bluuebunny/crossref_metadata_2025 huggingface dataset:
Thoracoscopic surgery approach to mediastinal mature teratomas: a single-center experience
Authors: Pham Lu Huu , Trinh Diep Ke , Nguyen Anh Viet , Nguyen Lanh Sy , Le Dung Thanh , Nguyen Dinh-Hoa , Doan Hung Quoc , Nguyen Uoc Huu
Published: February 2020

Background

Mediastinal mature teratomas are rare tumors with diverse surgical approaches. The aim of this study is to review our experience of thoracoscopic surgery management in patients with teratomas.

Methods

We retrospectively reviewed 28 consecutive patients with mediastinal mature teratomas who underwent thoracoscopic surgery at Viet Duc University Hospital from January 2008 to August2018. Patients were divided into 2 groups with 2 types of thoracoscopic surgery, closed thoracoscopic surgery (CTS) group and video-assisted thoracoscopic surgery (VATS) group. The selection of sugical approach was based on sizes, locations and characteristics of tumors. Post-operative outcomes were assessed and compared between these 2 groups.

Results

There were 14 female and 14 male patients with a median age of 41.2 ± 13.8 years. A total of 22 teratomas were located on the right side of the chest cavity and 6 on the left side. We performed CTS in 21 patients (75%) and VATS in 7 patients (25%) for tumor resection. There were 3 cases (10.7%) required conversion to minithoracotomy (5 cm in incision length). Skin appendages accounted for the highest rate (96.4%) in pathology. There was no record of mortality or tumor recurrence detected by computerized tomography.

Conclusion

A thoracoscopic surgery for a mediastinal mature teratoma was a feasible choice. Challenging factors such as large tumors, intraoperative bleeding and strong tumor cell adhesion were considered handling by conversion to mini-thoracotomy that could ensure safety procedures and complete removal of tumors. Extraction of tumor contents might be performed for patients with large mature cystic teratomas to facilitate thoracoscopic surgery.
Genotyping structural variants in pangenome graphs using the vg toolkit
Authors: Hickey Glenn , Heller David , Monlong Jean , Sibbesen Jonas A. , Sirén Jouni , Eizenga Jordan , Dawson Eric T. , Garrison Erik , Novak Adam M. , Paten Benedict
Published: February 2020

Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Authors: Holland Christian H. , Tanevski Jovan , Perales-Patón Javier , Gleixner Jan , Kumar Manu P. , Mereu Elisabetta , Joughin Brian A. , Stegle Oliver , Lauffenburger Douglas A. , Heyn Holger , Szalai Bence , Saez-Rodriguez Julio
Published: February 2020

Background

Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way.

Results

To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community.

Conclusions

Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.
Evaluating a couple-based intervention addressing sexual concerns for breast cancer survivors: study protocol for a randomized controlled trial
Authors: Reese Jennifer Barsky , Zimmaro Lauren A. , Lepore Stephen J. , Sorice Kristen A. , Handorf Elizabeth , Daly Mary B. , Schover Leslie R. , Kashy Deborah , Westbrook Kelly , Porter Laura S.
Published: February 2020

Background

Sexual concerns are distressing for breast cancer survivors and interfere with their intimate relationships. This study evaluates the efficacy of a four-session couple-based intervention delivered via telephone, called Intimacy Enhancement (IE). The IE intervention is grounded in social cognitive theory and integrates evidence-based techniques from cognitive behavioral couple therapy and sex therapy to address survivors’ sexual concerns and enhance their and their partners’ sexual, relationship, and psychological outcomes.

Methods

This trial is designed to evaluate the efficacy of the IE intervention in improving survivors’ sexual function, the primary study outcome. Secondary outcomes include survivors’ sexual distress, partners’ sexual function, and survivors’ and partners’ relationship intimacy and quality as well as psychological distress (depressive symptoms and anxiety symptoms). Additional aims are to examine whether treatment effects on patient sexual function are mediated by sexual communication and self-efficacy for coping with sexual concerns and to explore whether survivor age and race/ethnicity moderate intervention effects on survivors’ sexual function. Eligible adult female breast cancer survivors reporting sexual concerns and their intimate partners are recruited from two academic sites in the USA and are randomized to either the IE intervention or to a control condition of equal length offering education and support around breast cancer-related health topics (Living Healthy Together). The target sample size is 120 couples. Self-report outcome measures are administered to participants in both conditions at baseline (T1), post-treatment (T2), 3 months post-treatment (T3), and 6 months post-treatment (T4).

Discussion

Evidence-based interventions are needed to address sexual concerns for breast cancer survivors and to enhance their and their intimate partners’ sexual, relationship, and psychological well-being. This randomized controlled trial will allow us to examine the efficacy of a novel couple-based intervention delivered via telephone for breast cancer survivors experiencing sexual concerns and their intimate partners, in comparison with an attention control. Findings of this study could influence clinical care for women with breast cancer and inform theory guiding cancer-related sexual rehabilitation.

Trial registration

ClinicalTrials.gov, NCT03930797. Registered on 24 April 2019.
Onchocerca jakutensis ocular infection in Poland: a new vector-borne human health risk?
Authors: Wesołowska Maria , Zając-Pytrus Hanna , Masny Aleksander , Pytrus Wiktoria , Knysz Brygida , Golab Elzbieta , Sałamatin Rusłan
Published: February 2020

Background

Zoonotic onchocerciasis is a vector-borne disease, which involves many animal species, including large ungulates, boars, dogs, and sporadically, humans. So far, 39 cases of zoonotic onchocerciasis have been reported worldwide, 30 of which have been found in the last 20 years. Onchocerca nematodes are transmitted to humans by blood-sucking vectors during a blood meal. The following species have been responsible for zoonotic infections: Onchocerca cervicalis, O. dewittei japonica, O. gutturosa, O. jakutensis and O. lupi. In humans, the worms have usually been found in the subcutaneous tissues where they form subcutaneous nodules, induce inflammation of musculature, or penetrate the eye. Thirteen ocular zoonotic onchocerciasis cases have been reported so far. In the eye, nematodes were localized in the subconjunctival space, anterior chamber and within the vitreous body.

Methods

In a 39-year-old male patient, a writhing worm in the vitreous body of the left eye was detected and surgically removed. Laboratory identification of the worm was based on macroscopic and molecular identification, based on sequencing of the cytochrome c oxidase subunit 1 gene (cox1). Phylogenetic analysis of the first 250 nucleotide sequences showing the highest levels of similarity with the present isolate in a BLAST analysis was performed.

Results

Here, we report the first case worldwide of human ocular infection with O. jakutensis, a natural parasite of red deer. By exploiting a PCR assay, we detected the sequence almost identical to O. jakutensis (GenBank: KT001213.1; positions 1–650) with a single mismatch G/A at position 622. The sequence reported in this paper was deposited in the GenBank database under the accession number MK491767.

Conclusions

Our case together with the previous case reports indicate that zoonotic Onchocerca worms exhibit no tissue specificity and an eye infection has been described in over one third of human zoonotic onchocerciasis cases. In terms of the growing number of cases of zoonotic onchocerciasis in Europe, the USA and Japan, attention should be paid to the diagnosis of subcutaneous nodules and eye infestations.
Humoral immune response of pigs, Sus scrofa domesticus, upon repeated exposure to blood-feeding by Ornithodoros turicata Duges (Ixodida: Argasidae)
Authors: Kim Hee J. , Krishnavajhala Aparna , Armstrong Brittany A. , Pérez de León Adalberto A. , Filatov Serhii , Teel Pete D. , Lopez Job E.
Published: February 2020

Background

Ornithodoros turicatais an important vector of both human and veterinary pathogens. One primary concern is the global spread of African swine fever virus and the risk of its re-emergence in the Americas through potential transmission byO.turicatato domestic pigs and feral swine. Moreover, in Texas, African warthogs were introduced into the state for hunting purposes and evidence exists that they are reproducing and have spread to three counties in the state. Consequently, it is imperative to develop strategies to evaluate exposure of feral pigs and African warthogs toO. turicata.

Results

We report the development of an animal model to evaluate serological responses of pigs toO. turicatasalivary proteins after three exposures to tick feeding. Serological responses were assessed for ~ 120 days by enzyme-linked immunosorbent assay and immunoblotting using salivary gland extracts fromO. turicata.

Conclusions

Our findings indicate that domestic pigs seroconverted toO. turicatasalivary antigens that is foundational toward the development of a diagnostic assay to improve soft tick surveillance efforts.
Innate lymphoid cells in inflammatory arthritis
Authors: Fang Weiting , Zhang Yuanyuan , Chen Zhu
Published: February 2020

Aberrant activation and dysregulation of immune system is a common feature of many forms of inflammatory arthritis. Since their identification as a distinctive population of leukocytes, innate lymphoid cells (ILCs) have been considered crucial in maintaining tissue homeostasis and bridges between innate and adaptive immune system. Altered ILCs’ subset distribution and function have been observed in a variety of autoimmune and chronic inflammatory diseases and suggest a subset-specific role of ILCs in the pathogenesis of immune-mediated inflammation. In this review, we focus on the current knowledge of ILC subset and their role in inflammatory arthritis, including rheumatoid arthritis (RA), ankylosing spondylitis (AS), psoriatic arthritis (PsA), enteropathic arthritis, and other seronegative spondyloarthritis. By better understanding the biology and function of ILC subset in different disease settings, new therapeutic interventions can be anticipated by modulating dysregulated ILC responses toward promoting resolution of inflammation.
The prevalence of musculoskeletal pain among above 50-year-old population referred to the Kermanshah-Iran health bus in 2016
Authors: Shamsi MohammadBagher , Safari Ameneh , Samadzadeh Soheila , Yoosefpour Nasrin
Published: February 2020

Objective

Musculoskeletal disorders are one of the most important causes of disability. The aim of this study was to evaluate the prevalence of musculoskeletal disorders among the above 50-year-old population who referred to the health bus in Kermanshah. A questionnaire was used to collect data regarding musculoskeletal disorders of 589 people who voluntarily referred to the health bus. Means (SD) and range were used in descriptive statistics.

Results

The most prevalence of musculoskeletal complaints was related to the knee (338, 57.4%). After that, the low back pain had the most frequency (319, 54.3%). The lowest prevalence of musculoskeletal complaints was related to the thighs with a frequency of 95 (16.1%). The highest rate of musculoskeletal complaints over the past week in both genders with a frequency of 251 (59.3%) among women and 68 (41%) among men was related to the low back region The highest rate of musculoskeletal complaints over the past year was also related to the low back region, with a frequency of 220 (41%) among women and 61 (36.7%) among men. Concerning the physical health of the elderly, special attention is required for the knee joint and the low back region.
Visualization of very large high-dimensional data sets as minimum spanning trees
Authors: Probst Daniel , Reymond Jean-Louis
Published: February 2020

The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.
The effectiveness of solar disinfection water treatment method for reducing childhood diarrhea: a systematic review and meta-analysis protocol
Authors: Soboksa Negasa Eshete , Gari Sirak Robele , Hailu Abebe Beyene , Donacho Dereje Oljira , Alemu Bezatu Mengistie
Published: February 2020

Background

Several studies employing the effectiveness of solar disinfection water treatment method for reducing diarrhea have reported heterogeneous outcomes, necessitating a systematic review to provide an exhaustive summary of current evidence. Thus, the objective of this review is to pool out the available evidence on the effectiveness of solar disinfection water treatment method for reducing childhood diarrhea.

Methods

Searches will be conducted in PubMed/Medline, Scopus, Google Scholar, Cochrane Library databases, and reference of other studies published through in December 2019. Studies that compare the diarrhea incidence among the intervention group who were exposed to solar disinfection water treatment and the control group who were not exposed to such water treatment were included. The primary outcome of the study is the change in observed diarrhea incidence risk from baseline to post-intervention. Randomized controlled trial study designs will be included. Selected studies will be critically appraised by two independent reviewers. Extracted data will include details about the interventions, populations, study methods, and outcomes of significance to the review question and objectives. Effect sizes will be expressed as risk ratio, and their 95% confidence intervals will be calculated for analysis.

Discussion

This review and meta-analysis will systematically explore and integrate the evidence available on the effectiveness of solar disinfection water treatment method for reducing diarrhea. In this review, information about the potential impact of solar disinfection water treatment to inactivate pathogenic microbes for reducing diarrhea will be gathered and summarized. The findings from this study will provide directions for future research and public health professionals with an understanding of the importance of solar disinfection water treatment and point to directions for applicability of the interventions in the community.
Certain new dynamic nonlinear inequalities in two independent variables and applications
Authors: El-Deeb A. A. , Khan Zareen A.
Published: February 2020

Several inequalities were proved in 2018 by Boudeliou, in 2015 by Abdeldain and El-Deeb and in 1998 by Pachpatte. It is our aim in this paper to generalize these inequalities to time scales. Beside that, we also apply our inequalities to discrete and continuous calculus to obtain some new inequalities as special cases. Furthermore, we study the boundedness of some problems by applying our results.
Bespoke career up-skilling: the case of Mellon Skills Accelerator
Authors: Tsimas Konstantin
Published: February 2020

In the absence of a sufficient number of state-run institutional interventions, any action stemming from autonomous, voluntary private sector initiatives providing counseling and up-skilling to unemployed women is de facto important, especially when referring to confirmed successful and recurring efforts. This contribution provides a detailed discussion and analysis of the methodological approach and extraordinary results of the “Mellon Skills Accelerator” initiative, designed and delivered by knowl Social Enterprise to increase employability. It provides a preliminary evaluation of the initiative’s impact and suitability to be adopted as a standard course of action, across the Greek nation and possibly across Europe and beyond. The author has had first-hand experience of Mellon Skills Accelerator working as a volunteer counsel and coach with the organization.
Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine
Authors: Bogatyrev Said R. , Rolando Justin C. , Ismagilov Rustem F.
Published: February 2020

Background

The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract.

Results

In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine.

Conclusions

Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis.
Formal approach to model complex adaptive computing systems
Authors: Jarrar Abdessamad , Ait Wakrime Abderrahim , Balouki Youssef
Published: February 2020

Complex adaptive systems provide a significant number of concepts such as reaction, interaction, adaptation, and evolution. In general, these concepts are modelled employing different techniques which give an inexplicit vision on the system. Therefore, all concepts must be carefully modelled using the same approach to avoid contradiction and guarantee system homogeneity and correctness. However, developing a computing system that includes all these concepts using the same approach is not an easy task and requires a perfect understanding of the system’s behaviour. In this paper, we contribute as stepwise towards proposing an approach to model the most important concepts of complex adaptive systems while ensuring homogeneity and the correctness of models. For this aim, we present five standard agent-based models formalizing agent properties, reaction, interaction, adaptation, and evolution. These models are adapted to all cases of complex adaptive systems since they include an abstract description of these concepts. To implement our approach formally, we choose the Event-B method due to the strong assurance of bugs’ absence that it guarantees. Besides, it supports horizontal and vertical refinement which facilitates the specification process. Furthermore, the approach of this paper addresses the very abstract level of modelling which expand the use of this approach to other formal methods and tools.
The role of environmental stress and DNA methylation in the longitudinal course of bipolar disorder
Authors: Comes Ashley L. , Czamara Darina , Adorjan Kristina , Anderson-Schmidt Heike , Andlauer Till F. M. , Budde Monika , Gade Katrin , Hake Maria , Kalman Janos L. , Papiol Sergi , Reich-Erkelenz Daniela , Klöhn-Saghatolislam Farah , Schaupp Sabrina K. , Schulte Eva C. , Senner Fanny , Juckel Georg , Schmauß Max , Zimmermann Jörg , Reimer Jens , Reininghaus Eva , Anghelescu Ion-George , Konrad Carsten , Thiel Andreas , Figge Christian , von Hagen Martin , Koller Manfred , Dietrich Detlef E. , Stierl Sebastian , Scherk Harald , Witt Stephanie H. , Sivalingam Sugirthan , Degenhardt Franziska , Forstner Andreas J. , Rietschel Marcella , Nöthen Markus M. , Wiltfang Jens , Falkai Peter , Schulze Thomas G. , Heilbronner Urs
Published: February 2020

Background

Stressful life events influence the course of affective disorders, however, the mechanisms by which they bring about phenotypic change are not entirely known.

Methods

We explored the role of DNA methylation in response to recent stressful life events in a cohort of bipolar patients from the longitudinal PsyCourse study (n = 96). Peripheral blood DNA methylomes were profiled at two time points for over 850,000 methylation sites. The association between impact ratings of stressful life events and DNA methylation was assessed, first by interrogating methylation sites in the vicinity of candidate genes previously implicated in the stress response and, second, by conducting an exploratory epigenome-wide association analysis. Third, the association between epigenetic aging and change in stress and symptom measures over time was investigated.

Results

Investigation of methylation signatures over time revealed just over half of the CpG sites tested had an absolute difference in methylation of at least 1% over a 1-year period. Although not a single CpG site withstood correction for multiple testing, methylation at one site (cg15212455) was suggestively associated with stressful life events (p < 1.0 × 10−5). Epigenetic aging over a 1-year period was not associated with changes in stress or symptom measures.

Conclusions

To the best of our knowledge, our study is the first to investigate epigenome-wide methylation across time in bipolar patients and in relation to recent, non-traumatic stressful life events. Limited and inconclusive evidence warrants future longitudinal investigations in larger samples of well-characterized bipolar patients to give a complete picture regarding the role of DNA methylation in the course of bipolar disorder.
Habitat availability influences migration speed, refueling patterns and seasonal flyways of a fly-and-forage migrant
Authors: Hadjikyriakou Thomas G. , Nwankwo Emmanuel C. , Virani Munir Z. , Kirschel Alexander N. G.
Published: February 2020

Background

Despite our understanding of the principal factors that shape bird migration strategies, there is conflicting evidence regarding the role of habitat in shaping migration routes and schedules, including day and night activity and differences between autumn and spring. For fly-and-forage migrants, we predict that habitat characteristics might guide migration speed, route selection and migrating schedules.

Methods

We use solar-powered GPS transmitters, obtaining high accuracy data, to monitor the migratory movements of Eleonora’s falcon breeding in Cyprus, which is the easternmost breeding population of the species. We tested for potential preferences in habitat characteristics along the migration routes, separately for the northern, drier part and the more vegetated southern part of the trips. We also examined the relationship between migration speed and vegetative cover during day and at night, accounting for wind support.

Results

We found that tagged individuals repeatedly exhibited an anticlockwise loop migration pattern with spring routes being more easterly than autumn ones. We identified a preference for migration through vegetation-rich areas, where during daytime tagged individuals travel at slower migration speeds compared to vegetation-poor areas, indicating fly-and-forage activity. Birds roosted during most nights, combining refueling stopovers at selected vegetation-rich areas before or after crossing ecological barriers. Conversely, both during day and night, tagged individuals overflew unsuitable habitats more quickly.

Conclusions

Our results suggest that habitat is an important factor in Eleonora’s falcon migratory strategies. Active selection of vegetation rich areas in combination with reduced migration speeds there, allows the migrating falcons to combine migration during the day with fly-and-forage refueling, while roosting most nights.
Studies on the effects of mixed light-thermal ageing on parchment by vibrational spectroscopy and micro hot table method
Authors: Cappa Federica , Paganoni Ilaria , Carsote Cristina , Badea Elena , Schreiner Manfred
Published: February 2020

The damaging effects of mixed light-thermal ageing on parchment were studied by exposing mock-ups to artificial light (162 W/m2 irradiance) at controlled temperature and relative humidity (52 °C, 30% RH) for up to 748 h, with testing being made during this time incrementally. The physical–chemical changes (deterioration) resulting from these conditions were analysed by applying FTIR-ATR and Raman spectroscopy, colorimetric measurements and MHT. The deterioration found includes the formation of collagen-destabilised intermediate states which then progressively convert to disorganised structures, e.g. pregelatinised collagen and gelatin. The process is characterized by molecular changes of collagen associated with its photo-oxidation. These are shown by changes in the position and intensity of the main FTIR absorption bands of collagen, namely those of Amide I, Amide II, and Amide III, as well as by the occurrence and the increase of a shoulder at 1740 cm−1. The shrinking activity of the collagen fibres in the parchment mock-ups was measured by the micro-hot-table (MHT) method, which revealed the presence of multiple collagen populations with distinct thermal stabilities and confirmed the deterioration pattern suggested by the molecular changes.
Model studies of plus and double box shaped skirted footings resting on sand
Authors: Gnananandarao Tammineni , Dutta Rakesh Kumar , Khatri Vishwas Nandkishor
Published: February 2020

The paper presents the investigation on the model unskirted/skirted footings (plus and the double box) on sand. Skirt depth, sand relative density, footing interface condition and skirted footing type were varied parameters. Skirt depth (Ds) varied in this investigation was from 0.25 B to 1.5 B (B, footing width). The results show that the footing geometry and the skirt increased the bearing capacity and improved the overall behaviour. The results further revealed that the lowest percentage improvement for the square shaped footing with Ds/B = 0.25 was 26.08% at a relative density of 60%, whereas the highest improvement for the double box shaped footing with Ds/B = 1.50 was 364.12% at a relative density of 30%. The settlement reduction factors with the use of skirt from this investigation ranged from 0.16 to 1.0 and depended on the pressure applied and the depth ratio of the skirt. Finally, for the settlement reduction factor, an empirical equation was developed. This expression can be used to calculate the settlement of the plus and double box shaped skirted footings on sand.
Gaps in the structuring of organizations in the graduate employment context in Uganda
Authors: Ntale Peter Dithan , Ssempebwa Jude , Musisi Badiru , Musoke Genza Gyaviira , Joseph Kimoga , Mugimu C. B. , Muhammed Ngoma , Ntayi Joseph
Published: February 2020

The complexity of global challenges requires that organizations collaborate with one another. To do this, stakeholders need flexible structures that are designed in a way that allows organizations to collaborate. However, it is not known whether Uganda’s organizations are structured in a way that allows them to collaborate with one another, casting doubt as to whether they can manage the complexity of global challenges such as graduate unemployment. Informed by Hage and Aiken (1967), we studied the structures of selected organizations in Uganda and found out that their major components, i.e., centralization and formalization, are designed in a way that may not allow collaboration to occur. We found out that the organizational structures were exclusive in decision-making, had high power distance (HPD), jobs were strictly codified, and organizations enforced stringent rule observation. These gaps make it difficult for people interaction and involvement and deny them of their freedom to relate with one another, making it difficult for a collaboration between different agencies to occur. To enhance organizational collaboration, it is recommended that organizations should be restructured to become more inclusive, interactive, and democratic since organizations structured in this way have shown collaboration success and greater achievement of society needs.
Genetic diversity and spread of glyphosate-resistant flaxleaf fleabane
Authors: Minati Mohammed Hussein , Preston Christopher , Malone Jenna
Published: February 2020

Background

Continual application of herbicides for flaxleaf fleabane control readily results in the evolution of herbicide resistance. Flaxleaf fleabane has evolved resistance to different modes of action herbicides in many countries. Due to the comprehensive geographical distribution of flaxleaf fleabane in Australia, it was classified as a cosmopolitan weed and it therefore has no specific climatic requirement.

Results

The high percentage of polymorphisms in the samples of the susceptible population (79.8%, 75%) suggests that susceptible populations of flaxleaf fleabane, even within one site, originated from a number of parents. However, the percentage of polymorphism in the resistant populations (51.5%, 66.8%) suggests that resistant populations of flaxleaf fleabane within one site could have originated from fewer parents. In addition, any site containing resistant and susceptible populations of flaxleaf fleabane may have been populated by a large number of parents, evidenced by the relatively high percentage of polymorphisms detected by amplified fragment length polymorphism (AFLP) analysis (86.5%). Despite the large geographic distances between collection locations, populations from across states clustered in several groups showing a close genetic relationship among these populations over these large distances. These high levels of genetic diversity within and between populations confirmed in the sequencing of enolpyruvylshikimate-3-phosphate above support the results of AFLP studies and gave the author more confidence to report the genetic diversity seen within and between population studies.

Conclusion

To prevent further resistance spread, flaxleaf fleabane management in infested areas should focus on decreasing seed movement from resistant sites as well as reducing the selection pressure for resistance to glyphosate by adopting alternative management strategies.
Method validation for bifenthrin emulsifiable concentrate and uncertainty calculation using gas chromatographic approach
Authors: Nazir Arif , Iqbal Javaid , Iqbal Munawar , Abbas Mazhar , Nisar Numrah
Published: February 2020

Background

Bifenthrin is the third-generation synthetic pyrethroid insecticide having an effective control on the pest of cotton, vegetable, and fruits. This study is focused on the validation of the test procedure for the quantitative determination of bifenthrin contents in the emulsifiable concentrate and measurement of uncertainty. The purpose of this validation procedure is to demonstrate that it is suitable for the intended use. This was determined by gas chromatography with a flame ionization detector (FID). The estimation was carried out on Shimadzu GC equipped with TRB-5 (95% dimethyl, 5% diphenyl polysiloxane) column using a nitrogen carrier gas.

Results

Different parameters of validation (precision, accuracy, linearity, specificity, selectivity, and robustness) were executed. All steps of method validation were performed, and its uncertainty is determined. The method is simple, selective, accurate, precise, cost-effective, and suitable. The validation parameters are based on harmonized guidelines on the validation of the analytical test method.

Conclusions

Pesticide formulation bodies can use this method for the qualitative and quantitative determination of bifenthrin different formulations. These data verify that the method is validated, and all results are in an acceptable limit. The method is developed on GC. Moreover, the analysis time is also short as compared to that of HPLC. The developed method is simple reliable and has a realistic approach.
Comparing the broadband acoustic frequency response of single, clustered, and arrays of marine air guns
Authors: Landrø Martin , Langhammer Jan
Published: February 2020

Field data acquired from a seismic vessel by a seabed hydrophone is used to analyze the broadband response (10 Hz to 62.5 kHz) for various source configurations: single air guns, clustered air guns, and a full array consisting of 30 air guns. The various parts of the acoustic signal are analyzed in detail, and it is found that a high-frequency signal arriving prior to the main peak of a single air-gun signal most likely is caused by small vapor cavities collapsing at or close to the surface of the gun. This is confirmed by high-speed photographs taken when a small air gun is fired in a water tank. When the full array is used, a second type of cavitation signal is observed: ghost cavitation caused by acoustic stimulation by the negative pressure that is backscattered from the free surface. As this ghost signal from 30 different guns arrives at a specific location in the water, cavities might be formed, and they create a high-frequency acoustic signal.
Experimental study on the bifurcation of a density oscillator depending on density difference
Authors: Ito H. , Itasaka T. , Takeda N. , Kitahata H.
Published: February 2020

Hydrodynamic instabilities often cause spatio-temporal pattern formations and transitions between them. We investigate a model experimental system, a density oscillator, where the bifurcation from a resting state to an oscillatory state is triggered by the increase in the density difference of the two fluids. Our results show that the oscillation amplitude increases from zero and the period decreases above a critical density difference. The detailed data close to the bifurcation point provide a critical exponent consistent with the supercritical Hopf bifurcation.
Linguistic Diversity in Appalachia
Authors: Blanchette Frances , Reed Paul E. , Flannery Erin , Jackson Carrie N.
Published: February 2020

This study investigates how American English speakers from within and outside the Appalachian region interpret negative auxiliary inversion (NAI). Previously observed in Appalachian and other English varieties, NAI has surface syntax similar to yes-no questions but receives a declarative interpretation (e.g., Didn’t everybody watch Superbowl 53, meaning ‘not everybody watched’). Previous work shows that NAI is associated with a reading in which some but not all people participated in an event, as opposed to one in which no one participated. Results from an interpretation task revealed that Appalachian participants tended to obtain the ‘not all’ and not the ‘no one’ reading for NAI. In contrast, non-Appalachian participants’ interpretations exhibited greater inter- and intraspeaker variability. Appalachian participants with more ‘not all’ interpretations reported positive attitudes toward NAI use, and they also distinguished between attested and unattested syntactic subject types (e.g., everybody, many people, *few people) in a naturalness rating task. Appalachian participants with more ‘no one’ interpretations had more negative attitudes toward NAI use and made no distinction between subject types. These results highlight how individuals from Appalachia interpret NAI differently than individuals from outside the region and suggest that language attitudes may impact semantic interpretation within a nonmainstream speaker group.
Multiple lineages enable robust development of the neuropil-glia architecture in adult Drosophila
Authors: Kato Kentaro , Orihara-Ono Minako , Awasaki Takeshi
Published: February 2020

Neural remodeling is essential for the development of a functional nervous system and has been extensively studied in the metamorphosis of Drosophila. Despite the crucial roles of glial cells in brain functions, including learning and behavior, little is known of how adult glial cells develop in the context of neural remodeling. Here, we show that the architecture of neuropil-glia in the adult Drosophila brain, which is composed of astrocyte-like glia (ALG) and ensheathing glia (EG), robustly develops from two different populations in the larva: the larval EG and glial cell missing-positive (gcm+) cells. Whereas gcm+ cells proliferate and generate adult ALG and EG, larval EG dedifferentiate, proliferate and redifferentiate into the same glial subtypes. Each glial lineage occupies a certain brain area complementary to the other, and together they form the adult neuropil-glia architecture. Both lineages require the FGF receptor Heartless to proliferate, and the homeoprotein Prospero to differentiate into ALG. Lineage-specific inhibition of gliogenesis revealed that each lineage compensates for deficiency in the proliferation of the other. Together, the lineages ensure the robust development of adult neuropil-glia, thereby ensuring a functional brain.
Villin controls the formation and enlargement of punctate actin foci in pollen tubes
Authors: Zhao Wanying , Qu Xiaolu , Zhuang Yuhui , Wang Ludi , Bosch Maurice , Franklin-Tong Vernonica E. , Xue Yongbiao , Huang Shanjin
Published: February 2020

Self-incompatibility (SI) in the poppy Papaver rhoeas triggers dramatic alterations in actin within pollen tubes. However, how these actin alterations are mechanistically achieved remains largely unexplored. Here, we used treatment with the Ca2+ ionophore A23187 to mimic the SI-induced elevation in cytosolic Ca2+ and trigger formation of the distinctive F-actin foci. Live-cell imaging revealed that this remodeling involves F-actin fragmentation and depolymerization, accompanied by the rapid formation of punctate actin foci and subsequent increase in their size. We established that actin foci are generated and enlarged from crosslinking of fragmented actin filament structures. Moreover, we show that villins associate with actin structures and are involved in this actin reorganization process. Notably, we demonstrate that Arabidopsis VILLIN5 promotes actin depolymerization and formation of actin foci by fragmenting actin filaments, and controlling the enlargement of actin foci via bundling of actin filaments. Our study thus uncovers important novel insights about the molecular players and mechanisms involved in forming the distinctive actin foci in pollen tubes.
Mechanisms of malignancy in glioblastoma cells are linked to mitochondrial Ca2+ uniporter upregulation and higher intracellular Ca2+ levels
Authors: Li Xiaoyun , Spelat Renza , Bartolini Anna , Cesselli Daniela , Ius Tamara , Skrap Miran , Caponnetto Federica , Manini Ivana , Yang Yili , Torre Vincent
Published: February 2020

Glioblastoma (GBM) is one of the most malignant brain tumours and, despite advances in treatment modalities, it remains largely incurable. Ca2+ regulation and dynamics play crucial roles in different aspects of cancer, but they have never been investigated in detail in GBM. Here, we report that spontaneous Ca2+ waves in GBM cells cause unusual intracellular Ca2+ ([Ca2+]i) elevations (>1 μM), often propagating through tumour microtubes (TMs) connecting adjacent cells. This unusual [Ca2+]i elevation is not associated with the induction of cell death and is concomitant with overexpression of mitochondrial Ca2+ uniporter (MCU). We show that MCU silencing decreases proliferation and alters [Ca2+]i dynamics in U87 GBM cells, while MCU overexpression increases [Ca2+]i elevation in human astrocytes (HAs). These results suggest that changes in the expression level of MCU, a protein involved in intracellular Ca2+ regulation, influences GBM cell proliferation, contributing to GBM malignancy.

This article has an associated First Person interview with the first author of the paper.
Lamin is essential for nuclear localization of the GPI synthesis enzyme PIG-B and GPI-anchored protein production in Drosophila
Authors: Yamamoto-Hino Miki , Kawaguchi Kohei , Ono Masaya , Furukawa Kazuhiro , Goto Satoshi
Published: February 2020

Membrane lipid biosynthesis is a complex process that occurs in various intracellular compartments. In Drosophila, phosphatidylinositol glycan-B (PIG-B), which catalyzes addition of the third mannose in glycosylphosphatidylinositol (GPI), localizes to the nuclear envelope (NE). Although this NE localization is essential for Drosophila development, the underlying molecular mechanism remains unknown. To elucidate this mechanism, we identified PIG-B-interacting proteins by performing immunoprecipitation followed by proteomic analysis. We then examined which of these proteins are required for the NE localization of PIG-B. Knockdown of Lamin Dm0, a B-type lamin, led to mislocalization of PIG-B from the NE to the endoplasmic reticulum. Lamin Dm0 associated with PIG-B at the inner nuclear membrane, a process that required the tail domain of Lamin Dm0. Furthermore, GPI moieties were distributed abnormally in the Lamin Dm0 mutant. These data indicate that Lamin Dm0 is involved in the NE localization of PIG-B and is required for proper GPI-anchor modification of proteins.
Rapid cold hardening: ecological relevance, physiological mechanisms and new perspectives
Authors: Teets Nicholas M. , Gantz J. D. , Kawarasaki Yuta
Published: February 2020

Rapid cold hardening (RCH) is a type of phenotypic plasticity that allows ectotherms to quickly enhance cold tolerance in response to brief chilling (lasting minutes to hours). In this Review, we summarize the current state of knowledge of this important phenotype and provide new directions for research. As one of the fastest adaptive responses to temperature known, RCH allows ectotherms to cope with sudden cold snaps and to optimize their performance during diurnal cooling cycles. RCH and similar phenotypes have been observed across a diversity of ectotherms, including crustaceans, terrestrial arthropods, amphibians, reptiles, and fish. In addition to its well-defined role in enhancing survival to extreme cold, RCH also protects against nonlethal cold injury by preserving essential functions following cold stress, such as locomotion, reproduction, and energy balance. The capacity for RCH varies across species and across genotypes of the same species, indicating that RCH can be shaped by selection and is likely favored in thermally variable environments. Mechanistically, RCH is distinct from other rapid stress responses in that it typically does not involve synthesis of new gene products; rather, the existing cellular machinery regulates RCH through post-translational signaling mechanisms. However, the protective mechanisms that enhance cold hardiness are largely unknown. We provide evidence that RCH can be induced by multiple triggers in addition to low temperature, and that rapidly induced tolerance and cross-tolerance to a variety of environmental stressors may be a general feature of stress responses that requires further investigation.