bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of High Mountain Asia‐Land Data Assimilation System (Version 1) From 2003 to 2016: 2. The Impact of Assimilating Satellite‐Based Snow Cover and Freeze/Thaw Observations Into a Land Surface Model
Authors: Xue Yuan , Houser Paul R. , Maggioni Viviana , Mei Yiwen , Kumar Sujay V. , Yoon Yeosang
Published: March 2022

This second paper of the two‐part series focuses on demonstrating the impact of assimilating satellite‐based snow cover and freeze/thaw observations into the hyper‐resolution, offline terrestrial modeling system used for the High Mountain Asia (HMA) region from 2003 to 2016. To this end, this study systematically evaluates a total of six sets of 0.01° (∼1 km) model simulations forced by different precipitation forcings, with and without the dual assimilation scheme enabled, at point‐scale, basin‐scale, and domain‐scale. The key variables of interest include surface net shortwave radiation, surface net longwave radiation, skin temperature, near‐surface soil temperature, snow depth, snow water equivalent (SWE), and total runoff. First, the point‐scale assessment is mainly conducted via evaluating against ground‐based measurements. In general, the assimilation enabled estimates are better than no‐assimilation counterparts. Second, the basin‐scale runoff assessment demonstrates that across three snow‐dominated basins, the assimilation enabled experiment yields systematic improvements in all goodness‐of‐fit statistics through mitigating the negative effects brought by the fixed long‐term precipitation correction factors. For example, when forced by the bias‐corrected precipitation, the assimilation‐enabled experiment improves the bias by 69%, the root‐mean‐squared error by 30%, and the unbiased root‐mean‐squared error by 18% (relative to the no‐assimilation counterpart). Finally, the domain‐scale assessment is conducted via evaluating against satellite‐based SWE and skin temperature products. Both sets of domain‐scale analysis further corroborate the findings in the point‐scale evaluations. Overall, this study suggests the benefits of the proposed multi‐variate assimilation system in improving the cryospheric‐hydrological process within a land surface model for use in HMA.
Ice Shell Structure of Ganymede and Callisto Based on Impact Crater Morphology
Authors: Bjonnes E. , Johnson B. C. , Silber E. A. , Singer K. N. , Evans A. J.
Published: March 2022

Understanding the thermal structure of the ice shells around Ganymede and Callisto remains a critical step in unraveling the geologic histories of the moons. The depth‐diameter (d‐D) trends of pristine craters on each surface have an inflection point in crater morphology at approximately 26 km diameter, at which point observed crater depths transition from craters deepening with increasing crater diameter to craters shallowing with increasing crater diameter. In this work, we use iSALE‐2D to simulate impact crater formation in ice shells. We test conductive thermal gradients between 5 and 15 K/km and convective ice temperatures between 240 and 260 K in a modeled ice shell to determine if these observed d‐D trends correlate to specific thermal parameters. We find that the conductive thermal gradient has a more pronounced effect than the temperature of the underlying convective ice on reproducing the d‐D trends of craters up to 100 km in diameter, and that the inflection point in the observed crater depth trend on both Ganymede and Callisto is replicated in ice shells with a conductive thermal gradient of ∼10 K/km. With this conductive thermal gradient, the conductive ice was approximately 12–14 km thick on each body at the time they accrued these unmodified craters. The similar thermal constraints for both moons suggest that there are other differences between Ganymede and Callisto responsible for their divergent evolutionary paths, such as an increased proportion of strong impurities in Callisto's ice shell.
Winds From the Visible (513 nm) Images Obtained by the Venus Monitoring Camera Onboard Venus Express
Authors: Khatuntsev I. V. , Patsaeva M. V. , Zasova L. V. , Titov D. V. , Ignatiev N. I. , Gorinov D. A. , Turin A. V.
Published: March 2022

We present more than 250,000 wind vectors derived from the visible (513 nm) images captured by the Venus Monitoring Camera (VMC) onboard ESA's Venus Express orbiter in the Southern hemisphere from 01 July 2007 to 29 January 2013. From comparison to the wind velocity derived from tracking of the descent probes, these measurements correspond to 60 ± 3 km altitude, being between two levels 70 ± 2 km and 55 ± 2 km, probed by VMC in ultraviolet (UV) (365 nm) and NIR (965 nm) channels, respectively. The mean zonal wind suggests retrograde circulation with mean zonal wind speed decreasing from 76.5 to 61.5 m/s at 30°–65°S. In low latitudes, 10–20°S, it increased to 82 m/s over the course of the mission. The mean zonal flow depends on local solar time and latitude and is affected by the large‐scale topography. The meridional winds indicated equatorward flow of up to 7 m/s in the middle and low cloud opposite to that derived from simultaneous UV observations at the cloud top.
Mineral Protection and Resource Limitations Combine to Explain Profile‐Scale Soil Carbon Persistence
Authors: Lacroix E. M. , Masue‐Slowey Y. , Dlott G. A. , Keiluweit M. , Chadwick O. A. , Fendorf S.
Published: March 2022

The fate of soil carbon (C) is largely controlled by microbial oxidation of organic matter (OM), which is constrained by a variety of mechanisms. OM association with soil minerals provides pronounced protection against microbial decomposition. However, factors such as climate, occlusion, and resource limitations also contribute to OM preservation. We explore the factors explaining C distribution and age within an upland rainforest soil in Hawaiʻi, a site with abundant preferential flow paths (PFPs) and high short‐range order (SRO) mineral content. We characterized lateral and vertical changes in ∆14C, SRO mineral content, C‐functional group chemistry, and microbial community composition to elucidate the contributions of multiple protection mechanisms to OM preservation. Consistent with our expectation, SRO mineral content and ∆14C were strongly correlated (R2 = 0.95), indicating strong mineral protection of OM throughout the profile. Surprisingly, distance from PFP was also a significant predictor of ∆14C and improved model fit, particularly in the shallow horizons (R2 = 0.97). Elevated C/N ratios, decreased microbial abundance, and greater SRO mineral content suggest nitrogen limitations and enhanced mineral protection constrain OM turnover with distance from PFPs in deep, subsurface mineral horizons. Steady microbial abundance, increasing putative anaerobe abundance, and changes in C‐functional group chemistry indicate oxygen limitations constrain OM turnover in the matrix of shallow mineral horizons. Given that oxygen and nutrient limitations contribute to OM preservation in this high SRO system—an exemplar of mineral protection—resource limitations may play an even more important role in OM preservation in other well‐structured soils.
A Comparison of Methods for Identifying and Quantifying Ice Rafted Debris on the Antarctic Margin
Authors: McKay Robert , Albot Olga , Dunbar Gavin B. , Lee Jae Il , Lee Min Kyung , Yoo Kyu‐Cheul , Kim Sunghan , Turton Nikita , Kulhanek Denise , Patterson Molly , Levy Richard
Published: March 2022

Quantification of ice rafted debris (IRD) abundances in deep‐sea records is often used as a key proxy for identifying links between ice sheet instability and the oceanic overturning circulation. There currently exist multiple methods to determine IRD content in deep‐sea sediment cores. The preference for a given method is often determined by the accessibility to core material and destructive nature of some methods. While many studies have discussed the caveats between linking IRD to ice sheet dynamics, the uncertainties relating to the methodological approaches are often not considered in the interpretation or comparisons between different IRD datasets, particularly in the Antarctic. To address this, we compare three independent methodologies of obtaining IRD abundances and also discuss how different approaches will affect determinations of mass accumulation rates (MARs). The three methodologies we examine include: counting clasts >2 mm in x‐radiographs; the sieved weight percentage of the medium‐to‐coarse sand fraction (250 μm–2 mm); and volumetric estimates of the >125 μm sand fraction using laser diffraction particle size analysis. The x‐radiograph and sieve methods produced comparable results, while the laser particle size analysis, although showing comparable long‐term signals at most locations, in general has lower correlation to the other two methods and therefore a higher potential to obtain a noisy signal. We discuss the caveats associated with all methods, and emphasize that a combination of multiple methods should ideally be employed when assessing if a core is suitable for IRD study, and if sand or gravel fractions are accurately reflecting contents of IRD.
Active Tectonics of the North Tunisian Continental Margin
Authors: Camafort Miquel , Ranero César R. , Gràcia Eulàlia
Published: March 2022

A poorly defined boundary between the Nubia and Eurasian plates runs along the Northern Tunisian continental margin. The Tunisia margin is deformed by a slow NW–SE trending convergence resulting in a diffuse deformation zone with scarce and scattered seismicity compared to the seismic activity into the neighboring regions to the east and west along the boundary. The area has been poorly studied and therefore its recent evolution is almost unknown, particularly offshore. Here, we present a structural analysis of the active tectonics in this submarine continental margin. The data used for this analysis are high‐resolution bathymetric maps together with parametric echosounder images which have allowed to obtain a map of active faulting with unprecedented detail. The structural analysis supports a dominantly transpressive to compressive component of faulting, resulting from the current regional NW–SE trending compressive regime between plates. The North‐eastern Domain of the study region contains the highest number of active faults with numerous pockmarks aligned along them. This study shows that the plate boundary across the North Tunisia margin is incipient and poorly developed, which may be due to the fact that deformation is partitioned over a large number of structures, each accommodating a small percentage of convergence, with the exception of the Hayat fault system. The Hayat reverse fault, striking WSW–ENE, is the largest fault system that comparatively may accommodate a greater amount of displacement, and is probably responsible for the uplift of the North‐eastern Domain of the continental margin.
Crustal Mercury Addition Into the Giant Jinchuan Ni‐Cu Sulfide Deposit, China, and Its Geological Implications
Authors: Gao Lingjian , Long Ting‐Mao , Sun Deyou , Deng Changzhou , Tian Zhendong , Song Xie‐Yan , Yin Runsheng
Published: March 2022

Mercury (Hg) isotopes have shown their power of tracing Hg pollution sources in ecosystems, but their potentials for petrogenetic tracing are yet to be explored. Here we conducted Hg isotope analysis for samples collected from major orebodies of the world‐class Jinchuan Ni‐Cu sulfide deposit, China. These samples show large variations of δ202Hg (−2.65 to +0.19‰) and Δ199Hg (−0.16 to +0.19‰). Some of the Δ199Hg values significantly deviate from current estimates on the primitive mantle (Δ199Hg: 0.0 ± 0.1‰, 2SD). The pronounced Hg mass‐independent fractionation (Hg‐MIF) signals, with significant positive (>0.1‰) and negative (<0.1‰) Δ199Hg values similar to marine sediments and terrestrial soils, respectively, suggests the addition of crustal materials into the Jinchuan deposit, via crustal assimilation during mantle‐derived magma ascending to the crust. These samples show δ34S values (−1.09 to +1.38‰) identical to that of the primitive mantle (0.0 ± 2.0‰), which may indicate a major sulfur source from the mantle. However, δ34S provides poor constraints on the sulfur source, and the early reported anomalous Δ33S values (+0.12 to +2.67‰) in the Jinchuan deposit support the involvement of external sulfur from Archean and Proterozoic sedimentary rocks during the formation of this deposit, similar to the case of Hg. This study shows the powerful use of Hg isotopes as a petrogenic tracer and highlights the importance of interaction between mantle‐derived magmas and crustal materials on the formation of the Jinchuan Cu‐Ni sulfide deposit.
Evidence for a Global Slowdown in Seafloor Spreading Since 15 Ma
Authors: Dalton Colleen A. , Wilson Douglas S. , Herbert Timothy D.
Published: March 2022

The rate of ocean‐crust production exerts control over sea level, mantle heat loss, and climate. Different strategies to account for incomplete seafloor preservation have led to differing conclusions about how much production rates have changed since the Cretaceous, if at all. We construct a new global synthesis of crust production along 18 mid‐ocean ridges for the past 19 Myr at high temporal resolution. We find that the global production rate during 6–5 Ma was only 69%–75% of the 16–15 Ma interval. The reduction in crust production is mostly due to slower seafloor spreading along almost all ridge systems. While the total ridge length has varied little since 19 Ma, some fast‐spreading ridges have grown shorter and slow‐spreading ridges grown longer, amplifying the spreading‐rate changes. Our production curves represent a new data set for investigating the forces driving plate motions and the role of tectonic degassing on climate.
Effects of Oxygen Fugacity on Hydroxyl Incorporation in Garnet at 1–3 GPa and 800–1000°C and Implications for Water Storage in the Mantle
Authors: Zhang Kai , Liu Hanyong , Ionov Dmitri A. , Yang Xiaozhi
Published: March 2022

Garnet, an important mineral component in Earth's interior, usually contains minor water as structural OH, but experimental data on OH incorporation in the mineral as a function of chemical and thermodynamic parameters remain rare. In particular, the role of oxygen fugacity (fO2) that is variable in the Earth has not been well assessed. We examine the effects of fO2 on the incorporation of OH at 1–3 GPa and 800–1000°C, by H‐annealing gem‐quality spessartine‐rich, grossular‐rich, and pyrope‐rich garnets. For each type of annealed garnet, the OH peak positions and spectral shapes are the same, suggesting the same OH incorporation mechanism(s). Under identical conditions, spessartine‐rich and grossular‐rich garnets are rich in OH, with solubility orders of magnitudes greater than for pyrope‐rich garnets. Over the studied conditions, the solubility of OH increases with pressure and temperature but decreases with fO2. The negative correlation of fO2 and OH solubility is probably due to the Fe3+ to Fe2+ reduction at more reduced conditions and the coupled OH incorporation in the structure. The effects of fO2 on OH solubility are more significant in Fe‐rich garnets. The ascertained small OH solubility in peridotite garnets, together with comparisons with relevant studies, suggest that mantle garnet is unlikely to be a major water carrier. In combination with literature‐reported positive correlation of fO2 and OH solubility in olivine, the partition coefficient of OH between garnet and olivine in the upper mantle is expected to be redox‐dependent.
Alteration of barrier properties, stratum corneum ceramides and microbiome composition in response to lotion application on cosmetic dry skin
Authors: Murphy Barry , Grimshaw Sally , Hoptroff Michael , Paterson Sarah , Arnold David , Cawley Andrew , Adams Suzanne E. , Falciani Francesco , Dadd Tony , Eccles Richard , Mitchell Alex , Lathrop William F. , Marrero Diana , Yarova Galina , Villa Ana , Bajor John S. , Feng Lin , Mihalov Dawn , Mayes Andrew E.
Published: March 2022

Xerosis, commonly referred to as dry skin, is a common dermatological condition affecting almost a third of the population. Successful treatment of the condition traditionally involves the application of cosmetic products facilitating the moisturisation of the skin with a range of ingredients including glycerol and fatty acids. While the effectiveness of these treatments is not in question, limited information exists on the impact on the skin microbiome following use of these products and the improvement in skin hydration. Here, we describe improvements in skin barrier properties together with increased levels of cholesterol, ceramides and long-chain fatty acids following application of Body Lotion. Concomitant alterations in the skin microbiome are also seen via 16S rRNA metataxonomics, in combination with both traditional and novel informatics analysis. Following 5 weeks of lotion use, beneficial skin bacteria are increased, with improvements in microbiome functional potential, and increases in pathways associated with biosynthesis of multiple long chain fatty acids.
Towards a computational understanding of water oxidation at graphene-bound MnxOy and MnxOyM2+ particles
Authors: Terrett Richard N. L. , Tsekouras George , Tsuzuki Takuya , Swiegers Gerhard F. , Pace Ronald , Stranger Robert
Published: March 2022

DFT, QTAIM, and IGM calculations reveal details of ligand exchange and dioxygen release from an oxo-manganese water oxidation catalyst model.
NIR-II imaging-guided diagnosis and evaluation of the therapeutic effect on acute alcoholic liver injuryviaa nanoprobe
Authors: Nie Gang , Zhou Yinxing , Song Mengzi , Xu Jingya , Cui Zheng , Feng Yangzhen , Wang Huiling , Chen Dugang , Zhang Yu , Wang Kaiping
Published: March 2022

A NIR-II nanoprobe was developed and applied with excellent photostability and prominent biocompatibility to diagnose acute alcoholic liver injury in micein vivoand evaluate the therapeutic effects of a drug on AALI mice by NIR-II imaging.
Construction and application of a qualitative and quantitative analysis system of three boscalid polymorphs based on solid-state analytical methods and chemometric tools
Authors: Shang Zeren , Liu Mingdi , Hu Weiguo , Deng Tong , Su Xin , Hou Baohong , Wang Jingkang , Gong Junbo
Published: March 2022

A qualitative and quantitative analysis system for three boscalid polymorphs was constructed and applied for the first time.
Alginate promotes soil phosphorus solubilization synergistically with redox-active antibiotics through Fe(iii) reduction
Authors: Ge Xinfei , Wang Lijun , Yang Xiong , Qiu Guohong , Zhang Wenjun
Published: March 2022

This work reveals that alginate can enhance the beneficial physiological effect of redox-active antibiotics, and their synergistic effect can further promote the bioavailability of nutrients Fe and P.
Chemicals from lignin by diol-stabilized acidolysis: reaction pathways and kinetics
Authors: Zhang Zhenlei , Lahive Ciaran W. , Winkelman Jozef G. M. , Barta Katalin , Deuss Peter J.
Published: March 2022

Detailed kinetic modelling of metal triflate catalyzed diol-stabilized acidolysis that leads to a clearer vision of involved intermediates and pathways.
Homeoffice – fest etabliertes Arbeitsmodell auch nach der
Corona-Pandemie?
Authors: Sailer Larisa , Hoffmann Felix
Published: March 2022

Die Einhaltung der Covid-19-Pandemie-Maßnahmen forderte von vielen
Unternehmen die Einführung und Umsetzung von Homeoffice. Nicht nur die
Arbeitsprozesse, sondern auch die Teamführung musste binnen kurzer Zeit
an die neuen Anforderungen angepasst werden [1, 6]. Gerade für die
Führungskräfte des mittleren Managements stellte die
räumliche Dezentralisierung und Führung auf Distanz eine
Herausforderung dar [7,11]. Auch die AOK – Die Gesundheitskasse
Südlicher Oberrhein hat im Rahmen der Corona-Pandemie-Maßnahmen
ihren Mitarbeitern Homeoffice ermöglicht und das Arbeitsmodell optional
angeboten. Die Leitenden des mittleren Managements haben in der
Covid-19-Pandemie-Zeit Erfahrungen bzw. Erkenntnisse gesammelt und
wünschen für die Zukunft die feste Etablierung des flexiblen
Homeoffice-Arbeitsmodells.
Nutzen und Wirtschaftlichkeit der Topischen Behandlung Peripherer
Neuropathischer Schmerzen mit dem Capsaicin-Pflaster Qutenza – ein
Literaturüberblick
Authors: Thiem Helena , Kunde Katharina , Quandel Tamara , Schubert Tino
Published: March 2022

Hintergrund Periphere Neuropathien sind häufig und
beeinträchtigen die Lebensqualität der PatientInnen erheblich.
Die Behandlung ist komplex und kann, in Abhängigkeit von der
Grunderkrankung, bei vielen PatientInnen keine vollständige
Beschwerdefreiheit erzielen. Eine Therapieoption ist hochdosiertes Capsaicin
179 mg (oder 8%) in Form eines kutanen Pflasters (Qutenza). Die
vorliegende Literaturübersicht soll eine Einschätzung zu Nutzen
und Kosten dieser Therapie, auch im Vergleich zu systemischer Medikation,
bieten.

Methodik In der bibliografischen Datenbank PubMed wurde eine strukturierte
Literaturrecherche durchgeführt, um relevante Publikationen zur
topischen Therapie peripherer neuropathischer Schmerzen mit dem hochdosierten
Capsaicin-Pflaster zu identifizieren und hinsichtlich ihres Nutzens sowie unter
ökonomischen Gesichtspunkten zu bewerten. Die Ergebnisse der
eingeschlossenen Publikationen wurden extrahiert und narrativ
zusammengefasst.

Ergebnisse Es wurden insgesamt 29 Artikel in die Auswertung einbezogen. In
acht randomisierten kontrollierten Studien konnte die Wirksamkeit einer
Behandlung peripherer neuropathischer Schmerzen unterschiedlicher Genese mit
hochdosiertem Capsaicin in Form eines kutanen Pflasters belegt werden. Das
Capsaicin-Pflaster führte gegenüber der Standard-Therapie zu
einer vergleichbaren Reduktion der neuropathischen Schmerzsymptome bei deutlich
geringeren Nebenwirkungen. Für den Bereich der Wirtschaftlichkeit
konnten nur drei Publikationen ermittelt werden, die jedoch nicht das deutsche
Gesundheitssystem berücksichtigen. Die drei Analysen kommen zu dem
Schluss, dass die topische Capsaicin-Therapie im Vergleich zu den jeweils
untersuchten systemisch wirksamen Vergleichspräparaten kosteneffektiv
ist.

Schlussfolgerung Es konnte für periphere neuropathische Schmerzen
unterschiedlicher Genese der Nutzen einer topischen Behandlung mit dem kutanen
Capsaicin-Pflaster Qutenza nachgewiesen werden. In Bezug auf die
Wirtschaftlichkeit dieser Therapieoption, besonders in Hinblick auf das deutsche
Gesundheitssystem, sind weitere Analysen notwendig.
Renteneintrittswünsche und mögliche Determinanten bei
Hausärztinnen und Hausärzten
Authors: Bodendieck Erik , Jung Franziska Ulrike , Bleckwenn Markus , Hussenöder Felix , Luppa Melanie , Riedel-Heller Steffi G.
Published: March 2022

Einleitung In Hinblick auf den immer größer werdenden
Ärztemangel und gleichzeitig steigenden Versorgungsbedarf in der
Allgemeinbevölkerung war das Ziel der vorliegenden Untersuchung, ein
detailliertes Bild über Renteneintrittswünsche der aktiven
Hausärztinnen und Hausärzte (N=143) zu erfassen.

Methode Die Daten wurden im Rahmen einer Baseline-Befragung einer
Langzeitstudie erhoben (repräsentative Ärztebefragung). Es wurde
untersucht, inwiefern soziodemographische als auch berufsbezogene Variablen mit
einem vorzeitigen bzw. späteren Renteneintritt in Zusammenhang gebracht
werden können und welche Gründe für eine
ärztliche Tätigkeit über das Rentenalter hinaus
sprechen.

Ergebnisse Die Ergebnisse zeigen, dass die Hälfte der Befragten
zwischen 29 und 66 Jahren vorzeitig in den Ruhestand gehen möchte und
diese Entscheidung vor allem von Familienstand, aber auch von
Arbeitszufriedenheit und Arbeitsbelastung abhängig ist. Zu den
Gründen, die für einen späteren Eintritt sprechen,
zählen „Freude an der Arbeit“, „sich
nützlich und gebraucht fühlen“ und ein allgemein
„berufliches Interesse“.

Schlussfolgerung Renteneintrittswünsche sollten bei der
zukünftigen Planung der Versorgung berücksichtigt werden, um
Maßnahmen zu ergreifen, die einem ungewollten oder vorzeitigen Ausstieg
der Mediziner aus der Versorgung entgegenwirken.
Potent Anti-amoebic Effects of Ibogaine, Voacangine and the Root Bark Alkaloid Fraction of Tabernaemontana arborea
Authors: Carrero Julio César , Curay-Herrera Violeta , Chacón-Niño Lysette , Krengel Felix , Guzmán-Gutiérrez Silvia-Laura , Silva-Miranda Mayra , González-Ramírez Luisa-Carolina , Bobes Raúl J. , Espitia Clara , Reyes-Chilpa Ricardo , Laclette Juan-Pedro
Published: March 2022

Plants of Tabernaemontana species have several pharmacological activities including antimicrobial effects. Amoebiasis continues to be a public health problem, with increasing
evidence of resistance to metronidazole. In this study, we assessed the effect of the alkaloid fraction of T. arborea root bark and the alkaloids ibogaine and voacangine on the
viability and infectivity of Entamoeba histolytica trophozoites. Cultures were exposed to 0.1 – 10 µg/mL for 24, 48 and 72 h, and viability was then determined using a tetrazolium dye
reduction assay and type of cellular death analyzed by flow cytometry. Results showed that the alkaloid fraction, but mainly ibogaine and voacangine alkaloids, exhibited potent
dose-dependent anti-amoebic activity at 24 h post-exposure (IC50 4.5 and 8.1 µM, respectively), comparable to metronidazole (IC50 6.8 µM). However, the effect decreased
after 48 and 72 h of exposure to concentrations below 10 µg/mL, suggesting that the alkaloids probably were catabolized to less active derivatives by the trophozoites. The treatment of
trophozoites with the IC50 s for 24 h induced significant morphological changes in the trophozoites, slight increase in granularity, and death by apoptonecrosis. The capacity of
T. arborea alkaloids to inhibit the development of amoebic liver abscesses in hamsters was evaluated. Results showed that even when the treatments reduced the number of amoebic
trophozoites in tissue sections of livers, they were unable to limit the formation of abscesses, suggesting their rapid processing to inactive metabolites. This work leaves open the
possibility of using Tabernaemontana alkaloids as a new alternative for amoebiasis control.
TransPPMP: predicting pathogenicity of frameshift and non-sense mutations by a Transformer based on protein features
Authors: Nie Liangpeng , Quan Lijun , Wu Tingfang , He Ruji , Lyu Qiang
Published: March 2022

Motivation

Protein structure can be severely disrupted by frameshift and non-sense mutations at specific positions in the protein sequence. Frameshift and non-sense mutation cases can also be found in healthy individuals. A method to distinguish neutral and potentially disease-associated frameshift and non-sense mutations is of practical and fundamental importance. It would allow researchers to rapidly screen out the potentially pathogenic sites from a large number of mutated genes and then use these sites as drug targets to speed up diagnosis and improve access to treatment. The problem of how to distinguish between neutral and potentially disease-associated frameshift and non-sense mutations remains under-researched.

Results

We built a Transformer-based neural network model to predict the pathogenicity of frameshift and non-sense mutations on protein features and named it TransPPMP. The feature matrix of contextual sequences computed by the ESM pre-training model, type of mutation residue and the auxiliary features, including structure and function information, are combined as input features, and the focal loss function is designed to solve the sample imbalance problem during the training. In 10-fold cross-validation and independent blind test set, TransPPMP showed good robust performance and absolute advantages in all evaluation metrics compared with four other advanced methods, namely, ENTPRISE-X, VEST-indel, DDIG-in and CADD. In addition, we demonstrate the usefulness of the multi-head attention mechanism in Transformer to predict the pathogenicity of mutations—not only can multiple self-attention heads learn local and global interactions but also functional sites with a large influence on the mutated residue can be captured by attention focus. These could offer useful clues to study the pathogenicity mechanism of human complex diseases for which traditional machine learning methods fall short.

Availability and implementation

TransPPMP is available at https://github.com/lennylv/TransPPMP.

Supplementary information

Supplementary data are available at Bioinformatics online.
Utility of Follow-up Coronavirus Disease 2019 (COVID-19) Antigen Tests After Acute Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Among Healthcare Personnel
Authors: Tande Aaron J , Swift Melanie D , Challener Douglas W , Berbari Elie F , Tommaso Christopher P , Christopherson Darrin R , Binnicker Matthew J , Breeher Laura E
Published: March 2022

We report the utility of rapid antigen tests (RAgT) in a cohort of US healthcare personnel with coronavirus disease 2019 (COVID-19) infection who met symptom criteria to return to work at day 5 or later of isolation. In total, 11.9% of initial RAgT were negative. RAgT can be helpful to guide return to work decisions.
The early oblivion of the firstAeneidin Turkish: aiming at a moving target
Authors: Öyken Ekin
Published: March 2022

The first complete translation of Vergil’s Aeneid into Turkish was published in 1935–36, during the first decades of the Turkish Republic. The translator Ahmed Reşid (1870–1955) was an intellectual and statesman who not only witnessed but also played active roles in arguably the most radical sociocultural turn in the country’s long history. As Reşid did not know Latin, he used an intermediary French translation as his source text. If this alone might seem from a normative viewpoint an obstacle to success, a broader perspective that considers various approaches in current translation criticism reveals a more complete and nuanced image of Reşid's translation project. My aim here is to contextualize historically and to critically discuss this carefully made but too soon forgotten Vergil translation, by using a case-specific plurality of methods. I argue that Antoine Berman's hermeneutical model is especially useful for studies on classical reception including Vergil translations.
Changes in left ventricular geometry after subannular repair in type IIIb functional mitral regurgitation
Authors: Sinn Martin , Pausch Jonas , Ragab Haissam , Sequeira-Gross Tatiana , von Stumm Maria , Spink Clemens , Adam Gerhard , Reichenspurner Hermann , Bannas Peter , Lund Gunnar , Girdauskas Evaldas
Published: March 2022

OBJECTIVES

Papillary muscle repositioning in functional mitral regurgitation (FMR) alleviates mitral valve (MV) tenting by reducing the distance between papillary muscle tips and MV annular plane, i.e. apical left ventricular (LV) displacement. We aimed to quantify the effect of papillary muscle repositioning on papillary muscle geometry and to evaluate whether improved papillary muscle geometry after papillary muscle repositioning translates into the global LV reverse remodelling in FMR type IIIb.

METHODS

Patients with severe FMR type IIIb were prospectively enrolled and underwent pre- and postoperative 1.5-T cardiac magnetic resonance imaging. A new variable was defined, the papillary muscle to mitral annulus distance, which quantifies the distance between papillary muscle tips and MV annular plane. All parameters were measured by 2 independent investigators.

RESULTS

A total of 63 patients were enrolled. In all patients, papillary muscle to mitral annulus distance correlated significantly with established markers of LV remodelling and MV tenting severity. In patients who underwent subannular papillary muscle repositioning procedure (surgical cohort, n = 23), preoperative median papillary muscle to mitral annulus distance was 30 mm [interquartile range (IQR): 27–34 mm] and was significantly reduced postoperatively to 25 mm (IQR: 21–27 mm) (P = 0.001). LV end-diastolic diameter was reduced from 66 mm (IQR: 60–71) preoperatively to 58 mm (IQR: 53–67) after the surgery (P = 0.001).

CONCLUSIONS

MV repair with papillary muscle repositioning results in a papillary muscle to mitral annulus distance reduction and significantly improved MV tenting parameters. Improved papillary muscle geometry after papillary muscle repositioning is associated with a global LV reverse remodelling and may, thereby, improve the prognosis of FMR patients.
Process optimization for atrial fibrillation ablation
Authors: Boehmer Andreas A , Summ Alena , Vila Steffen , Rothe Moritz , Nussbaum Elena , Zezyk Celine , Dobre Bianca C , Kaess Bernhard , Ehrlich Joachim R
Published: March 2022

Aims

In the light of an increasing prevalence of atrial fibrillation (AF) and growing evidence for the superiority of early invasive rhythm control, the demand for ablation therapy is rising. Accordingly, ablation centres will have to maximize their capacity by either adding electrophysiology laboratory resources or optimizing process management. In order to optimize process management, we applied “Lean Six Sigma” method to a single ablation center. We compared procedural parameters, acute efficacy and safety of cryoballoon pulmonary vein isolation (cryoPVI) before and after modifications.

Methods and results

Patients (n = 713) undergoing cryoPVI (108 before and 605 after process optimization) were analysed. Within 3 years of process optimization, electrophysiology laboratory occupancy time (150.7 ± 44.4 vs. 94 ± 22.1 min, P < 0.001), procedure time (84.5 ± 21–47.4 ± 12 min, P < 0.001), left-atrial dwell time (53.9 ± 18.4–31.9 ± 9.9 min, P < 0.001), and fluoroscopy time (15.8 ± 5.1 vs. 6.2 ± 2.8 min, P < 0.001) decreased. Contrast dye use (116 ± 35 vs. 27 ± 15 mL, P < 0.001) and radiation dose (893 ± 1078 vs. 253 ± 249 cGy cm2, P < 0.001) were reduced by ∼77 and ∼72%, respectively. There was no difference in safety endpoint occurrence (3.7 vs. 1.5%, P = 0.11).

Conclusion

The process optimization of cryoPVI for AF therapy using the ‘Lean Six Sigma’ method significantly increases efficiency without compromising patient safety.
Industrial R&D and national innovation policy: an institutional reappraisal of the US national innovation system
Authors: Shaikh Ibrahim A , Randhawa Krithika
Published: March 2022

Studies highlight how the once envied US national innovation system (NIS) is now showing signs of slowing down. In this article, we unpack this issue from an industrial R&D perspective. First, we highlight that open innovation (OI) practices (i.e., external sources and markets for technologies) have increased the rate of inventive activity in the current wave of industrial R&D, but financialization skews the firms’ focus on short-term profits and shareholder value maximization. When OI intersects with an institutional context that propagates such shareholder-centric governance of R&D, three social costs are incurred by the US NIS: (i) irrational relationship between risks and rewards, (ii) weak antitrust and intellectual property (IP) rights that result in a lack of business dynamism, and (iii) austerity and weak demand-side policies. We contend that these social costs tilt the R&D trajectory toward incremental R&D at the expense of the blue-sky science needed to retain US leadership in technological innovation. Second, we document three social benefits that public-sector R&D agencies generate for the US NIS: (i) undertaking a technology brokerage role, (ii) creating radical R&D markets, and (iii) embracing stakeholder governance. We emphasize how a hidden “entrepreneurial network state” subtly creates and shapes breakthrough R&D and markets for private sector firms but cannot recoup the rewards for society due to political rhetoric that favors incumbent market power. Third, we recommend both incremental and radical policies to drive institutional reforms that promote a stakeholder-centric form of R&D governance so that the future wave of industrial R&D creates value for society. Overall, we draw attention to the role politics plays in industrial R&D and the US NIS and how small adjustments in institutional dimensions and governance modes can impact the US R&D trajectory and competitiveness.
Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families
Authors: Vicedomini R. , Bouly J.P. , Laine E. , Falciatore A. , Carbone A.
Published: March 2022

Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyze sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups. We validate ProfileView on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organization into functional subgroups and residues that characterize the functions. In addition, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions. On protein families with complex domain architecture, ProfileView functional classification reconciles domain combinations, unlike phylogenetic reconstruction. ProfileView proves to outperform the functional classification approach PANTHER, the two k-mer-based methods CUPP and eCAMI and a neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.
Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition
Authors: Quan Yujun , Wang Meijiao , Xu Chengpeng , Wang Xiaoxiao , Wu Yu , Qin Dandan , Lin Yuxuan , Lu Xukun , Lu Falong , Li Lei
Published: March 2022

Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
Call for Adoption of Synchronized Biweekly Dosing of Anti-EGFR Agent Cetuximab: Implications for Patients with Metastatic Colorectal Cancer, and Squamous Cell Carcinoma of the Head and Neck
Authors: Kasi Pashtoon Murtaza
Published: March 2022

This commentary highlights the article by Parikh and colleagues, regarding biweekly therapy with the anti-EGFR monoclonal antibody, cetuximab, for gastrointestinal cancer.
Differential Virulence Contributions of the Efflux Transporter MexAB-OprM in Pseudomonas syringae Infecting a Variety of Host Plants
Authors: Helmann Tyler C. , King Dana M. , Lindow Steven E.
Published: March 2022

Efflux transporters such as MexAB-OprM contribute to bacterial resistance to diverse antimicrobial compounds. Here, we show that MexB contributes to epiphytic and late-stage apoplastic growth of Pseudomonas syringae strain B728a, as well as lesion formation in common bean ( Phaseolus vulgaris). Although a ∆ mexB mutant formed fewer lesions after topical application to common bean, these lesions contain the same number of cells (105 to 107 cells) as those caused by the wild-type strain. The internalized population size of both the wild-type and the ∆ mexB mutant within small samples of surface-sterilized asymptomatic portions of leaves varied from undetectably low to as high as 105 cells/cm2. Localized bacterial populations within individual lesions consistently exceeded 105 cells/cm2. Strain B728a was capable of moderate to extensive apoplastic growth in diverse host plants, including lima bean ( P. lunatus), fava bean ( Vicia faba), pepper ( Capsicum annuum), Nicotiana benthamiana, sunflower ( Helianthus annuus), and tomato ( Solanum lycopersicum), but MexB was not required for growth in a subset of these plant species. A model is proposed that MexB provides resistance to as-yet-unidentified antimicrobials that differ between plant species.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Temporally Regulated Plant-Nematode Gene Networks Implicate Metabolic Pathways
Authors: Mishra Shova , Salichs Oscar , DiGennaro Peter
Published: March 2022

Root-knot nematodes (RKN) (Meloidogyne spp.) constantly communicate with their host to establish and maintain specialized feeding cells. They likely regulate this interaction by monitoring host biology. As plant host biology is influenced by light and gene expression varies correspondingly, RKN gene transcription and biology likely follow similar patterns. We profiled RKN transcripts over a period of 24 h and identified approximately 1,000 differentially expressed genes (DEG) in nematode and model host Medicago truncatula, with the majority of DEG occurring in the middle of the dark period. Many of the plant DEG are involved in defense-response pathways, while the nematode DEG are involved in establishing infection, suggesting a strong host-nematode interaction occurring during the dark. To identify interacting genes, we developed a plant-nematode gene network based on DEG signals. The phenylpropanoid pathway was identified as a significant plant-nematode interacting pathway, representing four of 33 genes in the network. We further examined if this pathway interacts similarly in another host, tomato, by quantifying phenolic and flavonoid compounds produced by this pathway. Phenolic compounds showed a significant increase in production during the day in uninoculated plants as compared with during the night. However, during the dark period, there was an increase in flavonoid content in infected plants when compared with uninfected controls, indicating potential host defense mechanisms active during the height of nematode activity at night. This study elucidated cross-species interacting pathways that could be targeted to develop novel management strategies to these important pests.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Effects of Macroautophagy and Mitophagy on the Pathogenicity of Fusarium graminearum
Authors: Chai Xicun , Liu Yutao , Ma Haixia , Wang Shipeng , Niyitanga Evode , He Chunxia
Published: March 2022

Fusarium graminearum is the main pathogen of Fusarium head blight (FHB), which causes huge economic losses every year. In this study, an attempt was made to control FHB from the point of view of the physiological behavior of the pathogen itself. Autophagic inhibitors and activators were used, and the pathogenicity-related indices of F. graminearum were measured. The results showed that under nitrogen-rich conditions, macroautophagy inhibition and activation greatly reduced the mycelium weight to 0.28 and 0.25 g/ml at 24 h, which were 17.82 and 24.77% lower than that of the control treatment, respectively. Mitophagy inhibition also significantly decreased the mycelium weight (P < 0.05). Conidial yield was found to be affected by factors related to autophagy occurrence. It was found that both autophagy inhibition and activation could reduce the conidiation of F. graminearum. The toxin contents in wheat medium of macroautophagy activation treatments were 0.678, 0.190, 0.402, and 0.195 μg/g when cultured for 8 and 24 h under 0% N and 100% N conditions, respectively, which were significantly higher than those of the control treatments (P < 0.05). The infection length was measured to characterize the infectivity of F. graminearum, and we found that the length was short under macroautophagy activation conditions. However, mitophagy did not seem to affect the infectivity of F. graminearum. In summary, the above results indicate that macroautophagy and mitophagy inhibition could reduce the pathogenicity of F. graminearum, which may provide a new perspective for management of plant fungal diseases.
Time-series monitoring of transgenic maize seedlings phenotyping exhibiting glyphosate tolerance
Authors: Tao Mingzhu , Feng Xuping , He Yong , Zhang Jinnuo , Bai Xiulin , Yang Guofeng , Wei Yuzhen
Published: March 2022

Developing herbicide resistant cultivars is one of the effective methods to solve the safety problem caused by the use of herbicide. In this study, hyperspectral image was used to develop more robust leaf chlorophyll content (LCC) prediction model based on different datasets to finally analyze the response of LCC to glyphosate-stress. Chlorophyll a fluorescence (ChlF) was used to dynamically monitor the photosynthetic physiological response of transgenic glyphosate-resistant and wild glyphosate–sensitive maize seedlings, and applying chemometrics methods to extract time-series features to screen resistant cultivars. Both the proposed two transfer strategies achieved the best prediction of LCC with a coefficient of determination value of 0.84, and relative root mean square error of 4.03 for the prediction set. Based on the predicted LCC and ChlF data, we found the antioxidant system of glyphosate-sensitive plants is too fragile to protect themselves from the damage, while glyphosate-resistant plants could overcome it by activating more powerful antioxidant system. φE0, VJ, ψE0, and M0could be used to indicate damage caused by glyphosate to differentiate resistant cultivars. This study provided a new methodology to monitor LCC to finally analyze glyphosate tolerance in a time-series manner, and verified the feasibility of ChlF in crop breeding.

Highlight

This study proposed a new methodology to monitor leaf chlorophyll content to finally analyze glyphosate tolerance in vivo, and verified the feasibility of chlorophyll a fluorescence in crop breeding.