julilili42/papers huggingface dataset:
Does error-driven learning occur in the absence of cues? Examination of the effects of updating connection weights to absent cues
2022-07-27

&lt;p&gt;The Rescorla-Wagner model has seen widespread success in modelling not only its original target of animal learning, but also several areas of human learning. However, despite its success, a number of studies with humans have found effects that are not predicted by the model, thus inspiring proposals for modifications to the model. One such proposal, by Van Hamme and Wasserman (1994, VHW), is that humans not only learn from present cues to all (present and absent) outcomes, as in the original model, but also learn from the absence of cues. They found evidence for this hypothesis in a causal rating experiment. However, behaviour in learning studies may depend on the task. We propose that error-driven learning should be considered to be a form of &lt;em&gt;implicit &lt;/em&gt;learning and that the results of VHW&rsquo;s contingency judgement task might stem from explicit strategies involving logic and reasoning. The present study investigates this question by a) running simulations with both the original and modified versions of the model; b) replicating the VHW experiment (Experiment 1); and c) extending the experiment with new stimuli and a post- test of learned and unseen stimuli (Experiment 2). Simulations show that the VHW modified model predicts that cues learnt at the beginning will be unlearnt when absent over the following blocks, so that they become negative predictors over time. In contrast, the original RW predicts that the absent cues remain steady (positive) predictors over the blocks. Results showed no significant difference in cue assignment between training and test, in line with the original RW model. Moreover, predictive cues in the training phase showed significantly higher ratings than a new cue introduced in the test phase, at least in some cases, also partially supporting the original RW. The results suggest that when an overt response is required to ab- sent cues, participants adjust ratings. But in later blocks when no response was required, there did not appear to be learning from the absent cues. We propose that in the development of human learning theory, attention should be paid to whether the behaviour (or other learning data) to be modelled results from implicit learning or involves higher level cognitive processes. We suggest that the RW may best capture implicit error-driven learning.&lt;/p&gt;
Reply on RC3
2022-07-27

<strong class="journal-contentHeaderColor">Abstract.</strong> The determination of the wind profile of the lower atmospheric boundary layer is an important aspect of meteorology and wind energy science. A suitable tool to capture the wind profile is the usage of small unmanned aircraft systems (UAS). This study describes an easily repeatable type of calibration process in order to obtain an estimation of the horizontal wind vector using a rotary-wing UAS in hovering conditions. This procedure works without using wind tunnels or meteorological masts: it requires only the data from the flight control unit and a particular set of calibration flights. A modified DJI S900 hexacopter has been used for this study. The UAS body has been encased in a styrofoam sphere, leaving only the rotors and the landing gear outside, in order to grant a higher level of isotropy with respect to the incoming wind flow. A model based on the characterization of the UAS drag coefficient is proposed for the estimation of the relative horizontal wind vector. Validation flights have been performed at the German Weather Service MOL-RAO observatory in Falkenberg, Brandenburg. By hovering aside of a 99 m high meteorological mast with ultrasonic anemometers, it was possible to prove the wind prediction capability and assess the accuracy of the model. The analysis of the power spectral density highlights how the system resolves atmospheric eddies up to 0.1 Hz frequency. The overall root mean square error is less than 0.7 ms<sup>-1</sup> for the wind speed while less than 8&deg; for the wind direction.
Reply on RC1
2022-07-27

<strong class="journal-contentHeaderColor">Abstract.</strong> The determination of the wind profile of the lower atmospheric boundary layer is an important aspect of meteorology and wind energy science. A suitable tool to capture the wind profile is the usage of small unmanned aircraft systems (UAS). This study describes an easily repeatable type of calibration process in order to obtain an estimation of the horizontal wind vector using a rotary-wing UAS in hovering conditions. This procedure works without using wind tunnels or meteorological masts: it requires only the data from the flight control unit and a particular set of calibration flights. A modified DJI S900 hexacopter has been used for this study. The UAS body has been encased in a styrofoam sphere, leaving only the rotors and the landing gear outside, in order to grant a higher level of isotropy with respect to the incoming wind flow. A model based on the characterization of the UAS drag coefficient is proposed for the estimation of the relative horizontal wind vector. Validation flights have been performed at the German Weather Service MOL-RAO observatory in Falkenberg, Brandenburg. By hovering aside of a 99 m high meteorological mast with ultrasonic anemometers, it was possible to prove the wind prediction capability and assess the accuracy of the model. The analysis of the power spectral density highlights how the system resolves atmospheric eddies up to 0.1 Hz frequency. The overall root mean square error is less than 0.7 ms<sup>-1</sup> for the wind speed while less than 8&deg; for the wind direction.
Report on 2104.11160v3
2022-07-27

We study the dynamics of a one-dimensional Rydberg lattice gas under facilitation (anti-blockade) conditions which implements a so-called kinetically constrained spin system.Here an atom can only be excited to a Rydberg state when one of its neighbors is already excited.Once two or more atoms are simultaneously excited mechanical forces emerge, which couple the internal electronic dynamics of this many-body system to external vibrational degrees of freedom in the lattice.This electron-phonon coupling results in a so-called phonon dressing of many-body states which in turn impacts on the facilitation dynamics.In our theoretical study we focus on a scenario in which all energy scales are sufficiently separated such that a perturbative treatment of the coupling between electronic and vibrational states is possible.This allows to analytically derive an effective Hamiltonian for the evolution of consecutive clusters of Rydberg excitations in the presence of phonon dressing.We analyze the spectrum of this Hamiltonian and show -by employing Fano resonance theory -that the interaction between Rydberg excitations and lattice vibrations leads to the emergence of slowly decaying bound states that inhibit fast relaxation of certain initial states.
Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense
2022-07-27

&lt;p&gt;This repository stores data produced from a genomic and epigenomic large-scale survey of natural populations of &lt;em&gt;Thlaspi arvense&lt;/em&gt;, investigating the genetic and environmental bases of epigenetic variation. 207 lines from across Europe were grown in common environment and scored for genetic and DNA methylation variation by Whole Genome Sequencing and Whole Genome Bisulfite Sequencing respectively. This repository includes:&lt;/p&gt; &lt;p&gt;1) The original mean&nbsp;methylation values for all lines, the respective processed values (corrected for non-conversion rate by subtracting the &quot;Surplus_0.6NCR&quot;, and optionally corrected for coverage and transformed), used for Genome Wide Association Studies (GWAS) and correlation with climatic variables. In addition, the weighted methylation values (Schultz et al. 2012) are available.&lt;/p&gt; &lt;p&gt;2) Differentially Methylated Regions and Variance Decomposition Analysis results, obtained with&nbsp;scripts available at&nbsp;https://github.com/Dario-Galanti/popDMRs_refine_VCA.&lt;/p&gt; &lt;p&gt;3) Gene Body Methylation (GBM) classification for each line and sequence context.&nbsp;A&nbsp;binomial test was applied to each coding sequence (CDS) to determine if its fraction of methylated cytosines was higher than average (Takuno and Gaut 2013). A 0 indicates a non-significant test, a 1 indicates a significant test. Code available at&nbsp;https://github.com/Dario-Galanti/WGBS_downstream/tree/main/WGBS_completeworkflow.&lt;/p&gt; &lt;p&gt;4)&nbsp;GWAS results (filtered for -log(p)&gt;1) for all processed mean&nbsp;methylation values are available with the &quot;.gwas&quot; extention and can be&nbsp;opened with Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/), using the reference genome published by Nunn et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34990041/).&lt;/p&gt;
Thinking about thinking: People underestimate how enjoyable and engaging just waiting is.
2022-07-28

The ability to engage in internal thoughts without external stimulation is a unique characteristic in humans. The current research tested the hypothesis that people metacognitively underestimate their capability to enjoy this process of "just thinking." Participants (university students; total N = 259) were asked to sit and wait in a quiet room without doing anything. Across six experiments, we consistently found that participants' predicted enjoyment and engagement for the waiting task were significantly less than what they actually experienced. This underappreciation of just thinking also led participants to proactively avoid the waiting task in favor of an alternative task (i.e., Internet news checking), despite their experiences not being statistically different. These results suggest an inherent difficulty in accurately appreciating how engaging just thinking can be, and could explain why people prefer keeping themselves busy, rather than taking a moment for reflection and imagination in our daily life. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
Generation of Leukaemia-Derived Dendritic Cells (DCleu) to Improve Anti-Leukaemic Activity in AML: Selection of the Most Efficient Response Modifier Combinations
2022-07-28

Dendritic cells (DC) and leukaemia derived DC (DCleu) are potent stimulators of anti-leukaemic activity in acute myeloid leukaemia (AML) and can be generated from mononuclear cells in vitro following standard DC/DCleu-generating protocols. With respect to future clinical applications though, DC/DCleu-generating protocols specifically designed for application in a whole-blood-(WB)-environment must be established. Therefore, we developed ten new DC/DCleu-generating protocols (kits; Kit-A/-C/-D/-E/-F/-G/-H/-I/-K/-M) for the generation of DC/DCleu from leukaemic WB, containing calcium-ionophore, granulocyte-macrophage-colony-stimulating-factor (GM-CSF), tumour-necrosis-factor-alpha, prostaglandin-E1 (PGE1), prostaglandin-E2 (PGE2) and/or picibanil (OK-432). All protocols were evaluated regarding their performance in generating DC/DCleu using refined classification and/or ranking systems; DC/DCleu were evaluated regarding their performance in stimulating anti-leukaemic activity using a cytotoxicity fluorolysis assay. Overall, we found the new kits capable to generate (mature) DC/DCleu from leukaemic WB. Through refined classification and ranking systems, we were able to select Kit-I (GM-CSF + OK-432), -K (GM-CSF + PGE2) and -M (GM-CSF + PGE1) as the most efficient kits in generating (mature) DC/DCleu, which are further competent to stimulate immunoreactive cells to show an improved anti-leukaemic cytotoxicity as well. This great performance of Kit-I, -K and -M in mediating DC/DCleu-based anti-leukaemic immunity in a WB-environment in vitro constitutes an important and directive step for translating DC/DCleu-based immunotherapy of AML into clinical application.
Malaria Transmission Intensity Likely Modifies RTS, S/AS01 Efficacy Due to a Rebound Effect in Ghana, Malawi, and Gabon
2022-07-28

Abstract Background RTS,S/AS01 is the first malaria vaccine to be approved and recommended for widespread implementation by the World Health Organization (WHO). Trials reported lower vaccine efficacies in higher-incidence sites, potentially due to a “rebound” in malaria cases in vaccinated children. When naturally acquired protection in the control group rises and vaccine protection in the vaccinated wanes concurrently, malaria incidence can become greater in the vaccinated than in the control group, resulting in negative vaccine efficacies. Methods Using data from the 2009–2014 phase III trial (NCT00866619) in Lilongwe, Malawi; Kintampo, Ghana; and Lambaréné, Gabon, we evaluate this hypothesis by estimating malaria incidence in each vaccine group over time and in varying transmission settings. After estimating transmission intensities using ecological variables, we fit models with 3-way interactions between vaccination, time, and transmission intensity. Results Over time, incidence decreased in the control group and increased in the vaccine group. Three-dose efficacy in the lowest-transmission-intensity group (0.25 cases per person-year [CPPY]) decreased from 88.2% to 15.0% over 4.5 years, compared with 81.6% to −27.7% in the highest-transmission-intensity group (3 CPPY). Conclusions These findings suggest that interventions, including the fourth RTS,S dose, that protect vaccinated individuals during the potential rebound period should be implemented for high-transmission settings.
Radiotherapy and hyperthermia for breast cancer patients at high risk of recurrence
2022-07-28

To evaluate the long-term efficacy of combined radiotherapy (RT) and hyperthermia (HT) in a large mono-institutional cohort of breast cancer (BC) patients affected by recurrent, newly diagnosed non-resectable or high risk resected tumor. Records of BC patients treated with RT + HT between 1995 and 2018 were retrospectively analyzed. RT doses of 50–70 Gy concurrent to a twice per week superficial HT were applied. For HT, a temperature between 41 and 42 °C was applied for approximately 1 h. Primary endpoint was local control (LC), secondary endpoints comprised toxicity, overall survival (OS), and progression-free survival (PFS). A total of 191 patients and 196 RT + HT treatments were analyzed. In 154 cases (78.6%) RT + HT was performed for patients with recurrent BC. Among these, 93 (47.4% of the entire cohort) had received RT prior to RT + HT. Median follow up was 12.7 years. LC at 2, 5, and 10 years was 76.4, 72.8, and 69.5%, respectively. OS at 2, 5, and 10 years was 73.5, 52.3, and 35.5%, respectively. PFS at 2, 5, and 10 years was 55.6, 41, and 33.6%, respectively. Predictive factors for LC were tumor stage, distant metastases, estrogen/progesterone receptor expression, resection status and number of HT fractions. At multivariate analysis tumor stage and receptor expression were significant. No acute or late toxicities higher than grade 3 were observed. Combined RT + HT offers long-term high LC rates with acceptable toxicity for patients with recurrent, newly diagnosed non-resectable or resected BC at high risk of relapse.
Impedance spectroscopy of ferroelectrics: The domain wall pinning element
2022-07-28

We introduce an equivalent-circuit element based on the theory of interface pinning in random systems to analyze the contribution of domain wall motion below the coercive field to the impedance of a ferroelectric, as a function of amplitude E0 and frequency f of an applied ac electric field. We demonstrate our model on a bulk PbZrxTi1−xO3 (PZT) reference sample and then investigate capacitor stacks, containing ferroelectric 0.5(Ba0.7Ca0.3)TiO3–0.5Ba(Zr0.2Ti0.8)O3 (BCZT) thin films, epitaxially grown by pulsed laser deposition on Nb-doped SrTiO3 single crystal substrates and covered with Au electrodes. Impedance spectra from f=10 Hz to 1 MHz were collected at different E0. Deconvolution of the spectra is achieved by fitting the measured impedance with an equivalent-circuit model of the capacitor stacks, and we extract for E0=2.5 kV/cm, a frequency-dependent permittivity of εr′(f)=458+7.3ln⁡(1Hz/2πf) for the BCZT films from the obtained fit parameters. From an extended Rayleigh analysis, we obtain a coupling strength of 0.187 cm/kV between dielectric nonlinearity and dielectric dispersion in the BCZT films and identify different domain-wall-motion regimes. Finally, we construct a schematic diagram of the different domain-wall-motion regimes and discuss the corresponding domain-wall dynamics. Our approach can be utilized to replace purely phenomenological constant phase elements (CPEs) in modeling the impedance response of ferroelectrics and extracting material properties.
Accurate sex prediction of cisgender and transgender individuals without brain size bias
2022-07-28

Abstract Brain size differs substantially between human males and females. This difference in total intracranial volume (TIV) can cause bias when employing machine-learning approaches for the investigation of sex differences in brain morphology. TIV-biased models will likely not capture actual qualitative sex differences in brain organization but rather learn to classify an individual’s sex based on brain size differences, thus leading to spurious and misleading conclusions, for example when comparing brain morphology between cisgender- and transgender individuals. Here, TIV bias in sex classification models applied to cis- and transgender individuals was systematically investigated by controlling for brain size either through featurewise confound removal or by matching training samples for TIV. Our results provide evidence that non-TIV-biased models can classify the sex of both cis- and transgender individuals with high accuracy, highlighting the importance of appropriate modelling to avoid bias in automated decision making. Teaser Accurate non-biased structural sex classification in cis- and transgender individuals by matching training samples for TIV
TB disease patterns by HIV and diabetes status
2022-07-28

BACKGROUND: TB is commonly categorised as pulmonary (PTB) or extrapulmonary TB (EPTB). Knowledge of TB disease patterns (PTB and/or EPTB) and determining risk factors remains limited. METHODS: This was a prospective cohort study using point-of-care ultrasound (POCUS) in Indian patients with presumed TB. Clinical and imaging data were used to develop refined case definitions for PTB, concurrent PTB and EPTB (PTB + EPTB) and EPTB without PTB (EPTB). These groups were analysed by HIV (HIV+/–) and diabetes mellitus (DM+/–) status. RESULTS: Of 172 HIV–/DM– patients with TB, 48% had PTB, 23% PTB + EPTB and 29% had EPTB, totalling 52% with any EPTB (PTB + EPTB or EPTB). In HIV+/DM– patients with TB ( n = 35), 6% had PTB, 40% had PTB + EPTB and 54% had EPTB, accounting for 94% with EPTB. In HIV–/DM+ patients with TB ( n = 61), 61% had PTB, 28% had PTB + EPTB and 11% had EPTB, representing 39% with EPTB. CONCLUSION: Refined case definitions revealed high proportions of EPTB even without HIV or DM. HIV further altered the TB disease pattern towards EPTB and DM towards PTB. Therefore, the dichotomy between PTB or EPTB does not represent the actual spectrum of TB disease. EPTB should receive higher priority in research and clinical practice.
Replication and Reproducibility in Primate Cognition Research
2022-07-28

Replication is an important tool used to test and develop scientific theories. Areas of biomedical and psychological research have experienced a replication crisis, in which many published findings failed to replicate. Following this, many other scientific disciplines have been interested in the robustness of their own findings. This chapter examines replication in primate cognitive studies. First, it discusses the frequency and success of replication studies in primate cognition and explores the challenges researchers face when designing and interpreting replication studies across the wide range of research designs used across the field. Next, it discusses the type of research that can probe the robustness of published findings, especially when replication studies are difficult to perform. The chapter concludes with a discussion of different roles that replication can have in primate cognition research.
The annual-hydrogen-yield-climatic-response ratio: evaluating the real-life performance of integrated solar water splitting devices
2022-07-28

Integrated solar water splitting devices that produce hydrogen without the use of power inverters operate outdoors and are hence exposed to varying weather conditions. As a result, they might sometimes work at non-optimal operation points below or above the maximum power point of the photovoltaic component, which would directly translate into efficiency losses. Up until now, however, no common parameter describing and quantifying this and other real-life operating related losses (e.g. spectral mismatch) exists in the community. Therefore, the annual-hydrogen-yield-climatic-response (AHYCR) ratio is introduced as a figure of merit to evaluate the outdoor performance of integrated solar water splitting devices. This value is defined as the ratio between the real annual hydrogen yield and the theoretical yield assuming the solar-to-hydrogen device efficiency at standard conditions. This parameter is derived for an exemplary system based on state-of-the-art AlGaAs//Si dual-junction solar cells and an anion exchange membrane electrolyzer using hourly resolved climate data from a location in southern California and from reanalysis data of Antarctica. Moreover, the advantage of devices operating at low current densities over completely decoupled PV-electrolysis is discussed. This work will help to evaluate, compare and optimize the climatic response of solar water splitting devices in different climate zones.
Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense
2022-07-28

This repository stores data produced from a genomic and epigenomic large-scale survey of natural populations of <em>Thlaspi arvense</em>, investigating the genetic and environmental bases of epigenetic variation. 207 lines from across Europe were grown in common environment and scored for genetic and DNA methylation variation by Whole Genome Sequencing and Whole Genome Bisulfite Sequencing respectively. This repository includes: 1) mean methylation values for all lines, the respective processed (transformed and/or corrected for coverage) values used for Genome Wide Association Studies (GWAS) and the weighted methylation values (Schultz et al. 2012). 2) Differentially Methylated Regions and Variance Decomposition Analysis results, obtained with scripts available at https://github.com/Dario-Galanti/popDMRs_refine_VCA. 3) Gene Body Methylation (GBM) classification for each line and sequence context. A binomial test was applied to each coding sequence (CDS) to determine if its fraction of methylated cytosines was higher than average (Takuno and Gaut 2013). A 0 indicates a non-significant test, a 1 indicates a significant test. Code available at https://github.com/Dario-Galanti/WGBS_downstream/tree/main/WGBS_completeworkflow. 4) GWAS results (filtered for -log(p)&gt;1) for all processed mean methylation values are available with the .gwas extention and can be opened with Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/), using the reference genome published by Nunn et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34990041/).