bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring the Physiological State in the Dark Fermentation of Maize/Grass Silage Using Flow Cytometry and Electrooptic Polarizability Measurements
Authors: Gómez-Camacho Carlos E. , Pellicer Alborch Klaus , Bockisch Anika , Neubauer Peter , Junne Stefan , Ruggeri Bernardo
Published: August 2020

Dark fermentation (DF), a key biohydrogen-producing process, is generally operated as a black-box, by monitoring different operative macroscopic process parameters without evaluating or tracking the physiology of the biotic phase. The biotic phase in DF is constituted by a large variety of microorganisms, mainly fermentative bacteria. The present study uses two (electro)optical techniques, flow cytometry (FC) and frequency-dependent polarizability anisotropy (FDPA) measurements, to gain insights into the physiology of open mixed consortia throughout the DF process. The mixed consortia for DF were obtained from a methanogenic sludge, selecting spore-forming bacteria by means of an acid treatment. Then, DF systems with and without pH control were studied, using as substrate a mixture of maize and grass silage (9:1 w/w). Over the course of fermentation, the butyric pathway was dominant in both systems, and relevant titers of acetate, formate, and ethanol were detected; while hydrogen yields amounted to 20.80 ± 0.05 and 17.08 ± 0.05 NmL/gVS under pH-regulated and non-regulated conditions, respectively. The cytometric pattern analysis of the culture together with microscopic observations made it possible, over the course of fermentation, to identify and track the predominant morphologies in play (i.e., free spore, rod-shaped, and endospore, which are typical of Clostridium spp.). Furthermore, the use of the fluorescent dye DiBAC4(3) in FC and FDPA measurements provided similar information regarding the physiological state (PS) of the mixed consortia during the different phases of the culture.
Paleorecords of Domesticated and Wild Grapevine in Romania: a Review
Authors: Brașoveanu Casandra , Bodi George , Danu Mihaela
Published: August 2020

This paper reviews the, so far available, paleorecords ofVitis sylvestrisC.C. Gmel andVitis viniferaL. from Romania. The study takes into consideration the presence ofVitispollen from Holocene peat sediment sequences and archaeological context, but also the presence of macrorests from various archaeological sites that date from Neolithic, Chalcolithic, Bronze Age, and La Tène. Both paleobotanical arguments and archaeological discoveries support the theory that places the beggining of viticulture in Romania a few millenia ago, in Neolithic period. Also, written evidences (works of classical authors, epigraphical sources) confirm, indirectly, the presence of grapevine in La Tène period. Occurrences ofVitis viniferaand those ofVitis sylvestrismanifest independently of the climate oscillations, being present both through colder and more humid episodes, as well as through drier and warmer events. Probably prehistoric communities have made a constant and deliberate effort, all along the Holocene, to maintain grapevine crops.
Younger Dryas and early Holocene subsistence in the northern Great Basin: multiproxy analysis of coprolites from the Paisley Caves, Oregon, USA
Authors: Blong John C. , Adams Martin E. , Sanchez Gabriel , Jenkins Dennis L. , Bull Ian D. , Shillito Lisa-Marie
Published: August 2020

Younger Dryas and early Holocene Western Stemmed Tradition occupants of the northern Great Basin appear to have practiced a broad-based subsistence strategy including the consumption of a wide variety of small animal and plant resources. However, much of our evidence for human diet and land use during this period comes from dry cave and rockshelter sites where it can be challenging to distinguish plant and small animal remains deposited as a result of human versus nonhuman activity. This study presents new direct evidence for Younger Dryas and early Holocene human diet in the northern Great Basin through multiproxy analysis of nine human coprolites from the Paisley Caves, Oregon, USA. The evidence indicates that Western Stemmed Tradition occupants consumed plants, small mammals, fish, and insects, including direct evidence for consumption of whole rodents and several types of beetle. Occupation of the caves occurred during the summer and fall by individuals foraging on wetland, sagebrush grassland, and riparian ecological landscapes suggesting geographical and seasonal variability in land-use patterns during the Younger Dryas and early Holocene periods. This research suggests that Western Stemmed Tradition settlement patterns were seasonally centered on productive valley bottom lakes and wetlands but also included forays to a variety of ecological landscapes. The results highlight the importance of plant and small animal resources in the human diet during the terminal Pleistocene settlement of North America and contribute to debates about the process of the peopling of the Americas.
Correction to: Potential risk assessment and spatial distribution of elemental concentrations in sediment
Authors: Ediagbonya T. F. , Balogun O. T.
Published: August 2020

In the print published article.
Erratum to: The political economy of adult learning systems
Authors: Ioannidou Alexandra , Desjardins Richard
Published: August 2020

In the Editorial of this issue, Miroslav Stefanik was accidentally stated as the single author of the article “Multi-layered Perspective on the Barriers to Learning Participation of Disadvantaged Adults”. The article is a joint authorship by Sofie Cabus, Petya Ilieva-Trichkova and Miroslav Stefanik
The Family Talk Intervention in palliative home care when a parent with dependent children has a life-threatening illness: A feasibility study from parents’ perspectives
Authors: Alvariza Anette , Jalmsell Li , Eklund Rakel , Lövgren Malin , Kreicbergs Ulrika
Published: August 2020

Objective

One of the main goals of the Family Talk Intervention (FTI) is to increase communication within families with dependent children about illness-related consequences and to support parenting. FTI is family-centered and includes six manual-based meetings led by two interventionists. This study aims to evaluate the feasibility of the FTI in terms of acceptability from the perspective of parents in families with dependent children where one parent receives specialized palliative home care.

Method

A descriptive design employing mixed methods was used to evaluate the FTI in specialized palliative home care. In total, 29 parents participated in interviews and responded to a questionnaire following FTI. Qualitative content analysis and descriptive statistics were used for analyses.

Results

FTI responded to both the ill parent's and the healthy co-parent's expectations, and they recommended FTI to other families. Parents found the design of FTI to be well-structured and flexible according to their families’ needs. Many parents reported a wish for additional meetings and would have wanted FTI to start earlier in the disease trajectory. Parents also would have wished for a more thorough briefing with the interventionists to prepare before the start. The importance of the interventionists was acknowledged by the parents; their professional competence, engagement, and support were vital for finding ways to open communication within the family. The FTI meetings provided them with a setting to share thoughts and views. Parents clearly expressed that they would never have shared thoughts and feelings in a similar way without the meetings.

Significance of results

According to parents, FTI was found acceptable in a palliative home care context with the potential to add valuable support for families with minor children when a parent is suffering from a life-threatening illness.
Physical Mechanisms Driving Oxygen Subduction in the Global Ocean
Authors: Portela Esther , Kolodziejczyk Nicolas , Vic Clément , Thierry Virginie
Published: August 2020

Future changes in subduction are suspected to be critical for the ocean deoxygenation predicted by climate models over the 21st century. However, the drivers of global oxygen subduction have not been fully described or quantified. Here, we address the physical mechanisms responsible for the oxygen transport across the late‐winter mixed layer base and their relation with water mass formation. Up to 70% of the global oxygen uptake takes place during Mode Water subduction mostly in the Southern Ocean and the North Atlantic. Te driving mechanisms are (i) the combination of strong currents with large mixed‐layer‐depth gradients at localized hot spots and (ii) the wind‐driven vertical velocity within the subtropical gyres. Oxygen diffusion, despite being underestimated in this study, is likely to play an important role in the global ocean oxygenation. The physical mass flux dominates the total oxygen subduction while the oxygen solubility plays a minor role in its modulation.
Linkage Between a Dominant Mode in the Lower Stratosphere and the Western Hemisphere Circulation Pattern
Authors: Tan Xin , Bao Ming
Published: August 2020

Based on the statistical analyses using ERA data sets, this study reveals a significant linkage between the tropospheric Western Hemisphere (WH) circulation pattern and the stratospheric EOF1 mode (North America [NA] pattern) of the wintertime daily height field at 50 hPa, which exhibits the displacement of the polar vortex to NA. The results of composite analysis indicate that the WH pattern leads the NA pattern at about 5 days. This time‐lagged linkage between the two patterns is further confirmed by the results of time‐lagged singular value decomposition (SVD) analyses. Through the linear interference with climatological waves, the WH pattern contributes to the enhanced (suppressed) wave‐2 (wave‐1) activity propagating into the stratosphere. The characteristics of planetary waves, with opposite sign of anomalous wave‐1 and wave‐2 activity, lead to the formation of the stratospheric NA pattern. We suggest the need for caution in interpreting the stratospheric influences on cold air outbreaks over NA.
Charge‐State‐Dependent Energization of Suprathermal Ions During Substorm Injections Observed by MMS in the Magnetotail
Authors: Bingham S. T. , Cohen I. J. , Mauk B. H. , Turner D. L. , Mitchell D. G. , Vines S. K. , Fuselier S. A. , Torbert R. B. , Burch J. L.
Published: August 2020

Understanding the energization processes and constituent composition of the plasma and energetic particles injected into the near‐Earth region from the tail is an important component of understanding magnetospheric dynamics. In this study, we present multiple case studies of the high‐energy (≳40 keV) suprathermal ion populations during energetic particle enhancement events observed by the Energetic Ion Spectrometer (EIS) on NASA's Magnetospheric Multiscale (MMS) mission in the magnetotail. We present results from correlation analysis of the flux response between different energy channels of different ion species (hydrogen, helium, and oxygen) for multiple cases. We demonstrate that this technique can be used to infer the dominant charge state of the heavy ions, despite the fact that charge is not directly measured by EIS. Using this technique, we find that the energization and dispersion of suprathermal ions during energetic particle enhancements concurrent with (or near) fast plasma flows are ordered by energy per charge state (E/q) throughout the magnetotail regions examined (~7 to 25 Earth radii). The ions with the highest energies (≳300 keV) are helium and oxygen of solar wind origin, which obtain their greater energization due to their higher charge states. Additionally, the case studies show that during these injections the flux ratio of enhancement is also well ordered by E/q. These results expand on previous results which showed that high‐energy total ion measurements in the magnetosphere are dominated by high‐charge‐state heavy ions and that protons are often not the dominant species above ~300 keV.
Seasonal and Latitudinal Variability of the Gravity Wave Spectrum in the Lower Stratosphere
Authors: Lindgren Erik A. , Sheshadri Aditi , Podglajen Aurélien , Carver Robert W.
Published: August 2020

Superpressure balloon data of unprecedented coverage from Loon LLC is used to investigate the seasonal and latitudinal variability of lower stratospheric gravity waves over the entire intrinsic frequency spectrum. We show that seasonal variability in both gravity wave amplitudes and spectral slopes exist for a wide range of intrinsic frequencies and provide estimates of spectral slopes in five latitudinal regions for all four seasons, in five different frequency windows. The spectral slopes can be used to infer gravity wave amplitudes of intrinsic frequencies as high as 70 cycles/day from gravity waves resolved in model and reanalysis data. We also show that a robust relationship between the phase of the quasi‐biennial oscillation and gravity wave amplitudes exists for intrinsic frequencies as high as the buoyancy frequency. These are the first estimates of seasonal and latitudinal variability of gravity wave spectral slopes and high‐frequency amplitudes and constitute a significant step toward obtaining observationally constrained gravity wave parameterizations in climate models.
Ionospheric Response to Strong Geomagnetic Storms During 2000–2005: An IMF Clock Angle Perspective
Authors: Chakraborty Sumanjit , Ray Sarbani , Datta Abhirup , Paul Ashik
Published: August 2020

This paper presents the equatorial ionospheric response to 11 strong‐to‐severe geomagnetic storms that occurred during the period 2000–2005, the declining phase of the Solar Cycle 23. The analysis has been performed using the global ion density plots of the Defense Meteorological Satellite Program (DMSP). Observations show that for about 91% of the cases, postsunset equatorial irregularities occurred within 3 hr from the time of northward to southward transition of the interplanetary magnetic field (IMF) clock angle, thus bringing out the importance of the role played by IMF By in the process of prompt penetration of electric field (PPEF) in addition to the IMF Bz. This is an improvement from the previously reported (Ray et al., 2015, https://doi.org/10.1002/2014RS005422) 4 hr window of equatorial spread F generation from the southward IMF Bz crossing −10 nT.
Process‐Level Evaluation of a Hyper‐Resolution Forest Snow Model Using Distributed Multisensor Observations
Authors: Mazzotti Giulia , Essery Richard , Webster Clare , Malle Johanna , Jonas Tobias
Published: August 2020

The complex dynamics of snow accumulation and melt processes under forest canopies entail major observational and modeling challenges, as they vary strongly in space and time. In this study, we present novel data sets acquired with mobile multisensor platforms in subalpine and boreal forest stands. These data sets include spatially and temporally resolved measurements of shortwave and longwave irradiance, air and snow surface temperatures, wind speed, and snow depth, all coregistered to canopy structure information. We then apply the energy balance snow model FSM2 to obtain concurrent, distributed simulations of the forest snowpack at very high (“hyper”) resolution (2 m). Our data sets allow us to assess the performance of alternative canopy representation strategies within FSM2 at the level of individual snow energy balance components and in a spatially explicit manner. We demonstrate the benefit of accounting for detailed spatial patterns of shortwave and longwave radiation transfer through the canopy and show the importance of describing wind attenuation by the canopy using stand‐scale metrics. With the proposed canopy representation, snowmelt dynamics in discontinuous forest stands were successfully reproduced. Hyper‐resolution simulations resolving these effects provide an optimal basis for assessing the snow‐hydrological impacts of forest disturbances and for validating and improving the representation of forest snow processes in land surface models intended for coarser‐scale applications.
Phase 2 study of irinotecan plus cetuximab rechallenge as third-line treatment in KRAS wild-type metastatic colorectal cancer: JACCRO CC-08
Authors: Masuishi Toshiki , Tsuji Akihito , Kotaka Masahito , Nakamura Masato , Kochi Mitsugu , Takagane Akinori , Shimada Ken , Denda Tadamichi , Segawa Yoshihiko , Tanioka Hiroaki , Hara Hiroki , Sagawa Tamotsu , Watanabe Takanori , Takahashi Takao , Negoro Yuji , Manaka Dai , Fujita Hideto , Suto Takeshi , Takeuchi Masahiro , Ichikawa Wataru , Fujii Masashi
Published: August 2020

Background

Regorafenib or trifluridine/tipiracil as third-line treatment have limited efficacy in metastatic colorectal cancer (mCRC).

Methods

This Phase 2 trial evaluated the efficacy and safety of irinotecan plus cetuximab rechallenge as third-line treatment in KRAS wild-type mCRC patients who achieved clinical benefit with first-line cetuximab-containing therapy. The primary endpoint was 3-month progression-free survival (PFS) rate. A sample size was calculated; 30 patients with a 3-month PFS rate of 45% deemed promising and 15% unacceptable. Patients with greater and less than the cut-off value of cetuximab-free intervals (CFIs) were classified into the long and short CFI groups, respectively, in subgroup analyses.

Results

Among 34 eligible patients who received treatment at least once, 3-month PFS rate was 44.1% (95% confidence interval, 27.4–60.8%). The median PFS and overall survival (OS) were 2.4 and 8.2 months, respectively. The response and disease control rates were 2.9 and 55.9%, respectively. PFS and OS were significantly longer in the long- than in the short CFI group.

Conclusions

Irinotecan plus cetuximab rechallenge as third-line treatment for KRAS wild-type mCRC was safe and had promising activity, especially in those with a long CFI, warranting further investigation in a Phase 3 randomised trial.

Clinical trial registration

UMIN000010638
Dynamics for El Niño-La Niña asymmetry constrain equatorial-Pacific warming pattern
Authors: Hayashi Michiya , Jin Fei-Fei , Stuecker Malte F.
Published: August 2020

The El Niño-Southern Oscillation (ENSO) results from the instability of and also modulates the strength of the tropical-Pacific cold tongue. While climate models reproduce observed ENSO amplitude relatively well, the majority still simulates its asymmetry between warm (El Niño) and cold (La Niña) phases very poorly. The causes of this major deficiency and consequences thereof are so far not well understood. Analysing both reanalyses and climate models, we here show that simulated ENSO asymmetry is largely proportional to subsurface nonlinear dynamical heating (NDH) along the equatorial Pacific thermocline. Most climate models suffer from too-weak NDH and too-weak linear dynamical ocean-atmosphere coupling. Nevertheless, a sizeable subset (about 1/3) having relatively realistic NDH shows that El Niño-likeness of the equatorial-Pacific warming pattern is linearly related to ENSO amplitude change in response to greenhouse warming. Therefore, better simulating the dynamics of ENSO asymmetry potentially reduces uncertainty in future projections.
Effective plans for hospital system response to earthquake emergencies
Authors: Ceferino Luis , Mitrani-Reiser Judith , Kiremidjian Anne , Deierlein Gregory , Bambarén Celso
Published: August 2020

Hospital systems play a critical role in treating injuries during disaster emergency responses. Simultaneously, natural disasters hinder their ability to operate at full capacity. Thus, cities must develop strategies that enable hospitals’ effective disaster operations. Here, we present a methodology to evaluate emergency response based on a model that assesses the loss of hospital functions and quantifies multiseverity injuries as a result of earthquake damage. The proposed methodology can design effective plans for patient transfers and allocation of ambulances and mobile operating rooms. This methodology is applied to Lima, Peru, subjected to a disaster scenario following a magnitude 8.0 earthquake. Our results show that the spatial distribution of healthcare demands mismatches the post-earthquake capacities of hospitals, leaving large zones on the periphery significantly underserved. This study demonstrates how plans that leverage hospital-system coordination can address this demand-capacity mismatch, reducing waiting times of critically injured patients by factors larger than two.
Author Correction: Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus
Authors: Ndeh Didier , Baslé Arnaud , Strahl Henrik , Yates Edwin A. , McClurgg Urszula L. , Henrissat Bernard , Terrapon Nicolas , Cartmell Alan
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Highly efficient eco-friendly X-ray scintillators based on an organic manganese halide
Authors: Xu Liang-Jin , Lin Xinsong , He Qingquan , Worku Michael , Ma Biwu
Published: August 2020

Scintillation based X-ray detection has received great attention for its application in a wide range of areas from security to healthcare. Here, we report highly efficient X-ray scintillators with state-of-the-art performance based on an organic metal halide, ethylenebis-triphenylphosphonium manganese (II) bromide ((C38H34P2)MnBr4), which can be prepared using a facile solution growth method at room temperature to form inch sized single crystals. This zero-dimensional organic metal halide hybrid exhibits green emission peaked at 517 nm with a photoluminescence quantum efficiency of ~ 95%. Its X-ray scintillation properties are characterized with an excellent linear response to X-ray dose rate, a high light yield of ~ 80,000 photon MeV−1, and a low detection limit of 72.8 nGy s−1. X-ray imaging tests show that scintillators based on (C38H34P2)MnBr4 powders provide an excellent visualization tool for X-ray radiography, and high resolution flexible scintillators can be fabricated by blending (C38H34P2)MnBr4 powders with polydimethylsiloxane.
Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma
Authors: Ianiro Gianluca , Rossi Ernesto , Thomas Andrew M. , Schinzari Giovanni , Masucci Luca , Quaranta Gianluca , Settanni Carlo Romano , Lopetuso Loris Riccardo , Armanini Federica , Blanco-Miguez Aitor , Asnicar Francesco , Consolandi Clarissa , Iacovelli Roberto , Sanguinetti Maurizio , Tortora Giampaolo , Gasbarrini Antonio , Segata Nicola , Cammarota Giovanni
Published: August 2020

Diarrhoea is one of the most burdensome and common adverse events of chemotherapeutics, and has no standardised therapy to date. Increasing evidence suggests that the gut microbiome can influence the development of chemotherapy-induced diarrhoea. Here we report findings from a randomised clinical trial of faecal microbiota transplantation (FMT) to treat diarrhoea induced by tyrosine kinase inhibitors (TKI) in patients with metastatic renal cell carcinoma (ClinicalTrials.gov number: NCT04040712). The primary outcome is the resolution of diarrhoea four weeks after the end of treatments. Twenty patients are randomised to receive FMT from healthy donors or placebo FMT (vehicle only). Donor FMT is more effective than placebo FMT in treating TKI-induced diarrhoea, and a successful engraftment is observed in subjects receiving donor faeces. No serious adverse events are observed in both treatment arms. The trial meets pre-specified endpoints. Our findings suggest that the therapeutic manipulation of gut microbiota may become a promising treatment option to manage TKI-dependent diarrhoea.
A Mn-N3 single-atom catalyst embedded in graphitic carbon nitride for efficient CO2 electroreduction
Authors: Feng Jiaqi , Gao Hongshuai , Zheng Lirong , Chen Zhipeng , Zeng Shaojuan , Jiang Chongyang , Dong Haifeng , Liu Licheng , Zhang Suojiang , Zhang Xiangping
Published: August 2020

Developing effective catalysts based on earth abundant elements is critical for CO2 electroreduction. However, simultaneously achieving a high Faradaic efficiency (FE) and high current density of CO (jCO) remains a challenge. Herein, we prepare a Mn single-atom catalyst (SAC) with a Mn-N3 site embedded in graphitic carbon nitride. The prepared catalyst exhibits a 98.8% CO FE with a jCO of 14.0 mA cm−2 at a low overpotential of 0.44 V in aqueous electrolyte, outperforming all reported Mn SACs. Moreover, a higher jCO of 29.7 mA cm−2 is obtained in an ionic liquid electrolyte at 0.62 V overpotential. In situ X-ray absorption spectra and density functional theory calculations demonstrate that the remarkable performance of the catalyst is attributed to the Mn-N3 site, which facilitates the formation of the key intermediate COOH* through a lowered free energy barrier.
Electric field control of radiative heat transfer in a superconducting circuit
Authors: Maillet Olivier , Subero Diego , Peltonen Joonas T. , Golubev Dmitry S. , Pekola Jukka P.
Published: August 2020

Heat is detrimental for the operation of quantum systems, yet it fundamentally behaves according to quantum mechanics, being phase coherent and universally quantum-limited regardless of its carriers. Due to their robustness, superconducting circuits integrating dissipative elements are ideal candidates to emulate many-body phenomena in quantum heat transport, hitherto scarcely explored experimentally. However, their ability to tackle the underlying full physical richness is severely hindered by the exclusive use of a magnetic flux as a control parameter and requires complementary approaches. Here, we introduce a dual, magnetic field-free circuit where charge quantization in a superconducting island enables thorough electric field control. We thus tune the thermal conductance, close to its quantum limit, of a single photonic channel between two mesoscopic reservoirs. We observe heat flow oscillations originating from the competition between Cooper-pair tunnelling and Coulomb repulsion in the island, well captured by a simple model. Our results highlight the consequences of charge-phase conjugation on heat transport, with promising applications in thermal management of quantum devices and design of microbolometers.
Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics
Authors: Zhou Zhiwei , Luo Mingdu , Chen Xi , Yin Yandong , Xiong Xin , Wang Ruohong , Zhu Zheng-Jiang
Published: August 2020

The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility – mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. Here, we curate an ion mobility CCS atlas, namely AllCCS, and develop an integrated strategy for metabolite annotation using known or unknown chemical structures. The AllCCS atlas covers vast chemical structures with >5000 experimental CCS records and ~12 million calculated CCS values for >1.6 million small molecules. We demonstrate the high accuracy and wide applicability of AllCCS with medium relative errors of 0.5–2% for a broad spectrum of small molecules. AllCCS combined with in silico MS/MS spectra facilitates multi-dimensional match and substantially improves the accuracy and coverage of both known and unknown metabolite annotation from biological samples. Together, AllCCS is a versatile resource that enables confident metabolite annotation, revealing comprehensive chemical and metabolic insights towards biological processes.
Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II
Authors: Parua Pabitra K. , Kalan Sampada , Benjamin Bradley , Sansó Miriam , Fisher Robert P.
Published: August 2020

Reversible phosphorylation of Pol II and accessory factors helps order the transcription cycle. Here, we define two kinase-phosphatase switches that operate at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3′ and 5′ ends of genes, respectively, and have overlapping but distinct specificities for Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between Kyrpides-Ouzounis-Woese (KOW) motifs 4 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation decreases as transcription complexes pass the cleavage and polyadenylation signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in termination first uncovered in yeast. Depletion of PP4-complex subunits increases phosphorylation of both Ser666 and the CTR, and promotes redistribution of promoter-proximally paused Pol II into gene bodies. These results suggest that switches comprising Cdk9 and either PP4 or PP1 govern pause release and the elongation-termination transition, respectively.
Anharmonic quantum nuclear densities from full dimensional vibrational eigenfunctions with application to protonated glycine
Authors: Aieta Chiara , Micciarelli Marco , Bertaina Gianluca , Ceotto Michele
Published: August 2020

The interpretation of molecular vibrational spectroscopic signals in terms of atomic motion is essential to understand molecular mechanisms and for chemical characterization. The signals are usually assigned after harmonic normal mode analysis, even if molecular vibrations are known to be anharmonic. Here we obtain the quantum anharmonic vibrational eigenfunctions of the 11-atom protonated glycine molecule and we calculate the density distribution of its nuclei and its geometry parameters, for both the ground and the O-H stretch excited states, using our semiclassical method based on ab initio molecular dynamics trajectories. Our quantum mechanical results describe a molecule elongated and more flexible with respect to what previously thought. More importantly, our method is able to assign each spectral peak in vibrational spectroscopy by showing quantitatively how normal modes involving different functional groups cooperate to originate that spectroscopic signal. The method will possibly allow for a better rationalization of experimental spectroscopy.
Direct observation of desorption of a melt of long polymer chains
Authors: Monnier Xavier , Napolitano Simone , Cangialosi Daniele
Published: August 2020

Tuning the thermodynamic state of a material has a tremendous impact on its performance. In the case of polymers placed in proximity of a solid wall, this is possible by annealing above the glass transition temperature, Tg, which induces the formation of an adsorbed layer. Whether heating to higher temperatures would result in desorption, thereby reverting the thermodynamic state of the interface, has so far remained elusive, due to the interference of degradation. Here, we employ fast scanning calorimetry, allowing to investigate the thermodynamics of the interface while heating at 104 K s−1. We show that applying such rate to adsorbed polymer layers permits avoiding degradation and, therefore, we provide clear-cut evidence of desorption of a polymer melt. We found that the enthalpy and temperature of desorption are independent of the annealing temperature, which, in analogy to crystallization/melting, indicates that adsorption/desorption is a first order thermodynamic transition.
Surveillance of cohesin-supported chromosome structure controls meiotic progression
Authors: Castellano-Pozo Maikel , Pacheco Sarai , Sioutas Georgios , Jaso-Tamame Angel Luis , Dore Marian H. , Karimi Mohammad M. , Martinez-Perez Enrique
Published: August 2020

Chromosome movements and programmed DNA double-strand breaks (DSBs) promote homologue pairing and initiate recombination at meiosis onset. Meiotic progression involves checkpoint-controlled termination of these events when all homologue pairs achieve synapsis and form crossover precursors. Exploiting the temporo-spatial organisation of the C. elegans germline and time-resolved methods of protein removal, we show that surveillance of the synaptonemal complex (SC) controls meiotic progression. In nuclei with fully synapsed homologues and crossover precursors, removing different meiosis-specific cohesin complexes, which are individually required for SC stability, or a SC central region component causes functional redeployment of the chromosome movement and DSB machinery, triggering whole-nucleus reorganisation. This apparent reversal of the meiotic programme requires CHK-2 kinase reactivation via signalling from chromosome axes containing HORMA proteins, but occurs in the absence of transcriptional changes. Our results uncover an unexpected plasticity of the meiotic programme and show how chromosome signalling orchestrates nuclear organisation and meiotic progression.
Insights into projected changes in marine heatwaves from a high-resolution ocean circulation model
Authors: Hayashida Hakase , Matear Richard J. , Strutton Peter G. , Zhang Xuebin
Published: August 2020

Global climate models project the intensification of marine heatwaves in coming decades due to global warming. However, the spatial resolution of these models is inadequate to resolve mesoscale processes that dominate variability in boundary current regions where societal and economic impacts of marine heatwaves are substantial. Here we compare the historical and projected changes in marine heatwaves in a 0.1° ocean model with 23 coarser-resolution climate models. Western boundary currents are the regions where the models disagree the most with observations and among themselves in simulating marine heatwaves of the past and the future. The lack of eddy-driven variability in the coarse-resolution models results in less intense marine heatwaves over the historical period and greater intensification in the coming decades. Although the projected changes agree well at the global scale, the greater spatial details around western boundary currents provided by the high-resolution model may be valuable for effective adaptation planning.
Author Correction: Humoral immune response to tick-borne encephalitis vaccination in allogeneic blood and marrow graft recipients
Authors: Harrison Nicole , Grabmeier-Pfistershammer Katharina , Graf Alexandra , Schwarzinger Ilse , Aberle Judith H. , Stiasny Karin , Greinix Hildegard , Rabitsch Werner , Kalhs Peter , Ramharter Michael , Burgmann Heinz , Forstner Christina
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Stunting of children under two from repeated pregnancy among young mothers
Authors: Maravilla Joemer Calderon , Betts Kim , Adair Linda , Alati Rosa
Published: August 2020

Repeated pregnancy leaves young mothers nutritionally deprived which may in turn lead to poor infant growth. We measure the occurrence and persistence of stunting among offspring of young mothers who experienced repeated pregnancies using data from the Cebu Longitudinal Health and Nutrition Survey. We selected mothers aged 14–24 years (n = 1,033) with singleton birth. We determined the length-for-age z scores (LAZ) at 12 and 24 months of the index child using the World Health Organisation 2007 growth standard. We fitted LAZ, stunting occurrence (i.e. LAZ < − 2) and persistence from 12 to 24 months into regression models and tested for the mediating effect of low birthweight and feeding practices. In these models, repeated pregnancy was analysed in an ordinal approach using number of past pregnancies of young mothers at birth of the index child. Compared to infants born to young mothers aged 14–24 years who had no previous pregnancies, those born to young mothers with repeated pregnancies have at least 0.15 (95% CI − 0.23, − 0.08) LAZ lower and are at higher chance of stunting by at least 40% (95% CI 1.19, 1.67) at 12 and 24 months. Similar cohorts of infants showed an elevated risk of persistent stunting from 12 through 24 months with a relative risk ratio of 1.51 (95% CI 1.21, 1.88). Optimal feeding practices substantially mediated stunting outcomes by further reducing the effects of repeated pregnancy to stunting occurrence and persistence by 19.95% and 18.09% respectively. Mediation tests also showed low birthweight in the causal pathway between repeated pregnancy and stunting. Repeated pregnancy in young mothers is a predictor of stunting among children under 2 years. Secondary pregnancy prevention measures and addressing suboptimal feeding practices are beneficial to mitigate the negative impact of repeated adolescent pregnancy on children.
Association of generalized and central obesity with serum and salivary cortisol secretion patterns in the elderly: findings from the cross sectional KORA-Age study
Authors: Ladwig Karl-Heinz , Schriever Sonja Charlotte , Atasoy Seryan , Bidlingmaier Martin , Kruse Johannes , Johar Hamimatunnisa
Published: August 2020

The study aimed to examine the sex specific association of obesity with cortisol metabolism in a sample of older community dwelling people. The cross-sectional analysis included 394 men and 375 women (aged 65–90 years) of the population-based KORA-Age study. Multivariable regression analyses were employed to examine the association between cortisol samples (serum and salivary samples of morning after awakening (M1), 30 min later (M2) and at late night (LNSC)). Obesity was calculated as waist-to-hip ratio (WHR) and body mass index (BMI). Cortisol levels were not significantly different between obesity measures except for elevated serum cortisol (P = 0.02) levels in individuals with a low WHR. Higher M1 levels were especially apparent in women with normal BMI. Serum cortisol levels were inversely related to WHR (P = 0.004) and CARAUC was inversely associated with BMI (P = 0.007). Sex-stratified analytic models revealed that both obesity measures showed a non-linear association with cortisol diurnal pattern (M1/LNSC) in men. Impaired cortisol patterns emerged at both very ends of the body weight distribution. These findings do not support a cortisol driven obesity etiology in an older population and even point to an inverse association of body weight with cortisol levels. Differences of cortisol secretion patterns in generalized and abdominal fat distribution were marginal.
Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome
Authors: Sidhu Navjot Singh , Pruthi Gomsie , Singh Sahildeep , Bishnoi Ritika , Singla Deepak
Published: August 2020

GRAS genes belong to the plant-specific transcription factors (TF’s) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF’s. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein–protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops.
Vitamin D supplementation and the outcomes of critically ill adult patients: a systematic review and meta-analysis of randomized controlled trials
Authors: Lan Shao-Huan , Lai Chih-Cheng , Chang Shen-Peng , Lu Li-Chin , Hung Shun-Hsing , Lin Wei-Ting
Published: August 2020

This meta-analysis assessed the association between vitamin D supplementation and the outcomes of critically ill adult patients. A literature search was conducted using the PubMed, Web of Science, EBSCO, Cochrane Library, Ovid MEDLINE, and Embase databases until March 21, 2020. We only included randomized controlled trials (RCTs) comparing the efficacy of vitamin D supplementation with placebo in critically ill adult patients. The primary outcome was their 28-day mortality. Overall, 9 RCTs with 1867 patients were included. In the pooled analysis of the 9 RCTs, no significant difference was observed in 28-day mortality between the vitamin D supplementation and placebo groups (20.4% vs 21.7%, OR, 0.73; 95% CI, 0.46–1.15; I2 = 51%). This result did not change as per the method of vitamin D supplementation (enteral route only: 19.9% vs 18.2%, OR, 1.19; 95% CI, 0.88–1.57; I2 = 10%; intramuscular or intravenous injection route: 25.6% vs 40.8%, OR, 0.48; 95% CI, 0.21–1.06; I2 = 19%) or daily dose (high dose: 20.9% vs 19.8%, OR, 0.83; 95% CI, 0.51–1.36; I2 = 53%; low dose: 15.6% vs 21.3%, OR, 0.74; 95% CI, 0.32–1.68; I2 = 0%). No significant difference was observed between the vitamin D supplementation and placebo groups regarding the length of ICU stay (standard mean difference [SMD], − 0.30; 95% CI, − 0.61 to 0.01; I2 = 60%), length of hospital stay (SMD, − 0.17; 95% CI, − 041 to 0.08; I2 = 65%), and duration of mechanical ventilation (SMD, − 0.41; 95% CI, − 081 to 0.00; I2 = 72%). In conclusion, this meta-analysis suggested that the administration of vitamin D did not provide additional advantages over placebo for critically ill patients. However, additional studies are needed to confirm our findings.
Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence
Authors: Fikere M. , Barbulescu D. M. , Malmberg M. M. , Spangenberg G. C. , Cogan N. O. I. , Daetwyler H. D.
Published: August 2020

Blackleg disease causes yield losses in canola (Brassica napusL.). To identify resistance genes and genomic regions, genome-wide association studies (GWAS) of 585 diverse winter and spring canola accessions were performed using imputed whole-genome sequence (WGS) and transcriptome genotype-by-sequencing (GBSt). Blackleg disease phenotypes were collected across three years in six trials. GWAS were performed in several ways and their respective power was judged by the number of significant single nucleotide polymorphisms (SNP), the false discovery rate (FDR), and the percentage of SNP that validated in additional field trials in two subsequent years. WGS GWAS with 1,234,708 million SNP detected a larger number of significant SNP, achieved a lower FDR and a higher validation rate than GBSt with 64,072 SNP. A meta-analysis combining survival and average internal infection resulted in lower FDR but also lower validation rates. The meta-analysis GWAS identified 79 genomic regions (674 SNP) conferring potential resistance toL. maculans. While several GWAS signals localised in regions of known Rlm genes, fifty-three new potential resistance regions were detected. Seventeen regions had underlying genes with putative functions related to disease defence or stress response inArabidopsis thaliana. This study provides insight into the genetic architecture and potential molecular mechanisms underlying canolaL. maculansresistance.
Climate and weather factors affecting winter sheltering by shoreline Copper Rockfish Sebastes caurinus in Howe Sound, British Columbia
Authors: Marliave J. B. , Borden L. A.
Published: August 2020

We monitored winter sheltering behavior of Copper Rockfish (Sebastes caurinus) in layered boulders at a shoreline in British Columbia and identified possible links to climate change and evolutionary adaptation. During late autumn and winter, these fish were inside the interstices of the boulder pile (termed “winter sheltering”); these fish were actively swimming above the boulders during spring through early fall. Sheltering duration did not vary between normal and most El Niño years (154–177 days). Sheltering longer than 6 months occurred during strong La Niña winters (197–241 days). Additionally, the proximate stimulus for entry into sheltering was intense Arctic outflow windstorms. Emergence from sheltering appears linked to water temperatures, occasionally related more to spring river flooding (snowmelt). The winter sheltering behavior we describe may be unique to shoreline populations in inland seas. Sheltering may confer a fitness advantage by conserving energy or reducing mortality from predation, thus increasing longevity and chances for successful reproduction. Our observations suggest that an ONI threshold of 0.8 °C or greater would be better suited than the current 0.5 °C threshold used to define ONI events.
Impact of hyperuricemia on mortality related to aortic diseases: a 3.8-year nationwide community-based cohort study
Authors: Otaki Yoichiro , Watanabe Tetsu , Konta Tsuneo , Watanabe Masafumi , Asahi Koichi , Yamagata Kunihiro , Fujimoto Shouichi , Tsuruya Kazuhiko , Narita Ichiei , Kasahara Masato , Shibagaki Yugo , Iseki Kunitoshi , Moriyama Toshiki , Kondo Masahide , Watanabe Tsuyoshi
Published: August 2020

Despite advances in medicine, aortic diseases (ADs) such as aortic dissection and aortic aneurysm rupture remain fatal with extremely high mortality rates. Owing to the relatively low prevalence of AD, the risk of AD-related death has not yet been elucidated. The aim of the present study was to examine whether hyperuricemia is a risk factor for AD-related mortality in the general population. We used a nationwide database of 474,725 subjects (age 40–75 years) who participated in the annual “Specific Health Check and Guidance in Japan” between 2008 and 2013. There were 115 deaths from aortic dissection and aortic aneurysm rupture during the follow-up period of 1,803,955 person-years. Kaplan–Meier analysis revealed that subjects with hyperuricemia had a higher rate of AD-related death than those without hyperuricemia. Multivariate Cox proportional hazard regression analysis demonstrated that hyperuricemia was an independent risk factor for AD-related death in the general population. The net reclassification index was improved by addition of hyperuricemia to the baseline model. This is the first report to demonstrate that hyperuricemia is a risk factor for AD-related death, indicating that hyperuricemia could be a crucial risk for AD-related death in the general population.
Targeting poor proteasomal function with radioiodine eliminates CT26 colon cancer stem cells resistant to bortezomib therapy
Authors: Lee Jin Hee , Jung Kyung-Ho , Park Jin Won , Moon Seung Hwan , Cho Young Seok , Lee Kyung-Han
Published: August 2020

We tested the hypothesis that tumor response to conventional bortezomib (BTZ) treatment is enhanced by targeted radiotherapy of resistant cancer stem cells (CSCs) that have characteristically poor proteasome function. This was accomplished by augmenting 131I uptake through expression of a sodium-iodide symporter (NIS) fusion protein that accumulates in cells with low proteasome activity. The NIS gene fused with the C-terminal of ornithine decarboxylase degron (NIS-cODC) was cloned. Stably expressing CT26/NIS-cODC cells and tumorsphere-derived CSCs were evaluated for NIS expression and radioiodine uptake. CT26/NIS-cODC cells implanted into mice underwent PET imaging, and tumor-bearing mice were treated with BTZ alone or with BTZ plus 131I. CT26/NIS-cODC cells accumulated NIS protein, which led to high radioiodine uptake when proteasome activity was inhibited or after enrichment for stemness. The cell population that survived BTZ treatment was enriched with CSCs that were susceptible to 131I treatment, which suppressed stemness features. Positron emission tomography and uptake measurements confirmed high 124I and 131I uptake of CT26/NIS-cODC CSCs implanted in living mice. In CT26/NIS-cODC tumor-bearing mice, whereas BTZ treatment modestly retarded tumor growth and increased stemness markers, combining 131I therapy suppressed stemness features and achieved greater antitumor effects. The NIS-cODC system offer radioiodine-targeted elimination of CSCs that are tolerant to proteasome inhibition therapy.