bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoscopically Assisted Marginal Mandibulectomy Using an Intraoral Approach Alone for Squamous Cell Carcinoma of the Posterior Mandibular Gingiva: A Technical Note
Authors: Shudo Atsushi 
Published: May 2021

Study Design: Technical note. Objective: Marginal mandibulectomy is a surgical procedure for treatment of mandibular gingival tumors. The intraoral approach to the posterior region of the mandible for marginal mandibulectomy is difficult due to limited access and operating field visibility; the conventional surgical procedure may require some skin incisions. This report discusses the effectiveness of endoscopic assistance in marginal mandibulectomy. Methods: This article describes endoscopically assisted marginal mandibulectomy using an intraoral approach alone for squamous cell carcinoma of the posterior mandibular gingiva. Results: The advantages of this surgical method are twofold: (1) superior visibility to the lower edge of the mandible without any skin incision; and (2) safe surgical confirmation of important anatomy on the buccolingual side (e.g., mental foramen, lingual nerve, mandibular foramen, and neurovascular bundle). This minimally invasive approach without any skin incision, as well as the superior visibility of the operating field, are important advantages of endoscopically assisted marginal mandibulectomy that cannot be obtained by other surgical methods. Conclusions: Endoscopically assisted marginal mandibulectomy using an intraoral approach alone may be useful because it avoids damage to facial skin and improves safety by employing an enlarged bright field.
Platelets and extracellular vesicles and their cross talk with cancer
Authors: Lazar Sophia , Goldfinger Lawrence E. 
Published: May 2021

Abstract
Platelets play significant and varied roles in cancer progression, as detailed throughout this review series, via direct interactions with cancer cells and by long-range indirect interactions mediated by platelet releasates. Microvesicles (MVs; also referred to as microparticles) released from activated platelets have emerged as major contributors to the platelet-cancer nexus. Interactions of platelet-derived MVs (PMVs) with cancer cells can promote disease progression through multiple mechanisms, but PMVs also harbor antitumor functions. This complex relationship derives from PMVs’ binding to both cancer cells and nontransformed cells in the tumor microenvironment and transferring platelet-derived contents to the target cell, each of which can have stimulatory or modulatory effects. MVs are extracellular vesicles of heterogeneous size, ranging from 100 nm to 1 µm in diameter, shed by living cells during the outward budding of the plasma membrane, entrapping local cytosolic contents in an apparently stochastic manner. Hence, PMVs are encapsulated by a lipid bilayer harboring surface proteins and lipids mirroring the platelet exterior, with internal components including platelet-derived mature messenger RNAs, pre-mRNAs, microRNAs, and other noncoding RNAs, proteins, second messengers, and mitochondria. Each of these elements engages in established and putative PMV functions in cancer. In addition, PMVs contribute to cancer comorbidities because of their roles in coagulation and thrombosis and via interactions with inflammatory cells. However, separating the effects of PMVs from those of platelets in cancer contexts continues to be a major hurdle. This review summarizes our emerging understanding of the complex roles of PMVs in the development and progression of cancer and cancer comorbidities.
Survival of HIV/AIDS patients treated under ART follow-up at the University hospital, northwest Ethiopia
Authors: Teka Zinabu , Mohammed Kasim , Workneh Gashu , Gizaw Zemichael 
Published: May 2021

Abstract
Introduction
The survival of HIV/AIDS patients on antiretroviral therapy (ART) is determined by a number of factors, including economic, demographic, behavioral, and institutional factors. Understanding the survival time and its trend is crucial to developing policies that will result in changes. The aim of this study was to compare the survival estimates of different subgroups and look into the predictors of HIV/AIDS patient survival.

Methods
A retrospective cohort study of HIV/AIDS patients receiving ART at the University of Gondar teaching hospital was carried out. To compare the survival of various groups, a Kaplan-Meier survival analysis was performed. The Cox proportional hazards model was used to identify factors influencing HIV/AIDS patient survival rates.

Results
In the current study, 5.91% of the 354 HIV/AIDS patients under ART follow-up were uncensored or died. Age (HR = 1.051) and lack of formal education (HR = 5.032) were associated with lower survival rate, whereas family size of one to two (HR = 0.167), three to four (HR = 0.120), no alcoholic consumption (HR = 0.294), no smoking and chat use (HR = 0.101), baseline weight (HR = 0.920), current weight (HR = 0.928), baseline CD4 cell count (HR = 0.990), baseline hemoglobin (HR = 0.800), and no TB diseases were associated with longer survival rate.

Conclusions
Fewer deaths were reported in a study area due to high patient adherence, compared to previous similar studies. Age, educational status, family size, alcohol consumption, tobacco and chat usage, baseline and current weight, baseline CD4 cell count, baseline hemoglobin, and tuberculosis (TB) diseases were all significant predictors of survival of HIV/AIDS patients.
Economic policy instruments for sustainable phosphorus management: taking into account climate and biodiversity targets
Authors: Garske Beatrice , Ekardt Felix 
Published: May 2021

AbstractBackgroundPhosphorus (P) is a vital and non-substitutable nutrient for agricultural production. However, P is often used inefficiently in European agriculture. To ensure food security while avoiding environmental damage caused by improper fertilization, a sustainable P management is required. Although P-related problems are partly addressed by existing agricultural and environmental legislation, e.g., in the EU, the current regulation lacks sufficient governance effect. In addition, the existing legal framework is strongly characterized by detailed command-and-control provisions and thus suffers from governance problems such as enforcement deficits, rebound and shifting effects. This paper focuses on how these challenges could be addressed by economic instruments. The article highlights not only the impact of the instruments on P management, but also on adjacent environmental areas. We pay particular attention to the governance effects on reaching international binding climate and biodiversity objectives, for which fertilization and agriculture play a major role.ResultsThe analysis builds on two economic instruments that ensure compliance with the climate target of the Paris Agreement and the Aichi targets of the Biodiversity Convention: a cap-and-trade scheme for fossil fuels and a cap-and-trade scheme for livestock products. We state that both instruments simultaneously address a large part of P-related problems. Moreover, if the two emissions trading schemes are combined with a livestock-to-land ratio at farm level, only little need for regulatory supplementation relating to P remains. The latter includes in particular a threshold value for contaminants in P-containing fertilizers. Furthermore, we discuss an almost complete phasing-out of fertilizers containing rock phosphate by means of a further certificate trading scheme.ConclusionsThe article shows that a wide variety of problems can be tackled with a few overarching instruments. This is true even for very specific and diverse problems such as those related to P use in agriculture.
Varicella zoster virus anterior uveitis complicated by thalamic stroke
Authors: Anthony Casey L. , Costarides Anastasios P. , Yeh Steven , Shantha Jessica G. 
Published: May 2021

AbstractWe report a case of varicella zoster virus (VZV)-associated anterior uveitis in a patient with weight loss, arthritis and signs of inflammatory bowel disease. Her clinical course included the development of a thalamic stroke secondary to VZV cerebral vasculopathy. Following antiviral therapy, the patient’s neurologic symptoms recovered and her ophthalmic findings improved.
Root Digger: a root placement program for phylogenetic trees
Authors: Bettisworth Ben , Stamatakis Alexandros 
Published: May 2021

Abstract
Background
In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position.

Results
We present a software called which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement. We find that is successful at finding roots when compared to similar tools such as IQ-TREE and MAD, and will occasionally outperform them. Additionally, we find that the exhaustive mode of is useful in quantifying and explaining uncertainty in rooting positions.

Conclusions
can be used on an existing phylogeny to find a root, or to asses the uncertainty of the root placement. is available under the MIT licence at https://www.github.com/computations/root_digger.
The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function
Authors: Krämer Andreas , Billaud Jean-Noël , Tugendreich Stuart , Shiffman Dan , Jones Martin , Green Jeff 
Published: May 2021

Abstract
Background
Leveraging previously identified viral interactions with human host proteins, we apply a machine learning-based approach to connect SARS-CoV-2 viral proteins to relevant host biological functions, diseases, and pathways in a large-scale knowledge graph derived from the biomedical literature. Our goal is to explore how SARS-CoV-2 could interfere with various host cell functions, and to identify drug targets amongst the host genes that could potentially be modulated against COVID-19 by repurposing existing drugs. The machine learning model employed here involves gene embeddings that leverage causal gene expression signatures curated from literature. In contrast to other network-based approaches for drug repurposing, our approach explicitly takes the direction of effects into account, distinguishing between activation and inhibition.

Results
We have constructed 70 networks connecting SARS-CoV-2 viral proteins to various biological functions, diseases, and pathways reflecting viral biology, clinical observations, and co-morbidities in the context of COVID-19. Results are presented in the form of interactive network visualizations through a web interface, the Coronavirus Network Explorer (CNE), that allows exploration of underlying experimental evidence. We find that existing drugs targeting genes in those networks are strongly enriched in the set of drugs that are already in clinical trials against COVID-19.

Conclusions
The approach presented here can identify biologically plausible hypotheses for COVID-19 pathogenesis, explicitly connected to the immunological, virological and pathological observations seen in SARS-CoV-2 infected patients. The discovery of repurposable drugs is driven by prior knowledge of relevant functional endpoints that reflect known viral biology or clinical observations, therefore suggesting potential mechanisms of action. We believe that the CNE offers relevant insights that go beyond more conventional network approaches, and can be a valuable tool for drug repurposing. The CNE is available at https://digitalinsights.qiagen.com/coronavirus-network-explorer.
Tamock: simulation of habitat-specific benchmark data in metagenomics
Authors: Gerner Samuel M. , Graf Alexandra B. , Rattei Thomas 
Published: May 2021

Abstract
Background
Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems. Conclusions from benchmark studies are therefore limited to the ecosystems they mimic. Ideally, simulations are therefore based on genomes, which resemble particular metagenomic communities realistically.

Results
We developed Tamock to facilitate the realistic simulation of metagenomic reads according to a metagenomic community, based on real sequence data. Benchmarks samples can be created from all genomes and taxonomic domains present in NCBI RefSeq. Tamock automatically determines taxonomic profiles from shotgun sequence data, selects reference genomes accordingly and uses them to simulate metagenomic reads. We present an example use case for Tamock by assessing assembly and binning method performance for selected microbiomes.

Conclusions
Tamock facilitates automated simulation of habitat-specific benchmark metagenomic data based on real sequence data and is implemented as a user-friendly command-line application, providing extensive additional information along with the simulated benchmark data. Resulting benchmarks enable an assessment of computational methods, workflows, and parameters specifically for a metagenomic habitat or ecosystem of a metagenomic study.

Availability
Source code, documentation and install instructions are freely available at GitHub (https://github.com/gerners/tamock).
Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders
Authors: Ávila Herrera Ivalú M. , Král Jiří , Pastuchová Markéta , Forman Martin , Musilová Jana , Kořínková Tereza , Šťáhlavský František , Zrzavá Magda , Nguyen Petr , Just Pavel , Haddad Charles R. , Hiřman Matyáš , Koubová Martina , Sadílek David , Huber Bernhard A. 
Published: May 2021

Abstract
Background
Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.

Results
Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.

Conclusions
The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome–autosome and autosome–sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.
Molecular evolutionary analysis of human primary microcephaly genes
Authors: Pervaiz Nashaiman , Kang Hongen , Bao Yiming , Abbasi Amir Ali 
Published: May 2021

Abstract
Background
There has been a rapid increase in the brain size relative to body size during mammalian evolutionary history. In particular, the enlarged and globular brain is the most distinctive anatomical feature of modern humans that set us apart from other extinct and extant primate species. Genetic basis of large brain size in modern humans has largely remained enigmatic. Genes associated with the pathological reduction of brain size (primary microcephaly-MCPH) have the characteristics and functions to be considered ideal candidates to unravel the genetic basis of evolutionary enlargement of human brain size. For instance, the brain size of microcephaly patients is similar to the brain size of Pan troglodyte and the very early hominids like the Sahelanthropus tchadensis and Australopithecus afarensis.

Results
The present study investigates the molecular evolutionary history of subset of autosomal recessive primary microcephaly (MCPH) genes; CEP135, ZNF335, PHC1, SASS6, CDK6, MFSD2A, CIT, and KIF14 across 48 mammalian species. Codon based substitutions site analysis indicated that ZNF335, SASS6, CIT, and KIF14 have experienced positive selection in eutherian evolutionary history. Estimation of divergent selection pressure revealed that almost all of the MCPH genes analyzed in the present study have maintained their functions throughout the history of placental mammals. Contrary to our expectations, human-specific adoptive evolution was not detected for any of the MCPH genes analyzed in the present study.

Conclusion
Based on these data it can be inferred that protein-coding sequence of MCPH genes might not be the sole determinant of increase in relative brain size during primate evolutionary history.
Sewage and sewage-contaminated environments are the most prominent sources to isolate phages against Pseudomonas aeruginosa
Authors: Aghaee Bahareh Lashtoo , Mirzaei Mohammadali Khan , Alikhani Mohammad Yousef , Mojtahedi Ali 
Published: May 2021

Abstract
Background
P. aeruginosa is the primary source of hospital-acquired infections. Unfortunately, antibiotic resistance is growing to precariously high levels, making the infections by this pathogen life-threatening and hard to cure. One possible alternative to antibiotics is to use phages. However, the isolation of phages suitable for phage therapy— be lytic, be efficient, and have a broad host range —against some target bacteria has proven difficult. To identify the best places to look for these phages against P. aeruginosa we screened hospital sewages, soils, and rivers in two cities.

Results
We isolated eighteen different phages, determined their host range, infection property, and plaque morphology. We found that the sewage and sewage-contaminated environments are the most reliable sources for the isolation of Pseudomonas phages. In addition, phages isolated from hospital sewage showed the highest efficiency in lysing the bacteria used for host range determination. In contrast, phages from the river had larger plaque size and lysed bacteria with higher levels of antibiotic resistance.

Conclusions
Our findings provided additional support for the importance of sewage as the source of phage isolation.
Analysis of culturable airborne fungi in outdoor environments in Tianjin, China
Authors: Nageen Yumna , Asemoloye Michael Dare , Põlme Sergei , Wang Xiao , Xu Shihan , Ramteke Pramod W. , Pecoraro Lorenzo 
Published: May 2021

Abstract
Background
Fungal spores dispersed in the atmosphere may become cause of different pathological conditions and allergies for human beings. A number of studies have been performed to analyze the diversity of airborne fungi in different environments worldwide, and in particular in many urban areas in China. We investigated, for the first time, the diversity, concentration and distribution of airborne fungi in Tianjin city. We sampled 8 outdoor environments, using open plate method, during a whole winter season. Isolated fungi were identified by morphological and molecular analysis. Environmental factors which could influence the airborne fungi concentration (temperature, humidity, wind speed, and air pressure) were monitored and analyzed. The effect of different urban site functions (busy areas with high traffic flow and commercial activities vs. green areas) on airborne fungal diversity was also analyzed.

Results
A total of 560 fungal strains, belonging to 110 species and 49 genera of Ascomycota (80 %), Basidiomycota (18 %), and Mucoromycota (2 %) were isolated in this study. The dominant fungal genus was Alternaria (22 %), followed by Cladosporium (18.4 %), Naganishia (14.1 %), Fusarium (5.9 %), Phoma (4.11 %), and Didymella (4.8 %). A fungal concentration ranging from 0 to 3224.13 CFU m− 3 was recorded during the whole study. Permutational multivariate analysis showed that the month was the most influential factor for airborne fungal community structure, probably because it can be regarded as a proxy of environmental variables, followed by wind speed. The two analyzed environments (busy vs. green) had no detectable effect on the air fungal community, which could be related to the relatively small size of parks in Tianjin and/or to the study season.

Conclusions
Our study shed light on the highly diverse community of airborne fungi characterizing the outdoor environments of Tianjin, and clarified the role that different environmental factors played in shaping the analyzed fungal community. The dominant presence of fungi with potential hazardous effect on human health, such as Alternaria, Cladosporium and Naganishia, deserves further attention. Our results may represent a valuable source of information for air quality monitoring, microbial pollution control, and airborne diseases prevention.