsina Kaniz , Sarker Palash Kumar , Sayem SM Abu
Published: April 2013

Amylases are one of the most important enzymes in present-day biotechnology. The present study was concerned with the production and partial characterization of extracellular amylase fromBacillus amyloliquefaciensP-001. The effect of various fermentation conditions on amylase production through shake-flask culture was investigated. Enzyme production was induced by a variety of starchy substrate but corn flour was found to be a suitable natural source for maximum production. Tryptone and ammonium nitrate (0.2%) as nitrogen sources gave higher yield compared to other nitrogen sources. Maximum enzyme production was obtained after 48 hrs of incubation in a fermentation medium with initial pH 9.0 at 42°C under continuous agitation at 150 rpm. The size of inoculum was also optimized which was found to be 1% (v/v). Enzyme production was 2.43 times higher after optimizing the production conditions as compared to the basal media. Studies on crude amylase revealed that optimum pH, temperature and reaction time of enzyme activity was 6.5, 60°C and 40 minutes respectively. About 73% of the activity retained after heating the crude enzyme solution at 50°C for 30 min. The enzyme was activated by Ca2+(relative activity 146.25%). It was strongly inhibited by Mn2+, Zn2+and Cu2+, but less affected by Mg2+and Fe2+.
Characterization of tetraspanins CD9, CD53, CD63, and CD81 in monocytes and macrophages in HIV-1 infection
Authors: Tippett Emma , Cameron Paul U , Marsh Mark , Crowe Suzanne M
Published: April 2013

Tetraspanins are differentially expressed in monocyte subsets and modified by inflammatory situations including HIV-1 infection.

Tetraspanins are a family of membrane-organizing proteins that mediate diverse functions. Little is known of their expression or function in myeloid cells. Here, expression of CD9, CD53, CD63, and CD81, tetraspanins that have been implicated in HIV-1 pathogenesis, were characterized in normal monocyte subsets, in MDM, and in HIV-1-infected donors. We show that tetraspanins are expressed differentially by monocyte subsets, with higher CD9 and CD63 and lower CD53 and CD81 levels on CD14++CD16− monocytes compared with CD14++CD16+ and CD14+CD16++ subsets. Maturation of monocytes resulted in increased CD9 expression and apparent relocation of CD63 and CD53 from surface to intracellular membranes. Expression was modulated by cytokines, and CD9 was a marker of anti-inflammatory and CD53 a marker of proinflammatory MDM. Tetraspanin expression on monocyte subsets from HIV-1-infected donors receiving antiretroviral therapy was unchanged compared with that in uninfected donors. However, CD53 expression was inversely correlated with viral load in HIV-1-infected donors not on therapy. This study is the first to comprehensively characterize tetraspanin expression on monocyte subsets and macrophages in health and during HIV-1 infection. It demonstrates regulation of tetraspanin expression by cytokines, and CD53 expression as a novel correlate of a proinflammatory phenotype. This paper characterizes tetraspanins in myeloid cells and shows that tetraspanins are expressed differentially in monocyte subsets and are modified in inflammatory conditions.
A new optimization approach for source-encoding full-waveform inversion
Authors: Moghaddam Peyman P. , Keers Henk , Herrmann Felix J. , Mulder Wim A.
Published: April 2013

Waveform inversion is the method of choice for determining a highly heterogeneous subsurface structure. However, conventional waveform inversion requires that the wavefield for each source is computed separately. This makes it very expensive for realistic 3D seismic surveys. Source-encoding waveform inversion, in which the sources are modeled simultaneously, is considerably faster than conventional waveform inversion but suffers from artifacts. These artifacts can partly be removed by assigning random weights to the source wavefields. We found that the misfit function, and therefore also its gradient, for source-encoding waveform inversion is an unbiased random estimation of the misfit function used in conventional waveform inversion. We found a new method of source-encoding waveform inversion that takes into account the random nature of the gradients used in the optimization. In this new method, the gradient at each iteration is a weighted average of past gradients such that the most recent gradients have the largest weights with exponential decay. This way we damped the random fluctuations of the gradient by incorporating information from the previous iterations. We compared this new method with existing source-encoding waveform inversion methods as well as conventional waveform inversion and found that the model misfit reduction is faster and smoother than those of existing source-encoding waveform inversion methods, and it approaches the model misfit reduction obtained in conventional waveform inversion.
Dynamics and navigation of autonomous underwater vehicles for submarine gravity surveying
Authors: Kinsey James C. , Tivey Maurice A. , Yoerger Dana R.
Published: April 2013

We investigated the effect of autonomous underwater vehicle (AUV) dynamics and navigation on underway submarine gravimetry. Our research was motivated by the need to obtain spatially dense marine gravity measurements close to the source of subkilometer-scale geologic features in the shallow oceanic crust. Such measurements have been previously obtained, for instance, with piloted submarines and towed sleds; however, the high cost and, in the case of on-bottom measurements, poor spatial sampling preclude routine acquisition of these measurements. Continuous underway gravity surveys with AUVs is a compelling cost-effective option, but this method requires separating the AUV accelerations from the measured gravity. We show that AUVs with a large distance between the center of buoyancy and the center of gravity have lower vertical accelerations than torpedo-shaped AUVs and consequentially are better suited for underway gravity surveys. Furthermore state estimators, which combine sensor measurements and models of the vehicle’s motion, provide superior estimates of the vehicle’s vertical accelerations than methods used in previous underway submarine gravity surveys. We simulated the use of these navigation methods in detecting dike swarms at the East Pacific Rise. Analysis showed that we can shorten filters used in reducing gravity data and consequentially provide improved measurements of the free-water anomaly with a minimal detectable spatial wavelength approximately 65% lower than previously reported results.
Noise reduction by vector median filtering
Authors: Liu Yike
Published: April 2013

The scalar median filter (SMF) is often used to reduce noise in scalar geophysical data. We present an extension of the SMF to a vector median filter (VMF) for suppressing noise contained in geophysical data represented by multidimensional, multicomponent vector fields. Although the SMF can be applied to each component of a vector field individually, the VMF is applied to all components simultaneously. Like the SMF, the VMF intends to suppress random noise while preserving discontinuities in the vector fields. Preserving such discontinuities is essential for exploration geophysics because discontinuities often manifest important geologic features such as faults and stratigraphic channels. The VMF is applied to synthetic and field data sets. The results are compared to those generated by using SMF, f-x deconvolution, and mean filters. Our results indicate that the VMF can reduce noise while preserving discontinuities more effectively than the alternatives. In addition, a fast VMF algorithm is described for reducing computation time.
Combined surface and borehole seismic imaging in a hard rock terrain: A field test of seismic interferometry
Authors: Hurich Charles , Deemer Sharon
Published: April 2013

Seismic images are inherently directionally biased by the source-receiver geometry. This directional bias is particularly problematic for seismic imaging in hard rock terrains where structural dips may have any orientation with respect to the surface. We tested a technique for partially mitigating directional bias by combining surface and borehole seismic data and evaluated the results of a first field test of the technique. In this technique, surface data acquired using standard 2D acquisition procedures were combined with borehole data derived from a walk-away vertical seismic profile (VSP). The VSP data were transformed into the borehole datum using seismic interferometry. The interferometry created virtual shot records comprising sources and receivers in the borehole. The virtual shot records were then processed, using standard common midpoint techniques, resulting in an image from the borehole datum. The combination of the surface and borehole data increased the range of illumination angles resulting in seismic images that included reflections from structures with a wider range of dips than is available to surface profiling alone. The field test demonstrated that the surface and borehole data provide complementary information, which is more than either data set alone can provide. The test also verified the robustness of the virtual source technique even when the original VSP data are highly contaminated by high-amplitude tube waves. These results demonstrated that the combined imaging approach has significant potential for application in the polydeformed hard rock domains often encountered in minerals exploration.
President's Page
Authors: Miller Rick
Published: April 2013

For nearly a decade now, SEG has actively and purposely scanned the horizon looking for opportunities to increase its offerings to and its support of the global applied geophysical community. Vision and flexibility have proven key to optimally positioning the Society for meeting member needs in a timely fashion. SEG's vision continues to be broadband with both near-term (on the order of years) and long-term (looking decades ahead of us) goals. It is imperative that we remain focused while cherry-picking our way through the range of opportunities routinely bombarding our Society. Staff and volunteers guided by a balanced and prioritized plan leads to proactive, rather than reactive, decisions.
An introduction to this special section: Marine and offshore technology
Authors: Clark Dean
Published: April 2013

For several years, the special section in TLE's April issue has focused on some aspect of offshore geophysical work. This has been deliberately done to put that issue into proximity with the massive Offshore Technology Conference (OTC) held annually in early May in Houston since 1969. OTC is almost universally regarded as the world's premier offshore-oriented conference, if not one of the biggest industry shows in general. It should be noted that OTC has expanded beyond the major event in Houston. There are now OTC Brasil, OTC Asia, and Arctic Technology conferences. SEG is one of the sponsoring societies for the OTC events, and, as such, it has representatives on the OTC Board of Directors (currently Wafik Beydoun) and the OTC (Houston) Program Committee (Joe Reilly, Charles Knobloch, and Rocco DeTomo). Additional volunteers also work within SEG's Technical Program Subcommittee to develop geosciences-oriented and other special-purpose sessions for OTC (Houston).
Seismic-derived seabed topography: Insights from the outer fold and thrust belt in the deep-water Niger Delta
Authors: Jibrin Babangida W. , Reston Tim J. , Westbrook Graham K.
Published: April 2013

Seafloor mapping of the outer fold and thrust belt in the deep-water Niger Delta using high-resolution 3D seismic data has revealed a variety of geomorphic features related to gravity-driven compressional tectonics, submarine sedimentary processes, and fluid migration as evidenced by bathymetric ridges caused by folding of the underlying sedimentary succession, gravity slide scars, submarine canyons and pockmarks all clearly imaged on the seismic-derived seabed bathymetry. The largest canyons, typically 25–35 km in length with widths of up to 5 km, incise an EW-trending arcuate zone of elevated bathymetry across the area. This ridge is the reference point for dividing the seabed topographic pattern into distal and proximal domains. Generally, seabed topography is gentle and less complex in the proximal domain and the major structures in the area include circular clusters of fluid-escape features primarily along channel margins and in places along discontinuities and ridges in the eastern half of the seabed. The large-scale distribution of these structures in the proximal parts of the study area may be related to fluid venting from shallow and or deeper reservoirs.
Full tensor CSEM and MT for subsalt structural imaging in the Red Sea: Implications for seismic and electromagnetic integration
Authors: Colombo Daniele , McNeice Gary , Curiel Ernesto Sandoval , Fox Adam
Published: April 2013

The mapping of complex salt, subsalt sediments, and basement structures in the Red Sea was addressed through the integration of coincident high-resolution wide-azimuth (WAZ) 3D seismic data, full tensor gravity gradiometry (FTG), and MT/CSEM techniques. The data acquisition was designed to enable advanced multi-geophysical integration schemes to image the subsalt geologic structures. Multi-offset, multicomponent electromagnetic measurements were recorded for both MT and CSEM with overlapping frequency bands. The analysis of the data and the preliminary 3D inversion results indicate that the two methods provide coherent information for the evaporitic overburden and the subsalt sediment sections. In addition, the MT data also show sensitivity to the deep basement structures. The obtained resistivity distributions strongly correlate with imaged seismic events from the 3D migrated seismic volumes and with the lateral- and vertical-velocity variations in the salt and presalt sections. These data suggest that the acquired electromagnetic data set can support the interval velocity-depth model building in areas of low seismic sensitivity such as the intrasalt and subsalt sections.
Modified Toxicity Probability Interval Design: A Safer and More Reliable Method Than the 3 + 3 Design for Practical Phase I Trials
Authors: Ji Yuan , Wang Sue-Jane
Published: April 2013

The 3 + 3 design is the most common choice among clinicians for phase I dose-escalation oncology trials. In recent reviews, more than 95% of phase I trials have been based on the 3 + 3 design. Given that it is intuitive and its implementation does not require a computer program, clinicians can conduct 3 + 3 dose escalations in practice with virtually no logistic cost, and trial protocols based on the 3 + 3 design pass institutional review board and biostatistics reviews quickly. However, the performance of the 3 + 3 design has rarely been compared with model-based designs in simulation studies with matched sample sizes. In the vast majority of statistical literature, the 3 + 3 design has been shown to be inferior in identifying true maximum-tolerated doses (MTDs), although the sample size required by the 3 + 3 design is often orders-of-magnitude smaller than model-based designs. In this article, through comparative simulation studies with matched sample sizes, we demonstrate that the 3 + 3 design has higher risks of exposing patients to toxic doses above the MTD than the modified toxicity probability interval (mTPI) design, a newly developed adaptive method. In addition, compared with the mTPI design, the 3 + 3 design does not yield higher probabilities in identifying the correct MTD, even when the sample size is matched. Given that the mTPI design is equally transparent, costless to implement with free software, and more flexible in practical situations, we highly encourage its adoption in early dose-escalation studies whenever the 3 + 3 design is also considered. We provide free software to allow direct comparisons of the 3 + 3 design with other model-based designs in simulation studies with matched sample sizes.
CIP4 coordinates with phospholipids and actin-associated proteins to localize to the protruding edge and produce actin ribs and veils
Authors: Saengsawang Witchuda , Taylor Kendra L. , Lumbard Derek C. , Mitok Kelly , Price Amanda , Pietila Lauren , Gomez Timothy M. , Dent Erik W.
Published: April 2013

CIP4, a member of the F-BAR family of proteins, plays important roles in a variety of cellular events by regulating both membrane and actin dynamics. In many cell types CIP4 functions in vesicle formation, endocytosis and membrane tubulation. However, recent data indicate that CIP4 is also involved in protrusion in some cell types, including cancer cells (lamellipodia and invadopodia) and neurons (ribbed lamellipodia and veils). In neurons, CIP4 localizes specifically to extending protrusions and functions to limit neurite outgrowth early in development. The mechanism by which CIP4 localizes to the protruding edge membrane and induces lamellipodial/veil protrusion and actin rib formation is not known. Here we show that CIP4 localization to the protruding edge of neurons is dependent on both the phospholipid content of the plasma membrane and the underlying organization of actin filaments. Inhibiting phosphatidylinositol 3,4,5-trisphosphate (PIP3) production decreases CIP4 at the membrane. CIP4 localization to the protruding edge is also dependent on Rac1/WAVE1, rather than Cdc42/N-WASP. Capping actin filaments with low concentrations of cytochalasin D or by overexpressing capping protein dramatically decreases CIP4 at the protruding edge, while inactivating Arp2/3 drives CIP4 to the protruding edge. We also demonstrate that CIP4 dynamically co-localizes with Ena/VASP and DAAM1, two proteins known to induce unbranched actin filament arrays and play important roles in neuronal development. Together, this is the first study to show that the localization of an F-BAR protein depends on both actin filament architecture and phospholipids at the protruding edge of developing neurons.
Negative regulation of p53 by Ras superfamily protein RBEL1A
Authors: Lui Ki , An Jie , Montalbano JoAnne , Shi Jingxue , Corcoran Chad , He Qin , Sun Hong , Sheikh M. Saeed , Huang Ying
Published: April 2013

We had previously reported that RBEL1A, a novel Ras-like GTPase, was overexpressed in multiple human malignancies and that its depletion suppressed cell growth. However, the underlying molecular mechanism remained to be elucidated. Here we report that depletion of endogenous RBEL1A results in p53 accumulation due to increased p53 half-life whereas increased expression of RBEL1A reduces p53 levels under unstressed and genotoxic stress conditions. RBEL1A directly interacts with p53 and MDM2, and strongly enhances MDM2-dependent p53 ubiquitination and degradation. We also found that RBEL1A modulation of p53 ubiquitination by MDM2 does not depend on its GTPase activity. We have also defined the p53 oligomeric domain and RBEL1A GTPase domain to be the critical regions for p53-RBEL1A interactions. Importantly, we have found that RBEL1A strongly interferes with p53 transactivation function; thus our results indicate that RBEL1A appears to function as a novel p53 negative regulator that facilitates MDM2-dependent p53 ubiquitination and degradation.
Detection of pinworm eggs in the dust of laboratory animals breeding facility, in the cages and on the hands of the technicians
Authors: Lytvynets A , Langrova I , Lachout J , Vadlejch J
Published: April 2013

Pinworms (Nematoda: Oxyurida) are common contaminants in most laboratory rodent colonies. The aim of the study was to monitor the transmission of Syphacia muris eggs in laboratory rat breeding facilities. Dust in a breeding room was investigated using special grids (free fallout, or through the help suction chamber). Furthermore, the ventilation system, breeding cages and the hands of the laboratory technical staff were examined. In the case of free fallout, the percentage of positive grids increased slightly over time: from 5.5% (after 24 h) to 8.2% (72 h). Similar values were also found when using the suction chamber (7.6%). Many more pinworm eggs were found in samples collected every second month from suction holes of the ventilation system (28.7%). One-half of the samples taken from the breeding cages (before washing) exhibited pinworm eggs (50.8%). Examination of the hands of technical staff showed positive detection in 37.9% of cases. In this study, certain transmission factors (dust, unclean cages and technicians) were proved to be significant in the distribution of pinworm infection in laboratory rodent facilities.
Treatment of male mice with gonadotropins to improve the fertilization rate and reproduction
Authors: Glage S , Wittur I , Elfers C , Hedrich H J , Dorsch M
Published: April 2013

The possibility of modifying the genome in mice has led to an exponential increase in the number of strains that have been developed for biomedical research. This will continue during the next few decades because international programmes plan to develop genetically-modified strains for every known mouse gene. Due to our own experiences and that of colleagues we know that the reproductive performance of many of these modified stains is impeded, despite that the modification is independent from genes that control reproduction. In some cases the spermatogenesis might be disturbed. The reason presumably lies in a defective endocrine function of the testes. This can cause reduced and/or abnormal sperm production. In livestock as well as in humans these disorders can be treated with gonadotropins. One treatment period lasts for the duration of spermatogenesis of the respective species. Up to now, nothing is known about such treatments in laboratory mice to restore or increase reproduction of genetically-modified strains. Spermatogenesis in the mouse lasts approximately 35 days. Therefore, we treated sexually mature male mice of C57BL/6 and BALB/c strains with gonadotropins for this period. The aim of this study was to test the principle suitability of such treatment for the improvement of sperm count, sperm motility, fertilization ability and reproduction.
Cubital Tunnel Syndrome Caused by a Synovial Cyst: Report of a Minimally Invasive Image-Guided Treatment
Authors: Flug Jonathan A , Kaplan Gary P , Luchs Jonathan S
Published: April 2013

Cubital tunnel syndrome is defined as ulnar neuropathy caused by compression in the region of the cubital tunnel and can be related to a variety of pathological aetiologies. Treatment involves decompression of the nerve and varies depending on the offending agent. We report the case of an 81-year-old man avid tennis player who presented with symptoms related to ulnar neuropathy. The patient was referred for an ultrasound of the elbow which demonstrated ulnar neuropathy related to compression by an 8 mm synovial cyst extending into the cubital tunnel. Magnetic resonance imaging of the elbow was performed confirming the cystic nature of this lesion. Ultrasound-guided aspiration of the cyst was performed followed by injection with corticosteroids. The patient experienced complete resolution of symptoms after treatment.
Consumer Fit Search, Retailer Shelf Layout, and Channel Interaction
Authors: Gu Zheyin (Jane) , Liu Yunchuan
Published: April 2013

This study examines the strategic implications of retailer shelf layout decisions in a market characterized by consumer fit uncertainty. A retailer can display competing products in the same location, allowing consumers to inspect various products all at once or in distant locations, which induces consumers to inspect one product first and then decide whether to incur the travel cost to inspect another product. We consider a model in which two competing manufacturers distribute two horizontally differentiated products through a common retailer. Our analysis shows when the two manufacturers offer products of the same fit probabilities, the retailer obtains a greater profit by displaying competing products in distant locations if the products' fit probabilities are not too high; otherwise, the retailer is better off displaying competing products in the same location. When manufacturers offer products of differentiated fit probabilities, a retailer is more likely to benefit from displaying competing products in distant locations with an increased fit difference between products. Finally, a retailer is more likely to benefit from displaying competing products in distant locations when facing less competition from other retailers.
Therapy-Related Views of Patients with Headache Undergoing Therapy with Turkish Music
Authors: Uçaner Burçin
Published: April 2013

In this study, posture and relaxing exercises accompanied by live Turkish music were performed every week for three weeks on 43 head-ache patients who are treated at the algology department. The study has been planned as active and passive therapy. Active therapy includes posture and relaxing exercises with Turkish music, while passive therapy includes listening to Turkish music in a relaxed steady position. After the third therapy session, patients were asked questions regarding the therapy and exercises. Almost all of the patients stated that the exercises and the Turkish music had positive effects on relieving their pain, helped them think positively, helped them relax and feel tranquil and that the therapy with Turkish music should be more common