bluuebunny/crossref_metadata_2025 huggingface dataset:
Smartphone and teamwork as a methodological tool for teaching and learning physics
Authors: Malndonado E A , Ramírez P , Avendaño W R
Published: January 2022

This research is based on the usefulness of mobile phones as a tool for students to learn about uniform rectilinear motion in vertical free fall, based on experimental practice. To evaluate whether these mobile devices allow better learning on the subject, a pre-test/post-test design was carried out with 43 students participating in the 9th grade in natural sciences. McNemar and Stuart-Maxwell non-parametric tests were applied. The proposal on the experimental practice gave satisfactory results when comparing the pre-test and post-test, in the analysis of the particular and global form of the answers.
High-energy bow tie multi-pass cells for nonlinear spectral broadening applications
Authors: Heyl Christoph M , Seidel Marcus , Escoto Esmerando , Schönberg Arthur , Carlström Stefanos , Arisholm Gunnar , Lang Tino , Hartl Ingmar
Published: January 2022

Multi-pass cells (MPCs) have emerged as very attractive tools for spectral broadening and post-compression applications. We discuss pulse energy limitations of standard MPCs considering basic geometrical scaling principles and introduce a novel energy scaling method using a MPC arranged in a bow tie geometry. Employing nonlinear pulse propagation simulations, we numerically demonstrate the compression of 125 mJ, 1 ps pulses to 50 fs using a compact 2 m long setup and outline routes to extend our approach into the Joule-regime.
2022 roadmap on 3D printing for energy
Authors: Tarancón Albert , Esposito Vincenzo , Torrell Marc , Di Vece Marcel , Son Jae Sung , Norby Poul , Bag Sourav , Grant Patrick S , Vogelpoth A , Linnenbrink S , Brucki M , Schopphoven T , Gasser A , Persembe Elif , Koufou Dionysia , Kuhn Simon , Ameloot Rob , Hou Xu , Engelbrecht Kurt , Bahl Christian R H , Pryds Nini , Wang Jie , Tsouris Costas , Miramontes Eduardo , Love Lonnie , Lai Canhai , Sun Xin , Kærn Martin Ryhl , Criscuolo Gennaro , Pedersen David Bue
Published: January 2022

The energy transition is one of the main challenges of our society and therefore a major driver for the scientific community. To ensure a smart transition to a sustainable future energy scenario different technologies such as energy harvesting using solar cells or windmills and chemical storage in batteries, super-capacitors or hydrogen have to be developed and ultimately deployed. New fabrication approaches based on additive manufacturing and the digitalization of the industrial processes increase the potential to achieve highly efficient and smart technologies required to increase the competitiveness of clean energy technologies against fossil fuels. In this frame, the present roadmap highlights the tremendous potential of 3D printing as a new route to fully automate the manufacturing of energy devices designed as digital files. This article gives numerous guidelines to maximize the performance and efficiency of the next generation of 3D printed devices for the energy transition while reducing the waste of critical raw materials. In particular, the paper is focused on the current status, present challenges and the expected and required advances of 3D printing for the fabrication of the most relevant energy technologies such as fuel cells and electrolysers, batteries, solar cells, super-capacitors, thermoelectric generators, chemical reactors and turbomachinery.
Fault tolerance and noise immunity in freespace diffractive optical neural networks
Authors: Panda Soumyashree S , Hegde Ravi S
Published: January 2022

Free-space diffractive optical networks are a class of trainable optical media that are currently being explored as a novel hardware platform for neural engines. The training phase of such systems is usually performed in a computer and the learned weights are then transferred onto optical hardware (‘ex-situ training’). Although this process of weight transfer has many practical advantages, it is often accompanied by performance degrading faults in the fabricated hardware. Being analog systems, these engines are also subject to performance degradation due to noises in the inputs and during optoelectronic conversion. Considering diffractive optical networks trained for image classification tasks on standard datasets, we numerically study the performance degradation arising out of weight faults and injected noises and methods to ameliorate these effects. Training regimens based on intentional fault and noise injection during the training phase are only found marginally successful at imparting fault tolerance or noise immunity. We propose an alternative training regimen using gradient based regularization terms in the training objective that are found to impart some degree of fault tolerance and noise immunity in comparison to injection based training regimen.
On the numbers 𝑛 relatively prime to Ω(𝑛)-𝜔(𝑛)
Authors: Ding Yuchen
Published: January 2022

Let

Ω
(
n
)

\Omega (n)

and

ω
(
n
)

\omega (n)

be the number of all prime factors and different prime factors of

n
n

, respectively. An elegant result of Alladi showed that the probability of

(
n
,
Ω
(
n
)
)
=
1

(n,\Omega (n))=1

or

(
n
,
ω
(
n
)
)
=
1

(n,\omega (n))=1

is

6

/

π
2

6/\pi ^2

. In the other aspect, denoting by

d
k

d_k

the density of the numbers

n
n

with

Ω
(
n
)
−
ω
(
n
)
=
k

\Omega (n)-\omega (n)=k

, then another elegant formula of Rényi states that

d
k

∼

c
0

/

2
k

d_k\sim c_0/2^k

as

k
k

tends to infinity, where
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="c 0 equals left-parenthesis 1 slash 4 right-parenthesis product Underscript p greater-than 2 Endscripts left-parenthesis 1 minus left-parenthesis p minus 1 right-parenthesis Superscript negative 2 Baseline right-parenthesis Superscript negative 1">

c
0

=
(
1

/

4
)

∏

p
>
2

(
1
−
(
p
−
1

)

−
2

)

−
1

c_0=(1/4)\prod _{p>2}(1-(p-1)^{-2})^{-1}

. In this paper, we investigate the numbers

n
n

which are relatively prime to

Ω
(
n
)
−
ω
(
n
)

\Omega (n)-\omega (n)

. Let

D

\mathscr {D}

denote the set of such numbers. It is proved that there exists a positive constant

c
1

c_1

such that

D

(
x
)
=

c
1

x
+

O

ε

(

x

log

1
+
ε

⁡
x
)

\mathscr {D}(x)=c_1x+O_{\varepsilon }(\sqrt {x}\log ^{1+\varepsilon }x)

for any

ε
>
0

\varepsilon >0

.
A remark on Strichartz estimates for Schrödinger equations with slowly decaying potentials
Authors: Taira Kouichi
Published: January 2022

In this short note, we prove Strichartz estimates for Schrödinger operators with slowly decaying singular potentials in dimension two. This is a generalization of the recent results by Mizutani, which are stated for dimension greater than two. The main ingredient of the proof is a variant of Kato’s smoothing estimate with a singular weight.
Neuropsychological Performance in Autoimmune Limbic Encephalitis: Evidence from an Immunotherapy-Naïve Cohort
Authors: Mueller Christoph , Langenbruch Lisa , Rau Johanna M H , Brix Tobias , Strippel Christine , Dik Andre , Golombeck Kristin S , Mönig Constanze , Johnen Andreas , Räuber Saskia , Wiendl Heinz , Meuth Sven G , Bölte Jens , Kovac Stjepana , Melzer Nico
Published: January 2022

Objective

Autoimmune limbic encephalitis (ALE) is characterized by memory impairment, psychiatric symptoms, and epileptic seizures. Though, the neuropsychological profile of ALE is not yet well defined. However, there is some evidence that neuropsychological impairments might exceed those related to the limbic system and that different autoantibodies (AABs) are associated with distinguishable pattern of neuropsychological impairments. We provide a comprehensive presentation of neuropsychological performance of ALE in an immune therapy-naïve sample.

Methods

We retrospectively analyzed 69 immunotherapy-naïve ALE-patients (26 seropositive—[8 LGI1-, 4 CASPR2-, 2 GABAB-R-, 3 Hu-, 4 GAD65-, 2 Ma2-, 2 unknown antigen, and 1 Yo-AABs] and 43 seronegative patients, mean age 56.0 years [21.9–78.2], mean disease duration 88 weeks [0–572]). Neuropsychological evaluations comprised of the domains memory, attention, praxis, executive functions, language, social cognition, and psychological symptoms. We compared these functions between seronegative −, seropositive patients with AABs against intracellular neural antigens and seropositive patients with AABs against surface membrane neural antigens.

Results

No effect of AAB group on neuropsychological performance could be detected. Overall, ALE predominantly presents with deficits in long-term memory and memory recognition, autobiographical-episodic memory loss, impairment of emotion recognition, and depressed mood. Furthermore, deficits in praxis of pantomimes and imitations, visuo-construction, and flexibility may occur.

Conclusion

ALE shows a wide spectrum of neuropsychological impairments, which might exceed the limbic system, with no evidence of differences between AAB groups. Neuropsychological assessment for diagnosing ALE should include long-term memory, memory recognition, autobiographical-episodic memory, emotion recognition, and a detailed investigation of depression.
Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia
Authors: Wang Ran , Zheng Xubin , Wang Jun , Wan Shibiao , Song Fangda , Wong Man Hon , Leung Kwong Sak , Cheng Lixin
Published: January 2022

The advances in single-cell RNA sequencing (scRNA-seq) technologies enable the characterization of transcriptomic profiles at the cellular level and demonstrate great promise in bulk sample analysis thereby offering opportunities to transfer gene signature from scRNA-seq to bulk data. However, the gene expression signatures identified from single cells are typically inapplicable to bulk RNA-seq data due to the profiling differences of distinct sequencing technologies. Here, we propose single-cell pair-wise gene expression (scPAGE), a novel method to develop single-cell gene pair signatures (scGPSs) that were beneficial to bulk RNA-seq classification to transfer knowledge across platforms. PAGE was adopted to tackle the challenge of profiling differences. We applied the method to acute myeloid leukemia (AML) and identified the scGPS from mouse scRNA-seq that allowed discriminating between AML and control cells. The scGPS was validated in bulk RNA-seq datasets and demonstrated better performance (average area under the curve [AUC] = 0.96) than the conventional gene expression strategies (average AUC$\le$ 0.88) suggesting its potential in disclosing the molecular mechanism of AML. The scGPS also outperformed its bulk counterpart, which highlighted the benefit of gene signature transfer. Furthermore, we confirmed the utility of scPAGE in sepsis as an example of other disease scenarios. scPAGE leveraged the advantages of single-cell profiles to enhance the analysis of bulk samples revealing great potential of transferring knowledge from single-cell to bulk transcriptome studies.
Quantifying Environmental Mitigation of Aerosol Viral Load in a Controlled Chamber With Participants Diagnosed With Coronavirus Disease 2019
Authors: Parhizkar Hooman , Dietz Leslie , Olsen-Martinez Andreas , Horve Patrick F , Barnatan Liliana , Northcutt Dale , Van Den Wymelenberg Kevin G
Published: January 2022

Background

Several studies indicate that coronavirus disease 2019 (COVID-19) is primarily transmitted within indoor spaces. Therefore, environmental characterization of severe acute respiratory syndrome coronavirus 2 viral load with respect to human activity, building parameters, and environmental mitigation strategies is critical to combat disease transmission.

Methods

We recruited 11 participants diagnosed with COVID-19 to individually occupy a controlled chamber and conduct specified physical activities under a range of environmental conditions; we collected human and environmental samples over a period of 3 days for each participant.

Results

Here we show that increased viral load, measured by lower RNA cycle threshold (CT) values, in nasal samples is associated with higher viral loads in environmental aerosols and on surfaces captured in both the near field (1.2 m) and far field (3.5 m). We also found that aerosol viral load in far field is correlated with the number of particles within the range of 1–2.5 µm. Furthermore, we found that increased ventilation and filtration significantly reduced aerosol and surface viral loads, while higher relative humidity resulted in lower aerosol and higher surface viral load, consistent with an increased rate of particle deposition at higher relative humidity. Data from near field aerosol trials with high expiratory activities suggest that respiratory particles of smaller sizes (0.3–1 µm) best characterize the variance of near field aerosol viral load.

Conclusions

Our findings indicate that building operation practices such as ventilation, filtration, and humidification substantially reduce the environmental aerosol viral load and therefore inhalation dose, and should be prioritized to improve building health and safety.
A cross-sectional study of the practice types of US adult primary care physician specialists
Authors: Young Richard A , Wilkinson Elizabeth , Barreto Tyler W , Newton Rebecca L , Turebylu Akshaj , Bullock Dana
Published: January 2022

Background

Many physicians listed as primary care in databases such as the American Medical Association (AMA) Masterfile do not provide traditional ambulatory primary care.

Objective

To compare physicians listed in the AMA Masterfile as primary care physician (PCPs) specialists for adult patients with their actual practice type.

Methods

We conducted a cross-sectional study of the AMA Masterfile report for PCPs who care for adults (listed as family medicine, internal medicine, medicine-paediatrics, and geriatrics) in the summer and fall of 2018 (spring of 2019 for Hartford, CT) in the primary counties of 8 metropolitan areas across the United States. We searched multiple websites to determine the actual practice type of each physician in the study counties. We correlated the 2 datasets: the AMA Masterfile list vs the results of our searches.

Results

Family physicians were more likely to function as traditional ambulatory PCPs than internists [1,738/2,101 (82.7%) vs 1,241/2,025 (60.9%), P < 0.001], and less likely to be hospitalists [83/2,101 (4.0%) vs 631/2,025 (31.0%), P < 0.001]. Other practice types included urgent care [105 (5.0%) family physicians, 16 (0.8%) internists] and emergency medicine [49 (2.3%) family physicians, 20 (1.0%) internists]. The AMA Masterfile identified 4,892 practicing PCPs for adult patients in the study counties, of which 3,084 (63.0%) matched by location and ambulatory PCP practice type [3,695 (75.5%) for ambulatory PCP practice type only].

Conclusions

We provide an updated estimate using a unique methodology to estimate how to correct the AMA Masterfile for PCPs who actually provide traditional ambulatory primary care to adult patients.
1. The Starting Point
Authors: John Peter
Published: January 2022

This chapter discusses what makes British politics distinctive and recognizable: its parliamentary democracy, uncodified constitution, and pattern of party government. It begins by outlining some recent events that have made British or UK politics so fascinating and controversial. The chapter then describes the political system, particularly the institutional rules that affect what happens and govern how politics takes place. Parliament, composed of the House of Commons, House of Lords, and the Crown, is the supreme legal authority in the UK. The chapter also provides a summary of the British constitution. It places the UK in a comparative context, to be studied alongside other nation states. Finally, the chapter sets out the information and concepts that help in understanding the nature of and limits to British democracy.
10. Delegating Upwards
Authors: John Peter
Published: January 2022

This chapter highlights the challenges presented by international politics. Much of what happens in British politics occurs because of Britain's relationship to the international stage. Relationships to other states, international bodies, and the international economy need to be managed by the UK's political leaders and foreign and defence bureaucracies, to manage how to deploy Britain's voice in international matters. Then there is the delegation of powers to international organizations and the making of treaties. The chapter specifically examines foreign policy and focuses on how functions are delegated to international organizations. It tells the story of the European Union (EU) as one of the most important international delegations culminating in the story of Brexit. This leads to a discussion of the UK's defence and security role. One key theme of the chapter is how success and failure in international politics feed back into domestic politics.
3. Growth Unlimited
Authors: Dryzek John S.
Published: January 2022

This chapter covers a response to the discourse of limits which stresses the unlimited capacity of ingenious humans to overcome ecological limits, especially when they are organized in capitalist markets. For Prometheans, long term trends show environmental improvement and declining resource scarcity, such that economic growth can therefore go on forever. This Promethean discourse has often been advanced by market economists, and has often been highly influential in government, especially in the United States. More recently a Promethean environmentalism looks forward to a ‘good Anthropocene’ in which government too plays a role in bringing natural systems under benign human control, so that technologies such as geoengineering can be used effectively against problems such as climate change. In the background of Promethean argument is an older cornucopian discourse that stresses natural abundance of resources and the capacity of ecosystems to absorb pollutants. Ecologists and Earth systems scientists are not convinced and remain critical of Promethean discourse.
5. Leave It to the People
Authors: Dryzek John S.
Published: January 2022

This chapter treats democracy as a way of approaching problems through involving a variety of interests and actors along with citizens in interactive problem solving within the basic institutional structure of liberal capitalist democracy. It is manifested in for example public consultation, alternative dispute resolution, policy dialogue, lay citizen deliberation, and public inquiries. The turn from government to more decentralized and networked governance can be seen as a kind of democratic pragmatism, though networks do not always enhance democracy. This problem solving must be a flexible process that involves many voices and cooperation across a plurality of perspectives. The degree of participation with which pragmatists are happy often corresponds to existing liberal democracies and enables congruence between the demands of rationality in social problem solving and democratic values, though efforts exist to deepen both the democratic and problem-solving capacity of participation.
9. Changing People
Authors: Dryzek John S.
Published: January 2022

This chapter delves into the world of radical green discourse, which is a diverse and lively place, home to a wide variety of ideologies, parties, movements, groups, and thinkers that befits imaginative and radical leanings. Those that stress green consciousness believe the way people experience and regard the world in which they live is the key to green change and confronting ecological crisis. This prioritization of consciousness is widespread in the green movement, among deep ecologists, ecological justice and citizenship advocates, bioregionalists, ecofeminists, ecotheologists, and lifestyle greens. Critics stress that consciousness change will not produce the desired results so long as environmentally destructive structures such as states and capitalist markets continue to dominate.
1. Why Study IR?
Authors: Sørensen Georg , Møller Jørgen , Jackson Robert
Published: January 2022

Introduction to International Relations provides a concise introduction to the principal international relations theories and approaches, and explores how theory can be used to analyse contemporary issues. Throughout the text, the chapters encourage readers to consider the strengths and weaknesses of the theories presented, and the major points of contention between them. In so doing, the text helps you to build a clear understanding of how major theoretical debates link up with each other, and how the structure of the discipline of international relations is established. The book places a strong emphasis throughout on the relationship between theory and practice, carefully explaining how theories organise and shape our view of the world. It also shows how a historical perspective can often refine theories and provide a frame of reference for contemporary problems of international relations. Topics include realism, liberalism, International Society, International Political Economy, social constructivism, post-positivism in international relations, major issues in IPE and IR, and foreign policy. Each chapter ends by discussing how different theories have attempted to integrate or combine international and domestic factors in their explanatory frameworks. The final chapter is dedicated to discussing the state of the world: are we seeing world chaos or world order? The text is accompanied by an Online Resource Centre, which includes: short case studies, review questions, annotated web links, and a flashcard glossary.
6. International Political Economy: Marxism, Mercantilism, Liberalism
Authors: Sørensen Georg , Møller Jørgen , Jackson Robert
Published: January 2022

This chapter examines the three most important classical theories within the field of International Political Economy (IPE): mercantilism, economic liberalism, and neo-Marxism. It considers the relationship between politics and economics, and between states and markets in world affairs, that IR has to be able to grasp. It suggests that IPE is about wealth, poverty, and power, about who gets what in the international economic and political system. The outlook of mercantilism has much in common with realism, while economic liberalism is an addition to liberalism. Mercantilism and economic liberalism thus represent views on IPE that are basically realist and liberal. The chapter concludes with a discussion about the original theoretical position of Marxism and how this has inspired neo-Marxist IPE theories.
10. Major Issues in IPE: Economic versus Political Power, Development, Globalization, How to Study the Real World
Authors: Sørensen Georg , Møller Jørgen , Jackson Robert
Published: January 2022

This chapter examines four major issues in International Political Economy (IPE). The first concerns power and the relationship between politics and economics, and more specifically whether politics is in charge of economics or whether it is the other way around. The second issue deals with development and underdevelopment in developing countries. The third is about the nature and extent of economic globalization, and currently takes places in a context of increasing inequality between and inside countries. The fourth and final issue concerns how to study the real world from an IPE perspective and it pits the hard science American School against the more qualitative and normative British School.
2. The history of EU institutions:
Authors: Dehousse Renaud , Magnette Paul
Published: January 2022

EU institutions have frequently been reformed since the origins of what is now the European Union (EU), and particularly so over the past twenty years. This chapter explains why and how this quasi-constant change has taken place. It begins by identifying five phases in this history: the founding, consolidation, relaunch, adaptation, and the current phase of reaction to functional challenges. The chapter then assesses the respective weight of state interests, ideas, and institutions in the evolution of EU institutions. In retrospect, institutional change in the EU appears to have followed a functionalist logic, leading to complex compromises that, in turn, prompt regular calls for ‘simplification’ and democratization.
6. The European Parliament:
Authors: Servent Ariadna Ripoll , Costa Olivier
Published: January 2022

The European Parliament (EP) symbolizes many of the struggles that characterize the process of European integration and is at the core of many theoretical and empirical debates about representation, accountability, and legitimacy. This chapter draws on a variety of theoretical approaches to explain the complex role the EP plays in the political system of the European Union (EU). It starts with a brief overview of the history and functions of the assembly, followed by a theoretical explanation of its empowerment over time. Then, it determines the extent to which the EP is capable of influencing policymaking, both in legislative and non-legislative domains, as well as for the appointment of the Commission. It presents the political structure of the assembly and underlines the role of parliamentary groups and committees. It discusses the representativeness of the EP and the democratic quality of its internal functioning. Finally, it addresses current and future challenges for the EP.
11. The institutions of Economic and Monetary Union:
Authors: Hodson Dermot
Published: January 2022

Since 1999, a subset of EU member states—known collectively as the euro area—has delegated exclusive competence for monetary policy to the European Central Bank (ECB), while giving limited powers to the European Commission, ECOFIN, and the Eurogroup in other areas of economic policy. The euro crisis provided the first major test of the Economic and Monetary Union (EMU), as a sovereign debt crisis spread between member states and threatened to tear the single currency apart. The ECB and two new institutions—the European Stability Mechanism and Euro Summit—helped to keep the euro area together but at significant economic and political cost. EU institutions were better prepared for the initial economic consequences of the COVID-19 pandemic, but the crisis still produced important institutional changes. The COVID-19 recovery fund Next Generation EU gives the Commission and Council a major new role in economic policy, albeit a temporary one for now. The EMU illustrates three key dimensions of EU institutional politics: the tension between intergovernmental versus supranational institutions, leaders versus followers, and legitimacy versus contestation. It also reveals the explanatory power of new institutionalism among other theoretical perspectives.
Challenging the Surge of Inflammatory Bowel Disease: The Role of the China Crohn’s and Colitis Foundation in the Healthcare Landscape of Inflammatory Bowel Disease
Authors: Peng Lishan , Hu Shurong , Yu Qiao , Chen Yan
Published: January 2022

Inflammatory bowel disease (IBD) is a chronic and lifelong disease, and patients must ultimately learn to live with and manage the condition. With advances in diagnostics and treatment in IBD, healthcare professionals (HCPs) and patients are now concerned with both quality of care (QOC) and quality of life (QOL). The China Crohn’s and Colitis Foundation (CCCF) is committed to improving the QOC and QOL for IBD patients by garnering social resources. This paper details how CCCF has worked for better IBD management over the past 5 years. The foundation has 4 main projects: education programs for IBD HCPs and patients, support activities, public awareness and advocacy, and research programs. CCCF is an increasingly influential public welfare organization providing advocacy for IBD patients in China. The foundation is now entering the next stage of its development in pursuing professional operations and helping to solve the social problems experienced by IBD patients. The CCCF ultimately plans to pioneer reforms in China’s medical system and hopefully provide a successful example of IBD advocacy for developing countries to emulate.
Patriarchy is a Judge: Young Feminists and LGBTQ+ Activists Performing Transitional Justice in Chile
Authors: Hiner Hillary , Badilla Manuela , López Ana , Zúñiga-Fajuri Alejandra , Hatibovic Fuad
Published: January 2022

In recent years many articles have discussed transitional justice in Chile with respect to the Pinochet dictatorship, and some of these have had a gendered perspective. In this article we seek to build upon this research, but touching upon recent human rights violations and political sexual violence that took place in Chile during the 18-O Uprising (October 2019 to January 2020). Key in our argument is that young feminists and sexual dissidents have been crucial in re-conceptualizing and making visible the Piñera government’s human rights abuses, both appealing to previous human rights and feminist discourses and practices, as well as inventing new, creative ways of expressing their claims for transitional justice and reparations, like the ‘Rapist in Your Path’ performance. We will use discussion groups and interviews with young feminists and LGBTQ+ people, as well as a revision of relevant national and international human rights reports, to make our argument.
Fiscal Responses to Foreign Aid: Does the Permanence of Aid Matter?
Authors: Abdelwahed Loujaina
Published: January 2022

This paper shows that failing to distinguish between permanent (low frequency) and temporary (high frequency) aid results in misleading estimates of the fiscal responses to aid. I focus on foreign grants received by sub-Saharan Africa over the period 1990–2016, and I separately identify the fiscal responses to permanent and temporary foreign aid. Permanent and temporary aid generates fiscal responses that are meaningfully different on the components of expenditure and domestic borrowing. Temporary aid is associated with fiscal adjustments, such as lower domestic borrowing and increasing recurrent expenditure, while permanent aid is associated with higher public investments. Results provide important policy implications regarding the macroeconomic effects of foreign aid and the design of aid programs to developing countries.
Hoop-like role of the cytosolic interface helix in Vibrio PomA, an ion-conducting membrane protein, in the bacterial flagellar motor
Authors: Nishikino Tatsuro , Sagara Yugo , Terashima Hiroyuki , Homma Michio , Kojima Seiji
Published: January 2022

Vibrio has a polar flagellum driven by sodium ions for swimming. The force-generating stator unit consists of PomA and PomB. PomA contains four transmembrane regions and a cytoplasmic domain of approximately 100 residues, which interacts with the rotor protein, FliG, to be important for the force generation of rotation. The 3D structure of the stator shows that the cytosolic interface (CI) helix of PomA is located parallel to the inner membrane. In this study, we investigated the function of CI helix and its role as stator. Systematic proline mutagenesis showed that residues K64, F66 and M67 were important for this function. The mutant stators did not assemble around the rotor. Moreover, the growth defect caused by PomB plug deletion was suppressed by these mutations. We speculate that the mutations affect the structure of the helices extending from TM3 and TM4 and reduce the structural stability of the stator complex. This study suggests that the helices parallel to the inner membrane play important roles in various processes, such as the hoop-like function in securing the stability of the stator complex and the ion conduction pathway, which may lead to the elucidation of the ion permeation and assembly mechanism of the stator.
Diptera (Dryomyzidae, Fanniidae, Muscidae, Piophilidae) Associated With Pig Carcasses in a Forest Habitat of Poland: Sex-Related Patterns of Visitation and Effectiveness of Sampling Methods
Authors: Bajerlein Daria , Jarmusz Mateusz , Gregor Aleksandra , Grzywacz Andrzej
Published: January 2022

Our knowledge on many necrophilous dipterans was limited for a long time mainly due to taxonomic issues. Therefore, findings on the sex-related associations with pig carcasses in Dryomyzidae, Fanniidae, Muscidae, and Piophilidae are presented. Moreover, the effectiveness of pitfall traps and sweep nets in fly sampling were compared, since the correct method of collecting insects is critical for the development and application of entomological tools for forensic purposes. The trapped numbers of all species differed significantly in respect to both sexes. The sex ratios were strongly female-biased in most species of Muscidae and in Fanniidae. More females were also collected in Piophilidae, but the proportion of males was higher when compared to muscids. Within Dryomyzidae, the sex ratio differed according to species. Only Dryomyza flaveola (Fabricius, 1794) (Diptera: Dryomyzidae) and Muscina pascuorum (Meigen, 1826) (Diptera: Muscidae) had male-biased sex ratios. Differences in residency patterns between sexes in Stearibia nigriceps (Meigen, 1826) (Diptera: Piophilidae), Liopiophila varipes (Meigen, 1830) (Diptera: Piophilidae), and D. flaveola were statistically insignificant. All studied species were recorded for each sampling method. The effect of the sampling method on the number of individuals was statistically significant for all dipterans but Piophilidae. Pitfall traps outcompeted the aerial sweep net in representing Dryomyzidae and Muscidae, whereas both methods were almost equally effective in the collection of Piophilidae. A varied effectiveness of sampling methods was observed in Fanniidae. The sampling method significantly affected the determination of the appearance time of flies on carcasses, but the effect of species and sampling method was insignificant. Implications for forensic entomology are discussed.
Comparing compact object distributions from mass- and presupernova core structure-based prescriptions
Authors: Patton Rachel A , Sukhbold Tuguldur , Eldridge J J
Published: January 2022

Binary population synthesis (BPS) employs prescriptions to predict final fates, explosion or implosion, and remnant masses based on one or two stellar parameters at the evolutionary cutoff imposed by the code, usually at or near central carbon ignition. In doing this, BPS disregards the integral role late-stage evolution plays in determining the final fate, remnant type, and remnant mass within the neutrino-driven explosion paradigm. To highlight differences between a popular prescription, which relies only on the core and final stellar mass and emerging methods, which rely on a star’s presupernova core structure, we generate a series of compact object distributions using three different methods for a sample population of single and binary stars computed in BPASS. The first method estimates remnant mass based on a star’s carbon–oxygen (CO) core mass and final total mass. The second method uses the presupernova core structure based on recent bare CO-core models combined with a parameterized explosion criterion to first determine final fate and remnant type, then remnant mass. The third method associates presupernova helium-core masses with remnant masses determined from public explosion models which rely implicitly on core structure. We find that the core-/final mass-based prescription favours lower mass remnants, including a large population of mass gap black holes, and predicts neutron star masses which span a wide range, whereas the structure-based prescriptions favour slightly higher mass remnants, mass gap black holes only as low as 3.5 M⊙, and predict NS mass distributions which cluster in a narrow range.
Reanalysis of c-type RR Lyrae variable BE Dor, period modulations and possible mechanism
Authors: Li L-J , Qian S-B , Zhu L-Y
Published: January 2022

We reanalysed the c-type RR Lyrae star BE Dor (MACHO 5.4644.8, OGLE-LMC-RRLYR-06002) that had been discovered to show cyclic period changes. The photometric data of several sky surveys (DASCH, MACHO, OGLE, ASAS-SN, and TESS) were used for analyses. The O − C diagram and pulsation period obtained from Fourier analysis show significant period modulations in BE Dor. However, different from the previous viewpoint, the changes are quasi-periodic and abrupt. Therefore, the light-traveltime effect caused by the companion motion cannot explain the changes. Noting a same subtype star KIC 9453114 with similar phenomena has a high macroturbulent velocity, and the degree of O − C changes seem to be positively correlated with these velocities, we consider that the mechanism leading to period modulation should be caused by the interaction between turbulent convection and magnetic field activity in the ionization zone, i.e. the viewpoint of Stothers. It may not explain the general Blazhko effect but should explain such period modulations in BE Dor and those other c-type RR Lyrae stars. We hope our discoveries and viewpoints can provide some information and inspiration for relevant research.
Folic acid deficiency increases sensitivity to DNA damage by glucose and methylglyoxal
Authors: Donnellan Leigh , Simpson Bradley S , Dhillon Varinderpal S , Costabile Maurizio , Fenech Michael , Deo Permal
Published: January 2022

Type 2 diabetes (T2D) is associated with elevated frequencies of micronuclei (MNi) and other DNA damage biomarkers. Interestingly, individuals with T2D are more likely to be deficient in micronutrients (folic acid, pyridoxal-phosphate, cobalamin) that play key roles in one-carbon metabolism and maintaining genomic integrity. Furthermore, it has recently been shown that deficiencies in these nutrients, in particular folic acid leaves cells susceptible to glucose-induced DNA damage. Therefore, we sought to investigate if the B lymphoblastoid WIL2-NS cell line cultured under folic acid-deficient conditions was more sensitive to DNA damage induced by glucose, or the reactive glycolytic byproduct methylglyoxal (MGO) and subsequent advanced glycation endproduct formation. Here, we show that only WIL2-NS cultured under folic acid-deficient conditions (23 nmol/l) experience an increase in MNi frequency when exposed to high concentrations of glucose (45 mmol/l) or MGO (100 µmol/l). Furthermore, we showed aminoguanidine, a well-validated MGO and free radical scavenger was able to prevent further MNi formation in folic acid-deficient cells exposed to high glucose, which may be due to a reduction in MGO-induced oxidative stress. Interestingly, we also observed an increase in MGO and other dicarbonyl stress biomarkers in folic acid-deficient cells, irrespective of glucose concentrations. Overall, our evidence shows that folic acid-deficient WIL2-NS cells are more susceptible to glucose and/or MGO-induced MNi formation. These results suggest that individuals with T2D experiencing hyperglycemia and folic acid deficiency may be at higher risk of chromosomal instability.
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection
Authors: Rigden Daniel J , Fernández Xosé M
Published: January 2022

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.
The fork protection complex recruits FACT to reorganize nucleosomes during replication
Authors: Safaric Barbara , Chacin Erika , Scherr Matthias J , Rajappa Lional , Gebhardt Christian , Kurat Christoph F , Cordes Thorben , Duderstadt Karl E
Published: January 2022

Chromosome replication depends on efficient removal of nucleosomes by accessory factors to ensure rapid access to genomic information. Here, we show this process requires recruitment of the nucleosome reorganization activity of the histone chaperone FACT. Using single-molecule FRET, we demonstrate that reorganization of nucleosomal DNA by FACT requires coordinated engagement by the middle and C-terminal domains of Spt16 and Pob3 but does not require the N-terminus of Spt16. Using structure-guided pulldowns, we demonstrate instead that the N-terminal region is critical for recruitment by the fork protection complex subunit Tof1. Using in vitro chromatin replication assays, we confirm the importance of these interactions for robust replication. Our findings support a mechanism in which nucleosomes are removed through the coordinated engagement of multiple FACT domains positioned at the replication fork by the fork protection complex.
Supramolecular CRISPR-OFF switches with host–guest chemistry
Authors: Xiong Wei , Liu Xingyu , Qi Qianqian , Ji Huimin , Liu Fengbo , Zhong Cheng , Liu Simin , Tian Tian , Zhou Xiang
Published: January 2022

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) technology is a powerful tool in biology and medicine. However, the safety and application of this technology is hampered by excessive activity of CRISPR machinery. It is particularly important to develop methods for switching off CRISPR activity in human cells. The current study demonstrates the concept of supramolecular CRISPR-OFF switches by employing host-guest chemistry. We demonstrate that the CRISPR systems show considerable tolerance to adamantoylation on guide RNAs (gRNAs), whereas supramolecular complexation tremendously affects the function of adamantoyl gRNAs. Host–guest chemistry is demonstrated to be novel and effective tools to reduce unwanted excessive activities of CRISPR complexes in human cells. This work indicates considerable potential of supramolecular strategy for controlling and enhancing CRISPR systems.
A Cas6-based RNA tracking platform functioning in a fluorescence-activation mode
Authors: Gao Feng , Zheng Ke , Li You-Bo , Jiang Feng , Han Chun-Yu
Published: January 2022

Given the fact that the localization of RNAs is closely associated with their functions, techniques developed for tracking the distribution of RNAs in live cells have greatly advanced the study of RNA biology. Recently, innovative application of fluorescent protein-labelled Cas9 and Cas13 into live-cell RNA tracking further enriches the toolbox. However, the Cas9/Cas13 platform, as well as the widely-used MS2-MCP technique, failed to solve the problem of high background noise. It was recently reported that CRISPR/Cas6 would exhibit allosteric alteration after interacting with the Cas6 binding site (CBS) on RNAs. Here, we exploited this feature and designed a Cas6-based switch platform for detecting target RNAs in vivo. Conjugating split-Venus fragments to both ends of the endoribonuclease-mutated Escherichia coli Cas6(dEcCas6) allowed ligand (CBS)-activated split-Venus complementation. We name this platform as Cas6 based Fluorescence Complementation (Cas6FC). In living cells, Cas6FC could detect target RNAs with nearly free background noise. Moreover, as minimal as one copy of CBS (29nt) tagged in an RNA of interest was able to turn on Cas6FC fluorescence, which greatly reduced the odds of potential alteration of conformation and localization of target RNAs. Thus, we developed a new RNA tracking platform inherently with high sensitivity and specificity.
Liquid biopsy in gliomas: A RANO review and proposals for clinical applications
Authors: Soffietti Riccardo , Bettegowda Chetan , Mellinghoff Ingo K , Warren Katherine E , Ahluwalia Manmeet S , De Groot John F , Galanis Evanthia , Gilbert Mark R , Jaeckle Kurt A , Le Rhun Emilie , Rudà Roberta , Seoane Joan , Thon Niklas , Umemura Yoshie , Weller Michael , van den Bent Martin J , Vogelbaum Michael A , Chang Susan M , Wen Patrick Y
Published: January 2022

Background

There is an extensive literature highlighting the utility of blood-based liquid biopsies in several extracranial tumors for diagnosis and monitoring.

Methods

The RANO (Response Assessment in Neuro-Oncology) group developed a multidisciplinary international Task Force to review the English literature on liquid biopsy in gliomas focusing on the most frequently used techniques, that is circulating tumor DNA, circulating tumor cells, and extracellular vesicles in blood and CSF.

Results

ctDNA has a higher sensitivity and capacity to represent the spatial and temporal heterogeneity in comparison to circulating tumor cells. Exosomes have the advantages to cross an intact blood-brain barrier and carry also RNA, miRNA, and proteins. Several clinical applications of liquid biopsies are suggested: to establish a diagnosis when tissue is not available, monitor the residual disease after surgery, distinguish progression from pseudoprogression, and predict the outcome.

Conclusions

There is a need for standardization of biofluid collection, choice of an analyte, and detection strategies along with rigorous testing in future clinical trials to validate findings and enable entry into clinical practice.