Accuracy of computed tomography in diagnosing malignancy in solitary pulmonary lesions

OBJECTIVE: To evaluate accuracy of Computed Tomography (CT) for diagnosing malignancy in solitary pulmonary lesions (SPLs). METHODS: A prospective cross-sectional study was conducted from 20-01-2007 to 30-06-2008 at the Radiology department, Aga Khan University Hospital (AKUH) Karachi. Fifty-three patients with solitary pulmonary lesions (SPLs) seen in prior chest x-rays or chest CT scans were referred to radiology department for CT guided biopsy. CT scan was performed for each patient prior to biopsy and CT evaluation of the SPLs was performed followed by CT guided Biopsy. Histopathological diagnosis of the lesion was taken as the gold standard. RESULTS: CT was found to be 100% sensitive, 30% specific and 87% accurate for diagnosing malignancy in solitary pulmonary lesions while PPV and NPV were 86% and 100% respectively. CONCLUSION: CT scan is highly sensitive yet non-specific and cannot be used as the definitive diagnostic modality for diagnosing malignancy in solitary pulmonary lesions

First Comprehensive In Silico

GalNAc-T1, a key candidate of GalNac-transferases genes family that is involved in mucin-type O-linked glycosylation pathway, is expressed in most biological tissues and cell types. Despite the reported association of GalNAc-T1 gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. Therefore, sequence- and structure-based computational tools were employed to screen the entire listed coding SNPs of GalNAc-T1 gene in order to identify and characterize them. Our concordant in silico analysis by SIFT, PolyPhen-2, PANTHER-cSNP, and SNPeffect tools, identified the potential nsSNPs (S143P, G258V, and Y414D variants) from 18 nsSNPs of GalNAc-T1. Additionally, 2 regulatory SNPs (rs72964406 and #x26; rs34304568) were also identified in GalNAc-T1 by using FastSNP tool. Using multiple computational approaches, we have systematically classified the functional mutations in regulatory and coding regions that can modify expression and function of GalNAc-T1 enzyme. These genetic variants can further assist in better understanding the wide range of disease susceptibility associated with the mucin-based cell signalling and pathogenic binding, and may help to develop novel therapeutic elements for associated diseases

Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution. Findings: Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates. After taking into account population growth and ageing, the absolute number of DALYs has remained stable. Since 2010, the pace of decline in global age-standardised DALY rates has accelerated in age groups younger than 50 years compared with the 1990–2010 time period, with the greatest annualised rate of decline occurring in the 0–9-year age group. Six infectious diseases were among the top ten causes of DALYs in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). In adolescents aged 10–24 years, three injury causes were among the top causes of DALYs: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). Five of the causes that were in the top ten for ages 10–24 years were also in the top ten in the 25–49-year age group: road injuries (ranked first), HIV/AIDS (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). In 2019, ischaemic heart disease and stroke were the top-ranked causes of DALYs in both the 50–74-year and 75-years-and-older age groups. Since 1990, there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries. In 2019, there were 11 countries where non-communicable disease and injury YLDs constituted more than half of all disease burden. Decreases in age-standardised DALY rates have accelerated over the past decade in countries at the lower end of the SDI range, while improvements have started to stagnate or even reverse in countries with higher SDI. Interpretation: As disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and developm nt investment is needed to identify new, more effective intervention strategies. With a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. The mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve. Funding: Bill & Melinda Gates Foundation. © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licens

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Distributed image and video coding based on compressed sensing : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computer Engineering at Massey University, New Zealand

Conventional methods for encoding of images and videos is a complex process with high computational demands. They are designed for application scenarios where the signals concerned are encoded once and played back many times. However, new applications such as wireless video sensor networks demand low cost and low power cameras with limited computing resources. The focus of this thesis is on such image and video coding systems where the computational burden is shifted from the encoder to the decoder. Three separate coding schemes have been developed { two for videos and one for images. Together they form a framework for distributed coding which is based on the theory of compressed sensing and distributed coding. Compressed sensing is a relatively new theory for the acquisition of sparse signals that allows the sampling rate to be much lower than the Nyquist limit. Distributed coding is based on the theorem by Slepian and Wolf, and Wyner and Ziv. It allows different correlated parts of a signal to be encoded independently without loss of coding efficiency. The decoding of these separately encoded parts are then decoded jointly in order to exploit the correlation between them. The main characteristics of the coding scheme proposed in this thesis are: (1) they do not require the use of traditional codecs; (2) only compressed sensing measurements are used for encoding and decoding; (3) no motion estimation and compensation are involved for videos. The first proposed coding scheme is for the encoding of whole video frames. The compressed sensing measurement of individual frames are separately encoded. These frames are divided into key and non-key frames with the key frames encoded at a higher rate than non-key ones. While the key frames are decoded independently, the non-key ones are decoded with the help of side information generated from the measurements of the key frames. The most important part of the decoder is a simple, yet effective, side information generation method which requires only minimal computation. The side information generated is simply added to the measurements of the non-key frames for use with any compressed sensing reconstruction algorithm. The other two coding schemes are block-based coding methods. Each image or frame is divided into non-overlapping image blocks in a similar way it is done in some existing coding standards. The coding of the blocks are performed in a distributed manner by classifying them into key blocks and nonkey blocks. An adaptive encoding strategy based on block similarity is also developed. Experimental analyses using publicly available test images and videos show that the performances of the simpler codecs proposed are better than other existing compressed sensing based codecs. The video codecs also out-perform conventional distributed video codec in terms of simplicity, compression ratio and decoding complexity. The basis of these coding methods is on the correlation of frames or blocks. This correlation is established through experimental analyses. These analyses also showed that the minimum square error between any pair of them can be effectively used as a measure of correlation. In conjunction with the development of the codecs, a quantization scheme that is tailored to the statistics of CS measurements has also been proposed. This scheme yields better results than a uniform quantizer and those used for JPEG. The quantizer is also robust against different statistics of individual images. Separate experimental evaluations also show that structurally random matrices are the best sensing matrices for acquiring images and the sparse reconstruction by separable approximation (SpaRSA) algorithm produces the best reconstructed image quality

Single stage cricoid split laryngoplasty with costochondral rib grafting is a novel approach to treat subglottic stenosis in a paediatric patient: A case report

Introduction and importance: Subglottic stenosis (SGS) appears to be a commonly encountered condition in the paediatric age group. Single stage cricoid split laryngoplasty with costochondral rib grafting in paediatric patients is a unique, innovative, and advanced operation in nature. Morbidity and mortality rates can be minimized with early diagnosis and prompt treatment.Presentation of case: Presenting the case of a 13-month-old child diagnosed with Grade II SGS who was managed for cricoid split laryngoplasty with a costochondral rib graft. It was a unique strategy for providing infants and neonates with symptomatic SGS with a safe and efficient substitute for long-term tracheostomy. When healing was completed, the patient regained the function of their airway. The approach was successful, and preventable to long-term tracheostomy.Discussion: Performing this procedure early in children has shown higher rates of success and it is safe and effective. Further extensive research and studies need to be conducted in this domain, and every patient\u27s status should be reviewed time and again to tend to their specific needs, and the choice of procedure should be made optimally based on clinical evaluations.Conclusion: Successful management of a 13-month-old child with Grade II subglottic stenosis through cricoid split laryngoplasty with costochondral rib grafting is a challenging and novel approach to treating single-stage SGS

DyxMnFe2-xO4 nanoparticles decorated over mesoporous silica for environmental remediation applications

An efficient, environment-friendly and economical catalyst to control contaminants of environment is an enduring interest in recent years. In this study, a new composite, DyxMnFe2-xO4nanoparticles decorated over mesoporous silica was synthesized and utilized for removal of organic pollutant. Highly crystalline nature of DyxMnFe2-xO4 nanoparticles and amorphous nature of material was confirmed by XRD (X-ray diffraction) technique. Infrared spectra of fabricated material before and after adsorption of dye molecules evidenced the successful adsorption of dye molecules by fabricated adsorbent. From field emission scanning electron microscopic (FESEM) images of Dy3+ substituted MnFe2O4 composite with mesoporous silica, it was clearly observed that ferrite particles of size 20−30 nm were decorated on the surface of mesoporous silica particles and distributed well over spherical silica balls homogeneously. Its magnificent mesoporous nature was revealed from BET (nitrogen adsorption-desorption measurements) analysis. Surface area, pore volume and average pore size was found 387.95 m2/g, 0.390 cm3/g and 4.02 nm respectively. Tri-modal pore size distribution showed its effective utilization in adsorption. The abundant (Si–OH) hydroxyl groups of mesoporous silica, the broad diffraction hump of silica depicted its superior loading capacity of target molecular specie inside its porous network. From band gap analysis, a red shift of 2.43 eV exhibited semiconductor photocatalysis of DyxMnFe2-xO4 nanoparticles. Degradation efficiency of bare MnFe2O4, DyxMnFe2-xO4 and mesoporous silica-based composite was tested using crystal violet dye. Its explored adsorption-photocatalysis synergy, degradation mechanism, kinetic investigation, easily recovery and remarkable recycling ability suggested that the new fabricated composite is best for environmental remediation

Synthesis of Carbon Nanotubes (CNTs) from Poultry Litter for Removal of Chromium (Cr (VI)) from Wastewater

Pakistan, an agricultural country, raises 146.5 million commercial and domestic poultry birds, which generate around 544,831 tons of waste per year. This waste finds its final disposal in agricultural land as soil fertilizer or disposal site amendment. The usage of poultry litter for this purpose is uncontrolled, which results in environmental degradation such as emission of greenhouse gases, e.g., methane. However, alternative options such as thermochemical conversion of poultry litter can offer better solutions where this waste can be used as a low-cost carbon source for the synthesis of Multiwalled Carbon Nanotubes (MWCNTs). In this study, efforts were made to utilize this cheap and plentiful carbon source for the synthesis of CNTs in the presence of Ni/Mo/MgO as a catalyst, through pyrolysis. For a better yield of carbon product, the optimum ratio for the catalysts (Ni/Mo/MgO) was found to be 4:0.2:1. Furthermore, the process parameters were also optimized for better carbon yield. A good yield of CNTs resulted from a pyrolysis time of 12 min, a temperature of 825 °C, and a catalyst weight of 100 mg. The structure and morphology of the produced nanotubes were confirmed through X-ray Diffractometer (X-RD) and Scanning Electron Microscopy (SEM). The environmental application of the nanotubes was tested in a synthetic chromium solution in the lab using a batch experiment. Different experimental conditions (pH, adsorbent dosage, and contact time) were optimized to improve the adsorption of Cr (VI) by carbon nanotubes and a UV-Visible spectrophotometer was used at 540 nm to measure the absorbance of Cr (VI). The results showed that up to 81.83% of Cr (VI) removal was achieved by using 8 mg of CNTs at pH 3 with 400 rpm at 180 min of contact time. Thus, it was concluded that poultry litter can be a useful source for the synthesis of MWCNTs and thereby removal of Cr (VI) from industrial tanneries’ wastewater

Structural and electrical properties of La3+ ions substituted MnFe2O4 ferrite nanoparticles synthesized via cost-effective reverse micelles strategy

La ^3+ ions substituted manganese ferrite (MnFe _2- _x La _x O _4 ) nanoparticles via reverse micelles strategy were synthesized and their structural and electrical properties are discussed in this article. Using low-cost precursors, mono-dispersed, and well crystalline MnFe _2- _x La _x O _4 nanoparticles were prepared at low temperature. X-ray diffraction (XRD) explored cubic spinel structure with minute secondary phase as LaFeO _3 . The crystallite size of MnFe _2- _x La _x O _4 was found to increase from 12.82 nm to 15.95 nm with increased La ^3+ ions contents. The room temperature Fourier transform infrared (FTIR) spectra were recorded in the wavenumber range 1000–400 cm ^−1 that showed the vibrational bands of octahedral and tetrahedral complexes. These bands are the fingerprints of spinel ferrites. Surface morphology characterized by field emission scanning electron microscopy (FESEM) revealed the relative spherical morphology of prepared spinel ferrite particles. The elemental composition analysis from Energy-dispersive x-ray (EDX) spectroscopy confirmed the presence of expected elements in the samples. The modification in resistivity and the enhancement in the dielectric parameters suggested the possible utilization of these soft ferrite nanoparticles in advanced electronics, especially the devices that are required to operate at high frequencies