bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topological physics of non-Hermitian optics and photonics: a review
Authors: Wang Hongfei , Zhang Xiujuan , Hua Jinguo , Lei Dangyuan , Lu Minghui , Chen Yanfeng 
Published: October 2021

Abstract
The notion of non-Hermitian optics and photonics rooted in quantum mechanics and photonic systems has recently attracted considerable attention ushering in tremendous progress on theoretical foundations and photonic applications, benefiting from the flexibility of photonic platforms. In this review, we first introduce the non-Hermitian topological physics from the symmetry of matrices and complex energy spectra to the characteristics of Jordan normal forms, exceptional points, biorthogonal eigenvectors, Bloch/non-Bloch band theories, topological invariants and topological classifications. We further review diverse non-Hermitian system branches ranging from classical optics, quantum photonics to disordered systems, nonlinear dynamics and optomechanics according to various physical equivalences and experimental implementations. In particular, we include cold atoms in optical lattices in quantum photonics due to their operability at quantum regimes. Finally, we summarize recent progress and limitations in this emerging field, giving an outlook on possible future research directions in theoretical frameworks and engineering aspects.
Pregnancy Reverses Abdominoplasty Aesthetic Outcome: Myth or Misconception? A Cross-Sectional Study
Authors: Averbuch Sagie Roni , Wiser Itay , Heller Lior , Klein Doron , Hadad Eran 
Published: October 2021

Abstract

Background
The common recommendation for female abdominoplasty candidates is to conclude family planning before undergoing the procedure. However, no evidence demonstrates a correlation between aesthetic outcome compromise, risk for fetal complications, or risk for maternal complications when abdominoplasty is followed by pregnancy.

Objectives
The aim of this study was to evaluate maternal, fetal, and aesthetic outcomes among pregnant females with a history of abdominoplasty.

Methods
The authors conducted an online survey among women who became pregnant after having an abdominoplasty. Participants were recruited via social media groups related to abdominoplasty. The survey included demographic-, aesthetic outcome-, and pregnancy-related questions utilizing a score from 1 (no effect) to 10 (worst effect) to assess abdominal aesthetic outcome compromise.

Results
Thirty-two participants completed the online survey, 15 (46.8%) of which reported their pregnancy was unplanned. Pregnancy-related findings included 5 (15.6%) late premature births (between gestational week 35 and 37), 1 miscarriage, and 1 emergency C-section. Compromised aesthetic outcomes following pregnancy included new abdominal stretch marks (50%, N = 16), widened abdominoplasty scar (28%, N = 9), abdominal skin excess (37.5%, N = 12), and abdominal bulge (25.8%, N = 8). A new hernia was reported by 2 participants (6.3%). The average abdominal aesthetic severity score was 2.7 (range, 1-8), and only 3 scores were above 5 (9.3%). Two women (6.2%) underwent abdominoplasty revision, and 18 (56.2%) stated they would recommend others to undergo abdominoplasty before pregnancy (56.3%).

Conclusions
This survey shows there is room to reevaluate whether future pregnancy should be considered a relative contraindication for undergoing abdominoplasty.

Level of Evidence: 4
Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies
Authors: Napolitano Francesco , Xu Xiaopeng , Gao Xin 
Published: October 2021

AbstractSARS-CoV-2 caused the first severe pandemic of the digital era. Computational approaches have been ubiquitously used in an attempt to timely and effectively cope with the resulting global health crisis. In order to extensively assess such contribution, we collected, categorized and prioritized over 17 000 COVID-19-related research articles including both peer-reviewed and preprint publications that make a relevant use of computational approaches. Using machine learning methods, we identified six broad application areas i.e. Molecular Pharmacology and Biomarkers, Molecular Virology, Epidemiology, Healthcare, Clinical Medicine and Clinical Imaging. We then used our prioritization model as a guidance through an extensive, systematic review of the most relevant studies. We believe that the remarkable contribution provided by computational applications during the ongoing pandemic motivates additional efforts toward their further development and adoption, with the aim of enhancing preparedness and critical response for current and future emergencies.
BioVAE: a pre-trained latent variable language model for biomedical text mining
Authors: Trieu Hai-Long , Miwa Makoto , Ananiadou Sophia 
Published: October 2021

Abstract

Summary
Large-scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large-scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs. In addition, our model can generate more accurate biomedical sentences than the original OPTIMUS output.

Availability and implementation
Our source code and pre-trained models are freely available: https://github.com/aistairc/BioVAE.

Supplementary information
Supplementary data are available at Bioinformatics online.
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study
Authors: Tadmor Arbel D , Phillips Rob 
Published: October 2021

AbstractMotivationMetagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome.ResultsTo address this problem, we developed a novel clustering approach called ‘metagenomic clustering by reference library’ (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed ‘signatures’, are iteratively clustered in a greedy fashion, retaining at each step the reference genes yielding the lowest E values, and terminating when signatures of remaining reference genes have a minimal overlap. The outcome of this computation is a non-redundant list of reference genes homologous to minimally overlapping sets of contigs, representing potential candidates for gene families present in the metagenome. Unlike metagenomic clustering methods, there is no need for contigs to overlap to be associated with a cluster, enabling MCRL to draw on more information encoded in the metagenome when computing tentative gene families. We demonstrate how MCRL can be used to extract candidate viral gene families from an oral metagenome and an oral virome that otherwise could not be determined using standard approaches. We evaluate the sensitivity, accuracy and robustness of our proposed method for the viral case study and compare it with existing analysis approaches.Availability and implementationhttps://github.com/a-tadmor/MCRL.Supplementary informationSupplementary data are available at Bioinformatics online.
Visual contrast perception in visual snow syndrome reveals abnormal neural gain but not neural noise
Authors: Brooks Cassandra J , Chan Yu Man , Fielding Joanne , White Owen B , Badcock David R , McKendrick Allison M 
Published: October 2021

Abstract
Visual snow syndrome is a neurological condition characterized by a persistent visual disturbance, visual snow, in conjunction with additional visual symptoms. Cortical hyperexcitability is a potential pathophysiological mechanism, which could be explained by increased gain in neural responses to visual input. Alternatively, neural noise in the visual pathway could be abnormally elevated.
We assessed these two potential competing neural mechanisms in our studies of visual contrast perception. Cortical hyperexcitation also occurs in migraine, which commonly co-occurs with visual snow syndrome. Therefore, to determine whether the effect of visual snow syndrome can be distinguished from interictal migraine, we recruited four participant groups: controls, migraine alone, visual snow syndrome alone and visual snow syndrome with migraine. In the first experiment, we estimated internal noise in 20 controls, 21 migraine participants and 32 visual snow syndrome participants (16 with migraine) using a luminance increment detection task. In the second experiment, we estimated neural contrast gain in 21 controls, 22 migraine participants and 35 visual snow syndrome participants (16 with migraine) using tasks assessing sensitivity to changes in contrast from a reference. Contrast gain and sensitivity were measured for the putative parvocellular and ‘on' and ‘off' magnocellular pathways, respectively.
We found that luminance increment thresholds and internal noise estimates were normal in both visual snow syndrome and migraine. Contrast gain measures for putative parvocellular processing and contrast sensitivity for putative off magnocellular processing were abnormally increased in visual snow syndrome, regardless of migraine status.
Therefore, our results indicate that visual snow syndrome is characterized by increased neural contrast gain but not abnormal neural noise within the targeted pathways.
VEGF signalling causes stalls in brain capillaries and reduces cerebral blood flow in Alzheimer’s mice
Authors: Ali Muhammad , Falkenhain Kaja , Njiru Brendah N , Murtaza-Ali Muhammad , Ruiz-Uribe Nancy E , Haft-Javaherian Mohammad , Catchers Stall , Nishimura Nozomi , Schaffer Chris B , Bracko Oliver 
Published: October 2021

Abstract
Increased incidence of stalled capillary blood flow caused by adhesion of leucocytes to the brain microvascular endothelium leads to a 17% reduction of cerebral blood flow and exacerbates short-term memory loss in multiple mouse models of Alzheimer’s disease.
Here, we report that vascular endothelial growth factor (VEGF) signalling at the luminal side of the brain microvasculature plays an integral role in the capillary stalling phenomenon of the APP/PS1 mouse model.
Administration of the anti-mouse VEGF-A164 antibody, an isoform that inhibits blood–brain barrier hyperpermeability, reduced the number of stalled capillaries within an hour of injection, leading to an immediate increase in average capillary blood flow but not capillary diameter. VEGF-A inhibition also reduced the overall endothelial nitric oxide synthase protein concentrations, increased occludin levels and decreased the penetration of circulating Evans Blue dye across the blood–brain barrier into the brain parenchyma, suggesting increased blood–brain barrier integrity. Capillaries prone to neutrophil adhesion after anti-VEGF-A treatment also had lower occludin concentrations than flowing capillaries.
Taken together, our findings demonstrate that VEGF-A signalling in APP/PS1 mice contributes to aberrant endothelial nitric oxide synthase /occludin-associated blood–brain barrier permeability, increases the incidence of capillary stalls, and leads to reductions in cerebral blood flow. Reducing leucocyte adhesion by inhibiting luminal VEGF signalling may provide a novel and well-tolerated strategy for improving brain microvascular blood flow in Alzheimer’s disease patients.
Abnormal whisker-dependent behaviors and altered cortico-hippocampal connectivity in Shank3b−/− mice
Authors: Balasco Luigi , Pagani Marco , Pangrazzi Luca , Chelini Gabriele , Ciancone Chama Alessandra Georgette , Shlosman Evgenia , Mattioni Lorenzo , Galbusera Alberto , Iurilli Giuliano , Provenzano Giovanni , Gozzi Alessandro , Bozzi Yuri 
Published: October 2021

Abstract
Abnormal tactile response is an integral feature of Autism Spectrum Disorders (ASDs), and hypo-responsiveness to tactile stimuli is often associated with the severity of ASDs core symptoms. Patients with Phelan-McDermid syndrome (PMS), caused by mutations in the SHANK3 gene, show ASD-like symptoms associated with aberrant tactile responses. The neural underpinnings of these abnormalities are still poorly understood. Here we investigated, in Shank3b−/− adult mice, the neural substrates of whisker-guided behaviors, a key component of rodents’ interaction with the surrounding environment. We assessed whisker-dependent behaviors in Shank3b−/− adult mice and age-matched controls, using the textured novel object recognition (tNORT) and whisker nuisance (WN) test. Shank3b−/− mice showed deficits in whisker-dependent texture discrimination in tNORT and behavioral hypo-responsiveness to repetitive whisker stimulation in WN. Sensory hypo-responsiveness was accompanied by a significantly reduced activation of the primary somatosensory cortex (S1) and hippocampus, as measured by c-fos mRNA induction, a proxy of neuronal activity following whisker stimulation. Moreover, resting-state fMRI showed a significantly reduced S1-hippocampal connectivity in Shank3b mutants, in the absence of altered connectivity between S1 and other somatosensory areas. Impaired crosstalk between hippocampus and S1 might underlie Shank3b−/− hypo-reactivity to whisker-dependent cues, highlighting a potentially generalizable somatosensory dysfunction in ASD.
Practical Attacks on Reduced-Round 3D and Saturnin
Authors: Hou Tao , Cui Ting , Zhang Jiyan 
Published: October 2021

Abstract3D, an advanced encryption standard-like cipher employed three-dimensional structure, was proposed in 2008. Its recommended number of rounds is 22. Although the longest key recovery attack can currently reach 13 rounds, the complexity of existing attacks for &gt;6 rounds seems to exceed the practically feasible complexity. Thus, a practical attack for 7-round 3D has yet to be developed. Recently, a lightweight block cipher called Saturnin has been selected as a second-round candidate in the National Institute of Standards and Technology standardization for lightweight cryptography. Saturnin also employs a three-dimensional structure and provides high security against quantum and classic attacks. In this paper, we investigate the yoyo attack on these two ciphers. Combined with the meet-in-the-middle technique, we apply the yoyo trick to 7-round 3D and recover the whole 512-bit secret key with $2^{15}$ plaintexts and adaptively chosen ciphertexts and $2^{16.5}$ complexity of full encryptions. To our best knowledge, it is the first practical key recovery attack for 7-round 3D to date. For Saturnin, we found a minor typo in its design report. The designers intended to make a super round containing two S-layers, but one was inadvertently omitted in the algorithm description. We propose a 5-super-round key recovery attack, which is suitable for both one-S-layer version and two-S-layer version. Since the round function of Saturnin has better diffusion, which leads that the meet-in-the-middle technique cannot be applied to this cipher directly. For the one-S-layer version, we address this problem by proposing a new technique called reducing key sets. This technique will fail on the other version, which proves the necessity of containing two S-layers in one-super-round. Finally, our attack requires $2^{39.1}$ plaintext pairs and adaptively chosen ciphertext pairs and $2^{46}$ one-round encryptions.
Pregnancy loss and risk of cardiovascular disease: the Nurses’ Health Study II
Authors: Wang Yi-Xin , Mínguez-Alarcón Lidia , Gaskins Audrey J. , Wang Liang , Ding Ming , Missmer Stacey A. , Rich-Edwards Janet W. , Manson JoAnn E. , Chavarro Jorge E. 
Published: October 2021

AbstractAimsThe aim of this study was to explore the association of pregnancy loss (PL) with the incidence of cardiovascular disease (CVD) and examine the extent to which this relation is mediated by subsequent metabolic disorders.Methods and resultsWe followed 95 465 ever-gravid women participating in the Nurses’ Health Study II between 1993 and 2017. Cox proportional hazards models were used to estimate the hazard ratios (HRs) of CVD, including coronary heart disease (CHD), and stroke, according to the occurrence of PL. A mediation analysis was conducted to explore the intermediating effect of subsequent type 2 diabetes, hypertension, or hypercholesterolaemia. During 2 205 392 person-years of follow-up (mean 23.10 years), 2225 (2.3%) incident CVD cases were documented. After adjusting for confounding factors, PL was associated with an HR of 1.21 [95% confidence interval (CI) 1.10–1.33] for CVD during follow-up. A similar association was observed for CHD (HR 1.20; 95% CI 1.07–1.35) and stroke (HR 1.23; 95% CI 1.04–1.44). The risk of CVD increased with the number of PLs [HR 1.18 (95% CI 1.06–1.31) for 1 and 1.34 (95% CI 1.13–1.59) for ≥2 times] and was greater for PL occurring early in reproductive lifespan [HR 1.40 (95% CI 1.21–1.62) for age ≤23 years, 1.25 (95% CI 1.09–1.43) for age 24–29 years, and 1.03 (95% CI 0.88–1.19) for age ≥30 years]. Hypertension, hypercholesterolaemia, and type 2 diabetes all explained &lt;1.80% of the association between PL and CVD.ConclusionPL was associated with a greater CVD risk, independently of subsequent development of metabolic disorders.
Angiographic and Clinical Predictors of Mild Non-Culprit Coronary Lesion Progression in Acute ST-Elevation Myocardial Infarction Managed by Primary Percutaneous Coronary Intervention: A Prospective Cohort Study
Authors: El-Awady Waleed Salem , Masoud Masoud Mohamed , Elmenshawy Mahmoud Diaa , Wageeh Shaimaa , Shehata Islam Elsayed 
Published: October 2021

Abstract

Aims
To identify the angiographic and clinical predictors of mild non-culprit coronary lesion (NCCL) progression in acute ST-elevation myocardial Infarction (STEMI).

Methods and Results
The present prospective cohort study evaluated 200 patients with acute STEMI underwent primary percutaneous coronary intervention (PPCI) (either PPCI or pharmaco-invasive PCI) divided into2groups based on whether the clinically driven non culprit lesion PCI existed or not into: Control group-1: 157 patients(78.5%) with non-progressed non culprit lesion (no additional PCI to the non-culprit lesion) and Study group-2: 43 patients(21.5%) with clinically driven non culprit lesion PCI (underwent additional PCI to progressed non-culprit lesions).
Our study end point was the clinically driven non culprit lesion PCI (additional PCI to progressed non-culprit lesions). Asymptomatic patients were followed up by exercise ECG at 12 months and myocardial perfusion stress testing at 24 months.
Multivariate regression analysis showed that the strongest independent predictor for progression of mild NCCL was complex morphology of culprit lesion (p &lt; 0.001).
Finally, a receiver operating characteristic (ROC) curve was performed to assess a cutoff value for predictors for NCCL progression after PPCI in Patients with STEMI.

Conclusions
Our novel angiographic independent predictor was complex morphology of culprit lesion. And our novel clinical independent predictors were CRP cutoff more than 7.05mg/l, peak cardiac troponin I value cutoff more than 27.5 ng/ml, and age cutoff less than 57.5 years, could be used for early prediction of mild NCCL progression after PPCI for acute STEMI patients. This could be used for early diagnosis to avoid repeated PCI and proper management for better outcomes.
Study of Global Longitudinal Strain and N Terminal Pro BNP as Predictors of Outcome in Acute ST-Segment Elevation Myocardial Infarction Patients Undergoing Primary Percutaneous Coronary Interventions
Authors: Magdy Gehan , El-tahhan Salah , Ahmed Fatema Al-zahraa , Hasanein Mahmoud 
Published: October 2021

Abstract

Background
Risk stratification of patients presenting with Acute ST-segment elevation myocardial infarction (STEMI) is of greatest importance as it may help to start early therapeutic procedures that could improve the outcome. Our study is designed to assess the prognostic value of N-terminal pro brain natriuretic peptide (NT-proBNP) and global longitudinal strain (GLS) of the left ventricle measured by 2 dimensional speckle tracking echocardiography (STE) in patients presenting with acute STEMI and treated by primary percutaneous coronary interventions (PPCI).

Patients and Methods
the study prospectively included 100 patients(their age 55.69 ±8.70 years, and 75% were males)presented to our institute (from march 2019 to December 2019) by acute STEMI and treated by PPCI within 12 hour of the onset of chest pain, excluding those with left ventricular ejection fraction ≤40%, left bundle branch block, atrial fibrillation, significant valvular disease, patients with non cardiac causes that interfere with NT-Pro BNP level eg.(renal failure, chronic obstructive pulmonary disease, acute respiratory distress syndrome, pneumonia, liver cirrhosis, hyperthyroidism, and on those on chemotherapy). All patients were subjected to peripheral samples of plasma for analysis of NT- proBNP and 2dimentional STE for calculation of the GLS, both were done within 24 hours of admission, and follow up of all patients were done for 6 months to assess outcome.

Results
The mean GLS for all patients was -10.41 ± 3.59%, and the mean NT- proBNP (2090.1 ± 1375.8) pg/ml. 20 patients (20%) had adverse events during the 6 month follow up including (1(1%) had all cause mortality, 2(2%) had cardiovascular mortality, 6(6%) had reinfarction, 11(11%) had heart failure hospitalization, and according to ROC curve analysis the GLS cut off value of (≤- 8) was able to discriminate patients with adverse outcome (AUC=0.971, p value&lt;0.001,CI=“0.940-1.001”,sensitivity=90%, specificity=91.67%, PPV=78.3%, NPV=96.5%) (figure 1, 2), also according to ROC curve analysis NT-pro BNP cut off value of (&gt;2318pg/ml) was able to discriminate patients with adverse outcome (AUC=0.802,p value&lt;0.001, CI=“0.685-0.920”, sensitivity=89%, specificity=75%, PPV=51.6%, NPV=91.8%) (Figure 3, 4).
There was a statistically significant inverse correlation between GLS and NT- ProBNP (r=-0.492*, p value&lt;0.001). In multivariate COX regression analysis for the parameters affecting the outcome, GLS was shown to be the most significant parameter in the prediction of reaching adverse outcome in STEMI patients (p value=0.003, OR “95%C.I”= 0.721 (0.580–0.896).

Conclusions
our study concluded that both GLS and NT-proBNP are significantly related to adverse outcome with more superiority of the GLS to NT- pro BNP in adverse outcome prediction in patients acute STEMI treated by PPCI.