Enhancing image captioning with depth information using a Transformer-based framework

Captioning images is a challenging scene-understanding task that connects computer vision and natural language processing. While image captioning models have been successful in producing excellent descriptions, the field has primarily focused on generating a single sentence for 2D images. This paper investigates whether integrating depth information with RGB images can enhance the captioning task and generate better descriptions. For this purpose, we propose a Transformer-based encoder-decoder framework for generating a multi-sentence description of a 3D scene. The RGB image and its corresponding depth map are provided as inputs to our framework, which combines them to produce a better understanding of the input scene. Depth maps could be ground truth or estimated, which makes our framework widely applicable to any RGB captioning dataset. We explored different fusion approaches to fuse RGB and depth images. The experiments are performed on the NYU-v2 dataset and the Stanford image paragraph captioning dataset. During our work with the NYU-v2 dataset, we found inconsistent labeling that prevents the benefit of using depth information to enhance the captioning task. The results were even worse than using RGB images only. As a result, we propose a cleaned version of the NYU-v2 dataset that is more consistent and informative. Our results on both datasets demonstrate that the proposed framework effectively benefits from depth information, whether it is ground truth or estimated, and generates better captions. Code, pre-trained models, and the cleaned version of the NYU-v2 dataset will be made publically available.Comment: 19 pages, 5 figures, 13 table

Xeno-free trans-differentiation of adipose tissue-derived mesenchymal stem cells into glial and neuronal cells.

Mesenchymal stem cells (MSCs) are undifferentiated cells that have the ability of self-renewal and trans-differentiation into other cell types. They hold out hope for finding a cure for many diseases. Nevertheless, there are still some obstacles that limit their clinical transplantation. One of these obstacles are the xenogeneic substances added in either proliferation or differentiation media with subsequent immunogenic and infectious transmission problems. In this study, we aimed to replace fetal bovine serum (FBS), the main nutrient source for MSC proliferation with xeno-free blood derivatives. We tested the effect of human activated pure platelet-rich plasma (P-PRP) and advanced platelet-rich fibrin (A-PRF) on the proliferation of human adipose derived-MSCs (AD-MSCs) at different concentrations. For the induction of MSC neural differentiation, we used human cerebrospinal fluid (CSF) at different concentrations in combination with P-PRP to effect xeno-free/species-specific neuronal/glial differentiation and we found that media with 10% CSF and 10% PRP promoted glial differentiation, while media with only 10% PRP induced a neuron-like phenotype

Application of the ANOVA method in the optimization of a thermoelectric cooler-based dehumidification system

© 2022 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).In recent studies, Thermo-Electric Coolers (TEC) have been utilized for dehumidification purposes, which is mainly based on the extraction of moisture from humid atmospheric air. The reviewed literature showed that the rate of water collection from the TEC-based system can be affected by various parameters such as the module’s input voltage, the heat sink orientation, and tilt angles. In this research, the analysis of variance (ANOVA) was used to examine the significance of these factors and their interaction within the system on the TEC-based dehumidification system. Four levels were investigated for both, the Peltier’s input voltage and the rotation angle, and three levels for the tilt angle. This study indicated the significance of the studied factors and their interactions within the dehumidification system along with performing an overall numerical optimization. The experiments were conducted under the same working conditions in an enclosed environment to minimize errors. According to the overall numerical optimization, which was validated experimentally, the optimum system performance was predicted to be obtained at approximately 6.8V Peltier input volt, 65° rotation angle, and 90° tilt angles, with predicted optimum productivities of 0.32278 L/kWh and 13.03 mL/hr. For the same set of parameters, the variation between the experiment and the numerical optimization was less than 4%. The experiments show that when optimizing water collection rates for thermoelectric cooling heat sinks​ under high humidity conditions, the orientation of the heat sink should be considered.Peer reviewe

Molecular Identification of Ladybird Beetles (Coccinella: Coccinellidae) Using DNA Barcodes

DNA barcoding is a molecular genetics technique commonly applied for species identification based on the cytochrome c oxidase subunit I (COI) gene located on the mitochondrial DNA genome. Based on our analysis, the DNA barcodes were generated from 16 specimen of Coccinella (family Coccinellidae). All the samples were collected from diverse sites in Egypt and Libya. Morphological traits based on the number of dorsal spots, DNA extraction, PCR amplification of COI, sequencing, nucleotide BLAST, and phylogenetics analyses were used to classify the specimens. A phylogenetic tree was constructed using the maximum likelihood method, including 46 COI sequences (the study and NCBI sequences). Three Coccinella clusters were defined and classified as Coccinella septempunctata, Coccinella novemnotata, and Coccinella undecimpunctata each species clustered into a unique branch. DNA barcodes discriminated clearly against the analyzed species. This study validated the COI efficiency as a marker for DNA barcoding of insects (Coccinella, family Coccinellidae)

Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability

The overall pattern of the SARS-CoV-2 pandemic so far has been a series of waves; surges in new cases followed by declines. The appearance of novel mutations and variants underlie the rises in infections, making surveillance of SARS-CoV-2 mutations and prediction of variant evolution of utmost importance. In this study, we sequenced 320 SARS-CoV-2 viral genomes isolated from patients from the outpatient COVID-19 clinic in the Children’s Cancer Hospital Egypt 57357 (CCHE 57357) and the Egypt Center for Research and Regenerative Medicine (ECRRM). The samples were collected between March and December 2021, covering the third and fourth waves of the pandemic. The third wave was found to be dominated by Nextclade 20D in our samples, with a small number of alpha variants. The delta variant was found to dominate the fourth wave samples, with the appearance of omicron variants late in 2021. Phylogenetic analysis reveals that the omicron variants are closest genetically to early pandemic variants. Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. Finally, we observed a large number of highly correlated mutations, and some negatively correlated mutations, and identified a general inclination toward mutations that lead to enhanced thermodynamic stability of the spike protein. Overall, this study contributes genetic and phylogenetic data, as well as provides insights into SARS-CoV-2 viral evolution that may eventually help in the prediction of evolving mutations for better vaccine development and drug targets

Perspective Chapter: The Toxic Silver (Hg)

In the late 1950s, residents of a Japanese fishing village known as “Minamata” began falling ill and dying at an alarming rate. The Japanese authorities stated that methyl-mercury-rich seafood and shellfish caused the sickness. Burning fossil fuels represent ≈52.7% of Hg emissions. The majorities of mercury’s compounds are volatile and thus travel hundreds of miles with wind before being deposited on the earth’s surface. High acidity and dissolved organic carbon increase Hg-mobility in soil to enter the food chain. Additionally, Hg is taken up by areal plant parts via gas exchange. Mercury has no identified role in plants while exhibiting high affinity to form complexes with soft ligands such as sulfur and this consequently inactivates amino acids and sulfur-containing antioxidants. Long-term human exposure to Hg leads to neurotoxicity in children and adults, immunological, cardiac, and motor reproductive and genetic disorders. Accordingly, remediating contaminated soils has become an obligation. Mercury, like other potentially toxic elements, is not biodegradable, and therefore, its remediation should encompass either removal of Hg from soils or even its immobilization. This chapter discusses Hg’s chemical behavior, sources, health dangers, and soil remediation methods to lower Hg levels

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P &lt; 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely