bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical practice guidelines for duodenal cancer 2021
Authors: Nakagawa Kenji , Sho Masayuki , Fujishiro Mitsuhiro , Kakushima Naomi , Horimatsu Takahiro , Okada Ken-ichi , Iguchi Mikitaka , Uraoka Toshio , Kato Motohiko , Yamamoto Yorimasa , Aoyama Toru , Akahori Takahiro , Eguchi Hidetoshi , Kanaji Shingo , Kanetaka Kengo , Kuroda Shinji , Nagakawa Yuichi , Nunobe Souya , Higuchi Ryota , Fujii Tsutomu , Yamashita Hiroharu , Yamada Suguru , Narita Yukiya , Honma Yoshitaka , Muro Kei , Ushiku Tetsuo , Ejima Yasuo , Yamaue Hiroki , Kodera Yasuhiro 
Published: October 2022

AbstractDuodenal cancer is considered to be a small intestinal carcinoma in terms of clinicopathology. In Japan, there are no established treatment guidelines based on sufficient scientific evidence; therefore, in daily clinical practice, treatment is based on the experience of individual physicians. However, with advances in diagnostic modalities, it is anticipated that opportunities for its detection will increase in future. We developed guidelines for duodenal cancer because this disease is considered to have a high medical need from both healthcare providers and patients for appropriate management. These guidelines were developed for use in actual clinical practice for patients suspected of having non-ampullary duodenal epithelial malignancy and for patients diagnosed with non-ampullary duodenal epithelial malignancy. In this study, a practice algorithm was developed in accordance with the Minds Practice Guideline Development Manual 2017, and Clinical Questions were set for each area of epidemiology and diagnosis, endoscopic treatment, surgical treatment, and chemotherapy. A draft recommendation was developed through a literature search and systematic review, followed by a vote on the recommendations. We made decisions based on actual clinical practice such that the level of evidence would not be the sole determinant of the recommendation. This guideline is the most standard guideline as of the time of preparation. It is important to decide how to handle each case in consultation with patients and their family, the treating physician, and other medical personnel, considering the actual situation at the facility (and the characteristics of the patient).
Perkinsus olseni and other parasites and abnormal tissue structures in New Zealand Greenshell™ mussels (Perna canaliculus) across different seasons
Authors: Muznebin Farhana , Alfaro Andrea C. , Webb Stephen C. 
Published: October 2022

AbstractThe New Zealand Greenshell™ mussel (Perna canaliculus) supports the largest aquaculture industry in the country. However, summer mortality events and potential disease outbreaks may threaten the growth of this industry. As an approach to gauging potential threats through the seasons, a detailed histopathological examination was conducted on 256 adult cultured mussels collected from a farm between April 2018 to September 2019, which covered the austral autumn, winter, spring and summer seasons. Histological sections followed by confirmatory in situ hybridization (ISH) resulted in the identification of Perkinsus olseni at an overall prevalence of 56%. Other parasites and pathogens were identified by histology: apicomplexan parasite X (APX) (78%), copepods (Pseudomyicola spinosus or Lichomolgus uncus) (1%), Microsporidium rapuae (1%), intracellular microcolonies of bacteria (IMCs) (2%) and bacilli and cocci bacteria (4%) in gills, mantle, gonads, digestive epithelium and digestive tubules. There was a significant association between P. olseni and APX infection in mussels. This is the first report on seasonal variations of P. olseni and APX in New Zealand Greenshell™ mussel. There was a significant association between seasons and the presence of P. olseni and APX in mussels. A significant positive association between the brown material accumulation and parasites (P. olseni and APX) and between haemocytosis and P. olseni infections were recorded. A significant association between presence of parasites and health condition (healthy and unhealthy) of mussels was observed. Moreover, a significant association between digestive tubule deterioration (large lumen, with a thin epithelial wall) and P. olseni infection was noted. Therefore, this study provides information regarding the infections of potential parasites and pathogens for the first time in P. canaliculus, their seasonal variations and host-parasite interactions within a commercial farm.
Protocol for iterative optimization of modified peptides bound to protein targets
Authors: Ochoa Rodrigo , Cossio Pilar , Fox Thomas 
Published: October 2022

AbstractPeptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Replacing natural by non-natural amino acids can avoid these problems, and potentially improve the affinity towards the target protein. Here, we present a computational pipeline to optimize peptides based on adding non-natural amino acids while improving their binding affinity. The workflow is an iterative computational evolution algorithm, inspired by the PARCE protocol, that performs single-point mutations on the peptide sequence using modules from the Rosetta framework. The modifications can be guided based on the structural properties or previous knowledge of the biological system. At each mutation step, the affinity to the protein is estimated by sampling the complex conformations and applying a consensus metric using various open protein-ligand scoring functions. The mutations are accepted based on the score differences, allowing for an iterative optimization of the initial peptide. The sampling/scoring scheme was benchmarked with a set of protein-peptide complexes where experimental affinity values have been reported. In addition, a basic application using a known protein-peptide complex is also provided. The structure- and dynamic-based approach allows users to optimize bound peptides, with the option to personalize the code for further applications. The protocol, called mPARCE, is available at: https://github.com/rochoa85/mPARCE/.
John squire and endothelial glycocalyx structure: an unfinished story
Authors: Arkill Kenton P. , Michel C. Charles , Rider Elizabeth V. M. , Wood Elise A. , Small Mathew O. , Brown Jennifer L. E. , Kinnaird Abigail L. 
Published: October 2022

AbstractJohn Squire did not only produce leading works in the muscle field, he also significantly contributed to the vascular permeability field by ultrastructural analysis of the endothelial glycocalyx. Presented here is a review of his involvement in the field by his main collaborator C.C. Michel and his last postdoctoral researcher KP Arkill. We end on a reinterpretation of his work that arguably links to our current understanding of endothelial glycocalyx structure and composition predicting 6 glycosaminoglycans fibres per syndecan core protein, only achieved in the endothelium by dimerization.
Industrial side streams as sustainable substrates for microbial production of poly(3-hydroxybutyrate) (PHB)
Authors: Vlaeminck Elodie , Uitterhaegen Evelien , Quataert Koen , Delmulle Tom , De Winter Karel , Soetaert Wim K. 
Published: October 2022

AbstractPoly(3-hydroxybutyrate) (PHB) is a microbially produced biopolymer that is emerging as a propitious alternative to petroleum-based plastics owing to its biodegradable and biocompatible properties. However, to date, the relatively high costs related to the PHB production process are hampering its widespread commercialization. Since feedstock costs add up to half of the total production costs, ample research has been focusing on the use of inexpensive industrial side streams as carbon sources. While various industrial side streams such as second-generation carbohydrates, lignocellulose, lipids, and glycerol have been extensively investigated in liquid fermentation processes, also gaseous sources, including carbon dioxide, carbon monoxide, and methane, are gaining attention as substrates for gas fermentation. In addition, recent studies have investigated two-stage processes to convert waste gases into PHB via organic acids or alcohols. In this review, a variety of different industrial side streams are discussed as more sustainable and economical carbon sources for microbial PHB production. In particular, a comprehensive overview of recent developments and remaining challenges in fermentation strategies using these feedstocks is provided, considering technical, environmental, and economic aspects to shed light on their industrial feasibility. As such, this review aims to contribute to the global shift towards a zero-waste bio-economy and more sustainable materials.
Pro-inflammatory RNA:DNA Hybrids Are p53 Independently Boosted by Hyperbaric Oxygen: a Subcellular Distribution Analysis by Automated Quantitative Imaging
Authors: De Santis Ilaria , Zanoni Michele , Pignatta Sara , Longobardi Pasquale , Tesei Anna , Bevilacqua Alessandro 
Published: October 2022

Abstract
Purpose
RNA:DNA hybrids are co-transcriptional products with acknowledged cytoplasmic pro-inflammatory role as activators of the cGAS-STING pathway. We recently proved them also as radiation-induced senescence messages for the abscopal effect mediation, demonstrating the need for a functional p53 for their production and release in A549 and H1299 tumour cells. However, little is known about their role under different stress conditions, especially in cancer cells.

Methods
In this work, we open the investigation making use of automated quantitative imaging to characterize the hybrid subcellular distribution in HeLa cells grown under different oxygen pressures or exposed to different ionizing radiation doses. After cell imaging by confocal fluorescent microscopy, we apply automated imaging methods developed on purpose to quantify hybrid foci and nuclear cluster intensity, regional and local density and dimension.

Results
We show that alteration of culture oxygenation increases hybrid cytoplasmic presence, especially when caused by an hyperoxic environment, with evident hybrid gathering at the cell membrane. Ionizing radiations always fail to increase hybrids, in accordance with the absence of functional p53 in HeLa cells. However, dose-dependent effects are still evident and suggest a threshold dose of 7.5 Gy for remarkable hybrid reduction.

Conclusion
Together with our previous results, these data demonstrate for the first time that different types of stress can increase hybrid production in cancer cells and by at least two different pathways, one p53-dependent triggerable by ionizing radiations and one p53-independent triggerable by oxidative stress. Together, our findings provide a starting point for understanding hybrid role in tumour stress response.
Nail and enthesis assessment in patients with psoriatic disease by high frequency ultrasonography: findings from a single-centre cross-sectional study
Authors: Ruscitti Piero , Esposito Maria , Gianneramo Camilla , Di Cola Ilenia , De Berardinis Andrea , Martinese Andrea , Nkamtse Tochap Gerard , Conforti Alessandro , Masciocchi Carlo , Cipriani Paola , Barile Antonio , Fargnoli Maria Concetta 
Published: October 2022

Abstract
Purpose
To characterize nail and enthesis abnormalities using high frequency ultrasound (HFUS) in patients with psoriasis (PSO), psoriatic arthritis (PSA) with PSO, and PSA sine PSO.

Material and Methods
Patients with PSO, PSA with PSO, and PSA sine PSO were evaluated and compared in a cross-sectional single centre study. Nail and enthesis abnormalities were evaluated by HFUS using high frequency probes (27 MHz). After a descriptive assessment, Brown University Nail Enthesis Scale (BUNES) and Madrid Sonography Enthesitis Index (MASEI) were used to assess nail and enthesis, respectively.

Results
Fifty-nine patients were enrolled (19 PSO, 22 PSA with PSO, 18 PSA sine PSO). In patients with PSO and in those with PSA and PSO, HFUS evaluation identified the following nail alterations characterised by thickened matrix, inhomogeneous echogenicity of the nail bed, and increased blood flow by power Doppler. In 38.9% patients with PSA sine PSO, a subclinical nail involvement was described. No difference was observed comparing BUNES values in three groups. In PSA patients with PSO and in those with PSA sine PSO, HFUS assessment of entheses mainly showed a hypoechoic aspect and thickness of the tendon, focal cortical erosion, and ossification. A subclinical enthesis involvement in 47.4% patients with PSO was observed. No difference was reported comparing MASEI values in three groups.

Conclusion
Qualitative and quantitative abnormalities of nail and enthesis were demonstrated by HFUS in patients with PSO, PSA with PSO, and PSA sine PSO, suggesting a practical additional tool to be used in clinical settings. Furthermore, HFUS highlighted a subclinical nail involvement in patients with PSA sine PSO and enthesis subclinical alterations in patients with PSO.
COVID-19 and its treatments: lights and shadows on testicular function
Authors: Pallotti Francesco , Esteves Sandro C. , Faja Fabiana , Buonacquisto Alessandra , Conflitti Anna Chiara , Hirsch Maria Neve , Lenzi Andrea , Paoli Donatella , Lombardo Francesco 
Published: October 2022

Abstract
Purpose
The SARS-CoV-2 pandemic has rapidly spread worldwide and, among the others, the male gender was quickly recognized as an independent risk factor for both the disease and its consequences. Since the possibility of long-term hormonal axis changes and male gamete impairment have been hypothesized but a relatively low levels of evidence has been reached, we focused this narrative mini-review on summarizing key state-of-the-art knowledge on male reproductive effects of COVID-19 as a quick reference for reproductive health specialists.

Methods
A comprehensive Medline/PubMed and Embase search was performed selecting all relevant, peer-reviewed papers in English published from 2020. Other relevant papers were selected from the reference lists.

Results
Available evidence indicates that the likelihood of direct testicular damage from SARS-CoV-2 is somewhat low, but there are many indirect ways (fever, cytokine imbalance, and drugs) through which the pituitary-gonadal axis and spermatogenesis may be disrupted. These alterations are probably transient, but as available evidence is low quality, it cannot be excluded that previous pathologies or comorbidities might modulate the risk of their persistence. On the other hand, available evidence shows high safety regarding andrological health for available vaccines, although studies are mainly focused on mRNA vaccines.

Conclusion
A careful andrological evaluation of men recovering from COVID-19 is highly recommended. Since available evidence is relatively scarce, a careful andrological follow-up and counseling of these patients are mandatory.
Aquinas’s Principle of Misericordia in Corporations: Implications for Workers and other Stakeholders
Authors: Robson Angus 
Published: October 2022

Abstract
Despite its central position in the history of European and Christian thought on the protection of human dignity, the virtue of mercy is currently a problematic and under-developed concept in business ethics, compared to related ideas of care, compassion or philanthropy. The aim of this article is to argue for its revival as a core principle of ethical business practice. The article is conceptual in method. An overview is provided of the scope of contemporary business ethics research on related topics and clarifies some of the similarities and differences between mercy and popular terms, such as compassion and prosocial behaviour. The question is then explored as to why mercy has so little traction in business ethics. Some of the history of the idea of mercy in European and Anglophone philosophy is discussed, from Anselm and Aquinas to the present day, showing how discourse on mercy came to be split into a wider concept of the prevention and alleviation of suffering (misericordia) and a narrower one of clemency or leniency. Aquinas’s wide concept of the virtue of misericordia is developed as the basis for a principle of mercy, which is applicable directly to corporations. The practical implications of this for standards of corporate behaviour towards employees and other stakeholders are then considered through the introduction of a ‘vulnerability grid’. The grid offers a critical contrast to other analysis tools, such as stakeholder power-interest matrices. Cases drawn from empirical studies are used to illustrate application of the grid and to challenge some common assumptions of stakeholder theory.
The information geometry of two-field functional integrals
Authors: Smith Eric 
Published: October 2022

AbstractTwo-field functional integrals (2FFI) are an important class of solution methods for generating functions of dissipative processes, including discrete-state stochastic processes, dissipative dynamical systems, and decohering quantum densities. The stationary trajectories of these integrals describe a conserved current by Liouville’s theorem, despite the absence of a conserved kinematic phase space current in the underlying stochastic process. We develop the information geometry of generating functions for discrete-state classical stochastic processes in the Doi-Peliti 2FFI form, and exhibit two quantities conserved along stationary trajectories. One is a Wigner function, familiar as a semiclassical density from quantum-mechanical time-dependent density-matrix methods. The second is an overlap function, between directions of variation in an underlying distribution and those in the directions of relative large-deviation probability that can be used to interrogate the distribution, and expressed as an inner product of vector fields in the Fisher information metric. To give an interpretation to the time invertibility implied by current conservation, we use generating functions to represent importance sampling protocols, and show that the conserved Fisher information is the differential of a sample volume under deformations of the nominal distribution and the likelihood ratio. We derive a pair of dual affine connections particular to Doi-Peliti theory for the way they separate the roles of the nominal distribution and likelihood ratio, distinguishing them from the standard dually-flat connection of Nagaoka and Amari defined on the importance distribution, and show that dual flatness in the affine coordinates of the coherent-state basis captures the special role played by coherent states in Doi-Peliti theory.
Microstructure evolution of pure titanium during hydrostatic extrusion
Authors: Wojtas Daniel , Maj Łukasz , Wierzbanowski Krzysztof , Jarzębska Anna , Chulist Robert , Kawałko Jakub , Trembecka-Wójciga Klaudia , Bieda-Niemiec Magdalena , Sztwiertnia Krzysztof 
Published: October 2022

Abstract
Regarding severely deformed materials of potentially high applicability in various industry branches, their microstructure evolution during processing is of vast significance as it enables to control or adjust the most essential properties, including mechanical strength or corrosion resistance. Within the present study, the microstructure development of commercially pure titanium (grade 2) in the multi-stage process of hydrostatic extrusion has been studied with the use of the well-established techniques, involving electron backscatter diffraction as well as transmission electron microscopy. Microstructural deformation-induced defects, including grain boundaries, dislocations, and twins, have been meticulously analyzed. In addition, a special emphasis has been placed on grain size, grain boundary character as well as misorientation gradients inside deformed grains. The main aim was to highlight the microstructural alterations triggered by hydroextrusion and single out their possible sources. The crystallographic texture was also studied. It has been concluded that hydrostatically extruded titanium is an exceptionally inhomogeneous material in terms of its microstructure as evidenced by discrepancies in grain size and shape, a great deal of dislocation-type features observed at every single stage of processing and the magnitude of deformation energy stored. Twinning, accompanied by grain subdivision phenomenon, was governing the microstructural development at low strains; whereas, the process of continuous dynamic recrystallization came to the fore at higher strains.
Selected mechanical properties resulting from the studied material microstructure are also presented and discussed.
Large Pleistocene tortoise tracks on the Cape south coast of South Africa
Authors: Helm Charles W. , Carr Andrew S. , Cawthra Hayley C. , De Vynck Jan C. , Dixon Mark G. , Lockley Martin G. , Stear Willo , Venter Jan A. 
Published: October 2022

AbstractAlthough tortoises (Testudinidae) are a familiar clade of reptiles, with a body fossil record extending to at least the Eocene, hitherto no tortoise ichnosites have been described. Here, a number of sites attributed to tortoise trackmakers are identified within Pleistocene aeolianites on South Africa's Cape south coast. These date from late Marine Isotope Stage 6 to Marine Isotope Stage 4. The findings indicate large trackmakers, with evidence of a trackmaker length of more than a meter—substantially longer than the largest extant tortoises in southern Africa. This suggests either the presence of an extinct very large tortoise species, or that Pleistocene leopard tortoises in the region were larger than their descendants. Variations in substrate properties are responsible for a variety of track and trace forms. A mismatch exists between the reported ichnological evidence for large tortoises, and the regional archaeological and body fossil records, which almost exclusively comprise smaller tortoises. The findings illustrate the potential of ichnology to complement and augment the paleontological and archaeological records.
Inadequate sleep duration may attenuate the anti-inflammatory effects of fish consumption in a healthy Japanese population: a cross-sectional study
Authors: Tani Shigemasa , Imatake Kazuhiro , Suzuki Yasuyuki , Yagi Tsukasa , Takahashi Atsuhiko , Matsumoto Naoya , Okumura Yasuo 
Published: October 2022

AbstractHigh fish consumption may be associated with lower inflammation, suppressing atherosclerotic CVD (ASCVD). Long sleep duration, as well as short sleep, may contribute to inflammation, thus facilitating ASCVD. This study investigated the overall association between fish consumption, sleep duration and leucocytes count. We conducted a cross-sectional study between April 2019 and March 2020 with a cohort of 8947 apparently healthy participants with no history of ASCVD (average age, 46·9 ± 12·3 years and 59 % males). The average frequency of fish consumption and sleep duration were 2·13 ± 1·26 d/week and 6·0 ± 0·97 h/d. Multivariate linear regression analysis revealed that increased fish consumption was an independent determinant of sleep duration (β = 0·084, P < 0·0001). Additionally, habitual aerobic exercise (β = 0·059, P < 0·0001) or cigarette smoking (β = −0·051, P < 0·0001) and homoeostasis model assessment-insulin resistance (HOMA-IR) (β = −0·039, P = 0·01) were independent determinants of sleep duration. Furthermore, multivariate linear regression analysis identified fish consumption as an independent determinant of leucocytes count (β = −0·091, P < 0·0001). However, a significant U-shaped curve was found between leucocytes count and sleep duration, with 6–7 h of sleep as the low value (P = 0·015). Higher fish consumption may be associated with a lower leucocytes count in the presence of adequate sleep duration and healthy lifestyle behaviors. However, long sleep duration was also related to increased inflammation, even in populations with high fish consumption. Further studies are needed to clarify the causality between these factors.