julilili42/papers huggingface dataset:
MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
2023-01-04

Abstract Transformer-based language models are successfully used to address massive text-related tasks. DNA methylation is an important epigenetic mechanism and its analysis provides valuable insights into gene regulation and biomarker identification. Several deep learning-based methods have been proposed to identify DNA methylation and each seeks to strike a balance between computational effort and accuracy. Here, we introduce MuLan-Methyl, a deep-learning framework for predicting DNA methylation sites, which is based on five popular transformer-based language models. The framework identifies methylation sites for three different types of DNA methylation, namely N6-adenine, N4-cytosine, and 5-hydroxymethylcytosine. Each of the employed language models is adapted to the task using the “pre-train and fine-tune” paradigm. Pre-training is performed on a custom corpus of DNA fragments and taxonomy lineages using self-supervised learning. Fine-tuning aims at predicting the DNA-methylation status of each type. The five models are used to collectively predict the DNA methylation status. We report excellent performance of MuLan-Methyl on a benchmark dataset. Moreover, we argue that the model captures characteristic differences between different species that are relevant for methylation. This work demonstrates that language models can be successfully adapted to applications in biological sequence analysis and that joint utilization of different language models improves model performance. Mulan-Methyl is open source and we provide a web server that implements the approach. Key points MuLan-Methyl aims at identifying three types of DNA-methylation sites. It uses an ensemble of five transformer-based language models, which were pre-trained and fine-tuned on a custom corpus. The self-attention mechanism of transformers give rise to importance scores, which can be used to extract motifs. The method performs favorably in comparison to existing methods. The implementation can be applied to chromosomal sequences to predict methylation sites.
Deciphering morbid curiosity: Psychological mechanisms underlying the voluntary viewing of negative images
2023-01-04

The principle of hedonism assumes that people pursue pleasure and positive experiences; however, we often observe that people voluntarily seek negative experiences in various daily settings—sometimes interpreted as the manifestation of “morbid curiosity.” This study tested four hypotheses to appraise people’s voluntary viewing of negative images: novelty/curiosity, metacognitive miscalibration, emotional arousal, and optimal stimulation. We used a paradigm in which participants could choose whether to view a positively or negatively valenced image. The results revealed that the rate of choosing to view positive and negative images decreased when participants had already seen the images previously. This result supports the novelty/curiosity hypotheses. However, contrary to the metacognitive miscalibration, emotional arousal, and optimal stimulation hypotheses, participants overestimated their negative feelings prior to viewing negative images, individual differences in sensation-seeking did not predict people’s choice of viewing negative images, and emotional arousal did not have an inverted-U relationship with choice behavior. These findings indicate a potential mechanism underlying people’s behavior in voluntarily seeking negative information, although we still observe a large unexplained variance vis-à-vis participants’ voluntary choice of negative images.
Pre- and Post-Portosystemic Shunt Placement Metabolomics Reveal Molecular Signatures for the Development of Hepatic Encephalopathy
2023-01-04

ABSTRACT Hepatic encephalopathy (HE) is a common complication of advanced liver disease causing brain dysfunction. This is likely due to the accumulation of unfiltered toxins within the bloodstream. A known risk factor for developing or worsening HE is the placement of a transjugular intrahepatic portosystemic shunt (TIPS), which connects the pre-hepatic and post-hepatic circulation allowing some blood to bypass the dysfunctional liver and decreases portal hypertension. To better understand the pathophysiology of post-TIPS HE, we conducted a multi-center prospective cohort study employing metabolomic analyses on hepatic vein and peripheral vein blood samples from participants with cirrhosis undergoing elective TIPS placement, measuring chemical modifications and changes in concentrations of metabolites resulting from TIPS placement. In doing so, we identified numerous alterations in metabolites, including bile acids, glycerophosphocholines, and bilirubins possibly implicated in the development and severity of HE.
Forming Mercury by a grazing giant collision involving similar mass bodies
2023-01-04

<title>Abstract</title> The planet Mercury is predominantly made up of an iron core, covered by a comparatively thin silicate layer, which has led to the idea that this configuration is the product of mantle stripping by a giant impact. In the literature, a classical hit-and-run impact has been explored in which a roughly Mars-mass proto-Mercury collides with an Earth-mass target, losing large parts of its mantle. However, such hit-and-run collisions between proto-planets of very different masses are rare in N-body simulations of terrestrial planet formation. On the other hand, hit-and-run collisions involving similar mass bodies appear to be more frequent. Our aim here is to investigate the conditions under which collisions of similar mass bodies are able to form a Mercury-like planet, fulfilling the necessary constraints in terms of mass and composition (silicate-to-iron mass ratio). We perform a series of smooth particle hydrodynamics (SPH) collision simulations. Our results show that it is possible to obtain Mercury-analogues from hit-and-run collisions involving a proto-Mercury roughly twice the mass of Mercury and targets of comparable mass (between 1 and 4 times higher), as long as the impact parameters (impact angle and velocity) are properly adjusted according to a set of well established scaling laws, while remaining compatible with the values typically observed in N-body simulations.
Quaternion lattices and quaternion fields
2023-01-04

Abstract Let <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>Q</mml:mi> <mml:mn>8</mml:mn> </mml:msub> </mml:math> be the quaternion group of order 8 and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>χ</mml:mi> </mml:math> its faithful irreducible character. Then <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>χ</mml:mi> </mml:math> can be realized over certain imaginary quadratic number fields <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>K</mml:mi> <mml:mo>=</mml:mo> <mml:mi>Q</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> </mml:mrow> <mml:msqrt> <mml:mrow> <mml:mo>-</mml:mo> <mml:mi>N</mml:mi> </mml:mrow> </mml:msqrt> <mml:mrow> <mml:mo>)</mml:mo> </mml:mrow> </mml:mrow> </mml:math> but not over their rings of integers (Feit, Serre); here N is a positive square-free integer. We show that this happens precisely when <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>Q</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> </mml:mrow> <mml:msqrt> <mml:mi>N</mml:mi> </mml:msqrt> <mml:mrow> <mml:mo>)</mml:mo> </mml:mrow> </mml:mrow> </mml:math> but not <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>Q</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> </mml:mrow> <mml:msqrt> <mml:mn>2</mml:mn> </mml:msqrt> <mml:mo>,</mml:mo> <mml:msqrt> <mml:mi>N</mml:mi> </mml:msqrt> <mml:mrow> <mml:mo>)</mml:mo> </mml:mrow> </mml:mrow> </mml:math> can be embedded into a <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>Q</mml:mi> <mml:mn>8</mml:mn> </mml:msub> </mml:math> -field over the rationals (Galois with group <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>Q</mml:mi> <mml:mn>8</mml:mn> </mml:msub> </mml:math> ) and N is not a sum of two integer squares. In particular, we get that <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>χ</mml:mi> </mml:math> cannot be integrally realized if N is (properly) divisible by some prime <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>q</mml:mi> <mml:mo>≡</mml:mo> <mml:mn>7</mml:mn> <mml:mspace /> <mml:mo>(</mml:mo> <mml:mrow> <mml:mtext>mod</mml:mtext> <mml:mspace /> </mml:mrow> <mml:mn>8</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> .
Prospective Evaluation of Children with Robin Sequence following Tübingen Palatal Plate Therapy
2023-01-05

Background: To assess the long-term functional orthodontic outcome of the Tübingen palatal plate (TPP) in children with Robin sequence (RS) in comparison to age- and sex-matched healthy controls. Methods: Between 09/2019 and 10/2020, we performed orthodontic assessments in 41 children at our Department of Orthodontics. Included were patients with RS (17 non-syndromic; four syndromic) and healthy controls (n = 22, average age in both groups 9.9 y). Facial analyses of 2D images, digital study casts and cephalometric measurements were made. Results: The orthodontic examinations showed no statistically significant group differences regarding functional extraoral, intraoral and pharyngeal parameters, or in skeletal patterns. The relationship between the upper and lower incisors was significantly increased (overjet 4 (2–10) vs. 3 (0–9) mm; p = 0.01) with a significant deficit in the lower face proportions (Jaw Index 4.15 (1.9–9.6) vs. 2.98 (0–9); p = 0.02; Facial convexity angle 157 (149–173) vs. 159 (149–170); p = 0.01). Conclusion: Children with RS treated with the TPP showed normal long-term functional orthodontic outcomes, thanks to the functional adaption of the stomatognathic system. However, soft tissue growth did not completely match skeletal growth, resulting in a more convex facial profile.
Ten simple rules for implementing open and reproducible research practices after attending a training course
2023-01-05

Open, reproducible, and replicable research practices are a fundamental part of science. Training is often organized on a grassroots level, offered by early career researchers, for early career researchers. Buffet style courses that cover many topics can inspire participants to try new things; however, they can also be overwhelming. Participants who want to implement new practices may not know where to start once they return to their research team. We describe ten simple rules to guide participants of relevant training courses in implementing robust research practices in their own projects, once they return to their research group. This includes (1) prioritizing and planning which practices to implement, which involves obtaining support and convincing others involved in the research project of the added value of implementing new practices; (2) managing problems that arise during implementation; and (3) making reproducible research and open science practices an integral part of a future research career. We also outline strategies that course organizers can use to prepare participants for implementation and support them during this process.
NK- and T-cell granzyme B and K expression correlates with age, CMV infection and influenza vaccine-induced antibody titres in older adults
2023-01-05

Granzymes are a family of serine-proteases that act as critical mediators in the cytolytic and immunomodulatory activities of immune cells such as CD8 + T-cells and natural killer (NK) cells. Previous work indicates that both granzyme B (GZB) and K (GZK) are increased with age in CD8 + T-cells, and in the case of GZB, contribute to dysfunctional immune processes observed in older adults. Here, we sought to determine how GZB and GZK expression in NK-cells, and CD4 + , CD8 + , and gamma-delta T-cells, quantified in terms of positive cell frequency and mean fluorescence intensity (MFI), differed with age, age-related health-traits and the antibody response to high-dose influenza vaccine. We found that the frequency and MFI of GZB-expressing NK-cells, and CD8 + and Vδ1+ T-cells, and GZK-expressing CD8 + T-cells was significantly higher in older (66–97 years old; n = 75) vs. younger (24–37 years old; n = 10) adults by up to 5-fold. There were no significant associations of GZB/GZK expression with sex, frailty or plasma levels of TNF or IL-6 in older adults, but those who were seropositive for cytomegalovirus (CMV) exhibited significantly higher frequencies of GZB+ NK-cells, and CD4 + , CD8 + and Vδ1+ T-cells, and GZK+ CD8 + T-cells (Cohen’s d = .5–1.5). Pre-vaccination frequencies of GZB+ NK-cells were positively correlated with vaccine antibody responses against A/H3N2 (d = .17), while the frequencies of GZK+ NK and CD8 + T-cells were inversely associated with A/H1N1 (d = −0.18 to −0.20). Interestingly, GZK+ NK-cell frequency was inversely correlated with pre-vaccination A/H1N1 antibody titres, as well as those measured over the previous 4 years, further supporting a role for this subset in influencing vaccine antibody-responses. These findings further our understanding of how granzyme expression in different lymphoid cell-types may change with age, while suggesting that they influence vaccine responsiveness in older adults.
ARTEM-IS for ERP: Agreed Reporting Template for EEG Methodology - International Standard for documenting studies on Event-Related Potentials
2023-01-05

Given that the choices made during recording, preprocessing and analysis of event-related potentials (ERP) data can affect study outcomes, it is critical that they are transparently reported to allow for reproducibility and replicability. Yet, systematic reviews of reporting practices in the field have shown that journal articles do not meet this goal and that guidelines for writing them better have not resulted in a sufficient improvement to reporting transparency.ARTEM-IS aims to address this issue by building dynamic, interactive web applications that support documenting information required by existing publication guidelines in the form of a standardised metadata template. Completing an ARTEM-IS form results in a human-reader-friendly PDF and a machine-readable JSON summary of methodological information, which allows for a level of reporting precision higher than what is typically found in journal articles. These can be used as supplements to a publication, as a memory aid when writing a paper, or as records that allow easier metadata extraction in comparison to verbal descriptions in papers.Here, we present the ARTEM-IS for ERP, which supports describing a typical ERP study, including most of its core methodological aspects (study description, experimental design, hardware, data acquisition, pre-processing, measurement, visualisation, additional comments). We discuss the current contents of the form, web application functionalities, current limitations, and potential directions for future developments. In addition, the process of building the form contents and the web application through a collaborative grassroots initiative is described. Finally, we argue that a wider adoption of ARTEM-IS can bring benefits to different stakeholders: researchers themselves or their collaborators, especially on large-scale projects, reviewers, readers of a paper, and the scientific community at large.
Spatial and temporal correlations in neural networks with structured connectivity
2023-01-06

Correlated fluctuations in the activity of neural populations reflect the network's dynamics and connectivity. The temporal and spatial dimensions of neural correlations are interdependent. However, prior theoretical work mainly analyzed correlations in either spatial or temporal domains, oblivious to their interplay. We show that the network dynamics and connectivity jointly define the spatiotemporal profile of neural correlations. We derive analytical expressions for pairwise correlations in networks of binary units with spatially arranged connectivity in one and two dimensions. We find that spatial interactions among units generate multiple timescales in auto- and cross-correlations. Each timescale is associated with fluctuations at a particular spatial frequency, making a hierarchical contribution to the correlations. External inputs can modulate the correlation timescales when spatial interactions are nonlinear, and the modulation effect depends on the operating regime of network dynamics. These theoretical results open new ways to relate connectivity and dynamics in cortical networks via measurements of spatiotemporal neural correlations.
CRISPR medicine for blood disorders: Progress and challenges in delivery
2023-01-06

Blood disorders are a group of diseases including hematological neoplasms, clotting disorders and orphan immune deficiency diseases that affects human health. Current improvements in genome editing based therapeutics demonstrated preclinical and clinical proof to treat different blood disorders. Genome editing components such as Cas nucleases, guide RNAs and base editors are supplied in the form of either a plasmid, an mRNA, or a ribonucleoprotein complex. The most common delivery vehicles for such components include viral vectors (e.g., AAVs and RV), non-viral vectors (e.g., LNPs and polymers) and physical delivery methods (e.g., electroporation and microinjection). Each of the delivery vehicles specified above has its own advantages and disadvantages and the development of a safe transferring method for ex vivo and in vivo application of genome editing components is still a big challenge. Moreover, the delivery of genome editing payload to the target blood cells possess key challenges to provide a possible cure for patients with inherited monogenic blood diseases and hematological neoplastic tumors. Here, we critically review and summarize the progress and challenges related to the delivery of genome editing elements to relevant blood cells in an ex vivo or in vivo setting. In addition, we have attempted to provide a future clinical perspective of genome editing to treat blood disorders with possible clinical grade improvements in delivery methods.
Prevalence, incidence, repair rate, and morbidity of groin hernias in Sierra Leone: cross-sectional household study
2023-01-06

Abstract Background Knowledge about the prevalence of groin hernias in sub-Saharan Africa is limited. Previous studies have demonstrated a higher incidence of the condition than the annual repair rate. This study aimed to investigate prevalence, incidence, annual repair rate, morbidity, and health-seeking behaviour of persons with groin hernias in Sierra Leone. Methods This population-based, cross-sectional household survey on groin hernias in Sierra Leone was part of the Prevalence Study on Surgical Conditions 2020 (PRESSCO 2020). Those who indicated possible groin hernia were asked problem-specific questions and underwent physical examination to confirm or exclude the diagnosis. Results 3626 study participants were interviewed. The prevalence of untreated groin hernia was 1.1 per cent (95 per cent c.i. 0.8 to 1.5 per cent), whereas the prevalence of untreated and treated groin hernia was 2.5 per cent (95 per cent c.i. 2.0 to 3.0 per cent). The proportion of recurrence was 13.1 per cent. An incidence of 389 (95 per cent c.i. 213 to 652) groin hernia cases per 100 000 people per year was identified, while a population-based annual hernia repair rate estimation was 470 (95 per cent c.i. 350 to 620) per 100 000 people. Out of 39 participants with groin hernia, non-ignorable pain was reported by eight and 27 reported financial shortcomings as a reason for not seeking healthcare. Conclusions Groin hernias are common in Sierra Leone and although the repair rate might match the incidence, the existing backlog of untreated hernias is likely to remain. It may be possible to reduce the number of recurrences through improved management. Measures to reduce financial barriers to treatment seem crucial to improve the health of people with groin hernias in Sierra Leone.
Power corrections to electroweak boson production from threshold resummation
2023-01-06

We study the power corrections for electroweak boson production that are implied by threshold resummation, which we have extended to massive particles produced at measured transverse momentum, , and rapidity. Power corrections in the resulting expressions arise from ambiguities in the low-scale behavior of the perturbative running coupling. Arguing for the relevance of the eikonal approximation, we show that such power corrections begin at order in full QCD, consistent with fixed-order, massive-gluon analysis. For large- Mellin moments, the leading behavior is , which exponentiates along with the logarithms of threshold resummation.
Ultrasound of the Biceps Muscle in Idiopathic Parkinson’s Disease with Deep Brain Stimulation: Rigidity Can Be Quantified by Shear Wave Elastography
2023-01-06

Rigidity in Parkinson’s disease (PD) is assessed by clinical scales, mostly the Unified Parkinson’s Disease Rating Scale of the Movement Disorders Society (MDS-UPDRS). While the MDS-UPDRS-III ranges on an integer from 0 to 4, we investigated whether muscle ultrasound shear wave elastography (SWE) offers a refined assessment. Ten PD patients (five treated with deep brain stimulation (DBS) and levodopa, five with levodopa only) and ten healthy controls were included. Over a period of 80 min, both the SWE value and the item 22b-c of the MDS-UPDRS-III were measured at 5 min intervals. The measurements were performed bilaterally at the biceps brachii muscle (BB) and flexor digitorum profundus muscle in flexion and passive extension. Rigidity was modified and tracked under various therapeutic conditions (with and without medication/DBS). The feasibility of SWE for objective quantification was evaluated by correlation with the UPDRS-III: considering all positions and muscles, there was already a weak correlation (r = 0.01, p &lt; 0.001)—in a targeted analysis, the BB in passive extension showed a markedly higher correlation (r = 0.494, p &lt; 0.001). The application of dopaminergic medication and DBS resulted in statistically significant short-term changes in both clinical rigidity and SWE measurements in the BB (p &lt; 0.001). We conclude that rigidity is reflected in the SWE measurements, indicating that SWE is a potential non-invasive quantitative assessment tool for PD.