bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the Two Most Common Phenology Algorithms Imbedded in Land Surface Models
Authors: Chen Baozhang 
Published: October 2022

AbstractA reasonable representation of plant phenology in land surface models (LSMs) is necessary to accurately simulate the momentum, heat, and mass interchanges between land and the atmosphere from ecosystem to global scales. Many process‐based phenology algorithms have been developed and coupled to LSMs to describe seasonal vegetation changes. The growing degree day (GDD) and the growing season index (GSI) algorithms are the two most well‐known algorithms used in LSMs for simulating phenophases. However, assessments of these two most commonly used phenology algorithms in LSMs are quite scarce. In this study, these two phenology algorithms were respectively coupled with the Community Land Model (CLM) and the Dynamic Land Model (DLM) to obtain four modeling scenarios. The simulation accuracy of phenophases and gross primary production (GPP) in the four scenarios was assessed against observations at the site scale, focusing on deciduous forests and grasses. The three main findings were as follows: (a) the difference in simulated phenological events between different LSMs coupled with the same phenological algorithm was small and less than 1 day, DLM performed better than CLM; (b) compared with the GSI algorithm and regardless of whether it was coupled with the DLM or CLM model, the GDD model performance was better for spring phenology and worse for autumn phenology; (c) GSI performance was better than GDD for GPP simulation over different vegetation function types across different bioclimatic zones: on average, the root mean square error and the index of agreement were about 8.0% higher and about 6.5% lower, respectively.
Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication
Authors: Larkin Alyse A , Hagstrom George I , Brock Melissa L , Garcia Nathan S , Martiny Adam C 
Published: October 2022

Abstract
Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (RObs) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in RObs that peaked between 19:00–22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in RObs that differed from spatial patterns in relative abundance. Finally, RObs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space.
Epstein Barr virus-mediated transformation of B cells from XIAP-deficient patients leads to increased expression of the tumor suppressor CADM1
Authors: Engelmann Christine , Schuhmachers Patrick , Zdimerova Hana , Virdi Sanamjeet , Hauri-Hohl Mathias , Pachlopnik Schmid Jana , Grundhoff Adam , Marsh Rebecca A. , Wong Wendy Wei-Lynn , Münz Christian 
Published: October 2022

AbstractX-linked lymphoproliferative disease (XLP) is either caused by loss of the SLAM-associated protein (SAP; XLP-1) or the X-linked inhibitor of apoptosis (XIAP; XLP-2). In both instances, infection with the oncogenic human Epstein Barr virus (EBV) leads to pathology, but EBV-associated lymphomas only emerge in XLP-1 patients. Therefore, we investigated the role of XIAP during B cell transformation by EBV. Using humanized mice, IAP inhibition in EBV-infected mice led to a loss of B cells and a tendency to lower viral titers and lymphomagenesis. Loss of memory B cells was also observed in four newly described patients with XIAP deficiency. EBV was able to transform their B cells into lymphoblastoid cell lines (LCLs) with similar growth characteristics to patient mothers’ LCLs in vitro and in vivo. Gene expression analysis revealed modest elevated lytic EBV gene transcription as well as the expression of the tumor suppressor cell adhesion molecule 1 (CADM1). CADM1 expression on EBV-infected B cells might therefore inhibit EBV-associated lymphomagenesis in patients and result in the absence of EBV-associated malignancies in XLP-2 patients.
DDX17 promotes the growth and metastasis of lung adenocarcinoma
Authors: Liu Xiaohui , Li Lu , Geng Chengjie , Wen Shiyuan , Zhang Cuiqiong , Deng Chunmiao , Gao Xuejuan , Zhang Gong , He Qing-yu , Liu Langxia 
Published: October 2022

AbstractDEAD box RNA helicase 17 (DDX17) has been shown to be an RNA binding protein involved in RNA metabolism and associated with cancer progression. However, the biological role of DDX17 in the pathogenesis of lung adenocarcinoma (LUAD) has not been well characterized. Here, we demonstrated that DDX17 promoted the proliferation, migration and invasion of H1299 and A549 lung adenocarcinoma cells. Analyses of public datasets showed that DDX17 is upregulated in LUAD specimens. Our tumor xenograft models confirmed the in vivo promoting role of DDX17 in the growth and metastasis of LUAD. Mechanistic analyses further revealed that DDX17 protein interacts with the mRNA of MYL9 and MAGEA6 and upregulates their levels. MYL9 could mediate the function of DDX17 to regulate the actin cytoskeleton rearrangement and cell adhesion, particularly by modulating the stress fiber and focal adhesion formation, whereas DDX17 might inhibit the autophagy process through MAGEA6/AMPKα1 axis in LUAD cells. Collectively, our study revealed the oncogenic role and pathways of DDX17 in LUAD.
PD-L1-directed PlGF/VEGF blockade synergizes with chemotherapy by targeting CD141+ cancer-associated fibroblasts in pancreatic cancer
Authors: Kim Duk Ki , Jeong Juhee , Lee Dong Sun , Hyeon Do Young , Park Geon Woo , Jeon Suwan , Lee Kyung Bun , Jang Jin-Young , Hwang Daehee , Kim Ho Min , Jung Keehoon 
Published: October 2022

AbstractPancreatic ductal adenocarcinoma (PDAC) has a poor 5-year overall survival rate. Patients with PDAC display limited benefits after undergoing chemotherapy or immunotherapy modalities. Herein, we reveal that chemotherapy upregulates placental growth factor (PlGF), which directly activates cancer-associated fibroblasts (CAFs) to induce fibrosis-associated collagen deposition in PDAC. Patients with poor prognosis have high PIGF/VEGF expression and an increased number of PIGF/VEGF receptor-expressing CAFs, associated with enhanced collagen deposition. We also develop a multi-paratopic VEGF decoy receptor (Ate-Grab) by fusing the single-chain Fv of atezolizumab (anti-PD-L1) to VEGF-Grab to target PD-L1-expressing CAFs. Ate-Grab exerts anti-tumor and anti-fibrotic effects in PDAC models via the PD-L1-directed PlGF/VEGF blockade. Furthermore, Ate-Grab synergizes with gemcitabine by relieving desmoplasia. Single-cell RNA sequencing identifies that a CD141+CAF population is reduced upon Ate-Grab and gemcitabine combination treatment. Overall, our results elucidate the mechanism underlying chemotherapy-induced fibrosis in PDAC and highlight a combinatorial therapeutic strategy for desmoplastic cancers.
Divergent regioselective Heck-type reaction of unactivated alkenes and N-fluoro-sulfonamides
Authors: Zhao Chunyang , Li Yang , Dong Yujiao , Li Miao , Xia Dan , Gao Shuangqiu , Zhang Qian , Liu Qun , Guan Wei , Fu Junkai 
Published: October 2022

AbstractThe control of regioselectivity in Heck-type reaction of unactivated alkenes represents a longstanding challenge due to several detachable hydrogens in β–H elimination step, which generally afford either one specific regioisomer or a mixture. Herein, a copper-catalyzed intermolecular Heck-type reaction of unactivated alkenes andN-fluoro-sulfonamides with divergent regioselectivities is reported. The complete switch of regioselectivity mainly depends on the choice of different additives. Employment of alcohol solvent gives access to vinyl products, while the addition of carboxylate leads to the formation of allylic products. In addition, exclusion of these two promoting factors results in β-lactams via a C–N reductive elimination. This protocol shows a broad substrate scope for both alkenes and structurally diverseN-fluoro-sulfonamides, producing the corresponding products with excellent regio- and stereoselectivities. Further control experiments and DFT calculations provide in-depth insights into the reaction mechanism, highlighting the distinct effect of the additives on a bidentate auxiliary-stabilized Cu(III) intermediate.
Reward salience but not spatial attention dominates the value representation in the orbitofrontal cortex
Authors: Zhang Wenyi , Xie Yang , Yang Tianming 
Published: October 2022

AbstractThe orbitofrontal cortex (OFC) encodes value and plays a key role in value-based decision-making. However, the attentional modulation of the OFC’s value encoding is poorly understood. We trained two monkeys to detect a luminance change at a cued location between a pair of visual stimuli, which were over-trained pictures associated with different amounts of juice reward and, thus, different reward salience. Both the monkeys’ behavior and the dorsolateral prefrontal cortex neuronal activities indicated that the monkeys actively directed their spatial attention toward the cued stimulus during the task. However, the OFC’s neuronal responses were dominated by the stimulus with higher reward salience and encoded its value. The value of the less salient stimulus was only weakly represented regardless of spatial attention. The results demonstrate that reward and spatial attention are distinctly represented in the prefrontal cortex and the OFC maintains a stable representation of reward salience minimally affected by attention.
REDD1 promotes obesity-induced metabolic dysfunction via atypical NF-κB activation
Authors: Lee Dong-Keon , Kim Taesam , Byeon Junyoung , Park Minsik , Kim Suji , Kim Joohwan , Choi Seunghwan , Lee Gihwan , Park Chanin , Lee Keun Woo , Kwon Yong Jung , Lee Jeong-Hyung , Kwon Young-Guen , Kim Young-Myeong 
Published: October 2022

AbstractRegulated in development and DNA damage response 1 (REDD1) expression is upregulated in response to metabolic imbalance and obesity. However, its role in obesity-associated complications is unclear. Here, we demonstrate that the REDD1–NF-κB axis is crucial for metabolic inflammation and dysregulation. Mice lacking Redd1 in the whole body or adipocytes exhibited restrained diet-induced obesity, inflammation, insulin resistance, and hepatic steatosis. Myeloid Redd1-deficient mice showed similar results, without restrained obesity and hepatic steatosis. Redd1-deficient adipose-derived stem cells lost their potential to differentiate into adipocytes; however, REDD1 overexpression stimulated preadipocyte differentiation and proinflammatory cytokine expression through atypical IKK-independent NF-κB activation by sequestering IκBα from the NF-κB/IκBα complex. REDD1 with mutated Lys219/220Ala, key amino acid residues for IκBα binding, could not stimulate NF-κB activation, adipogenesis, and inflammation in vitro and prevented obesity-related phenotypes in knock-in mice. The REDD1-atypical NF-κB activation axis is a therapeutic target for obesity, meta-inflammation, and metabolic complications.
Speed and accuracy instructions affect two aspects of skill learning differently
Authors: Vékony Teodóra , Pleche Claire , Pesthy Orsolya , Janacsek Karolina , Nemeth Dezso 
Published: October 2022

AbstractProcedural learning is key to optimal skill learning and is essential for functioning in everyday life. The findings of previous studies are contradictory regarding whether procedural learning can be modified by prioritizing speed or accuracy during learning. The conflicting results may be due to the fact that procedural learning is a multifaceted cognitive function. The purpose of our study is to determine whether and how speed and accuracy instructions affect two aspects of procedural learning: the learning of probability-based and serial-order-based regularities. Two groups of healthy individuals were instructed to practice on a cued probabilistic sequence learning task: one group focused on being fast and the other on being accurate during the learning phase. The speed instruction resulted in enhanced expression of probability-based but not serial-order-based knowledge. After a retention period, we instructed the participants to focus on speed and accuracy equally, and we tested their acquired knowledge. The acquired knowledge was comparable between groups in both types of learning. These findings suggest that different aspects of procedural learning can be affected differently by instructions. However, only momentary performance might be boosted by speed instruction; the acquired knowledge remains intact. In addition, as the accuracy instruction resulted in accuracy near ceiling level, the results illustrate that response errors are not needed for humans to learn in the procedural domain and draw attention to the fact that different instructions can separate competence from performance.
High-resolution bathymetries and shorelines for the Great Lakes of the White Nile basin
Authors: Hamilton Stuart E. , McGehee David D. , Nyamweya Chrispine , Ongore Collins , Makori Amina , Mangeni-Sande Richard , Kagoya Esther , Kashindye Benedicto B. , Elison Mboni , Shaban Sophia S. , Mlaponi Enock , Mwainge Venny M. , Ocaya Henry , Krach Noah , Ogari Zachary , Mugeni Bairon , Taabu-Munyaho Anthony , Kayanda Robert , Muhumuza Elias , Natugonza Vianny 
Published: October 2022

AbstractHRBS-GLWNB 2020 presents the first open-source and high-resolution bathymetry, shoreline, and water level data for Lakes Victoria, Albert, Edward, and George in East Africa. For each Lake, these data have three primary products collected for this project. The bathymetric datasets were created from approximately 18 million acoustic soundings. Over 8,200 km of shorelines are delineated across the three lakes from high-resolution satellite systems and uncrewed aerial vehicles. Finally, these data are tied together by creating lake surface elevation models collected from GPS and altimeter measures. The data repository includes additional derived products, including surface areas, water volumes, shoreline lengths, lake elevation levels, and geodetic information. These data can be used to make allocation decisions regarding the freshwater resources within Africa, manage food resources on which many tens of millions of people rely, and help preserve the region’s endemic biodiversity. Finally, as these data are tied to globally consistent geodetic models, they can be used in future global and regional climate change models.
Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages
Authors: Feng Lei , Zhang Yu , Liu Wei , Du Dewei , Jiang Wenbo , Wang Zihua , Wang Zhonghua , Hu Zhiyong 
Published: October 2022

AbstractHeat stress is an important issue in dairy cattle feeding management affecting summer health and economic efficiency. This experiment combined 16S rDNA sequencing(3,864,982 tags, 30 sequencing data), metagenomic sequencing(1,269,441,128 reads, 18 sequencing data), metabolomics analysis(72 sequencing data) and blood index analysis. Ten cows in each animal type (growing heifers, heifers, and lactating cows) were selected for sample collection in April and August. Here, we characterized both the changes in metabolites, rumen microbial communities and their functional potential and the effects of heat stress on serum biochemical, immune, oxidative stress, and hormonal indices derived from rumen fluid and serum samples from cows during different growth stages and in different climates. The generated data expand the resources for the rumen microbiome related to heat stress and age and provide useful datasets for research on developing therapeutic strategies to achieve high summer milk production in cows. These datasets will help researchers study the effects of heat stress on the physiological metabolism of Holstein cows and the time-dependent changes associated with growth stages.
Sub-terahertz silicon-based on-chip absorption spectroscopy using thin-film model for biological applications
Authors: Hosseini Farahabadi Seyed Ali , Entezami Milad , Abouali Hesam , Amarloo Hadi , Poudineh Mahla , Safavi-Naeini Safieddin 
Published: October 2022

AbstractSpectroscopy in the sub-terahertz (sub-THz) range of frequencies has been utilized to study the picosecond dynamics and interaction of biomolecules. However, widely used free-space THz spectrometers are typically limited in their functionality due to low signal-to-noise ratio and complex setup. On-chip spectrometers can revolutionize THz spectroscopy allowing integration, compactness, and low-cost fabrication. In this paper, a low-loss silicon-based platform is proposed for on-chip sub-THz spectroscopy. Through functionalization of silicon chip and immobilization of bio-particles, we demonstrate the ability to characterize low-loss nano-scale biomolecules across the G-band (0.14–0.22 THz). We also introduce an electromagnetic thin-film model to account for the loading effect of the immobilized biomolecules, i.e. dehydrated streptavidin and immunoglobulin antibody, as two key molecules in the biosensing discipline. The proposed platform was fabricated using a single mask micro-fabrication process, and then measured by a vector network analyzer (VNA), which offers high dynamic range and high spectral resolution measurements. The proposed planar platform is general and paves the way towards low-loss, cost-effective and integrated sub-THz biosensors for the detection and characterization of biomolecules.
In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis
Authors: Brankin Alice , Seifert Marva , Georghiou Sophia B. , Walker Timothy M. , Uplekar Swapna , Suresh Anita , Colman Rebecca E. 
Published: October 2022

AbstractUniversal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist.
Alarming antibiotics resistance of Helicobacter pylori from children in Southeast China over 6 years
Authors: Shu Xiaoli , Ye Diya , Hu Chenmin , Peng Kerong , Zhao Hong , Li Huamei , Jiang Mizu 
Published: October 2022

AbstractThe increasing rates of antibiotic resistance in Helicobacter pylori (H. pylori) are a major concern of the decreasing eradication rate. Large-scale and long-period studies on antimicrobial susceptibility of H. pylori in children are limited. This study aimed to describe the temporal changes of antibiotic resistance among children in southeast China. Gastric biopsies obtained from children were cultured for H. pylori from 2015 to 2020. Susceptibility to clarithromycin (CLA), amoxicillin (AML), metronidazole (MTZ), furazolidone (FZD), tetracycline (TET) and levofloxacin (LEV) was tested. Data from 2012 to 2014 reported previously were obtained for comparing the change in temporal trends of antibiotic resistance. A total of 1638 (52.7%) H. pylori strains were isolated from 3111 children recruited. The resistance rates to CLA, MTZ and LEV were 32.8%, 81.7% and 22.8%, respectively. There were 52.9% strains resistant to single resistance, 28.7% to double resistance, and 9.0% to triple resistance. The total resistance rate and resistance rates to CLA, MTZ, LEV, CLA + LEV and CLA + MTZ + LEV increased annually in a linear manner. All resistant patterns except single resistance increased obviously from 2015 to 2017 and 2018 to 2020 compared to that from 2012 to 2014. Double resistance to CLA + MTZ increased significantly with age. The resistance rate to CLA and triple resistance to CLA, MTZ and LEV increased in children with prior H. pylori treatment than that from children without prior treatment. The antibiotic resistance rates of H. pylori were high in a large pediatric population in southeast China from 2015 to 2020. Individual treatment based on susceptibility test is imperative and optimal regimens should be chosen in H. pylori eradication therapy.
CircRNA expression profiles of breast cancer and construction of a circRNA-miRNA-mRNA network
Authors: Xu Liping , Lyu Mengmeng , Yang Sujin , Zhang Jian , Yu Dandan 
Published: October 2022

AbstractCircRNAs are a group of endogenous small noncoding RNAs that are involved in multiple diseases including cancers. At present, the functions of circRNAs in breast cancer need to be further explored. In this study, 3 pairs of breast cancer and paracancer tissues with axillary lymph node metastasis were collected for circRNA high-throughput sequencing. We have identified 17,966 distinct circRNA candidates. Significant differential expressions were found in 136 circRNAs in breast cancer tissues relative to the matched paracancer tissues. We aslo identified differentially expressed 156 miRNAs and 1105 mRNAs in breast cancer tissues and normal breast tissues from public databases. Then we constructed a regulatory ceRNA network. 12 mRNAs were associated with prognosis of breast cancer. We also constructed a circRNAs-mediated subnetwork which might be related to prognosis of breast cancer. This article provides a better understanding of circRNAs-mediated ceRNA regulatory network by which circRNAs compete for endogenous RNAs in breast cancer.