bluuebunny/crossref_metadata_2025 huggingface dataset:
Silver nanoparticle effect on Salmonella enterica isolated from Northern West Egypt food, poultry, and calves
Authors: Torky Helmy Ahmed , Khaliel Samy Abd-Elsalam , Sedeek Eman Khalifa , Tawfik Rasha Gomaa , Bkheet Ahmad Abo Elmagd , Ebied Sawsan Khamees , Amin Heba said , Zahran Samir Ibrahim , Emara Hadeer Abd-Elhady , Nofal Abeer Mohamad , Elghazaly Eman Moneer
Published: August 2022

A total no. of 65 Salmonella enterica isolates recovered from food samples, feces of diarrheic calves, poultry, and hospital patient in large five cities at Northern West Egypt were obtained from the Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt. The 65 Salmonella enterica isolates had the invA gene were grouped into 11 Salmonella enterica serovars with dominance of S. Enteritidis and S. Kentucky serovars. Their resistance pattern were characterized by using 18 antibiotics from different classes. Approximately 80% of the isolates were multidrug resistant (MDR). Enterobacterial repetitive intergenic consequences polymerase chain reaction (ERIC-PCR) typing of 7 strains of S. Enteritidis showed 5 clusters with dissimilarity 25%. S. Enteritidis clusters in 2 main groups A and B. Group A have 2 human strain (HE2 and HE3) and one food origin (FE7) with a similarity 99%. Group B divided into B1 (FE2) and B2 (FE3) with a similarity ratio ≥ 93%, while ERIC-PCR analysis of 5 strains of S. Kentucky revealed 4 ERIC types, clustered in 2 main groups A and B with similarity 75%. We studied the effect of silver nanoparticles (Ag-NPs) on 10 antibiotic resistant strains of S. Enteritidis and S. Kentucky. The broth microdilution minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were detected. Evaluation of the affection using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed different ratios of Ag-NPs and microorganism as well as at different contact time ended finally with morphological alteration of the bacteria. We submitted new method in vivo to explore the activity of nanosilver in chicken.

Key points

• Importance of ERIC-PCR to determine the relatedness between Salmonella isolates.

• Effect of silver nanoparticles to confront the antibacterial resistance.

• Studying the effect of silver nanoparticles in vivo on infected chicken with Salmonella.
Immune phenotypes and checkpoint molecule expression of clonally expanded lymph node-infiltrating T cells in classical Hodgkin lymphoma
Authors: Ballhausen Alexej , Ben Hamza Amin , Welters Carlotta , Dietze Kerstin , Bullinger Lars , Rahn Hans-Peter , Hartmann Sylvia , Hansmann Martin-Leo , Hansmann Leo
Published: August 2022

Lymph node-infiltrating T cells have been of particular interest in classical Hodgkin lymphoma (cHL). High rates of complete therapeutic responses to antibody-mediated immune checkpoint blockade, even in relapsed/refractory patients, suggest the existence of a T cell-dominated, antigen-experienced, functionally inhibited and lymphoma-directed immune microenvironment. We asked whether clonally expanded T cells (1) were detectable in cHL lymph nodes, (2) showed characteristic immune phenotypes, and (3) were inhibited by immune checkpoint molecule expression. We applied high-dimensional FACS index sorting and single cell T cell receptor αβ sequencing to lymph node-infiltrating T cells from 10 treatment-naïve patients. T cells were predominantly CD4+ and showed memory differentiation. Expression of classical immune checkpoint molecules (CTLA-4, PD-1, TIM-3) was generally low (< 12.0% of T cells) and not different between CD4+ and CD8+ T cells. Degrees of clonal T cell expansion varied between patients (range: 1–18 expanded clones per patient) and was almost exclusively restricted to CD8+ T cells. Clonally expanded T cells showed non-naïve phenotypes and low checkpoint molecule expression similar to non-expanded T cells. Our data suggest that the therapeutic effects of immune checkpoint blockade require mechanisms in addition to dis-inhibition of pre-existing lymphoma-directed T cell responses. Future studies on immune checkpoint blockade-associated effects will identify molecular T cell targets, address dynamic aspects of cell compositions over time, and extend their focus beyond lymph node-infiltrating T cells.
Microbial carbon use efficiency of litter with distinct C/N ratios in soil at different temperatures, including microbial necromass as growth component
Authors: Börger Marie , Bublitz Tabata , Dyckmans Jens , Wachendorf Christine , Joergensen Rainer Georg
Published: August 2022

An incubation study was carried out to investigate the effects of litter quality, i.e. 15 N-labelled maize (C/N of 25.5) and Rhodes grass (C/N of 57.8) leaf litter on microbial carbon use efficiency (CUE) and priming effects in a moderate alkaline soil at two different temperatures (15 and 25 °C). CUE values were calculated from the isotopic composition of the particulate organic matter (POM) recovered as an index for the amount of non-decomposed litter. This approach allows the inclusion of microbial necromass growth components in the calculation of CUE values. Additionally, the soil was incubated for 10, 20, and 30 days to determine the optimum incubation period. Soil microbial CUE values of maize and Rhodes grass leaf litter, including microbial necromass C in the calculation of CUE, varied around 0.61, regardless of litter type, temperature, and incubation period. However, the optimum incubation time is between 20 and 30 days, depending on temperature. The strong priming effect on autochthonous soil organic carbon (SOC) mineralization was apparently not caused by N mining, as it was similar for both litter qualities. It most likely resulted from SOC being used by microbial co-metabolism. The litter-induced true priming effect was accompanied by a significant increase in autochthonous POM. The current approach, including microbial necromass as growth component, has been shown to be a strong tool for investigating CUE values and priming effects after application of litter and harvest residues to soil, probably under all environmental conditions.
Atrial fibrillation patterns and their cardiovascular risk profiles in the general population: the Rotterdam study
Authors: Tilly Martijn J. , Lu Zuolin , Geurts Sven , Ikram M. Arfan , Stricker Bruno H. , Kors Jan A. , de Maat Moniek P. M. , de Groot Natasja M. S. , Kavousi Maryam
Published: August 2022

Background

Clinical guidelines categorize atrial fibrillation (AF) based on the temporality of AF events. Due to its dependence on event duration, this classification is not applicable to population-based cohort settings. We aimed to develop a simple and standardized method to classify AF patterns at population level. Additionally, we compared the longitudinal trajectories of cardiovascular risk factors preceding the AF patterns, and between men and women.

Methods

Between 1990 and 2014, participants from the population-based Rotterdam study were followed for AF status, and categorized into ‘single-documented AF episode’, ‘multiple-documented AF episodes’, or ‘long-standing persistent AF’. Using repeated measurements we created linear mixed-effects models to assess the longitudinal evolution of risk factors prior to AF diagnosis.

Results

We included 14,061 participants (59.1% women, mean age 65.4 ± 10.2 years). After a median follow-up of 9.4 years (interquartile range 8.27), 1,137 (8.1%) participants were categorized as ‘single-documented AF episode’, 208 (1.5%) as ‘multiple-documented AF episodes’, and 57 (0.4%) as ‘long-standing persistent AF’. In men, we found poorer trajectories of weight and waist circumference preceding ‘long-standing persistent AF’ as compared to the other patterns. In women, we found worse trajectories of all risk factors between ‘long-standing persistent AF’ and the other patterns.

Conclusion

We developed a standardized method to classify AF patterns in the general population. Participants categorized as ‘long-standing persistent AF’ showed poorer trajectories of cardiovascular risk factors prior to AF diagnosis, as compared to the other patterns. Our findings highlight sex differences in AF pathophysiology and provide insight into possible risk factors of AF patterns.

Graphical abstract
Rainwater Charitable Foundation criteria for the neuropathologic diagnosis of progressive supranuclear palsy
Authors: Roemer Shanu F. , Grinberg Lea T. , Crary John F. , Seeley William W. , McKee Ann C. , Kovacs Gabor G. , Beach Thomas G. , Duyckaerts Charles , Ferrer Isidro A. , Gelpi Ellen , Lee Edward B. , Revesz Tamas , White Charles L. , Yoshida Mari , Pereira Felipe L. , Whitney Kristen , Ghayal Nikhil B. , Dickson Dennis W.
Published: August 2022

Neuropathologic criteria for progressive supranuclear palsy (PSP) proposed by a National Institute of Neurological Disorders and Stroke (NINDS) working group were published in 1994 and based on the presence of neurofibrillary tangles in basal ganglia and brainstem. These criteria did not stipulate detection methods or incorporate glial tau pathology. In this study, a group of 14 expert neuropathologists scored digital slides from 10 brain regions stained with hematoxylin and eosin (H&E) and phosphorylated tau (AT8) immunohistochemistry. The cases included 15 typical and atypical PSP cases and 10 other tauopathies. Blinded to clinical and neuropathological information, raters provided a categorical diagnosis (PSP or not-PSP) based upon provisional criteria that required neurofibrillary tangles or pretangles in two of three regions (substantia nigra, subthalamic nucleus, globus pallidus) and tufted astrocytes in one of two regions (peri-Rolandic cortices, putamen). The criteria showed high sensitivity (0.97) and specificity (0.91), as well as almost perfect inter-rater reliability for diagnosing PSP and differentiating it from other tauopathies (Fleiss kappa 0.826). Most cases (17/25) had 100% agreement across all 14 raters. The Rainwater Charitable Foundation criteria for the neuropathologic diagnosis of PSP feature a simplified diagnostic algorithm based on phosphorylated tau immunohistochemistry and incorporate tufted astrocytes as an essential diagnostic feature.
Mastoidectomy in surgical procedures to treat retraction pockets: a single-center experience and review of the literature
Authors: Immordino Angelo , Salvago Pietro , Sireci Federico , Lorusso Francesco , Immordino Palmira , Saguto Dario , Martines Francesco , Gallina Salvatore , Dispenza Francesco
Published: August 2022

Purpose

Retraction pocket (RP) is a common event affecting the middle ear when a negative pressure within it causes a retraction of a single part of the tympanic membrane (TM). Patients can be asymptomatic or can experience hearing loss, fullness feeling and/or ear discharge. RP can be stable or develop a cholesteatoma; aim of the study was to investigate if mastoidectomy may play a role in the surgical management of patients suffering from RP, both reporting our experience and discussing the existing literature.

Methods

Fifty-one patients affected by RP were referred for surgery and randomly divided into two groups. Patients of G1 group underwent tympanoplasty with mastoidectomy, patients of G2 group underwent tympanoplasty only. A systematic review of the literature was then carried out by applying the PRISMA guidelines.

Results

The mean follow-up lasted about 36 months. The G1 and G2 groups reached a postoperative mean air–bone gap (ABG) of 7.1 dB HL and 5.1 dB HL, respectively, with a mean ABG improvement of 13.2 dB HL and 12.4 dB HL. An ABG improvement was observed in the 59.7% of the G1 group and in the 63.2% of the G2 group, respectively (p > 0.5). Only one case of long-term complication was recognized in the G1 group. We combined, integrated and analyzed results of our prospective study with results of the literature review.

Conclusions

Based on the combined results of our study and literature review we may conclude that there is no evident benefit in performing mastoidectomy for the treatment of RP. In fact, no differences in ABG improvement or in RP recurrence were reported between the two groups.
Fourier analysis of collagen bundle orientation in myocardial infarction scars
Authors: Marcos-Garcés Víctor , Rios-Navarro Cesar , Gómez-Torres Fabián , Gavara Jose , de Dios Elena , Diaz Ana , Miñana Gema , Chorro Francisco Javier , Bodi Vicente , Ruiz-Sauri Amparo
Published: August 2022

Collagen bundle orientation (CBO) in myocardial infarct scars plays a major role in scar mechanics and complications after infarction. We aim to compare four histopathological methods for CBO measurement in myocardial scarring. Myocardial infarction was induced in 21 pigs by balloon coronary occlusion. Scar samples were obtained at 4 weeks, stained with Masson’s trichrome, Picrosirius red, and Hematoxylin–Eosin (H&E), and photographed using light, polarized light microscopy, and confocal microscopy, respectively. Masson’s trichrome images were also optimized to remove non-collagenous structures. Two observers measured CBO by means of a semi-automated, Fourier analysis protocol. Interrater reliability and comparability between techniques were studied by the intraclass correlation coefficient (ICC) and Bland–Altman (B&A) plots and limits of agreement. Fourier analysis showed an almost perfect interrater reliability for each technique (ICC ≥ 0.95, p < 0.001 in all cases). CBO showed more randomly oriented values in Masson’s trichrome and worse comparability with other techniques (ICC vs. Picrosirius red: 0.79 [0.47–0.91], p = 0.001; vs. H&E-confocal: 0.70 [0.26–0.88], p = 0.005). However, optimized Masson’s trichrome showed almost perfect agreement with Picrosirius red (ICC 0.84 [0.6–0.94], p < 0.001) and H&E-confocal (ICC 0.81 [0.54–0.92], p < 0.001), as well as these latter techniques between each other (ICC 0.84 [0.60–0.93], p < 0.001). In summary, a semi-automated, Fourier-based method can provide highly reproducible CBO measurements in four different histopathological techniques. Masson’s trichrome tends to provide more randomly oriented CBO index values, probably due to non-specific visualization of non-collagenous structures. However, optimization of Masson’s trichrome microphotographs to remove non-collagenous components provides an almost perfect comparability between this technique, Picrosirius red and H&E-confocal.
Evaluation of different imaging modalities for axillary lymph node staging in breast cancer patients to provide a personalized and optimized therapy algorithm
Authors: Diessner Joachim , Anders Laura , Herbert Saskia , Kiesel Matthias , Bley Thorsten , Schlaiss Tanja , Sauer Stephanie , Wöckel Achim , Bartmann Catharina
Published: August 2022

Purpose

The reliable detection of tumor-infiltrated axillary lymph nodes for breast cancer [BC] patients plays a decisive role in further therapy. We aimed to find out whether cross-sectional imaging techniques could improve sensitivity for pretherapeutic axillary staging in nodal-positive BC patients compared to conventional imaging such as mammography and sonography.

Methods

Data for breast cancer patients with tumor-infiltrated axillary lymph nodes having received surgery between 2014 and 2020 were included in this study.

All examinations (sonography, mammography, computed tomography [CT] and magnetic resonance imaging [MRI]) were interpreted by board-certified specialists in radiology. The sensitivity of different imaging modalities was calculated, and binary logistic regression analyses were performed to detect variables influencing the detection of positive lymph nodes.

Results

All included 382 breast cancer patients had received conventional imaging, while 52.61% of the patients had received cross-sectional imaging.

The sensitivity of the combination of all imaging modalities was 68.89%. The combination of MRI and CT showed 63.83% and the combination of sonography and mammography showed 36.11% sensitivity.

Conclusion

We could demonstrate that cross-sectional imaging can improve the sensitivity of the detection of tumor-infiltrated axillary lymph nodes in breast cancer patients. Only the safe detection of these lymph nodes at the time of diagnosis enables the evaluation of the response to neoadjuvant therapy, thereby allowing access to prognosis and improving new post-neoadjuvant therapies.
Entropy-Transport distances between unbalanced metric measure spaces
Authors: De Ponti Nicolò , Mondino Andrea
Published: August 2022

Inspired by the recent theory of Entropy-Transport problems and by the$${\mathbf {D}}$$D-distance of Sturm onnormalisedmetric measure spaces, we define a new class of complete and separable distances between metric measure spaces of possibly different total mass. We provide several explicit examples of such distances, where a prominent role is played by a geodesic metric based on the Hellinger-Kantorovich distance. Moreover, we discuss some limiting cases of the theory, recovering the “pure transport”$${\mathbf {D}}$$D-distance and introducing a new class of “pure entropic” distances. We also study in detail the topology induced by such Entropy-Transport metrics, showing some compactness and stability results for metric measure spaces satisfying Ricci curvature lower bounds in a synthetic sense.
Thermo-Poromechanical Properties of Pierre II Shale
Authors: Agofack Nicolaine , Cerasi Pierre , Sønstebø Eyvind , Stenebråten Jørn
Published: August 2022

During the injection of carbon dioxide (CO2) for CO2 capture and storage (CCS) operations, the near-well (including casing, cement, and rock around it) can undergo several thermal loadings. These loadings can significantly increase or decrease the pore pressure and can thus lead to mechanical failure of the cement sheath and rock formation. When these failures appear in the caprock, they can compromise the integrity of the storage site. The understanding of thermo-mechanical behaviour of a potential caprock shale is, therefore, of great importance for the success of CCS operations. In this paper, experiments were performed on Pierre II shale, under confining and initial pore pressures comparable to field conditions. A 60 °C loading amplitude (between 30 and 90 °C) was applied on the shale material both under undrained and drained conditions. The results, analysed within the framework of anisotropic thermo-poro-elasticity, highlight the anisotropic behaviour of the thermal expansion coefficients, as well as of the Skempton coefficient. The thermal pressurization coefficient was also evaluated and showed a potential pore pressure change as high as 0.11 MPa/°C.
On the mathematical fluid dynamics of atmospheric gravity (buoyancy) waves
Authors: Johnson R. S.
Published: August 2022

Starting from the general, governing equations for a viscous, compressible fluid written in rotating, spherical coordinates, with an associated prescription for its thermodynamics, we construct a general amplitude perturbation of the background state of the atmosphere. The background state, with a purely zonal flow (wind) is suitably non-dimensionalised and the thin-shell parameter introduced; this is the sole basis upon which we construct the asymptotic solution of this problem. A corresponding, but different, non-dimensionalisation is performed on the system representing the perturbation. This approach shows how the Boussinesq approximation arises, but it also shows that rotation (Coriolis) terms cannot be ignored. Furthermore, any consistent solution requires that changes in pressure, density and temperature, due to the passage of the wave, are all the same (asymptotic) size. Comparison is made with existing theories, and we comment on the new aspects that have been uncovered in this investigation. Finally, we indicate where these ideas might be taken in the future.
LCA as decision support tool in the food and feed sector: evidence from R&D case studies
Authors: Ott Denise , Goyal Shashank , Reuss Rosmarie , Gutzeit Herwig O. , Liebscher Jens , Dautz Jens , Degieter Margo , de Steur Hans , Zannini Emanuele
Published: August 2022

Biomass waste and waste-derived feedstocks are important resources for the development of sustainable value-added products. However, the provision and preparation of biomass as well as all possible downstream processing steps need to be thoroughly analyzed to gain environmentally sound and economically viable products. Additionally, its impacts are substantially determined by decisions made at early development stages. Therefore, sustainability assessment methods can support to improve the production process, reduce waste, and costs and help decision-making, at the industrial as well as policy levels. Life Cycle Assessment (LCA) is an analysis technique to assess environmental impacts associated with all product's life cycle stages. It is a well-established tool to drive development towards a sustainable direction, however, its application in the earlier research phase is surrounded by practical challenges. The overall objective of this paper is to provide an understanding of the environmental issues involved in the early stages of product and process development and the opportunities for life cycle assessment techniques to address these issues. Thus, herein two LCA case studies are presented, dealing with novel approaches for food and feed supply through implementing the valorization and upcycling of waste and side-streams, respectively. In both case studies, LCA is used as a decision support tool for R&D activities to launch environmentally sound products to market, as well as to highlight the usefulness of LCA for identifying environmental issues at an earlier stage of development, regardless of product, process, or service.
Computational Modelling for Alcohol Use Disorder
Authors: Colombo Matteo
Published: August 2022

In this paper, I examine Reinforcement Learning (RL) modelling practice in psychiatry, in the context of alcohol use disorders. I argue that the epistemic roles RL currently plays in the development of psychiatric classification and search for explanations of clinically relevant phenomena are best appreciated in terms of Chang’s (2004) account of epistemic iteration, and by distinguishing mechanistic and aetiological modes of computational explanation.
High-throughput sequencing analysis of nuclear-encoded mitochondrial genes reveals a genetic signature of human longevity
Authors: Gonzalez Brenda , Tare Archana , Ryu Seungjin , Johnson Simon C. , Atzmon Gil , Barzilai Nir , Kaeberlein Matt , Suh Yousin
Published: August 2022

Mitochondrial dysfunction is a well-known contributor to aging and age-related diseases. The precise mechanisms through which mitochondria impact human lifespan, however, remain unclear. We hypothesize that humans with exceptional longevity harbor rare variants in nuclear-encoded mitochondrial genes (mitonuclear genes) that confer resistance against age-related mitochondrial dysfunction. Here we report an integrated functional genomics study to identify rare functional variants in ~ 660 mitonuclear candidate genes discovered by target capture sequencing analysis of 496 centenarians and 572 controls of Ashkenazi Jewish descent. We identify and prioritize longevity-associated variants, genes, and mitochondrial pathways that are enriched with rare variants. We provide functional gene variants such as those in MTOR (Y2396Lfs*29), CPS1 (T1406N), and MFN2 (G548*) as well as LRPPRC (S1378G) that is predicted to affect mitochondrial translation. Taken together, our results suggest a functional role for specific mitonuclear genes and pathways in human longevity.
Algorithmus zur konservativen Behandlung von proximalen Humerusfrakturen
Authors: Razaeian Sam , Krettek Christian , Hawi Nael
Published: August 2022

Die proximale Humerusfraktur ist eine häufige Verletzung mit steigender Inzidenz. Die aktuelle S1-Leitlinie „Oberarmkopffraktur“ der federführenden Deutschen Gesellschaft für Unfallchirurgie e. V. (DGU) hält zwar fest, dass ein Großteil dieser Frakturen konservativ behandelt werden kann. Es stellt sich jedoch die Frage, wie genau sich jene konservative Therapie gestalten lässt. Nationale wie internationale Unterschiede in der Therapie unterstreichen ein uneinheitliches Management und den fehlenden Konsens in der Behandlung dieser so häufigen Verletzung. Im folgenden Artikel soll ein Einblick in die Erfahrungen der Autoren gewährt und eine mögliche alltagstaugliche Entscheidungshilfe vorgestellt werden, mit welcher diese stetig zunehmende Verletzungsart erfolgreich konservativ behandelt werden kann. Die Erfahrungen stützen sich dabei auf einen Patientenstrom von jährlich mehr als 200 Patienten eines Level-1-Traumazentrumes, von denen zwischen 01/2016 bis 09/2021 jährlich ca. 80 % erfolgreich einer konservativen Therapie zugeführt werden konnten und im Rahmen einer prospektiven Observationsstudie, dem Hannover Humerusregister (ClinicalTrials.gov Identifier: NCT03060876), systematisch nachkontrolliert wurden.
Total knee replacements using rotating hinge implants in polio patients: clinical and functional outcomes
Authors: Digennaro V. , Manzetti M. , Bulzacki Bogucki B. D. , Barile F. , Panciera A. , Viroli G. , Ferri R. , Cecchin D. , Ruffilli A. , Faldini C.
Published: August 2022

Little evidences are available in the literature concerning the outcomes of total knee replacement (TKR) in poliomyelitis patients with severe knee deformities or degeneration. Encouraging results have been reported concerning the use of constrained implants, i.e., rotating hinge knee prosthesis (RHK), compared to less constrained ones. The purpose of this paper is to report our experience with rotating hinge total knee replacement, using only RHK prosthesis, to determine functional results, complications, and survival of TKR in poliomyelitis patients. We performed a retrospective chart review of 14 patients with a history of knee osteoarthritis following poliomyelitis that underwent primary TKR, for a total of 15 surgical procedure (one bilateral case). Preoperative and postoperative clinical measurements have been conducted for all patients using the Knee Society Score (KSS). Hip-knee angle, recurvatum knee angle, and Insall-Salvati index were evaluated with full weight-bearing panoramic view X-ray preoperatively and postoperatively. The 2-year postoperative clinical KSS significantly improved from the preoperative scores. The average clinical KSS improved from 32,9 (range 3–48) preoperatively to 77,4 (range 60–88) postoperatively (P value < 0.005). The average functional KSS improved from 32,5 (range 10–60) preoperatively to 59,4 (range 30–95) postoperatively (P value < 0.005). TKR is a successful treatment in improving knee function and patient’s quality of life. Using constrained implants, especially rotating hinge implants in polio patients with a quadriceps muscle weakness, could be a good alternative to maintain a physiological kinematics and reducing the revision rate due to knee instability.
BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction
Authors: Asim Muhammad Nabeel , Ibrahim Muhammad Ali , Zehe Christoph , Trygg Johan , Dengel Andreas , Ahmed Sheraz
Published: August 2022

Background and objective:

Interactions of long non-coding ribonucleic acids (lncRNAs) with micro-ribonucleic acids (miRNAs) play an essential role in gene regulation, cellular metabolic, and pathological processes. Existing purely sequence based computational approaches lack robustness and efficiency mainly due to the high length variability of lncRNA sequences. Hence, the prime focus of the current study is to find optimal length trade-offs between highly flexible length lncRNA sequences.

Method

The paper at hand performs in-depth exploration of diverse copy padding, sequence truncation approaches, and presents a novel idea of utilizing only subregions of lncRNA sequences to generate fixed-length lncRNA sequences. Furthermore, it presents a novel bag of tricks-based deep learning approach “Bot-Net” which leverages a single layer long-short-term memory network regularized through DropConnect to capture higher order residue dependencies, pooling to retain most salient features, normalization to prevent exploding and vanishing gradient issues, learning rate decay, and dropout to regularize precise neural network for lncRNA–miRNA interaction prediction.

Results

BoT-Net outperforms the state-of-the-art lncRNA–miRNA interaction prediction approach by 2%, 8%, and 4% in terms of accuracy, specificity, and matthews correlation coefficient. Furthermore, a case study analysis indicates that BoT-Net also outperforms state-of-the-art lncRNA–protein interaction predictor on a benchmark dataset by accuracy of 10%, sensitivity of 19%, specificity of 6%, precision of 14%, and matthews correlation coefficient of 26%.

Conclusion

In the benchmark lncRNA–miRNA interaction prediction dataset, the length of the lncRNA sequence varies from 213 residues to 22,743 residues and in the benchmark lncRNA–protein interaction prediction dataset, lncRNA sequences vary from 15 residues to 1504 residues. For such highly flexible length sequences, fixed length generation using copy padding introduces a significant level of bias which makes a large number of lncRNA sequences very much identical to each other and eventually derail classifier generalizeability. Empirical evaluation reveals that within 50 residues of only the starting region of long lncRNA sequences, a highly informative distribution for lncRNA–miRNA interaction prediction is contained, a crucial finding exploited by the proposed BoT-Net approach to optimize the lncRNA fixed length generation process.

Availability:

BoT-Net web server can be accessed at https://sds_genetic_analysis.opendfki.de/lncmiRNA/.

Graphic Abstract
Effectiveness, Acceptability, and Mechanisms of Change of the Internet-Based Intervention StudiCare Mindfulness for College Students: a Randomized Controlled Trial
Authors: Küchler Ann-Marie , Kählke Fanny , Vollbrecht Danielle , Peip Katharina , Ebert David D. , Baumeister Harald
Published: August 2022

Objectives

College is an exhilarating but stressful time often associated with mental distress. The StudiCare project offers Internet- and mobile-based interventions (IMI) for college student mental health promotion. Within this framework, we evaluated the IMI StudiCare Mindfulness, and examined potential moderators and mediators of effectiveness.

Methods

In this randomized controlled trial, 150 college students with low to moderate mindfulness were randomly assigned to StudiCare Mindfulness or a waitlist control group (WL). StudiCare Mindfulness comprises 5 weekly online modules based on Acceptance Commitment Therapy and stress management. Assessments took place before (t0) and 6 weeks after (t1) randomization. Primary outcome was mindfulness. Secondary outcomes were stress, depression, anxiety, quality of life, intervention satisfaction, and adherence. Sociodemographic variables, pre-intervention symptomatology, personality traits, and attitudes towards IMI were examined as potential moderators.

Results

Intention-to-treat analyses (N = 149) showed a large effect of StudiCare Mindfulness on mindfulness (d = 1.37; 95% CI: 1.01–1.73) compared to WL at t1 (β = 1.18; 95% CI: 0.96–1.40). Effects on secondary outcomes were significant in favor of the intervention group except for physical quality of life. Mindfulness was found to mediate intervention effectiveness on depression, anxiety, and stress. Moderation analysis was non-significant except for baseline openness to experience, with lower openness associated with larger intervention effects on mindfulness.

Conclusions

This trial suggests that StudiCare Mindfulness may enhance mindfulness and reduce mental health problems. Its potential applicability as low-threshold prevention and treatment option on a population level should be subject to future trials.

Trial Registration

German Clinical Studies Trial Register TRN: DRKS00012559.
Finding Your Identity and Partner in a Trade Mark? Consumption, Innovation and the Law
Authors: Lai Jessica C. , Williams Janine L.
Published: August 2022

Trade marks are not traditionally considered to be central to innovation because they do not need to be innovative to be protected. Instead, trade marks are used to indicate the source of products and services. Of course, if consumers could not determine the source, this would reduce the incentive for traders to compete through innovative products and services. Here, we argue that trade marks implicate innovation in yet another way. Namely, because consumption can be based on identity characteristics and personality traits of trade marks, which can result in consumer-brand relationships that are either or both identity-related and/or partner-like, companies have incentives to innovate in accordance with the identity characteristics and personality traits. Failure to do so can result in negative reactions from consumers and relationship break-ups, which impacts innovation selection and hence societal good. We explore the implications of this for trade mark law theory and practice.
Investment expectations by vulnerable European firms in times of COVID
Authors: Coad Alex , Amaral-Garcia Sofia , Bauer Peter , Domnick Clemens , Harasztosi Peter , Pál Rozália , Teruel Mercedes
Published: August 2022

The effect of the COVID shock on European economies has been severe and also unequal, with some firms being affected much more strongly than others. To improve the effectiveness of policy interventions, policymakers need to understand which types of vulnerable firms have been suddenly pushed into dire circumstances. We seek to fill this important gap in our knowledge by providing evidence from the European Investment Bank Investment Survey 2016–2020 on how the COVID shock has affected the investment activity and investment-related framework conditions of vulnerable firms. While data on actual investment activity post-COVID is not yet available to us, we focus on investment expectations. We exploit the fact that the same questions relating to investment expectations have been asked in several previous survey waves, which enables a difference-in-differences approach to investigate how investment expectations might have suddenly changed, for vulnerable groups of firms, immediately after the onset of the COVID crisis. We focus on 4 groups of vulnerable firms: High-Growth Enterprises (HGEs), young and small firms, R&D investors and non-subsidiary firms. R&D investors are more likely to be pessimistic about investment plans as a consequence of the COVID shock, and (similarly) HGEs are less likely to be optimistic about investment plans. R&D investors are less likely to be optimistic about the availability of internal finance, while HGEs and R&D investors are more likely to be pessimistic about the availability of external finance. Subsidiary firms, interestingly, are more likely to report a decrease in expected investment, which is not necessarily evidence of financial constraints, because it could instead be part of a conservative group-level strategy and coordinated group-level reduction in investment. Event study graphs generally confirm our regression results.
Optimizing Tree-Based Contrast Subspace Mining Using Genetic Algorithm
Authors: Sia Florence , Alfred Rayner
Published: August 2022

Mining contrast subspace is a task of finding contrast subspace where a given query object is most similar to a target class but dissimilar to non-target class in a multidimensional data set. Recently, tree-based contrast subspace mining method has been introduced to find contrast subspace in numerical data set effectively. However, the contrast subspace search of the tree-based method may be trapped in local optima within the search space. This paper proposes a tree-based method which incorporates genetic algorithm to optimize the contrast subspace search by identifying global optima contrast subspace. The experiment results showed that the proposed method performed well on several cases compared to the variation of the tree-based method.
A New Route for Redress in the Samarco Case? An Overview of the Simplified Indemnification System’s (Un)Lawfulness
Authors: Garrido Alves Danilo B. , Arantes Prata Daniela , Manfredini de Abreu Camila
Published: August 2022

On 5 November 2015, the Fundão Dam collapsed, causing the most devastating tailings dam disaster to date. The dam was operated by Samarco S.A., a joint venture by Vale, Brazil’s biggest mining company, and BHP Billiton, the world’s largest mining company.1 Its tailings travelled down the Doce River for ca 700 kilometres until they reached the ocean, affecting 42 municipalities, two states, and thousands of communities along the way. The disaster caused myriad social, environmental and economic impacts: nineteen individuals were killed, and thousands endured physical or psychological harm; water resources and the soil were polluted; habitats were irreversibly destroyed; and the local economy suffered long-lasting damage. Traditional and indigenous communities were especially harmed, as their historical, social, religious and cultural relationships with their land led to even more profound harms.2
Reconstituting the Code of Capital: could a progressive European code of private law help us reduce inequality and regain democratic control?
Authors: Hesselink Martijn W.
Published: August 2022

Katharina Pistor’s powerful critique of the key role that private law plays in creating private wealth, producing inequalities, and undermining democracy, raises the urgent question of what could be done to set things right or, at least, could be a step in the right direction. This article argues that a progressive European code of private law could be a meaningful part of the solution. A progressive private law code would be a code aimed at making progress towards a more just society, where there is less inequality and where we have more democratic control over our future. The progressive EPL-code would be completely different, in crucial respects, from the civil codes of the member states. It would be European (not national), be mandatory (not optional), have ‘constitutional’ ie primary EU law status (not merely secondary), consist of fundamental principles (not detailed rules), prioritise justice (not economic growth), and be radically democratic (not technocratic).
Three times lucky: in dialogue with Rein Müllerson
Authors: Menéndez Agustín José , Müllerson Rein
Published: August 2022

The publication in 2017 of Dawn of a New World (I B Tauris) confirmed Rein Müllerson as one of the great international lawyers of his generation. His career is deeply marked by the recent history of Europe. He was a young director of the Department of International Law of the Academy of Sciences of Moscow in the 1980s, doubling down as legal advisor to Gorbachev during the decisive years of perestroika and glasnost. It is not an exaggeration to say that, in those hectic days, Müllerson saw history unfolding from the machine room of the Kremlin. In the 1990s, after a brief but very intense period as secretary of state of the newborn Estonian Republic, Müllerson joined academia again as professor of international law at the LSE first, then at King’s College. His inexhaustible stamina allowed him to wear a second hat as adviser on human rights to the United Nations, spending quite some time in Central Asia. After his retirement from King’s College, he returned in the 2010s to Tallinn as dean of the newly established School of Governance. The following text is the result of a number of conversations, some in Tallinn, others forced by circumstances through video connection. The range of issues is as wide as Müllerson’s interests, hopefully offering the reader views which are out of the common road. Not only because of the multiplicity of perspectives he is privy to, thanks to his extremely rich academic and personal trajectory, but also because of his commitment to diversity and pluralism.
Ecology and effects of metazoan parasites of fish in transitional waters
Authors: Giari Luisa , Castaldelli Giuseppe , Timi Juan Tomás
Published: August 2022

Given the abundance, heterogeneity and ubiquity of parasitic organisms, understanding how they influence biodiversity, evolution, health and ecosystem functionality is crucial, especially currently when anthropogenic pressures are altering host–parasite balances. This review describes the features, roles and impacts of metazoan parasites of fish occurring in transitional waters (TW). These aquatic ecosystems are highly productive and widespread around the globe and represent most favourable theatres for parasitism given the availability of hosts (invertebrates, fishes and birds) and an increased probability of parasite transmission, especially of those having complex life cycles. Fascinating examples of how parasitism can influence different hierarchical levels of biological systems, from host individuals and populations to entire aquatic communities, through effects on food webs come from this kind of ecosystem. Edible fish of commercial value found in TW can harbour some parasite species, significantly reducing host health, marketability and food safety, with possible economic and public health consequences. Many TW are historically exploited by humans as sources of relevant ecosystem services, including fisheries and aquaculture, and they are highly vulnerable ecosystems. Alteration of TW can be revealed through the study of parasite communities, contributing, as bioindicators, for assessing environmental changes, health and restoration. Fish parasites can provide much information about TW, but this potential appears to be not fully exploited. More studies are necessary to quantify the ecological, economic and medical impacts fish parasites can have on these important ecosystems.
Spatiotemporal Distributions and Source Apportionment of PM2.5‐Bound Antimony in Beijing, China
Authors: Yang Chenmeng , Wu Yunjie , Zhang Leiming , Sun Guangyi , Yao Heng , Li Zhonggen , Bi Xiangyang , Huang Qiang , Feng Xinbin
Published: August 2022

Antimony (Sb) is a toxic heavy metal, and PM2.5‐bound Sb (SbPM2.5) in the air impacts human health via inhalation pathways. In this study, we analyzed multiyear measurements of ambient SbPM2.5 in Beijing to characterize its spatiotemporal distributions, identify main sources, and predict future trends. The results show that ambient SbPM2.5 has been decreasing with fluctuations from 2005 to 2012 and decreased rapidly after 2013, which was likely a result of the government's enhanced air pollution control plan that targeted main sources of industrial Sb. Across the city, average SbPM2.5 concentrations were relatively higher at nonemission locomotive traffic sampling sites and in densely populated areas (9.45–19.45 ng/m3) and lower in background areas (0.6–0.9 ng/m3). Regional‐scale emissions and local human activities both affected the spatial distributions of SbPM2.5. Notably, SbPM2.5 concentration increased by 58.3% from 2006 to 2013 in one suburban background area, indicating the changing emission distributions and intensities over the study period. A neural network model was developed and tested to predict future SbPM2.5 levels, results from which showed that with simulated massive reductions in coal supplies and a rapid boom in the waste incineration industry, SbPM2.5 concentration would vary in a smaller range (from 4.08 to 4.38 ng/m3) over the next decade as compared to the observed range during 2011–2018 (19.0–5.44 ng/m3). The impact of the continued expansion of the waste incineration industry on SbPM2.5 pollution needs to be considered in future emission control policies.
Incorporating Uncertainty Into a Regression Neural Network Enables Identification of Decadal State‐Dependent Predictability in CESM2
Authors: Gordon Emily M. , Barnes Elizabeth A.
Published: August 2022

Predictable internal climate variability on decadal timescales (2–10 years) is associated with large‐scale oceanic processes, however these predictable signals may be masked by the noisy climate system. One approach to overcoming this problem is investigating state‐dependent predictability—how differences in prediction skill depend on the initial state of the system. We present a machine learning approach to identify state‐dependent predictability on decadal timescales in the Community Earth System Model version 2 pre‐industrial control simulation by incorporating uncertainty estimates into a regression neural network. We leverage the network's prediction of uncertainty to examine state dependent predictability in sea surface temperatures by focusing on predictions with the lowest uncertainty outputs. In particular, we study two regions of the global ocean—the North Atlantic and North Pacific—and find that skillful initial states identified by the neural network correspond to particular phases of Atlantic multi‐decadal variability and the interdecadal Pacific oscillation.
Revisiting the 1959 Hebgen Lake Earthquake Using Optical Image Correlation; New Constraints on Near‐Field 3D Ground Displacement
Authors: Andreuttiova Lucia , Hollingsworth James , Vermeesch Pieter , Mitchell Thomas M. , Bergman Eric
Published: August 2022

Near‐field surface displacement measurements allow us to quantify the on‐ and off‐fault proportion of earthquake‐related deformation. The Hebgen Lake earthquake was a large normal event with a complex surface rupture, which broke across mountainous terrain. This study takes advantage of high‐resolution historical aerial stereo‐imagery to measure three‐dimensional displacement from correlation of the orthorectified pre‐ and post‐earthquake image mosaics. The results reveal new strike‐slip ruptures which are possibly associated with the aftershocks from 18th August 1959. These structures likely reflect internal block deformation induced by the complex geometry of the mainshock. Additionally, comparison of our results with the existing displacement data shows that the optical image correlation‐derived offsets often exceed the field measurements by >50%. We attribute this difference to inelastic off‐fault deformation.
Autocyclic Secondary Channels Stabilize Deltaic Islands Undergoing Relative Sea Level Rise
Authors: Salter Gerard , Lamb Michael P.
Published: August 2022

Understanding what sets the size and stability of deltaic islands is critical for predicting how deltas will respond to sea level rise. Models of overbank sedimentation produce an exponentially decaying sedimentation profile, seemingly incompatible with island stability, which requires uniform sedimentation balancing sea level rise. However, secondary channels provide a mechanism for delivering sediment deeper into island interiors, potentially stabilizing islands. Using a 1D morphodynamic model, we found that autogenic secondary channels allow islands or parts of islands to maintain a stable profile dynamically through cycles of channel incision and aggradation. However, when islands are too large, secondary channels grow to become stable, primary channels, thereby bisecting the island, resulting in smaller, stable islands with more connectivity to the channel network. Rather than passively drowning, our results indicate that deltaic islands can respond to sea level rise through morphodynamic feedbacks that act to enhance island accretion.