bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bilateral Anterolateral Thigh Myocutaneous Flaps for Giant Complex Chest Wall Reconstruction
Authors: Song Dajiang , Li Juanjuan , Pafitanis Georgios , Li Zan 
Published: August 2021

BackgroundExtensive reconstruction of complex full-thickness chest wall oncological defects is challenging. Bilateral free anterolateral thigh (ALT) myocutaneous flap transfer for the complex reconstruction of a large area of the chest wall is discussed.Materials and MethodsWe reported a single unit's experience in 1-staged multilayered reconstruction of large full-thickness chest wall defects in 22 patients (16 primary chest wall tumor cases, 5 locally advanced breast cancer cases, and 1 osteoradionecrosis case) treated between 2011 and 2018. Bilateral ALT myocutaneous flaps together with traditional cement implant or unmovable/movable joint conformable titanium struts were used for chest wall reconstruction. The anatomical characteristics of pedicle origin and pattern of the venae comitantes of the ALT myocutaneous flap, recipient vessels, and anastomosis patterns were described.ResultsBilateral ALT myocutaneous flaps were used for soft tissue reconstruction in 22 cases. Different methods of flap harvesting and vascular anastomosis were selected as needed. No vein grafts or arteriovenous loops were required. We observed 3 vascular patterns of the flap pedicle, including 1 oblique branch and descending branch (59.1%, n = 26), 2 single descending branch (9.1%, n = 4), and 3 double branches of the descending branch (31.8%, n = 14). The flap was harvested pedicled with solely the oblique branch in 7 (15.9%) cases, solely the descending branch in 28 (63.6%) cases to minimize the donor site morbidity, and pedicled with the oblique and descending branch in 9 (20.5%) cases to achieve multiple vascular anastomosis choices. Stable skeletal reconstructions were achieved using traditional cement implant (13.6%, n = 3) or conformable titanium struts (86.4%, n = 19), with good fixation strength. Complication risk was low. An algorithmic approach to management is presented and recommended.ConclusionVarious forms of bilateral ALT myocutaneous flap transfer with different skeletal reconstruction presents as a reliable treatment for patients with large full-thickness chest wall defects. Anatomical variations in the pedicle and pattern of venae comitantes of the ALT myocutaneous flap are reported. In some challenging cases, finding the vessels in the recipient area is difficult. The clinical significance of each vascular pattern is delineated, and surgical technical considerations are discussed on the basis of the recipient area requirements and types of a flap's vascular anatomy.
Patient reported outcomes 6 to 12 months after interpersonal violence: A multicenter cohort study
Authors: Castillo-Angeles Manuel , Herrera-Escobar Juan P. , Toppo Alexander , Sanchez Sabrina E. , Kaafarani Haytham M. , Salim Ali , Haider Adil H. , Nehra Deepika 
Published: August 2021

PURPOSE
Violence continues to be a significant public health burden, but little is known about the long-term outcomes of these patients. Our goal was to determine the impact of violence-related trauma on long-term functional and psychosocial outcomes.

METHODS
We identified trauma patients with moderate to severe injuries (Injury Severity Score, ≥9) treated at one of three level 1 trauma centers. These patients were asked to complete a survey over the phone between 6 and 12 months after injury evaluating both functional and psychosocial outcomes (12-item Short Form Survey, Trauma Quality of Life, posttraumatic stress disorder [PTSD] screen, chronic pain, return to work). Patients were classified as having suffered a violent injury if the mechanism of injury was a stab, gunshot, or assault. Self-inflicted wounds were excluded. Adjusted logistic regression models were built to determine the association between a violent mechanism of injury and long-term outcomes.

RESULTS
A total of 1,050 moderate to severely injured patients were successfully followed, of whom 176 (16.8%) were victims of violence. For the victims of violence, mean age was 34.4 years (SD, 12.5 years), 85% were male, and 57.5% were Black; 30.7% reported newly needing help with at least one activity of daily living after the violence-related event. Fifty-nine (49.2%) of 120 patients who were working before their injury had not yet returned to work; 47.1% screened positive for PTSD, and 52.3% reported chronic pain. On multivariate analysis, a violent mechanism was significantly associated with PTSD (odds ratio, 2.57; 95% confidence interval, 1.59–4.17; p < 0.001) but not associated with chronic pain, return to work, or functional outcomes.

CONCLUSION
The physical and mental health burden after violence-related trauma is not insignificant. Further work is needed to identify intervention strategies and social support systems that may be beneficial to reduce this burden.

LEVEL OF EVIDENCE
Prognostic and epidemiological, level III.
Therapeutic strategies for C9orf72 amyotrophic lateral sclerosis and frontotemporal dementia
Authors: Hautbergue Guillaume M. , Cleary John D. , Guo Shu , Ranum Laura P.W. 
Published: August 2021

Purpose of review
An intronic G4C2 expansion mutation in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). Although there are currently no treatments for this insidious, fatal disease, intense research has led to promising therapeutic strategies, which will be discussed here.

Recent findings
Therapeutic strategies for C9-ALS/FTD have primarily focused on reducing the toxic effects of mutant expansion RNAs or the dipeptide repeat proteins (DPRs). The pathogenic effects of G4C2 expansion transcripts have been targeted using approaches aimed at promoting their degradation, inhibiting nuclear export or silencing transcription. Other promising strategies include immunotherapy to reduce the DPRs themselves, reducing RAN translation, removing the repeats using DNA or RNA editing and manipulation of downstream disease-altered stress granule pathways. Finally, understanding the molecular triggers that lead to pheno-conversion may lead to opportunities that can delay symptomatic disease onset.

Summary
A large body of evidence implicates RAN-translated DPRs as a main driver of C9-ALS/FTD. Promising therapeutic strategies for these devastating diseases are being rapidly developed with several approaches already in or approaching clinical trials.
On the philosophical, cognitive and mathematical foundations of symbiotic autonomous systems
Authors: Wang Yingxu , Karray Fakhri , Kwong Sam , Plataniotis Konstantinos N. , Leung Henry , Hou Ming  , Tunstel Edward , Rudas Imre J. , Trajkovic Ljiljana  , Kaynak Okyay , Kacprzyk Janusz  , Zhou Mengchu , Smith Michael H. , Chen Philip , Patel Shushma 
Published: August 2021

Symbiotic autonomous systems (SAS) are advanced intelligent and cognitive systems that exhibit autonomous collective intelligence enabled by coherent symbiosis of human–machine interactions in hybrid societies. Basic research in the emerging field of SAS has triggered advanced general-AI technologies that either function without human intervention or synergize humans and intelligent machines in coherent cognitive systems. This work presents a theoretical framework of SAS underpinned by the latest advances in intelligence, cognition, computer, and system sciences. SAS are characterized by the composition of autonomous and symbiotic systems that adopt bio-brain-social-inspired and heterogeneously synergized structures and autonomous behaviours. This paper explores the cognitive and mathematical foundations of SAS. The challenges to seamless human–machine interactions in a hybrid environment are addressed. SAS-based collective intelligence is explored in order to augment human capability by autonomous machine intelligence towards the next generation of general AI, cognitive computers, and trustworthy mission-critical intelligent systems. Emerging paradigms and engineering applications of SAS are elaborated via autonomous knowledge learning systems that symbiotically work between humans and cognitive robots.This article is part of the theme issue ‘Towards symbiotic autonomous systems'.
Engineering human-focused Industrial Cyber-Physical Systems in Industry 4.0 context
Authors: Walter Colombo Armando , Karnouskos Stamatis , Hanisch Christoph 
Published: August 2021

The world is increasingly interconnected, and this can also be seen in industry, where an ecosystem of digitalized assets, and humans with appropriate digital interfaces, constantly interact with each other. Digital transformation efforts in the industry rely on Industrial Cyber-Physical Systems that are driven by service-based cooperation among humans and digitalized industrial assets. This implies a radical paradigm change in their engineering and operation, which is focused on the symbiosis of digitalized assets and humans that cohabit a collaboration-driven industrial ecosystem. This work discusses how a digital transformation can effectively be achieved in an industrial ecosystem via a digitalization process performed along the three dimensions of the Reference Architecture Model for Industry 4.0, facilitated by the specification, development and implementation of an Asset Administration Shell. The discussion focus is put on humans and how the digitally transformed industrial environments empower her/his capabilities and interactions. It is also critically pointed out how one should go beyond technology and consider additional aspects. Therefore, it is argued that human-centred efforts in Industry 4.0 (I4.0) should be seen in the larger context of sustainability and circular economy in order to properly consider the interplay of the involved socio-technical dimensions.
This article is part of the theme issue ‘Towards symbiotic autonomous systems’.
Comparison of Wild Type DNA Sequence of Spike Protein from SARS-CoV-2 with Optimized Sequence on The Induction of Protective Responses Against SARS-Cov-2 Challenge in Mouse Model
Authors: Jiang Sheng , Wu Shuting , Zhao Gan , He Yue , Hou Jiawang , Ding Yuan , Bao Linlin , Liu Jiangning , Qin Chuan , Cheng Alex , Jiang Brian , Wu John , Yan Jian , Patel Ami , Weiner David B. , Humeau Laurent , Broderick Kate , Wang Bin 
Published: August 2021

ABSTRACTCOVID-19 caused by SARS-CoV-2 has been spreading worldwide. To date, several vaccine candidates moved into EUA or CA applications. Although DNA vaccine is on phase III clinical trial, it is a promised technology platform with many advantages. Here, we showed that the pGX9501 DNA vaccine encoded the spike full-length protein-induced strong humoral and cellular immune responses in mice with higher neutralizing antibodies, blocking the hACE2-RBD binding against live virus infection in vitro. Importantly, higher levels of IFN-γ expression in CD8+ and CD4+ T cell and specific cytotoxic lymphocyte (CTL) killings effect were also observed in the pGX9501-immunized group. It provided subsequent protection against virus challenges in the hACE2 transgenic mouse model. Overall, pGX9501 was a promising DNA vaccine candidate against COVID-19, inducing strong humoral immunity and cellular immunity that contributed to the vaccine’s protective effects.
Third Generation Cytogenetic Analysis (TGCA): diagnostic application of long-read sequencing
Authors: Magini Pamela , Mingrino Alessandra , Gega Barbara , Mattei Gianluca , Semeraro Roberto , Bolognini Davide , Mongelli Patrizia , Desiderio Laura , Pittalis Maria Carla , Pippucci Tommaso , Magi Alberto 
Published: August 2021

AbstractUnbalanced Structural Variants (uSVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from three to fifteen days. Long read sequencing approaches, such as Oxford Nanopore Technologies (ONT), have the ability to reduce time to results for the detection of uSVs with the same resolution of current state-of-the-art diagnostic tests.Here we compared ONT to molecular karyotyping for the detection of pathogenic uSVs of 7 patients with previously diagnosed causative CNVs of different sizes and allelic fractions. Larger chromosomal anomalies included trisomy 21 and mosaic tetrasomy 12p. Among smaller CNVs we tested two reciprocal genomic imbalances in 7q11.23 (1.367 Mb), a 170 kb deletion encompassing NRXN1 and mosaic 6q27 (1.231 Mb) and 2q23.1 (408 kb) deletions. DNA libraries were prepared following ONT standard protocols and sequenced on the GridION device for 48 h. Data generated during runs were analysed in online mode, using NanoGLADIATOR.We were capable to identify all pathogenic CNVs with detection time inversely proportional to size and allelic fraction. Aneuploidies were called after only 30 minutes of sequencing, while 30 hours were needed to call CNVs < 500 kb also in mosaic state (44%). These results demonstrate the clinical utility of our approach that allows the molecular diagnosis of genomic disorders within a 30 minutes to 30 hours time-frame.
Estimation of effective concentrations enforced by complex linker architectures from conformational ensembles
Authors: Kjaergaard Magnus 
Published: August 2021

AbstractProteins and protein assemblies often tether interaction partners to strengthen interactions, to regulate activity through auto-inhibition or -activation, or to boost enzyme catalysis. Tethered reactions are regulated by the architecture of the tether, which defines an effective concentration of the interactor. Effective concentrations can be estimated theoretically for simple linkers via polymer models, but there is currently no general method for estimating effective concentrations for complex linker architectures consisting of both flexible and folded domains. We describe how effective concentrations can be estimated computationally for any protein linker architecture by defining a realistic conformational ensemble. We benchmark against prediction from a worm-like chain and values measured by competition experiments and find minor differences likely due to excluded volume effects. Systematic variation of the properties of flexible and folded segments show that the effective concentration is mainly determined by the combination of the total length of flexible segments and the distance between the termini of the folded domains. We show that a folded domain in a disordered linker can increase the effective concentration beyond what can be achieved by a fully disordered linker by focusing the end-to-end distance at the appropriate spacing. This suggests that complex linker architecture may have advantages over simple flexible linkers and emphasizes that annotation as a linker should depend on the molecular context.
Antiviral face mask functionalized with solidified hand soap: low-cost infection prevention clothing against enveloped viruses such as SARS-CoV-2
Authors: Cano-Vicent Alba , Tuñón-Molina Alberto , Martí Miguel , Muramoto Yukiko , Noda Takeshi , Takayama Kazuo , Serrano-Aroca Ángel 
Published: August 2021

ABSTRACTInfection prevention clothing is becoming an essential protective tool in the current pandemic, especially because now we know that SARS-CoV-2 can easily infect humans in poorly ventilated indoor spaces. However, commercial infection prevention clothing is made of fabrics that are not capable of inactivating the virus. Therefore, viral infections of symptomatic and asymptomatic individuals wearing protective clothing such as masks can occur through aerosol transmission or by contact with the contaminated surfaces of the masks, which are suspected as an increasing source of highly infectious biological waste. Herein, we report an easy fabrication method of a novel antiviral non-woven fabric containing polymer filaments that were coated with solidified hand soap. This extra protective fabric is capable of inactivating enveloped viruses such as SARS-CoV-2 and phi 6 in one minute of contact. In this study, this antiviral fabric was used to fabricate an antiviral face mask and did not show any cytotoxic effect in human keratinocyte HaCaT cells. Furthermore, this antiviral non-woven fabric could be used for the fabrication of other infection prevention clothing such as caps, scrubs, shirts, trousers, disposable gowns, overalls, hoods, aprons, and shoe covers. Therefore, this low-cost technology could provide a wide range of infection protective tools to combat COVID-19 and future pandemics in developed and underdeveloped countries.
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
Authors: Romero-Losada Ana B. , Arvanitidou Christina , de los Reyes Pedro , García-González Mercedes , Romero-Campero Francisco J. 
Published: August 2021

AbstractBackgroundMicroalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae physiology and the biosynthesis of compounds of biotechnological interest are largely uncharacterized. This hinders the development of microalgae full potential as cell-factories. The recent application of omics technologies into microalgae research aims at unraveling these systems. Nevertheless, the lack of specific tools for analysing omics raw data generated from microalgae to provide biological meaningful information are hampering the impact of these technologies. The purpose of ALGAEFUN with MARACAS consists in providing researchers in microalgae with an enabling tool that will allow them to exploit transcriptomic and cistromic high-throughput sequencing data.ResultsALGAEFUN with MARACAS consists of two different tools. First, MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS) implements a fully automatic computational pipeline receiving as input RNA-seq (RNA sequencing) or ChIP-seq (chromatin immunoprecipitation sequencing) raw data from microalgae studies. MARACAS generates sets of differentially expressed genes or lists of genomic loci for RNA-seq and ChIP-seq analysis respectively. Second, ALGAEFUN (microALGAE FUNctional enrichment tool) is a web-based application where gene sets generated from RNA-seq analysis as well as lists of genomic loci from ChIP-seq analysis can be used as input. On the one hand, it can be used to perform Gene Ontology and biological pathways enrichment analysis over gene sets. On the other hand, using the results of ChIP-seq data analysis, it identifies a set of potential target genes and analyses the distribution of the loci over gene features. Graphical representation of the results as well as tables with gene annotations are generated and can be downloaded for further analysis.ConclusionsALGAEFUN with MARACAS provides an integrated environment for the microalgae research community that facilitates the process of obtaining relevant biological information from raw RNA-seq and ChIP-seq data. These applications are designed to assist researchers in the interpretation of gene lists and genomic loci based on functional enrichment analysis. ALGAEFUN with MARACAS is publicly available on https://greennetwork.us.es/AlgaeFUN/.
Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data
Authors: Combrisson Etienne , Allegra Michele , Basanisi Ruggero , Ince Robin A. A. , Giordano Bruno , Bastin Julien , Brovelli Andrea 
Published: August 2021

AbstractThe reproducibility crisis in neuroimaging and in particular in the case of underpowered studies has introduced doubts on our ability to reproduce, replicate and generalize findings. As a response, we have seen the emergence of suggested guidelines and principles for neuroscientists known asGood Scientific Practicefor conducting more reliable research. Still, every study remains almost unique in its combination of analytical and statistical approaches. While it is understandable considering the diversity of designs and brain data recording, it also represents a striking point against reproducibility. Here, we propose a non-parametric permutation-based statistical framework, primarily designed for neurophysiological data, in order to perform group-level inferences on non-negative measures of information encompassing metrics from information-theory, machine-learning or measures of distances. The framework supports both fixed- and random-effect models to adapt to inter-individuals and inter-sessions variability. Using numerical simulations, we compared the accuracy in ground-truth retrieving of both group models, such as test- and cluster-wise corrections for multiple comparisons. We then reproduced and extended existing results using both spatially uniform MEG and non-uniform intracranial neurophysiological data. We showed how the framework can be used to extract stereotypical task- and behavior-related effects across the population covering scales from the local level of brain regions, inter-areal functional connectivity to measures summarizing network properties. We also present an open-source Python toolbox called Frites1that includes the proposed statistical pipeline using information-theoretic metrics such as single-trial functional connectivity estimations for the extraction of cognitive brain networks. Taken together, we believe that this framework deserves careful attention as its robustness and flexibility could be the starting point toward the uniformization of statistical approaches.Graphical abstractHighlightsGroup-level statistics for extracting neurophysiological cognitive brain networksCombining non-parametric permutations with measures of informationFixed- and random-effect models, test- and cluster-wise correctionsMulti-level inferences, from local regions to inter-areal functional connectivityA Python open-source toolbox calledFritesincludes the proposed statistical methods
Anterior thalamic nuclei: A critical substrate for non-spatial paired-associate memory in rats
Authors: Hamilton Jennifer J , Dalrymple-Alford John C 
Published: August 2021

AbstractInjury or dysfunction in the anterior thalamic nuclei (ATN) may be the key contributory factor in many instances of diencephalic amnesia. Experimental ATN lesions impair spatial memory and temporal discriminations, but there is only limited support for a more general role in non-spatial memory. To extend evidence on the effects of ATN lesions, we examined the acquisition of bi-conditional associations between odour and object pairings presented in a runway, either with or without a temporal gap between these items. Intact adult male rats acquired both the no-trace and 10-second trace versions of this non-spatial task. Intact rats trained in the trace version showed elevated Zif268 activation in the dorsal CA1 of the hippocampus, suggesting that the temporal component recruited additional neural processing. ATN lesions completely blocked acquisition on both versions of this association-memory task. This deficit was not due to poor inhibition to non-rewarded cues or impaired sensory processing, because rats with ATN lesions were unimpaired in the acquisition of simple odour discriminations and simple object discriminations using similar task demands in the same apparatus. This evidence challenges the view that impairments in arbitrary paired-associate learning after ATN lesions require the use of multimodal spatial stimuli. It suggests that diencephalic amnesia associated with the ATN stems from degraded attention to stimulus-stimulus associations and their representation across a distributed memory system.