bluuebunny/crossref_metadata_2025_split huggingface dataset:
The microbial rare biosphere: current concepts, methods and ecological principles
Authors: Pascoal Francisco , Costa Rodrigo , Magalhães Catarina 
Published: November 2020

ABSTRACTOur ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the ‘rare biosphere’, across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
Progress in the elimination of lymphatic filariasis in the Western Pacific Region: successes and challenges
Authors: Yajima Aya , Ichimori Kazuyo 
Published: November 2020

Abstract
The Western Pacific Region is the largest and most diverse region in the world, made up of 37 countries and territories in the Pacific, Oceania and parts of Asia, with a population of more than 1.9 billion people stretching over an area from China and Mongolia in the north to New Zealand in the south. In 1999, 22 countries and territories in the Pacific joined together and launched the Pacific Programme to Eliminate Lymphatic Filariasis. Shortly after, the Global Programme to Eliminate Lymphatic Filariasis was launched in 2000. In 2004, 12 countries in the Asia subregion of the Western Pacific Region and Southeast Asian Region joined and developed the Mekong-Plus Strategic Plan for Elimination of Lymphatic Filariasis. Since then, significant efforts have been made by all endemic countries, with annual mass drug administration (MDA) as a principal strategy, through strong partnership with the WHO and other donors and partners. As a result, by the end of 2019, 10 of 22 endemic countries in the region, including 8 of 16 countries in the Pacific and 2 countries in the Asia subregion, achieved WHO validation for elimination of lymphatic filariasis (LF) as a public health problem. All the other countries are either progressing with post-MDA surveillance or accelerating efforts by adoption of the new triple drug therapy strategy and enhancement of MDA campaigns to tackle persistent transmission. Some 85% of the originally endemic implementation units have stopped MDA and the number of people requiring MDA for LF in the Western Pacific Region was reduced by 72% from 2000 to 2018. This paper reviews the progress, key success factors and remaining challenges and indicates the way forward to achieve LF elimination in the Western Pacific Region.
Simultaneous Detection of Anions and Carbohydrates in Cyanobacteria by Two-Dimensional Ion Chromatography
Authors: Jiang Lijun , Bao Yan , Guo Liang , Cui He , Wang Qi , Liu Kai , Hao Xiaoxian , Qiu Ruchen , Guo Zhiyan , Fa Yun 
Published: November 2020

Abstract

Background
The simultaneous analysis of several anions and carbohydrates by one-dimensional chromatography with a single detector is often complicated by the presence of overlapping peaks. To overcome this problem, analytes are usually analyzed separately making analysis long and tedious.

Objective
A method combining two-dimensional ion chromatography (2D-IC) and valve switching was developed for the simultaneous determination of anions (F−, Cl−, NO2−, SO42−, NO3−, and PO43−) and carbohydrates (glycerin, glucosyl glycerol, trehalose, mannose, glucose, galactose, fructose, ribose, and sucrose) in cyanobacteria.

Method
Interfering color compounds were removed by first passing the sample through graphitized carbon solid phase extraction (SPE) cartridges. Samples were applied to an AS11-HC column, which was used to separate the anions followed by quantification using a conductance detector. Carbohydrates eluted from the AS11-HC column were trapped and separated on a MA1 column and simultaneously quantified using electrochemical detection in the second dimension with valve switching.

Results
The following parameters were established: LOD, 0.001–0.030 (mg/L); LOQ, 0.001–0.010 (mg/L); linearity (R2), 0.9940; repeatability, 0.39–3.02%; and spiked recovery, 90.1–107%.

Conclusions
The proposed method is adequately linear, accurate, and repeatable. The 2D-IC method provides fast, high-resolution, and completely automated procedure for the simultaneous determination of anions and carbohydrates without co-elution compared to the 1D ion chromatography method. This study provides application perspectives for use in biotechnology and other research fields.

Highlights
An accurate and effective 2D-IC method was developed for determining anions and carbohydrates in cyanobacteria. The method includes pre-treating samples with graphitized carbon SPE cartridges.
Differentiation of Milk and Whey Protein Concentrates by Microbiome Profiling Using 16S Metagenomics
Authors: Thompson Christopher M , Gao Quanyin , Chang Peter , Swanson Gary 
Published: November 2020

Abstract

Background
Protein powder identification presents a challenge in quality control. There is current deliberation of the specificity of methods for the identification of milk proteins, and the consensus identification method of whey protein from the United States Pharmacopeia Food Chemical Codex relies on a combined analysis of the testing of ash, fat, lactose, loss on drying, and protein. These methods are non-specific. Milk and whey proteins both contain background DNA content. Both milk and whey proteins retain source DNA (cow), but also have bacterial DNA from natural flora, the dairy plant, and in whey protein, the cheesemaking process. The DNA in these materials is retained post-processing, even after the pasteurization process.

Objective
By utilizing 16S metagenomics, the bacterial DNA in protein powders can be sequenced and cross-referenced to a curated library to ultimately create a microbiome profile of these raw materials. This microbiome can be measured for alpha and beta diversity, specifically how many and which species of bacteria are present.

Method
Using 16S metagenomics, we measure alpha and beta diversity of the microbiome profile of each protein powder and use principle coordinate analysis to produce differential groupings, providing a novel identification method for raw materials.

Results
In this study, we demonstrate that the microbiome of cow proteins can be used for raw material identification, as the microbiome of milk and whey proteins differ significantly. We also demonstrate that the microbiome of whey protein concentrate can differ from supplier to supplier.

Conclusions
Microbiome profiling by 16S metagenomics can be an important forensic tool for quality control.

Highlights
Principle Coordinate Analysis can be used as a statistical tool for protein differentiation using the protein microbiome.
Teaching classics with objects? The acquisition of classical antiquities by British schools, 1860–1950
Authors: Croker Ollie 
Published: November 2020

Abstract
British secondary schools amassed collections of antiquities from the mid-nineteenth century onwards. These ordinarily contained classical objects, sometimes alongside Egyptian antiquities, and accompanied collections of natural history, geology and ethnography. This paper uses the collection formed by Bedford Modern School, now housed at the Higgins Museum, Bedford, to study the phenomenon of school classical collections. The analysis presented here places school collections within a wider history of ‘object lessons’, but suggests that these collections were more than merely teaching aids. School museums could act as signifiers of power and prestige, connection to alumni and wider local communities, and to a heritage of learning and scholarship embodied by classical antiquities. Furthermore, these collections illustrate the personalities and interests of individual collectors – usually the schoolmasters who were instrumental in their formation.
QKI-5 regulates the alternative splicing of cytoskeletal gene ADD3 in lung cancer
Authors: Wang Jin-Zhu , Fu Xing , Fang Zhaoyuan , Liu Hui , Zong Feng-Yang , Zhu Hong , Yu Yan-Fei , Zhang Xiao-Ying , Wang Shen-Fei , Huang Ying , Hui Jingyi 
Published: November 2020

Abstract
Accumulating evidence indicates that the alternative splicing program undergoes extensive changes during cancer development and progression. The RNA-binding protein QKI-5 is frequently downregulated and exhibits anti-tumor activity in lung cancer. Howeve-r, little is known about the functional targets and regulatory mechanism of QKI-5. Here, we report that upregulation of exon 14 inclusion of cytoskeletal gene Adducin 3 (ADD3) significantly correlates with a poor prognosis in lung cancer. QKI-5 inhibits cell proliferation and migration in part through suppressing the splicing of ADD3 exon 14. Through genome-wide mapping of QKI-5 binding sites in vivo at nucleotide resolution by iCLIP-seq analysis, we found that QKI-5 regulates alternative splicing of its target mRNAs in a binding position-dependent manner. By binding to multiple sites in an upstream intron region, QKI-5 represses the splicing of ADD3 exon 14. We also identified several QKI mutations in tumors, which cause dysregulation of the splicing of QKI targets ADD3 and NUMB. Taken together, our results reveal that QKI-mediated alternative splicing of ADD3 is a key lung cancer-associated splicing event, which underlies in part the tumor suppressor function of QKI.
“The Way of Progress and Civilization”: Racial Hierarchy and US State Building in Haiti and the Dominican Republic (1915–1922)
Authors: Pampinella Stephen 
Published: November 2020

AbstractRacial stratification remains critically undertheorized in hierarchy studies. Postcolonial analyses demonstrate how diffuse systems of racial knowledge produce unequal subjectivities in world politics, but they are often criticized for making overdetermined explanations that do not account for agency or contingency. To rectify this theoretical lacuna, I develop a postcolonial-practice theory approach to explain variation in the intensity and duration of governance hierarchies. I argue that racialized discourses constitute the habitualized dispositions of dominant and subordinate actors and make possible specific governance practices. This approach can account for puzzling cases of successful resistance by some subordinates while others languish under intense domination. Two such cases are US state building interventions in Haiti and the Dominican Republic during the early twentieth century. By using a variety of primary archival and public sources, I demonstrate how ideas about racial differences among Anglo-Americans, Dominicans, and Haitians led US policymakers to enact a more long-term and domineering occupation of Haiti compared to the Dominican Republic. Once Dominican elites articulated a European–Spanish identity in opposition to Blackness, they mobilized support from other Latin American states and made US withdrawal practical. A postcolonial-practice explanation is useful because it addresses the limitations of both narrow and broad approaches to the study of hierarchy. Its focus on the contestation of US hierarchies further contributes to hegemonic-order theory while illustrating how the dynamics of inclusion and exclusion shape imperial rule and strategies of anti-imperial resistance.
Sector-Specific Associations, Trust, and Survival of PPPs: A Behavioral Experiment Based on the Centipede Game
Authors: Weißmüller Kristina S , Vogel Rick 
Published: November 2020

AbstractPublic-private partnerships (PPPs) have become widespread in the delivery of public services. This study explores behavioral mechanisms of building and eroding trust in partnering across sectors at the micro-level of interaction between public and private partners. Combining classic theoretical concepts on the development of interorganizational trust and administrative behavior, this study derives theory suggesting that partners’ sector affiliation may have adverse signaling effects on individuals’ intention to uphold effective partnerships over time, and that this intent may be moderated by sector-specific associations. Tested with a novel and dynamic multi-stage behavioral experiment based on the classic centipede game conducted with German graduate students (N = 482; Obs. = 4,338), results suggest that sector affiliation functions as a strong but potentially misleading signal for partners’ strategic behavior in PPPs and that sector-specific associations asymmetrically moderate respondents’ will to collaborate. These findings contribute to a more nuanced theoretical understanding of the micro-foundations of strategic behavior, particularly at nascent stages of PPPs, calling into question basic assumptions about coordination efficiency in cross-sectoral partnerships.
Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children
Authors: Coleman Andrea , Bialasiewicz Seweryn , Marsh Robyn L , Grahn Håkansson Eva , Cottrell Kyra , Wood Amanda , Jayasundara Nadeesha , Ware Robert S , Zaugg Julian , Sidjabat Hanna E , Adams Jasmyn , Ferguson Josephine , Brown Matthew , Roos Kristian , Cervin Anders 
Published: November 2020

Abstract

Background
We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health.

Methods
In total, 103 Indigenous Australian children aged 2–7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children’s ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis.

Results
Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P &lt; .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P &lt; .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children.

Conclusions
Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.
Jejunal diverticular disease: a report of three cases
Authors: Ghandour Richard , Khalifeh Georges , Orm Nasr Bou , Rakka Mohamad , Dbouk Samer , El Sahili Riad , Mcheimeche Hussein 
Published: November 2020

Abstract
Jejunal diverticula (JD) are a rare medical entity. They are often unnoticed, until complications occur. We report herein three cases of such diverticula, analyzed retrospectively, and depicting some of these complications: small bowel obstruction due to enterolith in a giant diverticulum treated surgically, incidental intraoperative finding on an anastomotic jejunal limb affecting the surgical plan and diverticulitis with anemia. In all three cases, the diagnosis of JD was unexpected, which illustrates the importance of being familiar with this disease for adequate management.
‘Arianism’ Ante Litteram in Origen’s Peri Archōn 4.4.1
Authors: Ip Pui Him 
Published: November 2020

Abstract
In Peri Archōn 4.4.1, Origen argues against a form of ‘Arianism’ ante litteram. Previous scholarship has suggested that the view targeted by Origen could be a form of Basilidean system. In this paper, I make a fresh attempt to identify the polemical context of this passage. I first identify a more reliable control for delimiting the possible targets using Origen’s classification of heresies reported in Pamphilus’ Apology and Book 32 of the Commentary on John. Synthesis of the two reports suggests that Origen is unlikely to have targeted Basilides’ teachings in Peri Archōn 4.4.1. I then analyse two further pieces of evidence to substantiate an alternative identification: psilanthropism or monarchianism. Where Origen explicitly rejects ἦν ποτε ὅτε οὐκ ἦν (or variants), one finds these two positions as the immediate polemical context. Further, analysis of Peri Archōn 1.2.1–4 reveals that, as in Peri Archōn 4.4.1, these positions are placed alongside Valentinian emanationism as the twin polemical targets of Origen’s Christology. This fresh identification opens up a new perspective for reassessing the development of the fourth-century ‘Arian’ controversy prospectively, that is, through the lens of the third-century polemical landscape.
APOBEC3 enzymes mediate efficacy of cisplatin and are epistatic with base excision repair and mismatch repair in platinum response
Authors: Conner Kayla L , Shaik Asra N , Marshall Katie A , Floyd Ashley M , Ekinci Elmira , Lindquist Jacob , Sawant Akshada , Lei Wen , Adolph Madison B , Chelico Linda , Siriwardena Sachini U , Bhagwat Ashok , Kim Seongho , Cote Michele L , Patrick Steve M 
Published: November 2020

AbstractIdentifying the mechanisms mediating cisplatin response is essential for improving patient response. Previous research has identified base excision repair (BER) and mismatch repair (MMR) activity in sensitizing cells to cisplatin. Cisplatin forms DNA adducts including interstrand cross-links (ICLs) that distort the DNA helix, forcing adjacent cytosines to become extrahelical. These extrahelical cytosines provide a substrate for cytosine deaminases. Herein, we show that APOBEC3 (A3) enzymes are capable of deaminating the extrahelical cytosines to uracils and sensitizing breast cancer cells to cisplatin. Knockdown of A3s results in resistance to cisplatin and induction of A3 expression in cells with low A3 expression increases sensitivity to cisplatin. We show that the actions of A3s are epistatic with BER and MMR. We propose that A3-induced cytosine deamination to uracil at cisplatin ICLs results in repair of uracils by BER, which blocks ICL DNA repair and enhances cisplatin efficacy and improves breast cancer outcomes.
Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform
Authors: Maiolo Massimo , Ulzega Simone , Gil Manuel , Anisimova Maria 
Published: November 2020

Abstract
Recently we presented a frequentist dynamic programming (DP) approach for multiple sequence alignment based on the explicit model of indel evolution Poisson Indel Process (PIP). This phylogeny-aware approach produces evolutionary meaningful gap patterns and is robust to the ‘over-alignment’ bias. Despite linear time complexity for the computation of marginal likelihoods, the overall method’s complexity is cubic in sequence length. Inspired by the popular aligner MAFFT, we propose a new technique to accelerate the evolutionary indel based alignment. Amino acid sequences are converted to sequences representing their physicochemical properties, and homologous blocks are identified by multi-scale short-time Fourier transform. Three three-dimensional DP matrices are then created under PIP, with homologous blocks defining sparse structures where most cells are excluded from the calculations. The homologous blocks are connected through intermediate ‘linking blocks’. The homologous and linking blocks are aligned under PIP as independent DP sub-matrices and their tracebacks merged to yield the final alignment. The new algorithm can largely profit from parallel computing, yielding a theoretical speed-up estimated to be proportional to the cubic power of the number of sub-blocks in the DP matrices. We compare the new method to the original PIP approach and demonstrate it on real data.
Detection capability of the Migdal effect for argon and xenon nuclei with position-sensitive gaseous detectors
Authors: Nakamura Kiseki D , Miuchi Kentaro , Kazama Shingo , Shoji Yutaro , Ibe Masahiro , Nakano Wakutaka 
Published: November 2020

Abstract
The Migdal effect is attracting interest because of the potential to enhance the sensitivities of direct dark matter searches to the low-mass region. In spite of its great importance, the Migdal effect has not been experimentally observed yet. A realistic experimental approach towards the first observation of the Migdal effect in the neutron scattering was studied with Monte Carlo simulations. In this study, the potential background rate was studied together with the event rate of the Migdal effect by a neutron source. It was found that a table-top-sized $\sim (30~\mbox{cm})^3$ position-sensitive gaseous detector filled with argon or xenon target gas can detect characteristic signatures of the Migdal effect with sufficient rates (O($10^2\sim10^3$) events per day). A simulation result of a simple experimental set-up showed two significant background sources, namely the intrinsic neutrons and the neutron-induced gamma-rays. It is found that the intrinsic neutron background rate for the argon gas is at an acceptable level and some future study of the reduction of the gamma-rays from the laboratory would make the observation of the Migdal effect possible. The background for the xenon gas, on the other hand, is found to be much more serious than for the argon gas. Future works on the isotope separation as well as the reduction of the gamma-rays from the detector and laboratory will be needed before the Migdal effect can be observed for the xenon gas case.
ASSESSMENT OF OCCUPATIONAL RADIATION DOSES OF MEDICAL RADIATION WORKERS IN TWO COMMUNITY HOSPITALS
Authors: Osei Ernest , Nuru Faiza , Moore Michael 
Published: November 2020

Abstract
The International Commission on Radiological Protection recommends the adoption of the linear, no-threshold model as a predictive risk model for radiation protection purposes since the relationship between low-dose radiation exposure and cancer risk is unclear. Medical radiation workers are subject to occupational exposures and differences in workload, area of work and types of exposure can lead to variations in exposures between different occupational groups. We investigated the occupational exposures of 572 workers from four departments in two community hospitals and stratified into 22 occupational groups in order to identify groups with the highest radiation exposure. The occupational doses from 2015 to 2019 were analyzed to identify the dose distribution of each occupational group, total number of monitored workers, annual and collective deep (Hp(10)), eye (Hp(3)) and shallow (Hp(0.07)) doses. We further determined the individual and occupational group lifetime doses as well as the probability that monitored workers’ lifetime doses will exceed a specified lifetime dose level. The occupational groups with the highest radiation exposures were the nuclear medicine technologists, diagnostic imaging radiologists and diagnostic cardiologists. Although our data suggest that occupational doses reported are low, it is essential that exposure of occupationally exposed personnel are always kept as low as reasonably achievable with an effective radiation protection program.