bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inversion-based method for estimating total organic carbon and porosity and for diagnosing mineral constituents from multiple well logs in shale-gas formations
Authors: Heidari Zoya , Torres-Verdín Carlos 
Published: September 2013

Reliable estimates of petrophysical and compositional properties of organic shale are critical for detecting perforation zones or candidates for hydro-fracturing jobs. Current methods for in situ formation evaluation of organic shale largely rely on qualitative responses and empirical formulas. Even core measurements can be inconsistent and inaccurate when evaluating clay minerals and other grain constituents.We implement a recently introduced inversion-based method for organic-shale evaluation from conventional well logs. The objective is to estimate total porosity, total organic carbon (TOC), and volumetric/weight concentrations of mineral/fluid constituents. After detecting bed boundaries, the first step of the method is to perform separate inversion of individual well logs to estimate bed physical properties such as density, neutron migration length, electrical conductivity, photoelectric factor (PEF), and thorium, uranium , and potassium volumetric/weight concentrations. Next, a multilayer petrophysical model specific to organic shale is constructed with an initial guess obtained from conventional well-log interpretation or X-ray diffraction data; bed physical properties are calculated with the initial layer-by-layer values. Final estimates of organic shale petrophysical and compositional properties are obtained by progressively minimizing the difference between calculated and measured bed properties. A unique advantage of this method is the correction of shoulder-bed effects on well logs, which are prevalent in shale-gas plays. Another advantage is the explicit calculation of accurate well-log responses for specific petrophysical, mineral, fluid, and kerogen properties based on chemical formulas and volumetric concentrations of minerals/kerogen and fluid constituents.Examples are described of the successful application of the new organic-shale evaluation method in the Haynesville shale-gas formation. This formation includes complex solid compositions and thin beds where rapid depth variations of mineral/fluid constituents are commonplace. Comparison of estimates for total porosity, total water saturation, and TOC obtained with (a) commercial software for multimineral analysis, (b) our organic-shale evaluation method, and (c) core/X-ray diffraction measurements indicates a significant improvement in estimates of total porosity and water saturation yielded by our interpretation method. The estimated TOC is also in agreement with core laboratory measurements.
Fragile X mental retardation protein regulates trans-synaptic signaling inDrosophila
Authors: Friedman Samuel H. , Dani Neil , Rushton Emma , Broadie Kendal 
Published: September 2013

SummaryFragile X syndrome (FXS), the most common inherited determinant of intellectual disability and autism spectrum disorders, is caused by loss of the fragile X mental retardation 1 (FMR1) gene product (FMRP), an mRNA-binding translational repressor. A number of conserved FMRP targets have been identified in the well-characterized Drosophila FXS disease model, but FMRP is highly pleiotropic in function and the full spectrum of FMRP targets has yet to be revealed. In this study, screens for upregulated neural proteins in Drosophila fmr1 (dfmr1) null mutants reveal strong elevation of two synaptic heparan sulfate proteoglycans (HSPGs): GPI-anchored glypican Dally-like protein (Dlp) and transmembrane Syndecan (Sdc). Our recent work has shown that Dlp and Sdc act as co-receptors regulating extracellular ligands upstream of intracellular signal transduction in multiple trans-synaptic pathways that drive synaptogenesis. Consistently, dfmr1 null synapses exhibit altered WNT signaling, with changes in both Wingless (Wg) ligand abundance and downstream Frizzled-2 (Fz2) receptor C-terminal nuclear import. Similarly, a parallel anterograde signaling ligand, Jelly belly (Jeb), and downstream ERK phosphorylation (dpERK) are depressed at dfmr1 null synapses. In contrast, the retrograde BMP ligand Glass bottom boat (Gbb) and downstream signaling via phosphorylation of the transcription factor MAD (pMAD) seem not to be affected. To determine whether HSPG upregulation is causative for synaptogenic defects, HSPGs were genetically reduced to control levels in the dfmr1 null background. HSPG correction restored both (1) Wg and Jeb trans-synaptic signaling, and (2) synaptic architecture and transmission strength back to wild-type levels. Taken together, these data suggest that FMRP negatively regulates HSPG co-receptors controlling trans-synaptic signaling during synaptogenesis, and that loss of this regulation causes synaptic structure and function defects characterizing the FXS disease state.
An insert-based enzymatic cell culture system to rapidly and reversibly induce hypoxia: investigations of hypoxia-induced cell damage, protein expression and phosphorylation in neuronal IMR-32 cells
Authors: Huang Ying , Zitta Karina , Bein Berthold , Steinfath Markus , Albrecht Martin 
Published: September 2013

Summary
Ischemia-reperfusion injury and tissue hypoxia are of high clinical relevance because they are associated with various pathophysiological conditions such as myocardial infarction and stroke. Nevertheless, the underlying mechanisms causing cell damage are still not fully understood, which is at least partially due to the lack of cell culture systems for the induction of rapid and transient hypoxic conditions. The aim of the study was to establish a model that is suitable for the investigation of cellular and molecular effects associated with transient and long-term hypoxia and to gain insights into hypoxia-mediated mechanisms employing a neuronal culture system. A semipermeable membrane insert system in combination with the hypoxia-inducing enzymes glucose oxidase and catalase was employed to rapidly and reversibly generate hypoxic conditions in the culture medium. Hydrogen peroxide assays, glucose measurements and western blotting were performed to validate the system and to evaluate the effects of the generated hypoxia on neuronal IMR-32 cells. Using the insert-based two-enzyme model, hypoxic conditions were rapidly induced in the culture medium. Glucose concentrations gradually decreased, whereas levels of hydrogen peroxide were not altered. Moreover, a rapid and reversible (on-off) generation of hypoxia could be performed by the addition and subsequent removal of the enzyme-containing inserts. Employing neuronal IMR-32 cells, we showed that 3 hours of hypoxia led to morphological signs of cellular damage and significantly increased levels of lactate dehydrogenase (a biochemical marker of cell damage). Hypoxic conditions also increased the amounts of cellular procaspase-3 and catalase as well as phosphorylation of the pro-survival kinase Akt, but not Erk1/2 or STAT5. In summary, we present a novel framework for investigating hypoxia-mediated mechanisms at the cellular level. We claim that the model, the first of its kind, enables researches to rapidly and reversibly induce hypoxic conditions in vitro without unwanted interference of the hypoxia-inducing agent on the cultured cells. The system could help to further unravel hypoxia-associated mechanisms that are clinically relevant in various tissues and organs.
Chemicals-Inspired Biomaterials: Developing Biomaterials Inspired by Material Science Based on POSS
Authors: Tanaka Kazuo , Chujo Yoshiki 
Published: September 2013

Abstract
The concept of “chemicals-inspired biomaterials” and several examples are demonstrated in this review. The idea and background for the design of chemicals-inspired biomaterials which are constructed based on the chemistry and characteristics in material science are explained. As an example, we show several chemicals-inspired materials utilizing polyhedral oligomeric silsesquioxane (POSS) as a building block to apply the material functions of the POSS chemicals for fabricating a series of biomaterials having superior properties. Initially, the filler effects of POSS are explained. Because of the robust silica cube, POSS derivatives can show significant effect as a filler reinforcing the thermal and mechanical properties of conventional plastics simply by mixing. Based on these results, we designed rigid chelators for the complexation with gadolinium ions as an MRI contrast agent. It is demonstrated that the enhancement of the rigidity is a valid strategy for the improvement of the sensitivity. Next, we assembled the functional molecules into the POSS-core dendrimer. We observed from the dendrimer complexes that photon upconversion can be accomplished via an optical process which should be suppressed in electroluminescence devices. The last topic concerns the selective encapsulation by the POSS-core dendrimer for biomolecules. From the study of POSS-based ionic liquids, it was found that the strength of the hydrogen bonds with the ion pair moiety was significantly increased by tethering to POSS. Based on this enhancement, we accomplished selective encapsulation with the POSS-core dendrimer. The results and the prominent properties of the chemicals-inspired biomaterials are shown in this review.
Asymmetric Aldol Reaction on Water Using an Organocatalyst Tethered on a Thermoresponsive Block Copolymer
Authors: Suzuki Noriyuki , Inoue Takahiro , Asada Takumi , Akebi Ryuji , Kobayashi Go , Rikukawa Masahiro , Masuyama Yoshiro , Ogasawara Masamichi , Takahashi Tamotsu , Thang San H 
Published: September 2013

Abstract
l-Proline moieties, which serve as organocatalysts, were tethered on block copolymers that consisted of thermoresponsive poly(N-isopropylacrylamide) and PEG-grafted polyacrylate blocks. The copolymer dissolved in water at temperatures below the LCST (25 °C), whereas they formed micelles at temperatures above the LCST (50 °C). Aldol reactions between an arylaldehyde and a ketone were conducted in this aqueous solution. The aldol products were obtained in high yield with high diastereo- and enantioselectivity (96% ee). The catalyst solution could be reused up to three times.
Review of postoperative CT and ultrasound for endovascular aneurysm repair using Talent stent graft: Can we simplify the surveillance protocol and reduce the number of CT scans?
Authors: Nyheim Thomas , Staxrud Lars Erik , Rosen L , Slagsvold Carl Erik , Sandbæk Gunnar , Jørgensen Jørgen J 
Published: September 2013

Background Simplifying a postoperative surveillance protocol for endovascular aneurysm repair (EVAR) requires quality control comparing computerized tomography (CT) and ultrasound (US) results of abdominal aortic aneurysm (AAA) diameter measurements and endoleaks. Purpose To test if US is comparable to CT, then assess a simplified follow-up with our conventional surveillance to assess patient safety. Material and Methods During 2001-2006, data on 56 patients treated with Talent stent graft were prospectively registered. Median follow-up was 41.5 months (range, 2-94 months), with CT, US, and plain film abdomen X-rays (PFA) at 1, 6, and 12 months, then yearly. Bland-Altman plot was used to assess the agreement between CT and US measuring the AAA diameters and mixed model by the time effect to assess the difference in diameter over time. Sensitivity and specificity for detection of endoleaks by US, with CT as ‘gold standard’ were calculated. A simplified surveillance protocol with US/PFA at 6 and 8 weeks, CT/US/PFA at 1 year, and yearly US/PFA thereafter, was evaluated. CT was carried out when poor visibility, endoleak detected, AAA diameter increase (≥5 mm) on US or migration (≥10 mm) on PFA. This regime was compared with our conventional follow-up protocol. Results Diameter measurements on US appear comparable to CT with 91% specificity and 85% sensitivity for endoleaks detected by US. Using the simplified surveillance protocol no endoleaks, migrations, or endotension requiring treatment were overlooked. The simplified protocol generated 53 selective CT scans, avoiding approximately 144 CT scans. If further simplified by omitting the 1-year CT scan, one type II endoleak would be missed with a 1-year delay, eliminating a further 45 CT scans. Conclusion US appears comparable to CT in the follow-up of Talent stent grafts in our institution. The proposed simplified surveillance protocol seems safe and can lead to a significant reduction in the number of CT scans.
Ultrasound-guided percutaneous laser and ethanol ablation of rabbit VX2 liver tumors
Authors: Zou Xiaojuan , Liu Qing , Zhou Xiaodong , He Guangbin , Yu Ming , Han Zenghui , Meng Xin , Su Haili 
Published: September 2013

Background Only a small percentage of patients with hepatocellular carcinoma (HCC) may benefit out of surgical resection. Thus, lots of these patients are in need of local control, such as percutaneous ethanol injection (PEI), percutaneous laser ablation (PLA), or radiofrequency thermal ablation (RF). Purpose To investigate the effects of ultrasound-guided PLA combined with PEI on rabbit VX2 liver tumors, using conventional gray-scale ultrasonography (US), color/power Doppler (CD/PD)US, contrast-enhanced (CE) US, and histologic examination. Material and Methods VX2 tumors were implanted in the livers of 80 rabbits. Fourteen days after implantation, animals were randomly separated into four groups of 20 rabbits. Treatment of the four groups was with: (i) PLA; (ii) PEI; (iii) combined therapy of PLA immediately followed by PEI; and (iv) combined therapy of PEI immediately followed by PLA. Conventional gray-scale US, CD US, PD US, and CE US were performed before and after ablation. The effects on ablated areas were assessed by histologic examination. Results Conventional gray-scale US showed a clear boundary around the ablated area in groups 1, 3, and 4. An isoechoic treated region with an irregular boundary was seen in group 2. On CE US, coagulated areas demonstrated a perfusion defect. Both conventional gray-scale US and CE US showed that the ablated volume in group 4 was larger than that in groups 1, 2, and 3. CD US and PD US demonstrated residual tumor in the periphery of ablated areas in groups 1 and 2, but not in groups 3 and 4. CE US demonstrated no residual tumor in group 4, unlike in groups 1, 2, and 3. Examination of treated tumors demonstrated necrosis in the ablated zones and increasing surrounding fibrous bands in the four treatment groups. Residual viable tissue in group 4 was less than that in groups 1, 2, and 3. Conclusion Combined therapy of PEI immediately followed by PLA can coagulate significantly larger volumes of tumor and reduce residual tumor.
Interventional embolization of giant thoracic tumors before surgical resection
Authors: Liu Feng-Yong , Wang Mao-Qiang , Fan Qing-Sheng , Duan Feng , Wang Zhi-Jun , Song Peng 
Published: September 2013

Background Preoperative embolization of tumors is a well-established procedure that has been successfully applied in various clinical situations. Preoperative embolization can reduce the vascularity of tumors resulting in a clearer operative field, less difficult dissection, decreased blood loss, and, in some cases, a decrease in tumor size. However, few studies have been conducted regarding the preoperative embolization of giant thoracic tumors. Purpose To examine the effectiveness and safety of interventional embolization of giant thoracic tumors before surgical resection. Material and Methods A total of 14 consecutive patients with giant thoracic tumors received angiography and the feeding arteries of the tumors were embolized using polyvinyl alcohol (PVA) particles and gelatin sponges 1 day before surgical resection. The patient records were retrospectively reviewed and data regarding diagnoses, embolization, and surgical resection were recorded. Results Angiography revealed the feeding arteries of the tumors to be characterized by multiple branches and thickened vessel trunks with abnormal distal branches superimposed of the tumor shadow. Embolization was successfully without complications in all patients, and all feeding vessels of each tumor were occluded. Embolization reduced the severity of bleeding during surgery and decreased the difficulty of resection of the tumor. No intraoperative or postoperative complications occurred. Conclusion Interventional embolization is a safe and efficient method to facilitate the surgical resection of giant thoracic tumors.
Visualization and simulation of the human heart based on ECG
Authors: Sochocka Anna , Kawa Tomasz , Płaneta Roman 
Published: September 2013

Abstract
The aim of this study was to develop a three-dimensional (3D) animation of the heart that can show its components and function using electrocardiography. Another aim of the study was to increase knowledge on computer graphics and animation as well as to create a useful educational tool that, through play, will also teach. Because the heart is one of the most important organs and a very complex one, the authors decided to create a 3D model. This article presents the current state of knowledge in the use of computer-generated models of the human heart as a learning aid and for creating simulation. The authors describe the tools used to implement the program and sources that were used for modeling the heart. The result is presented in the form of descriptions and screenshots on how to use the program. At the end of the article, a description is placed of further developments that will be applied to the program.
A serious game – a new training addressing particularly prospective memory in the elderly
Authors: Laskowska Ilona , Zając-Lamparska Ludmiła , Wiłkość Monika , Malicki Michał , Szałkowska Agnieszka , Jurgielewicz Anna , Lewandowski Paweł , Węgrzyn Paweł , Roterman-Konieczna Irena , Izdebski Paweł 
Published: September 2013

Abstract
A training in the form of a computer game that aims at improving five cognitive functions in the elderly has been developed: visuospatial memory, attention, memory for prose, working memory and prospective memory. It was devised as a collaboration among the Department of Cognitive Psychology in Warsaw, Department of Individual Differences Psychology in Bydgoszcz, Faculty of Physics, Astronomy and Applied Computer Science – Game Academy in Cracow, and Department of Human Psychology and Department of Psychiatry of Ludwik Rydygier Collegium Medicum in Bydgoszcz. This software is an example of the so-called serious games. To the best of our knowledge it is the first one to focus particularly on prospective memory. This is the first report concerning the present training, which is currently being elaborated. The next step in its development will be testing its validity.
Linking macroalgal δ
15N-values to nitrogen sources and effects of nutrient stress on coral condition in an upwelling region
Authors: Huang Hui , Li Xiu Bao , Titlyanov Eduard A. , Ye Cheng , Titlyanova Tamara V. , Guo Ya Ping , Zhang Jing 
Published: September 2013

Abstract
Land-based sewage pollution is a major threat to the health of near-shore coral reefs. Macroalgal δ
15N-values are useful indicators for tracking nitrogen sources and sewage input; however, the direct link between δ
15N-values of macroalgae and the coral condition, including live coral cover, species richness, and juvenile coral density, is unclear. Macroalgal δ
15N-values of two species, Lobophora variegata and Tricleocarpa oblongata, were measured in Wenchang (northeast Hainan Island, South China Sea) in both the dry and wet seasons, to assess the influence of nitrogen sources and nutrient stress resulting from sewage input or upwelling on the condition of corals. Macroalgal δ
15N-values showed that shallow stations between the reef and the coast were severely affected by sewage input (e.g., river discharges and aquaculture ponds), whereas deep stations on the outside of the reef were influenced by upwelling-based nutrients. Correlation and redundancy analysis demonstrated that δ
15N-values of L. variegata had a stronger relation with coral condition than any other environmental parameter (e.g., water quality index, turbidity, and dissolved nutrients), with significant negative correlations in both the dry and wet seasons. Thus, macroalgal δ
15N-values can be used to determine where nutrient stress is negatively affecting corals, highlighting the links of human activities and coastal upwelling with marine ecosystems.
The first record of Grateloupia subpectinata from the New Zealand region and comparison with G. prolifera, a species endemic to the Chatham Islands
Authors: Nelson Wendy A. , Kim Su Yeon , D’Archino Roberta , Boo Sung Min 
Published: September 2013

Abstract
A finely pinnately branched species of Grateloupia not seen previously in New Zealand was collected in Tauranga, New Zealand, growing on a tug boat. Molecular sequencing data (rbcL) revealed it to be Grateloupia subpectinata, a species first described from Japan, and also reported as native to Korea and China, and introduced to Britain, France, and Australia. The only species of Grateloupia with morphology similar to G. subpectinata in the New Zealand region is G. prolifera from the Chatham Islands. A sequence of this species was obtained for comparative purposes and found to be distinct from G. subpectinata.
Optimization of Trickle-Bed Reactors (TBRs) for Hydrodesulfurization (HDS) and Hydrodearomatization (HDA) of Diesel using Single and Multiple Objectives
Authors: Srinivas Bhadri , Karthik Srikanth , Sankararao B. 
Published: September 2013

Abstract
This article describes the formulation, solution and analysis of two single-objective optimization and one multi-objective optimization (MOO) problems on trickle-bed reactors (TBRs) involving hydrodesulfurization (HDS) and hydrodearomatization (HDA). The model used by Chowdhury et al. (AIChE J 2002;48:26) for TBR involving HDS and HDA is used in this study, to solve these optimization problems. The correctness of algorithm and the numerical procedure used in this study to solve the model equations are validated with the results of Chowdhury et al. (AIChE J 2002;48:26), before the model is used for optimization. Objective functions chosen in our optimization studies are minimization of sulfur concentration and maximization of total conversion of aromatics at the exit of TBR. Decision variables considered are reactor temperature, reactor pressure and liquid hourly space velocity (LHSV). Two single-objective optimization and one MOO problems are formulated and solved using simple genetic algorithm (SGA) and NSGA-II, respectively, to obtain the optimal values of reactor operating conditions. Pareto set for the MOO problem is generated which show that conflicting nature of the objective functions. Specifically, we have shown that the simultaneous minimization of exit sulfur and maximization of aromatics removal conflict each other in hydrotreating.
Enrichment of target sequences for next-generation sequencing applications in research and diagnostics
Authors: Altmüller Janine , Budde Birgit S. , Nürnberg Peter 
Published: September 2013

Abstract
Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.