bluuebunny/crossref_metadata_2025 huggingface dataset:
Exposure of Human Platelets to Plasmin Results in the Expression of Irreversibly Active Fibrinogen Receptors
Authors: Rabhi-Sabile Samia , Pidard Dominique
Published: July 2018

Although plasmin can trigger strong platelet responses such as shape change and exocytosis of internal granules, limited platelet aggregation is induced by this proteinase, owing to its capacity to rapidly proteolyse secreted adhesive proteins. In this context, we have investigated the state of activation of the fibrinogen receptor, the integrin αIIbβ3, on platelets exposed to plasmin. Following incubation with plasmin at 37 °C, washing, and resuspension, platelets exhibit a moderate, low-velocity aggregation when stirred in the presence of fibrinogen. Optimum aggregability is observed when platelets have been exposed to plasmin activity of ≈0.5 CU/ml for 20 min, and aggregation is insensitive to the presence of antagonists such as prostaglandin (PG) E1 and apyrase. Plasmin-induced platelet aggregability is associated with the expression of active fibrinogen receptors on the cell surface, which, using a l25I-fibrinogen binding assay, can be quantified to ≈2,300 molecules per platelet. Exposure of active αIIbβ3 receptors appears to depend partially, but not totally on a metabolic activation and granule exocytosis at the time of incubation with plasmin. In contrast with a-thrombin, plasmin-induced activation of αIIbβ3 is sustained and cannot be reversed by exposure of platelets to PGE1. Immunoblotting analysis of the receptor subunits shows no extensive proteolytic modification of αIIbβ3 by plasmin, and only reveals a limited proteolysis of the aminoterminal domain of the αIIb subunit. In addition to their capacity to aggregate in the presence of fibrinogen alone, plasmin-treated platelets also show a potentiated aggregability in response to low doses of ADP. Thus, plasmin has the potential to activate the platelet fibrinogen receptor in such a way that it remains irreversibly available to fibrinogen on the surface of nonaggregated cells, a feature that may participate to pathological states of in vivo platelet hyperaggregability.
Augmentation of Vascular Endothelial Barrier Function by Heparin and Low Molecular Weight Heparin
Authors: Bannon P G , Kim Mi-Jurng , Dean R T , Dawes J
Published: July 2018

Glycosaminoglycans (GAGs) are an important component of endothelial barrier function. Early passage human umbilical vein endothelial cells were grown to confluence on transparent micropore filters and barrier function assessed as transendothelial electrical resistance (TEER) and permeability to albumin and sucrose. Unfractionated heparin and the LMW heparin Clexane decreased endothelial permeability to both sucrose and albumin and increased TEER. Chondroitin 6-sulphate also augmented barrier function, but other GAGs had no effect. Interleukin-1 increased permeability to albumin and sucrose and decreased TEER. Although heparin attenuated the effect of IL-1 on TEER and sucrose permeability, it could not restore the barrier to albumin transfer. Denuded endothelial matrix presented a negligible barrier, which was not enhanced by heparin. When sulphation of endogenous GAGs was inhibited by chlorate, barrier function was compromised and was not restored by exogenous heparin. Thus heparin enhances the barrier function of resting endothelium, but cannot completely overcome the increased permeability resulting from exposure to IL-1 or substitute for endogenous GAGs.
Identification of Eight Point Mutations in Protein S Deficiency Type I – Analysis of 15 Pedigrees
Authors: Reitsma P H , Gómez E , Poort S R , Bertina R M
Published: July 2018

We describe molecular genetic studies of 15 patients with protein S deficiency type I (i. e. reduced total protein S antigen). All the exons of the PROS 1 gene were analyzed both by PCR and direct sequencing in all 15 probands. This analysis led to the identification of point mutations affecting eight individuals. One of these mutations (codon -25, insertion of T) has been described previously in a Dutch pedigree. The other mutations are novel and all are located in exons that code for the protein S domain that is homologous to the steroid hormone binding globulins. They include two amino acid replacements (one individual with 340 Gly → Val, and two individuals with 467 → Val Gly), and four frameshift mutations due to either one bp deletions (in codon 261 deletion of T and in codon 267 deletion of G) or insertions (in codon 565 insertion T and after codon 578 insertion of C). Studies performed in six families (totalling 43 subjects) showed cosegregation of the genetic abnormality with reduced plasma protein S levels, and provided genetic evidence for a heterozygous protein S deficiency in 25 of them. The yield of mutations in this study (53%) confirms that the percentage of protein S deficient cases in which a point mutation is found remains low.
Detection of Ten New Mutations by Screening the Gene Encoding Factor IX of Danish Hemophilia B Patients
Authors: Schwartz Marianne , Ingerslev Jørgen , Scheibel Elma , Nielsen Lise Rud
Published: July 2018

Hemophilia B is caused by a wide range of mutations. In order to characterize the mutations among patients in Denmark, we have systematically screened the entire coding region, the promoter region and exon flanking sequences of the gene encoding factor IX using single strand conformation and heteroduplex analyses. Patients from 32 different families were examined, and point mutations (23 different) were found in all of them. Ten of the mutations have not been reported by others; they include a splice site mutation, a single base pair deletion, and missense mutations. Notably, the study contains a female patient and a previously described Leyden mutation. In ten families with sporadic cases of hemophilia B, all 10 mothers were found to be carriers. The origin of two of these mutations was established.
Protection of Single-chain Urokinase-type Plasminogen Activator (scu-PA) in Aprotinin Treated Cardiac Surgical Patients Undergoing Cardiopulmonary Bypass
Authors: Spannagl M , Dooijewaard G , Dietrich W , Kluft C
Published: July 2018

Intraoperative high-dose aprotinin administration has been shown to reduce the intra-and postoperative blood loss in cardiac surgery. The haemostatic effect has been attributed to platelet preserving properties and to inhibition of contact activation reducing thrombotic and fibrinolytic activity during and after cardiopulmonary bypass (CPB).

Here we report on the effects of aprotinin on urokinase-type plasminogen activator, especially on the protection of the zymogen singlechain urokinase-type plasminogen activator (scu-PA). scu-PA occurs cell associated as well as free in the circulation (concentration 50 pM, half-life 5 min), and is potentially activated by kallikrein and plasmin, both potent targets for aprotinin. The generated active two-chain u-PA (tcu-PA) is a powerful activator of fibrinolysis.

Sixteen male patients undergoing myocardial revascularization were randomly assigned to aprotinin treatment (A) or control group (C).

Plasma concentration of total u-PA antigen and of the specific forms scu-PA(zymogen) and tcu-PA(active enzyme) were measured at different stages intraoperatively and two hours postoperatively. After an initial drop due to haemodilution at the onset of CPB, the concentrations of circulating u-PA forms restored intraoperatively in A, but remained subnormal in C until the end of the observation period. The concentration of total u-PA antigen of shed mediastinal blood was both in A and C two-fold higher than in the circulation, but the antigen was preserved as the zymogen scu-PA in A and largely converted to an inactive, non activatable form in C. Intra- and postoperative blood losses were less than half the amount in A as compared to C.

It is concluded that without aprotinin administration activation of circulatory scu-PA occurs, accompanied by stimulation of fibrinolysis and bleeding, finally resulting in elimination of tcu-PA complexed with endogenous inhibitors. Furthermore, cellular release of scu-PA occurs at or near the bleeding sites, as evidenced by the two-fold higher u-PA antigen concentration in the shed mediastinal blood. The released scu-PA is also activated and subsequently converted to an inactive form unless aprotinin is administered. High-dose aprotinin application during CPB effectively protects circulating and released scu-PA from activation and attenuates bleeding consequences.
Fine-needle Aspiration Cytology to Identify a Rare Mimicker of Breast Cancer: Plasma Cell Mastitis
Authors: Ortiz-Mendoza Carlos Manuel , Sánchez Norma Alicia Acosta , Dircio Arturo Catarino
Published: July 2018

There are rare benign diseases that can mimic malignant breast neoplasms in the clinical exam and in mammography. We evaluated the contribution of an accessible procedure to most clinicians, the fine-needle aspiration cytology, to identify a rare mimicker of malignant breast neoplasms. A type 2 diabetic 85-year-old female presented with a 6-month history of a left breast lump. The physical exam and mammography were compatible with breast cancer. Nevertheless, after fine-needle aspiration cytology, the diagnosis was plasma cell mastitis. Once this rare diagnosis was established, the tumor was extirpated, and the final histologic diagnosis corroborated chronic plasma cell mastitis. The patient's postoperative evolution was uneventful, and no other treatment was needed. Fine-needle aspiration cytology could be a valuable tool to identify rare mimickers of malignant breast neoplasms.
Temporomandibular Joint Ankylosis with Maxillary Extension: Proposal for Modification of Sawhney's Classification
Authors: Braimah Ramat Oyebunmi , Taiwo Abdurrazaq Olanrewaju , Ibikunle Adebayo Aremu , Oladejo Taoheed , Adeyemi Mike , Adejobi Adewale Francis , Abubakar Siddiq
Published: July 2018

Temporomandibular joint (TMJ) is a unique joint in which both jaws must open synchronously for function. Any pathology in one or both joints results in functional problems with associated poor quality of life. TMJ ankylosis (TMJA) is a joint pathology as a result of bony and/or fibrous adhesion of the joint apparatus, resulting in partial or total loss of function. This is a retrospective study from two tertiary referral centers in northwest region of Nigeria from 2012 to 2016. Data retrieved include gender, age, etiology of ankylosis, duration of ankylosis, laterality of ankylosis, type of imaging technique, type of airway management, types of incision, surgical procedure, interpositional materials used, and complications. Data were analyzed using SPSS for Window version 20.0 (IBM Corp.). Results were presented as simple frequencies and descriptive statistics. A total of 36 patients with TMJA were seen during the study period; out of which 7 (19.4%) patients had maxillary extension of the ankylotic mass. There was a male: female ratio of 1.3:1. Four (57.1%) patients were within the age group between 5 and 10 years, two (28.6%) within the age group between 11 and 15 years, while only one (14.3%) was within the age group between 31 and 35 years. All the cases (7 [100%]) of maxillary extension were secondary to cancrum oris (noma). Cheek scarring as a result of management of cancrum oris was observed. In addition, intraoral fibrosis eliminating the upper and lower buccal sulci extending to the molar regions was also noted. With the involvement of the maxilla in the ankylotic mass, the authors have proposed modification of Sawhney's classification by the addition of Class V. The authors have suggested a name for the new classification to be “Modified Sawhney's Classification of Temporomandibular Joint Ankylosis”. Aggressive postoperative physiotherapy for a sufficient period of time (minimum of 6 months) is paramount.
Outcomes of a Negative Rapid Influenza Diagnostic Test in Pregnant Women
Authors: Has Phinnara , Fitzgerald Kelly , Hughes Brenna , Datkhaeva Ilina
Published: July 2018

Objective The objective of this study was to evaluate the negative predictive value (NPV) of a rapid influenza diagnostic test (RIDT) compared with polymerase chain reaction (PCR) in pregnant women.

Study Design Retrospective cohort study of pregnant women with a negative RIDT followed by confirmatory PCR for influenza A, H1N1, and B during the influenza seasons from 2012 to 2015.

Results The NPV of the RIDT was 85.4% (211 of 247), 93.5% (231 of 247), and 97.9% (242 of 247) for influenza A, H1N1, and B, respectively. Antiviral treatment was administered to 47.2% (17 of 36) of women with a false-negative RIDT for influenza A compared with 9.0% (19 of 211) of women with a true-negative RIDT (p< 0.001). Patients were more likely to receive antiviral treatment if they were feverish (adjusted odds ratio [aOR]: 6.05, 95% confidence interval [CI]: 1.83–20.03), had cough (aOR: 6.43, 95% CI: 1.06–39.26), dyspnea (aOR: 6.41, 95% CI: 1.63–25.29), or had a subsequently positive PCR (aOR: 9.41, 95% CI: 3.13–28.31).

Conclusion Up to 14.5% of women with a negative RIDT in pregnancy had positive influenza A by PCR of whom more than half did not receive antiviral treatment.
Chronic Hypertension in Pregnancy: New Concepts for Classification and Management
Authors: Sibai Baha , Chahine Khalil
Published: July 2018

Chronic hypertension in pregnancy is traditionally classified according to degree of blood pressure (BP) elevation. Alternatively, stratifying women as high or low risk based on the etiology of hypertension, baseline work-up, and comorbid medical conditions will better inform clinicians about thresholds to initiate antihypertensive therapy, target BPs, frequency of antepartum visits, and timing of delivery. Women classified as high-risk chronic hypertension as described here require stricter BP management and more frequent follow-up visits as their associated rates of adverse maternal and/or fetal/neonatal outcomes appear higher than women classified as low-risk chronic hypertension. The latter group can in most cases be managed similarly to the general obstetric population.
Narrative Analyse: Ein Schlüssel zum Verstehen der Patient-Behandler-Beziehung
Authors: Koch Roland , Preiser Christine
Published: July 2018

Hintergrund Ein wesentlicher Aspekt von Balintarbeit sind Erzählungen über Begegnungen zwischen Patient und Behandler. Der Akt des Erzählens ist sowohl eine bewusste, kohärente Auseinandersetzung mit Erinnerung als auch ein Kommunikationsprozess im sozialen Kontext der Balintgruppe.

Methode Mittels narrativer Analysemethoden können Erzählungen auf Selbstdarstellung und Selbstherstellung des Erzählenden untersucht werden. Beispielhaft werden die Methode der Analyse von Handlungskraft und die Methode der sozialen Positionierung aufgeführt.

Ergebnisse Zwei verschiedene Erzählungen über Patient-Behandler-Begegnungen werden analysiert. Anhand der Texte wird demonstriert, wie Narrative Analyse von der Auswahl der Texte bis zur Diskussion konkret funktioniert. Dabei spielt die interdisziplinäre Zusammenarbeit zwischen Sozialwissenschaftlern und Medizinern eine tragende Rolle.

Diskussion Narrative Analyse ist geeignet, um die Patient-Behandler-Beziehung in Erzählungen zu analysieren. Sie liefert einen Schlüssel sowohl für eine empirische interdisziplinäre Forschungsarbeit als auch für eine durch narrative Denkweise verstärkte Reflektion der Rolle von Erzählungen bei der Balintarbeit.
Graphdiyne under pressure: A Raman study
Authors: Wang Yan , Yao Mingguang , Chen Yanhuan , Dong Jiajun , Yang Xigui , Du Mingrun , Liu Ran , Liu Huibiao , Li Yuliang , Liu Bingbing
Published: July 2018

High pressure Raman spectra of graphdiyne (GDY) have been studied up to 34.63 GPa. We found that sp-hybridized carbons in GDY are highly active and start to undergo a bonding change at around 5.2 GPa. Such a bonding change affects the C-C stretching vibration of sp2 hexagon rings in GDY, leading to an anomaly in the corresponding G-band pressure coefficient. A three-dimensional sp2 structure is proposed to form via pressure-induced interlayer cross-linking of sp carbons in GDY and is stable up to at least 34.63 GPa. Our study presents an important example in the study of graphyne family under pressure.
The constraint equations of Lovelock gravity theories: A new σ
k-Yamabe problem
Authors: Lachaume Xavier
Published: July 2018

This paper is devoted to the study of the constraint equations of the Lovelock gravity theories. In the case of a conformally flat, time-symmetric, and space-like manifold, we show that the Hamiltonian constraint equation becomes a generalisation of the σk-Yamabe problem. That is to say, the prescription of a linear combination of the σk-curvatures of the manifold. We search solutions in a conformal class for a compact manifold. Using the existing results on the σk-Yamabe problem, we describe some cases in which they can be extended to this new problem. This requires to study the concavity of some polynomial. We do it in two ways: regarding the concavity of a root of this polynomial, which is connected to algebraic properties of the polynomial; and seeking analytically a concavifying function. This gives several cases in which a conformal solution exists. Finally we show an implicit function theorem in the case of a manifold with negative scalar curvature, and find a conformal solution when the Lovelock theories are close to General Relativity.
Analytic modeling of dipolar field requirements for robust coupling in a non-identical biaxial two-magnet system
Authors: Kani Nickvash , Rakheja Shaloo , Naeemi Azad
Published: July 2018

Magnetic bodies interact with each other through magnetic dipolar fields that depend on the instantaneous magnetization vectors of the coupled magnetic bodies in a system. Previous studies have shown that reliable, deterministic coupling can be achieved in identical two-magnet systems and is a function of the longitudinal and perpendicular components of the dipolar field. In this work, we extend previous work significantly by developing analytic models that map the regions of dipolar field driven magnetization reversal of a non-identical two-magnet system. Models are obtained for mono-domain magnetic bodies with biaxial magnetic anisotropy. The analytic models presented map the necessary requirements for a deterministically coupled two-magnet system. In these deterministic, stable reversals, the two-magnet system stabilizes in an anti-parallel configuration along the natural free-axis of the system, regardless of thermal effects. However, non-deterministic reversals can also occur in certain non-identical systems. These pseudo-reversals occur because only one of the nanomagnets meets the critical field requirements. In this case, the system reversal is a result of thermal drift and therefore complex function system parameters and observation time. We also note that multi-magnet systems may find steady-state orientations away from the free-axis if the perpendicular components of the dipolar field are too large. We present models which accurately map the field magnitudes which result in these meta-stable reversals. Lastly, models to interpret the impact of dipolar coupling on the critical current requirement for spin-transfer-torque driven magnetization switching are also presented in this manuscript. This work greatly expands our understanding of the complex-field interaction in multi-magnet systems and is crucial when evaluating complex magnetic devices.
Optically transparent coding metasurfaces based on indium tin oxide films
Authors: Jing Hong Bo , Ma Qian , Bai Guo Dong , Bao Lei , Luo Jun , Cui Tie Jun
Published: July 2018

We describe optically transparent coding metasurfaces based on indium tin oxide (ITO) thin films with high optical transparency and good electric conductivity. Four optically transparent coding metasurfaces are designed to realize desired scattering patterns. Three of them produce anomalous reflections for normally incident electromagnetic (EM) waves by encoding specific digital coding patterns. The fourth achieves diffusion-like scattering to reduce the backward radar cross section (RCS) by encoding an optimized random coding sequence. An ITO coding element based on a glass substrate is applied to reflect 0° and 180° phase responses. Based on this element, three coding schemes for beam deflection and one scheme for the RCS reduction are presented. The consistency of simulation and measurement results fully proves the powerful abilities of the optically transparent coding metasurfaces on manipulating EM waves. The center working frequency of metasurfaces is 12 GHz, in which the reflection beam angles of three schemes are 24.6°, 12°, and 36°, respectively. The diffusion-like scattering is verified by experiments, in which the RCS reduction is more than 10 dB. Considering the high-transparency property of the designed metasurfaces, we expect the proposed method to be exploited for many applications in the microwave and optical spectral ranges.
IGLIAS: A new experimental set-up for low temperature irradiation studies at large irradiation facilities
Authors: Augé B. , Been T. , Boduch P. , Chabot M. , Dartois E. , Madi T. , Ramillon J. M. , Ropars F. , Rothard H. , Voivenel P.
Published: July 2018

We designed and built a mobile experimental set-up for studying the interaction of ion beams with solid samples in a wide temperature range from 9 to 300 K. It is either possible to mount up to three samples prepared ex situ or to prepare samples by condensation of molecules from gases or vapours onto IR or Visible-ultraviolet (Vis-UV) transparent windows. The physico-chemical evolution during irradiation can be followed in situ with different analysis techniques including Fourier transform infrared spectroscopy, Vis-UV, and quadrupole mass spectrometry.
Impact of UV spot position on forward and reverse photocurrent symmetry in a gold-diamond-gold detector
Authors: Liu Kang , Wang Weihua , Dai Bing , Yang Lei , Zhao Jiwen , Xue Jingjing , Liu Benjian , Lv Zhijun , Bi Minghao , Shu Guoyang , Sun Mingqi , Yao Kaili , Gao Ge , Han Jiecai , Zhu Jiaqi
Published: July 2018

A UV detector based on a planar quadrant electrode structure with a 100-μm isolating cross-gap deposited on chemical vapor deposition diamond was fabricated. An asymmetrical behavior was observed for the amplitude of photocurrent when in forward and reverse bias. A linear relationship between the sum of the photocurrents at biases U and −U, and the light spot position was also observed. The aim of this study is to clarify the mechanism underlying this asymmetrical behavior and exhibit its potential application based on this behavior. A mechanism involving lowering of the contact barrier height between gold and i-diamond by carrier generation upon UV illumination was adopted to account for the photocurrent behavior and confirmed when an opposite asymmetrical photocurrent behavior was observed in other samples. In addition, position-sensitive detection performance, based on this asymmetrical photocurrent behavior, was preliminarily studied. The results exhibited the potential for application as a position-sensitive detector.
Evolution of surface topography of 304L stainless steel irradiated by long pulse laser
Authors: Li Ninghui , Mou Lingqian , Li Zewen , Kang Min , Wang Xingsheng
Published: July 2018

The evolution of surface topography of 304L stainless steel, induced by long pulse laser with a wavelength of 1070 nm and a pulse width of 10 μs and a pulse number of 400 in air, was investigated in the fluence range between around 3 J/cm2 and 210 J/cm2. Three-dimensional (3D) morphologies and two-dimensional (2D) cross-sectional profiles of microstructures at different laser fluences were compared. Furthermore, surface profiles of the microstructures were quantified by using the inner diameter, the outer diameter, the elevation of central area and the rim height thereof. The trends of the above four geometrical parameters and surface profiles suggest five laser fluence ranges, where the corresponding topographies change from bump to crater. Energy dispersive spectrometer (EDS) was used to analyze surface elements of different microstructures, and the results showed that the content of oxygen had a great influence on surface tension and surface topography. In this study, a complex picture was drawn where melting, vaporization, solidification, melt displacement, melt expulsion and plasma shielding take place at different laser fluences.
Characterization of an atmospheric pressure plasma jet array and its application to cancer cell treatment using plasma activated medium
Authors: Kim Dong Yeong , Kim Sun Ja , Joh Hea Min , Chung T. H.
Published: July 2018

An atmospheric pressure plasma jet array source driven by a pulsed bipolar voltage of several tens of kilohertz was characterized and utilized for cancer cell treatment. Electrical and optical emission characteristics of plasma jet array were obtained as functions of the applied voltage, gas flow rate, and pulse frequency, and the optimal operating parameters were obtained. The emission intensities from reactive oxygen and nitrogen species (RONS) in a gas phase, such as OH, NO, H, and O, were measured by optical emission spectroscopy. In the plasma-liquid interaction experiment, the OH concentration was measured using the TA solution. The nitrite concentration in the plasma treated media (DW, HBSS, and DMEM) was measured using Griess reaction assay. Human skin cancer cells injected with plasma treated liquid were observed for changes in cell viability using the MTS assay. The results demonstrate that the plasma jet array source can be a good candidate for delivering RONS to liquid for plasma activated medium (PAM).
Pore diameter dependence of catalytic activity: p-nitrobenzaldehyde conversion to an aldol product in amine-functionalized mesoporous silica
Authors: García Andres , Slowing Igor I. , Evans James W.
Published: July 2018

The reaction yield for conversion of p-nitrobenzaldehyde (PNB) to an aldol product in amine-functionalized mesoporous silica nanoparticles (MSN) exhibits a 20-fold enhancement for a modest increase in pore diameter, d. This enhanced catalytic activity is shown to reflect a strong increase in the “passing propensity,” P, of reactant and product species inside the pores. We find that P ≈ 0, corresponding to single-file diffusion, applies for the smallest d which still significantly exceeds the linear dimensions of PNB and the aldol product. However, in this regime of narrow pores, these elongated species must align with each other and with the pore axis in order to pass. Thus, P reflects both translational and rotational diffusion. Langevin simulation accounting for these features is used to determine P versus d. The results are also augmented by analytic theory for small and large d where simulation is inefficient. The connection with the catalytic activity and yield is achieved by the incorporation of results for P into a multi-scale modeling framework. Specifically, we apply a spatially coarse-grained (CG) stochastic model for the overall catalytic reaction-diffusion process in MSN. Pores are treated as linear arrays of cells from the ends of which species adsorb and desorb, and between which species hop and exchange, with the exchange rate reflecting P. CG model predictions including yield are assessed by Kinetic Monte Carlo simulation.
Thickness dependence of superconductivity in single-crystal Ta4Pd3Te16 nanoribbons
Authors: Bao Lin , Bi Yiqing , Liu Xiaotong , Yang Xiaohui , Hao Tingting , Tian Shibing , Wang Zongli , Li Junjie , Gu Changzhi
Published: July 2018

We present the thickness-dependent electrical properties of mechanically exfoliated single crystal Ta4Pd3Te16 nanoribbons. By decreasing the nanoribbon thickness in the range of 500–20 nm, we observed a suppression of superconductivity driven by both the thickness and the external magnetic field. In particular, for the thinner nanoribbons with the thickness less than 40 nm, there is a non-zero resistance state extending down to low temperature, followed by the loss of superconductivity when the thickness is decreased to the order of the coherence length. We found that the theory of a thermally activated phase slip can well describe the temperature dependence of the resistance below Tc. The disorder-induced enhanced Coulomb interaction with the decrease in the thickness is expected to be dominant in the gradual crossover behavior from superconducting to normal or very weakly insulating behavior in the low-dimensional system.
Measuring genome-wide genetic variation to reassess subspecies classifications in Dodonaea viscosa (Sapindaceae)
Authors: Christmas Matthew J. , Biffin Ed , Lowe Andrew J.
Published: July 2018

Subspecies are traditionally defined on the basis of geographic discontinuities in phenotypic traits, and their circumscription is useful to distinguish morphologically differentiated populations. However, the robustness of morphology-based subspecies classifications in the genomics era is coming under increasing scrutiny, and phylogenies inferred from molecular data may not match with morphological approaches. The division of the shrub Dodonaea viscosa into seven subspecies within Australia has been based mainly on variation in leaf shape, which is a notably variable phenotypic character in this species. So as to assess the alignment between genetic variation and subspecies assignment, we genotyped 67 D. viscosa plants, including representatives from each of the seven subspecies, for 941 single nucleotide polymorphisms. We used network- and Bayesian-based methods to assess genetic relatedness between sampled individuals. Structure analysis identified two genetic clusters, with a further substructure being identified within one of the clusters. Genetic clusters partially aligned with subspecies classifications, particularly for the three most morphologically distinct subspecies (ssp. mucronata, ssp. viscosa and ssp. burmanniana). Subspecies inhabiting the arid zone (ssp. mucronata and ssp. angustissima) exhibited the most distinct genetic clustering. For subspecies inhabiting more temperate regions of its range (ssp. angustifolia, ssp. cuneata and ssp. spatulata), genetic groups did not correspond well with subspecies classifications, but rather were better explained by the geographic origin of individuals. We suggest that the current subspecific classification of the hopbush does not accurately reflect the evolutionary history of this species, and recommend that phenotypic variation be reassessed in light of the genetic structure we describe here. The roles of environmental change, selection and geographic isolation are discussed in an attempt to explain the contemporary distribution of genetic variation in D. viscosa in Australia.
Comparing length-measurement methods and estimating growth parameters of free-swimming whale sharks (Rhincodon typus) near the South Ari Atoll, Maldives
Authors: Perry Cameron T. , Figueiredo Joana , Vaudo Jeremy J. , Hancock James , Rees Richard , Shivji Mahmood
Published: July 2018

Whale sharks (Rhincodon typus) are an endangered species whose growth and reproductive biology are poorly understood. Given their conservation concern, estimating growth parameters, as traditionally derived from vertebral samples of dead animals, is challenging. We used a non-invasive approach to investigate growth parameters of whale sharks frequenting the South Ari Atoll, Maldives, by analysing repeat measurements of free-swimming sharks over a 10-year period. Total lengths of the sharks were estimated by three measurement methods. Visual estimates underestimated the sizes of large sharks, whereas laser and tape measurements yielded results that were similar to one another. The Maldives aggregation consisted of primarily male (91%) juvenile (total length=3.16–8.00m) sharks and sharks new to the area were significantly smaller than were returning sharks, which suggests that this site may constitute a secondary nursery ground. Estimates of von Bertalanffy (VBG) growth parameters for combined sexes (L∞=19.6m, k=0.021year–1) were calculated from 186 encounters with 44 sharks. For males, VBG parameters (L∞=18.1m, k=0.023year–1) were calculated from 177 encounters with 40 sharks and correspond to a male age at maturity of ~25 years and longevity of ~130 years. Differences between these estimates and those from other studies underscore the need for regional studies.
From dragonflies to Facebook: digital disruption creates new opportunities for wetland science and conservation
Authors: Davis Jenny
Published: July 2018

This paper describes a project that started with a proto-science communication project on wetland dragonfly biodiversity in 1998, stopped when a funding hurdle appeared in 2002, restarted with the development of an app in 2016, and culminated with the completion of a successful citizen science project in 2017. Digital disruption, in the form of an app to replace a field guide that was never printed due to lack of funds, and using digital media to facilitate a citizen science project, was the key to completing the initial project and collecting data on dragonflies (locally valued wetland species) that previously would have been difficult to achieve. The invitation to write this paper from a less formal perspective provided the opportunity to describe the unconventional progress of a project spanning 20 years, to acknowledge the contributions of family and friends, and to emphasise the new opportunities that digital tools, media and skills can provide for wetland science and biodiversity conservation.
Observing carbon cycle–climate feedbacks from space
Authors: Sellers Piers J. , Schimel David S. , Moore Berrien , Liu Junjie , Eldering Annmarie
Published: July 2018

The impact of human emissions of carbon dioxide and methane on climate is an accepted central concern for current society. It is increasingly evident that atmospheric concentrations of carbon dioxide and methane are not simply a function of emissions but that there are myriad feedbacks forced by changes in climate that affect atmospheric concentrations. If these feedbacks change with changing climate, which is likely, then the effect of the human enterprise on climate will change. Quantifying, understanding, and articulating the feedbacks within the carbon–climate system at the process level are crucial if we are to employ Earth system models to inform effective mitigation regimes that would lead to a stable climate. Recent advances using space-based, more highly resolved measurements of carbon exchange and its component processes—photosynthesis, respiration, and biomass burning—suggest that remote sensing can add key spatial and process resolution to the existing in situ systems needed to provide enhanced understanding and advancements in Earth system models. Information about emissions and feedbacks from a long-term carbon–climate observing system is essential to better stewardship of the planet.
Unrestrained markerless trait stacking in
Nannochloropsis gaditana
through combined genome editing and marker recycling technologies
Authors: Verruto John , Francis Kristie , Wang Yingjun , Low Melisa C. , Greiner Jessica , Tacke Sarah , Kuzminov Fedor , Lambert William , McCarren Jay , Ajjawi Imad , Bauman Nicholas , Kalb Ryan , Hannum Gregory , Moellering Eric R.
Published: July 2018

Significance

Stacking traits in microalgae is limited by a lack of robust genome modification tools and selectable marker availability. This presents a key hurdle in developing strains for renewable products including biofuels. Here, we overcome these limitations by combining inducible Cre recombinase with constitutive Cas9 nuclease expression in the industrial strain,
Nannochloropsis gaditana
. With this system, we demonstrate marker- and reporter-free recapitulation of an important lipid productivity trait. In addition, we generate a strain harboring seven-gene knockouts within the photosystem antennae encoding genes. The combined use of relatively mature (Cre) and emerging (CAS9) genome modification technologies can thus accelerate the pace of industrial strain development and facilitate basic research into functionally redundant gene families.
WDR5 modulates cell motility and morphology and controls nuclear changes induced by a 3D environment
Authors: Wang Pengbo , Dreger Marcel , Madrazo Elena , Williams Craig J. , Samaniego Rafael , Hodson Nigel W. , Monroy Francisco , Baena Esther , Sánchez-Mateos Paloma , Hurlstone Adam , Redondo-Muñoz Javier
Published: July 2018

Significance

Cells require nuclear deformation to squeeze through tissue matrices. We have discovered that WD repeat domain 5 (WDR5; an epigenetic modulator of H3K4 methylation) is fundamental for cell polarity and migration in vitro and in vivo, independent of transcription. We have uncovered that the interactions between cells and the surrounding 3D confined conditions induce the upregulation of H3K4me3. Moreover, 3D environments control the deformability and the mechanical properties of the nucleus. We have identified that loss of WDR5 abrogates the H3K4 methylation and the nuclear changes induced by 3D conditions. Mechanistically, we found that myosin light chain kinase and myosin function were required for WDR5-mediated H3K4 methylation in 3D matrices. Our findings uncover functions of the epigenetic machinery when cells move through constricted conditions.
Rhinovirus induces an anabolic reprogramming in host cell metabolism essential for viral replication
Authors: Gualdoni Guido A. , Mayer Katharina A. , Kapsch Anna-Maria , Kreuzberg Katharina , Puck Alexander , Kienzl Philip , Oberndorfer Felicitas , Frühwirth Karin , Winkler Stefan , Blaas Dieter , Zlabinger Gerhard J. , Stöckl Johannes
Published: July 2018

Significance

Rhinovirus (RV) is the causative agent of the common cold and other respiratory tract infections. Despite the vast prevalence, effective treatment or prevention strategies are lacking. Here, we analyzed metabolic alterations in infected cells and found a pronounced reprogramming of host cell metabolism toward an anabolic state, which involved enhancement of glucose uptake and glycogenolysis. We further demonstrate that these alterations can be reverted by treatment with 2-deoxyglucose, a glycolysis inhibitor, which results in a disruption of RV replication in vitro and in vivo. Thus, we show how the specific metabolic fingerprint of viral infection can be used to generate targets for antiviral therapy.
1.1-billion-year-old porphyrins establish a marine ecosystem dominated by bacterial primary producers
Authors: Gueneli N. , McKenna A. M. , Ohkouchi N. , Boreham C. J. , Beghin J. , Javaux E. J. , Brocks J. J.
Published: July 2018

Significance

The oceans of Earth’s middle age, 1.8–0.8 billion years ago, were devoid of animal-like life. According to one hypothesis, the emergence of large, active organisms was restrained by the limited supply of large food particles such as algae. Through the discovery of molecular fossils of the photopigment chlorophyll in 1.1-billion-year-old marine sedimentary rocks, we were able to quantify the abundance of different phototrophs. The nitrogen isotopic values of the fossil pigments showed that the oceans were dominated by cyanobacteria, while larger planktonic algae were scarce. This supports the hypothesis that small cells at the base of the food chain limited the flow of energy to higher trophic levels, potentially retarding the emergence of large and complex life.
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
Authors: Duren Zhana , Chen Xi , Zamanighomi Mahdi , Zeng Wanwen , Satpathy Ansuman T. , Chang Howard Y. , Wang Yong , Wong Wing Hung
Published: July 2018

Significance

Biological samples are often heterogeneous mixtures of different types of cells. Suppose we have two single-cell datasets, each providing information on a different cellular feature and generated on a different sample from this mixture. Then, the clustering of cells in the two samples should be coupled as both clusterings are reflecting the underlying cell types in the same mixture. This “coupled clustering” problem is a new problem not covered by existing clustering methods. In this paper, we develop an approach for its solution based on the coupling of two nonnegative matrix factorizations. The method should be useful for integrative single-cell genomics analysis tasks such as the joint analysis of single-cell RNA-sequencing and single-cell ATAC-sequencing data.
Observation of highly stable and symmetric lanthanide octa-boron inverse sandwich complexes
Authors: Li Wan-Lu , Chen Teng-Teng , Xing Deng-Hui , Chen Xin , Li Jun , Wang Lai-Sheng
Published: July 2018

Significance

Lanthanide borides constitute an important class of materials with wide industrial applications, but clusters of lanthanide borides have been rarely investigated. It is of great interest to study these nanosystems, which may provide molecular-level understanding of the emergence of new properties and provide insight into designing new boride materials. We have produced lanthanide boride clusters and probed their electronic structure and chemical bonding. Two Ln
2
B
8
−
clusters are presented, and they are found to possess inverse sandwich structures. The neutral Ln
2
B
8
complexes are found to possess
D
8h
symmetry with strong Ln–B
8
bonding. A unique (d–p)δ bond is found to be important for the Ln–B
8
–Ln interactions. The Ln
2
B
8
inverse sandwich complexes broaden the structural chemistry of the lanthanide elements and provide insights into bonding in lanthanide boride materials.
Systems genetic analysis of inversion polymorphisms in the malaria mosquito
Anopheles gambiae
Authors: Cheng Changde , Tan John C. , Hahn Matthew W. , Besansky Nora J.
Published: July 2018

Significance

Chromosomal inversions play an important role in local adaptation. Strong evidence exists of selection acting on inversions, but the genic targets inside them are largely unknown. Here we take a systems genetics approach, analyzing two inversion systems implicated in climatic adaption by
Anopheles gambiae
. We profiled physiology, behavior, and transcription in four different karyotypic backgrounds derived from a common parental colony. Acclimation to different climatic regimes resulted in pervasive inversion-driven phenotypic differences whose magnitude and direction depended upon gender, environment, and epistatic interactions between inversions. Inversion-affected loci were significantly enriched inside inversions, as predicted by local adaptation theory. Drug perturbation supported lipid homeostasis and energy balance as inversion-regulated functions, a finding supported by research on climatic adaptation in multiple systems.
Local magnetism in MnSiPt rules the chemical bond
Authors: Rosner Helge , Leithe-Jasper Andreas , Carrillo-Cabrera Wilder , Schnelle Walter , Ackerbauer Sarah V. , Gamza Monika B. , Grin Yuri
Published: July 2018

Significance

A crystal structure can be understood as a result of bonding interactions (covalent, ionic, van der Waals, etc.) between the constituting atoms. If the forces caused by these interactions are equilibrated, the so-stabilized crystal structure should have the lowest energy. In such an atomic configuration, additional weaker atomic interactions may further reduce the total energy, influencing the final atomic arrangement. Indeed, in the intermetallic compound MnSiPt, a 3D framework is formed by polar covalent bonds between Mn, Si, and Pt atoms. Without taking into account the local spin polarization of manganese atoms, they would form Mn–Mn bonds within the framework. Surprisingly, the local magnetic moments of manganese prevent the formation of Mn–Mn bonds, thus changing decisively and significantly the final atomic arrangement.
Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins
Authors: Hudait Arpa , Moberg Daniel R. , Qiu Yuqing , Odendahl Nathan , Paesani Francesco , Molinero Valeria
Published: July 2018

Significance

Antifreeze proteins have evolved to inhibit ice growth in organisms living at subfreezing temperatures; the mechanism by which these proteins recognize and bind ice is not understood. It has been proposed that antifreeze proteins recognize ice by preordering water at the ice-binding site already in solution. Here we use multiresolution molecular simulations to demonstrate that preordering of interfacial water is not needed for ice recognition by antifreeze proteins. We predict that preordering could emerge on the large ice-binding surfaces of aggregates of ice-nucleating proteins, where it may assist with ice nucleation.
The Obligatory Coding Principle in diachronic perspective
Authors: Creissels Denis
Published: July 2018

The Obligatory Coding Principle accounts for the
inventories of possible coding frames in languages that, according
to the current terminology, can be characterized as consistently
accusative or consistently ergative in their system of argument
coding. In coding frame inventories fully consistent with the
Obligatory Coding principle, every coding frame includes a given
type of coding, either A (in obligatory A coding
languages) or P (in obligatory P coding
languages). However, languages with coding frame
inventories violating this principle are not exceptional. This
chapter examines the types of evolutions that may result either in
global shifts affecting the Obligatory Coding Principle, in
systematic violations of the Obligatory Coding Principle, or in the
gradual spreading of non-canonical coding frames. The idea
underlying this study is that, before discussing the theoretical
status of this kind of generalization, it is crucial to clarify its
involvement in diachronic processes.
Incipient hierarchical alignment in four Central Salish languages
from the Proto-Salish middle
Authors: Zahir Zalmai
Published: July 2018

There are three distinct transitive constructions in four Coast
Salish languages, Squamish, Halkomelem, Klallam and Lushootseed. In
the V-tr construction, both A and P are unmarked for case;
in the V-mid construction (often considered antipassive), A
is unmarked and P marked; in the V-tr-mid construction
(often considered passive), P is unmarked and A marked.
Individually, none of these constructions is a hierarchical system,
but in combination, asymmetries in their distribution are well on
the way to creating a person-based hierarchical system. This paper
discusses the diachronic development of each of these constructions,
then describes their differential distribution into the four
functional domains: local (SAP A → SAP P), direct
(SAP → 3P), nonlocal (3A → 3P), and
inverse (3A → SAP P). While the distribution is not
identical in each of the languages, the trend is clear: the
etymologically passive V-tr-mid construction cannot occur
in the direct domain and has become the pragmatically
unmarked construction in the inverse domain, whereas the
etymologically antipassive V-mid construction cannot occur
in the inverse domain. While it only occurs in the
direct and nonlocal domains, even there it is
rare, giving the appearance that its function is still that of an
antipassive. In combination, the result is that whenever the two
core arguments of a clause are an SAP and a third person, regardless
of grammatical role the SAP participant is always an unmarked core
argument, whereas the third person is most often marked, leading to
a situation where the oblique case in these languages is beginning
to resemble the obviative case-marker of inverse languages.