julilili42/papers huggingface dataset:
Lesions in a songbird vocal circuit increase variability in song syntax
2024-01-10

Complex skills like speech and dance are composed of ordered sequences of simpler elements, but the neuronal basis for the syntactic ordering of actions is poorly understood. Birdsong is a learned vocal behavior composed of syntactically ordered syllables, controlled in part by the songbird premotor nucleus HVC (proper name). Here, we test whether one of HVC’s recurrent inputs, mMAN (medial magnocellular nucleus of the anterior nidopallium), contributes to sequencing in adult male Bengalese finches ( Lonchura striata domestica ). Bengalese finch song includes several patterns: (1) chunks, comprising stereotyped syllable sequences; (2) branch points , where a given syllable can be followed probabilistically by multiple syllables; and (3) repeat phrases , where individual syllables are repeated variable numbers of times. We found that following bilateral lesions of mMAN, acoustic structure of syllables remained largely intact, but sequencing became more variable, as evidenced by ‘breaks’ in previously stereotyped chunks, increased uncertainty at branch points, and increased variability in repeat numbers. Our results show that mMAN contributes to the variable sequencing of vocal elements in Bengalese finch song and demonstrate the influence of recurrent projections to HVC. Furthermore, they highlight the utility of species with complex syntax in investigating neuronal control of ordered sequences.
Evolution of the temporal skull openings in land vertebrates: A hypothetical framework on the basis of biomechanics
2024-01-10

Abstract The complex constructions of land vertebrate skulls have inspired a number of functional analyses. In the present study, we provide a basic view on skull biomechanics and offer a framework for more general observations using advanced modeling approaches in the future. We concentrate our discussion on the cranial openings in the temporal skull region and work out two major, feeding‐related factors that largely influence the shape of the skull. We argue that (1) the place where the most forceful biting is conducted and (2) the handling of resisting food (sideward movements) constitute the formation and shaping of either one or two temporal arcades surrounding these openings. Diversity in temporal skull anatomy among amniotes can be explained by specific modulations of these factors with different amounts of acting forces which inevitably lead to deposition or reduction of bone material. For example, forceful anterior bite favors an infratemporal bar, whereas forceful posterior bite favors formation of an upper temporal arcade. Transverse forces (inertia and resistance of seized objects) as well as neck posture also influence the shaping of the temporal region. Considering their individual skull morphotypes, we finally provide hypotheses on the feeding adaptation in a variety of major tetrapod groups. We did not consider ligaments, internal bone structure, or cranial kinesis in our considerations. Involving those in quantitative tests of our hypotheses, such as finite element system synthesis, will provide a comprehensive picture on cranial mechanics and evolution in the future.
Spike desensitisation as a mechanism for high-contrast selectivity in retinal ganglion cells
2024-01-10

In the vertebrate retina, several dozens of parallel channels relay information about the visual world to the brain. These channels are represented by the different types of retinal ganglion cells (RGCs), whose responses are rendered selective for distinct sets of visual features by various mechanisms. These mechanisms can be roughly grouped into synaptic interactions and cell-intrinsic mechanisms, with the latter including dendritic morphology as well as ion channel complement and distribution. Here, we investigate how strongly ion channel complement can shape RGC output by comparing two mouse RGC types, the well-described ON alpha cell and a little-studied ON cell that is EGFP-labelled in the Igfbp5 mouse line and displays an unusual selectivity for stimuli with high contrast. Using patch-clamp recordings and computational modelling, we show that a higher activation threshold and a pronounced slow inactivation of the voltage-gated Na + channels contribute to the distinct contrast tuning and transient responses in ON Igfbp5 RGCs, respectively. In contrast, such a mechanism could not be observed in ON alpha cells. This study provides an example for the powerful role that the last stage of retinal processing can play in shaping RGC responses.
Interleukin-1ß / Interleukin (IL)-1-Receptor-Antagonist (IL1-RA) Axis in Invasive Bladder Cancer – An Exploratory Analysis of Clinical and Tumor Biological Significance
2024-01-10

Background: Previous data indicate a role of IL-1 and IL-1RA imbalance in bladder carcinoma (BC) and inhibition of IL-1 signaling might be considered a treatment option. Objective: To assess expression patterns and the prognostic role of IL-1ß and IL-1RA in invasive BC and to evaluate their interaction with AKT signaling and proliferation. Design, Setting, and Participants: The study included two independent cohorts of n=92 and n=102 patients who underwent radical cystectomy for BC. Specimen from BC and benign urothelium (n=22 and n=39) were processed to a tissue microarray and immunohistochemically stained for IL-1ß, IL-1RA, AKT and Ki-67. Expression scores were correlated to clinical variables and Ki-67 and AKT expression. Outcome measurements and statistical analysis: Association with outcome was assessed using Wilcoxon Kruskal-Wallis tests, Chi-square tests or linear regression, dependent on the variable’s category. Kaplan–Meier and Cox proportional hazard analyses were used to estimate recurrence-free (RFS), cancer-specific (CSS) and overall survival (OS). Results: Both, IL-1ß and IL-1RA were significantly overexpressed in invasive BC compared to benign urothelium in both cohorts (p&amp;amp;lt;0.005). IL-1ß was associated with vascular invasion (210 vs. 183, p&amp;amp;lt;0.02), lymphatic invasion (210 vs. 180, &amp;amp;lt;0.05) and G3 cancer (192 vs. 188, &amp;amp;lt;0.04). Survival analysis revealed favorable RFS, CSS, and OS in case of high IL-1ß expression (p&amp;amp;lt;0.02, &amp;amp;lt;0.03 and &amp;amp;lt;0.006, respectively). Multivariate analyses revealed an independent impact of (low) IL1ß expression on RFS, CSS and OS. IL-1ß and IL-1ß/IL-1RA ratio were positively correlated to AKT expression (p&amp;amp;lt;0.05 and &amp;amp;lt;0.01, respectively). Additionally, high expression of Ki-67 (&amp;amp;gt;15%) correlated with higher levels of IL-1β (p=0.01). Conclusions: Overexpression of IL-1ß and IL-1RA is frequently found in BC, with a prognostic significance observed for IL-1ß protein expression. The observed link between the IL-1ß / IL-1RA axis and AKT signaling may indicate possible autophagy activation processes beside the known tumor-promoting effects of AKT.
Towards patient-relevant, trial-ready digital motor outcomes for SPG7: a cross-sectional prospective multi-center study (PROSPAX)
2024-01-10

Abstract Background and Objectives With targeted treatment trials on the horizon, identification of sensitive and valid outcome measures becomes a priority for the &gt;100 spastic ataxias. Digital-motor measures, assessed by wearable sensors, are prime outcome candidates for SPG7 and other spastic ataxias. We here aimed to identify candidate digital-motor outcomes for SPG7 – as one of the most common spastic ataxias – that: (i) reflect patient-relevant health aspects, even in mild, trial-relevant disease stages; (ii) are suitable for a multi-center setting; and (iii) assess mobility also during uninstructed walking simulating real-life. Methods Cross-sectional multi-center study (7 centers, 6 countries). Unaided walking was assessed in 65 patients with SPG7 and 50 unrelated healthy controls using 3 wearable sensors (Opal APDM). Digital gait measures were correlated to measures of disease severity (SARA, SPRS; including mobility-relevant subscores SPRS 1315291292025 , SARA PG ) and activities of daily living (FARS-ADL). The task set included lab-based defined gait tasks, complemented by uninstructed ‘supervised free walking’. Results Among 30 hypothesis-based gait measures, 18 demonstrated at least moderate effect size (Cliff’s δ&gt;0.5) in discriminating SPG7 patients from controls, and 17 even in mild disease stages (SPRS mobility ≤9). Spatiotemporal variability measures such as the spatial variability composite measure SPcmp (ρ=0.67, p=&lt;0.0001), Stride Time CV (ρ=0.67, p=&lt;0.0001) and Swing CV (ρ=0.64, p=&lt;0.0001) showed the highest correlations with clinician-reported mobility scores (SPRS mobility ), and overall disease severity (SPRS, SARA). Overall, top-ranked measures also correlated with patient-relevant functional deficits in everyday life activities (FARS-ADL). In mild disease stages (SPRS mobility ≤9, n=41), Swing CV (ρ=0.53, p=&lt;0.0001) and SPcmp (ρ=0.50, p=&lt;0.0001) correlated with SPRS mobility . In the uninstructed ‘supervised free walking’ task, the correlations between spatiotemporal variability measures (Stride Time CV, Stride Length CV, Swing CV) and SPRS mobility could be confirmed; additionally, Gait Speed (ρ=-0.59, p=&lt;0.0001) was highly correlated with SPRS mobility . Discussion We here identified trial-ready digital-motor candidate outcomes for the spastic ataxia SPG7, all characterized by proven multi-center applicability, ability to discriminate patients from controls, and correlation with measures of disease severity – even in mild disease stages –, and patient-relevant everyday function. If validated longitudinally, these sensor outcomes might inform future natural history and treatment trials in SPG7 and other spastic ataxias.
Autotrophic growth of E. coli is achieved by a small number of genetic changes
2024-01-10

Abstract Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. 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 E. 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.
Who said it? Native and non-native listeners' source memory for object-speaker associations
2024-01-10

Memory for who said what can help native and non-native listeners identify critical information for use in conversations. In two experiments, source memory for object-speaker associations was tested for listeners varying in language proficiency. Native and non-native participants of English first heard speakers name objects with prototypical color (e.g., broccoli) before they had to indicate who had previously named each object. Speakers either consistently named objects of one color, or they randomly named objects of different colors. While both listener groups associated objects with speakers successfully, in Experiment 1, with black and white images, native listeners showed an advantage in source memory in the color consistent condition over the random condition, while non-native listeners had no such advantage. The finding for non-native listeners was replicated in Experiment 2 with color images. The results confirm the role of source memory representations in communication, but also suggest that encoding object-speaker association in L2 may be less sensitive to consistent patterns in the input.
OSIRIS – The Online Scintillator Internal Radioactivity Investigation System of JUNO
2024-01-10

The Online Scintillator Internal Radioactivity Investigation System is an 18-ton pre-detector of\\nJUNO, currently under commissioning in south-west China. During the 6-month filling phase\\nof the JUNO main detector, it will be responsible for the monitoring of the radiopurity of the\\nliquid scintillator filled into the JUNO central detector. Fast 214/212Bi/214/212Po coincidences\\nserve as a main measurement channel for OSIRIS’ high sensitivity to 238U/232Th contaminations\\nin the liquid scintillator. In addition, contamination measurements of 85Kr and 14C are also\\nforeseen. OSIRIS is located 700m underground in the JUNO laboratory near the central detector.\\nIts cylindrical central vessel is surrounded by 64 JUNO 20-inch PMTs and embedded into a water\\nCherenkov muon veto. Calibration of the detector will be done by an automated calibration unit\\nfeaturing radioactive sources and a fast pulsed LED, as well as by a pico-second laser calibration\\nsystem responsible for time- and charge calibration. After OSIRIS’ main purpose of monitoring\\nthe liquid scintillator has been fulfilled, a consecutive physics phase addressing solar neutrinos\\nand 0νββ decay is foreseen.
JUNO’s Sensitivity to the Neutrino Mass Ordering
2024-01-10

The Jiangmen Underground Neutrino Observatory (JUNO) is a 20 kt liquid scintillator detector\\nequipped with 17612 20-inch PMTs as well as 25600 3-inch PMTs located 700 m underground\\nin southern China. It features a broad physics program with a primary goal of determining the\\nneutrino mass ordering to 3σ in about 6 years. With an unprecedented energy resolution better than\\n3% at 1 MeV, it will measure the spectrum of antineutrinos emitted from two nuclear power plants\\nlocated 53 km from the detector. For the success of JUNO’s neutrino mass ordering determination\\nand its oscillation parameter precision measurement program, an accurate knowledge of the emitted\\nreactor neutrino spectrum is crucial. Therefore, a satellite detector with 2.8 tons of gadolinium-doped\\nliquid scintillator will be constructed in a distance of 30 m from one of the reactor cores\\nto provide a precise measurement of the unoscillated spectrum with an energy resolution better\\nthan 2% at 1 MeV. This contribution will present studies on the sensitivity of the JUNO detector\\nto determine the neutrino mass ordering in combination with its satellite detector called TAO.
Author Response: Autotrophic growth of E. coli is achieved by a small number of genetic changes
2024-01-10

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. 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 E. 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.
Lesions in a songbird vocal circuit increase variability in song syntax
2024-01-10

Abstract Complex motor skills like speech and dance are composed of ordered sequences of simpler elements, but the neuronal basis for syntactic ordering of individual actions into sequences is poorly understood. Birdsong is a learned vocal behavior composed of syntactically ordered sequences of individual syllables. Activity in song premotor nucleus HVC (proper name) has been linked to the control of syllable sequencing, but sequencing may also be affected by its recurrent inputs. We here test the contribution of one of HVC’s inputs, mMAN (medial magnocellular nucleus of the anterior nidopallium), to the variable songs of adult male Bengalese finches (Lonchura striata domestica). The syntax of Bengalese song includes several patterns: 1) chunks, where syllables follow stereotypical order 2) branch points, where a given syllable can be followed by two or more different syllables in a probabilistic manner and 3) repeat phrases, where an individual syllable is repeated a variable number of times. We found that after bilateral lesions of mMAN, the acoustic structure of syllables remained largely intact, but sequencing became more variable for each of these patterns, seen by ‘breaks’ in previously stereotyped chunks, increased uncertainty at branch points and increased variability of repeat numbers. This increase in sequencing variability highlights the potential importance of regions projecting to HVC in the ordering of vocal elements. Previous studies on zebra finches found little effect of mMAN lesions on their relatively stereotyped adult song. In contrast, our results suggest that mMAN contributes to sequencing the variable songs of Bengalese finches and highlight the utility of species with more complex song syntax in investigating neuronal control of ordered motor sequences.
Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration
2024-01-10

&lt;p&gt;Data and code for the analysis in Ollonen et al., 2024, Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration, Nature Ecology and Evolution.&nbsp;&lt;/p&gt; &lt;p&gt;Raw landmark data, R scripts for the analysis and surface files used for the analysis as well as figure visualisations.&nbsp;&lt;/p&gt; &lt;p&gt;Cite the original article, not the dataset citation!!!&lt;/p&gt;
Consensus definitions of perception-action-integration in action control
2024-01-11

The literature on action control is rife with differences in terminology. This consensus statement contributes shared definitions for perception-action integration concepts as informed by the framework of event coding.
Towards an Integrated Perspective of Teachers’ Technology Integration: A Preliminary Model and Future Research Directions
2024-01-11

Technology integration is regarded as a crucial and complex endeavour to enhance students’ learning and prepare them to participate in a digital society. Although the research landscape on teachers’ technology integration is vivid and stimulating, an analytical model which synthesises different strands of research to model antecedents (i.e., teachers’ professional competences), processes and outcomes of technology integration in an integrated manner is missing. That said, previous research was often rather product-oriented and ignored potential effects on students’ learning processes and their achievement. To fill this gap, in this paper, we outline a preliminary model, the TPTI-model (teachers’ professional competence for technology integration), in which we deliberately link different research perspectives on teachers’ professional competences, professional vision and students’ learning (processes) to model technology integration during teaching. Based on the preliminary TPTI-model, we propose future research directions, which may allow to gain a better understanding of the teacher- and student-related conditions as well as processes of technology integration and their effects on students’ learning.
Complexation by Particulate Organic Matter Alters Iron Redox Behavior
2024-01-11

The role of iron (Fe) in environmental redox processes, such as microbial respiration and pollutant turnover, is influenced by its association with organic matter, particularly in redox-dynamic systems such as wetlands. While the association between Fe and dissolved organic matter (DOM) has been studied extensively, the association between Fe and particulate organic matter (POM), which differs in size and composition from DOM, is poorly understood. In this work, we investigated the complexation of aqueous Fe(II) by mineral-free POM over a full redox cycle using wet chemical and spectroscopic (X-ray absorption and Mössbauer spectroscopy) techniques. The mass of Fe(II) complexed by POM under anoxic conditions ranged from 18.9 ± 1.2 mg Fe·g–1 POM at pH 4.5 to 37.6 ± 1.5 mg Fe·g–1 POM at pH 7. Part of the complexed Fe(II) was oxidized to Fe(III) (21–46%) under anoxic conditions, indicating that complexation by POM altered the Fe(II) redox stability. We then exposed POM-complexed Fe to O2 at pH 5.5 and 7 to simulate oxidizing conditions. Upon exposure to aqueous O2, the complexed Fe(II) was rapidly and completely oxidized at pH 5.5 and pH 7, faster than uncomplexed Fe(II), suggesting that complexation by POM promoted abiotic Fe(II) oxidation. The resulting Fe(III)-POM consisted of Fe(III)-organic phases and poorly crystalline Fe(III) (oxyhydr)oxides. The results of this work demonstrate that POM acts as a major complexant of Fe and alters Fe redox behavior, thereby affecting the role of Fe in environmental redox processes.
Magnetism and metallicity in moiré transition metal dichalcogenides
2024-01-11

The ability to control the properties of twisted bilayer transition metal dichalcogenides in situ makes them an ideal platform for investigating the interplay of strong correlations and geometric frustration. Of particular interest are the low energy scales, which make it possible to experimentally access both temperature and magnetic fields that are of the order of the bandwidth or the correlation scale. In this manuscript, we analyze the moiré Hubbard model, believed to describe the low energy physics of an important subclass of the twisted bilayer compounds. We establish its magnetic and the metal–insulator phase diagram for the full range of magnetic fields up to the fully spin-polarized state. We find a rich phase diagram including fully and partially polarized insulating and metallic phases of which we determine the interplay of magnetic order, Zeeman-field, and metallicity, and make connection to recent experiments.