bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD5L as a promising biological therapeutic for treating sepsis
Authors: Oliveira Liliana , Silva M. Carolina , Gomes Ana P. , Santos Rita F. , Cardoso Marcos S. , Nóvoa Ana , Luche Hervé , Cavadas Bruno , Amorim Irina , Gärtner Fátima , Malissen Bernard , Mallo Moisés , Carmo Alexandre M. 
Published: May 2024

AbstractSepsis results from systemic, dysregulated inflammatory responses to infection, culminating in multiple organ failure. Here, we demonstrate the utility of CD5L for treating experimental sepsis caused by cecal ligation and puncture (CLP). We show that CD5L’s important features include its ability to enhance neutrophil recruitment and activation by increasing circulating levels of CXCL1, and to promote neutrophil phagocytosis. CD5L-deficient mice exhibit impaired neutrophil recruitment and compromised bacterial control, rendering them susceptible to attenuated CLP. CD5L-/- peritoneal cells from mice subjected to medium-grade CLP exhibit a heightened pro-inflammatory transcriptional profile, reflecting a loss of control of the immune response to the infection. Intravenous administration of recombinant CD5L (rCD5L) in immunocompetent C57BL/6 wild-type (WT) mice significantly ameliorates measures of disease in the setting of high-grade CLP-induced sepsis. Furthermore, rCD5L lowers endotoxin and damage-associated molecular pattern (DAMP) levels, and protects WT mice from LPS-induced endotoxic shock. These findings warrant the investigation of rCD5L as a possible treatment for sepsis in humans.
Introduction of the difluoromethyl group at the meta- or para-position of pyridines through regioselectivity switch
Authors: Xu Pengwei , Wang Zhe , Guo Shu-Min , Studer Armido 
Published: May 2024

AbstractDifluoromethyl pyridines have gained significant attention in medicinal and agricultural chemistry. The direct C−H-difluoromethylation of pyridines represents a highly efficient economic way to access these azines. However, the direct meta-difluoromethylation of pyridines has remained elusive and methods for site-switchable regioselective meta- and para-difluoromethylation are unknown. Here, we demonstrate the meta-C−H-difluoromethylation of pyridines through a radical process by using oxazino pyridine intermediates, which are easily accessed from pyridines. The selectivity can be readily switched to para by in situ transformation of the oxazino pyridines to pyridinium salts upon acid treatment. The preparation of various meta- and para-difluoromethylated pyridines through this approach is presented. The mild conditions used also allow for the late-stage meta- or para-difluoromethylation of pyridine containing drugs. Sequential double functionalization of pyridines is presented, which further underlines the value of this work.
Carbon storage through China’s planted forest expansion
Authors: Cheng Kai , Yang Haitao , Tao Shengli , Su Yanjun , Guan Hongcan , Ren Yu , Hu Tianyu , Li Wenkai , Xu Guangcai , Chen Mengxi , Lu Xiancheng , Yang Zekun , Tang Yanhong , Ma Keping , Fang Jingyun , Guo Qinghua 
Published: May 2024

AbstractChina’s extensive planted forests play a crucial role in carbon storage, vital for climate change mitigation. However, the complex spatiotemporal dynamics of China’s planted forest area and its carbon storage remain uncaptured. Here we reveal such changes in China’s planted forests from 1990 to 2020 using satellite and field data. Results show a doubling of planted forest area, a trend that intensified post-2000. These changes lead to China’s planted forest carbon storage increasing from 675.6 ± 12.5 Tg C in 1990 to 1,873.1 ± 16.2 Tg C in 2020, with an average rate of ~ 40 Tg C yr−1. The area expansion of planted forests contributed ~ 53% (637.2 ± 5.4 Tg C) of the total above increased carbon storage in planted forests compared with planted forest growth. This proactive policy-driven expansion of planted forests has catalyzed a swift increase in carbon storage, aligning with China’s Carbon Neutrality Target for 2060.
TRIM25 predominately associates with anti-viral stress granules
Authors: Shang Zehua , Zhang Sitao , Wang Jinrui , Zhou Lili , Zhang Xinyue , Billadeau Daniel D. , Yang Peiguo , Zhang Lingqiang , Zhou Fangfang , Bai Peng , Jia Da 
Published: May 2024

AbstractStress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25’s ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
A renewably sourced, circular photopolymer resin for additive manufacturing
Authors: Machado Thiago O. , Stubbs Connor J. , Chiaradia Viviane , Alraddadi Maher A. , Brandolese Arianna , Worch Joshua C. , Dove Andrew P. 
Published: May 2024

AbstractThe additive manufacturing of photopolymer resins by means of vat photopolymerization enables the rapid fabrication of bespoke 3D-printed parts. Advances in methodology have continually improved resolution and manufacturing speed, yet both the process design and resin technology have remained largely consistent since its inception in the 1980s1. Liquid resin formulations, which are composed of reactive monomers and/or oligomers containing (meth)acrylates and epoxides, rapidly photopolymerize to create crosslinked polymer networks on exposure to a light stimulus in the presence of a photoinitiator2. These resin components are mostly obtained from petroleum feedstocks, although recent progress has been made through the derivatization of renewable biomass3–6 and the introduction of hydrolytically degradable bonds7–9. However, the resulting materials are still akin to conventional crosslinked rubbers and thermosets, thus limiting the recyclability of printed parts. At present, no existing photopolymer resin can be depolymerized and directly re-used in a circular, closed-loop pathway. Here we describe a photopolymer resin platform derived entirely from renewable lipoates that can be 3D-printed into high-resolution parts, efficiently deconstructed and subsequently reprinted in a circular manner. Previous inefficiencies with methods using internal dynamic covalent bonds10–17 to recycle and reprint 3D-printed photopolymers are resolved by exchanging conventional (meth)acrylates for dynamic cyclic disulfide species in lipoates. The lipoate resin platform is highly modular, whereby the composition and network architecture can be tuned to access printed materials with varied thermal and mechanical properties that are comparable to several commercial acrylic resins.
Physiological temperature drives TRPM4 ligand recognition and gating
Authors: Hu Jinhong , Park Sung Jin , Walter Tyler , Orozco Ian J. , O‘Dea Garrett , Ye Xinyu , Du Juan , Lü Wei 
Published: May 2024

AbstractTemperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity1,2. However, its impact is often overlooked in biophysical studies that are typically performed at non-physiological temperatures, potentially leading to inaccurate mechanistic and pharmacological insights. Here we demonstrate temperature-dependent changes in the structure and function of TRPM4, a temperature-sensitive Ca2+-activated ion channel3–7. By studying TRPM4 prepared at physiological temperature using single-particle cryo-electron microscopy, we identified a ‘warm’ conformation that is distinct from those observed at lower temperatures. This conformation is driven by a temperature-dependent Ca2+-binding site in the intracellular domain, and is essential for TRPM4 function in physiological contexts. We demonstrated that ligands, exemplified by decavanadate (a positive modulator)8 and ATP (an inhibitor)9, bind to different locations of TRPM4 at physiological temperatures than at lower temperatures10,11, and that these sites have bona fide functional relevance. We elucidated the TRPM4 gating mechanism by capturing structural snapshots of its different functional states at physiological temperatures, revealing the channel opening that is not observed at lower temperatures. Our study provides an example of temperature-dependent ligand recognition and modulation of an ion channel, underscoring the importance of studying macromolecules at physiological temperatures. It also provides a potential molecular framework for deciphering how thermosensitive TRPM channels perceive temperature changes.
A multi-institutional meningioma MRI dataset for automated multi-sequence image segmentation
Authors: LaBella Dominic , Khanna Omaditya , McBurney-Lin Shan , Mclean Ryan , Nedelec Pierre , Rashid Arif S. , Tahon Nourel hoda , Altes Talissa , Baid Ujjwal , Bhalerao Radhika , Dhemesh Yaseen , Floyd Scott , Godfrey Devon , Hilal Fathi , Janas Anastasia , Kazerooni Anahita , Kent Collin , Kirkpatrick John , Kofler Florian , Leu Kevin , Maleki Nazanin , Menze Bjoern , Pajot Maxence , Reitman Zachary J. , Rudie Jeffrey D. , Saluja Rachit , Velichko Yury , Wang Chunhao , Warman Pranav I. , Sollmann Nico , Diffley David , Nandolia Khanak K. , Warren Daniel I , Hussain Ali , Fehringer John Pascal , Bronstein Yulia , Deptula Lisa , Stein Evan G. , Taherzadeh Mahsa , Portela de Oliveira Eduardo , Haughey Aoife , Kontzialis Marinos , Saba Luca , Turner Benjamin , Brüßeler Melanie M. T. , Ansari Shehbaz , Gkampenis Athanasios , Weiss David Maximilian , Mansour Aya , Shawali Islam H. , Yordanov Nikolay , Stein Joel M. , Hourani Roula , Moshebah Mohammed Yahya , Abouelatta Ahmed Magdy , Rizvi Tanvir , Willms Klara , Martin Dann C. , Okar Abdullah , D’Anna Gennaro , Taha Ahmed , Sharifi Yasaman , Faghani Shahriar , Kite Dominic , Pinho Marco , Haider Muhammad Ammar , Alonso-Basanta Michelle , Villanueva-Meyer Javier , Rauschecker Andreas M. , Nada Ayman , Aboian Mariam , Flanders Adam , Bakas Spyridon , Calabrese Evan 
Published: May 2024

AbstractMeningiomas are the most common primary intracranial tumors and can be associated with significant morbidity and mortality. Radiologists, neurosurgeons, neuro-oncologists, and radiation oncologists rely on brain MRI for diagnosis, treatment planning, and longitudinal treatment monitoring. However, automated, objective, and quantitative tools for non-invasive assessment of meningiomas on multi-sequence MR images are not available. Here we present the BraTS Pre-operative Meningioma Dataset, as the largest multi-institutional expert annotated multilabel meningioma multi-sequence MR image dataset to date. This dataset includes 1,141 multi-sequence MR images from six sites, each with four structural MRI sequences (T2-, T2/FLAIR-, pre-contrast T1-, and post-contrast T1-weighted) accompanied by expert manually refined segmentations of three distinct meningioma sub-compartments: enhancing tumor, non-enhancing tumor, and surrounding non-enhancing T2/FLAIR hyperintensity. Basic demographic data are provided including age at time of initial imaging, sex, and CNS WHO grade. The goal of releasing this dataset is to facilitate the development of automated computational methods for meningioma segmentation and expedite their incorporation into clinical practice, ultimately targeting improvement in the care of meningioma patients.
Comparison of δ13C and δ15N of ecologically relevant amino acids among beluga whale tissues
Authors: Matthews Cory J. D. , Smith Emma A. Elliott , Ferguson Steven H. 
Published: May 2024

AbstractEcological applications of compound-specific stable isotope analysis (CSIA) of amino acids (AAs) include 1) tracking carbon pathways in food webs using essential AA (AAESS) δ13C values, and 2) estimating consumer trophic position (TP) by comparing relative differences of ‘trophic’ and ‘source’ AA δ15N values. Despite the significance of these applications, few studies have examined AA-specific SI patterns among tissues with different AA compositions and metabolism/turnover rates, which could cause differential drawdown of body AA pools and impart tissue-specific isotopic fractionation. To address this knowledge gap, especially in the absence of controlled diet studies examining this issue in captive marine mammals, we used a paired-sample design to compare δ13C and δ15N values of 11 AAs in commonly sampled tissues (skin, muscle, and dentine) from wild beluga whales (Delphinapterus leucas). δ13C of two AAs, glutamic acid/glutamine (Glx, a non-essential AA) and, notably, threonine (an essential AA), differed between skin and muscle. Furthermore, δ15N of three AAs (alanine, glycine, and proline) differed significantly among the three tissues, with glycine δ15N differences of approximately 10 ‰ among tissues supporting recent findings it is unsuitable as a source AA. Significant δ15N differences in AAs such as proline, a trophic AA used as an alternative to Glx in TP estimation, highlight tissue selection as a potential source of error in ecological applications of CSIA-AA. Amino acids that differed among tissues play key roles in metabolic pathways (e.g., ketogenic and gluconeogenic AAs), pointing to potential physiological applications of CSIA-AA in studies of free-ranging animals. These findings underscore the complexity of isotopic dynamics within tissues and emphasize the need for a nuanced approach when applying CSIA-AA in ecological research.
Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis
Authors: Farooq Saba , Faiz Sirmast , Wahab Atia-tul , Choudhary M. Iqbal 
Published: May 2024

AbstractHepatitis is a major public health issue, affecting 10–17 million people worldwide, with its prevalence continuously increasing. The Hepatitis C virus (HCV) is responsible for liver related diseases, which include liver cirrhosis, hepatocellular carcinoma, and chronic hepatitis. Pakistan is experiencing a serious rise in HCV cases. This study aimed to assess the prevalence and distribution of HCV genotypes in Sindh, Pakistan. Serum samples from HCV-positive patients were collected from various local hospitals in Sindh. These samples were first screened for HCV antibodies using ELISA. Samples that tested positive for HCV RNA underwent further genotyping through sequencing using the standard Sanger method. The genotypes were identified by comparing the sequences with those available in the National Center for Biotechnology Information (NCBI) database, and a phylogenetic tree was constructed. The phylogenetic analysis showed that all isolates in this study were clustered with genotypes 3a and 3b, except for one sequence that was clustered with genotype 1a. No isolates were found to be clustered with reference genomes of genotypes 2, 4, 5, 6, and 7 suggesting that genotype 3a is endemic in this region. The analyzed sequences demonstrated a 98% similarity with reference and isolated sequences. In summary, sequencing of the HCV 5′ UTR essential for identifying the predominant genotype of HCV RNA in the Sindh region Further research on the distribution of HCV genotypes in other regions of Pakistan could aid in improving screening processes, identifying more effective treatment options, and developing suitable prevention strategies.
Assessing internal displacement patterns in Ukraine during the beginning of the Russian invasion in 2022
Authors: Shibuya Yuya , Jones Nicholas , Sekimoto Yoshihide 
Published: May 2024

AbstractGiven the worldwide increase of forcibly displaced populations, particularly internally displaced persons (IDPs), it’s crucial to have an up-to-date and precise tracking framework for population movements. Here, we study how the spatial and temporal pattern of a large-scale internal population movement can be monitored using human mobility datasets by exploring the case of IDPs in Ukraine at the beginning of the Russian invasion of 2022. Specifically, this study examines the sizes and travel distances of internal displacements based on GPS human mobility data, using the combinations of mobility pattern estimation methods such as truncated power law fitting and visualizing the results for humanitarian operations. Our analysis reveals that, although the city of Kyiv started to lose its population around 5 weeks before the invasion, a significant drop happened in the second week of the invasion (4.3 times larger than the size of the population lost in 5 weeks before the invasion), and the population coming to the city increased again from the third week of the invasion, indicating that displaced people started to back to their homes. Meanwhile, adjacent southern areas of Kyiv and the areas close to the western borders experienced many migrants from the first week of the invasion and from the second to third weeks of the invasion, respectively. In addition, people from relatively higher-wealth areas tended to relocate their home locations far away from their original locations compared to those from other areas. For example, 19 % of people who originally lived in higher wealth areas in the North region, including the city of Kyiv, moved their home location more than 500 km, while only 9 % of those who originally lived in lower wealth areas in the North region moved their home location more than 500 km.
Enhancing cardiovascular risk prediction through AI-enabled calcium-omics
Authors: Hoori Ammar , Al-Kindi Sadeer , Hu Tao , Song Yingnan , Wu Hao , Lee Juhwan , Tashtish Nour , Fu Pingfu , Gilkeson Robert , Rajagopalan Sanjay , Wilson David L. 
Published: May 2024

AbstractWhole-heart coronary calcium Agatston score is a well-established predictor of major adverse cardiovascular events (MACE), but it does not account for individual calcification features related to the pathophysiology of the disease (e.g., multiple-vessel disease, spread of the disease along the vessel, stable calcifications, numbers of lesions, and density). We used novel, hand-crafted calcification features (calcium-omics); Cox time-to-event modeling; elastic net; and up and down synthetic sampling methods for imbalanced data, to assess MACE risk. We used 2457 CT calcium score (CTCS) images enriched for MACE events from our large no-cost CLARIFY program (ClinicalTrials.gov Identifier: NCT04075162). Among calcium-omics features, numbers of calcifications, LAD mass, and diffusivity (a measure of spatial distribution) were especially important determinants of increased risk, with dense calcification (> 1000HU, stable calcifications) associated with reduced risk Our calcium-omics model with (training/testing, 80/20) gave C-index (80.5%/71.6%) and 2-year AUC (82.4%/74.8%). Although the C-index is notoriously impervious to model improvements, calcium-omics compared favorably to Agatston and gave a significant difference (P < 0.001). The calcium-omics model identified 73.5% of MACE cases in the high-risk group, a 13.2% improvement as compared to Agatston, suggesting that calcium-omics could be used to better identity candidates for intensive follow-up and therapies. The categorical net-reclassification index was NRI = 0.153. Our findings from this exploratory study suggest the utility of calcium-omics in improved risk prediction. These promising results will pave the way for more extensive, multi-institutional studies of calcium-omics.
Lissajous curves as aerial search patterns
Authors: Steckenrider J. Josiah , Miller Mitchell , Blankenship Rory , Trujillo Victor , Bluman James 
Published: May 2024

AbstractManned and unmanned systems are prevalent in a wide range of aerial searching applications. For aircraft whose trajectory is not or cannot be planned on-the-fly, optimal deterministic search pattern generation is a critical area of research. Lissajous curves have recently caught attention as excellent candidates for all kinds of aerial search applications, but little fundamental research has been done to understand how best to design Lissajous pattern (LP)s for this use. This paper examines the optimization of these search patterns from analytical, numerical, and data-driven perspectives to establish the state of the field in Lissajous curves for aerial search. From an analytical perspective, it was found that the average expected distance between a Lissajous searcher and a random target on a unit square approaches 0.586 as search time increases. Furthermore, an analytical approximation for the average searcher speed was found to guarantee error of no more than 22.1%. Important outcomes from the numerical optimization of Lissajous search patterns include the development of an intuitive evaluation criterion and the conclusion that irrational frequency ratios near 0.8 typically yield highest performance. Finally, while a robust predictive model for fast pattern optimization is yet out of reach, initial results indicate that such an approach shows promise.
New alternatives to the Lennard-Jones potential
Authors: Moscato Pablo , Haque Mohammad Nazmul 
Published: May 2024

AbstractWe present a new method for approximating two-body interatomic potentials from existing ab initio data based on representing the unknown function as an analytic continued fraction. In this study, our method was first inspired by a representation of the unknown potential as a Dirichlet polynomial, i.e., the partial sum of some terms of a Dirichlet series. Our method allows for a close and computationally efficient approximation of the ab initio data for the noble gases Xenon (Xe), Krypton (Kr), Argon (Ar), and Neon (Ne), which are proportional to $$r^{-6}$$

r

-
6

and to a very simple $$depth=1$$

d
e
p
t
h
=
1

truncated continued fraction with integer coefficients and depending on $$n^{-r}$$

n

-
r

only, where n is a natural number (with $$n=13$$

n
=
13

for Xe, $$n=16$$

n
=
16

for Kr, $$n=17$$

n
=
17

for Ar, and $$n=27$$

n
=
27

for Neon). For Helium (He), the data is well approximated with a function having only one variable $$n^{-r}$$

n

-
r

with $$n=31$$

n
=
31

and a truncated continued fraction with $$depth=2$$

d
e
p
t
h
=
2

(i.e., the third convergent of the expansion). Also, for He, we have found an interesting $$depth=0$$

d
e
p
t
h
=
0

result, a Dirichlet polynomial of the form $$k_1 \, 6^{-r} + k_2 \, 48^{-r} + k_3 \, 72^{-r}$$

k
1

6

-
r

+

k
2

48

-
r

+

k
3

72

-
r

(with $$k_1, k_2, k_3$$

k
1

,

k
2

,

k
3

all integers), which provides a surprisingly good fit, not only in the attractive but also in the repulsive region. We also discuss lessons learned while facing the surprisingly challenging non-linear optimisation tasks in fitting these approximations and opportunities for parallelisation.