iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences.

SUMMARY: We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to cluster DNA sequences, without the need for sequence alignment or taxonomic identifiers. iDeLUCS is scalable and user-friendly: its graphical user interface, with support for hardware acceleration, allows the practitioner to fine-tune the different hyper-parameters involved in the training process without requiring extensive knowledge of deep learning. The performance of iDeLUCS was evaluated on a diverse set of datasets: several real genomic datasets from organisms in kingdoms Animalia, Protista, Fungi, Bacteria, and Archaea, three datasets of viral genomes, a dataset of simulated metagenomic reads from microbial genomes, and multiple datasets of synthetic DNA sequences. The performance of iDeLUCS was compared to that of two classical clustering algorithms (k-means++ and GMM) and two clustering algorithms specialized in DNA sequences (MeShClust v3.0 and DeLUCS), using both intrinsic cluster evaluation metrics and external evaluation metrics. In terms of unsupervised clustering accuracy, iDeLUCS outperforms the two classical algorithms by an average of ∼20%, and the two specialized algorithms by an average of ∼12%, on the datasets of real DNA sequences analyzed. Overall, our results indicate that iDeLUCS is a robust clustering method suitable for the clustering of large and diverse datasets of unlabeled DNA sequences. AVAILABILITY AND IMPLEMENTATION: iDeLUCS is available at https://github.com/Kari-Genomics-Lab/iDeLUCS under the terms of the MIT licence.

Microclimate, airborne particles, and microbiological monitoring protocol for conservation of rock-art caves: The case of the world-heritage site La Garma cave (Spain).

Cave heritage is often threatened by tourism or even scientific activities, which can lead to irreversible deterioration. We present a preventive conservation monitoring protocol to protect caves with rock art, focusing on La Garma Cave (Spain), a World Heritage Site with valuable archaeological materials and Palaeolithic paintings. This study assessed the suitability of the cave for tourist use through continuous microclimate and airborne particles monitoring, biofilm analysis, aerobiological monitoring and experimental visits. Our findings indicate several factors that make it inadvisable to adapt the cave for tourist use. Human presence and transit within the cave cause cumulative effects on the temperature of environmentally very stable and fragile sectors and significant resuspension of particles from the cave sediments. These environmental perturbations represent severe impacts as they affect the natural aerodynamic control of airborne particles and determine bacterial dispersal throughout the cave. This monitoring protocol provides part of the evidence to design strategies for sustainable cave management.

Recovery rate and factors associated with smell and taste disruption in patients with coronavirus disease 2019.

PURPOSE: To determine the occurrence of olfactory and gustatory disruptions in COVID-19 patients, their association with demographic and clinical features and prognosis. MATERIAL AND METHODS: This observational cohort study involved consecutively diagnosed COVID-19 patients tested between March the 3rd 2020 and March the 24th 2020, in a geographically defined cohort area. All COVID-19 patients were evaluated in a University Hospital. The primary outcome of interest is the prevalence of smell and taste alterations, factors associated and recovery rate. Univariate and multivariate analysis by logistic regression was performed to detect factors associated to these symptoms. RESULTS: 151 patients were included and 99 (65.6%) reported olfactory or gustatory symptoms. Olfactory dysfunction was reported by 75 patients (49.7%). Isolated anosmia was found in 2 patients (1.3%). Gustatory dysfunction was reported by 91 patients (60.3%). Factors associated with higher prevalence of smell dysfunction included age, sex, and comorbidities. The time to smell disruption development was significantly shorter in mild to moderate patients than in severe patients (p = 0.043). In 85.3% of patients with smell disruption, the symptom had been resolved in the first 2 months. 14.7% of patients remained symptomatic after 3 months of follow-up. CONCLUSIONS: Olfactory and gustatory dysfunction was common in COVID-19 patients. Smell disruption has high recovery rate and was associated with age, sex, and clinical severity. It may be beneficial to investigate the appearance of taste and/or smell disruptions in individual patients, with respect to diagnosis and prognosis.

Recommendations for head and neck surgical oncology practice in a setting of acute severe resource constraint during the COVID-19 pandemic: an international consensus.

The speed and scale of the global COVID-19 pandemic has resulted in unprecedented pressures on health services worldwide, requiring new methods of service delivery during the health crisis. In the setting of severe resource constraint and high risk of infection to patients and clinicians, there is an urgent need to identify consensus statements on head and neck surgical oncology practice. We completed a modified Delphi consensus process of three rounds with 40 international experts in head and neck cancer surgical, radiation, and medical oncology, representing 35 international professional societies and national clinical trial groups. Endorsed by 39 societies and professional bodies, these consensus practice recommendations aim to decrease inconsistency of practice, reduce uncertainty in care, and provide reassurance for clinicians worldwide for head and neck surgical oncology in the context of the COVID-19 pandemic and in the setting of acute severe resource constraint and high risk of infection to patients and staff.

Neural entrainment to music is sensitive to melodic spectral complexity.

During auditory perception, neural oscillations are known to entrain to acoustic dynamics but their role in the processing of auditory information remains unclear. As a complex temporal structure that can be parameterized acoustically, music is particularly suited to address this issue. In a combined behavioral and EEG experiment in human participants, we investigated the relative contribution of temporal (acoustic dynamics) and nontemporal (melodic spectral complexity) dimensions of stimulation on neural entrainment, a stimulus-brain coupling phenomenon operationally defined here as the temporal coherence between acoustical and neural dynamics. We first highlight that low-frequency neural oscillations robustly entrain to complex acoustic temporal modulations, which underscores the fine-grained nature of this coupling mechanism. We also reveal that enhancing melodic spectral complexity, in terms of pitch, harmony, and pitch variation, increases neural entrainment. Importantly, this manipulation enhances activity in the theta (5 Hz) range, a frequency-selective effect independent of the note rate of the melodies, which may reflect internal temporal constraints of the neural processes involved. Moreover, while both emotional arousal ratings and neural entrainment were positively modulated by spectral complexity, no direct relationship between arousal and neural entrainment was observed. Overall, these results indicate that neural entrainment to music is sensitive to the spectral content of auditory information and indexes an auditory level of processing that should be distinguished from higher-order emotional processing stages.NEW & NOTEWORTHY Low-frequency (<10 Hz) cortical neural oscillations are known to entrain to acoustic dynamics, the so-called neural entrainment phenomenon, but their functional implication in the processing of auditory information remains unclear. In a behavioral and EEG experiment capitalizing on parameterized musical textures, we disentangle the contribution of stimulus dynamics, melodic spectral complexity, and emotional judgments on neural entrainment and highlight their respective spatial and spectral neural signature.

Uncovering mental representations of smiled speech using reverse correlation.

Which spectral cues underlie the perceptual processing of smiles in speech? Here, the question was addressed using reverse-correlation in the case of the isolated vowel [a]. Listeners were presented with hundreds of pairs of utterances with randomly manipulated spectral characteristics and were asked to indicate, in each pair, which was the most smiling. The analyses revealed that they relied on robust spectral representations that specifically encoded vowel's formants. These findings demonstrate the causal role played by formants in the perception of smile. Overall, this paper suggests a general method to estimate the spectral bases of high-level (e.g., emotional/social/paralinguistic) speech representations.

DAVID: An open-source platform for real-time transformation of infra-segmental emotional cues in running speech.

We present an open-source software platform that transforms emotional cues expressed by speech signals using audio effects like pitch shifting, inflection, vibrato, and filtering. The emotional transformations can be applied to any audio file, but can also run in real time, using live input from a microphone, with less than 20-ms latency. We anticipate that this tool will be useful for the study of emotions in psychology and neuroscience, because it enables a high level of control over the acoustical and emotional content of experimental stimuli in a variety of laboratory situations, including real-time social situations. We present here results of a series of validation experiments aiming to position the tool against several methodological requirements: that transformed emotions be recognized at above-chance levels, valid in several languages (French, English, Swedish, and Japanese) and with a naturalness comparable to natural speech.

Respiratory mechanics in infants with severe bronchiolitis on controlled mechanical ventilation.

BACKGROUND: Analysis of respiratory mechanics during mechanical ventilation (MV) is able to estimate resistive, elastic and inertial components of the working pressure of the respiratory system. Our aim was to discriminate the components of the working pressure of the respiratory system in infants on MV with severe bronchiolitis admitted to two PICU's. METHODS: Infants younger than 1 year old with acute respiratory failure caused by severe bronchiolitis underwent neuromuscular blockade, tracheal intubation and volume controlled MV. Shortly after intubation studies of pulmonary mechanics were performed using inspiratory and expiratory breath hold. The maximum inspiratory and expiratory flow (QI and QE) as well as peak inspiratory (PIP), plateau (PPL) and total expiratory pressures (tPEEP) were measured. Inspiratory and expiratory resistances (RawI and RawE) and Time Constants (KTI and KTE) were calculated. RESULTS: We included 16 patients, of median age 2.5 (1-5.8) months. Bronchiolitis due to respiratory syncytial virus was the main etiology (93.8%) and 31.3% had comorbidities. Measured respiratory pressures were PIP 29 (26-31), PPL 24 (20-26), tPEEP 9 [8-11] cmH2O. Elastic component of the working pressure was significantly higher than resistive and both higher than threshold (tPEEP - PEEP) (P < 0.01). QI was significantly lower than QE [5 (4.27-6.75) v/s 16.5 (12-23.8) L/min. RawI and RawE were 38.8 (32-53) and 40.5 (22-55) cmH2O/L/s; KTI and KTE [0.18 (0.12-0.30) v/s 0.18 (0.13-0.22) s], and KTI:KTE ratio was 1:1.04 (1:0.59-1.42). CONCLUSIONS: Analysis of respiratory mechanics of infants with severe bronchiolitis receiving MV shows that the elastic component of the working pressure of the respiratory system is the most important. The elastic and resistive components in conjunction with flow profile are characteristic of restrictive diseases. A better understanding of lung mechanics in this group of patients may lead to change the traditional ventilatory approach to severe bronchiolitis.

Combined analysis of cross-reacting antibodies anti-ß1AR and anti-B13 in advanced stages of Chagas heart disease.

OBJECTIVE: Autoantibodies cross-reacting with the ß1 adrenergic receptor (anti-ß1AR and anti-p2ß) and cardiac myosin antigens (anti-B13) have been related to the pathogenesis of chronic Chagas heart disease (CCHD). Studies exploring their levels in different stages are scarce. We aimed to evaluate the relationship of these autoantibodies with the clinical profile of chronic patients, especially regarding their classificatory accuracy in severe presentation with heart failure. METHODS AND RESULTS: We conducted a cross-sectional study of 155 T. cruzi-seropositive patients and 26 age- and gender-matched healthy controls. They were categorised in three stages of CCHD. Serum antibodies were measured by specific immunoassays. Symptomatic individuals showed increased levels of anti-ß1AR and anti-B13, while anti-p2ß antibodies were similar between groups. A composite logistic regression model including anti-B13, anti-ß1AR antibody levels and age was able to predict systolic heart failure yielding an area under the curve of 83% (sensitivity of 67% and specificity of 89%). CONCLUSIONS: In our study, anti-ß1AR and anti-B13 antibodies were higher in individuals with chronic Chagas heart disease stage III, mainly in those with dilated cardiomyopathy associated with systolic heart failure. Logistic regression analysis showed that both antibodies were good predictors of severe CCHD. As well as being involved in disease progression, anti-ß1AR and anti-B13 antibodies may be used as a serum marker of poor prognosis in terms of heart compromise.

Minimally invasive video-assisted submandibular sialadenectomy: surgical technique and results from two institutions.

BACKGROUND: Submandibular gland excision is traditionally performed using a transcervical approach. However, innovative surgical trials have recently been conducted to investigate techniques that can prevent or reduce visible scarring and nerve injury. The aim of the present study was to evaluate the feasibility of a new approach to submandibular gland excision that is based on the use of a minimally invasive video-assisted technique and an ultrasound scalpel in an endoscopic neck surgery program with a low annual flow of procedures. METHODS: We retrospectively studied 15 patients with submandibular gland disease who underwent minimally invasive video-assisted submandibular sialadenectomy performed by two surgeons at two institutions. Eight patients had proximally located salivary calculi, three had chronic sialadenitis, and four had benign neoplasms. All dissections were carried out by a single-port gasless approach, using the Miccoli technique, involving endoscope magnification and an ultrasonic scalpel. RESULTS: All 15 submandibular gland resections were performed successfully, with no conversions to conventional open resection. The operative time ranged from 45 to 125 min (median 84 min). A total of 67 % of patients were discharged the day after surgery, and the maximum length of stay was 3 days. One patient experienced postoperative bleeding, and one experienced postoperative infection. There was no neural injury. The incision scar healed well in all cases, and all patients reported excellent cosmetic results. CONCLUSIONS: Endoscopic submandibular gland resection using a minimally invasive video-assisted technique, endoscopic magnification, and ultrasonic scalpel was feasible and resulted in excellent surgical outcomes.

Transoral ultrasonic total laryngectomy (TOUSS-TL): description of a new endoscopic approach and report of two cases.

The minimally invasive total laryngectomy avoids a wide surgical field and so it has the potential benefit of reducing the local morbidity, especially on radiated patients. This approach has been previously described on a robotic basis, the transoral robotic total laryngectomy (TORS-TL). We have designed a minimally invasive approach for total laryngectomy (TL) using the transoral ultrasonic surgery technique (TOUSS). TOUSS is a transoral, endoscopic, non-robotic approach for laryngeal and pharyngeal tumors, based on the ultrasonic scalpel as a resection tool. Two patients with a laryngeal squamous cell carcinoma with indication for total laryngectomy were surgically treated: one primary TL for a subglottic carcinoma and one salvage TL with partial pharyngectomy for a local relapse after chemoradiotherapy of a glottic carcinoma. The tumors were completely removed with free surgical margin in both patients. The functional recovery was satisfactory in terms of swallowing and speech (a tracheoesophageal puncture and voice prosthesis placement were done in the same procedure). No intraoperative complications were observed. The patient with previous chemoradiotherapy had a pharyngocutaneous fistula which closed spontaneously without additional surgery. We have demonstrated that transoral endoscopic approach to the larynx and pharynx is feasible without a robotic platform. TOUSS-TL can easily spread the transoral endoscopic philosophy as well as the benefits of a minimally invasive way to remove the entire larynx. Further research will show the advantages in terms of complications and functional outcomes.

TransOral endoscopic UltraSonic Surgery (TOUSS): a preliminary report of a novel robotless alternative to TORS.

The objective of this study is to describe and evaluate the feasibility of TransOral UltraSonic Surgery (TOUSS), a new endoscopic alternative to transoral robotic surgery for approaching pharyngeal and laryngeal tumours based on ultrasonic scalpel as a resection tool. This is a prospective study on 11 consecutive patients with pharyngeal and supraglottic carcinomas between December 2013 and August 2014. All tumours were resected transorally with 35 cm ThunderbeatTM. Exposure was achieved using GyrusTM FK-retractor and Olympus ENDOEYE Flex 5 mm 2D/10 mm 3D deflecting tip video laparoscopes. We evaluated tumour staging, surgical margins, surgical time, blood transfusions, tracheostomy, enteral feeding, postoperative pain and hospital stay. The operating room setup and procedure are described. This series comprised seven early and four locally advanced carcinomas. The mean setup for TOUSS and resection time were 16 and 70.9 minutes. No major intraoperative complications were identified. The average time of nasogastric feeding tube dependence (n = 9) was 13 days. Gastrostomy was performed in one patient. The average hospital stay was 14.3 days. Postoperative pain was satisfactory treated with nonsteroidal anti-inflammatory drugs. We have described TOUSS as a new feasible and intuitive procedure to approach endoscopically pharyngeal and supraglottic tumours, with good intraoperative conditions and functional outcomes.

Spatiotemporal Gait Patterns During Overt and Covert Evaluation in Patients With Parkinson´s Disease and Healthy Subjects: Is There a Hawthorne Effect?

Parkinson's disease (PD) and aging lead to gait impairments. Some of the disturbances of gait are focused on step length, cadence, and temporal variability of gait cycle. Under experimental conditions gait can be overtly evaluated, but patients with PD are prone to expectancy effects; thus it seems relevant to determine if such evaluation truly reflects the spontaneous gait pattern in such patients, and also in healthy subjects. Thirty subjects (15 subjects with PD and 15 healthy control subjects) were asked to walk using their natural, preferred gait pattern. In half of the trials subjects were made aware that they were being evaluated (overt evaluation), while in the rest of the trials the evaluation was performed covertly (covert evaluation). During covert evaluation the gait pattern was modified in all groups. Gait speed was significantly increased (P = .022); step cadence and average step length were also significantly modified, the average step length increased (P = .002) and the cadence was reduced (P ≤ .001). Stride cycle time variability was unchanged significantly (P = .084). These changes were not significantly different compared between elderly and young healthy controls either. Due to the small sample size, a note of caution is in order; however, the significant results suggest that covert evaluation of gait might be considered to complement experimental evaluations of gait.

The effects of expectancy on corticospinal excitability: passively preparing to observe a movement.

The corticospinal tract excitability is modulated when preparing movements. Earlier to movement execution, the excitability of the spinal cord increases waiting for supraspinal commands to release the movement. Movement execution and movement observation share processes within the motor system, although movement observation research has focused on processes later to movement onset. We used single and paired pulse transcranial magnetic stimulation on M1 (n = 12), and electrical cervicomedullary stimulation (n = 7), to understand the modulation of the corticospinal system during the "preparation" to observe a third person's movement. Subjects passively observed a hand that would remain still or make an index finger extension. The observer's corticospinal excitability rose when "expecting to see a movement" vs. when "expecting to see a still hand." The modulation took origin at a spinal level and not at the corticocortical networks explored. We conclude that expectancy of seeing movements increases the excitability of the spinal cord.

Efficacy and safety of canagliflozin versus glimepiride in patients with type 2 diabetes inadequately controlled with metformin (CANTATA-SU): 52 week results from a randomised, double-blind, phase 3 non-inferiority trial.

BACKGROUND: Sodium-glucose cotransporter 2 (SGLT2) inhibitors improve glycaemia in patients with type 2 diabetes by enhancing urinary glucose excretion. We compared the efficacy and safety of canagliflozin, an SGLT2 inhibitor, with glimepiride in patients with type 2 diabetes inadequately controlled with metformin. METHODS: We undertook this 52 week, randomised, double-blind, active-controlled, phase 3 non-inferiority trial at 157 centres in 19 countries between Aug 28, 2009, and Dec 21, 2011. Patients aged 18-80 years with type 2 diabetes and glycated haemoglobin A1c (HbA1c) of 7·0-9·5% on stable metformin were randomly assigned (1:1:1) by computer-generated random sequence via an interactive voice or web response system to receive canagliflozin 100 mg or 300 mg, or glimepiride (up-titrated to 6 mg or 8 mg per day) orally once daily. Patients, study investigators, and local sponsor personnel were masked to treatment. The primary endpoint was change in HbA1c from baseline to week 52, with a non-inferiority margin of 0·3% for the comparison of each canagliflozin dose with glimepiride. If non-inferiority was shown, we assessed superiority on the basis of an upper bound of the 95% CI for the difference of each canagliflozin dose versus glimepiride of less than 0·0%. Analysis was done in a modified intention-to-treat population, including all randomised patients who received at least one dose of study drug. This study is registered with ClinicalTrials.gov, number NCT00968812. FINDINGS: 1450 of 1452 randomised patients received at least one dose of glimepiride (n=482), canagliflozin 100 mg (n=483), or canagliflozin 300 mg (n=485). For lowering of HbA1c at 52 weeks, canagliflozin 100 mg was non-inferior to glimepiride (least-squares mean difference -0·01% [95% CI -0·11 to 0·09]), and canagliflozin 300 mg was superior to glimepiride (-0·12% [-0·22 to -0·02]). 39 (8%) patients had serious adverse events in the glimepiride group versus 24 (5%) in the canagliflozin 100 mg group and 26 (5%) in the 300 mg group. In the canagliflozin 100 mg and 300 mg groups versus the glimepiride group, we recorded a greater number of genital mycotic infections (women: 26 [11%] and 34 [14%] vs five [2%]; men: 17 [7%] and 20 [8%] vs three [1%]), urinary tract infections (31 [6%] for both canagliflozin doses vs 22 [5%]), and osmotic diuresis-related events (pollakiuria: 12 [3%] for both doses vs one [<1%]; polyuria: four [<1%] for both doses vs two [<1%]). INTERPRETATION: Canagliflozin provides greater HbA1c reduction than does glimepiride, and is well tolerated in patients with type 2 diabetes receiving metformin. These findings support the use of canagliflozin as a viable treatment option for patients who do not achieve sufficient glycaemic control with metformin therapy. FUNDING: Janssen Research & Development, LLC.

Erratum: Under the Skin of a Lion: Unique Evidence of Upper Paleolithic Exploitation and Use of Cave Lion (Panthera spelaea) from the Lower Gallery of La Garma (Spain).

[This corrects the article DOI: 10.1371/journal.pone.0163591.].

Fatigue insights from walking tests in spinal cord injury and multiple sclerosis individuals.

In the last decade, fatigue in clinical populations has been re-conceptualized, including dimensions such as perceived fatigue (trait and state fatigue) and fatigability. The aim of this study was to evaluate different expressions of fatigue in Spinal Cord Injury (SCI) and Multiple Sclerosis (MS) participants compared to able-bodied controls, during activities of daily living, especially during gait. A total of 67 participants were included in this study (23 with SCI, 23 with MS, and 21 able-bodied controls). All participants performed two functional tests (6-Minute Walk Test and 10-Meter Walk Test) and they completed the Fatigue Severity Scale (FSS). The rate of trait fatigue was different between groups, with MS participants showing the highest rate. Moreover, scores on functional tests and state fatigue were different between groups after the tests. Our results indicate that trait fatigue and state fatigue in individuals with SCI and MS are different with respect to able-bodied population. Both SCI and MS groups experienced more trait fatigue than control group in daily life. In addition, walking tasks produced similar levels of state fatigue between healthy people and patients with MS/SCI. However, these tests induced longer-lasting levels of state fatigue in the patients.

Plasticlusters: A marine litter microhabitat in a marina of Tunisia, N Africa.

Plastic debris is a significant and rapidly developing ecological issue in coastal marine ecosystems, especially in areas where it accumulates. This study introduces "plasticlusters", a new form of floating debris agglomeration found in the Yasmine Hammamet marina (Tunisia, North-Africa), loosely attached to pontoon ropes around the water surface level. The analysis of two samples revealed that they were formed primarily by average 2.11 mm polystyrene fragments, 3.43 mm fibers, 104 mm polypropylene and polyethylene sheets, and 122 mm decomposing seagrass leaves. They were inhabited by several taxa, including at least 2 cryptogenic and 5 non-indigenous species (NIS). Unlike other plastic formations, plasticlusters provide a novel and potentially temporal microhabitat to fouling assemblages due to their loose and unconsolidated structure which, combined with marinas being NIS hubs, could enhance NIS dispersion. The results of this study raise concerns about the combined ecological effects of debris accumulation and biocontamination inside marinas.