bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of CSDE1 in translational reprogramming and human diseases
Authors: Guo Ao-Xiang , Cui Jia-Jia , Wang Lei-Yun , Yin Ji-Ye 
Published: January 2020

Abstract
CSDE1 (cold shock domain containing E1) plays a key role in translational reprogramming, which determines the fate of a number of RNAs during biological processes. Interestingly, the role of CSDE1 is bidirectional. It not only promotes and represses the translation of RNAs but also increases and decreases the abundance of RNAs. However, the mechanisms underlying this phenomenon are still unknown. In this review, we propose a “protein-RNA connector” model to explain this bidirectional role and depict its three versions: sequential connection, mutual connection and facilitating connection. As described in this molecular model, CSDE1 binds to RNAs and cooperates with other protein regulators. CSDE1 connects with different RNAs and their regulators for different purposes. The triple complex of CSDE1, a regulator and an RNA reprograms translation in different directions for each transcript. Meanwhile, a number of recent studies have found important roles for CSDE1 in human diseases. This model will help us to understand the role of CSDE1 in translational reprogramming and human diseases.

Graphical abstract
Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer
Authors: Yang Dan , He Yang , Wu Bo , Deng Yan , Wang Nan , Li Menglin , Liu Yang 
Published: January 2020

Abstract
Background
Ovarian cancer (OC) ranks fifth as a cause of gynecological cancer-associated death globally. Until now, the molecular mechanisms underlying the tumorigenesis and prognosis of OC have not been fully understood. This study aims to identify hub genes and therapeutic drugs involved in OC.

Methods
Four gene expression profiles (GSE54388, GSE69428, GSE36668, and GSE40595) were downloaded from the Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) in OC tissues and normal tissues with an adjusted P-value < 0.05 and a |log fold change (FC)| > 1.0 were first identified by GEO2R and FunRich software. Next, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were performed for functional enrichment analysis of these DEGs. Then, the hub genes were identified by the cytoHubba plugin and the other bioinformatics approaches including protein-protein interaction (PPI) network analysis, module analysis, survival analysis, and miRNA-hub gene network construction was also performed. Finally, the GEPIA2 and DGIdb databases were utilized to verify the expression levels of hub genes and to select the candidate drugs for OC, respectively.

Results
A total of 171 DEGs were identified, including 114 upregulated and 57 downregulated DEGs. The results of the GO analysis indicated that the upregulated DEGs were mainly involved in cell division, nucleus, and protein binding, whereas the biological functions showing enrichment in the downregulated DEGs were mainly negative regulation of transcription from RNA polymerase II promoter, protein complex and apicolateral plasma membrane, and glycosaminoglycan binding. As for the KEGG-pathway, the upregulated DEGs were mainly associated with metabolic pathways, biosynthesis of antibiotics, biosynthesis of amino acids, cell cycle, and HTLV-I infection. Additionally, 10 hub genes (KIF4A, CDC20, CCNB2, TOP2A, RRM2, TYMS, KIF11, BIRC5, BUB1B, and FOXM1) were identified and survival analysis of these hub genes showed that OC patients with the high-expression of CCNB2, TYMS, KIF11, KIF4A, BIRC5, BUB1B, FOXM1, and CDC20 were statistically more likely to have poorer progression free survival. Meanwhile, the expression levels of the hub genes based on GEPIA2 were in accordance with those based on GEO. Finally, DGIdb database was used to identify 62 small molecules as the potentially targeted drugs for OC treatment.

Conclusions
In summary, the data may produce new insights regarding OC pathogenesis and treatment. Hub genes and candidate drugs may improve individualized diagnosis and therapy for OC in future.
Studying the evolution of exception handling anti-patterns in a long-lived large-scale project
Authors: de Sousa Dêmora B C , Maia Paulo Henrique M. , Rocha Lincoln S , Viana Windson 
Published: January 2020

AbstractException handling is a well-known technique used to improve software robustness. However, recent studies report that developers typically neglect exception handling (mostly novice ones). We believe the quality of exception handling code in a software project is directly affected (i) by the absence, or lack of awareness, of an explicit exception handling policy and guidelines and (ii) by a silent rising of exception handling anti-patterns. In this paper, we investigate this phenomenon in a case study of a long-lived large-scale Java Web system in a Public Education Institution, trying to better understand the relationship between (i) and (ii), and the impact of developers’ turnover, skills, and guidance in (ii). Our case study takes into account the technical and human aspects. As a first step, we surveyed 21 developers regarding their perception of exception handling in the system’s institution. Next, we analysed the evolution of exception handling anti-patterns across 15 releases of the target system. We conducted a semi-structured interview with three senior software engineers, representatives of the development team, to present partial results of the case and raise possible causes for the found problems. The interviewed professionals and a second analysis of the code identified the high team turnover as the source of this phenomenon, since the public procurement process for hiring new developers has mostly attracted novice ones. These findings suggest that the absence of an explicit exception handling policy impacts negatively in the developers’ perception and implementation of exception handling. Furthermore, the absence of such policy has been leading developers to replicate existing anti-patterns and spread them through new features added during system evolution. We also observed that most developers have low skills regarding exception handling in general and low knowledge regarding the design and implementation of exception handling in the system. The system maintainer now has a diagnosis of the major causes of the quality problems in the exception handling code and was able to lead the required measures to repair this technical debt.
Does political risk matter for economic and financial risks in Venezuela?
Authors: Kirikkaleli Dervis 
Published: January 2020

AbstractIn this paper, the time–frequency dependency of political risk as well as economic and financial risks is explored in Venezuela using quarterly data from 1984Q1 to 2018Q4. The present study uses the wavelet coherence technique, which allows the investigation of both the long and short-term causal relationships between political risk and economic and financial risks in Venezuela. The findings of this study indicate that: (i) significant vulnerabilities in political risk, economic risk, and financial risk are observed at different time periods and different frequency levels; (ii) political risk has a strong power for explaining economic risk from 1995 to 2005 in the long run, while between 1984 and 2010, economic risk and political risk are positively correlated at different frequency levels; (iii) in the long run, changes in political risk significantly lead to changes in financial risk in Venezuela.
Epistatic interaction between PKD2 and ABCG2 influences the pathogenesis of hyperuricemia and gout
Authors: Dong Zheng , Zhou Jingru , Jiang Shuai , Li Yuan , Zhao Dongbao , Yang Chengde , Ma Yanyun , He Hongjun , Ji Hengdong , Jin Li , Zou Hejian , Wang Jiucun 
Published: January 2020

Abstract
Background
Genetic background affects serum urate concentration and gout risk, especially regarding these variants in the urate-transporter gene ABCG2. However, the role of epistasis between PKD2 and ABCG2 on the pathogenesis of gout is poorly understood. Here we assess this epistatic interaction in the progression from elevated serum urate to gout.

Results
We identified two epistatic interaction pairs (rs2728121: rs1481012 and rs2728121: rs2231137) were associated with urate levels in 4914 Chinese individuals (Pint = 0.018 and 0.004, respectively). Using subgroup analysis for gender and BMI, we found the degree of associations was varied by gender and BMI. The SNP pair rs2728121:rs1481012 influenced urate levels in females and overweight subjects (Pint = 0.006 and 0.022, respectively), but rs2728121:rs2231137 did in males, overweight and normal-weight subjects (Pint = 0.017, 0.047 and 0.013, respectively). Consistent results were also observed in associations between these epistatic interactions with hyperuricemia. Next, the SNP pair rs2728121:rs2231137 was identified to influence the development of gout from both hyperuricemia and healthy (Pint = 0.035 and 0.001, respectively), especially in males (Pint = 0.030 and 0.001, respectively). Furthermore, we demonstrated that interacting regions were enriched by regulatory elements. Finally, we observed a strong gene co-expression pattern between PKD2 and ABCG2 (r = 0.743, P = 5.83E-06).

Conclusion
Our findings indicate epistasis between PKD2 and ABCG2 influence serum urate concentrations, hyperuricemia and gout risk, thus providing insight into the pathogenesis of gout.
Aboveground biomass, growth and yield for some selected introduced tree species, namely Cupressus lusitanica, Eucalyptus saligna, and Pinus patula in Central Highlands of Ethiopia
Authors: Tesfaye Mehari Alebachew , Gardi Oliver , Anbessa Tesfaye Bekele , Blaser Jurgen 
Published: January 2020

AbstractBackgroundSpecies of the generaEucalyptus,Cupressus, andPinusare the most widely planted tree species in the country in general and in Chilimo dry Afromontane forest in particular. Eucalyptus covers 90% of the total planted forest area in the country. However, only limited information exists in the country regarding aboveground biomass (AGB), belowground biomass (BGB), growth, and yield. This study was conducted to assess the variables on 25 and 30 years of age for three planted species:Cupressus lusitanica,Eucalyptus saligna, andPinus patulain Chilimo plantation forest, in the Central Highlands of Ethiopia. A two-times inventory was conducted in 2012 and 2017. A total of nine square sampled plots of 400 m2each, three plots underCupressus lusitanica, 3Eucalyptus saligna, and 3Pinus patulawere used for data collection. Data on height, diameter, soil, and tree stumps were collected. Percent C, % N, and bulk density was performed following chemical procedure.ResultsThe aboveground biomass ranged from 125.76 to 228.67 t C ha−1and the basal area and number of stems from 3.76 to 25.50 m2 ha−1and 483 to 1175 N ha−1, respectively. The mean annual basal area and volume increment were between 0.97 and 1.20 m2 ha−1 year−1and 10.79 and 16.22 m3 ha−1 year−1. Both carbon and nitrogen stock of the planted forest was non-significant among the tree species.ConclusionThe aboveground biomass, growth, and yield significantly varied among the species.Cupressus lusitanicahad the highest aboveground biomass, volume, and basal area, whileEucalyptus salignahad the lowest value .To a depth of 1 m, total carbon stored ranged from 130.13 to 234.26 t C ha−1. The total annual carbon sequestration potential was 12,575.18 t CO2eq.Eucalyptus has the highest carbon stock density and growth rate than other species.
Changing wildfire, changing forests: the effects of climate change on fire regimes and vegetation in the Pacific Northwest, USA
Authors: Halofsky Jessica E. , Peterson David L. , Harvey Brian J. 
Published: January 2020

AbstractBackgroundWildfires in the Pacific Northwest (Washington, Oregon, Idaho, and western Montana, USA) have been immense in recent years, capturing the attention of resource managers, fire scientists, and the general public. This paper synthesizes understanding of the potential effects of changing climate and fire regimes on Pacific Northwest forests, including effects on disturbance and stress interactions, forest structure and composition, and post-fire ecological processes. We frame this information in a risk assessment context, and conclude with management implications and future research needs.ResultsLarge and severe fires in the Pacific Northwest are associated with warm and dry conditions, and such conditions will likely occur with increasing frequency in a warming climate. According to projections based on historical records, current trends, and simulation modeling, protracted warmer and drier conditions will drive lower fuel moisture and longer fire seasons in the future, likely increasing the frequency and extent of fires compared to the twentieth century. Interactions between fire and other disturbances, such as drought and insect outbreaks, are likely to be the primary drivers of ecosystem change in a warming climate. Reburns are also likely to occur more frequently with warming and drought, with potential effects on tree regeneration and species composition. Hotter, drier sites may be particularly at risk for regeneration failures.ConclusionResource managers will likely be unable to affect the total area burned by fire, as this trend is driven strongly by climate. However, fuel treatments, when implemented in a spatially strategic manner, can help to decrease fire intensity and severity and improve forest resilience to fire, insects, and drought. Where fuel treatments are less effective (wetter, high-elevation, and coastal forests), managers may consider implementing fuel breaks around high-value resources. When and where post-fire planting is an option, planting different genetic stock than has been used in the past may increase seedling survival. Planting seedlings on cooler, wetter microsites may also help to increase survival. In the driest topographic locations, managers may need to consider where they will try to forestall change and where they will allow conversions to vegetation other than what is currently dominant.
Pathologic assessment of tumor-associated macrophages and their histologic localization in invasive breast carcinoma
Authors: Mwafy Shorouk E. , El-Guindy Dina M. 
Published: January 2020

Abstract
Background
Tumor-associated macrophages (TAMs) are important in regulating cross-talk between tumor cells and tumor microenvironment. TAMs are involved in multiple steps of tumor progression and invasion. This study aimed to compare CD163 expression with the widely used CD68 pan-macrophage marker in invasive breast carcinoma. Furthermore, it focused on assessing the significance of TAMs localization in relation to clinicopathological parameters.

Results
CD68 and CD163 immunohistochemical expressions within TAMs infiltrating both tumor nest (TN) and tumor stroma (TS) were evaluated in 60 specimens with invasive breast carcinoma. High CD68-positive stromal TAMs was significantly related to larger tumor, nodal metastasis and vascular invasion (p = 0.003, 0.037, 0.032, respectively), whereas high CD163-positive stromal TAMs was significantly related to larger tumors, nodal metastasis, stage III tumors, vascular invasion, estrogen receptor (ER) negativity, and triple-negative subtype (p = 0.023, < 0.001, 0.001, 0.022, 0.002, 0.017, respectively). On multivariate analysis, high CD68-positive TAMs infiltrating TS was significantly associated with larger tumor and positive nodal metastasis (p = 0.006 and 0.016, respectively), whereas high CD163 TAMs density within TS was significantly associated with positive vascular invasion, nodal metastasis, and molecular subtypes (p = 0.003, 0.001, and 0.009, respectively).

Conclusion
TAMs within tumor stroma and tumor nest have different levels of association with poor prognostic parameters. So, it is of great importance to consider the histologic localization of TAMs in addition to the degree of TAMs infiltration.
Germline and Somatic Tumor Testing in Epithelial Ovarian Cancer: ASCO Guideline
Authors: Konstantinopoulos Panagiotis A. , Norquist Barbara , Lacchetti Christina , Armstrong Deborah , Grisham Rachel N. , Goodfellow Paul J. , Kohn Elise C. , Levine Douglas A. , Liu Joyce F. , Lu Karen H. , Sparacio Dorinda , Annunziata Christina M. 
Published: January 2020

PURPOSE To provide recommendations on genetic and tumor testing for women diagnosed with epithelial ovarian cancer based on available evidence and expert consensus. METHODS A literature search and prospectively defined study selection criteria sought systematic reviews, meta-analyses, randomized controlled trials (RCTs), and comparative observational studies published from 2007 through 2019. Guideline recommendations were based on the review of the evidence. RESULTS The systematic review identified 19 eligible studies. The evidence consisted of systematic reviews of observational data, consensus guidelines, and RCTs. RECOMMENDATIONS All women diagnosed with epithelial ovarian cancer should have germline genetic testing for BRCA1/2 and other ovarian cancer susceptibility genes. In women who do not carry a germline pathogenic or likely pathogenic BRCA1/2 variant, somatic tumor testing for BRCA1/2 pathogenic or likely pathogenic variants should be performed. Women with identified germline or somatic pathogenic or likely pathogenic variants in BRCA1/2 genes should be offered treatments that are US Food and Drug Administration (FDA) approved in the upfront and the recurrent setting. Women diagnosed with clear cell, endometrioid, or mucinous ovarian cancer should be offered somatic tumor testing for mismatch repair deficiency (dMMR). Women with identified dMMR should be offered FDA-approved treatment based on these results. Genetic evaluations should be conducted in conjunction with health care providers familiar with the diagnosis and management of hereditary cancer. First- or second-degree blood relatives of a patient with ovarian cancer with a known germline pathogenic cancer susceptibility gene variant should be offered individualized genetic risk evaluation, counseling, and genetic testing. Clinical decision making should not be made based on a variant of uncertain significance. Women with epithelial ovarian cancer should have testing at the time of diagnosis.
Treaty 6 Cree Annuity Spending in the Territorial Economy of Western Canada, 1873–1905
Authors: Colpitts George 
Published: January 2020

AbstractBefore mass settlement occurred in Western Canada at the turn of the twentieth century, Indigenous people used treaty monetization and town spending to subvert the very forces of liberalism encouraged with the expansion of a colonial market economy. After 1880, the Cree of Treaty 6, in particular, chose to collectively spend their annuities in new towns to support traditional dances and ceremonies and, especially, to join together in large multiband gatherings. Despite increasingly restrictive government policies, particularly the pass system that limited Indigenous movement beyond reserves, town “Treaty Days” spending only declined in prevalence in the late 1890s when treaty annuities began quickly losing their extraordinary spending power.
A Comparison of Historical Evidence for Droughts in the Pre-Columbian Maya Codices with Climatological Evidence for Droughts during the Early and Late Classic Periods
Authors: Bricker Harvey M. , Bricker Victoria R. 
Published: January 2020

Abstract
An examination of several historical texts in the Maya codices reveals that droughts were a significant concern to the pre-Columbian Maya that ultimately resulted in the collapse of their civilization. The effects of such droughts mentioned in those texts include damage to crops, famine, and wildfires. The dates assigned to five droughts in the codical texts agree with dates obtained from the analysis of lacustrine cores and stalagmites in caves by climatologists.
Lamin A/C modulates spatial organization and function of the Hsp70 gene locus via nuclear myosin I
Authors: Pradhan Roopali , Nallappa Muhunden Jayakrishnan , Sengupta Kundan 
Published: January 2020

ABSTRACT
The structure–function relationship of the nucleus is tightly regulated, especially during heat shock. Typically, heat shock activates molecular chaperones that prevent protein misfolding and preserve genome integrity. However, the molecular mechanisms that regulate nuclear structure–function relationships during heat shock remain unclear. Here, we show that lamin A and C (hereafter lamin A/C; both lamin A and C are encoded by LMNA) are required for heat-shock-mediated transcriptional induction of the Hsp70 gene locus (HSPA genes). Interestingly, lamin A/C regulates redistribution of nuclear myosin I (NM1) into the nucleus upon heat shock, and depletion of either lamin A/C or NM1 abrogates heat-shock-induced repositioning of Hsp70 gene locus away from the nuclear envelope. Lamins and NM1 also regulate spatial positioning of the SC35 (also known as SRSF2) speckles – important nuclear landmarks that modulates Hsp70 gene locus expression upon heat shock. This suggests an intricate crosstalk between nuclear lamins, NM1 and SC35 organization in modulating transcriptional responses of the Hsp70 gene locus during heat shock. Taken together, this study unravels a novel role for lamin A/C in the regulation of the spatial dynamics and function of the Hsp70 gene locus upon heat shock, via the nuclear motor protein NM1.
This article has an associated First Person interview with the first author of the paper.
Effects of a titin mutation on force enhancement and force depression in mouse soleus muscles
Authors: Tahir Uzma , Monroy Jenna A. , Rice Nicole A. , Nishikawa Kiisa C. 
Published: January 2020

ABSTRACTThe active isometric force produced by muscles varies with muscle length in accordance with the force–length relationship. Compared with isometric contractions at the same final length, force increases after active lengthening (force enhancement) and decreases after active shortening (force depression). In addition to cross-bridges, titin has been suggested to contribute to force enhancement and depression. Although titin is too compliant in passive muscles to contribute to active tension at short sarcomere lengths on the ascending limb and plateau of the force–length relationship, recent evidence suggests that activation increases titin stiffness. To test the hypothesis that titin plays a role in force enhancement and depression, we investigated isovelocity stretching and shortening in active and passive wild-type and mdm (muscular dystrophy with myositis) soleus muscles. Skeletal muscles from mdm mice have a small deletion in the N2A region of titin and show no increase in titin stiffness during active stretch. We found that: (1) force enhancement and depression were reduced in mdm soleus compared with wild-type muscles relative to passive force after stretch or shortening to the same final length; (2) force enhancement and force depression increased with amplitude of stretch across all activation levels in wild-type muscles; and (3) maximum shortening velocity of wild-type and mdm muscles estimated from isovelocity experiments was similar, although active stress was reduced in mdm compared with wild-type muscles. The results of this study suggest a role for titin in force enhancement and depression, which contribute importantly to muscle force during natural movements.