bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of secondary electron intensities for dopant profiling in ion implanted semiconductors: a correlative study combining SE, SIMS and ECV methods
Authors: Shyam Kumar C N , Tabean Saba , Morisset Audrey , Wyss Philippe , Lehmann Mario , Haug Franz-Josef , Jeangros Quentin , Hessler-Wyser Aïcha , Valle Nathalie , Wirtz Tom , Eswara Santhana 
Published: June 2021

Abstract
This study evaluates the secondary electron (SE) dopant contrast in scanning electron microscopy (SEM) and helium ion microscopy (HIM) on boron implanted silicon sample. Complementary techniques like secondary ion mass spectrometry and electrochemical capacitance voltage (ECV) measurements are used to understand the dopant profile and active dopant distribution before and after a thermal firing, a step carried out to remove implantation damage and to electrically activate the implanted boron. Thermal firing resulted in an activation efficiency of 33%. HIM showed higher contrast than SEM having more defined peak with a lower background contribution. Variations in dopant concentration near the peak maximum were observed in ECV measurements, which was not observed in the intensity profiles from both SEM and HIM. This study demonstrates the effectiveness of SE dopant profiling as a quick tool to map the electrically active dopant concentrations even in far-from-equilibrium materials such as ion implanted samples.
From sub- to superdiffusion: fractional Brownian motion of membraneless organelles in early C. elegans embryos
Authors: Benelli Rebecca , Weiss Matthias 
Published: June 2021

Abstract
Fractional Brownian motion (FBM) is a prevalent Gaussian stochastic process that has frequently been linked to subdiffusive motion in complex fluids, e.g. inside living cells. In contrast, examples for a superdiffusive FBM in complex fluids are sparse, and a covering of all FBM regimes in the same sample is basically lacking. Here we show that membraneless organelles in the single-cell state of C. elegans embryos, so-called p-granules, constitute an experimental example in which the whole range of FBM processes, from the sub- to the superdiffusive regime, can be observed. The majority of p-granules is subdiffusive, featuring an antipersistent velocity autocorrelation function (VACF). A smaller fraction of trajectories shows normal diffusion or even superdiffusion with a persistent VACF. For all trajectories, from sub- to superdiffusive, the VACF, its characteristic values, and the trajectories’ power-spectral density are well matched by FBM predictions. Moreover, static localization errors, a frequent problem in single-particle tracking experiments, are shown to not affect the conclusion that p-granule motion is best described by FBM from the sub- to the superdiffusive regime.
Suspended nanocrystalline diamond ridge waveguides designed for the mid-infrared
Authors: Rahmati A T , Mashanovich G Z , Nezhad M P 
Published: June 2021

Abstract
A comprehensive study and design of air-clad suspended ridge diamond waveguides for operation across the 2.5–16 µm spectral range is presented, specifically targeting nanocrystalline diamond (NCD) thin films directly grown on silicon substrates. Three film thicknesses of 520, 1000 and 2000 nm are considered, to cover overlapping sub-bands of 2.5–5, 4–9 and 8–16 µm, respectively. Within each sub-band, the waveguide dimensions for single mode quasi-TE operation are found and the waveguide material losses and bending losses are estimated at each design point. In addition, in each case the minimum required undercut depth and etch hole placement for optical isolation of the waveguide mode from the silicon substrate is also quantified. We also estimate the losses associated with scattering from surface roughness, which is an unavoidable byproduct of the NCD thin film growth process. Our results indicate that despite the relatively low film thickness-to-wavelength ratio, mechanically stable waveguides with good optical confinement and low material and bending losses can be realised to cover the full 2.5–16 µm range. In addition, scattering loss estimations predict a drastic drop in roughness-induced scattering losses above 6 µm, even for relatively rough films. In addition to highlighting the utility of suspended NCD as a versatile platform for mid-infrared integrated photonics, the approaches and results presented here can be used to inform the design of suspended air-clad waveguides in other material platforms.
Self-imaging vectorial singularity networks in 3d structured light fields
Authors: Droop Ramon , Otte Eileen , Denz Cornelia 
Published: June 2021

Abstract
We transfer on-demand structuring of three-dimensional scalar amplitude and phase patterns to polarization-structured, vectorial light fields and its singularities. Our approach allows inheriting non-diffracting as well as self-imaging propagation properties to tailored singular ellipse fields, including self-replicating amplitude, polarization, and singularity configurations. It is experimentally realized by amplitude, phase and polarization modulation of the angular spectrum of the light field. We demonstrate the customization of complex singularity formations embedded in three-dimensionally (3d) tailored vectorial field. Our findings show that embedded networks of polarization singularities can be customized to propagate in a robust way along curved trajectories, creating and annihilating during propagation. This 3d structuring of vectorial singular light fields opens new perspectives for in-depth singularity studies and for advancing applications as optical micro-manipulation and material machining.
Magnetic sensors-A review and recent technologies
Authors: Khan Mohammed Asadullah , Sun Jian , Li Bodong , Przybysz Alexander , Kosel Jürgen 
Published: June 2021

Abstract
Magnetic field sensors are an integral part of many industrial and biomedical applications, and their utilization continues to grow at a high rate. The development is driven both by new use cases and demand like internet of things as well as by new technologies and capabilities like flexible and stretchable devices. Magnetic field sensors exploit different physical principles for their operation, resulting in different specifications with respect to sensitivity, linearity, field range, power consumption, costs etc. In this review, we will focus on solid state magnetic field sensors that enable miniaturization and are suitable for integrated approaches to satisfy the needs of growing application areas like biosensors, ubiquitous sensor networks, wearables, smart things etc. Such applications require a high sensitivity, low power consumption, flexible substrates and miniaturization. Hence, the sensor types covered in this review are Hall Effect, Giant Magnetoresistance, Tunnel Magnetoresistance, Anisotropic Magnetoresistance and Giant Magnetoimpedance.
BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning
Authors: Cheng Jun , Bendjama Kaïdre , Rittner Karola , Malone Brandon 
Published: June 2021

AbstractMotivationIncreasingly comprehensive characterization of cancer-associated genetic alterations has paved the way for the development of highly specific therapeutic vaccines. Predicting precisely the binding and presentation of peptides to major histocompatibility complex (MHC) alleles is an important step toward such therapies. Recent data suggest that presentation of both class I and II epitopes are critical for the induction of a sustained effective immune response. However, the prediction performance for MHC class II has been limited compared to class I.ResultsWe present a transformer neural network model which leverages self-supervised pretraining from a large corpus of protein sequences. We also propose a multiple instance learning (MIL) framework to deconvolve mass spectrometry data where multiple potential MHC alleles may have presented each peptide. We show that pretraining boosted the performance for these tasks. Combining pretraining and the novel MIL approach, our model outperforms state-of-the-art models based on peptide and MHC sequence only for both binding and cell surface presentation predictions.Availability and implementationOur source code is available at https://github.com/s6juncheng/BERTMHC under a noncommercial license. A webserver is available at https://bertmhc.privacy.nlehd.de/Supplementary informationSupplementary data are available at Bioinformatics online.
TIGA: target illumination GWAS analytics
Authors: Yang Jeremy J , Grissa Dhouha , Lambert Christophe G , Bologa Cristian G , Mathias Stephen L , Waller Anna , Wild David J , Jensen Lars Juhl , Oprea Tudor I 
Published: June 2021

Abstract

Motivation
Genome-wide association studies can reveal important genotype–phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study.

Results
Here, we describe rational ranking, filtering and interpretation of inferred gene–trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene–trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene–trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.
This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists.

Availability and implementation
Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Comparison of laparoscopic versus robot-assisted versus transanal total mesorectal excision surgery for rectal cancer: a retrospective propensity score-matched cohort study of short-term outcomes
Authors: Hol J C , Burghgraef T A , Rutgers M L W , Crolla R M P H , van Geloven N A W , Hompes R , Leijtens J W A , Polat F , Pronk A , Smits A B , Tuynman J B , Verdaasdonk E G G , Consten E C J , Sietses C 
Published: June 2021

Abstract

Background
Laparoscopic total mesorectal excision (TME) surgery for rectal cancer has important technical limitations. Robot-assisted and transanal TME (TaTME) may overcome these limitations, potentially leading to lower conversion rates and reduced morbidity. However, comparative data between the three approaches are lacking. The aim of this study was to compare short-term outcomes for laparoscopic TME, robot-assisted TME and TaTME in expert centres.

Methods
Patients undergoing rectal cancer surgery between 2015 and 2017 in expert centres for laparoscopic, robot-assisted or TaTME were included. Outcomes for TME surgery performed by the specialized technique in the expert centres were compared after propensity score matching. The primary outcome was conversion rate. Secondary outcomes were morbidity and pathological outcomes.

Results
A total of 1078 patients were included. In rectal cancer surgery in general, the overall rate of primary anastomosis was 39.4, 61.9 and 61.9 per cent in laparoscopic, robot-assisted and TaTME centres respectively (P &lt; 0.001). For specialized techniques in expert centres excluding abdominoperineal resection (APR), the rate of primary anastomosis was 66.7 per cent in laparoscopic, 89.8 per cent in robot-assisted and 84.3 per cent in TaTME (P &lt; 0.001). Conversion rates were 3.7 , 4.6 and 1.9 per cent in laparoscopic, robot-assisted and TaTME respectively (P = 0.134). The number of incomplete specimens, circumferential resection margin involvement rate and morbidity rates did not differ.

Conclusion
In the minimally invasive treatment of rectal cancer more primary anastomoses are created in robotic and TaTME expert centres.
Subacromial spacer implantation: an alternative to arthroscopic superior capsular reconstruction. A systematic review
Authors: Osti Leonardo , Milani Lorenzo , Ferrari Silvana , Maffulli Nicola 
Published: June 2021

Abstract

Introduction
This systematic review evaluated and compared the use of a subacromial spacer implantation (SSI) with arthroscopic superior capsular repair (ASCR) in the management of massive irreparable rotator cuff tears (MIRCTs) with an assessment of clinical and imaging outcomes.

Sources of data
This systematic review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched in PubMed, Medline and Embase database literature using the keywords ‘subacromial spacer’, ‘subacromial balloon’, ‘subacromial device’, ‘arthroscopy’, ‘superior capsular reconstruction’, ‘irreparable rotator cuff tears’, ‘satisfaction’ and ‘quality of life’.

Areas of agreement
We included a total of 29 articles (14 about SSI and 15 about ASCR) dealing with outcomes, satisfaction and patients’ quality of life.

Areas of controversy
The use of a subacromial spacer showed similar results in terms of patients’ satisfaction and quality of life when compared with ASCR.

Growing points
SSI can be implanted quickly and has a low complication rate. It can therefore be considered a good alternative for the management of MIRCTs.

Areas timely for developing research
The subacromial spacer is a biodegradable implant easily implanted at arthroscopy. It can lead good clinical and imaging outcomes in MIRCTs. Similarly, ASCR can be performed with either an autograft or synthetic allograft transplantation, with satisfactory results. Long-term prospective studies are needed to compare SSI and ASCR to verify their effectiveness.
Interactive rather than independent effect of APOE and sex potentiates tau deposition in women
Authors: Wang Yi-Ting T , Pascoal Tharick A , Therriault Joseph , Kang Min Su , Benedet Andréa L , Savard Melissa , Tissot Cécile , Lussier Firoza Z , Arias Jaime Fernandez , Mathotaarachchi Sulantha , Rajah Maria Natasha , Gauthier Serge , Rosa-Neto Pedro ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: June 2021

Abstract
The apolipoprotein E gene (APOE) is the most important genetic risk factor for sporadic Alzheimer disease, with the ε4 allele being associated with increased cerebral amyloid-β and tau pathologies. Although APOE has been suggested to have a stronger effect in women as compared to men, there is a lack of comprehensive assessment on how the interactive effect of APOE and sex modulates regional vulnerability to tau accumulation. We previously have shown the regional vulnerability to the interactive effect of tau and APOE, yet the sex difference was not specifically addressed. In this study, we leveraged PET imaging data from the Translational Biomarkers in Aging and Dementia cohort at McGill University Research Centre for Studies in Aging to elucidate the APOE-by-sex interactive effect on tau burden. We hypothesized sex-dependent regional vulnerability to tau deposition. PET radiopharmaceuticals [18F]AZD4694 and [18F]MK6240 were used to assess amyloid-β and tau level respectively in 277 subjects from the Translational Biomarkers in Aging and Dementia cohort. We found that the interaction between APOE and sex, rather than their independent main effects, was associated with abnormal tau accumulation in medial temporal regions. Specifically, we found that female APOEε4 carriers showed significantly higher tau burden in early tau deposition regions including the hippocampus, entorhinal and parahippocampal cortices, after accounting for age, educational attainment, clinical diagnosis and neocortical amyloid load. We replicated these findings in 221 subjects from the Alzheimer’s Disease Neuroimaging Initiative cohort, in which a different tau-PET radioligand, [18F]flortaucipir, was used to assess tau burden. In conclusion, this study provides evidence from two cohort studies that interactive rather than independent effect of APOE and sex potentiates early tau deposition in women. Our results have important implications for clinical trials and practice, which should take into consideration both APOEε4 carriage status and sex for identifying individuals with the highest probability of developing tau accumulation and clinical progression.
LncRNA PCBP1-AS1 correlated with the functional states of cancer cells and inhibited lung adenocarcinoma metastasis by suppressing the EMT progression
Authors: Li Zhihua , Pan Cheng , Wang Zhibo , Deng Xiaheng , Zhu Quan , Wu Weibing , Chen Liang 
Published: June 2021

Abstract
The development of single-cell RNA sequencing (scRNA-seq) provided us an unprecedented chance to identify novel oncogenes or tumor suppressors at single-cell resolution. Long non-coding RNAs (lncRNAs) related to the functional states of cancer cells might play vital roles in the progression of lung adenocarcinoma (LUAD). In this study, lncRNAs that were associated with the functional states of LUAD cells identified in scRNA-seq studies were screened based on the CancerSEA database. Differential gene expression analysis and survival analysis were performed in TCGA, GEO and our JSPH databases. Finally, transwell and tail vein metastasis assays were used to reveal the functions of our identified novel prognostic lncRNAs. A total of 849 lncRNAs were initially identified. Among them, 11 lncRNAs were found significantly associated with LUAD prognosis in the TCGA database. Two of them (PCBP1-AS1 and ZSCAN16-AS1) were further validated in independent GEO datasets. ScRNA-seq analysis showed that PCBP1-AS1 and ZSCAN16-AS1 were significantly negatively correlated with most of the functional states of LUAD cells, especially with metastasis. Functionally, PCBP1-AS1 was aberrantly downregulated in LUAD cells and tumor tissues. Knockdown of PCBP1-AS1 significantly promoted the migration and invasion of LUAD cells. Consistently, PCBP1-AS1 overexpression suppressed the metastasis of LUAD in vitro and in vivo. Besides, PCBP1-AS1 inhibition induced decreased E-cadherin expression and increased N-cadherin, Vimentin and Snail expression. In conclusion, PCBP1-AS1 could suppress the metastasis of LUAD by targeting the epithelial–mesenchymal transition pathway and might serve as a prognostic biomarker and a potential therapeutic target of LUAD.
Adenosine A2A Receptors Contribute to the Radial Migration of Cortical Projection Neurons through the Regulation of Neuronal Polarization and Axon Formation
Authors: Alçada-Morais Sofia , Gonçalves Nélio , Moreno-Juan Verónica , Andres Belén , Ferreira Sofia , Marques Joana M , Magalhães Joana , Rocha João M M , Xu Xinli , Partidário Matilde , Cunha Rodrigo A , López-Bendito Guillermina , Rodrigues Ricardo J 
Published: June 2021

Abstract
Cortical interneurons born in the subpallium reach the cortex through tangential migration, whereas pyramidal cells reach their final position by radial migration. Purinergic signaling via P2Y1 receptors controls the migration of intermediate precursor cells from the ventricular zone to the subventricular zone. It was also reported that the blockade of A2A receptors (A2AR) controls the tangential migration of somatostatin+ interneurons. Here we found that A2AR control radial migration of cortical projection neurons. In A2AR-knockout (KO) mouse embryos or naïve mouse embryos exposed to an A2AR antagonist, we observed an accumulation of early-born migrating neurons in the lower intermediate zone at late embryogenesis. In utero knockdown of A2AR also caused an accumulation of neurons at the lower intermediate zone before birth. This entails the presently identified ability of A2AR to promote multipolar–bipolar transition and axon formation, critical for the transition of migrating neurons from the intermediate zone to the cortical plate. This effect seems to require extracellular ATP-derived adenosine since a similar accumulation of neurons at the lower intermediate zone was observed in mice lacking ecto-5′-nucleotidase (CD73-KO). These findings frame adenosine as a fine-tune regulator of the wiring of cortical inhibitory and excitatory networks.
Recovery From COVID-19-Related Olfactory Disorders and Quality of Life: Insights From an Observational Online Study
Authors: Ferdenzi Camille , Bousquet Christophe , Aguera Pierre-Emmanuel , Dantec Morgane , Daudé Christelle , Fornoni Lesly , Fournel Arnaud , Kassan Aurélien , Mantel Marylou , Moranges Maëlle , Moussy Erwan , Richard Ortegón Stéphane , Rouby Catherine , Bensafi Moustafa 
Published: June 2021

Abstract
Although olfactory disorders (OD) are among the most significant symptoms of COVID-19, recovery time from COVID-19-related OD and their consequences on the quality of life remain poorly documented. We investigated the characteristics and behavioral consequences of COVID-19-related OD using a large-scale study involving 3111 French respondents (78% women) to an online questionnaire over a period of 9 months covering different epidemic waves (from 8 April 2020 to 13 January 2021). In the patients who subjectively recovered from COVID-19-related OD (N = 609), recovery occurred on average after 16 days and most of the time within 1 month (“normal” recovery range); 49 subjectively recovered in 1–2.5 months, and several cases took up to 6.5 months. Among the patients with ongoing OD (N = 2502), 974 were outside the “normal” recovery range (persistent OD) and reported OD for 1–10 months. Developing a persistent OD was more likely with increasing age and in women and was more often associated with parosmia and phantosmia. The deleterious impact of COVID-19-related OD on the quality of life was significantly aggravated by OD duration and was more pronounced in women. Because persistent OD is not infrequent after COVID-19, has deleterious consequences on the quality of life, and receives few solutions from the health practitioners, it would be beneficial to implement screening and treatment programs to minimize the long-term behavioral consequences of COVID-19-related OD.
Increased Household Secondary Attacks Rates With Variant of Concern Severe Acute Respiratory Syndrome Coronavirus 2 Index Cases
Authors: Buchan Sarah A , Tibebu Semra , Daneman Nick , Whelan Michael , Vanniyasingam Thuva , Murti Michelle , Brown Kevin A 
Published: June 2021

Abstract
We compared secondary attack rates in households with B.1.1.7 variant of concern (VOC) versus non-VOC index cases in a matched cohort in Ontario, Canada. The secondary attack rate for VOC index cases was 1.31 times higher than non-VOC index cases. This increase was particularly accentuated for asymptomatic or presymptomatic index cases.