julilili42/papers huggingface dataset:
Landscape positioning of Neolithic mustatil stone structures along the margins of the Nefud Desert, Saudi Arabia
2024-09-11

Monumental rectangular stone structures called mustatils are an important emerging feature of the Holocene archaeological record of northwestern Arabia. To date, few have been excavated, with available radiocarbon dates suggesting an age range of ca. 5400–4200 BC. Here we present a rigorous spatial analysis to identify the patterning and landscape context of 169 mustatils in the southern and western margins of the Nefud Desert. This included: (1) a systematic survey of satellite imagery to identify mustatils; (2) viewshed analysis to examine location and landscape visibility; (3) a point process model to understand how diverse environmental and landscape variables affect mustatil locations; (4) mark correlation function to assess spatial patterning of mustatils based on their size. Results indicate that mustatil locations are determined most by proximity to water (likely locations of enhanced surface water occurrence under the enhanced humidity of the Mid-Holocene), on east facing slopes, close to rocky areas, at elevations between 880 and 950 masl, and on or near topographic ridges (positive topographic position index). Viewshed analysis showed that mustatils are preferentially located in areas that have good views, but not the best that are available, indicating complex landscape positioning that balances a range of topographic and behavioural factors. Using a rank permutation method with size (length) of mustatils as a proxy for labour mobilization we show that mustatils within clusters are not arranged hierarchically based on size, and were likely built by non-stratified groups of people. Our analyses show that people were choosing multiple factors when deciding where to build mustatils, and that the distribution of mustatils may relate to different groups of people resulting in the construction of complex ritual landscapes. As one of the earliest examples of large-scale monumental stone structure construction in global prehistory, understanding mustatils can enlighten us on human-environment interaction during the Neolithic.
Power-to-vitamins: producing folate (vitamin B9) from renewable electric power and CO2 with a microbial protein system
2024-09-12

We recently proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO<sub>2</sub>. Two stages were operated in series: Clostridium ljungdahlii in Stage A to reduce CO<sub>2</sub> with H<sub>2</sub> into acetate, and Saccharomyces cerevisiae in Stage B to utilize O<sub>2</sub> and produce microbial protein from acetate. Renewable energy can be used to power water electrolysis to produce H<sub>2</sub> and O<sub>2</sub>. A drawback of Stage A was the need for continuous vitamin supplementation. In this study, by using the more robust thermophilic acetogen Thermoanaerobacter kivui instead of C. ljungdahlii, vitamin supplementation was no longer needed. Additionally, S. cerevisiae produced folate when grown with acetate as a sole carbon source, achieving a total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g l<sup>-1</sup>. The developed Power-to-Vitamin system enables folate production from renewable power and CO<sub>2</sub> with zero or negative net-carbon emissions.
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions
2024-09-12

Abstract Bacteria employ CRISPR-Cas systems for defense by integrating invader-derived sequences, termed spacers, into the CRISPR array, which constitutes an immunity memory. While spacer deletions occur randomly across the array, newly acquired spacers are predominantly integrated at the leader end. Consequently, spacer arrays can be used to derive the chronology of spacer insertions. Reconstruction of ancestral spacer acquisitions and deletions could help unravel the coevolution of phages and bacteria, the evolutionary dynamics in microbiomes, or track pathogens. However, standard reconstruction methods produce misleading results by overlooking insertion order and joint deletions of spacers. Here, we present SpacerPlacer, a maximum likelihood-based ancestral reconstruction approach for CRISPR array evolution. We used SpacerPlacer to reconstruct and investigate ancestral deletion events of 4565 CRISPR arrays, revealing that spacer deletions occur 374 times more frequently than mutations and are regularly deleted jointly, with an average of 2.7 spacers. Surprisingly, we observed a decrease in the spacer deletion frequency towards both ends of the reconstructed arrays. While the resulting trailer-end conservation is commonly observed, a reduced deletion frequency is now also detectable towards the variable leader end. Finally, our results point to the hypothesis that frequent loss of recently acquired spacers may provide a selective advantage.
Revisited and revalorized: Technological and refitting studies at the Middle Stone Age open-air knapping site Jojosi 1 (KwaZulu-Natal, South Africa)
2024-09-12

<title>Abstract</title> The Middle Stone Age (MSA) of southern Africa is mainly known from rock shelters and caves. How early modern humans interacted with their landscapes remains comparatively understudied. The site of Jojosi 1, situated north of Nquthu in north central KwaZulu-Natal, is set within erosional badlands, known locally as “dongas.” This locality offers a rare opportunity to study MSA technology and settlement dynamics in an open-air context. A. Mazel initially discovered and excavated Jojosi 1 in 1991, but did not publish the lithic assemblage. Here, we report on the site’s rediscovery coupled with the first lithic analysis and luminescence dating. This work provides insights into the site formation processes of Jojosi 1 and lithic reduction strategies, raw material provisioning, and landscape use. Our techno-typological analysis draws upon Mazel’s collection of 7529 artefacts while combining attribute analysis and refitting studies. The results show the exclusive use of hornfels and its reduction via platform and Levallois methods to produce flakes and blades. Retouched tools are scarce and comprise mostly notched or denticulate pieces but lack backed tools, unifacial, and bifacial points. The museum collection features abundant small debitage and a strong component of cortical, initial stage, and core preparation flakes. The 48 refitted artefacts and ample small debitage in a spatially constricted band suggest high assemblage integrity with minimal post-depositional disturbance. Infrared stimulated luminescence dating of coarse grain feldspars brackets the archaeological occurrence to ~ 139 − 106 ka. Comparisons with contemporary lithic assemblages link the assemblage to the early Middle Stone Age in southern Africa. We interpret Jojosi 1 as a knapping event aimed at blank production and exploitation of local high-quality hornfels. With little evidence for other behaviours, the site likely reflects an ephemeral knapping workshop on a source of abundant hornfels slabs. Our ongoing excavations in the Jojosi Dongas will be able to test this hypothesis and will work to characterise the technological adaptations and settlement dynamics of the MSA hunter-gatherers in this area.
The High-Resolution Archaeology of Shared Courtyards at Old Dongola (14th–16th Century a.d., Sudan): an Intensive Approach to Domestic Open Spaces
2024-09-12

Identifying the dynamics of domestic open spaces remains a challenging task. This research applies an adjusted theoretical framework of activity areas to characterize domestic open spaces in the 14th-16th century a.d. in Old Dongola, Sudan. Activity areas were defined as sedimentations of residues of recurring cycles of changing actions rather than stable components of space. To identify domestic space, this research utilizes high-resolution methods: analyses of multiple chemical elements, spatial distribution of objects, and botanical remains of courtyard occupational surfaces, combined with spatial statistics using local Moran's I autocorrelation. The relationships between the remains of human and non-human actions are discussed in terms of the material affordances affecting their deposition within the archaeological layers. Application of these methods allowed for the identification of areas of domestic tasks related to high concentrations of elements, as well as clusters of tools located on their edges. Botanical data corroborated often vague identifications of activities based on geochemistry.
Debris flows and sediment transport at Yucaipa Ridge and impacts to Oak Glen and Forest Falls area, southern California, following the 2020 El Dorado and Apple Fires
2024-09-12

ABSTRACT The 2020 El Dorado and Apple Fires burned a combined area of ~225 km2 in the San Bernardino Mountains, California, USA, including much of the steep terrain of Yucaipa Ridge. Wildfire increases the potential for debris flows, flooding, and rockfall hazards. A California Watershed Emergency Response Team assessed these hazards to assist affected portions of San Bernardino and Riverside counties with their emergency preparedness efforts. These assessments identified high hazard sites in the Forest Falls and Oak Glen areas on the north and south flanks of Yucaipa Ridge, respectively. Subsequent monitoring by the California Geological Survey documented 16 flow events from nine study area basins and their impacts to downstream communities generated by six storms between fall 2020 and August 2023. Tropical Storms Kay (2022) and Hilary (2023) and monsoonal thunderstorms on August 13, 2022, produced the most widespread and severe impacts. Observations of flow characteristics were then used to determine flow type behavior and estimate flow velocities and discharge for 11 flow events, and the total volume of mobilized debris was estimated for three flow events. Debris flow velocities were found to range from 2.1 to 11.2 m/s (4.7–25 mph) and associated discharge values were estimated to range from 12 to 311 m3/s (~425–11,000 cfs). Observed discharges were then used to assess and calibrate previous flow bulking multipliers for post-fire emergency planning. Volumes of debris mobilized during three events were estimated based on hydraulic methods, field observations, and lidar differencing, respectively, with resulting volumes ranging from ~19,000 m3 to more than 100,000 m3. Rainfall data were also acquired and reviewed to assess rainfall intensity thresholds for the generation of post-fire debris flows. Concurrently, studies were conducted to assess sediment transport and yields based on the distribution of fractured rock outcrops, colluvial debris, and dry ravel generated by fire impacts, as documented by repeat surveys of selected source basin areas. The surveys showed a mixture of fractured rock outcrops, and steep soil mantled slopes provided both coarse (&amp;gt;3 m) boulders and fine sediment. The latter was preferentially delivered to debris flow prone channels as post-fire dry ravel. Debris flows generated by Tropical Storms Kay and Hilary mobilized all of these grain size fractions downstream to alluvial fans and developed areas.
Model for efficient dynamical ranking in networks
2024-09-12

We present a physics-inspired method for inferring dynamic rankings in directed temporal networks—networks in which each directed and timestamped edge reflects the outcome and timing of a pairwise interaction. The inferred ranking of each node is real-valued and varies in time as each new edge, encoding an outcome like a win or loss, raises or lowers the node's estimated strength or prestige, as is often observed in real scenarios including sequences of games, tournaments, or interactions in animal hierarchies. Our method works by solving a linear system of equations and requires only one parameter to be tuned. As a result, the corresponding algorithm is scalable and efficient. We test our method by evaluating its ability to predict interactions (edges' existence) and their outcomes (edges' directions) in a variety of applications, including both synthetic and real data. Our analysis shows that in many cases our method's performance is better than existing methods for predicting dynamic rankings and interaction outcomes. Published by the American Physical Society 2024
Short-term vital parameter forecasting in the intensive care unit: A benchmark study leveraging data from patients after cardiothoracic surgery
2024-09-12

Patients in an Intensive Care Unit (ICU) are closely and continuously monitored, and many machine learning (ML) solutions have been proposed to predict specific outcomes like death, bleeding, or organ failure. Forecasting of vital parameters is a more general approach to ML-based patient monitoring, but the literature on its feasibility and robust benchmarks of achievable accuracy are scarce. We implemented five univariate statistical models (the naïve model, the Theta method, exponential smoothing, the autoregressive integrated moving average model, and an autoregressive single-layer neural network), two univariate neural networks (N-BEATS and N-HiTS), and two multivariate neural networks designed for sequential data (a recurrent neural network with gated recurrent unit, GRU, and a Transformer network) to produce forecasts for six vital parameters recorded at five-minute intervals during intensive care monitoring. Vital parameters were the diastolic, systolic, and mean arterial blood pressure, central venous pressure, peripheral oxygen saturation (measured by non-invasive pulse oximetry) and heart rate, and forecasts were made for 5 through 120 minutes into the future. Patients used in this study recovered from cardiothoracic surgery in an ICU. The patient cohort used for model development (n = 22,348) and internal testing (n = 2,483) originated from a heart center in Germany, while a patient sub-set from the eICU collaborative research database, an American multicenter ICU cohort, was used for external testing (n = 7,477). The GRU was the predominant method in this study. Uni- and multivariate neural network models proved to be superior to univariate statistical models across vital parameters and forecast horizons, and their advantage steadily became more pronounced for increasing forecast horizons. With this study, we established an extensive set of benchmarks for forecast performance in the ICU. Our findings suggest that supplying physicians with short-term forecasts of vital parameters in the ICU is feasible, and that multivariate neural networks are most suited for the task due to their ability to learn patterns across thousands of patients.
Naphtho[1,2-b][1,4]diazepinedione-based P2X4 Receptor Antagonists from Structure-Activity Relationships Study Towards PET Tracer Development
2024-09-12

The P2X4 receptor, a ligand-gated ion channel, is implicated in various pathological conditions, including neuropathic pain and cancer. This study reports the development of 1,4-naphthodiazepinedione-based P2X4 receptor antagonists aimed at both therapeutic applications and potential use as PET tracers for imaging P2X4 receptor expression in cancer and neuroinflammatory diseases. Structure-activity relationship studies aided by docking studies and molecular dynamics simulations led to a series of compounds with potent P2X4 receptor antagonism, promising in vitro inhibition of interleukin-1β release in THP-1 cells and suitability for radiolabeling with fluorine-18. The most potent compounds were further evaluated for their physicochemical properties, metabolic stability, and in vivo biodistribution using PET imaging in mice. While these antagonists exhibited strong receptor binding and serum stability, rapid in vivo metabolism limited their potential as PET tracers, highlighting the need for further structural optimization. This study advances the understanding of P2X4 receptor antagonism and underscores the challenges in developing effective PET tracers for this target.
Dosage by design – 3D printing individualized cabozantinib tablets with immediate release
2024-09-13

Production of patient-specific dosage forms is important to improve patient adherence and effectiveness while reducing the prevalence and severity of adverse effects. Due to its possibility of rapid prototyping 3D printing can be used to produce individual dosages while utilizing techniques such as hot melt extrusion to increase the bioavailability of poorly soluble drugs. In this work, Parteck MXP and Kollicoat IR were used as water-soluble polymer bases for formulation development for 3D printing of various dosages incorporating cabozantinib while enabling immediate release. The effect of tablet design and the excipients sorbitol, croscarmellose sodium, and sodium starch glycolate was investigated for this goal. A way to calculate the size of tablets for predetermined dosages is proposed to enable the printing of individual strengths from one formulation. Rheological data were collected to deepen the understanding of the role of melt viscosity in 3D printing and hot melt extrusion processes. The production of immediate-release cabozantinib tablets containing every therapeutically relevant dosage in a single unit produced by two-step 3D printing was realized.
Yoga as Potential Therapy for Burnout: Health Technology Assessment Report on Efficacy, Safety, Economic, Social, Ethical, Legal and Organizational Aspects
2024-09-13

Abstract Purpose of Review This health technology assessment aimed to systematically assess the efficacy and safety of yoga as therapy for burnout. Economic, ethical, legal, social and organizational aspects were considered as well. Recent Findings Yoga as a therapy has been shown to have positive effects on a range of symptoms, including stress, anxiety and depression. Regarding work-related stress and burnout, the effects of yoga have mainly been examined in a preventative context. Summary Meta-analyses revealed no effects on burnout severity comparing yoga with passive controls in general. Compared with passive controls, yoga had a positive effect on subjective stress. Compared to active control, yoga had an effect on the burnout subscale depersonalization on individual study level. Yoga may have positive effects on burnout, but the results are mixed. Common definitions and standardized diagnostic tools are necessary to improve research and further assess yoga as therapy for burnout. Trial Registration The HTA is registered with PROSPERO, CRD42022299405, on 6th February 2022.
Drowning Out Dissent: The Thai Military’s Quest to Fabricate Popular Support on Twitter
2024-09-13

Why and how do autocracies discursively conduct digital astroturfing against their populations? As these regimes increasingly co-opt social media to manipulate online political discourse, the current political disinformation literature continues to privilege a Cold War paradigm, focusing on countries that dominate Western foreign policy priorities and concerns. Its normative underpinnings overshadow other understudied cases that have also been weaponizing social media to manipulate domestic online discourses. Concurrently, findings from ethnographic interviews and big data approaches remain theoretically disconnected from the long-held logics of regime stabilization. I argue that regime digital astroturfing follows offline events that spark online discourses with collective action potential. In countering these discourses, regime-linked digital astroturfers exploit social media affordances to discursively cheerlead the regime and devalue regime challengers to create a semblance of popular support for the former. I adopt a mixed-methods approach informed by Contextual Text Coding to examine 14,430 tweets linked to the Royal Thai Army in February 2020 to subject my central propositions to empirical scrutiny. My findings demonstrated that astroturfing efforts on Twitter throughout this period, which discursively cheerleaded the military/autocratic regime of General Prayut Chan-o-cha and devalued their pro-democratic opposition with negative frames, were spurred by a mass shooting incident in the city of Korat that exposed the ruling elites to widespread online backlash. This contribution deepens case-specific knowledge about an understudied case in the literature and also strengthens our understanding about the adaptations of authoritarian legitimation strategies in the digital era and the militarization of social media communication.
Sliding Ferroelectricity Induced Ultrafast Switchable Photovoltaic Response in ε‐InSe Layers
2024-09-14

Abstract 2D sliding ferroelectric semiconductors have greatly expanded the ferroelectrics family with the flexibility of bandgap and material properties, which hold great promise for ultrathin device applications that combine ferroelectrics with optoelectronics. Besides the induced different resistance states for non‐volatile memories, the switchable ferroelectric polarizations can also modulate the photogenerated carriers for potentially ultrafast optoelectronic devices. Here, it is demonstrated that the room temperature sliding ferroelectricity can be used for ultrafast switchable photovoltaic response in ε‐InSe layers. By first‐principles calculations and experimental characterizations, it is revealed that the ferroelectricity with out‐of‐plane (OOP) polarization only exists in even layer ε‐InSe. The ferroelectricity is also demonstrated in ε‐InSe‐based vertical devices, which exhibit high on‐off ratios (≈10 4 ) and non‐volatile storage capabilities. Moreover, the OOP ferroelectricity enables an ultrafast (≈3 ps) bulk photovoltaic response in the near‐infrared band, rendering it a promising material for self‐powered reconfigurable and ultrafast photodetector. This work reveals the essential role of ferroelectric polarization on the photogenerated carrier dynamics and paves the way for hybrid multifunctional ferroelectric and optoelectronic devices.
Long-term memory formation for voices during sleep in three-month-old infants
2024-09-14

The ability to form long-term memories begins in early infancy. However, little is known about the specific mechanisms that guide memory formation during this developmental stage. We demonstrate the emergence of a long-term memory for a novel voice in three-month-old infants using the EEG mismatch response (MMR) to the word "baby". In an oddball-paradigm, a frequent standard, and two rare deviant voices (novel and mother) were presented before (baseline), and after (test) familiarizing the infants with the novel voice and a subsequent nap. Only the mother deviant but not the novel deviant elicited a late frontal MMR (∼850 ms) at baseline, possibly reflecting a long-term memory representation for the mother's voice. Yet, MMRs to the novel and mother deviant significantly increased in similarity after voice familiarization and sleep. Moreover, both MMRs showed an additional early (∼250 ms) frontal negative component that is potentially related to deviance processing in short-term memory. Enhanced spindle activity during the nap predicted an increase in late MMR amplitude to the novel deviant and increased MMR similarity between novel and mother deviant. Our findings indicate that the late positive MMR in infants might reflect emergent long-term memory that benefits from sleep spindles.