bluuebunny/crossref_metadata_2025 huggingface dataset:
Medical, Genomic, and Evolutionary Aspects of the Peptide Sharing between Pathogens, Primates, and Humans
Authors: Kanduc Darja , Shoenfeld Yehuda
Published: September 2020

Comparing mammalian proteomes for molecular mimicry with infectious pathogens highlights the highest levels of heptapeptide sharing between pathogens and human, murine, and rat proteomes, while the peptide sharing level is minimal (or absent) with proteomes from nonhuman primates such as gorilla, chimpanzee, and rhesus macaque. From the medical point of view, the data might be useful to clinicians and vaccinologists to develop and evaluate immunomodulatory and immunotherapeutic approaches. As a matter of fact, primates seem to be unreliable animal models for revealing potential autoimmune events in preclinical testing of immunotherapies. In terms of genomics, the scarce or absent peptide sharing between pathogens and primates versus the massive peptide sharing existing between pathogens and humans lets foresee mechanisms of pathogen sequence insertion/deletion/alteration that have differently operated in mammals over evolutionary timescales. Why and how the human genome has been colonized by pathogen sequences and why and how primates escaped such a colonization appears to be the new scientific challenge in our efforts to understand not only the origin of Homo sapiens but also his autoimmune diseasome.
Different Hydraulic Constructs to Optimize the Venous Drainage of DIEP Flaps in Breast Reconstruction: Decisional Algorithm and Review of the Literature
Authors: Pignatti Marco , Pinto Valentina , Giorgini Federico A. , Lozano Miralles Maria Elisa , D'Arpa Salvatore , Cipriani Riccardo , De Santis Giorgio
Published: September 2020

Background Venous congestion is the most common perfusion-related complication of deep inferior epigastric artery perforator (DIEP) flap. Several hydraulic constructs can be created for venous superdrainage in case of flap venous engorgement or as a preventive measure. These can be classified based on the choice of the draining vein of the flap, either a second deep inferior epigastric vein (DIEV) or a superficial inferior epigastric vein (SIEV), and of the recipient vein, either a vein of the chest or the DIEV.

Methods We conducted a comprehensive systematic literature review in Medline, Scopus, EMBASE, Cochrane Library, and Google Scholar to find publications that reported on venous congestion in DIEP flap. The keywords used were DIEP Flap, breast reconstruction, venous congestion, supercharging, superdrainage, SIEV, and DIEV.

Results Based on the studies found in the literature, we developed an algorithm to guide the surgeon's decision when choosing the veins for the superdrainage anastomosis.

Conclusion Several alternatives for venous anastomosis in superdrainage are available. We propose an algorithm to simplify the choice. The use of the ipsilateral SIEV to be connected to a vein of the chest appears to be advantageous. The anatomical position that allows the easiest anastomosis dictates which chest vein to favor.
Evaluation of Galectin-3 as a Novel Diagnostic Biomarker in Patients with Heart Failure with Preserved Ejection Fraction
Authors: Kanukurti Jyothirmayi , Mohammed Noorjahan , Sreedevi N. N. , Khan Siraj Ahmed , Baba K.S.S. Sai , Bhaskar M. Vijaya , Satish O. Sai , Naushad Shaik Mohammad , Mohan Iyyapu Krishna
Published: September 2020

Background Heart failure is a complex cardiovascular disease with a variety of etiologies and heterogeneity. The N-terminal pro-B-type natriuretic peptide (NT-proBNP) value has limited usefulness in diagnosing heart failure with preserved ejection fraction (HFpEF).

Aim The aim of the present study is to evaluate serum Galectin-3 as a diagnostic biomarker in patients with HFpEF and to compare Galectin-3 with NT-proBNP levels.

Materials and Methods A cross-sectional case–control study including 63 cases of heart failure with ejection fraction ≥50% confirmed by echocardiography. NT-proBNP levels in serum were measured by electrochemiluminescence immunoassay and Galectin-3 levels in serum were measured by using an enzyme-linked-immunosorbent serologic assay kit.

Results The median levels of serum Galectin-3 and NT-proBNP in patients were significantly higher than those of controls (26.59 vs. 5.27 and 927 vs. 49.3, p < 0.0001). A positive correlation was observed between serum levels of Galection-3 and NT-ProBNP (r: 0.21, p = 0.048). At cut-off values of 10.1 ng/mL and 160 pg/mL, serum Galectin-3 has 77.78% sensitivity, 95% specificity with an area under the curve (AUC) of 0.93, and serum NT-proBNP has 71.43% sensitivity, 100% specificity with an AUC of 0.87, respectively, for diagnosing HFpEF. The comparison of receiver operating characteristics curves showed that Galectin-3 has better AUC compared with NT-proBNP in diagnosing HFpEF. Serum Galectin-3 showed a positive correlation with NT-proBNP and lipid parameters.

Conclusion Galectin-3 with higher sensitivity and AUC can be used as a valuable biomarker for the diagnosis of HFpEF. Simultaneous testing of both Galectin-3 and NT-proBNP can further improve the detection of patients with HFpEF.
Not everything helps the same for everyone: relevance of extracurricular activities for academic achievement
Authors: Balaguer Álvaro , Benítez Edgar , Albertos Aranzazu , Lara Sonia
Published: September 2020

Participation in organized Extracurricular Activities has contributed to improve academic achievement. However, this does not happen in the same way; it depends on sex, age, or parental educational level. Our objective is to know the importance of these factor interactions’ in the explanation of academic achievement. The sample consisted of 1148 adolescents, aged between 12 and 18 years, 52% of whom were female. Participants completed the Extracurricular Activities questionnaire, and academic and sociodemographic data were collected. The results show that differences in academic achievement depend on the adolescent stage. In early adolescence, girls improve in academic achievement, as well as with better parental education, reading of books and activity duration. On the contrary, in the middle and late adolescence, academic achievement improves with not participating in collective sports and reduced activity breadth, although parental educational level follows the same trend as in the early adolescence. These results reinforce the evolutionary hypothesis of specialization in the choice of activities throughout adolescence. In this sense, some proposals for schools that advocate for greater integration of curricular and non-curricular elements are discussed.
Rise of nations: Why do empires expand and fall?
Authors: Vakulenko S. , Lyakhov D. A. , Weber A. G. , Lukichev D. , Michels D. L.
Published: September 2020

We consider centralized networks composed of multiple satellites arranged around a few dominating super-egoistic centers. These so-called empires are organized using a divide and rule framework enforcing strong center–satellite interactions while keeping the pairwise interactions between the satellites sufficiently weak. We present a stochastic stability analysis, in which we consider these dynamical systems as stable if the centers have sufficient resources while the satellites have no value. Our model is based on a Hopfield type network that proved its significance in the field of artificial intelligence. Using this model, it is shown that the divide and rule framework provides important advantages: it allows for completely controlling the dynamics in a straight-forward way by adjusting center–satellite interactions. Moreover, it is shown that such empires should only have a single ruling center to provide sufficient stability. To survive, empires should have switching mechanisms implementing adequate behavior models by choosing appropriate local attractors in order to correctly respond to internal and external challenges. By an analogy with Bose–Einstein condensation, we show that if the noise correlations are negative for each pair of nodes, then the most stable structure with respect to noise is a globally connected network. For social systems, we show that controllability by their centers is only possible if the centers evolve slowly. Except for short periods when the state approaches a certain stable state, the development of such structures is very slow and negatively correlated with the size of the system’s structure. Hence, increasing size eventually ends up in the “control trap.”
Dynamical phase transitions and their relation to structural and thermodynamic aspects of glass physics
Authors: Royall C. Patrick , Turci Francesco , Speck Thomas
Published: September 2020

We review recent developments in structural–dynamical phase transitions in trajectory space based on dynamic facilitation theory. An open question is how the dynamic facilitation perspective on the glass transition may be reconciled with thermodynamic theories that posit collective reorganization accompanied by a growing static length scale and, eventually, a vanishing configurational entropy. In contrast, dynamic facilitation theory invokes a dynamical phase transition between an active phase (close to the normal liquid) and an inactive phase, which is glassy and whose order parameter is either a time-averaged dynamic or structural quantity. In particular, the dynamical phase transition in systems with non-trivial thermodynamics manifests signatures of a lower critical point that lies between the mode-coupling crossover and the putative Kauzmann temperature, at which a thermodynamic phase transition to an ideal glass state would occur. We review these findings and discuss such criticality in the context of the low-temperature decrease in configurational entropy predicted by thermodynamic theories of the glass transition.
Research on the propagation properties of THz circularly polarized wave in BGK model inhomogeneous dusty plasma
Authors: Yutong Liu , Wei Chen , Lixia Yang , Zhixiang Huang , Lixin Guo , Linjing Guo , Qingqing Deng
Published: September 2020

When a hypersonic vehicle flies near space, a layer of complex dusty plasma will form around the vehicle under the influence of high temperature, which will cause radar signal attenuation (ATT) to different degrees and lead to communication barriers. Therefore, studying the interaction mechanism between electromagnetic waves and dusty plasma is important. In this paper, the Bhatnagar–Gross–Krook collision model of non-uniform dusty plasma is derived on the basis of Boltzmann's approximate equation. In addition, the modified expression of a dielectric coefficient of weakly ionized dusty plasma is obtained under the condition of magnetization. With the Wentzel–Kramers–Brillouin method, the ATT coefficients of terahertz wave with different external magnetic fields and dusty plasma parameters are calculated. Results show that a strong external magnetic field will cause the ATT of the right-hand circular polarized wave to produce a low absorption band, whereas the ATT of the left-hand circular polarized wave will evidently weaken. The electron concentration, dust concentration, dust particle radius, collision frequency, and charging frequency also influence the ATT under the external magnetic field. These studies provide theoretical references for the research on the blackouts of hypersonic vehicles.
Characteristics of closed currents and magnetic fields outside the dense pinch column in a plasma focus discharge
Authors: Kubes P. , Paduch M. , Sadowski M. J. , Cikhardtova B. , Cikhardt J. , Klir D. , Kravarik J. , Kwiatkowski R. , Munzar V. , Rezac K. , Szymaszek A. , Tomaszewski K. , Zielinska E. , Zaloga D. , Akel M.
Published: September 2020

This paper describes the structure of a higher extreme ultraviolet (XUV) emission and plasma density region which surrounds a pinched dense-plasma column. It is interpreted as a toroidal-like plasma formation, which is flowing by a closed current with poloidal and toroidal components upon its surface. This current produces a local magnetic field, which separates the external discharge current from the surface of the dense pinch column. We estimated the values of closed currents as well as magnetic- and plasma-pressures in this column and its surrounding on the basis of the measured distribution of interferometric fringes and intense XUV emission, recorded during the pinch stagnation phase. The considered layer forms the region in which the magnetic energy can be conserved, and during its decay, the acceleration of fast deuterons can take place.
Ion beam diagnostic for the assessment of miniaturized electric propulsion systems
Authors: Habl L. , Rafalskyi D. , Lafleur T.
Published: September 2020

An automated plume diagnostic system is presented for two-dimensional mapping of the ion beam produced by using miniaturized electric propulsion devices. The instrument is designed to operate with noble and reactive gases and consists of a semi-circular probe array with a unique angular distribution following a Gaussian shape for improved beam profile resolution. To demonstrate the operation of the diagnostic system, a series of experiments are conducted with a low-power gridded ion thruster using xenon and iodine propellants. The two-dimensional current density maps generated are used to calculate important beam properties for performance estimates, including the total ion current and the effective divergence angle, and we show how the measurements can be used to assess and optimize the design of ion optics for gridded ion thrusters. All current density measurements with the new instrument are corrected for secondary electron emission (SEE) due to ion bombardment, and using a separate, specially designed, electrostatic probe, we present the first measurements of the SEE yield for iodine ions impacting molybdenum and SAE 304 stainless steel surfaces.
Investigation and improvement of the spin self-sustaining magnetometer
Authors: Zhao Q. , Fan B. L. , Wang S. G. , Wang L. J.
Published: September 2020

The spin self-sustaining atomic magnetometer has the advantage of 1/τ measurement and great development potential in many applications. In this paper, we investigated the main elements that affect the stability and accuracy of the self-sustaining magnetometer and proposed the methods to improve its performance based on the measurement results. The correlation coefficient between fluctuations of the magnetic field generated by coils and the spin Larmor precession frequency is 0.97, which mainly dominates the stability in a short term. The accuracy of the magnetometer is affected by the power and frequency of the pump light. The Larmor precession frequency coefficient related to the pump light power is 26 mHz/mW, and the effect on the Larmor precession frequency is minimized when the pump light frequency is red detuned by 200 MHz from the 85Rb transition D1 line F = 3 to F′ = 3. The 1/τ measurement time after these corrections can be extended to 10 s, and the sensitivity achieved is 149 fT/Hz, which is close to the quantum projection noise limit of the system.
Piezoplasmonics: Strain-induced tunability of plasmon resonance in AlAs quantum wells
Authors: Khisameeva A. R. , Muravev V. M. , Kukushkin I. V.
Published: September 2020

We demonstrate tuning of a two-dimensional (2D) plasmon spectrum in modulation-doped AlAs quantum wells via the application of in-plane uniaxial strain. We show that the dramatic change in the plasma spectrum is caused by strain-induced redistribution of charge carriers between anisotropic Xx and Xy valleys. The discovered piezoplasmonic effect provides a tool to study the band structure of 2D systems. We use the piezoplasmonic effect to measure how the inter-valley energy splitting depends on the deformation. This dependency yields the AlAs deformation potential of E2=(5.6±0.3) eV.
Theoretical spectroscopy of isotopically dilute water and hydrophobicity
Authors: Reddy Kambham Devendra , Biswas Rajib
Published: September 2020

Hydrophobic solutes significantly alter the water hydrogen bond network. The local alteration of solvation structures gets reflected in the vibrational spectroscopic signal. Although it is possible to detect this microscopic feature by modern infrared spectroscopy, bulk phase spectra often come with a formidable challenge of establishing the connection of experimental spectra to molecular structures. Theoretical spectroscopy can serve as a more powerful tool where spectroscopic data cannot provide the microscopic picture. In the present work, we build a theoretical spectroscopic map based on a hybrid quantum–classical molecular simulation approach using a methane–water system. The single oscillator O–H stretch frequency is well correlated with a collective variable solvation energy. We construct the spectroscopic maps for fundamental transition frequencies and also the transition dipoles. A bimodal frequency distribution with a blue-shifted population of transition frequency illustrates the presence of gas like water molecules in the hydration shell of methane. This observation is further complemented by a shell-wise decomposition of the O–H stretch frequencies. We observe a significant increase in the ordering of the first solvation water molecules, except those which are directly facing the methane molecule. This is manifested in the redshift of the observed transition frequencies. Temperature dependent simulations depict that the water molecules facing the methane molecule behave similarly to the high temperature water, and a few of the first shell water molecules behave more like cold water.
Pendant drop tensiometry: A machine learning approach
Authors: Kratz Felix S. , Kierfeld Jan
Published: September 2020

Modern pendant drop tensiometry relies on the numerical solution of the Young–Laplace equation and allows us to determine the surface tension from a single picture of a pendant drop with high precision. Most of these techniques solve the Young–Laplace equation many times over to find the material parameters that provide a fit to a supplied image of a real droplet. Here, we introduce a machine learning approach to solve this problem in a computationally more efficient way. We train a deep neural network to determine the surface tension of a given droplet shape using a large training set of numerically generated droplet shapes. We show that the deep learning approach is superior to the current state of the art shape fitting approach in speed and precision, in particular if shapes in the training set reflect the sensitivity of the droplet shape with respect to surface tension. In order to derive such an optimized training set, we clarify the role of the Worthington number as a quality indicator in conventional shape fitting and in the machine learning approach. Our approach demonstrates the capabilities of deep neural networks in the material parameter determination from rheological deformation experiments, in general.
Seeding method for ice nucleation under shear
Authors: Goswami Amrita , Dalal Indranil Saha , Singh Jayant K.
Published: September 2020

Hydrodynamic flow can have complex and far-reaching consequences on the rate of homogeneous nucleation. We present a general formalism for calculating the nucleation rates of simply sheared systems. We have derived an extension to the conventional Classical Nucleation Theory, explicitly embodying the shear rate. Seeded molecular dynamics simulations form the backbone of our approach. The framework can be used for moderate supercooling, at which temperatures brute-force methods are practically infeasible. The competing energetic and kinetic effects of shear arise naturally from the equations. We show how the theory can be used to identify shear regimes of ice nucleation behavior for the mW water model, unifying disparate trends reported in the literature. At each temperature, we define a crossover shear rate in the limit of 1000 s−1–10 000 s−1, beyond which the nucleation rate increases steadily up to a maximum, at the optimal shear rate. For 235 K, 240 K, 255 K, and 260 K, the optimal shear rates are in the range of ≈106 s−1–107 s−1. For very high shear rates beyond 108 s−1, nucleation is strongly inhibited. Our results indicate that the optimal shear rates have a non-monotonic dependence on temperature.
Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin
Authors: Young Melanie J. , Dutoit Ludovic , Robertson Fiona , van Heezik Yolanda , Seddon Philip J. , Robertson Bruce C.
Published: September 2020

Abstract
Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin.
Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples.
Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2.
Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified.
Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species.
Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.
Biotic rescaling reveals importance of species interactions for variation in biodiversity responses to climate change
Authors: Vandvik Vigdis , Skarpaas Olav , Klanderud Kari , Telford Richard J. , Halbritter Aud H. , Goldberg Deborah E.
Published: September 2020

Significance

Evidence of climate change impacts on biodiversity is accumulating, but a growing literature also reveals highly variable rates and even directions of these responses. We propose that this complexity arises because biological processes do not respond to climate in direct and linear ways and, therefore, that complex biodiversity responses could be simplified by rescaling climate in terms of the underlying biological processes. Applying this “plant’s eye view” approach to a montane grassland climate change experiment, we find that variation in local extinction and colonization rates in response to temperature and precipitation change across landscapes emerge from unexpected and understudied biotic interactions. Thus, biotic rescaling can simultaneously test mechanistic hypotheses and enhance generality in understanding of biodiversity responses to climate change.
DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination
Authors: Crowe Jennifer L. , Wang Xiaobin S. , Shao Zhengping , Lee Brian J. , Estes Verna M. , Zha Shan
Published: September 2020

Significance

DNA-dependent protein kinase (DNA-PK), which is composed of the KU heterodimer and the large catalytic subunit (DNA-PKcs), is a classical nonhomologous end-joining (cNHEJ) factor with important roles in immunoglobulin class switch recombination. Activated DNA-PK phosphorylates many substrates, including DNA-PKcs itself at the T2609 cluster. Using knockin mouse models, we found that while the loss of T2609 phosphorylation of DNA-PKcs does not affect class switch recombination (CSR) efficiency, the CSR junctions recovered from T2609A B cells are generated by the alternative end-joining pathway, providing the evidence for a role of DNA-PKcs T2609 phosphorylation in DNA repair pathway choice.
Ethnic antagonism erodes Republicans’ commitment to democracy
Authors: Bartels Larry M.
Published: September 2020

Significance

Growing partisan polarization and democratic “backsliding” in various parts of the world have raised concerns about the attachment of ordinary Americans to democratic institutions and procedures. I find that substantial numbers of Republicans endorse statements contemplating violations of key democratic norms, including respect for the law and for the outcomes of elections and eschewing the use of force in pursuit of political ends. The strongest predictor by far of these antidemocratic attitudes is ethnic antagonism—especially concerns about the political power and claims on government resources of immigrants, African-Americans, and Latinos. The strong tendency of ethnocentric Republicans to countenance violence and lawlessness, even prospectively and hypothetically, underlines the significance of ethnic conflict in contemporary US politics.
The breakdown of antiracist norms: A natural experiment on hate speech after terrorist attacks
Authors: Álvarez-Benjumea Amalia , Winter Fabian
Published: September 2020

Significance

Surges in hateful and xenophobic content online are often found after terrorist attacks. We find that this effect is highly dependent on the local context and the respective social norms. Prejudiced attitudes are likely to be voiced only if the perceived social acceptability of expressing prejudice increases. Since antihate norms play an important role in containing the expression of prejudice, understanding how terrorist attacks may impact the strength of the social norm is essential to understanding societal responses to terrorist attacks.
POLQ suppresses interhomolog recombination and loss of heterozygosity at targeted DNA breaks
Authors: Davis Luther , Khoo Kevin J. , Zhang Yinbo , Maizels Nancy
Published: September 2020

Significance

This manuscript identifies a pathway of recombination which joins DNA ends on two homologous chromosomes in human cells. This pathway supports efficient recombination at targeted DSBs and nicks, at frequencies exceeding those of the spontaneous recombination events that ameliorate genetic diseases in human blood and skin cells. Recombination is further stimulated by depletion of POLQ, a factor with both DNA polymerase and helicase activities. POLQ depletion causes an especially dramatic increase in the frequency of copy-neutral loss of heterozygosity (cnLOH) events. These results have immediate practical implications for therapeutic correction of both compound heterozygous and autosomal dominant mutations, and they identify a mechanistic origin for prominent but poorly understood mutagenic signatures in cancer.
Direct kinetic fingerprinting and digital counting of single protein molecules
Authors: Chatterjee Tanmay , Knappik Achim , Sandford Erin , Tewari Muneesh , Choi Sung Won , Strong William B. , Thrush Evan P. , Oh Kenneth J. , Liu Ning , Walter Nils G. , Johnson-Buck Alexander
Published: September 2020

Significance

The sensitive measurement of specific protein biomarkers is important for medical diagnostics and research. However, existing methods for quantifying proteins use antibody probes that cannot distinguish between specific and nonspecific binding, limiting their sensitivity and specificity. This work establishes a method for distinguishing between specific binding to the target protein and nonspecific binding to assay surfaces using single-molecule kinetic measurements with dynamically binding probes. This is significant because it permits extremely sensitive protein measurements without requiring a high-affinity detection antibody or any washing steps, enabling streamlined and sensitive quantification of proteins even when no pair of high-quality, tightly binding antibodies is available.
Defining an amyloid link Between Parkinson’s disease and melanoma
Authors: Dean Dexter N. , Lee Jennifer C.
Published: September 2020

An epidemiological connection exists between Parkinson’s disease (PD) and melanoma. α-Synuclein (α-syn), the hallmark pathological amyloid observed in PD, is also elevated in melanoma, where its expression is inversely correlated with melanin content. We present a hypothesis that there is an amyloid link between α-syn and Pmel17 (premelanosomal protein), a functional amyloid that promotes melanogenesis. Using SK-MEL 28 human melanoma cells, we show that endogenous α-syn is present in melanosomes, the organelle where melanin polymerization occurs. Using in vitro cross-seeding experiments, we show that α-syn fibrils stimulate the aggregation of a Pmel17 fragment constituting the repeat domain (RPT), an amyloidogenic domain essential for fibril formation in melanosomes. The cross-seeded fibrils exhibited α-syn−like ultrastructural features that could be faithfully propagated over multiple generations. This cross-seeding was unidirectional, as RPT fibrils did not influence α-syn aggregation. These results support our hypothesis that α-syn, a pathogenic amyloid, modulates Pmel17 aggregation in the melanosome, defining a molecular link between PD and melanoma.
Human γδ T cells recognize CD1b by two distinct mechanisms
Authors: Reijneveld Josephine F. , Ocampo Tonatiuh A. , Shahine Adam , Gully Benjamin S. , Vantourout Pierre , Hayday Adrian C. , Rossjohn Jamie , Moody D. Branch , Van Rhijn Ildiko
Published: September 2020

Significance

γδ T cells are an abundant component of the human immune system that protect against infection and cancer. Here we show that γδ T cells recognize CD1b proteins, which are known for their capacity to present lipid antigens to αβ T cells. Recognition of CD1b is dependent on the presented lipid antigen for some γδ T cells, but a lipid-independent pattern was also observed. Thus, γδ T cells show diversity in the type of protein recognized as well as differing surfaces of the protein.
Public perceptions of federal science advisory boards depend on their composition
Authors: Drummond Caitlin , Gray Sara Goto , Raimi Kaitlin T. , Wilson Robyn , Árvai Joseph
Published: September 2020

The United States Environmental Protection Agency (EPA) Science Advisory Board (SAB) provides expert advice to inform agency decision-making. Recent regulations have decreased the representation of academic scientists on the EPA SAB and increased the representation of industry scientists. In an experiment, we asked how the US public views the goals and legitimacy of the board as a function of its composition. Respondents perceived SABs with a majority of industry scientists to be more likely to promote business interests than SABs with a majority of academic scientists. Liberals were less likely than conservatives to perceive industry-majority SABs as promoting human health and the environment, and making unbiased and evidence-based decisions. Our findings underscore the potential for politicization of scientific advice to the government.
Cat-flap micro-pendulum for low noise optomechanics
Authors: Ying Ma-ke , Chen Xu , Hsu Yu-ying , Tsai Dung-sheng , Pan Huang-wei , Chao Shiuh , Sunderland Andrew , Page Michael , Neil Benjamin , Ju Li , Zhao chun-nong , Blair David
Published: September 2020

Microresonators with high Q-factor are essential components for optomechanical experiments. Here we report on the development of ‘cat-flap’ micro-pendulums consisting of sub-millimetre scale micromirrors supported by nanometre-thickness flexures. The micromirror pendulum is designed to achieve the lowest possible flexure stiffness, which enables maximal dilution of mechanical losses through the use of optical springs. An angular spring constant of

1
×

10

−
9

N

⋅

m/radian

, corresponding to a fundamental frequency (in the absence of gravity) of 18 Hz has been demonstrated. It is shown that Q-factors up to

10
8

at an optical spring frequency of 25 kHz could be achieved with these pendulums. By extrapolating the measurement results to a sample with a double thickness mirror pad, we estimate that it may be possible to achieve a Q-factor of

5
×

10
8

at 100 kHz at room temperature.
Emission spectroscopic diagnostics of weakly ionized argon-diluted plasmas: glow discharge and inductively coupled plasma
Authors: Weiss Zdeněk
Published: September 2020

An extensive study of Mn, Fe, Ti, Cr, Cu emission spectra from a Grimm-type glow discharge (GDOES) and an inductively coupled plasma (ICP), in argon, was performed, using the formalism of population functions (experimental Boltzmann plots) and transition rate diagrams. Emission characteristics of both spectral sources were compared, with the following results: in both discharges the excitation of neutral metal atoms (Me I) is dominated by electron impact (EI), however, in the excitation of singly charged ions (Me II) the charge transfer between Ar+ ions and Me I plays a significant role, especially in GDOES. Relative populations of singly charged excited ions compared to the population of excited neutral atoms of the same element are much higher in ICP than GDOES. Deviations from local thermodynamic equilibrium were identified. Besides charge transfer reactions with Ar+ ions they are caused by a low electron density in the plasma. The experimental ‘excitation temperatures’ follow a pattern predicted by computer simulations with a collisional-radiative model: they are lower than the actual electron temperature, while this deviation is greater for the Me I system than Me II.
Break-even year: a concept for understanding intergenerational trade-offs in climate change mitigation policy
Authors: Brown Patrick T , Moreno-Cruz Juan , Caldeira Ken
Published: September 2020

Global climate change mitigation is often framed in public discussions as a tradeoff between environmental protection and harm to the economy. However, climate-economy models have consistently calculated that the immediate implementation of greenhouse gas emissions restriction (via e.g. a global carbon price) would be in humanity’s best interest on purely economic grounds. Despite this, the implementation of global climate policy has been notoriously difficult to achieve. This evokes an apparent paradox: if the implementation of a global carbon price is not only beneficial to the environment, but is also ‘economically optimal’, why has it been so difficult to enact? One potential reason for this difficulty is that economically optimal greenhouse gas emissions restrictions are not economically beneficial for the generation of people that launch them. The purpose of this article is to explore this issue by introducing the concept of the break-even year, which we define as the year when the economically optimal policy begins to produce global mean net economic benefits. We show that in a commonly used climate-economy model (DICE), the break-even year is relatively far into the future—around 2080 for mitigation policy beginning in the early 2020s. Notably, the break-even year is not sensitive to the uncertain magnitudes of the costs of climate change mitigation policy or the costs of economic damages from climate change. This result makes it explicit and understandable why an economically optimal policy can be difficult to implement in practice.
The pleurogram, an under-investigated functional trait in seeds
Authors: Rodrigues-Junior Ailton G , Baskin Carol C , Baskin Jerry M , De-Paula Orlando C
Published: September 2020

Background

A structure called the pleurogram makes up a large part of the seed coat of some species in subfamilies Caesalpinioideae and Mimosoideae of Fabaceae, but little is known about its function. It has been hypothesized that this structure acts as a hygroscopic valve during the maturation drying of seeds. However, a new hypothesis has recently emerged that proposes a distinct function for the pleurogram.

Scope

Here, we provide an overview of the structure and function of the pleurogram, which is diverse and complex. This large structure can be dislodged, thereby creating a pathway for water entry into water-impermeable seeds. However, the pleurogram is non-functional as a pathway of water into the seed of some species. Thus, the evolutionary history of species with a pleurogram may be related to a loss/gain in its function. A complete model for the function of the pleurogram is proposed.

Conclusions

The pleurogram may act on several stages of the seed, from maturation to germination. As a hygroscopic valve, it regulates dehydration of the seed during maturation. As a pathway for water entry into the seed, the pleurogram acts as a water gap in seeds with physical dormancy, thereby regulating dormancy break/germination. The occurrence of a pleurogram in several genera of legumes and Cucurbitaceae is confirmed. Single or multiple pleurograms can serve as (the) point(s) of water entry into seeds that do not otherwise have a hilar water gap.
Fast gap-affine pairwise alignment using the wavefront algorithm
Authors: Marco-Sola Santiago , Moure Juan Carlos , Moreto Miquel , Espinosa Antonio
Published: September 2020

Motivation

Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields.

Results

In this article, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s2) memory. Furthermore, our algorithm exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code. We evaluate the performance of our algorithm, together with other state-of-the-art implementations. As a result, we demonstrate that the WFA runs 20–300× faster than other methods aligning short Illumina-like sequences, and 10–100× faster using long noisy reads like those produced by Oxford Nanopore Technologies.

Availability and implementation

The WFA algorithm is implemented within the wavefront-aligner library, and it is publicly available at https://github.com/smarco/WFA.
Evaluation of treatment effect modification by biomarkers measured pre- and post-randomization in the presence of non-monotone missingness
Authors: Zhuang Yingying , Huang Ying , Gilbert Peter B
Published: September 2020

In vaccine studies, an important research question is to study effect modification of clinical treatment efficacy by intermediate biomarker-based principal strata. In settings where participants entering a trial may have prior exposure and therefore variable baseline biomarker values, clinical treatment efficacy may further depend jointly on a biomarker measured at baseline and measured at a fixed time after vaccination. This makes it important to conduct a bivariate effect modification analysis by both the intermediate biomarker-based principal strata and the baseline biomarker values. Existing research allows this assessment if the sampling of baseline and intermediate biomarkers follows a monotone pattern, i.e., if participants who have the biomarker measured post-randomization would also have the biomarker measured at baseline. However, additional complications in study design could happen in practice. For example, in a dengue correlates study, baseline biomarker values were only available from a fraction of participants who have biomarkers measured post-randomization. How to conduct the bivariate effect modification analysis in these studies remains an open research question. In this article, we propose approaches for bivariate effect modification analysis in the complicated sampling design based on an estimated likelihood framework. We demonstrate advantages of the proposed method over existing methods through numerical studies and illustrate our method with data sets from two phase 3 dengue vaccine efficacy trials.
‘Inspiring Conversations’: A Comparative Analysis of the Involvement of Experts by Experience in Italian and Scottish Social Work Education
Authors: Cabiati Elena , Levy Susan
Published: September 2020

The involvement of service users and carers, Experts by Experience (EBE), in social work education at the Catholic University of Milan, Italy, and the University of Dundee, Scotland, is rooted and connected epistemologically and pedagogically. Differences emerge in how these roots are manifest in the models of EBE involvement adopted in the two universities. This article explores these similarities and differences through discussion of the different models of EBE involvement in use at the two European universities, and thus provides a comparative European insight into approaches, experiences and impact of EBE involvement in social work education. The authors contextualise the pedagogy and core values underpinning EBE involvement and introduce the concept of ‘inspiring conversations’. The comparative analysis is centred on five areas of EBE involvement in social work education: context and types of involvement; recruitment of EBE; roles and responsibilities of EBE; resource implications; and impact and outcomes of involvement. The article calls for a focus on ‘Coherence’, ‘Prudence’ and ‘Sustainability’ as a foundation for other universities to enhance their social work programmes through cultivating EBE involvement to co-create knowledge to inform future innovative practice.
Quality Assessment of Sitopaladi Churna Using High-Performance Liquid Chromatography Coupled with Multivariate Analysis
Authors: Patel Nikunj D , Prajapati Prajesh N , Kanaki Niranjan S
Published: September 2020

“Sitopaladi churna,” a well-known formulation of Ayurveda, is prescribed to treat the disease like Bronchitis, Pneumonia, allergic conditions, viral infection of the respiratory tract and as a natural antioxidant. A novel method based on reversed-phase high-performance liquid chromatography (RP-HPLC) coupled to photodiode array detector was established and validated for sitopaladi churna. Here, HPLC fingerprints data obtained for 28 samples including standard sample were then treated to chemometric analysis like principal component analysis and hierarchical clustering analysis for further analysis to evaluate the differences in market samples of sitopaladi churna. Additionally, one major marker compound, piperine was quantified and it also facilitated for relative retention time. The simulative mean spectrum was also generated. The validation results showed that the developed method was simple, precise and stable. Thus, the developed chromatographic method adjoined with multivariate analysis can be used as an efficient and practical approach for quality assessment of sitopaladi churna.
Diagnostic Value of Clinical Features to Distinguish Enteric Fever From Other Febrile Illnesses in Bangladesh, Nepal, and Pakistan
Authors: Aiemjoy Kristen , Tamrakar Dipesh , Saha Shampa , Naga Shiva R , Yu Alexander T , Longley Ashley , Date Kashmira , Hemlock Caitlin , Qamar Farah N , Saha Samir K , Luby Stephen P , Garrett Denise O , Andrews Jason R , Bogoch Isaac I
Published: September 2020

Background

Enteric fever, a bacterial infection caused by Salmonella enterica serotypes Typhi and Paratyphi A, frequently presents as a nonlocalizing febrile illness that is difficult to distinguish from other infectious causes of fever. Blood culture is not widely available in endemic settings and, even when available, results can take up to 5 days. We evaluated the diagnostic performance of clinical features, including both reported symptoms and clinical signs, of enteric fever among patients participating in the Surveillance for Enteric Fever in Asia Project (SEAP), a 3-year surveillance study in Bangladesh, Nepal, and Pakistan.

Methods

Outpatients presenting with ≥3 consecutive days of reported fever and inpatients with clinically suspected enteric fever from all 6 SEAP study hospitals were eligible to participate. We evaluated the diagnostic performance of select clinical features against blood culture results among outpatients using mixed-effect regression models with a random effect for study site hospital. We also compared the clinical features of S. Typhi to S. Paratyphi A among both outpatients and inpatients.

Results

We enrolled 20 899 outpatients, of whom 2116 (10.1%) had positive blood cultures for S. Typhi and 297 (1.4%) had positive cultures for S. Paratyphi A. The sensitivity of absence of cough was the highest among all evaluated features, at 65.5% (95% confidence interval [CI], 55.0–74.7), followed by measured fever at presentation at 59.0% (95% CI, 51.6–65.9) and being unable to complete normal activities for 3 or more days at 51.0% (95% CI, 23.8–77.6). A combined case definition of 3 or more consecutive days of reported fever and 1 or more of the following (a) either the absence of cough, (b) fever at presentation, or (c) 3 or more consecutive days of being unable to conduct usual activity--yielded a sensitivity of 94.6% (95% CI, 93.4–95.5) and specificity of 13.6% (95% CI, 9.8–17.5).

Conclusions

Clinical features do not accurately distinguish blood culture–confirmed enteric fever from other febrile syndromes. Rapid, affordable, and accurate diagnostics are urgently needed, particularly in settings with limited or no blood culture capacity.