bluuebunny/crossref_metadata_2025 huggingface dataset:
Urinary profiles of methoxyphenamine and its metabolite after inhalation of methoxyphenamine smoke in humans: aiming to distinguish between active and passive exposure
Authors: Morinaka Haruka , Kaizaki-Mitsumoto Asuka , Morohoshi Hokuto , Uchida Naoki , Numazawa Satoshi
Published: January 2023

Purpose

Methamphetamine (METH) is commonly abused through smoking. However, the lack of evidence regarding differences in urinary METH excretion after its active and passive inhalation has resulted in complications where the accused claims passive exposure. This study aimed to determine the differences in urinary excretion after active and passive inhalation of the drug, using methoxyphenamine (MPA) as a model for METH.

Methods

Body temperature and locomotor activity were measured in mice as indicators of central nervous system toxicity. Six healthy adult male subjects were exposed to passive or active inhalation of MPA smoke in a small room, and urine samples were taken. MPA concentrations were measured using liquid chromatography–tandem mass spectrometry (LC–MS/MS).

Results

There were no signs of toxicity in mice exposed to MPA smoke, ensuring the safety of the clinical study. Urinary MPA concentrations were significantly lower with passive inhalation compared with those of active inhalation. The maximum urinary MPA concentration in passive inhalation was 13.4 ng/mL, which was 1/60 of active inhalation with 800 ng/mL. The urinary excretion in passive inhalation until 24 h was 8.21 μg, which was 1/76 of active inhalation with 625 μg.

Conclusions

Since METH and MPA are expected to be excreted similarly, urinary METH concentrations in passively exposed persons are expected to be lower than the cutoff value of the screening kit. If the urine screening test is positive, the suspect should be considered a METH user.

Trial registration number: jRCTs031210604, registration date: Feb. 9, 2022.
Distortional effects of separate accounting and formula apportionment on factor allocation
Authors: Ortmann Regina , Pummerer Erich
Published: January 2023

We examine distortions caused by tax base allocation systems–separate accounting (SA) or formula apportionment (FA)–with respect to the allocation of assets and workforce within multinational entities (MNEs). The effects of both systems are intensively debated by EU Member States as they are striving to implement a European tax system. Its introduction would lead to a switch from SA to FA. Moreover, Pillar One of the recent global tax reform includes a mix of both tax base allocation systems. We find that, against the claims of the EU, FA does not necessarily create lower distortions of the factor allocation. Decisive for that assessment is the level of profit shifting under SA. Our results indicate that, in tendency, the factor allocation is more severely distorted by FA when the profit shifting possibilities were rather low under SA. In contrast to former studies, we highlight the importance of analyzing the status quo under the recently applied system (SA) in order to be able to assess the consequences of a switch from SA to FA. Our results are interesting for policy-makers as they help anticipating reactions of MNEs to a change in the applied tax base allocation system and for companies as a basis for future tax planning.
Understanding the bioeconomy through its instruments: standardizing sustainability, neoliberalizing bioeconomies?
Authors: Vogelpohl Thomas
Published: January 2023

Sustainability standards have been one of the hopefuls for decades when it comes to ensuring the sustainability of biomass for the bioeconomy, especially in the wake of their evolvement from voluntary, non-governmental to hybrid, public–private governance instruments in recent years. In addition to doubts regarding their legitimacy and effectiveness, however, they have also been associated with a neoliberalization of nature that integrates natural resources into a free market logic. Drawing on a conceptual framework that builds on political ecology and the political sociology of policy instruments, this paper challenges this notion. To this end, it examines sustainability standards in three countries/regions particularly prominent for the bioeconomy—the EU, Brazil, and Indonesia—to illustrate how these can be differentiated in terms of their neoliberal orientation, and what can be inferred from this for the orientation and state of the respective bioeconomies. The results show that the introduction of sustainability standards is not necessarily accompanied by a neoliberalization of nature. Rather, it is shown that the standards and their specific designs—and thus also their intrinsic understanding of sustainability as integration—are primarily intended to serve the material interests of the state and the respective industrial factions, for which neoliberal configurations are sometimes seen as rather obstructive, sometimes as rather useful. The sustainability standards, and thus the bioeconomies for which they stand, therefore, rather serve as instruments to stay on the path of modernization and industrial development already taken or envisaged, or, put differently, as strategies to avoid social–ecological transformation.
Do civil engineering fronts emerge from interdisciplinary research?
Authors: He Jie , Yao Junlan , Chen Xin , Liu Fang , Zhu Hehua
Published: January 2023

Interdisciplinary research is considered a source of innovativeness and creativity, serving as a key mechanism for creating recombination necessary for the evolution of science systems. The aim of this study is to quantitatively establish the connection between interdisciplinary research and the research fronts that have recently emerged in civil engineering. The degree of interdisciplinarity of the research fronts was measured by developing metrics from bibliographic analyses. As indicated by the consistent increase in the metrics of interdisciplinarity over time, research fronts tend to emerge in studies with increasing diversity in the disciplines involved. The active disciplines involved in the fronts vary over time. The most active disciplines are no longer fundamental but those associated with energy, environment, and sustainable development, focusing on solutions to climate change and integrating intelligence technologies.
An analysis of the sensitivity of cutting force coefficients and their influence on the variability of stability diagrams
Authors: Bergmann Jim A. , Wöste Florian , Wiederkehr Petra
Published: January 2023

Process forces are an integral characteristic for the evaluation of machining operations, which can be calculated using, for instance, empirical models. An adequate prediction is essential, especially as it provides input data for subsequent models, e.g., for stability analysis of milling processes. However, the calibration of force model coefficients is not unambiguous and may have multiple local optima, which can significantly affect the accuracy of the approximation of the cutting forces. In this context, the selection of experiments used for calibration is crucial to obtain adequate results. In this paper, a systematic analysis of the selection of the required calibration experiments and the influence of the resulting parametrization of the coefficients on the predicted milling forces and the stability limit was conducted.Based on the results, designs of calibration experiments could be identified, with which the influence of varying undeformed chip thicknesses could be represented adequately. By applying these force model parameterizations for stability analysis, an improvement in the prediction of stability limits was achieved.
Encountering ideas about teaching and learning mathematics in undergraduate mathematics courses
Authors: Burroughs Elizabeth A. , Arnold Elizabeth G. , Álvarez James A. M. , Kercher Andrew , Tremaine Rachel , Fulton Elizabeth , Turner Kyle
Published: January 2023

We study the ideas about teaching and learning mathematics that undergraduate students generate when they encounter tasks designed to embed approximations of teaching practice in mathematics courses taken by a general population of students. These tasks attend to the dual goals of developing an understanding of mathematics content and an understanding of how teachers provide classroom experiences that foster mathematics learning. The study employs a qualitative, multiple-case study methodology, with four cases bounded by the content areas of abstract algebra, single variable calculus, discrete mathematics, and introductory statistics. The data for the study come from undergraduate students’ written work on mathematical tasks, interviews with a subset of students from each course, and interviews with each instructor throughout the term during which they implemented the tasks. Our findings indicate that students identified the broad applicability of teaching skills (discussed by 32 of the 61 interviewed students), recognized the value of examining hypothetical learners’ mathematical work (discussed by 59 of the 61 interviewed students), and reported empathy for hypothetical learners (discussed by 38 of the 61 interviewed students). These findings persisted across the course content and course levels we studied, leading us to conclude that our findings can transfer to additional mathematics courses in secondary mathematics teacher preparation.
Predictors of adolescents’ change in reading literacy: the role of reading strategies, reading motivation, and declarative metacognition
Authors: Heyne Nora , Gnambs Timo , Lockl Kathrin , Neuenhaus Nora
Published: January 2023

Declarative metacognition, use of reading strategies and reading motivation are important predictors of reading literacy. Moreover, reading motivation’s strong links with reading strategy use and declarative metacognition raise questions about whether motivation moderates the effects of the latter on reading literacy and its development during secondary school. Whereas most previous research implemented cross-sectional analyses focusing on one or more of the aforementioned variables, this study takes a longitudinal perspective to examine how reading motivation (reading for enjoyment versus interest), declarative metacognition and reading strategy use – directly or in interaction – concurrently predict reading literacy in Grade 7 and subsequent changes until Grade 9. Applying structural equation models to a sample of 4,037 secondary school students from the German National Educational Panel Study, the results revealed that reading for enjoyment and declarative metacognition had strong effects on reading literacy in Grade 7. In contrast, reading for interest exhibited a small negative effect and the effects of strategy use were negligible. Longitudinal analyses replicated the cross-sectional pattern with more modest effect sizes. Contrary to our hypotheses, the effects of declarative metacognition and reading strategy use on reading literacy at Grade 7 as well as changes in reading literacy until Grade 9 were not moderated by aspects of reading motivation. Finally, regarding the trajectory of reading literacy, our results challenge previous assumptions on the importance of reading for interest and reading strategies use, but also confirm earlier findings on the relevance of declarative metacognition and reading for enjoyment.
Quantum chemical studies on hydrogen bonds in helical secondary structures
Authors: Takano Yu , Kondo Hiroko X. , Nakamura Haruki
Published: January 2023

We present a brief review of our recent computational studies of hydrogen bonds (H-bonds) in helical secondary structures of proteins, α-helix and 310-helix, using a Negative Fragmentation Approach with density functional theory. We found that the depolarized electronic structures of the carbonyl oxygen of the ith residue and the amide hydrogen of the (i + 4)th residue cause weaker H-bond in an α-helix than in an isolated H-bond. Our calculations showed that the H-bond energies in the 310-helix were also weaker than those of the isolated H-bonds. In the 310-helices, the adjacent N–H group at the (i + 1)th residue was closer to the C=O group of the H-bond pair than the adjacent C=O group in the 310-helices, whereas the adjacent C=O group at the (i + 1)th residue was close to the H-bond acceptor in α-helices. Therefore, the destabilization of the H-bond is attributed to the depolarization caused by the adjacent residue of the helical backbone connecting the H-bond donor and acceptor. The differences in the change in electron density revealed that such depolarizations were caused by the local electronic interactions in their neighborhood inside the helical structure and redistributed the electron density. We also present the improvements in the force field of classical molecular simulation, based on our findings.
Expression systems for bovine rhodopsin: a review of the progress made in the Khorana laboratory
Authors: Reeves Philip J.
Published: January 2023

Here I will review the development of gene expression systems for production of bovine rhodopsin in the Khorana laboratory with particular focus on stable mammalian cell lines made using human embryonic kidney cells (HEK293S). The synthesis of a gene encoding bovine rhodopsin was completed in 1986. This gene was expertly designed with the built-in capacity for DNA duplex cassette replacement mutagenesis which made site-directed mutagenesis relatively straightforward. Intense effort was expended over several years in order to identify a gene expression system capable of producing rhodopsin in milligram amounts as required for biophysical studies. Mammalian expression systems, both transient and stable, were found to be the most favourable based on several criteria including receptor expression levels, correct folding and post translational processing, and capacity for purification of fully functional receptor. Transient expression using COS-1 cells was preferred for routine small-scale production of rhodopsin mutants, while HEK293S stable cell lines were used when milligram amounts of rhodopsin mutants were needed; for example, when conducting NMR studies.
A systematic scoping review of digital health technologies during COVID-19: a new normal in primary health care delivery
Authors: Ndayishimiye Costase , Lopes Henrique , Middleton John
Published: January 2023

This scoping review compiled information concerning digital health technologies (DHTs) evolution to support primary health care (PHC) during COVID-19 and lessons for the future of PHC. The identified literature was published during the COVID-19 peak years (2019–2021), retrieved from PubMed, Scopus, and Google Scholar, as well as hand searched on the internet. Predefined inclusion criteria were used, thematic analysis was applied, and reporting followed the PRISMA for Scoping Reviews.

A total of 46 studies were included in the final synthesis (40 articles, one book, two book chapters, one working paper, and two technical reports). These studies scrutinized various aspects of DHTs, entailing 19 types of DHTs with 20 areas of use that can be compressed into five bigger PHC functions: general PHC service delivery (teleconsultations, e-diagnosis, e-prescription, etc.); behavior promotion and digital health literacy (e.g., combating vaccine hesitancy); surveillance functions; vaccination and drugs; and enhancing system decision-making for proper follow-up of ongoing PHC interventions during COVID-19.

DHTs have the potential to solve some of the problems that have plagued us even prior to COVID-19. Therefore, this study uses a forward-looking viewpoint to further stimulate the use of evidence-based DHT, making it more inclusive, educative, and satisfying to people’s needs, both under normal conditions and during outbreaks. More research with narrowed research questions is needed, with a particular emphasis on quality assurance in the use of DHTs, technical aspects (standards for digital health tools, infrastructure, and platforms), and financial perspectives (payment for digital health services and adoption incentives).
Justice in Finnish Food Policies
Authors: Puupponen Antti , Huttunen Suvi , Kortetmäki Teea , Lähteenmäki-Uutela Anu , Kaljonen Minna
Published: January 2023

The need to create more sustainable food systems calls for careful attention to justice in making the transition. However, to achieve a just transition and create policies to support the goal of developing sustainable food systems, we need more knowledge of the ways current policies tackle justice. This knowledge can reveal blind spots and development needs and increase the transparency of potentially conflicting goals, which is essential for designing just transition policies. From the normative perspective of food justice, a food system should produce three principal outcomes: food security and nutrition, livelihoods and fair income, and environmental sustainability. In this article, we take these outcomes as the starting point to study how they relate to the distributive, procedural, and recognitive aspects of food justice in the context of Finnish food policies. Our data consist of Finnish policy strategies relating to the national food system and data from interviews with experts involved in the policy processes. Our results suggest that food security and farmer livelihoods have dominated justice related considerations at the cost of environmental sustainability. Although these are important for distributive justice and for recognizing vulnerabilities, the current setting reveals risks regarding the possibilities of transitioning to a low-carbon food system. The invisibility of the often-invisible groups is also notable in the policy documents. To promote justice more broadly, there should be greater emphasis on environmental sustainability as well as procedural and recognitive justice and opportunities for diverse people to participate in food policymaking.
A Fur-regulated type VI secretion system contributes to oxidative stress resistance and virulence in Yersinia pseudotuberculosis
Authors: Zuo Yuxin , Li Changfu , Yu Danyang , Wang Kenan , Liu Yuqi , Wei Zhiyan , Yang Yantao , Wang Yao , Shen Xihui , Zhu Lingfang
Published: January 2023

The type VI secretion system (T6SS) is a widespread protein secretion apparatus deployed by many Gram-negative bacterial species to interact with competitor bacteria, host organisms, and the environment. Yersinia pseudotuberculosis T6SS4 was recently reported to be involved in manganese acquisition; however, the underlying regulatory mechanism still remains unclear. In this study, we discovered that T6SS4 is regulated by ferric uptake regulator (Fur) in response to manganese ions (Mn2+), and this negative regulation of Fur was proceeded by specifically recognizing the promoter region of T6SS4 in Y. pseudotuberculosis. Furthermore, T6SS4 is induced by low Mn2+ and oxidative stress conditions via Fur, acting as a Mn2+-responsive transcriptional regulator to maintain intracellular manganese homeostasis, which plays important role in the transport of Mn2+ for survival under oxidative stress. Our results provide evidence that T6SS4 can enhance the oxidative stress resistance and virulence for Y. pseudotuberculosis. This study provides new insights into the regulation of T6SS4 via the Mn2+-dependent transcriptional regulator Fur, and expands our knowledge of the regulatory mechanisms and functions of T6SS from Y. pseudotuberculosis.
High-performance 800–1050 nm seed pulses based on spectral broadening and filtering for petawatt lasers
Authors: Liang Wenhai , Chen Renjing , Xu Yilin , Xuan Yaping , Wang Peng , Liu Jun , Li Ruxin
Published: January 2023

High-performance 86 μJ, 11.2 fs pulses with a spectrum range of 800–1050 nm are generated based on 1030 nm, 190 fs Yb femtosecond pulses by using multi-plate-based spectral broadening and filtering. Taking advantage of single beam configuration, the obtained pulses have excellent power and spectral stabilities. Since the output spectrum is obtained by spectrally filtering the broadened components, the temporal contrast of the output pulses is enhanced by at least four orders of magnitude. Together with the robust and simple setup, the proposed method is expected to be a competitive option for the generation of seed pulses for 10s–100s petawatt lasers.
Hypersonic flow over spherically blunted cone capsules for atmospheric entry. Part 2. Vibrational non-equilibrium effects
Authors: Martinez Schramm Jan , Hannemann Klaus , Hornung H.G.
Published: January 2023

Atmospheric entry capsules shaped as spherically blunted, large apex-angle cones are widely used in space missions. In Part 1 of this study (Hornung, Martinez Schramm & Hannemann, J. Fluid Mech., vol. 871, 2019, pp. 1097–1116) we explored flows over the two elements of the capsule shape, the sphere and the sharp cone with detached shock, theoretically and computationally. Using a large number of inviscid, perfect-gas computations, analytical functions of two independent variables, the normal-shock density ratio

$\varepsilon$

and a cone-angle parameter

$\eta$

(which is a function of

$\varepsilon$

and the cone half-angle

$\theta$

) were found for the dimensionless shock wave stand-off distance and the drag coefficient of a sharp cone. An analytical description was found for the shock stand-off distance in the transition from the 90

$^\circ$

cone (flat-faced cylinder) to the sphere. In Part 1, it was speculated that the perfect-gas results have relevance to non-equilibrium situations if the normal-shock density ratio is replaced by the density ratio based on the average density along the stagnation streamline. In Part 2, the investigation is extended to blunted-cone capsule shapes. High-precision force measurements and schlieren image analysis are performed in the High-Enthalpy Shock Tunnel Göttingen (HEG) of the German Aerospace Centre using air as the test gas, at conditions where vibrational non-equilibrium effects are significant. Accordingly, results are compared with viscous numerical predictions using different physico-chemical models. A theoretical model is constructed for the density profile along the stagnation streamline that is determined by the free stream conditions and gives the average density. Comparisons of the experimental and numerical results for the dimensionless shock stand-off distance and the drag coefficient, with the extension of the analytical functions of Part 1 to vibrationally relaxing flow, exhibit very good agreement in all of a range of geometries.
Reinforcement-learning-based control of convectively unstable flows
Authors: Xu Da , Zhang Mengqi
Published: January 2023

This work reports the application of a model-free deep reinforcement learning (DRL) based flow control strategy to suppress perturbations evolving in the one-dimensional linearised Kuramoto–Sivashinsky (KS) equation and two-dimensional boundary layer flows. The former is commonly used to model the disturbance developing in flat-plate boundary layer flows. These flow systems are convectively unstable, being able to amplify the upstream disturbance, and are thus difficult to control. The control action is implemented through a volumetric force at a fixed position, and the control performance is evaluated by the reduction of perturbation amplitude downstream. We first demonstrate the effectiveness of the DRL-based control in the KS system subjected to a random upstream noise. The amplitude of perturbation monitored downstream is reduced significantly, and the learnt policy is shown to be robust to both measurement and external noise. One of our focuses is to place sensors optimally in the DRL control using the gradient-free particle swarm optimisation algorithm. After the optimisation process for different numbers of sensors, a specific eight-sensor placement is found to yield the best control performance. The optimised sensor placement in the KS equation is applied directly to control two-dimensional Blasius boundary layer flows, and can efficiently reduce the downstream perturbation energy. Via flow analyses, the control mechanism found by DRL is the opposition control. Besides, it is found that when the flow instability information is embedded in the reward function of DRL to penalise the instability, the control performance can be further improved in this convectively unstable flow.
Gender and Ambition Among Potential Law Clerks
Authors: Badas Alex , Stauffer Katelyn E.
Published: January 2023

Law clerks hold immense responsibilities and exert influence over the judges they work with. However, women remain underrepresented in these positions. We argue that one reason for this underrepresentation is that – like potential political candidates – female law students may have lower levels of ambition compared to men. Using a survey of student editors at thirty-three top law reviews, we find that there is a gender gap in ambition for clerkships with the Supreme Court and Federal Courts of Appeal. Examining potential sources of this difference, we find that while women view themselves to be just as qualified for these positions as men, men are more willing to apply with lower feelings of qualification. Likewise, while women and men report similar levels of encouragement, more encouragement is required before women express ambition to hold these posts. The findings presented here have implications for research on judicial politics, political ambition, and women’s representation.
Chasing collective variables using temporal data-driven strategies
Authors: Chen Haochuan , Chipot Christophe
Published: January 2023

The convergence of free-energy calculations based on importance sampling depends heavily on the choice of collective variables (CVs), which in principle, should include the slow degrees of freedom of the biological processes to be investigated. Autoencoders (AEs), as emerging data-driven dimension reduction tools, have been utilised for discovering CVs. AEs, however, are often treated as black boxes, and what AEs actually encode during training, and whether the latent variables from encoders are suitable as CVs for further free-energy calculations remains unknown. In this contribution, we review AEs and their time-series-based variants, including time-lagged AEs (TAEs) and modified TAEs, as well as the closely related model variational approach for Markov processes networks (VAMPnets). We then show through numerical examples that AEs learn the high-variance modes instead of the slow modes. In stark contrast, time series-based models are able to capture the slow modes. Moreover, both modified TAEs with extensions from slow feature analysis and the state-free reversible VAMPnets (SRVs) can yield orthogonal multidimensional CVs. As an illustration, we employ SRVs to discover the CVs of the isomerizations of N-acetyl-N′-methylalanylamide and trialanine by iterative learning with trajectories from biased simulations. Last, through numerical experiments with anisotropic diffusion, we investigate the potential relationship of time-series-based models and committor probabilities.
Is it ethical to advertise unhealthy foods to children?
Authors: Boyland E.
Published: January 2023

The marketing of foods and non-alcoholic beverages (hereafter: food) high in fats, salt and/or sugar (HFSS) has been strongly implicated in the rising levels of childhood obesity worldwide. Multiple ethical concerns arise from the practice of exposing children to such marketing and efforts to monitor and restrict it through regulatory policies. There is considerable evidence that exposure to powerful food marketing messages affects children's food behaviours in ways that are detrimental to good dietary health. Children are particularly vulnerable to being exploited and deceived by food marketing messages based on their cognitive and developmental immaturity. HFSS food marketing also affects numerous child rights enshrined within the UN Convention on the Rights of the Child (of which the UK is a signatory) including the right to the enjoyment of the highest attainable standard of health. The debate has become somewhat polarised between the public health community's evidence-based assertion that all marketing is inherently exploitative and the rebuttal from food and marketing industry stakeholders that provided the marketing is ‘accurate and truthful’ and there is no ethical need to regulate. This polarisation is reflected in the complexity of policymaking decisions regarding the rationale for mandatory government-led policies or industry self-regulation. There are also ethical considerations inherent in the monitoring of children's food marketing exposure, particularly in the digital sphere, by researchers for the purposes of informing policy design, scope and implementation. This review paper will explore the latest evidence on these issues and consider the implications for public health research, policy, and practice.
Evaluation of perfusion index and left ventricular output changes in low cardiac output syndrome after arterial switch operation
Authors: Öztürk Dilek Yavuzcan , Öztürk Erkut , Dıkmen Rahime Tuten , Ozcanoglu Hatice Dilek , Toprak Hamza Halil , Tuzun Behzat , Tanıdır İbrahim Cansaran , Hatemi Ali Can , Cetinkaya Merih
Published: January 2023

Introduction:

Transposition of great arteries is one of newborns' most common cyanotic CHDs, and its treatment is arterial switch operation in the first days of life. Low cardiac output syndrome may develop in the early postoperative period. In this study, we evaluated perfusion index and left ventricular output blood flow changes in patients who underwent arterial switch operation and developed low cardiac output syndrome.

Methods:

This study was conducted prospectively in newborns with transposition of great arteries who underwent arterial switch operation between 1st August 2020 and 1st August 2022. Low cardiac output syndrome score and left ventricular output were investigated. Initially, 6th, 12th, 18th, and 24th hour perfusion index and left ventricular output values of patients with and without low cardiac output syndrome were recorded. The results were evaluated statistically.

Results:

A total of 60 patients were included in the study. Sex distribution was equal. The median age at the time of surgery was 5 days (interquartile range 3–7 days), and the median weight was 3.1 kg (interquartile range 2.9–3. 4). Low cardiac output syndrome was detected in 30% (n = 18) of cases. The median perfusion index of patients who developed low cardiac output syndrome was significantly lower at the 12th, 18th, and 24th hours (p < 0.05) (0.99 versus 1.25, 0.86 versus 1.21, and 0.96 versus 1.33, respectively). Similarly, the median left ventricular output of patients who developed low cardiac output syndrome was significantly lower at 12th, 18th, and 24th hours (p < 0.05) (95 versus 110 ml/kg/min, 89 versus 109 ml/kg/min, and 92 versus 112 ml/kg/min, respectively). There was a significant correlation between perfusion index values and left ventricular output at all measurements (r > 0.500, p < 0.05).

Conclusion:

Perfusion index and left ventricular output measurements decreased in newborns who developed low cardiac output syndrome after arterial switch operation, especially at 12th and 18th hours. Serial perfusion index and left ventricular output measurements can be instructive in predicting low cardiac output syndrome development.
Hemispheric Reconstructions: Post-Emancipation Social Movements and Capitalist Reaction in Colombia and the United States
Authors: Sanders James E.
Published: January 2023

As historians have begun to conceptualize the U.S. Civil War as a global event, so too must they consider Reconstruction as a political process that transcended national boundaries. The United States and Colombia both abolished slavery during civil wars; ex-slaves in both societies struggled for full citizenship and landholding, partially succeeding for a time; in both societies, a harsh reaction ripped full citizenship from the freedpeople and denied their claims to the land. These events, usually studied only as part of a national story in either the United States or Colombia, can also be understood, and perhaps be better understood, as a history of hemispheric and transnational processes—of race, of republican politics, of contests over equality, of capitalism. This essay examines the words and actions of historical actors, especially U.S. African Americans and afrocolombianos, to note the impressive commonalities of discourse (which was almost exactly the same in many cases) and political repertoires. This article focuses first on the agency of African Americans in both societies to create post-emancipation social movements for citizenship and land and then on the, largely successful, reactions against these movements.
Statistical Properties of Plateau‐Like Turbulence Spectra in the Martian Magnetosheath: MAVEN Observations
Authors: Jiang Wence , Li Hui , Liu Xiaodong , Verscharen Daniel , Wang Chi
Published: January 2023

The Martian magnetosheath provides us with a natural laboratory to study plasma turbulence in the presence of pickup ions and locally generated instabilities. Unlike the typical magnetic‐field spectra with a single spectral scaling at magnetohydrodynamics (MHD) scales in Earth's magnetosheath, the magnetic‐field spectra in the Martian magnetosheath during 4 years of Mars Atmosphere and Volatile EvolutioN observations frequently present an additional spectral break‐point with a shallow slope at MHD scales which we define as a plateau‐like spectral feature. The average occurrence rate of plateau‐like magnetic‐field spectra is 56.6% of our measurement intervals. At moderate pick‐up angles, the occurrence rate increases to a maximum of ∼70.0%. Furthermore, we present a positive correlation with the local ion density and anti‐correlations with the local βi and the solar Extreme Ultra Violet irradiance. A similar occurrence rate in the quasi‐perpendicular and the quasi‐parallel magnetosheath (60.1% vs. 52.9%) indicates that the plateau‐like spectra are more likely formed locally than in the upstream solar wind. Our results suggest that energy injection from pickup ion driven micro‐instabilities, for example, in the form of proton cyclotron waves, has insufficient time to evolve into a fully developed cascade in such a confined space like the Martian magnetosheath.
Martian Meteoric Mg+: Atmospheric Distribution and Variability From MAVEN/IUVS
Authors: Crismani M. M. J. , Tyo R. M. , Schneider N. M. , Plane J. M. C. , Feng W. , Carrillo‐Sánchez J. D. , Villanueva G. L. , Jain S. , Deighan J. , Curry S.
Published: January 2023

Since the discovery of atmospheric Mg+ on Mars in 2015 by the Mars Atmosphere and Volatile Evolution mission, there have been almost continuous observations of this meteoric ion layer in a variety of seasons, local times, and latitudes. Here, we present the most comprehensive set of observations of the persistent metal ion layer at Mars, constructing the first grand composite maps from pooled medians of subsamples of a metallic ion species. These maps demonstrate that Mg+ appears in almost all conditions when illuminated, with peak density values varying between 100 and 500 cm−3, dependent on season and local time. There exists significant latitudinal variation within a given season, indicating that Mg+ is not simply an inert tracer, but may instead be influenced by the meteoric input distribution and/or atmospheric dynamics and chemistry. Geographic maps of Mg+ density as a function of latitude and longitude indicate the influence of atmospheric tides, and there is no apparent correlation with remnant crustal magnetic fields. This work also presents counter‐intuitive results, such as a reduction of Mg+ ions in the northern hemisphere during Northern Winter in an apparent correlation with dust aerosols.
Proteins of the XMRV retrovirus implicated in chronic fatigue syndrome and prostate cancer are homologous to human proteins relevant to both diseases.
Authors: Carter Christopher
Published: January 2023

The XMRV retrovirus has been implicated in chronic fatigue syndrome and prostate cancer. A homology search comparing retroviral with human proteins revealed short contiguous amino acid strings (typically 5-8 aa) matching human proteins whose dysfunction might be expected to cause fatigue, including mitochondrial proteins related to oxidative phosphorylation, glutamate receptors and their synaptic scaffolds, muscular acetylcholine receptor scaffolds and structural proteins, components of the immune system, and phosphatidylinositol signalling inter alia. Viral proteins are also homologous to members of the oestrogen, peroxisome proliferator, and CREB activated receptor networks, all of which are implicated in prostate cancer, and to a protein, SRCAP, that controls the expression of the prostate-specific antigen. These short matches are often predicted to be antigenic, and antibodies to XMRV proteins may target their human homologues. This is supported by the presence of autoantibodies to muscarinic receptors , vimentin and LAMINB1 (all XMRV homologues) in chronic fatigue syndrome sufferers. Homologous XMRV proteins might also interfere with the protein interactomes of their human homologues. Viral mimicry of human proteins is extensive and often relevant to disease. For example Epstein-Barr viral proteins aligns with multiple sclerosis autoantigens, while HIV-1 proteins align with several components of the immune system. Mutant proteins in Huntington's disease and cystic fibrosis also align with proteins from common phages or viruses. This suggests a common theme of viral derived autoimmunity/network interference in many human disorders, which could radically change the shape of future therapy. Such viral mimicry likely relates to the idea that life evolved from viruses, leaving behind a legacy of viral derived human proteins whose homology to the current virome may be responsible for many human diseases and syndromes. Vaccination programmes or immunosuppression may be beneficial in many of these conditions.
PrOCoil - Advances in predicting two- and three-stranded coiled coils
Authors: Mahrenholz* Carsten , Abfalter* Ingrid , Bodenhofer Ulrich , Volkmer Rudolf , Hochreiter Sepp
Published: January 2023

*Overview* ∣ Coiled coils are usually described as consisting of two up to seven α-helices that are wrapped around each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies. Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad repeat, where n denotes the heptad number. In these repeats, a and d are hydrophobic amino acids at core positions crucial for the tertiary structure. In contrast, the polar positions b, c, and f are hydrophilic and e and g are charged residues.Due to their ability to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of larger protein complexes. Hence, they are in the focus of current research, for instance, as potential oncogenes and in the context of viral fusion proteins. Since structure and occurrence are well known, it might stand to reason that we have a clearly drawn picture of coiled coils. Most remarkably, however, the complex rules that govern oligomer formation, and thus the key to biological function, are poorly understood.*Approach* ∣ To find rules that determine oligomerization, we applied support vector machines and statistical methods to classify dimers and trimers on the basis of their amino acid sequences. The data set for this classification task was collected by searching the entire RCSB Protein Data Base for coiled coil structures, extracting the according amino acid sequences, and sorting them into types of oligomers based on properties of their 3D structures. We then extracted important features in the form of specific amino acids at certain key positions or amino acid patterns that are characteristic for each type of oligomer. Amino acid patterns were retrieved from our new coiled coil kernel, which detects amino acid co-occurrences. The relevance of the selected patterns was ensured by statistical tests and the excellent classification results measured by cross-validation.*Results* ∣ We discovered that a complex network of amino acid dependencies and sequence positions previously thought irrelevant to direct coiled coil interaction have an undeniable impact on stoichiometry. Our online-tool PrOCoil, classifies coiled coils with an outstanding accuracy of 86% and is also able to visualize the contribution of each individual amino acid to the overall oligomeric tendency of a given coiled coil sequence. A "web version":http://www.bioinf.jku.at/software/procoil/ and an "R package":http://www.bioinf.jku.at/software/procoil/procoilR.html of our prediction and profiling software (PrOCoil) are available to the scientific community.
Process Makna - A Semantic Wiki for Scientific Workflows
Authors: Paschke Adrian , Zhao Zhili
Published: January 2023

Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of a business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution.
Para-(benzoyl)-phenylalanine as a potential inhibitor against leptospirosis
Authors: Pradhan Dibyabhaba , Priyadarshini Vani , Munikumar Manne , Umamaheswari Amineni
Published: January 2023

Leptospirosis is a zoonotic disease of global concern caused by Leptospira interrogans. Subtractive genomic approach, metabolic pathway analysis and multi strain genome comparisons of Leptospira interrogans serovars had proposed 88 common drug targets from 5,124 genes of serovar Copenhageni and 4,727 genes of serovar Lai. Three potential drug targets (lpxC, lpxD and lpxB) were identified from Lipid A biosynthesis process of lipopolysaccharide (LPS) biosynthesis pathway. Lipid A is one of the three components of LPS that contains multiple hydrophobic fatty acid chains which anchor the LPS into the bacterial membrane. Designing inhibitory drug molecules targeting Lipid A biosynthesis would dissolve the structural integrity of membrane structure leading to cell lysis and death of Leptospira. LpxC being the first enzyme among the three drug targets of Lipid A biosynthesis pathway; blocking the enzyme with suitable inhibitor would stop synthesizing substrates for lpxD and lpxB. Also, there is no alternative mechanism in Leptospira to replace the catalytic activity rendered by lpxC; hence, the drug target was selected herein for rational drug design. The lpxC tertiary structure was modeled incorporating inhibitor BB-78485 using Modeller9v8. The lpxC 3D structure reliability was assessed through various model validation techniques. Ligand based virtual screening was performed from one million entries of ligand.Info metadatabase. The leads were ranked using computational docking technique of Glidev5.5. Twelve leads with better binding affinity than BB-78485 (XPGscore -7.98 Kcal/mol) were proposed as potential inhibitors of lpxC. Para-(benzoyl)-phenylalanine, the best ranked inhibitor (XPGscore -10.34Kcal/mol), would be intriguing for rational drug design against leptospirosis.
Use of Semantic Technologies - Semantic Chemistry
Authors: Todor Alexandru , Paschke Adrian , Heineke Stephan
Published: January 2023

Our Chemical e-Science Information Cloud (ChemCloud) – a Semantic Web based eScience infrastructure – integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and our well-established databases at FIZ Chemie such as ChemInform for organic reaction data, InfoTherm the leading source for thermophysical data, Chemisches Zentralblatt, the complete chemistry knowledge from 1830 to 1969, and ChemgaPedia the largest and most frequented e-Learning platform for Chemistry and related sciences in German language.
Cu2+ uptake by Chlorococcum hemicolum - A Xeric Chlorophycean Alga
Authors: Harish Mr. , Sundaramoorthy S. , Kumar Devendra , Vaijapurkar S.G.
Published: January 2023

Bioremediation of copper by xeric chlorophycean bioremediator, Chlorococcum hemicolum was investigated. The growth rates at various concentrations of Cu2+ were assessed in terms of protein level and 8 mg L-1 (37.67 % level in growth kinetics) is the tolerance limit. Absorption/adsorption kinetics was estimated after 240 hrs of Cu2+ treatments. Absorptions were higher than adsorption with maximum accumulation factor (AF) of 1.40. The Cu2+ concentration and absorption were linearly related (r = 0.99; p>0.01). Other biochemical parameters like total sugar, chlorophyll and carotenoids were also quantified to correlate the state of metabolism and these exhibited reduction due to heavy metal stress.
BRIF Workshop Introduction
Authors: Cambon-Thomsen Anne
Published: January 2023

This presentation aims at introducing the place of BRIF in the landscape of data sharing, the BRIF concept, a presentation of the working group, the ongoing debates and the workshop objectives.
Bio-resources for sharing: which communities and what specific needs
Authors: Metspalu Andres
Published: January 2023

Biobanks are an important source to obtain samples and data for research purposes for a wide array of communities. In fact, sharing of bio-resources and data is an integral part of a biobank's role. For an effective partnership a list of requirements or needs have to be met, assuring quality of the resources shared as well as quality of the collaboration in general. Tracking and documenting bio-resource sharing and collaborations of a biobank can be seen as one indicator of the "impact" a biobank has to the field. As an example, the practice of the Estonian Genome Center of the University of Tartu is presented.
D2RQ Platform – Treating Non-RDF Databases as Virtual RDF Graphs
Authors: Oldakowski Radoslaw
Published: January 2023

D2RQ is a complete solution to map and expose relational databases as RDF.
SBGN Activity Flow Update
Authors: Mi Huaiyu
Published: January 2023

SBGN Activity Flow specification was released in September 2009. In this talk, a brief review is provided on the specification, and a number of issues raised by the community are discussed. Particular focus was on the issue of graphical representation of entity decoration of a biological activity. A number of proposals from the community are discussed in detail.
Models of Multifunctional Central Pattern Generators: Polyrhythmic Bursting
Authors: Shilnikov Andrey
Published: January 2023

We demonstrate a motif of three reciprocally inhibitory cells that is able to produce multiple patterns of bursting rhythms. Through the examination of the qualitative geometric structure of two-dimensional maps for phase lag between the cells we reveal the organizing centers of emergent polyrhythmic patterns and their bifurcations, as the asymmetry of the synaptic coupling is varied. The presence of multistability and the types of attractors in the network are shown to be determined by the duty cycle of bursting. This analysis does not require knowledge of the equations that model the system, and so provides a powerful new approach to studying regulatory networks. Thus, the approach is applicable to a variety of biological phenomena beyond motor control.