bluuebunny/crossref_metadata_2025 huggingface dataset:
RETRACTED ARTICLE: In vitro and in vivo responses of macrophages to magnesium-doped titanium
Authors: Li Bin , Cao Huiliang , Zhao Yaochao , Cheng Mengqi , Qin Hui , Cheng Tao , Hu Yan , Zhang Xianlong , Liu Xuanyong
Published: February 2017

Modulating immune response to biomaterials through changing macrophage polarization has been proven to be a promising strategy to elicit beneficial outcomes in tissue repair. The objective of this study was to evaluate the response of macrophage polarization to titanium doped with magnesium (0.1~0.35%), which was prepared through the magnesium plasma immersion ion implantation (Mg PIII) technique. The M1/M2 polarization profile of macrophages was investigated using a murine cell line RAW 264.7 in vitro and a murine air pouch model in vivo. Our results demonstrated that the Mg PIII-treated titanium induced a higher percentage of M2 macrophages and higher concentrations of the anti-inflammatory cytokines interleukin (IL)-4 and IL-10. Genes encoding two growth factors, bone morphogenetic protein 2 (BMP2) and vascular endothelial growth factor (VEGF) were up-regulated, thus indicating the ability of the M2 phenotype to promote wound healing. The nuclear factor κB (NF-κB) signalling pathway was down-regulated. In vivo the Mg PIII -treated titanium elicited a similar effect on macrophage polarization and induced thinner fibrous capsule formation and a decrease in infiltrated cells. These results indicate that Mg PIII treatment has the immunomodulatory potential to elicit the pro-healing M2-polarized macrophage phenotype, thus providing new insight into the development of immunomodulatory biomaterials.
Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid
Authors: Chen Zhong , Ji Lexiang , Wang Jia , Jin Jinpu , Yang Xiaoyu , Rao Pian , Gao Kai , Liao Weihua , Ye Meixia , An Xinmin
Published: February 2017

Abscisic acid (ABA) plays a fundamental role in plant response and adaptation to abiotic stresses, such as drought, high salinity and low temperature. Populus hopeiensis exhibits exceptional tolerance to water-deficit environments and is therefore an excellent choice for studying drought tolerance in trees. This study provides a global view of transcriptome dynamics in P. hopeiensis in response to exogenous ABA using Illumina RNA-sequencing. Endogenous ABA content increased and reached a peak at 8 h after ABA treatment and then significantly decreased at latter time points. Differential expression analysis and Gene ontology enrichment revealed that the number of transcripts exhibited significant increase during the first 8 hours after ABA treatment, which then significantly decreased at 12 and 24 h. Transcription factors (TFs) analysis showed that six different patterns were observed based on the expression of the six TFs families (AP2/ERF, NAC, MYB, MYB-related, bZIP and WRKY) and the majority of differentially expressed TFs increased rapidly after ABA treatment. This study provides a robust resource for investigating the functions of genes induced by ABA and will help to develop a better understanding of the molecular regulatory mechanism in response to drought in poplar.
Serum lipid alterations identified in chronic hepatitis B, hepatitis B virus-associated cirrhosis and carcinoma patients
Authors: Wu Tao , Zheng Xiaojiao , Yang Ming , Zhao Aihua , Li Meng , Chen Tianlu , Panee Jun , Jia Wei , Ji Guang
Published: February 2017

The incidences of chronic hepatitis B (CHB), Hepatitis B virus (HBV)-associated cirrhosis and HBV-associated carcinoma are high and increasing. This study was designed to evaluate serum lipid metabolite changes that are associated with the progression from CHB to HBV-associated cirrhosis and ultimately to HBV-associated HCC. A targeted metabolomic assay was performed in fasting sera from 136 CHB patients, 104 HBV-associated cirrhosis, and 95 HBV-associated HCC using ultra-performance liquid chromatography triple quadrupole mass spectrometry. A total of 140 metabolites were identified. Clear separations between each two groups were obtained using the partial least squares discriminate analysis of 9 lipid metabolites. Progressively lower levels of long-chain lysophosphatidylcholines (lysoPC a C18:2, lysoPC a C20:3, lysoPC a C20:4) were observed from CHB to cirrhosis to carcinoma; lower levels of lysoPC a C20:4 were found in patients with higher model for end-stage liver disease in the same disease group; and lysoPC a C20:3 levels were lower in Child-Pugh Class C than in Class A and Class B in HBV-associated cirrhosis and HBV-associated HCC groups. The octadecadienyl carnitine level was higher in HBV-associated cirrhosis group than in other two groups. Serum levels of selected long-chain lysoPCs are promising markers for the progression of HBV-associated liver diseases.
Identification of a novel type III secretion-associated outer membrane-bound protein from Xanthomonas campestris pv. campestris
Authors: Li Lei , Li Rui-Fang , Ming Zhen-Hua , Lu Guang-Tao , Tang Ji-Liang
Published: February 2017

Many bacterial pathogens employ the type III secretion system (T3SS) to translocate effector proteins into eukaryotic cells to overcome host defenses. To date, most of our knowledge about the T3SS molecular architecture comes from the studies on animal pathogens. In plant pathogens, nine Hrc proteins are believed to be structural components of the T3SS, of which HrcC and HrcJ form the outer and inner rings of the T3SS, respectively. Here, we demonstrated that a novel outer membrane-bound protein (HpaM) of Xanthomonas campestris pv. campestris is critical for the type III secretion and is structurally and functionally conserved in phytopathogenic Xanthomonas spp. We showed that the C-terminus of HpaM extends into the periplasm to interact physically with HrcJ and the middle part of HpaM interacts physically with HrcC. It is clear that the outer and inner rings compose the main basal body of the T3SS apparatus in animal pathogens. Therefore, we presume that HpaM may act as a T3SS structural component, or play a role in assisting assembling or affecting the stability of the T3SS apparatus. HpaM is a highly prevalent and specific protein in Xanthomonas spp., suggesting that the T3SS of Xanthomonas is distinctive in some aspects from other pathogens.
Fatigue-related impairments in oculomotor control are prevented by norepinephrine-dopamine reuptake inhibition
Authors: Connell Charlotte J. W. , Thompson Benjamin , Turuwhenua Jason , Srzich Alexa , Gant Nicholas
Published: February 2017

Fatigue-induced reductions in saccade velocity have been reported following acute, prolonged exercise. Interestingly, the detrimental impact of fatigue on oculomotor control can be prevented by a moderate dose of caffeine. This effect may be related to central catecholamine upregulation via caffeine’s action as an adenosine antagonist. To test this hypothesis, we compared the protective effect of caffeine on oculomotor control post-exercise to that of a norepinephrine-dopamine reuptake inhibitor. Within a placebo-controlled crossover design, 12 cyclists consumed placebo, caffeine or a norepinephrine-dopamine reuptake inhibitor (bupropion) during 180 minutes of stationary cycling. Saccades, smooth pursuit and optokinetic nystagmus were measured using infrared oculography. Exercise fatigue was associated with an 8 ± 11% reduction in the peak velocity of prosaccades, and a 10 ± 11% decrement in antisaccade peak velocity. Optokinetic nystagmus quick phases decreased in velocity by 15 ± 17%. These differences were statistically significant (p < 0.05). Norepinephrine-dopamine reuptake inhibition and caffeine prevented fatigue-related decrements in eye movement velocity. Pursuit eye movements and visual attention were unaffected. These findings show that norepinephrine-dopamine reuptake inhibition protects oculomotor function during exercise fatigue. Caffeine’s fatigue-reversing effects on eye movements appear to be mediated, at least in part, via modulation of central catecholamines.
Caesium-rich micro-particles: A window into the meltdown events at the Fukushima Daiichi Nuclear Power Plant
Authors: Furuki Genki , Imoto Junpei , Ochiai Asumi , Yamasaki Shinya , Nanba Kenji , Ohnuki Toshihiko , Grambow Bernd , Ewing Rodney C. , Utsunomiya Satoshi
Published: February 2017

The nuclear disaster at the Fukushima Daiichi Nuclear Power Plant (FDNPP) in March 2011 caused partial meltdowns of three reactors. During the meltdowns, a type of condensed particle, a caesium-rich micro-particle (CsMP), formed inside the reactors via unknown processes. Here we report the chemical and physical processes of CsMP formation inside the reactors during the meltdowns based on atomic-resolution electron microscopy of CsMPs discovered near the FDNPP. All of the CsMPs (with sizes of 2.0–3.4 μm) comprise SiO2 glass matrices and ~10-nm-sized Zn–Fe-oxide nanoparticles associated with a wide range of Cs concentrations (1.1–19 wt% Cs as Cs2O). Trace amounts of U are also associated with the Zn–Fe oxides. The nano-texture in the CsMPs records multiple reaction-process steps during meltdown in the severe FDNPP accident: Melted fuel (molten core)-concrete interactions (MCCIs), incorporating various airborne fission product nanoparticles, including CsOH and CsCl, proceeded via SiO2 condensation over aggregates of Zn-Fe oxide nanoparticles originating from the failure of the reactor pressure vessels. Still, CsMPs provide a mechanism by which volatile and low-volatility radionuclides such as U can reach the environment and should be considered in the migration model of Cs and radionuclides in the current environment surrounding the FDNPP.
Particle size specific distribution of perfluoro alkyl substances in atmospheric particulate matter in Asian cities
Authors: Ge H. , Yamazaki E. , Yamashita N. , Taniyasu S. , Ogata A. , Furuuchi M.
Published: February 2017

PM0.1was found to be a major contributor to the mass fraction of perfluoro alkyl substances, which is more influenced by the type of land use than country differences.
Energetics competition in centrally four-coordinated water clusters and Raman spectroscopic signature for hydrogen bonding
Authors: Wang Bo , Jiang Wanrun , Gao Yang , Zhang Zhiyuan , Sun Changqing , Liu Fang , Wang Zhigang
Published: February 2017

Viaseparating the H-bonded neighbour molecules of centrally four-coordinated water molecules from other molecules in outer cages, the calculations discover these two regions interact competitively with the central molecule.
Synthesis of In2O3 nanoparticle/TiO2 nanobelt heterostructures for near room temperature ethanol sensing
Authors: Li Yujie , Yang Hongru , Tian Jian , Hu Xiaolin , Cui Hongzhi
Published: February 2017

The obtained In2O3 nanoparticle/TiO2 nanobelt heterostructures exhibit a high sensitive toward ethanol at near room temperature of 45 °C and low detection limit of 1 ppm.
2D free-standing Ge-doped ZnO: excellent electron-emitter and excitation-power-dependent photoluminescence redshift
Authors: Sun Yong , Wang Chengxin
Published: February 2017

Ge-Doped ZnO 2D nanostructures show large current-emission capabilities (>35 mA cm−2) and an excitation power-dependent PL redshift.
Charge transfer induced polymerization of EDOT confined between 2D titanium carbide layers
Authors: Chen Chi , Boota Muhammad , Xie Xiuqiang , Zhao Mengqiang , Anasori Babak , Ren Chang E. , Miao Ling , Jiang Jianjun , Gogotsi Yury
Published: February 2017

In situpolymerization of 3,4-ethylenedioxythiophene (EDOT) is achieved on the surface of 2D Ti3C2TxMXene without using any oxidant, resulting in improved lithium ion storage capability of Ti3C2Tx/poly-EDOT hybrids.
Durable vesicles for reconstitution of membrane proteins in biotechnology
Authors: Beales Paul A. , Khan Sanobar , Muench Stephen P. , Jeuken Lars J.C.
Published: February 2017

The application of membrane proteins in biotechnology requires robust, durable reconstitution systems that enhance their stability and support their functionality in a range of working environments. Vesicular architectures are highly desirable to provide the compartmentalisation to utilise the functional transmembrane transport and signalling properties of membrane proteins. Proteoliposomes provide a native-like membrane environment to support membrane protein function, but can lack the required chemical and physical stability. Amphiphilic block copolymers can also self-assemble into polymersomes: tough vesicles with improved stability compared with liposomes. This review discusses the reconstitution of membrane proteins into polymersomes and the more recent development of hybrid vesicles, which blend the robust nature of block copolymers with the biofunctionality of lipids. These novel synthetic vesicles hold great promise for enabling membrane proteins within biotechnologies by supporting their enhanced in vitro performance and could also contribute to fundamental biochemical and biophysical research by improving the stability of membrane proteins that are challenging to work with.
The short and the long: non-coding RNAs and growth factors in cancer progression
Authors: Sas-Chen Aldema , Srivastava Swati , Yarden Yosef
Published: February 2017

A relatively well-understood multistep process enables mutation-bearing cells to form primary tumours, which later use the circulation system to colonize new locations and form metastases. However, in which way the emerging abundance of different non-coding RNAs supports tumour progression is poorly understood. Here, we review new lines of evidence linking long and short types of non-coding RNAs to signalling pathways activated in the course of cancer progression by growth factors and by the tumour micro-environment. Resolving the new dimension of non-coding RNAs in oncogenesis will probably translate to earlier detection of cancer and improved therapeutic strategies.
Deciphering the RAS/ERK pathway in vivo
Authors: Dorard Coralie , Vucak Georg , Baccarini Manuela
Published: February 2017

The RAS/ERK pathway has been intensely studied for about three decades, not least because of its role in human pathologies. ERK activation is observed in the majority of human cancers; in about one-third of them, it is driven by mutational activation of pathway components. The pathway is arguably one of the best targets for molecule-based pharmacological intervention, and several small-molecule inhibitors are in clinical use. Genetically engineered mouse models have greatly contributed to our understanding of signaling pathways in development, tissue homeostasis, and disease. In the specific case of the RAS/ERK pathway, they have revealed unique biological roles of structurally and functionally similar proteins, new kinase-independent effectors, and unsuspected relationships with other cascades. This short review summarizes the contribution of mouse models to our current understanding of the pathway.
Constraints in cancer evolution
Authors: Venkatesan Subramanian , Birkbak Nicolai J. , Swanton Charles
Published: February 2017

Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution. The presence of (1) parallel evolution, (2) convergent evolution and (3) the biological impact of acquiring mutations in specific orders suggest that cancer evolution may be exploitable. These constraints on cancer evolution may help us identify cancer evolutionary rule books, which could eventually inform both diagnostic and therapeutic approaches to improve survival outcomes.
Imaging and Outcomes for a New Entity: Low-Grade Sinonasal Sarcoma with Neural and Myogenic Features
Authors: Cannon Richard , Wiggins Richard , Witt Benjamin , Dundar Yusuf , Johnston Tawni , Hunt Jason
Published: February 2017

Objectives Low-grade sinonasal sarcoma with neural and myogenic features (LGSSNMF) is a new, rare tumor. Our goal is to describe the imaging characteristics and surgical outcomes of this unique skull base malignancy.

Design Retrospective case series.

Setting Academic medical center.

Participants There were three patients who met inclusion criteria with a confirmed LGSSNMF.

Main Outcome Measures Imaging and histopathological characteristics, treatments, survival and recurrence outcomes, complications, morbidity, and mortality.

Results Patients presented with diplopia, facial discomfort, a supraorbital mass, and nasal obstruction. Magnetic resonance imaging and computed tomography imaging in all cases showed an enhancing sinonasal mass with associated hyperostotic bone formation that involved the frontal sinus, invaded the lamina papyracea and anterior skull base, and had intracranial extension. One patient underwent a purely endoscopic surgical resection and the second underwent a craniofacial resection, while the last is pending treatment. All patients recovered well, without morbidity or long-term complications, and are currently without evidence of disease (mean follow-up of 2.1 years). One patient recurred after 17 months and underwent a repeat endoscopic skull base and dural resection.

Conclusions The surgical outcomes and imaging of this unique, locally aggressive skull base tumor are characterized.
Evidence of Early Pulmonary Hypertension Is Associated with Increased Mortality in Very Low Birth Weight Infants
Authors: Berenz Andrew , Vergales Jeffrey , Swanson Jonathan , Sinkin Robert
Published: February 2017

Objective The objective of this study was to describe the inhospital outcomes of a high-risk cohort of very low birth weight infants with evidence of pulmonary hypertension (PHT) within the first 2 weeks after delivery.

Design A retrospective cohort study of consecutively admitted neonates with birth weight < 1,500 g admitted to a Level IV neonatal intensive care unit who were evaluated by echocardiogram between 72 hours and 14 days.

Results A total of 343 eligible infants were included in the cohort with a median gestational age of 25.5 weeks and birth weight of 790 g. Evidence of early PHT was associated with birth weight Z-score (odds ratio [OR]: 0.65, confidence interval [CI]: 0.48–0.87) and maternal African American race (OR: 1.9, CI: 1.03–3.69). Early PHT was associated with decreased in-hospital survival compared with those with no evidence of PHT (OR: 2.0, CI: 1.02–3.90), and was associated with an increased rate of moderate-to-severe bronchopulmonary dysplasia at 36 weeks postmenstrual age (OR: 2.92, CI: 1.24–6.89).

Conclusion The presence of early PHT on echocardiogram between 72 hours and 14 days of age was associated with decreased in-hospital survival and worse pulmonary outcomes. This population represents a group of infants who warrant further investigation to improve outcomes.
Hypogonadotropic Hypogonadism in Non-Functioning Pituitary Adenomas: Impact of Intervention
Authors: Monteiro Diana , Freitas Paula , Vieira Romana , Carvalho Davide
Published: February 2017

To determine the prevalence of hypogonadotropic hypogonadism (HH) among patients with non-functioning pituitary adenomas (NFPA) and the post-surgery outcome on pituitary gonadotropins secretion (PGS); to determine the prevalence of erectile dysfunction (ED) on male patients with NFPA, to evaluate the impact of testosterone replacement therapy (TRT) in those with HH.

Retrospective evaluation of gonadal function in 109 NFPA patients (45 males), with a mean age of 51.8 years, diagnosed on the last 10 years. ED questionnaire applied to 34 male patients.

Male patients with NFPA were significantly older (males 58.1±15.8 vs. females 47.4±16.94; p=0.001). Most patients had macroadenomas (67%; p=0.001) and only a minority were incidentalomas (19%; p<0.001). Prevalence of HH was 40% (60% on males, 25% on females; p<0.001). Surgery was performed in 54% of all patients (71% of males, 42% of females; p<0.003). After intervention, 14% became HH, 69% maintained previous function and 17% improved. On the questionnaire, 76% reported having ED, 54% of which had HH and 21% were under TRT. Of the patients under TRT, 79% still had ED. Median age of patients with ED was significantly higher [with ED 65 vs. without 49 years; p=0.012). There was no BMI difference between patients with or without TRT (28.0 vs. 27.4 Kg/m2).

NFPA was more frequent in older rather than younger patients. Males were older, had more HH and surgery. There was no significant improvement of pituitary function with surgery (17%) and 13% became iatrogenic HH. TRT had a low efficacy to improve ED in these patients.
Exploring the “Middle Earth” of network spectra via a Gaussian matrix function
Authors: Estrada Ernesto , Alhomaidhi Alhanouf Ali , Al-Thukair Fawzi
Published: February 2017

We study a Gaussian matrix function of the adjacency matrix of artificial and real-world networks. We motivate the use of this function on the basis of a dynamical process modeled by the time-dependent Schrödinger equation with a squared Hamiltonian. In particular, we study the Gaussian Estrada index—an index characterizing the importance of eigenvalues close to zero. This index accounts for the information contained in the eigenvalues close to zero in the spectra of networks. Such a method is a generalization of the so-called “Folded Spectrum Method” used in quantum molecular sciences. Here, we obtain bounds for this index in simple graphs, proving that it reaches its maximum for star graphs followed by complete bipartite graphs. We also obtain formulas for the Estrada Gaussian index of Erdős-Rényi random graphs and for the Barabási-Albert graphs. We also show that in real-world networks, this index is related to the existence of important structural patterns, such as complete bipartite subgraphs (bicliques). Such bicliques appear naturally in many real-world networks as a consequence of the evolutionary processes giving rise to them. In general, the Gaussian matrix function of the adjacency matrix of networks characterizes important structural information not described in previously used matrix functions of graphs.
Magnetization reversal processes of isotropic permanent magnets with various inter-grain exchange interactions
Authors: Tsukahara Hiroshi , Iwano Kaoru , Mitsumata Chiharu , Ishikawa Tadashi , Ono Kanta
Published: February 2017

We performed a large-scale micromagnetics simulation on a supercomputing system to investigate the properties of isotropic nanocrystalline permanent magnets consisting of cubic grains. In the simulation, we solved the Landau–Lifshitz–Gilbert equation under a periodic boundary condition for accurate calculation of the magnetization dynamics inside the nanocrystalline isotropic magnet. We reduced the inter-grain exchange interaction perpendicular and parallel to the external field independently. Propagation of the magnetization reversal process is inhibited by reducing the inter-grain exchange interaction perpendicular to the external field, and the coercivity is enhanced by this restraint. In contrast, when we reduce the inter-grain exchange interaction parallel to the external field, the coercivity decreases because the magnetization reversal process propagates owing to dipole interaction. These behaviors show that the coercivity of an isotropic permanent magnet depends on the direction of the inter-grain exchange interaction.
Effect of magnetic fields on green color formation in frog skin
Authors: Kashiwagi H. , Kashiwagi A. , Iwasaka M.
Published: February 2017

The present work is focused on a dynamic and efficient optical control system that is made possible by investigation of the body surfaces of various animals. Specifically, we expect Japanese tree frog (Hyla japonica) skin to provide a model for a flexible display device actuator mechanism. Tree frogs change body color from their original green to other colors in response to background colors. The color formation is controlled not only by chromatophores, but also by guanine microcrystals in iridophores. We collected sample microcrystals from the frog’s dorsal skin and made a model display sheet using the green skin layers. The transparent chamber that contained the crystal suspension was layered to enhance light reflection. Sheet color was observed while the angle of light incidence was varied, with and without magnetic field exposure at 0.3 T. A slight increase in red and green intensity was detected. Additionally, reflected intensity increased with increasing angle of incidence. These results indicate that the guanine crystal platelets in frog skin can efficiently switch the reflected light direction under application of a magnetic field. This in turn suggests that a several-micron-sized microcrystal of this type is a candidate material for development of flexible optical chips for ambient light control.
Realisation of a joint consumer engagement strategy in the Nepean Blue Mountains region
Authors: Blignault Ilse , Aspinall Diana , Reay Lizz , Hyman Kay
Published: February 2017

Ensuring consumer engagement at different levels of the health system – direct care, organisational design and governance and policy – has become a strategic priority. This case study explored, through interviews with six purposively selected ‘insiders’ and document review, how one Medicare Local (now a Primary Health Network, PHN) and Local Health District worked together with consumers, to establish a common consumer engagement structure and mechanisms to support locally responsive, integrated and consumer-centred services. The two healthcare organisations worked as partners across the health system, sharing ownership and responsibility. Critical success factors included a consumer champion working with other highly motivated consumers concerned with improving the health system, a budget, and ongoing commitment from the Medicare Local or PHN and the Local Health District at executive and board level. Shared boundaries were an enormous advantage. Activities were jointly planned and executed, with consumer participation paramount. Training and mentoring enhanced consumer capacity and confidence. Bringing everyone on board and building on existing structures required time, effort and resources. The initiative produced immediate and lasting benefits, with consumer engagement now embedded in organisational governance and practice.
Hemoglobin phase of oxygenation and deoxygenation in early brain development measured using fNIRS
Authors: Watanabe Hama , Shitara Yoshihiko , Aoki Yoshinori , Inoue Takanobu , Tsuchida Shinya , Takahashi Naoto , Taga Gentaro
Published: February 2017

Significance

We propose time-averaged hemoglobin phase of oxygenation and deoxygenation (hPod) measured using functional near-infrared spectroscopy as a method for the detection of the developmental status of the hemodynamic and metabolic processes of the brain. hPod values exhibit initially rapid changes from in-phase to antiphase patterns in neonates and infants. These changes become more gradual in later development. We also describe the impact of early preterm birth on brain development.
Marian apparitions in cultural contexts: applying Jungian depth psychological principles to mass visions of the Virgin Mary at Zeitoun
Authors: Musso Valeria Céspedes
Published: February 2017

This paper provides a depth-psychological analysis of the mass visions of the Virgin Mary taking place at Zeitoun, Egypt, during the late 1960s. A review of the literature points to a prevailing socio-political approach to examining visions of the Virgin Mary, while I argue that a satisfactory psychoanalytical approach is generally lacking. The interpretation I propose draws on Jung’s theoretical model inFlying Saucerswith the aim of merging depth-psychology and historical material surrounding the Zeitoun phenomenon. Common themes and symbols are extracted and interpreted from the empirical material and analysed along with Egyptian social and political data. This study concludes with a discussion on how depth-psychological principles grounded in empirical and historical material could be applied in order to explicate cases of mass visions.
La Racha: Speed and Violence in Tijuana
Authors: Yeh Rihan
Published: February 2017

Perched at the edge of California, Tijuana occupies a strategic location for capitalist mobilities of all sorts. This essay examines how the violence of drug trafficking and the speed of the transnational assembly plants came into resonance during a period often known locally as the racha, or streak, of violence, when Mexico’s so-called war on drug trafficking was perceived by many to be at its worst. The semiotic underpinnings of the racha, I argue, lie in the qualia of speed and slowness as these are valorized in supply-chain provisioning of the assembly plants and then calqued onto automotive traffic in the city. Speed and slowness here, though, are bound up with a highly equivocal sense of individual agency. By tracking these qualia across spheres of practice and, finally, into narratives of violence, I show how the racha took shape as a public crisis in the ability to assign individual agency securely.
Total and Fetal Circulating Cell-Free DNA, Angiogenic, and Antiangiogenic Factors in Preeclampsia and HELLP Syndrome
Authors: Muñoz-Hernández Rocío , Medrano-Campillo Pablo , Miranda Maria L. , Macher Hada C. , Praena-Fernández Jose Manuel , Vallejo-Vaz Antonio J. , Dominguez-Simeon María J. , Moreno-Luna Rafael , Stiefel Pablo
Published: February 2017

BACKGROUND

Preeclampsia (PE) is a hypertensive disorder of pregnancy characterized by hypertension and proteinuria. The HELLP syndrome is the most severe form of PE. The aim of the present study was to determine different potential biomarkers that may help us perform an early diagnosis of the disease, assess on the severity of the disease, and/or predict maternal or fetal adverse outcomes.

METHODS

We measured serum levels of total and fetal circulating cell-free DNA (cfDNA), soluble endoglin, soluble form of vascular endothelial growth factor receptor, and placental growth factor in a healthy control group of pregnant women (n = 26), patients with mild (n = 37) and severe PE (n = 25), and patients with HELLP syndrome (n = 16).

RESULTS

We observed a gradual and strong relationship between all the biomarkers mentioned and the range of severity of PE, with the highest levels in patients with HELLP syndrome. Nevertheless, only the values of total cfDNA were able to significantly differentiate severe PE and HELLP syndrome (20957 ± 2784 vs. 43184 ± 8647 GE/ml, P = 0.01). Receiver operating characteristic (ROC) curves were constructed (i) for the healthy group with respect to the groups with PE and (ii) for patients with PE with respect to the group with HELLP syndrome; sensitivity and specificity values at different cutoff levels were calculated in each case. The maximum ROC area under the curve value for PE and HELLP syndrome (with respect to controls) was 0.91 (P < 0.001).

CONCLUSIONS

The measured biomarkers of cell damage, angiogenesis, and antiangiogenesis may reflect the severity of PE, with higher levels in patients who develop HELLP syndrome. In addition, these biomarkers may also help predict adverse fetal and maternal outcomes.
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells
Authors: Yang Pengyi , Oldfield Andrew , Kim Taiyun , Yang Andrian , Yang Jean Yee Hwa , Ho Joshua W K
Published: February 2017

Motivation

DNA binding proteins such as chromatin remodellers, transcription factors (TFs), histone modifiers and co-factors often bind cooperatively to activate or repress their target genes in a cell type-specific manner. Nonetheless, the precise role of cooperative binding in defining cell-type identity is still largely uncharacterized.

Results

Here, we collected and analyzed 214 public datasets representing chromatin immunoprecipitation followed by sequencing (ChIP-Seq) of 104 DNA binding proteins in embryonic stem cell (ESC) lines. We classified their binding sites into those proximal to gene promoters and those in distal regions, and developed a web resource called Proximal And Distal (PAD) clustering to identify their co-localization at these respective regions. Using this extensive dataset, we discovered an extensive co-localization of BRG1 and CHD7 at distal but not proximal regions. The comparison of co-localization sites to those bound by either BRG1 or CHD7 alone showed an enrichment of ESC master TFs binding and active chromatin architecture at co-localization sites. Most notably, our analysis reveals the co-dependency of BRG1 and CHD7 at distal regions on regulating expression of their common target genes in ESC. This work sheds light on cooperative binding of TF binding proteins in regulating gene expression in ESC, and demonstrates the utility of integrative analysis of a manually curated compendium of genome-wide protein binding profiles in our online resource PAD.

Availability and Implementation

PAD is freely available at http://pad.victorchang.edu.au/ and its source code is available via an open source GPL 3.0 license at https://github.com/VCCRI/PAD/

Supplementary information

Supplementary data are available at Bioinformatics online.
Marginal likelihood estimation of negative binomial parameters with applications to RNA-seq data
Authors: León-Novelo Luis , Fuentes Claudio , Emerson Sarah
Published: February 2017

RNA-Seq data characteristically exhibits large variances, which need to be appropriately accounted for in any proposed model. We first explore the effects of this variability on the maximum likelihood estimator (MLE) of the dispersion parameter of the negative binomial distribution, and propose instead to use an estimator obtained via maximization of the marginal likelihood in a conjugate Bayesian framework. We show, via simulation studies, that the marginal MLE can better control this variation and produce a more stable and reliable estimator. We then formulate a conjugate Bayesian hierarchical model, and use this new estimator to propose a Bayesian hypothesis test to detect differentially expressed genes in RNA-Seq data. We use numerical studies to show that our much simpler approach is competitive with other negative binomial based procedures, and we use a real data set to illustrate the implementation and flexibility of the procedure.
Bayesian inference for causal mechanisms with application to a randomized study for postoperative pain control
Authors: Baccini Michela , Mattei Alessandra , Mealli Fabrizia
Published: February 2017

We conduct principal stratification and mediation analysis to investigate to what extent the positive overall effect of treatment on postoperative pain control is mediated by postoperative self administration of intra-venous analgesia by patients in a prospective, randomized, double-blind study. Using the Bayesian approach for inference, we estimate both associative and dissociative principal strata effects arising in principal stratification, as well as natural effects from mediation analysis. We highlight that principal stratification and mediation analysis focus on different causal estimands, answer different causal questions, and involve different sets of structural assumptions.
SERAPHIN haemodynamic substudy: the effect of the dual endothelin receptor antagonist macitentan on haemodynamic parameters and NT-proBNP levels and their association with disease progression in patients with pulmonary arterial hypertension
Authors: Galiè Nazzareno , Jansa Pavel , Pulido Tomás , Channick Richard N. , Delcroix Marion , Ghofrani Hossein-Ardeschir , Le Brun Franck-Olivier , Mehta Sanjay , Perchenet Loïc , Rubin Lewis J. , Sastry B.K.S. , Simonneau Gérald , Sitbon Olivier , Souza Rogério , Torbicki Adam
Published: February 2017

Aims

The effect of macitentan on haemodynamic parameters and NT-proBNP levels was evaluated in pulmonary arterial hypertension (PAH) patients in the SERAPHIN study. Association between these parameters and disease progression, assessed by the primary endpoint (time to first morbidity/mortality event), was explored.

Methods and results

Of the 742 randomized patients, 187 with right heart catheterization at baseline and month 6 participated in a haemodynamic sub-study. Prespecified endpoints included change from baseline to month 6 in cardiac index (CI), right atrial pressure (RAP), mean pulmonary arterial pressure (mPAP), pulmonary vascular resistance (PVR), mixed-venous oxygen saturation, and NT-proBNP. Exploratory analyses examined associations between CI, RAP, and NT-proBNP and disease progression using the Kaplan-Meier method and Cox regression models. Macitentan improved CI, RAP, mPAP, PVR and NT-proBNP vs. placebo at month 6. Absolute levels of CI, RAP and NT-proBNP at baseline and month 6, but not their changes, were associated with morbidity/mortality events. Patients with CI > 2.5 L/min/m2, RAP < 8 mmHg, or NT-proBNP < 750 fmol/ml at month 6 had a lower risk of morbidity/mortality than those not meeting these thresholds (HR 0.49, 95% CL 0.28–0.86; HR 0.72, 95% CL 0.42–1.22; and HR 0.22, 95% CL 0.15–0.33, respectively).

Conclusions

For all treatment groups, baseline and month 6 values of CI, RAP, and NT-proBNP, but not their changes, were associated with morbidity/mortality events, confirming their relevance in predicting disease progression in patients with PAH. By improving those parameters, macitentan increased the likelihood of reaching threshold values associated with lower risk of morbidity/mortality.
Effects of current and future coastal upwelling conditions on the fertilization success of the red abalone (Haliotis rufescens)
Authors: Boch Charles A. , Litvin Steven Y. , Micheli Fiorenza , De Leo Giulio , Aalto Emil A. , Lovera Christopher , Brock Woodson C. , Monismith Stephen , Barry James P.
Published: February 2017

Acidification, deoxygenation, and warming are escalating changes in coastal waters throughout the world ocean, with potentially severe consequences for marine life and ocean-based economies. To examine the influence of these oceanographic changes on a key biological process, we measured the effects of current and expected future conditions in the California Current Large Marine Ecosystem on the fertilization success of the red abalone (Haliotis rufescens). Laboratory experiments were used to assess abalone fertilization success during simultaneous exposure to various levels of seawater pH (gradient from 7.95 to 7.2), dissolved oxygen (DO) (∼60 and 180 µm.kg SW) and temperature (9, 13, and 18 °C). Fertilization success declined continuously with decreasing pH but dropped precipitously below a threshold near pH 7.55 in cool (9 °C—upwelling) to average (13 °C) seawater temperatures. Variation in DO had a negligible effect on fertilization. In contrast, warmer waters (18 °C) often associated with El Niño Southern Oscillation conditions in central California acted antagonistically with decreasing pH, largely reducing the strong negative influence below the pH threshold. Experimental approaches that examine the interactive effects of multiple environmental drivers and also strive to characterize the functional response of organisms along gradients in environmental change are becoming increasingly important in advancing our understanding of the real-world consequences of changing ocean conditions.
Cutting through the Gordian knot: unravelling morphological, molecular, and biogeographical patterns in the genus Zapteryx (guitarfish) from the Mexican Pacific
Authors: Castillo-Páez Ana , Sandoval-Castillo Jonathan , Corro-Espinosa David , Tovar-Ávila Javier , Blanco-Parra María-Del-Pilar , Saavedra-Sotelo Nancy C. , Sosa-Nishizaki Oscar , Galván-Magaña Felipe , Rocha-Olivares Axayácatl
Published: February 2017

Defining species boundaries is important not only for the appropriate attribution of life history and ecological traits but also for sustainable fishery management and for the conservation of biodiversity. Problems arise from taxonomic uncertainty and incorrect species delineation leading to historical misidentification. This is the case of Pacific guitarfishes in the genus Zapteryx. We use a molecular phylogenetic approach combining mitochondrial and nuclear loci to investigate genetic variation in fish along the Mexican Pacific coast. Our analyses reveal a lack of nuclear and mitochondrial distinction between rays identified morphologically as banded guitarfish Z. exasperata and as southern banded guitarfish Z. xyster, casting doubts on the validity of their current systematics. However, we detected two mitochondrial lineages in accordance with the number of species described for the Pacific: a “northern” lineage corresponding to Z. exasperata and a “southern” lineage possibly attributable to Z. xyster. The poorly understood phenotypic plasticity in coloration and size of the evolutionary lineage of Z. exasperata and its apparently wider than currently thought geographic distribution (at least to Oaxaca) are the major sources of confusion regarding the taxonomic and geographic delineation of these nominal species. In light of our findings, eastern Pacific guitarfishes in the genus Zapteryx require a thorough taxonomic revision using morphological and genetic data to unveil what appears to be a complex pattern of diversification.
Galactic rotation in Gaia DR1
Authors: Bovy Jo
Published: February 2017

The spatial variations of the velocity field of local stars provide direct evidence of Galactic differential rotation. The local divergence, shear and vorticity of the velocity field – the traditional Oort constants – can be measured based purely on astrometric measurements and in particular depend linearly on proper motion and parallax. I use data for 304 267 main-sequence stars from the Gaia DR1 Tycho-Gaia Astrometric Solution to perform a local, precise measurement of the Oort constants at a typical heliocentric distance of 230 pc. The pattern of proper motions for these stars clearly displays the expected effects from differential rotation. I measure the Oort constants to be: A = 15.3 ± 0.4 km s−1 kpc−1, B = −11.9 ± 0.4 km s−1 kpc−1, C = −3.2 ± 0.4 km s−1 kpc−1 and K = −3.3 ± 0.6 km s−1 kpc−1, with no colour trend over a wide range of stellar populations. These first confident measurements of C and K clearly demonstrate the importance of non-axisymmetry for the velocity field of local stars and they provide strong constraints on non-axisymmetric models of the Milky Way.
Comparison Between CTA and Digital Subtraction Angiography in the Diagnosis of Ruptured Aneurysms
Authors: Philipp Lucas R. , McCracken D. Jay , McCracken Courtney E. , Halani Sameer H. , Lovasik Brendan P. , Salehani Arsalaan A. , Boulter Jason H. , Cawley C. Michael , Grossberg Jonathan A. , Barrow Daniel L. , Pradilla Gustavo
Published: February 2017

BACKGROUND: Computerized tomography angiography (CTA) is commonly used to diagnose ruptured cerebral aneurysms with sensitivities reported as high as 97% to 100%. Studies validating CTA accuracy in the setting of subarachnoid hemorrhage (SAH) are scarce and limited by small sample sizes.

OBJECTIVE: To evaluate the diagnostic accuracy of CTA in detecting intracranial aneurysms in the setting of SAH.

METHODS: A single-center, retrospective cohort of 643 patients was reviewed. A total of 401 patients were identified whose diagnostic workup included both CTA and confirmatory digital subtraction angiography (DSA). Aneurysms missed by CTA but diagnosed by DSA were further stratified by size and location.

RESULTS: Three hundred and thirty aneurysms were detected by CTA while DSA detected a total of 431 aneurysms. False positive CTA results were seen for 24 aneurysms. DSA identified 125 aneurysms that were missed by CTA and 83.2% of those were <5 mm in diameter. The sensitivity of CTA was 57.6% for aneurysms smaller than 5 mm in size, and 45% for aneurysms originating from the internal carotid artery. The overall sensitivity of CTA in the setting of SAH was 70.7%.

CONCLUSION: The accuracy of CTA in the diagnosis of ruptured intracranial aneurysm may be lower than previously reported. CTA has a low sensitivity for aneurysms less than 5 mm in size, in locations adjacent to bony structures, and for those arising from small caliber parent vessels. It is our recommendation that CTA should be used with caution when used alone in the diagnosis of ruptured intracranial aneurysms.
Endovascular Rescue Therapies for Refractory Vasospasm After Subarachnoid Hemorrhage: A Prospective Evaluation Study Using Multimodal, Continuous Event Neuromonitoring
Authors: Albanna Walid , Weiss Miriam , Müller Marguerite , Brockmann Marc Alexander , Rieg Annette , Conzen Catharina , Clusmann Hans , Höllig Anke , Schubert Gerrit Alexander
Published: February 2017

BACKGROUND: Critical hypoperfusion and metabolic derangement are frequently encountered with refractory vasospasm. Endovascular rescue therapies (ERT) have proven beneficial in selected cases. However, angioplasty (AP) and intraarterial lysis (IAL) are measures of last resort and prospective, quantitative results regarding the efficacy (cerebral oxygenation, metabolism) are largely lacking.

OBJECTIVE: To evaluate the efficacy of ERTs for medically refractory vasospasm using multimodal, continuous event neuromonitoring.

METHODS: To detect cerebral compromise in a timely fashion, sedated patients with aneurysmal subarachnoid hemorrhage received continuous neuromonitoring (ptiO2 measurement, intraparenchymal microdialysis). ERT (AP and/or IAL) was considered in cases of clinically relevant vasospasm refractory to conservative treatment measures. Oxygen saturation and cerebral and systemic metabolism before and after events of ERT was recorded.

RESULTS: We prospectively included 13 consecutive patients and recorded a total of 25 ERT events: AP (n = 10), IAL (n = 11), or both (AP + IAL, n = 4). Average cerebral ptiO2 was 10 ± 11 torr before and 49 ± 22 torr after ERT (P < .001), with a lactate-pyruvate ratio decreasing from 146.6 ± 119.0 to 27.9 ± 10.7 after ERT (P < .001). Comparable improvement was observed for each type of intervention (AP, IAL, or both). No significant alterations in systemic metabolism could be detected after ERT

CONCLUSION: Multimodal event neuromonitoring is able to quantify treatment efficacy in subarachnoid hemorrhage-related vasospasm. In our small cohort of highly selected cases, ERT was associated with improvement in cerebral oxygenation and metabolism with reasonable outcome. Event neuromonitoring may facilitate individual and timely optimization of treatment modality according to the individual clinical course.