bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study of horizontal-to-vertical component spectral ratio as a proxy for site classification in central Asia
Authors: Sedaghati Farhad , Rahpeyma Sahar , Ansari Anooshiravan , Pezeshk Shahram , Zare Mehdi , Daneshvaran Siamak 
Published: July 2020

SUMMARYTien Shan of central Asia is known as one of the world's largest, youngest and most active intracontinental orogens. In this study, we implemented the horizontal-to-vertical spectral ratio (HVSR) technique as a widely used first-order approximation of the site effect parameters (i.e. fundamental frequency and site amplification). A set of data including 2119 strong-motion recordings from 468 earthquakes with hypocentral distances up to 500 km and small to moderate moment magnitudes ($ {M_{\rm{w}}}\sim $3.0–5.5) recorded by 24 broad-band stations from five different networks, located in Afghanistan, Tajikistan and Kyrgyzstan was deployed to investigate site-specific characteristics. We fitted a Gaussian-shape pulse function to evaluate fundamental frequencies and site amplifications. The HVSRs analysis revealed that although the majority of the stations (16 out of 24) show flat amplification functions, there are few stations with single sharp amplification functions. Then, we classified the stations based on the predominant frequency. Furthermore, we approximated the time-averaged shear wave velocity in the uppermost 30 m (${V_{{\rm{S}}30}}$) using the fundamental frequency and its corresponding amplitude. Moreover, we compared the HVSRs obtained from P waves, S waves, coda and pre-event noise. All peak frequencies including the fundamental frequency estimated from different seismic phases are in good agreement; whereas generally, the amplitude of the P-wave window is the lowest, the amplitudes of the S wave and noise windows are similar to the whole record and the amplitudes of early and late coda windows are the highest. We also observed that the HVSRs of noise using a 5 s window may have anomalous high amplitudes and peaks. These anomalous high amplitudes and peaks in the noise HVSRs indicate the existence of some unnatural sources or artefacts such as traffic and wind with specific resonance frequencies, suggesting 5 s ambient noise window is insufficient to capture site characteristics. Finally, to assess the reliability of the determined geotechnical results, we implemented a blind theoretical HVSR inversion to obtain representative shear wave velocity profiles as well as ${V_{{\rm{S}}30}}$ along with associated uncertainties for stations characterized by a single-peak HVSR curve using a Bayesian statistical framework.
Fto-modulated lipid niche regulates adult neurogenesis through modulating adenosine metabolism
Authors: Gao Hui , Cheng Xuejun , Chen Junchen , Ji Chai , Guo Hongfeng , Qu Wenzheng , Dong Xiaoxue , Chen Yingyan , Ma Linghan , Shu Qiang , Li Xuekun 
Published: July 2020

Abstract
Adult neurogenesis is regulated by diverse factors including the local environment, i.e. the neurogenic niche. However, whether the lipid in the brain regulates adult neurogenesis and related mechanisms remains largely unknown. In the present study, we found that lipid accumulates in the brain during postnatal neuronal development. Conditional knockout of Fto (cKO) in lipid not only reduced the level of lipid in the brain but also impaired the learning and memory of mice. In addition, Fto deficiency in lipid did not affect the proliferation of adult neural stem cells (aNSCs), but it did inhibit adult neurogenesis by inducing cell apoptosis. Mechanistically, specific deleting Fto in lipid altered gene expression and increased adenosine secretion of adipocytes. The treatment of adenosine promoted the apoptosis of newborn neurons. As a whole, these results reveal the important function of the lipid niche and its associated mechanism in regulating adult neurogenesis.
How context and attention shape behaviors in online communities: a modified garbage can model
Authors: Foss Nicolai J. , Jeppesen Lars Bo , Rullani Francesco 
Published: July 2020

AbstractOnline communities have emerged as important organizational forms, but there are many gaps in our understanding. In particular, researchers have mainly focused on individual-level drivers of behaviors in communities, while downplaying (formal, informal) context at various levels. We theorize that different dimensions of context (i.e. omnibus and discrete context) influence decision-making in online communities through mechanisms involving community members’ attention. Specifically, context influences which problems members perceive and which solutions they retrieve and apply, thereby shaping the process of matching solutions and problems. We derive four hypotheses about contribution behaviors in online communities and how such behaviors are influenced by context. The empirical setting for our study is the open-source software community. We find support for our hypotheses in a unique dataset that captures the behavior of 24,057 community members who used the SourceForge.net online platform from 2000 to 2002.
Major Histocompatibility Complex Class I Chain–Related A and B (MICA and MICB) Gene, Allele, and Haplotype Associations With Dengue Infections in Ethnic Thais
Authors: Luangtrakool Panpimon , Vejbaesya Sasijit , Luangtrakool Komon , Ngamhawornwong Somporn , Apisawes Kusuma , Kalayanarooj Siripen , Macareo Louis R , Fernandez Stefan , Jarman Richard G , Collins Robert W M , Cox Steven T , Srikiatkhachorn Anon , Rothman Alan L , Stephens Henry A F 
Published: July 2020

Abstract

Background
Major histocompatibility complex class I chain–related (MIC) A and B (MICA and MICB) are polymorphic stress molecules recognized by natural killer cells. This study was performed to analyze MIC gene profiles in hospitalized Thai children with acute dengue illness.

Methods
MIC allele profiles were determined in a discovery cohort of patients with dengue fever or dengue hemorrhagic fever (DHF) (n = 166) and controls (n = 149). A replication cohort of patients with dengue (n = 222) was used to confirm specific MICB associations with disease.

Results
MICA*045 and MICB*004 associated with susceptibility to DHF in secondary dengue virus (DENV) infections (odds ratio [OR], 3.22; [95% confidence interval (CI), 1.18–8.84] and 1.99 [1.07–2.13], respectively), and MICB*002 with protection from DHF in secondary DENV infections (OR, 0.41; 95% CI, .21–.68). The protective effect of MICB*002 against secondary DHF was confirmed in the replication cohort (OR, 0.43; 95% CI, .22–.82) and was stronger when MICB*002 is present in individuals also carrying HLA-B*18, B*40, and B*44 alleles which form the B44 supertype of functionally related alleles (0.29, 95% CI, .14–.60).

Conclusions
Given that MICB*002 is a low expresser of soluble proteins, these data indicate that surface expression of MICB*002 with B44 supertype alleles on DENV-infected cells confer a protective advantage in controlling DENV infection using natural killer cells.
Adoptive Transfer of Serum Samples From Children With Invasive Staphylococcal Infection and Protection Against Staphylococcus aureus Sepsis
Authors: Tsai Chih-Ming , Soper Nicole , Bennett Monique , Fallon Jonathan K , Michell Ashlin R , Alter Galit , Liu George Y , Thomsen Isaac 
Published: July 2020

Abstract
A successful Staphylococcus aureus vaccine remains elusive, and one controversy in the field is whether humans generate a protective adaptive immune response to infection. We developed a bacterial challenge murine assay that directly assesses the protective capacity of adoptively transferred human serum samples. We first validated the model by showing that postpneumococcal vaccine serum samples from humans induced effective clearance of Streptococcus pneumoniae in mice. We then found that human serum samples adoptively transferred from children with invasive S. aureus infections exhibited protection from disease in a murine model, with some samples conferring near complete protection. These findings demonstrate that human serum samples are capable of conferring a protective adaptive response generated by humans during invasive staphylococcal disease, allowing for the study of protective factors in a murine model. Identification of the protective factors present in the most efficacious serum samples would be of high interest as potential staphylococcal vaccine candidates or passive therapeutics.
An Inflammatory Composite Score Predicts Mycobacterial Immune Reconstitution Inflammatory Syndrome in People with Advanced HIV: A Prospective International Cohort Study
Authors: Vinhaes Caian L , Sheikh Virginia , Oliveira-de-Souza Deivide , Wang Jing , Rupert Adam , Roby Gregg , Arriaga María B , Fukutani Kiyoshi F , Sawe Fred , Shaffer Doug , Ananworanich Jintanat , Phanuphak Nittaya , Andrade Bruno B , Sereti Irini 
Published: July 2020

Abstract

Background
Immune reconstitution inflammatory syndrome (IRIS) is a common cause of morbidity among people with human immunodeficiency virus (PWH) who initiate antiretroviral therapy (ART) with severe lymphopenia. Easily accessible tools that reliably predict emergence and elucidate pathogenesis of IRIS are needed to facilitate improved clinical management.

Methods
Plasma levels of biomarkers were measured before ART initiation in a large multinational cohort of ART-naive PWH with severe immunosuppression (CD4+ count &lt;100 cells/mm3) in United States, Kenya, and Thailand. We performed a series of multiparametric analyses of inflammatory and clinical biomarkers and developed a composite score merging relevant biomarkers for use in a prediction model.

Results
We identified a distinct baseline inflammatory profile and changes in inflammatory networks among biomarkers in participants who subsequently developed mycobacterial or viral IRIS. We also developed a composite score incorporating biomarkers associated with IRIS (interleukin-6 [IL-6], IL-10, IL-27, sCD14, interferon-γ, tumor necrosis factor-α, hyaluronic acid, D-dimer, body mass index, and hemoglobin) that accurately predicted mycobacterial IRIS and death in this cohort.

Conclusions
Systemic inflammatory profiles in PWH with severe immunosuppression are predictive of IRIS. Composite scores for the prediction of mycobacterial IRIS and death could be useful for risk stratification in PWH and lymphopenia initiating ART.

Clinical Trials Registration
NCT00286767.
Choosing to Fight, Choosing to Die: Examining How ISIS Foreign Fighters Select Their Operational Roles
Authors: Evans Tyler , Milton Daniel J , Young Joseph K 
Published: July 2020

AbstractUnderstanding why and how individuals participate in militant organizations has been the focus of an increasing amount of scholarship. Traditionally, these studies focus at either the individual or organizational level of explanation. This article advances the discussion on individual participation in militant organizations by combining primary and secondary sources at both levels to explain how the Islamic State of Iraq and Syria (ISIS) attracted individuals into its organization as either suicide bombers or frontline fighters. First, at the individual level, we analyze a primary source dataset of over 4,000 personnel files from foreign fighters who went to Syria to join ISIS between 2013 and 2014. Second, at the organizational level, we examine trends in Islamic State propaganda and messaging to see how the recruitment of individuals into the organization placed them on certain operational paths. Two specific takeaways emerge. First, foreign fighters in 2013–2014 volunteered to become suicide bombers with relatively less frequency than in past iterations of the conflict in Iraq and Syria. Second, fighters from Western countries and fighters from countries undergoing a civil war were especially less likely to volunteer for a suicide role. More broadly, this analytical essay makes a case for the value of looking inside an organization as well as at individuals to get a more complete picture about group-level behavior.
Benedict XIV’s donation of Amazonian objects to the Istituto delle Scienze of Bologna (1751): origins and history
Authors: Tacconi Samuele 
Published: July 2020

Abstract
In 1751 Pope Benedict XIV made a donation of Amazonian objects to the Istituto delle Scienze in Bologna, a scientific academy located in the city of his birth. This article reconstructs the history of this group of objects back to its origins in the Jesuit missions of the upper Amazon basin, by presenting and examining new documentary evidence. The encounter between a Jesuit missionary and Pope Benedict XIV is analysed in the context of the early modern reception of the New World and its peoples in Catholic Europe. Finally, an overview is presented of the items in this collection, which represent some of the scarcest and oldest known examples of native material culture from the region.
AgeStrucNb: Software for Simulating and Detecting Changes in the Effective Number of Breeders (Nb)
Authors: Antao Tiago , Cosart Ted , Trethewey Brian , Waples Robin S , Ackerman Mike W , Luikart Gordon , Hand Brian K 
Published: July 2020

Abstract
Estimation of the effective number of breeders per reproductive event (Nb) using single sample DNA-marker-based methods has rapidly grown in recent years. However, estimating Nb is difficult in age-structured populations because the performance of estimators is influenced by the Nb / Ne ratio, which varies among species with different life histories. We provide a computer program, AgeStrucNb, to simulate age-structured populations (including life history) and also estimate Nb. The AgeStrucNb program is composed of 4 major components to simulate, subsample, estimate, and then visualize Nb time series data. AgeStrucNb allows users to also quantify the precision and accuracy of any set of loci or sample size to estimate Nb for many species and populations. AgeStrucNb allows users to conduct power analysis to evaluate sensitivity to detect changes in Nb or the power to detect a correlation between trends in Nb and environmental variables (e.g., temperature, habitat quality, predator or pathogen abundance) that could be driving changes in Nb. The software provides Nb estimates for empirical data sets using the LDNe (linkage disequilibrium) method, includes publication-quality output graphs, and outputs genotype files in Genepop format for use in other programs. AgeStrucNb will help advance the application of genetic markers for monitoring Nb, which will help biologists to detect population declines and growth, which is crucial for research and conservation of natural and managed populations.
The relationship between molar morphology and ecology withinNeotoma
Authors: Tomé Catalina P , Whiteman-Jennings Winifred , Smith Felisa A 
Published: July 2020

AbstractThe extensive diversity in dental form across mammals and its strong relationship with function provides insights into the diet, habitat, and behavior, of both extant and extinct taxa. Understanding the extent of variation in dental morphology across species allows for more accurate identification of fossils and a better ability to infer relationships between form and function and ecology. We examined variation in the size and shape of the first upper molar among the genus Neotoma. We employed elliptical Fourier analysis to quantify differences in the shape of 2D outlines for 23 populations and six species of Neotoma, varying in body size and habitat preference. As expected, molar length is a strong predictor of body size and is significantly and negatively correlated with temperature, particularly in species whose ranges span large latitudinal gradients. We found that differences in molar shape separate species into three general morpho-groups, with no evidence of a phylogenetic signal. While outline analysis could not robustly classify all molars to the species level, it did perform well for Neotoma cinerea, probably because of the greater degree of folding and more acute angling of molar lophs. In contrast, wider lophs with shallower enamel infolding was characteristic of species specializing on softer, more succulent resources (i.e., Neotoma albigula and Neotoma micropus). Neotoma floridana were inaccurately classified to species in the majority of cases, but were the only molars correctly identified to locality 100% of the time, suggesting that dietary specializations at a local level may drive morphological changes within the species as well as across the genus.
p16/ki67 and E6/E7 mRNA Accuracy and Prognostic Value in Triaging HPV DNA-Positive Women
Authors: Giorgi Rossi Paolo , Carozzi Francesca , Ronco Guglielmo , Allia Elena , Bisanzi Simonetta , Gillio-Tos Anna , De Marco Laura , Rizzolo Raffaella , Gustinucci Daniela , Del Mistro Annarosa , Frayle Helena , Confortini Massimo , Iossa Anna , Cesarini Elena , Bulletti Simonetta , Passamonti Basilio , Gori Silvia , Toniolo Laura , Barca Alessandra , Bonvicini Laura , Mancuso Pamela , Venturelli Francesco , Benevolo Maria ,   the New Technology for Cervical Cancer 2 Working Group
Published: July 2020

Abstract

Background
The study presents cross-sectional accuracy of E6 and E7 (E6/E7) mRNA detection and p16/ki67 dual staining, alone or in combination with cytology and human papillomavirus (HPV)16/18 genotyping, as a triage test in HPV DNA-positive women and their impact on cervical intraepithelial neoplasia (CIN2+) overdiagnosis.

Methods
Women aged 25-64 years were recruited. HPV DNA-positive women were triaged with cytology and tested for E6/E7 mRNA and p16/ki67. Cytology positive women were referred to colposcopy, and negatives were randomly assigned to immediate colposcopy or to 1-year HPV retesting. Lesions found within 24 months since recruitment were included. All P values were 2-sided.

Results
40 509 women were recruited, and 3147 (7.8%) tested HPV DNA positive; 174 CIN2+ were found: sensitivity was 61.0% (95% confidence interval [CI] = 53.6 to 68.0), 94.4% (95% CI = 89.1 to 97.3), and 75.2% (95% CI = 68.1 to 81.6) for cytology, E6/E7 mRNA, and p16/ki67, respectively. Immediate referral was 25.6%, 66.8%, and 28.3%, respectively. Overall referral was 65.3%, 78.3%, and 63.3%, respectively. Cytology or p16/ki67, when combined with HPV16/18 typing, reached higher sensitivity with a small impact on referral. Among the 2306 HPV DNA-positive and cytology-negative women, relative CIN2+ detection in those randomly assigned at 1-year retesting vs immediate colposcopy suggests a -28% CIN2+ regression (95% CI = -57% to +20%); regression was higher in E6/E7 mRNA-negatives (Pinteraction = .29). HPV clearance at 1 year in E6/E7 mRNA and in p16/ki67 negative women was about 2 times higher than in positive women (Pinteraction &lt; .001 for both).

Conclusions
p16/ki67 showed good performance as a triage test. E6/E7 mRNA showed the highest sensitivity, at the price of too high a positivity rate to be efficient for triage. However, when negative, it showed a good prognostic value for clearance and CIN2+ regression.
MYB134-RNAi poplar plants show reduced tannin synthesis in leaves but not roots, and increased susceptibility to oxidative stress
Authors: Gourlay Geraldine , Ma Dawei , Schmidt Axel , Constabel C Peter 
Published: July 2020

Abstract
The importance of the poplar MYB134 gene in controlling condensed tannin (CT) biosynthesis was tested by suppressing its expression using RNA interference (RNAi). MYB134-RNAi plants grew normally but showed reduced accumulation of stress-induced CTs in leaves. RNA-seq analysis indicated that flavonoid- and CT-related genes, as well as additional CT regulators, were strongly and specifically down-regulated by MYB134 suppression. This confirmed that the primary MYB134 target is the leaf flavonoid and CT pathway. Root CT accumulation was not impacted by MYB suppression, suggesting that additional CT regulators are active in roots and emphasizing the complexity of the regulation of CTs in poplar. To test the effect of CT down-regulation on oxidative stress resistance, leaves of MYB134-RNAi and control plants were exposed to the reactive oxygen species generator methyl viologen. MYB134-RNAi leaves sustained significantly more photosystem II damage, as seen in reduced chlorophyll fluorescence, compared with wild-type leaves. MYB134-RNAi leaves also contained more hydrogen peroxide, a reactive oxygen species, compared with the wild type. Our data thus corroborate the hypothesis that CT can act as an antioxidant in vivo and protect against oxidative stress. Overall, MYB134 was shown to be a central player in the regulation of CT synthesis in leaves.
SN 2018zd: an unusual stellar explosion as part of the diverse Type II Supernova landscape
Authors: Zhang Jujia , Wang Xiaofeng , József Vinkó , Zhai Qian , Zhang Tianmeng , Filippenko Alexei V , Brink Thomas G , Zheng WeiKang , Wyrzykowski Łukasz , Mikołajczyk Przemysław , Huang Fang , Rui Liming , Mo Jun , Sai Hanna , Zhang Xinhan , Wang Huijuan , DerKacy James M , Baron Eddie , Sárneczky K , Bódi A , Csörnyei G , Hanyecz O , Ignácz B , Kalup Cs , Kriskovics L , Könyves-Tóth R , Ordasi A , Pál A , Sódor Á , Szakáts R , Vida K , Zsidi G 
Published: July 2020

ABSTRACT
We present extensive observations of SN 2018zd covering the first ∼450 d after the explosion. This SN shows a possible shock-breakout signal ∼3.6 h after the explosion in the unfiltered light curve, and prominent flash-ionization spectral features within the first week. The unusual photospheric temperature rise (rapidly from ∼12 000 to above 18 000 K) within the earliest few days suggests that the ejecta were continuously heated. Both the significant temperature rise and the flash spectral features can be explained by the interaction of the SN ejecta with the massive stellar wind ($0.18^{+0.05}_{-0.10}\, \rm M_{\odot }$), which accounts for the luminous peak ($L_{\rm max} = [1.36\pm 0.63] \times 10^{43}\, \rm erg\, s^{-1}$) of SN 2018zd. The luminous peak and low expansion velocity (v ≈ 3300 km s−1) make SN 2018zd like a member of the LLEV (luminous SNe II with low expansion velocities) events originating due to circumstellar interaction. The relatively fast post-peak decline allows a classification of SN 2018zd as a transition event morphologically linking SNe IIP and SNe IIL. In the radioactive-decay phase, SN 2018zd experienced a significant flux drop and behaved more like a low-luminosity SN IIP both spectroscopically and photometrically. This contrast indicates that circumstellar interaction plays a vital role in modifying the observed light curves of SNe II. Comparing nebular-phase spectra with model predictions suggests that SN 2018zd arose from a star of $\sim 12\, \rm M_{\odot }$. Given the relatively small amount of 56Ni ($0.013\!-\!0.035 \rm M_{\odot }$), the massive stellar wind, and the faint X-ray radiation, the progenitor of SN 2018zd could be a massive asymptotic giant branch star that collapsed owing to electron capture.