bluuebunny/crossref_metadata_2025 huggingface dataset:
Designing Symmetric Gradient Honeycomb Structures with Carbon-Coated Iron-Based Composites for High-Efficiency Microwave Absorption
Authors: Zhang Yu , Yang Shu-Hao , Xin Yue , Cai Bo , Hu Peng-Fei , Dai Hai-Yang , Liang Chen-Ming , Meng Yun-Tong , Su Ji-Hao , Zhang Xiao-Juan , Lu Min , Wang Guang-Sheng
Published: July 2024

The impedance matching of absorbers is a vital factor affecting their microwave absorption (MA) properties. In this work, we controllably synthesized Material of Institute Lavoisier 88C (MIL-88C) with varying aspect ratios (AR) as a precursor by regulating oil bath conditions, followed by one-step thermal decomposition to obtain carbon-coated iron-based composites. Modifying the precursor MIL-88C (Fe) preparation conditions, such as the molar ratio between metal ions and organic ligands (M/O), oil bath temperature, and oil bath time, influenced the phases, graphitization degree, and AR of the derivatives, enabling low filler loading, achieving well-matched impedance, and ensuring outstanding MA properties. The MOF-derivatives 2 (MD2)/polyvinylidene Difluoride (PVDF), MD3/PVDF, and MD4/PVDF absorbers all exhibited excellent MA properties with optimal filler loadings below 20 wt% and as low as 5 wt%. The MD2/PVDF (5 wt%) achieved a maximum effective absorption bandwidth (EAB) of 5.52 GHz (1.90 mm). The MD3/PVDF (10 wt%) possessed a minimum reflection loss (RLmin) value of − 67.4 at 12.56 GHz (2.13 mm). A symmetric gradient honeycomb structure (SGHS) was constructed utilizing the high-frequency structure simulator (HFSS) to further extend the EAB, achieving an EAB of 14.6 GHz and a RLmin of − 59.0 dB. This research offers a viable inspiration to creating structures or materials with high-efficiency MA properties.
Analyzing water level variability in Odisha: insights from multi-year data and spatial analysis
Authors: Mohanty Litan Kumar , Panda Banajarani , Samantaray Sambit , Dixit Ankur , Bhange Sandesh
Published: July 2024

A comprehensive analysis of long-term water level trends is essential for freshwater sustainability. Given that Odisha heavily relies on agriculture, the monitoring and management of groundwater and its fluctuations are imperative for ensuring future sustainability in the state. Here, we analyzed the trend in Groundwater using water level data for a 30-year period (1990–2020) for the entire Odisha region. Moreover, to determine the long term variability, critical zones of future groundwater variability and controlling parameters of the water level change, we used spatio-temporal water level data of 746 locations. Water level rise of coastal districts during post-monsoon (POM), corresponds to the intensity of rainfall received, thus rising, however other districts of Odisha, showing decline in water level during the same season is due to shortage of rainfall, increase in population at a sudden, and over pumping due to industrial activities. Similarly, during pre-monsoon (PRM), water level shows an increasing trend in hard rock terrain of Odisha implying rabi crop irrigation, high density drainage network and lesser population density. Feature selection techniques were used in this study to know the parameters controlling most to this water level fluctuation in the entire Odisha state. Precipitation followed by landuse & landcover, lithology and population density are controlling the most for the long term water level change. Drainage, elevation, lithology and slope are positively related to the water level change while others are negatively related. It is also inferred that the districts like Mayurbhanj, Sundargarh, Keonjhar, Kandhamal, Boudh, Dhenkanal, Gajapati, Koraput and Kalahandi contain most of the high critical zone concerning future availability of groundwater while most of the coastal regions are safe.
A Note on Rounding Error in The Variables: Understanding Its Influence on Statistical Estimators
Authors: Ahmad Amar
Published: July 2024

When estimating the variance, higher moments, and regression coefficients using rounded data, bias is commonly introduced into these estimates. Sheppard’s correction can be used to approximately adjust for this bias under certain conditions. This study investegated the conditions that allow for the valid application of Sheppard’s corrections. A significant observation from the research was that the rounding error-often displaying a uniform distribution-was not independent of the original, unrounded variable. The study provided a thorough investigation of instances where variables, distributed uniformly, undergo rounding. This investigation yielded crucial insights into the statistical behavior and potential ramifications of such variables within statistical analyses. An integral part of this study was the computation and discussion of the density function of the rounding error. Deriving this density function facilitated a nuanced analysis of the differences between the moments of rounded data and the original, unrounded data. Sheppard’s regularities, under which Sheppard’s correction is applied, were discussed. The letter also carefully considered the effects of rounding error on regression estimates. In this context, Sheppard’s correction was implemented to the biased regression parameters to evaluate its efficacy in providing more accurate estimations. Further, our research provides new insights into how rounding can affect statistical outcomes, depending on the underlying distribution of the data. We have discovered that the impact is minimal under uniform distribution assumptions but becomes significantly pronounced under non-uniform distributions. This highlights the importance of considering the distributional characteristics of data when applying rounding corrections to ensure the reliability of statistical inferences.
A Multiple Environment Available Path Planning Based on an Improved A* Algorithm
Authors: Sun Yu , Yuan Qingni , Gao Qingyang , Xu Liangyao
Published: July 2024

The objective of the path planning for a mobile robot is to generate a collision-free path from a starting position to a target position, aiming to realize a higher quality of path planning, an improved A* algorithm and a hybrid approach incorporating the dynamic window algorithm have been proposed for robot path planning in various environments in this paper. In global path planning, first, a bidirectional search strategy was introduced into to improve the searching efficiency, and an adaptive heuristic function was designed to reduce redundant search nodes. In the meantime, a filtering function for key path nodes and an enhanced jump point optimization method help to remove redundant nodes in the path, reduce turning angles, greatly shorten the path length, and smooth the path using cubic B-spline curves. Furthermore, in local path planning, the combination of key path nodes and the dynamic window approach (DWA) algorithm is utilized to achieve obstacle avoidance in dynamic environments and adjust the heading angle of the section enables seamless locomotion of the robot. Finally, the simulation experiments and physical experiments on the robot were conducted to validate that the proposed improved algorithm significantly improves the speed of path planning while also reducing the length of the planned path and improve the reliability of the algorithm when compared with other algorithms.
Caveats to the Interface of Law and Social Science
Authors: Yegge Robert B.
Published: July 2024

Thus far I have attempted to describe what social science might offer to law and what law might offer to social science. In each case some caveats were offered. At this point, further warning flags should be posted.
The ‘Good Death’ versus ‘Euthanasia”
Authors: Trowell Hugh
Published: July 2024

We pray for a good death and a perfect end in every service of Compline. When is death (thanatos) good (eu-) ? Every man must answer this according to his definition of goodness. Does goodness depend merely on the absence of pain in the sufferer or of grief in the spectators? Death is such a negative subject that to make it good one must see some positive content of love, compassion, even bravery and perhaps immortality set around it, within it and beyond it. Only then is death euthanatos (the good death).

Dictionaries define euthanasia as ‘gentle easy death’, but euthanasia is a euphemism which like a shroud hides the reality. When the sprightly old lady died in her sleep no one would call it euthanasia, but it is. If a man had a stroke and sank slowly and gently without pain to death in a couple of days and the doctor gave only one brandy, no one would accuse him of assisting euthanasia.
Pain in the Christian Life
Authors: Mahoney John
Published: July 2024

Christians are accused of discounting human suffering. Catholics are charged with increasing people’s sufferings in order to keep the rules of the Church, sometimes with regarding suffering as a just punishment, and even with considering it as something good and desirable in itself. In addition, your profession and mine are closely and continually connected with suffering in a variety of forms, and while on occasion we may be forgiven for seeing life in terms of little else, the possibility of this one-sided view at least prevents us from evading the fact that there is a great deal of suffering in ordinary life and that as both Christians and professionals we are compelled to think seriously of it.

Suppose we begin with this idea of suffering as a punishment, or a judgment, or a visitation of divine wrath. It is not uncommon to meet people who regard their sufferings as a judgment, and who gloomily go further and say that not only is God punishing them, but he is quite right to do so.
Intensive Radiosonde Observations of Environmental Conditions on the Development of a Mesoscale Convective System in the Baiu Frontal Zone
Authors: Manda A. , Tachibana Y. , Nakamura H. , Takikawa T. , Nishina A. , Moteki Q. , Zhao N. , Iizuka S.
Published: July 2024

Mesoscale convective systems (MCSs) that occur in the Baiu frontal zone (BFZ) can cause devastating flash floods during early summer in Japan; however, the environmental conditions necessary for their development require further investigation. High‐frequency atmospheric soundings, conducted using multiple marine vessels in the East China Sea on 19 June 2022, captured the detailed environmental conditions pertaining to the development of an MCS within the BFZ. The MCS, which developed rapidly without any remarkable preceding synoptic or mesoscale disturbance in the mid‐ or upper troposphere, caused intense precipitation exceeding 80 mm/hr. The MCS persisted for approximately 6 hr, and it intensified when the influx of nearly saturated air near the sea surface toward a weak surface front overlapped with the influx of free‐tropospheric moist air. The influx of nearly saturated air near the sea surface ensured conditional instability within the lower troposphere. The influx of moist air in the free troposphere contributed to the near‐saturation conditions above the boundary layer, a feature inherent to the BFZ, and played an important role in minimizing the reduction in the buoyancy of air parcels. The results of this study indicate that a better forecast of the horizontal distribution of free tropospheric moist air is beneficial for limiting the potential area of genesis of MCS in the BFZ, and a more comprehensive understanding of the vertical variations in moisture transport contributes to an improved forecast skill for MCS in the BFZ.
Improved Estimates of Sub‐Regional Groundwater Storage Anomaly Using Coordinated Forward Modeling
Authors: Ma Yalin , Pan Yun , Zhang Chong , Yeh Pat J.‐F. , Xu Li , Huang Zhiyong , Gong Huili
Published: July 2024

Groundwater storage anomaly (GWSA) can be estimated either at the large scale from the Gravity Recovery and Climate Experiment (GRACE) or at the local scale based on in situ observed groundwater level (GWL) and aquifer storage parameters. Yet, the accuracy of GRACE‐based estimate is affected by leakage errors, while that of local GWL‐based estimate requires the reliable specific yield (Sy) data that are usually not available. Here, we developed a novel approach, the coordinated forward modeling (CoFM), based on the iterative forward modeling to improve GWSA estimation at the sub‐regional scale smaller than the typical GRACE footprint. It is achieved by solving Sy through iterative comparisons between GRACE‐based and observation‐based GWSA at 0.5° grid scale, and then re‐calculating GWSA using the updated Sy and observed GWL. The utility of CoFM is explored by using the hypothetical experiments and a real case study in the Piedmont Plain (PP, ∼54,000 km2) and East‐central Plain (ECP, ∼86,000 km2) of North China Plain. Results show that CoFM can detect GWSA at 0.5° grid scale in the hypothetical experiments given the large spatial variability of GWL. While in the real case study, the CoFM distinguishes between the divergent unconfined GWSA trends (2005–2016) in PP (−41.80 ± 0.55 mm/yr) and ECP (−7.57 ± 0.60 mm/yr) caused by the differences in hydrogeological conditions and groundwater use. The improvement made by CoFM can be attributed to the use of the distributed GWL information to constrain GRACE leakage errors. This study highlights a practical important solution for improving sub‐regional GWSA estimation through the joint use of large‐scale GRACE data and local‐scale well observations.
Exploring the Mechanisms of the Soil Moisture‐Air Temperature Hypersensitive Coupling Regime
Authors: Hsu Hsin , Dirmeyer Paul A. , Seo Eunkyo
Published: July 2024

High temperature extremes accompanied by drought have led to serious ramifications for environmental and socio‐economic systems. Thus, improving the predictability of heat‐wave events is a high priority. One key to achieving this is to better understand land‐atmosphere interactions. Recent studies have documented a hypersensitive regime in the soil moisture‐temperature relationship: when soil dries below a critical low threshold, called the soil moisture breakpoint, air temperatures increase at a greater rate as soil moisture declines. Whether such a hypersensitive regime is rooted in land surface processes and whether this soil moisture breakpoint corresponds to a known plant critical value, the permanent wilting point (WP), below which latent heat flux almost ceases, remains unclear. In this study, we explore the mechanisms linking low soil moisture to high air temperatures. From in situ observations, we confirm that the hypersensitive regime acts throughout the chain of energy processes from land to atmosphere. A simple energy‐balance model indicates that the hypersensitive regime occurs when there is a dramatic drop in evaporative cooling, which happens when soil moisture dries toward the permanent WP, suggesting that the soil moisture breakpoint is slightly above the permanent WP. Precisely how a model represents the relationship between evapotranspiration and soil moisture is found to be essential to describe the occurrence of the hypersensitive regime. Thus, we advocate that weather and climate models should ensure a realistic representation of land‐atmosphere interactions to obtain reliable forecasts of extremes and climate projections, aiding the assessment of heatwave vulnerability and adaptation.
Open Access GNSS Data for Studies of the Lithosphere
Authors: Stamps D. Sarah , Kreemer Corné
Published: July 2024

Various types of Global Navigation Satellite System (GNSS) data are used for a wide range of applications. When modeled correctly, millimeter precision daily GNSS position time‐series yield velocities and other derived products that can be used for investigations of lithospheric processes and properties. In this review paper, we describe the specific types of GNSS data and data products that are valuable for studies of the lithosphere, such as coseismic offsets, post‐seismic decay in time‐series, seasonal signals, secular velocities, and strain rates, and how those data are derived. We also discuss the applications of several types of GNSS data and data products. We provide open access resources for precision GNSS daily position time‐series, quality secular velocity solutions, and daily GNSS RINEX files for researchers interested in processing their own data.
Cryo-EM unveils kinesin KIF1A’s processivity mechanism and the impact of its pathogenic variant P305L
Authors: Benoit Matthieu P. M. H. , Rao Lu , Asenjo Ana B. , Gennerich Arne , Sosa Hernando
Published: July 2024

Mutations in the microtubule-associated motor protein KIF1A lead to severe neurological conditions known as KIF1A-associated neurological disorders (KAND). Despite insights into its molecular mechanism, high-resolution structures of KIF1A-microtubule complexes remain undefined. Here, we present 2.7-3.5 Å resolution structures of dimeric microtubule-bound KIF1A, including the pathogenic P305L mutant, across various nucleotide states. Our structures reveal that KIF1A binds microtubules in one- and two-heads-bound configurations, with both heads exhibiting distinct conformations with tight inter-head connection. Notably, KIF1A’s class-specific loop 12 (K-loop) forms electrostatic interactions with the C-terminal tails of both α- and β-tubulin. The P305L mutation does not disrupt these interactions but alters loop-12’s conformation, impairing strong microtubule-binding. Structure-function analysis reveals the K-loop and head-head coordination as major determinants of KIF1A’s superprocessive motility. Our findings advance the understanding of KIF1A’s molecular mechanism and provide a basis for developing structure-guided therapeutics against KAND.
Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2
Authors: Li Huanyu Z. , Pike Ashley C. W. , Lotsaris Irina , Chi Gamma , Hansen Jesper S. , Lee Sarah C. , Rödström Karin E. J. , Bushell Simon R. , Speedman David , Evans Adam , Wang Dong , He Didi , Shrestha Leela , Nasrallah Chady , Burgess-Brown Nicola A. , Vandenberg Robert J. , Dafforn Timothy R. , Carpenter Elisabeth P. , Sauer David B.
Published: July 2024

Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes that link substrate release and opening of the cytoplasmic gate and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria.
HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy
Authors: Lee Guinevere Q. , Khadka Pragya , Gowanlock Sarah N. , Copertino Dennis C. , Duncan Maggie C. , Omondi F. Harrison , Kinloch Natalie N. , Kasule Jingo , Kityamuweesi Taddeo , Buule Paul , Jamiru Samiri , Tomusange Stephen , Anok Aggrey , Chen Zhengming , Jones R. Brad , Galiwango Ronald M. , Reynolds Steven J. , Quinn Thomas C. , Brumme Zabrina L. , Redd Andrew D. , Prodger Jessica L.
Published: July 2024

The primary obstacle to curing HIV-1 is a reservoir of CD4+ cells that contain stably integrated provirus. Previous studies characterizing the proviral landscape, which have been predominantly conducted in males in the United States and Europe living with HIV-1 subtype B, have revealed that most proviruses that persist during antiretroviral therapy (ART) are defective. In contrast, less is known about proviral landscapes in females with non-B subtypes, which represents the largest group of individuals living with HIV-1. Here, we analyze genomic DNA from resting CD4+ T-cells from 16 female and seven male Ugandans with HIV-1 receiving suppressive ART (n = 23). We perform near-full-length proviral sequencing at limiting dilution to examine the proviral genetic landscape, yielding 607 HIV-1 subtype A1, D, and recombinant proviral sequences (mean 26/person). We observe that intact genomes are relatively rare and clonal expansion occurs in both intact and defective genomes. Our modification of the primers and probes of the Intact Proviral DNA Assay (IPDA), developed for subtype B, rescues intact provirus detection in Ugandan samples for which the original IPDA fails. This work will facilitate research on HIV-1 persistence and cure strategies in Africa, where the burden of HIV-1 is heaviest.
Structural evolution during inverse vulcanization
Authors: Zheng Botuo , Zhong Liling , Wang Xiaoxiao , Lin Peiyao , Yang Zezhou , Bai Tianwen , Shen Hang , Zhang Huagui
Published: July 2024

Inverse vulcanization exploits S8 to synthesize polysulfides. However, evolution of products and its mechanism during inverse vulcanization remains elusive. Herein, inverse vulcanization curves are obtained to describe the inverse vulcanization process in terms of three stages: induction, curing and over-cure. The typical curves exhibit a moduli increment before declining or plateauing, reflecting the process of polysulfide network formation and loosing depending on monomers. For aromatic alkenes, in the over-cure, the crosslinked polysulfide evolves significantly into a sparse network with accelerated relaxation, due to the degradation of alkenyl moieties into thiocarbonyls. The inverse vulcanization product of olefins degrades slowly with fluctuated relaxation time and modulus because of the generation of thiophene moieties, while the inverse vulcanization curve of dicyclopentadiene has a plateau following curing stage. Confirmed by calculations, the mechanisms reveal the alkenyl groups react spontaneously into thiocarbonyls or thiophenes via similar sulfur-substituted alkenyl intermediates but with different energy barriers.
Improving laboratory animal genetic reporting: LAG-R guidelines
Authors: Teboul Lydia , Amos-Landgraf James , Benavides Fernando J. , Birling Marie-Christine , Brown Steve D. M. , Bryda Elizabeth , Bunton-Stasyshyn Rosie , Chin Hsian-Jean , Crispo Martina , Delerue Fabien , Dobbie Michael , Franklin Craig L. , Fuchtbauer Ernst-Martin , Gao Xiang , Golzio Christelle , Haffner Rebecca , Hérault Yann , Hrabe de Angelis Martin , Lloyd Kevin C. Kent , Magnuson Terry R. , Montoliu Lluis , Murray Stephen A. , Nam Ki-Hoan , Nutter Lauryl M. J. , Pailhoux Eric , Pardo Manuel de Villena Fernando , Peterson Kevin , Reinholdt Laura , Sedlacek Radislav , Seong Je Kyung , Shiroishi Toshihiko , Smith Cynthia , Takeo Toru , Tinsley Louise , Vilotte Jean-Luc , Warming Søren , Wells Sara , Whitelaw C. Bruce , Yoshiki Atsushi ,   Asian Mouse Mutagenesis Resource Association, Yoshiki Atsushi , Wang Chi-Kuang ,   CELPHEDIA infrastructure, Marvel Jacqueline , Zarubica Ana ,   INFRAFRONTIER consortium, Wells Sara ,   International Mammalian Genome Society,   International Mouse Phenotyping Consortium, Heaney Jason , Wells Sara ,   International Society for Transgenic Technologies,   Mutant Mouse Resource and Research Centers, Korf Ian F. , Lutz Cathleen ,   Phenomics Australia, Kueh Andrew J. , Thomas Paul Q. , Arkell Ruth M. , Mann Graham J. ,   RRRC- Rat Resource and Research Center, Pavlovic Guillaume
Published: July 2024

The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals’ genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.
Chiral multiferroicity in two-dimensional hybrid organic-inorganic perovskites
Authors: Zheng Haining , Ghosh Arup , Swamynadhan M. J. , Zhang Qihan , Wong Walter P. D. , Wu Zhenyue , Zhang Rongrong , Chen Jingsheng , Cimpoesu Fanica , Ghosh Saurabh , Campbell Branton J. , Wang Kai , Stroppa Alessandro , Mahendiran Ramanathan , Loh Kian Ping
Published: July 2024

Chiral multiferroics offer remarkable capabilities for controlling quantum devices at multiple levels. However, these materials are rare due to the competing requirements of long-range orders and strict symmetry constraints. In this study, we present experimental evidence that the coexistence of ferroelectric, magnetic orders, and crystallographic chirality is achievable in hybrid organic-inorganic perovskites [(R/S)-β-methylphenethylamine]2CuCl4. By employing Landau symmetry mode analysis, we investigate the interplay between chirality and ferroic orders and propose a novel mechanism for chirality transfer in hybrid systems. This mechanism involves the coupling of non-chiral distortions, characterized by defining a pseudo-scalar quantity, $$\xi={{{{{\bf{p}}}}}}{{\cdot }}{{{{{\bf{r}}}}}}$$
ξ
=
p
⋅
r
($${{{{{\bf{p}}}}}}$$
p
represents the ferroelectric displacement vector and $${{{{{\bf{r}}}}}}$$
r
denotes the ferro-rotational vector), which distinguishes between (R)- and (S)-chirality based on its sign. Moreover, the reversal of this descriptor’s sign can be associated with coordinated transitions in ferroelectric distortions, Jahn-Teller antiferro-distortions, and Dzyaloshinskii-Moriya vectors, indicating the mediating role of crystallographic chirality in magnetoelectric correlations.
Cyprocide selectively kills nematodes via cytochrome P450 bioactivation
Authors: Knox Jessica , Burns Andrew R. , Cooke Brittany , Cammalleri Savina R. , Kitner Megan , Ching Justin , Castelli Jack M. P. , Puumala Emily , Snider Jamie , Koury Emily , Collins J. B. , Geissah Salma , Dowling James J. , Andersen Erik C. , Stagljar Igor , Cowen Leah E. , Lautens Mark , Zasada Inga , Roy Peter J.
Published: July 2024

Left unchecked, plant-parasitic nematodes have the potential to devastate crops globally. Highly effective but non-selective nematicides are justifiably being phased-out, leaving farmers with limited options for managing nematode infestation. Here, we report our discovery of a 1,3,4-oxadiazole thioether scaffold called Cyprocide that selectively kills nematodes including diverse species of plant-parasitic nematodes. Cyprocide is bioactivated into a lethal reactive electrophilic metabolite by specific nematode cytochrome P450 enzymes. Cyprocide fails to kill organisms beyond nematodes, suggesting that the targeted lethality of this pro-nematicide derives from P450 substrate selectivity. Our findings demonstrate that Cyprocide is a selective nematicidal scaffold with broad-spectrum activity that holds the potential to help safeguard our global food supply.
Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria
Authors: Tian Ran , Zhang Yaolei , Kang Hui , Zhang Fan , Jin Zhihong , Wang Jiahao , Zhang Peijun , Zhou Xuming , Lanyon Janet M. , Sneath Helen L. , Woolford Lucy , Fan Guangyi , Li Songhai , Seim Inge
Published: July 2024

Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
Strain-graded quantum dots with spectrally pure, stable and polarized emission
Authors: Jung Dongju , Park Jeong Woo , Min Sejong , Lee Hak June , Park Jin Su , Kim Gui-Min , Shin Doyoon , Im Seongbin , Lim Jaemin , Kim Ka Hyung , Chae Jong Ah , Lee Doh C. , Pugin Raphaël , Bulliard Xavier , Hwang Euyheon , Park Ji-Sang , Park Young-Shin , Bae Wan Ki
Published: July 2024

Structural deformation modifies the bandgap, exciton fine structure and phonon energy of semiconductors, providing an additional knob to control their optical properties. The impact can be exploited in colloidal semiconductor quantum dots (QDs), wherein structural stresses can be imposed in three dimensions while defect formation is suppressed by controlling surface growth kinetics. Yet, the control over the structural deformation of QDs free from optically active defects has not been reached. Here, we demonstrate strain-graded CdSe-ZnSe core-shell QDs with compositionally abrupt interface by the coherent pseudomorphic heteroepitaxy. Resulting QDs tolerate mutual elastic deformation of varying magnitudes at the interface with high structural fidelity, allowing for spectrally stable and pure emission of photons at accelerated rates with near unity luminescence efficiency. We capitalize on the asymmetric strain effect together with the quantum confinement effect to expand emission envelope of QDs spanning the entire visible region and exemplify their use in photonic applications.
Development and characterization of amino donor-acceptor Stenhouse adducts
Authors: Reyes Cesar A. , Lee Hye Joon , Karanovic Connie , Picazo Elias
Published: July 2024

Donor-acceptor Stenhouse adducts (DASAs) are molecular photoswitches spurring wide interest because of their dynamic photophysical properties, complex photoswitching mechanism, and diverse applications. Despite breakthroughs in modularity for the donor, acceptor, and triene compartments, the backbone heteroatom remains static due to synthetic challenges. We provide a predictive tool and sought-after strategy to vary the heteroatom, introduce amino DASA photoswitches, and analyze backbone heteroatom effects on photophysical properties. Amino DASA synthesis is enabled by aza-Piancatelli rearrangements on pyrrole substrates, imparting an aromaticity-breaking rearrangement that capitalizes on nitrogen’s additional bonding orbital and the inductive properties of sulfonyl groups. Amino DASA structure is confirmed by single crystal X-ray diffraction, the photochromic properties are characterized, and the photoswitch isomerization is investigated. Overall, the discovered pyrrole rearrangement enables the study of the DASA backbone heteroatom compartment and furthers our insight into the structure-property relationship of this complex photoswitch.
In silico fragment-based discovery of CIB1-directed anti-tumor agents by FRASE-bot
Authors: An Yi , Lim Jiwoong , Glavatskikh Marta , Wang Xiaowen , Norris-Drouin Jacqueline , Hardy P. Brian , Leisner Tina M. , Pearce Kenneth H. , Kireev Dmitri
Published: July 2024

Chemical probes are an indispensable tool for translating biological discoveries into new therapies, though are increasingly difficult to identify since novel therapeutic targets are often hard-to-drug proteins. We introduce FRASE-based hit-finding robot (FRASE-bot), to expedite drug discovery for unconventional therapeutic targets. FRASE-bot mines available 3D structures of ligand-protein complexes to create a database of FRAgments in Structural Environments (FRASE). The FRASE database can be screened to identify structural environments similar to those in the target protein and seed the target structure with relevant ligand fragments. A neural network model is used to retain fragments with the highest likelihood of being native binders. The seeded fragments then inform ultra-large-scale virtual screening of commercially available compounds. We apply FRASE-bot to identify ligands for Calcium and Integrin Binding protein 1 (CIB1), a promising drug target implicated in triple negative breast cancer. FRASE-based virtual screening identifies a small-molecule CIB1 ligand (with binding confirmed in a TR-FRET assay) showing specific cell-killing activity in CIB1-dependent cancer cells, but not in CIB1-depletion-insensitive cells.
Uplift of the Tibetan Plateau driven by mantle delamination from the overriding plate
Authors: Xie Yuan , Balázs Attila , Gerya Taras , Xiong Xiong
Published: July 2024

The geodynamic evolution of the Tibetan Plateau remains highly debated. Any model of its evolution must explain the plateau’s growth as constrained by palaeo-altitude studies, the spatio-temporal distribution of magmatic activity, and the lithospheric mantle removal inferred from seismic velocity anomalies in the underlying mantle. Several conflicting models have been proposed, but none of these explains the first-order topographic, magmatic and seismic features self-consistently. Here we propose and test numerically an evolutionary model of the plateau that involves gradual peeling of the lithospheric mantle from the overriding plate and consequent mantle and crustal melting and uplift. We show that this model successfully reproduces the successive surface uplift of the plateau to more than 4 km above sea level and is consistent with the observed migration of magmatism and geometry of the lithosphere–asthenosphere boundary resulting from subduction of the Indian plate and delamination of the mantle lithosphere of the Eurasian plate. These comparisons indicate that mantle delamination from the overriding plate is the driving force behind the uplift of the Tibetan Plateau and, potentially, orogenic plateaus more generally.
Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping
Authors: Netskar Herman , Pfefferle Aline , Goodridge Jodie P. , Sohlberg Ebba , Dufva Olli , Teichmann Sarah A. , Brownlie Demi , Michaëlsson Jakob , Marquardt Nicole , Clancy Trevor , Horowitz Amir , Malmberg Karl-Johan
Published: July 2024

The functional diversity of natural killer (NK) cell repertoires stems from differentiation, homeostatic, receptor–ligand interactions and adaptive-like responses to viral infections. In the present study, we generated a single-cell transcriptional reference map of healthy human blood- and tissue-derived NK cells, with temporal resolution and fate-specific expression of gene-regulatory networks defining NK cell differentiation. Transfer learning facilitated incorporation of tumor-infiltrating NK cell transcriptomes (39 datasets, 7 solid tumors, 427 patients) into the reference map to analyze tumor microenvironment (TME)-induced perturbations. Of the six functionally distinct NK cell states identified, a dysfunctional stressed CD56bright state susceptible to TME-induced immunosuppression and a cytotoxic TME-resistant effector CD56dim state were commonly enriched across tumor types, the ratio of which was predictive of patient outcome in malignant melanoma and osteosarcoma. This resource may inform the design of new NK cell therapies and can be extended through transfer learning to interrogate new datasets from experimental perturbations or disease conditions.
Benefits for children with suspected cancer from routine whole-genome sequencing
Authors: Hodder Angus , Leiter Sarah M. , Kennedy Jonathan , Addy Dilys , Ahmed Munaza , Ajithkumar Thankamma , Allinson Kieren , Ancliff Phil , Bailey Shivani , Barnard Gemma , Burke G. A. Amos , Burns Charlotte , Cano-Flanagan Julian , Chalker Jane , Coleman Nicholas , Cheng Danny , Clinch Yasmin , Dryden Caryl , Ghorashian Sara , Griffin Blanche , Horan Gail , Hubank Michael , May Phillippa , McDerra Joanna , Nagrecha Rajvi , Nicholson James , O’Connor David , Pavasovic Vesna , Quaegebeur Annelies , Rao Anupama , Roberts Thomas , Samarasinghe Sujith , Stasevich Iryna , Tadross John A. , Trayers Claire , Trotman Jamie , Vora Ajay , Watkins James , Chitty Lyn S. , Bowdin Sarah , Armstrong Ruth , Murray Matthew J. , Hook Catherine E. , Tarpey Patrick , Vedi Aditi , Bartram Jack , Behjati Sam
Published: July 2024

Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.
Neural representation of human experimenters in the bat hippocampus
Authors: Snyder Madeleine C. , Qi Kevin K. , Yartsev Michael M.
Published: July 2024

Here we conducted wireless electrophysiological recording of hippocampal neurons from Egyptian fruit bats in the presence of human experimenters. In flying bats, many neurons modulated their activity depending on the identity of the human at the landing target. In stationary bats, many neurons carried significant spatial information about the position and identity of humans traversing the environment. Our results reveal that hippocampal activity is robustly modulated by the presence, movement and identity of human experimenters.
Quick methylene blue dye elimination via SDS-Ag nanoparticles catalysts
Authors: Almarashi Jamal Q. M. , Gadallah A.-S. , Shaban Mohamed , Ellabban M. A. , Hbaieb Kais , Kordy Mohamed G. M. , Zayed Mohamed , Mohamed Abdel-Aleam H.
Published: July 2024

Methylene blue dye, being toxic, carcinogenic and non-biodegradable, poses a serious threat for human health and environmental safety. The effective and time-saving removal of such industrial dye necessitates the use of innovative technologies such as silver nanoparticle-based catalysis. Utilizing a pulsed Nd:YAG laser operating at the second harmonic generation of 532 nm with 2.6 J energy per pulse and 10 ns pulse duration, Ag nanoparticles were synthesized via an eco-friendly method with sodium dodecyl sulphate (SDS) as a capping agent. Different exposure times (15, 30, and 45 min) resulted in varying nanoparticle sizes. Characterization was achieved through UV–Vis absorption spectroscopy, scanning electron microscopy (SEM) imaging, and energy dispersive X-ray (EDX). Lorentzian fitting was used to model nanoparticle size, aligning well with SEM results. Mie’s theory was applied to evaluate the absorption, scattering, and extinction cross-sectional area spectra. EDX revealed increasing Ag and carbon content with exposure time. The SDS-caped AgNPs nanoparticles were tested as catalyst for methylene blue degradation, achieving up to 92.5% removal in just 12 min with a rate constant of 0.2626 min−1, suggesting efficient and time-saving catalyst compared to previously reported Ag-based nanocatalysts.
The association of rs17713054 with Neanderthal origin at 3p21.31 locus with the severity of COVID-19 in Iranian patients
Authors: Yaghmouri Mohammad , Safdari Lord Javad , Amini Masoumeh , Yekaninejad Mir Saeed , Izadi Pantea
Published: July 2024

Since the COVID-19 pandemic, the diversity of clinical manifestations in patients has been a tremendous challenge. It seems that genetic variations, as one of the players, contribute to the variety of symptoms. Genome-wide association studies have demonstrated the influence of certain genomic regions on the disease prognosis. Particularly, a haplotype at 3p21.31 locus, inherited from Neanderthals, showed an association with COVID-19 severity. Despite several studies regarding this haplotype, some key variants are not sufficiently addressed. In the present study, we investigated the association of rs17713054 at 3p21.31 with COVID-19 severity. We analyzed the genotype of 251 Iranian COVID-19 patients (151 patients with asymptomatic to mild form as control and 100 patients with severe to critical symptoms without any comorbidities as case group) using the ARMS-PCR method. Results demonstrated that the A allele confers an almost twofold increased risk for COVID-19 severity (Pvalue = 0.008). The AA genotype also raises the risk by more than 11 times following the recessive model (Pvalue = 0.013). In conclusion, the A allele in rs17713054 was a risk allele in Iranian patients and was independently associated with COVID-19 severity. More studies are beneficial to confirm these findings in other populations and to develop strategies for risk assessment, prevention, and personalized medicine.
Impending role of inflammatory markers and their specificity and sensitivity in breast cancer patients
Authors: Malik Samina , Waquar Sulayman , Idrees Nimra , Malik Arif
Published: July 2024

Cancer and related disorders are the most common cause of cancer-related mortality with the incidence of 1 in 9 among the pre-menopausal Pakistani females. among the most common ailments worldwide, indicating the importance of developing particular techniques that could help attenuate the effects of breast cancer and related outcomes. The primary aim of the current study was to review the role of inflammatory and stress markers in the development and progression of breast cancer. Four hundred ninety-eight (n = 498) patients with breast cancer and four hundred and ninety-eight (n = 498) age- and sex-matched controls were selected for this case‒control study. Serum samples were obtained, and the levels of stress and inflammatory markers, including Matrix metalloproteases (MMPs), Interleukins (ILs), Heat shock proteins (HSPs), Malondialdehyde (MDA), Nitric Oxide (NO), inducible Nitric Oxide Synthase (iNOS) and Tumour necrosis factor-alpha (TNF-α), were determined. Most (62%) patients had metastatic breast cancer (stage III or IV) with an adverse grade (65% with Grade III and 35% with Grade II). The present study showed that the levels of oxidants such as MDA, ILs, MMPs and HSPs were significantly greater, while the levels of antioxidants such as Superoxide Dismutase (SOD), Glutathione (GSH), Catalase (CAT), vitamin A, C and D were significantly lower in breast cancer patients than in controls, suggesting their diagnostic importance and role in the pathophysiology of breast cancer. Oxidants, including IL-1, HSP27 and MMP9, which are highly specific and sensitive, may be used to develop the pathophysiological pathways of metastatic breast cancer in these patients. These pathways include cell invasion, cell migration and epithelial–mesenchymal transition. Therefore, we concluded that an increase in growth factors, e.g., Vascular Endothelial Growth Factor (VEGF), Tumour Growth Factor-beta (TGF-β) and B-cell lymphoma (Bcl2), under the influence of these variables plays a crucial role in the metastasis of breast cancer.
Salt stress amelioration and nutrient strengthening in spinach (Spinacia oleracea L.) via biochar amendment and zinc fortification: seed priming versus foliar application
Authors: Ahmad Shoaib , Khan Sehrish Adiba , Hussain Afzal , Zhang Lidan , Owdah Alomrani Sarah , Ahmad Azeem , Al-Ghanim Khalid A. , Ali Alshehri Mohammad , Ali Shafaqat , Sarker Pallab K.
Published: July 2024

Soil salinity is a major nutritional challenge with poor agriculture production characterized by high sodium (Na+) ions in the soil. Zinc oxide nanoparticles (ZnO NPs) and biochar have received attention as a sustainable strategy to reduce biotic and abiotic stress. However, there is a lack of information regarding the incorporation of ZnO NPs with biochar to ameliorate the salinity stress (0, 50,100 mM). Therefore, the current study aimed to investigate the potentials of ZnO NPs application (priming and foliar) alone and with a combination of biochar on the growth and nutrient availability of spinach plants under salinity stress. Results demonstrated that salinity stress at a higher rate (100 mM) showed maximum growth retardation by inducing oxidative stress, resulted in reduced photosynthetic rate and nutrient availability. ZnO NPs (priming and foliar) alone enhanced growth, chlorophyll contents and gas exchange parameters by improving the antioxidant enzymes activity of spinach under salinity stress. While, a significant and more pronounced effect was observed at combined treatments of ZnO NPs with biochar amendment. More importantly, ZnO NPs foliar application with biochar significantly reduced the Na+ contents in root 57.69%, and leaves 61.27% of spinach as compared to the respective control. Furthermore, higher nutrient contents were also found at the combined treatment of ZnO NPs foliar application with biochar. Overall, ZnO NPs combined application with biochar proved to be an efficient and sustainable strategy to alleviate salinity stress and improve crop nutritional quality under salinity stress. We inferred that ZnO NPs foliar application with a combination of biochar is more effectual in improving crop nutritional status and salinity mitigation than priming treatments with a combination of biochar.
Generalized div-curl based regularization for physically constrained deformable image registration
Authors: Tzitzimpasis Paris , Ries Mario , Raaymakers Bas W. , Zachiu Cornel
Published: July 2024

Variational image registration methods commonly employ a similarity metric and a regularization term that renders the minimization problem well-posed. However, many frequently used regularizations such as smoothness or curvature do not necessarily reflect the underlying physics that apply to anatomical deformations. This, in turn, can make the accurate estimation of complex deformations particularly challenging. Here, we present a new highly flexible regularization inspired from the physics of fluid dynamics which allows applying independent penalties on the divergence and curl of the deformations and/or their nth order derivative. The complexity of the proposed generalized div-curl regularization renders the problem particularly challenging using conventional optimization techniques. To this end, we develop a transformation model and an optimization scheme that uses the divergence and curl components of the deformation as control parameters for the registration. We demonstrate that the original unconstrained minimization problem reduces to a constrained problem for which we propose the use of the augmented Lagrangian method. Doing this, the equations of motion greatly simplify and become managable. Our experiments indicate that the proposed framework can be applied on a variety of different registration problems and produce highly accurate deformations with the desired physical properties.