bluuebunny/crossref_metadata_2025 huggingface dataset:
Intranasal PAMAM-G3 scavenges cell-free DNA attenuating the allergic airway inflammation
Authors: Chen Xiumin , Chen Changhui , Tu Zhaoxu , Guo Zeling , Lu Tong , Li Jian , Wen Yihui , Chen Dehua , Lei Wenbin , Wen Weiping , Li Hang
Published: May 2024

Allergic airway inflammation (AAI), including allergic rhinitis (AR) and allergic asthma, is driven by epithelial barrier dysfunction and type 2 inflammation. However, the underlying mechanism remains uncertain and available treatments are constrained. Consequently, we aim to explore the role of cell-free DNA (cfDNA) in AAI and assess the potential alleviating effects of cationic polymers (CPs) through cfDNA elimination. Levels of cfDNA were evaluated in AR patients, allergen-stimulated human bronchial epithelium (BEAS-2B cells) and primary human nasal epithelium from both AR and healthy control (HC), and AAI murine model. Polyamidoamine dendrimers-generation 3 (PAMAM-G3), a classic type of cationic polymers, were applied to investigate whether the clearance of cfDNA could ameliorate airway epithelial dysfunction and inhibit AAI. The levels of cfDNA in the plasma and nasal secretion from AR were higher than those from HC (P < 0.05). Additionally, cfDNA levels in the exhaled breath condensate (EBC) were positively correlated with Interleukin (IL)-5 levels in EBC (R = 0.4191, P = 0.0001). Plasma cfDNA levels negatively correlated with the duration of allergen immunotherapy treatment (R = −0.4297, P = 0.006). Allergen stimulated cfDNA secretion in vitro (P < 0.001) and in vivo (P < 0.0001), which could be effectively scavenged with PAMAM-G3. The application of PAMAM-G3 inhibited epithelial barrier dysfunction in vitro and attenuated the development of AAI in vivo. This study elucidates that cfDNA, a promising biomarker for monitoring disease severity, aggravates AAI and the application of intranasal PAMAM-G3 could potentially be a novel therapeutic intervention for AAI.
Universal scaling law for chiral antiferromagnetism
Authors: Xu Shijie , Dai Bingqian , Jiang Yuhao , Xiong Danrong , Cheng Houyi , Tai Lixuan , Tang Meng , Sun Yadong , He Yu , Yang Baolin , Peng Yong , Wang Kang L. , Zhao Weisheng
Published: May 2024

The chiral antiferromagnetic (AFM) materials, which have been widely investigated due to their rich physics, such as non-zero Berry phase and topology, provide a platform for the development of antiferromagnetic spintronics. Here, we find two distinctive anomalous Hall effect (AHE) contributions in the chiral AFM Mn3Pt, originating from a time-reversal symmetry breaking induced intrinsic mechanism and a skew scattering induced topological AHE due to an out-of-plane spin canting with respect to the Kagome plane. We propose a universal AHE scaling law to explain the AHE resistivity ($${{\rho }}_{AH}$$

ρ

A
H

) in this chiral magnet, with both a scalar spin chirality (SSC)-induced skew scattering topological AHE term, $${a}_{sk}$$

a

s
k

and non-collinear spin-texture induced intrinsic anomalous Hall term, $${{b}}_{{in}}$$

b

i
n

. We found that $${{{a}}}_{{{sk}}}$$

a

s
k

and $${{{b}}}_{{{in}}}$$

b

i
n

can be effectively modulated by the interfacial electron scattering, exhibiting a linear relation with the inverse film thickness. Moreover, the scaling law can explain the anomalous Hall effect in various chiral magnets and has far-reaching implications for chiral-based spintronics devices.
A sparse quantized hopfield network for online-continual memory
Authors: Alonso Nicholas , Krichmar Jeffrey L.
Published: May 2024

An important difference between brains and deep neural networks is the way they learn. Nervous systems learn online where a stream of noisy data points are presented in a non-independent, identically distributed way. Further, synaptic plasticity in the brain depends only on information local to synapses. Deep networks, on the other hand, typically use non-local learning algorithms and are trained in an offline, non-noisy, independent, identically distributed setting. Understanding how neural networks learn under the same constraints as the brain is an open problem for neuroscience and neuromorphic computing. A standard approach to this problem has yet to be established. In this paper, we propose that discrete graphical models that learn via an online maximum a posteriori learning algorithm could provide such an approach. We implement this kind of model in a neural network called the Sparse Quantized Hopfield Network. We show our model outperforms state-of-the-art neural networks on associative memory tasks, outperforms these networks in online, continual settings, learns efficiently with noisy inputs, and is better than baselines on an episodic memory task.
Synthetic intrinsically disordered protein fusion tags that enhance protein solubility
Authors: Tang Nicholas C. , Su Jonathan C. , Shmidov Yulia , Kelly Garrett , Deshpande Sonal , Sirohi Parul , Peterson Nikhil , Chilkoti Ashutosh
Published: May 2024

We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.
The environmental sustainability of digital content consumption
Authors: Istrate Robert , Tulus Victor , Grass Robert N. , Vanbever Laurent , Stark Wendelin J. , Guillén-Gosálbez Gonzalo
Published: May 2024

Internet access has reached 60% of the global population, with the average user spending over 40% of their waking life on the Internet, yet the environmental implications remain poorly understood. Here, we assess the environmental impacts of digital content consumption in relation to the Earth’s carrying capacity, finding that currently the global average consumption of web surfing, social media, video and music streaming, and video conferencing could account for approximately 40% of the per capita carbon budget consistent with limiting global warming to 1.5 °C, as well as around 55% of the per capita carrying capacity for mineral and metal resources use and over 10% for five other impact categories. Decarbonising electricity would substantially mitigate the climate impacts linked to Internet consumption, while the use of mineral and metal resources would remain of concern. A synergistic combination of rapid decarbonisation and additional measures aimed at reducing the use of fresh raw materials in electronic devices (e.g., lifetime extension) is paramount to prevent the growing Internet demand from exacerbating the pressure on the finite Earth’s carrying capacity.
Using genome and transcriptome data from African-ancestry female participants to identify putative breast cancer susceptibility genes
Authors: Ping Jie , Jia Guochong , Cai Qiuyin , Guo Xingyi , Tao Ran , Ambrosone Christine , Huo Dezheng , Ambs Stefan , Barnard Mollie E. , Chen Yu , Garcia-Closas Montserrat , Gu Jian , Hu Jennifer J. , John Esther M. , Li Christopher I. , Nathanson Katherine , Nemesure Barbara , Olopade Olufunmilayo I. , Pal Tuya , Press Michael F. , Sanderson Maureen , Sandler Dale P. , Yoshimatsu Toshio , Adejumo Prisca O. , Ahearn Thomas , Brewster Abenaa M. , Hennis Anselm J. M. , Makumbi Timothy , Ndom Paul , O’Brien Katie M. , Olshan Andrew F. , Oluwasanu Mojisola M. , Reid Sonya , Yao Song , Butler Ebonee N. , Huang Maosheng , Ntekim Atara , Li Bingshan , Troester Melissa A. , Palmer Julie R. , Haiman Christopher A. , Long Jirong , Zheng Wei
Published: May 2024

African-ancestry (AA) participants are underrepresented in genetics research. Here, we conducted a transcriptome-wide association study (TWAS) in AA female participants to identify putative breast cancer susceptibility genes. We built genetic models to predict levels of gene expression, exon junction, and 3′ UTR alternative polyadenylation using genomic and transcriptomic data generated in normal breast tissues from 150 AA participants and then used these models to perform association analyses using genomic data from 18,034 cases and 22,104 controls. At Bonferroni-corrected P < 0.05, we identified six genes associated with breast cancer risk, including four genes not previously reported (CTD-3080P12.3, EN1, LINC01956 and NUP210L). Most of these genes showed a stronger association with risk of estrogen-receptor (ER) negative or triple-negative than ER-positive breast cancer. We also replicated the associations with 29 genes reported in previous TWAS at P < 0.05 (one-sided), providing further support for an association of these genes with breast cancer risk. Our study sheds new light on the genetic basis of breast cancer and highlights the value of conducting research in AA populations.
Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls
Authors: Tsitkov Stanislav , Valentine Kelsey , Kozareva Velina , Donde Aneesh , Frank Aaron , Lei Susan ,   the Answer ALS Consortium, Workman Michael J. , Lim Ryan G. , Wu Jie , Wu Zhuoxing , Ornelas Loren , Panther Lindsay , Galvez Erick , Perez Daniel , Meepe Imara , Valencia Viviana , Gomez Emilda , Liu Chunyan , Moran Ruby , Pinedo Louis , Ho Richie , Kaye Julia A. , Thompson Terri , Shear Dillon , Baloh Robert , Banuelos Maria G. , Garcia Veronica , Holewenski Ronald , Karpov Oleg , Manalo Danica-Mae , Mandefro Berhan , Matlock Andrea , Pandey Rakhi , Sundararaman Niveda , Trost Hannah , Vaibhav Vineet , Venkatraman Vidya , Wang Oliver , Glass Jonathan D. , Jamil Arish , Amirani Naufa , Lima Leandro , Raja Krishna , Robinson Wesley , Thomas Reuben , Vertudes Edward , Wyman Stacia , Agurto Carla , Cecchi Guillermo , Norel Raquel , Ahmad Omar , Baxi Emily G. , Cerezo Aianna , Coyne Alyssa N. , Hayes Lindsey , Krakauer John W. , Maragakis Nicholas , Mosmiller Elizabeth , Roy Promit , Zeiler Steven , Adam Miriam , Albistami Noura , Ehrenberger Tobias , Huynh Nhan , New Connie , Lenail Alex , Li Jonathan , Patel-Murray Natasha Leanna , Raghav Yogindra , Ramamoorthy Divya , Im Egun , Sachs Karen , Wassie Brook T. , Berry James , Cudkowicz Merit E. , Farrar Alanna , Thrower Sara , Luppino Sarah , Pothier Lindsay , Sherman Alexander V. , Sinani Ervin , Vigneswaran Prasha , Yu Hong , Beavers Jay C. , Bellard Mary , Bruce Elizabeth , Ajroud-Driss Senda , Alibazoglu Deniz , Ben Joslin  , Harms Matthew B. , Heintzman Sarah , Kolb Stephen , Prina Carolyn , Heitzman Daragh , Morgan Todd , Miramontes Ricardo , Stocksdale Jennifer , Wang Keona , Jockel-Balsarotti Jennifer , Karanja Elizabeth , Markway Jesse , McCallum Molly , Miller Tim , Roggenbuck Jennifer , E. Van Eyk Jennifer , Finkbeiner Steve , Rothstein Jeffrey D. , Thompson Leslie M. , Sareen Dhruv , Svendsen Clive N. , Fraenkel Ernest
Published: May 2024

Amyotrophic Lateral Sclerosis (ALS), like many other neurodegenerative diseases, is highly heritable, but with only a small fraction of cases explained by monogenic disease alleles. To better understand sporadic ALS, we report epigenomic profiles, as measured by ATAC-seq, of motor neuron cultures derived from a diverse group of 380 ALS patients and 80 healthy controls. We find that chromatin accessibility is heavily influenced by sex, the iPSC cell type of origin, ancestry, and the inherent variance arising from sequencing. Once these covariates are corrected for, we are able to identify ALS-specific signals in the data. Additionally, we find that the ATAC-seq data is able to predict ALS disease progression rates with similar accuracy to methods based on biomarkers and clinical status. These results suggest that iPSC-derived motor neurons recapitulate important disease-relevant epigenomic changes.
Stereospecific syn-dihalogenations and regiodivergent syn-interhalogenation of alkenes via vicinal double electrophilic activation strategy
Authors: Moon Hyeon , Jung Jungi , Choi Jun-Ho , Chung Won-jin
Published: May 2024

Whereas the conventionalanti-dihalogenation of alkenes is a valuable synthetic tool with highly predictable stereospecificity, the restricted reaction mechanism makes it challenging to alter the diastereochemical course into the complementarysyn-dihalogenation process. Only a few notable achievements were made recently by inverting one of the stereocenters afteranti-addition using a carefully designed reagent system. Here, we report a conceptually distinctive strategy for the simultaneous double electrophilic activation of the two alkene carbons from the same side. Then, the resulting vicinal leaving groups can be displaced iteratively by nucleophilic halides to complete thesyn-dihalogenation. For this purpose, thianthrenium dication is employed, and all possible combinations of chlorine and bromine are added onto internal alkenes successfully, particularly resulting in thesyn-dibromination and the regiodivergentsyn-bromochlorination.
Circulating fatty acids and risk of hepatocellular carcinoma and chronic liver disease mortality in the UK Biobank
Authors: Liu Zhening , Huang Hangkai , Xie Jiarong , Xu Yingying , Xu Chengfu
Published: May 2024

Nuclear magnetic resonance (NMR)-based plasma fatty acids are objective biomarkers of many diseases. Herein, we aim to explore the associations of NMR-based plasma fatty acids with the risk of hepatocellular carcinoma (HCC) and chronic liver disease (CLD) mortality in 252,398 UK Biobank participants. Here we show plasma levels of n-3 poly-unsaturated fatty acids (PUFA) and n-6 PUFA are negatively associated with the risk of incident HCC [HRQ4vsQ1: 0.48 (95% CI: 0.33–0.69) and 0.48 (95% CI: 0.28–0.81), respectively] and CLD mortality [HRQ4vsQ1: 0.21 (95% CI: 0.13–0.33) and 0.15 (95% CI: 0.08–0.30), respectively], whereas plasma levels of saturated fatty acids are positively associated with these outcomes [HRQ4vsQ1: 3.55 (95% CI: 2.25–5.61) for HCC and 6.34 (95% CI: 3.68–10.92) for CLD mortality]. Furthermore, fibrosis stage significantly modifies the associations between PUFA and CLD mortality. This study contributes to the limited prospective evidence on the associations between plasma-specific fatty acids and end-stage liver outcomes.
Weyl spin-momentum locking in a chiral topological semimetal
Authors: Krieger Jonas A. , Stolz Samuel , Robredo Iñigo , Manna Kaustuv , McFarlane Emily C. , Date Mihir , Pal Banabir , Yang Jiabao , B. Guedes Eduardo , Dil J. Hugo , Polley Craig M. , Leandersson Mats , Shekhar Chandra , Borrmann Horst , Yang Qun , Lin Mao , Strocov Vladimir N. , Caputo Marco , Watson Matthew D. , Kim Timur K. , Cacho Cephise , Mazzola Federico , Fujii Jun , Vobornik Ivana , Parkin Stuart S. P. , Bradlyn Barry , Felser Claudia , Vergniory Maia G. , Schröter Niels B. M.
Published: May 2024

Spin-orbit coupling in noncentrosymmetric crystals leads to spin-momentum locking – a directional relationship between an electron’s spin angular momentum and its linear momentum. Isotropic orthogonal Rashba spin-momentum locking has been studied for decades, while its counterpart, isotropic parallel Weyl spin-momentum locking has remained elusive in experiments. Theory predicts that Weyl spin-momentum locking can only be realized in structurally chiral cubic crystals in the vicinity of Kramers-Weyl or multifold fermions. Here, we use spin- and angle-resolved photoemission spectroscopy to evidence Weyl spin-momentum locking of multifold fermions in the chiral topological semimetal PtGa. We find that the electron spin of the Fermi arc surface states is orthogonal to their Fermi surface contour for momenta close to the projection of the bulk multifold fermion at the Γ point, which is consistent with Weyl spin-momentum locking of the latter. The direct measurement of the bulk spin texture of the multifold fermion at the R point also displays Weyl spin-momentum locking. The discovery of Weyl spin-momentum locking may lead to energy-efficient memory devices and Josephson diodes based on chiral topological semimetals.
Response of treatment-naive brain metastases to stereotactic radiosurgery
Authors: Ene Chibawanye I. , Abi Faraj Christina , Beckham Thomas H. , Weinberg Jeffrey S. , Andersen Clark R. , Haider Ali S. , Rao Ganesh , Ferguson Sherise D. , Alvarez-Brenkenridge Christopher A. , Kim Betty Y. S. , Heimberger Amy B. , McCutcheon Ian E. , Prabhu Sujit S. , Wang Chenyang Michael , Ghia Amol J. , McGovern Susan L. , Chung Caroline , McAleer Mary Frances , Tom Martin C. , Perni Subha , Swanson Todd A. , Yeboa Debra N. , Briere Tina M. , Huse Jason T. , Fuller Gregory N. , Lang Frederick F. , Li Jing , Suki Dima , Sawaya Raymond E.
Published: May 2024

With improvements in survival for patients with metastatic cancer, long-term local control of brain metastases has become an increasingly important clinical priority. While consensus guidelines recommend surgery followed by stereotactic radiosurgery (SRS) for lesions >3 cm, smaller lesions (≤3 cm) treated with SRS alone elicit variable responses. To determine factors influencing this variable response to SRS, we analyzed outcomes of brain metastases ≤3 cm diameter in patients with no prior systemic therapy treated with frame-based single-fraction SRS. Following SRS, 259 out of 1733 (15%) treated lesions demonstrated MRI findings concerning for local treatment failure (LTF), of which 202 /1733 (12%) demonstrated LTF and 54/1733 (3%) had an adverse radiation effect. Multivariate analysis demonstrated tumor size (>1.5 cm) and melanoma histology were associated with higher LTF rates. Our results demonstrate that brain metastases ≤3 cm are not uniformly responsive to SRS and suggest that prospective studies to evaluate the effect of SRS alone or in combination with surgery on brain metastases ≤3 cm matched by tumor size and histology are warranted. These studies will help establish multi-disciplinary treatment guidelines that improve local control while minimizing radiation necrosis during treatment of brain metastasis ≤3 cm.
HPK1 citron homology domain regulates phosphorylation of SLP76 and modulates kinase domain interaction dynamics
Authors: Chitre Avantika S. , Wu Ping , Walters Benjamin T. , Wang Xiangdan , Bouyssou Alexandre , Du Xiangnan , Lehoux Isabelle , Fong Rina , Arata Alisa , Chan Joyce , Wang Die , Franke Yvonne , Grogan Jane L. , Mellman Ira , Comps-Agrar Laetitia , Wang Weiru
Published: May 2024

Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T-cell receptor signaling and as such is an attractive target for cancer immunotherapy. Although the role of the HPK1 kinase domain (KD) has been extensively characterized, the function of its citron homology domain (CHD) remains elusive. Through a combination of structural, biochemical, and mechanistic studies, we characterize the structure-function of CHD in relationship to KD. Crystallography and hydrogen-deuterium exchange mass spectrometry reveal that CHD adopts a seven-bladed β-propellor fold that binds to KD. Mutagenesis associated with binding and functional studies show a direct correlation between domain-domain interaction and negative regulation of kinase activity. We further demonstrate that the CHD provides stability to HPK1 protein in cells as well as contributes to the docking of its substrate SLP76. Altogether, this study highlights the importance of the CHD in the direct and indirect regulation of HPK1 function.
Arbitrary engineering of spatial caustics with 3D-printed metasurfaces
Authors: Zhou Xiaoyan , Wang Hongtao , Liu Shuxi , Wang Hao , Chan John You En , Pan Cheng-Feng , Zhao Daomu , Yang Joel K. W. , Qiu Cheng-Wei
Published: May 2024

Caustics occur in diverse physical systems, spanning the nano-scale in electron microscopy to astronomical-scale in gravitational lensing. As envelopes of rays, optical caustics result in sharp edges or extended networks. Caustics in structured light, characterized by complex-amplitude distributions, have innovated numerous applications including particle manipulation, high-resolution imaging techniques, and optical communication. However, these applications have encountered limitations due to a major challenge in engineering caustic fields with customizable propagation trajectories and in-plane intensity profiles. Here, we introduce the “compensation phase” via 3D-printed metasurfaces to shape caustic fields with curved trajectories in free space. The in-plane caustic patterns can be preserved or morphed from one structure to another during propagation. Large-scale fabrication of these metasurfaces is enabled by the fast-prototyping and cost-effective two-photon polymerization lithography. Our optical elements with the ultra-thin profile and sub-millimeter extension offer a compact solution to generating caustic structured light for beam shaping, high-resolution microscopy, and light-matter-interaction studies.
Endogenous clock-mediated regulation of intracellular oxygen dynamics is essential for diazotrophic growth of unicellular cyanobacteria
Authors: Bandyopadhyay Anindita , Sengupta Annesha , Elvitigala Thanura , Pakrasi Himadri B.
Published: May 2024

The discovery of nitrogen fixation in unicellular cyanobacteria provided the first clues for the existence of a circadian clock in prokaryotes. However, recalcitrance to genetic manipulation barred their use as model systems for deciphering the clock function. Here, we explore the circadian clock in the now genetically amenable Cyanothece 51142, a unicellular, nitrogen-fixing cyanobacterium. Unlike non-diazotrophic clock models, Cyanothece 51142 exhibits conspicuous self-sustained rhythms in various discernable phenotypes, offering a platform to directly study the effects of the clock on the physiology of an organism. Deletion of kaiA, an essential clock component in the cyanobacterial system, impacted the regulation of oxygen cycling and hindered nitrogenase activity. Our findings imply a role for the KaiA component of the clock in regulating the intracellular oxygen dynamics in unicellular diazotrophic cyanobacteria and suggest that its addition to the KaiBC clock was likely an adaptive strategy that ensured optimal nitrogen fixation as microbes evolved from an anaerobic to an aerobic atmosphere under nitrogen constraints.
Regulatory sequence-based discovery of anti-defense genes in archaeal viruses
Authors: Bhoobalan-Chitty Yuvaraj , Xu Shuanshuan , Martinez-Alvarez Laura , Karamycheva Svetlana , Makarova Kira S. , Koonin Eugene V. , Peng Xu
Published: May 2024

In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.
Selective production of methylindan and tetralin with xylose or hemicellulose
Authors: Zou Zhufan , Yu Zhenjie , Guan Weixiang , Liu Yanfang , Yao Yumin , Han Yang , Li Guangyi , Wang Aiqin , Cong Yu , Liang Xinmiao , Zhang Tao , Li Ning
Published: May 2024

Indan and tetralin are widely used as fuel additives and the intermediates in the manufacture of thermal-stable jet fuel, many chemicals, medicines, and shockproof agents for rubber industry. Herein, we disclose a two-step route to selectively produce 5-methyl-2,3-dihydro-1H-indene (abbreviated as methylindan) and tetralin with xylose or the hemicelluloses from agricultural or forestry waste. Firstly, cyclopentanone (CPO) was selectively formed with ~60% carbon yield by the direct hydrogenolysis of xylose or hemicelluloses on a non-noble bimetallic Cu-La/SBA-15 catalyst. Subsequently, methylindan and tetralin were selectively produced with CPO via a cascade self-aldol condensation/rearrangement/aromatization reaction catalyzed by a commercial H-ZSM-5 zeolite. When we used cyclohexanone (another lignocellulosic cycloketone) in the second step, the main product switched to dimethyltetralin. This work gives insights into the selective production of bicyclic aromatics with lignocellulose.
Globally occurring pelagiphage infections create ribosome-deprived cells
Authors: Brüwer Jan D. , Sidhu Chandni , Zhao Yanlin , Eich Andreas , Rößler Leonard , Orellana Luis H. , Fuchs Bernhard M.
Published: May 2024

Phages play an essential role in controlling bacterial populations. Those infecting Pelagibacterales (SAR11), the dominant bacteria in surface oceans, have been studied in silico and by cultivation attempts. However, little is known about the quantity of phage-infected cells in the environment. Using fluorescence in situ hybridization techniques, we here show pelagiphage-infected SAR11 cells across multiple global ecosystems and present evidence for tight community control of pelagiphages on the SAR11 hosts in a case study. Up to 19% of SAR11 cells were phage-infected during a phytoplankton bloom, coinciding with a ~90% reduction in SAR11 cell abundance within 5 days. Frequently, a fraction of the infected SAR11 cells were devoid of detectable ribosomes, which appear to be a yet undescribed possible stage during pelagiphage infection. We dubbed such cells zombies and propose, among other possible explanations, a mechanism in which ribosomal RNA is used as a resource for the synthesis of new phage genomes. On a global scale, we detected phage-infected SAR11 and zombie cells in the Atlantic, Pacific, and Southern Oceans. Our findings illuminate the important impact of pelagiphages on SAR11 populations and unveil the presence of ribosome-deprived zombie cells as part of the infection cycle.
Body-part specificity for learning of multiple prior distributions in human coincidence timing
Authors: Matsumura Yoshiki , Roach Neil W. , Heron James , Miyazaki Makoto
Published: May 2024

During timing tasks, the brain learns the statistical distribution of target intervals and integrates this prior knowledge with sensory inputs to optimise task performance. Daily events can have different temporal statistics (e.g., fastball/slowball in baseball batting), making it important to learn and retain multiple priors. However, the rules governing this process are not yet understood. Here, we demonstrate that the learning of multiple prior distributions in a coincidence timing task is characterised by body-part specificity. In our experiments, two prior distributions (short and long intervals) were imposed on participants. When using only one body part for timing responses, regardless of the priors, participants learned a single prior by generalising over the two distributions. However, when the two priors were assigned to different body parts, participants concurrently learned the two independent priors. Moreover, body-part specific prior acquisition was faster when the priors were assigned to anatomically distant body parts (e.g., hand/foot) than when they were assigned to close body parts (e.g., index/middle fingers). This suggests that the body-part specific learning of priors is organised according to somatotopy.
Predictability of B cell clonal persistence and immunosurveillance in breast cancer
Authors: Sammut Stephen-John , Galson Jacob D. , Minter Ralph , Sun Bo , Chin Suet-Feung , De Mattos-Arruda Leticia , Finch Donna K. , Schätzle Sebastian , Dias Jorge , Rueda Oscar M. , Seoane Joan , Osbourn Jane , Caldas Carlos , Bashford-Rogers Rachael J. M.
Published: May 2024

B cells and T cells are important components of the adaptive immune system and mediate anticancer immunity. The T cell landscape in cancer is well characterized, but the contribution of B cells to anticancer immunosurveillance is less well explored. Here we show an integrative analysis of the B cell and T cell receptor repertoire from individuals with metastatic breast cancer and individuals with early breast cancer during neoadjuvant therapy. Using immune receptor, RNA and whole-exome sequencing, we show that both B cell and T cell responses seem to coevolve with the metastatic cancer genomes and mirror tumor mutational and neoantigen architecture. B cell clones associated with metastatic immunosurveillance and temporal persistence were more expanded and distinct from site-specific clones. B cell clonal immunosurveillance and temporal persistence are predictable from the clonal structure, with higher-centrality B cell antigen receptors more likely to be detected across multiple metastases or across time. This predictability was generalizable across other immune-mediated disorders. This work lays a foundation for prioritizing antibody sequences for therapeutic targeting in cancer.
Mapping annual 10-m soybean cropland with spatiotemporal sample migration
Authors: Zhang Hongchi , Lou Zihang , Peng Dailiang , Zhang Bing , Luo Wang , Huang Jianxi , Zhang Xiaoyang , Yu Le , Wang Fumin , Huang Linsheng , Liu Guohua , Gao Shuang , Hu Jinkang , Yang Songlin , Cheng Enhui
Published: May 2024

China, as the world’s biggest soybean importer and fourth-largest producer, needs accurate mapping of its planting areas for global food supply stability. The challenge lies in gathering and collating ground survey data for different crops. We proposed a spatiotemporal migration method leveraging vegetation indices’ temporal characteristics. This method uses a feature space of six integrals from the crops’ phenological curves and a concavity-convexity index to distinguish soybean and non-soybean samples in cropland. Using a limited number of actual samples and our method, we extracted features from optical time-series images throughout the soybean growing season. The cloud and rain-affected data were supplemented with SAR data. We then used the random forest algorithm for classification. Consequently, we developed the 10-meter resolution ChinaSoybean10 maps for the ten primary soybean-producing provinces from 2019 to 2022. The map showed an overall accuracy of about 93%, aligning significantly with the statistical yearbook data, confirming its reliability. This research aids soybean growth monitoring, yield estimation, strategy development, resource management, and food scarcity mitigation, and promotes sustainable agriculture.
Exploration of the photothermal role of curcumin-loaded targeted carbon nanotubes as a potential therapy for melanoma cancer
Authors: Kargar Bahareh , Fazeli Mehdi , Sobhani Zahra , Hosseinzadeh Saeid , Solhjoo Aida , Akbarizadeh Amin Reza
Published: May 2024

In this research, the hydrophilic structure of multi-walled carbon nanotubes (MWCNTs) was modified by synthesizing polycitric acid (PCA) and attaching folic acid (FA) to create MWCNT–PCA–FA. This modified nanocomplex was utilized as a carrier for the lipophilic compound curcumin (Cur). Characterization techniques including TGA, TEM, and UV–visible spectrophotometry were used to analyze the nanocomplex. The mechanism of cancer cell death induced by MWCNT–PCA–FA was studied extensively using the MTT assay, colony formation analysis, cell cycle assessment via flow cytometry, and apoptosis studies. Furthermore, we assessed the antitumor efficacy of these targeted nanocomplexes following exposure to laser radiation. The results showed that the nanocomposites and free Cur had significant toxicity on melanoma cancer cells (B16F10 cells) while having minimal impact on normal cells (NHDF cells). This selectivity for cancerous cells demonstrates the potential of these compounds as therapeutic agents. Furthermore, MWCNT–PCA–FA/Cur showed superior cytotoxicity compared to free Cur alone. Colony formation studies confirmed these results. The researchers found that MWCNT–FA–PCA/Cur effectively induced programmed cell death. In photothermal analysis, MWCNT–PCA–FA/Cur combined with laser treatment achieved the highest mortality rate. These promising results suggest that this multifunctional therapeutic nanoplatform holds the potential for combination cancer therapies that utilize various established therapeutic methods.
The effects of probiotics supplementation on Helicobacter pylori standard treatment: an umbrella review of systematic reviews with meta-analyses
Authors: Yang Zihan , Zhou Yueyang , Han Ziying , He Kun , Zhang Yuelun , Wu Dong , Chen Hongda
Published: May 2024

Helicobacter pylori infection, a worldwide health issue, is typically treated with standard antibiotic therapies. However, these treatments often face resistance and non-compliance due to side effects. In this umbrella review, we aimed to comprehensively assess the impact of probiotics supplementation in different preparations on Helicobacter pylori standard treatment. We searched PubMed, Embase and Cochrane Central Register of Controlled Trials in the Cochrane Library from inception to June 1, 2023, to identify systematic reviews with meta-analyses that focused on eradication rates, total side effects and other outcomes of interest. The most comprehensive meta-analysis was selected for data extraction. AMSTAR 2 was used to assess quality of meta-analyses. Overall, 28 unique meta-analyses based on 534 RCTs were included. The results suggests that probiotics supplementation with pooled probiotic strains was significantly associated with improved eradication rates (RR 1.10, 95% CI 1.06–1.14) and reduced risk of total side effects (RR 0.54, 95% CI 0.42–0.70) compared with standard therapy alone. Single-strained or multi-strained preparation of probiotics supplementation showed similar results. Despite Bifidobacterium spp. showing the highest potential for eradication, the study quality was critically low for most meta-analyses, necessitating further high-quality research to explore the optimal probiotic strains or their combinations for Helicobacter pylori treatment.aq_start?>Kindly check and confirm the edit made in article title.
The fine line between automation and augmentation in website usability evaluation
Authors: Esposito Andrea , Desolda Giuseppe , Lanzilotti Rosa
Published: May 2024

Artificial Intelligence (AI) systems are becoming widespread in all aspects of society, bringing benefits to the whole economy. There is a growing understanding of the potential benefits and risks of this type of technology. While the benefits are more efficient decision processes and industrial productivity, the risks may include a potential progressive disengagement of human beings in crucial aspects of decision-making. In this respect, a new perspective is emerging that aims at reconsidering the centrality of human beings while reaping the benefits of AI systems to augment rather than replace professional skills: Human-Centred AI (HCAI) is a novel framework that posits that high levels of human control do not contradict high levels of computer automation. In this paper, we investigate the two antipodes, automation vs augmentation, in the context of website usability evaluation. Specifically, we have analyzed whether the level of automation provided by a tool for semi-automatic usability evaluation can support evaluators in identifying usability problems. Three different visualizations, each one corresponding to a different level of automation, ranging from a full-automation approach to an augmentation approach, were compared in an experimental study. We found that a fully automated approach could help evaluators detect a significant number of medium and high-severity usability problems, which are the most critical in a software system; however, it also emerged that it was possible to detect more low-severity usability problems using one of the augmented approaches proposed in this paper.
Heteroepitaxial GaAs thin-films on flexible, large-area, single-crystal-like substrates for wide-ranging optoelectronic applications
Authors: Radhakrishnan Gokul , Kim Kyunghoon , Droopad Ravi , Goyal Amit
Published: May 2024

Recent advances in semiconductor based electronic devices can be attributed to the technological demands of ever increasing, application specific markets. These rapidly evolving markets for devices such as displays, wireless communication, photovoltaics, medical devices, etc. are demanding electronic devices that are increasingly thinner, smaller, lighter and flexible. High-quality, III-V epitaxial thin-films deposited on single-crystal substrates have yielded extremely high-performance, but are extremely expensive and rigid. Here we demonstrate heteroepitaxial deposition of GaAs thin-films on large-grained, single-crystal-like, biaxially-aligned, flexible, metallic substrates. We use molecular beam epitaxy (MBE) for the controlled growth of high quality GaAs layers on lattice matched Ge capped, flexible metal substrates. The structural, optical, interfacial and electrical characteristics and properties of the heteroepitaxial GaAs layers are analyzed and discussed. The results show that heteroepitaxial GaAs layers with good crystalline and optoelectronic properties can be realized for flexible, III-V based semiconductor devices. III-V materials integrated on large-grained, single-crystal-like, flexible, metallic substrates offer a potential route towards fabrication of large-area, high-performance electronic devices.
Accelerating material property prediction using generically complete isometry invariants
Authors: Balasingham Jonathan , Zamaraev Viktor , Kurlin Vitaliy
Published: May 2024

Periodic material or crystal property prediction using machine learning has grown popular in recent years as it provides a computationally efficient replacement for classical simulation methods. A crucial first step for any of these algorithms is the representation used for a periodic crystal. While similar objects like molecules and proteins have a finite number of atoms and their representation can be built based upon a finite point cloud interpretation, periodic crystals are unbounded in size, making their representation more challenging. In the present work, we adapt the Pointwise Distance Distribution (PDD), a continuous and generically complete isometry invariant for periodic point sets, as a representation for our learning algorithm. The PDD distinguished all (more than 660 thousand) periodic crystals in the Cambridge Structural Database as purely periodic sets of points without atomic types. We develop a transformer model with a modified self-attention mechanism that combines PDD with compositional information via a spatial encoding method. This model is tested on the crystals of the Materials Project and Jarvis-DFT databases and shown to produce accuracy on par with state-of-the-art methods while being several times faster in both training and prediction time.
Combined effect of seasons and life history in an anuran strengthens the response and relationship between their physiology and gut microbiota
Authors: Park Jun-Kyu , Do Yuno
Published: May 2024

Gut microbiota impact host physiology, though simultaneous investigations in ectothermic vertebrates are rare. Particularly, amphibians may exhibit more complex interactions between host physiology and the effects of gut microbiota due to the combination of seasonal changes and complex life histories. In this study, we assessed the relationships among food resources, gut bacterial communities, and host physiology in frogs (Phelophylax nigromaculatus), taking into account seasonal and life history variations. We found that food sources were not correlated with physiological parameters but had some relationships with the gut bacterial community. Variations in gut bacterial community and host physiology were influenced by the combined effects of seasonal differences and life history, though mostly driven by seasonal differences. An increase in Firmicutes was associated with higher fat content, reflecting potential fat storage in frogs during the non-breeding season. The increase in Bacteroidetes resulted in lower fat content in adult frogs and decreased immunity in juvenile frogs during the breeding season, demonstrating a direct link. Our results suggest that the gut microbiome may act as a link between food conditions and physiological status, and that the combined effect of seasons and life history could reinforce the relationship between gut microbiota and physiological status in ectothermic animals. While food sources may influence the gut microbiota of ectotherms, we contend that temperature-correlated seasonal variation, which predominately influences most ectotherms, is a significant factor.
Cinnamaldehyde ameliorates STZ-induced diabetes through modulation of autophagic process in adipocyte and hepatic tissues on rats
Authors: Ghazal Nesma A. , Agamia Yara T. , Meky Basant K. , Assem Nagwa M. , Abdel-Rehim Wafaa M. , Shaker Sara A.
Published: May 2024

Type 2 diabetes mellitus is a worldwide public health issue. In the globe, Egypt has the ninth-highest incidence of diabetes. Due to its crucial role in preserving cellular homeostasis, the autophagy process has drawn a lot of attention in recent years, Therefore, the purpose of this study was to evaluate the traditional medication metformin with the novel therapeutic effects of cinnamondehyde on adipocyte and hepatic autophagy in a model of high-fat diet/streptozotocin-diabetic rats. The study was conducted on 40 male albino rats, classified into 2 main groups, the control group and the diabetic group, which was subdivided into 4 subgroups (8 rats each): untreated diabetic rats, diabetic rats received oral cinnamaldehyde 40 mg/kg/day, diabetic rats received oral metformin 200 mg/kg/day and diabetic rats received a combination of both cinnamaldehyde and metformin daily for 4 weeks. The outcomes demonstrated that cinnamaldehyde enhanced the lipid profile and glucose homeostasis. Moreover, Cinnamaldehyde had the opposite effects on autophagy in both tissues; by altering the expression of genes that control autophagy, such as miRNA 30a and mammalian target of rapamycin (mTOR), it reduced autophagy in adipocytes and stimulated it in hepatic tissues. It may be inferred that by increasing the treatment efficacy of metformin and lowering its side effects, cinnamaldehyde could be utilized as an adjuvant therapy with metformin for the treatment of type 2 diabetes.
Control strategy for current limitation and maximum capacity utilization of grid connected PV inverter under unbalanced grid conditions
Authors: Joshi Jyoti , Jately Vibhu , Kala Peeyush , Sharma Abhishek , Lim Wei Hong , Azzopardi Brian
Published: May 2024

Under grid voltage sags, over current protection and exploiting the maximum capacity of the inverter are the two main goals of grid-connected PV inverters. To facilitate low-voltage ride-through (LVRT), it is imperative to ensure that inverter currents are sinusoidal and remain within permissible limits throughout the inverter operation. An improved LVRT control strategy for a two-stage three-phase grid-connected PV system is presented here to address these challenges. To provide over current limitation as well as to ensure maximum exploitation of the inverter capacity, a control strategy is proposed, and performance the strategy is evaluated based on the three generation scenarios on a 2-kW grid connected PV system. An active power curtailment (APC) loop is activated only in high power generation scenario to limit the current’s amplitude below the inverter’s rated current. The superior performance of the proposed strategy is established by comparison with two recent LVRT control strategies. The proposed method not only injects necessary active and reactive power but also minimizes overcurrent with increased exploitation of the inverter’s capacity under unbalanced grid voltage sag.
Multiscale and multimodal imaging for three-dimensional vascular and histomorphological organ structure analysis of the pancreas
Authors: Salg Gabriel Alexander , Steinle Verena , Labode Jonas , Wagner Willi , Studier-Fischer Alexander , Reiser Johanna , Farjallah Elyes , Guettlein Michelle , Albers Jonas , Hilgenfeld Tim , Giese Nathalia A. , Stiller Wolfram , Nickel Felix , Loos Martin , Michalski Christoph W. , Kauczor Hans-Ulrich , Hackert Thilo , Dullin Christian , Mayer Philipp , Kenngott Hannes Goetz
Published: May 2024

Exocrine and endocrine pancreas are interconnected anatomically and functionally, with vasculature facilitating bidirectional communication. Our understanding of this network remains limited, largely due to two-dimensional histology and missing combination with three-dimensional imaging. In this study, a multiscale 3D-imaging process was used to analyze a porcine pancreas. Clinical computed tomography, digital volume tomography, micro-computed tomography and Synchrotron-based propagation-based imaging were applied consecutively. Fields of view correlated inversely with attainable resolution from a whole organism level down to capillary structures with a voxel edge length of 2.0 µm. Segmented vascular networks from 3D-imaging data were correlated with tissue sections stained by immunohistochemistry and revealed highly vascularized regions to be intra-islet capillaries of islets of Langerhans. Generated 3D-datasets allowed for three-dimensional qualitative and quantitative organ and vessel structure analysis. Beyond this study, the method shows potential for application across a wide range of patho-morphology analyses and might possibly provide microstructural blueprints for biotissue engineering.
Statistical downscaling of GRACE terrestrial water storage changes based on the Australian Water Outlook model
Authors: Kalu Ikechukwu , Ndehedehe Christopher E. , Ferreira Vagner G. , Janardhanan Sreekanth , Currell Matthew , Kennard Mark J.
Published: May 2024

The coarse spatial resolution of the Gravity Recovery and Climate Experiment (GRACE) dataset has limited its application in local water resource management and accounting. Despite efforts to improve GRACE spatial resolution, achieving high resolution downscaled grids that correspond to local hydrological behaviour and patterns is still limited. To overcome this issue, we propose a novel statistical downscaling approach to improve the spatial resolution of GRACE-terrestrial water storage changes (ΔTWS) using precipitation, evapotranspiration (ET), and runoff data from the Australian Water Outlook. These water budget components drive changes in the GRACE water column in much of the global land area. Here, the GRACE dataset is downscaled from the original resolution of 1.0° × 1.0° to 0.05° × 0.05° over a large hydro-geologic basin in northern Australia (the Cambrian Limestone Aquifer—CLA), capturing sub- grid heterogeneity in ΔTWS of the region. The downscaled results are validated using data from 12 in-situ groundwater monitoring stations and water budget estimates of the CLA’s land water storage changes from April 2002 to June 2017. The change in water storage over time (ds/dt) estimated from the water budget model was weakly correlated (r = 0.34) with the downscaled GRACE ΔTWS. The weak relationship was attributed to the possible uncertainties inherent in the ET datasets used in the water budget, particularly during the summer months. Our proposed methodology provides an opportunity to improve freshwater reporting using GRACE and enhances the feasibility of downscaling efforts for other hydrological data to strengthen local-scale applications.