bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Clearcutting and Residual Biomass Harvesting on Hillslope Mercury Mobilization and Downgradient Mercury Accumulation
Authors: McCarter Colin P. R. , Eggert Susan L. , Sebestyen Stephen D. , Kolka Randall K. , Mitchell Carl P. J. 
Published: March 2022

AbstractMercury (Hg) in forest runoff varies geographically and in relation to silvicultural practices. There is also considerable uncertainty about how forest management practices, such as residual biomass removal, affect Hg mobilization, and downgradient cumulative effects. In this study, total Hg, dissolved organic carbon (DOC), and sulfate (SO42−) mobilization in runoff were compared among unharvested and harvested hillslopes with and without residual biomass removal, and peat soil and invertebrate methylmercury (MeHg) concentrations were assessed in a down‐gradient peatland. Using a before‐after‐control‐impact design, runoff from three adjacent hillslopes was monitored pre‐harvest (2010–2011) and post‐harvest (2012–2013) from snowmelt to freeze‐up at the USDA Forest Service’s Marcell Experimental Forest in northern Minnesota. Dilution, due to increased available hillslope soil water, led to decreased THg and DOC concentrations after harvest at both harvested hillslopes. Sulfate concentrations did not statistically change following harvest. Compared to its removal, leaving residual biomass significantly increased yields of all solutes but only DOC yields significantly increased when the residual biomass was removed. In the adjacent down‐gradient peatland, peat MeHg concentrations decreased, whereas no change was observed in peat below the unharvested hillslope. There was no discernible change post‐harvest in MeHg levels among several peatland macroinvertebrate taxa. This study provides a much‐needed hillslope‐scale understanding of Hg response to forest management practices, highlighting that increased solute yields from hillslopes do not necessarily stimulate Hg methylation or invertebrate bioaccumulation in down‐gradient peatland systems.
S6K1 controls adiponectin expression by inducing a transcriptional switch: BMAL1-to-EZH2
Authors: Yi Sang Ah , Jeon Ye Ji , Lee Min Gyu , Nam Ki Hong , Ann Sora , Lee Jaecheol , Han Jeung-Whan 
Published: March 2022

AbstractAdiponectin (encoded by Adipoq), a fat-derived hormone, alleviates risk factors associated with metabolic disorders. Although many transcription factors are known to control adiponectin expression, the mechanism underlying its fluctuation with regard to metabolic status remains unclear. Here, we show that ribosomal protein S6 kinase 1 (S6K1) controls adiponectin expression by inducing a transcriptional switch between two transcriptional machineries, BMAL1 and EZH2. Active S6K1 induced a suppressive histone code cascade, H2BS36p-EZH2-H3K27me3, leading to suppression of adiponectin expression. Moreover, active S6K1 phosphorylated BMAL1, an important transcription factor regulating the circadian clock system, at serine 42, which led to its dissociation from the Adipoq promoter region. This response resulted in EZH2 recruitment and subsequent H3K27me3 modification of the Adipoq promoter. Upon fasting, inactivation of S6K1 induced the opposite transcriptional switch, EZH2-to-BMAL1, promoting adiponectin expression. Consistently, S6K1-depleted mice exhibited lower H3K27me3 levels and elevated adiponectin expression. These findings identify a novel epigenetic switch system by which S6K1 controls the production of adiponectin, which displays beneficial effects on metabolism.
Multiphoton single-molecule localization by sequential excitation with light minima
Authors: Masullo Luciano A. , Stefani Fernando D. 
Published: March 2022

AbstractUsing sequential excitation with a minimum of light to localize single fluorescent molecules represented a breakthrough because it delivers 1–2 nm precision with moderate photon counts, enabling tracking and super-resolution imaging with true molecular resolution. Expanding this concept to multi-photon regimes may be a useful complement to reach even higher localization precision and get deeper into biological specimens.
Design of protein-binding proteins from the target structure alone
Authors: Cao Longxing , Coventry Brian , Goreshnik Inna , Huang Buwei , Sheffler William , Park Joon Sung , Jude Kevin M. , Marković Iva , Kadam Rameshwar U. , Verschueren Koen H. G. , Verstraete Kenneth , Walsh Scott Thomas Russell , Bennett Nathaniel , Phal Ashish , Yang Aerin , Kozodoy Lisa , DeWitt Michelle , Picton Lora , Miller Lauren , Strauch Eva-Maria , DeBouver Nicholas D. , Pires Allison , Bera Asim K. , Halabiya Samer , Hammerson Bradley , Yang Wei , Bernard Steffen , Stewart Lance , Wilson Ian A. , Ruohola-Baker Hannele , Schlessinger Joseph , Lee Sangwon , Savvides Savvas N. , Garcia K. Christopher , Baker David 
Published: March 2022

AbstractThe design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1–5. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
Functional movement screen dataset collected with two Azure Kinect depth sensors
Authors: Xing Qing-Jun , Shen Yuan-Yuan , Cao Run , Zong Shou-Xin , Zhao Shu-Xiang , Shen Yan-Fei 
Published: March 2022

AbstractThis paper presents a dataset for vision-based autonomous Functional Movement Screen (FMS) collected from 45 human subjects of different ages (18–59 years old) executing the following movements: deep squat, hurdle step, in-line lunge, shoulder mobility, active straight raise, trunk stability push-up and rotary stability. Specifically, shoulder mobility was performed only once by different subjects, while the other movements were repeated for three episodes each. Each episode was saved as one record and was annotated from 0 to 3 by three FMS experts. The main strength of our database is twofold. One is the multimodal data provided, including color images, depth images, quaternions, 3D human skeleton joints and 2D pixel trajectories of 32 joints. The other is the multiview data collected from the two synchronized Azure Kinect sensors in front of and on the side of the subjects. Finally, our dataset contains a total of 1812 recordings, with 3624 episodes. The size of the dataset is 190 GB. This dataset provides the opportunity for automatic action quality evaluation of FMS.
Pomegranate fruit juice adulteration with apple juice: detection by UV–visible spectroscopy combined with multivariate statistical analysis
Authors: Pappalardo Lucia 
Published: March 2022

AbstractPomegranate is rich in high value nutritional substances known to be beneficial against several diseases and its use in medicine is known since ancient times. Due to its properties and delicious taste, pomegranate fresh fruit juices demand has been growing worldwide and its adulteration is becoming a problem. Low-cost, user friendly and fast detection methods are therefore desirable in order to easily and rapidly detect adulteration of short shelf-life fresh fruit juices. For this purpose fresh squeezed arils pomegranate juice samples adulterated with less expensive apple juice concentrate were investigated by UV–visible spectroscopy combined with multivariate statistical analysis. Unsupervised principle component analysis (PCA), supervised projection to latent structure discriminant analysis (PLS-DA) and orthogonal projection to latent structure discriminant analysis (OPLS-DA) were performed on the full spectra. OPLS-DA analysis of UV–visible spectra proved to be a suitable method to detect pomegranate juices adulterated by more than 20% v/v apple juice concentrate.
Evidence of antagonistic predictive effects of miRNAs in breast cancer cohorts through data-driven networks
Authors: Miglioli Cesare , Bakalli Gaetan , Orso Samuel , Karemera Mucyo , Molinari Roberto , Guerrier Stéphane , Mili Nabil 
Published: March 2022

AbstractNon-coding micro RNAs (miRNAs) dysregulation seems to play an important role in the pathways involved in breast cancer occurrence and progression. In different studies, opposite functions may be assigned to the same miRNA, either promoting the disease or protecting from it. Our research tackles the following issues: (i) why aren’t there any concordant findings in many research studies regarding the role of miRNAs in the progression of breast cancer? (ii) could a miRNA have either an activating effect or an inhibiting one in cancer progression according to the other miRNAs with which it interacts? For this purpose, we analyse the AHUS dataset made available on the ArrayExpress platform by Haakensen et al. The breast tissue specimens were collected over 7 years between 2003 and 2009. miRNA-expression profiling was obtained for 55 invasive carcinomas and 70 normal breast tissue samples. Our statistical analysis is based on a recently developed model and feature selection technique which, instead of selecting a single model (i.e. a unique combination of miRNAs), delivers a set of models with equivalent predictive capabilities that allows to interpret and visualize the interaction of these features. As a result, we discover a set of 112 indistinguishable models (in a predictive sense) each with 4 or 5 miRNAs. Within this set, by comparing the model coefficients, we are able to identify three classes of miRNA: (i) oncogenic miRNAs; (ii) protective miRNAs; (iii) undefined miRNAs which can play both an oncogenic and a protective role according to the network with which they interact. These results shed new light on the biological action of miRNAs in breast cancer and may contribute to explain why, in some cases, different studies attribute opposite functions to the same miRNA.
Oxidative stress facilitates exogenous mitochondria internalization and survival in retinal ganglion precursor-like cells
Authors: Aharoni-Simon Michal , Ben-Yaakov Keren , Sharvit-Bader Maya , Raz Daniel , Haim Yasmin , Ghannam Waleed , Porat Noga , Leiba Hana , Marcovich Arie , Eisenberg-Lerner Avital , Rotfogel Ziv 
Published: March 2022

AbstractOcular cells are highly dependent on mitochondrial function due to their high demand of energy supply and their constant exposure to oxidative stress. Indeed, mitochondrial dysfunction is highly implicated in various acute, chronic, and genetic disorders of the visual system. It has recently been shown that mitochondrial transplantation (MitoPlant) temporarily protects retinal ganglion cells (RGCs) from cell death during ocular ischemia. Here, we characterized MitoPlant dynamics in retinal ganglion precursor-like cells, in steady state and under oxidative stress. We developed a new method for detection of transplanted mitochondria using qPCR, based on a difference in the mtDNA sequence of C57BL/6 and BALB/c mouse strains. Using this approach, we show internalization of exogenous mitochondria already three hours after transplantation, and a decline in mitochondrial content after twenty four hours. Interestingly, exposure of target cells to moderate oxidative stress prior to MitoPlant dramatically enhanced mitochondrial uptake and extended the survival of mitochondria in recipient cells by more than three fold. Understanding the factors that regulate the exogenous mitochondrial uptake and their survival may promote the application of MitoPlant for treatment of chronic and genetic mitochondrial diseases.
Misperception influence on zero-determinant strategies in iterated Prisoner’s Dilemma
Authors: Cheng Zhaoyang , Chen Guanpu , Hong Yiguang 
Published: March 2022

AbstractZero-determinant (ZD) strategies have attracted wide attention in Iterated Prisoner’s Dilemma (IPD) games, since the player equipped with ZD strategies can unilaterally enforce the two players’ expected utilities subjected to a linear relation. On the other hand, uncertainties, which may be caused by misperception, occur in IPD inevitably in practical circumstances. To better understand the situation, we consider the influence of misperception on ZD strategies in IPD, where the two players, player X and player Y, have different cognitions, but player X detects the misperception and it is believed to make ZD strategies by player Y. We provide a necessary and sufficient condition for the ZD strategies in IPD with misperception, where there is also a linear relationship between players’ utilities in player X’s cognition. Then we explore bounds of players’ expected utility deviation from a linear relationship in player X’s cognition with also improving its own utility.
Safety, pharmacokinetics, and pharmacodynamics of milvexian in healthy Japanese participants
Authors: Perera Vidya , Wang Zhaoqing , Lubin Susan , Ueno Takayo , Shiozaki Tomomi , Chen Wei , Xu Xiaohui , Seiffert Dietmar , DeSouza Mary , Murthy Bindu 
Published: March 2022

AbstractThis randomized, double-blind, placebo-controlled, multiple ascending–dose study evaluated safety, tolerability, pharmacokinetics, and pharmacodynamics of multiple doses of milvexian, an oral small-molecule FXIa inhibitor, in healthy Japanese participants. Participants received oral milvexian daily under fasted (50 mg and 200 mg) or fed conditions (500 mg) or placebo over 14 days; 24 participants (8/cohort: 6 milvexian; 2 placebo) were planned. Due to an unblinding event, participants in one cohort (200 mg daily) were discontinued, and a second cohort enrolled; 32 participants were included in safety and pharmacodynamic analyses, and 24/32 in pharmacokinetic analyses. Milvexian up to 500 mg daily for 14 days was generally well tolerated, with no deaths, serious adverse events, or discontinuations due to adverse events. Milvexian exposure increased between 50-mg and 200-mg doses. Median Tmax was similar with 50-mg and 200-mg doses (2.5–3.0 h) and delayed under fed conditions (500 mg, 7.0–8.0 h). Median T1/2 was similar across doses (8.9–11.9 h). Multiple oral milvexian administrations resulted in concentration-related prolongation of aPTT and decreased FXI clotting activity.
Milvexian was generally safe and well tolerated. The pharmacokinetic and pharmacodynamic profile of milvexian demonstrates suitability for further clinical development in Japanese participants.
The uptake characteristics of Prussian-blue nanoparticles for rare metal ions for recycling of precious metals from nuclear and electronic wastes
Authors: Watanabe Shinta , Inaba Yusuke , Harigai Miki , Takeshita Kenji , Onoe Jun 
Published: March 2022

AbstractWe have examined the uptake mechanisms of platinum-group-metals (PGMs) and molybdenum (Mo) ions into Prussian blue nanoparticles (PBNPs) in a nitric acid solution for 24-h sorption test, using inductively coupled plasma atomic emission spectroscopy, powder XRD, and UV–Vis-NIR spectroscopy in combination with first-principles calculations, and revealed that the Ru4+ and Pd2+ ions are incorporated into PBNPs by substitution with Fe3+ and Fe2+ ions of the PB framework, respectively, whereas the Rh3+ ion is incorporated into PBNPs by substitution mainly with Fe3+ and minorly with Fe2+ ion, and Mo6+ ion is incorporated into PBNPs by substitution with both Fe2+ and Fe3+ ions, with maintaining the crystal structure before and after the sorption test. Assuming that the amount of Fe elusion is equal to that of PGMs/Mo substitution, the substitution efficiency is estimated to be 39.0% for Ru, 47.8% for Rh, 87% for Pd, and 17.1% for Mo6+. This implies that 0.13 g of Ru, 0.16 g of Rh, 0.30 g of Pd, and 0.107 g of Mo can be recovered by using 1 g PBNPs with a chemical form of KFe(III)[Fe(II)(CN)6].
Differential early diagnosis of benign versus malignant lung cancer using systematic pathway flux analysis of peripheral blood leukocytes
Authors: Li Jian , Li Xiaoyu , Li Ming , Qiu Hong , Saad Christian , Zhao Bo , Li Fan , Wu Xiaowei , Kuang Dong , Tang Fengjuan , Chen Yaobing , Shu Hongge , Zhang Jing , Wang Qiuxia , Huang He , Qi Shankang , Ye Changkun , Bryant Amy , Yuan Xianglin , Kurts Christian , Hu Guangyuan , Cheng Weiting , Mei Qi 
Published: March 2022

AbstractEarly diagnosis of lung cancer is critically important to reduce disease severity and improve overall survival. Newer, minimally invasive biopsy procedures often fail to provide adequate specimens for accurate tumor subtyping or staging which is necessary to inform appropriate use of molecular targeted therapies and immune checkpoint inhibitors. Thus newer approaches to diagnosis and staging in early lung cancer are needed. This exploratory pilot study obtained peripheral blood samples from 139 individuals with clinically evident pulmonary nodules (benign and malignant), as well as ten healthy persons. They were divided into three cohorts: original cohort (n = 99), control cohort (n = 10), and validation cohort (n = 40). Average RNAseq sequencing of leukocytes in these samples were conducted. Subsequently, data was integrated into artificial intelligence (AI)-based computational approach with system-wide gene expression technology to develop a rapid, effective, non-invasive immune index for early diagnosis of lung cancer. An immune-related index system, IM-Index, was defined and validated for the diagnostic application. IM-Index was applied to assess the malignancies of pulmonary nodules of 109 participants (original + control cohorts) with high accuracy (AUC: 0.822 [95% CI: 0.75–0.91, p < 0.001]), and to differentiate between phases of cancer immunoediting concept (odds ratio: 1.17 [95% CI: 1.1–1.25, p < 0.001]). The predictive ability of IM-Index was validated in a validation cohort with a AUC: 0.883 (95% CI: 0.73–1.00, p < 0.001). The difference between molecular mechanisms of adenocarcinoma and squamous carcinoma histology was also determined via the IM-Index (OR: 1.2 [95% CI 1.14–1.35, p = 0.019]). In addition, a structural metabolic behavior pattern and signaling property in host immunity were found (bonferroni correction, p = 1.32e − 16). Taken together our findings indicate that this AI-based approach may be used for “Super Early” cancer diagnosis and amend the current immunotherpay for lung cancer.
Efficient generation of few-cycle pulses beyond 10 μm from an optical parametric amplifier pumped by a 1-µm laser system
Authors: Heiner Zsuzsanna , Petrov Valentin , Panyutin Vladimir L. , Badikov Valeriy V. , Kato Kiyoshi , Miyata Kentaro , Mero Mark 
Published: March 2022

AbstractNonlinear vibrational spectroscopy profits from broadband sources emitting in the molecular fingerprint region. Yet, broadband lasers operating at wavelengths above 7 μm have been lacking, while traditional cascaded parametric frequency down-conversion schemes suffer from exceedingly low conversion efficiencies. Here we present efficient, direct frequency down-conversion of femtosecond 100-kHz, 1.03-μm pulses to the mid-infrared from 7.5 to 13.3 μm in a supercontinuum-seeded, tunable, single-stage optical parametric amplifier based on the wide-bandgap material Cd0.65Hg0.35Ga2S4. The amplifier delivers near transform-limited, few-cycle pulses with an average power > 30 mW at center wavelengths between 8.8 and 10.6 μm, at conversion efficiencies far surpassing that of optical parametric amplification followed by difference-frequency generation or intrapulse difference-frequency generation. The pulse duration at 10.6 μm is 101 fs corresponding to 2.9 optical cycles with a spectral coverage of 760–1160 cm−1. CdxHg1−xGa2S4 is an attractive alternative to LiGaS2 and BaGa4S7 in small-scale, Yb-laser-pumped, few-cycle mid-infrared optical parametric amplifiers and offers a much higher nonlinear figure of merit compared to those materials. Leveraging the inherent spatial variation of composition in CdxHg1−xGa2S4, an approach is proposed to give access to a significant fraction of the molecular fingerprint region using a single crystal at a fixed phase matching angle.
Combining elemental and immunochemical analyses to characterize diagenetic alteration patterns in ancient skeletal remains
Authors: Gatti L. , Lugli Federico , Sciutto Giorgia , Zangheri M. , Prati S. , Mirasoli M. , Silvestrini S. , Benazzi S. , Tütken T. , Douka K. , Collina C. , Boschin F. , Romandini M. , Iacumin P. , Guardigli M. , Roda A. , Mazzeo R. 
Published: March 2022

AbstractBones and teeth are biological archives, but their structure and composition are subjected to alteration overtime due to biological and chemical degradation postmortem, influenced by burial environment and conditions. Nevertheless, organic fraction preservation is mandatory for several archeometric analyses and applications. The mutual protection between biomineral and organic fractions in bones and teeth may lead to a limited diagenetic alteration, promoting a better conservation of the organic fraction. However, the correlation between elemental variations and the presence of organic materials (e.g., collagen) in the same specimen is still unclear. To fill this gap, chemiluminescent (CL) immunochemical imaging analysis has been applied for the first time for collagen localization. Then, Laser Ablation–Inductively Coupled Plasma–Mass Spectrometry (LA–ICP–MS) and CL imaging were combined to investigate the correlation between elemental (i.e., REE, U, Sr, Ba) and collagen distribution. Teeth and bones from various archeological contexts, chronological periods, and characterized by different collagen content were analyzed. Immunochemical analysis revealed a heterogeneous distribution of collagen, especially in highly degraded samples. Subsequently, LA–ICP–MS showed a correlation between the presence of uranium and rare earth elements and areas with low amount of collagen. The innovative integration between the two methods permitted to clarify the mutual relation between elemental variation and collagen preservation overtime, thus contributing to unravel the effects of diagenetic alteration in bones and teeth.