bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Tryptophan Modification upon Digestion of Antithrombin III by Elastase
Authors: Scully M F , Shah N , Ellis V , Kakkar V V
Published: July 2018

Chemical modification of tryptophan residues in antithrombin III by dimethyl (2-hydroxy-5-nitrobenzyl) sulfonium bromide (HNBSB) generates products with similar levels of modification (equivalent to 0.9 mole 2-hydroxy-5-nitrobenzyl [HNB] incorporated/mole of antithrombin III) but with high or low affinity for heparin-Sepharose. Upon digestion with pancreatic or neutrophil elastase the low affinity forms generate a product of molecular weight form (55 kDa) not seen in digests of native antithrombin III or modified forms with high affinity for heparin. When measured as loss of activity the obserued rate of digestion of the latter in the absence of heparin was more rapid than that of native antithrombin III. The differences in digestion are considered to be related to conformation at differences between the various forms.
Antithrombotic and Anticoagulant Activity of Depolymerized Fragment of the Glycosaminoglycan Extracted from Stichopus japonicus Selenka
Authors: Suzuki Norihiko , Kitazato Kenji , Takamatsu Junki , Saito Hidehiko
Published: July 2018

The antithrombotic and anticoagulant activities of depolymerized fragment (DHG-l) of glycosaminoglycan extracted from Stichopw japonicus Selenka (FGAG) were compared with those of unfractionated heparin (UFH) or low molecular weight heparin (LMWH). DHG-1 at more than 0.3 mg/kg i. v. significantly prevented death of mice treated with thrombin (800 U/kg i.u.). Under the same conditions, FGAG, UFH and LMWH significantly prevented death of mice at more than 0.3, 0.3 and 0.6 mg/kg i.v., respectively. In normal plasma, the concentration required to double the activated partial thromboplastin time (doubling APTT) of DHG-I, FGAG, LMWH and UFH were 12.0, 2.4, 5.8, and 1.2 μg/ml, respectively. In antithrombin III (AT Ill)-depleted plasma, doubling APTT of DHG-1, FGAG, and UFH were 11.3, 2.1, and 18.5 μg/ml, respectively. Prothrombin activation in contact-activated plasma was inhibited completely for 60 s at doubling APTT by all glycosaminoglycans used in this study. DHG-I, however, showed much less antithrombin activity than UFH as tested by thrombin clotting time in plasma and chromogenic assay in the presence of AT III. Moreover, DHG-1 showed much less inhibitory activity on factor Xa, factor IXa, and glass surface-induced factor IXa generation than UFH

These results suggested that DHG-1 is one of the promising antithrombotic agents with quite different anticoagulant property from UFH or LMWH.
Antithrombotic Activity of a Novel C-Terminal Hirudin Analog in Experimental Animals
Authors: Broersma R J , Kutcher L W , Heminger E F , Krstenansky J L , Marshall F N
Published: July 2018

A synthetic hirudinsgs55-65 C-terminal fragment analog was evaluated for anticoagulant activity and in models of experimental thrombosis in mice and rats. Intravenous injection caused doserelated inhibition of thrombin and anticoagulation in rat blood samples, protection from thromboembolism in mice and inhibition of stasis-induced venous thrombosis in rats. Antithrombotic effectiveness corresponded with anticoagulant activity. Anephric animals exhibited longer duration of activity than normal animals suggesting the kidney as a major route of elimination.
Plasminogen Activation In Vivo upon Intravenous Infusion of DDAVP
Authors: Levi Marcel , Boer Jan Paul de , Roem Dorina , Cate Jan Wouter ten , Hack C Erik
Published: July 2018

Infusion of desamino-d-arginine vasopressin (DDAVP) results in an increase in plasma plasminogen activator activity. Whether this increase results in the generation of plasmin in vivo has never been established.

A novel sensitive radioimmunoassay (RIA) for the measurement of the complex between plasmin and its main inhibitor α2 antiplasmin (PAP complex) was developed using monoclonal antibodies preferentially reacting with complexed and inactivated α2-antiplasmin and monoclonal antibodies against plasmin. The assay was validated in healthy volunteers and in patients with an activated fibrinolytic system.

Infusion of DDAVP in a randomized placebo controlled crossover study resulted in all volunteers in a 6.6-fold increase in PAP complex, which was maximal between 15 and 30 min after the start of the infusion. Hereafter, plasma levels of PAP complex decreased with an apparent half-life of disappearance of about 120 min. Infusion of DDAVP did not induce generation of thrombin, as measured by plasma levels of prothrombin fragment F1+2 and thrombin-antithrombin III (TAT) complex.

We conclude that the increase in plasminogen activator activity upon the infusion of DDAVP results in the in vivo generation of plasmin, in the absence of coagulation activation. Studying the DDAVP induced increase in PAP complex of patients with thromboembolic disease and a defective plasminogen activator response upon DDAVP may provide more insight into the role of the fibrinolytic system in the pathogenesis of thrombosis.
Type I Congenital Plasminogen Deficiency Is not a Risk Factor for Thrombosis
Authors: Shigekiyo T , Uno Y , Tomonari A , Satoh K , Hondo H , Ueda S , Saito S
Published: July 2018

The risk of thrombosis in type I congenital plasminogen (PLG) deficiency has been suggested, but is still not confirmed. We studied 40 members of two unrelated families with this disease, and found that 21 were heterozygotes of type I congenital PLG deficiency. Three of them had thrombosis, but the other 18 had no thrombosis. The percentages of family members with no history of thrombosis up to a given age among subjects with type I congenital PLG deficiency and healthy controls were analyzed by the Kaplan-Meier method. No significant difference between the two groups was observed by the generalized Wilcoxon test (p = 0.23). These results suggest that there is no significant correlation between type I congenital PLG deficiency and thrombosis.
Extracorporeal Model for Study of Factors Affecting Thrombus Formation
Authors: Benis Anthony M , Nossel Hymie L , Aledort Louis M , Koffsky Robert M , Stevenson James F , Leonard Edward F , Shiang Howard , Litwak Robert S
Published: July 2018

Factors determining thrombus formation on a foreign surface were studied with the use of plastic flow chambers introduced into extracorporeal shunts. Silicone rubber shunts, joining the carotid artery and jugular vein, were implanted in dogs and remained patent for several weeks. The flow chamber geometry consisted of a 4.8 mm diameter straight tube having a 3.2 × 3.2 mm circumferential cavity in the wall. Chambers were introduced sequentially into the shunts for exposure times of 10 to 30 minutes and regulated blood flow rates of 100 to 400 ml/min. The dry weight of thrombus accumulated in the chamber (5 to 50 mg) was found to increase with exposure time up to 20 minutes and to decrease with increasing flow rate. Various components of the process of thrombus formation were altered by the administration of acetylsalicylic acid, heparin and lysozyme, used alone and in pairs. Heparin was found to be the most effective antithrombotic agent, dry weights of accumulated thrombus being on the order of 50 percent lower when compared to control values. The efficacy of heparin was found to be unaffected by the presence of aspirin and lysozyme, which themselves were not effective antithrombotic agents under the conditions of these experiments. The technique described here may provide a useful animal model for studying the influence of blood flow and different biomaterials on thrombus formation.
The Effects of Infusion of Thrombin or Endotoxin in Rabbits Treated with Cortisone
Authors: Stafford Benjamin T , Rapaport Samuel I , Shen Stephen M.-C
Published: July 2018

Rabbits treated for 4 days with cortisone to prepare for the generalized Shwartzman reaction (GSR) were infused with thrombin or endotoxin. Whereas endotoxin induced the GSR, infusion of from 120-400 U/kg of thrombin over 1 to 2½ hr failed to induce the GSR. Mean values for fibrinogen consumption after thrombin or endotoxin, calculated from changes in plasma fibrinogen concentration and plasma 12 5I-fibrinogen radioactivity, were as follows: for rabbits infused with thrombin, from 43 to 61 mg/kg over a 3 hr period; for rabbits infused with endotoxin, 58.5 mg/kg over a 6 hr period. A small peak of non-clottable protein radioactivity, indicative of secondary fibrinolysis, was found in animals infused with thrombin but not in animals infused with endotoxin. A striking late rise in plasma fibrinogen levels was noted in animals infused with endotoxin. It was not noted in animals infused with thrombin. This observation provides further evidence that endotoxin stimulates fibrinogen synthesis by mechanisms independent of intravascular clotting or fibrinolysis. The failure to produce the GSR with thrombin in cortisone-treated rabbits leads us to conclude that depression of reticuloendothelial cell clearance of fibrin can not account for the preparatory effect of cortisone for the GSR after endotoxin.
Collagen-Induced Platelet Aggregation: The Role of Adenine Nucleotides and the Release Reaction
Authors: Kattlove Herman , Gomez M. Hugo
Published: July 2018

Collagen-induced platelet aggregation is associated with the release of ADP and the catabolism of radioactive ATP. These studies demonstrate that the amount of human platelet ADP released and ATP catabolized increase with time of stirring of the collagen-platelet rich plasma (PRP) mixture and with increasing amounts of collagen. These changes in adenine nucleotides occurred simultaneously with the aggregation. No early changes preceding aggregation were noted. Stirring the collagen-PRP mixture maximized ADP release and ATP catabolism; some ADP release and ATP catabolism occurred with minimal agitation. Incubation of PRP with metabolic poisons (2-deoxyglucose with either KCN or oligomycin), which lowered platelet ATP content, also reduced collagen-induced release of ADP and aggregation. However, platelet adhesion to collagen was unaffected by metabolic poisons. These data suggest that collagen directly stimulates ADP release. The demonstration of release in EDTA–PRP further suggests that platelet aggregation is not required for collagen-induced ADP release.
Decision-Making Factors for Ulnar Nerve Transposition in Cubital Tunnel Surgery
Authors: DeGeorge Brent , Kakar Sanjeev
Published: July 2018

Background We designed a survey to ascertain the current perspectives of hand surgeons on the evaluation and management of ulnar nerve instability at the elbow. The secondary aim was to assess the concordance of hand surgeons on definitions of the terms “subluxated” and “dislocated” for classification of ulnar nerve instability.

Methods A questionnaire, including demographic practice variables, cubital tunnel practice patterns, preoperative imaging and electrodiagnostic evaluation, and a series of standardized intraoperative photographs of ulnar nerve instability at the elbow were developed and distributed to the current American Society for Surgery of the Hand (ASSH) membership.

Results A total of 690 (26.8%) members completed the survey; 84.2% of respondents indicated that they evaluate for ulnar nerve instability preoperatively with clinical examination, whereas only 6.1% indicated they routinely obtained dynamic ultrasound. Respondents indicated that the factors most strongly influencing their decision to proceed with anterior transposition of the ulnar nerve were subluxation on physical examination (89.6%), history consistent with ulnar nerve subluxation (85.8%), and muscle atrophy (43.2%). On review of clinical photographs, respondents demonstrated varying degrees of agreement on the terms “subluxated” or “dislocated” and recommendations for ulnar nerve transposition at intermediate degrees of ulnar nerve instability.

Conclusion ASSH members routinely evaluate for ulnar nerve instability with history and clinical examination without uniform use of preoperative ultrasound, and nearly half of the time the decision to transpose the ulnar nerve is made intraoperatively. Definitions for the degree of ulnar nerve instability at the elbow are not uniformly agreed upon, and further development of a classification system may be warranted to standardize treatment.
A computational method of productivity forecast of a multi-angle fractured horizontal well using the discrete fracture model
Authors: Zhang Jinlin , Mu Longxin , Jin Jianli , Li Xiangling
Published: July 2018

Multi-staged fracturing for horizontal wells is an important technique of stimulation in a naturally-fractured reservoir (NFR). Due to the complexity of the in-situ stress and the impact of natural fractures, there is usually a certain angle between the hydraulic fractures and the wellbore, which makes the production forecast of the fractured horizontal well very difficult. Based on the discrete fracture model (DFM), a computational method for the productivity of a multi-angle fractured horizontal well in NFR is established. The result of a practical case shows that the error between the computing results and the field data is less than 5% for considering the effect of the arbitrary of natural fractures and the angular of hydraulic fractures. A sensitivity analysis that was carried out indicates that the angle between the fracture and the wellbore has a significant impact on the horizontal well productivity. With the increase of fracture aperture, the productivity increases. Due to the interference that exists between fractures, the higher the fracture numbers there are does not mean the better productivity is.
Study of oxidation processes in Mo/Be multilayers
Authors: Nechay A. N. , Chkhalo N. I. , Drozdov M. N. , Garakhin S. A. , Pariev D. E. , Polkovnikov V. N. , Salashchenko N. N. , Svechnikov M. V. , Vainer Yu. A. , Meltchakov E. , Delmotte F.
Published: July 2018

The results of an investigation on oxidation processes in Mo/Be multilayer nanofilms are presented. The films annealed both in ambient atmosphere and in vacuum. The extreme ultraviolet (EUV) and X-ray reflectivity of the samples at 11.34 and at 0.154 nm respectively were measured before and after the treatment. No noticeable changes in film thicknesses and boundaries were observed during the annealing at temperatures up to 300°C. An oxidation mechanism of the nanofilms Mo/Be is established and the activation energy of the oxidation process is estimated to be 38 kJ/mol. To determine an absolute quantity of oxygen in the oxidized layers, a simple technique based on the EUV reflectivity data is proposed, and the range of its applicability is subsequently analysed.
Approximate controllability of the Jaynes-Cummings dynamics
Authors: Pinna Lorenzo , Panati Gianluca
Published: July 2018

We investigate the controllability of the Jaynes-Cummings dynamics in the resonant and nearly resonant regime. We analyze two different types of control operators acting on the bosonic part, corresponding—in the application to cavity Quantum Electro Dynamics—to an external electric and magnetic field, respectively. For these models, we prove approximate controllability for all values of the coupling constant g∈R, except those in a countable set S* which is explicitly characterized in the statement. The proof relies on a spectral analysis which yields the non-resonance of the spectrum for every g∈R\S*.
Inverting the thermal radiative contrast of vanadium dioxide by metasurfaces based on localized gap-plasmons
Authors: Ito Kota , Watari Toshio , Nishikawa Kazutaka , Yoshimoto Hiroshi , Iizuka Hideo
Published: July 2018

Vanadium dioxide (VO2) is a promising phase-change material (PCM) in controlling radiative heat transfer because of the large permittivity contrast between the phases and the moderate metal-insulator transition temperature of 340 K. Widely adopted bare VO2 films on a dielectric substrate permit more radiative heat in the insulating state compared to that in the metallic state. In this paper, we present PCM-insulator-metal metasurfaces that invert the thermal radiative contrast, which means that the radiative heat flux is more promoted in the metallic state. The metasurfaces exhibit similar but broader resonance compared to conventional metal-insulator-metal metamaterials based on localized gap-plasmons when VO2 is in the metallic state. The broad resonance facilitates to maximize the radiative thermal exchange and is explained by the damping of the gap-plasmon mode dominated by the optical loss of VO2. The measured electromagnetic response of the fabricated metasurfaces agrees well with numerical simulations, and it also demonstrates that the resonant wavelength is tuned by the temperature. High emission or absorption contrast at a specific temperature is numerically obtained by geometrical optimization albeit lossy amorphous silicon or alumina is employed as the insulating layer to satisfy the fabrication requirement. We believe that the presented metasurface design contributes to intelligent thermal management systems with flexibility.
GaAs/GaNAs core-multishell nanowires with nitrogen composition exceeding 2%
Authors: Yukimune M. , Fujiwara R. , Ikeda H. , Yano K. , Takada K. , Jansson M. , Chen W. M. , Buyanova I. A. , Ishikawa F.
Published: July 2018

We report the growth of GaAs/GaNAs/GaAs core-multishell nanowires having N compositions exceeding 2%. The structures were grown by plasma-assisted molecular beam epitaxy using constituent Ga-induced vapor-liquid-solid growth on Si(111) substrates. The GaNAs shell nominally contains 0%, 2%, and 3% nitrogen. The axial cross-sectional scanning transmission electron microscopy measurements confirm the existence of core-multishell structure. The room temperature micro-photoluminescence measurements reveal a red-shift of the detected emission with increasing N content in the nanowires, consistent with the expected changes in the GaNAs bandgap energy due to the bowing effect.
Deep and fast free-space electro-absorption modulation in a mobility-independent graphene-loaded Bragg resonator
Authors: Doukas Spyros , Chatzilari Alma , Dagkli Alva , Papagiannopoulos Andreas , Lidorikis Elefterios
Published: July 2018

Deep and fast electro-optic modulation is critical for high-speed near infrared signal processing. We combine the electro-absorption tunability of graphene with the high-Q resonance of a Bragg-based Fabry-Perot resonator at λ = 1550 nm and show that ∼100% free-space signal modulation at small insertion loss and GHz speed can always be achieved independently of graphene quality (mobility), provided that the device operates in the reflection mode and is tuned in critical coupling with graphene. Remarkably, the critical coupling mechanism produces a higher extinction ratio for lower graphene mobility. We use practical considerations to optimize the device architecture and operation as a function of graphene mobility. With a small modification, this scheme can be turned into a very sensitive acousto-absorption modulator with an extinction ratio of ∼30 dB/Å or an index sensor with a sensitivity of 107%/RIU. These designs can be extended throughout the IR spectrum by appropriate material selection and scaling of layer dimensions.
Improving accuracy of nanothermal measurements via spatially distributed scanning thermal microscope probes
Authors: Spiece J. , Evangeli C. , Lulla K. , Robson A. , Robinson B. , Kolosov O.
Published: July 2018

Advances in material design and device miniaturization lead to physical properties that may significantly differ from the bulk ones. In particular, thermal transport is strongly affected when the device dimensions approach the mean free path of heat carriers. Scanning Thermal Microscopy (SThM) is arguably the best approach for probing nanoscale thermal properties with few tens of nm lateral resolution. Typical SThM probes based on microfabricated Pd resistive probes (PdRP) using a spatially distributed heater and a nanoscale tip in contact with the sample provide high sensitivity and operation in ambient, vacuum, and liquid environments. Although some aspects of the response of this sensor have been studied, both for static and dynamic measurements, here we build an analytical model of the PdRP sensor taking into account finite dimensions of the heater that improves the precision and stability of the quantitative measurements. In particular, we analyse the probe response for heat flowing through a tip to the sample and due to probe self-heating and theoretically and experimentally demonstrate that they can differ by more than 50%, hence introducing significant correction in the SThM measurements. Furthermore, we analyzed the effect of environmental parameters such as sample and microscope stage temperatures and laser illumination, which allowed reducing the experimental scatter by a factor of 10. Finally, varying these parameters, we measured absolute values of heat resistances and compared these to the model for both ambient and vacuum SThM operations, providing a comprehensive pathway improving the precision of the nanothermal measurements in SThM.
Control of misfit strain in ferroelectric BaTiO3 thin-film capacitors with SrRuO3-based electrodes on (Ba, Sr)TiO3-buffered SrTiO3 substrates
Authors: Noguchi Yuji , Maki Hisashi , Kitanaka Yuuki , Matsuo Hiroki , Miyayama Masaru
Published: July 2018

We investigate ferroelectric BaTiO3 capacitors with SrRuO3-based electrodes employing a (BaxSr1−x)TiO3 (BST) buffer layer on (100) SrTiO3 substrates prepared by pulsed laser deposition. Structural analysis by high-resolution X-ray diffraction reciprocal space mapping shows that the BST (x = 0.5 and 0.7) layers are relaxed and have their bulk in-plane lattices in the upper part owing to strain relief. The bottom electrodes on the buffer layers grow heteroepitaxially but cannot withstand a tensile stress and then show a diminution of the in-plane lattice. On the BST (x = 0.7) layer, compared with the capacitor with an SrRuO3 electrode, that with a Ba0.1Sr0.9RuO3 one has a reduced in-plane lattice relaxation of the BaTiO3 film and then exhibits a larger remanent polarization (Pr) of 34 μC/cm2 associated with a smaller shift of the hysteresis loop. The polarization hysteresis shift is attributed to a flexoelectric effect stemming from the coupling between out-of-plane polarization and a strain gradient in the BaTiO3 film. We conclude that a reduced misfit strain relaxation in the ferroelectric film achieved with the Ba0.1Sr0.9RuO3 electrode on the thicker BST (x = 0.7) buffer layer is the origin of an enhanced Pr with a smaller hysteresis shift.
Oxygen aging time: A dominant step for spiro-OMeTAD in perovskite solar cells
Authors: Liu Guilin , Xi Xi , Chen Rulong , Chen Liping , Chen Guoqing
Published: July 2018

Perovskite solar cells (PSCs) are emerging as a new type of energy device which have drawn tremendous attention in the scientific community. However, details of the fabrication process, such as about the aging time of the hole transport layer, are worth clarified. Commonly, PSCs were sealed in oxygen conditions over 24 h, but further long-time-aging lacks a deep study. In this article, PSCs were sealed in oxygen from 0 h to 120 h. We have found that trapping centers and accumulated charges in perovskite crystals increased after 48-h aging treatment, leading to an increased recombination rate. As a result, the short circuit current density decreased from initially 20 mA/cm2 to lower than 10 mA/cm2, which was the main reason for the decrease in the power conversion efficiency. The current falling was further checked by the transient photocurrent technique. Although the current dropping was slightly related to differential capacitance, the accumulated charge in the bulk of cells strongly increased by 50% along with the aging time. Compared to 24-h-sealed PSCs, the lifetime of free carriers in both open circuit and short circuit conditions was significantly decreased after 48-h aging treatment, indicating that the decomposition occurred inside perovskite crystals.
Passivity-based fractional-order sliding-mode control design and implementation of grid-connected photovoltaic systems
Authors: Yang Bo , Yu Tao , Shu Hongchun , Zhu Dena , Sang Yiyan , Jiang Lin
Published: July 2018

In order to achieve the maximum power point tracking of photovoltaic (PV) systems in the presence of time-varying stochastic operation conditions and various uncertainties/disturbances, a passivity-based fractional-order sliding-mode control (PbFoSMC) scheme is proposed. The design can be classified into two steps, i.e., (a) construct a storage function in terms of the tracking error of DC-link voltage, DC-link current, and q-axis current for the PV system, upon which the actual characteristics of each term is thoroughly analyzed. Moreover, the beneficial terms are carefully retained to enhance the dynamical responses of the closed-loop system while the detrimental terms are fully removed to realize a global control consistency; (b) based on the passivized system, a fractional-order sliding-mode control (FoSMC) is incorporated as an additional input, which can considerably improve the control performance with the aim of rapid uncertainties/disturbances rejection. Four case studies, including the solar irradiance change, temperature variation, power grid voltage drop, and PV inverter parameter uncertainties, are undertaken to evaluate the effectiveness of PbFoSMC in comparison to that of proportional-integral-derivative control, passivity-based control, and sliding-mode control (SMC), respectively. At last, a dSpace based hardware-in-loop test is carried out to validate the implementation feasibility of PbFoSMC.
Surface morphology of GaN nucleation layer grown by MOCVD with different carrier gas
Authors: Su Xingliang , Ye Teng , Wang Shen , Shi Yujun , Fan Leilei , Liu Lei , Zhang Geng , Shi Xurong , Wei Min , Zhou Haitao , Jiao Hujun
Published: July 2018

GaN nucleation layers were grown on sapphire substrate by metal organic chemical vapor deposition (MOCVD) with different carrier gas. The morphology of nucleation layer which is crucial to GaN crystal quality was systematically studied using nitrogen and hydrogen as carrier gas. The GaN nucleation layer tends to form larger islands under H2 ambient, and forms higher density nucleation islands and thicker nucleation layer under N2 ambient.
Simultaneous measurement of exchangeable Al and other cations in acidic soils
Authors: Conyers Mark , Poile Graeme
Published: July 2018

It is both time consuming and costly to undertake two extractions of acidic soils when there is a need to measure exchangeable Al along with the other cations. There is some evidence that, although 1 M KCl is the standard procedure for exchangeable Al, the extraction of soil with 0.1 M BaCl2 + 0.1 M NH4Cl gives similar values. It would then be possible to measure all cations from one extraction. There is also concern that the assumption of trivalence of Al does not hold true in all situations, as commonly held to be true in the literature of the 1950s to the 1970s. Two experiments were conducted: the first a simple comparison of three extraction procedures in common use in New South Wales and the second a repeated comparison of two extractions but with more detailed measurements to enable interpretation of the results. During the second experiment we also measured the charge on the extracted Al by titration. The three methods for extraction of Al gave similar results despite very different procedures with respect to physical mixing, soil–solution contact time and strength of electrolyte, indicating that the pool of exchangeable Al was operationally well defined. The average charge on KCl-extracted Al was within error of 3 moles per mole of Al, supporting the current trivalent model of Alex. The 0.1 M BaCl2 + 0.1 M NH4Cl procedure estimated Alex successfully on acid soils of low effective cation exchange capacity (ECEC) (<10 cmolc/kg) and so can be used for extraction of all cations. However, as ECEC increased the 0.1 M BaCl2 + 0.1 M NH4Cl extraction tended to underestimate Alex compared with KCl on soils with above ~1.5 to 2 cmolc/kg of Alex.
Chromatin organization by an interplay of loop extrusion and compartmental segregation
Authors: Nuebler Johannes , Fudenberg Geoffrey , Imakaev Maxim , Abdennur Nezar , Mirny Leonid A.
Published: July 2018

Significance

Human DNA is 2 m long and is folded into a 10-μm-sized cellular nucleus. Experiments have revealed two major features of genome organization: Segregation of alternating active and inactive regions into compartments, and formation of compacted local domains. These were hypothesized to be formed by different mechanisms: Compartments can be formed by microphase separation and domains by active, motor-driven, loop extrusion. Here, we integrate these mechanisms into a polymer model and show that their interplay coherently explains diverse experimental data for wild-type and mutant cells. Our results provide a framework for the interpretation of chromosome organization in cellular phenotypes and highlight that chromatin is a complex, active matter shaped by an interplay of phase segregation and loop extrusion.
Human impact on the diversity and virulence of the ubiquitous zoonotic parasite
Toxoplasma gondii
Authors: Shwab E. Keats , Saraf Pooja , Zhu Xing-Quan , Zhou Dong-Hui , McFerrin Brent M. , Ajzenberg Daniel , Schares Gereon , Hammond-Aryee Kenneth , van Helden Paul , Higgins Steven A. , Gerhold Richard W. , Rosenthal Benjamin M. , Zhao Xiaopeng , Dubey Jitender P. , Su Chunlei
Published: July 2018

Significance

A majority of emerging infectious diseases in humans are transmitted from animals. It is generally agreed that our behavior can influence our exposure to such pathogens, but little is known regarding our role in shaping evolution in such pathogens. Such understanding would aid in their control, to the benefit of public health. Our results indicate that expansion of agriculture influenced not only the biogeography but also the virulence of
Toxoplasma gondii
. By linking landscape ecology to parasite virulence, our framework contributes a fundamentally unique perspective on the ecology and evolution of infectious disease.
Zyxin promotes colon cancer tumorigenesis in a mitotic phosphorylation-dependent manner and through CDK8-mediated YAP activation
Authors: Zhou Jiuli , Zeng Yongji , Cui Lian , Chen Xingcheng , Stauffer Seth , Wang Zhan , Yu Fang , Lele Subodh M. , Talmon Geoffrey A. , Black Adrian R. , Chen Yuanhong , Dong Jixin
Published: July 2018

Significance

Zyxin is a member of the cell–cell adhesion complex and controls cell cytoskeleton and motility. Analysis from clinical samples revealed that Zyxin is highly expressed in colon cancer compared with normal tissue, suggesting an oncogenic role for Zyxin in cancer. Depletion of Zyxin resulted in significantly impaired colon cancer cell proliferation, migration, cellular transformation, and tumor formation in xenograft animal models. We also showed that Zyxin is phosphorylated by CDK1 during mitosis. Mitotic phosphorylation is required for Zyxin activity in promoting colon cancer growth. Zyxin regulates YAP activity through the colon cancer oncogene CDK8. We further showed that CDK8 directly phosphorylates YAP and promotes its activation. These observations identify the Zyxin–CDK8–YAP axis as a potential therapeutic target in cancer.
Folding artificial mucosa with cell-laden hydrogels guided by mechanics models
Authors: Chan Hon Fai , Zhao Ruike , Parada German A. , Meng Hu , Leong Kam W. , Griffith Linda G. , Zhao Xuanhe
Published: July 2018

Significance

While mucosal folding is a ubiquitous phenomenon observed in many hollow or tubular human tissues/organs, recapitulating the process for tissue engineering has yet to be achieved. Here we fold a cell-laden hydrogel film to recapitulate the folding of a physiologically mimicking artificial mucosa. We attach the cell-laden hydrogel film onto a prestretched tough-hydrogel substrate, which after relaxation induces controlled patterns in the artificial mucosa. A combination of theory and numerical simulations predicts the folding conditions and the morphologies, thereby guiding the design of surface folding. This simple strategy can facilitate the understanding and engineering of mucosa for tissues/organs such as stomach, colon, and intestine. The work also demonstrates a paradigm in tissue engineering via harnessing mechanical instabilities guided by quantitative mechanics models.
Induction of oligoclonal CD8 T cell responses against pulmonary metastatic cancer by a phospholipid-conjugated TLR7 agonist
Authors: Hosoya Tadashi , Sato-Kaneko Fumi , Ahmadi Alast , Yao Shiyin , Lao Fitzgerald , Kitaura Kazutaka , Matsutani Takaji , Carson Dennis A. , Hayashi Tomoko
Published: July 2018

Significance

A major goal of cancer immunotherapy is the expansion and/or reactivation of cytotoxic CD8
+
T cell responses against malignant cells. We previously showed that the direct injection of toll-like receptor 7 (TLR7) agonists into primary tumors can induce tumor-specific oligoclonal T cell responses whose magnitude correlates with therapeutic efficacy. However, tumors are not always accessible to local therapy. Here, we demonstrate in murine lung metastasis models that single systemic administration of a phospholipid conjugated TLR7 agonist can also expand tumor-specific cytotoxic T cells that are shared by different animals. The expansion can be achieved without causing apparent toxicity. Similar technology combining immune repertoire analysis and immunomodulatory drugs can help to guide the development of optimal immunotherapeutic regimens in cancer patients.
Effects of SiO2 particle size on the corrosion resistance of fluoropolymer/SiO2 composite coatings
Authors: Lu J. P. , Chen L. , Song R. G.
Published: July 2018

The surfaces of SiO2 ultra-fine particles with different sizes have been modified by γ-(2, 3-epoxypropoxy)propytrimethoxysilane (KH-560) silane coupling agent. Then the homogeneous fluoropolymer/SiO2 composite coatings have been successfully prepared on mild steel substrates. The surface grafting of KH-560 on SiO2 particles was detected by means of Fourier transform infrared spectroscopy, thermo gravimetric analysis and transmission electron microscopy. The surface morphologies and corrosion resistance of fluoropolymer/SiO2 composite coatings were characterised by field emission scanning electron microscopy, potentiodynamic polarisation as well as electrochemical impedance. The results showed that KH-560-modified SiO2 particles can decrease agglomeration effectively, and the particles play a beneficial role in improving the corrosion resistance of the coated steel significantly. There exists an obvious effect of SiO2 particles size on the corrosion resistance of fluoropolymer/SiO2 composite coatings. Also, the SiO2 particles with diameter of 150 nm are of the best effect among all particle sizes.
Shedding of CD16 disassembles the NK cell immune synapse and boosts serial engagement of target cells
Authors: Srpan Katja , Ambrose Ashley , Karampatzakis Alexandros , Saeed Mezida , Cartwright Adam N.R. , Guldevall Karolin , De Matos Gabriela Dos Santos Cruz , Önfelt Björn , Davis Daniel M.
Published: July 2018

Natural Killer (NK) cells can engage multiple virally infected or tumor cells sequentially and deliver perforin for cytolytic killing of these targets. Using microscopy to visualize degranulation from individual NK cells, we found that repeated activation via the Fc receptor CD16 decreased the amount of perforin secreted. However, perforin secretion was restored upon subsequent activation via a different activating receptor, NKG2D. Repeated stimulation via NKG2D also decreased perforin secretion, but this was not rescued by stimulation via CD16. These different outcomes of sequential stimulation could be accounted for by shedding of CD16 being triggered by cellular activation. The use of pharmacological inhibitors and NK cells transfected to express a noncleavable form of CD16 revealed that CD16 shedding also increased NK cell motility and facilitated detachment of NK cells from target cells. Disassembly of the immune synapse caused by CD16 shedding aided NK cell survival and boosted serial engagement of target cells. Thus, counterintuitively, shedding of CD16 may positively impact immune responses.
Mangrove Mapping Using SPOT 6 at East Lombok Indonesia
Authors: Rudiastuti Aninda W , Yuwono Doddy M , Hartini Sri
Published: July 2018

Accumulated biomass estimation in mangrove forest is important for assessing its productivity and sustainability. It is also important on revealing the potential amount of carbon that can be emitted in the form of carbon dioxide when deforestation took place. Mangrove as a part of the coastal ecosystem is related to Blue Carbon, especially in controlling climate change. This is due to its ability in utilizing carbon dioxide for photosynthesis and store it in stock biomass and sediment. This study addressed to estimate the mangrove extent at East Lombok as a part of One Map Mangrove Bali – Nusa Tenggara, and also trying to estimate its above ground biomass (AGB). Those are indispensable, especially for eastern part of Lombok which has the greatest mangroves area and mostly in good condition such as Gili Lawang and Gili Sulat. Forest biomass can be estimated through combination of field measurement and remote sensing - GIS methods. SPOT 6 and another high resolution-imagery were used as primary remotely sensed data. On screen digitation using RGB-NIR bands and Normalized Difference Vegetation Index (NDVI) image transformation are applied for the initial canopy density classification. For field measurement at 2016, plot sample sized 10 m x 10 m were used for mangrove parameter inventory. Non-destructive biomass estimation applied in this research which is applicable for mangrove ecosystems, using allometric equations. AGB estimation model also applied in mangrove area at two small islands. Bruguiera sp. and Rhizopora sp. dominated in East Lombok. While, Sonneratia sp., and Avicennia sp dominantly appeared in seaward zone of mangrove zonation. The spatial analysis resulted mangrove area in East Lombok is 1759.5778 ha. The estimation results of above ground biomass (trees and saplings) using 12 sample plots in East Lombok is 12,667.316 kg, while there are 881,677 kg of AGB of mangrove in Gili Lawang and Gili Sulat based on the AGBs model applied.
Modeling Deforestation and Green Houses Gas Emissions in Morowali Utara District, Central Sulawesi Province, Indonesia
Authors: Nahib Irmadi , Suwarno Yatin
Published: July 2018

Land use cover conversion from forest to another land was constributing for total green houses gas (GHS) emission, especially from forestry sector. The Central Sulawesi Province has forest area about 4.258 million ha. The deforestation in Central Sulawesi Province for period 2000-2009 reached 432,111.50 Ha (10.15 %). Morowali Utara District is one of district in Central Sulawesi Province, which contribution 15,20 % total deforestation in Central Sulawesi province. This study aims to calculate the rate of deforestation and simulation carbon emission in Morowali Utara District by using REDD+ model. The main data used in this study are land use or cover map (2003, 2009 and 2015), driver variable (distance from : forest edge, roads, streams, and slope) as the explanatory variables of deforestation. The results show that the deforestation on the period 2003-2015 reached 62,017.47 (9,19 %) or the rate of deforestation 5,168.12 ha year−1. Logistic regression model for prediction of deforestation is Y1 = −2.2649 + 0.001126 X1 − 0.000152 X2 − 0.000225 X3 + 0.010704 X4 (ROC = 0,7408), meanwhile the amount of carbon that the REDD project will protect given a departure from the business as usual deforestation scenario up to 18.868 million tCO2e.
Differential coexpression in human tissues and the confounding effect of mean expression levels
Authors: Farahbod Marjan , Pavlidis Paul
Published: July 2018

Motivation

Differential coexpression—the alteration of gene coexpression patterns observed in different biological conditions—has been proposed to be a mechanism for revealing rewiring of transcription regulatory networks. Despite wide use of methods for differential coexpression analysis, the phenomenon has not been well-studied. In particular, in many applications, differential coexpression is confounded with differential expression, that is, changes in average levels of expression across conditions. This confounding, despite affecting the interpretation of the differential coexpression, has rarely been studied.

Results

We constructed high-quality coexpression networks for five human tissues and identified coexpression links (gene pairs) that were specific to each tissue. Between 3 and 32% of coexpression links were tissue-specific (differentially coexpressed) and this specificity is reproducible in an external dataset. However, we show that up to 75% of the observed differential coexpression is substantially explained by average expression levels of the genes. ‘Pure’ differential coexpression independent from differential expression is a minority and is less reproducible in external datasets. We also investigated the functional relevance of pure differential coexpression. Our conclusion is that to a large extent, differential coexpression is more parsimoniously explained by changes in average expression levels and pure links have little impact on network-based functional analysis.

Supplementary information

Supplementary data are available at Bioinformatics online.
The indirect influence of quasars on reionization
Authors: Seiler Jacob , Hutter Anne , Sinha Manodeep , Croton Darren
Published: July 2018

The exact role of quasars during the Epoch of Reionization remains uncertain. With consensus leaning towards quasars producing a negligible amount of ionizing photons, we pose an alternate question: Can quasars indirectly contribute to reionization by allowing ionizing photons from stars to escape more easily? Using the semi-analytic galaxy evolution model to evolve a galaxy population through cosmic time, we construct an idealized scenario in which the escape fraction of stellar ionizing photons (fesc) is boosted following quasar wind events, potentially for several dynamical times. We find that under this scenario, the mean value of fesc as a function of galaxy stellar mass peaks for intermediate mass galaxies. This mass dependence will have consequences for the 21-cm power spectrum, enhancing power at small scales and suppressing it at large scales. This hints that whilst quasars may not directly contribute to the ionizing photon budget, they could influence reionization indirectly by altering the topology of ionized regions.
Characteristics of Adult Cigarette Smokers Who “Relight” and the Effects of Exposure to Tobacco Smoke Constituents
Authors: Allen Sophia I , Wasserman Emily , Veldheer Susan , Yingst Jessica , Hrabovsky Shari , Liao Jason , Krebs Nicolle M , Horn Kimberly , Reinhart Lisa , Modesto Jennifer , Putt Kayla , Evins A Eden , Muscat Joshua E , Richie John P , Foulds Jonathan
Published: July 2018

Introduction

About half of smokers relight their cigarette, a habit that is a risk factor for chronic bronchitis and possibly lung cancer. Little is known about the characteristics of smokers who relight and their dependence on nicotine. It is unknown whether relighting affects exposure to tobacco smoke constituents. This study examined the characteristics of relighters of usual brand cigarettes and whether relighting affects exposure to selected tobacco smoke constituents.

Methods

We explored relighting status and frequency, using baseline data from 248 adult smokers participating in studies of reduced nicotine cigarettes in relation to demographic and cigarette characteristics, smoking behaviors, nicotine dependence, biomarkers of exposure (exhaled carbon monoxide, blood cotinine), and biomarkers of oxidative stress (ratio of oxidized/reduced glutathione).

Results

69.4% (n = 172) of subjects reported relighting, and they relit an average of five cigarettes out of 20. Both relighters and non-relighters smoked a mean of 20 cigarettes per day (p = .6). Relighting was significantly associated with higher nicotine dependence, use of longer rod cigarettes, older age, lower income, and unemployment. There were no significant associations between relighting and blood cotinine, exhaled carbon monoxide or measures of oxidized/reduced blood glutathione.

Conclusions

The majority of subjects were relighters, who had higher levels of nicotine dependence than non-relighters. Relighters had similar levels of plasma cotinine and exhaled carbon monoxide to non-relighters.

Implications

No study has compared the cigarette characteristics and biomarkers of exposure of adult cigarette smokers who relight with those who do not. Relighting behavior was common in our sample and was associated with low income, not currently working, higher nicotine dependence, cigarette rod length, daily cigarette use years, and a lifetime history of depressed mood.
Management After Percutaneous Cholecystostomy: What Should We do With the Catheter?
Authors: Charrier Thibaut , Kepenekian Vahan , Muller Arnaud , Valette Pierre-Jean , Glehen Olivier , Cotte Eddy , Passot Guillaume
Published: July 2018

Background:

Percutaneous cholecystostomy (PC) is an alternative to cholecystectomy for acute calculous cholecystitis (ACC) in patients with high mortality risk, but the catheters’ and patients’ management remains unclear. This study aimed to determine outcomes after PC and to define surgical strategy.

Methods:

All patients who underwent PC between 2009 and 2014 for ACC in a single institution were reviewed for outcomes and postdrainage management.

Results:

Forty-one patients underwent PC with a median age of 77 years. Twenty patients (45%) presented American Society of Anesthesiologists (ASA) score 3-4, and all had cholecystitis grade II or III. The 6-month mortality was 17% (7/41 patients). Twelve patients (29%) presented PC-related complications. Catheters were removed, clamped, left open, and dislodged for 17, 9, 5, and 5 patients, respectively. Three patients died after PC, and data were missing for 2 patients. Twenty-five (61%) patients underwent cholecystectomy after PC, and were significantly younger (median age, 70 vs. 83; P<0.010), and presented with higher ASA score (ASA: 3-4, 36% vs. 68%; P=0.041) and more grade III cholecystitis (16% vs. 44%; P=0.050). Among 16 patients who did not undergo cholecystectomy, none presented recurrent gallstone disease (median survival, 7 mo; range, 0 to 55).

Conclusions:

The risk of complications associated with the catheter is high. To prevent morbidity related to PC, we suggest removing the catheter when ACC is controlled.