bluuebunny/crossref_metadata_2025 huggingface dataset:
Adapting the motet(s)? The case of Hé bergier in Oxford MS Douce 308
Authors: LEACH ELIZABETH EVA
Published: October 2019

The present article seeks to further recent discussion of the diversity of the motet in the long thirteenth century by considering a specific, rather unusual example of motet-related materials in a songbook. It examines a two-stanza pastourelle in the songbook that forms part of Oxford, Bodleian Library, MS Douce 308, and its connection to a network of related materials in various thirteenth-century motet sources. In so doing, it proposes the ostensibly unlikely scenario that this monophonic song derives from two separate motets that may already have been linked through their shared tenor and possibly also performed together in some way. This article brings the important conclusions of Fred Büttner in regard to these materials to Anglophone scholarship, while nuancing his reasoning in light of more recent scholarly work on thirteenth-century motets copied in songbooks.
Cheap, fast, good: the Roman glassblowing revolution reconsidered
Authors: Larson Katherine A.
Published: October 2019

Among the most dramatic changes in ancient material culture was the widespread adoption of glass vessels for tableware and storage during the 1st c. B.C. and 1st c. A.D. As shown by the quantity of glass finds from occupation sites of the Imperial era, glassware was much more prominent in daily life than it had been previously. This shift occurred concurrently with the widespread adoption of glassblowing. This change in consumer behavior points to a complex process of experimentation, development, and gradual adaptation on the part of both producers and consumers. The transition from centuries-old technologies of core-forming, casting and sagging to blowing required a complete reconfiguration of every stage of glass production, from the increased supply of raw material to the development of new tools and workshop space, and in the training of craftsmen.
Roma e le prime importazioni di alimenti ispanici trasportati in anfora
Authors: Rizzo Giorgio , Moreno Megías Violeta
Published: October 2019

Un noto passo di Strabone (3.2.6),1 che potrebbe riferirsi al periodo in cui Posidonio (una delle sue fonti) si trovò nella valle del Baetis e a Gades, all’inizio del I sec. a.C., restituisce l’immagine di un’economia della Turdetania, la regione che dal 27 a.C. costituì parte della provincia della Baetica, già molto fiorente, in grado di alimentare esportazioni di generi alimentari — soprattutto grano, vino ed olio di ottima qualità (oὺ πoλὺ μóvov, ὰλλὰ καìκὰλλιστov), ma anche prodotti derivati dalla lavorazione del pesce . di notevole entità e varietà. Nel testo di Strabone questi flussi verso il mercato di Roma e dell’Italia centromeridionale sono materializzati dalle navi di grandi dimensioni in entrata nei porti di Dicearchia (Pozzuoli) e Ostia.
Notes on the elogium of a benefactor at Pompeii
Authors: Bodel John , Bendlin Andreas , Bernard Seth , Bruun Christer , Edmondson Jonathan
Published: October 2019

The rediscovery in the summer of 2017 of a large monumental tomb of unusual form outside the Stabian Gate at Pompeii caused an immediate sensation, and the swift initial publication by M. Osanna in JRA 31 (2018) of the long funerary inscription fronting the W side of the base, facing the road, has been welcomed gratefully by the scholarly community. The text — at 183 words, by far the longest funerary inscription yet found at Pompeii — records a series of extraordinary benefactions by an unnamed local worthy, beginning with a banquet held on the occasion of his coming-of-age ceremony and continuing, it seems, well into his adult life, up to the final years of the town when the monument was built. As Osanna and others have recognized, the inscription, which seems to allude to an historical event (Tac., Ann. 14.17), the riot between Nucerians and Pompeians around Pompeii’s amphitheater in A.D. 59, provides valuable if ambivalent new information relevant to the demographic, economic and social history of Pompeii that will require full discussion in a variety of contexts over time. The present collection of remarks, a collaborative effort, is offered in the spirit of debate and is intended as an interim contribution toward a more complete understanding of the text.1
Capricorno Alae VII Phrygum … (i) Interim report on the fort near Tel Shalem
Authors: Arubas Benjamin , Heinzelmann Michael , Mevorah David , Overman Andrew
Published: October 2019

A multi-disciplinary research project has been begun in the fields next to the site of Tel Shalem (fig. 1), the locus of important discoveries since the 1970s (primarily the bronze statue of Hadrian). Recent geophysical prospections have detected the clear layout of a Roman fort and possibly even two successive forts. Two short excavation seasons carried out in 2017 and 2019, with a focus on the principia, resulted in finds that shed new light on the nature, history and identity of the site.
The man who came late to dinner. A sundial, a raven, and a missed dinner party on a mosaic at Tarsus
Authors: Dunbabin Katherine M. D. , Adak Adıbelli Işık , Çavuş Mehmet , Alper Doğukan
Published: October 2019

In 2012, construction works at the traditional olive market at Tarsus, in Eski Ömerli district, revealed large-scale architectural remains of the Roman period; the construction works were halted and a salvage excavation was initiated by Tarsus Museum. The remains that appeared at the first stage of the excavations were interpreted as those of a reservoir from the Roman Imperial period, stretching along a N–S axis. On the E side, a structure projects from the E wall of the reservoir, containing a pool that collects water flowing from drainage pipes set in the reservoir’s façade. The pool was extended in two stages in late antiquity.1 Two metres north of this pool and 3 m from the E wall of the reservoir, the excavations revealed a mosaic pavement (9.73 x 5.05 m), apparently forming part of the floor of a building running parallel to the reservoir’s wall (fig. 1).
Burnswark Hill: the opening shot of the Antonine reconquest of Scotland?
Authors: Reid John H. , Nicholson Andrew
Published: October 2019

This paper represents an interim report of the Burnswark Project that has utilised the techniques of battlefield archaeology to locate and accurately identify missiles across a substantial field of conflict in SW Scotland. The distribution, characteristics, dating and proposed historical context of these missiles are argued to support their use in a dramatic episode of ‘exemplary force’ by the Roman army. The magnitude of the event might be seen to be compatible with an emperor establishing his legitimacy as a military leader.
What makes a ban on plastic bags effective? The case of Nepal
Authors: Bharadwaj Bishal , Baland Jean Marie , Nepal Mani
Published: October 2019

The extensive use of plastic bags in Nepal has led to growing concern in recent years. We investigate the impact of a municipal plastic bags ban on bags use behavior, based on a field survey carried out among consumers and retailers across selected municipalities. Our results indicate that the effectiveness of the ban critically depends on its enforcement and sanctioning system. In particular, our results suggest that the perceived sanction is a critical determinant of plastic bags use, as a doubling of the perceived sanction could reduce plastic bags use by two-thirds for retailers and by one-half for consumers. While the nominal amount of the fine does not seem to play a role, the probability of being detected appears to play a key role in the perceived sanction. This implies that effective monitoring of the ban by the municipal authorities is critical for the success of the policy.
DEFINABLE SETS OF BERKOVICH CURVES
Authors: Cubides Kovacsics Pablo , Poineau Jérôme
Published: October 2019

In this article, we functorially associate definable sets to$k$-analytic curves, and definable maps to analytic morphisms between them, for a large class of$k$-analytic curves. Given a$k$-analytic curve$X$, our association allows us to have definable versions of several usual notions of Berkovich analytic geometry such as the branch emanating from a point and the residue curve at a point of type 2. We also characterize the definable subsets of the definable counterpart of$X$and show that they satisfy a bijective relation with the radial subsets of$X$. As an application, we recover (and slightly extend) results of Temkin concerning the radiality of the set of points with a given prescribed multiplicity with respect to a morphism of$k$-analytic curves. In the case of the analytification of an algebraic curve, our construction can also be seen as an explicit version of Hrushovski and Loeser’s theorem on iso-definability of curves. However, our approach can also be applied to strictly$k$-affinoid curves and arbitrary morphisms between them, which are currently not in the scope of their setting.
Establishment of the early-life microbiome: a DOHaD perspective
Authors: Stinson Lisa F.
Published: October 2019

The human microbiome plays a number of critical roles in host physiology. Evidence from longitudinal cohort studies and animal models strongly supports the theory that maldevelopment of the microbiome in early life can programme later-life disease. The early-life microbiome develops in a clear stepwise manner over the first 3 years of life. During this highly dynamic time, insults such as antibiotic use and formula feeding can adversely affect the composition and temporal development of the microbiome. Such experiences predispose infants for the development of chronic health conditions later in life. This review highlights key factors that disrupt the early-life microbiome and highlights major non-communicable diseases which are underpinned by early-life dysbiosis.
Disfluent, But Fast
Authors: Bahník Štěpán
Published: October 2019

Abstract. Processing fluency, a metacognitive feeling of ease of cognitive processing, serves as a cue in various types of judgments. Processing fluency is sometimes evaluated by response times, with shorter response times indicating higher fluency. The present study examined existence of the opposite association; that is, it tested whether disfluency may lead to faster decision times when it serves as a strong cue in judgment. Retrieval fluency was manipulated in an experiment using previous presentation and phonological fluency by varying pronounceability of pseudowords. Participants liked easy-to-pronounce and previously presented words more. Importantly, their decisions were faster for hard-to-pronounce and easy-to-pronounce pseudowords than for pseudowords moderate in pronounceability. The results thus showed an inverted-U shaped relationship between fluency and decision times. The findings suggest that disfluency can lead to faster decision times and thus demonstrate the importance of separating different processes comprising judgment when response times are used as a measure of processing fluency.
Underestimation of Global Photosynthesis in Earth System Models Due to Representation of Vegetation Structure
Authors: Braghiere R. K. , Quaife T. , Black E. , He L. , Chen J. M.
Published: October 2019

The impact of vegetation structure on the absorption of shortwave radiation in Earth System Models (ESMs) is potentially important for accurate modeling of the carbon cycle and hence climate projections. A proportion of incident shortwave radiation is used by plants to photosynthesize and canopy structure has a direct impact on the fraction of this radiation which is absorbed. This paper evaluates how modeled carbon assimilation of the terrestrial biosphere is impacted when clumping derived from satellite data is incorporated. We evaluated impacts of clumping on photosynthesis using the Joint UK Land Environment Simulator, the land surface scheme of the UK Earth System Model. At the global level, Gross Primary Productivity (GPP) increased by 5.53 ± 1.02 PgC/year with the strongest absolute increase in the tropics. This is contrary to previous studies that have shown a decrease in photosynthesis when similar clumping data sets have been used to modify light interception in models. In our study additional transmission of light through upper canopy layers leads to enhanced absorption in lower layers in which photosynthesis tends to be light limited. We show that this result is related to the complexity of canopy scheme being used.
Acceleration of the Extreme Sea Level Rise Along the Chinese Coast
Authors: Feng Jianlong , Li Delei , Wang Tao , Liu Qiulin , Deng Lijing , Zhao Liang
Published: October 2019

Using high‐frequency tide gauge observations from 1980 to 2017, we analyzed changes in extreme sea levels (ESLs) along the Chinese coast to examine whether extreme sea‐level rise acceleration could be observed. The results indicated that the ESL has risen with fluctuations along the Chinese coast. The ESL also featured significant decadal variabilities. The ESL rise was accelerated at most tide gauges throughout the whole study period, especially after the 1980s, while the acceleration patterns varied with station location. The mean sea level (MSL) change was confirmed as the major driver of the ESL change according to the analysis. However, the skew surge may also have affected the extremes at many of the tide gauges, which was observed after detrending. The extreme/MSL had a significant positive correlation with the Atlantic Multidecadal Oscillation, which is supposed to affect the MSL through a combination of variation in sea surface temperature, pressure system, and wind. That sea level oscillation is dominated by Atlantic Multidecadal Oscillation should be taken into consideration when studying accelerations in the rate of ESLs and of MSLs along the Chinese coast.
Broader Impacts of the Metasomatic Underplating Hypothesis
Authors: Park Jeffrey , Rye Danny M.
Published: October 2019

The “metasomatic underplating” hypothesis argues that crustal fractures develop during hot spot magma ascent to allow seawater to infiltrate and to serpentinize the sub‐Moho mantle. Published seismic velocities and layer thicknesses support estimates that 1 km of seawater could be chemically bound within an underplated layer, which may require 2–4 Myr to mature. If a serpentinized mantle layer underlies hot spot tracks and/or aseismic ridges, their buoyancy can induce flat‐slab behavior within subduction zones (e.g., beneath central Chile and Peru), weaken slab rheology, and foster slab tears. During serpentinization, metasomatic underplating would produce more serpentine and talc and less brucite and magnetite, if seawater equilibrates with silica in the gabbroic oceanic crust as it descends to the Moho. The restricted solubility of carbonate with temperature may induce seawater CO2 to sequester in the crust as carbonate concretions or intergrowths. Consumption of seawater H2O by serpentinization raises its salinity so that Fe cations stabilize in chloride complexes and depart the open system. Alkali cations in seawater contribute to the sodic metasomatism of pyroxenes, analogous to alterations observed in abyssal peridotites.
The Role of Winter Warming in Permafrost Change Over the Qinghai‐Tibet Plateau
Authors: Zhang Guofei , Nan Zhuotong , Wu Xiaobo , Ji Hailong , Zhao Shuping
Published: October 2019

Winter warming is fast than summer warming on the Qinghai‐Tibet Plateau (QTP). However, no assessment of winter warming effects on permafrost has been attempted. Here we conducted hypothetical control experiments and used the Noah land surface model to evaluate the impacts of winter warming on the QTP permafrost. The results show that air temperature in winter (November–April) was increasing at a rate of 0.66 °C/decade during 1980s−2000s, over double that in summer (May–October). The mean annual ground temperature of permafrost increased by 0.13 °C/decade. The summer warming dominated the variations in thermal regime of permafrost before 2000. After that, the influence of winter warming on permafrost thermal regime has gradually grown and exceeded that of summer warming. Winter warming has amplified the thermal degradation of permafrost. Our findings reveal that alpine continuous permafrost on the northern QTP has experienced a prominent regional warming due to rapid winter warming since 2000.
Short‐ and Long‐Wavelength TIDs Generated by the Great American Eclipse of 21 August 2017
Authors: Eisenbeis J. , Occhipinti G. , Astafyeva E. , Rolland L.
Published: October 2019

On the 21 August 2017 the eclipse shadow drastically changed the state of the ionosphere over the United States. This effect on the ionosphere is visible in the total electron content measured by Global Navigation Satellite Systems (GNSS). The shadow moved with the supersonic speed of ~1,000 m/s over Oregon to ~650 m/s over South Carolina. In order to exhaustively explore the ionospheric signature of the eclipse, we use data of total electron content from ~3,000 GNSS stations seeing multiple Global Positioning System (GPS) and Global Navigation Satellite System (GLONASS) satellites to visualize the phenomena. This tremendous dataset allows high‐resolution characterization of the frequency content and wavelengths—using an omega‐k analysis based on 3‐D fast Fourier transform—of the eclipse signature in the ionosphere in order to fully identify traveling ionospheric disturbances (TIDs). We confirm the generation of TIDs associated with the eclipse including TIDs interpreted as bow waves in previous studies. Additionally, we reveal, for the first time, short (50–100 km) and long (500–600 km) wavelength TIDs with periods between 30 and 65 min. The sources of the revealed short wavelength TIDs are co‐located with the regions of stronger gradient of the EUV related to sunspots. Our work confirms and describes physical properties of the waves observable in the ionosphere during the Great American Eclipse.
Logarithmic Model Joint Inversion Method for Coseismic and Postseismic Slip: Application to the 2017 Mw 7.3 Sarpol Zahāb Earthquake, Iran
Authors: Liu Xiaoge , Xu Wenbin
Published: October 2019

Interferometric synthetic aperture radar (InSAR) has become an important technique for studying earthquake cycle deformation. However, due to the limited satellite revisit time, it is often difficult to fully separate coseismic and postseismic slip from InSAR data. Nevertheless, accurately estimating spatiotemporal coseismic and postseismic fault slip distribution models is important for quantifying earthquake slip, understanding the kinematics of seismogenic faulting, and evaluating seismic hazards. Here, we develop a logarithmic model‐based method (LogSIM) for the joint inversion of coseismic and postseismic fault slip using InSAR data from multiple platforms in different orbits. This method considers the nature of early postseismic slip following logarithmic decay. The coseismic slip, the decay time constant, and the decay amplitude of the logarithmic model can be jointly estimated from unwrapped interferograms without the need for InSAR time series calculations, thereby reducing the number of unknown parameters and stabilizing the inversion. The robustness of LogSIM is first validated with synthetic experiments. We then apply LogSIM to invert for the coseismic and postseismic slip models of the 2017 Mw 7.3 Sarpol Zahāb earthquake. We find that the maximum afterslip value and postseismic moment release during the first four months reported in previous studies are underestimated by ~26% and ~31%, respectively, due to the unavailability of the first five days of postseismic deformation. The estimated afterslip distribution spatially overlaps with the aftershocks in the updip region of the fault plane. LogSIM could potentially be extended to integrate different space geodetic data in earthquake cycle deformation modeling.
AquaSat: A Data Set to Enable Remote Sensing of Water Quality for Inland Waters
Authors: Ross Matthew R. V. , Topp Simon N. , Appling Alison P. , Yang Xiao , Kuhn Catherine , Butman David , Simard Marc , Pavelsky Tamlin M.
Published: October 2019

Satellite estimates of inland water quality have the potential to vastly expand our ability to observe and monitor the dynamics of large water bodies. For almost 50 years, we have been able to remotely sense key water quality constituents like total suspended sediment, dissolved organic carbon, chlorophyll a, and Secchi disk depth. Nonetheless, remote sensing of water quality is poorly integrated into inland water sciences, in part due to a lack of publicly available training data and a perception that remote estimates are unreliable. Remote sensing models of water quality can be improved by training and validation on larger data sets of coincident field and satellite observations, here called matchups. To facilitate model development and deeper integration of remote sensing into inland water science, we have built AquaSat, the largest such matchup data set ever assembled. AquaSat contains more than 600,000 matchups, covering 1984–2019, of ground‐based total suspended sediment, dissolved organic carbon, chlorophyll a, and SDDSecchi disk depth measurements paired with spectral reflectance from Landsat 5, 7, and 8 collected within ±1 day of each other. To build AquaSat, we developed open source tools in R and Python and applied them to existing public data sets covering the contiguous United States, including the Water Quality Portal, LAGOS‐NE, and the Landsat archive. In addition to publishing the data set, we are also publishing our full code architecture to facilitate expanding and improving AquaSat. We anticipate that this work will help make remote sensing of inland water accessible to more hydrologists, ecologists, and limnologists while facilitating novel data‐driven approaches to monitoring and understanding critical water resources at large spatiotemporal scales.
The interrelationship between cerebral ischemic stroke and glioma: a comprehensive study of recent reports
Authors: Ghosh Mrinal K. , Chakraborty Dipankar , Sarkar Sibani , Bhowmik Arijit , Basu Malini
Published: October 2019

Glioma and cerebral ischemic stroke are two major events that lead to patient death worldwide. Although these conditions have different physiological incidences, ~10% of ischemic stroke patients develop cerebral cancer, especially glioma, in the postischemic stages. Additionally, the high proliferation, venous thrombosis and hypercoagulability of the glioma mass increase the significant risk of thromboembolism, including ischemic stroke. Surprisingly, these events share several common pathways, viz. hypoxia, cerebral inflammation, angiogenesis, etc., but the proper mechanism behind this co-occurrence has yet to be discovered. The hypercoagulability and presence of the D-dimer level in stroke are different in cancer patients than in the noncancerous population. Other factors such as atherosclerosis and coagulopathy involved in the pathogenesis of stroke are partially responsible for cancer, and the reverse is also partially true. Based on clinical and neurosurgical experience, the neuronal structures and functions in the brain and spine are observed to change after a progressive attack of ischemia that leads to hypoxia and atrophy. The major population of cancer cells cannot survive in an adverse ischemic environment that excludes cancer stem cells (CSCs). Cancer cells in stroke patients have already metastasized, but early-stage cancer patients also suffer stroke for multiple reasons. Therefore, stroke is an early manifestation of cancer. Stroke and cancer share many factors that result in an increased risk of stroke in cancer patients, and vice-versa. The intricate mechanisms for stroke with and without cancer are different. This review summarizes the current clinical reports, pathophysiology, probable causes of co-occurrence, prognoses, and treatment possibilities.
Reminiscent capillarity in subnanopores
Authors: Deroche Irena , Daou T. Jean , Picard Cyril , Coasne Benoit
Published: October 2019

Fluids in large and small pores display different behaviors with a crossover described through the concept of critical capillarity. Here we report experimental and simulation data for various siliceous zeolites and adsorbates that show unexpected reminiscent capillarity for such nanoporous materials. For pore sizes D exceeding the fluid molecule size, the filling pressures p are found to follow a generic behavior kBT ln p ∼ γ/ρD where γ and ρ are the fluid surface tension and density. This result is rationalized by showing that the filling chemical potential for such ultra-small pores is the sum of an adsorption energy and a capillary energy that remains meaningful even for severe confinements. A phenomenological model, based on Derjaguin’s formalism to bridge macroscopic and molecular theories for condensation in porous materials, is developed to account for the behavior of fluids confined down to the molecular scale from simple parameters.
Integrated molecular characterization of chondrosarcoma reveals critical determinants of disease progression
Authors: Nicolle Rémy , Ayadi Mira , Gomez-Brouchet Anne , Armenoult Lucile , Banneau Guillaume , Elarouci Nabila , Tallegas Matthias , Decouvelaere Anne-Valérie , Aubert Sébastien , Rédini Françoise , Marie Béatrice , Labit-Bouvier Corinne , Reina Nicolas , Karanian Marie , le Nail Louis-Romée , Anract Philippe , Gouin François , Larousserie Frédérique , de Reyniès Aurélien , de Pinieux Gonzague
Published: October 2019

Chondrosarcomas are primary cancers of cartilaginous tissue with highly contrasting prognoses. These tumors are defined by recurrent mutations in the IDH genes and other genetic alterations including inactivation of CDKN2A and COL2A1; however, these have no clinical value. Here we use multi-omics molecular profiles from a series of cartilage tumors and find an mRNA classification that identifies two subtypes of chondrosarcomas defined by a balance in tumor differentiation and cell cycle activation. The microRNA classification reveals the importance of the loss of expression of the 14q32 locus in defining the level of malignancy. Finally, DNA methylation is associated with IDH mutations. We can use the multi-omics classifications to predict outcome. We propose an mRNA-only classifier to reproduce the integrated multi-omics classification, and its application to relapsed tumor samples shows the progressive nature of the classification. Thus, it may be possible to use mRNA-based signatures to detect patients with high-risk chondrosarcomas.
How to control single-molecule rotation
Authors: Simpson Grant J. , García-López Víctor , Daniel Boese A. , Tour James M. , Grill Leonhard
Published: October 2019

The orientation of molecules is crucial in many chemical processes. Here, we report how single dipolar molecules can be oriented with maximum precision using the electric field of a scanning tunneling microscope. Rotation is found to occur around a fixed pivot point that is caused by the specific interaction of an oxygen atom in the molecule with the Ag(111) surface. Both directions of rotation are realized at will with 100% directionality. Consequently, the internal dipole moment of an individual molecule can be spatially mapped via its behavior in an applied electric field. The importance of the oxygen-surface interaction is demonstrated by the addition of a silver atom between a single molecule and the surface and the consequent loss of the pivot point.
Understanding resonant charge transport through weakly coupled single-molecule junctions
Authors: Thomas James O. , Limburg Bart , Sowa Jakub K. , Willick Kyle , Baugh Jonathan , Briggs G. Andrew D. , Gauger Erik M. , Anderson Harry L. , Mol Jan A.
Published: October 2019

Off-resonant charge transport through molecular junctions has been extensively studied since the advent of single-molecule electronics and is now well understood within the framework of the non-interacting Landauer approach. Conversely, gaining a qualitative and quantitative understanding of the resonant transport regime has proven more elusive. Here, we study resonant charge transport through graphene-based zinc-porphyrin junctions. We experimentally demonstrate an inadequacy of non-interacting Landauer theory as well as the conventional single-mode Franck–Condon model. Instead, we model overall charge transport as a sequence of non-adiabatic electron transfers, with rates depending on both outer and inner-sphere vibrational interactions. We show that the transport properties of our molecular junctions are determined by a combination of electron–electron and electron-vibrational coupling, and are sensitive to interactions with the wider local environment. Furthermore, we assess the importance of nuclear tunnelling and examine the suitability of semi-classical Marcus theory as a description of charge transport in molecular devices.
Topology, landscapes, and biomolecular energy transport
Authors: Elenewski Justin E. , Velizhanin Kirill A. , Zwolak Michael
Published: October 2019

While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics. While the former determines transport pathways via pairwise interactions, the latter reflects frustration within the landscape for local conformational rearrangements. Unlike transport through small-molecule systems, such as alkanes, nonlinearity dominates over coherent processes at even quite short time- and length-scales. Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules. The approach demonstrates that vibrational energy transport can probe otherwise inaccessible aspects of macromolecular dynamics and interactions that underly biological function.
Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection
Authors: Ulz Peter , Perakis Samantha , Zhou Qing , Moser Tina , Belic Jelena , Lazzeri Isaac , Wölfler Albert , Zebisch Armin , Gerger Armin , Pristauz Gunda , Petru Edgar , White Brandon , Roberts Charles E. S. , John John St. , Schimek Michael G. , Geigl Jochen B. , Bauernhofer Thomas , Sill Heinz , Bock Christoph , Heitzer Ellen , Speicher Michael R.
Published: October 2019

Deregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. Here we develop and validate a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyze whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a bioinformatics pipeline developed by us that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observe patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of detection of early-stage colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.
Gel electrophoresis separation and origins of light emission in fluorophores prepared from citric acid and ethylenediamine
Authors: Kokorina Alina A. , Bakal Artem A. , Shpuntova Daria V. , Kostritskiy Alexandr Yu. , Beloglazova Natalia V. , De Saeger Sarah , Sukhorukov Gleb B. , Sapelkin Andrei V. , Goryacheva Irina Yu.
Published: October 2019

We investigated light emission of hydrothermally treated citric acid and ethylenediamine (EDA) with various precursor ratios using gel-electrophoresis. We show that this relatively simple approach can deliver significant insights into the origins of photoluminescence. We found that products of the synthesis consist of both positively and negatively charged species and exhibit large dispersion in electrophoretic mobility (i.e. charge-to-size ratio). We observed that despite the large dispersion of the reaction products the blue light emission is confined to discrete bands clearly identifiable in the gel. We demonstrate clear evidence that this emission originates from the negatively charged light molecular fraction with the highest mobility which shows no excitation-dependent light emission. This molecular fluorophore exhibits spectral characteristics similar to previously reported 1,2,3,5-tetrahydro-5-oxo-imidazo[1,2-a]pyridine-7-carboxylic acid (IPCA). Secondary gel electrophoresis run performed on the bands extracted from the first run indicates that no further separation takes place. On the basis of our experimental results, we conclude that relatively stable binding exists between IPCA and EDA-derived product. Thus, the products of the reaction contain IPCA both in molecular form and in complexes with EDA-derived products. We conclude that excitation-dependent emission is related to the fluorophore binding to the positively charged EDA-derived products with a positive charge.
Vitamin K1 prevents diabetic cataract by inhibiting lens aldose reductase 2 (ALR2) activity
Authors: Thiagarajan R. , Varsha M. K. N. Sai , Srinivasan V. , Ravichandran R. , Saraboji K.
Published: October 2019

This study investigated the potential of vitamin K1 as a novel lens aldose reductase inhibitor in a streptozotocin-induced diabetic cataract model. A single, intraperitoneal injection of streptozotocin (STZ) (35 mg/kg) resulted in hyperglycemia, activation of lens aldose reductase 2 (ALR2) and accumulation of sorbitol in eye lens which could have contributed to diabetic cataract formation. However, when diabetic rats were treated with vitamin K1 (5 mg/kg, sc, twice a week) it resulted in lowering of blood glucose and inhibition of lens aldose reductase activity because of which there was a corresponding decrease in lens sorbitol accumulation. These results suggest that vitamin K1 is a potent inhibitor of lens aldose reductase enzyme and we made an attempt to understand the nature of this inhibition using crude lens homogenate as well as recombinant human aldose reductase enzyme. Our results from protein docking and spectrofluorimetric analyses clearly show that vitamin K1 is a potent inhibitor of ALR2 and this inhibition is primarily mediated by the blockage of DL-glyceraldehyde binding to ALR2. At the same time docking also suggests that vitamin K1 overlaps at the NADPH binding site of ALR2, which probably shows that vitamin K1 could possibly bind both these sites in the enzyme. Another deduction that we can derive from the experiments performed with pure protein is that ALR2 has three levels of affinity, first for NADPH, second for vitamin K1 and third for the substrate DL-glyceraldehyde. This was evident based on the dose-dependency experiments performed with both NADPH and DL-glyceraldehyde. Overall, our study shows the potential of vitamin K1 as an ALR2 inhibitor which primarily blocks enzyme activity by inhibiting substrate interaction of the enzyme. Further structural studies are needed to fully comprehend the exact nature of binding and inhibition of ALR2 by vitamin K1 that could open up possibilities of its therapeutic application.
Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function
Authors: Brawner Kyle M. , Yeramilli Venkata A. , Duck Lennard W. , Van Der Pol William , Smythies Lesley E. , Morrow Casey D. , Elson Charles O. , Martin Colin A.
Published: October 2019

The intestinal microbiota is critical for maintaining homeostasis. Dysbiosis, an imbalance in the microbial community, contributes to the susceptibility of several diseases. Many factors are known to influence gut microbial composition, including diet. We have previously shown that fecal immunoglobulin (Ig) A levels are decreased in mice fed a diet free of aryl hydrocarbon receptor (AhR) ligands. Here, we hypothesize this IgA decrease is secondary to diet-induced dysbiosis. We assigned mice to a conventional diet, an AhR ligand-free diet, or an AhR ligand-free diet supplemented with the dietary AhR ligand indole-3-carbinol (I3C). We observed a global alteration of fecal microbiota upon dietary AhR ligand deprivation. Compared to mice on the conventional diet, familyErysipelotrichaceaewas enriched in the feces of mice on the AhR ligand-free diet but returned to normal levels upon dietary supplementation with I3C.Faecalibaculum rodentium, anErysipelotrichaceaespecies, depleted its growth media of AhR ligands. Cultured fecal bacteria from mice on the AhR ligand-free diet, but not the other two diets, were able to alter IgA levelsin vitro, as wasF.rodentiumalone. Our data point to the critical role of AhR dietary ligands in shaping the composition and proper functioning of gut microbiota.
Cerium-based UiO-66 metal–organic frameworks explored as efficient redox catalysts: titanium incorporation and generation of abundant oxygen vacancies
Authors: Zhang Yajun , Chen Hanjiao , Pan Yi , Zeng Xiaoliang , Jiang Xiaofang , Long Zhou , Hou Xiandeng
Published: October 2019

For the first time, UiO-66(Ce) was endowed with greatly improved redox photocatalytic activity via Ti incorporation, based on the formation of oxygen vacancies.
Rhodium-mediated 18F-oxyfluorination of diazoketones using a fluorine-18-containing hypervalent iodine reagent
Authors: Cortés González Miguel A. , Jiang Xingguo , Nordeman Patrik , Antoni Gunnar , Szabó Kálmán J.
Published: October 2019

α-[18F]Fluoro ethers were obtained from diazocarbonyl compounds using a hypervalent iodine based fluorine-18 reagent.
Discovery of two types of new porphyrin–C70 co-crystals: influence of intermolecular contact on the inherent resistance
Authors: Yu Weidong , Yan Qianwen , Nie Yanmei , Liang Shuang , Li Sanghao , Zhang Yin , Lin Mingyuan , Yan Jun
Published: October 2019

Two types of supramolecular aggregates based on C70 were synthesised and their inherent resistances were analysed.
Evaluating lithium diffusion mechanisms in the complex spinel Li2NiGe3O8
Authors: Martin Daniel Z. C. , Haworth Abby R. , Schmidt Whitney L. , Baker Peter J. , Boston Rebecca , Johnston Karen E. , Reeves-McLaren Nik
Published: October 2019

Li+-ion diffusion in the all-solid-state battery electrolyte candidate material Li2NiGe3O8was investigated andDLi= 3.89 × 10−12cm2s−1calculated.
Nanotubols under H2O2 exposure: is it possible to poly-hydroxylate carbon nanotubes?
Authors: Vicente-Santiago J. , Cornejo-Jacob J. , Valdez-Pérez D. , Ruiz-García J. , Guirado-López R. A.
Published: October 2019

We present a combined experimental and theoretical study dedicated to analyze the variations in the surface chemistry of hydroxylated multiwalled carbon nanotubes (MWCNTs), so called nanotubols, when exposed to H2O2 at high temperatures.
Enhanced functional properties of soft polymer–ceramic composites by swift heavy ion irradiation
Authors: Mohanty Hari Sankar , Sharma Saurabh Kumar , RaviKant RaviKant , Kulriya Pawan Kumar , Kumar Ashok , Thomas Reji , Pradhan Dillip K.
Published: October 2019

Variations of different physical properties with the fluence (ions per cm2) of Li3+ion irradiation.
Understanding electro-catalysis by using density functional theory
Authors: Chen Z. W. , Chen L. X. , Wen Z. , Jiang Q.
Published: October 2019

DFT calculations are indispensable for understanding the electro-catalysis through explanation of the experimental phenomena, prediction of experimental results, and guiding of the experimental investigation.
Quantum–classical approach to the reaction dynamics in a superfluid helium nanodroplet. The Ne2 dimer and Ne–Ne adduct formation reaction Ne + Ne-doped nanodroplet
Authors: Blancafort-Jorquera Miquel , Vilà Arnau , González Miguel
Published: October 2019

The Ne + Ne@(4He)N reaction dynamics was studied using a quantum–classical approach. The angular momentum plays a critical role: the Ne–Ne adduct formation dominates the reactivity (instead of the Ne2 dimer) and quantized vortices are produced.
Spin transport properties of 1,4,5,8-naphthalenetetracarboxylic dianhydride based molecular devices
Authors: Wang Wenjing , Gao Denglei , Huang Yucheng , Zhou Tao , Wang Sufan
Published: October 2019

NTCDA carbon based molecular devices have been designed, and spin-dependent transport properties via carbon and oxygen linkage to the zigzag graphene nanoribbon electrodes have been investigated.
Luminescence of the Mn2+ ion in non-Oh and Td coordination environments: the missing case of square pyramid
Authors: Artem'ev Alexander V. , Davydova Maria P. , Berezin Alexey S. , Brel Valery K. , Morgalyuk Vasilii P. , Bagryanskaya Irina Yu. , Samsonenko Denis G.
Published: October 2019

The luminescence of Mn2+ ion in a square-pyramidal (C4v) ligand field was discovered. The molecular complexes with such coordination geometry exhibit red emission with enhanced Stokes shift and millisecond lifetimes.
Insights into the solvent-assisted degradation of organophosphorus compounds by a Zr-based metal–organic framework
Authors: Harvey Jacob A. , Pearce Charles J. , Hall Morgan G. , Bruni Eric J. , DeCoste Jared B. , Sava Gallis Dorina F.
Published: October 2019

Insights into the MOF-based degradation of organophosphorus compounds in non-/aqueous solvents highlights the effect of solvent size on reaction rates.
Correction: Endoplasmic reticulum targeting tumour selective photocytotoxic oxovanadium(iv) complexes having vitamin-B6 and acridinyl moieties
Authors: Banerjee Samya , Dixit Akanksha , Karande Anjali A. , Chakravarty Akhil R.
Published: October 2019

Correction for ‘Endoplasmic reticulum targeting tumour selective photocytotoxic oxovanadium(iv) complexes having vitamin-B6 and acridinyl moieties’ by Samya Banerjee et al., Dalton Trans., 2016, 45, 783–796.
Electrochemical TEMPO-catalyzed multicomponent C(sp3)–H α-carbamoylation of free cyclic secondary amines
Authors: Pan Na , Ling Johanne , Zapata Ramiro , Pulicani Jean-Pierre , Grimaud Laurence , Vitale Maxime R.
Published: October 2019

The electrochemical α-carbamoylation of free cyclic secondary amines has been realized under an original TEMPO-catalyzed multicomponent coupling.
Synthesis of novel cationic carbon dots and application to quantitative detection of K+ in human serum samples
Authors: Gao Zideng , Wang Shunyi , Xu Zijun , Liu Jin , Huang Yuanfang , Hu Shuwen , Ren Xueqin
Published: October 2019

Novel cationic carbon dots were synthesized in a simple way and applied to detect K+ in human serum samples with ultra-high sensitivity.
One-pot synthesis of PtIn/3D-GNs composites with high alloying degree for electro-photo synergistic catalysis
Authors: Ye Yixiang , Wang Yanli , Li Zhongshui , Ye Yanzhu , Liu Ying , Zou Xiaohuan , Lin Shen
Published: October 2019

Alloyed PtIn/3D-GNs composites exhibit efficient electro-photo-catalysis under irradiation, deriving from the synergy between the charge separation of In2O3 and SPR excitation of In(0).
“Naked-eye” detection of CN− from aqueous phase and other extracellular matrices: an experimental and theoretical approach mimicking the logic gate concept
Authors: Bej Sourav , Das Riyanka , Hirani Harish , Ghosh Somnath , Banerjee Priyabrata
Published: October 2019

Selective and real-field detection of a toxic anion (CN−) from aqueous and extracellular matrices by a cost-effective chemosensor.
Membrane domain modulation of Aβ1–42oligomer interactions with supported lipid bilayers: an atomic force microscopy investigation
Authors: Azouz Mehdi , Cullin Christophe , Lecomte Sophie , Lafleur Michel
Published: October 2019

Lipid domains favour membrane perturbations induced by Aβ1–42, an amyloid peptide identified as a trigger of Alzheimer's disease. It is proposed that lipid packing defects at domain interfaces could act as adsorption and nucleation sites.
Structured and intrinsically disordered domains within Amphiphysin1 work together to sense and drive membrane curvature
Authors: Zeno Wade F. , Snead Wilton T. , Thatte Ajay S. , Stachowiak Jeanne C.
Published: October 2019

Cellular membranes undergo remodeling during many cellular processes including endocytosis. Here we elucidated the functional role of the disordered domain in Amphiphysin1 by gradually truncating it, creating a family of mutant proteins.
Efficient photosynthesis in dynamic light environments: a chloroplast's perspective
Authors: Kaiser Elias , Correa Galvis Viviana , Armbruster Ute
Published: October 2019

In nature, light availability for photosynthesis can undergo massive changes on a very short timescale. Photosynthesis in such dynamic light environments requires that plants can respond swiftly. Expanding our knowledge of the rapid responses that underlie dynamic photosynthesis is an important endeavor: it provides insights into nature's design of a highly dynamic energy conversion system and hereby can open up new strategies for improving photosynthesis in the field. The present review focuses on three processes that have previously been identified as promising engineering targets for enhancing crop yield by accelerating dynamic photosynthesis, all three of them involving or being linked to processes in the chloroplast, i.e. relaxation of non-photochemical quenching, Calvin–Benson–Bassham cycle enzyme activation/deactivation and dynamics of stomatal conductance. We dissect these three processes on the functional and molecular level to reveal gaps in our understanding and critically discuss current strategies to improve photosynthesis in the field.
The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics
Authors: Strand Deserah D. , D'Andrea Lucio , Bock Ralph
Published: October 2019

The thylakoid NAD(P)H dehydrogenase-like (NDH) complex is a large protein complex that reduces plastoquinone and pumps protons into the lumen generating protonmotive force. In plants, the complex consists of both nuclear and chloroplast-encoded subunits. Despite its perceived importance for stress tolerance and ATP generation, chloroplast-encoded NDH subunits have been lost numerous times during evolution in species occupying seemingly unrelated environmental niches. We have generated a phylogenetic tree that reveals independent losses in multiple phylogenetic lineages, and we use this tree as a reference to discuss possible evolutionary contexts that may have relaxed selective pressure for retention of ndh genes. While we are still yet unable to pinpoint a singular specific lifestyle that negates the need for NDH, we are able to rule out several long-standing explanations. In light of this, we discuss the biochemical changes that would be required for the chloroplast to dispense with NDH functionality with regards to known and proposed NDH-related reactions.
Warfarin therapy: Rat poison and the prevention of thrombosis
Authors: Scully Mike
Published: October 2019

Thrombosis, which has been defined as blood clotting in the wrong place, is among the principal causes of death in the Western world. One of the drugs that is most frequently used to prevent arterial thrombosis is the oral anti-coagulant, warfarin, which was first marketed as rat poison in the 1940s. In 1999, warfarin was the eleventh most prescribed drug in the USA, with annual sales of approximately US$500 m.