bluuebunny/crossref_metadata_2025 huggingface dataset:
Isomorphisms and elementary equivalence of Chevalley groups over commutative rings
Authors: Bunina E. I.
Published: April 2019

It is proved that two Chevalley groups with indecomposable root systems of rank

over commutative rings (which contain in addition

for the types

,

,

,

, and

, and

for the type

) are isomorphic or elementarily equivalent if and only if the corresponding root systems coincide, the weight lattices of the representation of the Lie algebra coincide, and the rings are isomorphic or elementarily equivalent, respectively. The isomorphisms of adjoint (elementary) Chevalley groups over the rings of the above types are also described.

Bibliography: 25 titles.
Two-sided estimates for domains of univalence for classes of holomorphic self-maps of a disc with two fixed points
Authors: Kudryavtseva O. S. , Solodov A. P.
Published: April 2019

We investigate the class of holomorphic maps of a disc into itself that have an interior and a boundary fixed point, as well as the class of holomorphic maps of a half-plane into itself that have a fixed point in the interior of the domain and a fixed point at infinity. Two-sided estimates for domains of univalence are obtained for these function classes in terms of the values of the angular derivative at the boundary fixed point and the position of the interior fixed point.

Bibliography: 21 titles.
On maximizers of a convolution operator in

-spaces
Authors: Kalachev G. V. , Sadov S. Yu.
Published: April 2019

The paper is concerned with convolution operators in

, whose kernels are in

, which act from

into

, where

. It is shown that for

there exists a maximizer (a function with

-norm 1) at which the supremum of the

-norm of the convolution is attained. A special analysis is carried out for the cases in which one of the exponents

,

, or

is

or

.

Bibliography: 12 titles.
The Pliś metric and Lipschitz stability of minimization problems
Authors: Balashov M. V.
Published: April 2019

We study the metric introduced by Pliś on the set of convex closed bounded subsets of a Banach space. For a real Hilbert space it is proved that metric projection and (under certain conditions) metric antiprojection from a point onto a set satisfy a Lipschitz condition with respect to the set in the Pliś metric. It is proved that solutions of a broad class of minimization problems are also Lipschitz stable with respect to the set. Several examples are discussed.

Bibliography: 18 titles.
Convex trigonometry with applications to sub-Finsler geometry
Authors: Lokutsievskiy L. V.
Published: April 2019

A new convenient method for describing flat convex compact sets and their polar sets is proposed. It generalizes the classical trigonometric functions

and

. It is apparent that this method can be very useful for an explicit description of solutions of optimal control problems with two-dimensional control. Using this method a series of sub-Finsler problems with two-dimensional control lying in an arbitrary convex set

is investigated. Namely, problems on the Heisenberg, Engel, and Cartan groups and also Grushin’s and Martinet’s cases are considered. Particular attention is paid to the case when

is a convex polygon.

Bibliography: 13 titles.
An approach problem for a control system and a compact set in the phase space in the presence of phase constraints
Authors: Ershov A. A. , Ushakov A. V. , Ushakov V. N.
Published: April 2019

A control system with a phase constraint is considered in a finite-dimensional Euclidean space. The problem of making this system approach the target set at a fixed time instant is studied. A method for constructing an approximate solution to the approach problem is given, which involves the concept of the solvability set of an approach problem.

Bibliography: 24 titles.
Conflict across representational gaps: Threats to and opportunities for improved communication
Authors: Cronin Matthew A. , Weingart Laurie R.
Published: April 2019

Often, the senders and receivers of scientific communication have different knowledge bases. While such communication is essential for solving the complex social and technological problems that affect multiple stakeholders, a diversity of knowledge among communicators can create representational gaps (rGaps). rGaps occur when senders make assumptions that receivers do not, creating conflict over the meaning and value of the information communicated. Such conflict could, if managed, promote learning and innovation as communicators reconcile their assumptions. More often, however, rGaps cause conflict to transform from a debate that informs to an argument that divides. Managing rGap conflict so that it does not degrade communication requires relationship building to mitigate the negative by-products of persistent conflict while maintaining appropriate levels of cognitive distinctiveness among diverse stakeholders. Thus, we provide a framework for identifying and leveraging rGaps through managed conflict so that communication between those with different perspectives builds rather than burns bridges.
Same-sex marriage legalization associated with reduced implicit and explicit antigay bias
Authors: Ofosu Eugene K. , Chambers Michelle K. , Chen Jacqueline M. , Hehman Eric
Published: April 2019

The current research tested whether the passing of government legislation, signaling the prevailing attitudes of the local majority, was associated with changes in citizens’ attitudes. Specifically, with ∼1 million responses over a 12-y window, we tested whether state-by-state same-sex marriage legislation was associated with decreases in antigay implicit and explicit bias. Results across five operationalizations consistently provide support for this possibility. Both implicit and explicit bias were decreasing before same-sex marriage legalization, but decreased at a sharper rate following legalization. Moderating this effect was whether states passed legislation locally. Although states passing legislation experienced a greater decrease in bias following legislation, states that never passed legislation demonstrated increased antigay bias following federal legalization. Our work highlights how government legislation can inform individuals’ attitudes, even when these attitudes may be deeply entrenched and socially and politically volatile.
Fast and robust active neuron segmentation in two-photon calcium imaging using spatiotemporal deep learning
Authors: Soltanian-Zadeh Somayyeh , Sahingur Kaan , Blau Sarah , Gong Yiyang , Farsiu Sina
Published: April 2019

Calcium imaging records large-scale neuronal activity with cellular resolution in vivo. Automated, fast, and reliable active neuron segmentation is a critical step in the analysis workflow of utilizing neuronal signals in real-time behavioral studies for discovery of neuronal coding properties. Here, to exploit the full spatiotemporal information in two-photon calcium imaging movies, we propose a 3D convolutional neural network to identify and segment active neurons. By utilizing a variety of two-photon microscopy datasets, we show that our method outperforms state-of-the-art techniques and is on a par with manual segmentation. Furthermore, we demonstrate that the network trained on data recorded at a specific cortical layer can be used to accurately segment active neurons from another layer with different neuron density. Finally, our work documents significant tabulation flaws in one of the most cited and active online scientific challenges in neuron segmentation. As our computationally fast method is an invaluable tool for a large spectrum of real-time optogenetic experiments, we have made our open-source software and carefully annotated dataset freely available online.
A diecast mineralization process forms the tough mantis shrimp dactyl club
Authors: Amini Shahrouz , Tadayon Maryam , Loke Jun Jie , Kumar Akshita , Kanagavel Deepankumar , Le Ferrand Hortense , Duchamp Martial , Raida Manfred , Sobota Radoslaw M. , Chen Liyan , Hoon Shawn , Miserez Ali
Published: April 2019

Biomineralization, the process by which mineralized tissues grow and harden via biogenic mineral deposition, is a relatively lengthy process in many mineral-producing organisms, resulting in challenges to study the growth and biomineralization of complex hard mineralized tissues. Arthropods are ideal model organisms to study biomineralization because they regularly molt their exoskeletons and grow new ones in a relatively fast timescale, providing opportunities to track mineralization of entire tissues. Here, we monitored the biomineralization of the mantis shrimp dactyl club—a model bioapatite-based mineralized structure with exceptional mechanical properties—immediately after ecdysis until the formation of the fully functional club and unveil an unusual development mechanism. A flexible membrane initially folded within the club cavity expands to form the new club’s envelope. Mineralization proceeds inwards by mineral deposition from this membrane, which contains proteins regulating mineralization. Building a transcriptome of the club tissue and probing it with proteomic data, we identified and sequenced Club Mineralization Protein 1 (CMP-1), an abundant mildly phosphorylated protein from the flexible membrane suggested to be involved in calcium phosphate mineralization of the club, as indicated by in vitro studies using recombinant CMP-1. This work provides a comprehensive picture of the development of a complex hard tissue, from the secretion of its organic macromolecular template to the formation of the fully functional club.
Intrinsic planar polarity mechanisms influence the position-dependent regulation of synapse properties in inner hair cells
Authors: Jean Philippe , Özçete Özge Demet , Tarchini Basile , Moser Tobias
Published: April 2019

Significance

The wide dynamic range of sound encoding enables perception of sounds varying over six orders of magnitude, thought to be collectively achieved by distinct classes of type I spiral ganglion neurons (SGNs) contacting each inner hair cell (IHC). These synaptic contacts have been shown to vary according to the SGN firing properties along the modiolar–pillar axis. It has also been shown that the IHCs spatially segregate active zones (AZs) with different Ca2+-influx properties, proposing an attractive candidate mechanism for the diverse sound encoding properties among SGNs. Our study, combining confocal/STED immunofluorescence microscopy, patch-clamp, and Ca2+imaging, proposes that Gαi and LGN, involved in planar polarity mechanisms at the IHC apex, contribute to establish the spatial gradient of IHC AZ properties.
Distinct segregation patterns of yeast cell-peripheral proteins uncovered by a method for protein segregatome analysis
Authors: Sugiyama Shinju , Tanaka Motomasa
Published: April 2019

Protein segregation contributes to various cellular processes such as polarization, differentiation, and aging. However, the difficulty in global determination of protein segregation hampers our understanding of its mechanisms and physiological roles. Here, by developing a quantitative proteomics technique, we globally monitored segregation of preexisting and newly synthesized proteins during cell division of budding yeast, and identified crucial domains that determine the segregation of cell-peripheral proteins. Remarkably, the proteomic and subsequent microscopic analyses demonstrated that the flow through the bud neck of the proteins that harbor both endoplasmic reticulum (ER) membrane-spanning and plasma membrane (PM)-binding domains is not restricted by the previously suggested ER membrane or PM diffusion barriers but by septin-mediated partitioning of the PM-associated ER (pmaER). Furthermore, the proteomic analysis revealed that although the PM-spanning t-SNARE Sso2 was retained in mother cells, its paralog Sso1 unexpectedly showed symmetric localization. We found that the transport of Sso1 to buds was required for enhancement of polarized cell growth and resistance to cell-wall stress. Taken together, these data resolve long-standing questions about septin-mediated compartmentalization of the cell periphery, and provide new mechanistic insights into the segregation of cell-periphery proteins and their cellular functions.
Structural insight into TRPV5 channel function and modulation
Authors: Dang Shangyu , van Goor Mark K. , Asarnow Daniel , Wang YongQiang , Julius David , Cheng Yifan , van der Wijst Jenny
Published: April 2019

TRPV5 (transient receptor potential vanilloid 5) is a unique calcium-selective TRP channel essential for calcium homeostasis. Unlike other TRPV channels, TRPV5 and its close homolog, TRPV6, do not exhibit thermosensitivity or ligand-dependent activation but are constitutively open at physiological membrane potentials and modulated by calmodulin (CaM) in a calcium-dependent manner. Here we report high-resolution electron cryomicroscopy structures of truncated and full-length TRPV5 in lipid nanodiscs, as well as of a TRPV5 W583A mutant and TRPV5 in complex with CaM. These structures highlight the mechanism of calcium regulation and reveal a flexible stoichiometry of CaM binding to TRPV5.
GUN1 interacts with MORF2 to regulate plastid RNA editing during retrograde signaling
Authors: Zhao Xiaobo , Huang Jianyan , Chory Joanne
Published: April 2019

During development or under stress, chloroplasts generate signals that regulate the expression of a large number of nuclear genes, a process called retrograde signaling. GENOMES UNCOUPLED 1 (GUN1) is an important regulator of this pathway. In this study, we have discovered an unexpected role for GUN1 in plastid RNA editing, as
gun1
mutations affect RNA-editing efficiency at multiple sites in plastids during retrograde signaling. GUN1 plays a direct role in RNA editing by physically interacting with MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2).
MORF2
overexpression causes widespread RNA-editing changes and a strong
genomes uncoupled
(
gun
) molecular phenotype similar to
gun1
. MORF2 further interacts with RNA-editing site-specificity factors: ORGANELLE TRANSCRIPT PROCESSING 81 (OTP81), ORGANELLE TRANSCRIPT PROCESSING 84 (OTP84), and YELLOW SEEDLINGS 1 (YS1). We further show that
otp81
,
otp84
, and
ys1
single mutants each exhibit a very weak
gun
phenotype, but combining the three mutations enhances the phenotype. Our study uncovers a role for GUN1 in the regulation of RNA-editing efficiency in damaged chloroplasts and suggests that MORF2 is involved in retrograde signaling.
Characterizing the cultural niches of North American birds
Authors: Schuetz Justin G. , Johnston Alison
Published: April 2019

Significance

Conservation of species is driven largely by human decisions, so it is important to understand how and why people value species differently. We combine information from Google searches with millions of bird observations to characterize public interest in North American birds. We describe different relationships between people and birds based on the volume and spatial patterns of these searches. For example, “celebrity” birds attract high numbers of Google searches, even where they do not occur; large birds are generally more popular than small birds; and endangered species attract interest in the regions where they occur. Our results provide a framework for beginning to explore complex relationships between humans and other species and help to inform bird conservation strategies.
Functional connectomics of affective and psychotic pathology
Authors: Baker Justin T. , Dillon Daniel G. , Patrick Lauren M. , Roffman Joshua L. , Brady Roscoe O. , Pizzagalli Diego A. , Öngür Dost , Holmes Avram J.
Published: April 2019

Significance

Historically, most research on the biological origins of psychiatric illness has focused on individual diagnostic categories, studied in isolation. Mounting evidence indicates that nominally distinct psychiatric diagnoses are not separated by clear neurobiological boundaries. Here, we derive functional connectomic signatures in over 1,000 individuals, including patients presenting with different categories of impairment (psychosis), clinical diagnoses, and severity of illness as reflected in treatment seeking. Our analyses reveal features of connectome functioning that are commonly disrupted across distinct forms of pathology, scaling with clinical severity. Conversely, other aspects of network connectivity were preferentially disrupted in patients with psychotic illness. These data have important implications for the establishment of functional connectome fingerprints of severe mental disease.
Disconnection description of triple-junction motion
Authors: Thomas Spencer L. , Wei Chaozhen , Han Jian , Xiang Yang , Srolovitz David J.
Published: April 2019

Significance

Many materials of industrial and scientific interest (including metals and ceramics) are polycrystalline. The defect microstructure of these materials has a profound impact on their properties and utility. Microstructure engineering yields materials with greatly enhanced qualities, but the microstructure typically evolves over time via the motion of grain boundaries and triple junctions. One must understand and guide this evolution to produce reliable enhanced materials. Much has been discovered in recent decades regarding the motion of grain boundaries—less so regarding triple junctions. This work presents observations of triple-junction migration from atomistic simulations, explains these observations by extending recent developments in grain boundary theory to triple junctions, and presents a continuum model of triple-junction migration based on this theory.
Functional characterization of 3D protein structures informed by human genetic diversity
Authors: Hicks Michael , Bartha Istvan , di Iulio Julia , Venter J. Craig , Telenti Amalio
Published: April 2019

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. Structural intolerance data correlated with deep mutational scanning functional readouts for PPARG, MAPK1/ERK2, UBE2I, SUMO1, PTEN, CALM1, CALM2, and TPK1 and with shallow mutagenesis data for 1,026 proteins. The 3D structural intolerance analysis revealed different features for ligand binding pockets and orthosteric and allosteric sites. Large-scale data on human genetic variation support a definition of functional 3D sites proteome-wide.
Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution
Authors: Heng Jacob S. , Rattner Amir , Stein-O’Brien Genevieve L. , Winer Briana L. , Jones Bryan W. , Vernon Hilary J. , Goff Loyal A. , Nathans Jeremy
Published: April 2019

The mammalian CNS is capable of tolerating chronic hypoxia, but cell type-specific responses to this stress have not been systematically characterized. In the Norrin KO (NdpKO) mouse, a model of familial exudative vitreoretinopathy (FEVR), developmental hypovascularization of the retina produces chronic hypoxia of inner nuclear-layer (INL) neurons and Muller glia. We used single-cell RNA sequencing, untargeted metabolomics, and metabolite labeling from13C-glucose to compare WT andNdpKOretinas. InNdpKOretinas, we observe gene expression responses consistent with hypoxia in Muller glia and retinal neurons, and we find a metabolic shift that combines reduced flux through the TCA cycle with increased synthesis of serine, glycine, and glutathione. We also used single-cell RNA sequencing to compare the responses of individual cell types inNdpKOretinas with those in the hypoxic cerebral cortex of mice that were housed for 1 week in a reduced oxygen environment (7.5% oxygen). In the hypoxic cerebral cortex, glial transcriptome responses most closely resemble the response of Muller glia in theNdpKOretina. In both retina and brain, vascular endothelial cells activate a previously dormant tip cell gene expression program, which likely underlies the adaptive neoangiogenic response to chronic hypoxia. These analyses of retina and brain transcriptomes at single-cell resolution reveal both shared and cell type-specific changes in gene expression in response to chronic hypoxia, implying both shared and distinct cell type-specific physiologic responses.
Inherited predisposition to malignant mesothelioma and overall survival following platinum chemotherapy
Authors: Hassan Raffit , Morrow Betsy , Thomas Anish , Walsh Tom , Lee Ming K. , Gulsuner Suleyman , Gadiraju Meghana , Panou Vasiliki , Gao Shaojian , Mian Idrees , Khan Javed , Raffeld Mark , Patel Snehal , Xi Liqiang , Wei Jun S. , Hesdorffer Mary , Zhang Jingli , Calzone Kathleen , Desai Arpita , Padiernos Emerson , Alewine Christine , Schrump David S. , Steinberg Seth M. , Kindler Hedy L. , King Mary-Claire , Churpek Jane E.
Published: April 2019

Significance

Survival from malignant mesothelioma, particularly pleural mesothelioma, is very poor. For patients with some cancers, overall survival following platinum chemotherapy is better for patients with germline mutations in DNA repair and related genes than for patients without such mutations. We evaluated this relationship for patients with malignant mesothelioma. Following platinum chemotherapy, overall survival was significantly longer for patients with loss-of-function mutations in
BAP1
and DNA repair genes compared with patients with no such mutations. The effect of genotype was highly significant for patients with pleural mesothelioma, but not for patients with peritoneal mesothelioma, and remained significant after adjusting for gender and age at diagnosis. These patients may benefit from DNA repair targeted therapies such as poly-ADP ribose polymerase inhibitors.
Giant nonvolatile resistive switching in a Mott oxide and ferroelectric hybrid
Authors: Salev Pavel , del Valle Javier , Kalcheim Yoav , Schuller Ivan K.
Published: April 2019

Significance

New materials are currently investigated as a basis for energy-efficient computational paradigms such as neuromorphic computing. In materials exhibiting a metal–insulator transition (MIT), a small stimulus can trigger a large change in electrical conductivity. This can be used to mimic brain-spiking activity in biologically inspired electronics. Enabling continuous, nonvolatile, and reversible tuning of the MIT is important for implementing learning algorithms. Here we demonstrate an unprecedentedly large, voltage-controlled MIT temperature modulation and resistive switching in a Mott-oxide/ferroelectric heterostructure. Our results imply this effect is produced by strain tuning of the structural phase transition (SPT) which is coupled to the MIT. Since many Mott oxides have concurrent MIT and SPT, our results are directly relevant to a broad range of correlated oxides heterostructures.
Constitutive release of CPS1 in bile and its role as a protective cytokine during acute liver injury
Authors: Park Min-Jung , D’Alecy Louis G. , Anderson Michelle A. , Basrur Venkatesha , Feng Yongjia , Brady Graham F. , Kim Dong-il , Wu Jun , Nesvizhskii Alexey I. , Lahann Joerg , Lukacs Nicholas W. , Fontana Robert J. , Omary M. Bishr
Published: April 2019

Carbamoyl phosphate synthetase-1 (CPS1) is the major mitochondrial urea cycle enzyme in hepatocytes. It is released into mouse and human blood during acute liver injury, where is has a short half-life. The function of CPS1 in blood and the reason for its short half-life in serum are unknown. We show that CPS1 is released normally into mouse and human bile, and pathologically into blood during acute liver injury. Other cytoplasmic and mitochondrial urea cycle enzymes are also found in normal mouse bile. Serum, bile, and purified CPS1 manifest sedimentation properties that overlap with extracellular vesicles, due to the propensity of CPS1 to aggregate despite being released primarily as a soluble protein. During liver injury, CPS1 in blood is rapidly sequestered by monocytes, leading to monocyte M2-polarization and homing to the liver independent of its enzyme activity. Recombinant CPS1 (rCPS1), but not control r-transferrin, increases hepatic macrophage numbers and phagocytic activity. Notably, rCPS1 does not activate hepatic macrophages directly; rather, it activates bone marrow and circulating monocytes that then home to the liver. rCPS1 administration prevents mouse liver damage induced by Fas ligand or acetaminophen, but this protection is absent in macrophage-deficient mice. Moreover, rCPS1 protects from acetaminophen-induced liver injury even when given therapeutically after injury induction. In summary, CPS1 is normally found in bile but is released by hepatocytes into blood upon liver damage. We demonstrate a nonenzymatic function of CPS1 as an antiinflammatory protective cytokine during acute liver injury.
Reduced default mode network functional connectivity in patients with recurrent major depressive disorder
Authors: Yan Chao-Gan , Chen Xiao , Li Le , Castellanos Francisco Xavier , Bai Tong-Jian , Bo Qi-Jing , Cao Jun , Chen Guan-Mao , Chen Ning-Xuan , Chen Wei , Cheng Chang , Cheng Yu-Qi , Cui Xi-Long , Duan Jia , Fang Yi-Ru , Gong Qi-Yong , Guo Wen-Bin , Hou Zheng-Hua , Hu Lan , Kuang Li , Li Feng , Li Kai-Ming , Li Tao , Liu Yan-Song , Liu Zhe-Ning , Long Yi-Cheng , Luo Qing-Hua , Meng Hua-Qing , Peng Dai-Hui , Qiu Hai-Tang , Qiu Jiang , Shen Yue-Di , Shi Yu-Shu , Wang Chuan-Yue , Wang Fei , Wang Kai , Wang Li , Wang Xiang , Wang Ying , Wu Xiao-Ping , Wu Xin-Ran , Xie Chun-Ming , Xie Guang-Rong , Xie Hai-Yan , Xie Peng , Xu Xiu-Feng , Yang Hong , Yang Jian , Yao Jia-Shu , Yao Shu-Qiao , Yin Ying-Ying , Yuan Yong-Gui , Zhang Ai-Xia , Zhang Hong , Zhang Ke-Rang , Zhang Lei , Zhang Zhi-Jun , Zhou Ru-Bai , Zhou Yi-Ting , Zhu Jun-Juan , Zou Chao-Jie , Si Tian-Mei , Zuo Xi-Nian , Zhao Jing-Ping , Zang Yu-Feng
Published: April 2019

Major depressive disorder (MDD) is common and disabling, but its neuropathophysiology remains unclear. Most studies of functional brain networks in MDD have had limited statistical power and data analysis approaches have varied widely. The REST-meta-MDD Project of resting-state fMRI (R-fMRI) addresses these issues. Twenty-five research groups in China established the REST-meta-MDD Consortium by contributing R-fMRI data from 1,300 patients with MDD and 1,128 normal controls (NCs). Data were preprocessed locally with a standardized protocol before aggregated group analyses. We focused on functional connectivity (FC) within the default mode network (DMN), frequently reported to be increased in MDD. Instead, we found decreased DMN FC when we compared 848 patients with MDD to 794 NCs from 17 sites after data exclusion. We found FC reduction only in recurrent MDD, not in first-episode drug-naïve MDD. Decreased DMN FC was associated with medication usage but not with MDD duration. DMN FC was also positively related to symptom severity but only in recurrent MDD. Exploratory analyses also revealed alterations in FC of visual, sensory-motor, and dorsal attention networks in MDD. We confirmed the key role of DMN in MDD but found reduced rather than increased FC within the DMN. Future studies should test whether decreased DMN FC mediates response to treatment. All R-fMRI indices of data contributed by the REST-meta-MDD consortium are being shared publicly via the R-fMRI Maps Project.
On the chain-melted phase of matter
Authors: Naden Robinson Victor , Zong Hongxiang , Ackland Graeme J. , Woolman Gavin , Hermann Andreas
Published: April 2019

Various single elements form incommensurate crystal structures under pressure, where a zeolite-type “host” sublattice surrounds a “guest” sublattice comprising 1D chains of atoms. On “chain melting,” diffraction peaks from the guest sublattice vanish, while those from the host remain. Diffusion of the guest atoms is expected to be confined to the channels in the host sublattice, which suggests 1D melting. Here, we present atomistic simulations of potassium to investigate this phenomenon and demonstrate that the chain-melted phase has no long-ranged order either along or between the chains. This 3D disorder provides the extensive entropy necessary to make the chain melt a true thermodynamic phase of matter, yet with the unique property that diffusion remains confined to 1D only. Calculations necessitated the development of an interatomic forcefield using machine learning, which we show fully reproduces potassium’s phase diagram, including the chain-melted state and 14 known phase transitions.
Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan
Authors: Zhang Lei , Dong Xiao , Lee Moonsook , Maslov Alexander Y. , Wang Tao , Vijg Jan
Published: April 2019

Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell–specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.
Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions
Authors: Dooner Hugo K. , Wang Qinghua , Huang Jun T. , Li Yubin , He Limei , Xiong Wenwei , Du Chunguang
Published: April 2019

While studying spontaneous mutations at the maize
bronze
(
bz
) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new
bz
mutations from several
Bz
stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable
bz
mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous
wx
mutations [Wessler S (1997)
The Mutants of Maize
, pp 385–386]. Similar mutations were recovered at the closely linked
sh
locus. These events occurred with a frequency of 2–4 × 10
−5
in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like
Hopscotch
,
Magellan
, and
Bs2
, a
Bs1
variant, were described previously; others, like
Foto
and
Focou
in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of
Hopscotch
,
Magellan
, and
Bs2
occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.
‘Cold spray +’ as a new hybrid additive manufacturing technology: a literature review
Authors: Li Wenya , Cao Congcong , Wang Guoqing , Wang Feifan , Xu Yaxin , Yang Xiawei
Published: April 2019

Cold spray (CS) is a new solid state coating technique that has attracted considerable attention as it is quite suitable for mass production of metallic materials or metal matrix composites. More recently, cold spray additive manufacturing (CSAM) has been proposed to fabricate/repair components or produce welding joint. However, inherently deficient in ductility/plasticity of CSAMed materials limits its application. Therefore, many hybrid processes have been proposed to further explore CS, which can be grouped together as ‘cold spray +’ hybrid processes (laser, shot peening and friction stir processing). This review will summarise the state-of-the-art of the ‘cold spray +’ processes to show their abilities and their effectiveness. Recommendations for further research and development have been incorporated to help widespread the process.
Rejection of the biophoton hypothesis on the origin of photoreceptor dark noise
Authors: Govardovskii Victor I. , Astakhova Luba A. , Rotov Alexander Yu. , Firsov Michael L.
Published: April 2019

Rod photoreceptors of the vertebrate retina produce, in darkness, spontaneous discrete current waves virtually identical to responses to single photons. The waves comprise an irreducible source of noise (discrete dark noise) that may limit the threshold sensitivity of vision. The waves obviously originate from acts of random activation of single rhodopsin molecules. Until recently, it was generally accepted that the activation occurs due to the rhodopsin thermal motion. Yet, a few years ago it was proposed that rhodopsin molecules are activated not by heat but rather by real photons generated within the retina by chemiluminescence. Using a high-sensitive photomultiplier, we measured intensities of biophoton emission from isolated retinas and eyecups of frogs (Rana ridibunda) and fish (sterlet, Acipenser ruthenus). Retinal samples were placed in a perfusion chamber and emitted photons collected by a high-aperture quartz lens. The collected light was sent to the photomultiplier cathode through a rotating chopper so that a long-lasting synchronous accumulation of the light signal was possible. The absolute intensity of bio-emission was estimated by the response of the measuring system to a calibrated light source. The intensity of the source, in turn, was quantified by measuring rhodopsin bleaching with single-rod microspectrophotometry. We also measured the frequency of discrete dark waves in rods of the two species with suction pipette recordings. Expressed as the rate constant of rhodopsin activation, it was 1.2 × 10−11/s in frogs and 7.6 × 10−11/s in sterlets. Approximately two thirds of retinal samples of each species produced reliably measurable biophoton emissions. However, its intensity was ≥100 times lower than necessary to produce the discrete dark noise. We argue that this is just a lower estimate of the discrepancy between the hypothesis and experiment. We conclude that the biophoton hypothesis on the origin of discrete dark noise in photoreceptors must be rejected.
The effect of low temperature atmospheric nitrogen plasma on MC3T3-E1 preosteoblast proliferation and differentiation in vitro
Authors: Przekora Agata , Pawlat Joanna , Terebun Piotr , Duday David , Canal Cristina , Hermans Sophie , Audemar Maïté , Labay Cédric , Thomann Jean-Sébastien , Ginalska Grazyna
Published: April 2019

The aim of this work was to evaluate the impact of atmospheric pressure nitrogen plasma on viability, proliferation, and osteogenic differentiation of normal mouse calvarial preosteoblasts (MC3T3-E1 Subclone 4), which were maintained in Hanks’ balanced salt solution (HBSS) during plasma exposure. Obtained results clearly demonstrated that short-time (4, 8, and 16 s) nitrogen plasma treatment is non-toxic to the MC3T3-E1 cells, does not affect cell morphology, promotes preosteoblasts’ proliferation, enhances osteogenic differentiation by increasing bone alkaline phosphatase and osteocalcin concentration, but inhibits mineralization of extracellular matrix. The best results were achieved for 16 s exposure time and when the preosteoblasts were left in HBSS for 3 h after plasma treatment. Presented studies indicate great clinical potential of cold atmospheric nitrogen plasma for regenerative medicine applications to improve bone healing process.
Uncertainty analysis in structured laser illumination planar imaging (SLIPI) applied to non-linear signals: gas-phase phosphor thermometry
Authors: Fan Luming , Hochgreb Simone
Published: April 2019

Recent studies have used structured laser illumination planar imaging (SLIPI) combined with phosphor thermography to remove multiple scatter effects and near-wall reflections, which lead to biases in temperature measurements and reduced spatial resolution. We show that for the typical non-linear pump-signal range under which thermographic phosphors are used, errors may arise in the reconstruction of the temperature field using SLIPI. In this study, synthetic laser induced phosphorescence (LIP) images are generated numerically by adapting the synthetic PIV image generator for the purpose. The simulations are combined with phosphorescent signal yield functions obtained from experimental data to investigate the application of SLIPI to gas-phase phosphor thermography. We conclude that whilst SLIPI is effective in removing scattering noise for phosphors for which the two-colour signal ratio is insensitive to the laser fluence, it creates a bias in the temperature measurement otherwise. We also show that the extent of multiple scatter in LIP images is always overestimated by SLIPI, owning to the non-linear emission behaviour and particle image diffraction.
Response of the QED(2) vacuum to a quench: Long-term oscillations of the electric field and the pair creation rate
Authors: Otto A , Graeveling D , Kämpfer B
Published: April 2019

We consider—within QED(2)—the backreaction to the Schwinger pair creation in a time dependent, spatially homogeneous electric field. Our focus is the screening of the external field as a quench and the subsequent long-term evolution of the resulting electric field. Our numerical solutions of the self consistent, fully backreacted dynamical equations exhibit a self-sustaining oscillation of both the electric field and the pair number depending on the coupling strength.
The 2019 mathematical oncology roadmap
Authors: Rockne Russell C , Hawkins-Daarud Andrea , Swanson Kristin R , Sluka James P , Glazier James A , Macklin Paul , Hormuth David A , Jarrett Angela M , Lima Ernesto A B F , Tinsley Oden J , Biros George , Yankeelov Thomas E , Curtius Kit , Al Bakir Ibrahim , Wodarz Dominik , Komarova Natalia , Aparicio Luis , Bordyuh Mykola , Rabadan Raul , Finley Stacey D , Enderling Heiko , Caudell Jimmy , Moros Eduardo G , Anderson Alexander R A , Gatenby Robert A , Kaznatcheev Artem , Jeavons Peter , Krishnan Nikhil , Pelesko Julia , Wadhwa Raoul R , Yoon Nara , Nichol Daniel , Marusyk Andriy , Hinczewski Michael , Scott Jacob G
Published: April 2019

Whether the nom de guerre is Mathematical Oncology, Computational or Systems Biology, Theoretical Biology, Evolutionary Oncology, Bioinformatics, or simply Basic Science, there is no denying that mathematics continues to play an increasingly prominent role in cancer research. Mathematical Oncology—defined here simply as the use of mathematics in cancer research—complements and overlaps with a number of other fields that rely on mathematics as a core methodology. As a result, Mathematical Oncology has a broad scope, ranging from theoretical studies to clinical trials designed with mathematical models. This Roadmap differentiates Mathematical Oncology from related fields and demonstrates specific areas of focus within this unique field of research. The dominant theme of this Roadmap is the personalization of medicine through mathematics, modelling, and simulation. This is achieved through the use of patient-specific clinical data to: develop individualized screening strategies to detect cancer earlier; make predictions of response to therapy; design adaptive, patient-specific treatment plans to overcome therapy resistance; and establish domain-specific standards to share model predictions and to make models and simulations reproducible. The cover art for this Roadmap was chosen as an apt metaphor for the beautiful, strange, and evolving relationship between mathematics and cancer.
Inclusive Language in Spanish as Interpellation to Educational Authorities
Authors: Banegas Darío Luis , López María Fernanda
Published: April 2019

The aim of this commentary is to discuss and promote discussion on some linguistic and pedagogical issues around the use of gender inclusive language, particularly the -e morpheme in plural forms, in Spanish. Its speakers are experiencing and becoming aware of language change in real time concerning the use of morphosyntactic choices that seek embrace gender equality, diversity, representation, and diversity. This language change impacts directly on formal education and educational administrators who are under pressure not only from different social actors but also from their own beliefs on whether they should promote, ignore, or mitigate the linguistic changes that society is producing through their situated practices. Against this background, to what extent are educational authorities professionally prepared to encourage academic discussions on inclusive language in education? How can applied linguists help? Having these questions as our Southern Cross, our commentary lies at the intersection of language change and educational authorities’ professional knowledge.
The genomic architecture of antimalarial drug resistance
Authors: Cowell Annie N , Winzeler Elizabeth A
Published: April 2019

Plasmodium falciparum and Plasmodium vivax, the two protozoan parasite species that cause the majority of cases of human malaria, have developed resistance to nearly all known antimalarials. The ability of malaria parasites to develop resistance is primarily due to the high numbers of parasites in the infected person’s bloodstream during the asexual blood stage of infection in conjunction with the mutability of their genomes. Identifying the genetic mutations that mediate antimalarial resistance has deepened our understanding of how the parasites evade our treatments and reveals molecular markers that can be used to track the emergence of resistance in clinical samples. In this review, we examine known genetic mutations that lead to resistance to the major classes of antimalarial medications: the 4-aminoquinolines (chloroquine, amodiaquine and piperaquine), antifolate drugs, aryl amino-alcohols (quinine, lumefantrine and mefloquine), artemisinin compounds, antibiotics (clindamycin and doxycycline) and a napthoquinone (atovaquone). We discuss how the evolution of antimalarial resistance informs strategies to design the next generation of antimalarial therapies.
Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data
Authors: Han Zhijie , Xue Weiwei , Tao Lin , Lou Yan , Qiu Yunqing , Zhu Feng
Published: April 2019

The pathogenesis of multiple sclerosis (MS) is significantly regulated by long noncoding RNAs (lncRNAs), the expression of which is substantially influenced by a number of MS-associated risk single nucleotide polymorphisms (SNPs). It is thus hypothesized that the dysregulation of lncRNA induced by genomic variants may be one of the key molecular mechanisms for the pathology of MS. However, due to the lack of sufficient data on lncRNA expression and SNP genotypes of the same MS patients, such molecular mechanisms underlying the pathology of MS remain elusive. In this study, a bioinformatics strategy was applied to obtain lncRNA expression and SNP genotype data simultaneously from 142 samples (51 MS patients and 91 controls) based on RNA-seq data, and an expression quantitative trait loci (eQTL) analysis was conducted. In total, 2383 differentially expressed lncRNAs were identified as specifically expressing in brain-related tissues, and 517 of them were affected by SNPs. Then, the functional characterization, secondary structure changes and tissue and disease specificity of the cis-eQTL SNPs and lncRNA were assessed. The cis-eQTL SNPs were substantially and specifically enriched in neurological disease and intergenic region, and the secondary structure was altered in 17.6% of all lncRNAs in MS. Finally, the weighted gene coexpression network and gene set enrichment analyses were used to investigate how the influence of SNPs on lncRNAs contributed to the pathogenesis of MS. As a result, the regulation of lncRNAs by SNPs was found to mainly influence the antigen processing/presentation and mitogen-activated protein kinases (MAPK) signaling pathway in MS. These results revealed the effectiveness of the strategy proposed in this study and give insight into the mechanism (SNP-mediated modulation of lncRNAs) underlying the pathology of MS.
MINERVA API and plugins: opening molecular network analysis and visualization to the community
Authors: Hoksza David , Gawron Piotr , Ostaszewski Marek , Smula Ewa , Schneider Reinhard
Published: April 2019

The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform’s visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network.

Availability and implementation

Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.