bluuebunny/crossref_metadata_2025_split huggingface dataset:
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks
Authors: Vlaic Sebastian , Conrad Theresia , Tokarski-Schnelle Christian , Gustafsson Mika , Dahmen Uta , Guthke Reinhard , Schuster Stefan 
Published: January 2018

AbstractThe identification of disease-associated modules based on protein-protein interaction networks (PPINs) and gene expression data has provided new insights into the mechanistic nature of diverse diseases. However, their identification is hampered by the detection of protein communities within large-scale, whole-genome PPINs. A presented successful strategy detects a PPIN’s community structure based on the maximal clique enumeration problem (MCE), which is a non-deterministic polynomial time-hard problem. This renders the approach computationally challenging for large PPINs implying the need for new strategies. We present ModuleDiscoverer, a novel approach for the identification of regulatory modules from PPINs and gene expression data. Following the MCE-based approach, ModuleDiscoverer uses a randomization heuristic-based approximation of the community structure. Given a PPIN of Rattus norvegicus and public gene expression data, we identify the regulatory module underlying a rodent model of non-alcoholic steatohepatitis (NASH), a severe form of non-alcoholic fatty liver disease (NAFLD). The module is validated using single-nucleotide polymorphism (SNP) data from independent genome-wide association studies and gene enrichment tests. Based on gene enrichment tests, we find that ModuleDiscoverer performs comparably to three existing module-detecting algorithms. However, only our NASH-module is significantly enriched with genes linked to NAFLD-associated SNPs. ModuleDiscoverer is available at http://www.hki-jena.de/index.php/0/2/490 (Others/ModuleDiscoverer).
Optimal swimming strategies and behavioral plasticity of oceanic whitetip sharks
Authors: Papastamatiou Yannis P. , Iosilevskii Gil , Leos-Barajas Vianey , Brooks Edd J. , Howey Lucy A. , Chapman Demian D. , Watanabe Yuuki Y. 
Published: January 2018

AbstractAnimal behavior should optimize the difference between the energy they gain from prey and the energy they spend searching for prey. This is all the more critical for predators occupying the pelagic environment, as prey is sparse and patchily distributed. We theoretically derive two canonical swimming strategies for pelagic predators, that maximize their energy surplus while foraging. They predict that while searching, a pelagic predator should maintain small dive angles, swim at speeds near those that minimize the cost of transport, and maintain constant speed throughout the dive. Using biologging sensors, we show that oceanic whitetip shark (Carcharhinus longimanus) behavior matches these predictions. We estimate that daily energy requirements of an adult shark can be met by consuming approximately 1–1.5 kg of prey (1.5% body mass) per day; shark-borne video footage shows a shark encountering potential prey numbers exceeding that amount. Oceanic whitetip sharks showed incredible plasticity in their behavioral strategies, ranging from short low-energy bursts on descents, to high-speed vertical surface breaches from considerable depth. Oceanic whitetips live a life of energy speculation with minimization, very different to those of tunas and billfish.
Winner-take-all in a phase oscillator system with adaptation
Authors: Burylko Oleksandr , Kazanovich Yakov , Borisyuk Roman 
Published: January 2018

AbstractWe consider a system of generalized phase oscillators with a central element and radial connections. In contrast to conventional phase oscillators of the Kuramoto type, the dynamic variables in our system include not only the phase of each oscillator but also the natural frequency of the central oscillator, and the connection strengths from the peripheral oscillators to the central oscillator. With appropriate parameter values the system demonstrates winner-take-all behavior in terms of the competition between peripheral oscillators for the synchronization with the central oscillator. Conditions for the winner-take-all regime are derived for stationary and non-stationary types of system dynamics. Bifurcation analysis of the transition from stationary to non-stationary winner-take-all dynamics is presented. A new bifurcation type called a Saddle Node on Invariant Torus (SNIT) bifurcation was observed and is described in detail. Computer simulations of the system allow an optimal choice of parameters for winner-take-all implementation.
Neural correlates of perceptual separation-induced enhancement of prepulse inhibition of startle in humans
Authors: Lei Ming , Zhang Changxin , Li Liang 
Published: January 2018

AbstractPrepulse inhibition (PPI) is the suppression of the startle reflex when the intense startling stimulus is shortly preceded by a weaker non-startling stimulus (prepulse). In rats, the auditory precedence-effect-induced perceived spatial separation between the fear-conditioned prepulse and a noise masker facilitates selective attention to the prepulse and enhances PPI. However, whether the perceptual separation between the prepulse and a noise masker can also enhance PPI in humans remains unclear. Also, the relationship between the PPI enhancement and the change in early cortical representations of prepulse signals is unclear. This study for the first time reveals that in a sound-attenuated laboratory environment, relative to the listening condition with perceptual co-location between the prepulse stimulus and a noise-masking stimulus, the perceptual separation between the two stimuli significantly enhances the group-mean PPI. More importantly, the early cortical responses (N1/P2 complex) to the prepulse stimulus are also enhanced by the perceptual separation in most listeners, and the perceptual-separation-induced enhancement of the N1 component is positively correlated with the perceptual-separation-induced PPI enhancement. Thus, the perceptual separation enhances PPI through facilitating selective attention to the prepulse, leading to an enhancement of the early cortical representation of the prepulse signal in temporal auditory cortical fields.
Kirigami-based Elastic Metamaterials with Anisotropic Mass Density for Subwavelength Flexural Wave Control
Authors: Zhu R. , Yasuda H. , Huang G. L. , Yang J. K. 
Published: January 2018

AbstractA novel design of an elastic metamaterial with anisotropic mass density is proposed to manipulate flexural waves at a subwavelength scale. The three-dimensional metamaterial is inspired by kirigami, which can be easily manufactured by cutting and folding a thin metallic plate. By attaching the resonant kirigami structures periodically on the top of a host plate, a metamaterial plate can be constructed without any perforation that degrades the strength of the pristine plate. An analytical model is developed to understand the working mechanism of the proposed elastic metamaterial and the dispersion curves are calculated by using an extended plane wave expansion method. As a result, we verify an anisotropic effective mass density stemming from the coupling between the local resonance of the kirigami cells and the global flexural wave propagations in the host plate. Finally, numerical simulations on the directional flexural wave propagation in a two-dimensional array of kirigami metamaterial as well as super-resolution imaging through an elastic hyperlens are conducted to demonstrate the subwavelength-scale flexural wave control abilities. The proposed kirigami-based metamaterial has the advantages of no-perforation design and subwavelength flexural wave manipulation capability, which can be highly useful for engineering applications including non-destructive evaluations and structural health monitoring.
Angiopoietins bind thrombomodulin and inhibit its function as a thrombin cofactor
Authors: Daly Christopher , Qian Xiaozhong , Castanaro Carla , Pasnikowski Elizabeth , Jiang Xiabo , Thomson Benjamin R. , Quaggin Susan E. , Papadopoulos Nicholas , Wei Yang , Rudge John S. , Thurston Gavin , Yancopoulos George D. , Davis Samuel 
Published: January 2018

AbstractAngiopoietin-1 (Ang1) and Angiopoietin-2 (Ang2) are ligands for Tie2, an endothelial-specific receptor tyrosine kinase that is an essential regulator of angiogenesis. Here we report the identification, via expression cloning, of thrombomodulin (TM) as another receptor for Ang1 and Ang2. Thrombomodulin is an endothelial cell surface molecule that plays an essential role as a coagulation inhibitor via its function as a cofactor in the thrombin-mediated activation of protein C, an anticoagulant protein, as well as thrombin-activatable fibrinolysis inhibitor (TAFI). Ang1 and Ang2 inhibited the thrombin/TM-mediated generation of activated protein C and TAFI in cultured endothelial cells, and inhibited the binding of thrombin to TM in vitro. Ang2 appears to bind TM with higher affinity than Ang1 and is a more potent inhibitor of TM function. Consistent with a potential role for angiopoietins in coagulation, administration of thrombin to mice rapidly increased plasma Ang1 levels, presumably reflecting release from activated platelets (previously shown to contain high levels of Ang1). In addition, Ang1 levels were significantly elevated in plasma prepared from wound blood, suggesting that Ang1 is released from activated platelets at sites of vessel injury. Our results imply a previously undescribed role for angiopoietins in the regulation of hemostasis.
A green method to leach vanadium and chromium from residue using NaOH-H2O2
Authors: Peng Hao , Liu Zuohua , Tao Changyuan 
Published: January 2018

AbstractHydrogen peroxide as an oxidant was applied in leaching of vanadium and chromium in concentrated NaOH solution. Under the optimal reaction conditions (the liquid to solid ratio of 4.0 ml/g, residue particle size of <200 mesh, the mass ratio of NaOH-to-residue of 1.0 g/g, the volume ratio of H2O2-to-residue of 1.2 ml/g, reaction temperature of 90 °C and reaction time of 120 min), the leaching efficiency of vanadium and chromium could reach up to 98.60% and 86.49%, respectively. Compared with the current liquid-phase oxidation technologies, the reaction temperature was 90–310 °C lower, and the NaOH concentration of the reaction medium is lower by more than 50 wt% (the mass ratio of NaOH-to-residue of 1.0 g/g equals to concentration of 20 wt%). The kinetics study revealed that leaching process of chromium and vanadium were interpreted with shrinking core model under chemical reaction control. The apparent activation energy of chromium and vanadium dissolution was 22.19 kJ/mol and 6.95 kJ/mol, respectively.
Calcium-phosphate complex increased during subchondral bone remodeling affects earlystage osteoarthritis
Authors: Jung Youn-Kwan , Han Min-Su , Park Hye-Ri , Lee Eun-Ju , Jang Ji-Ae , Kim Gun-Woo , Lee Sun-Young , Moon DaeWon , Han Seungwoo 
Published: January 2018

AbstractAn activation of osteoclasts and subchondral bone remodeling is a major histologic feature of early-stage osteoarthritis (OA), which can be accompanied by an increase of calcium (Ca) and phosphate (Pi) level in the subchondral milieu. Considering articular cartilage gets most of nutrition from subchondral bone by diffusion, these micro-environmental changes in subchondral bone can affect the physiology of articular chondrocytes. Here, we have shown that Ca is increased and co-localized with Pi in articular cartilage of early-stage OA. The Ca-Pi complex increased the production of MMP-3 and MMP-13 in the hypertrophic chondrocytes, which was dependent on nuclear factor-kappa B (NF-kB), p38 and extracellular signal-regulated kinase (Erk) 1/2 mitogen-activated protein (MAP) kinase and Signal transducer and activator of transcription 3 (STAT3) signaling. The Ca-Pi complexes increased the expression of endocytosis markers, and the inhibition of the formation of the Ca-Pi complex ameliorated the Ca-Pi complex-mediated increases of MMPs expression in hypertrophic chondrocytes. Our data provide insight regarding the Ca-Pi complex as a potential catabolic mediator in the subchondral milieu and support the pathogenic role of subchondral bone in the early stages of cartilage degeneration.
Characterization of isoprene-derived secondary organic aerosols at a rural site in North China Plain with implications for anthropogenic pollution effects
Authors: Li Jianjun , Wang Gehui , Wu Can , Cao Cong , Ren Yanqin , Wang Jiayuan , Li Jin , Cao Junji , Zeng Limin , Zhu Tong 
Published: January 2018

AbstractIsoprene is the most abundant non-methane volatile organic compound (VOC) and the largest contributor to secondary organic aerosol (SOA) burden on a global scale. In order to examine the influence of high concentrations of anthropogenic pollutants on isoprene-derived SOA (SOA
i
) formation, summertime PM2.5 filter samples were collected with a three-hour sampling interval at a rural site in the North China Plain (NCP), and determined for SOA
i
tracers and other chemical species. RO2+NO pathway derived 2-methylglyceric acid presented a relatively higher contribution to the SOA
i
due to the high-NOx (~20 ppb) conditions in the NCP that suppressed the reactive uptake of RO2+HO2 reaction derived isoprene epoxydiols. Compared to particle acidity and water content, sulfate plays a dominant role in the heterogeneous formation process of SOA
i
. Diurnal variation and correlation of 2-methyltetrols with ozone suggested an important effect of isoprene ozonolysis on SOA
i
formation. SOA
i
increased linearly with levoglucosan during June 10–18, which can be attributed to an increasing emission of isoprene caused by the field burning of wheat straw and a favorable aqueous SOA formation during the aging process of the biomass burning plume. Our results suggested that isoprene oxidation is highly influenced by intensive anthropogenic activities in the NCP.
Clinical Value of 99mTc-3PRGD2 SPECT/CT in Differentiated Thyroid Carcinoma with Negative 131I Whole-Body Scan and Elevated Thyroglobulin Level
Authors: Gao Rui , Zhang Guang-Jian , Wang Yuan-Bo , Liu Yan , Wang Fan , Jia Xi , Liang Yi-Qian , Yang Ai-Min 
Published: January 2018

AbstractThe aim of this study was to assess the usefulness of integrin imaging with 99mTc-PEG4-E[PEG4-c(RGDfK)]2 (99mTc-3PRGD2) single photon emission computed tomography (SPECT)/computed tomography (CT) in detecting recurrent disease in patients with differentiated thyroid cancer (DTC), negative radioiodine whole-body scan (WBS) and high serum thyroglobulin (Tg). Thirty-seven patients who underwent total thyroidectomy followed by radioactive iodine ablation and had negative radioiodine WBS but elevated Tg levels were included. 99mTc-3PRGD2 SPECT/CT was performed 1 week after the negative diagnostic 131I WBS. Diagnostic performance indicators, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), for 99mTc-3PRGD2 SPECT/CT was calculated. The correlations between SPECT/CT results and clinic-pathological characteristics were examined. In 30 (81.1%) of the 37 patients, 99mTc-3PRGD2 SPECT/CT showed positive uptake. The sensitivity, specificity, PPV, and NPV of SPECT/CT to detect recurrent disease at follow-up were 96.6%, 75%, 93.3% and 85.7%, respectively. The sensitivity and PPV of SPECT/CT increased with increasing serum Tg levels. 99mTc-3PRGD2 SPECT/CT showed high sensitivity and PPV in the detection of recurrence among DTC patients with higher Tg levels and negative WBS, and the probability of obtaining a positive SPECT/CT result was related with the level of Tg.
Racial Differences in Four Leukemia Subtypes: Comprehensive Descriptive Epidemiology
Authors: Zhao Yinjun , Wang Yu , Ma Shuangge 
Published: January 2018

AbstractLeukemia is a malignant progressive disease and has four major subtypes. Different racial groups differ significantly in multiple aspects. Our goal is to systematically and comprehensively quantify racial differences in leukemia. The SEER database is analyzed, and comprehensive descriptive analysis is provided for the four major subtypes, namely ALL (acute lymphoblastic leukemia), CLL (chronic lymphoblastic leukemia), AML (acute myeloid leukemia), and CML (chronic myeloid leukemia), and for two age groups (≤14 and >14) separately. The racial groups studied include NHW (non-Hispanic White), HW (Hispanic White), BL (Black), and API (Asian and Pacific Islander). Univariate and multivariate analyses are conducted to quantify racial differences in patients’ characteristics, incidence, and survival. For patients’ characteristics, significant racial differences are observed in gender, age at diagnosis, diagnosis era, using radiation for treatment, registry, cancer history, and histology type. For incidence, significant racial differences are observed, and the patterns vary across subtypes, gender, and age groups. For most of the subtypes and gender and age groups, Blacks have the worst five-year survival, and significant racial differences exist. This study provides a comprehensive epidemiologic description of racial differences for the four major leukemia subtypes in the U.S. population.
The details of past actions on a smartphone touchscreen are reflected by intrinsic sensorimotor dynamics
Authors: Balerna Myriam , Ghosh Arko 
Published: January 2018

AbstractUnconstrained day-to-day activities are difficult to quantify and how the corresponding movements shape the brain remain unclear. Here, we recorded all touchscreen smartphone interactions at a sub-second precision and show that the unconstrained day-to-day behavior captured on the phone reflects in the simple sensorimotor computations measured in the laboratory. The behavioral diversity on the phone, the speed of interactions, the amount of social & non-social interactions, all uniquely influenced the trial-to-trial motor variability used to measure the amount of intrinsic neuronal noise. Surprisingly, both the motor performance and the early somatosensory cortical signals (assessed using EEG in passive conditions) became noisier with increased social interactions. Inter-individual differences in how people use the smartphone can help thus decompose the structure of low-level sensorimotor computations.
Skull Base Reconstruction in the Pediatric Patient
Authors: Duek Irit , Pener-Tessler Alon , Yanko-Arzi Ravit , Zaretski Arik , Abergel Avraham , Safadi Ahmad , Fliss Dan 
Published: January 2018

Introduction Pediatric skull base and craniofacial reconstruction presents a unique challenge since the potential benefits of therapy must be balanced against the cumulative impact of multimodality treatment on craniofacial growth, donor-site morbidity, and the potential for serious psychosocial issues.
Objectives To suggest an algorithm for skull base reconstruction in children and adolescents after tumor resection.
Materials and Methods Comprehensive literature review and summary of our experience.
Results We advocate soft-tissue reconstruction as the primary technique, reserving bony flaps for definitive procedures in survivors who have reached skeletal maturity. Free soft-tissue transfer in microvascular technique is the mainstay for reconstruction of large, three-dimensional defects, involving more than one anatomic region of the skull base, as well as defects involving an irradiated field. However, to reduce total operative time, intraoperative blood loss, postoperative hospital stay, and donor-site morbidity, locoregional flaps are better be considered the flap of first choice for skull base reconstruction in children and adolescents, as long as the flap is large enough to cover the defect. Our “workhorse” for dural reconstruction is the double-layer fascia lata. Advances in endoscopic surgery, image guidance, alloplastic grafts, and biomaterials have increased the armamentarium for reconstruction of small and mid-sized defects.
Conclusions Skull base reconstruction using locoregional flaps or free flaps may be safely performed in pediatrics. Although the general principles of skull base reconstruction are applicable to nearly all patients, the unique demands of skull base surgery in pediatrics merit special attention. Multidisciplinary care in experienced centers is of utmost importance.
Developmental Considerations in Pediatric Skull Base Surgery
Authors: LoPresti Melissa , Sellin Jonathan , DeMonte Franco 
Published: January 2018

Objectives To review developmental surgical anatomy and technical nuances related to pediatric skull base surgery.
Design Retrospective, single-center case series with literature review.
Setting MD Anderson Cancer Center.
Participants Patients undergoing pediatric skull base surgery.
Main Outcome Measures Review developmental anatomy of the pediatric skull base as it relates to technical nuance of various surgical approaches and insight gained from a 25-year institutional experience with this unique patient population.
Results Thirty-nine patients meeting these criteria were identified over a 13-year period from 2003 to 2016 and compared to a previously reported earlier cohort from 1992 to 2002. The most common benign pathologies included nerve sheath tumors (11%), juvenile nasopharyngeal angiofibromas (9.5%), and craniopharyngiomas (4.8%). The most common malignancies were chondrosarcoma (11%), chordoma (11%), and rabdomyosarcoma (11%). Varied surgical approaches were utilized and were similar between the two cohorts save for the increased use of endoscopic surgical techniques in the most recent cohort. The most common sites of tumor origin were the infratemporal fossa, sinonasal cavities, clivus, temporal bone, and parasellar region. Gross total resection and postoperative complication rates were similar between the two patient cohorts.
Conclusions Pediatric skull base tumors, while rare, often are treated surgically, necessitating an in depth understanding of the anatomy of the developing skull base.
Effect of N-Acetylserotonin on TLR-4 and MyD88 Expression during Intestinal Ischemia-Reperfusion in a Rat Model
Authors: Ben Shahar Yoav , Halabi Salim , Bitterman Nir , Dorfman Tatiana , Pollak Yulia , Coran Arnold , Bitterman Arie , Sukhotnik Igor 
Published: January 2018

Background Accumulating evidence indicates that changes in intestinal toll-like receptors (TLRs) precede histological injury in a rodent model of necrotizing enterocolitis. N-acetylserotonin (NAS) is a naturally occurring chemical intermediate in the biosynthesis of melatonin. A recent study has shown that treatment with NAS prevents gut mucosal damage and inhibits programmed cell death following intestinal ischemia-reperfusion (IR). The objective of this study was to determine the effects of NAS on TLR-4, myeloid differentiation factor 88 (Myd88), and TNF-α receptor-associated factor 6 (TRAF6) expression in intestinal mucosa following intestinal IR in a rat.
Materials and Methods Male Sprague-Dawley rats were randomly assigned to one of the four experimental groups: 1) Sham rats underwent laparotomy; 2) Sham-NAS rats underwent laparotomy and were treated with intraperitoneal (IP) NAS (20 mg/kg); 3) IR rats underwent occlusion of both superior mesenteric artery and portal vein for 20 minutes followed by 48 hours of reperfusion; and 4) IR-NAS rats underwent IR and were treated with IP NAS immediately before abdominal closure. Intestinal structural changes, mucosal TLR-4, MyD88, and TRAF6 mucosal gene, and protein expression were examined using real-time PCR, Western blot, and immunohistochemistry.
Results Significant mucosal damage in IR rats was accompanied by a significant upregulation of TLR-4, MyD88, and TRAF6 gene and protein expression in intestinal mucosa compared with control animals. The administration of NAS decreased the intestinal injury score, inhibited cell apoptosis, and significantly reduced the expression of TLR-4, MyD88, and TRAF6.
Conclusion Treatment with NAS is associated with downregulation of TLR-4, MyD88, and TRAF6 expression along with a concomitant decrease in intestinal mucosal injury caused by intestinal IR in a rat.