bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning regularized representations of categorically labelled surface EMG enables simultaneous and proportional myoelectric control
Authors: Olsson Alexander E. , Malešević Nebojša , Björkman Anders , Antfolk Christian 
Published: February 2021

Abstract
Background
Processing the surface electromyogram (sEMG) to decode movement intent is a promising approach for natural control of upper extremity prostheses. To this end, this paper introduces and evaluates a new framework which allows for simultaneous and proportional myoelectric control over multiple degrees of freedom (DoFs) in real-time. The framework uses multitask neural networks and domain-informed regularization in order to automatically find nonlinear mappings from the forearm sEMG envelope to multivariate and continuous encodings of concurrent hand- and wrist kinematics, despite only requiring categorical movement instruction stimuli signals for calibration.

Methods
Forearm sEMG with 8 channels was collected from healthy human subjects (N = 20) and used to calibrate two myoelectric control interfaces, each with two output DoFs. The interfaces were built from (I) the proposed framework, termed Myoelectric Representation Learning (MRL), and, to allow for comparisons, from (II) a standard pattern recognition framework based on Linear Discriminant Analysis (LDA). The online performances of both interfaces were assessed with a Fitts’s law type test generating 5 quantitative performance metrics. The temporal stabilities of the interfaces were evaluated by conducting identical tests without recalibration 7 days after the initial experiment session.

Results
Metric-wise two-way repeated measures ANOVA with factors method (MRL vs LDA) and session (day 1 vs day 7) revealed a significant ($$p<0.05$$

p
<
0.05

) advantage for MRL over LDA in 5 out of 5 performance metrics, with metric-wise effect sizes (Cohen’s $$d$$
d
) separating MRL from LDA ranging from $$\left|d\right|=0.62$$

d

=
0.62

to $$\left|d\right|=1.13$$

d

=
1.13

. No significant effect on any metric was detected for neither session nor interaction between method and session, indicating that none of the methods deteriorated significantly in control efficacy during one week of intermission.

Conclusions
The results suggest that MRL is able to successfully generate stable mappings from EMG to kinematics, thereby enabling myoelectric control with real-time performance superior to that of the current commercial standard for pattern recognition (as represented by LDA). It is thus postulated that the presented MRL approach can be of practical utility for muscle-computer interfaces.
Systematic review of gut microbiota and attention-deficit hyperactivity disorder (ADHD)
Authors: Sukmajaya Alverina Cynthia , Lusida Maria Inge , Soetjipto  , Setiawati Yunias 
Published: February 2021

Abstract
Background
Gut–brain axis (GBA) is a system widely studied nowadays, especially in the neuropsychiatry field. It is postulated to correlate with many psychiatric conditions, one of them being attention-deficit hyperactivity disorder (ADHD). ADHD is a disorder that affects many aspects of life, including but not limited to financial, psychosocial, and cultural aspects. Multiple studies have made a comparison of the gut microbiota between ADHD and healthy controls. Our aims were to review the existing studies analyzing the gut microbiota between human samples in ADHD and healthy individuals.

Methods
The literature was obtained using Google Scholar, Pubmed, and Science Direct search engine. The keywords used were “ADHD”, “gut microbiota”, “stool”, “gut”, and “microbiota”. The selected studies were all case–control studies, which identify the gut microbiota between ADHD and healthy individuals.

Result
We found six studies which were eligible for review. The model and methods of each study is different. Forty-nine bacterial taxa were found, yet none of them can explain the precise relationship between ADHD and the gut microbiota. Bifidobacterium was found in higher amount in ADHD patients, but other study stated that the abundance of this genus was lower in ADHD with post-micronutrient treatment. This may suggest that micronutrient can modulate the population of Bifidobacterium and improve the behavior of ADHD patients. Other notable findings include a significantly lower population of Dialister in unmedicated ADHD, which rose after patients were medicated. A smaller amount of Faecalibacterium were also found in ADHD patients. This may explain the pathogenesis of ADHD, as Faecalibacterium is known for its anti-inflammatory products. It is possible the scarcity of this genera could induce overproduction of pro-inflammatory cytokines, which is in accordance with the high level of pro-inflammatory cytokines found in children with ADHD.

Conclusion
There were no studies that examined which bacterial taxa correlated most to ADHD. This might occur due to the different model and methods in each study. Further study is needed to identify the correlation between gut microbiota and ADHD.
Finite element analysis of wedge and biconcave deformity in four different height restoration after augmentation of osteoporotic vertebral compression fractures
Authors: Zuo Xiao-Hua , Chen Yin-Bing , Xie Peng , Zhang Wen-Dong , Xue Xiang-Yun , Zhang Qian-Xi , Shan Ben , Zhang Xiao-Bing , Bao Hong-Guang , Si Yan-Na 
Published: February 2021

AbstractPurposeBiomechanical comparison of wedge and biconcave deformity of different height restoration after augmentation of osteoporotic vertebral compression fractures was analyzed by three-dimensional finite element analysis (FEA).MethodsThree-dimensional finite element model (FEM) of T11-L2 segment was constructed from CT scan of elderly osteoporosis patient. The von Mises stresses of vertebrae, intervertebral disc, facet joints, displacement, and range of motion (ROM) of wedge and biconcave deformity were compared at four different heights (Genant 0–3 grade) after T12 vertebral augmentation.ResultsIn wedge deformity, the stress of T12 decreased as the vertebral height in neutral position, flexion, extension, and left axial rotation, whereas increased sharply in bending at Genant 0; L1 and L2 decreased in all positions excluding flexion of L2, and T11 increased in neutral position, flexion, extension, and right axial rotation at Genant 0. No significant changes in biconcave deformity. The stress of T11-T12, T12-L1, and L1-L2 intervertebral disc gradually increased or decreased under other positions in wedge fracture, whereas L1-L2 no significant change in biconcave fracture. The utmost overall facet joint stress is at Genant 3, whereas there is no significant change under the same position in biconcave fracture. The displacement and ROM of the wedge fracture had ups and downs, while a decline in all positions excluding extension in biconcave fracture.ConclusionsThe vertebral restoration height after augmentation to Genant 0 affects the von Mises stress, displacement, and ROM in wedge deformity, which may increase the risk of fracture, whereas restored or not in biconcave deformity.
Remodeling Alzheimer-amyloidosis models by seeding
Authors: Ulm Brittany S. , Borchelt David R. , Moore Brenda D. 
Published: February 2021

AbstractAlzheimer’s disease (AD) is among the most prevalent neurodegenerative diseases, with brain pathology defined by extracellular amyloid beta deposits and intracellular tau aggregates. To aid in research efforts to improve understanding of this disease, transgenic murine models have been developed that replicate aspects of AD pathology. Familial AD is associated with mutations in the amyloid precursor protein and in the presenilins (associated with amyloidosis); transgenic amyloid models feature one or more of these mutant genes. Recent advances in seeding methods provide a means to alter the morphology of resultant amyloid deposits and the age that pathology develops. In this review, we discuss the variety of factors that influence the seeding of amyloid beta pathology, including the source of seed, the time interval after seeding, the nature of the transgenic host, and the preparation of the seeding inoculum.
Novel hybrid polyester-polyacrylate hydrogels enriched with platelet-derived growth factor for chondrogenic differentiation of adipose-derived mesenchymal stem cells in vitro
Authors: Valipour Fereshteh , Valipour Farzaneh , Rahbarghazi Reza , Navali Amir Mohammad , Rashidi Mohammad Reza , Davaran Soodabeh 
Published: February 2021

AbstractBackgroundThe goal of the present study was to create a new biodegradable hybrid PCL-P (HEMA-NIPAAm) thermosensitive hydrogel scaffold by grafting PNIPAAm-based copolymers with biodegradable polyesters to promote the chondrogenic differentiation of human progenitor cells (adipose-derived stem cells-hASCs) in the presence of the platelet-derived growth factor (PDGF-BB). Different mixture ratios including 50 mmol ε-caprolactone and 10 mmol HEMA (S-1), 30 mmol ε-caprolactone and 10 mmol HEMA (S-2), 10 mmol ε-caprolactone and 30 mmol HEMA (S-3) were copolymerized followed by the addition of NIPAAm.ResultsA mild to moderate swelling and wettability rates were found in S-2 group copmpared to the S-1 ans S-3 samples. After 7 weeks, S-2 degradation rate reached ~ 43.78%. According to the LCST values, S-2, reaching 37 °C, was selected for different in vitro assays. SEM imaging showed nanoparticulate structure of the scaffold with particle size dimensions of about 62–85 nm. Compressive strength, Young’s modulus, and compressive strain (%) of S-2 were 44.8 MPa, 0.7 MPa, and 75.5%. An evaluation of total proteins showed that the scaffold had the potential to gradually release PDGF-BB. When hASCs were cultured on PCL-P (HEMA-NIPAAm) in the presence of PDGF-BB, the cells effectively attached and flattened on the scaffold surface for a period of at least 14 days, the longest time point evaluated, with increased cell viability rates as measured by performing an MTT assay (p < 0.05). Finally, a real-time RT-PCR analysis demonstrated that the combination of PCL-P (HEMA-NIPAAm) and PDGF-BB promoted the chondrogenesis of hASCs over a period of 14 days by up-regulating the expression of aggrecan, type-II collagen, SOX9, and integrin β1 compared with the non-treated control group (p < 0.05).ConclusionThese results demonstrate that the PCL-P(HEMA-NIPAAm) hydrogel scaffold carrying PDGF-BB as a matrix for hASC cell seeding is a valuable system that may be used in the future as a three-dimensional construct for implantation in cartilage injuries.
DASSI: differential architecture search for splice identification from DNA sequences
Authors: Moosa Shabir , Amira Prof. Abbes , Boughorbel Dr. Sabri 
Published: February 2021

AbstractBackgroundThe data explosion caused by unprecedented advancements in the field of genomics is constantly challenging the conventional methods used in the interpretation of the human genome. The demand for robust algorithms over the recent years has brought huge success in the field of Deep Learning (DL) in solving many difficult tasks in image, speech and natural language processing by automating the manual process of architecture design. This has been fueled through the development of new DL architectures. Yet genomics possesses unique challenges that requires customization and development of new DL models.MethodsWe proposed a new model, DASSI, by adapting a differential architecture search method and applying it to the Splice Site (SS) recognition task on DNA sequences to discover new high-performance convolutional architectures in an automated manner. We evaluated the discovered model against state-of-the-art tools to classify true and false SS in Homo sapiens (Human), Arabidopsis thaliana (Plant), Caenorhabditis elegans (Worm) and Drosophila melanogaster (Fly).ResultsOur experimental evaluation demonstrated that the discovered architecture outperformed baseline models and fixed architectures and showed competitive results against state-of-the-art models used in classification of splice sites. The proposed model - DASSI has a compact architecture and showed very good results on a transfer learning task. The benchmarking experiments of execution time and precision on architecture search and evaluation process showed better performance on recently available GPUs making it feasible to adopt architecture search based methods on large datasets.ConclusionsWe proposed the use of differential architecture search method (DASSI) to perform SS classification on raw DNA sequences, and discovered new neural network models with low number of tunable parameters and competitive performance compared with manually engineered architectures. We have extensively benchmarked DASSI model with other state-of-the-art models and assessed its computational efficiency. The results have shown a high potential of using automated architecture search mechanism for solving various problems in the field of genomics.
Extracting single-trial neural interaction using latent dynamical systems model
Authors: Huh Namjung , Kim Sung-Phil , Lee Joonyeol , Sohn Jeong-woo 
Published: February 2021

AbstractIn systems neuroscience, advances in simultaneous recording technology have helped reveal the population dynamics that underlie the complex neural correlates of animal behavior and cognitive processes. To investigate these correlates, neural interactions are typically abstracted from spike trains of pairs of neurons accumulated over the course of many trials. However, the resultant averaged values do not lead to understanding of neural computation in which the responses of populations are highly variable even under identical external conditions. Accordingly, neural interactions within the population also show strong fluctuations. In the present study, we introduce an analysis method reflecting the temporal variation of neural interactions, in which cross-correlograms on rate estimates are applied via a latent dynamical systems model. Using this method, we were able to predict time-varying neural interactions within a single trial. In addition, the pairwise connections estimated in our analysis increased along behavioral epochs among neurons categorized within similar functional groups. Thus, our analysis method revealed that neurons in the same groups communicate more as the population gets involved in the assigned task. We also showed that the characteristics of neural interaction from our model differ from the results of a typical model employing cross-correlation coefficients. This suggests that our model can extract nonoverlapping information about network topology, unlike the typical model.
CD19 CAR-T expressing PD-1/CD28 chimeric switch receptor as a salvage therapy for DLBCL patients treated with different CD19-directed CAR T-cell therapies
Authors: Liang Yun , Liu Hui , Lu Zheming , Lei Wen , Zhang Chaoting , Li Ping , Liang Aibin , Young Ken H. , Qian Wenbin 
Published: February 2021

AbstractCD19-targeted chimeric antigen receptor T (CAR T) cell therapy is a promising option to treat relapsed/refractory diffuse large B-cell lymphoma (R/R DLBCL). However, the majority of CAR T-treated patients will eventually progress and require salvage treatment, for which there is no current standard. In this study, we analyzed data from 6 patients with R/R DLBCL who experienced progression following CD19-CAR T therapy, and then received CD19-specific CAR T cells that express a PD-1/CD28 chimeric switch-receptor (CD19-PD-1/CD28-CAR T) as salvage therapy at our institution. After the second infusion of CAR T cells, 3 of 6 patients achieved complete remissions and the duration of the response of responsive patients ranged from 8 to 25 months. One patient showed a stable disease. In contrast, 2/6 patients died on 60 days because of progression disease. Importantly, no severe neurologic toxicity or cytokine release syndrome was observed. These data suggest that CD19-PD-1/CD28-CAR-T cells, a novel anti-CD19 CAR-T cell therapy, elicit a potent and durable anticancer response, and can be used in the post-CD19-CAR T failure setting.
Incidental finding of APC deletion in a child: double trouble or double chance? – a case report
Authors: Rosina Erica , Rinaldi Berardo , Silipigni Rosamaria , Bergamaschi Luca , Gattuso Giovanna , Signoroni Stefano , Guerneri Silvana , Carnevali Alessandra , Marchisio Paola Giovanna , Milani Donatella 
Published: February 2021

Abstract
Background
22q11.2 deletion syndrome is one of the most common genomic disorders, characterized by the variable presence of facial dysmorphisms, congenital cardiac defects, velopharyngeal insufficiency/cleft palate, thymic hypoplasia/aplasia, immunodeficiency, parathyroid hypoplasia, developmental delay, learning disabilities, psychiatric disorders, renal, ocular, and skeletal malformations, hearing loss and laryngeal abnormalities. Chromosomal microarray (CMA) hybridization is one of the most performed diagnostic tests but as a genome wide analysis, it can point out relevant incidental copy number variations.

Case presentation
We report the case of a 2-year-old boy that came to our attention for mild psychomotor delay, poor growth, and minor facial anomalies. Considering a diagnosis of 22q11.2 deletion syndrome, we performed CMA that not only confirmed our diagnosis, but also pointed out an additional de novo 5q21.3q22.2 microdeletion, encompassing APC gene. As a result of the genetic testing we enrolled the patient in a tailored surveillance protocol that enabled the early detection of a hepatoblastoma. The child underwent surgical and chemotherapic treatments with complete cancer eradication.

Conclusions
The concurrent finding of an expected result and an additional deletion of APC gene represents an example of a relevant issue about the health and ethical management of secondary findings revealed by genome-wide tests. Furthermore, this report highlights the need to develop dedicated surveillance guidelines for children with APC-related polyposis and raise the question whether to suspect and screen for APC-related conditions in cases of sporadic hepatoblastomas.
Monitoring circulating dipeptidyl peptidase 3 (DPP3) predicts improvement of organ failure and survival in sepsis: a prospective observational multinational study
Authors:   AdrenOSS-1 Study Investigators, Blet Alice , Deniau Benjamin , Santos Karine , van Lier Dirk P. T. , Azibani Feriel , Wittebole Xavier , Chousterman Benjamin G. , Gayat Etienne , Hartmann Oliver , Struck Joachim , Bergmann Andreas , Antonelli Massimo , Beishuizen Albertus , Constantin Jean-Michel , Damoisel Charles , Deye Nicolas , Di Somma Salvatore , Dugernier Thierry , François Bruno , Gaudry Stephane , Huberlant Vincent , Lascarrou Jean-Baptiste , Marx Gernot , Mercier Emmanuelle , Oueslati Haikel , Pickkers Peter , Sonneville Romain , Legrand Matthieu , Laterre Pierre-François , Mebazaa Alexandre 
Published: February 2021

Abstract
Background
Dipeptidyl peptidase 3 (DPP3) is a cytosolic enzyme involved in the degradation of various cardiovascular and endorphin mediators. High levels of circulating DPP3 (cDPP3) indicate a high risk of organ dysfunction and mortality in cardiogenic shock patients.

Methods
The aim was to assess relationships between cDPP3 during the initial intensive care unit (ICU) stay and short-term outcome in the AdrenOSS-1, a prospective observational multinational study in twenty-four ICU centers in five countries. AdrenOSS-1 included 585 patients admitted to the ICU with severe sepsis or septic shock. The primary outcome was 28-day mortality. Secondary outcomes included organ failure as defined by the Sequential Organ Failure Assessment (SOFA) score, organ support with focus on vasopressor/inotropic use and need for renal replacement therapy. cDPP3 levels were measured upon admission and 24 h later.

Results
Median [IQR] cDPP3 concentration upon admission was 26.5 [16.2–40.4] ng/mL. Initial SOFA score was 7 [5–10], and 28-day mortality was 22%. We found marked associations between cDPP3 upon ICU admission and 28-day mortality (unadjusted standardized HR 1.8 [CI 1.6–2.1]; adjusted HR 1.5 [CI 1.3–1.8]) and between cDPP3 levels and change in renal and liver SOFA score (p = 0.0077 and 0.0009, respectively). The higher the initial cDPP3 was, the greater the need for organ support and vasopressors upon admission; the longer the need for vasopressor(s), mechanical ventilation or RRT and the higher the need for fluid load (all p < 0.005). In patients with cDPP3 > 40.4 ng/mL upon admission, a decrease in cDPP3 below 40.4 ng/mL after 24 h was associated with an improvement of organ function at 48 h and better 28-day outcome. By contrast, persistently elevated cDPP3 at 24 h was associated with worsening organ function and high 28-day mortality.

Conclusions
Admission levels and rapid changes in cDPP3 predict outcome during sepsis.
Trial Registration ClinicalTrials.gov, NCT02393781. Registered on March 19, 2015.
Deploying unsupervised clustering analysis to derive clinical phenotypes and risk factors associated with mortality risk in 2022 critically ill patients with COVID-19 in Spain
Authors:   on behalf of COVID-19 SEMICYUC Working Group, Rodríguez Alejandro , Ruiz-Botella Manuel , Martín-Loeches Ignacio , Jimenez Herrera María , Solé-Violan Jordi , Gómez Josep , Bodí María , Trefler Sandra , Papiol Elisabeth , Díaz Emili , Suberviola Borja , Vallverdu Montserrat , Mayor-Vázquez Eric , Albaya Moreno Antonio , Canabal Berlanga Alfonso , Sánchez Miguel , del Valle Ortíz María , Ballesteros Juan Carlos , Martín Iglesias Lorena , Marín-Corral Judith , López Ramos Esther , Hidalgo Valverde Virginia , Vidaur Tello Loreto Vidaur , Sancho Chinesta Susana , Gonzáles de Molina Francisco Javier , Herrero García Sandra , Sena Pérez Carmen Carolina , Pozo Laderas Juan Carlos , Rodríguez García Raquel , Estella Angel , Ferrer Ricard 
Published: February 2021

Abstract
Background
The identification of factors associated with Intensive Care Unit (ICU) mortality and derived clinical phenotypes in COVID-19 patients could help for a more tailored approach to clinical decision-making that improves prognostic outcomes.

Methods
Prospective, multicenter, observational study of critically ill patients with confirmed COVID-19 disease and acute respiratory failure admitted from 63 ICUs in Spain. The objective was to utilize an unsupervised clustering analysis to derive clinical COVID-19 phenotypes and to analyze patient’s factors associated with mortality risk. Patient features including demographics and clinical data at ICU admission were analyzed. Generalized linear models were used to determine ICU morality risk factors. The prognostic models were validated and their performance was measured using accuracy test, sensitivity, specificity and ROC curves.

Results
The database included a total of 2022 patients (mean age 64 [IQR 5–71] years, 1423 (70.4%) male, median APACHE II score (13 [IQR 10–17]) and SOFA score (5 [IQR 3–7]) points. The ICU mortality rate was 32.6%. Of the 3 derived phenotypes, the A (mild) phenotype (537; 26.7%) included older age (< 65 years), fewer abnormal laboratory values and less development of complications, B (moderate) phenotype (623, 30.8%) had similar characteristics of A phenotype but were more likely to present shock. The C (severe) phenotype was the most common (857; 42.5%) and was characterized by the interplay of older age (> 65 years), high severity of illness and a higher likelihood of development shock. Crude ICU mortality was 20.3%, 25% and 45.4% for A, B and C phenotype respectively. The ICU mortality risk factors and model performance differed between whole population and phenotype classifications.

Conclusion
The presented machine learning model identified three clinical phenotypes that significantly correlated with host-response patterns and ICU mortality. Different risk factors across the whole population and clinical phenotypes were observed which may limit the application of a “one-size-fits-all” model in practice.