bluuebunny/crossref_metadata_2025 huggingface dataset:
Big Data Analytics for Assistance Operation Identification in Ice-Covered Waters
Authors: Liu Cong , Musharraf Mashrura , Kujala Pentti , Toivola Jarkko
Published: October 2022

In winter, shipping activities in the Baltic Sea area involve risks because of the harsh navigational environment. To ensure maritime safety and the efficiency of the transport system, icebreaker assistance is needed when the ship is not able to navigate independently in the prevailing ice condition. The existing ship operation mode determination practices are primarily based on empirical knowledge. To better understand when the assistance operation is needed for various ships operating in real ice conditions from a quantitative perspective, this paper proposes the use of a data-driven assistance operation identification model. The model combines different data types, including Automatic Identification System (AIS) data and ice data that portray the real operational conditions in the Baltic Sea. The aim is to measure temporal-spatial similarities among trajectories of icebreakers and potentially assisted ship(s) using clustering algorithms, automatically identifying assistance scenarios in ice-covered waters. Both the static voyage features (e.g., ship types, departures /destinations, voyage length) and the dynamic navigation features (e.g., speed, course, and ship trajectory spatial distance) are considered in the model. The outcomes of the model would assist in better understanding of ship behaviors and coupled kinematics of ships linking with the following distance and speed under icebreaker assistance in various ice conditions. They would also contribute to data-driven ship operation mode determination, therefore supporting the development of an intelligent decision support system in winter navigation.
Control Co-Design of a Hydrokinetic Turbine With Open-Loop Optimal Control
Authors: Jiang Boxi , Amini Mohammad Reza , Liao Yingqian , Martins Joaquim R. R. A. , Sun Jing
Published: October 2022

This paper introduces a control co-design (CCD) framework to simultaneously explore the physical parameters and control spaces for a hydro-kinetic turbine (HKT) rotor optimization. The optimization formulation incorporates a coupled dynamic-hydrodynamic model to maximize the rotor power efficiency for various time-variant flow profiles. The open-loop optimal control is applied for maximum power tracking, and the blade element momentum theory (BEMT) is used to model the hydrodynamics. Case studies with different control constraints are investigated for CCD. Sensitivity analyses were conducted with respect to different flow profiles and initial geometries. Comparisons are made between CCD and the sequential process, with physical design followed by a control design process under the same conditions. The results demonstrate the benefits of CCD and reveal that, with control constraints, CCD leads to increased energy production compared to the design obtained from the sequential design process.
Prediction of Inclined Surface Spreading Extent for High Flashpoint Fuel in Large Compartments Under Ship Motion
Authors: Baeg Dae Yu , Lee Hyun Ho , Lee Seung Yul , Kim Seon Jin , Kim Jeong Hwan , Seo Jung Kwan
Published: October 2022

Fire accidents can occur on in-service ships and offshore installations due to the spillage of fuels from components such as storage tanks and valves under accidental and extreme conditions. In such accidents, the liquefied fuel spread area on the decks are affected by ship motion and properties of the fuel, which may cause a pool fire to develop into a large-scale fire, resulting in casualties and severe damage to property and the environment. Therefore, the effects of surface spread extent on the structural response of ships and offshore installations should be examined. Additional safety measures are particularly necessary on ships with large compartments, such as Ro-Ro ships. However, these fire hazards and their preventive measures have not been sufficiently explored. Thus, in this study, fuel discharge experiments were conducted to investigate the fuel spreading behavior at different substrate slopes and discharge rates. Based on the results, empirical formulae that predict the spreading extent of liquefied fuel in large compartments were derived. Additionally, the proposed formulae were used to investigate the variation of heat release rate in different spillage scenarios.
Advanced Laboratory Setup to Determine and Verify Cement Sheath Integrity
Authors: Taghipour Ali , Feneuil Blandine , Vrålstad Torbjørn , Skorpa Ragnhild
Published: October 2022

It is crucial to ensure that stored CO2 does not leak into the atmosphere. As the last step in the Carbon Capture and Storage (CCS) process, CO2 is injected into underground formations, and it should remain stored there for eternity. However, when reusing old petroleum wells for CO2 storage, defects in the cement sheath, such as microannuli or radial cracks, might be present from production operations such as shut down/startups or from the injection process itself. Thus, causing a possible leak path for CO2 through the cement. Upon reaction with CO2 the cement carbonates, and this carbonation process may in fact seal the cracks in the cement. This so-called self-healing effect has been studied experimentally for many years, but, to the best of our knowledge, none of these studies were performed with realistic well geometries with cracked cement sheaths.

An advanced experimental setup has been developed to study the sealing process of realistic cracks in the cement sheath by flowing CO2 through radial cracks and investigate the effect of flow rate and exposure time for different cement systems. The setup consists of a modular based downscaled section of a wellbore with rock, cement, and casing, and allows for a confining pressure up to 100 bar around the rock. Pressure cycling experiments are performed on the cement sheath by increasing the pressure from inside the casing, causing realistic radial cracks in the cement sheath. When these cracks are connected axially through the sample, they provide a leak path for fluids through the cement. This novel setup allows for a direct exposure of the bottom of a microannuli or radial crack with CO2, and thus measure the flow through the cracks and study the possible healing effects by CO2. The novelty of the setup lies in a movable support of the cement sheath. The first position allows a firm support for the cement upon curing, and the second, at a lower level opens the ports for CO2 exposure and exposes the full bottom surface of the cement sheath. The cracks in the cement sheath were visualized using μ-CT both prior to and after CO2 experiments.

The paper describes in detail the novel laboratory setup and the applicability of the setup.
Flowability of Dry and Water Wet Barite Powder
Authors: Skorpa Ragnhild , Feneuil Blandine , von Hafenbrädl Franz Otto , Ratnayake Chandana
Published: October 2022

Barite is added to drilling fluids as weight material to increase its density. Over time, when the drilling fluids are left static in the annulus, gravitational forces will make the barite settle out. This settled barite is today the main reason for casing cut and removal process, which accounts for up to 50% of time related to P&A operations. Knowledge of settled barite on top of cement behind casing is also essential for perf, wash & cement procedures.

The most compact barite sediment can be characterized as a non-elastic dense wet particle sediment where the packing of the particles and the particle size of the grains varies. To fully understand the packing mechanism of the consolidated barite sediments characterization of barite powder (both dry and wet) is important.

In this study we have done comparable measurements with a Jenike shear test, which measures direct shear strength under different loading conditions, and compared these to rheological measurements using an Anton Paar powder module under the same loading conditions. Experiments were performed on both dry and wet (by 2.5 wt% and 5 wt% water) barite and with 1, 3, 6 and 9 kPa loading.

The results from the Jenike test and the powder module were found to be complimentary. At a low water content, the sample showed an increase in flowability, while with a high-water content a decrease the flowability was observed compared to that of dry barite.
Practical Application of Pressure and Temperature Dependent Viscosity Calculations in Well Cementing Simulations
Authors: Flamant Nicolas C. , Pelipenko Sviatoslav
Published: October 2022

During well cementing and drilling operations, proper control of downhole pressure is critical for controlling the well, i.e. avoiding formation fluids influx or fracturing the formation, and hence ensuring successful well construction operations. At the planning stage, well control is investigated using numerical hydraulics simulations. During actual operations, annular pressure-while-drilling (APWD) is often, but not systematically, available while drilling but not while cementing. Here again well control relies on simulations. Accurate prediction of downhole pressures is therefore a key requirement for well control, whether at the planning stage or in real-time during operations.

Fluid properties are a key input to the hydraulics simulations, in particular fluid viscosity, which is required to estimate friction pressure losses. A difficulty is the dependence of viscosity on pressure and temperature. At a given shear rate, the viscosity of drilling and cementing fluids continuously changes within the flow path, and variations of several tens of percent are common. Hence it is paramount to measure cementing and drilling fluids viscosity over the pressure and temperature domain that will be experienced in the well, but also to fit to the measurements a pressure and temperature dependent rheological model that will allow the hydraulics simulator to obtain viscosity at any shear rate, temperature, and pressure values.

We first provide an overview of the algorithms needed to analyze rheological lab measurements, where care must be taken to account for potential wall slip effects. We then review how to account for pressure and temperature effects, via the use of Arrhenius and Barus laws, and why the modeling needs should inform the test requirements.
Digital Twin Based Structural Health Monitoring of Offshore Crane
Authors: Rølvåg Terje , Stranden Øystein
Published: October 2022

This paper presents a novel approach for implementation of digital twin (DT) based Structural Health Monitoring (SHM) of an Palfinger offshore knuckle boom crane. Contrary to most harbor gantry cranes, knuckle boom cranes are highly nonlinear mechanisms that cannot be represented by static reduced order twin models. Such cranes need to be solved by non-linear finite element solvers. The digital twin representation of the Palfinger crane is modelled and simulated real-time in a nonlinear finite element (FE) program, driven by inputs from physical sensors. Model reduction techniques are applied to enable DT co-simulation running two times faster than the physical crane. The inputs from the standard crane instrumentation are processed for noise reduction and singularity removal and converted to hydraulic actuator inputs. A simple inverse method for estimation of the crane payload is implemented based on hydraulic pressures. Structural loads due to wave induced ship motions are predicted based on sensor signals from the ship IMU. Based on the standard ship and crane instrumentation, the digital twin allows for real-time determination of stresses, strains and loads at an unlimited number of hot spots. Hence, a digital twin can be an effective tool for predictive maintenance of real offshore knuckle boom cranes with minor additional costs. The presented approach is described in a general manner and is applicable for offshore cranes used in the industry.
Optimization of Semi-Submersible Hull Design for Floating Offshore Wind Turbines
Authors: Hsu I-Jen , Ivanov Glib , Ma Kai-Tung , Huang Zheng-Zhang , Wu Hua-Tung , Huang Yun-Tzu , Chou Mike
Published: October 2022

As wind energy developers start venturing into deeper waters with depths greater than 65 meters, the floating offshore wind turbines (FOWTs) are becoming the preferred solutions there over bottom-fixed structures. This paper summarizes the design of a semi-submersible platform for hosting a 15MW turbine. While semi-submersible origins from the oil & gas industry, the FOWT presents a different set of requisites and conditions for designing it. Recent existing and planned projects can be characterized by excessive use of steel and dimensions, compared to bottom-fixed structures. This paper aims to optimize the hull structure of a semi-submersible platform to be as cost-effective as possible while fulfilling the following design considerations: strength, vessel stability in still water and dynamic conditions, constructability, and operability. Meanwhile, the design is made to satisfy the rule requirements of major classification societies. Through a literature survey, data on existing semi-submersible projects is gathered and analyzed. The ratios of vessel displacement to hull steel weight relations are presented to show the trend. A high-level overview of class rules is given. An example platform, TaidaFloat, designed to carry a 15MW turbine is introduced. Its application is targeting a water depth from 65 to 100 meters with a deployment in Taiwan Strait in mind. The platform is designed against some limits and constraints, e.g. ensuring that it meets stability criteria. Its internal structural arrangement is preliminarily developed, and the steel weight is compared to recent projects. Features of the design are introduced, and their advantages are summarized.
SALVAGING FLAWED DISCOURSES SURROUNDING NZ’S ‘COUNTER-TERRORISM LEGISLATION BILL’
Authors: Veale Kevin
Published: October 2022

Public-facing announcements from Labour minister Kris Faafoi and Prime Minister Jacinda Ardern around the ‘Counter-Terrorism Legislation Bill’ that that was introduced to Parliament on the 13th of April 2021 has included a number of flawed discourses that risk making the legislation less effective. The current focus on ‘lone actors’ speaks to a misunderstanding of online community dynamics within the hate-groups that motivate terror attacks. Additionally, there is little attention either in the foundational document for the ‘Christchurch Call to Action Summit’ or the discussions surrounding the ‘Counter-Terrorism Legislation Bill’ of the ways that online economies drive the expansion of extremist groups and raise the odds of terrorist actions. This article will explore the background to these issues, what makes the current discursive framing from the government around the legislation problematic, and what initiatives could be concretely taken to mitigate these issues.
PARĀOA RĒWENA: The Relegation of Aotearoa New Zealand's Indigenous Bread
Authors: Neill Lindsay , Sturny Arno
Published: October 2022

National identity is linked to food. Exemplifying that, many people associate Turkey with pide, Italy with focaccia and, of course, France with the baguette. But what about Aotearoa New Zealand, what breads signifies a New Zealand/Kiwi identity? This paper explores a contender for that role, a bread commonly associated with Māori, Aotearoa New Zealand’s tangata whenua: parāoa rēwena. This research asked eight expert chef/bakers about their views and experiences of parāoa rēwena. Four of the participants self-identified as Māori, and four as Pākehā. Working within a qualitative paradigm and using thematic analysis, this research revealed bifurcated views about parāoa rēwena that clearly differentiated the opinions and experiences of our participants. Within these differences, our findings revealed that the self-identifying Pākehā participants tended to hold imperial views reflecting colonial dominance, whereas the self-identifying Māori participants expressed a more holistic approach to andmindset about parāoa rēwena. Consequently, this paper proposes that parāoa rēwena becoming the national bread of Aotearoa New Zealand is more likely to occur as an initiative promoted by Māori and not Pākehā. In this way, within an exploration of parāoa rēwena, this paper reflects the politics of palatability in Aotearoa New Zealand as a metaphor of the relationship between Māori and Pākehā.
Plasmon resonance-based study of the peroxidaselike catalytic effect of gold nanoparticles
Authors: Zheng Minjie , Cai Yujuan , Zhang Jun , Li Liying , Tai Zhigang
Published: October 2022

In this paper, the peroxidaselike catalytic effect of gold nanoparticles (AuNPs) was explored in dye wastewater treatment by visible light excitation. Using hydrogen peroxide as a substrate, the peroxidaselike reaction was evaluated with AuNPs catalyzing the substrate oxidative degradation of the organic dye rhodamine B (RhB). The synthesized AuNPs were characterized by transmission electron microscopy. The degradation of RhB was observed by a UV-visible spectrophotometer. The results showed that under visible light irradiation, the AuNPs exhibited good peroxidaselike catalytic activity for the oxidative degradation of RhB by hydrogen peroxide. By studying the light wavelength and light intensity-dependent reaction rates, radical trapping, and hole acceptor incorporation, it was found that AuNPs can absorb photon energy and generate hot electrons through a localized surface plasmon resonance effect under light irradiation. Subsequently, hot electrons flow into the molecular orbitals of H2O2 based on energy matching, activating the molecule and transforming it into the transition state, which is proceeded by breakdown to release hydroxyl radicals (⋅OH) for oxidative destruction of RhB.
Growth of (SmxGa1−x)2O3 by molecular beam epitaxy
Authors: Stewart Anthony D. , Gila Brent P. , Abernathy Cammy R. , Pearton S. J.
Published: October 2022

The (SmxGa1−x)2O3 alloy system is a potential new dielectric for compound semiconductors such as GaAs. Using molecular beam epitaxy under metal-modulated growth conditions, we grew the binary oxide, Sm2O3, at two substrate temperatures (100 and 500 °C) and optimized the structural, morphological, and electrical properties of the films. Decreasing the Sm cell temperature suppressed the formation of the monoclinic phase and promoted the growth of the cubic phase. Next, the ternary oxide, (SmxGa1−x)2O3, was deposited to investigate the effects of Ga incorporation. Optimization experiments were used to determine the effects of substrate temperature and samarium cell temperature (i.e., growth rate) on film stoichiometry, phase distribution, and microstructure in these films. Films grown at 500 °C showed significant surface roughness and the presence of multiple crystalline phases. Since all of the Sm-based oxides (i.e., samarium oxide with and without gallium) were found to have unbonded Sm metal, annealing experiments were carried out in oxygen and forming gas to determine the effects of annealing on film stoichiometry. The motivation behind annealing in forming gas was to see whether this commonly used technique for reducing interface densities could improve the film quality. GaAs metal-oxide-semiconductor diodes with (SmxGa1−x)2O3 showed breakdown fields at 1 mA/cm2 of 4.35 MV/cm, which decreased with increasing Sm unbonded metal content in the films.
Mixed plastics waste valorization through tandem chemical oxidation and biological funneling
Authors: Sullivan Kevin P. , Werner Allison Z. , Ramirez Kelsey J. , Ellis Lucas D. , Bussard Jeremy R. , Black Brenna A. , Brandner David G. , Bratti Felicia , Buss Bonnie L. , Dong Xueming , Haugen Stefan J. , Ingraham Morgan A. , Konev Mikhail O. , Michener William E. , Miscall Joel , Pardo Isabel , Woodworth Sean P. , Guss Adam M. , Román-Leshkov Yuriy , Stahl Shannon S. , Beckham Gregg T.
Published: October 2022

Mixed plastics waste represents an abundant and largely untapped feedstock for the production of valuable products. The chemical diversity and complexity of these materials, however, present major barriers to realizing this opportunity. In this work, we show that metal-catalyzed autoxidation depolymerizes comingled polymers into a mixture of oxygenated small molecules that are advantaged substrates for biological conversion. We engineer a robust soil bacterium,
Pseudomonas putida
, to funnel these oxygenated compounds into a single exemplary chemical product, either β-ketoadipate or polyhydroxyalkanoates. This hybrid process establishes a strategy for the selective conversion of mixed plastics waste into useful chemical products.
Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device
Authors: Reed Brian D. , Meyer Michael J. , Abramzon Valentin , Ad Omer , Ad Omer , Adcock Pat , Ahmad Faisal R. , Alppay Gün , Ball James A. , Beach James , Belhachemi Dominique , Bellofiore Anthony , Bellos Michael , Beltrán Juan Felipe , Betts Andrew , Bhuiya Mohammad Wadud , Blacklock Kristin , Boer Robert , Boisvert David , Brault Norman D. , Buxbaum Aaron , Caprio Steve , Choi Changhoon , Christian Thomas D. , Clancy Robert , Clark Joseph , Connolly Thomas , Croce Kathren Fink , Cullen Richard , Davey Mel , Davidson Jack , Elshenawy Mohamed M. , Ferrigno Michael , Frier Daniel , Gudipati Saketh , Hamill Stephanie , He Zhaoyu , Hosali Sharath , Huang Haidong , Huang Le , Kabiri Ali , Kriger Gennadiy , Lathrop Brittany , Li An , Lim Peter , Liu Stephen , Luo Feixiang , Lv Caixia , Ma Xiaoxiao , McCormack Evan , Millham Michele , Nani Roger , Pandey Manjula , Parillo John , Patel Gayatri , Pike Douglas H. , Preston Kyle , Pichard-Kostuch Adeline , Rearick Kyle , Rearick Todd , Ribezzi-Crivellari Marco , Schmid Gerard , Schultz Jonathan , Shi Xinghua , Singh Badri , Srivastava Nikita , Stewman Shannon F. , Thurston TR , Thurston T. R. , Trioli Philip , Tullman Jennifer , Wang Xin , Wang Yen-Chih , Webster Eric A. G. , Zhang Zhizhuo , Zuniga Jorge , Patel Smita S. , Griffiths Andrew D. , van Oijen Antoine M. , McKenna Michael , Dyer Matthew D. , Rothberg Jonathan M.
Published: October 2022

Studies of the proteome would benefit greatly from methods to directly sequence and digitally quantify proteins and detect posttranslational modifications with single-molecule sensitivity. Here, we demonstrate single-molecule protein sequencing using a dynamic approach in which single peptides are probed in real time by a mixture of dye-labeled N-terminal amino acid recognizers and simultaneously cleaved by aminopeptidases. We annotate amino acids and identify the peptide sequence by measuring fluorescence intensity, lifetime, and binding kinetics on an integrated semiconductor chip. Our results demonstrate the kinetic principles that allow recognizers to identify multiple amino acids in an information-rich manner that enables discrimination of single amino acid substitutions and posttranslational modifications. With further development, we anticipate that this approach will offer a sensitive, scalable, and accessible platform for single-molecule proteomic studies and applications.
A bacterial phospholipid phosphatase inhibits host pyroptosis by hijacking ubiquitin
Authors: Chai Qiyao , Yu Shanshan , Zhong Yanzhao , Lu Zhe , Qiu Changgen , Yu Yang , Zhang Xinwen , Zhang Yong , Lei Zehui , Qiang Lihua , Li Bing-Xi , Pang Yu , Qiu Xiao-Bo , Wang Jing , Liu Cui Hua
Published: October 2022

The inflammasome-mediated cleavage of gasdermin D (GSDMD) causes pyroptosis and inflammatory cytokine release to control pathogen infection, but how pathogens evade this immune response remains largely unexplored. Here we identify the known protein phosphatase PtpB from
Mycobacterium tuberculosis
as a phospholipid phosphatase inhibiting the host inflammasome-pyroptosis pathway. Mechanistically, PtpB dephosphorylated phosphatidylinositol-4-monophosphate and phosphatidylinositol-(4,5)-bisphosphate in host cell membrane, thus disrupting the membrane localization of the cleaved GSDMD to inhibit cytokine release and pyroptosis of macrophages. Notably, this phosphatase activity requires PtpB binding to ubiquitin. Disrupting phospholipid phosphatase activity or the ubiquitin-interacting motif of PtpB enhanced host GSDMD-dependent immune responses and reduced intracellular pathogen survival. Thus, pathogens inhibit pyroptosis and counteract host immunity by altering host membrane composition.
Evolution of increased complexity and specificity at the dawn of form I Rubiscos
Authors: Schulz Luca , Guo Zhijun , Zarzycki Jan , Steinchen Wieland , Schuller Jan M. , Heimerl Thomas , Prinz Simone , Mueller-Cajar Oliver , Erb Tobias J. , Hochberg Georg K. A.
Published: October 2022

The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.
Peptide ligand-mediated trade-off between plant growth and stress response
Authors: Ogawa-Ohnishi Mari , Yamashita Tomohide , Kakita Mitsuru , Nakayama Takuya , Ohkubo Yuri , Hayashi Yoko , Yamashita Yasuko , Nomura Taizo , Noda Saki , Shinohara Hidefumi , Matsubayashi Yoshikatsu
Published: October 2022

Deciding whether to grow or to divert energy to stress responses is a major physiological trade-off for plants surviving in fluctuating environments. We show that three leucine-rich repeat receptor kinases (LRR-RKs) act as direct ligand-perceiving receptors for PLANT PEPTIDE CONTAINING SULFATED TYROSINE (PSY)-family peptides and mediate switching between two opposing pathways. By contrast to known LRR-RKs, which activate signaling upon ligand binding, PSY receptors (PSYRs) activate the expression of various genes encoding stress response transcription factors upon depletion of the ligands. Loss of PSYRs results in defects in plant tolerance to both biotic and abiotic stresses. This ligand-deprivation–dependent activation system potentially enables plants to exert tuned regulation of stress responses in the tissues proximal to metabolically dysfunctional damaged sites where ligand production is impaired.
Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP
2
Authors: Yin Ying , Zhang Feng , Feng Shasha , Butay Kevin John , Borgnia Mario J. , Im Wonpil , Lee Seok-Yong
Published: October 2022

The transient receptor potential melastatin 8 (TRPM8) channel is the primary molecular transducer responsible for the cool sensation elicited by menthol and cold in mammals. TRPM8 activation is controlled by cooling compounds together with the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP
2
). Our knowledge of cold sensation and the therapeutic potential of TRPM8 for neuroinflammatory diseases and pain will be enhanced by understanding the structural basis of cooling agonist- and PIP
2
-dependent TRPM8 activation. We present cryo–electron microscopy structures of mouse TRPM8 in closed, intermediate, and open states along the ligand- and PIP
2
-dependent gating pathway. Our results uncover two discrete agonist sites, state-dependent rearrangements in the gate positions, and a disordered-to-ordered transition of the gate-forming S6—elucidating the molecular basis of chemically induced cool sensation in mammals.
Natural monuments
Elderflora: A Modern History of Ancient Trees
Jared Farmer
Basic Books, 2022. 448 pp.
Authors: Stahle D. W.
Published: October 2022

Reverence for old trees sparked early forest conservation efforts, even as ancient woodlands were cut with impunity
In Science Journals
Authors: Funk Michael A. , Stern Peter , Grocholski Brent , Ray L. Bryan , Hines Pamela J. , Lavine Marc S. , Czajka Caitlin , Wong Wei , Hurtley Stella M. , Alderton Gemma , Szuromi Phil , Olingy Claire
Published: October 2022

Highlights from the
Science
family of journals
In Other Journals
Authors: Jiang Di , Wible Brad , Maroso Mattia , Kelly Priscilla N. , Funk Michael A. , Uzogara Ekeoma , Stajic Jelena
Published: October 2022

Editors’ selections from the current scientific literature
Secrets of Tibet’s hot-spring snakes revealed
Authors: Pennisi Elizabeth
Published: October 2022

Mutations helped animals adapt to extreme temperatures, low oxygen
Integrative Assessment of Reduced Listeria monocytogenes Susceptibility to Benzalkonium Chloride in Produce Processing Environments
Authors: He Yingshu , Xu Tongzhou , Li Shaoting , Mann David A. , Britton Brianna , Oliver Haley F. , den Bakker Hendrik C. , Deng Xiangyu
Published: October 2022

Our study demonstrates an integrative approach to improve food safety assessment and control strategies in food processing environments through the collective leveraging of genomic surveys, laboratory assays, and processing facility sampling. In the example of assessing reduced
Listeria
susceptibility to a widely used sanitizer, this approach yielded multifaceted evidence that incorporates population genetic signals, experimental findings, and real-world constraints to help address a lasting debate of policy and practical importance.
Context-Dependent Roles for Toll-Like Receptors 2 and 9 in the Pathogenesis of Staphylococcus aureus Osteomyelitis
Authors: Petronglo Jenna R. , Putnam Nicole E. , Ford Caleb A. , Cruz-Victorio Virginia , Curry Jacob M. , Butrico Casey E. , Fulbright Laura E. , Johnson Joshua R. , Peck Sun H. , Fatah Sana R. , Cassat James E.
Published: October 2022

Staphylococcus aureus
is the major causative agent of bacterial osteomyelitis, an invasive infection of bone. Inflammation generated by the immune response to
S. aureus
contributes to bone damage by altering bone homeostasis.
ppe51
Variants Enable Growth of Mycobacterium tuberculosis at Acidic pH by Selectively Promoting Glycerol Uptake
Authors: Dechow Shelby J. , Baker Jacob J. , Murto Megan , Abramovitch Robert B.
Published: October 2022

It is puzzling why
Mycobacterium tuberculosis
(Mtb) cannot grow on glycerol at acidic pH, as it has a carbon source and oxygen, everything it needs to grow. In this study, we found that Mtb limits uptake of glycerol at acidic pH to restrict its growth and that mutations in
ppe51
promote uptake of glycerol at acidic pH and enable growth.
Hepatitis B Virus Core Protein Is Not Required for Covalently Closed Circular DNA Transcriptional Regulation
Authors: Zhong Youquan , Wu Chuanjian , Xu Zaichao , Teng Yan , Zhao Li , Zhao Kaitao , Wang Jingjing , Wang Wen , Zhan Qiong , Zhu Chengliang , Chen Xinwen , Liang Kaiwei , Cheng Xiaoming , Xia Yuchen
Published: October 2022

Hepatitis B virus (HBV) core protein (HBc) has emerged as a promising antiviral target. However, whether HBc can regulate HBV covalently closed circular DNA (cccDNA) transcription remains elusive. This study illustrated that HBc has no effect on epigenetic regulation of cccDNA, and it does not participate in cccDNA transcription. Given that HBc is dispensable for cccDNA transcription, novel cccDNA-targeting therapeutics are needed for an HBV cure.
Altered Gut Microbial Profile Accompanied by Abnormal Fatty Acid Metabolism Activity Exacerbates Endometrial Cancer Progression
Authors: Zhao Shan-Shan , Chen Lei , Yang Jing , Wu Zhen-Hua , Wang Xiao-Yu , Zhang Qi , Liu Wen-Jie , Liu Hui-Xin
Published: October 2022

A growing number of studies have shown the connection between gut microbiota, obesity, and cancer. However, to our knowledge, the association between gut microbiota and endometrial cancer progression in humans has not been studied.
Post-acute sequelae of covid-19 six to 12 months after infection: population based study
Authors: Peter Raphael S , Nieters Alexandra , Kräusslich Hans-Georg , Brockmann Stefan O , Göpel Siri , Kindle Gerhard , Merle Uta , Steinacker Jürgen M , Rothenbacher Dietrich , Kern Winfried V
Published: October 2022

Objectives

To describe symptoms and symptom clusters of post-covid syndrome six to 12 months after acute infection, describe risk factors, and examine the association of symptom clusters with general health and working capacity.

Design

Population based, cross sectional study

Setting

Adults aged 18-65 years with confirmed SARS-CoV-2 infection between October 2020 and March 2021 notified to health authorities in four geographically defined regions in southern Germany.

Participants

50 457 patients were invited to participate in the study, of whom 12 053 (24%) responded and 11 710 (58.8% (n=6881) female; mean age 44.1 years; 3.6% (412/11 602) previously admitted with covid-19; mean follow-up time 8.5 months) could be included in the analyses.

Main outcome measures

Symptom frequencies (six to 12 months after versus before acute infection), symptom severity and clustering, risk factors, and associations with general health recovery and working capacity.

Results

The symptom clusters fatigue (37.2% (4213/11 312), 95% confidence interval 36.4% to 38.1%) and neurocognitive impairment (31.3% (3561/11 361), 30.5% to 32.2%) contributed most to reduced health recovery and working capacity, but chest symptoms, anxiety/depression, headache/dizziness, and pain syndromes were also prevalent and relevant for working capacity, with some differences according to sex and age. Considering new symptoms with at least moderate impairment of daily life and ≤80% recovered general health or working capacity, the overall estimate for post-covid syndrome was 28.5% (3289/11 536, 27.7% to 29.3%) among participants or at least 6.5% (3289/50 457) in the infected adult population (assuming that all non-responders had completely recovered). The true value is likely to be between these estimates.

Conclusions

Despite the limitation of a low response rate and possible selection and recall biases, this study suggests a considerable burden of self-reported post-acute symptom clusters and possible sequelae, notably fatigue and neurocognitive impairment, six to 12 months after acute SARS-CoV-2 infection, even among young and middle aged adults after mild infection, with a substantial impact on general health and working capacity.

Trial registration

German registry of clinical studies DRKS 00027012.
Scoping and targeted reviews to support development of SPIRIT and CONSORT extensions for randomised controlled trials with surrogate primary endpoints: protocol
Authors: Manyara Anthony Muchai , Davies Philippa , Stewart Derek , Wells Valerie , Weir Christopher , Young Amber , Taylor Rod , Ciani Oriana
Published: October 2022

Introduction

Using a surrogate endpoint as a substitute for a primary patient-relevant outcome enables randomised controlled trials (RCTs) to be conducted more efficiently, that is, with shorter time, smaller sample size and lower cost. However, there is currently no consensus-driven guideline for the reporting of RCTs using a surrogate endpoint as a primary outcome; therefore, we seek to develop SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) and CONSORT (Consolidated Standards of Reporting Trials) extensions to improve the design and reporting of these trials. As an initial step, scoping and targeted reviews will identify potential items for inclusion in the extensions and participants to contribute to a Delphi consensus process.

Methods and analysis

The scoping review will search and include literature reporting on the current understanding, limitations and guidance on using surrogate endpoints in trials. Relevant literature will be identified through: (1) bibliographic databases; (2) grey literature; (3) handsearching of reference lists and (4) solicitation from experts. Data from eligible records will be thematically analysed into potential items for inclusion in extensions. The targeted review will search for RCT reports and protocols published from 2017 to 2021 in six high impact general medical journals. Trial corresponding author contacts will be listed as potential participants for the Delphi exercise.

Ethics and dissemination

Ethical approval is not required. The reviews will support the development of SPIRIT and CONSORT extensions for reporting surrogate primary endpoints (surrogate endpoint as the primary outcome). The findings will be published in open-access publications.

This review has been prospectively registered in the OSF Registration DOI: 10.17605/OSF.IO/WP3QH.
Analysis of nicotine dependence among daily smokers in China: evidence from a cross-sectional study in Zhejiang Province
Authors: Xu Yue , Xu Shuiyang , Wu Qingqing , Chen Heni , Yao Dingming , Hu XiuJing , Zhang Xuehai
Published: October 2022

Objective

The current study aimed to assess the level of nicotine dependence and its influencing factors among daily smokers in Zhejiang, China.

Setting

The 2020 Global Adult Tobacco Survey was conducted in Zhejiang, China.

Participants

1244 daily smokers aged ≥15 years.

Measures

Respondents were asked questions regarding their age, sex, residence, education level, occupation, household income, age of starting daily smoking and nicotine dependence.

Results

The findings revealed that 17.4% of daily smokers were highly dependent on nicotine, and the mean Fagerström Test for Nicotine Dependence score of daily smokers was (3.1±2.4). Age, educational level, occupation and age of starting daily smoking had significant effects on high nicotine dependence, whereas residence, sex and yearly household income were not significant factors. Compared with the age group ≥60 years, the proportion of respondents with a higher nicotine dependence level was lower in the age group of 15–39 years (OR=0.45). Daily smokers with a higher education level had a lower nicotine dependence level than those with a lower education level: primary or less (OR=3.07) and secondary (OR=2.62). Government institution staff (OR=4.02), unemployed persons (OR=3.08) and industrial workers (OR=2.46) had significantly higher nicotine dependence levels than did workers in the other occupation categories. People who started daily smoking at ≤18 years of age had a higher nicotine dependence level (OR=2.25) than those who started later.

Conclusions

This study elucidated that nearly one-fifth of daily smokers in Zhejiang, China, have high nicotine dependence levels. Improved health information on tobacco smoking is needed to encourage daily smokers to quit smoking, particularly among young males, unemployed persons and those with lower education levels.
How commercial actors used different types of power to influence policy on restricting food marketing: a qualitative study with policy actors in Thailand
Authors: Phulkerd Sirinya , Collin Jeff , Ngqangashe Yandisa , Thow Anne Marie , Schram Ashley , Huckel Schneider Carmen , Friel Sharon
Published: October 2022

Objectives

There is limited research focused explicitly on understanding how commercial actors use different forms of power to influence policy decision making in Thailand. This study aimed to identify how the food industry has used structural, instrumental and discursive power to influence policy on restricting food marketing in Thailand.

Study design

Qualitative study using in-depth semistructured interviews

Settings

Thailand.

Participants

The interviews were conducted with 20 participants (of a total of 29 invited actors) from government, civil society, technical experts, international organisation and the food and advertising industry. Interview data were identified in the transcripts and analysed using abductive methods.

Results

Non-commercial actors perceived the commercial actors’ structural power (its economic influence and structurally privileged position) as central to understanding the government having not implemented policy to restrict food marketing. The commercial actors’ instrumental power was observed through sponsorship, campaign and lobbying activities. Discursive power was used by the industry to shift responsibility away from the food companies and onto their customers, by focusing their messaging on freedom of consumer choice and consumer health literacy.

Conclusions

This study examined different types of power that commercial actors were perceived to use to influence policy to restrict food marketing in Thailand. The study showed arguments and institutional processes used to enhance commercial actors’ ability to shape the policy decision for nutrition, public opinion and the broader regulatory environment. The findings help governments and other stakeholders to anticipate industry efforts to counter policy. The findings also suggest the need for governance structures that counter industry power, including comprehensive monitoring and enforcement in policy implementation.
Koori Quit Pack mailout smoking cessation support for Aboriginal and Torres Strait Islander people who smoke: a feasibility study protocol
Authors: Kennedy Michelle , Mersha Amanual Getnet , Maddox Raglan , Chamberlain Catherine , Maidment Sian , O'Mara Peter , Segan Cathy , Hunt Marina , Clarke Kerindy , Donaldson Belinda , Bonevski Billie
Published: October 2022

Introduction

Smoking remains the leading preventable cause of death for Aboriginal and Torres Strait Islander people in Australia. Aboriginal and Torres Strait Islander people who smoke are more likely to make a quit attempt than their non-Aboriginal counterparts but less likely to sustain the quit attempt. There is little available evidence specifically for and by Indigenous peoples to inform best practice smoking cessation care.

The provision of a free Koori Quit Pack with optional nicotine replacement therapy sent by mail may be a feasible, acceptable and effective way to access stop smoking support for Aboriginal and Torres Strait Islander peoples.

Methods and analysis

An Aboriginal-led, multisite non-randomised single-group, pre–post feasibility study across three states in Australia will be conducted. Participants will be recruited via service-targeted social media advertising and during usual care at their Aboriginal Community Controlled Health Services. Through a process of self-referral, Aboriginal and Torres Strait Islander people who smoke daily will complete a survey and receive mailout smoking cessation support. Data will be collected over the phone by an Aboriginal Research Assistant. This pilot study will inform the development of a larger, powered trial.

Ethics and dissemination

Ethics approval has been obtained from the Aboriginal Health & Medical Research Council Ethics Committee of New South Wales (NSW) (#1894/21) and the University of Newcastle (#H-2022-0174). Findings will be reported through peer-reviewed journals and presentations at relevant local, national and international conferences. The findings will be shared with the NSW and Victoria Quitline, Aboriginal Health and Medical Research Council and Victorian Aboriginal Community Controlled Organisation and the National Heart Foundation.

Trial registration number

ACTRN12622000654752.
Retrospective spatial analysis of cases of COVID-19 in a single military accommodation block corridor, RMAS, January–March 21
Authors: Taylor Hannah , Routledge M , Fawcett J , Ross D
Published: October 2022

Shared ablutions and stairwells, corridor cross-ventilation and non-deliberate perflation (natural draft blowing through a space) are potential risk factors for COVID-19 transmission in corridor-based accommodation. This paper uses retrospective spatial analysis to identify potential built environmental risk factors during the January–March 2021 outbreak in Victory College, Royal Military Academy Sandhurst.

Distance was measured in units of single room spacing. Odds, ORs and 95% CIs were calculated to identify and measure associations between distance from exposure and having COVID-19. Distance response trends were assessed using Pearson’s χ2for trend test. Linear relationships were tested using the t-test or rank-sum test.

Stairwells and ablutions were not identified as likely sources of infection for all corridor occupants. Assuming occupants used their nearest ablutions, closer distance among those attributed to using ablutions 2 (one of four sets of ablutions), was identified as a risk factor (p=0.05). Testing distance response by χ2linear trend testing showed a potential association between nearest adjacent positive room and COVID-19 (p=0.06), strongest if dominant air movement along the corridor length was from the left (p=0.10) compared with the right (p=0.24).

Formal qualitative spatial analysis and environmental assessment of ventilation and air movement has a role in outbreak investigation in assessing factors related to the built environment. Environmental investigations would best inform outbreak investigations if undertaken contemporaneously. Pre-emptive and retrospective studies can help inform public health advice to military establishments in business continuity planning for isolation facilities, during outbreaks or in future development of the built environment.
Novel scoring system based on clinical examination for prediction of in-hospital mortality in acute coronary syndrome patients: a retrospective cohort study
Authors: Pramudyo Miftah , Bijaksana Transiska Liesmadona , Yahya Achmad Fauzi , Putra Iwan Cahyo Santosa
Published: October 2022

Background

This study aims to develop PADjadjaran Mortality in Acute coronary syndrome (PADMA) Score to predict in-hospital mortality in acute coronary syndrome (ACS) patients based on clinical examination only. Additionally, we also compared the predictive value of the PADMA Score with the Global Registry of Acute Coronary Events (GRACE), Canada Acute Coronary Syndrome (C-ACS), and The Portuguese Registry of Acute Coronary Syndromes (ProACS) risk scores.

Methods

This retrospective cohort study included all ACS patients aged≥18 years who were admitted to Dr. Hasan Sadikin Central General Hospital from January 2018 to January 2022. Patients’ demographic, comorbidities and clinical presentation data were collected and analysed using multivariate logistic regression to create two models of scoring system (probability and cut-off model) to predict in-hospital all-cause mortality. The area under the curve (AUC) among PADMA, GRACE, C-ACS and ProACS risk scores was compared using the fisher Z test.

Results

Multivariate regression analysis of 1359 patients showed that older age, history of cerebrovascular disease, tachycardia, high Shock Index and Killip class III and IV were independent mortality predictors and included in the PADMA Score. PADMA Score ranged from 0 to 20, with a score≥5 that can predict all-cause mortality with 82.78% sensitivity and 72.35% specificity. The difference in AUC between PADMA and GRACE scores was insignificant (p=0.126). Moreover, the AUC of the PADMA Score was significantly higher compared with the C-ACS (p=0.002) and ProACS risk scores (p<0.001).

Conclusion

PADMA Score is a simple scoring system to predict in-hospital mortality in ACS patients. PADMA Score≥5 showed an accurate discriminative capability to predict in-hospital mortality, comparable with the GRACE Score and superior to C-ACS and ProACS scores.