julilili42/papers huggingface dataset:
Make your own laboratory: A comparative perspective on the logistics and dynamics of DIY biology spaces and communities
2025-08-25

Do-It-Yourself (DIY) biology, also known as biohacking or community biology, is a grassroots movement where people conduct biological experiments outside formal institutions. DIY biologists set up their laboratories in garages and community spaces and often acquire their equipment and materials from online marketplaces. While their needs for material resources are comparable to those of academic and industrial laboratories, DIY biologists face greater challenges in acquiring such resources, reflecting the structural disparities between institutional and extra-institutional science. This paper examines how DIY biology spaces are materialized and explores the challenges encountered during this process. Materializing refers to the efforts of DIY biologists to transform their visions of grassroots science into material and immaterial results. Drawing on semi-structured interviews with 23 DIY biologists across Great Britain, Germany, and Canada, alongside observations from online and in-person events, this study highlights how these practitioners position themselves within their respective countries’ life science landscapes. The findings indicate that DIY biologists actively negotiate boundaries between institutional and extra-institutional science, engaging in debates over funding sources, including partnerships with industry, and seeking alternative models of community sustainability. Country-specific innovation and economic ecosystems shape these negotiations. For instance, Canadian DIY biologists embrace entrepreneurial narratives akin to ‘garage start-ups,’ aligning with a neoliberal ethos of innovation. In contrast, their German counterparts gravitate toward the principles of Mittelstand entrepreneurship emphasizing stability, regional embeddedness, and responsibility. Despite their diverse approaches, DIY biologists in all three contexts face systemic challenges tied to neoliberal funding structures, particularly a scarcity of financial resources. These insights contribute to understanding how grassroots science adapts to, and resists, broader socio-economic forces, illuminating the dynamics through which science is materialized outside traditional institutions.
Humanized Fruit Flies as a Novel Pre-Clinical Test Model for Membrane Drug Transporters
2025-08-25

Background: Membrane transport proteins are critical determinants of systemic and intracellular drug levels, thereby contributing substantially to drug response and/or adverse drug reactions. Therefore, the U.S. Food and Drug Administration and the European Medicines Agency, the regulatory authorities for drug approval in the U.S. and Europe, respectively, recommend pre-clinical testing of selected drug transporters during the drug development process to elucidate clinically relevant drug–drug interactions (DDIs). In the current proof-of-principle study, we describe the generation of fruit flies expressing human membrane drug transporters in their salivary glands to enable DDI studies in a time-saving manner and at low costs. Methods: Using the Gal4/upstream activation sequence (UAS) expression system, we established fruit flies expressing human organic cation transporters (hOCTs) 1 and 2 and genetic variants thereof. Both transporters are key drug uptake transporters in humans and are recommended for pre-clinical DDI studies. After injecting fluorescent hOCT substrates, their accumulation in salivary gland cells was observed by confocal laser scanning microscopy. Results: We demonstrate the feasibility of expressing hOCT1 and hOCT2 in the salivary glands of fruit fly embryos and subsequent alteration by clinically relevant genetic variants, corroborating results from mammalian cell experiments. Moreover, we show an OCT-dependent accumulation of the prototypic fluorescent OCT substrates ethidium (Et+) and 4-Di-1-ASP (4-(4-(dimethylamino)styryl)-N-methylpyridinium, ASP+) in the salivary gland cells and subsequent inhibition by clinically-used OCT drug inhibitors. Conclusions: Based on the handling procedure and the lack of need for Animal Protection Act approval, we propose that the humanized Drosophila melanogaster fruit fly model opens a new avenue for pre-clinical functional transporter studies.
Long‐Term Outcomes After Cardiac Arrest: Protocol for the Extended Follow‐Up Sub‐Study of the STEPCARE Trial
2025-08-26

ABSTRACT Background The international multi‐center randomized controlled STEPCARE‐trial will investigate optimal management of sedation, temperature, and mean arterial pressure (MAP) during intensive care in out‐of‐hospital cardiac arrest (OHCA) patients due to various etiologies. The primary outcome is mortality at 6 months. This protocol describes an extended follow‐up sub‐study of the STEPCARE‐trial with the main objective to provide detailed long‐term outcomes for survivors and caregivers. It will focus on potential neuroprotection and improved recovery for different targets of sedation, temperature, and MAP management at 6 and 12 months post‐OHCA. Methods All survivors and one caregiver per survivor at selected STEPCARE sites will be invited to participate. Randomization is stratified by site. This sub‐study extends the main STEPCARE follow‐up at 6 months by undertaking detailed assessments, face‐to‐face meetings, inclusion of a caregiver, and repeating the assessments at 12 months. Our main outcome for survivors is cognitive function measured by the Montreal Cognitive Assessment, and for caregivers, the caregiver burden measured by the Zarit Burden Interview. Additional outcomes include symptoms of anxiety, depression, post‐traumatic stress disorder, fatigue, physical function, life satisfaction, and life impact (disability), assessed by psychometrically robust measures. The estimated sample size is 600. Efforts to improve interrater reliability and decrease missing data are integral to the study design. Conclusion These detailed long‐term outcomes will explore the possible benefits or risks of fever, sedation, and blood pressure management in post‐OHCA survivors. Additionally, this study will explore survivorship after cardiac arrest from various perspectives, including different causes of arrest. ClinicalTrials.gov: NCT0207942.
Closed-loop coupling of both physiological spindle model and spinal pathways for sensorimotor control of human center-out reaching
2025-08-26

The development of new studies that consider different structures of the hierarchical sensorimotor control system is essential to enable a more holistic understanding about movement. The incorporation of more biological proprioceptive and neuronal circuit models to muscles can turn neuromusculoskeletal systems more appropriate to investigate and elucidate motor control. Specifically, further studies that consider the closed-loop between proprioception and central nervous system may allow to better understand the yet open question about the importance of afferent feedback for sensorimotor learning and execution in the intact biological system. Therefore, this study aims to investigate the processing of spindle afferent firings by spiking neuronal network and their relevance for sensorimotor control. We integrated our previously published physiological model of the muscle spindle in a biological arm model, corresponding to a musculoskeletal system able to reproduce biological motion inside of the demoa multi-body simulation framework. We coupled this musculoskeletal system to physiologically-motivated neuronal spinal pathways, which were implemented based on literature in the NEST spiking neural network simulator, intended to perform human center-out reaching arising from spinal synaptic learning. As result, the spindle connections to the spinal neurons were strengthened for the more difficult targets (i.e. higher above placed targets) under perturbation, highlighting the importance of spindle proprioception to succeed in more difficult scenarios. Furthermore, an additionally-implemented simpler spinal network (that does not include the pathways with spindle proprioception) presented an inferior performance in the task by not being able to reach all the evaluated targets.
Optimizing Carrier Balance in CsPbBr3 Nanocrystal LEDs: The Role of Alkyl Ligands and Polar Electron Transport Layers
2025-08-26

Abstract The study of lead halide perovskite nanocrystal based light‐emitting diodes (LEDs) has advanced significantly, with notable improvements in stability and optical properties. However, optimizing charge carrier injection and transport remains a challenge. Efficient electroluminescence requires a balanced transport of both holes and electrons within the emitting material. Here, cubic CsPbBr 3 nanocrystals passivated with oleylamine and oleic acid are investigated, comparing them to ligand‐exchanged nanocrystals with didodecyldimethylammonium bromide (DDABr). Nuclear magnetic resonance spectroscopy and transmission electron microscopy confirm successful ligand exchange, revealing reduced ligand coverage in DDABr‐treated nanocrystals. Photoelectron spectroscopy, spectroelectrochemistry, and single‐carrier devices indicate improved hole injection in DDABr‐capped nanocrystals. Density functional theory calculations further reveal the influence of ligand type and coverage on energy levels, with oleic acid introducing localized states in native nanocrystals. Additionally, incorporation of a polar electron transport layer enhances LED performance by over an order of magnitude in DDABr‐capped nanocrystals, driven by improved charge balance arising from the spontaneous orientation polarization of the electron transport layer. These findings highlight the critical role of ligand selection, passivation degree, and charge transport control by the adjacent organic transport layers in optimizing LED efficiency.
Second-Harmonic Generation and Photoluminescence Properties of Colloidal WS2 Monolayers deposited from Solution
2025-08-26

Monolayered WS2 exhibits a direct band gap, strongly bound excitons, trions and biexcitons as well as no inversion symmetry in the 2D crystal structure (D3h), allowing frequency doubling by second-harmonic generation. The recent progress in colloidal synthesis of transition metal dichalcogenides enables the scalable production of phase pure monolayer-dominated WS2. In this work, we use parabolic mirror-assisted microscopy to investigate the linear and nonlinear optical properties of deposited colloidal WS2. Spatial and spectral resolution of one- and two-photon photoluminescence and second-harmonic generation correlates structural motifs of the WS2 layers including orientation and agglomeration to the local optical response. We find exciton and trion emission at 613 nm and 639 nm respectively, with significantly varying contribution to the overall intensity between one- and two-photon excitation. This is attributed to the increased carrier density under high fluences needed for two-photon excitation. By evaluating the second-harmonic generation intensity, the nonlinear susceptibility of colloidally synthesized WS2 nanosheets is calculated to range from 4.28-7.55 nm/V, averaging higher than a commercial WS2 monolayer reference sample. Our results show that colloidal WS2 is suitable for large area coverage creating an isotropic WS2 film, while retaining the highly sought after linear and nonlinear optical properties of WS2 monolayers, even under surface ligand separated aggregation.
Analytical and modelling strategies for thermal histories from in situ (U-Th-Sm)/He data of single apatites
2025-08-27

Abstract. (U-Th-Sm)/He is a thermochronometric method used to reconstruct the rates and timing of geological processes. Recent developments in analytical approaches, specifically laser ablation (in situ) measurements, allow quantifying the distribution of parent isotopes (U, Th, and, in apatites, Sm) and decay products (4He) within individual mineral grains. This is particularly important to understand potential date over-dispersion, which can arise from the heterogeneous distribution of parent isotopes, and to develop thermal history modelling for single-grain (U-Th-Sm)/He techniques. We build on previous studies and combine in situ 4He concentration profile measurements with parent nuclide distribution mapping in natural apatites to explore analytical and modelling strategies for single-grain thermal history reconstructions. Specifically, we investigate the effects of laser ablation spot size, the number and location of ablation spots in a grain, and grain size on data resolution and suitability for thermal history modelling. In doing so, we introduce the calculation of Caw, which is the concentration of parent nuclides at each ablation site weighted by alpha-particle stopping distances to account for the redistribution of 4He in the crystal from high-energy alpha decay. We present stacked U, Th, and Sm maps measured at different ablation depths in two apatite grains from South Germany (one with homogeneous and one with zoned parent isotope distribution) and one apatite from the McClure Mountain Syenite age standard. Furthermore, we show in situ 4He profiles of the two South German apatites and inversions for thermal histories. Our results indicate that, for our study and instrument set-up, four to six spot measurements with various distances from the grain rim enable measuring an in situ 4He profile. We determined that the optimal spot diameter for in situ 4He profile measurements for apatite grains with (U-Th-Sm)/He dates as young as 16 Ma is 20–30 μm. Additionally, a six-spot in situ 4He profile requires a minimum grain diameter (measured perpendicular to the c-axis) of 145 μm. Combined with information from detailed parent nuclide maps, the in situ 4He profiles offer a possibility to reconstruct the thermal histories of single grains, potentially including zoned and irregularly shaped crystals.
Evolution of Shear‐Zone Fractures Presages the Disintegration of Thwaites Eastern Ice Shelf
2025-08-27

Abstract Thwaites Eastern Ice Shelf (TEIS) is a partially confined floating extension of Thwaites Glacier, anchored by an offshore pinning point at its northern terminus. Over the past two decades, the shelf has experienced progressive fracturing around a prominent shear zone upstream of its pinning point, gradually compromising its structural integrity. Here we present an analysis of shear‐zone fracture evolution from 2002 to 2022 and its control on the flow dynamics of the ice shelf using satellite remote sensing and in situ GPS observations. We compiled multi‐year statistics of fracture length and orientation from Landsat and Sentinel‐1 imagery and compared their changes with evolving flow dynamics and surface strain rates. Ongoing disintegration driven by the shelf's shearing against the pinning point occurred in two stages: propagation of large shearing fractures approximately parallel to flow earlier in the record, followed by the rapid formation of smaller tensile fractures approximately perpendicular to flow later in the record. We also observed velocity perturbations originating from the shear zone and propagating across the main ice shelf, observationally demonstrating the direct impact that shear‐zone disintegration has on the dynamics of TEIS.
Benjamini–Schramm vs. Plancherel convergence
2025-08-27

We show that Plancherel convergence is strictly stronger than Benjamini–Schramm convergence. In order to do so, we introduce two criteria for Plancherel and Benjamini–Schramm convergence in terms of counting functions of the length spectrum.
Moiré-Orbital-Resolved Excitonic Mott Insulating States and Their Optical and Electric Control in van der Waals Heterostructures
2025-08-27

Moiré potential formed in van der Waals heterostructures is predicted to feature multiple local minima functioning as orbital degree of freedom, which is an important ingredient for understanding intriguing strong correlation phenomena. However, an experimental demonstration of this moiré-orbital enabled quantum state engineering is still unexplored. Here, we report clear evidence of moiré-orbital resolved excitonic Mott insulating states in multiannealing H-type WSe_{2}/WS_{2} heterobilayers and demonstrate their application in generating spatially ordered excitonic quantum phases. This moiré orbital is evidenced by interlayer exciton emissions with an energy separation of ∼65 meV and further supported by our multiple field-dependent characterizations. Remarkably, the moiré orbital allows a sequential formation of correlated Mott insulating states, with the extracted onsite Hubbard interaction reaching ∼30 meV. A combined optical and electric doping allows control of strongly correlated quantum phases with various spatially ordered fermionic-bosonic orbital components.
Development of a QCM-D-Based Aptasensor for the Real-Time Detection of β-Lactoglobulin
2025-08-27

The prevalence of food allergies has been steadily increasing in recent years. β-lactoglobulin (β-LG), the main allergenic protein of milk and dairy allergies, is more commonly observed in infants and children. In this study, a β-LG-specific aptamer was selected using the combinatorial chemistry process known as systematic evolution of ligands by exponential enrichment (SELEX), and a quartz crystal microbalance with dissipation monitoring (QCM-D)-based aptasensor was developed using a novel surface functionalization technique, which mimics an artificial cell membrane on the QCM-D sensor surface, creating a physiologically relevant environment for the binding of the target to the sensor. Through SELEX combined with next-generation sequencing (NGS), the aptamer Apt 356 was identified. Its binding to β-LG was confirmed via dot blot analysis. The selected Apt 356 was then used for the development of a QCM-D-based sensor. To fabricate the sensor, the quartz surface was functionalized with a supported lipid bilayer (SLB). The β-LG-specific aptamer was immobilized onto this SLB. The results demonstrated that the QCM-D system allows real-time observation and evaluation of the binding of β-LG. While there have been some studies on aptasensors for the β-LG protein, to the best of our knowledge, this is the first QCM-D-based aptasensor developed specifically for β-LG protein detection.
Sleep‘s contribution to memory formation
2025-08-28

The brain state of sleep contributes in a specific way to the formation of long-term memory. Over the past 10 years, research on the psychological and neuronal mechanisms underlying this process has rapidly increased, including studies in humans and rodents across early and late life. Intended to comprehensively cover this research, our review reveals that the majority of findings is consistent with the concept of long-term memory formation during sleep as an active systems consolidation process that concurs with widespread synaptic down-selection. In this concept, the repeated neuronal replay of encoded representations, particularly in the hippocampus, in conjunction with brain oscillations hallmarking non-rapid eye movement (NonREM) sleep, provide mechanisms for regulating information flow across brain networks. This interplay drives the consolidation of newly encoded memory into neocortical long-term stores, whereby this neocorticalisation of representations goes along with a transformation of memories into more abstract representations. The findings, however, remain controversial as to the nature of memory transformation: What kind of information is eventually consolidated into neocortical networks and how is storage of this information achieved at the synaptic level? Further, the role of REM sleep to consolidation of, particularly, emotional memory and in shaping representations at the synaptic level are unclear. Future research also needs to elaborate on how consolidation during sleep differs from that during wakefulness, as well as on the changes in sleep-dependent consolidation across the lifespan. A promising new area arising from this research pertains to brain-stimulation techniques developed to enhance memory consolidation during human sleep.
Noninvasive Monitoring of Inflammatory Processes by Myeloid Cell–Directed PET Tracers in an Experimental Severe Acute Respiratory Syndrome Coronavirus 2 Infection Model
2025-08-28

Monitoring the presence and distribution of distinct immune cell populations is key in deciphering immunopathologic disease mechanisms. Considering the crucial role of myeloid cells in provoking hyperinflammatory responses associated with coronavirus disease 2019, a camelid-derived single-domain antibody specifically recognizing human signal-regulatory protein-α (SIRPα) as a biomarker for myeloid cells has been generated and radiolabeled with <sup>64</sup>Cu, that is, [<sup>64</sup>Cu]copper-SIRPα-nanobody ([<sup>64</sup>Cu]Cu-SIRPα-Nb), for in vivo PET imaging. In this study, this PET tracer was used and validated to monitor the temporal dynamics of inflammatory processes during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in nonhuman primates. For further validation, the signal of [<sup>64</sup>Cu]Cu-SIRPα-Nb was compared with the signal of TSPO-targeting [<sup>18</sup>F]fluorine-<i>N</i>,<i>N</i>-diethyl-2-(2-(4-(2-fluoroethoxy)phenyl)-5,7-dimethylpyrazolo[1,5a]pyrimidin-3-yl)acetamide ([<sup>18</sup>F]F-DPA714). <b>Methods:</b> Six cynomolgus macaques (<i>Macaca fascicularis</i>) were experimentally infected with SARS-CoV-2 and subsequently monitored for 7 wk. We performed a baseline [<sup>64</sup>Cu]Cu-SIRPα-Nb PET/CT before infection, followed by repetitive PET/CT on days 3, 10, 24, and 52 after infection covering the head, thorax, and abdominal region. Of the 6 macaques, 3 underwent additional TSPO-targeting [<sup>18</sup>F]F-DPA714 PET/CT investigations at baseline and at days 2, 9, 23, and 51 after infection. Tracheal and nasal swabs were taken to monitor the course of infection, and changes in blood count and inflammatory mediators in the periphery blood were monitored. <b>Results:</b> Detection of subgenomic SARS-CoV-2 messenger RNA from tracheal and nasal swab samples confirmed viral infection of all animals. CT scans identified initial pulmonary lesions 2 days after infection. [<sup>64</sup>Cu]Cu-SIRPα-Nb PET/CT revealed increased tracer uptake in the mediastinal lymph nodes of all animals, but not in the lung lesions, 3 days after infection. [<sup>18</sup>F]F-DPA714 PET/CT showed increased uptake in both anatomically affected and unaffected lung tissues. The increased [<sup>64</sup>Cu]Cu-SIRPα-Nb uptake in the spleen and bone marrow of all animals was more pronounced 3 and 7 wk after infection. We detected individual differences in [<sup>64</sup>Cu]Cu-SIRPα-Nb uptake within the bone marrow and spleen, whereas [<sup>18</sup>F]F-DPA714 exhibited rather homogeneous uptake patterns. <b>Conclusion:</b> Our findings indicate that [<sup>64</sup>Cu]Cu-SIRPα-Nb is a versatile tool for quantitative monitoring of whole-body distribution, temporal distribution, and accumulation dynamics of myeloid cell subpopulations even in moderately inflamed tissues and affected lymphatic organs during SARS-CoV-2 infection.