bluuebunny/crossref_metadata_2025_split huggingface dataset:
An introduction to geological mapping of our world and others
Authors: Butler Robert W. H. , Torvela Taija , Williams Lucy 
Published: January 2024

Abstract
Map-making is a fundamental tool for developing geological knowledge. It involves data collection and interpretation and has its roots in the earliest discoveries in Earth Sciences. It is the starting point for stratigraphic and structural interpretations, metamorphic facies, geochronology and modelling studies – and underpins civil engineering. From the beginning, geological mapping rapidly evolved into far more than being a simple spatial catalogue of observable rock types and landforms on the Earth's land-surface; deductive reasoning allowing this knowledge to infer subsurface Earth structure. The same approaches are down-scaled to deduce processes on the grain-scale; or up-scaled to look out to extra-terrestrial objects. This is an introduction to fourteen papers in this Special Publication that celebrates geological mapping, its historical importance and future directions, and its use in applied geology together with developing knowledge of Earth and planetary evolution and processes. Geological mapping has a long tradition of adopting evolving technologies. This introduction considers the challenges faced in synthesizing interpretations, sharing competing interpretations on maps and the role of open-access digital resources in facing these challenges.
Cretaceous fossil birds from China
Authors: Zhou Zhonghe , Wang Min 
Published: January 2024

Abstract
The explosive radiation of early birds has been well documented by the extraordinary discoveries of the Early Cretaceous fossil birds in China in the past three decades. They have greatly expanded the diversity, disparity and temporal distribution of Mesozoic birds, refining our knowledge of the evolutionary path leading to the characteristic avian body plan, including feathers and powered flight, locomotion and habitat differentiation, diet and digestion, reproduction and development, feather colours and display. In addition, studies on the geological background of the Jehol Biota that produced the majority of the Chinese Cretaceous birds have provided important clues to our understanding of the taphonomy as well as the interaction between deep geological process and biological evolution in northeastern China and East Asia during the Early Cretaceous. Future multidisciplinary studies are expected to advance our knowledge of the palaeogeography of Early Cretaceous birds, what impacted the changes in the diversity of early birds in China, and the roles that early birds played in the Early Cretaceous terrestrial ecosystem.
Siberian Jehol Biota
Authors: Bugdaeva Eugenia V. , Golovneva Lina B. 
Published: January 2024

Abstract

Volcanogenic-sedimentary and coal-bearing deposits, which contain abundant fossils of a lacustrine fauna and terrestrial flora, are widespread in the territory of Transbaikalia (Russia), Mongolia and Northeastern China. These ecosystems are known under the name ‘Jehol Biota’, which occurs in the Yixian and Jiufotang formations. The discovery of ‘feathered’ dinosaurs and of the earliest angiosperms in western Liaoning Province (China) made them world famous. The history of this biota began in the nineteenth century, when the discoveries in Transbaikalia of the remains of conchostracans, ostracods, insects, fish and plants collected during the expedition of A.F. Middendorf were described. The Barremian–Aptian sedimentary sequences of Transbaikalia (Russia), Mongolia and Northeastern China are very similar. The appearance and evolution of the Jehol Biota occurred against the background of extensive volcanism and tectonic revival, after which normal sedimentary rocks were deposited, culminating in relief peneplanation, swamp development and peat formation. The northern limit of the distribution of this biota is determined to be up to
c.
54° modern north latitude. The existence of the Siberian Jehol Biota in extreme climatic conditions is confirmed, as was indicated for the Jehol Biota from NE China.
Sublithospheric Diamonds: Plate Tectonics from Earth's Deepest Mantle Samples
Authors: Shirey Steven B. , Pearson D. Graham , Stachel Thomas , Walter Michael J. 
Published: January 2024

Sublithospheric diamonds and the inclusions they may carry crystallize in the asthenosphere, transition zone, or uppermost lower mantle (from 300 to ∼800 km), and are the deepest minerals so far recognized to form by plate tectonics. These diamonds are distinctive in their deformation features, low nitrogen content, and inclusions of these major mantle minerals: majoritic garnet, clinopyroxene, ringwoodite, CaSi perovskite, ferropericlase, and bridgmanite or their retrograde equivalents. The stable isotopic compositions of elements within these diamonds (δ11B, δ13C, δ15N) and their inclusions (δ18O, δ56Fe) are typically well outside normal mantle ranges, showing that these elements were either organic (C) or modified by seawater alteration (B, O, Fe) at relatively low temperatures. Metamorphic minerals in cold slabs are effective hosts that transport C as CO3 and H as H2O, OH, or CH4 below the island arc and mantle wedge. Warming of the slab generates carbonatitic melts, supercritical aqueous fluids, or metallic liquids, forming three types of sublithospheric diamonds. Diamond crystallization occurs by movement and reduction of mobile fluids as they pass through host mantle via fractures—a process that creates chemical heterogeneity and may promote deep focus earthquakes. Geobarometry of majoritic garnet inclusions and diamond ages suggest upward transport, perhaps to the base of mantle lithosphere. From there, diamonds are carried to Earth's surface by eruptions of kimberlite magma. Mineral assemblages in sublithospheric diamonds directly trace Earth's deep volatile cycle, demonstrating how the hydrosphere of a rocky planet can connect to its solid interior.
▪Sublithospheric diamonds from the deep upper mantle, transition zone, and lower mantle host Earth's deepest obtainable mineral samples.▪Low-temperature seawater alteration of the ocean floor captures organic and inorganic carbon at the surface eventually to become some of the most precious gem diamonds.▪Subduction transports fluids in metamorphic minerals to great depth. Fluids released by slab heating migrate, react with host mantle to induce diamond crystallization, and may trigger earthquakes.▪Sublithospheric diamonds are powerful tracers of subduction—a plate tectonic process that deeply recycles part of Earth's planetary volatile budget.
Intranasal administration of sugarcane ash causes chronic kidney disease in rats
Authors: Roncal-Jimenez Carlos A. , Rogers Keegan L. , Stem Arthur , Wijkstrom Julia , Wernerson Annika , Fox Jacob , Garcia Trabanino Ramon , Brindley Stephen , Garcia Gabriela , Miyazaki Makoto , Miyazaki-Anzai Shinobu , Sasai Fumihiko , Urra Manuel , Cara-Fuentes Gabriel , Sánchez-Lozada L. Gabriela , Rodriguez-Iturbe Bernardo , Butler Dawson Jaime , Madero Magdalena , Brown Jared M. , Johnson Richard J. 
Published: January 2024

Silica nanoparticles found in sugarcane ash have been postulated to be a toxicant contributing to chronic kidney disease (CKD) of unknown etiology. However, although the administration of manufactured silica nanoparticles is known to cause chronic tubulointerstitial disease in rats, the effect of administering sugarcane ash on kidney pathology remains unknown. Here, we investigated whether sugarcane ash can induce CKD in rats. Sugarcane ash was administered for 13 wk into the nares of rats (5 mg/day for 5 days/wk), and blood, urine, and kidney tissues were collected at 13 wk (at the end of ash administration) and in a separate group of rats at 24 wk (11 wk after ash administration was stopped). Kidney histology was evaluated, and inflammation and fibrosis (collagen deposition) were measured. Sugarcane ash exposure led to the accumulation of silica in the kidneys, lungs, liver, and spleen of rats. Mild proteinuria developed, although renal function was largely maintained. However, biopsies showed focal glomeruli with segmental glomerulosclerosis as well as tubulointerstitial inflammation and fibrosis that tended to worsen even after the ash administration had been stopped. Staining for the lysosomal marker lysosomal associated membrane protein-1 showed decreased staining in ash-administered rats consistent with lysosomal activation. In conclusion, sugarcane ash containing silica nanoparticles can cause CKD in rats. NEW & NEWSWORTHY Epidemics of chronic kidney disease of unknown etiology have been reported in many areas of the world. In Central America, it occurs most commonly in sugarcane workers. Although heat stress is a major risk factor, there is some evidence that there may be a toxin. Here we show that sugarcane ash containing silica nanoparticles can induce chronic kidney disease in rats with similar features as observed in humans.
Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft-tissue Sarcomas: Clinical Outcomes and Biological Correlates
Authors: Haddox Candace L. , Nathenson Michael J. , Mazzola Emanuele , Lin Jia-Ren , Baginska Joanna , Nau Allison , Weirather Jason L. , Choy Edwin , Marino-Enriquez Adrian , Morgan Jeffrey A. , Cote Gregory M. , Merriam Priscilla , Wagner Andrew J. , Sorger Peter K. , Santagata Sandro , George Suzanne 
Published: January 2024

Abstract

Purpose:
Eribulin modulates the tumor-immune microenvironment via cGAS-STING signaling in preclinical models. This non-randomized phase II trial evaluated the combination of eribulin and pembrolizumab in patients with soft-tissue sarcomas (STS).

Patients and Methods:
Patients enrolled in one of three cohorts: leiomyosarcoma (LMS), liposarcomas (LPS), or other STS that may benefit from PD-1 inhibitors, including undifferentiated pleomorphic sarcoma (UPS). Eribulin was administered at 1.4 mg/m2 i.v. (days 1 and 8) with fixed-dose pembrolizumab 200 mg i.v. (day 1) of each 21-day cycle, until progression, unacceptable toxicity, or completion of 2 years of treatment. The primary endpoint was the 12-week progression-free survival rate (PFS-12) in each cohort. Secondary endpoints included the objective response rate, median PFS, safety profile, and overall survival (OS). Pretreatment and on-treatment blood specimens were evaluated in patients who achieved durable disease control (DDC) or progression within 12 weeks [early progression (EP)]. Multiplexed immunofluorescence was performed on archival LPS samples from patients with DDC or EP.

Results:
Fifty-seven patients enrolled (LMS, n = 19; LPS, n = 20; UPS/Other, n = 18). The PFS-12 was 36.8% (90% confidence interval: 22.5–60.4) for LMS, 69.6% (54.5–89.0) for LPS, and 52.6% (36.8–75.3) for UPS/Other cohorts. All 3 patients in the UPS/Other cohort with angiosarcoma achieved RECIST responses. Toxicity was manageable. Higher IFNα and IL4 serum levels were associated with clinical benefit. Immune aggregates expressing PD-1 and PD-L1 were observed in a patient that completed 2 years of treatment.

Conclusions:
The combination of eribulin and pembrolizumab demonstrated promising activity in LPS and angiosarcoma.
Simvastatin Overcomes Resistance to Tyrosine Kinase Inhibitors in Patient-derived, Oncogene-driven Lung Adenocarcinoma Models
Authors: Ma Weijie , Wei Sixi , Li Qianping , Zeng Jie , Xiao Wenwu , Zhou Chihong , Yoneda Ken Y. , Zeki Amir A. , Li Tianhong 
Published: January 2024

Abstract
There is an unmet clinical need to develop novel strategies to overcome resistance to tyrosine kinase inhibitors (TKI) in patients with oncogene-driven lung adenocarcinoma (LUAD). The objective of this study was to determine whether simvastatin could overcome TKI resistance using the in vitro and in vivo LUAD models. Human LUAD cell lines, tumor cells, and patient-derived xenograft (PDX) models from TKI-resistant LUAD were treated with simvastatin, either alone or in combination with a matched TKI. Tumor growth inhibition was measured by the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay and expression of molecular targets was assessed by immunoblots. Tumors were assessed by histopathology, IHC stain, immunoblots, and RNA sequencing. We found that simvastatin had a potent antitumor effect in tested LUAD cell lines and PDX tumors, regardless of tumor genotypes. Simvastatin and TKI combination did not have antagonistic cytotoxicity in these LUAD models. In an osimertinib-resistant LUAD PDX model, simvastatin and osimertinib combination resulted in a greater reduction in tumor volume than simvastatin alone (P &lt; 0.001). Immunoblots and IHC stain also confirmed that simvastatin inhibited TKI targets. In addition to inhibiting 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase, RNA sequencing and Western blots identified the proliferation, migration, and invasion-related genes (such as PI3K/Akt/mTOR, YAP/TAZ, focal adhesion, extracellular matrix receptor), proteasome-related genes, and integrin (α3β1, αvβ3) signaling pathways as the significantly downregulated targets in these PDX tumors treated with simvastatin and a TKI. The addition of simvastatin is a safe approach to overcome acquired resistance to TKIs in several oncogene-driven LUAD models, which deserve further investigation.
miR-217 Regulates Normal and Tumor Cell Fate Following Induction of Endoplasmic Reticulum Stress
Authors: Dey Neekkan , Koumenis Costas , Ruggero Davide , Fuchs Serge Y. , Diehl J. Alan 
Published: January 2024

Abstract

Rapidly proliferating cancer cells require a microenvironment where essential metabolic nutrients like glucose, oxygen, and growth factors become scarce as the tumor volume surpasses the established vascular capacity of the tissue. Limits in nutrient availability typically trigger growth arrest and/or apoptosis to prevent cellular expansion. However, tumor cells frequently co-opt cellular survival pathways thereby favoring cell survival under this environmental stress. The unfolded protein response (UPR) pathway is typically engaged by tumor cells to favor adaptation to stress. PERK, an endoplasmic reticulum (ER) protein kinase and UPR effector is activated in tumor cells and contributes tumor cell adaptation by limiting protein translation and balancing redox stress. PERK also induces miRNAs that contribute to tumor adaptation. miR-211 and miR-216b were previously identified as PERK-ATF4–regulated miRNAs that regulate cell survival. We have identified another PERK-responsive miRNA, miR-217, with increased expression under prolonged ER stress. Key targets of miR-217 are identified as TRPM1, the host gene for miR-211 and EZH2. Evidence is provided that miR-217 expression is essential for the rapid loss of miR-211 in prolonged ER stress and provides a functional link for determining whether cells adapt to stress or commit to apoptosis.

Implications:
PERK-dependent induction of miR-217 limits accumulation and function of the prosurvival miRNA, miR-211, to establish cell fate and promote cell commitment to apoptosis.
Implications of Mitral Annular Calcification on Outcomes Following Mitral Transcatheter Edge-to-Edge Repair
Authors: Shechter Alon , Lee Mirae , Kaewkes Danon , Patel Vivek , Koren Ofir , Chakravarty Tarun , Koseki Keita , Nagasaka Takashi , Skaf Sabah , Makar Moody , Makkar Raj R. , Siegel Robert J. 
Published: January 2024

BACKGROUND:
Limited data exist regarding the impact of mitral annular calcification (MAC) on outcomes of transcatheter edge-to-edge repair for mitral regurgitation (MR).

METHODS:
We retrospectively analyzed 968 individuals (median age, 79 [interquartile range, 70–86] years; 60.0% males; 51.8% with functional MR) who underwent an isolated, first-time intervention. Stratified by MAC extent per baseline transthoracic echocardiogram, the cohort was assessed for residual MR, functional status, all-cause mortality, heart failure hospitalizations, and mitral reinterventions post-procedure.

RESULTS:

Patients with above-mild MAC (n=101; 10.4%) were older and more likely to be female, exhibited a greater burden of comorbidities, and presented more often with severe, primary MR. Procedural aspects and technical success rate were unaffected by MAC magnitude, as was the significant improvement from baseline in MR severity and functional status along the first postprocedural year. However, the persistence of above-moderate MR or functional classes III and IV at 1 year and the cumulative incidence of reinterventions at 2 years were overall more pronounced within the above-mild MAC group (significant MR or functional impairment, 44.7% versus 29.9%,
P
=0.060; reinterventions, 11.9% versus 6.2%,
P
=0.033; log-rank
P
=0.035). No link was demonstrated between MAC degree and the cumulative incidence or risk of mortality and mortality or heart failure hospitalizations. Differences in outcomes frequencies were mostly confined to the primary MR subgroup, in which patients with above-mild MAC also experienced earlier, more frequent 2-year heart failure hospitalizations (20.8% versus 9.6%;
P
=0.016; log-rank
P
=0.020).

CONCLUSIONS:
Mitral transcatheter edge-to-edge repair in patients with and without above-mild MAC is equally feasible and safe; however, its postprocedural course is less favorable among those with primary MR.
CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by
TTN
Truncation Variants
Authors: Ghahremani Shahnaz , Kanwal Aditya , Pettinato Anthony , Ladha Feria , Legere Nicholas , Thakar Ketan , Zhu Yanfen , Tjong Harianto , Wilderman Andrea , Stump W. Tom , Greenberg Lina , Greenberg Michael J. , Cotney Justin , Wei Chia-Lin , Hinson J. Travis 
Published: January 2024

BACKGROUND:

TTN
truncation variants (TTNtvs) are the most common genetic lesion identified in individuals with dilated cardiomyopathy, a disease with high morbidity and mortality rates. TTNtvs reduce normal TTN (titin) protein levels, produce truncated proteins, and impair sarcomere content and function. Therapeutics targeting TTNtvs have been elusive because of the immense size of TTN, the rarity of specific TTNtvs, and incomplete knowledge of TTNtv pathogenicity.

METHODS:
We adapted CRISPR activation using dCas9-VPR to functionally interrogate TTNtv pathogenicity and develop a therapeutic in human cardiomyocytes and 3-dimensional cardiac microtissues engineered from induced pluripotent stem cell models harboring a dilated cardiomyopathy–associated TTNtv. We performed guide RNA screening with custom TTN reporter assays, agarose gel electrophoresis to quantify TTN protein levels and isoforms, and RNA sequencing to identify molecular consequences of TTN activation. Cardiomyocyte epigenetic assays were also used to nominate DNA regulatory elements to enable cardiomyocyte-specific TTN activation.

RESULTS:

CRISPR activation of TTN using single guide RNAs targeting either the
TTN
promoter or regulatory elements in spatial proximity to the
TTN
promoter through 3-dimensional chromatin interactions rescued TTN protein deficits disturbed by TTNtvs. Increasing TTN protein levels normalized sarcomere content and contractile function despite increasing truncated TTN protein. In addition to
TTN
transcripts, CRISPR activation also increased levels of myofibril assembly-related and sarcomere-related transcripts.

CONCLUSIONS:
TTN CRISPR activation rescued TTNtv-related functional deficits despite increasing truncated TTN levels, which provides evidence to support haploinsufficiency as a relevant genetic mechanism underlying heterozygous TTNtvs. CRISPR activation could be developed as a therapeutic to treat a large proportion of TTNtvs.
High-Serum Brain-Derived Neurotrophic Factor Levels Are Associated With Decreased Risk of Poststroke Cognitive Impairment
Authors: Chang Xinyue , You Jiaxing , Yang Pinni , He Yu , Liu Yi , Shi Mengyao , Guo Daoxia , Peng Yanbo , Chen Jing , Wang Aili , Xu Tan , He Jiang , Zhang Yonghong , Zhu Zhengbao 
Published: January 2024

BACKGROUND:
BDNF (brain-derived neurotrophic factor) is widely implicated in the pathophysiological process of stroke, but the effect of BDNF on poststroke cognitive impairment (PSCI) remains unclear. We aimed to investigate the association between baseline serum BDNF and the risk of PSCI at 3 months in a multicenter study based on a preplanned ancillary study of the CATIS trial (China Antihypertensive Trial in Acute Ischemic Stroke).

METHODS:
We examined serum BDNF levels at baseline and used the Mini-Mental State Examination and Montreal Cognitive Assessment to evaluate cognitive function at 3-month follow-up after ischemic stroke. PSCI was defined as Mini-Mental State Examination score <27 or Montreal Cognitive Assessment score <25. Logistic regression analyses were performed to evaluate the association between serum BDNF and the risk of 3-month PSCI.

RESULTS:

In this ancillary study, a total of 660 patients with ischemic stroke with hypertension were included, and 593 patients (mean age, 59.90±10.44 years; 410 males and 183 females) were finally included in this analysis. According to mini-mental state examination score, after adjustment for age, sex, education, baseline National Institutes of Health Stroke Scale score,
APOE ɛ4
carriers, and other potential confounders, the odds ratio of PSCI for the highest tertile of BDNF was 0.60 ([95% CI, 0.39–0.94];
P
=0.024) compared with the lowest tertile. Multiple-adjusted spline regression model showed a linear association of serum BDNF levels with PSCI at 3 months (
P
value for linearity=0.010). Adding serum BDNF to conventional prognostic factors slightly improved the risk reclassification of PSCI (net reclassification improvement: 27.46%,
P
=0.001; integrated discrimination index: 1.02%,
P
=0.015). Similar significant findings were observed when PSCI was defined by the Montreal Cognitive Assessment score.

CONCLUSIONS:
Elevated serum BDNF levels were associated with a decreased risk of PSCI at 3 months, suggesting that serum BDNF might be a potential predictive biomarker for PSCI among patients with ischemic stroke with hypertension.
In their own language: cues guiding sticky spiral placement by Micrathena duodecimspinosa (Araneae: Araneidae)
Authors: Eberhard William G. 
Published: January 2024

Abstract
Orb-web construction behaviour, a classic example of ‘innate’ behaviour, is highly flexible. Determining which cues guide construction behaviour is complicated by the strong correlations between some variables, and the difficulty of manipulating of some web variables in biologically realistic ways. This study utilized a new experimental technique, adding sticky lines to webs during construction, to examine cues that guide sticky spiral spacing. Deflections and subsequent reductions in spacing produced by experiments that involved relatively long radii resembled the reduced spacing pattern on short radii in control webs; radius length was thus not the cue eliciting reduced spacing in control webs. An alternative, that smaller inter-radius distances elicited reduced spacing, was supported by experimentally removing radii to increase the distances between radii. The new technique also elicited variation in responses that suggested that spiders may use mental cues such as memories or expectations of line positions to guide sticky spiral placement.
Tahirih and the Religious World of Nineteenth-century Qazvin
Authors: Momen Moojan 
Published: January 2024

Abstract
Nineteenth Century Qazvin was a maelstrom of religious controversy and conflict. Uṣūlīs, Akhbārīs, Shaykhīs, Bābīs, and Bahā’īs all interacted in conflict with each other and sometimes even in violence. This paper will first try to create a religious map of Qazvin in the early 19th Century. The central figure for much of the religious conflict in the city was Qurrat al-ʿAyn Tahirih, the daughter of an Uṣūlī scholar, who became a Shaykhī and then a Bābī. This paper will look at the circle of women around her and how she interacted with them. Although she herself was killed in 1852, the impact that she had on the women of the city had a lasting direct effect until the end of the nineteenth century and an indirect one up the present time.