Interoperable workflows by exchanging grid-based data between quantum-chemical program packages.

Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.

Comparing RNA extraction methods to face the variations in RNA quality using two human biological matrices.

BACKGROUND: Nucleic acids, RNA among them, are widely used in biomedicine and Biotechnology. Because of their susceptibility to degradation by RNases, the handling and extraction process of RNA from cells and tissues require specialized personnel and standardized methods to guarantee high purity and integrity. Due to the diversity of techniques found in the market, a comparative study between different RNA extraction methods is useful to facilitate the best choice for the researcher or in research service platforms such as biobanks to see the traceability of the samples. METHODS AND RESULTS: In this study, we have compared seven different RNA extraction methods: manual (TRIzol™), semiautomated (QIAGEN™, Bio-Rad, Monarch®, and Canvax™), and fully automated (QIAcube™ and Maxwell®) processes, from two biological matrices: human Jurkat T cells and peripheral blood mononuclear cells (PBMC). Results showed marked differences in the RNA quality and functionality according to the method employed for RNA extraction and the matrix used. DISCUSSION: QIAcube™ and semi-automated extraction methods were perceived as the best options because of their lower variability, good functionality, and lower cost (P < 0.001). These data contribute to facilitating researchers or research service platforms (Biobanks) in decision-making practices and emphasize the relevance of the selection of the RNA extraction method in each experimental procedure or traceability study to guarantee both quality standards and its reproducibility.

Entropy is a good approximation to the electronic (static) correlation energy.

For an electronic system, given a mean field method and a distribution of orbital occupation numbers that are close to the natural occupations of the correlated system, we provide formal evidence and computational support to the hypothesis that the entropy (or more precisely -σS, where σ is a parameter and S is the entropy) of such a distribution is a good approximation to the correlation energy. Underpinning the formal evidence are mild assumptions: the correlation energy is strictly a functional of the occupation numbers, and the occupation numbers derive from an invertible distribution. Computational support centers around employing different mean field methods and occupation number distributions (Fermi-Dirac, Gaussian, and linear), for which our claims are verified for a series of pilot calculations involving bond breaking and chemical reactions. This work establishes a formal footing for those methods employing entropy as a measure of electronic correlation energy (e.g., i-DMFT [Wang and Baerends, Phys. Rev. Lett. 128, 013001 (2022)] and TAO-DFT [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)]) and sets the stage for the widespread use of entropy functionals for approximating the (static) electronic correlation.

Measurement of yield and quality of DNA in human buffy coat is extraction method dependent.

During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.

Current use of biologic therapies for musculoskeletal disease: A survey of board-certified equine specialists.

OBJECTIVE: To evaluate the use of mesenchymal stem cells (MSCs), autologous conditioned serum (ACS), platelet-rich plasma (PRP), and autologous protein solution (APS) for the treatment of equine musculoskeletal disease by diplomates of the American College of Veterinary Surgery (ACVS), and American College of Veterinary Sports Medicine and Rehabilitation (ACVSMR). STUDY DESIGN: Cross-sectional study. SAMPLE POPULATION: Diplomates (n = 423). METHODS: An email link was sent to ACVS and ACVMR diplomates. A survey contained 59 questions regarding demographics, as well as indications, frequency, adverse effects, and limitations of use. Responses were analyzed using Fisher's exact test. RESULTS: One hundred and fifty four surveys were analyzed. Years in practice and type of practice were not associated with biologic therapy use. PRP was the most used therapy (120/137; 87.5%). PRP and MSCs were most often administered intralesionally while ACS and APS were most often administered intra-articularly. ACS (50/104; 48.1%) treatment was repeated commonly within 2 weeks of initial injection. MSCs (39/90; 43.3%) and PRP (38/100; 38%) were commonly repeated 1-2 months after initial injection and APS was typically repeated >4 months after initial injection (21/53; 39.6%). Local inflammation and expense were the most common adverse effect and limitation of use. CONCLUSION: Diplomates most commonly utilized PRP and MSC intralesionally for soft-tissue injuries, and ACS and ACP intra-articularly for joint injury. Protocols for repeated administration varied widely. Local inflammation was a clinical concern with the use of biologics. CLINICAL SIGNIFICANCE: Biologic therapies are used commonly by ACVS and ACVSMR diplomates for soft tissue and joint disease.

A scoping review of the detection, epidemiology and control of Cyclospora cayetanensis with an emphasis on produce, water and soil.

Cyclospora cayetanensis is a parasite causing cyclosporiasis (an illness in humans). Produce (fruits, vegetables, herbs), water and soil contaminated with C. cayetanensis have been implicated in human infection. The objective was to conduct a scoping review of primary research in English on the detection, epidemiology and control of C. cayetanensis with an emphasis on produce, water and soil. MEDLINE® (Web of ScienceTM), Agricola (ProQuest), CABI Global Health, and Food Science and Technology Abstracts (EBSCOhost) were searched from 1979 to February 2020. Of the 349 relevant primary research studies identified, there were 75 detection-method studies, 40 molecular characterisation studies, 38 studies of Cyclospora in the environment (33 prevalence studies, 10 studies of factors associated with environmental contamination), 246 human infection studies (212 prevalence/incidence studies, 32 outbreak studies, 60 studies of environmental factors associated with non-outbreak human infection) and eight control studies. There appears to be sufficient literature for a systematic review of prevalence and factors associated with human infection with C. cayetanensis. There is a dearth of publicly available detection-method studies in soil (n = 0) and water (n = 2), prevalence studies on soil (n = 1) and studies of the control of Cyclospora (particularly on produce prior to retail (n = 0)).

Spotting intruders: Species distribution models for managing invasive intertidal macroalgae.

Invasive macroalgae represent one of the major threats to marine biodiversity, ecosystem functioning and structure, as well as being important drivers of ecosystem services depletion. Many such species have become well established along the west coast of the Iberian Peninsula. However, the lack of information about the distribution of the invaders and the factors determining their occurrence make bioinvasions a difficult issue to manage. Such information is key to enabling the design and implementation of effective management plans. The present study aimed to map the current probability of presence of six invasive macroalgae: Grateloupia turuturu, Asparagopsis armata, Colpomenia peregrina, Sargassum muticum, Undaria pinnatifida, and Codium fragile ssp. fragile. For this purpose, an extensive field survey was carried out along the coast of the north-western Iberian Peninsula. Species distribution models (SDMs) were then used to map the presence probability of these invasive species throughout the study region on the basis of environmental and anthropogenic predictor variables. The southern Galician rias were identified as the main hotspots of macroalgal invasion, with a high probability of occurrence for most of the species considered. Conversely, the probability of presence on the Portuguese coast was generally low. Physico-chemical variables were the most important factors for predicting the distribution of invasive macroalgae contributing between 57.27 and 85.24% to the ensemble models. However, anthropogenic factors (including size of vessels, number of shipping lines, distance from ports, population density, etc.) considerably improved the estimates of the probability of occurrence for most of the target species. This study is one of the few to include anthropogenic factors in SDMs for invasive macroalgae. The findings suggest that management actions aimed at controlling these species should strengthen control and surveillance at ports, particularly in southern Galician rias. Early detection should be of main concern for risk assessment plans on the Portuguese coast.

Quantitative interactions between Candida albicans and the mutans streptococci in patients with Down Syndrome.

BACKGROUND: Oral microorganisms produce damage through the transfer to bloodstream, colonizing other tissues or direct damage in the oral cavity. Aim to study the quantitative interactions between C. albicans and the mutans streptococci and ms serotypes in the saliva of the oral cavity of patients with Down syndrome (DS). MATERIAL AND METHODS: Included 120 patients of both genders, 60 patients with Down syndrome (DS) and 60 pa- tients as a control group (CG). Samples of saliva were taken, and bacteria and fungi were grown on TYCSB and Saboureaud agar. Microbiological, serological and quantitative analyses were performed to determine the kind of isolated of microorganisms corresponding to the ms c, e, f and k for species S. mutans and d and g for S. sobrinus and C. albicans. Electronic scanning microscopy was employed to visualize and confirm the colonies under study. Statistics analysis included t-test proofs for matched data test, Scheffé and ANOVA. RESULTS: Forming units (CFU) per mL of saliva of C. albicans a significant difference was observed among DS

Effect of CRHR1 and CRHR2 gene polymorphisms and childhood trauma in suicide attempt.

Family, twin, and adoption studies have suggested that genetic factors might be involved in suicidal behavior. Corticotropin-releasing receptor type 1 (CRHR1) and 2 (CRHR2) genes play a key role in the activation and modulation of the hypothalamic-pituitary-adrenal (HPA) axis, which is considered a major stress regulator. Childhood trauma is an environmental risk factor associated with suicide attempt (SA) and it has been related to HPA axis dysregulation. This study aimed at analyzing the relationship of CRHR1 and CRHR2 genes with childhood trauma concerning the development of SA. In this study, we included 366 affective disorder patients. Among them, 183 patients had SA at least once and 183 had not SA. Information regarding SA and childhood trauma was obtained from medical records. Multifactor Dimensionality Reduction program was used to detect gene-environment interactions between CRHR1 (rs110402, rs242924, and rs16940665) and CRHR2 (rs2190242, rs2284217, and rs2014663) with childhood trauma in SA. The analysis showed an interaction of CRHR1 and CRHR2 with childhood trauma, thus conferring increased risk of having presented at least one SA (OR 7.44; 95% CI 4.58-12.07; p < 0.0001). In addition, we observed the following in the trauma subtypes analysis: physical negligence (OR 4.72; 95% CI 3.01-7.40; p < 0.0001), emotional abuse (OR 5.76; 95% CI 3.67-9.05; p < 0.0001), and sexual abuse (OR 5.70; 95% CI 3.62-8.97; p < 0.0001). Our results suggested that genetic variants of CRHR1 and CRHR2 genes in addition to physical negligence, and emotional and sexual abuse, contribute to increase risk of presented at least one SA.

Quality assessment on the long-term cryopreservation and nucleic acids extraction processes implemented in the andalusian public biobank.

Human samples are commonly collected and long-term stored in biobanks for current and future analyses. Even though techniques for freezing human blood are well established, the storage time can compromise the cell viability as well as the yield and quality of nucleic acids (RNA and DNA) extracted from them. In this study, a protocol to obtain peripheral blood mononuclear cells (PBMCs) from 70 subjects, which were stored at - 196 °C from EDTA tubes for a long-term, was assessed. In parallel; a protocol to obtain DNA from the same subjects, which were stored at - 80 °C from citrate tubes, was also studied. Samples stored from 2008 to 2012 were studied and the results obtained showed that there were no statistically significant differences in the RNA or DNA extracted in terms of purity, integrity and functionality The freezing protocol used by the Málaga Biobank shows that viable PBMCs and DNA could be kept for a period of, at least, 10 years, with a high quality and performance. Furthermore, RNA extracted from these PBMCs presents also a good quality and performance. Therefore, the samples frozen according to the conditions of the protocols assessed in this study could be optimal for biomedical research.

Pneumonia eosinofilic in pediatrics, clinical cases. / Neumonía eosinofílica en pediatría, a propósito de dos casos clínicos.

INTRODUCTION: Eosinophilic Pneumonia (EP) is a very rare disorder in Pediatrics. It is characterized by the infiltra tion of eosinophils in the pulmonary and alveolar interstitium, and may be primary or secondary as well as present an acute or chronic progress. OBJECTIVE: to present 2 pediatric EP clinical cases which were diagnosed at the pediatric intensive care unit of Clinica Indisa in Santiago, Chile between 2014 and 2017. CLINICAL CASES: Two older infants, who were hospitalized due to respiratory failure with a diagnosis of viral pneumonia. Both have asthmatic mothers. Additionally, they both had febrile syn drome, persistent condensation images in the chest x-rays, and peripheral eosinophilia throughout the course of the disease. One of the infants required oxygen for more than one month, and there was no eosinophilia in the bronchoalveolar lavage (BAL). In this case, the diagnosis of EP was reached via pulmonary biopsy. The other infant required mechanic ventilation for 28 days, and was diagnosed due to eosinophilia greater than 25% in the bronchoalveolar lavage. Both patients had excellent res ponse to systemic corticosteroids. CONCLUSION: After ruling out other causes, EP should be suspected in children with pneumonia diagnosis, and persistent symptoms that do not respond positively to treatment, especially if associated with peripheral eosinophilia. The diagnosis of EP in pediatrics is confirmed with eosinophilia greater than 20% in BAL and, in some cases, it is necessary to perform a lung biopsy.

Autodisplay of an avidin with biotin-binding activity on the surface of Escherichia coli.

OBJECTIVES: To display a recombinant avidin fused to the autotransporter ShdA to bind biotinylated molecules on the surface of Escherichia coli. RESULTS: Two chimeric protein constructs containing avidin fused to the autotransporter ShdA were expressed on the surface of Escherichia coli DH5α. One fusion protein contained 476 amino acids of the ShdA α and ß domains, whereas the second consisted of a 314 amino acid from α and truncated ß domains. Protein production was verified by SDS-PAGE using an antibody to the molecular FLAG-tag. The surface display of the avidin-shdA fusion protein was confirmed by confocal microscopy and flow cytometry analysis, and the biotin-binding activity was evaluated by fluorescence microscopy and flow cytometry using biotin-4-fluorescein and biotinylated-ovalbumin (OVA). CONCLUSIONS: Expression of a recombinant avidin with biotin-binding activity on the surface of E. coli was achieved using the autotransporter ShdA. This system is an alternative to bind biotinylated molecules to E. coli.

Early mobilization: Why, what for and how?

Early mobilization strategies in the intensive care unit may result in the prevention and reduction of polyneuromyopathy in the critical patient, improved quality of life, shortened ICU and hospital stay, and lesser mortality during hospitalization. However, it is well known that factors such as the protocol used, the population included in the studies, the timing of the strategy, the severity of the patients and different barriers directly influence the outcomes. This study examines the main protocols described in the literature and their associated results. The main techniques used were kinesitherapy, transfer and locomotion training, as well as neuromuscular electrical stimulation and cycle ergometry. Although two trials and a meta-analysis found no positive results with mobilization, programs that focus on specific populations, such as patients with weakness due to immobility and with preserved neuromuscular excitability can derive more positive effects from such treatment.

PET-CT in presurgical lymph node staging in non-small cell lung cancer: the importance of false-negative and false-positive findings. / La PET-TC en la estadificación ganglionar prequirúrgica del carcinoma de pulmón de células no pequeñas: implicación de los falsos negativos y falsos positivos.

OBJECTIVE: To assess the importance of false-negative and false-positive findings in computed tomography (CT) and 18F-FDG positron emission tomography (PET) in mediastinal lymph node staging in patients undergoing surgery for non-small cell lung cancer (NSCLC). MATERIAL AND METHODS: This retrospective study included 113 consecutive patients and 120 resected NSCLCs; 22 patients received neoadjuvant treatment. We compared the findings on preoperative 18F-FDG PET-CT studies with the postoperative pathology findings. Lymph node size and primary tumor size were measured with CT, and lymph nodes and primary tumors were evaluated qualitatively and semiquantitatively (using standardized uptake values (SUVmax)) with PET. RESULTS: Metastatic lymph nodes were found in 26 (21.7%) of the 120 tumors and in 41 (7.7%) of the 528 lymph node stations analyzed. 18F-FDG PET-CT yielded 53.8% sensitivity, 76.6% specificity, 38.9% positive predictive value, 85.7% negative predictive value, and 71.7% diagnostic accuracy. The false-negative rate was 14.2%. Multivariable analysis found that the factors associated with false-negative findings were a moderate degree of differentiation in the primary tumor (p = 0.005) and an SUVmax of the primary tumor >4 (p = 0.027). The false-positive rate was 61.1%, and the multivariable analysis found that lymph node size >1cm was associated with false-positive findings (p < 0.001). CONCLUSIONS: In mediastinal lymph node staging in patients with NSCLC, 18F-FDG PET-CT improves the specificity and negative predictive value and helps clinicians to select the patients that will benefit from surgery. Given the high rate of false positives, histological confirmation of positive cases is recommendable.

[Preoperative and follow-up cardiac magnetic resonance imaging of candidates for surgical ventricular restoration]. / Resonancia magnética cardíaca prequirúrgica y de seguimiento en pacientes candidatos a endoventriculoplastia.

PURPOSE: To assess pre and post-operative cardiac MRI (CMR) findings in patients with left endoventriculoplasty repair for ventricular aneurysm due to ischemic heart disease. MATERIAL AND METHODS: Data were retrospectively gathered on 21 patients with diagnosis of ventricular aneurysm secondary to ischemic heart disease undergoing left endoventriculoplasty repair between January 2007 and March 2013. Pre and post-operative CMR was performed in 12 patients. The following data were evaluated in pre-operative and post-operative CMR studies: quantitative analysis of left ventricular ejection fraction (LVEF), left ventricular end-diastolic (LVEDV) and end-systolic (LVESV) volume index, presence of valvular disease and intracardiac thrombi. The time between surgery and post-operative CRM studies was 3-24 months. RESULTS: Significant differences were found in the pre and post-operative LVEF, LVEDV and LVESV data. EF showed a median increase of 10% (IQR 2-15) (p=0.003). The LVEDV showed a median decrease of 38 ml/m(2) (IQR 18-52) (p=0.006) and the LVESV showed a median decrease of 45 ml/m(2) (IQR:12-60) (p=0.008). Post-operative ventricular volume reduction was significantly higher in those patients with preoperative LVESV >110 ml/m(2) (59 ml/m(2) and 12 ml/m(2), p=0.006). CONCLUSION: In patients with ischemic heart disease that are candidates for left endoventriculoplasty, CMR is a reliable non-invasive and reproducible technique for the evaluation of the scar before the surgery and the ventricular volumes and its evolution after endoventricular surgical repair.

Effects of region of birth, educational level and age on late presentation among men who have sex with men newly diagnosed with HIV in a network of STI/HIV counselling and testing clinics in Spain.

This paper analyses late presentation (LP) of HIV infection, and its determinants, among men who have sex with men (MSM) in Spain, newly diagnosed with HIV (2003-2011) in 15 sexually transmitted infection/HIV counselling and testing clinics. LP was defined as <350 CD4 cells/µL or AIDS. In total, 3,081 MSM were included (2,499 having CD4/AIDS); overall LP was 25.3%. LP was higher in men older than 34 years, those not previously HIV-tested (adjusted odds ratio (aOR):3.1; 95% confidence intervals (CI):2.3-4.2) , and those tested > 12 months before diagnosis (12-24 months (aOR:1.4; 95% CI:1.0-2.0); > 24 months (aOR:2.2; 95% CI:1.7-3.0)). LP was less likely in MSM reporting a known HIV-infected partner as infection source or symptoms compatible with acute retroviral syndrome. 'Region of birth' interacted with 'educational level' and 'steady partner as infection source': only African and Latin-American MSM with low educational level were more likely to present late; Latin-American men attributing their infection to steady partner, but no other MSM, had LP more frequently. In Spain, HIV testing among MSM should be promoted, especially those > 34 years old and migrants with low educational level. The current recommendation that MSM be tested at least once a year is appropriate.

Trends in HIV testing, prevalence among first-time testers, and incidence in most-at-risk populations in Spain: the EPI-VIH Study, 2000 to 2009.

During 2000 to 2009, data on people undergoing HIV testing and on those newly diagnosed with HIV were collected in a network of 20 Spanish clinics specialising in sexually transmitted infections and/or HIV testing and counselling. The number of tests performed, overall and disaggregated by different variables, was obtained. HIV prevalence among first-time testers and HIV incidence among repeat testers were calculated. To evaluate trends, joinpoint regression models were fitted. In total, 236,939 HIV tests were performed for 165,745 individuals. Overall HIV prevalence among persons seeking HIV testing was 2.5% (95% CI: 2.4 to 2.6). Prevalence was highest in male sex workers who had sex with other men (19.0% (95% CI: 16.7 to 21.4)) and was lowest in female sex workers (0.8% (95% CI: 0.7 to 0.9)). Significant trends in prevalence were observed in men who have sex with men (MSM) (increasing) and heterosexual individuals (decreasing). The incidence analysis included 30,679 persons, 64,104 person-years (py) of follow-up and 642 seroconversions. The overall incidence rate (IR) was 1.0/100 py (95% CI: 0.9/100 to 1.1/100). Incidence was significantly higher in men and transgender females than in women (1.8/100 py (95% CI: 1.6 to 1.9), 1.2/100 py (95% CI: 0.5 to 2.8) and 0.1/100 py (95% CI: 0.09 to 0.2) respectively) and increased with age until 35­39 years. IRs in MSM and people who inject drugs were significantly greater than in heterosexual individuals (2.5/100 py (95% CI: 2.3 to 2.7), 1.6/100 py (95% CI: 1.1 to 2.2) and 0.1/100 py (95% CI: 0.09 to 0.2) respectively), and an upward trend was observed in MSM. Our results call for HIV prevention to be reinforced in MSM and transgender women in Spain.

Absorption and deposition of xanthophylls in broilers challenged with three dosages of Eimeria acervulina oocysts.

1. An experiment was designed to evaluate the effect of different doses of oocysts of Eimeria acervulina on intestinal absorption and skin deposition of xanthophylls (XAs) in broilers. 2. A total of 192 broiler chickens were randomly assigned to 4 groups: an uninfected control group and three groups inoculated with either 1 × 10(2), 1 × 10(4) or 1 × 10(5) sporulated oocysts of E. acervulina by gavaging at 21 d. There were 4 replicate pens (2 male and 2 female) per group. 3. Plasma xanthophyll (PX) and skin yellowness (SY) were measured in live birds weekly. At 42 d of age, SY was measured in the breast and abdomen after chilling and in the breast 24 h post-processing on refrigerated carcasses. 4. In general, in all challenged treatments, and for the duration of the study, the average PX decreased by 0.02 µg/ml (R(2) = 61.6%) for every 1000 inoculated oocysts, whereas PX increased by 1.26 µg/ml/d in uninfected birds. 5. The average SY in live birds from 21 to 42 d of age decreased by 0.019 b*/every 1000 oocysts administered, while SY of uninfected controls increased by 0.57 b*/d. It was also noted that in all treatments females had a greater SY (6.17 b*) than males for the duration of the study. The SY of the breast and abdomen was correlated (r = 0.76) in chilled carcasses. Breast SY in 24 h refrigerated carcasses was greater in the control group and for female birds. 6. Oocyst excretion was different between inoculated treatments only on 7 d post-inoculation (PI). Coccidia lesion scores in the duodenum averaged 1+ in infected birds and 2+ in birds given the highest oocyst dose.

Direct laser acceleration: A model for the electron injection from the walls of a cylindrical guiding structure.

We use analytical methods and particle-in-cell simulation to investigate the origin of electrons accelerated by the process of direct laser acceleration driven by high-power laser pulses in preformed narrow cylindrical plasma channels. The simulation shows that the majority of accelerated electrons are originally located along the interface between the channel wall and the channel interior. The analytical model based on the electron hydrodynamics illustrates the underlying physical mechanism of the release of electrons from the channel wall when irradiated by an intense laser, the subsequent electron dynamics, and the corresponding evolution of the channel density profile. The quantitative predictions of the total charge of released electrons and the average electron density inside the channel are validated by comparison with the simulation results.