bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRCA1 and BRCA2 pathogenic variants and prostate cancer risk: systematic review and meta-analysis
Authors: Nyberg Tommy , Tischkowitz Marc , Antoniou Antonis C. 
Published: December 2021

Abstract
Background
BRCA1 and BRCA2 pathogenic variants (PVs) are associated with prostate cancer (PCa) risk, but a wide range of relative risks (RRs) has been reported.

Methods
We systematically searched PubMed, Embase, MEDLINE and Cochrane Library in June 2021 for studies that estimated PCa RRs for male BRCA1/2 carriers, with no time or language restrictions. The literature search identified 27 studies (BRCA1: n = 20, BRCA2: n = 21).

Results
The heterogeneity between the published estimates was high (BRCA1: I2 = 30%, BRCA2: I2 = 83%); this could partly be explained by selection for age, family history or aggressive disease, and study-level differences in ethnicity composition, use of historical controls, and location of PVs within BRCA2. The pooled RRs were 2.08 (95% CI 1.38–3.12) for Ashkenazi Jewish BRCA2 carriers, 4.35 (95% CI 3.50–5.41) for non-Ashkenazi European ancestry BRCA2 carriers, and 1.18 (95% CI 0.95–1.47) for BRCA1 carriers. At ages <65 years, the RRs were 7.14 (95% CI 5.33–9.56) for non-Ashkenazi European ancestry BRCA2 and 1.78 (95% CI 1.09–2.91) for BRCA1 carriers.

Conclusions
These PCa risk estimates will assist in guiding clinical management. The study-level subgroup analyses indicate that risks may be modified by age and ethnicity, and for BRCA2 carriers by PV location within the gene, which may guide future risk-estimation studies.
A single-agent extension of the SIR model describes the impact of mobility restrictions on the COVID-19 epidemic
Authors: Paoluzzi Matteo , Gnan Nicoletta , Grassi Francesca , Salvetti Marco , Vanacore Nicola , Crisanti Andrea 
Published: December 2021

AbstractMobility restrictions are successfully used to contain the diffusion of epidemics. In this work we explore their effect on the epidemic growth by investigating an extension of the Susceptible-Infected-Removed (SIR) model in which individual mobility is taken into account. In the model individual agents move on a chessboard with a Lévy walk and, within each square, epidemic spreading follows the standard SIR model. These simple rules allow to reproduce the sub-exponential growth of the epidemic evolution observed during the Covid-19 epidemic waves in several countries and which cannot be captured by the standard SIR model. We show that we can tune the slowing-down of the epidemic spreading by changing the dynamics of the agents from Lévy to Brownian and we investigate how the interplay among different containment strategies mitigate the epidemic spreading. Finally we demonstrate that we can reproduce the epidemic evolution of the first and second COVID-19 waves in Italy using only 3 parameters, i.e , the infection rate, the removing rate, and the mobility in the country. We provide an estimate of the peak reduction due to imposed mobility restrictions, i. e., the so-called flattening the curve effect. Although based on few ingredients, the model captures the kinetic of the epidemic waves, returning mobility values that are consistent with a lock-down intervention during the first wave and milder limitations, associated to a weaker peak reduction, during the second wave.
Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori
Authors: Tamrakar Anubhav , Singh Rahul , Kumar Amit , Makde Ravindra D. , Ashish  , Kodgire Prashant 
Published: December 2021

AbstractHelicobacter pylori is a Gram-negative bacterium that causes chronic inflammations in the stomach area and is involved in ulcers, which can develop into gastric malignancies. H. pylori attaches and colonizes to the human epithelium using some of their outer membrane proteins (OMPs). HomB and HomA are the most studied OMPs from H. pylori as they play a crucial role in adherence, hyper biofilm formation, antibiotic resistance and are also associated with severe gastric malignancies. The role of HomA and HomB in pathogenesis concerning their structure and function has not been evaluated yet. In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. Further, biophysical experiments suggested that HomA and HomB are dimeric and most likely the cysteine residues present on surface-exposed loops participate in protein–protein interactions. Our study provides essential structural information of unexplored proteins of the Hom family that can help in a better understanding of H. pylori pathogenesis.
The effects of violet and blue light irradiation on ESKAPE pathogens and human cells in presence of cell culture media
Authors: Bauer Richard , Hoenes Katharina , Meurle Tobias , Hessling Martin , Spellerberg Barbara 
Published: December 2021

AbstractBacteria belonging to the group of ESKAPE pathogens are responsible for the majority of nosocomial infections. Due to the increase of antibiotic resistance, alternative treatment strategies are of high clinical relevance. In this context visible light as disinfection technique represents an interesting option as microbial pathogens can be inactivated without adjuvants. However cytotoxic effects of visible light on host cells have also been reported. We compared the cytotoxicity of violet and blue light irradiation on monocytic THP-1 and alveolar epithelium A549 cells with the inactivation effect on ESKAPE pathogens. THP-1 cells displayed a higher susceptibility to irradiation than A549 cells with first cytotoxic effects occurring at 300 J cm−2 (405 nm) and 400 J cm−2 (450 nm) in comparison to 300 J cm−2 and 1000 J cm−2, respectively. We could define conditions in which a significant reduction of colony forming units for all ESKAPE pathogens, except Enterococcus faecium, was achieved at 405 nm while avoiding cytotoxicity. Irradiation at 450 nm demonstrated a more variable effect which was species and medium dependent. In summary a significant reduction of viable bacteria could be achieved at subtoxic irradiation doses, supporting a potential use of visible light as an antimicrobial agent in clinical settings.
The GAPS Programme at TNG
Authors: Fossati L. , Guilluy G. , Shaikhislamov I. F. , Carleo I. , Borsa F. , Bonomo A. S. , Giacobbe P. , Rainer M. , Cecchi-Pestellini C. , Khodachenko M. L. , Efimov M. A. , Rumenskikh M. S. , Miroshnichenko I. B. , Berezutsky A. G. , Nascimbeni V. , Brogi M. , Lanza A. F. , Mancini L. , Affer L. , Benatti S. , Biazzo K. , Bignamini A. , Carosati D. , Claudi R. , Cosentino R. , Covino E. , Desidera S. , Fiorenzano A. , Harutyunyan A. , Maggio A. , Malavolta L. , Maldonado J. , Micela G. , Molinari E. , Pagano I. , Pedani M. , Piotto G. , Poretti E. , Scandariato G. , Sozzetti A. , Stoev H. 
Published: December 2021

Context. Because of its proximity to an active K-type star, the hot Jupiter WASP-80b has been identified as a possible excellent target for detecting and measuring He I absorption in the upper atmosphere.
Aims. Our aim was to look for, and eventually measure and model, metastable He I atmospheric absorption.
Methods. We observed four primary transits of WASP-80b in the optical and near-infrared using the HARPS-N and GIANO-B high-resolution spectrographs attached to the Telescopio Nazionale Galileo telescope, focusing the analysis on the He I triplet. We further employed a three-dimensional hydrodynamic aeronomy model to understand the observational results.
Results. We did not find any signature of planetary absorption at the position of the He I triplet with an upper limit of 0.7% (i.e. 1.11 planetary radii; 95% confidence level). We re-estimated the high-energy stellar emission, which we combined with a stellar photospheric model, to generate the input for the hydrodynamic modelling. We determined that, assuming a solar He to H abundance ratio, He I absorption should have been detected. Considering a stellar wind 25 times weaker than solar, we could reproduce the non-detection only by assuming a He to H abundance ratio about 16 times smaller than solar. Instead, considering a stellar wind ten times stronger than solar, we could reproduce the non-detection only with a He to H abundance ratio about ten times smaller than solar. We attempted to understand this result by collecting all past He I measurements and looking for correlations with high-energy stellar emission and planetary gravity, but without success.
Conclusions. WASP-80b is not the only planet with an estimated sub-solar He to H abundance ratio, which suggests the presence of efficient physical mechanisms (e.g. phase separation, magnetic fields) capable of significantly modifying the He to H content in the upper atmosphere of hot Jupiters. The planetary macroscopic properties and the shape of the stellar spectral energy distribution are not sufficient for predicting the presence or absence of detectable metastable He in a planetary atmosphere, since the He abundance also appears to play a major role.
SunnyNet: A neural network approach to 3D non-LTE radiative transfer
Authors: Chappell Bruce A. , Pereira Tiago M. D. 
Published: December 2021

Context. Computing spectra from 3D simulations of stellar atmospheres when allowing for departures from local thermodynamic equilibrium (non-LTE) is computationally very intensive.
Aims. We develop a machine learning based method to speed up 3D non-LTE radiative transfer calculations in optically thick stellar atmospheres.
Methods. Making use of a variety of 3D simulations of the solar atmosphere, we trained a convolutional neural network, SunnyNet, to learn the translation from LTE to non-LTE atomic populations. Non-LTE populations computed with an existing 3D code were considered as the true values. The network was then used to predict non-LTE populations for other 3D simulations, and synthetic spectra were computed from its predicted non-LTE populations. We used a six-level model atom of hydrogen and Hα spectra as test cases.
Results. SunnyNet gives reasonable predictions for non-LTE populations with a dramatic speedup of about 105 times when running on a single GPU and compared to existing codes. When using different snapshots of the same simulation for training and testing, SunnyNet’s predictions are within 20–40% of the true values for most points, which results in average differences of a few percent in Hα spectra. Predicted Hα intensity maps agree very well with existing codes. Most importantly, they show the telltale signs of 3D radiative transfer in the morphology of chromospheric fibrils. The results are not as reliable when the training and testing are done with different families of simulations. SunnyNet is open source and publicly available.
Partially Resorbable Mesh Inclusion between Dissected Layers during Surgical Repair of Aortic Dissection
Authors: Cavozza Corrado , Regesta Tommaso , Campanella Antonio , Camporini Glauco , Audo Andrea 
Published: December 2021

AbstractSurgical management of aortic dissection is technically challenging for different reasons. Reapproximation of dissected layers because of fragility of the dissected aortic wall layers is of major concern. Many techniques have been described to restore the integrity of aortic wall. Inclusion of a partially resorbable mesh fixed with glue, between the dissected layers, may be a simple and effective method for providing a secure and viable end-to-end anastomosis between aortic stump and a Dacron graft.
High-Frequency Three-Dimensional Lumen Volume Ultrasound Is a Sensitive Method to Detect Early Aneurysmal Change in Elastase-Induced Murine Abdominal Aortic Aneurysm
Authors: Waduud Mohammed A. , Kandavelu Parkavi , Reay Melanie , Paradine Katherine , Scott David J. A. , Bailey Marc A. 
Published: December 2021

Abstract
Objective The aim of this study was to investigate the reproducibility of anterior–posterior diameter (APdmax) and three-dimensional lumen volume (3DLV) measurements of abdominal aortic aneurysms (AAA) in a classical murine AAA model. We also compared the magnitude of change in the aortic size detected with each method of assessment.
Methods Periadventitial application of porcine pancreatic elastase (PPE AAA) or sham surgery was performed in two cohorts of mice. Cohort 1 was used to assess for observer variability with the APdmax and 3DLV measurements. Cohort 2 highlighted the relationship between APdmax and 3DLV and changes in AAA detected.
Results There was no significant observer variability detected with APdmax measurement. Similarly, no significant intraobserver variability was evident with 3DLV; however, a small but significant interobserver difference was present. APdmax and 3DLV measurements of PPE AAA significantly correlated. However, changes in the AAA morphology were detected earlier with 3DLV.
Conclusion APdmax and 3DLV are both reliable methods for measuring an AAA. Both these methods correlate with each other. However, changes in AAA morphology were detected earlier with 3DLV, which is important to detect subtle but important changes to aortic geometry in a laboratory setting. 3DLV measurement of AAA is a simple, reproducible, and comprehensive method for assessing changes in disease morphology.
A Unique Case of an Expanded Polytetrafluoroethylene Graft Rupture 14 Years after Abdominal Aortic Aneurysm Open Repair Managed with Placement of a Thoracic Endograft
Authors: Alexopoulou-Prounia Loukia , Kakkos Stavros K. , Papageorgopoulou Chrysanthi P. , Katsanos Konstantinos , Zampakis Peter , Tsantrizos Polyzois , Ntouvas Ioannis 
Published: December 2021

AbstractWe report a unique case of expanded polytetrafluoroethylene (ePTFE) tube graft rupture that occurred 14 years after abdominal aortic aneurysm (AAA) repair. Endovascular repair with a thoracic endograft was performed. Postoperatively, an increase in the size of the existing hematoma with active extravasation occurred and was managed with iliolumbar artery embolization. Τo the best of our knowledge, rupture of ePTFE graft used for AAA repair has not been reported in the literature.
Massive Sternal Osteophyte Compressing Aortic Arch Branch Graft
Authors: Ellauzi Hesham , Cardella Jonathan , Zafar Mohammad A. , Ziganshin Bulat A. , Elefteriades John A. 
Published: December 2021

AbstractWe present a dramatic computed tomography scan demonstrating compression of a brachiocephalic graft by a massive sternal osteophyte, coming to light many years after aortic arch replacement surgery.
A New Era of Diagnosis and Therapy in Acute Aortic Syndromes: The Mainz–Essen Experience (Part II)—Management and Outcomes
Authors: Bossone Eduardo , Gorla Riccardo , Ranieri Brigida , Russo Valentina , Jakob Heinz , Erbel Raimund 
Published: December 2021

AbstractOver the years, the cardiovascular department of Johannes Gutenberg University in Mainz-West-German Heart Centre in Essen (Germany) designed and implemented the hybrid operating room (2003) along with advanced endovascular and surgical procedures, including the frozen elephant trunk technique. For the study purpose, the Mainz–Essen experience on acute aortic syndromes was summarized by considering original articles from single-center or multicenter studies performed at West German Heart Centre, Essen, Germany, or at the cardiovascular department of Johannes Gutenberg University, Mainz, Germany. We present the 35-year-long Mainz–Essen research, education, and patient management journey in creating an integrated multidisciplinary “Aortic Center” in the heart of Europe.
Role of Extra-anatomic Ascending to Descending Bypass in Complex Thoracic Aortic Pathology
Authors: Camporrotondo Mariano , Pagni Sebastian 
Published: December 2021

AbstractComplex pathology of the distal arch and proximal descending thoracic aorta is usually approached by stent endografting or in situ graft replacement. Oftentimes, these options are not feasible due to unfavorable anatomy, multiple previous procedures, active infection, or presence of concomitant cardiac disease. Thoracic aortic extra-anatomic bypass, as part of an open surgical strategy, is a useful and often the only curative option left for the treatment in these patients. Herein, we describe two cases that illustrate the utility of extra-anatomic thoracic aortic bypass for complex aortic disease.
Ruptured Popliteal Artery Aneurysm
Authors: Rossi Umberto G. , Petrocelli Francesco , Cariati Maurizio 
Published: December 2021

AbstractRupture of a popliteal artery aneurysm is an uncommon event in an uncommon disease. We present the case of an 88-year-old female with a ruptured popliteal artery aneurysm that was diagnosed by multidetector computed tomography and treated by an endovascular approach.
Revisiting the phase transition sequence in L-methionine: Description of the disordering mechanism in an essential amino acid
Authors: Guinet Yannick , Paccou Laurent , Danède Florence , Hédoux Alain 
Published: December 2021

Raman spectroscopy investigations on L-methionine (L-Met) performed in a large temperature range (170–420 K) and in a wide spectral window (5–3600 cm−1) have revealed an extended disordering mechanism triggered by thermally activated motions of the terminal side-chain atoms, from 250 up to 390 K. This very progressive disordering process is characterized by two thermodynamic features, the first corresponding to a broad endotherm (250 → 310 K) marking the beginning of the process, while the second ending the disordering transformation is a sharp endothermic peak at 390 K. These thermodynamic events are correlated with the softening of lattice vibrations and the increase of the quasielastic scattering, considered as the signatures of displacive phase transitions. The amorphous-like band-shape of the low-frequency Raman spectrum collected above 390 K, resulting from the strong anharmonicity of local motions, is contrasting with the detection of additional Bragg peaks above 390 K by x-ray diffraction, consistent with the Cp jump accompanying the endothermic peak. These observations suggest that L-Met is progressively dynamically disordered adopting additional configurations in the crystalline lattice through rotations of CH3 and the side-chain flexibility not clearly detected by x-ray diffraction. These results should be crucial for considering the stability of dried proteins composed of methionine residues.
Vibration Control in Nanostructural Problems
Authors: Kumar Puneet , Srinivas J. , Ryvkin Michael 
Published: December 2021

In the nanotechnological era, an astounding demand for energy efficient and light-weight structures has emerged in fields such as nanomanufacturing, nanomachines, nanoelectronics, nanomedicine, aerospace, satellite-launching vehicles, and nuclear and solar energy. In this line, miniature structures (i.e., micro- and nanostructures) have received considerable attention in recent years owing to their small size, low weight, simple fabrication, and high-frequency operations. Nanostructures, such as nanobeams, nanoplates, nanoshells, nanowires, nanorods, nanorings, and nanohelices, have provided the most exciting trend in the current research scenario and have shown wide applications in various nano- and micro-sized devices and systems such as nanoresonators, nanoactuators, nanobots, biosensors, nanoprobes, nanogyroscopes, and micro- and nanoelectromechanical systems (MEMS/NEMS).
Sometimes, these structures may encounter large-amplitude vibrations and dynamic chaos during operational conditions. These undesired phenomena often cause unpleasant motion, disturbing noise, and unacceptable levels of dynamic stresses in nanostructural problems which may lead to potential fatigue failure, degraded performance, energy losses, and decreased reliability. Such detrimental effects need to be mitigated for the safety, reliability, and continuous operation of the nanodevice or system. Hence, a suitable vibration control strategy can only address this problem by integrating the self-controlling and self-monitoring capabilities into the structure. This chapter is devoted to study and summarize the various available vibration control techniques for nanostructural problems. A comprehensive insight into active, hybrid, and semi-active vibration control strategies for nanostructures is presented which will certainly enrich and generate interesting applications in nanodevices and systems.
Design and testing of a novel multipath-actuation compliant manipulator
Authors: Yang Xu , Ji Lichao , Zhu Wule , Shang Ying , Li Shizhen 
Published: December 2021

Abstract
In this paper, a novel multipath-actuation compliant manipulator (MCM) driven by piezoelectric actuators is proposed. Specifically, the monolithic MCM employs two vertically arranged compliant limbs with multipath motion transmission to actuate a symmetrically constrained planar mechanism, realizing x- and y-directional motion. For each limb, the multiple branched chains are configured in different paths but all contribute to the output motion, which results in a large displacement amplification ratio as well as a high working bandwidth. The ideal motion transmission of the proposed MCM is revealed by a specially established rigid-body kinematics model. Finite element analysis is carried out to predict the realistic static and dynamic performance of designed MCM. Moreover, a monolithic MCM prototype is fabricated, which is demonstrated to have a large displacement amplification ratio of 11.05, a high resonance frequency of 969 Hz, and a fine motion resolution of 25.48 nm. With promising static and dynamic characteristics, the proposed MCM can be widely used in practical applications.
Evaluating Helium Variations By Modeling Red Giant Branch Bump of Large Magellanic Cluster NGC 1978
Authors: Ji Xin , Li Cheng-Yuan , Deng Li-Cai 
Published: December 2021

Abstract
Many evidences show that the Multiple Population (MP) features exist not only in old clusters but also in intermediate-age clusters in the Megallanic Clouds (MCs), which are characterized by star-to-star abundance scatter of several elements, including helium (He). The red giant branch bump (RGBB)'s photometric properties are proved to be related to the variation in helium abundances of the member stars in star clusters. We use the “Modules for Experiments in Stellar Astrophysics” (MESA) stellar evolution code to calculate the evolution sequences of stars along the red giant branch (RGB) with changing helium content. Following the RGB sequences, we then generate a luminosity function of the RGB stars within the grid of input helium abundances, which are compared with the observational data of an intermediate-age MC cluster NGC 1978.
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
Authors: Lee Soohyun , Bakker Clara R , Vitzthum Carl , Alver Burak H , Park Peter J 
Published: December 2021

AbstractSummaryAs the amount of 3D chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.Availability and implementationThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/pairsqc.