julilili42/papers huggingface dataset:
Prior Specification for More Stable Bayesian Estimation of Multilevel Latent Variable Models in Small Samples: A Comparative Investigation of Two Different Approaches
2021-01-25

Bayesian approaches for estimating multilevel latent variable models can be beneficial in small samples. Prior distributions can be used to overcome small sample problems, for example, when priors that increase the accuracy of estimation are chosen. This article discusses two different but not mutually exclusive approaches for specifying priors. Both approaches aim at stabilizing estimators in such a way that the Mean Squared Error (MSE) of the estimator of the between-group slope will be small. In the first approach, the MSE is decreased by specifying a slightly informative prior for the group-level variance of the predictor variable, whereas in the second approach, the decrease is achieved directly by using a slightly informative prior for the slope. Mathematical and graphical inspections suggest that both approaches can be effective for reducing the MSE in small samples, thus rendering them attractive in these situations. The article also discusses how these approaches can be implemented in M plus .
Probing Bias-Induced Electron Density Shifts in Metal–Molecule Interfaces via Tip-Enhanced Raman Scattering
2021-01-25

Surface charging effects at metal-molecule interfaces, for example, charge transfer, charge transport, charge injection, and so on, have a strong impact on the performance of organic electronics. Only having molecules bound or adsorbed on different metals results in a doping-like behavior at the interface by the different work functions of the metals and creates hybrid surface states, which strongly affect the efficiencies. With the ongoing downsizing and thinning of the organic components, the impact of the interface will even further increase. However, most of the investigations only monitor the interface without the additional charging effects from applying a voltage to the interface. In this work we present a spectroscopic approach based on tip-enhanced Raman spectroscopy (TERS) to study metal-molecule interfaces with an applied voltage simulating the electric field strength in real devices. We monitor how an intrinsic inductive effect of partial functional groups in molecules can shift the molecular electron density (ED) distribution when a bias voltage is applied. Therefore, we choose two molecules as model systems, which are similar in size and binding condition to a smooth gold surface, but with different electronic structure. By placing the tip 1 nm over the molecular surface at a fixed position and changing the applied bias voltage, we record electric-field-dependent tip-enhanced Raman spectra. Specific vibrational bands exhibit voltage-dependent intensity changes related to the shift of the local ED inside the molecules. We believe this experiment is valuable to gain deeper insights into charged metal-molecule interfaces.
Using Crowd-Sourced Speech Data to Study Socially Constrained Variation in Nonmodal Phonation
2021-01-25

This study examines the status of nonmodal phonation (e.g. breathy and creaky voice) in British English using smartphone recordings from over 2,500 speakers. With this novel data collection method, it uncovers effects that have not been reported in past work, such as a relationship between speakers’ education and their production of nonmodal phonation. The results also confirm that previous findings on nonmodal phonation, including the greater use of creaky voice by male speakers than female speakers, extend to a much larger and more diverse sample than has been considered previously. This confirmation supports the validity of using crowd-sourced data for phonetic analyses. The acoustic correlates that were examined include fundamental frequency, H1*-H2*, cepstral peak prominence, and harmonic-to-noise ratio.
Complementary Role of Computed Tomography Texture Analysis for Differentiation of Hepatocellular Carcinoma from Intrahepatic Peripheral Cholangiocellular Carcinoma on Single Portal-Venous Phase Computed Tomography
2021-01-25

Kaspar Ekert1*, Thomas Horger2, Aenne Oelker2, Karolin Baumgartner1, Hans Bösmüller3#, Michael Bitzer4 and Marius Horger1# Author Affiliations 1Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany 2Technical University Munich, Boltzmannstraße 3, 85748 Garching, Germany 3Department of General and molecular Pathology and pathological Anatomy, Liebermeisterstraße 8, 72076 Tübingen, Germany 4Department of Internal Medicine I, Eberhard-Karls-University, Otfried-Müller-Str. 10, 72076, Tübingen, Germany #both authors share equal contribution Received: January 16, 2021 | Published: January 25, 2021 Corresponding author: Kaspar Ekert, Eberhard Karls University, Department of Radiology, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany DOI: 10.26717/BJSTR.2021.33.005392
Magnetic Bead-Based Immunoassay Allows Rapid, Inexpensive, and Quantitative Detection of Human SARS-CoV-2 Antibodies
2021-01-26

Immunological methods to detect SARS-CoV-2 seroconversion in humans are important to track COVID-19 cases and the humoral response to SARS-CoV-2 infections and immunization to future vaccines. The aim of this work was to develop a simple chromogenic magnetic bead-based immunoassay which allows rapid, inexpensive, and quantitative detection of human antibodies against SARS-CoV-2 in serum, plasma, or blood. Recombinant 6xHis-tagged SARS-CoV-2 Nucleocapsid protein was mobilized on the surface of Ni<sup>2+</sup> magnetic beads and challenged with serum or blood samples obtained from controls or COVID-19 cases. The beads were washed, incubated with anti-human IgG-HPR conjugate, and immersed into a solution containing a chromogenic HPR substrate. Bead transfer and homogenization between solutions was aided by a simple low-cost device. The method was validated by two independent laboratories, and the performance to detect SARS-CoV-2 seroconversion in humans was in the same range as obtained using the gold standard immunoassays ELISA and Luminex, though requiring only a fraction of consumables, instrumentation, time to deliver results, and volume of sample. Furthermore, the results obtained with the method described can be visually interpreted without compromising accuracy as demonstrated by validation at a point-of-care unit. The magnetic bead immunoassay throughput can be customized on demand and is readily adapted to be used with any other 6xHis tagged protein or peptide as antigen to track other diseases.
Breast Cancer Risk Factors and Survival by Tumor Subtype: Pooled Analyses from the Breast Cancer Association Consortium
2021-01-26

Abstract Background: It is not known whether modifiable lifestyle factors that predict survival after invasive breast cancer differ by subtype. Methods: We analyzed data for 121,435 women diagnosed with breast cancer from 67 studies in the Breast Cancer Association Consortium with 16,890 deaths (8,554 breast cancer specific) over 10 years. Cox regression was used to estimate associations between risk factors and 10-year all-cause mortality and breast cancer–specific mortality overall, by estrogen receptor (ER) status, and by intrinsic-like subtype. Results: There was no evidence of heterogeneous associations between risk factors and mortality by subtype (Padj &amp;gt; 0.30). The strongest associations were between all-cause mortality and BMI ≥30 versus 18.5–25 kg/m2 [HR (95% confidence interval (CI), 1.19 (1.06–1.34)]; current versus never smoking [1.37 (1.27–1.47)], high versus low physical activity [0.43 (0.21–0.86)], age ≥30 years versus &amp;lt;20 years at first pregnancy [0.79 (0.72–0.86)]; &amp;gt;0–&amp;lt;5 years versus ≥10 years since last full-term birth [1.31 (1.11–1.55)]; ever versus never use of oral contraceptives [0.91 (0.87–0.96)]; ever versus never use of menopausal hormone therapy, including current estrogen–progestin therapy [0.61 (0.54–0.69)]. Similar associations with breast cancer mortality were weaker; for example, 1.11 (1.02–1.21) for current versus never smoking. Conclusions: We confirm associations between modifiable lifestyle factors and 10-year all-cause mortality. There was no strong evidence that associations differed by ER status or intrinsic-like subtype. Impact: Given the large dataset and lack of evidence that associations between modifiable risk factors and 10-year mortality differed by subtype, these associations could be cautiously used in prognostication models to inform patient-centered care.
A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans
2021-01-26

Abstract Deafness, the most frequent sensory deficit in humans, is extremely heterogeneous with hundreds of genes involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein, as a new deafness gene. Homozygosity mapping followed by exome sequencing identified a 14.96 Mb locus on chromosome 4p15.32p15.1 containing a likely pathogenic missense variant in CLRN2 (c.494C &gt; A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C &gt; A variant leads to two events: (1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and (2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients.
Four pages are indeed necessary for planar graphs
2021-01-26

An embedding of a graph in a book consists of a linear order of its vertices along the spine of the book and of an assignment of its edges to the pages of the book, so that no two edges on the same page cross. The book thickness of a graph is the minimum number of pages over all its book embeddings. Accordingly, the book thickness of a class of graphs is the maximum book thickness over all its members. In this paper, we address a long-standing open problem regarding the exact book thickness of the class of planar graphs, which previously was known to be either three or four. We settle this problem by constructing planar graphs that require four pages in all of their book embeddings, thus establishing that the book thickness of the class of planar graphs is four.
The selection gap in teacher education: Adverse effects of ethnicity, gender, and socio‐economic status on situational judgement test performance
2021-01-26

Background Situational judgement tests (SJTs) measure non‐cognitive attributes and have recently drawn attention as a selection method for initial teacher education programmes. To date, very little is known about adverse impact in teacher selection SJT performance. Aims This study aimed to shed light on adverse effects of gender, ethnicity, and socio‐economic status (SES) on SJT scores, by exploring both main effects and interactions, and considering both overall SJT performance and separate SJT domain scores (mindset, emotion regulation, and conscientiousness). Sample A total of 2,808 prospective teachers from the United Kingdom completed the SJTs as part of the initial stage of selection into a teacher education programme. Methods In addition to SJT scores, the variables gender (female vs. male), ethnicity (majority group vs. minority group), and home SES background (higher SES status vs. lower SES status) were used in the analyses. Regression models and moderated regression models were employed. Results and conclusions Results from the regression models revealed that gender effects (females scoring higher than males) were restricted to emotion regulation, while ethnicity effects (ethnic majority group members scoring higher than ethnic minority group members) emerged for SJT overall scores and all three domains. Moderated regression modelling results furthermore showed significant interactions (gender and ethnicity) for SJT overall scores and two domains. Considering the importance of reducing subgroup differences in selection test scores to ensure equal access to teacher education, this study’s findings are a critical contribution. The partially differentiated results for overall vs. domain‐specific scores point towards the promise of applying a domain‐level perspective in research on teacher selection SJTs.
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2
2021-01-26

Abstract A detailed understanding of antibody-based SARS-CoV-2 immunity has critical implications for overcoming the COVID-19 pandemic and for informing on vaccination strategies. In this study, we evaluated the dynamics of the SARS-CoV-2 antibody response in a cohort of 963 recovered individuals over a period of 10 months. Investigating a total of 2,146 samples, we detected an initial SARS-CoV-2 antibody response in 94.4% of individuals, with 82% and 79% exhibiting serum and IgG neutralization, respectively. Approximately 3% of recovered patients demonstrated exceptional SARS-CoV-2 neutralizing activity, defining them as ‘elite neutralizers’. These individuals also possessed effective cross-neutralizing IgG antibodies to SARS-CoV-1 without any known prior exposure to this virus. By applying multivariate statistical modeling, we found that sero-reactivity, age, time since disease onset, and fever are key factors predicting SARS-CoV-2 neutralizing activity in mild courses of COVID-19. Investigating longevity of the antibody response, we detected loss of anti-spike reactivity in 13% of individuals 10 months after infection. Moreover, neutralizing activity had an initial half-life of 6.7 weeks in serum versus 30.8 weeks in purified IgG samples indicating the presence of a more stable and long-term memory IgG B cell repertoire in the majority of individuals recovered from COVID-19. Our results demonstrate a broad spectrum of the initial SARS-CoV-2 neutralizing antibody response depending on clinical characteristics, with antibodies being maintained in the majority of individuals for the first 10 months after mild course of COVID-19.
Macrophage and Lymphocyte Infiltration Is Associated with Volumetric Tumor Size but Not with Volumetric Growth in the Tübingen Schwannoma Cohort
2021-01-26

Most patients with vestibular schwannomas can be cured with microsurgical resection, or tumor growth can be stabilized by radiotherapy in certain cases. Recurrence is rare but usually difficult to treat. Treatment alternatives to local therapies are not established. There is growing evidence of the role of inflammatory processes in schwannomas, which may be exploitable by targeted innovative therapies. To further define the impact of inflammation with tumor growth in vestibular schwannoma, we performed immunohistochemical analyses of CD3, CD8, CD68 and CD163 to assess lymphocyte and macrophage infiltration in 923 tumor tissue samples of surgically resected vestibular schwannomas. An inflammatory score was compared with tumor size and volumetric growth. We observed a significantly larger preoperative tumor size with increased expression rates of CD3, CD8, CD68 and CD163 (p &lt; 0.0001, p &lt; 0.0001, p = 0.0015 and p &lt; 0.0001, respectively), but no differences in percentual volumetric tumor growth. When all four markers were combined as an inflammatory score, tumors with high inflammatory infiltration showed slower percentual growth in a multivariate analysis, including MIB1 expression (p = 0.0249). We conclude that inflammatory cell infiltration increases with larger tumor size but is associated with slower percentual volumetric tumor growth.
Agreement between careHPV and hybrid capture 2 in detecting high‐risk HPV in women in Tanzania
2021-01-26

Abstract Introduction Visual inspection of the cervix with acetic acid is used to control the burden of cervical cancer in low‐ and middle‐income countries. This method has some limitations and HPV DNA testing may be an alternative, but it is expensive and requires a laboratory setup. Cheaper and faster HPV tests have been developed. This study describe the agreement between a fast HPV test ( care HPV) and hybrid capture 2 (HC2) in detection of high‐risk HPV among Tanzanian women. Material and methods The study involved women attending routine cervical cancer screening at the Ocean Road Cancer Institute and Kilimanjaro Christian Medical Centre in Tanzania. The women were offered HIV testing. Two cervical samples were subsequently obtained; the first sample was processed at the clinics using care HPV and the second sample was transported to Denmark and Germany for cytology and HC2 analysis. Kappa statistic was calculated to assess the agreement between care HPV and HC2. The sensitivity, specificity and predictive values of care HPV were calculated using HC2 as reference. The analyses were done for the overall study population and stratified by testing site and HIV status. Results A total of 4080 women were enrolled, with 437 being excluded due to invalid information, lack of care HPV or HC2 results. Overall agreement between the tests was substantial with a kappa value of 0.69 (95% confidence interval [CI] 0.66‐0.72). The sensitivity and specificity of care HPV was 90.7% (95% CI 89.6‐91.8) and 84.2% (95% CI 81.2–86.8), respectively. The agreement was similar in the stratified analyses where the kappa values were 0.75 (95% CI 0.70‐0.79) in women aged 25‐34, 0.66 (95% CI 0.62‐0.70) in women aged 35–60, 0.73 (95% CI 0.70‐0.77) at the Ocean Road Cancer Institute, 0.64 (95% CI 0.60‐0.69) at the Kilimanjaro Christian Medical Center, 0.73 (95% CI 0.68‐0.79) in HIV‐positive and 0.66 (95% CI 0.63‐0.70) in HIV‐negative women. The kappa value of 0.64 (95% CI 0.39‐0.88) for cervical high‐grade lesions indicates a substantial agreement between care HPV and HC2 in detecting HPV among women with cervical high‐grade lesions. Conclusions A substantial agreement was found between care HPV and HC2 in detecting HPV overall as well as detecting HPV among women with cervical high‐grade lesions. However, given the limited resources available in low and middle‐income countries, the HPV testing assay should be weighed against the cost‐effectiveness of the test.
Genetic overlap between Alzheimer’s disease and depression mapped onto the brain
2021-01-26

ABSTRACT Background Alzheimer’s disease (AD) and depression are debilitating brain disorders that are often comorbid. Shared brain mechanisms have been implicated, yet findings are inconsistent, reflecting the complexity of the underlying pathophysiology. As both disorders are (partly) heritable, characterizing their genetic overlap may provide etiological clues. While previous studies have indicated negligible genetic correlations, this study aims to expose the genetic overlap that may remain hidden due to mixed directions of effects. Methods We applied Gaussian mixture modelling, through MiXeR, and conjunctional false discovery rate (cFDR) analysis, through pleioFDR, to genome-wide association study (GWAS) summary statistics of AD (n=79,145) and depression (n=450,619). The effects of identified overlapping loci on AD and depression were tested in 403,029 participants of the UK Biobank (mean age 57.21 52.0% female), and mapped onto brain morphology in 30,699 individuals with brain MRI data. Results MiXer estimated 98 causal genetic variants overlapping between the two disorders, with 0.44 concordant directions of effects. Through pleioFDR, we identified a SNP in the TMEM106B gene, which was significantly associated with AD (B=-0.002, p=9.1×10 −4 ) and depression (B=0.007, p=3.2×10 −9 ) in the UK Biobank. This SNP was also associated with several regions of the corpus callosum volume anterior (B&gt;0.024, p&lt;8.6×10 −4 ), third ventricle volume ventricle (B=-0.025, p=5.0×10 −6 ), and inferior temporal gyrus surface area (B=0.017, p=5.3×10 −4 ). Discussion Our results indicate there is substantial genetic overlap, with mixed directions of effects, between AD and depression. These findings illustrate the value of biostatistical tools that capture such overlap, providing insight into the genetic architectures of these disorders.
Small proteins modulate ion channel-like ACD6 to regulate immunity inArabidopsis thaliana
2021-01-26

SUMMARY ACCELERATED CELL DEATH 6 (ACD6) mediates a trade-off between growth and defense in Arabidopsis thaliana . However, the precise biochemical mechanism by which ACD6 and related proteins in plants act remains enigmatic. Here, we identified two loci, MODULATOR OF HYPERACTIVE ACD6 1 ( MHA1 ) and its paralog MHA1-LIKE ( MHA1L ), that code for ∼7 kDa proteins that differentially interact with specific ACD6 variants. MHA1L enhances accumulation of an ACD6 complex, thereby increasing activity of the ACD6 standard allele for regulating plant growth and defenses. ACD6 is a multipass transmembrane protein with intracellular ankyrin repeats that are structurally similar to those found in mammalian ion channels. Several lines of evidence link increased ACD6 activity to enhanced calcium influx, likely mediated by ACD6 itself and with MHA1L as a direct regulator of ACD6.
Estimation of the SARS-CoV-2 infection fatality rate in Germany
2021-01-26

ABSTRACT Assessing the infection fatality rate (IFR) of SARS-CoV-2 is one of the most controversial issues during the pandemic. Due to asymptomatic or mild courses of COVID-19, many infections remain undetected. Reported case fatality rates – COVID-19-associated deaths divided by number of detected infections – are therefore poor estimates of the IFR. Endogenous changes of the population at risk of a SARS-CoV-2 infection, changing test practices and an improved understanding of the pathogenesis of COVID-19 further exacerbate the estimation of the IFR. Here, we propose a strategy to estimate the IFR of SARS-CoV-2 in Germany that combines official data on reported cases and fatalities supplied by the Robert Koch Institute (RKI) with data from seroepidemiological studies in two infection hotspots, the Austrian town Ischgl and the German municipality Gangelt, respectively. For this purpose, we use the law of total probability to derive an approximate formula for the IFR that is based on a set of assumptions regarding data quality and test specificity and sensitivity. The resulting estimate of the IFR in Germany of 0.83% (95% CI: [0.69%; 0.98%]) that is based on a combination of the RKI and Ischgl data is notably higher than the IFR estimate reported in the Gangelt study (0.36% [0.29%; 0.45%]). It is closer to the consolidated estimate based on a meta-analysis (0.68% [0.53%; 0.82%]), where the difference can be explained by Germany’s disadvantageous age structure. As a result of virus mutations, vaccination strategies, and improved therapy, a re-estimation of the IFR will eventually be mandated; the proposed method is able to account for such developments.
Code for: Selective exposure in action: Do visitors of product evaluation portals select reviews in a biased manner?
2021-01-26

Code for: Winter, K., Zapf, B., Hütter, M., Tichy, N., &amp; Sassenberg, K. (2021). Selective exposure in action: Do visitors of product evaluation portals select reviews in a biased manner? Cyberpsychology: Journal of Psychosocial Research on Cyberspace, 15(1), article 4. https://doi.org/10.5817/CP2021-1-4