bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bridging nestedness and economic complexity in multilayer world trade networks
Authors: Ren Zhuo-Ming , Zeng An , Zhang Yi-Cheng 
Published: November 2020

AbstractUnderstanding the complexity of international trading is critical for a variety of issues ranging from quantifying the competitiveness of individual nations to forecasting the collective evolution of the world economy. Despite the significant progress made in this direction, the international trading system is mainly modeled with a single network in the previous works such as the monopartite product space network and the bipartite country-product network to capture economic complexity. In order to better capture the more detailed dynamics, we characterize the international trading system with a multilayer network with each layer representing the transnational trading relations of a product. This framework immediately reveals the nested structure in each layer and accordingly allows us to develop an alternative measure of the complexity of products. The metric provides a ranking of products’ complexity more consistent with common understanding. The nested structure of a network layer seems to correlate with the asymmetric export relations resulted from the technology barriers, and the evolution of product complexity indicates that the growth of product nestedness is faster than the relevance decay. Finally, we remark a comparison of trade competitive by nestedness between China and the United States to explore the evolution of the economy industries, and the aggregated nestedness index can predict a nation’s future economic growth.
Inhibition of 3-phosphoinositide–dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts
Authors: An Sugyun , Cho Si-Young , Kang Junsoo , Lee Soobeom , Kim Hyung-Su , Min Dae-Jin , Son EuiDong , Cho Kwang-Hyun 
Published: November 2020

Significance
Recent studies showed that cellular senescence, previously considered an irreversible biological phenomenon, may represent a reversible state, but the mechanism for the reversion is not well elucidated. To identify targets the inhibition of which would convert senescent cells into quiescent cells, we constructed a molecular regulatory network model of cellular senescence. From the model simulation, we identified PDK1 as a promising target that can revert the senescent state into a quiescent state. We validated this prediction in experiments with human dermal fibroblasts, which showed that PDK1 inhibition eradicates senescence hallmarks by suppressing both nuclear factor κB and mTOR signaling through the inactivation of a positive feedback loop composed of PDK1, AKT, IKBKB, and PTEN, resulting in restored skin regeneration capacity.
Distemper, extinction, and vaccination of the Amur tiger
Authors: Gilbert Martin , Sulikhan Nadezhda , Uphyrkina Olga , Goncharuk Mikhail , Kerley Linda , Castro Enrique Hernandez , Reeve Richard , Seimon Tracie , McAloose Denise , Seryodkin Ivan V. , Naidenko Sergey V. , Davis Christopher A. , Wilkie Gavin S. , Vattipally Sreenu B. , Adamson Walt E. , Hinds Chris , Thomson Emma C. , Willett Brian J. , Hosie Margaret J. , Logan Nicola , McDonald Michael , Ossiboff Robert J. , Shevtsova Elena I. , Belyakin Stepan , Yurlova Anna A. , Osofsky Steven A. , Miquelle Dale G. , Matthews Louise , Cleaveland Sarah 
Published: November 2020

Significance
The decline and progressive fragmentation of many threatened populations increase extinction vulnerability due to outbreaks of infectious disease. Vaccination is one of the few tools available to mitigate these threats, but its use is often hampered by insufficient epidemiological understanding and historic controversies over endangered wildlife vaccination. Using the example of Amur tigers and CDV, we describe a holistic approach to select appropriate disease mitigation strategies based on key epidemiological evidence from the field. We then assess the protection of vaccinated tigers against the locally circulating CDV strain and use modeling to compare the efficacy and cost of potential vaccination programs. This practical approach provides conservation managers with an evidence-based rationale to address disease-mediated extinction risks for threatened wildlife populations.
Using dynamic monitoring of choices to predict and understand risk preferences
Authors: Stillman Paul E. , Krajbich Ian , Ferguson Melissa J. 
Published: November 2020

SignificanceChoices that consist of risky versus certain options are pervasive and consequential, leading many researchers to investigate when and which individuals select risk over certainty. The present research takes an alternative approach and measures computer mouse movements to assess how people arrive at these decisions. We show that measuring mouse movements while participants are deciding between a risky gamble and a certain payout powerfully detects their conflict about the options, and that this conflict strongly predicts their risk preferences. Further, mouse movements are predictive of risk preferences even when choice outcomes are not. The present research thus demonstrates the unique utility of dynamic measures of choice, as well as the predictive and theoretical importance of conflict in risky decision-making.
Mapping transmembrane binding partners for E-cadherin ectodomains
Authors: Shafraz Omer , Xie Bin , Yamada Soichiro , Sivasankar Sanjeevi 
Published: November 2020

SignificanceWhile transmembrane proteins are essential for cellular function, it is extremely challenging to identify their interactions using traditional biochemical methods. Here we combine proximity labeling and single molecule binding assays to discover transmembrane protein interactions in cells. We initially screen for transmembrane proteins that are located proximal to a protein of interest (the “bait”), by tagging both the extracellular and cytoplasmic regions of the bait with the proximity labeling enzyme, BioID. We then directly test binding interactions between proximal proteins and the bait using single molecule atomic force microscopy. Using this approach, we identify previously unknown direct interactions between a number of transmembrane proteins and the extracellular region of E-cadherin, an essential cell–cell adhesion protein.
Ultrarare heterozygous pathogenic variants of genes causing dominant forms of early-onset deafness underlie severe presbycusis
Authors: Boucher Sophie , Tai Fabienne Wong Jun , Delmaghani Sedigheh , Lelli Andrea , Singh-Estivalet Amrit , Dupont Typhaine , Niasme-Grare Magali , Michel Vincent , Wolff Nicolas , Bahloul Amel , Bouyacoub Yosra , Bouccara Didier , Fraysse Bernard , Deguine Olivier , Collet Lionel , Thai-Van Hung , Ionescu Eugen , Kemeny Jean-Louis , Giraudet Fabrice , Lavieille Jean-Pierre , Devèze Arnaud , Roudevitch-Pujol Anne-Laure , Vincent Christophe , Renard Christian , Franco-Vidal Valérie , Thibult-Apt Claire , Darrouzet Vincent , Bizaguet Eric , Coez Arnaud , Aschard Hugues , Michalski Nicolas , Lefevre Gaëlle M. , Aubois Anne , Avan Paul , Bonnet Crystel , Petit Christine 
Published: November 2020

Significance
Presbycusis, or age-related hearing loss, is a major public health issue and the principal potentially modifiable risk factor for dementia. It is caused by environmental factors and largely uncharacterized genetic factors. We compared DNA sequences across genomic coding regions between familial or sporadic cases of severe presbycusis and controls with normal hearing. The frequency of ultrarare predicted pathogenic variants in genes known to cause dominant early-onset forms of deafness was significantly higher in both familial and sporadic cases than in controls. Pathogenicity of many of these variants was established with complementary analyses. Ultrarare variants have a large effect size and are known to cause monogenic disorders. These findings open up possibilities for curing these forms of presbycusis by gene therapy.
Mutation-oriented profiling of autoinhibitory kinase conformations predicts RAF inhibitor efficacies
Authors: Mayrhofer Johanna E. , Enzler Florian , Feichtner Andreas , Röck Ruth , Fleischmann Jakob , Raffeiner Andrea , Tschaikner Philipp , Ogris Egon , Huber Roland G. , Hartl Markus , Schneider Rainer , Troppmair Jakob , Torres-Quesada Omar , Stefan Eduard 
Published: November 2020

SignificanceThe pharmaceutical targeting of mutated BRAF has shown promising clinical outcomes in patients with melanoma. However, more than 300 reported BRAF patient mutations and the occurrence of a kinase-drug resistance mechanism hamper patient-oriented therapies. We have developed an extendable and cell-based kinase conformation reporter platform (KinCon) to predict and compare the effect of kinase drugs. We systematically evaluated drug efficacies by assessing KinCon reporter dynamics in response to different drugs and patient mutations. Our findings suggest that FDA-approved melanoma inhibitors may have the potential to block non-V600E–mutated BRAF activities also in non–small-cell lung cancers (NSCLC). We assume that widespread analyses of KinCon:drug interactions may assist in the future in identifying patient mutation–specific and thus more effective kinase inhibitors.
Development of cyclic peptides with potent in vivo osteogenic activity through RaPID-based affinity maturation
Authors: Bashiruddin Nasir K. , Hayashi Mikihito , Nagano Masanobu , Wu Yan , Matsunaga Yukiko , Takagi Junichi , Nakashima Tomoki , Suga Hiroaki 
Published: November 2020

Significance
Osteoporosis affects over 75 million people globally, and this number is increasing with global median age. Therefore, the development of therapeutics with novel mechanisms of action is of high importance. Inhibition of the PlexinB1-Semaphorin4D interaction on osteoblasts has been shown to be a potential target for developing osteoanabolic modalities. Here, using a novel affinity maturation approach for cyclic peptides, we were able to develop cyclic peptide that tightly binds human and mouse PlexinB1 and inhibits its interaction with Semaphorin4D. Chemical dimerization of this peptide resulted in further increases in activity and demonstrated complete rescue of bone loss in an osteoporosis mouse model.
Conservation cobenefits from air pollution regulation: Evidence from birds
Authors: Liang Yuanning , Rudik Ivan , Zou Eric Yongchen , Johnston Alison , Rodewald Amanda D. , Kling Catherine L. 
Published: November 2020

Significance
Understanding the drivers of abundance and biodiversity decline across numerous taxa is imperative for designing conservation policy. We use highly detailed citizen science data to show that there is a strong, robust negative association between bird abundance and ambient ozone concentrations in the United States. In particular, we find that a regulation aimed at reducing ozone precursors has significantly bolstered populations in the eastern United States. Our estimated effects suggest that the large decline in average US ozone concentrations over the past several decades has averted the loss of potentially billions of birds. Environmental policies nominally aimed at humans can also provide substantial benefits to other species.
Layer and rhythm specificity for predictive routing
Authors: Bastos André M. , Lundqvist Mikael , Waite Ayan S. , Kopell Nancy , Miller Earl K. 
Published: November 2020

Significance
An established theoretical model, predictive coding, states that the brain is constantly building models (signifying changing predictions) of the environment. The brain does this by forming predictions and signaling sensory inputs which deviate from predictions (“prediction errors”). Various hypotheses exist about how predictive coding could be implemented in the brain. We recorded neural spiking and oscillations with laminar resolution in a network of cortical areas as monkeys performed a working memory task with changing stimulus predictability. Predictability modulated the patterns of feedforward/feedback flow, cortical layers, and oscillations used to process a visual stimulus. These data support the theory of predictive coding but suggest an alternate model for its neural implementation: predictive routing.
Targeting a scavenger receptor on tumor-associated macrophages activates tumor cell killing by natural killer cells
Authors: Eisinger Silke , Sarhan Dhifaf , Boura Vanessa F. , Ibarlucea-Benitez Itziar , Tyystjärvi Sofia , Oliynyk Ganna , Arsenian-Henriksson Marie , Lane David , Wikström Stina L. , Kiessling Rolf , Virgilio Tommaso , Gonzalez Santiago F. , Kaczynska Dagmara , Kanatani Shigeaki , Daskalaki Evangelia , Wheelock Craig E. , Sedimbi Saikiran , Chambers Benedict J. , Ravetch Jeffrey V. , Karlsson Mikael C. I. 
Published: November 2020

SignificanceHere we report that targeting the pattern recognition receptor MARCO on macrophages within the tumor alters their polarization and in turn activate natural killer (NK) cells to kill the tumor. We describe the mechanism of action, including that NK cells are induced to use receptor-mediated killing of the cancer cells. Furthermore, we find that this type of treatment works in combination with T cell-targeted checkpoint therapies. We then transfer this finding to humans and find that similar subpopulations of human macrophages also block NK cells. Finally, we find that targeting these human macrophages with a new specific antibody that we generated can activate these to release NK cell killing, thus generating a venue for combinatory treatments for cancer.
A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns
Authors: Steinbrenner Adam D. , Muñoz-Amatriaín Maria , Chaparro Antonio F. , Aguilar-Venegas Jessica Montserrat , Lo Sassoum , Okuda Satohiro , Glauser Gaetan , Dongiovanni Julien , Shi Da , Hall Marlo , Crubaugh Daniel , Holton Nicholas , Zipfel Cyril , Abagyan Ruben , Turlings Ted C. J. , Close Timothy J. , Huffaker Alisa , Schmelz Eric A. 
Published: November 2020

SignificancePlants respond to biotic attack using an immune system of receptors to recognize molecules associated with danger. We identified an immune receptor, termed inceptin receptor (INR), able to confer responses to defined inceptin peptide fragments present in caterpillar oral secretions. Like many plant immune receptors, INR is encoded only by certain plant species but can be transferred across families to confer new signaling and defense functions. While INR is only found in the genomes of cowpea, common bean, and related legumes, it confers defined elicitor responses to transgenic tobacco and suppresses the growth of attacking beet armyworm larvae. INR expands the breadth of plant pattern recognition receptors to detection of chewing insect herbivores.
Cytocidal macrophages in symbiosis with CD4 and CD8 T cells cause acute diabetes following checkpoint blockade of PD-1 in NOD mice
Authors: Hu Hao , Zakharov Pavel N. , Peterson Orion J. , Unanue Emil R. 
Published: November 2020

SignificanceImmune checkpoint inhibitors have achieved great success in the treatment of a number of malignancies. Unfortunately, immune-related adverse events develop in patients, particularly endocrine autoimmunity, including type 1 diabetes. We examined the nonobese diabetic mouse that develops fulminant autoimmune diabetes after anti–PD-1 blockade, uncovering an unexplored pathway by which PD-1 blockade facilitated diabetes progression. Analysis of the pancreatic islets showed strong cellular interactions among T cells and activated macrophages, and their dramatic changes after anti–PD-1 antibody treatment. Monocyte-derived macrophages played a major role in causing acute diabetes development. Their temporal depletion dramatically protected mice from β-cell demise. We identify the blood monocytes as a possible target for the control of the autoimmune complications brought about by checkpoint inhibitors.
The Arg/N-degron pathway targets transcription factors and regulates specific genes
Authors: Vu Tri T. M. , Mitchell Dylan C. , Gygi Steven P. , Varshavsky Alexander 
Published: November 2020

Significance
The Arg/N-degron pathway targets proteins for degradation by recognizing their N-terminal or internal degradation signals. In the present study, we compared wild-type human cells to their double-knockout (2-KO) counterparts that lacked the UBR1/UBR2 ubiquitin ligases of the Arg/N-degron pathway. We found that a number of specific genes were either strongly induced or strongly repressed in 2-KO cells. In addition, specific transcription factors, including glucocorticoid receptor, were identified here as physiological substrates of the Arg/N-degron pathway. We discuss the emerged role of this proteolytic system as a regulator of mammalian gene expression.
Lexical convergence reflects complex historical processes
Authors: Chechuro Ilia 
Published: November 2020

Abstract
This paper is an illustration of how deep historical and
anthropological analyses may be of use in studies of linguistic convergence
and in contact linguistics. The study reported here aims at investigating
the lexical influence of Russian on East Caucasian languages. In this study,
I use an extended version of the DagLoans wordlist created by the members of
the Linguistic Convergence Laboratory (HSE, Moscow). I collect this list in
the languages belonging to two different linguistic areas of Daghestan: the
Rutul area and the Tsezic area. The two areas share many
sociolinguistic features, such as the neighboring languages, multilingualism
and migration patterns. However, the wordlists show completely different
counts for loanwords coming from source languages with similar status
(Azerbaijani and Georgian on the one hand and Russian on the other). In
order to explain the observed counts, I discuss historical and
anthropological data from the two regions and propose several possible
explanations. With these explanations, I intend to show that studies of
language contact cannot be based exclusively on geographical proximity and
surface sociolinguistic profiling and should be refined by more detailed
information such as cultural influence, as well as a deeper historical
investigation.
The ideological background of language change in Permic-speaking
communities
Authors: Edygarova Svetlana 
Published: November 2020

Abstract
In the present paper I examine the language ideologies
which existed in the Soviet Union and which exist in Russia today, and their
impact on language change in Permic-speaking communities. In particular, I
investigate how different ideologies viewed possible sources for “enriching”
these languages and what kind of attitudes they held towards borrowing and
language purism. In the article I present the example of Russian relational
adjectives and investigate the ways in which they have been integrated by
the Permic languages during the Soviet era and after perestroika. Based on
the results of a translation test, I also analyze how modern Permic speakers
integrate Russian relational adjectives.
Russian influence on Surgut Khanty and Estonian aspect is limited but
similar
Authors: Gugán Katalin , Tamm Anne 
Published: November 2020

Abstract
In the present paper, we investigate evidence for a
causal link between the sociolinguistic contact type and the type of
structural change in borrowing. We build our argument via a comparative and
contrastive study of the aspectual system of Surgut Khanty (Ob-Ugric,
Uralic), Estonian (Finnic, Uralic) and Russian (Slavic, Indo-European). We
relate our findings to earlier findings on the functional similarity of
typologically distant languages in slight borrowing situations. Comparing
the category of aspect in two Uralic languages, Estonian and Surgut Khanty,
we claim that the structural changes in Estonian and Surgut Khanty are
similar in the domain of aspect, despite the differences in the social
conditions of contacts with Russian and additional influences from
typologically diverging contact languages. We attribute the similarity to
the low intensity of borrowing.
Quotative indexes in Permic
Authors: Teptiuk Denys 
Published: November 2020

Abstract
In this paper, I discuss the use of quotative indexes in
new media texts of the Permic languages Komi and Udmurt. I focus on
quotative strategies that emerge under the influence of Russian. Even though
both Permic languages are found nowadays relatively equally under the
influence of Russian, its impact is realized to different extents. In
Udmurt, both matter and pattern replication can be observed (the quotative
particles mol and deskatʹ, new quotative
tipa, the complementizers čto and
budto), while in Komi, only the pattern replication of
the complementizer strategy is noticed. It leads to the conclusion that Komi
speakers keep control over the separation of linguistic repertoire in the
written form, while Udmurt speakers use already conventionalized markers
from the contact language as new quotatives.
Why do two Uralic languages (Surgut Khanty and Erzya) use different
code-switching strategies?
Authors: Janurik Boglárka , Schön Zsófia 
Published: November 2020

Abstract
In this paper, we study the code-switching types
occurring in two contact situations, in Surgut Khanty–Russian and in
Erzya–Russian bilingual utterances. Using Myers-Scotton’s Matrix Language
Frame Model (1993, 2002, 2006), we analyze the subtypes of insertion in
narrative texts and semi-structured interviews. It might be assumed that the
code-switching types would be similar in the two contact situations, as
Surgut Khanty and Erzya share many structural properties (e.g. the lack of
gender as a grammatical category). Our results show that most Russian
elements do occur in both cases as insertions, but the distribution and
frequency of these types differ. This discrepancy can be attributed to the
history and length of the contact situations. Finally, we use Auer’s 1999 continuum model to
portray these differences.
The choice of forms in contact varieties
Authors: Fedorova Kapitolina 
Published: November 2020

Abstract
The article addresses the issue of language choice in
contact situations on the basis of linguistic intersection in the
Russian-Chinese border area. It aims to analyze morphological forms found in
Russian-Chinese communication, both in the past (in data on Russian-Chinese
pidgin) and in the present, and to reveal the nature of the motivations that determine
speakers’ choice of forms. The analysis of three sets of data – (1)
historical data on Russian-Chinese Pidgin; (2) modern data on actual
interethnic communication; (3) metalinguistic data obtained from consultants
without reference to a particular ethnic group (Chinese) – find more
similarities between the first two sets. It shows therefore that choice of
morphological forms can depend on social settings and linguistic stereotypes
rather than linguistic structure per se.
Geometric spin–orbit coupling and chirality-induced spin selectivity
Authors: Shitade Atsuo , Minamitani Emi 
Published: November 2020

Abstract
We report a new type of spin–orbit coupling (SOC) called geometric SOC. Starting from the relativistic theory in curved space, we derive an effective nonrelativistic Hamiltonian in a generic curve embedded into flat three dimensions. The geometric SOC is O(m
−1), in which m is the electron mass, and hence much larger than the conventional SOC of O(m
−2). The energy scale is estimated to be a hundred meV for a nanoscale helix. We calculate the current-induced spin polarization in a coupled-helix model as a representative of the chirality-induced spin selectivity. We find that it depends on the chirality of the helix and is of the order of 0.01ℏ per nm when a charge current of 1 μA is applied.