julilili42/papers huggingface dataset:
Community effort to unravel the complex human neuronal landscape exemplified for the striatum
2024-02-20

<title>Abstract</title> Precise determination of cellular identity and molecular phenotypes through advanced high-throughput technologies is crucial for understanding intricate tissue functions, especially in complex organs like the brain. Given the complexity of the brain, community efforts are needed but currently underexploited to unravel the function of the human brain. In this study, we present findings from a multi-center investigation performed as a community effort involving seven genome centers. We analyzed single-nucleus transcriptomes obtained from NeuN+ neurons from the putamen and caudate nucleus of both healthy individuals and Parkinson's Disease (PD) patients. Our results demonstrate the potential for establishing community-wide standards, fostering collaborative networks, and enhancing brain cell classification efforts. We propose a transcriptional architecture that encodes synaptic communication patterns in the striatum, comprising of cell-adhesion molecules (CAMs), transmitter/modulator receptors, ion channels, signaling proteins, neuropeptides, vesicular release components, and transcription factors. This classification serves as a foundation for mapping and integrating publicly available datasets, showcasing the value of deep sampling in defined brain regions for comprehensive brain-wide analyses. Importantly, this nomenclature can serve as a template for other brain regions. This community effort enabled the precise mapping of cellular alterations in Parkinson's Disease. Transcriptional changes predominantly occurred in specific cell states of medium spiny neurons within the putamen matrix, pointing towards increased excitability. Additionally, a disbalance in specific interneuron cell states was associated with heightened glutamatergic signaling, further contributing to increased overall excitability.
Generalizable Neural Models of Emotional Engagement and Disengagement
2024-02-20

Emotional experiences are never static but continuously evolve in response to internal and external contexts. Little is known about how neural patterns change as a function of these experiences, particularly in response to complex, real-world stimuli. This study aimed to identify generalizable neural patterns as individuals collectively engage and disengage from emotions dynamically. To do so, we analyzed functional magnetic resonance imaging (fMRI) along with subjective emotional annotations from two independent studies as individuals watched negative and neutral movie clips. We used predictive modeling to test if a model trained to predict a group emotional signature response in one study generalizes to the other study and vice versa. Disengagement patterns generalized specifically across intense clips. They were supported by connections within and between the sensorimotor and salience networks, maybe reflecting the processing of feeling states as individuals regulate their emotions. Prediction success for the engagement signature was mixed, primarily linked to connections within the visual and between the visual and dorsal attention networks, supporting visual attention orienting as emotions intensify. This work offers potential pathways for identifying generalizable neural patterns contributing to future affective research and clinical applications aiming to better understand dynamic emotional responses to naturalistic stimuli.
Detection of X-Ray Polarization from the Blazar 1ES 1959+650 with the Imaging X-Ray Polarimetry Explorer
2024-02-21

Abstract Observations of linear polarization in the 2–8 keV energy range with the Imaging X-ray Polarimetry Explorer (IXPE) explore the magnetic field geometry and dynamics of the regions generating nonthermal radiation in relativistic jets of blazars. These jets, particularly in blazars whose spectral energy distribution peaks at X-ray energies, emit X-rays via synchrotron radiation from high-energy particles within the jet. IXPE observations of the X-ray-selected BL Lac–type blazar 1ES 1959+650 on 2022 May 3–4 showed a significant linear polarization degree of Π x = 8.0% ± 2.3% at an electric-vector position angle ψ x = 123° ± 8°. However, on 2022 June 9–12, only an upper limit of Π x ≤ 5.1% could be derived (at the 99% confidence level). The degree of optical polarization at that time, Π O ∼ 5%, is comparable to the X-ray measurement. We investigate possible scenarios for these findings, including temporal and geometrical depolarization effects. Unlike some other X-ray-selected BL Lac objects, there is no significant chromatic dependence of the measured polarization in 1ES 1959+650, and its low X-ray polarization may be attributed to turbulence in the jet flow with dynamical timescales shorter than 1 day.
Ochre-based compound adhesives at the Mousterian type-site document complex cognition and high investment
2024-02-21

Ancient adhesives used in multicomponent tools may be among our best material evidences of cultural evolution and cognitive processes in early humans. African Homo sapiens is known to have made compound adhesives from naturally sticky substances and ochre, a technical behavior proposed to mark the advent of elaborate cognitive processes in our species. Foragers of the European Middle Paleolithic also used glues, but evidence of ochre-based compound adhesives is unknown. Here, we present evidence of this kind. Bitumen was mixed with high loads of goethite ochre to make compound adhesives at the type-site of the Mousterian, Le Moustier (France). Ochre loads were so high that they lowered the adhesive’s performance in classical hafting situations where stone implements are glued to handles. However, when used as handheld grips on cutting or scraping tools, a behavior known from Neanderthals, high-ochre adhesives present a real benefit, improving their solidity and rigidity. Our findings help understand the implications of Pleistocene adhesive making.
Presenilin‐1 mutation position influences amyloidosis, small vessel disease, and dementia with disease stage
2024-02-21

Abstract INTRODUCTION Amyloidosis, including cerebral amyloid angiopathy, and markers of small vessel disease (SVD) vary across dominantly inherited Alzheimer's disease (DIAD) presenilin‐1 ( PSEN1) mutation carriers. We investigated how mutation position relative to codon 200 (pre‐/postcodon 200) influences these pathologic features and dementia at different stages. METHODS Individuals from families with known PSEN1 mutations ( n = 393) underwent neuroimaging and clinical assessments. We cross‐sectionally evaluated regional Pittsburgh compound B‐positron emission tomography uptake, magnetic resonance imaging markers of SVD (diffusion tensor imaging‐based white matter injury, white matter hyperintensity volumes, and microhemorrhages), and cognition. RESULTS Postcodon 200 carriers had lower amyloid burden in all regions but worse markers of SVD and worse Clinical Dementia Rating ® scores compared to precodon 200 carriers as a function of estimated years to symptom onset. Markers of SVD partially mediated the mutation position effects on clinical measures. DISCUSSION We demonstrated the genotypic variability behind spatiotemporal amyloidosis, SVD, and clinical presentation in DIAD, which may inform patient prognosis and clinical trials. Highlights Mutation position influences Aβ burden, SVD, and dementia. PSEN1 pre‐200 group had stronger associations between Aβ burden and disease stage. PSEN1 post‐200 group had stronger associations between SVD markers and disease stage. PSEN1 post‐200 group had worse dementia score than pre‐200 in late disease stage. Diffusion tensor imaging‐based SVD markers mediated mutation position effects on dementia in the late stage.
The Occurrence of Suids in the Post-Olduvai to Pre-Jaramillo Pleistocene of Europe and Implications for Late Villafranchian Biochronology and Faunal Dynamics
2024-02-21

It has been proposed that suids were absent from Europe during the post-Olduvai to pre-Jaramillo Early Pleistocene (from less than 1.8 to more than 1.2 Ma) and that their “re-appearance” in the late Early Pleistocene would mark the end of the late Villafranchian and the beginning of the Epivillafranchian. Arguments enumerated in favor of this “suid gap” are the lack of suid remains from extensively sampled fossil localities of this age and the high reproductive potential (r-strategy) of suids, which would translate in a high commonness of their remains in the fossil record. However, here it shown that while suids’ reproductive potential is certainly exceptional within artiodactyls, there is no direct relationship between the reproductive strategy and preservation rate of a taxon in the fossil record. In Early Pleistocene localities of Europe and adjoining areas, where suids are present in a fossil assemblage, they are always rare. In terms of number of occurrences (frequency), suids range from being moderately common (~2.0–1.8 Ma) to moderately rare (~1.1–1.0 Ma). Suid material is also described herein from Peyrolles (Issoire, France; reference locality for MNQ 19), a site dated at 1.47 Ma, providing direct evidence for the presence of suids within the purported “suid gap”. The case of suids underlines an important source of caveat in inferring faunal dynamics of the late Early Pleistocene of western Europe—including the dispersal of hominins—i.e., the unequal geographical distribution of the paleontological sites of post-Olduvai to pre-Jaramillo age. Indeed, Peyrolles is the only large mammal site in western Europe located outside the Iberian and Italian Peninsulas reliably dated around 1.5 Ma. In the post-Olduvai to pre-Jaramillo period, there is a paucity of radiometric estimates (or they have too coarse a resolution) and of paleomagnetic excursions detectable in continental deposits. Basically, for this time span, there is a high dependence on biochronological correlations, although, at the same time, these correlations are less reliable—because these are based on a few sites not covering the entire spectrum of environments present in Europe and the sites are not independently dated with methods that outperform biochronology—than those for other periods.
Exploring the current state of clinical and practical teaching in obstetrics and gynecology in the era of competency-based education: a nationwide survey among German teaching coordinators
2024-02-21

Abstract Background Obstetrics and gynecology (OB/GYN) is an essential medical field that focuses on women’s health. Universities aim to provide high-quality healthcare services to women through comprehensive education of medical students. In Germany, medical education is undergoing a phase of restructuring towards the implementation of competency-based learning. The objective of the current survey was to gain insights into the teaching methods, resources, and challenges at German medical universities in the field OB/GYN. This aims to document the current state of medical education and derive potential suggestions for improvements in the era of competency-based learning. The survey was conducted with teaching coordinators from the majority of OB/GYN departments at German universities. Methods A questionnaire was sent to the teaching coordinators in all 41 OB/GYN departments at German university hospitals. The survey was delivered via email with a link to an online survey platform. Results The study received 30 responses from 41 universities. Differences were observed in the work environment of teaching coordinators concerning release from clinical duties for teaching purposes and specialized academic training. Overall, medical education and student motivation were perceived positively, with noticeable gaps, particularly in practical gynecological training. Deficiencies in supervision and feedback mechanisms were also evident. Subfields such as urogynecology and reproductive medicine appear to be underrepresented in the curriculum, correlating with poorer student performance. E-learning was widely utilized and considered advantageous. Conclusion The present study provides valuable insights into the current state of medical education in OB/GYN at German universities from the perspective of teaching experts. We highlight current deficits, discuss approaches to overcome present obstacles, and provide suggestions for improvement.
Pistol: Pupil Invisible Supportive Tool in the Wild
2024-02-21

Abstract This paper is an in the wild evaluation of the eye tracking tool Pistol. Pistol supports Pupil Invisible projects and other eye trackers (Dikablis, Emke GmbH, Look, Pupil, and many more) in offline mode. For all eye tracking recordings, Pistol is able to compute pupil and iris ellipse, eye aperture, eye lids, 3D eye ball, optical vector estimation, and eye movement types. For Pupil Invisible projects, it also supports the detection of a special marker and allows the 2D and 3D gaze estimation mapped on the scene camera. In this extended journal paper for Pistol we focus on challenging in the wild situations, such as reflections on glasses, eye tracking during sport, changing lightning conditions, and this for two eye trackers. The tool Pistol can be downloaded here Link
Colonic Electrical Stimulation for Chronic Constipation: A Perspective Review
2024-02-21

Chronic constipation affects around 20% of the population and there is no efficient solution. This perspective review explores the potential of colonic electric stimulation (CES) using neural implants and methods of bioelectronic medicine as a therapeutic way to treat chronic constipation. The review covers the neurophysiology of colonic peristaltic function, the pathophysiology of chronic constipation, the technical aspects of CES, including stimulation parameters, electrode placement, and neuromodulation target selection, as well as a comprehensive analysis of various animal models highlighting their advantages and limitations in elucidating the mechanistic insights and translational relevance for CES. Finally, the main challenges and trends in CES are discussed.
Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes
2024-02-21

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO 2 . Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis ( pgi ), central-carbon regulation ( crp ), and RNA transcription ( rpoB ). The pgi mutation reduces the enzyme’s activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module ( rpiB ) and the energy module ( fdoGH ), as well as an increased ratio of NADH/NAD + - the cycle’s electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.
Effects of Miosis on the Visual Acuity Space under Varying Conditions of Contrast and Ambient Luminance in Presbyopia
2024-02-21

Background: Presbyopia is an age-related ocular condition, typically affecting individuals aged over 40 years, characterized by a gradual and irreversible decline in the eye’s ability to focus on nearby objects. Correction methods for presbyopia encompass the use of corrective lenses, surgical interventions (corneal or lens based), and, more recently, the FDA-approved topical administration of 1.25% pilocarpine. While prior research has demonstrated the efficacy of daily pilocarpine eye drop application in enhancing near visual acuity by increasing the depth of focus leveraging the pinhole effect, limited knowledge exists regarding its influence on visual acuity under varying conditions of contrast and ambient luminance. Methods: This study aims to investigate the impact of these variables on visual acuity, employing the VA-CAL test, among 11 emmetropic and 11 presbyopic volunteers who reported subjective difficulties with near vision. This study includes evaluations under natural conditions with a pinhole occluder (diameter of 2 mm), and subsequent administration of 1% pilocarpine (Pilomann, Bausch + Lomb, Laval, Canada). Results: The VA-CAL results demonstrate the expected, statistically significant effects of contrast and ambient luminance on visual acuity in both emmetropic and presbyopic volunteers. Furthermore, in emmetropic individuals, the application of pilocarpine resulted in a statistically significant reduction in visual acuity. In contrast, presbyopes did not exhibit statistically significant differences in the visual acuity space under either the pinhole or pilocarpine conditions when compared to natural conditions. Conclusions: The pharmacological treatment of presbyopia with pilocarpine eye drops, intended to enhance near vision, does not adversely affect visual acuity in presbyopes. This suggests that pilocarpine may offer a viable alternative for individuals averse to wearing corrective eyewear.
The revised International Code of Medical Ethics unites doctors under one global medical ethos
2024-02-21

The World Medical Association's revised International Code of Medical Ethics offers a core set of ethical norms for all doctors worldwide to follow, write <b>Ramin W Parsa-Parsi</b>, <b>Raanan Gillon</b>, and <b>Urban Wiesing</b>
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
2024-02-21

Abstract Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the re-identification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder that leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes these information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.
Teaming up with an AI: Exploring human-AI collaboration in a writing scenario with ChatGPT
2024-02-21

Recent advancements in artificial intelligence (AI) technologies, particularly in generative pre-trained transformer large language models, have significantly enhanced the capabilities of text-generative AI tools – a development that opens new avenues for human-AI collaboration across various domains. However, the dynamics of human interaction with AI-based chatbots, such as ChatGPT, remain largely unexplored. We observed and analyzed how people interact with ChatGPT in a collaborative writing setting to address this research gap. A total of 135 participants took part in this exploratory lab study, which consisted of engaging with ChatGPT to compose a text discussing a prohibition of alcohol in public in relation to a given statement on risky alcohol consumption. During the writing task, all screen activity was logged. In addition to the writing task, further insights on user behavior and experience were gained by applying questionnaires and conducting an additional short interview with a randomly selected subset of 18 participants. Our results reveal high satisfaction with ChatGPT regarding quality aspects, mainly cognitive rather than affect-based trust in ChatGPT’s responses, and higher ratings on perceived competence than on warmth. Compared to other types of prompts, mostly content-related prompts for data, facts, and information were sent to ChatGPT. Mixed-method analysis showed that affinity for technology integration and current use of ChatGPT were positively associated with the frequency of complete text requests. Moreover, prompts for complete texts were associated with more copy-paste behavior. These first insights into co-writing with ChatGPT can inform future research on how successful human-AI collaborative writing can be designed.
Distribution of initial caries lesions in relation to fixed orthodontic therapy. A systematic review and meta-analysis
2024-02-22

Abstract Background Initial caries lesion (ICLs) adjacent to orthodontic brackets are the most common side effect of orthodontic treatment with fixed appliances. The reported prevalence is uncertain and varies considerably across studies, from 27% to 97%. Objectives This paper was designed to evaluate and synthesize the available evidence on the prevalence and incidence rates of ICLs in relation to orthodontic treatment. Selection criteria: The review (Prospero protocol CRD42023412952) included randomized and non-randomized clinical trials of interventions, cohort studies, and cross-sectional studies, published after 1990 on the prevalence or incidence of ICLs during or after orthodontic treatment with fixed appliances. Search methods: Pubmed, Scopus, and Embase databases were searched from 1990 until 01 May 2023. The risk of bias assessment was performed with RoB 2 and ROBINS-I tool and the Joanna Briggs Institute Critical Appraisal Checklist. Data collection and analysis: The proportion of individuals with ICLs, reported as the number/percentage of individuals/teeth with ICLs or mean number of ICLs per subject, were used to synthesize results. Results The search yielded a total of 468 papers; 21 studies were included in the systematic review, 2 of which were not included in the meta-analysis. The prevalence rate [95%CI] of ICLs was 0.57% [0.48; 0.65] in 1448 patients, 0.22% [0.14; 0.33] in 11583 teeth, with a mean number of lesions equal to 2.24 [1.79; 2.70] in 484 patients evaluated. The incidence rate of new carious lesions developed during orthodontic treatment was 0.48% [0.33; 0.63] in 533 patients, 0.15% [0.08; 0.26] in 1890 teeth with a mean number of ICLs equal to 2.29 [1.12; 3.46] in 208 patients evaluated. Limitations Although the high number of included studies and the overall good quality, there was a significant heterogeneity in the collected data. Conclusion The prevalence and incidence rates of ICLs in subjects undergoing orthodontic treatment are quite high and raise some concerns in terms of risk assessment of orthodontic treatment. ICLs represent an alarming challenge for both patients and professionals. Effective caries prevention strategies during treatment need to be considered and implemented where appropriate.