bluuebunny/crossref_metadata_2025 huggingface dataset:
DPHL: A DIA Pan-Human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Authors: Zhu Tiansheng , Zhu Yi , Xuan Yue , Gao Huanhuan , Cai Xue , Piersma Sander R. , Pham Thang V. , Schelfhorst Tim , Haas Richard R.G.D. , Bijnsdorp Irene V. , Sun Rui , Yue Liang , Ruan Guan , Zhang Qiushi , Hu Mo , Zhou Yue , Van Houdt Winan J. , Le Large Tessa Y.S. , Cloos Jacqueline , Wojtuszkiewicz Anna , Koppers-Lalic Danijela , Böttger Franziska , Scheepbouwer Chantal , Brakenhoff Ruud H. , van Leenders Geert J.L.H. , Ijzermans Jan N.M. , Martens John W.M. , Steenbergen Renske D.M. , Grieken Nicole C. , Selvarajan Sathiyamoorthy , Mantoo Sangeeta , Lee Sze S. , Yeow Serene J.Y. , Alkaff Syed M.F. , Xiang Nan , Sun Yaoting , Yi Xiao , Dai Shaozheng , Liu Wei , Lu Tian , Wu Zhicheng , Liang Xiao , Wang Man , Shao Yingkuan , Zheng Xi , Xu Kailun , Yang Qin , Meng Yifan , Lu Cong , Zhu Jiang , Zheng Jin'e , Wang Bo , Lou Sai , Dai Yibei , Xu Chao , Yu Chenhuan , Ying Huazhong , Lim Tony K. , Wu Jianmin , Gao Xiaofei , Luan Zhongzhi , Teng Xiaodong , Wu Peng , Huang Shi'ang , Tao Zhihua , Iyer Narayanan G. , Zhou Shuigeng , Shao Wenguang , Lam Henry , Ma Ding , Ji Jiafu , Kon Oi L. , Zheng Shu , Aebersold Ruedi , Jimenez Connie R. , Guo Tiannan
Published: August 2020

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.
Legal Governance on Fintech Risks: Effects and Lessons from China
Authors: YUAN Kang , XU Duoqi
Published: August 2020

Fintech risks have a special type of structure and formation mechanism; regular updates and a complete financial legal system are needed to implement an effective legal governance. China’s fintech development is leading the world, but its lagging legal development does not match its rank in the field. Due to the difficult co-ordination of regulatory goals, unclear allocation of regulatory power, insufficient risk identification, and incomplete regulation tools, China’s legal governance on fintech risks has been swinging between the paths of suppressive, indulging, and adaptive regulation. It is urgently necessary to follow the fintech-risk law and fully tap into the local resources and explore the intervening path with more proactivity, foresight, and refined characteristics, through specification of the legal status and governing power of the intervening entity, the institutional basis and legal effect of interventional means, and the governing key and constitutional rules of intervening objects, to establish a legal-governance system on fintech risks that is innovation-friendly, regulatorily effective, and safe at the bottom line, fully covering the whole process.
Investigation and Analysis of 108 Cases of Home Isolated Patients With Mild COVID-19
Authors: Li Hang , Peng Yuan-Yuan , Lu Jin-Ping
Published: August 2020

Background:

Coronavirus disease 2019 (COVID-19) began to spread across Wuhan, China, by the end of 2019, and patients were unable to be hospitalized because medical resources were limited.

Methods:

A questionnaire survey was conducted among 108 participants with mild COVID-19 who have isolated at home under the guidance of doctors. The results of the questionnaire and outpatient data were integrated to evaluate participants’ compliance with various epidemic prevention measures.

Results:

During isolation, most participants were able to follow epidemic prevention measures under the guidance of doctors. After 14 d from the start of isolation, 45.37% of the participants recovered. Approximately half of the participants were relieved of symptoms, and most of them were transferred to mobile cabin hospitals to continue isolation. Three participants with worsening symptoms were transferred to the designated hospitals. There were no deaths of the participants, but there were 7 family members that were infected.

Conclusions:

During a period of home isolation under the guidance of a doctor, individuals can comply with epidemic prevention measures and symptoms can be improved. Scientific home isolation may be an effective way to relieve the strain of medical and social resources during the epidemic of COVID-19.
Methicillin-resistant Staphylococcus aureus (MRSA) screening upon inpatient hospital admission: Is there concordance between nasal swab results and samples taken from skin and soft tissue?
Authors: Petry Natasha J. , Montgomery Anna D. , Hammer Kimberly D. P. , Lo Tze Shien
Published: August 2020

Background:

Methicillin-resistant Staphylococcus aureus (MRSA) infections are associated with increased mortality and healthcare costs. In 2007, a Veterans’ Affairs (VA) hospital implemented a MRSA nasal screening program, following a nationwide VA mandate, in an effort to reduce healthcare-associated MRSA infections.

Objective:

To evaluate the correlation between the nasal screening results for MRSA and culture results of wound and tissue sites.

Methods:

This retrospective study was conducted on inpatients at our VA hospital. Patients were included if they had undergone nasal screening for MRSA plus culture of a wound or tissue site within 30 days of hospital admission.

Results:

In total, 337 patients underwent nasal screening and wound culture and 211 underwent nasal screening and wound and tissue cultures. The prevalence of MRSA nasal colonization was 14.2% for wound samples and 15.2% for tissue samples. The sensitivities of MRSA nasal screening for detecting MRSA were 64.6% for wound cultures and 65.5% for tissue cultures. Specificities were 86.2% and 88.8% for wound and tissue cultures, respectively. The positive predictive values (PPVs) were 43.7% and 51.2% for wound and tissue cultures, respectively, and the negative predictive values (NPVs) were high at 93.6% and 93.5%, respectively.

Conclusions:

In cases of wound or tissue samples for which culture results are pending, a negative MRSA nasal swab may be a component of the decision to withhold or discontinue MRSA-active agents.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid contamination of surfaces on a coronavirus disease 2019 (COVID-19) ward and intensive care unit
Authors: Redmond Sarah N. , Dousa Khalid M. , Jones Lucas D. , Li Daniel F. , Cadnum Jennifer L. , Navas Maria E. , Kachaluba Nataliya M. , Silva Sandra Y. , Zabarsky Trina F. , Eckstein Elizabeth C. , Procop Gary W. , Donskey Curtis J.
Published: August 2020

On coronavirus disease 2019 (COVID-19) wards, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid was frequently detected on high-touch surfaces, floors, and socks inside patient rooms. Contamination of floors and shoes was common outside patient rooms on the COVID-19 wards but decreased after improvements in floor cleaning and disinfection were implemented.
From History Book to Digital Humanities Database: The Basic Annals of the Shiji
Authors: Li Bin , Li Yaxin , Yang Qian , Wang Yaqi , Chen Rui
Published: August 2020

The Shiji (史記 Records of the Grand Historian) is of great value for Chinese history before 90 BCE. Many online databases provide character-based search of the Shiji. We go beyond simple search by creating an word-based open-access database of the Basic Annals (本纪) of the Shiji that allows the exploration of relationships between persons and the relationships between persons and named places.
Using Philologic For Digital Textual and Intertextual Analyses of the Twenty-Four Chinese Histories 二十四史
Authors: Tharsen Jeffrey , Gladstone Clovis
Published: August 2020

What does it mean to be able to study Chinese history at scale? What methods, tools, and approaches will allow us to understand Chinese history and historiography from a larger perspective over the longue durée, including linguistic, philosophical, ethnographic, and literary concerns? In this article we present what we feel is one potential key to answering these questions and provide an overview of the utility and value of harnessing this framework for text-based historical research as a means to expand one's scholarship to virtually limitless scales.
Introduction to the Special Issue
Authors: Bol Peter K.
Published: August 2020

This issue of the Journal of Chinese History aims to take stock of the effects of “the digital” on the study of Chinese history. We are doing this through a combination of research articles whose authors have made extensive use of digital resources and technologies and a set of introductions to non-commercial, open-access utilities and tools that scholars have created to support research in a digital environment. These hardly exhaust the universe of research or tools.
Director Networks, Political Connections, and Earnings Quality in Malaysia
Authors: Abdul Wahab Effiezal Aswadi , Jamaludin Mohd Faizal , Agustia Dian , Harymawan Iman
Published: August 2020

This article investigates the relationship between director networks and earnings quality in Malaysia. Using data on 4,416 individual directors who served on the boards of 745 firms listed on Bursa, Malaysia during 2011, we map the entire network of directors and generate measures to reflect the size and quality of information within the network. We find a negative and significant relationship between the overall connectedness of a director's network and the firm's earnings quality. In addition, we find a negative and significant relationship between the political connectedness of the director's network and earnings quality. Our results are robust for different measures of earnings quality.
The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0–55 cal kBP)
Authors: Reimer Paula J , Austin William E N , Bard Edouard , Bayliss Alex , Blackwell Paul G , Bronk Ramsey Christopher , Butzin Martin , Cheng Hai , Edwards R Lawrence , Friedrich Michael , Grootes Pieter M , Guilderson Thomas P , Hajdas Irka , Heaton Timothy J , Hogg Alan G , Hughen Konrad A , Kromer Bernd , Manning Sturt W , Muscheler Raimund , Palmer Jonathan G , Pearson Charlotte , van der Plicht Johannes , Reimer Ron W , Richards David A , Scott E Marian , Southon John R , Turney Christian S M , Wacker Lukas , Adolphi Florian , Büntgen Ulf , Capano Manuela , Fahrni Simon M , Fogtmann-Schulz Alexandra , Friedrich Ronny , Köhler Peter , Kudsk Sabrina , Miyake Fusa , Olsen Jesper , Reinig Frederick , Sakamoto Minoru , Sookdeo Adam , Talamo Sahra
Published: August 2020

Radiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
SHCal20 Southern Hemisphere Calibration, 0–55,000 Years cal BP
Authors: Hogg Alan G , Heaton Timothy J , Hua Quan , Palmer Jonathan G , Turney Chris SM , Southon John , Bayliss Alex , Blackwell Paul G , Boswijk Gretel , Bronk Ramsey Christopher , Pearson Charlotte , Petchey Fiona , Reimer Paula , Reimer Ron , Wacker Lukas
Published: August 2020

Early researchers of radiocarbon levels in Southern Hemisphere tree rings identified a variable North-South hemispheric offset, necessitating construction of a separate radiocarbon calibration curve for the South. We present here SHCal20, a revised calibration curve from 0–55,000 cal BP, based upon SHCal13 and fortified by the addition of 14 new tree-ring data sets in the 2140–0, 3520–3453, 3608–3590 and 13,140–11,375 cal BP time intervals. We detail the statistical approaches used for curve construction and present recommendations for the use of the Northern Hemisphere curve (IntCal20), the Southern Hemisphere curve (SHCal20) and suggest where application of an equal mixture of the curves might be more appropriate. Using our Bayesian spline with errors-in-variables methodology, and based upon a comparison of Southern Hemisphere tree-ring data compared with contemporaneous Northern Hemisphere data, we estimate the mean Southern Hemisphere offset to be 36 ± 2714C yrs older.
When prey becomes killer: does a double lethal attack on a blue shark reveal a precise defensive strategy in young swordfish?
Authors: Romeo Teresa , Battaglia Pietro , Macaluso Domenico , Tagliavia Giuseppe , Vicchio Teresa Manuela , Falautano Manuela , Serena Fabrizio , Andaloro Franco
Published: August 2020

In this paper a rare case of a double swordfish mortal attack against an adult blue shark (Prionace glauca) is reported. A female blue shark, with a total length of 3 m, was found stranded along the southern Sicilian coast (Strait of Sicily, Mediterranean Sea) on 30 May 2018. The analysis of this carcass revealed the presence of two swordfish bill fragments, impaled in the shark head; the former on the snout, the latter near the eye. The results of anatomical and computed tomography scanning analysis on the head of the blue shark showed that the larger bill fragment (19.7 cm) probably determined the death of this animal, having been impaled in a vital point, just behind the right eye. The analysis of both these events and other similar swordfish-shark interactions reported in the literature makes possible the hypothesis that young swordfish specimens put in place a precise defensive strategy against their potential predators or competitors, aimed at hitting vulnerable and vital points and delivering a mortal blow.
Talking about frailty: health professional perspectives and an ideological dilemma
Authors: Cluley Victoria , Martin Graham , Radnor Zoe , Banerjee Jay
Published: August 2020

Frailty is increasingly used in clinical settings to describe a physiological state resulting from a combination of age-related co-morbidities. Frailty also has a strong ‘lay’ meaning that conjures a particular way of being. Recent studies have reported how frail older people perceive the term frailty, showing that frailty is often an unwanted and resisted label. While there are many scores and measures that clinicians can use to determine frailty, little has been published regarding how health-care professionals use and make sense of the term. This paper reports the findings of a qualitative study that explored how health professionals perceive frailty. Forty situated interviews were conducted with health-care professionals working in an emergency department in the English Midlands. The interview talk was analysed using discourse analysis. The findings show that the health professionals negotiate an ‘ideological dilemma’ – a tension between contradictory sets of meanings and consequences for action – based on their ‘lay’ and clinical experience of the term frailty. It is concluded that this dilemma could have a negative impact on the assessment of frailty depending on the system of assessment used.
Pleasure and time in senior dance: bringing temporality into focus in the field of ageing
Authors: Krekula Clary
Published: August 2020

Population ageing and discourses on healthy ageing have led to a growing interest in social dancing for seniors. While senior dance has been described as both common and contributing to good health, the fundamental connection between bodily and temporal dimensions has been fairly neglected. As a result, there is a risk of portraying dance among older adults as a general practice, while at the same time the senior dance's potential to shed light on relations between temporality and ageing is not utilised. Based on qualitative interviews with 25 women and eight men, aged 52–81, in Sweden, whose main leisure activity was dancing, this article sheds light on this knowledge gap by illustrating the pleasurable experiences of senior dance. The results illustrate that the pleasurable experiences of dancing can be understood as three different experiences of temporality: embodied experience of extended present, an interaction with synchronised transcending subjectivities and age identities with unbroken temporality. The results also highlight the central role that temporal aspects play in processes around subjectivities in later life, as well as the close connection between ageing embodiment and temporality. They also illustrate the ability of dance to create wellbeing, not only through its physical elements, but also through the sociality that constitutes the core of dancing. In light of these results, the article argues that the temporal processes relate to individuals’ diverse relationship with the world and that they therefore play a central role in subjective experiences of ageing.
Using elicited imitation to measure global oral proficiency in SLA research: A close replication study
Authors: McManus Kevin , Liu Yingying
Published: August 2020

We closely replicated Wu and Ortega (2013), who found that an elicited imitation test (EIT) reliably distinguished low-level from high-level language abilities among instructed second language (L2) learners of Mandarin Chinese. The original study sampled learners (1) from second-level courses to represent low-level language abilities and (2) from third-, fourth- and graduate-level courses to represent high-level language abilities. Results showed high-level learners outperformed low-level learners on the Mandarin EIT. Our close replication used Wu and Ortega's (2013) materials and procedures in order to understand (1) the extent to which this EIT can additionally distinguish between finer-grained language abilities and (2) the ways in which the broad grouping of language abilities in the high group may have contributed to the findings. Sixty-five instructed L2 learners from four instructional levels were assigned to one of three groups: Beginner (first-level courses), Low (second-level courses), High (third- and fourth-level courses). Consistent with the original study, our results showed clear between-group differences, indicating that the EIT can distinguish between both broad (beginner vs high) and finer-grained (beginner vs low, low vs high) language abilities. These results are discussed in light of the original study's findings with implications for proficiency assessment in second language acquisition (SLA) research.
Robustness of randomized rumour spreading
Authors: Daknama Rami , Panagiotou Konstantinos , Reisser Simon
Published: August 2020

In this work we consider three well-studied broadcast protocols: push, pull and push&pull. A key property of all these models, which is also an important reason for their popularity, is that they are presumed to be very robust, since they are simple, randomized and, crucially, do not utilize explicitly the global structure of the underlying graph. While sporadic results exist, there has been no systematic theoretical treatment quantifying the robustness of these models. Here we investigate this question with respect to two orthogonal aspects: (adversarial) modifications of the underlying graph and message transmission failures.

We explore in particular the following notion of local resilience: beginning with a graph, we investigate up to which fraction of the edges an adversary may delete at each vertex, so that the protocols need significantly more rounds to broadcast the information. Our main findings establish a separation among the three models. On one hand, pull is robust with respect to all parameters that we consider. On the other hand, push may slow down significantly, even if the adversary may modify the degrees of the vertices by an arbitrarily small positive fraction only. Finally, push&pull is robust when no message transmission failures are considered, otherwise it may be slowed down.

On the technical side, we develop two novel methods for the analysis of randomized rumour-spreading protocols. First, we exploit the notion of self-bounding functions to facilitate significantly the round-based analysis: we show that for any graph the variance of the growth of informed vertices is bounded by its expectation, so that concentration results follow immediately. Second, in order to control adversarial modifications of the graph we make use of a powerful tool from extremal graph theory, namely Szemerédi’s Regularity Lemma.
Immediate effects of the implementation of nutritional warnings in Uruguay: awareness, self-reported use and increased understanding
Authors: Ares Gastón , Antúnez Lucía , Curutchet María Rosa , Galicia Luis , Moratorio Ximena , Giménez Ana , Bove Isabel
Published: August 2020

Objective:

To assess the effects of nutritional warnings during the first month after the date of full compliance by the food industry in Uruguay in terms of citizen awareness, self-reported use and ability to understand nutritional information.

Design:

The present work encompassed two online studies, conducted before (Study 1) and during the first month after the date of full compliance by the food industry (Study 2). An after-only design was used to assess awareness of the policy, exposure to nutritional warnings on food packages and self-reported use of warnings for making purchase decisions in Study 2. An after-only with control group experimental design was used to assess the effect of nutritional warnings on understanding of nutrition information in Studies 1 and 2.

Setting:

Uruguay, one of the Latin American countries, that has recently implemented nutritional warnings.

Participants:

A non-probabilistic sample of 1772 participants was recruited using Facebook advertisements targeted at Uruguayan adult users.

Results:

High awareness and self-reported use of nutritional warnings during the first month after the date of full compliance in Uruguay were observed. In addition, the before and after comparison showed that the implementation of warnings increased citizens’ ability to use nutritional information to compare products and to identify products with excessive content of sugar, fat, saturated fat and sodium.

Conclusions:

The current study confirms results from experimental studies and provides additional evidence to support the implementation of nutritional warnings as one of the public policies that can contribute to tackle obesity and non-communicable diseases.
Factors affecting the fate of β-carotene in the human gastrointestinal tract: A narrative review
Authors: Maurya Vaibhav Kumar , Singh Jagmeet , Ranjan Vijay , Gothandam Kodiveri Muthukaliannan , Bohn Torsten , Pareek Sunil
Published: August 2020

Abstract. Carotenoids and their metabolites play crucial roles in human health such as in immunity, cell differentiation, embryonic development, maintenance of plasma membrane integrity, and gastrointestinal functions, in addition to counteracting night blindness and other eye-related diseases. However, carotenoid bioavailability is highly variable and often low. The bioavailability of β-carotene, among the most frequently consumed carotenoid from the diet, is determined by food matrix related factors such as carotenoid dose, its location in food the matrix, the physical state in food, the presence of other food compounds in the matrix such as dietary fiber, dietary lipids, other micronutrients present such as minerals, and food processing, influencing also the size of food particles, and the presence of absorption inhibitors (fat replacers and anti-obesity drugs) or enhancers (nano-/micro-formulations). However, also host-related factors such as physiochemical interactions by gastrointestinal secretions (enzyme and salts) and other host-related factors such as surgery, age, disease, obesity, and genetic variations have shown to play a role. This review contributes to the knowledge regarding factors affecting the bioavailability of β-carotene (food and host-relegated), as well as highlights in vitro models employed to evaluate β-carotene bioavailability aspects.
Evaluating a Recovery-Oriented Intensive Outpatient Program for Veterans at Risk for Suicide
Authors: Roush Jared F. , O'Brien Karen M. , Ruha Allyson L.
Published: August 2020

Abstract. Background: Suicide is the 10th leading cause of death in the United States and suicide risk is elevated among military veterans. Risk for suicide is inherently transdiagnostic, complex, and multifaceted, which means a comprehensive psychotherapeutic approach to risk mitigation is required. Aims: Our aims were to summarize findings from an evaluation of an interdisciplinary, recovery-oriented intensive outpatient program (IR-IOP) that includes evidence-based suicide prevention stategies for veterans with varying psychiatric diagnoses who are at risk for suicide. Method: Veterans completed the Patient Health Questionnaire-9 and the Beck Scale for Suicide Ideation prior to and following their participation in the IR-IOP. Results: A significant decrease in the severity of suicide ideation was found between pre- and posttreatment. Limitations: This program evaluation utilized archival data and, as such, there was not a control group and posttreatment follow-up data were not collected. Conclusion: Preliminary findings suggest an IR-IOP for veterans with heterogenous psychiatric diagnoses utilizing a multifaceted psychotherapeutic approach to suicide prevention may be effective in reducing suicide ideation.
Reasons for Living and Suicide Attempts Among Young Adults With Lifetime Suicide Ideation
Authors: Christensen Kirsten , Hom Melanie A. , Stanley Ian H. , Joiner Thomas E.
Published: August 2020

Abstract. Background: Previous work suggests that reasons for living (RFL) are associated with suicide ideation; however, the relationship between RFL and suicide attempts among individuals with suicide ideation remains unclear. Such an examination is necessary to delineate whether RFL are associated with suicide attempts above and beyond their association with suicide ideation. Aims: This study examined the relationship between RFL and suicide attempts among young adults with a lifetime history of suicide ideation. Method: Undergraduate students ( N = 163) completed surveys assessing demographics, suicidal thoughts and behaviors, and RFL. Results: Individuals with a history of both suicide ideation and attempt reported significantly lower RFL than individuals with a history of suicide ideation but no suicide attempt. Among individual RFL-YA subscales, only Coping Beliefs was significantly associated with a suicide attempt history. Limitations: The cross-sectional nature of this study precludes any conclusions about the potential protective effects of RFL against suicide attempts, and the college student sample limits generalizability of the findings. Conclusion: Further research is needed to understand whether RFL prospectively predict suicide attempts among individuals with suicide ideation and whether interventions that bolster RFL might reduce suicide risk.
Decadal‐Scale Recovery of Carbon Stocks After Wildfires Throughout the Boreal Forests
Authors: Palviainen M. , Laurén A. , Pumpanen J. , Bergeron Y. , Bond‐Lamberty B. , Larjavaara M. , Kashian D. M. , Köster K. , Prokushkin A. , Chen H. Y. H. , Seedre M. , Wardle D. A. , Gundale M. J. , Nilsson M.‐C. , Wang C. , Berninger F.
Published: August 2020

Boreal forests store 30% of the world's terrestrial carbon (C). Consequently, climate change mediated alterations in the boreal forest fire regime can have a significant impact on the global C budget. Here we synthesize the effects of forest fires on the stocks and recovery rates of C in boreal forests using 368 plots from 16 long‐term (≥100 year) fire chronosequences distributed throughout the boreal zone. Forest fires led to a decrease in total C stocks (excluding mineral soil) by an average of 60% (range from <10% to >80%), which was primarily a result of C stock declines in the living trees and soil organic layer. Total C stocks increased with time since fire largely following a sigmoidal shape Gompertz function, with an average asymptote of 8.1 kg C m−2. Total C stocks accumulated at a rate of 2–60 g m−2 yr−1 during the first 100 years. Potential evapotranspiration (PET) was identified as a significant driver of C stocks and their post‐fire recovery, likely because it integrates temperature, radiation, and the length of the growing season. If the fire return interval shortens to ≤100 years in the future, our findings indicate that many boreal forests will be prevented from reaching their full C storage potential. However, our results also suggest that climate warming‐induced increases in PET may speed up the post‐fire recovery of C stocks.
Magnetopause Reconnection as Influenced by the Dipole Tilt Under Southward IMF Conditions: Hybrid Simulation and MMS Observation
Authors: Guo Zhifang , Lin Yu , Wang Xueyi , Vines Sarah K. , Lee S. H. , Chen Yuxi
Published: August 2020

Using a three‐dimensional (3‐D) global‐scale hybrid code, the Magnetospheric Multiscale (MMS) reconnection event around 02:13 UT on 18 November 2015, highlighted in the Geospace Environment Modeling (GEM) Dayside Kinetic Challenge, is simulated, in which the interplanetary magnetic field (IMF) points southward and the geomagnetic field has a −27° dipole tilt angle. Strong southward plasma jets are found near the magnetopause as a result of the dayside reconnection. Our results indicate that the subsolar magnetopause reconnection X line shifts from the subsolar point toward the Northern Hemisphere due to the effect of the tilted geomagnetic dipole angle, consistent with the MMS observation. Subsequently, the reconnection X lines or sites and reconnection flux ropes above the equator propagate northward along the magnetopause. The formation and global distribution of the X lines and the structure of the magnetopause reconnection are investigated in detail with the simulation. Mirror mode waves are also found in the middle of the magnetosheath downstream of the quasi‐perpendicular shock where the plasma properties are consistent with the mirror instability condition. As a special outcome of the GEM challenge event, the spatial and temporal variations in reconnection, the electromagnetic power spectra, and the associated D‐shaped ion velocity distributions in the simulated reconnection event are compared with the MMS observation.
The clinical-phenotype continuum in DYNC1H1-related disorders—genomic profiling and proposal for a novel classification
Authors: Becker Lena-Luise , Dafsari Hormos Salimi , Schallner Jens , Abdin Dalia , Seifert Michael , Petit Florence , Smol Thomas , Bok Levinus , Rodan Lance , Krapels Ingrid , Spranger Stephanie , Weschke Bernhard , Johnson Katherine , Straub Volker , Kaindl Angela M. , Di Donato Nataliya , von der Hagen Maja , Cirak Sebahattin
Published: August 2020

Mutations in the cytoplasmic dynein 1 heavy chain gene (DYNC1H1) have been identified in rare neuromuscular (NMD) and neurodevelopmental (NDD) disorders such as spinal muscular atrophy with lower extremity dominance (SMALED) and autosomal dominant mental retardation syndrome 13 (MRD13). Phenotypes and genotypes of ten pediatric patients with pathogenic DYNC1H1 variants were analyzed in a multi-center study. Data mining of large-scale genomic variant databases was used to investigate domain-specific vulnerability and conservation of DYNC1H1. We identified ten patients with nine novel mutations in the DYNC1H1 gene. These patients exhibit a broad spectrum of clinical findings, suggesting an overlapping disease manifestation with intermixed phenotypes ranging from neuropathy (peripheral nervous system, PNS) to severe intellectual disability (central nervous system, CNS). Genomic profiling of healthy and patient variant datasets underlines the domain-specific effects of genetic variation in DYNC1H1, specifically on toleration towards missense variants in the linker domain. A retrospective analysis of all published mutations revealed domain-specific genotype–phenotype correlations, i.e., mutations in the dimerization domain with reductions in lower limb strength in DYNC1H1–NMD and motor domain with cerebral malformations in DYNC1H1–NDD. We highlight that the current classification into distinct disease entities does not sufficiently reflect the clinical disease manifestation that clinicians face in the diagnostic work-up of DYNC1H1-related disorders. We propose a novel clinical classification for DYNC1H1-related disorders encompassing a spectrum from DYNC1H1–NMD with an exclusive PNS phenotype to DYNC1H1–NDD with concomitant CNS involvement.
Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community
Authors: Fritts Ryan K , Bird Jordan T , Behringer Megan G , Lipzen Anna , Martin Joel , Lynch Michael , McKinlay James B
Published: August 2020

Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.
Loss of NARS1 impairs progenitor proliferation in cortical brain organoids and leads to microcephaly
Authors: Wang Lu , Li Zhen , Sievert David , Smith Desirée E. C. , Mendes Marisa I. , Chen Dillon Y. , Stanley Valentina , Ghosh Shereen , Wang Yulu , Kara Majdi , Aslanger Ayca Dilruba , Rosti Rasim O. , Houlden Henry , Salomons Gajja S. , Gleeson Joseph G.
Published: August 2020

Asparaginyl-tRNA synthetase1 (NARS1) is a member of the ubiquitously expressed cytoplasmic Class IIa family of tRNA synthetases required for protein translation. Here, we identify biallelic missense and frameshift mutations in NARS1 in seven patients from three unrelated families with microcephaly and neurodevelopmental delay. Patient cells show reduced NARS1 protein, impaired NARS1 activity and impaired global protein synthesis. Cortical brain organoid modeling shows reduced proliferation of radial glial cells (RGCs), leading to smaller organoids characteristic of microcephaly. Single-cell analysis reveals altered constituents of both astrocytic and RGC lineages, suggesting a requirement for NARS1 in RGC proliferation. Our findings demonstrate that NARS1 is required to meet protein synthetic needs and to support RGC proliferation in human brain development.
Spatiotemporal data analysis with chronological networks
Authors: Ferreira Leonardo N. , Vega-Oliveros Didier A. , Cotacallapa Moshé , Cardoso Manoel F. , Quiles Marcos G. , Zhao Liang , Macau Elbert E. N.
Published: August 2020

The number of spatiotemporal data sets has increased rapidly in the last years, which demands robust and fast methods to extract information from this kind of data. Here, we propose a network-based model, called Chronnet, for spatiotemporal data analysis. The network construction process consists of dividing a geometric space into grid cells represented by nodes connected chronologically. Strong links in the network represent consecutive recurrent events between cells. The chronnet construction process is fast, making the model suitable to process large data sets. Using artificial and real data sets, we show how chronnets can capture data properties beyond simple statistics, like frequent patterns, spatial changes, outliers, and spatiotemporal clusters. Therefore, we conclude that chronnets represent a robust tool for the analysis of spatiotemporal data sets.
Bacterial polyphosphates interfere with the innate host defense to infection
Authors: Roewe Julian , Stavrides Georgios , Strueve Marcel , Sharma Arjun , Marini Federico , Mann Amrit , Smith Stephanie A. , Kaya Ziya , Strobl Birgit , Mueller Mathias , Reinhardt Christoph , Morrissey James H. , Bosmann Markus
Published: August 2020

Polyphosphates are linear polymers and ubiquitous metabolites. Bacterial polyphosphates are long chains of hundreds of phosphate units. Here, we report that mouse survival of peritoneal Escherichia coli sepsis is compromised by long-chain polyphosphates, and improves with bacterial polyphosphatekinase deficiency or neutralization using recombinant exopolyphosphatase. Polyphosphate activities are chain-length dependent, impair pathogen clearance, antagonize phagocyte recruitment, diminish phagocytosis and decrease production of iNOS and cytokines. Macrophages bind and internalize polyphosphates, in which their effects are independent of P2Y1 and RAGE receptors. The M1 polarization driven by E. coli derived LPS is misdirected by polyphosphates in favor of an M2 resembling phenotype. Long-chain polyphosphates modulate the expression of more than 1800 LPS/TLR4-regulated genes in macrophages. This interference includes suppression of hundreds of type I interferon-regulated genes due to lower interferon production and responsiveness, blunted STAT1 phosphorylation and reduced MHCII expression. In conclusion, prokaryotic polyphosphates disturb multiple macrophage functions for evading host immunity.
Revealing electronic state-switching at conical intersections in alkyl iodides by ultrafast XUV transient absorption spectroscopy
Authors: Chang Kristina F. , Reduzzi Maurizio , Wang Han , Poullain Sonia M. , Kobayashi Yuki , Barreau Lou , Prendergast David , Neumark Daniel M. , Leone Stephen R.
Published: August 2020

Conical intersections between electronic states often dictate the chemistry of photoexcited molecules. Recently developed sources of ultrashort extreme ultraviolet (XUV) pulses tuned to element-specific transitions in molecules allow for the unambiguous detection of electronic state-switching at a conical intersection. Here, the fragmentation of photoexcited iso-propyl iodide and tert-butyl iodide molecules (i-C3H7I and t-C4H9I) through a conical intersection between 3Q0/1Q1 spin–orbit states is revealed by ultrafast XUV transient absorption measuring iodine 4d core-to-valence transitions. The electronic state-sensitivity of the technique allows for a complete mapping of molecular dissociation from photoexcitation to photoproducts. In both molecules, the sub-100 fs transfer of a photoexcited wave packet from the 3Q0 state into the 1Q1 state at the conical intersection is captured. The results show how differences in the electronic state-switching of the wave packet in i-C3H7I and t-C4H9I directly lead to differences in the photoproduct branching ratio of the two systems.
Children’s family income is associated with cognitive function and volume of anterior not posterior hippocampus
Authors: Decker Alexandra L. , Duncan Katherine , Finn Amy S. , Mabbott Donald J.
Published: August 2020

Children from lower income backgrounds tend to have poorer memory and language abilities than their wealthier peers. It has been proposed that these cognitive gaps reflect the effects of income-related stress on hippocampal structure, but the empirical evidence for this relationship has not been clear. Here, we examine how family income gaps in cognition relate to the anterior hippocampus, given its high sensitivity to stress, versus the posterior hippocampus. We find that anterior (but not posterior) hippocampal volumes positively correlate with family income up to an annual income of ~$75,000. Income-related differences in the anterior (but not posterior) hippocampus also predicted the strength of the gaps in memory and language. These findings add anatomical specificity to current theories by suggesting a stronger relationship between family income and anterior than posterior hippocampal volumes and offer a potential mechanism through which children from different income homes differ cognitively.
Neural mechanisms underlying the effects of physical fatigue on effort-based choice
Authors: Hogan Patrick S. , Chen Steven X. , Teh Wen Wen , Chib Vikram S.
Published: August 2020

Physical fatigue crucially influences our decisions to partake in effortful action. However, there is a limited understanding of how fatigue impacts effort-based decision-making at the level of brain and behavior. We use functional magnetic resonance imaging to record markers of brain activity while human participants engage in uncertain choices for prospective physical effort, before and after bouts of exertion. Using computational modeling of choice behavior we find that fatiguing exertions cause participants to increase their subjective cost of effort, compared to a baseline/rested state. We describe a mechanism by which signals related to motor cortical state in premotor cortex influence effort value computations, instantiated by insula, thereby increasing an individual’s subjective valuation of prospective physical effort while fatigued. Our findings provide a neurobiological account of how information about bodily state modulates decisions to engage in physical activity.
A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus
Authors: Georgi Fanny , Kuttler Fabien , Murer Luca , Andriasyan Vardan , Witte Robert , Yakimovich Artur , Turcatti Gerardo , Greber Urs F.
Published: August 2020

Human adenoviruses (HAdVs) are fatal to immuno-suppressed individuals, but no effective anti-HAdV therapy is available. Here, we present a novel image-based high-throughput screening (HTS) platform, which scores the full viral replication cycle from virus entry to dissemination of progeny and second-round infections. We analysed 1,280 small molecular weight compounds of the Prestwick Chemical Library (PCL) for interference with HAdV-C2 infection in a quadruplicate, blinded format, and performed robust image analyses and hit filtering. We present the entire set of the screening data including all images, image analyses and data processing pipelines. The data are made available at the Image Data Resource (IDR, idr0081). Our screen identified Nelfinavir mesylate as an inhibitor of HAdV-C2 multi-round plaque formation, but not single round infection. Nelfinavir has been FDA-approved for anti-retroviral therapy in humans. Our results underscore the power of image-based full cycle infection assays in identifying viral inhibitors with clinical potential.
Publisher Correction: Large-scale metabolic interaction network of the mouse and human gut microbiota
Authors: Lim Roktaek , Cabatbat Josephine Jill T. , Martin Thomas L. P. , Kim Haneul , Kim Seunghyeon , Sung Jaeyun , Ghim Cheol-Min , Kim Pan-Jun
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
RNA N6-methyladenosine modification is required for miR-98/MYCN axis-mediated inhibition of neuroblastoma progression
Authors: Cheng Junmei , Xu Lingling , Deng Liqiang , Xue Lan , Meng Qingmei , Wei Furong , Wang Jinghua
Published: August 2020

Neuroblastoma (NB) is one of the most common malignant tumors of the sympathetic nervous system in childhood. NB severely threatens patient’s health and life. However, more effective diagnosis and treatment methods are badly needed in clinics all over the world. MYCN is well recognized as a genetic biomarker of high risk and poor outcome in NB. miRNAs are small RNAs and miR-98 involved in the pathogenesis of various cancers. The role and mechanism of miR-98 in NB remains to be investigated. Here we found that miR-98 was decreased in human MYCN-high-expression NB tissues, and its down-regulation was associated with poor prognosis of NB. Over-expression of miR-98 inhibited cell proliferation, migration and invasion of NB cells. The analysis by employing the software of miRanda predicted the possible binding sites of miR-98 in the 3′-UTR of MYCN, and experimental data illustrated that miR-98 directly bound to MYCN 3′-UTR and decreased MYCN expression. Over-expression of MYCN rescued the decreased malignant phenotype caused by over-expression of miR-98 in NB. N6-methyladenosine modification in 3′-UTR of MYCN promoted its interaction with miR-98. The data collectively demonstrated that RNA m6A modification was required for miR-98/MYCN axis-mediated inhibition of neuroblastoma progression, and miR-98 might be novel targets for NB detection and treatment.