bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractInternet 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

AbstractAfrican-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

AbstractAmyotrophic 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

AbstractWhereas 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

AbstractNuclear 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

AbstractSpin-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

AbstractWith 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

AbstractHematopoietic 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

AbstractCaustics 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

AbstractThe 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

AbstractIn 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

AbstractIndan 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

AbstractPhages 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

AbstractDuring 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

AbstractB 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.