bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for lymph node metastasis of ovarian, fallopian tube and primary peritoneal cancer in hereditary breast and ovarian cancer syndrome
Authors: Mitamura Takashi , Sekine Masayuki , Arai Masami , Shibata Yuka , Kato Momoko , Yokoyama Shiro , Yamashita Hiroko , Watari Hidemichi , Yabe Ichiro , Nomura Hiroyuki , Enomoto Takayuki , Nakamura Seigo ,   the Registration Committee of the Japanese HBOC Consortium
Published: June 2020

Abstract

Background
To establish an individualized surgical strategy for lymphadenectomy in ovarian cancer patients with the germline BRCA1 and BRCA2 pathogenic variants (BRCA1+ and BRCA2+), we investigated the clinicopathological characteristics that are involved in the increased risk of lymph node metastasis.

Methods
We retrospectively reviewed the data of Japanese women registered in the database of the Japanese Hereditary Breast and Ovarian Cancer Consortium, who underwent BRCA1 and BRCA2 genetic testing.

Results
We evaluated the predictors of lymph node metastasis in all patients with the information of age at the diagnosis, disease site, histological subtype, 2014 FIGO stage, personal breast cancer history and family history; 233, 153 and 32 patients in the BRCA− (no pathogenic variant), BRCA1+ and BRCA2+ groups, respectively. The prevalence of lymph node metastasis was not markedly different between BRCA− (20.0%), BRCA1+ (18.4%) and BRCA2+ (26.2%). Multivariate analysis revealed an absence of a family history of ovarian cancer as an independent predictor for an increased risk of lymph node metastasis in BRCA1+, and the prevalence of lymph node metastasis was 11.7 and 42.0% in the groups with and without a family history of ovarian cancer, respectively. This subgroup without a family history of ovarian cancer did not show any correlation with a particular variant of BRCA1, including two common variants of c.188 T &gt; A and c.2800C &gt; T.

Conclusions
This study suggested that certain genetic factors related to the penetrance of hereditary breast and ovarian cancer syndrome altered the frequency of lymph node metastasis in BRCA1+ ovarian cancer, and family history may be useful to personalize the indication of lymphadenectomy.
Influenza-Associated Medical Visits Prevented by Influenza Vaccination in Young Children in Thailand, 2012–2014
Authors: Rolfes Melissa A , Olsen Sonja J , Kittikraisak Wanitchaya , Suntarattiwong Piyarat , Klungthong Chonticha , Ellison Damon , Mott Joshua A , Chotpitayasunondh Tawee 
Published: June 2020

Abstract
Despite recommendations, few children aged 6–35 months in Thailand receive seasonal influenza vaccination. Using previously estimated incidence and vaccine effectiveness data from the period 2012–2014, we estimate that up to 121 000 medical visits could be prevented each year with 50% coverage and expanded recommendations to children aged &lt;5 years.
Insights into the control of metabolism and biomass accumulation in a staple C4 grass
Authors: Billakurthi Kumari , Schreier Tina B 
Published: June 2020

This article comments on:
Chen J, Zhu M, Liu R, Zhang M, Lv Y, Liu Y, Xiao X, Yuan J, Cai H. 2020. BIOMASS YIELD 1 regulates Sorghum biomass and grain yield via the shikimate pathway. Journal of Experimental Botany 71, 5506–5520.
Is this an early stage merger? A case study on molecular gas and star formation properties of Arp 240
Authors: He Hao , Wilson C D , Sliwa Kazimierz , Iono Daisuke , Saito Toshiki 
Published: June 2020

ABSTRACT
We present new high-resolution 12CO J = 1–0, J = 2–1, and 13CO J = 1–0 maps of the early stage merger Arp 240 (NGC 5257/8) obtained with the Atacama Large Millimeter/submillimeter Array (ALMA). Simulations in the literature suggest that the merger has just completed its first passage; however, we find that this system has a lower global gas fraction but a higher star formation efficiency (SFE) compared to typical close galaxy pairs, which suggests that this system may already be in an advanced merger stage. We combine the ALMA data with 12CO J = 3–2 observations from the Submillimeter Array and carry out RADEX modelling on several different regions. Both, the RADEX modelling and a local thermal equilibrium (LTE) analysis show that the regions are most likely to have a CO-to-H2 conversion factor αCO close to or perhaps even smaller than the typical value for (ultra)luminous infrared galaxies. Using 33-GHz data from the Very Large Array to measure the star formation rate, we find that most star-forming regions have molecular gas depletion times of less than 100 Myr. We calculated the SFE per free-fall time for different regions and find some regions appear to have values greater than 100 per cent. We find these regions generally show evidence for young massive clusters (YMCs). After exploring various factors, we argue that this is mainly due to the fact that radio continuum emission in those regions is dominated by that from YMCs, which results in an overestimate of the SFE per free-fall time.
Corruption, Opportunity Networks, and Gender
Authors: Wiesehomeier Nina , Verge Tània 
Published: June 2020

Abstract
Given the gender stereotype that women are more ethical than men, people should assess female politicians as being less corruptible. Yet information about access to networks suggests that opportunities to engage in unethical behavior may counter this perception. Using a conjoint analysis in a nationally representative survey in Spain, a country shaken by corruption scandals, we asked respondents to identify the more corruptible politician between two hypothetical local councilors by imagining an investor willing to offer a bribe to advance business interests. Results indicate that female politicians do symbolically stand for honesty. However, this assessment is offset by embeddedness cues signaling a woman politician’s access to opportunity networks. We discuss our findings in light of instrumentalist arguments for an increase of women in politics as a means to combat corruption.
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach
Authors: Laudanno Giovanni , Haegeman Bart , Rabosky Daniel L , Etienne Rampal S 
Published: June 2020

AbstractThe branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth–death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation]
Globe-hopping
Authors: Chistikov Dmitry , Goulko Olga , Kent Adrian , Paterson Mike 
Published: June 2020

We consider versions of the grasshopper problem (Goulko & Kent 2017
Proc. R. Soc. A
473
, 20170494) on the circle and the sphere, which are relevant to Bell inequalities. For a circle of circumference 2
π
, we show that for unconstrained lawns of any length and arbitrary jump lengths, the supremum of the probability for the grasshopper’s jump to stay on the lawn is one. For antipodal lawns, which by definition contain precisely one of each pair of opposite points and have length
π
, we show this is true except when the jump length
ϕ
is of the form
π
(
p
/
q
) with
p
,
q
coprime and
p
odd. For these jump lengths, we show the optimal probability is 1 − 1/
q
and construct optimal lawns. For a
pair
of antipodal lawns, we show that the optimal probability of jumping from one onto the other is 1 − 1/
q
for
p
,
q
coprime,
p
odd and
q
even, and one in all other cases. For an antipodal lawn on the sphere, it is known (Kent & Pitalúa-García 2014
Phys. Rev. A
90
, 062124) that if
ϕ
=
π
/
q
, where

q
∈

N

, then the optimal retention probability of 1 − 1/
q
for the grasshopper’s jump is provided by a hemispherical lawn. We show that in all other cases where 0 <
ϕ
<
π
/2, hemispherical lawns are not optimal, disproving the hemispherical colouring maximality hypotheses (Kent & Pitalúa-García 2014
Phys. Rev. A
90
, 062124). We discuss the implications for Bell experiments and related cryptographic tests.
SARS-CoV-2 mutations altering regulatory properties: deciphering host’s and virus’s perspectives
Authors: Islam Abul Bashar Mir Md. Khademul , Khan Md. Abdullah-Al-Kamran 
Published: June 2020

AbstractSince the first recorded case of the SARS-CoV-2, it has acquired several mutations in its genome while spreading throughout the globe. However, apart from some changes in protein coding, functional importance of these mutations in disease pathophysiology are still largely unknown. In this study, we investigated the significance of these mutations both from the host’s and virus’s perspective by analyzing the host miRNA binding and virus’s internal ribosome entry site (IRES), respectively. Strikingly, we observed that due to the acquired mutations, host miRNAs bind differently compared to the reference; where few of the miRNAs lost and few gained the binding affinity for targeting the viral genome. Moreover, functional enrichment analysis suggests that targets of both of these gained and lost miRNAs might be involved in various host immune signaling pathways. Also, we sought to shed some insights on the impacts of mutations on the IRES structure of SARS-CoV-2. Remarkably, we detected that three particular mutations in the IRES can disrupt its secondary structure which can further make the virus less functional. These results could be valuable in exploring the functional importance of the mutations of SARS-CoV-2 and could provide novel insights into the differences observed different parts of the world.
Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology
Authors: Paris Kristina A. , Santiago Ulises , Camacho Carlos J. 
Published: June 2020

AbstractCell surface receptor engagement is a critical aspect of viral infection. This paper compares the dynamics of virus-receptor interactions for SARS-CoV (CoV1) and CoV2. At low (endosomal) pH, the binding free energy landscape of CoV1 and CoV2 interactions with the angiotensin-converting enzyme 2 (ACE2) receptor is almost the same. However, at neutral pH the landscape is different due to the loss of a pH-switch (His445Lys) in the receptor binding domain (RBD) of CoV2 relative to CoV1. Namely, CoV1 stabilizes a transition state above the bound state. In situations where small external strains are applied by, say, shear flow in the respiratory system, the off rate of the viral particle is enhanced. As a result, CoV1 virions are expected to detach from cell surfaces in time scales that are much faster than the time needed for other receptors to reach out and stabilize virus attachment. On the other hand, the loss of this pH-switch, which sequence alignments show is unique to CoV2, eliminates the transition state and allows the virus to stay bound to the ACE2 receptor for time scales compatible with the recruitment of additional ACE2 receptors diffusing in the cell membrane. This has important implications for viral infection and its pathology. CoV1 does not trigger high infectivity in the nasal area because it either rapidly drifts down the respiratory tract or is exhaled. By contrast, this novel mutation in CoV2 should not only retain the infection in the nasal cavity until ACE2-rich cells are sufficiently depleted, but also require fewer particles for infection. This mechanism explains observed longer incubation times, extended period of viral shedding, and higher rate of transmission. These considerations governing viral entry suggest that number of ACE2-rich cells in human nasal mucosa, which should be significantly smaller for children (and females relative to males), should also correlate with onset of viral load that could be a determinant of higher virus susceptibility. Critical implications for the development of new vaccines to combat current and future pandemics that, like SARS-CoV2, export evolutionarily successful strains via higher transmission rates by viral retention in nasal epithelium are also discussed.
Evolution and spread of SARS-CoV-2 likely to be affected by climate
Authors: Bajaj Priyanka , Arya Prakash Chandra 
Published: June 2020

AbstractCOVID-19 pandemic has been extensively studied by many researchers. However, it is still unclear why it was restricted to higher latitudes during the initial days and later cascaded in the tropics. Here, we analyzed 176 SARS-CoV-2 genomes across different latitudes and climate (Koppen’s climate) that provided insights about within species virus evolution and its relation to abiotic factors. Two genetically variant groups, named as G1 and G2 were identified, well defined by four mutations. The G1 group (ancestor), is mainly restricted to warm and moist, temperate climate (Koppen’s C climate) while its descendent G2 group surpasses the climatic restrictions of G1, initially cascading into neighboring cold climate (D) of higher latitudes and later into hot climate of the tropics (A). It appears that the gradation of temperate climate (Cfa-Cfb) to cold climate (Dfa-Dfb) drives the evolution of G1 into G2 variant group which later adapted to tropical climate (A) as well. It seems this virus followed inverse latitudinal gradient in the beginning due to its preference towards temperate (C) and cold climate (D). Our work elucidates virus evolutionary studies combined with climatic studies can provide crucial information about the pathogenesis and natural spreading pathways in such outbreaks which is hard to achieve through individual studies. Mutational insights gained may help design an efficacious vaccine.Graphical AbstractIn BriefThe authors elucidate adaptation of SARS-CoV-2 to different climates by studying phylogenetics and the distribution of strains on Koppen’s climate map.HighlightsPhylogenetic network divides SARS-CoV-2 strains into two variant groups, G1 and G2.G1 strains is restricted to Koppen’s“temperate”climate (mainlyCfa-Cfb).G2 strains has evolved from G1 to sustain in other climates mainly “humid-continental” (Dfa-Dfb)and “tropical-savannah” (Aw)climate.
The Lifelines COVID-19 Cohort: a questionnaire-based study to investigate COVID-19 infection and its health and societal impacts in a Dutch population-based cohort
Authors: Intyre Kate Mc , Lanting Pauline , Deelen Patrick , Wiersma Henry , Vonk Judith M. , Ori Anil P.S. , Jankipersadsing Soesma A. , Warmerdam Robert , van Blokland Irene , Boulogne Floranne , Dijkema Marjolein X.L. , Herkert Johanna C. , Claringbould Annique , Bakker Olivier , Lopera Maya Esteban A. , Bültmann Ute , Zhernakova Alexandra , Reijneveld Sijmen A. , Zijlstra Elianne , Swertz Morris , Brouwer Sandra , van Ooijen R. , Angelini Viola , Dekker Louise , Sijtsma Anna , Scherjon Sicco A. , Dekens Jackie , Mierau Jochen O. , Boezen H. Marike , Franke Lude 
Published: June 2020

AbstractThe COVID-19 pandemic has affected billions of people around the world not only through the infection itself but also through its wider impact on public health and daily life. To assess the effects of the pandemic, a team of researchers across a wide range of disciplines developed and implemented the Lifelines COVID-19 questionnaire, leading to the development of the Lifelines COVID-19 cohort. This cohort is recruited from participants of the Lifelines prospective population cohort and the Lifelines NEXT birth cohort, and participants were asked to fill out detailed questionnaires about their physical and mental health and experiences on a weekly basis starting in late March of 2020 and on a bi-weekly basis staring in June 2020. The Lifelines region covers the three Northern provinces of the Netherlands— Drenthe, Groningen and Friesland—which together account for ∼10% of the Dutch population. To date, >70,000 people have responded to the questionnaires at least once, and the questionnaire program is still ongoing. Data collected by the questionnaires will be used to address four aspects of the outbreak: (1) how the COVID-19 pandemic developed in the three northern provinces of the Netherlands, (2) which environmental risk factors predict disease susceptibility and severity, (3) which genetic risk factors predict disease susceptibility and severity and (4) what are the psychological and societal impacts of the crisis.Informed consentAll Lifelines and Lifelines NEXT participants have provided informed consent that provide the opportunity for add-on research.Research involving human participantsBoth the Lifelines and the Lifelines NEXT studies were approved by the ethics committee of the University Medical Center Groningen.
Breath-borne VOC Biomarkers for COVID-19
Authors: Chen Haoxuan , Qi Xiao , Ma Jianxin , Zhang Chunyang , Feng Huasong , Yao Maosheng 
Published: June 2020

AbstractRapid diagnosis of COVID-19 is key to controlling the pandemic. Here we report the potential breath-borne volatile organic compound (VOC) biomarkers for COVID-19. Higher levels of ethyl butanoate were detected in exhaled breath of COVID-19 patients (N=10) than healthy controls/health care workers (N=21), lung cancer (LC) patients (N=7) and backgrounds. In contrast, breath-borne butyraldehyde and isopropanol (an efficient SARS-CoV-2 inactivation agent) were significantly higher for non-COVID-19 respiratory infections (URTI) (N=22) than COVID-19, HC, LC patients and backgrounds. Breath-borne isopropanol emission from COVID-19 patients varied greatly up to ∼100-fold difference. COVID-19 patients had lower acetone levels than other subjects, except LC patients. The monitoring of ethyl butanoate, butyraldehyde and isopropanol could lend considerable support in rapidly screening COVID-19; and alerting the presence of COVID-19 patient in particular environments.One Sentence SummaryCOVID-19 patients emit distinctive VOC profiles
A chromosome-level genome assembly and annotation of the humpback grouperCromileptes altivelas
Authors: Sun Yun , Zhang Dongdong , Shi Jianzhi , Chen Guisen , Wu Ying , Shen Yang , Cao Zhenjie , Zhang Linlin , Zhou Yongcan 
Published: June 2020

AbstractCromileptes altivelasthat belongs to Serranidae in the order Perciformes, is widely distributed throughout the tropical waters of the Indo-West Pacific regions. Due to their excellent food quality and abundant nutrients, it has become a popular marine food fish with high market values. Here, we reported a chromosome-level genome assembly and annotation of the humpback grouper genome using more than 103X PacBio long-reads and high-throughput chromosome conformation capture (Hi-C) technologies. The N50 contig length of the assembly is as large as 4.14 Mbp, the final assembly is 1.07 Gb with N50 of scaffold 44.78 Mb, and 99.24% of the scaffold sequences were anchored into 24 chromosomes. The high-quality genome assembly also showed high gene completeness with 27,067 protein coding genes and 3,710 ncRNAs. This high accurate genome assembly and annotation will not only provide an essential genome resource forC. altivelasbreeding and restocking, but will also serve as a key resource for studying fish genomics and genetics.
The Effect of Uncertainty on Prediction Error in the Action-Perception Loop
Authors: Perrykkad Kelsey , Lawson Rebecca P. , Jamadar Sharna , Hohwy Jakob 
Published: June 2020

AbstractAmong all their sensations, agents need to distinguish between those caused by themselves and those caused by external causes. The ability to infer agency is particularly challenging under conditions of uncertainty. Within the predictive processing framework, this should happen through active control of prediction error that closes the action-perception loop. Here we use a novel, temporally-sensitive, behavioural proxy for prediction error to show that it is minimised most quickly when variability is low, but also when volatility is high. Further, when human participants report agency, they show steeper prediction error minimisation. We demonstrate broad effects of uncertainty on accuracy of agency judgements, movement, policy selection, and hypothesis switching. Measuring autism traits, we find differences in policy selection, sensitivity to uncertainty and hypothesis switching despite no difference in overall accuracy.
Disentangling the biological information encoded in disordered mitochondrial morphology through its rapid elicitation by iCMM
Authors: Miyamoto Takafumi , Uosaki Hideki , Mizunoe Yuhei , Goto Satoi , Yamanaka Daisuke , Masuda Masato , Yoneyama Yosuke , Nakamura Hideki , Hattori Naoko , Takeuchi Yoshinori , Sekiya Motohiro , Matsuzaka Takashi , Hakuno Fumihiko , Takahashi Shin-Ichiro , Yahagi Naoya , Ito Koichi , Shimano Hitoshi 
Published: June 2020

AbstractMitochondrial morphology is dynamically changed in conjunction with spatiotemporal functionality. Although considerable efforts have been made to understand why abnormal mitochondrial morphology occurs in various diseases, the biological significance of mitochondrial morphology in states of health and disease remains to be elucidated owing to technical limitations. In the present study, we developed a novel method, termed inducible Counter Mitochondrial Morphology (iCMM), to purposely manipulate mitochondrial morphological patterns on a minutes timescale, using a chemically inducible dimerization system. Using iCMM, we showed that mitochondrial morphological changes rapidly lead to the characteristic reconstitution of various biological information, which is difficult to investigate by conventional genetic engineering. The manipulation of mitochondrial morphology using iCMM can improve our understanding of the interplay between mitochondrial morphology and cellular functions.
Development of optogenetic tools to manipulate cell cycle checkpoints
Authors: Goto Yuhei , Aoki Kazuhiro 
Published: June 2020

SUMMARYIn order to understand the systematic regulation of the cell cycle, we need more precise tools for cell-cycle perturbation. Optogenetics is a powerful technique for precisely controlling cellular signaling at higher spatial and temporal resolution. Here, we report optogenetic tools for the rapid and reversible control of cell-cycle checkpoints with a red/far-red light photoreceptor, phytochrome B (PhyB). We established fission yeast cells producing phycocyanobilin as a chromophore of PhyB, and demonstrated light-dependent protein recruitment to the plasma membrane, nucleus, and kinetochore. Using this system, we developed optogenetic manipulation of the cell cycle in two ways: the Opto-G2/M checkpoint triggered G2/M cell cycle arrest in response to red light, and Opto-SAC induced a spindle assembly checkpoint (SAC) in response to red light and then quickly released the SAC by far-red light.