bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants
Authors: Mao Lingfeng , Kawaide Hiroshi , Higuchi Toshiya , Chen Meihong , Miyamoto Koji , Hirata Yoshiki , Kimura Honoka , Miyazaki Sho , Teruya Miyu , Fujiwara Kaoru , Tomita Keisuke , Yamane Hisakazu , Hayashi Ken-ichiro , Nojiri Hideaki , Jia Lei , Qiu Jie , Ye Chuyu , Timko Michael P. , Fan Longjiang , Okada Kazunori
Published: May 2020

Momilactones are bioactive diterpenoids that contribute to plant defense against pathogens and allelopathic interactions between plants. Both cultivated and wild grass species ofOryzaandEchinochloa crus-galli(barnyard grass) produce momilactones using a biosynthetic gene cluster (BGC) in their genomes. The bryophyteCalohypnum plumiforme(formerlyHypnum plumaeforme) also produces momilactones, and the bifunctional diterpene cyclase geneCpDTC1/HpDTC1,which is responsible for the production of the diterpene framework, has been characterized. To understand the molecular architecture of the momilactone biosynthetic genes in the moss genome and their evolutionary relationships with other momilactone-producing plants, we sequenced and annotated theC. plumiformegenome. The data revealed a 150-kb genomic region that contains two cytochrome P450 genes, theCpDTC1/HpDTC1gene and the “dehydrogenase momilactone A synthase” gene tandemly arranged and inductively transcribed following stress exposure. The predicted enzymatic functions in yeast and recombinant assay and the successful pathway reconstitution inNicotiana benthamianasuggest that it is a functional BGC responsible for momilactone production. Furthermore, in a survey of genomic sequences of a broad range of plant species, we found that momilactone BGC is limited to the two grasses (OryzaandEchinochloa) andC. plumiforme, with no synteny among these genomes. These results indicate that while the gene cluster inC. plumiformeis functionally similar to that in rice and barnyard grass, it is likely a product of convergent evolution. To the best of our knowledge, this report of a BGC for a specialized plant defense metabolite in bryophytes is unique.
The
Veiled Virgin
illustrates visual segmentation of shape by cause
Authors: Phillips Flip , Fleming Roland W.
Published: May 2020

Three-dimensional (3D) shape perception is one of the most important functions of vision. It is crucial for many tasks, from object recognition to tool use, and yet how the brain represents shape remains poorly understood. Most theories focus on purely geometrical computations (e.g., estimating depths, curvatures, symmetries). Here, however, we find that shape perception also involves sophisticated inferences that parse shapes into features with distinct causal origins. Inspired by marble sculptures such as Strazza’s
The Veiled Virgin
(1850), which vividly depict figures swathed in cloth, we created composite shapes by wrapping unfamiliar forms in textile, so that the observable surface relief was the result of complex interactions between the underlying object and overlying fabric. Making sense of such structures requires segmenting the shape based on their causes, to distinguish whether lumps and ridges are due to the shrouded object or to the ripples and folds of the overlying cloth. Three-dimensional scans of the objects with and without the textile provided ground-truth measures of the true physical surface reliefs, against which observers’ judgments could be compared. In a virtual painting task, participants indicated which surface ridges appeared to be caused by the hidden object and which were due to the drapery. In another experiment, participants indicated the perceived depth profile of both surface layers. Their responses reveal that they can robustly distinguish features belonging to the textile from those due to the underlying object. Together, these findings reveal the operation of visual shape-segmentation processes that parse shapes based on their causal origin.
Kinetics of pHLIP peptide insertion into and exit from a membrane
Authors: Slaybaugh Gregory , Weerakkody Dhammika , Engelman Donald M. , Andreev Oleg A. , Reshetnyak Yana K.
Published: May 2020

Significance

The process of peptide insertion across a membrane is of fundamental interest. Obtained in this study’s results, combined with our recent constant-pH molecular dynamics simulations and kinetics experiments with liposomes of different bilayer thicknesses, allowed us to complete a generalized model of the insertion/exit and folding/unfolding of polypeptides of the pHLIP family and expand the general view of peptide conformations and dynamic excursions of the bilayer that can accompany interactions with peptides. In addition to fundamental significance, pH-dependent pHLIP insertion into membranes of acidic cells within diseased tissues finds wide application in medicine for targeted delivery of imaging and therapeutic agents.
Dynamics and functional diversity of the smallest phytoplankton on the Northeast US Shelf
Authors: Fowler Bethany L. , Neubert Michael G. , Hunter-Cevera Kristen R. , Olson Robert J. , Shalapyonok Alexi , Solow Andrew R. , Sosik Heidi M.
Published: May 2020

Picophytoplankton are the most abundant primary producers in the ocean. Knowledge of their community dynamics is key to understanding their role in marine food webs and global biogeochemical cycles. To this end, we analyzed a 16-y time series of observations of a phytoplankton community at a nearshore site on the Northeast US Shelf. We used a size-structured population model to estimate in situ division rates for the picoeukaryote assemblage and compared the dynamics with those of the picocyanobacteriaSynechococcusat the same location. We found that the picoeukaryotes divide at roughly twice the rate of the more abundantSynechococcusand are subject to greater loss rates (likely from viral lysis and zooplankton grazing). We describe the dynamics of these groups across short and long timescales and conclude that, despite their taxonomic differences, their populations respond similarly to changes in the biotic and abiotic environment. Both groups appear to be temperature limited in the spring and light limited in the fall and to experience greater mortality during the day than at night. Compared withSynechococcus, the picoeukaryotes are subject to greater top-down control and contribute more to the region’s primary productivity than their standing stocks suggest.
foxl3
, a sexual switch in germ cells, initiates two independent molecular pathways for commitment to oogenesis in medaka
Authors: Kikuchi Mariko , Nishimura Toshiya , Ishishita Satoshi , Matsuda Yoichi , Tanaka Minoru
Published: May 2020

Significance

In teleost fish, unlike mammals, retinoic acid (RA) does not exert a conspicuous feminization effect of germ cells. Instead, in the teleost fish medaka,
foxl3
serves as a germ cell-autonomous factor acting at the very beginning of the sexual fate decision. This study shows that
foxl3
initiates oogenesis through two genetically independent pathways, meiosis and follicular development. One pathway, involving
rec8a
, drives female-specific regulation of meiosis. The other, involving
fbxo47
, both directs follicular development and suppresses spermatogenesis commitment. The involvement of two evolutionarily conserved factors in oogenesis suggests the existence of an RA-independent pathway that promotes oogenesis, common in vertebrates. In addition, our findings reveal the timing of the establishment of germ cell feminization.
Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required forToxoplasmaapical complex biogenesis
Authors: Back Peter S. , O’Shaughnessy William J. , Moon Andy S. , Dewangan Pravin S. , Hu Xiaoyu , Sha Jihui , Wohlschlegel James A. , Bradley Peter J. , Reese Michael L.
Published: May 2020

Apicomplexan parasites use a specialized cilium structure called the apical complex to organize their secretory organelles and invasion machinery. The apical complex is integrally associated with both the parasite plasma membrane and an intermediate filament cytoskeleton called the inner-membrane complex (IMC). While the apical complex is essential to the parasitic lifestyle, little is known about the regulation of apical complex biogenesis. Here, we identify AC9 (apical cap protein 9), a largely intrinsically disordered component of theToxoplasma gondiiIMC, as essential for apical complex development, and therefore for host cell invasion and egress. Parasites lacking AC9 fail to successfully assemble the tubulin-rich core of their apical complex, called the conoid. We use proximity biotinylation to identify the AC9 interaction network, which includes the kinase extracellular signal-regulated kinase 7 (ERK7). Like AC9, ERK7 is required for apical complex biogenesis. We demonstrate that AC9 directly binds ERK7 through a conserved C-terminal motif and that this interaction is essential for ERK7 localization and function at the apical cap. The crystal structure of the ERK7–AC9 complex reveals that AC9 is not only a scaffold but also inhibits ERK7 through an unusual set of contacts that displaces nucleotide from the kinase active site. ERK7 is an ancient and autoactivating member of the mitogen-activated kinase (MAPK) family and its regulation is poorly understood in all organisms. We propose that AC9 dually regulates ERK7 by scaffolding and concentrating it at its site of action while maintaining it in an “off” state until the specific binding of a true substrate.
Lumefantrine, an antimalarial drug, reverses radiation and temozolomide resistance in glioblastoma
Authors: Rajesh Yetirajam , Biswas Angana , Kumar Utkarsh , Banerjee Indranil , Das Subhayan , Maji Santanu , Das Swadesh K. , Emdad Luni , Cavenee Webster K. , Mandal Mahitosh , Fisher Paul B.
Published: May 2020

Significance

No current therapies prevent recurrence in patients with glioblastoma multiforme (GBM). Extracellular matrix (ECM) remodeling and epithelial mesenchymal transition (EMT) are important processes regulating GBM progression and acquisition of radiation and temozolomide (radio/TMZ) resistance. Fli-1 choreographs ECM remodeling and EMT in GBM via transcriptional regulation of HSPB1. Lumefantrine, an antimalarial drug, inhibits the transcriptional activities of Fli-1 and its downstream targets HSPB1, ECM remodeling, and EMT. Lumefantrine is selectively cytotoxic and promotes apoptosis in GBM and reverses radio/TMZ resistance in GBM. This drug can easily be repurposed for management of GBM. Identification of drugs like lumefantrine from FDA-approved therapeutic agents and uncommon sources provides opportunities to broaden the breadth and versatility of current therapeutic regimens for GBM.
Tenofovir prodrugs potently inhibit Epstein–Barr virus lytic DNA replication by targeting the viral DNA polymerase
Authors: Drosu Natalia C. , Edelman Elazer R. , Housman David E.
Published: May 2020

Significance

Epstein–Barr virus (EBV)-associated diseases represent a major cause of morbidity worldwide, accounting for at least 1.5% of the global cancer burden, and contributing to autoimmunity. Viral reactivation from latency is associated with an increased risk of EBV-driven cancers, and thus may be a target for disease prevention. Anti-EBV agents that are safe, effective, and suitable for continuous long-term treatment are needed to address questions of whether suppression of lytic reactivation can reduce the incidence of EBV-associated diseases. Here we report that tenofovir disoproxil fumarate and tenofovir alafenamide, drugs with excellent safety profiles used for HIV prophylaxis, are potent inhibitors of EBV. This study identifies compounds that enable clinical investigations of antiviral therapy for EBV in efforts toward disease prevention.
Reading scientific translations in the first half of sixteenth-century Europe
through Hernando Colón’s library
Authors: Sumillera Rocío G.
Published: May 2020

The humanist Hernando Colón (1488–1539),
second son to Christopher Columbus, has been acknowledged as one of the greatest
collectors of manuscripts and printed works of sixteenth-century Europe. Hernando
acquired all kinds of works (from cheap pamphlets to expensive illustrated volumes),
in a variety of European cities (from London to Seville, from Rome to Nuremberg),
written in various languages (Latin, Spanish, French, Italian, German,
Greek, Catalan), and dealing with topics ranging from theology and law, to cartography and
astrology charts. This chapter examines the translated scientific texts in
Hernando’s library to shed light on a number of determining factors that can account
for the fortunes of the dissemination of scientific literature in translation,
including the cities where these translated texts were published and purchased, and
issues such as language combinations, translators and printers.
Translating the Iron Curtain
Authors: Ottersbach Simon
Published: May 2020

This chapter, taking as a case study Radio Free Europe (RFE), demonstrates the potential of studying from a translational perspective the Cultural Cold War with its many forms of cultural and scientific contacts, both within, but also between the two blocs. As an international radio broadcaster from Munich to Central and Eastern Europe, RFE was an intermediator between ‘East’ and ‘West’. RFE had to translate the perceived reality of an Iron Curtain for audiences on both sides of this curtain, with each audience requiring individualised translations of the Cold War’s bipolarity. Thus, looking at the Cultural Cold War from a translational perspective will help us to further deconstruct the Cold War’s bipolar separation and help uncover the many transsystemic interactions.
The Latin translation of Philosophical Transactions
(1671–1681)
Authors: Toribio Pablo
Published: May 2020

“The story of the Latin edition of the
early volumes [of Philosophical Transactions] is a complex one and
not easy to reconstruct” (Kronick
2004: 165). The lengthiest available account (Johns 1998: 514–521) is based on the edition of the
Oldenburg-Sand correspondence by Hall and Hall
(1973–1977). This chapter engages with the primary texts involved and
provides a substantially revised account of the Neo-Latin translation of
Philosophical Transactions, challenging previous assumptions and
also revealing for the first time the presence of theologically heterodox
material.
Energetic visions
Authors: Leber Christoffer
Published: May 2020

In the aftermath of the revolutions of
1848, anticlerical and freethought organisations had evolved a powerful opposition
to the Church and generally to conservatism in Europe. Amongst these organisations, the
German Monist League (founded in 1906) became one of the main representatives of secularism in
Wilhelmine Germany. The League not only opposed the Christian
churches, but also popularised a scientific worldview which sought to unite the
material and spiritual worlds. Monist thinkers translated scientific knowledge into
a popular language, transferring it to new domains of knowledge, such as ethics,
politics, gender, sexuality, law and education. This chapter argues that Monist thinkers
used scientific knowledge as a way to essentialise and
legitimise their ethical and educational reform goals. By doing
so, they transformed scientific knowledge itself.
An (imagined) community
Authors: Savelieva Irina
Published: May 2020

Conducted from 1996 to 2002, the project Translation Literature in the Social Sciences changed the face of post-Soviet Russian academia. Not only did it result in the translation of more than 400 key publications in human and social sciences, but it also created a community of scholars and translators specialising in social sciences and humanities, many of whom have continued shaping the Russian academic landscape until today. This chapter discusses the aims, scope and results of the translation project, as well as the ramifications that it had for contemporary academia. Particular attention is paid to the transformation and changing praxis of translations from Soviet to post-Soviet Russia.
From Textbook Pluralism to Modern Hyperpluralism
Authors: Cameron Charles M. , Gray Cody , Kastellec Jonathan P. , Park Jee-Kwang
Published: May 2020

We examine interest group involvement in Supreme Court nominations from 1930 to 2017, finding dramatic shifts in the number and type of groups, as well as their choice of tactics. Whereas the early period was dominated by labor unions, “core” civil rights groups, and groups affiliated with the “old right,” the modern period is dominated by public interest/citizen groups and “identity” groups. We also find a shift from more traditional “inside” tactics to the heavy use of “outside/grassroots” mobilization tactics. Finally, we show that the calculus of mobilization has increasingly been based on a nominee’s ideology over time.
High-frame-rate volume imaging using sparse-random-aperture compounding
Authors: Bernal Miguel , Cunitz Bryan , Rohrbach Daniel , Daigle Ron
Published: May 2020

High-frame-rate volume imaging (HFR-VI) aims to provide high-quality images with high-temporal information. Despite its potential, HFR-VI translation into clinical applications has been challenging due to the high cost of the equipment required to drive matrix probes with a large number of elements. The goal of this study is to introduce and test sparse-random-aperture compounding (SRAC), a technique that allows use of matrix probes with an ultrasound system that has fewer channels while maintaining high frame rates.

Four scanning methods were implemented with a 256-channel system using a 4-to-1 multiplexer and a 3 MHz matrix probe with 1024 elements. These methods used three types of waves, either single-diverging waves (SDW), multiplane-diverging waves (MDW) or wide beams (WB); and were driven using one to four SRAC. All methods were also implemented in a 1024-channel multisystem. The main-lobe-to-side-lobe ratio (MLSLR) and the contrast ratio (CR) were studied using a string phantom and a CIRS phantom, respectively.

The results showed an increase in the MLSLR and CR as a function of the number of SRAC. The multisystem provided the best results for the MLSLR. However, four SRAC outperformed the multisystem with respect to CR. The method using SDW provided the highest frame rates (i.e. 1875 and 7500 Hz for four and one SRAC, respectively), however it provided the lowest image quality. The two methods using MDWs showed a good compromise between image quality and frame rate (i.e. 187 to 750 Hz for four and one SRAC). WB provided the best image quality at the expense of frame rate (i.e. 18 to 75 Hz for four and one SRAC).

Our results suggest that SRAC in combination with the tested scanning methods can provide a low-channel count alternative for HFR-VI systems and allows a tunable tradeoff between image quality and frame rate guided by the desired application.
A novel OFDR-based distributed optical fiber sensing tape: design, optimization, calibration and application
Authors: You Runzhou , Ren Liang , Song Gangbing
Published: May 2020

The significance of implementing structural health monitoring (SHM) system for civil engineering, especially infrastructure engineering, has been recognized. Distributed optical fiber sensor (DOFS) based on optical frequency domain reflectometer (OFDR) offers an attractive technique for in situ strain measurement due to its high resolution and high precision. However, a main challenge that naturally arises is how to guarantee sensors survival in harsh construction and service environments. In this paper, a new, but simple, packaging technique is proposed to solve this issue. The novel sensing tape is fabricated by embedding DOFS into two fiberglass tapes and its strain transfer mechanism is analyzed in detail to provide scientific criteria for the choice of the material parameters. Then, a calibration test is carried out to evaluate the performance of the sensing tape in distributed strain measurement. Finally, the tape sensor is applied to the surface strain monitoring of the reinforced concrete (RC) beam tested in three-point bending. Experimental results verify that the sensing tape works well on concrete materials and the strain measured has the capability to reveal and localize cracks. Both analytical and experimental results demonstrate that the proposed packaging technique is feasible and effective.
Investigation of nitrogen enriched silicon for particle detectors
Authors: Hönig J.C. , Baselga M. , Vignali M. Centis , Diehl L. , Dierlamm A. , Fretwurst E. , Kaminski P. , Moll M. , Moos F. , Mori R. , Parzefall U. , Pellegrini G. , Rafí J.M. , Schwandt J. , Wiik-Fuchs L.
Published: May 2020

This article explores the viability of nitrogen enriched silicon for particle physics application. For that purpose silicon diodes and strip sensors were produced using high resistivity float zone silicon, diffusion oxygenated float zone silicon, nitrogen enriched float zone silicon and magnetic Czochralski silicon. The article features comparative studies using secondary ion mass spectrometry, electrical characterization, edge transient current technique, source and thermally stimulated current spectroscopy measurements on sensors that were irradiated up to a fluence of 1015 neq/cm2. Irradiations were performed with 23 MeV protons at the facilities in Karlsruhe (KIT), with 24 GeV/c protons at CERN (PS-IRRAD) and neutrons at the research reactor in Ljubljana. Secondary ion mass spectrometry measurements give evidence for nitrogen loss after processing, which makes gaining from nitrogen enrichment difficult.
Prevention and control measures for coastal erosion in northern high-latitude communities: a systematic review based on Alaskan case studies
Authors: Liew Min , Xiao Ming , Jones Benjamin M , Farquharson Louise M , Romanovsky Vladimir E
Published: May 2020

Erosion along high-latitude coasts has been accelerating in recent decades, resulting in land loss and infrastructure damage, threatening the wellbeing of local communities, and forcing undesired community relocations. This review paper evaluates the state of practice of current coastal stabilization measures across several coastal communities in northern high latitudes. After considering global practices and those in northern high latitude and arctic settings, this paper then explores new and potential coastal stabilization measures to address erosion specific to northern high-latitude coastlines. The challenges in constructing the current erosion control measures and the cost of the measures over the last four decades in northern high-latitude regions are presented through case histories. The synthesis shows that among the current erosion controls being used at high latitudes, revetments built with rocks have the least reported failures and are the most common measures applied along northern high-latitude coastlines including permafrost coasts, while riprap is the most common material used. For seawalls, bulkheads, and groin systems, reported failures are common and mostly associated with displacement, deflection, settlement, vandalism, and material ruptures. Revetments have been successfully implemented at sites with a wide range of mean annual erosion rates (0.3–2.4 m/year) and episodic erosion (6.0–22.9 m) due to the low costs and easy construction, inspection, and decommissioning. No successful case history has been reported for the non-engineered expedient measures that are constructed in the event of an emergency, except for the expedient vegetation measure using root-wads and willows. Soft erosion prevention measures, which include both beach nourishment and dynamically stable beaches, have been considered in this review. The effectiveness of beach nourishment in Utqiaġvik, Alaska, which is affected by permafrost, is inconclusive. Dynamically stable beaches are effective in preventing erosion, and observations show that they experience only minor damages after single storm events. The analysis also shows that more measures have been constructed on a spit (relative to bluffs, islands, barrier islands, and river mouths), which is a landform where many Alaskan coastal communities reside. The emerging erosion control measures that can potentially be adapted to mitigate coastal erosion in high-latitude regions include geosynthetics, static bay beach concept, refrigerating techniques, and biogeochemical applications. However, this review shows that there is a lack of case studies that evaluated the performance of these new measures in high-latitude environments. This paper identifies research gaps so that these emerging measures can be upscaled for full-scale applications on permafrost coasts.
Global food self-sufficiency in the 21st century under sustainable intensification of agriculture
Authors: Beltran-Peña Areidy , Rosa Lorenzo , D’Odorico Paolo
Published: May 2020

Meeting the increasing global demand for agricultural products without depleting the limited resources of the planet is a major challenge that humanity is facing. Most studies on global food security do not make projections past the year 2050, just as climate change and increasing demand for food are expected to intensify. Moreover, past studies do not account for the water sustainability limits of irrigation expansion to presently rainfed areas. Here we perform an integrated assessment that considers a range of factors affecting future food production and demand throughout the 21st century. We evaluate the self-sufficiency of 165 countries under sustainability, middle-of-the-road, and business-as-usual scenarios considering changes in diet, population, agricultural intensification, and climate. We find that under both the middle-of-the-road and business-as-usual trajectories global food self-sufficiency is likely to decline despite increased food production through sustainable agricultural intensification since projected food demand exceeds potential production. Contrarily, under a sustainability scenario, we estimate that there will be enough food production to feed the global population. However, most countries in Africa and the Middle East will continue to be heavily reliant on imports throughout the 21st century under all scenarios. These results highlight future hotspots of crop production deficits, reliance on food imports, and vulnerability to food supply shocks.
The influence of crystal thickness and interlayer interactions on the properties of heavy ion irradiated MoS2
Authors: Isherwood Liam H , Hennighausen Zachariah , Son Seok-Kyun , Spencer Ben F , Wady Paul T , Shubeita Samir M , Kar Swastik , Casiraghi Cinzia , Baidak Aliaksandr
Published: May 2020

Ion irradiation is a versatile tool to introduce controlled defects into two-dimensional (2D) MoS2 on account of its unique spatial resolution and plethora of ion types and energies available. In order to fully realise the potential of this technique, a holistic understanding of ion-induced defect production in 2D MoS2 crystals of different thicknesses is mandatory. X-ray photoelectron spectroscopy, electron diffraction and Raman spectroscopy show that thinner MoS2 crystals are more susceptible to radiation damage caused by 225 keV Xe+ ions. However, the rate of defect production in quadrilayer and bulk crystals is not significantly different under our experimental conditions. The rate at which S atoms are sputtered as a function of radiation exposure is considerably higher for monolayer MoS2, compared to bulk crystals, leading to MoO3 formation. P-doping of MoS2 is observed and attributed to the acceptor states introduced by vacancies and charge transfer interactions with adsorbed species. Moreover, the out-of-plane vibrational properties of irradiated MoS2 crystals are shown to be strongly thickness-dependent: in mono- and bilayer MoS2, the confinement of phonons by defects results in a blueshift of the

A

1
g

mode. Whereas, a redshift is observed in bulk crystals due to attenuation of the effective restoring forces acting on S atoms caused by vacancies in adjacent MoS2 layers. Consequently, the

A

1
g

frequency of tri- and quadrilayer crystals is statistically invariant on account oft competition between phonon confinement effects and interlayer interactions. The

A

1
g

linewidth is observed to decrease in bi- and trilayer crystals after low dose irradiation and is attributed to layer decoupling. This work shows that there is a complex interplay between defect production, crystal thickness and interlayer interactions in MoS2. Our results demonstrate that ion irradiation is an effective tool to modulate the electronic, vibrational and structural properties of MoS2, which may prove beneficial for practical applications.
On defectivity of families of full-dimensional point configurations
Authors: Borger Christopher , Nill Benjamin
Published: May 2020

The mixed discriminant of a family of point configurations can be considered as a generalization of the

A
A

-discriminant of one Laurent polynomial to a family of Laurent polynomials. Generalizing the concept of defectivity, a family of point configurations is called defective if the mixed discriminant is trivial. Using a recent criterion by Furukawa and Ito we give a necessary condition for defectivity of a family in the case that all point configurations are full-dimensional. This implies the conjecture by Cattani, Cueto, Dickenstein, Di Rocco, and Sturmfels that a family of

n
n

full-dimensional configurations in

Z

n

{\mathbb {Z}}^n

is defective if and only if the mixed volume of the convex hulls of its elements is

1
1

.
Dr AFC: drug repositioning through anti-fibrosis characteristic
Authors: Wu Dingfeng , Gao Wenxing , Li Xiaoyi , Tian Chuan , Jiao Na , Fang Sa , Xiao Jing , Xu Zhifeng , Zhu Lixin , Zhang Guoqing , Zhu Ruixin
Published: May 2020

Fibrosis is a key component in the pathogenic mechanism of a variety of diseases. These diseases involving fibrosis may share common mechanisms and therapeutic targets, and therefore common intervention strategies and medicines may be applicable for these diseases. For this reason, deliberately introducing anti-fibrosis characteristics into predictive modeling may lead to more success in drug repositioning. In this study, anti-fibrosis knowledge base was first built by collecting data from multiple resources. Both structural and biological profiles were then derived from the knowledge base and used for constructing machine learning models including Structural Profile Prediction Model (SPPM) and Biological Profile Prediction Model (BPPM). Three external public data sets were employed for validation purpose and further exploration of potential repositioning drugs in wider chemical space. The resulting SPPM and BPPM models achieve area under the receiver operating characteristic curve (area under the curve) of 0.879 and 0.972 in the training set, and 0.814 and 0.874 in the testing set. Additionally, our results also demonstrate that substantial amount of multi-targeting natural products possess notable anti-fibrosis characteristics and might serve as encouraging candidates in fibrosis treatment and drug repositioning. To leverage our methodology and findings, we developed repositioning prediction platform, drug repositioning based on anti-fibrosis characteristic that is freely accessible via https://www.biosino.org/drafc.
Subconscious Biases in Coral Reef Fish Studies
Authors: Bellwood David R , Hemingson Christopher R , Tebbett Sterling B
Published: May 2020

In complex, diverse ecosystems, one is faced with an exceptionally challenging decision: which species to examine first and why? This raises the question: Is there evidence of subconscious biases in study species selection? Likewise, is there evidence of this bias in selecting methods, locations, and times? We addressed these questions by surveying the literature on the most diverse group of vertebrates (fishes) in an iconic high-diversity ecosystem (coral reefs). The evidence suggests that we select study species that are predominantly yellow. Reef fish studies also selectively examine fishes that are behaviorally bold and in warm, calm, attractive locations. Our findings call for a reevaluation of study species selection and methodological approaches, recognizing the potential for subconscious biases to drive selection for species that are attractive rather than important and for methods that give only a partial view of ecosystems. Given the challenges faced by high-diversity ecosystems, we may need to question our decision-making processes.
Reduction of Coronavirus Burden With Mass Azithromycin Distribution
Authors: Doan Thuy , Hinterwirth Armin , Arzika Ahmed M , Worden Lee , Chen Cindi , Zhong Lina , Oldenburg Catherine E , Keenan Jeremy D , Lietman Thomas M
Published: May 2020

We evaluated the potential antiviral effects of azithromycin on the nasopharyngeal virome of Nigerien children who had received multiple rounds of mass drug administration. We found that the respiratory burden of non–severe acute respiratory syndrome coronaviruses was decreased with azithromycin distributions.

Clinical Trials Registration. NCT02047981.
Exposed Neophasia terlooii (Lepidoptera: Pieridae) Eggs are Resistant to Desiccation During Quiescence
Authors: Halbritter D A
Published: May 2020

Terrestrial insects face the risk of desiccation owing to their small size and high surface area to volume ratios. Insect eggs adhered to exposed substrates are especially prone to extremes in temperature and available moisture. The potential of butterfly egg clusters to withstand desiccation in saturated and unsaturated atmospheres was investigated in this study. Butterflies in the genus Neophasia (Lepidoptera: Pieridae) lay their eggs along live pine needles and they must survive long intervals without available liquid water while overwintering. After 2 d in a desiccating environment, groups of Neophasia terlooii Behr eggs were exposed to several different humidified chambers for 8 d at 5°C. Group masses were monitored over time and the change in mass was compared to the pre-desiccation mass. Changes in mass were minimal, ranging from a 3% increase in the saturated chamber (100% RH) to a 2% decrease in the driest chamber (<10% RH). Ambient humidity was recorded from among the pine needles of a live tree branch in the natural habitat for 2 wk at the start of the overwintering period. Daytime relative humidity among the pine needles dropped as low as 14.5% but rose as high as 92% at night. In the absence of precipitation, N. terlooii eggs can remain within 2% of their starting weight for 10 d at a constant RH of <10% at 5°C. The mechanism for avoiding desiccation and the physical properties of the egg coating are discussed in the context of life in an arid environment.
A Method for a Long-Term Marking of Spotted Lanternfly (Hemiptera: Fulgoridae) Using a Stable Isotope of Nitrogen
Authors: Porras Mitzy F , López-Londoño Tomás , Rost John , Biddinger David , Calvin Dennis , Rajotte Edwin G
Published: May 2020

Developing a lifelong marking method for Lycorma delicatula (White, 1845) is crucial to investigate ecological processes. Here we validate a marking method using stable isotope enrichment (15N) of host plants to track spotted lanternfly (SLF), an invasive species causing economic damage on grapes, hardwood forest and landscape tree species. To validate this method, we first determined the isotope dosage to be sprayed on the host plants and subsequently detected in SLF. Second, we examined whether 15N mark remains detectable from the nymphal to adult stage. We demonstrated that two stable isotope dosages applied to the host plants were assimilated by the insect and equally detectable in the exoskeleton, wings, and mature eggs ready to be oviposited. This safe and reliable method can be used to examine fundamental processes of the biology and ecology of SLF that range from dietary resources and resource allocation to food-web structure and dispersal patterns.
Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting
Authors: Cox Diana C , Guan Xiangnan , Xia Zheng , Cooper Thomas A
Published: May 2020

mRNA processing is highly regulated during development through changes in RNA-binding protein (RBP) activities. CUG-BP, Elav-like family member 1 (CELF1, also called CUGBP1) is an RBP, the expression of which decreases in skeletal muscle soon after birth. CELF1 regulates multiple nuclear and cytoplasmic RNA processing events. In the nucleus, CELF1 regulates networks of postnatal alternative splicing (AS) transitions, while in the cytoplasm, CELF1 regulates mRNA stability and translation. Stabilization and misregulation of CELF1 has been implicated in human diseases including myotonic dystrophy type 1, Alzheimer’s disease and multiple cancers. To understand the contribution of nuclear and cytoplasmic CELF1 activity to normal and pathogenic skeletal muscle biology, we generated transgenic mice for doxycycline-inducible and skeletal muscle-specific expression of active CELF1 mutants engineered to be localized predominantly to either the nucleus or the cytoplasm. Adult mice expressing nuclear, but not cytoplasmic, CELF1 are characterized by strong histopathological defects, muscle loss within 10 days and changes in AS. In contrast, mice expressing cytoplasmic CELF1 display changes in protein levels of targets known to be regulated at the level of translation by CELF1, with minimal changes in AS. These changes are in the absence of overt histopathological changes or muscle loss. RNA-sequencing revealed extensive gene expression and AS changes in mice overexpressing nuclear and naturally localized CELF1 protein, with affected genes involved in cytoskeleton dynamics, membrane dynamics, RNA processing and zinc ion binding. These results support a stronger role for nuclear CELF1 functions as compared to cytoplasmic CELF1 functions in skeletal muscle wasting.
Functional genomics in autoimmune diseases
Authors: Ding James , Frantzeskos Antonios , Orozco Gisela
Published: May 2020

Associations between genetic loci and increased susceptibility to autoimmune disease have been well characterized, however, translating this knowledge into mechanistic insight and patient benefit remains a challenge. While improvements in the precision, completeness and accuracy of our genetic understanding of autoimmune diseases will undoubtedly be helpful, meeting this challenge will require two interlinked problems to be addressed: first which of the highly correlated variants at an individual locus is responsible for increased disease risk, and second what are the downstream effects of this variant. Given that the majority of loci are thought to affect non-coding regulatory elements, the second question is often reframed as what are the target gene(s) and pathways affected by causal variants. Currently, these questions are being addressed using a wide variety of novel techniques and datasets. In many cases, these approaches are complementary and it is likely that the most accurate picture will be generated by consolidating information relating to transcription, regulatory activity, chromatin accessibility, chromatin conformation and readouts from functional experiments, such as genome editing and reporter assays. It is clear that it will be necessary to gather this information from disease relevant cell types and conditions and that by doing so our understanding of disease etiology will be improved. This review is focused on the field of autoimmune disease functional genomics with a particular focus on the most exciting and significant research to be published within the last couple of years.
Robustness of potential biological removal to monitoring, environmental, and management uncertainties
Authors: Punt André E , Siple Margaret , Francis Tessa B , Hammond Phillip S , Heinemann Dennis , Long Kristy J , Moore Jeffrey E , Sepúlveda Maritza , Reeves Randall R , Sigurðsson Guðjón Már , Vikingsson Gísli , Wade Paul R , Williams Rob , Zerbini Alexandre N
Published: May 2020

The potential biological removal (PBR) formula used to determine a reference point for human-caused mortality of marine mammals in the United States has been shown to be robust to several sources of uncertainty. This study investigates the consequences of the quality of monitoring on PBR performance. It also explores stochastic and demographic uncertainty, catastrophic events, sublethal effects of interactions with fishing gear, and the situation of a marine mammal population subject to bycatch in two fisheries, only one of which is managed. Results are presented for two pinniped and two cetacean life histories. Bias in abundance estimates and whether there is a linear relationship between abundance estimates and true abundance most influence conservation performance. Catastrophic events and trends in natural mortality have larger effects than environmental stochasticity. Managing only one of two fisheries with significant bycatch leads, as expected, to a lower probability of achieving conservation management goals, and better outcomes would be achieved if bycatch in all fisheries were managed. The results are qualitatively the same for the four life histories, but estimates of the probability of population recovery differ.
The European Union’s Plan to Amend the ‘First Country of Asylum’ and ‘Safe Third Country’ Concepts
Authors: Marx Reinhard
Published: May 2020

This article examines the European Commission’s 2016 proposals relating to asylum procedures and the Dublin mechanism. In particular, it analyses what State responsibility for protection means in the context of the ‘first country of asylum’ and ‘safe third country’ concepts, which are addressed in the Commission’s Asylum Procedures Proposal. What effect does the common responsibility of all parties to the Refugee Convention have on a particular State’s individual obligations when it examines a refugee’s application for protection? Can a State simply transfer asylum seekers to another State without seeking assurances from that ‘safe third country’ that they will be granted access to refugee status determination procedures? Does a State’s responsibility end after it removes an asylum seeker or is it obliged to cooperate with the destination State? Does merely transiting through a country mean that it is a ‘safe third country’ to which an asylum seeker can be returned? Can an asylum seeker be sent to a State that is safe in one or two regions, but is otherwise unstable? The article considers these and other questions, taking a sceptical approach to the European Commission’s proposal relating to the ‘safe third country’ concept.
Combination rhIL-15 and Anti-PD-L1 (Avelumab) Enhances HIVGag-Specific CD8 T-Cell Function
Authors: Goshu Bruktawit A , Chen Hui , Moussa Maha , Cheng Jie , Catalfamo Marta
Published: May 2020

In chronic HIV infection, virus-specific cytotoxic CD8 T cells showed expression of checkpoint receptors and impaired function. Therefore, restoration of CD8 T-cell function is critical in cure strategies. Here, we show that in vitro blockade of programmed cell death ligand 1 (PD-L1) by an anti-PD-L1 antibody (avelumab) in combination with recombinant human interleukin-15 (rhIL-15) synergistically enhanced cytokine secretion by proliferating HIVGag-specific CD8 T cells. In addition, these CD8 T cells have a CXCR3+PD1−/low phenotype, suggesting a potential to traffic into peripheral tissues. In vitro, proliferating CD8 T cells express PD-L1 suggesting that anti-PD-L1 treatment also targets virus-specific CD8 T cells. Together, these data indicate that rhIL-15/avelumab combination therapy could be a useful strategy to enhance CD8 T-cell function in cure strategies.
Anchialine adjustments: an updated phylogeny and classification for the family Barbouriidae Christoffersen, 1987 (Decapoda: Caridea)
Authors: Ditter Robert E , Mejía-Ortíz Luis M , Bracken-Grissom Heather D
Published: May 2020

Barbouriidae Christoffersen, 1987 is a family comprised of 4 genera and 11 species of enigmatic shrimps restricted to anchialine or marine caves whose evolutionary history and relationships remain elusive. We investigated the evolutionary relationships among members of Barbouriidae with the inclusion of four genera and nine species, and newly collected material from Belize, the Bahamas, and the Yucatán Peninsula, Mexico. Phylogenetic analyses based on seven mitochondrial and nuclear gene regions and genetic distances calculated using partial 16S gene regions have identified a need to revisit the relationships and classification within Barbouriidae. More specifically, we find evidence to suggest Janicea Manning & Hart, 1984 as a junior synonym of Parhippolyte Borradaile, 1900, B. yanezi Mejía, Zarza & López, 2008 as a synonym of Barbouria cubensis (von Martens, 1872), and define two new subfamilies, Calliasmatinae Holthuis, 1973 and Barbouriinae Christoffersen, 1987. Included is a dichotomous key for the species of Barbouriidae that summarizes previous literature and includes new morphological characters. Our findings shed light on existing inaccuracies and gaps in molecular data from barbouriids. We also provide further clarity into evolutionary relationships among genera of Barbouriidae and their allies, suggesting phylogeographic divisions within the family. Our findings suggest an early Atlantic-Pacific divide among genera originating from a shallow-water reef ancestor.
Gouverneur’ syndrome in a young Hispanic patient: A case report of a rare presentation of a rectal adenocarcinoma tumor
Authors: Mejias Emanuel , Robles Yarret , Olivella Gerardo , Bolaños Guillermo
Published: May 2020

This is an unusual case report of 32-year-old Hispanic male who presented with an early-onset advanced stage colorectal cancer with an enterovesical fistula. A 32-year-old man presented to our institution referring suprapubic pain, urinary frequency, dysuria and tenesmus for several weeks suggesting Gouverneur’s syndrome. Patient had been treated with oral antibiotics for his recurrent urinary tract infections without resolution. Associated unintentional weight loss, decreased appetite and suprapubic pain raised concern for occult malignancy. Abdominopelvic computed tomography scan revealed a rectal mass with invasion to bladder. Colonoscopy biopsy confirmed diagnosis of moderately differentiated rectal adenocarcinoma. This report provides vital information about clinical presentations of enterovesical fistula in an imposed rectal adenocarcinoma in a young Hispanic adult with no previous family or medical history. A thorough clinical assessment must be taken to ensure accurate diagnosis and early detection of colorectal cancer in the young Hispanic population.
Variation in zinc concentration of sweetcorn kernels reflects source–sink dynamics influenced by kernel number
Authors: Cheah Zhong Xiang , O’Hare Tim J , Harper Stephen M , Bell Michael J
Published: May 2020

Grain yield and mineral nutrient concentration in cereal crops are usually inversely correlated, undermining biofortification efforts. Here, sink size, expressed as kernel number per cob, was manipulated by controlling the time when the silks of sweetcorn (Zea mays) cv. Hybrix 5 and var. HiZeax 103146 were exposed to pollen. Twelve other varieties were manually pollinated to achieve the maximum potential kernel number per cob, and kernel Zn concentration was correlated with kernel number and kernel mass. As kernel number increased, kernel Zn concentration decreased, with the decrease occurring to similar extents in the embryo tissue and the rest of the kernel. However, total kernel Zn accumulated per cob increased with increasing kernel number, as the small decreases in individual kernel Zn concentration were more than offset by increases in kernel number. When both kernel number and mass were considered, 90% of the variation in kernel Zn concentration was accounted for. Differential distribution of assimilates and Zn to sweetcorn cobs led to significant decreases in kernel Zn concentration with increasing kernel number. This suggests there will be challenges to achieving high kernel Zn concentrations in modern high-yielding sweetcorn varieties unless genotypes with higher Zn translocation rates into kernels can be identified.