julilili42/papers huggingface dataset:
Maize mutants in miR394 ‐regulated genes show improved drought tolerance
2025-03-01

Abstract Water limitation represents one of the major threats to agricultural production, which often leads to drought stress and results in compromised growth, development and yield of crop species. Drought tolerance has been intensively studied in search of potential targets for molecular approaches to crop improvement. However, drought adaptive traits are complex, and our understanding of the physiological and genetic basis of drought tolerance is still incomplete. The miR394‐LCR pathway is a conserved regulatory module shown to participate in several aspects of plant growth and development, including stress response. Here, we characterized the miR394 pathway in maize, which harbours two genetic loci producing an evolutionarily conserved mature zma‐miR394 targeting two transcripts coding for F‐Box proteins, named hereby ZmLCR1 and ZmLCR2. Arabidopsis plants overexpressing the zma‐MIR394B gene showed high tolerance to drought conditions compared to control plants. Moreover, analysis of the growth and development of single and double maize mutant plants in ZmLCR genes indicate that these mutations do not affect plant fitness when they grow in normal watering conditions, but mutants showed better survival than wild‐type plants under water deprivation conditions. This increased drought tolerance is based on more efficient intrinsic water use, changes in root architecture and increased epicuticular wax content under water‐limiting conditions. Our results indicate that the miR394‐regulated ZmLCR genes are involved in drought stress tolerance and are remarkable candidates for maize crop improvement.
The reliability of replications: a study in computational reproductions
2025-03-01

This study investigates researcher variability in computational reproduction, an activity for which it is least expected. Eighty-five independent teams attempted numerical replication of results from an original study of policy preferences and immigration. Reproduction teams were randomly grouped into a ‘transparent group’ receiving original study and code or ‘opaque group’ receiving only a method and results description and no code. The transparent group mostly verified original results (95.7% same sign and p -value cutoff), while the opaque group had less success (89.3%). Second-decimal place exact numerical reproductions were less common (76.9 and 48.1%). Qualitative investigation of the workflows revealed many causes of error, including mistakes and procedural variations. When curating mistakes, we still find that only the transparent group was reliably successful. Our findings imply a need for transparency, but also more. Institutional checks and less subjective difficulty for researchers ‘doing reproduction’ would help, implying a need for better training. We also urge increased awareness of complexity in the research process and in ‘push button’ replications.
Correlates of Vocal Tract Evolution in Late Pliocene and Pleistocene Hominins
2025-03-01

Abstract Despite decades of research on the emergence of human speech capacities, an integrative account consistent with hominin evolution remains lacking. We review paleoanthropological and archaeological findings in search of a timeline for the emergence of modern human articulatory morphological features. Our synthesis shows that several behavioral innovations coincide with morphological changes to the would-be speech articulators. We find that significant reductions of the mandible and masticatory muscles and vocal tract anatomy coincide in the hominin fossil record with the incorporation of processed and (ultimately) cooked food, the appearance and development of rudimentary stone tools, increases in brain size, and likely changes to social life and organization. Many changes are likely mutually reinforcing; for example, gracilization of the hominin mandible may have been maintainable in the lineage because food processing had already been outsourced to the hands and stone tools, reducing selection pressures for robust mandibles in the process. We highlight correlates of the evolution of craniofacial and vocal tract features in the hominin lineage and outline a timeline by which our ancestors became ‘pre-adapted’ for the evolution of fully modern human speech.
Lossless single-molecule counting to absolute quantify proteoforms
2025-03-01

A novel immunoassay, termed Protein Interaction Coupling (PICO), is introduced to deliver clear, reference-free quantification of proteoforms - precise quantification. PICO employs a compartmentalized, homogeneous single-molecule assay with lossless and sensitive signal generation, capable of detecting down to a few molecules per reaction. Additionally, it utilizes a background-free, digital enumeration principle, known as decouplexing. PICO is presented as mathematical theories, providing a theoretical understanding of its chemistry. Consequently, PICO demonstrates precise quantification, as exemplified with recombinant and non-recombinant ErbB2 and multi-tagged peptide rTRX targets, validating quantification against internal and external references in both analytical and cellular matrices. Furthermore, PICO enables combinatorial multiplexing (cplex), a readout between any two antibodies, demonstrated by an 8-plex antibody, 12-cplex PICO, measuring functional changes of the ErbB pathway upon mock and dactolisib treatment delivering quantitative cellular stoichiometry. PICO possesses significant potential for versatile, standardized, and accurate protein measurements, offering insights into physiological and perturbed cellular processes.
BFEX: A Toolbox for Finite Element Analysis With Fossils and Blender
2025-03-01

ABSTRACT (1) Finite Element Analysis (FEA) has become a common method when studying fossils. As computer systems and tools advance, new software like Fossils is developed to make FE analyses more efficient. (2) However, the preparation of input data for analysis remains time‐consuming. In particular, surface mesh cleaning and the selection of groups of nodes for the boundary conditions (muscle forces and prescribed displacements) usually require graphical programs that are either not well adapted to this task or require an expensive license. (3) To address this, we introduce BFEX (Blender Finite Element eXporter), a Blender add‐on that simplifies model creation for FEA with Fossils. (4) This approach helps streamline the entire process, making it more user‐friendly.
Integrative phylogenomics sheds light on the diversity and evolution of fluorescence in coral-dwelling gall crabs
2025-03-01

Fluorescence is a notable adaptation in marine environments, helping to counteract the loss of longer wavelengths as light diminishes with depth. Studied to some extent in cnidarians and reef fish, its presence and functions in crustaceans are less understood. Recently, fluorescence was discovered in gall crabs (Cryptochiridae). To investigate the evolutionary significance of fluorescence in these coral-dwelling decapods, we combined a multivariate examination of 27 fluorescent morphological traits with phylogenomic analysis across 14 crab genera from the Red Sea and Indian Ocean. Fluorescence first evolved in the genus Opecarcinus and was subsequently retained showing varying levels of expression. We identified four distinct fluorescent morphologies (fluotypes) with high phenotypic variability, some of which show distinct distributions across the phylogeny. Along with differences in the crabs’ microhabitats, these findings suggest that fluorescence may be shaped by selective pressures, such as visibility to potential viewers, and could thus play a role in camouflage, aiding concealment against complex coral reef backgrounds. This study provides a deeper understanding of evolutionary dynamics in cryptochirids and introduces a new workflow, providing guidance for future research on fluorescence in marine invertebrates. Further research into behavioural functions and fluorophore identification are required to explain the observed variability in Cryptochiridae.
Suppression of Methanogenesis by Microbial Reduction of Iron‐Organic Carbon Associations in Fully Thawed Permafrost Soil
2025-03-01

Abstract Global methane (CH 4 ) emissions from thawing permafrost peatlands are expected to increase substantially in the future. Net emission of CH 4 depends on the presence of more favorable terminal electron acceptors for microbial respiration, such as ferric iron (Fe(III)). In soils with high OC content, Fe(III) is often coprecipitated with organic carbon (OC). The presence of Fe(III)‐OC coprecipitates could either suppress CH 4 emissions due to inhibition of methanogenesis and stimulation of anaerobic methane oxidation coupled to Fe(III) reduction, or enhance emissions by providing additional OC. Here, we investigated the role of Fe(III)‐OC coprecipitates in net CH 4 release in a fully thawed, waterlogged permafrost peatland (Stordalen Mire, Abisko, Sweden). We synthesized Fe(III)‐OC coprecipitates using natural organic matter from the field site and added them to waterlogged soil in a microcosm experiment and in situ, and followed Fe speciation and changes in greenhouse gas emissions over time. Fe(III)‐OC coprecipitates were partially reduced (22%) within 42 days in the microcosm experiment, while almost full reduction (92 ± 4%) occurred in situ within 53 days. This led to a decrease in CH 4 emissions by 94% and 40% in the microcosm and field experiments, respectively, compared to no‐coprecipitate controls. A decrease in both RNA‐based mcrA copy numbers and relative abundance of detected methanogens indicated that methanogenesis was mainly inhibited by the addition of the coprecipitates due to microbial Fe(III) reduction. In conclusion, Fe(III)‐OC coprecipitates temporarily suppress net CH 4 emissions in fully thawed permafrost soils, and might play a similar role in mitigating CH 4 release in other (periodically) flooded soils.
Conduct Disorder Is Associated With Heightened Action Initiation and Reduced Learning From Punishment but Not Reward
2025-03-01

These findings provide empirical support for a reduced ability to learn from punishment in CD, while reward learning is typical. Our results also suggest that behaviors that appear superficially to reflect reward learning differences may reflect heightened impulsive action initiation instead. Such asymmetric learning from reward and punishment, with increased action initiation, could have important implications for tailoring learning-based interventions to help individuals with CD.
Burning, Cleaning, Dumping, and Dissolution: Site Formation Processes and Stratigraphy of Pre‐110,000‐Year‐Old MSA l Deposits in Cave 1, Klasies River Main Site, South Africa
2025-03-01

ABSTRACT Understanding the formation and stratigraphy of sequences in southern African Middle Stone Age (MSA) sites is vital for contextualizing evidence for the evolution of modern human behaviors and cognition. Deposits at these sites often have complex formation histories, typically involving a range of anthropogenic, geogenic, and biogenic depositional and post‐depositional processes, and micro‐laminated deposits are common. Consequently, archaeological micromorphology and related micro‐analyses are now routinely a major component of MSA geoarchaeological research in the region. In the past few decades, microscale studies of the formation of anthropogenic features and deposits at MSA sites have begun to provide important behavioral information, including evidence for varying occupational intensities and the structuring and maintenance of living spaces. Here, a microscale geoarchaeological approach is applied to deposits dating to the MSA I cultural phase (&gt; 110 ka) in the Cave 1 Witness Baulk. The results show that humans played a considerable role in site formation and that subsequent diagenesis affected the guano, charcoal, ash, and shell, with particular impact on the carbonates which were variably dissolved, altered, or recrystallized. This latter process helped to preserve ash through reduced dissolution potential. Spatial and temporal patterns in these factors influence the macroscopic properties of the deposits in any particular area, with significant implications for the correlation of extant deposits across areas excavated at low resolution during the 1960s. Different, variably preserved, anthropogenic features and deposits were found to make up a significant proportion of the deposits. Inferred behaviors range from repeated long‐term low‐intensity use of individually stacked hearths to the formation of dumped deposits (including shell middens) due to repeated hearth maintenance and patterned discarding of food waste during more intensive occupations. Differences in occupational intensity and frequency both within and between the two recognized MSA I members could indicate adaptation to changing conditions as temperatures and sea levels fluctuated during Marine Isotope Stage 5e and early Stage 5d, but changes in geogenic depositional rates over the same period could skew our perception of occupational frequency. The current limited and low‐resolution dating evidence prevents correlation with any specific event/s, which might have affected behavior and/or depositional rates.
Differentiation in Cognitive Abilities Beyond g : The Emergence of Domain-Specific Variance in Childhood
2025-03-01

Understanding how the structure of cognitive abilities changes depending on age and ability (age and ability differentiation) has critical implications for cognitive-ability assessments and cognitive-developmental theories. Most differentiation research has focused on general intelligence; however, we argue that the investments children make in specific domains and school-taught subjects should rather affect their domain-specific ability structures. Leveraging a representative longitudinal sample of 17,979 U.S. children who were assessed in mathematics, reading, science, working memory, and cognitive flexibility, we found that loadings on a general intelligence factor remained similar, whereas most domain-specific factor loadings increased over time. Hence, age and ability differentiation are conceptually distinct, with the former pertaining to specific abilities and the latter to general intelligence. We find some evidence that domain-specific abilities can compensate for lower general intelligence. Overall, our results encourage a nuanced understanding of children’s cognitive development.
Screening of Covalent Kinase Inhibitors Yields Hits for Cysteine Protease USP7 / HAUSP
2025-03-01

The screening and evaluation of the kinase library revealed several initial hits of interest. Seven S<sub>N</sub>Ar warheads and one acrylamide warhead compound covalently modified the target protein (USP7) and showed clear shifts in the melting temperatures ranging from -6.0 °C to +1.7 °C.
Interplay of structural and electronic properties and their impact on thin films of metal-free organic radicals (Final report on DFG funded projects, reference number: CA852/11-1 and CA852/11-3, Project number: 394233453)
2025-03-01

The project and its extension concentrate on radical thin films. I have identified and refined the growth protocols for various radicals and multi-radicals, enabling their evaporation while pre-serving their radical nature. Additionally, I have explored the influence of different functional groups on thin film properties. During these years, I have addressed a variety of aspects, demonstrating the feasibility of using radicals in fields ranging from quantum technologies to spintronics. By using primarily X-ray-based techniques, including at synchrotron facilities, I have linked structural, electronic, and magnetic properties. I have also examined how the interaction strength between the (multi-)radicals and the substrate affects the interface formation, growth modes, and film processes of the radical thin films. Furthermore, I have focused on evaluating film stability, which is crucial for understanding their chemistry when exposed to air prior to performing electron spin resonance (ESR) spectroscopy—a traditional (ex-situ) technique used for radicals—and for determining film stability in environments simulating working devic-es. I have developed a protocol to study the effects of air exposure on radical thin films and utilized this method. Finally, I have conducted and interpreted X-ray magnetic circular dichro-ism (XMCD) investigations, revealing the interplay between structure and magnetic behavior in radical thin films.
Age‐ and gender‐specific molecular characteristics of diffuse large B‐cell lymphoma: Results from clinical trials of the DSHNHL/GLA
2025-03-01

Abstract Diffuse large B‐cell lymphoma (DLBCL) is the most common non‐Hodgkin lymphoma. Despite a high cure rate, too many patients show refractory (ref) or relapsed (rel) disease. This study examines the frequency of recurring gene mutations and their interplay with well‐known biomarkers in female and male patients between 18 and 80 years with ref/rel DLBCL compared to patients with complete remission (CR) to identify biological risk factors associated with treatment response, using cohorts of R‐CHOP‐like treated DLBCL enrolled in clinical trials of the DSHNHL. The biomarker profile of patients differed between younger and elderly patients with ref/rel DLBCL, with a higher frequency of BCL2 translocations in younger patients, and higher numbers of ABC subtypes and MYC protein expression in the elderly. Amplicon sequencing revealed generally higher mutation frequencies in the younger cohort. Mutations in CREBBP and TNFRSF14 were associated with shorter overall survival (OS) only in younger patients. A higher proportion of GNA13 mutations was detected in female patients of the elderly DLBCL patient cohort, clearly emphasizing the striking differences in biomarker distribution between younger and elderly as well as female and male patients.
Does the Brain Care Which Direction We Read? A Cross‐Cultural tDCS Study on Functional Lateralization of Number Processing
2025-03-01

ABSTRACT Purpose The potential influence of culture on functional lateralization was rarely investigated, yet it may be an important factor in our understanding of the human brain. In numerical processing, evidence was found for differential directional preferences of space–number associations in cultures with opposite reading direction systems. This may affect finger‐counting preferences like the starting hand, which in turn have previously been associated with differing lateralization. Such studies raise the question of whether number culture may also play a distinct role in the lateralization of the intraparietal sulcus (IPS), the hallmark region of numerical magnitude processing. Method In our preregistered cross‐cultural study, we applied anodal transcranial direct current stimulation (tDCS) over the left versus right IPS to investigate the effect of stimulation as compared to sham in Iranians (with right‐to‐left reading system) and Germans (with left‐to‐right reading system). Finding Results indicated no overall effect of stimulation; however, exploratory analyses revealed that tDCS over the left and right IPS facilitated number processing in Iranians compared to Germans after controlling for training effects. Finger‐counting direction was not found to be decisive for this effect. Conclusion At the end, number processing might be bilaterally represented in the IPS; however, our exploratory analyses emphasize the need for further investigation on the potential role of culture in the representations of numbers.
Cathodal Transcranial Direct Current Stimulation Does Not Change Implicit Associations Against Alcohol in Alcohol Use Disorder: A Preregistered Clinical Trial
2025-03-01

ABSTRACT Addictive behaviour is shaped by the dynamic interaction of implicit, bottom‐up and explicit, top‐down cognitive processes. In alcohol use disorder (AUD), implicit alcohol‐related associations have been shown to predict increased subsequent alcohol consumption and are linked to the risk of relapse. Explicit cognitive processes, exerting prefrontal top‐down control, are particularly significant during the critical period following the decision to abstain. This study aims to map implicit and explicit cognitive processes in recently abstinent individuals with AUD and to explore the effect of cathodal transcranial direct current stimulation (tDCS) on implicit associations by modulating top‐down control. In this preregistered, double‐blind, sham‐controlled clinical trial, 30 abstinent individuals with AUD participated in two experimental sessions. They received either 2 mA cathodal tDCS to the left dorsolateral prefrontal cortex (dlPFC) or sham tDCS in a crossover design. During tDCS, participants completed the alcohol approach implicit association test (IAT) and the drinking identity IAT, along with two control tasks. Additionally, we collected explicit ratings of the IAT stimuli and assessed craving before and after each experimental session. Preregistered ANOVAs revealed significant implicit alcohol–avoidance and non–drinking identity biases. Cathodal tDCS did not modulate IAT scores. Explicit ratings showed a preference for non‐alcoholic drinks and non‐drinking identity, correlating moderately with IAT scores. Exploratory analyses indicated that cathodal tDCS mitigated the increase in nicotine craving during the experimental session. This preregistered clinical trial provides robust evidence that single‐session cathodal tDCS to the left dorsolateral prefrontal cortex does not modulate implicit associations in AUD, with Bayesian analyses corroborating the absence of tDCS effects. Our results emphasize the impact of contextual factors on the interplay between explicit and implicit cognitive processes and underscore the importance of investigating multisession stimulation paradigms in future research.
In Situ Uncrewed Aircraft Measurements of Turbulent Kinetic Energy over Heterogeneous Terrain
2025-03-01

Abstract Turbulent kinetic energy (TKE) is a key variable in understanding the energy dynamics within the atmospheric boundary layer. Accurate characterization of TKE is crucial for several applications, especially in regions characterized by complexity and heterogeneity. This study investigates the comparison between a moving sensor, an uncrewed aircraft system (UAS), and a stationary sensor, a sonic anemometer, in the heterogeneous terrain of the boundary layer field site Falkenberg (Lindenberg, Germany) operated by the German Weather Service (DWD). The UAS, a multipurpose airborne sensor carrier (MASC-3), was operated during three measurement campaigns in July 2020, June 2021, and November 2022, respectively. The comparison pairs UAS measurements with data collected by a sonic anemometer positioned at a height of 90 m on a meteorological tower. The analysis focuses on careful data processing and precise synchronization of the time series from both sensors, so that the same air mass is taken into account when calculating turbulence statistics. The study examines several parameters that can affect the quality of the comparison. The analysis showed that the bias and scatter between the two sensors are a function of the wind direction: the best agreement was recorded when the wind came from the south, a region of flat terrain (bias of 21%, scatter of 53%). Conversely, less favorable statistics were obtained when the wind blew from a sector between west to north, regions that are predominantly characterized by forest cover (bias of 68%, scatter of 103%). This result illustrates the difficulties of comparing UAS measurements along a 1.5–2.0-km long path with stationary point measurements above a heterogeneous land surface.