bluuebunny/crossref_metadata_2025_split huggingface dataset:
On critical hope and the anthropos of non-anthropocentric discourses. Some thoughts on archaeology in the Anthropocene
Authors: Hacıgüzeller Piraye 
Published: December 2021

AbstractIn this essay I scrutinize the non-anthropocentric discourses used by the social sciences and humanities narratives and critiques of the Anthropocene. Although not always predominant within the academic Anthropocene debate, such discursive strands remain politically and ethically inspiring and influential in that debate and for the public discourse concerning the epoch. I stress that these discourses inherit the hope for human progress that characterizes critical theory of the Frankfurt school, i.e. ‘critical hope’, a type of hope that renders the non-anthropocentric discourses self-contradictory. Even when they manage to escape the hold of critical hope, these discourses, I argue, suffer from ethical and political failings due to their inherent lack of focus on human–human relations and largely ahistorical nature. I conclude the essay by advocating an Anthropocene archaeology that remains critical of and learns from the ethical and political shortcomings of non-anthropocentric perspectives and making a related call for a slow archaeology of the Anthropocene.
Political–Economic Determinants of External Import Protection under a Preferential Trade Agreement
Authors: Tovar Patricia 
Published: December 2021

AbstractThe stalling of WTO multilateralism and the proliferation of preferential trade agreements in recent decades have drawn substantial attention to the impacts of preferential liberalization. A critical question is how they affect the trade barriers imposed against outsiders. I examine the relationship between preferential trade liberalization and protection against non-member countries by testing the predictions of a political–economy model based on the previous literature. Focusing on a specific model allows me to uncover the mechanisms via which preferential liberalization affects external import protection, whereas most of the existing literature has focused on establishing the sign of the effect only. Furthermore, I focus on not only tariffs, as most studies do, but also on the temporary trade barriers of antidumping and safeguards. I test the predictions for Latin America and obtain results that provide solid evidence supporting two mechanisms from the theory, which lead to lower protection against non-members of a preferential trade agreement. First, a lower preferential import protection level means that the increase in preferential imports from increasing the external tariff creates a smaller increase in tariff revenue. Second, as preferential import protection is cut, there is a decrease in the markup and sales of domestic firms, and thus raising the external import protection generates less profit. Moreover, this second effect is present when the political motivation of the government is sufficiently strong.
Can we determine burdensome transitions in the last year of life based on time of occurrence and frequency? An explanatory mixed-methods study
Authors: Schippel Nicolas , Dust Gloria , von Reeken Christian , Voltz Raymond , Strupp Julia , Rietz Christian 
Published: December 2021

Abstract

Objective
Burdensome transitions are typically defined as having a transition in the last three days or multiple hospitalizations in the last three months of life, which is seldom verified with qualitative accounts from persons concerned. This study analyses types and frequencies of transitions in the last year of life and indicators of burdensome transitions from the perspective of bereaved relatives.

Method
Cross-sectional explanatory mixed-methods study with 351 surveyed and 41 interviewed bereaved relatives in a German urban area. Frequencies, t-tests, and Spearman correlations were computed for quantitative data. Qualitative data were analyzed using content analysis with provisional and descriptive coding/subcoding.

Results
Transitions rise sharply during the last year of life. 8.2% of patients experience a transition in the last three days and 7.8% three or more hospitalizations in the last three months of life. An empathetic way of telling patients about the prospect of death is associated with fewer transitions in the last month of life (r = 0.185, p = 0.046). Professionals being aware of the preferred place of death corresponds to fewer hospitalizations in the last three months of life (1.28 vs. 0.97, p = 0.021). Qualitative data do not confirm that burden in transitions is linked to having transitions in the last three days or multiple hospitalizations in the last three months of life. Burden is associated with (1) late and non-empathetic communication about the prospect of death, (2) not coordinating care across settings, and (3) not considering patients’ preferences.

Significance of results
Time of occurrence and frequency appear to be imperfect proxies for burdensome transitions. The subjective burden seems to be associated rather with insufficient information, preparation, and management of transitions.
De novo assembly, annotation and molecular marker identification from the leaf transcriptome of Ocimum gratissimum L.
Authors: Tanuja  , Parasar Nibir Ranjan , Kumar Ravichandiran , Natarajan Purushothaman , Parani Madasamy 
Published: December 2021

AbstractOcimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.
Small- and Wide-Angle X-Ray Scattering (SAXS/WAXS) with Temperature-Controlled Stages Makes Phase Identification Faster than Ever
Authors: Wu Han , Stacey Duncan 
Published: December 2021

Abstract:X-ray diffraction (XRD) is a fingerprint technique for the analysis of atomic and molecular structures of crystalline materials, from polymers and plastics, through to structural composites and biomaterials. These all have crystallographic phases in the nanostructure, which greatly influence the macro properties of the material—from insulin and hemoglobin to semiconductors and solar cells. Here, we look at how XRD analysis using a small- and wide-angle X-ray scattering (SAXS/WAXS) system under full vacuum brings the possibility of crystallographic sample characterization, with temperature and environmental control, direct to the laboratory, and how this improves the workflow for phase identification.
The lack of statistical power of subgroup analyses in meta-analyses: a cautionary note
Authors: Cuijpers Pim , Griffin Jason W. , Furukawa Toshi A. 
Published: December 2021

Abstract
One of the most used methods to examine sources of heterogeneity in meta-analyses is the so-called ‘subgroup analysis’. In a subgroup analysis, the included studies are divided into two or more subgroups, and it is tested whether the pooled effect sizes found in these subgroups differ significantly from each other. Subgroup analyses can be considered as a core component of most published meta-analyses. One important problem of subgroup analyses is the lack of statistical power to find significant differences between subgroups. In this paper, we explore the power problems of subgroup analyses in more detail, using ‘metapower’, a recently developed statistical package in R to examine power in meta-analyses, including subgroup analyses. We show that subgroup analyses require many more included studies in a meta-analysis than are needed for the main analyses. We work out an example of an ‘average’ meta-analysis, in which a subgroup analysis requires 3–4 times the number of studies that are needed for the main analysis to have sufficient power. This number of studies increases exponentially with decreasing effect sizes and when the studies are not evenly divided over the subgroups. Higher heterogeneity also requires increasing numbers of studies. We conclude that subgroup analyses remain an important method to examine potential sources of heterogeneity in meta-analyses, but that meta-analysts should keep in mind that power is very low for most subgroup analyses. As in any statistical evaluation, researchers should not rely on a test and p-value to interpret results, but should compare the confidence intervals and interpret results carefully.
Characterizing Methane Emission Hotspots From Thawing Permafrost
Authors: Elder C. D. , Thompson D. R. , Thorpe A. K. , Chandanpurkar H. A. , Hanke P. J. , Hasson N. , James S. R. , Minsley B. J. , Pastick N. J. , Olefeldt D. , Walter Anthony K. M. , Miller C. E. 
Published: December 2021

AbstractMethane (CH4) emissions from climate‐sensitive ecosystems within the northern permafrost region represent a potentially large but highly uncertain source, with current estimates spanning a factor of seven (11–75 Tg CH4 yr−1). Accelerating permafrost thaw threatens significant increases in pan‐Arctic CH4 emissions, amplifying the permafrost carbon feedback. We used airborne imaging spectroscopy with meter‐scale spatial resolution and broad coverage to identify a previously undiscovered CH4 emission hotspot adjacent to a thermokarst lake in interior Alaska. Hotspot emissions were confined to <1% of the 10 ha lake study area. Ground‐based chamber measurements confirmed average daily fluxes from the hotspot of 1,170 mg CH4 m−2 d−1, with extreme daily maxima up to 24,200 mg CH4 m−2 d−1. Ground‐based geophysical measurements revealed thawed permafrost directly beneath the CH4 hotspot, extending to a depth of ∼15 m, indicating that the intense CH4 emissions likely originated from recently thawed permafrost. Hotspot emissions accounted for ∼40% of total diffusive CH4 emissions from the lake study site. Combining study site findings with hotspot statistics from our 70,000 km2 airborne survey across Alaska and northwestern Canada, we estimate that pan‐Arctic terrestrial thermokarst hotspots currently emit 1.1 (0.1–5.2) Tg CH4 yr−1, or roughly 4% of the annual pan‐Arctic wetland budget from just 0.01% of the northern permafrost land area. Our results suggest that significant proportions of pan‐Arctic CH4 emissions originate from disproportionately small areas of previously undetermined thermokarst emissions hotspots, and that pan‐Arctic CH4 emissions may increase non‐linearly as thermokarst processes increase under a warming climate.
Regulation of common neurological disorders by gut microbial metabolites
Authors: Park Jeongho , Kim Chang H. 
Published: December 2021

AbstractThe gut is connected to the CNS by immunological mediators, lymphocytes, neurotransmitters, microbes and microbial metabolites. A mounting body of evidence indicates that the microbiome exerts significant effects on immune cells and CNS cells. These effects frequently result in the suppression or exacerbation of inflammatory responses, the latter of which can lead to severe tissue damage, altered synapse formation and disrupted maintenance of the CNS. Herein, we review recent progress in research on the microbial regulation of CNS diseases with a focus on major gut microbial metabolites, such as short-chain fatty acids, tryptophan metabolites, and secondary bile acids. Pathological changes in the CNS are associated with dysbiosis and altered levels of microbial metabolites, which can further exacerbate various neurological disorders. The cellular and molecular mechanisms by which these gut microbial metabolites regulate inflammatory diseases in the CNS are discussed. We highlight the similarities and differences in the impact on four major CNS diseases, i.e., multiple sclerosis, Parkinson’s disease, Alzheimer’s disease, and autism spectrum disorder, to identify common cellular and molecular networks governing the regulation of cellular constituents and pathogenesis in the CNS by microbial metabolites.
GTF2E2 is a novel biomarker for recurrence after surgery and promotes progression of esophageal squamous cell carcinoma via miR-139-5p/GTF2E2/FUS axis
Authors: Zhang Yujie , Zhang Yuxin , Ai Bo , Gong Juejun , Li Yichen , Yu Shiying , Cai Xiuyu , Zhang Li 
Published: December 2021

AbstractEsophageal squamous cell carcinoma (ESCC) is one of the most lethal gastrointestinal malignancies with high mortality. Recurrence develops within only a few years after curative resection and perioperative adjuvant therapy in 30–50% of these patients. Therefore, it is essential to identify postoperative recurrence biomarkers to facilitate selecting the following surveillance and therapeutic strategies. The general transcription factor IIE subunit beta (GTF2E2) is crucial for physiological and pathological functions, but its roles in the aggression and recurrence of ESCC remain ambiguous. In this study, we found that GTF2E2 was highly expressed in ESCC samples, and elevated GTF2E2 expression predicted early recurrence after surgery for ESCC patients. High expression of GTF2E2 associated with more aggressive clinic features and poor prognosis. GTF2E2 promoted the proliferation and mobility of ESCC cells in vitro and in vivo. We further revealed that miR-139-5p repressed GTF2E2 expression by downregulating its mRNA through binding with Argonaute 2 (Ago2). Rescue assays suggested that miR-139-5p affected GTF2E2-mediated ESCC progression. Moreover, GTF2E2 positively interacted with FUS promoter and regulated FUS expression, and the phenotype changes caused by GTF2E2 manipulation were recovered by rescuing FUS expression in ESCC cells. Additionally, we demonstrated that GTF2E2 promotes ESCC cells progression via activation of the AKT/ERK/mTOR pathway. In conclusion, GTF2E2 may serve as a novel biomarker for recurrence after surgery and a potential therapeutic target for ESCC patients, and it promotes ESCC progression via miR-139-5p/GTF2E2/FUS axis.
Secreted frizzled related-protein 2 (Sfrp2) deficiency decreases adult skeletal stem cell function in mice
Authors: de Castro Luis Fernandez , Sworder Brian J. , Mui Byron , Futrega Kathryn , Berendsen Agnes , Phillips Matthew D. , Burbach Nathan J. , Cherman Natasha , Kuznetsov Sergei , Gabet Yankel , Holmbeck Kenn , Robey Pamela G. 
Published: December 2021

AbstractIn a previous transcriptomic study of human bone marrow stromal cells (BMSCs, also known as bone marrow-derived “mesenchymal stem cells”), SFRP2 was highly over-represented in a subset of multipotent BMSCs (skeletal stem cells, SSCs), which recreate a bone/marrow organ in an in vivo ectopic bone formation assay. SFRPs modulate WNT signaling, which is essential to maintain skeletal homeostasis, but the specific role of SFRP2 in BMSCs/SSCs is unclear. Here, we evaluated Sfrp2 deficiency on BMSC/SSC function in models of skeletal organogenesis and regeneration. The skeleton of Sfrp2-deficient (KO) mice is overtly normal; but their BMSCs/SSCs exhibit reduced colony-forming efficiency, reflecting low SSC self-renewal/abundancy. Sfrp2 KO BMSCs/SSCs formed less trabecular bone than those from WT littermates in the ectopic bone formation assay. Moreover, regeneration of a cortical drilled hole defect was dramatically impaired in Sfrp2 KO mice. Sfrp2-deficient BMSCs/SSCs exhibited poor in vitro osteogenic differentiation as measured by Runx2 and Osterix expression and calcium accumulation. Interestingly, activation of the Wnt co-receptor, Lrp6, and expression of Wnt target genes, Axin2, C-myc and Cyclin D1, were reduced in Sfrp2-deficient BMSCs/SSCs. Addition of recombinant Sfrp2 restored most of these activities, suggesting that Sfrp2 acts as a Wnt agonist. We demonstrate that Sfrp2 plays a role in self-renewal of SSCs and in the recruitment and differentiation of adult SSCs during bone healing. SFRP2 is also a useful marker of BMSC/SSC multipotency, and a factor to potentially improve the quality of ex vivo expanded BMSC/SSC products.
PIAS1 alleviates diabetic peripheral neuropathy through SUMOlation of PPAR-γ and miR-124-induced downregulation of EZH2/STAT3
Authors: Hou Zixin , Chen Ji , Yang Huan , Hu Xiaoling , Yang Fengrui 
Published: December 2021

AbstractDiabetic peripheral neuropathy (DPN) is a frequently occurring chronic complication of diabetes. In this study, we aim to explore the regulatory mechanism of protein inhibitor of activated STAT1 (PIAS1) in DPN in terms of autophagy and apoptosis of Schwann cells. The SUMOlation of PPAR-γ by PIAS1 was examined, and ChIP was performed to verify the binding of PPAR-γ to miR-124 promoter region. Dual-luciferase gene reporter assay was used to validate the binding affinity between miR-124 and EZH2/STAT3. Following loss‐ and gain‐of-function experiments, in vitro assays in high glucose-treated Schwann cells (SC4) and in vivo assays in db/db and ob/ob mice were performed to detect the effects of PIAS1 on autophagy and apoptosis of Schwann cells as well as symptoms of DPN by regulating the PPAR-γ-miR-124-EZH2/STAT3. The expression of PIAS1, PPAR-γ, and miR-124 was downregulated in the sciatic nerve tissue of diabetic mice. PIAS1 enhanced the expression of PPAR-γ through direct binding and SUMOlation of PPAR-γ. PPAR-γ enhanced the expression of miR-124 by enhancing the promoter activity of miR-124. Furthermore, miR-124 targeted and inversely modulated EZH2 and STAT3, promoting the autophagy of Schwann cells and inhibiting their apoptosis. In vivo experiments further substantiated that PIAS1 could promote the autophagy and inhibit the apoptosis of Schwann cells through the PPAR-γ-miR-124-EZH2/STAT3 axis. In conclusion, PIAS1 promoted SUMOlation of PPAR-γ to stabilize PPAR-γ expression, which upregulated miR-124 to inactivate EZH2/STAT3, thereby inhibiting apoptosis and promoting autophagy of Schwann cells to suppress the development of DPN.
The cytosolic iron–sulfur cluster assembly (CIA) pathway is required for replication stress tolerance of cancer cells to Chk1 and ATR inhibitors
Authors: Redwood Abena B. , Zhang Xiaomei , Seth Sahil B. , Ge Zhongqi , Bindeman Wendy E. , Zhou Xinhui , Sinha Vidya C. , Heffernan Timothy P. , Piwnica-Worms Helen 
Published: December 2021

AbstractThe relationship between ATR/Chk1 activity and replication stress, coupled with the development of potent and tolerable inhibitors of this pathway, has led to the clinical exploration of ATR and Chk1 inhibitors (ATRi/Chk1i) as anticancer therapies for single-agent or combinatorial application. The clinical efficacy of these therapies relies on the ability to ascertain which patient populations are most likely to benefit, so there is intense interest in identifying predictive biomarkers of response. To comprehensively evaluate the components that modulate cancer cell sensitivity to replication stress induced by Chk1i, we performed a synthetic-lethal drop-out screen in a cell line derived from a patient with triple-negative breast cancer (TNBC), using a pooled barcoded shRNA library targeting ~350 genes involved in DNA replication, DNA damage repair, and cycle progression. In addition, we sought to compare the relative requirement of these genes when DNA fidelity is challenged by clinically relevant anticancer breast cancer drugs, including cisplatin and PARP1/2 inhibitors, that have different mechanisms of action. This global comparison is critical for understanding not only which agents should be used together for combinatorial therapies in breast cancer patients, but also the genetic context in which these therapies will be most effective, and when a single-agent therapy will be sufficient to provide maximum therapeutic benefit to the patient. We identified unique potentiators of response to ATRi/Chk1i and describe a new role for components of the cytosolic iron–sulfur assembly (CIA) pathway, MMS19 and CIA2B-FAM96B, in replication stress tolerance of TNBC.
Connected-UNets: a deep learning architecture for breast mass segmentation
Authors: Baccouche Asma , Garcia-Zapirain Begonya , Castillo Olea Cristian , Elmaghraby Adel S. 
Published: December 2021

AbstractBreast cancer analysis implies that radiologists inspect mammograms to detect suspicious breast lesions and identify mass tumors. Artificial intelligence techniques offer automatic systems for breast mass segmentation to assist radiologists in their diagnosis. With the rapid development of deep learning and its application to medical imaging challenges, UNet and its variations is one of the state-of-the-art models for medical image segmentation that showed promising performance on mammography. In this paper, we propose an architecture, called Connected-UNets, which connects two UNets using additional modified skip connections. We integrate Atrous Spatial Pyramid Pooling (ASPP) in the two standard UNets to emphasize the contextual information within the encoder–decoder network architecture. We also apply the proposed architecture on the Attention UNet (AUNet) and the Residual UNet (ResUNet). We evaluated the proposed architectures on two publically available datasets, the Curated Breast Imaging Subset of Digital Database for Screening Mammography (CBIS-DDSM) and INbreast, and additionally on a private dataset. Experiments were also conducted using additional synthetic data using the cycle-consistent Generative Adversarial Network (CycleGAN) model between two unpaired datasets to augment and enhance the images. Qualitative and quantitative results show that the proposed architecture can achieve better automatic mass segmentation with a high Dice score of 89.52%, 95.28%, and 95.88% and Intersection over Union (IoU) score of 80.02%, 91.03%, and 92.27%, respectively, on CBIS-DDSM, INbreast, and the private dataset.