julilili42/papers huggingface dataset:
Proof Systems for Super- Strict Implication
2023-06-05

Abstract This paper studies proof systems for the logics of super-strict implication <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>ST</mml:mi> <mml:mn>2</mml:mn> </mml:mrow> </mml:math> – <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>ST</mml:mi> <mml:mn>5</mml:mn> </mml:mrow> </mml:math> , which correspond to C.I. Lewis’ systems <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>S</mml:mi> <mml:mn>2</mml:mn> </mml:mrow> </mml:math> – <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>S</mml:mi> <mml:mn>5</mml:mn> </mml:mrow> </mml:math> freed of paradoxes of strict implication. First, Hilbert-style axiomatic systems are introduced and shown to be sound and complete by simulating <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>STn</mml:mi> </mml:math> in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>Sn</mml:mi> </mml:math> and backsimulating <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>Sn</mml:mi> </mml:math> in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>STn</mml:mi> </mml:math> , respectively (for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>n</mml:mi> <mml:mo>=</mml:mo> <mml:mn>2</mml:mn> <mml:mo>,</mml:mo> <mml:mo>...</mml:mo> <mml:mo>,</mml:mo> <mml:mn>5</mml:mn> </mml:mrow> </mml:math> ). Next, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>G</mml:mi> <mml:mn>3</mml:mn> </mml:mrow> </mml:math> -style labelled sequent calculi are investigated. It is shown that these calculi have the good structural properties that are distinctive of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>G</mml:mi> <mml:mn>3</mml:mn> </mml:mrow> </mml:math> -style calculi, that they are sound and complete, and it is shown that the proof search for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>G</mml:mi> <mml:mn>3</mml:mn> <mml:mo>.</mml:mo> <mml:mi>ST</mml:mi> <mml:mn>2</mml:mn> </mml:mrow> </mml:math> is terminating and therefore the logic is decidable.
Asymmetric distribution of color-opponent response types across mouse visual cortex supports superior color vision in the sky
2023-06-05

Color is an important visual feature that informs behavior, and the retinal basis for color vision has been studied across various vertebrate species. While many studies have investigated how color information is processed in visual brain areas of primate species, we have limited understanding of how it is organized beyond the retina in other species, including most dichromatic mammals. In this study, we systematically characterized how color is represented in the primary visual cortex (V1) of mice. Using large-scale neuronal recordings and a luminance and color noise stimulus, we found that more than a third of neurons in mouse V1 are color-opponent in their receptive field center, while the receptive field surround predominantly captures luminance contrast. Furthermore, we found that color-opponency is especially pronounced in posterior V1 that encodes the sky, matching the statistics of natural scenes experienced by mice. Using unsupervised clustering, we demonstrate that the asymmetry in color representations across cortex can be explained by an uneven distribution of green-On/UV-Off color-opponent response types that are represented in the upper visual field. Finally, a simple model with natural scene-inspired parametric stimuli shows that green-On/UV-Off color-opponent response types may enhance the detection of “predatory”-like dark UV-objects in noisy daylight scenes. The results from this study highlight the relevance of color processing in the mouse visual system and contribute to our understanding of how color information is organized in the visual hierarchy across species.
Enhanced 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification and a Domain-specific Loss Function
2023-06-05

DNA 5-methylcytosine modification has been widely studied in mammals and plays an important role in epigenetics. Several computational methods exist that attempt to determine the methylation state of a DNA sequence centered at a possible methylation site. Here, we introduce a novel deep-learning framework, MR-DNA, that predicts the methylation state of a single nucleotide located in a gene promoter region. The idea is to adapt the named-entity recognition approach to methylation-site prediction and to incorporate biological rules during model construction. MR-DNA has a stacked model architecture consisting of a pre-trained MuLan-Methyl-DistilBERT language model and a conditional random field algorithm, trained with a self-defined methyl loss function. The resulting fine-tuned model achieves an accuracy of 97.9% on an independent test dataset of samples. An advantage of this formulation of the methylation-site identification task is that it predicts on every nucleotide of a sequence of a given length, unlike previous methods that the predict methylation state of DNA sequences of a short fixed length. For training and testing purposes, we provide a database of DNA sequences containing verified 5mC-methylation sites, calculated from data for eight human cell lines downloaded from the ENCODE database.
Managers perception of hospital employees’ effort-reward imbalance
2023-06-06

Abstract Objective Hospitals are frequently associated with poor working conditions that can lead to work stress and increase the risk for reduced employee well-being. Managers can shape and improve working conditions and thereby, the health of their teams. Thus, as a prerequisite, managers need to be aware of their employees’ stress levels. This study had two objectives: At first, it aimed to test the criterion validity of the Effort-Reward Imbalance (ERI) questionnaire measuring psychosocial workload in hospital employees. Secondly, mean scales of the ERI questionnaire filled in by employees were compared with mean scales of an adapted ERI questionnaire, in which managers assessed working conditions of their employees. Methods Managers (n = 141) from three hospitals located in Germany assessed working conditions of their employees with an adapted external, other-oriented questionnaire. Employees (n = 197) of the mentioned hospitals completed the short version of the ERI questionnaire to assess their working conditions. Confirmatory factor analyses (CFA) were applied to test factorial validity, using the ERI scales for the two study groups. Criterion validity was assessed with multiple linear regression analysis of associations between ERI scales and well-being among employees. Results The questionnaires demonstrated acceptable psychometric properties in terms of internal consistency of scales, although some indices of model fit resulting from CFA were of borderline significance. Concerning the first objective, effort, reward, and the ratio of effort-reward imbalance were significantly associated with well-being of employees. With regard to the second objective, first tentative findings showed that managers’ ratings of their employees’ effort at work was quite accurate, whereas their reward was overestimated. Conclusions With its documented criterion validity the ERI questionnaire can be used as a screening tool of workload among hospital employees. Moreover, in the context of work-related health promotion, managers’ perceptions of their employees’ workload deserve increased attention as first findings point to some discrepancies between their perceptions and those provided by employees.
I-PREGNO – prevention of unhealthy weight gain and psychosocial stress in families during pregnancy and postpartum using an mHealth enhanced intervention: a study protocol of two cluster randomized controlled trials
2023-06-06

Abstract Background The transition to parenthood represents a critical life period with psychosocial, and behavioral changes and challenges for parents. This often increases stress and leads to unhealthy weight gain in families, especially in psychosocially burdened families. Although universal and selective prevention programs are offered to families, specific support often fails to reach psychosocially burdened families. Digital technologies are a chance to overcome this problem by enabling a low-threshold access for parents in need. However, there is currently a lack of smartphone-based interventions that are tailored to the needs of psychosocially burdened families. Aims The research project I-PREGNO aims to develop and evaluate a self-guided, smartphone-based intervention in combination with face-to-face counseling delivered by healthcare professionals for the prevention of unhealthy weight gain and psychosocial problems. The intervention is specifically tailored to the needs of psychosocially burdened families during the pregnancy and postpartum period. Methods In two cluster randomized controlled trials in Germany and Austria (N = 400) psychosocially burdened families will be recruited and randomized to i) treatment as usual (TAU), or ii) I-PREGNO intervention (self-guided I-PREGNO app with counseling sessions) and TAU. We expect higher acceptance and better outcomes on parental weight gain and psychosocial stress in the intervention group. Discussion The intervention offers a low cost and low-threshold intervention and considers the life situation of psychosocially burdened families who are a neglected group in traditional prevention programs. After positive evaluation, the intervention may easily be implemented in existing perinatal care structures in European countries such as Germany and Austria. Trial registration Both trials were registered prospectively at the German Clinical Trials Register (Germany: DRKS00029673; Austria: DRKS00029934) in July and August 2022.
Cerebral venous sinus thrombosis due to vaccine-induced immune thrombotic thrombocytopenia in middle-income countries
2023-06-06

Background: Adenovirus-based COVID-19 vaccines are extensively used in low- and middle-income countries (LMICs). Remarkably, cases of cerebral venous sinus thrombosis due to vaccine-induced immune thrombotic thrombocytopenia (CVST-VITT) have rarely been reported from LMICs. Aims: We studied the frequency, manifestations, treatment, and outcomes of CVST-VITT in LMICs. Methods: We report data from an international registry on CVST after COVID-19 vaccination. VITT was classified according to the Pavord criteria. We compared CVST-VITT cases from LMICs to cases from high-income countries (HICs). Results: Until August 2022, 228 CVST cases were reported, of which 63 were from LMICs (all middle-income countries [MICs]: Brazil, China, India, Iran, Mexico, Pakistan, Turkey). Of these 63, 32 (51%) met the VITT criteria, compared to 103 of 165 (62%) from HICs. Only 5 of the 32 (16%) CVST-VITT cases from MICs had definite VITT, mostly because anti-platelet factor 4 antibodies were often not tested. The median age was 26 (interquartile range [IQR] 20–37) versus 47 (IQR 32–58) years, and the proportion of women was 25 of 32 (78%) versus 77 of 103 (75%) in MICs versus HICs, respectively. Patients from MICs were diagnosed later than patients from HICs (1/32 [3%] vs. 65/103 [63%] diagnosed before May 2021). Clinical manifestations, including intracranial hemorrhage, were largely similar as was intravenous immunoglobulin use. In-hospital mortality was lower in MICs (7/31 [23%, 95% confidence interval (CI) 11–40]) than in HICs (44/102 [43%, 95% CI 34–53], p = 0.039). Conclusions: The number of CVST-VITT cases reported from LMICs was small despite the widespread use of adenoviral vaccines. Clinical manifestations and treatment of CVST-VITT cases were largely similar in MICs and HICs, while mortality was lower in patients from MICs.
The radio shut-off, glitch, and X-ray burst in 1E 1547.0−5408 interpreted through magnetic reconfiguration
2023-06-06

ABSTRACT A short X-ray burst was observed from the radio-loud magnetar 1E 1547.0–5408 in 2022 April. Unusually however, the source stopped showing radio pulsations weeks prior to the burst. After recovery, radio timing revealed that the object had also undergone a modest glitch. A model for the overall event is constructed where an initially mild perturbation adjusts the magnetic geometry near the polar caps, leading to shallow fractures. Crustal ejecta or particles leaking from a pair-plasma fireball pollute the magnetospheric gaps, shutting off the pulsar mechanism, but the energy release is not yet large enough to noticeably enhance the X-ray flux. This perturbation gradually ramps, eventuating in a large-scale energy redistribution which fuels the burst. The star’s mass quadrupole moment changes in tandem, issuing a glitch. Some quantitative estimates for the magnetic reconfiguration under this interpretation are provided, based on a quasi-static model where the fluid evolves through a sequence of hydromagnetic equilibria.
Engaging learners with games–Insights from functional near-infrared spectroscopy
2023-06-06

The use of game elements in learning tasks is thought to facilitate emotional and behavioral responses as well as learner engagement. So far, however, little is known about the underlying neural mechanisms of game-based learning. In the current study, we added game elements to a number line estimation task assessing fraction understanding and compared brain activation patterns to a non-game-based task version. Forty-one participants performed both task versions in counterbalanced order while frontal brain activation patterns were assessed using near-infrared spectroscopy (within-subject, cross-sectional study design). Additionally, heart rate, subjective user experience, and task performance were recorded. Task performance, mood, flow experience, as well as heart rate did not differ between task versions. However, the game-based task-version was rated as more attractive, stimulating and novel compared to the non-game-based task version. Additionally, completing the game-based task version was associated with stronger activation in frontal brain areas generally involved in emotional and reward processing as well as attentional processes. These results provide new neurofunctional evidence substantiating that game elements in learning tasks seem to facilitate learning through emotional and cognitive engagement.
TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data
2023-06-06

Although Top-down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise its adoption. In this context, there are numerous improvements that are possible in the area of open science including the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include e.g. increased data sharing practices and availability of tailored open data standards. Additionally, the field would benefit from the development of open analysis workflows that can enable e.g. data reuse of public datasets, something that is increasingly common in other proteomics fields. We present an open and modular platform for the analysis and visualisation of TD proteomics data called TopDownApp. It can be used as a flexible analysis platform, through the use of a common workflow engine, common data formats for input/output, and software containerisation. It can also serve as a tool for visual inspection through its simple setup. As a key point, it can also be used as a development platform for new tools through the use of Python, a modular design, software containerisation and common data formats. TopDownApp is open source and freely available at: https://github.com/mwalzer/TopDownApp.
Onsite versus home-office: differences in sleep patterns according to workplace
2023-06-06

Abstract Background and objective This study aimed to evaluate the sleep patterns of students and employees working onsite versus those working from home during the COVID-19 pandemic using actigraphy. Methods A total of 75 students/employees (onsite: N = 40, home-office: N = 35; age range: 19–56 years; 32% male; 42.7% students, 49.3% employees) were studied between December 2020 and January 2022 using actigraphy, a sleep diary, and an online questionnaire assessing sociodemographics and morningness–eveningness. Independent-sample t -tests, paired-sample tests, and a multivariate general linear model adjusting for age (fixed factors: sex and work environment) were applied. Results Overall, onsite workers had significantly earlier rise times (7:05 [SD: 1:11] versus 7:44 [1:08] hours) and midpoints of sleep (2:57 [0:58] versus 3:33 [0:58] hours) on weekdays compared to home-office workers. Sleep efficiency, sleep duration, variability of sleep timing, and social jetlag did not differ between the groups. Discussion Home-office workers showed a delay in sleep timing that did not affect any other sleep parameters such as sleep efficiency or nighttime sleep duration. The work environment had only marginal impact on sleep patterns and thus sleep health in this sample. Sleep timing variability did not differ between groups.
Influence of Alkyl Chain Variation on Cocrystal Formation and Molecular Charge Transfer in DIP:Perylene Diimide Binary Systems
2023-06-06

We present a comprehensive investigation of cocrystal formation and charge transfer effects in weakly interacting organic semiconductor mixtures. As a model system, we choose diindenoperylene (DIP) as a donor molecule and several perylene diimide derivatives (PDI) as acceptor molecules that differ in the n-alkyl side chain in the imide position and in the cyano (CN) group in the bay position. We identified the optimized side groups for the acceptors in thin films with the donor DIP concerning the mixing behavior and molecular charge transfer (CT) effects. The two systems, which form a well-defined cocrystal and show excited-state charge transfer effects, are DIP:PTCDI-C3 with an n-propyl side chain and DIP:PTCDI-C8-CN2 with incorporated cyano groups. Important for the mixing behavior and the charge transfer effects with DIP are the intermolecular interactions of the pure perylene diimide derivatives and the orientation of these molecules on the substrate (SiO2). For the DIP:PTCDI-C3 system, a sharp CT peak in absorption with a well-defined CT energy is observed. In contrast, the DIP:PTCDI-C8-CN2 mixed films show a broad CT band in absorption and two different CT energies. The mixing behavior and charge transfer effects with DIP are strongly influenced by the structure of the acceptors, which are easily chemically tunable in the desired way.
Monsoon-driven changes in aeolian and fluvial sediment input to the central Red Sea recorded throughout the last 200,000 years
2023-06-06

Abstract. Climatic and associated hydrological changes controlled the transport processes and composition of the sediments in the central Red Sea during the last ca. 200 kyr. Three different source areas for mineral dust are identified. The dominant source is located in the eastern Sahara (Sudan and southernmost Egypt). We identify its imprint on Red Sea sediments by high smectite and Ti contents, high 87Sr/86Sr and low εNd. The availability of deflatable sediments was controlled by the intensity of tropical rainfall and vegetation cover over northern Africa linked to the African monsoon. Intense dust input to the Red Sea occurred during arid phases, low input during humid phases. A second, less significant source indicated by palygorskite input is probably located on the eastern Arabian Peninsula and/or Mesopotamia, while the presence of kaolinite suggests an additional minor dust source in northern Egypt. Our grain size data reflect episodes of fluvial sediment discharge to the central Red Sea and document the variable strength in response to all of the precession-paced insolation maxima during our study interval including both those that were strong enough to trigger sapropel formation in the eastern Mediterranean Sea and those that were not. The African Humid Period most strongly expressed in our Red Sea record was the one during the Eemian last interglacial at ca. 125 ka, followed by those at 198 ka, 108 ka, 84 ka and 6 ka.
Why shot noise does not generally detect pairing in mesoscopic superconducting tunnel junctions
2023-06-06

The shot noise in tunneling experiments reflects the Poissonian nature of the tunneling process. The shot noise power is proportional to both the magnitude of the current and the effective charge of the carrier. Shot noise spectroscopy thus enables, in principle, to determine the effective charge q of the charge carriers that tunnel. This can be used to detect electron pairing in superconductors: in the normal state, the noise corresponds to single electron tunneling (q = 1e), while in the paired state, the noise corresponds to q = 2e. Here, we use a newly developed amplifier to reveal that in typical mesoscopic superconducting junctions, the shot noise does not reflect the signatures of pairing and instead stays at a level corresponding to q = 1e. We show that transparency can control the shot noise and this q = 1e is due to the large number of tunneling channels with each having very low transparency. Our results indicate that in typical mesoscopic superconducting junctions one should expect q = 1e noise, and lead to design guidelines for junctions that allow the detection of electron pairing.
Dataset on simulations of Kinetic of Fe(II) oxidation
2023-06-06

This upload contains simulation and fitting data matching figures in the publication &amp;quot;Kinetic constraints for the formation of microniches for microaerophilic Fe(II) oxidation&amp;rdquo;, Peiffer et al, submitted to GCA.\\n\\n\\nIt further contains the matlab code used for the simulations (micro_n_iteration_v1.m) \\n&amp;nbsp;
Pembrolizumab plus axitinib versus sunitinib as first-line therapy for advanced clear cell renal cell carcinoma: 5-year analysis of KEYNOTE-426.
2023-06-07

LBA4501 Background: At the first interim analysis of the randomized, open-label, phase 3 KEYNOTE-426 (NCT02853331) study, 1L pembro + axi showed statistically significant OS, PFS, and ORR over sun for advanced ccRCC. We report results with 5-y minimum follow-up. Methods: Adults with confirmed locally advanced or metastatic ccRCC with or without sarcomatoid features, no previous systemic therapy for metastatic ccRCC, KPS ≥70%, and ≥1 lesion measurable per RECIST v1.1 were randomly assigned 1:1 to receive pembro 200 mg IV Q3W for 35 doses (~2 y) + axi 5 mg PO BID or sun 50 mg PO QD on a 4-wk-on/2-wk-off schedule. Dual primary end points were OS and PFS per RECIST v1.1 by blinded independent central review (BICR). Secondary end points included ORR and DOR per RECIST v1.1 by BICR, and safety. A post hoc analysis adjusting for the effect of subsequent therapy on OS using a 2-stage adjustment model was conducted. Results: Of 861 enrolled patients (pts), 432 were assigned to pembro + axi and 429 to sun. Median study follow-up was 67.2 mo (range, 60.0-75.0). Efficacy for the ITT population and IMDC risk subgroups are shown in table. For pembro + axi vs sun, the 60-mo OS rates were 41.9% vs 37.1%, and the 60-mo PFS rates were 18.3% vs 7.3%. Median DOR (range) was 23.6 mo (1.4+ to 68.6+) for pembro + axi and 15.3 mo (2.3-68.3) for sun. In pts who discontinued treatment, 237/381 pts (62.2%) in the pembro + axi arm and 300/406 pts (73.9%) in the sun arm received subsequent anticancer treatment. The HR for OS when adjusted for subsequent therapy was 0.67 (95% CI, 0.52-0.84). Clinical data on pts who completed 2 y of pembro will be presented. No new safety signals were observed. Conclusions: After 5 y of follow-up, pembro + axi had sustained OS, PFS, and ORR benefits over sun in advanced ccRCC. These results are the longest follow-up to date of an anti–PD-1/L1 inhibitor + VEGFR TKI in this pt population and continue to support the use of pembro + axi as a 1L standard of care for advanced ccRCC. Clinical trial information: NCT02853331 .