bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Bloodmeals from Sand Flies (Diptera: Psychodidae) Collected in the Parque Nacional do Viruá, State of Roraima, Brazil
Authors: Rodrigues Bruno Leite , Costa Glaucilene da Silva , Shimabukuro Paloma Helena Fernandes 
Published: April 2021

Abstract
The transmission of pathogens that cause leishmaniases occurs by the bite of female sand flies (Diptera: Psychodidae) in their vertebrate hosts, which makes the identification of their bloodmeal sources an important step for the control and epidemiology of these diseases. In Brazil, the state of Roraima has a great diversity of sand flies, vertebrate hosts, and protozoan Leishmania, but little is known about the host blood-feeding preferences of sand flies. Thus, we evaluated the bloodmeal sources of sand flies collected from their sylvatic habitats in Parque Nacional do Viruá, Roraima. Fieldwork was carried-out between 13th and 18th August 2019 using CDC light traps. Sand flies were slide-mounted and morphologically identified using the head and last segments of the abdomen. Engorged females had their DNA extracted, followed by amplification and sequencing of the cytochrome b (cytb) molecular marker for vertebrates. Sequences were analyzed and compared with those from GenBank using the BLASTn search tool, in addition to the reconstruction of a phylogenetic tree to demonstrate the clustering pattern of these sequences. A total of 1,209 sand flies were identified, comprising 20 species, in which the most abundant were Psychodopygus ayrozai (Barretto and Coutinho) (42.10%) and Psychodopygus chagasi (Costa Lima) (26.22%). Bloodmeal source identification was successfully performed for 34 sand flies, that confirm four vertebrate species, being the most abundant the armadillo Dasypus novemcinctus Linnaeus, 1758 (Cingulata: Dasypodidae).
Nomograms for Differentiated Thyroid Carcinoma Patients Based on the Eighth AJCC Staging and Competing Risks Model
Authors: Li Chengzhuo , Xu Fengshuo , Huang Qiao , Han Didi , Zheng Shuai , Wu Wentao , Zhao Fanfan , Feng Xiaojie , Lyu Jun 
Published: April 2021

Abstract

Background
Differentiated thyroid carcinoma (DTC) patients have a long survival period and good prognosis, so they are easily affected by competing risk events. The purpose of this study was to use the competing risks model to identify prognostic factors for cause-specific death (CSD) and death due to other causes (DOC) in patients with DTC.

Methods
Our screening process identified 34 585 DTC patients in the Surveillance, Epidemiology, and End Results database and randomly divided them into a training cohort and a validation cohort. We used the Fine and Gray subdistribution hazards model to establish the CSD and DOC nomograms. The distinguishing ability and consistency of the nomograms were evaluated using the consistency indexes and calibration plots.

Results
Our analysis of a competing risks model revealed that pathological grade, tumor size, histological type, American Joint Committee on Cancer (AJCC)–8 stage, surgery status, adjuvant radiotherapy status, adjuvant chemotherapy status, and log odds of positive lymph nodes are prognostic factors for CSD, and age at diagnosis, year of diagnosis, sex, pathological grade, tumor size, AJCC-8 stage, surgery status, adjuvant radiotherapy status, and lymph node ratio are prognostic factors for DOC. The 1-year, 3-year, and 5-year concordance indexes in the validation cohorts were 0.942, 0.931, and 0.913 for the CSD nomogram and 0.813, 0.746, and 0.776 for the DOC nomogram. The calibration plots showed good consistency in both nomograms.

Conclusions
Our nomograms can be used as a tool to help clinicians individually predict the probability of CSD and DOC in DTC patients at 1 year, 3 years, and 5 years, which has certain guiding value in clinical applications.
Poor-Prognosis Metastatic Cancers in Adolescents and Young Adults: Incidence Patterns, Trends, and Disparities
Authors: Sheth Bhutada Jessica , Hwang Amie , Liu Lihua , Deapen Dennis , Freyer David R 
Published: April 2021

Abstract

Background
For adolescents and young adults (AYAs, aged 15-39 years) with cancer, metastatic disease at diagnosis is the strongest predictor of mortality, but its associations with age and sociodemographic factors are largely unexplored.

Methods
Using Surveillance, Epidemiology, and End Results Program data from 2000 to 2016, we collected incident cases of poor-prognosis metastatic cancer (5-year survival &lt; 50%) and compared the proportion, incidence, time trends, and incidence rate ratios for race and ethnicity, sex, and socioeconomic status among AYAs, middle-aged adults (aged 40-64 years) and older adults (aged 65-79 years).

Results
From 2000 to 2016, a total of 17 210 incident cases of poor-prognosis metastatic cancer were diagnosed in AYAs, 121 274 in middle-aged adults, and 364 228 in older adults. Compared with older patients, the proportion of AYAs having metastatic disease was equivalent or substantially lower in nearly every site except stomach and breast cancers, which were statistically significantly higher for AYAs compared with middle-aged and older adults (stomach: 57.3% vs 46.4% and 39.5%; breast: 6.6% vs 4.4% and 5.6%, respectively; 2-sided P &lt; .001 for all comparisons). Incidence rates rose significantly faster among AYAs for breast, stomach, and kidney cancers and among AYAs and middle-aged adults for colorectal cancer. Markedly higher incidence rate ratios were noted for AYA racial and ethnic minorities with breast, stomach, and especially kidney cancer, where only non-Hispanic Black AYAs were at considerably higher risk. For most sites, incidence rate ratios were higher among male patients and individuals of low socioeconomic status across age groups.

Conclusions
For most cancers, AYAs are not more likely to present with metastases than middle-aged and older adults. Further investigation is warranted for the disproportionate rise in incidence of metastatic breast, stomach, and kidney cancer among AYAs and their excess burden among AYA racial and ethnic minorities. The rising incidence of colorectal cancer among AYAs and middle-aged adults remains an additional concern.
Estimating Marginal Costs of Additional Water Flow from a Loblolly Pine Stand in South Georgia, United States
Authors: Bawa Ranjit , Dwivedi Puneet 
Published: April 2021

AbstractCertain silvicultural operations enhance the flow of ecosystem services derived from forestlands. Monetary estimates of an increased flow of such services that can impact forest management decisions are generally lacking. Here we use a growth-and-yield model to estimate physical changes in water yield and assign monetary values to these changes under different regimes of forest thinning and planting density in a loblolly pine (Pinus taeda L.) stand located in South Georgia. The model is expanded to develop corresponding measures of water yield and net present value per each management scenario. Results show an expected inverse relationship between average annual water yield and economic rent. Further, the marginal costs associated with producing an extra liter of water (per unit area) decrease as thinning intensifies and planting density declines (US$1.35/kL to US$0.72/kL under a site index of 18.3 m and US$1.20/kL to US$0.66/kL, assuming a site index of 21.3 m) relative to our baseline scenario. We emphasize that a landowner’s profits may be negatively affected by the provision of improved water yield downstream as it competes with timber extraction. Monetary payments are needed to encourage the net production of water from existing loblolly pine stands in South Georgia, United States.
The sexual dimorphism displayed by the roots of mulberry (Morus alba) saplings depends on the sex of the neighboring plants
Authors: Zhang Chunyan , Zhu Juan , Liu Gang , Huang Youyou , Huang Gaiqun , Xu Xiao 
Published: April 2021

Abstract

Aims
Dioecious plants present sexual dimorphism, but how the root traits and nutrient uptake of female and male plants in dioecious species response to the sexual identity change of the neighbor plants are poorly understood.

Methods
Mulberry (Morus alba L.), a dioecious plant widely distributed in China, was employed in our study. Male and female plants were grown with neighbors of the same and opposite sex for 3 months. At harvest, the root anatomy, root morphology, nutrient concentrations and biomass accumulation were measured.

Important Findings
When grown with the opposite sex, the males showed decreases in root xylem size, biomass of root and stem and increases in root N, P and K concentrations compared with grown with the same sex. By contrast, females showed significant increases in xylem size, fine root system (e.g. fine root length, root surface area and root volume), root carbon isotope composition (δ 13C) and root N, P and K concentrations. The changes in the δ 13C and N, P and K concentrations in male and female plants were associated with the changes of root traits. These results demonstrated that the sexual identity of the neighboring plants affected root anatomy and morphology of female and male mulberry plants. Meanwhile, the responses of female and male plants to the sex change of the neighboring plants showed sexual dimorphism, which influenced water-use efficiency and resource acquisition. These findings are important for understanding the population dynamics of other dioecious species in forestry and natural systems.
Provenance-specific ecophysiological responses to drought in Cunninghamia lanceolata
Authors: Gao Shuang , Cai Ze-Yu , Yang Cong-Cong , Luo Jian-Xun , Zhang Sheng 
Published: April 2021

Abstract

Aims
Cunninghamia lanceolata is one of the most important coniferous species in southern China, but its high sensitivity to drought restricts its expansion. Understanding the intraspecific variation of physiological responses to drought can help us manage this plantation better.

Methods
We selected 3-year-old seedlings of C. lanceolata, which originated from the low precipitation (LP), middle precipitation (MP) and high precipitation (HP) habitats, respectively. Seedlings were grown under drought stress (20% of soil volumetric water content) for 40 days. The ecophysiological responses and adaptive strategies with different drought tolerance were investigated.

Important Findings
LP provenance possessed the best tolerance to drought stress, suggesting that considerably increased carbohydrates and nitrogen-containing compounds as osmotic protective materials, which were driven by fast carbon and nitrogen metabolisms. In addition, the highest peroxidase activity could effectively eliminate hydrogen peroxide in drought-stressed LP provenance. The MP provenance reserved a large amount of non-structural carbohydrates, which may act as a certain buffer for encountering drought stress. Importantly, timely closure of stomata to reduce needle transpiration when encountering a water deficiency would help them adapt to long-term drought. MP provenance adopted a conservative water-saving strategy. However, HP provenance regulated root growth (increased root/shoot ratio) and reduced penetration potential to help them absorb water. The different strategies among provenances may be related to the long-term domestication of the geographical environments. Therefore, our results underline the importance of provenance-specific responses to drought stress. It is highly significant to accelerate the selection of drought-resistant germplasms and to cultivate high-yield plantations in the future.
Barriers to adverse drug reaction reporting in Malaysia: a narrative review based on theoretical domains framework
Authors: Shaik Rahmat Shakirin , Karuppannan Mahmathi 
Published: April 2021

Abstract

Objectives
This review aims to determine the common barriers to adverse drug reaction (ADR) reporting in Malaysia based on theoretical domains framework (TDF).

Methods
Three online databases, PubMed (Medline), Scopus and Web of Science, were searched from 2000 to 2020 to identify related quantitative and qualitative studies.

Key findings
Eleven articles were reviewed – nine quantitative and two qualitative studies. Three domains from TDF were identified as the most common: (1) knowledge, (2) skills and (3) environmental context and resources. Lack of awareness of an ADR reporting system, lack of clinical and ADR knowledge and lack of time were identified as the main barriers. Additionally, assumption of healthcare professionals (HCPs) of ADR to be too insignificant or too well known and unavailability of the ADR form were also reported as barriers for reporting an ADR.

Conclusions
The findings from this narrative review could be useful for the policymakers in planning strategies at the national level to improve the reporting rate of ADR in Malaysia. It is necessary to promote and publicize pharmacovigilance activities and to enhance communication and engagement between the Malaysian ADR Advisory Committee and the HCPs and consumers. There is also a need to increase training and continuous education related to ADR and pharmacovigilance system and making ADR reporting compulsory for all HCPs.
Remodelling (Un)certainty: Outsourcing and Auditing Refugee Reception in Switzerland
Authors: Alberti Camilla 
Published: April 2021

AbstractBy approaching outsourcing through an ethnographic lens, this article focuses on the policies that enable public authorities to deal with the many uncertainties of refugee reception. It investigates how cantonal (subnational) governments in Switzerland remodel these uncertainties by implementing the policy of reception through private intermediaries, namely actors, instruments, and rationalities from the private sphere. The analysis shows that by thickening the interface between the decision-making and implementation spheres, these elements constitute a multilayer buffer zone that dilutes, absorbs, and also shifts the insecurities related to the governance of refugee reception. The article argues that the use of private intermediaries enables the state to ‘navigate within’ unpredictable temporalities and realities, but also to ‘govern through’ uncertainty as it is transferred and (re)produced in the implementation work carried out by the mandated organizations. This article thus apprehends uncertainty as a structural and organisational condition and a mechanism that together shape how different governmental actors engage with (the reception of) refugees.
Efficacy and safety of pentamidine isethionate for tegumentary and visceral human leishmaniasis: a systematic review
Authors: Piccica Matteo , Lagi Filippo , Bartoloni Alessandro , Zammarchi Lorenzo 
Published: April 2021

Abstract

Rationale for Review
We performed a systematic review of the literature to investigate the efficacy and safety of pentamidine isethionate for the treatment of human tegumentary and visceral leishmaniasis.

Key findings
A total of 616 papers were evaluated, and 88 studies reporting data on 3108 cases of leishmaniasis (2082 patients with tegumentary leishmaniasis and 1026 with visceral leishmaniasis) were finally included. The majority of available studies were on New World cutaneous leishmaniasis and visceral leishmaniasis caused by Leishmania donovani. At the same time, few data are available for Old World cutaneous leishmaniasis, mucosal leishmaniasis, and visceral leishmaniasis caused by L. infantum. Pooled cure rate for tegumentary leishmaniasis was 78.8% (CI 95%, 76.9–80.6%) and 92.7% (CI 95%, 88.3–97.1%) according to controlled randomized trial and observational studies and case report and case series respectively. Pooled cure rate for visceral leishmaniasis was 84.8% (CI 95%, 82.6–87.1%) and 90.7% (CI 95%, 84.1–97.3%) according to controlled randomized trial and observational studies and case report and case series, respectively. Comparable cure rate was observed in recurrent and refractory cases of visceral leishmaniasis. Concerning the safety profile, among about 2000 treated subjects with some available information, the most relevant side effects were six cases of arrhythmia (including four cases of fatal ventricular fibrillation), 20 cases of irreversible diabetes, 26 cases of muscular aseptic abscess following intramuscular administration.

Conclusions/recommendations
Pentamidine isethionate is associated with a similar cure rate of the first-line anti-leishmanial drugs. Severe and irreversible adverse effect appear to be rare. The drug may still have a role in the treatment of any form of human leishmaniasis when the first-line option has failed or in patients who cannot tolerate other drugs also in the setting of travel medicine. In difficult cases, the drug can also be considered as a component of a combination treatment regimen.
Nestorius and Nestorianism
Authors: Adams Robert Merrihew 
Published: April 2021

Abstract
This paper has three parts. The first outlines the history of Nestorianism. From the end of the fifth century all the way into the thirteenth century (c.e.), quite a large population—in fact most Christians in Asia—belonged to branches of the Nestorian church. The second part provides a brief biography of Nestorius, after whom this church was named. The third part explores two elements of Nestorius’s christology, as they are found in his posthumously discovered theological writings. (1) Does Christ have one nature or two (both human and divine), and if two, how can one person have two natures? (2) To what extent was Adam, the first man, created for a role that Christ eventually fulfilled?
ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics
Authors: Theodorakis Evangelos , Antonakis Andreas N , Baltsavia Ismini , Pavlopoulos Georgios A , Samiotaki Martina , Amoutzias Grigoris D , Theodosiou Theodosios , Acuto Oreste , Efstathiou Georgios , Iliopoulos Ioannis 
Published: April 2021

Abstract
Bottom-up proteomics analyses have been proved over the last years to be a powerful tool in the characterization of the proteome and are crucial for understanding cellular and organism behaviour. Through differential proteomic analysis researchers can shed light on groups of proteins or individual proteins that play key roles in certain, normal or pathological conditions. However, several tools for the analysis of such complex datasets are powerful, but hard-to-use with steep learning curves. In addition, some other tools are easy to use, but are weak in terms of analytical power. Previously, we have introduced ProteoSign, a powerful, yet user-friendly open-source online platform for protein differential expression/abundance analysis designed with the end-proteomics user in mind. Part of Proteosign's power stems from the utilization of the well-established Linear Models For Microarray Data (LIMMA) methodology. Here, we present a substantial upgrade of this computational resource, called ProteoSign v2, where we introduce major improvements, also based on user feedback. The new version offers more plot options, supports additional experimental designs, analyzes updated input datasets and performs a gene enrichment analysis of the differentially expressed proteins. We also introduce the deployment of the Docker technology and significantly increase the speed of a full analysis. ProteoSign v2 is available at http://bioinformatics.med.uoc.gr/ProteoSign.
MoiRNAiFold: a novel tool for complex in silico RNA design
Authors: Minuesa Gerard , Alsina Cristina , Garcia-Martin Juan Antonio , Oliveros Juan Carlos , Dotu Ivan 
Published: April 2021

Abstract
Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/).
The emerging determinants of replication fork stability
Authors: Thakar Tanay , Moldovan George-Lucian 
Published: April 2021

AbstractA universal response to replication stress is replication fork reversal, where the nascent complementary DNA strands are annealed to form a protective four-way junction allowing forks to avert DNA damage while replication stress is resolved. However, reversed forks are in turn susceptible to nucleolytic digestion of the regressed nascent DNA arms and rely on dedicated mechanisms to protect their integrity. The most well studied fork protection mechanism involves the BRCA pathway and its ability to catalyze RAD51 nucleofilament formation on the reversed arms of stalled replication forks. Importantly, the inability to prevent the degradation of reversed forks has emerged as a hallmark of BRCA deficiency and underlies genome instability and chemosensitivity in BRCA-deficient cells. In the past decade, multiple factors underlying fork stability have been discovered. These factors either cooperate with the BRCA pathway, operate independently from it to augment fork stability in its absence, or act as enablers of fork degradation. In this review, we examine these novel determinants of fork stability, explore the emergent conceptual underpinnings underlying fork protection, as well as the impact of fork protection on cellular viability and cancer therapy.
ProteoVision: web server for advanced visualization of ribosomal proteins
Authors: Penev Petar I , McCann Holly M , Meade Caeden D , Alvarez-Carreño Claudia , Maddala Aparna , Bernier Chad R , Chivukula Vasanta L , Ahmad Maria , Gulen Burak , Sharma Aakash , Williams Loren Dean , Petrov Anton S 
Published: April 2021

AbstractProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/.