bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of Specialist Beech-Feeding Underwing Moths From Taiwan (Lepidoptera: Erebidae: Catocalinae) and Its Implication to Biodiversity Conservation of Taiwan Beech Forests
Authors: Hsu Yu-Feng , Wang Li-Hao , Huang Chia-Lung , Braby Michael F , Lin Wen-Jie , Lin Rung-Juen , Hsu Yu-Ming 
Published: December 2020

Abstract
Deciduous Beech (Fagus spp.) forests have a highly disjunct distribution in the Northern Hemisphere, with greatest diversity in eastern Asia. Although Fagus supports a rich phytophagous insect fauna, the diversity, composition, and host specialization of insects associated with these trees in Asia are less well known compared with Europe and North America. For instance, two species of Catocala moths, both considered endemic to Japan, were previously known as the only beech-feeding specialists of this genus. However, two Catocala species were recently discovered from Taiwan during a survey of phytophagous insects on Taiwan Beech Fagus hayatae, a threatened plant. Identification of these two species of moths was determined by mtDNA (COI barcodes), adult morphology, including wing pattern and genitalia, and biology. Based on these multiple sources of evidence, we conclude that one species represents an undescribed species and the other a new subspecies of a species previously known only from mainland China. The taxonomic treatments in the present work include Catocala seiohbo sanctocula Hsu & Huang, subsp. nov., C. nimbosa Hsu & Wang, sp. nov. and C. nubila ohshimai, stat. nov. In Taiwan, Catocala spp. occur mainly in large, undisturbed patches of Taiwan Beech forest and are codependent on F. hayatae. Thus, they are not only considered to be at risk of co-extinction, but may serve as potential indicator species to monitor the extent and health of this threatened ecological community.
Why we need to evaluate long-term antidepressant use in older patients with depression
Authors: Batelaan Neeltje , Scholten Willemijn , Rhebergen Didi , Van Balkom Anton 
Published: December 2020

Abstract
In this commentary, we address current clinical practice of long-term antidepressant use in older adults with depression, and recommend improvements. Compared with younger adults, older adults more frequently use antidepressants in the long term, although they may not always benefit from them, and in spite of an increased risk for adverse events. Unfortunately, evaluations of long-term antidepressant use are sparse, especially in older age groups. To prevent and reduce inappropriate long-term use and adverse events, antidepressant use in older age groups should be regularly evaluated.
Individual Factors of Botulinum Type A in Treatment of Gummy Smile: A Prospective Study
Authors: Gong Xi , Huang Hongyuan , Gu Chenyang , Li Facheng , Zou Lidong , An Yang , Han Xuefeng , Tang Zhihui 
Published: December 2020

Abstract

Background
Botulinum type A (BTX-A) injection is a promising treatment for gummy smile (GS), although its effects are varied and inconsistent.

Objectives
The aim of this study was to explore the effect of individual factors on BTX-A treatment for GS, and to establish treatment expectations.

Methods
In this prospective clinical study, a standardized technique comprising bilateral single-point injections of 2 U BTX-A (total, 4 U) was administered to all GS patients. Data were collected at baseline and after 4, 12, and 32 weeks of follow-up. Twenty-nine potential individual factors were analyzed by correlation and regression analysis to exclude confounding bias.

Results
Ninety-four patients completed the BTX-A treatment. After adjusting for potential confounding factors, the correlation and regression analysis confirmed the following formula: anterior gingival exposure (GE) at 4 weeks = 1.44 + (0.94 × baseline anterior GE) − (1.88 × sex) (where male = 1 and female = 2). The confidence interval (CI) of the prediction showed that for all female participants with baseline anterior GE &lt;5.3 mm, the 95% CI of anterior GE was 0.3 to 3.0 mm after 4 weeks of treatment, and 3.0 to 8.9 mm with baseline anterior GE ≥6 mm. For male patients with baseline anterior GEs of 3 and ≥4.6 mm, the 95% CIs were 1.5 to 3.3 mm and 3.2 to 8.9 mm, respectively.

Conclusions
The effect of average-dose BTX-A treatment for GS depended on GS severity and patient’s sex, rather than GS etiology and other factors. Female participants with baseline anterior GE &lt;5.3 mm were more likely to show complete improvement after 4 weeks of treatment. However, female participants with baseline anterior GE ≥6.0 mm or male participants were less likely to show complete improvement at 4 weeks.

Level of Evidence: 4
Riboexp: an interpretable reinforcement learning framework for ribosome density modeling
Authors: Hu Hailin , Liu Xianggen , Xiao An , Li YangYang , Zhang Chengdong , Jiang Tao , Zhao Dan , Song Sen , Zeng Jianyang 
Published: December 2020

AbstractTranslation elongation is a crucial phase during protein biosynthesis. In this study, we develop a novel deep reinforcement learning-based framework, named Riboexp, to model the determinants of the uneven distribution of ribosomes on mRNA transcripts during translation elongation. In particular, our model employs a policy network to perform a context-dependent feature selection in the setting of ribosome density prediction. Our extensive tests demonstrated that Riboexp can significantly outperform the state-of-the-art methods in predicting ribosome density by up to 5.9% in terms of per-gene Pearson correlation coefficient on the datasets from three species. In addition, Riboexp can indicate more informative sequence features for the prediction task than other commonly used attribution methods in deep learning. In-depth analyses also revealed the meaningful biological insights generated by the Riboexp framework. Moreover, the application of Riboexp in codon optimization resulted in an increase of protein production by around 31% over the previous state-of-the-art method that models ribosome density. These results have established Riboexp as a powerful and useful computational tool in the studies of translation dynamics and protein synthesis. Availability: The data and code of this study are available on GitHub: https://github.com/Liuxg16/Riboexp. Contact:zengjy321@tsinghua.edu.cn; songsen@tsinghua.edu.cn
IGD: high-performance search for large-scale genomic interval datasets
Authors: Feng Jianglin , Sheffield Nathan C 
Published: December 2020

Abstract

Summary
Databases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions.

Availabilityand implementation
https://github.com/databio/IGD.

Supplementary information
Supplementary data are available at Bioinformatics online.
The software for interactive evaluation of mass spectra stability and reproducibility
Authors: Zhvansky E S , Sorokin A A , Bormotov D S , Bocharov K V , Zavorotnyuk D S , Ivanov D G , Nikolaev E N , Popov I A 
Published: December 2020

Abstract

Summary
Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra.

Availability and implementation
Source code, example datasets, binaries and other information are available at https://github.com/EvgenyZhvansky/R_matrix.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improving circRNA–disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks
Authors: Lu Chengqian , Zeng Min , Wu Fang-Xiang , Li Min , Wang Jianxin 
Published: December 2020

Abstract

Motivation
Emerging studies indicate that circular RNAs (circRNAs) are widely involved in the progression of human diseases. Due to its special structure which is stable, circRNAs are promising diagnostic and prognostic biomarkers for diseases. However, the experimental verification of circRNA–disease associations is expensive and limited to small-scale. Effective computational methods for predicting potential circRNA–disease associations are regarded as a matter of urgency. Although several models have been proposed, over-reliance on known associations and the absence of characteristics of biological functions make precise predictions are still challenging.

Results
In this study, we propose a method for predicting CircRNA–disease associations based on sequence and ontology representations, named CDASOR, with convolutional and recurrent neural networks. For sequences of circRNAs, we encode them with continuous k-mers, get low-dimensional vectors of k-mers, extract their local feature vectors with 1D CNN and learn their long-term dependencies with bi-directional long short-term memory. For diseases, we serialize disease ontology into sentences containing the hierarchy of ontology, obtain low-dimensional vectors for disease ontology terms and get terms’ dependencies. Furthermore, we get association patterns of circRNAs and diseases from known circRNA–disease associations with neural networks. After the above steps, we get circRNAs’ and diseases’ high-level representations, which are informative to improve the prediction. The experimental results show that CDASOR provides an accurate prediction. Importing the characteristics of biological functions, CDASOR achieves impressive predictions in the de novo test. In addition, 6 of the top-10 predicted results are verified by the published literature in the case studies.

Availability and implementation
The code and data of CDASOR are freely available at https://github.com/BioinformaticsCSU/CDASOR.
The Use of Digital Platforms for Community-Based Monitoring
Authors: Johnson Noor , Druckenmiller Matthew L , Danielsen Finn , Pulsifer Peter L 
Published: December 2020

AbstractEnvironmental observing programs that are based on Indigenous and local knowledge increasingly use digital technologies. Digital platforms may improve data management in community-based monitoring (CBM) programs, but little is known about how their use translates into tangible results. Drawing on published literature and a survey of 18 platforms, we examine why and how digital platforms are used in CBM programs and illuminate potential challenges and opportunities. Digital platforms make it easy to collect, archive, and share CBM data, facilitate data use, and support understanding larger-scale environmental patterns through interlinking with other platforms. Digital platforms, however, also introduce new challenges, with implications for the sustainability of CBM programs and communities’ abilities to maintain control of their own data. We expect that increased data access and strengthened technical capacity will create further demand within many communities for ethically developed platforms that aid in both local and larger-scale decision-making.
Great Expectations: Deconstructing the Process Pathways Underlying Beaver-Related Restoration
Authors: Nash Caroline S , Grant Gordon E , Charnley Susan , Dunham jason B , Gosnell Hannah , Hausner Mark B , Pilliod David S , Taylor Jimmy D 
Published: December 2020

ABSTRACTBeaver-related restoration is a process-based strategy that seeks to address wide-ranging ecological objectives by reestablishing dam building in degraded stream systems. Although the beaver-related restoration has broad appeal, especially in water-limited systems, its effectiveness is not yet well documented. In this article, we present a process-expectation framework that links beaver-related restoration tactics to commonly expected outcomes by identifying the set of process pathways that must occur to achieve those expected outcomes. We explore the contingency implicit within this framework using social and biophysical data from project and research sites. This analysis reveals that outcomes are often predicated on complex process pathways over which humans have limited control. Consequently, expectations often shift through the course of projects, suggesting that a more useful paradigm for evaluating process-based restoration would be to identify relevant processes and to rigorously document how projects do or do not proceed along expected process pathways using both quantitative and qualitative data.
How does Lived Experience of Incarceration Impact Upon the Helping Process in Social Work Practice?: A Scoping Review
Authors: Duvnjak Angella , Stewart Victoria , Young Peter , Turvey Leah 
Published: December 2020

Abstract
Whilst the value of lived experience in the helping process is recognised in a range of settings including mental health, disability and substance addiction, the understanding of therole of lived experience of incarceration in the helping process is less developed. This is relevant to the question of gatekeeping into the social work profession. A heightened focus on risk has resulted in limited opportunity for those with a history of incarceration from studying and practising social work. Little is known about how a lived experience of incarceration influences the helping relationship, and in turn we know very little about the implications for service users of having reduced access to social workers who have experienced imprisonment. To better understand the current state of knowledge regarding the role of lived experience of incarceration in the helping process, a scoping review of the literature was undertaken. A thematic analysis of sixty-one articles published before 2019 was undertaken and consensus was achieved on four themes: stigma and discrimination; trust and authenticity; role modelling and hope; and, power and agency. The findings include recommendations for more nuanced policy regarding the restriction of those with a lived experience of incarceration entering the social work profession.
Dual Analysis of N-methyl-2-pyridone-5-carboxamide and N-1-methylnicotinamide in Urine by HPLC with UV Detection
Authors: Nguyen Van Long , Saldanha Roxanne , Fitzpatrick Michael 
Published: December 2020

Abstract
N-methyl-2-pyridone-5-carboxamide (2PYr) and N-1-methylnicotinamide (NMN) are metabolites of the water soluble Vitamin B3 (Nicotinamide). Limited methodologies exist for their dual chromatographic analysis in urine samples. In this study, we developed a method for analysis of both 2PYr and NMN by ultraviolet detection. Urine samples were treated to a salting-out assisted liquid/liquid extraction for the extraction of 2PYr and cation exchange for NMN. Both analytes were separated on a Biphenyl 100 × 2.1 mm, 2.6-μm column. The new assay’s performance (specifically 2PYr) was compared against the existing testing protocol (based on a previously published method). Linearity for both analytes was above 0.99 (r 2) up to a concentration range of: 1500 μmol/L (2PYr) and 150 μmol/L (NMN). Intra-assay and inter-assay precision of the method was below 8% (coefficient of variation) except at the lower limit of quantification where it was below 20%. Recovery of 2PYr was above 80% and NMN above 90%. A significant positive bias was observed with 2PYr against the existing method. This new method allows for both 2PYr and NMN to be chromatographed and overcomes sample preparation issues in urine 2PYr analysis.
Human Immunodeficiency Virus (HIV) Care Models During the Coronavirus Disease 2019 (COVID-19) Era
Authors: Guaraldi Giovanni , Milic Jovana , Martinez Esteban , Kamarulzaman Adeeba , Mussini Cristina , Waters Laura , Pozniak Anton , Mallon Patrick , Rockstroh Jürgen K , Lazarus Jeffrey V 
Published: December 2020

Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an unprecedented global challenge that substantially risks reversing the progress in ending human immunodeficiency virus (HIV). At the same time, it may offer the opportunity for a new era of HIV management. This viewpoint presents the impact of COVID-19 on HIV care, including the Joint United Nations Programme on HIV/AIDS (UNAIDS) “three 90s” targets. It outlines how to enhance a patient-centered care approach, now known as the “fourth 90,” by integrating face-to-face patient–physician and telemedicine encounters. It suggests a framework for prevention and treatment of multimorbidity and frailty, to achieve a good health-related quality of life, and to preserve intrinsic capacity in all people living with HIV.
Whiskers as a novel tissue for tracking reproductive and stress-related hormones in North Pacific otariid pinnipeds
Authors: Keogh Mandy J , Charapata Patrick , Fadely Brian S , Zeppelin Tonya , Rea Lorrie , Waite Jason N , Burkanov Vladimir , Marshall Chris , Jones Aubree , Sprowls Caitlin , Wooller Matthew J 
Published: December 2020

Abstract
Keratinized tissues, including whiskers, are ideal for acquiring a record of physiological parameters. Most tissues provide a snapshot of physiological status; however, whiskers may support longitudinal sampling for reproductive and stress-related hormones, if hormones are incorporated as whiskers grow and concentrations change with physiological state. Whiskers from female Steller sea lions (Eumetopias jubatus) and northern fur seals (Callorhinus ursinus) were serially sectioned and pulverized and steroid hormones were extracted. Standard methods were used to validate enzyme immunoassay kits for cortisol, progesterone, 17β-estradiol and testosterone. All hormones were measurable in whisker segments from both species with progesterone concentrations showing cyclical patterns, which appear to signify previous pregnancies or luteal phases. Yearly progesterone concentrations were greater in years a pup was produced compared with years when no pup was observed. Free-ranging female Steller sea lions had reproductive rates between 0 and 1.0 (0.53 ± 0.33, n = 12) using a yearly progesterone concentration of 30 pg/mg or greater to classify a reproductive year as producing a pup and below 30 pg/mg as non-reproductive. Cortisol concentrations were greater near the root and rapidly declined, lacking any obvious patterns, throughout the rest of the whisker. Progesterone and testosterone concentrations were able to help determine sex of unknown individuals. Immunohistochemistry revealed that steroid hormones most likely do not leach out of whiskers based on the deposition patterns of progesterone and cortisol being present throughout the whisker length. Overall, measuring steroid hormones in whiskers can reveal individual reproductive histories over multiple years in sea lions and fur seals. Cyclical patterns of δ15N were useful for identifying periods of up to ~10 years of growth within whiskers, and measuring both stable isotopes and hormones may be useful for differentiating periods of active gestation from diapause and potentially track multi-year reproductive histories of female otariids.
Do Viruses From Managed Honey Bees (Hymenoptera: Apidae) Endanger Wild Bees in Native Prairies?
Authors: Pritchard Zoe A , Hendriksma Harmen P , St Clair Ashley L , Stein David S , Dolezal Adam G , O’Neal Matthew E , Toth Amy L 
Published: December 2020

AbstractPopulations of wild and managed pollinators are declining in North America, and causes include increases in disease pressure and decreases in flowering resources. Tallgrass prairies can provide floral resources for managed honey bees (Hymenoptera: Apidae, Apis mellifera Linnaeus) and wild bees. Honey bees kept near prairies may compete with wild bees for floral resources, and potentially transfer viral pathogens to wild bees. Measurements of these potential interactions are lacking, especially in the context of native habitat conservation. To address this, we assessed abundance and richness of wild bees in prairies with and without honey bee hives present, and the potential spillover of several honey bee viruses to bumble bees (Hymenoptera: Apidae, Bombus Latrielle). We found no indication that the presence of honey bee hives over 2 yr had a negative effect on population size of wild bee taxa, though a potential longer-term effect remains unknown. All levels of viruses quantified in bumble bees were lower than those observed in honey bees. Higher levels of deformed wing virus and Israeli acute paralysis virus were found in Bombus griseocollis DeGeer (Hymenoptera: Apidae) collected at sites with hives than those without hives. These data suggest that the presence of honey bees in tallgrass prairie could increase wild bee exposure to viruses. Additional studies on cross-species transmission of viruses are needed to inform decisions regarding the cohabitation of managed bees within habitat utilized by wild bees.
Percutaneous coronary intervention in patients with cancer and readmissions within 90 days for acute myocardial infarction and bleeding in the USA
Authors: Kwok Chun Shing , Wong Chun Wai , Kontopantelis Evangelos , Barac Ana , Brown Sherry-Ann , Velagapudi Poonam , Hilliard Anthony A , Bharadwaj Aditya S , Chadi Alraies M , Mohamed Mohamed , Bhatt Deepak L , Mamas Mamas A 
Published: December 2020

Abstract

Aims
The post-discharge outcomes of patients with cancer who undergo PCI are not well understood. This study evaluates the rates of readmissions within 90 days for acute myocardial infarction (AMI) and bleeding among patients with cancer who undergo percutaneous coronary intervention (PCI).

Methods and results
Patients treated with PCI in the years from 2010 to 2014 in the US Nationwide Readmission Database were evaluated for the influence of cancer on 90-day readmissions for AMI and bleeding. A total of 1 933 324 patients were included in the analysis (2.7% active cancer, 6.8% previous history of cancer). The 90-day readmission for AMI after PCI was higher in patients with active cancer (12.1% in lung, 10.8% in colon, 7.5% in breast, 7.0% in prostate, and 9.1% for all cancers) compared to 5.6% among patients with no cancer. The 90-day readmission for bleeding after PCI was higher in patients with active cancer (4.2% in colon, 1.5% in lung, 1.4% in prostate, 0.6% in breast, and 1.6% in all cancer) compared to 0.6% among patients with no cancer. The average time to AMI readmission ranged from 26.7 days for lung cancer to 30.5 days in colon cancer, while the average time to bleeding readmission had a higher range from 38.2 days in colon cancer to 42.7 days in breast cancer.

Conclusions
Following PCI, patients with cancer have increased risk for readmissions for AMI or bleeding, with the magnitude of risk depending on both cancer type and the presence of metastasis.