julilili42/papers huggingface dataset:
A recurrent missense variant in ITPR3 causes demyelinating Charcot-Marie-Tooth with variable severity
2024-06-24

Abstract Charcot-Marie-Tooth (CMT) disease is a neuromuscular disorder affecting the peripheral nervous system. The diagnostic yield in demyelinating CMT (CMT1) is typically ∼80%–95%, of which at least 60% is due to the PMP22 gene duplication. The remainder of CMT1 is more genetically heterogeneous. We used whole exome and whole genome sequencing data included in the GENESIS database to investigate novel causal genes and mutations in a cohort of ∼2670 individuals with CMT neuropathy. A recurrent heterozygous missense variant p.Thr1424Met in the recently described CMT gene ITPR3, encoding IP3R3 (inositol 1,4,5-trisphosphate receptor 3), was identified. This previously reported p.Thr1424Met change was present in 33 affected individuals from nine unrelated families from multiple populations, representing an unusual recurrence rate at a mutational hotspot, strengthening the gene-disease relationship (gnomAD v4 allele frequency 1.76 × 10−6). Sanger sequencing confirmed the co-segregation of the CMT phenotype with the presence of the mutation in autosomal dominant and de novo inheritance patterns, including a four-generation family with multiple affected second-degree cousins. Probands from all families presented with slow nerve conduction velocities, matching the diagnostic category of CMT1. Remarkably, we observed a uniquely variable clinical phenotype for age at onset and phenotype severity in p.Thr1424Met carrying patients, even within families. Finally, we present data supportive of a dominant-negative effect of the p.Thr1424Met mutation with associated changes in protein expression in patient-derived cells.
Tree diversity increases carbon stocks and fluxes above- but not belowground in a tropical forest experiment
2024-06-24

International commitments advocate large-scale forest restoration as a nature-based solution to climate change mitigation through carbon (C) sequestration. Mounting evidence suggests that mixed compared to monospecific planted forests may sequester more C, exhibit lower susceptibility to climate extremes and offer a broader range of ecosystem services. However, experimental studies comprehensively examining the control of tree diversity on multiple C stocks and fluxes above- and belowground are lacking. To address this gap, we leverage data from the Sardinilla experiment in Panama, the oldest tropical tree diversity experiment which features a gradient of one–, two–, three–, and five–species mixtures of native tree species. Over 16 years, we measured multiple above- and belowground C stocks and fluxes, ranging from tree aboveground C, over leaf litter C production, to soil organic carbon (SOC). We show that tree diversity significantly increased aboveground C stocks and fluxes, with a 57% higher gain in aboveground tree C in five-species mixtures compared to monocultures (35.7±1.8 vs 22.8±3.4 Mg C ha -1 ) 16 years after planting. In contrast, we observed a net reduction in SOC (on average -11.2±1.1 Mg C ha -1 ) and no significant difference in SOC 3 stocks (the predominantly tree-derived, i.e., C 3 plant-derived SOC fraction) between five-species mixtures and monocultures (13.0±0.9 vs 15.1±1.3 Mg C ha -1 ). Positive tree diversity effects persisted despite repeated climate extremes and strengthened over time for aboveground tree growth. Structural equation models showed that higher tree growth in mixtures enhanced leaf litter and coarse woody debris C fluxes to the soil, resulting in a tightly linked C cycle aboveground. However, we did not observe significant links between above- and belowground C stocks and fluxes. Our study elucidates the mechanisms through which higher tree diversity bolsters the climate mitigation potential of tropical forest restoration. Restoration schemes should prioritize mixed over monospecific planted forests.
White Clover does not Increase Soil N2O Emissions Compared to Ryegrass in Non-Frozen Winter, but Increases CH4 Uptake
2024-06-24

Abstract As one of the most important forage species in Europe, white clover ( Trifolium repens ) is a legume that is well recognized for its potential to increase productivity especially under reduced N input. It is hypothesized that legumes have the potential to decrease overwinter soil greenhouse gas (GHG) emissions due to more efficient N recycling as compared to non-legume forbs. We conducted a field experiment recording high-resolution soil nitrous oxide (N 2 O) and methane (CH 4 ) fluxes during the winter months (December 2019 to March 2020) on a five-year-old grassland in central Germany with white clover, fertilized and unfertilized perennial ryegrass ( Lolium perenne ), and bare soil. White clover and fertilized ryegrass stimulated soil N 2 O emissions by 174% and 212% as compared to bare soil, and by 36% and 56% as compared to unfertilized ryegrass, respectively, due to their greater N availability and higher water-filled pore space (WFPS). The estimated cumulative CH 4 fluxes under white clover were a net CH 4 sink, whereas ryegrass and bare soil were net CH 4 sources. Soil N 2 O fluxes were predominantly regulated by both mineral N and WFPS, while CH 4 fluxes were mainly explained by WFPS. N-fertilization during the growing season did not affect off-season N 2 O and CH 4 fluxes in perennial ryegrass plots. The combined non-CO 2 global warming potential highlighted the possible mitigation effect of white clover on overwinter GHG emissions. Our findings suggest that GHG emissions from legumes are not offsetting their productive benefits during the non-frozen winter seasons.
Leptochelins A–C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria
2024-06-25

Metals are important cofactors in the metabolic processes of cyanobacteria, including photosynthesis, cellular respiration, DNA replication, and the biosynthesis of primary and secondary metabolites. In adaptation to the marine environment, cyanobacteria use metallophores to acquire trace metals when necessary as well as to reduce potential toxicity from excessive metal concentrations. Leptochelins A-C were identified as structurally novel metallophores from three geographically dispersed cyanobacteria of the genus <i>Leptothoe</i>. Determination of the complex structures of these metabolites presented numerous challenges, but they were ultimately solved using integrated data from NMR, mass spectrometry and deductions from the biosynthetic gene cluster. The leptochelins are comprised of halogenated linear NRPS-PKS hybrid products with multiple heterocycles that have potential for hexadentate and tetradentate coordination with metal ions. The genomes of the three leptochelin producers were sequenced, and retrobiosynthetic analysis revealed one candidate biosynthetic gene cluster (BGC) consistent with the structure of leptochelin. The putative BGC is highly homologous in all three <i>Leptothoe</i> strains, and all possess genetic signatures associated with metallophores. Postcolumn infusion of metals using an LC-MS metabolomics workflow performed with leptochelins A and B revealed promiscuous binding of iron, copper, cobalt, and zinc, with greatest preference for copper. Iron depletion and copper toxicity experiments support the hypothesis that leptochelin metallophores may play key ecological roles in iron acquisition and in copper detoxification. In addition, the leptochelins possess significant cytotoxicity against several cancer cell lines.
Temporal trends of skin and soft tissue infections caused by methicillin-resistant Staphylococcus aureus in Gabon
2024-06-25

Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of mortality due to bacterial antimicrobial resistance. While S. aureus is common in skin and soft tissue infections (SSTI) in Africa, data on MRSA rates are scarce and reports vary widely across the continent (5%-80%). In this study, we describe the proportion of MRSA causing SSTI in Lambaréné, Gabon, over an 11-year period. Methods We retrospectively analyzed data from 953 bacterial specimens collected from inpatients and outpatients with SSTI at the Albert Schweitzer Hospital, Lambaréné, Gabon, between 2009 and 2019. We determined temporal changes in the prevalence of MRSA and identified risk factors for SSTI with MRSA. Results 68% of all specimens with bacterial growth yielded S. aureus (n = 499/731), of which 7% (36/497) with antimicrobial susceptibility testing were identified as MRSA. Age above 18 years, admission to the surgical ward, and deep-seated infections were significantly associated with MRSA as the causative agent. After an initial decline from 7% in 2009, there was a marked increase in the proportion of MRSA among all S. aureus from SSTI from 3 to 20% between 2012 and 2019. The resistance rate to erythromycin was significantly higher in MRSA than in methicillin-susceptible S. aureus (73% vs. 10%), and clindamycin resistance was detected exclusively in MRSA isolates (8%). Conclusion The increasing proportion of MRSA causing SSTI over the 11-year period contrasts with many European countries where MRSA is on decline. Continuous surveillance of MRSA lineages in the hospital and community along with antibiotic stewardship programs could address the increasing trend of MRSA.
Cystic vestibular schwannoma – a subgroup analysis from a comparative study between radiosurgery and microsurgery
2024-06-25

Abstract Some vestibular schwannoma (VS) show cystic morphology. It is known that these cystic VS bear different risk profiles compared to solid VS in surgical treatment. Still, there has not been a direct comparative study comparing both SRS and SURGERY effectiveness in cystic VS. This retrospective bi-center cohort study aims to analyze the management of cystic VS compared to solid VS in a dual center study with both microsurgery ( SURGERY ) and stereotactic radiosurgery ( SRS ). Cystic morphology was defined as presence of any T2-hyperintense and Gadolinium-contrast-negative cyst of any size in the pre-interventional MRI. A matched subgroup analysis was carried out by determining a subgroup of matched SURGERY- treated solid VS and SRS -treated solid VS. Functional status, and post-interventional tumor volume size was then compared. From 2005 to 2011, N = 901 patients with primary and solitary VS were treated in both study sites. Of these, 6% showed cystic morphology. The incidence of cystic VS increased with tumor size: 1.75% in Koos I, 4.07% in Koos II, 4.84% in Koos III, and the highest incidence with 15.43% in Koos IV. Shunt-Dependency was significantly more often in cystic VS compared to solid VS ( p = 0.024) and patients with cystic VS presented with significantly worse Charlson Comorbidity Index (CCI) compared to solid VS ( p &lt; 0.001). The rate of GTR was 87% in cystic VS and therefore significantly lower, compared to 96% in solid VS ( p = 0.037). The incidence of dynamic volume change (decrease and increase) after SRS was significantly more common in cystic VS compared to the matched solid VS ( p = 0.042). The incidence of tumor progression with SRS in cystic VS was 25%. When comparing EOR in the SURGERY- treated cystic to solid VS, the rate for tumor recurrence was significantly lower in GTR with 4% compared to STR with 50% ( p = 0.042). Tumor control in cystic VS is superior in SURGERY , when treated with a high extent of resection grade, compared to SRS . Therapeutic response of SRS was worse in cystic compared to solid VS. However, when cystic VS was treated surgically, the rate of GTR is lower compared to the overall, and solid VS cohort. The significantly higher number of patients with relevant post-operative facial palsy in cystic VS is accredited to the increased tumor size not its sole cystic morphology. Cystic VS should be surgically treated in specialized centers.
EMOKINE: A software package and computational framework for scaling up the creation of highly controlled emotional full-body movement datasets
2024-06-25

Abstract EMOKINE is a software package and dataset creation suite for emotional full-body movement research in experimental psychology, affective neuroscience, and computer vision. A computational framework, comprehensive instructions, a pilot dataset, observer ratings, and kinematic feature extraction code are provided to facilitate future dataset creations at scale. In addition, the EMOKINE framework outlines how complex sequences of movements may advance emotion research. Traditionally, often emotional-‘action’-based stimuli are used in such research, like hand-waving or walking motions. Here instead, a pilot dataset is provided with short dance choreographies, repeated several times by a dancer who expressed different emotional intentions at each repetition: anger, contentment, fear, joy, neutrality, and sadness. The dataset was simultaneously filmed professionally, and recorded using XSENS® motion capture technology (17 sensors, 240 frames/second). Thirty-two statistics from 12 kinematic features were extracted offline, for the first time in one single dataset: speed, acceleration, angular speed, angular acceleration, limb contraction, distance to center of mass, quantity of motion, dimensionless jerk (integral), head angle (with regards to vertical axis and to back), and space (convex hull 2D and 3D). Average, median absolute deviation (MAD), and maximum value were computed as applicable. The EMOKINE software is appliable to other motion-capture systems and is openly available on the Zenodo Repository. Releases on GitHub include: (i) the code to extract the 32 statistics, (ii) a rigging plugin for Python for MVNX file-conversion to Blender format (MVNX=output file XSENS® system), and (iii) a Python-script-powered custom software to assist with blurring faces; latter two under GPLv3 licenses.
Computational methods for climate change frame analysis: Techniques, critiques, and cautious ways forward
2024-06-25

Abstract Frame analysis is a popular methodological paradigm to investigate how climate change is reported in the media, how it is negotiated by political actors, and perceived by publics. Its scope of application extends across various academic disciplines and transcends traditional boundaries of research such as those between quantitative and qualitative methods. Recent transformations of the media landscape have a strong influence on how frame analysis is conducted and how it is used to investigate climate change communication. Online data mining and computational methods have now become increasingly mainstream to investigate discursive elements in online media. Scholars have highlighted the potential, but also the risks associated with sophisticated computational methods, such as machine learning, increasingly used in the context of frame analysis. This advanced review gathers the scientific literature on computational frame analysis for analyzing climate change communication and discusses ways of dealing with associated risks and caveats by incorporating ideas from Science &amp; Technology Studies (STS) and other stances of critical scholarship. Recommended ways forward include combining methods, practicing theoretical interdisciplinarity, infrastructuring reflexivity in research constellations, and embracing transparency, documentation, and accessibility of methods. This article is categorized under: The Social Status of Climate Change Knowledge &gt; Sociology/Anthropology of Climate Knowledge Perceptions, Behavior, and Communication of Climate Change &gt; Communication Climate, History, Society, Culture &gt; Technological Aspects and Ideas
Multiple evolutionary pressures shape identical consonant avoidance in the world’s languages
2024-06-25

Languages disfavor word forms containing sequences of similar or identical consonants, due to the biomechanical and cognitive difficulties posed by patterns of this sort. However, the specific evolutionary processes responsible for this phenomenon are not fully understood. Words containing sequences of identical consonants may be more likely to arise than those without; processes of word form mutation may be more likely to remove than create sequences of identical consonants in word forms; finally, words containing identical consonants may die out more frequently than those without. Phylogenetic analyses of the evolution of homologous word forms indicate that words with identical consonants arise less frequently than those without. However, words with identical consonants do not die out more frequently than those without. Further analyses reveal that forms with identical consonants are replaced in basic meaning functions more frequently than words without. Taken together, results suggest that the underrepresentation of sequences of identical consonants is overwhelmingly a by-product of constraints on word form coinage, though processes related to word usage also serve to ensure that such patterns are infrequent in more salient vocabulary items. These findings clarify aspects of processes of lexical evolution and competition that take place during language change, optimizing communicative systems.
Dating the Neanderthal environment: Detailed luminescence chronology of a palaeochannel sediment core at the Palaeolithic site of Lichtenberg in the Lower Saxony, northern Germany
2024-06-25

Northern Germany is famous for its numerous Neanderthal (Middle Palaeolithic) archaeological sites and well-preserved palaeoclimate records. Nevertheless, our understanding of how hominins responded to climate fluctuations and adapted to changing environments in this region remains limited because there are only a few reliable, highly-resolved chronological frameworks of long stratigraphic successions. Most of the Middle Palaeolithic sites in this region lack a reliable chronostratigraphy beyond the radiocarbon dating range. In this study, we present a high-resolution optically stimulated luminescence (OSL) chronology derived from a ∼21 m long sediment core (Li-BPa) that was drilled in close proximity to the known Neanderthal site of Lichtenberg. Quartz OSL dating was applied to the upper 6.5 m of the core. Subsequently, the obtained quartz OSL ages were compared with feldspar post-infrared (IR) IRSL (pIRIR) measured at 290 °C (pIRIR<sub>290</sub>), pulsed IR<sub>50</sub> (pre-pIRIR<sub>225</sub>), and pulsed pIRIR<sub>225</sub> ages to select a suitable feldspar signal to date older samples. A comparison of the quartz and feldspar ages indicates that only fading-corrected pulsed IR<sub>50</sub> (pre-pIRIR<sub>225</sub>) and pIRIR<sub>225</sub> ages agree well with quartz OSL ages. Finally, the age framework of the sediment sequence was established based on the 11 quartz OSL ages and 23 fading-corrected pulsed IR<sub>50</sub> (pre-pIRIR<sub>225</sub>) and pulsed pIRIR<sub>225</sub> ages. The resulting Bacon age-depth model agrees with litho- and biostratigraphic designations, indicating that the whole sequence was deposited between ca. 275 ka and ca. 24 ka, corresponding to the Saalian to Weichselian periods.
An AINTEGUMENTA phospho-switch controls bilateral stem cell activity during secondary growth
2024-06-25

Abstract Plant stem cells have the remarkable ability to give rise to distinct tissues and organs throughout development. Two concentric cylinders of actively dividing stem cells are the main drivers of radial thickening during secondary growth, each producing distinct vascular cell types towards the inside and the outside. While the molecular mechanisms underlying their initiation have been well studied, it remains unclear how these stem cell layers determine which cell type is generated. Here, we demonstrate that the cross-talk between the ERECTA (ER) receptor pathway and auxin signalling controls the amount and choice of output tissue in these two stem cell regions. Mechanistically, we show that the ER pathway phosphorylates the transcription factor AINTEGUMENTA, thereby modulating bilateral stem cell activity and favouring the differentiation of only one type of cell. Our results thus show that the phosphorylation status of ANT regulates root girth and biomass accumulation by influencing bilateral stem cell production. This highlights the critical role of post-translational modifications in plant growth and development. Significance This study uncovers a critical regulatory mechanism governing bilateral stem cell activity during plant radial growth. Stem cells in the cambia proliferate and differentiate into specialized tissues like wood and cork, key sites of biomass accumulation. By exploring the interplay between the ERECTA (ER) receptor and auxin signalling, we reveal how these pathways modulate stem cell differentiation and radial thickening through the phosphorylation of the transcription factor AINTEGUMENTA (ANT). Phosphorylation status of ANT modulates stem cell activity, dictating the production of specific vascular cell types like wood thus controlling root girth. This research underscores the importance of post-translational modifications in plant development and provides a novel regulation underpinning stem cell differentiation, with significant implications for enhancing biomass accumulation as wood.
Spike generation in electroreceptor afferents introduces additional spectral response components by weakly nonlinear interactions
2024-06-25

Abstract Spiking thresholds in neurons or rectification at synapses are essential for neuronal computations rendering neuronal processing inherently nonlinear. Nevertheless, linear response theory has been instrumental for understanding, for example, the impact of noise or neuronal synchrony on signal transmission, or the emergence of oscillatory activity, but is valid only at low stimulus amplitudes or large levels of intrinsic noise. At higher signal-to-noise ratios, however, nonlinear response components become relevant. Theoretical results for leaky integrate-and-fire neurons in the weakly nonlinear regime suggest strong responses at the sum of two input frequencies if these frequencies or their sum match the neuron’s baseline firing rate. We here analyze nonlinear responses in two types of primary electroreceptor afferents, the P-units of the active and the ampullary cells of the passive electrosensory system of the wave-type electric fish Apteronotus leptorhynchus . In our combined experimental and modeling approach we identify these predicted nonlinear responses in low-noise P-units and, much stronger, in ampullary cells. Our results provide experimental evidence for nonlinear responses of spike generators in the weakly nonlinear regime. We conclude that such nonlinear responses occur in any sensory neuron that operates in similar regimes particularly at near-threshold stimulus conditions.
Effects of exposure to plus-size fashion models on weight-related attitudes in bulimia nervosa: Findings from an exploratory study
2024-06-25

These exploratory results imply that the positive effects of plus-sized model images on reducing negative assumptions about people with high weight may not be limited to healthy individuals but also seem to extend to women with BN. Further controlled studies with larger samples and long-term assessments are needed to confirm these findings.