bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pruning: a tool to optimize the layout of large scale arrays for ultra-high-energy air-shower detection
Authors: Benoit-Lévy Aurélien , Kotera Kumiko , Tueros Matías 
Published: April 2024

Abstract
The deployment of several large scale arrays is envisioned
to study astroparticles at ultra-high energies. In order to
circumvent the heavy computational costs of exploring and optimizing
their layouts, we have developed a pruning method. It consists in
i) running a set of microscopic simulations and interpolate them
over a dense, regularly spaced array of detection units, and
ii) pruning the unnecessary units out of the layout, in order to
obtain the shower footprint on a newly shaped layout. This method
offers flexibility to test various layout parameters, instrumental
constraints, and physical inputs, with a drastic reduction in the
required CPU time. The method can be universally applied to optimize
arrays of any size, and using any detection techniques.

For demonstration, we apply the pruning tool to radio antenna
layouts, which allows us to discuss the interplay between the energy
and inclination of air-showers on the size of the radio footprint
and the intensity of the signal on the ground. Some rule-of-thumb
conclusions that can be drawn for this specific case are: i) a
hexagonal geometry is more efficient than a triangular geometry,
ii) the detection efficiency of the array is stable to changes in
the spacing between radio antennas around 1000 m step size,
iii) for a given number of antennas, adding a granular infill on top
of a coarse hexagonal array is more efficient than instrumenting the
full array with a less dense spacing.
Key drivers and pressures of global water scarcity hotspots
Authors: Leijnse Myrthe , F P Bierkens Marc , H M Gommans Kim , Lin Daisy , Tait Alex , Wanders Niko 
Published: April 2024

Abstract
Global freshwater resources are vital to humanity and Earth’s ecosystems, yet about one third of the global population is affected by water scarcity for at least one month per year. In these areas, the overuse of freshwater resources can lead to the threat of depletion, marking them as the global ‘water scarcity hotspots’. This study combines outputs from a global hydrological model (PCR-GLOBWB 2) with an extensive literature search to provide a comprehensive intercomparison of the key drivers, pressures, states, impacts and responses (DPSIR) that shape the water gap between water demand and availability at the most important water scarcity hotspots worldwide. Hydroclimatic change, population growth, and water use for the industrial, municipal and agricultural sectors are the most important driving and pressuring forces on the water gap, affecting both water quality and quantity. These drivers and pressures have been showing increasing trends at all hotspots, which is concerning for the future development of the water gap. Additionally, we identify and characterize seven clusters of hotspots based on shared DPSIR patterns, revealing their common mechanisms. Our work highlights the diversity of water scarcity related issues at hotspots, especially the variety of impacts involved and governmental responses in place. The results of our DPSIR analysis provide valuable insights for building causal networks representing water gap dynamics at the hotspots. They form a foundation for conceptual models that illuminate human-water interactions, trade-offs, and synergies at the hotspots, while guiding policymakers in addressing the multifaceted challenge of closing the water gap.
Preconditioning of mountain permafrost towards degradation detected by electrical resistivity
Authors: Hauck Christian , Hilbich Christin 
Published: April 2024

Abstract
Warming permafrost has been detected worldwide and is projected to continue during the next century by many modelling studies. In mountain regions, this can lead to potentially hazardous impacts on short time-scales by an increased tendency for slope instabilities. However, time scales of permafrost thaw and the role of the ice content are less clear, especially in heterogeneous mountain terrain, where ice content can vary between zero and supersaturated conditions over small distances. Warming of permafrost near the freezing point shows therefore complex inter-annual behaviour due to latent heat effects during thawing and the influence of the snow-cover, which is governed by highly non-linear processes itself. Here, we demonstrate a preconditioning effect within near-surface layers in mountain permafrost that causes non-linear degradation and accelerates thaw. We hypothesise that a summer heat wave, as has occurred in the Central European summers 2003, 2015 and 2022, will enhance permafrost degradation if the active layer and the top of the permafrost layer are already preconditioned, i.e. have reduced latent heat content. This preconditioning can already be effectuated by a singular warm year, leading to exceptionally strong melting of the ground ice. On sloping terrain this ice-loss can be considered as irreversible, as large parts of the melted water will drain during the process, and an equivalent build-up of ice in cold years does not happen on similar time-scales as the melting. We propose a simple geophysical approach based on electrical resistivity tomography surveys that can assess the state of preconditioning in the absence of boreholes. In addition, we will show that resistivity data from a total of 124 permafrost sites in the Andes, Europe, and Antarctic adhere to a distinct power law behaviour between unfrozen and frozen states, which confirms the consistent electrical behaviour of permafrost and active layer materials over a wide range of landforms and material composition.
Polar-coordinate line-projection light-curing continuous 3D printing for tubular structures
Authors: Wang Huiyuan , Liu Siqin , Yin Xincheng , Huang Mingming , Fu Yanzhe , Chen Xun , Wang Chao , Sun Jingyong , Yan Xin , Han Jianmin , Yang Jiping , Wang Zhijian , Wang Lizhen , Fan Yubo , Li Jiebo 
Published: April 2024

Abstract
3D printing techniques offer an effective method in fabricating complex radially multi-material structures. However, it is challenging for complex and delicate radially multi-material model geometries without supporting structures, such as tissue vessels and tubular graft, among others. In this work, we tackle these challenges by developing a polar digital light processing technique which uses a rod as the printing platform. The 3D model fabrication is accomplished through line projection. The rotation and translation of the rod are synchronized to project and illuminate the photosensitive material volume. By controlling the distance between the rod and the printing window, we achieved the printing of tubular structures with a minimum wall thickness as thin as 50 micrometers. By controlling the width of fine slits at the printing window, we achieved the printing of structures with a minimum feature size of 10 micrometers. Our process accomplished the fabrication of thin-walled tubular graft structure with a thickness of only 100 micrometers and lengths of several centimeters within a timeframe of just 100 s. Additionally, it enables the printing of axial multi-material structures, thereby achieving adjustable mechanical strength. This method is conducive to rapid customization of tubular grafts and the manufacturing of tubular components in fields such as dentistry, aerospace, and more.
Fusarium wilt constrains mungbean yield due to reduction in source availability
Authors: Van Haeften Shanice , Kang Yichen , Dudley Caitlin , Potgieter Andries , Robinson Hannah , Dinglasan Eric , Wenham Kylie , Noble Thomas , Kelly Lisa , Douglas Colin A , Hickey Lee , Smith Millicent R 
Published: April 2024

Abstract
Mungbean is an important source of plant protein for consumers and a high-value export crop for growers across Asia, Australia and Africa. However, many commercial cultivars are highly vulnerable to biotic stresses, which rapidly reduce yield within the season. Fusarium oxysporum is a soil-borne pathogen that is a growing concern for mungbean growers globally. This pathogen causes Fusarium wilt by infecting the root system of the plant resulting in devastating yield reductions. To understand the impact of Fusarium on mungbean development and productivity and to identify tolerant genotypes, a panel of 23 diverse accessions was studied. Field trials conducted in 2016 and 2021 in Warwick, Queensland, Australia under rainfed conditions investigated the variation in phenology, canopy and yield component traits under disease and disease-free conditions. Analyses revealed a high degree of genetic variation for all traits. By comparing the performance of these traits across these two environments, we identified key traits that underpin yield under disease and disease-free conditions. Aboveground biomass components at 50 % flowering were identified as significant drivers of yield development under disease-free conditions and when impacted by Fusarium resulted in up to 96 % yield reduction. Additionally, eight genotypes were identified to be tolerant to Fusarium. These genotypes were found to display differing phenological and morphological behaviours, thereby demonstrating the potential to breed tolerant lines with a range of diverse trait variations. The identification of tolerant genotypes that sustain yield under disease pressure may be exploited in crop improvement programs.
Phyllodulcin from the hexane fraction of Hydrangea macrophylla inhibits glucose-induced lipid accumulation and reactive oxygen species generation in Caenorhabditis elegans
Authors: Cho Myogyeong , Park Harin , Lee Sang Hyun , Kim Myo-Jeong , Jang Miran 
Published: April 2024

ABSTRACT
We confirmed that the hexane layer of Hydrangea macrophylla leaf extract (HLH) is rich in phyllodulcin (PD), an alternative sweetener, through high performance liquid chromatography (HPLC) analysis. To investigate in vivo activity of HLH and its PD, acute toxicity and growth rate of Caenorhabditis elegans were tested and there are no clinical abnormalities at 125-500 µg/mL of HLH. HLH decreased the total lipid and triglyceride contents dose-dependently in glucose-induced obese worms. Also, HLH increased survival rates under oxidative and thermal stress and decreased body reactive oxygen species (ROS) contents significantly. Such antioxidant properties of HLH were attributed to the enhanced activity of the antioxidant enzyme catalase. To determine whether the effect of HLH was due to PD, worms were treated with PD (concentration contained in HLH), and inhibitory effects on total lipids and ROS were observed. Our results suggest that HLH and its PD as a natural alternative sweetener can be used as materials to improve metabolic diseases.
WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences
Authors: Glidden-Handgis George , Wheeler Travis J 
Published: April 2024

Abstract

Background
Software for labeling biological sequences typically produces a theory-based statistic for each match (the E-value) that indicates the likelihood of seeing that match’s score by chance. E-values accurately predict false match rate for comparisons of random (shuffled) sequences, and thus provide a reasoned mechanism for setting score thresholds that enable high sensitivity with low expected false match rate. This threshold-setting strategy is challenged by real biological sequences, which contain regions of local repetition and low sequence complexity that cause excess matches between non-homologous sequences. Knowing this, tool developers often develop benchmarks that use realistic-seeming decoy sequences to explore empirical tradeoffs between sensitivity and false match rate. A recent trend has been to employ reversed biological sequences as realistic decoys, because these preserve the distribution of letters and the existence of local repeats, while disrupting the original sequence’s functional properties. However, we and others have observed that sequences appear to produce high scoring alignments to their reversals with surprising frequency, leading to overstatement of false match risk that may negatively affect downstream analysis.

Results
We demonstrate that an alignment between a sequence S and its (possibly mutated) reversal tends to produce higher scores than alignment between truly unrelated sequences, even when S is a shuffled string with no notable repetitive or low-complexity regions. This phenomenon is due to the unintuitive fact that (even randomly shuffled) sequences contain palindromes that are on average longer than the longest common substrings (LCS) shared between permuted variants of the same sequence. Though the expected palindrome length is only slightly larger than the expected LCS, the distribution of alignment scores involving reversed sequences is strongly right-shifted, leading to greatly increased frequency of high-scoring alignments to reversed sequences.

Impact
Overestimates of false match risk can motivate unnecessarily high score thresholds, leading to potentially reduced true match sensitivity. Also, when tool sensitivity is only reported up to the score of the first matched decoy sequence, a large decoy set consisting of reversed sequences can obscure sensitivity differences between tools. As a result of these observations, we advise that reversed biological sequences be used as decoys only when care is taken to remove positive matches in the original (un-reversed) sequences, or when overstatement of false labeling is not a concern. Though the primary focus of the analysis is on sequence annotation, we also demonstrate that the prevalence of internal palindromes may lead to an overstatement of the rate of false labels in protein identification with mass spectrometry.
Midfacial toddler excoriation syndrome (MiTES): case series, diagnostic criteria and evidence for a pathogenic mechanism
Authors: Sarveswaran Nivedita , Pamela Yunisa , Reddy Akhila A N , Mustari Akash P , Parthasarathi Anchala , Mancini Anthony J , Bishnoi Anuradha , Inamadar Arun C , Olabi Bayanne , Browne Fiona , Deshmukh Gargi N , McWilliam Kenneth , Vinay Keshavamurthy , Srinivas Sahana , Ibbs Samantha , Natarajan Sivakumar , Rao Vadlamudi R , Zawar Vijay , Gowda Vykuntaraju K , Shaikh Samiha S , Moss Celia , Woods Christopher G , Drissi Ichrak 
Published: April 2024

Abstract

Background
PRDM12 polyalanine tract expansions cause two different disorders: midfacial toddler excoriation syndrome (MiTES; itch with normal pain sensation associated with 18 homozygous alanines (18A); and congenital insensitivity to pain (CIP) with normal itch associated with 19 homozygous alanines (19A). Knowledge of the phenotype, genotype and disease mechanism of MiTES is incomplete. Why 18A vs. 19A PRDM12 can cause almost opposite phenotypes is unknown; no other polyalanine or polyglutamine tract expansion disease causes two such disparate phenotypes.

Objectives
To assess the genotype and phenotype of nine new, nine atypical and six previously reported patients diagnosed with MiTES.

Methods
Using cell lines with homozygous PR domain zinc finger protein 12 (PRDM12) containing 12 alanines (12A; normal), 18A (MiTES) and 19A (CIP), we examined PRDM12 aggregation and subcellular localization by image-separation confocal microscopy and subcellular fractionation Western blotting.

Results
MiTES presents in the first year of life; in all cases the condition regresses over the first decade, leaving scarring. The MiTES phenotype is highly distinctive. Features overlapping with PRDM12 CIP are rarely found. The genotype–phenotype study of the PRDM12 polyalanine tract shows that having 7–15 alanines is normal; 16–18 alanines is associated with MiTES; 19 alanines leads to CIP; and no clinically atypical cases of MiTES had a polyalanine tract expansion. PRDM12 aggregation and subcellular localization differed significantly between 18A and normal 12A cell lines and between 18A and 19A cell lines. MiTES is a new protein-aggregation disease.

Conclusions
We provide diagnostic criteria for MiTES and improved longitudinal data. MiTES and CIP are distinct phenotypes, despite their genotypes varying by a single alanine in the PRDM12 polyalanine tract. We found clear distinctions between the cellular phenotypes of normal, MiTES and CIP cells. We hypothesize that the developmental environment of the trigeminal ganglion is unique and critically sensitive to pre- and postnatal levels of PRDM12.
Health-related quality of life in patients with conditions affecting the hand: meta-analysis
Authors: Geoghegan Luke , Carolina Maria , French James , Harrison Conrad J , Rodrigues Jeremy N 
Published: April 2024

Abstract

Background
Health state utility values provide the quality component of quality-adjusted life years and are essential for health economic analyses, such as the National Institute for Health and Care Excellence Technology Appraisal. The aims of this systematic review were to: catalogue utility values for health states experienced by patients with hand conditions; provide pooled utility estimates for common hand conditions; and determine how utilities have been estimated.

Methods
A PRISMA-compliant systematic review and meta-analysis was conducted (registered in PROSPERO, the international prospective register of systematic reviews (CRD42021226098)). Five databases were searched from inception until April 2023 (Embase, MEDLINE, PsycINFO, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), and the Cochrane Central Register of Controlled Trials (CENTRAL)). All studies that reported primary utility values for hand health states in adult patients were eligible for inclusion. Pooled utility estimates were determined across conditions and intervention status using random-effects meta-analysis.

Results
A total of 10 254 articles were identified; 57 studies met the full inclusion criteria and reported 363 distinct health state utility values. Health state utility values were estimated using a range of methods; the most common measure was the EQ-5D. Pooled utility estimates for carpal tunnel syndrome and hand osteoarthritis before surgical intervention were 0.69 (95% c.i. 0.66 to 0.73) and 0.63 (95% c.i. 0.60 to 0.67) respectively.

Conclusion
Pooled utility estimates for patients with untreated carpal tunnel syndrome and hand osteoarthritis are 11% and 18% lower than age-matched population norms respectively. Hand conditions have a significant detrimental impact on health-related quality of life and this study provides catalogued utility values for use in future economic analyses to support the delivery of value-based hand surgery.
Abnormal gamma phase-amplitude coupling in the parahippocampal cortex is associated with network hyperexcitability in Alzheimer’s disease
Authors: Prabhu Pooja , Morise Hirofumi , Kudo Kiwamu , Beagle Alexander , Mizuiri Danielle , Syed Faatimah , Kotegar Karunakar A , Findlay Anne , Miller Bruce L , Kramer Joel H , Rankin Katherine P , Garcia Paul A , Kirsch Heidi E , Vossel Keith , Nagarajan Srikantan S , Ranasinghe Kamalini G 
Published: April 2024

Abstract
While animal models of Alzheimer’s disease (AD) have shown altered gamma oscillations (∼40 Hz) in local neural circuits, the low signal-to-noise ratio of gamma in the resting human brain precludes its quantification via conventional spectral estimates. Phase-amplitude coupling (PAC) indicating the dynamic integration between the gamma amplitude and the phase of low-frequency (4–12 Hz) oscillations is a useful alternative to capture local gamma activity. In addition, PAC is also an index of neuronal excitability as the phase of low-frequency oscillations that modulate gamma amplitude, effectively regulates the excitability of local neuronal firing. In this study, we sought to examine the local neuronal activity and excitability using gamma PAC, within brain regions vulnerable to early AD pathophysiology—entorhinal cortex and parahippocampus, in a clinical population of patients with AD and age-matched controls. Our clinical cohorts consisted of a well-characterized cohort of AD patients (n = 50; age, 60 ± 8 years) with positive AD biomarkers, and age-matched, cognitively unimpaired controls (n = 35; age, 63 ± 5.8 years). We identified the presence or the absence of epileptiform activity in AD patients (AD patients with epileptiform activity, AD-EPI+, n = 20; AD patients without epileptiform activity, AD-EPI−, n = 30) using long-term electroencephalography (LTM-EEG) and 1-hour long magnetoencephalography (MEG) with simultaneous EEG. Using the source reconstructed MEG data, we computed gamma PAC as the coupling between amplitude of the gamma frequency (30–40 Hz) with phase of the theta (4–8 Hz) and alpha (8–12 Hz) frequency oscillations, within entorhinal and parahippocampal cortices. We found that patients with AD have reduced gamma PAC in the left parahippocampal cortex, compared to age-matched controls. Furthermore, AD-EPI+ patients showed greater reductions in gamma PAC than AD-EPI− in bilateral parahippocampal cortices. In contrast, entorhinal cortices did not show gamma PAC abnormalities in patients with AD. Our findings demonstrate the spatial patterns of altered gamma oscillations indicating possible region-specific manifestations of network hyperexcitability within medial temporal lobe regions vulnerable to AD pathophysiology. Greater deficits in AD-EPI+ suggests that reduced gamma PAC is a sensitive index of network hyperexcitability in AD patients. Collectively, the current results emphasize the importance of investigating the role of neural circuit hyperexcitability in early AD pathophysiology and explore its potential as a modifiable contributor to AD pathobiology.
Development of 3D printed electrospun vascular graft loaded with tetramethylpyrazine for reducing thrombosis and restraining aneurysmal dilatation
Authors: Shen Yihong , Pan Yanjun , Liang Fubang , Song Jiahui , Yu Xiao , Cui Jie , Cai Guangfang , EL-Newehy Mohamed , Abdulhameed Meera Moydeen , Gu Hongbing , Sun Binbin , Yin Meng , Mo Xiumei 
Published: April 2024

Abstract

Background
Small-diameter vascular grafts have become the focus of attention in tissue engineering. Thrombosis and aneurysmal dilatation are the two major complications of the loss of vascular access after surgery. Therefore, we focused on fabricating 3D printed electrospun vascular grafts loaded with tetramethylpyrazine (TMP) to overcome these limitations.

Methods
Based on electrospinning and 3D printing, 3D-printed electrospun vascular grafts loaded with TMP were fabricated. The inner layer of the graft was composed of electrospun poly(L-lactic-co-caprolactone) (PLCL) nanofibers and the outer layer consisted of 3D printed polycaprolactone (PCL) microfibers. The characterization and mechanical properties were tested. The blood compatibility and in vitro cytocompatibility of the grafts were also evaluated. Additionally, rat abdominal aortas were replaced with these 3D-printed electrospun grafts to evaluate their biosafety.

Results
Mechanical tests demonstrated that the addition of PCL microfibers could improve the mechanical properties. In vitro experimental data proved that the introduction of TMP effectively inhibited platelet adhesion. Afterwards, rat abdominal aorta was replaced with 3D-printed electrospun grafts. The 3D-printed electrospun graft loaded with TMP showed good biocompatibility and mechanical strength within 6 months and maintained substantial patency without the occurrence of acute thrombosis. Moreover, no obvious aneurysmal dilatation was observed.

Conclusions
The study demonstrated that 3D-printed electrospun vascular grafts loaded with TMP may have the potential for injured vascular healing.