bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Queuing Technology on Customer Experience in Physical Retail Environments
Authors: Obermeier Gabriele , Zimmermann Robert , Auinger Andreas
Published: July 2020

Queuing systems manage the order of customers waiting for their service encounter fairly and equitably and influence the perception of their experience in a physical retail store. In this field study, we investigate a self-service and a human-operated queuing system, both offering additional features, designed to offer a higher level of personalization and convenience for the customer’s waiting time. Our study shows that advanced queuing technologies in stores, with generally low customer frequency and short waiting times, show no statistically significant effect on a customer’s perception of the overall customer experience, satisfaction or intention to repurchase. However, customers were satisfied with the technologies and evaluated their queuing experience as effortless, easy and quick, which shows general support for those technologies. Beyond the statistical analysis, our mixed-method approach contributes to a broad understanding of advanced queuing technology for practitioners, retailers and developers of such systems.
Phase transition and chaos in charged SYK model
Authors: Sorokhaibam Nilakash
Published: July 2020

Abstract

We study chaotic-integrable transition and the nature of quantum chaos in SYK model with chemical potential. We use a novel numerical technique to calculate the partition function explicitly. We show the phase transition in the presence of large chemical potential. We also show that a mass-like term consisting of two fermion random interaction (q = 2 SYK term) does not give rise to a sharp transition. We find that turning on the chemical potential suppresses the Lyapunov exponent in the chaotic phase exponentially.
Radiomics in radiation oncology—basics, methods, and limitations
Authors: Lohmann Philipp , Bousabarah Khaled , Hoevels Mauritius , Treuer Harald
Published: July 2020

Over the past years, the quantity and complexity of imaging data available for the clinical management of patients with solid tumors has increased substantially. Without the support of methods from the field of artificial intelligence (AI) and machine learning, a complete evaluation of the available image information is hardly feasible in clinical routine. Especially in radiotherapy planning, manual detection and segmentation of lesions is laborious, time consuming, and shows significant variability among observers. Here, AI already offers techniques to support radiation oncologists, whereby ultimately, the productivity and the quality are increased, potentially leading to an improved patient outcome. Besides detection and segmentation of lesions, AI allows the extraction of a vast number of quantitative imaging features from structural or functional imaging data that are typically not accessible by means of human perception. These features can be used alone or in combination with other clinical parameters to generate mathematical models that allow, for example, prediction of the response to radiotherapy. Within the large field of AI, radiomics is the subdiscipline that deals with the extraction of quantitative image features as well as the generation of predictive or prognostic mathematical models. This review gives an overview of the basics, methods, and limitations of radiomics, with a focus on patients with brain tumors treated by radiation therapy.
Nomogram Analysis and Internal Validation to Predict the Risk of Cystobiliary Communication in Patients Undergoing Hydatid Liver Cyst Surgery
Authors: Wang Zhan , Xu Jin , Pang MingQuan , Guo Bin , Xu XiaoLei , Wang HaiJiu , Zhou Ying , Ren Li , Zhang LingQiang , Ma Jie , Fan HaiNing
Published: July 2020

Purpose

Biliary leakage caused by cystobiliary communication (CBC) is a common clinical concern. This study sought to identify predictors of CBC in hepatic cystic echinococcosis (HCE) patients undergoing hydatid liver cyst surgery and establish nomograms to predict CBC.

Methods

A predictive model was established in a training cohort of 310 HCE patients diagnosed between January 2013 and May 2017. Upon revision of the records of clinical parameters and imaging features of these patients, the lasso regression model was used to optimize feature selection for the CBC risk model. Combined with feature selection, a CBC nomogram was developed with multivariable logistic regression. C‐index and calibration plots were used to analyze and evaluate the discrimination and calibration. The net benefit and predictive accuracy of the nomogram were performed via decision curve analysis (DCA) and receiver operating characteristic (ROC) curve. An independent validation cohort of 132 patients recruited from June 2017 to May 2019 was used to evaluate the practicability of the nomogram.

Results

Predictors contained four features, namely alkaline phosphatase (ALP), glutamyl transpeptidase (GGT), cyst size and cyst location. The C‐index of the nomogram is 0.791 (95% CI, 0.736–0.845), while the C‐index verified by bootstrap is 0.746, indicating high prediction accuracy. The area under the curve (AUC) of the CBC in training was 0.766. ROC curve analysis demonstrated high sensitivity and specificity. Decision curve analysis confirmed the CBC nomogram was clinically useful when the intervention was determined at the non‐adherence possibility threshold of 8%.

Conclusion

The nomogram developed using the ALP, GGT, cyst size and cyst location could be used to facilitate the CBC risk prediction in HCE patients.
Case study of an autoantibody panel for early detection of lung cancer and ground-glass nodules
Authors: Huo Yunli , Guo Zijian , Gao Xuehui , Liu Zhongjuan , Zhang Ruili , Qin Xuzhen
Published: July 2020

Purpose

Increasing lung cancer incidence in China with a high death rate due to late diagnosis highlights the need for biomarkers, such as panels of autoantibodies (AAbs), for prediction and early lung cancer diagnosis. We conducted a study to further evaluate the clinical performance of an AAb diagnostic kit.

Methods

Using enzyme-linked immunosorbent assay, levels of seven AAbs in serum samples from 121 patients with newly diagnosed lung cancer, 84 controls (34 healthy individuals and 50 patients with benign lung disease), and 100 indeterminate solid nodules, were measured. Participants were followed up until 6 months after a positive test result to confirm lung cancer diagnosis.

Results

The seven AAb concentration was significantly higher in lung cancer patients than in controls (P < 0.05). The seven AAb sensitivity and specificity for newly diagnosed lung cancer were 45.5% and 85.3%, respectively, while the seven AAb combined area under the curve (in lung cancer patients versus controls) was 0.660. Of the 28 patients with solid nodules with positive test results, 8 and 3 were diagnosed with lung cancer and benign lung disease, respectively, during follow-up. The positive predictive value of the experiment was 72.7%.

Conclusion

Positive AAb test results were associated with a high risk of lung cancer. The seven-AAb panel also had a high predictive value for detecting lung cancer in patients with solid nodules. Our seven lung cancer autoantibody types can provide an important early warning sign in the clinical setting.
Discrimination of Low-Energy Acetabular Fractures from Controls Using Computed Tomography-Based Bone Characteristics
Authors: Gebre Robel K. , Hirvasniemi Jukka , Lantto Iikka , Saarakkala Simo , Leppilahti Juhana , Jämsä Timo
Published: July 2020

The incidence of low-energy acetabular fractures has increased. However, the structural factors for these fractures remain unclear. The objective of this study was to extract trabecular bone architecture and proximal femur geometry (PFG) measures from clinical computed tomography (CT) images to (1) identify possible structural risk factors of acetabular fractures, and (2) to discriminate fracture cases from controls using machine learning methods. CT images of 107 acetabular fracture subjects (25 females, 82 males) and 107 age-gender matched controls were examined. Three volumes of interest, one at the acetabulum and two at the femoral head, were extracted to calculate bone volume fraction (BV/TV), gray-level co-occurrence matrix and histogram of the gray values (GV). The PFG was defined by neck shaft angle and femoral neck axis length. Relationships between the variables were assessed by statistical mean comparisons and correlation analyses. Bayesian logistic regression and Elastic net machine learning models were implemented for classification. We found lower BV/TV at the femoral head (0.51 vs. 0.55, p = 0.012) and lower mean GV at both the acetabulum (98.81 vs. 115.33, p < 0.001) and femoral head (150.63 vs. 163.47, p = 0.005) of fracture subjects when compared to their matched controls. The trabeculae within the femoral heads of the acetabular fracture sides differed in structure, density and texture from the corresponding control sides of the fracture subjects. Moreover, the PFG and trabecular architectural variables, alone and in combination, were able to discriminate fracture cases from controls (area under the receiver operating characteristics curve 0.70 to 0.79). In conclusion, lower density in the acetabulum and femoral head with abnormal trabecular structure and texture at the femoral head, appear to be risk factors for low-energy acetabular fractures.
A formula for hidden regular variation behavior for symmetric stable distributions
Authors: Forsström Malin Palö , Steif Jeffrey E.
Published: July 2020

We develop a formula for the power-law decay of various sets for symmetric stable random vectors in terms of how many vectors from the support of the corresponding spectral measure are needed to enter the set. One sees different decay rates in “different directions”, illustrating the phenomenon of hidden regular variation. We give several examples and obtain quite varied behavior, including sets which do not have exact power-law decay.
Phenomenology of imagining and the pragmatics of fictional language
Authors: Summa Michela
Published: July 2020

This paper focuses on the performative character of fictional language. While assuming that all speaking is a form of acting, it aims to shed light on the nature of fictional, and particularly literary, speech acts. To this aim, relevant input can be found in (a) the discussion of the ontological status of fictional entities and of their constitution and in (b) the inquiry into the interaction between author and receiver of a fictional work. Based on the critical assessment of different approaches in the debate on speech-act theory and literary fiction, the article first clarifies why the study of the performative character of fictional language cannot be reduced to either the discussion of the status of singular speech acts in the fiction or the inquiry into the pretend or unserious nature of fictional speech acts formulated by an author. While referring to Roman Ingarden’s, Jean-Paul Sartre’s, and Wolfgang Iser’s work, it subsequently argues that such a performative character should be understood as a specific serious affordance—or appeal—to imagine and thus to participate in the constitution of the fictional world.
Alleviation of salinity stress in plants by endophytic plant-fungal symbiosis: Current knowledge, perspectives and future directions
Authors: Gupta Sneha , Schillaci Martino , Walker Robert , Smith Penelope M. C. , Watt Michelle , Roessner Ute
Published: July 2020

Salinization of soil with sodium chloride ions inhibits plant functions, causing reduction of yield of crops. Salt tolerant microorganisms have been studied to enhance crop growth under salinity. This review describes the performance of endophytic fungi applied to crops as a supplement to plant genetics or soil management to alleviate salt stress in crops. This is achieved via inducing systemic resistance, increasing the levels of beneficial metabolites, activating antioxidant systems to scavenge ROS, and modulating plant growth phytohormones. Colonization by endophytic fungi improves nutrient uptake and maintains ionic homeostasis by modulating ion accumulation, thereby restricting the transport of Na+ to leaves and ensuring a low cytosolic Na+:K+ ratio in plants. Participating endophytic fungi enhance transcripts of genes encoding the high Affinity Potassium Transporter 1 (HKT1) and the inward-rectifying K+ channels KAT1 and KAT2, which play key roles in regulating Na+ and K+ homeostasis. Endophytic-induced interplay of strigolactones play regulatory roles in salt tolerance by interacting with phytohormones. Future research requires further attention on the biochemical, molecular and genetic mechanisms crucial for salt stress resistance requires further attention for future research. Furthermore, to design strategies for sustained plant health with endophytic fungi, a new wave of exploration of plant-endophyte responses to combinations of stresses is mandatory.
Seropositivity for pathogens associated with chronic infections is a risk factor for all-cause mortality in the elderly: findings from the Memory and Morbidity in Augsburg Elderly (MEMO) Study
Authors: Zeeb Marius , Kerrinnes Tobias , Cicin-Sain Luka , Guzman Carlos A. , Puppe Wolfram , Schulz Thomas F. , Peters Annette , Berger Klaus , Castell Stefanie , Karch André
Published: July 2020

Immunostimulation by chronic infection has been linked to an increased risk for different non-communicable diseases, which in turn are leading causes of death in high- and middle-income countries. Thus, we investigated if a positive serostatus for pathogens responsible for common chronic infections is individually or synergistically related to reduced overall survival in community dwelling elderly. We used data of 365 individuals from the German MEMO (Memory and Morbidity in Augsburg Elderly) cohort study with a median age of 73 years at baseline and a median follow-up of 14 years. We examined the effect of a positive serostatus at baseline for selected pathogens associated with chronic infections (Helicobacter pylori, Borrelia burgdorferi sensu lato, Toxoplasma gondii, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1/2, and human herpesvirus 6) on all-cause mortality with multivariable parametric survival models. We found a reduced survival time in individuals with a positive serostatus for Helicobacter pylori (accelerated failure time (AFT) − 15.92, 95% CI − 29.96; − 1.88), cytomegalovirus (AFT − 22.81, 95% CI − 36.41; − 9.22) and Borrelia burgdorferi sensu lato (AFT − 25.25, 95% CI − 43.40; − 7.10), after adjusting for potential confounders. The number of infectious agents an individual was seropositive for had a linear effect on all-cause mortality (AFT per additional infection − 12.42 95% CI − 18.55; − 6.30). Our results suggest an effect of seropositivity for Helicobacter pylori, cytomegalovirus, and Borrelia burgdorferi sensu lato on all-cause mortality in older community dwelling individuals. Further research with larger cohorts and additional biomarkers is required, to assess mediators and molecular pathways of this effect.
Wie authentisch führe ich? Prüfung der Selbsteinschätzungsform des Deutschen Inventars Authentischer Führung
Authors: Reineboth Magdalena , Le Thu Ha Nensy , Franke-Bartholdt Luise , Frömmer Dirk , Wegge Jürgen , Strobel Anja
Published: July 2020

Dieser Beitrag der Zeitschrift „Gruppe. Interaktion. Organisation. (GIO)“ beschäftigt sich mit der Prüfung und Validierung der Selbsteinschätzungsform des Deutschen Inventars Authentischer Führung.

Authentische Führung hat sich in den letzten Jahren als ein zentrales positives Führungskonzept herausgebildet. Allerdings liegt im deutschsprachigen Raum bisher nur ein Instrument zur Fremdeinschätzung vor: Das Deutsche Inventar authentischer Führung (DIAF-F). In diesem Beitrag wird ein Instrument zur Selbsteinschätzung authentischer Führung (DIAF-S) mit den Komponenten Selbstbewusstheit, Transparenz in Beziehungen, ausgewogene Informationsverarbeitung und verinnerlichte moralische Perspektive vorgestellt und erprobt. Zur ersten Validierung des neuen Verfahrens wurden Daten vonN = 91 Führungskräften undN = 259 Mitarbeitenden erfasst. Für die Gesamtskala und drei der vier Komponenten ergaben sich interne Konsistenzen im befriedigenden bis guten Bereich. Das DIAF‑S wies bedeutsame Zusammenhänge mit organisationalen Außenkriterien (durch Führungskraft eingeschätzte Arbeitsleistung der Mitarbeitenden, Voice-Verhalten und Moral Courage) auf. Zudem zeigte sich für einen Großteil der Komponenten die erwartete moderate Übereinstimmung zwischen selbst- und fremdeingeschätzter authentischer Führung. Mittels konfirmatorischer Faktorenanalysen ließ sich eine Verwendung der vierfaktoriellen Struktur analog zur Fremdbeurteilung rechtfertigen. Eine explorative Faktorenanalyse legte eher eine dreifaktorielle Struktur der selbsteingeschätzten authentischen Führung nahe. Vor diesem Hintergrund werden alternative Modelle authentischer Führung diskutiert. Insgesamt betrachtet stellt das DIAF‑S ein weitgehend reliables und valides Instrument für die Selbsteinschätzung authentischer Führung und damit eine wichtige Ergänzung zum DIAF‑F dar.
Extraction of pumpkin peel extract using supercritical CO2 and subcritical water technology: Enhancing oxidative stability of canola oil
Authors: Salami Azadeh , Asefi Narmela , Kenari Reza Esmaeilzadeh , Gharekhani Mehdi
Published: July 2020

In this study, subcritical water extraction (SWE) and the supercritical fluid extraction (SFE) methods were used for the extraction of pumpkin peel extract. Total phenolic content and carotenoid compounds of extracts were measured. The extracts were added to canola oil at a concentration of 400 ppm and were stored at 30 °C for 60 days. The peroxide, carbonyl and acid values of the oil samples were measured, then compared with 100 ppm of tert-butylhydroquinone (TBHQ) synthetic antioxidants. The results showed that the total phenol content of obtained extract by SFE (353.5 mg GA/100 g extract) was higher than by SWE (213.6 mg GA/100 g extract), while the carotenoid content was higher for obtained extract by SWE (15.22 mg/100 g extract) compared to SFE (11.48 mg/100 g extract). The result of oil oxidation showed that the oxidative stability of the oil containing the mixed extract (SFE–SWE) is higher than the separate extract, consequently showing higher performance in preventing oil oxidation compared to TBHQ.
Microstructure and luminescent properties of Eu3+-activated MgGa2O4:Mn2+ ceramic phosphors
Authors: Luchechko A. , Shpotyuk Y. , Kravets O. , Zaremba O. , Szmuc K. , Cebulski J. , Ingram A. , Golovchak R. , Shpotyuk O.
Published: July 2020

Mn2+ and the trivalent europium (Eu3+)-doped MgGa2O4 ceramics are characterized using a multi-experimental approach. The formation of spinel-structured ceramics is ascertained from X-ray diffraction (XRD) analysis. Morphology investigations with transmission electron microscopy (TEM) show irregularly shaped grains and grain boundaries with a homogeneous distribution of Eu3+ ions. The inability of Eu activator to penetrate the bulk of ceramic grains is inferred from positron annihilation lifetime spectroscopy data. The Eu doping is shown to enhance the positron trapping rate due to the occupancy of vacancy-type defects at ceramic grains by Eu3+ ions. Both Mn2+ and Eu3+ doped samples show a broad multi-color luminescence in 350–650 nm range under 240 nm and 270–300 nm excitations. Blue emission is concluded to originate from host defects, whereas green emission and narrow lines in the red region of the spectrum are attributed to Mn2+ and Eu3+ ions, respectively. High asymmetry around Eu3+ ions can be concluded from the photoluminescence and positron annihilation lifetime spectra analysis.
Researching the political economy of adult learning systems. Theoretical amendments and empirical findings
Authors: Schemmann Michael , Herbrechter Dörthe , Engels Martina
Published: July 2020

The article relates to different approaches which emphasize a multi-level perspective as well as the institutional conditions that shape adult education. With reference to both the political economy approach and the governance perspective, it is outlined how these more general approaches can be theoretically amended by neo-institutional ideas especially when considering the institutional conditions that shape adult education at an organizational level. Based on a re-analysis of interview data, the findings provide first empirical indications of how institutional conditions of adult education organizations (e.g. the actors involved and their institutionalized relationships of interdependency) can be further specified when neo-institutional ideas are taken into account.
DNA double-strand break end resection: a critical relay point for determining the pathway of repair and signaling
Authors: Katsuki Yoko , Jeggo Penny A. , Uchihara Yuki , Takata Minoru , Shibata Atsushi
Published: July 2020

A DNA double-strand break (DSB) is considered the most critical DNA lesion because it causes cell death and severe mutations if it is not repaired or repaired incorrectly. Accumulating evidence has shown that the majority of DSBs are repaired by DNA non-homologous end joining (NHEJ), the first utilized repair pathway in human cells. In contrast, the repair pathway is sometimes diverted into using homologous recombination (HR), which has increased precision under specific circumstances: e.g., when DSBs are generated at transcriptionally active loci or are not readily repaired due to the complexity of damage at the DSB ends or due to highly compacted chromatin. DSB end resection (resection) is considered the most critical turning point for directing repair towards HR. After resection, the HR process is finalized by RAD51 loading and recombination. Thus, understanding the process of resection is critically important to understand the regulation of the choice of DSB repair pathway. In addition, resection is also an important factor influencing DNA damage signaling because unresected ends preferentially activate ATM, whereas longer resected ends activate ATR. Thus, DSB end resection is a key relay point that determines the repair pathway and the signal balance. In this review, we summarize the mechanism underlying DSB end resection and further discuss how it is involved in cancer therapy.
Breaking up is hard to do – Making up can be even harder! (Tales of atomising and sintering)
Authors: Kearns Martin A. , Coleman Andrew J.
Published: July 2020

As well as having a strong focus on product consistency, Sandvik Osprey has sought over the years to understand more of its customers’ experience of its products through characterisation and customisation of its growing product range. By controlling the alloying, atomising and sizing processes, powder producers can subtly influence the compounding, moulding and sintering behavior in customers’ processes delivering various positive outcomes. In this retrospective, examples are given in case studies on fluidity, strength and surface finish in 17-4PH, high temperature stability in HK30 turbocharger alloy, improved processing windows and tolerance control in tool steels and martensitic stainless steels and the exceptional mechanical properties developed in Ni base superalloys for auto and aero applications. While primarily relating to MIM, the benefits described are potentially applicable in emerging binder jet technologies where additional emphasis is put on powder flow and packing density.
Jam v International Finance Corporation: The US Supreme Court Decision and its Aftermath
Authors: SIMONS Marco , GRAZIANO MacKennan
Published: July 2020

A year ago, in Jam v International Finance Corporation, fishing and farming families from rural India achieved a historic US Supreme Court victory over one of the world’s largest financial institutions. The Supreme Court decided that the World Bank Group, and similar international organizations, do not automatically enjoy ‘absolute’ immunity from suit, but instead can be sued under the same circumstances as foreign governments can be sued in United States (US) courts – including suits based on their commercial activities in the US.
Dynamic network prediction
Authors: Goyal Ravi , De Gruttola Victor
Published: July 2020

We present a statistical framework for generating predicted dynamic networks based on the observed evolution of social relationships in a population. The framework includes a novel and flexible procedure to sample dynamic networks given a probability distribution on evolving network properties; it permits the use of a broad class of approaches to model trends, seasonal variability, uncertainty, and changes in population composition. Current methods do not account for the variability in the observed historical networks when predicting the network structure; the proposed method provides a principled approach to incorporate uncertainty in prediction. This advance aids in the designing of network-based interventions, as development of such interventions often requires prediction of the network structure in the presence and absence of the intervention. Two simulation studies are conducted to demonstrate the usefulness of generating predicted networks when designing network-based interventions. The framework is also illustrated by investigating results of potential interventions on bill passage rates using a dynamic network that represents the sponsor/co-sponsor relationships among senators derived from bills introduced in the U.S. Senate from 2003 to 2016.
Dosimetric evaluation of 3 and/or 4 field radiation therapy of breast cancers: clinical experience
Authors: Osei Ernest , Dang Susan , Darko Johnson , Fleming Katrina , Rachakonda Ramana
Published: July 2020

Background:

Breast cancer is the most commonly diagnosed cancer among women and the second leading cause of cancer-related death in Canadian women. Surgery is often the first line of treatment for low-risk early stage patients, followed by adjuvant radiation therapy to reduce the risk of local recurrence and prevent metastasis after lumpectomy or mastectomy. For high-risk patients with node positive disease or are at greater risk of nodal metastasis, radiation therapy will involve treatment of the intact breast or chest-wall as well as the regional lymph nodes.

Materials and methods:

We retrospectively evaluated the treatment plans of 354 patients with breast cancer with nodes positive or were at high risk of nodal involvement treated at our cancer centre. All patients were treated with a prescription dose of 50 Gy in 25 fractions to the intact breast or chest-wall and 50 Gy in 25 fractions to the supraclavicular region and, based on patient suitability and tolerance, were treated either using the deep inspiration breath hold (DIBH) or free-breathing (FB) techniques.

Results:

Based on patient suitability and tolerance, 130 (36·7%) patients were treated with DIBH and 224 (63·3%) with FB techniques. There were 169 (47·7%) patients treated with intact breast, whereas 185 (52·3%) were treated for post-mastectomy chest-wall. The mean PTV_eval V92%, V95%, V100% and V105% for all patients are 99·4 ± 0·7, 97·6 ± 1·6, 74·8 ± 7·9 and 1·5 ± 3·2%, respectively. The mean ipsilateral lung V10Gy, V20Gy and V30Gy are 30·0 ± 5·3, 22·4 ± 4·7 and 18·4 ± 4·3% for intact breast and 30·9 ± 5·8, 23·5 ± 5·4 and 19·4 ± 5·0% for post-mastectomy patients with FB, respectively. The corresponding values for patients treated using DIBH are 26·3 ± 5·9, 18·9 ± 5·0 and 15·6 ± 4·7% for intact breast and 27·5 ± 6·5, 20·6 ± 5·7 and 17·1 ± 5·2% for post-mastectomy patients, respectively. The mean heart V10Gy, V20Gy, is 1·8 ± 1·7, 0·9 ± 1·0 for intact breast and 3·1 ± 2·2, 1·7 ± 1·6 for post-mastectomy patients with FB, respectively. The corresponding values with the DIBH are 0·5 ± 0·7, 0·1 ± 0·4 for intact breast and 1·1 ± 1·4, 0·4 ± 0·7 for post-mastectomy patients, respectively.

Conclusion:

The use of 3 and/or 4 field hybrid intensity-modulated radiation therapy technique for radiation therapy of high-risk node positive breast cancer patients provides an efficient and reliable method for achieving superior dose uniformity, conformity and homogeneity in the breast or post-mastectomy chest-wall volume with minimal doses to the organs at risk. The development and implementation of a consistent treatment plan acceptability criteria in radiotherapy programmes would establish an evaluation process to define a consistent, standardised and transparent treatment path for all patients that would reduce significant variations in the acceptability of treatment plans.
INTS10–INTS13–INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module
Authors: Sabath Kevin , Stäubli Melanie L. , Marti Sabrina , Leitner Alexander , Moes Murielle , Jonas Stefanie
Published: July 2020

The Integrator complex processes 3′-ends of spliceosomal small nuclear RNAs (snRNAs). Furthermore, it regulates transcription of protein coding genes by terminating transcription after unstable pausing. The molecular basis for Integrator’s functions remains obscure. Here, we show that INTS10, Asunder/INTS13 and INTS14 form a separable, functional Integrator module. The structure of INTS13-INTS14 reveals a strongly entwined complex with a unique chain interlink. Unexpected structural homology to the Ku70-Ku80 DNA repair complex suggests nucleic acid affinity. Indeed, the module displays affinity for DNA and RNA but prefers RNA hairpins. While the module plays an accessory role in snRNA maturation, it has a stronger influence on transcription termination after pausing. Asunder/INTS13 directly binds Integrator’s cleavage module via a conserved C-terminal motif that is involved in snRNA processing and required for spermatogenesis. Collectively, our data establish INTS10-INTS13-INTS14 as a nucleic acid-binding module and suggest that it brings cleavage module and target transcripts into proximity.
A supervised learning framework for chromatin loop detection in genome-wide contact maps
Authors: Salameh Tarik J. , Wang Xiaotao , Song Fan , Zhang Bo , Wright Sage M. , Khunsriraksakul Chachrit , Ruan Yijun , Yue Feng
Published: July 2020

Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on a genome-wide map. However, given the availability of orthogonal data types such as ChIA-PET, HiChIP, Capture Hi-C, and high-throughput imaging, a supervised learning approach could facilitate the discovery of a comprehensive set of chromatin interactions. Here, we present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps. We compare Peakachu with current enrichment-based approaches, and find that Peakachu identifies a unique set of short-range interactions. We show that our models perform well in different platforms, across different sequencing depths, and across different species. We apply this framework to predict chromatin loops in 56 Hi-C datasets, and release the results at the 3D Genome Browser.
EEF1A1 deacetylation enables transcriptional activation of remyelination
Authors: Duman Mert , Vaquié Adrien , Nocera Gianluigi , Heller Manfred , Stumpe Michael , Siva Sankar Devanarayanan , Dengjel Jörn , Meijer Dies , Yamaguchi Teppei , Matthias Patrick , Zeis Thomas , Schaeren-Wiemers Nicole , Hayoz Antoinette , Ruff Sophie , Jacob Claire
Published: July 2020

Remyelination of the peripheral and central nervous systems (PNS and CNS, respectively) is a prerequisite for functional recovery after lesion. However, this process is not always optimal and becomes inefficient in the course of multiple sclerosis. Here we show that, when acetylated, eukaryotic elongation factor 1A1 (eEF1A1) negatively regulates PNS and CNS remyelination. Acetylated eEF1A1 (Ac-eEF1A1) translocates into the nucleus of myelinating cells where it binds to Sox10, a key transcription factor for PNS and CNS myelination and remyelination, to drag Sox10 out of the nucleus. We show that the lysine acetyltransferase Tip60 acetylates eEF1A1, whereas the histone deacetylase HDAC2 deacetylates eEF1A1. Promoting eEF1A1 deacetylation maintains the activation of Sox10 target genes and increases PNS and CNS remyelination efficiency. Taken together, these data identify a major mechanism of Sox10 regulation, which appears promising for future translational studies on PNS and CNS remyelination.
The structures of two archaeal type IV pili illuminate evolutionary relationships
Authors: Wang Fengbin , Baquero Diana P. , Su Zhangli , Beltran Leticia C. , Prangishvili David , Krupovic Mart , Egelman Edward H.
Published: July 2020

We have determined the cryo-electron microscopic (cryo-EM) structures of two archaeal type IV pili (T4P), from Pyrobaculum arsenaticum and Saccharolobus solfataricus, at 3.8 Å and 3.4 Å resolution, respectively. This triples the number of high resolution archaeal T4P structures, and allows us to pinpoint the evolutionary divergence of bacterial T4P, archaeal T4P and archaeal flagellar filaments. We suggest that extensive glycosylation previously observed in T4P of Sulfolobus islandicus is a response to an acidic environment, as at even higher temperatures in a neutral environment much less glycosylation is present for Pyrobaculum than for Sulfolobus and Saccharolobus pili. Consequently, the Pyrobaculum filaments do not display the remarkable stability of the Sulfolobus filaments in vitro. We identify the Saccharolobus and Pyrobaculum T4P as host receptors recognized by rudivirus SSRV1 and tristromavirus PFV2, respectively. Our results illuminate the evolutionary relationships among bacterial and archaeal T4P filaments and provide insights into archaeal virus-host interactions.
Publisher Correction: Metabolic characteristics of CD8+ T cell subsets in young and aged individuals are not predictive of functionality
Authors: Quinn Kylie M. , Hussain Tabinda , Kraus Felix , Formosa Luke E. , Lam Wai K. , Dagley Michael J. , Saunders Eleanor C. , Assmus Lisa M. , Wynne-Jones Erica , Loh Liyen , van de Sandt Carolien E. , Cooper Lucy , Good-Jacobson Kim L. , Kedzierska Katherine , Mackay Laura K. , McConville Malcolm J. , Ramm Georg , Ryan Michael T. , La Gruta Nicole L.
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Photo-oxidation of PE-HD affecting polymer/fuel interaction and bacterial attachment
Authors: Erdmann Maren , Kleinbub Sherin , Wachtendorf Volker , Schutter Jan David , Niebergall Ute , Böhning Martin , Koerdt Andrea
Published: July 2020

In the present study, a simple approach was used to investigate the effect of UV-exposure on two high density polyethylene materials (PE-HD), commonly used for storage tanks, on fuel sorption behavior and colonization by microorganisms. The aim was to investigate whether the sorption behavior of the fuels (diesel/biodiesel) and the colonization by microorganisms, frequently occurring in the fuel, is affected and may lead to undesirable or safety-relevant material changes. We showed that the UV-irradiation leads to significant changes of the sorption behavior due to chemi-crystallization and crosslinking. The fuel sorption is affected by the UV-induced formation of polar carbonyl and hydroxyl groups predominantly occurring at the surface. With respect to microbial colonization behavior forBacillus subtilisandPseudomonas aeruginosa, isolated from a contaminated diesel sample, differences of the initial adhesion could be shown depending on the initial type of polyethylene as well as on the degree of UV-induced degradation.
TGF-β regulates Sca-1 expression and plasticity of pre-neoplastic mammary epithelial stem cells
Authors: Remšík Ján , Pícková Markéta , Vacek Ondřej , Fedr Radek , Binó Lucia , Hampl Aleš , Souček Karel
Published: July 2020

The epithelial-mesenchymal plasticity, in tight association with stemness, contributes to the mammary gland homeostasis, evolution of early neoplastic lesions and cancer dissemination. Focused on cell surfaceome, we used mouse models of pre-neoplastic mammary epithelial and cancer stem cells to reveal the connection between cell surface markers and distinct cell phenotypes. We mechanistically dissected the TGF-β family-driven regulation of Sca-1, one of the most commonly used adult stem cell markers. We further provided evidence that TGF-β disrupts the lineage commitment and promotes the accumulation of tumor-initiating cells in pre-neoplastic cells.
Semimytilus algosus: first known hermaphroditic mussel with doubly uniparental inheritance of mitochondrial DNA
Authors: Lubośny Marek , Przyłucka Aleksandra , Śmietanka Beata , Burzyński Artur
Published: July 2020

Doubly uniparental inheritance (DUI) of mitochondrial DNA is a rare phenomenon occurring in some freshwater and marine bivalves and is usually characterized by the mitochondrial heteroplasmy of male individuals. Previous research on freshwater Unionida mussels showed that hermaphroditic species do not have DUI even if their closest gonochoristic counterparts do. No records showing DUI in a hermaphrodite have ever been reported. Here we show for the first time that the hermaphroditic musselSemimytilus algosus(Mytilida), very likely has DUI, based on the complete sequences of both mitochondrial DNAs and the distribution of mtDNA types between male and female gonads. The two mitogenomes show considerable divergence (34.7%). The presumably paternal M type mitogenome dominated the male gonads of most studied mussels, while remaining at very low or undetectable levels in the female gonads of the same individuals. If indeed DUI can function in the context of simultaneous hermaphroditism, a change of paradigm regarding its involvement in sex determination is needed. It is apparently associated with gonadal differentiation rather than with sex determination in bivalves.
Multivariable logistic and linear regression models for identification of clinically useful biomarkers for osteoarthritis
Authors: Liem Yulia , Judge Andrew , Kirwan John , Ourradi Khadija , Li Yunfei , Sharif Mohammed
Published: July 2020

Osteoarthritis (OA) is the most common chronic degenerative joint disease which causes substantial joint pain, deformity and loss of activities of daily living. Currently, there are over 500 million OA cases worldwide, and there is an urgent need to identify biomarkers for early detection, and monitoring disease progression in patients without obvious radiographic damage to the joint. We have used regression modelling to describe the association of 19 of the currently available biomarkers (predictors) with key radiographic and clinical features of OA (outcomes) in one of the largest and best characterised OA cohort (NIH Osteoarthritis Initiative). We demonstrate that of the 19 currently available biomarkers only 4 (serum Coll2-1 NO2, CS846, COMP and urinary CTXII) were consistently associated with established radiographic and/or clinical features of OA. These biomarkers are independent of one another and provide additional predictive power over, and above established predictors of OA such as age, gender, BMI and race. We also show that that urinary CTXII had the strongest and consistent associations with clinical symptoms of OA as well as radiographic evidence of joint damage. Accordingly, urinary CTXII may aid in early diagnosis of OA in symptomatic patients without radiographic evidence of OA.
‘Alexandrian’ glass confirmed by hafnium isotopes
Authors: Barfod Gry H. , Freestone Ian C. , Lesher Charles E. , Lichtenberger Achim , Raja Rubina
Published: July 2020

Archaeological glass contains information about the movement of goods and ancient economies, yet our understanding of critical aspects of the ancient glass industry is fragmentary. During Roman times, distinct glass types produced in coastal regions of Egypt and the Levant used evaporitic soda (natron) mixed with Nile-derived sands. In the Levant, furnaces for producing colourless Roman glass by addition of manganese have been uncovered, whereas the source of the desirable antimony-decolourised Roman glass remains an enigma. In the Edict of Diocletian, this colourless glass is listed as “Alexandrian” referring to Egypt, but its origin has been ambiguous. Previous studies have found overlapping strontium and neodymium isotope ratios for Levantine and Egyptian glass. Here, we confirm these findings and show for the first time, based on glasses from the ancient city of Gerasa, that hafnium (Hf) isotopes are different in Egyptian and Levantine natron glasses, and that Sb Roman glass is Egyptian. Our work illustrates the value of Hf isotopes in provenancing archaeological glass. We attribute the striking difference in Hf isotopes of Egyptian versus Levantine glasses to sorting of zircons in Nile sediments during longshore drift and aeolian transport along the south-eastern Mediterranean coast leaving behind a less juvenile fraction.
Study of the bioremediatory capacity of wild yeasts
Authors: García-Béjar Beatriz , Arévalo-Villena María , Guisantes-Batan Eduardo , Rodríguez-Flores Juana , Briones Ana
Published: July 2020

Microbial detoxification has been proposed as a new alternative for removing toxins and pollutants. In this study, the biodetoxification activities of yeasts against aflatoxin B1 and zinc were evaluated by HPLC and voltammetric techniques. The strains with the best activity were also subjected to complementary assays, namely biocontrol capability and heavy-metal resistance. The results indicate that the detoxification capability is toxin- and strain-dependent and is not directly related to cell growth. Therefore, we can assume that there are some other mechanisms involved in the process, which must be studied in the future. Only 33 of the 213 strains studied were capable of removing over 50% of aflatoxin B1, Rhodotrorula mucilaginosa being the best-performing species detected. As for zinc, there were 39 strains that eliminated over 50% of the heavy metal, with Diutina rugosa showing the best results. Complementary experiments were carried out on the strains with the best detoxification activity. Biocontrol tests against mycotoxigenic moulds showed that almost 50% of strains had an inhibitory effect on growth. Additionally, 53% of the strains grew in the presence of 100 mg/L of zinc. It has been proven that yeasts can be useful tools for biodetoxification, although further experiments must be carried out in order to ascertain the mechanisms involved.
Development and validation of a nomogram prognostic model for esophageal cancer patients with oligometastases
Authors: Li Butuo , Wang Ruiqing , Zhang Ting , Sun Xiubin , Jiang Chao , Li Wanlong , Zou Bing , Xie Peng , Meng Xue , Sun Xindong , Wang Linlin , Yu Jinming
Published: July 2020

Platinum-based chemotherapy is recommended as the standard treatment for metastatic esophageal cancer (EC) patients; however, the outcome is poor. Oligometastasis is less aggressive and has limited growth potential. However, the prognostic factors for EC patients with oligometastases was largely unknown. Thus, we intend to determine the prognostic factors, and develop and validate nomograms for prediction of survival for EC patients with oligometastases. In this study, characteristics of 273 oligometastatic EC patients were analyzed using univariate and multivariate Cox models to determine the independent prognostic factors for progression-free survival (PFS) and overall survival (OS). The result showed that history of alcohol consumption, longer tumor, no local radiotherapy for EC, and no local treatment for metastases were independent factors for PFS. Sex, esophageal fistula, number of metastatic organs, and local radiotherapy for EC were independent prognostic factors for OS. On the basis of Cox models, the respective nomogram for prediction of PFS and OS was established with the corrected concordance index of 0.739 and 0.696 after internal cross-validation. In conclusion, local treatment for metastases and local radiotherapy for EC were demonstrated to be beneficial for oligometastatic EC patients, and the validated nomograms are valuable in prognosis prediction and could guide individualized management for these patients.
Assessment of a self-assembling peptide gel, SPG-178, in providing a clear operative field for trabeculectomy surgery for glaucoma in an animal model
Authors: Matsushita Kenji , Kawashima Rumi , Uesugi Koji , Okada Haruka , Sakaguchi Hirokazu , Quantock Andrew J. , Nishida Kohji
Published: July 2020

The presence of blood during ophthalmic surgery is problematic, as it can obstruct a surgeon’s view of the operative field. This is particularly true when performing trabeculectomy surgery to enhance ocular fluid outflow and reduce intraocular pressure as a treatment for glaucoma, one of the most common vision loss conditions worldwide. In this study, we investigated the performance of a transparent, self-assembling peptide gel (SPG-178) and its ability to maintain visibility during trabeculectomy surgery. Unlike the hyaluronic acid gel commonly used in ophthalmic surgery, SPG-178 did not permit the ingress of blood into the gel itself. Rather, it forced blood to flow peripherally to the gel. Moreover, if bleeding occurred under the SPG-178 gel, perfusion with saline was able to effectively flush the blood away along the interface between the SPG-178 and the ocular tissue (in this case scleral) to clear the surgical field of view. In experimental trabeculectomy surgeries with mitomycin C used as an adjuvant, there were no differences in the postoperative recovery of intraocular pressure or bleb morphology with or without the use of SPG-178. SPG-178, therefore, when used in a gel formulation, represents a new material for use in intraocular surgery to ensure a clear operative field with likely beneficial treatment outcomes.