Potential of Capparis decidua plant and eggshell composite adsorbent for effective removal of anionic dyes from aqueous medium

The presence of hazardous dyes in wastewater poses significant threats to both ecosystems and the natural environment. Conventional methods for treating dye-contaminated water have several limitations, including high costs and complex operational processes. This study investigated a sustainable bio-sorbent composite derived from the Capparis decidua plant and eggshells, and evaluated its effectiveness in removing anionic dyes namely tartrazine (E-102), methyl orange (MO), and their mixed system. The research examines the influence of initial concentration, contact time, pH, adsorbent dosage, and temperature on the adsorption properties of anionic dyes. Optimal removal of tartrazine (E-102), methyl orange (MO), and their mixed system was achieved at a pH of 3. The equilibrium was achieved at 80 min for MO and mixed systems, and 100 min for E-102. The adsorption process showed an exothermic nature, indicating reduced capacity with increasing temperature, consistent with heat release during adsorption. Positive entropy values indicated increased disorder at the solid-liquid interface, attributed to molecular rearrangements and interactions between dye molecules and the adsorbent. Isotherm analysis using Langmuir, Freundlich, Temkin, and Redlich-Peterson models revealed that the Langmuir model best fit the experimental data. The maximum adsorption capacities of 50.97 mg/g, 52.24 mg/g, and 56.23 mg/g were achieved for E-102, MO, and the mixed system under optimized conditions, respectively. The pseudo-second-order kinetic model demonstrated the best fit, indicating that adsorption occurs through physical and chemical interactions such as electrostatic attraction, pore filling, and hydrogen bonding. Hence, the developed bio-sorbent could be a sustainable and cost-effective solution for the treatment of anionic dyes from industrial effluents.

Simultaneous adsorption of methylene blue and amoxicillin by starch-impregnated MgAl layered double hydroxide: Parametric optimization, isothermal studies and thermo-kinetic analysis

Textile and pharmaceutical effluents contain significant amounts of dyes and antibiotics, which pose a serious threat to the ecosystem when discharged directly. Therefore, they should be treated by facile treatment techniques using low-cost materials. Layered double hydroxide (LDH) and its hybrids have emerged as robust and economic adsorbents for water treatment. Herein, magnesium/aluminum LDH and its starch-based composite were synthesized by a co-precipitation technique. The physicochemical features of the developed adsorbents were thoroughly characterized using various analytical tools. The developed materials were tested for the eradication of methylene blue (MB) and amoxicillin (AMX) in batch mode adsorption by varying operating conditions. Adsorption performance depends on the solution's pH. Under optimum adsorption conditions of pH 11, adsorbent dosage of 50 mg/L, and treatment time of 120 min, starch-impregnated MgAl-LDH exhibited maximum MB and AMX adsorption capacities of 114.94 and 48.08 mg/g, respectively. The adsorption mechanism states that hydrogen bonds and weak van der Waals forces are responsible for the removal of pollutants by the developed materials. Moreover, equilibrium and kinetic studies revealed that the removal of dye and antibiotic followed the Freundlich and Langmuir models with the pseudo-second-order reaction kinetics, respectively. The spent adsorbents were regenerated using 0.1 M HCl (for MB) and methanol (for AMX) eluent, and reusability studies ensured that the developed adsorbents retained their performance for up to four consecutive adsorption/desorption cycles. MgAl-LDH and its starch-based hybrid could thus be used to effectively remove organic contaminants from wastewater streams on a commercial scale.

Iodine supplementation through its biofortification in Brassica species depending on the type of soil

Iodine is an essential microelement for humans and its deficiency leads to iodine deficiency disorder (IDD) which is a common problem faced by people in hilly areas. Biofortification of iodine is an option to overcome the IDD problem. Herein, we investigated the iodine uptake and accumulation in the edible portion of vegetables such as Brassica napus (BNP) and Brassica pekinensis (BPK) which were grown on two different soils such as sandy soil (SS) and silty loam soil (SLS) with different concentrations of iodine application (used in sodium iodide form) such as 0 ppm, 50 ppm, and 100 ppm. The concentration of iodine was determined by the oxidation of iodide, and nutrients were examined by double acid digestion. Different concentrations of iodine were noticed in silty loam and sandy soils, roots, and shoots of BNP and BPK, while the concentration follows the order: soils > roots > shoots. Iodine concentrations in the roots of BNP and BPK ranged from 46 to 223.7 μg/g which shows a strong correlation with other soil nutrients. Moreover, a large amount of iodine was lost due to the leaching. It is concluded that the biofortification of iodine increases its concentration in Brassica species. This work provides a reference for the iodine biofortification in plant species which will be helpful to control IDD.

The Burden of Vitamin D Deficiency in Patients of Chronic Liver Disease

Objective: To determine the frequency of vitamin D deficiency in chronic liver disease patients. Study design: Cross-sectional study. Place and Duration of Study: Gastroenterology Department, Liaquat National Hospital and Medical College, Karachi Pakistan, from Jan to Dec 2020. Methodology: Patients between the age of 18 to 50 years, of either gender, already diagnosed case of chronic liver diseases for 6 months and had sun exposure of at least 15 minutes twice weekly were included in this study. History was taken after taking informed written consent, the clinical assessment was done, and blood samples were sent for serum vitamin D levels to determine the results. Results: The study included 177 patients with chronic liver disease. One hundred eleven patients (62.7%) were males and 66 patients (37.3%) were females, with the mean age of 45.0 ± 6.306 years. Vitamin D deficiency was observed in 100 patients (56.5%). Conclusion: The frequency of vitamin D deficiency was quite high. It increases with age and body mass index and is predominant in the male gender, while no association was noted with sun exposure time.

The impact of environment degrading factors and remittances on health expenditure: an asymmetric ARDL and dynamic simulated ARDL approach

This paper investigates the impact of CO₂ emissions, air pollution (PM2.5) exposure, foreign remittances, energy consumption, renewable energy consumption, trade openness, and gross domestic product per capita on health expenditure in a panel of the 27 highest emitting countries from 2000 to 2019. Focusing on objectives, panel ARDL, and dynamic simulated ARDL models are used to examine the short-run and long-run impact of the variables on health expenditure. An asymmetric or nonlinear ARDL model is used to test the asymmetric effect of CO₂ emissions, air pollution exposure, and foreign remittance inflows on health expenditure. The results show that environment-degrading factors, remittances, and GDP per capita significantly impact health expenditure. There is an asymmetric effect of remittances, CO₂ emissions, and air pollution (PM2.5) exposure on health expenditure. Based on the results, the study suggests policymakers should make policies regarding environment-degrading elements as these factors cause huge increases in health spending in a country. Consumption of renewable energy helps reduce health expenditure as it does not cause environmental degradation, irrespective of other forms of energy, and it is suggested that policies relating to foreign remittance inflows should be encouraged and made efficient.

EFFICACY OF ALFUZOSIN VERSUS CONTROL GROUP IN UPPER URETERIC STONE EXPULSION IN ADULT POPULATION OF LAHORE, PAKISTAN

Background: Urinary stone disease is one of the commonest urological diseases worldwide. The objective of this study was to compare the efficacy of alfuzosin versus control group in upper ureteric stone expulsion in adult population of district Lahore, Pakistan.Materials Methods: This trial was conducted in Department of Urology, Sheikh Zayed Hospital, Lahore, Pakistan form January 2017 to June 2017. All adult patients with upper ureteric stone size 5-10 mm were eligible. Those with multiple stones, having fever, severe pain, history of surgery in past two weeks and growth on urine culture or pyuria were excluded. Experimental and control groups each had 30 patients. Experimental group received Tab. alfuzosin 10 mg daily for four weeks and Tab. diclofenac sodium 50 mg SOS for acute pain. The control group received Tab. diclofenac sodium 50 mg SOS for acute pain. We followed all patients for four weeks for expulsion of ureteric stones by X-ray KUB or CT KUB. Sex, age and stone size were matching variables. Stone expulsion (yes, no) was research variable. We compared count of stone expulsion between two groups by using McNemar chi-square test at alpha 0.5 using GraphPad.Results: Out of 30 patients in experimental group, 23 (76.67%) were men and seven (23.33%) women and out of 30 in control group, 20 (66.67%) were men and 10 (33.33%) women, almost similar in both groups. Mean age in experimental group was 39.45±10.33 years and in control group it was 37.38±8.28 years, almost similar in both groups. Mean stone size was 7.45±1.47 (5-10) mm in the experimental and 7.28±1.68 (5-10) mm in control group, being comparable in both the groups. In experimental group, stone expulsion was achieved in 23 (76.67%) cases and not in seven (23.33%) cases and in control group, it was achieved in 16 (53.33%) cases and not in 14 (46.67%) cases. There was statistically no significant difference in efficacy of alfuzosin versus control group (p=.1213).Conclusion: Our study showed no difference in efficacy of alfuzosin versus control group for upper ureteric stone expulsion in adult population of district Lahore, Pakistan.

Efficacy of Tamsulosin as Compared to Placebo, in Reducing Post Operative Flank Pain during Voiding, in Patients with Ureteric Stent

Objective: To evaluate the efficacy of tamsulosin in reducing post operative flank pain during voiding, in patients with ureteric stent. Study Design: This is a Randomized control trial (RCT) study. Place and Duration: Study carried out at Department of Urology, Jinnah Post Graduate Medical Centre, Hospital, Karachi, Pakistan, from June 2016 to November 2016. Methodology: 60 patients aged between 15 – 45years, undergone placement of ureteric stent to treat ureteric and renal calculi and have pain score >4, were included in the study. Divided into two groups ‘group A’ and ‘group B’. In group ‘A’ and group ‘B’ Tamsulosin and Placebo was given respectively in patients with ureteric stent and reduction in post-operative flank pain was measured and compared. Tamsulosin was given post operatively when NPO is broken after 2 hours – 6 hours.  Patients having uretral trauma, patients having BPH,  patient underwent TURP or TURBT, patent having urinary tract infection and  patients with pregnancy or lactating females were excluded. All patients were received intravenous antibiotic (Ceftrixone 1gr). Also all patients were receive oral analgesic (diclofenic sodium 50mg BID) and antispasmodics (Drotaverine 80mg BID). Patients were discharged after 24 hours. Postoperatively stent related flank pain during voiding was assessed via Pain Scale. Results: 60 Patients who got operated for ureteric stent. In group ‘A’ there were 21 males (70%) and 9 females (30%), the mean age of group A was 35.67±5.99 as In group ‘B’ there were of 21 males (70%) and 9 females (30%) and mean age of group B was 35.04±6.42 (Table 1). Mean Pain score in ‘Group A’ (Tamsulosin) in week 1, 2, 3, 4, 5, 6 was 4.1, 3.5, 2.9, 2.3, 1.9, 1.3 respectively as shown in Table 2. Mean Pain score in ‘group B’ (Placebo) in week1, 2, 3, 4, 5, 6 was 6.9, 6.3, 5.9, 5.6, 5, 4.2 respectively as shown in Table 2.  Average pain score in ‘group A’ and ‘group B’ came out to be 2.67 and 5.64 respectively (P value 0.005).  Conclusion: Alpha blockers reduces the post-operative flank pain and voiding complaints in patients with ureteric stent. Our study shows that the efficacy of Tamsulosin in reducing post-operatice flank pain in patients with uretercic stent is better than placebo.

Antigenic structure of wild poliovirus type 1 strains endemic in Pakistan is highly conserved and completely neutralized by Sabin's Oral Polio Vaccine

BACKGROUND

Elimination of poliovirus in Pakistan and Afghanistan is challenged by notions against the role of oral polio vaccine in eradicating contemporary wild poliovirus strains.

METHODS

1,055 WPV1 strains isolated between 2013-2018 were categorized into 68 antigenic groups and tested for neutralization by OPV derived antibodies. Molecular docking was conducted to determine neutralization efficiency of antibodies against wild poliovirus. The clinical significance of WPV1 variants was assessed to ascertain their role in patient's outcome.

RESULTS

We found that 88% of WPV1 strains isolated from paralytic children belonged to a single antigenic lineage identical to WPV1 strain detected in 1993. WPV1 antigenic variants were effectively neutralized by OPV derived antibodies with geometric mean titers comparable to the neutralization titers found for three strains in OPV (OPV1-3: 7.96-9.149, 95%CI: 6.864-10.171; WPV1 strains: 7.542-8.786, 95%CI: 6.493-9.869). Docking examination underscored a strong antigen-antibody interaction despite variations within the VP1 epitopes. No significant association (p-value = 0.78) of clinical prognosis was inferred among patients infected with antigenically diverse WPV1 strains and patients' outcome including death.

CONCLUSIONS

Our findings substantiate the robustness of OPV to neutralize the contemporary WPV1 strains endemic in Pakistan and Afghanistan. The vaccination coverage must be augmented to achieve eradication early on.

Urdu text in natural scene images: a new dataset and preliminary text detection

Text detection in natural scene images for content analysis is an interesting task. The research community has seen some great developments for English/Mandarin text detection. However, Urdu text extraction in natural scene images is a task not well addressed. In this work, firstly, a new dataset is introduced for Urdu text in natural scene images. The dataset comprises of 500 standalone images acquired from real scenes. Secondly, the channel enhanced Maximally Stable Extremal Region (MSER) method is applied to extract Urdu text regions as candidates in an image. Two-stage filtering mechanism is applied to eliminate non-candidate regions. In the first stage, text and noise are classified based on their geometric properties. In the second stage, a support vector machine classifier is trained to discard non-text candidate regions. After this, text candidate regions are linked using centroid-based vertical and horizontal distances. Text lines are further analyzed by a different classifier based on HOG features to remove non-text regions. Extensive experimentation is performed on the locally developed dataset to evaluate the performance. The experimental results show good performance on test set images. The dataset will be made available for research use. To the best of our knowledge, the work is the first of its kind for the Urdu language and would provide a good dataset for free research use and serve as a baseline performance on the task of Urdu text extraction.

Detection of SARs-CoV-2 in wastewater using the existing environmental surveillance network: A potential supplementary system for monitoring COVID-19 transmission

The ongoing COVID-19 pandemic is caused by SARs-CoV-2. The virus is transmitted from person to person through droplet infections i.e. when infected person is in close contact with another person. In January 2020, first report of detection of SARS-CoV-2 in faeces, has made it clear that human wastewater might contain this virus. This may illustrate the probability of environmentally facilitated transmission, mainly the sewage, however, environmental conditions that could facilitate faecal oral transmission is not yet clear. We used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID 19 patients and quarantine center strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as supplementary system to monitor viral tracking and circulation in cities with lower COVID-19 testing capacity or heavily populated areas where door-to-door tracing may not be possible. However, attention is needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.

The Burden of Duodenal Ulcers Among Dyspeptic Patients

INTRODUCTION

Dyspepsia is a common presenting complaint of various upper gastrointestinal disorders. Duodenal ulcer is one of the rare endoscopic findings in patients with dyspepsia, but it can present with upper gastrointestinal bleed. The aim of this study was to determine the frequency of duodenal ulcers among dyspeptic patients undergoing esophagogastroduodenoscopy (EGD).

SUBJECT AND METHODS

All patients who fulfilled the inclusion criteria were recruited during the period of six months, i.e., from July to December 2020 in the Department of Gastroenterology, Liaquat National Hospital and Medical College, Karachi. After obtaining informed and written consent, history, and clinical examination, the EGD was performed to assess the outcome, i.e., frequency of duodenal ulcers.

RESULTS

A total of 156 patients with dyspepsia were included. Eighty-seven (55.8%) were male and 69 (44.2%) were female with the mean age of 36.96+11.71 years. The most common symptom at presentation was epigastric burning seen in 76 patients (48.7%) followed by postprandial fullness in 59 patients (37%). Duodenal ulcers were noted in 18 patients (11.5%) and were significantly associated with alcohol intake, smoking, epigastric pain, postprandial fullness with p-values of 0.001, 0.001, 0.001, and 0.013, respectively.

CONCLUSION

Duodenal ulcer is an uncommon endoscopic finding in patients with dyspepsia; it is seen in younger age, smokers, alcohol use, and patients presenting with epigastric pain and postprandial fullness.

Genetic Epidemiology Reveals 3 Chronic Reservoir Areas With Recurrent Population Mobility Challenging Poliovirus Eradication in Pakistan

BACKGROUND

Pakistan is among 3 countries endemic for wild poliovirus type 1 (WPV1) circulation that are still struggling for eradication of poliomyelitis. Active clinical and environmental surveillance with meticulous laboratory investigations provide insights into poliovirus transmission patterns and genomic diversity to inform decisions for strategic operations required to achieve eradication.

METHODS

We analyzed epidemiological and virological data to comprehend the current epidemiological status of WPV1 in Pakistan during 2015-2017. Stool specimens of patients with acute flaccid paralysis (AFP) and sewage samples collected from 60 environmental sites were tested. Viral culturing, intratypic differentiation by real-time polymerase chain reaction, and nucleic acid sequencing of the VP1 region of the poliovirus genome to determine genetic relatedness among WPV1 strains were applied.

RESULTS

Poliovirus isolates were grouped into 11 distinct clusters, which had ≥95% nucleotide homology in the VP1 coding region. Most of the poliovirus burden was shared by 3 major reservoirs: Karachi, Peshawar, and Quetta block (64.2% in 2015, 75.4% in 2016, and 76.7% in 2017).

CONCLUSIONS

Environmental surveillance reveals importations and pockets of unimmunized children that dictate intensive target mop-up campaigns to contain poliovirus transmission. A decrease in the number of orphan isolates reflects effective combination of AFP and environmental surveillance in Pakistan. The genetic data reflect sustained transmission within reservoir areas, further expanded by periodic importations to areas of high immunity reflected by immediate termination of imported viruses. Improved immunization coverage with high-quality surveillance is vital for global certification of polio eradication.

Air pollutants, economic growth and public health: implications for sustainable development in OECD countries

The rapid economic growth over recent years and the resulting environmental pollution in OECD countries are a serious concern for the health of the general public. A comprehensive analysis of environmental pollutants, economic growth, and public health is done using data from 28 OECD economies from 2002 to 2018. Panel fully modified least squares and the panel vector error correction model are used. The results show that there is long-run causality from renewable energy and carbon dioxide (CO₂) emissions to healthcare spending. Renewable energy and healthcare spending are positively and significantly related. It is concluded that investment in renewable energy leads to a reduction in air pollution, improvements in healthcare, and the promotion of economic growth.

Spectrum of genetic variants in moderate to severe sporadic hearing loss in Pakistan

Hearing loss affects 380 million people worldwide due to environmental or genetic causes. Determining the cause of deafness in individuals without previous family history of hearing loss is challenging and has been relatively unexplored in Pakistan. We investigated the spectrum of genetic variants in hearing loss in a cohort of singleton affected individuals born to consanguineous parents. Twenty-one individuals with moderate to severe hearing loss were recruited. We performed whole-exome sequencing on DNA samples from the participants, which identified seventeen variants in ten known deafness genes and one novel candidate gene. All identified variants were homozygous except for two. Eleven of the variants were novel, including one multi-exonic homozygous deletion in OTOA. A missense variant in ESRRB was implicated for recessively inherited moderate to severe hearing loss. Two individuals were heterozygous for variants in MYO7A and CHD7, respectively, consistent with de novo variants or dominant inheritance with incomplete penetrance as the reason for their hearing loss. Our results indicate that similar to familial cases of deafness, variants in a large number of genes are responsible for moderate to severe hearing loss in sporadic individuals born to consanguineous couples.

Future challenges and emerging role of academic libraries in Pakistan: A phenomenology approach

This study was carried out to investigate the current and prospective challenges faced by academic libraries in Pakistan and to present possible solutions addressing these challenges. The research design was qualitative, adopting the phenomenology approach. In-depth interviews of 14 senior academic library leaders from public and private sector universities of Pakistan were conducted. Leadership crisis was identified as the top challenge followed by those related to changing user behavior, human resources, financial, technological issues, and changes in higher education. Prospective challenges encompassed issues related to technological modalities, human resources, research data management and library space. While the study participants indicated their readiness to cope with these challenges, they agreed that there was a need of collective effort for human capacity building, initiation of compatible smart services, effective policy making and creation of societal awareness. The support from key players such as the library professionals, library associations, top management, LIS schools, HEC and other funding agencies was deemed to be vital for this purpose.

Assessment of clinical features and determinants of mortality among cancer patients with septic shock of pulmonary origin: a prospective analysis

BACKGROUND

Pneumonia-associated septic shock (PASS) in patients with cancer inflicts healthcare burden attributed to high morbidity and mortality. Current study was aimed to evaluate the clinical outcomes, microbiological characteristics, risk factors and impact of life-support interventions on 28-day mortality among cancer patients with PASS.

METHODS

A prospective observational study was conducted among cancer patients with PASS admitted to intensive care unit (ICU) of 'Shaukat Khanum Memorial Cancer Hospital'. Data were analysed using appropriate statistical methods.

RESULTS

Out of 100 patients who sought medical care during the study period, 59 (59%) were male and majority had solid tumour than haematological malignancies (68% vs 32%). Nosocomial pneumonia was most frequent (90%) followed by healthcare-associated pneumonia (HCAP) (9%) and community-acquired pneumonia (CAP) (1%). The most common causative pathogen was Pseudomonas aeruginosa, 21 (32%). Overall mortality rate was 76% including 15% hospital and 61% ICU mortality. Sequential Organ Failure Assessment (SOFA) score at first day (HR 3.8; 95% CI 1.7 to 8.9; p=0.002), SOFA score at seventh day (HR 8.9; 95% CI 3.6 to 22.7; p=<0.001), invasive mechanical ventilation (HR 8.0; 95% CI 3.2 to 20; p<0.001) and performance status (HR 5.4; 95% CI 2.5 to 11.3; p<0.001) were found to be independently associated with 28-day mortality. Receiver operating characteristic curve analysis accentuates the excellent predictive accuracy of Cox regression model for mortality indicated by area under the curve of 0.892 (95% CI 0.801 to 0.983, p<0.001).

CONCLUSION

Our analysis demonstrates substantial mortality associated with PASS among patients with cancer. Timely recognition of patients with high predilection of increased mortality could be of value in improving the disease burden.

Multi-sensor fusion based on multiple classifier systems for human activity identification

Multimodal sensors in healthcare applications have been increasingly researched because it facilitates automatic and comprehensive monitoring of human behaviors, high-intensity sports management, energy expenditure estimation, and postural detection. Recent studies have shown the importance of multi-sensor fusion to achieve robustness, high-performance generalization, provide diversity and tackle challenging issue that maybe difficult with single sensor values. The aim of this study is to propose an innovative multi-sensor fusion framework to improve human activity detection performances and reduce misrecognition rate. The study proposes a multi-view ensemble algorithm to integrate predicted values of different motion sensors. To this end, computationally efficient classification algorithms such as decision tree, logistic regression and k-Nearest Neighbors were used to implement diverse, flexible and dynamic human activity detection systems. To provide compact feature vector representation, we studied hybrid bio-inspired evolutionary search algorithm and correlation-based feature selection method and evaluate their impact on extracted feature vectors from individual sensor modality. Furthermore, we utilized Synthetic Over-sampling minority Techniques (SMOTE) algorithm to reduce the impact of class imbalance and improve performance results. With the above methods, this paper provides unified framework to resolve major challenges in human activity identification. The performance results obtained using two publicly available datasets showed significant improvement over baseline methods in the detection of specific activity details and reduced error rate. The performance results of our evaluation showed 3% to 24% improvement in accuracy, recall, precision, F-measure and detection ability (AUC) compared to single sensors and feature-level fusion. The benefit of the proposed multi-sensor fusion is the ability to utilize distinct feature characteristics of individual sensor and multiple classifier systems to improve recognition accuracy. In addition, the study suggests a promising potential of hybrid feature selection approach, diversity-based multiple classifier systems to improve mobile and wearable sensor-based human activity detection and health monitoring system.

Bi-allelic Pro291Leu variant in KCNQ4 leads to early onset non-syndromic hearing loss

Variants of KCNQ4 are one of the most common causes of dominantly inherited nonsyndromic hearing loss. We investigated a consanguineous family in which two individuals had prelignual hearing loss, apparently inherited in a recessive mode. Whole-exome sequencing analyses demonstrated genetic heterogeneity as variants in two different genes segregated with the phenotype in two branches of the family. Members in one branch were homozygous for a pathogenic variant of TMC1. The other two affected individuals were homozygous for a missense pathogenic variant in KCNQ4 c.872C>T; p.(Pro291Leu). These two individuals had prelingual, progressive moderate to severe hearing loss, while a heterozygous carrier had late onset mild hearing loss. Our work demonstrates that p.Pro291L variant is semi-dominantly inherited. This is the first report of semi-dominance of a KCNQ4 variant.

Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations

Background

Enteroviruses are common human pathogens occasionally associated with severe disease, notoriously paralytic poliomyelitis caused by poliovirus. Other enterovirus serotypes such as enterovirus A71 and D68 have been linked to severe neurological syndromes. New enterovirus serotypes continue to emerge, some believed to be derived from nonhuman primates. However, little is known about the circulation patterns of many enterovirus serotypes and, in particular, the detailed enterovirus composition of sewage samples.

Methods

We used a next-generation sequencing approach analyzing reverse transcriptase polymerase chain reaction products synthesized directly from sewage concentrates.

Results

We determined whole-capsid genome sequences of multiple enterovirus strains from all 4 A to D species present in environmental samples from the United Kingdom, Senegal, and Pakistan.

Conclusions

Our results indicate complex enterovirus circulation patterns in human populations with differences in serotype composition between samples and evidence of sustained and widespread circulation of many enterovirus serotypes. Our analyses revealed known and divergent enterovirus strains, some of public health relevance and genetically linked to clinical isolates. Enteroviruses identified in sewage included vaccine-derived poliovirus and enterovirus D-68 stains, new enterovirus A71 and coxsackievirus A16 genogroups indigenous to Pakistan, and many strains from rarely reported serotypes. We show how this approach can be used for the early detection of emerging pathogens and to improve our understanding of enterovirus circulation in humans.

Exome sequencing identifies a novel frameshift variant causing hypomagnesemia with secondary hypocalcemia

Hypomagnesemia with secondary hypocalcemia is a rare autosomal-recessive disorder characterized by intense hypomagnesemia associated with hypocalcemia (HSH). Mutations in the TRPM6 gene, encoding the epithelial Mg²⁺ channel TRPM6, have been proven to be the molecular cause of this disease. This study identified causal mutations in a 2-month-old male patient of hypomagnesemia from a consanguineous marriage. Biochemical analyses indicated the diagnosis of HSH due to primary gastrointestinal loss of magnesium. Whole exome sequencing of the trio (i.e. proband and both parents) was carried out with mean coverage of > 150×. ANNOVAR was used to annotate functional consequences of genetic variation from exome sequencing data. After variant filtering and annotation, a number of single nucleotide variants (SNVs) and 2 bp deletion at exon26:c.4402_4403delCT in TRPM6 gene were identified. This deletion which resulted in a novel frameshift mutation in exon 26 of this gene was confirmed by Sanger sequencing. With these investigations in hand, the patient was managed with magnesium sulphate. The patient remained asymptomatic and was developmentally and neurologically normal till his last follow up.

Epidemiological and molecular investigation of a measles outbreak in Punjab, Pakistan, 2013-2015

Despite the availability of an effective vaccine, the measles virus continues to cause significant morbidity and mortality in children worldwide. Molecular characterization of wild-type measles strains is an invaluable component of epidemiological studies or surveillance systems that provides important information pertinent to outbreak linkages and transmission pathways. Serum samples and throat swabs were collected from suspected measles cases from the Punjab province of Pakistan (2013-2015) and further tested for measles immunoglobulin M (IgM) through enzyme-linked immunosorbent assay and reverse-transcriptase polymerase chain reaction for molecular characterization. Among the total of 5415 blood samples, 59% tested positive for measles IgM. Males had a higher infection rate (55%) than females (45%), and the highest frequency of positive cases (63%) was found in the age group of 0 to 5 years. Partial sequencing of the nucleoprotein gene showed that 27 strains belonged to the B3 genotype, whereas 2 viruses were identified as D4. On phylogenetic analysis, Pakistani B3 strains were found to be closely related to previously reported indigenous strains and those from neighboring countries of Iran and Qatar. This is the first report on the detection of the measles B3 genotype from Punjab, Pakistan. The current study shows a high burden of measles infections in Punjab province owing to poor routine immunization coverage in major cities. It is imperative that national health authorities adopt strategic steps on an urgent basis for improvement of routine immunization coverage. Molecular epidemiology of the measles viruses circulating in different parts of the country can provide useful data to manage future outbreaks.

Evaluation of the bag-mediated filtration system as a novel tool for poliovirus environmental surveillance: Results from a comparative field study in Pakistan

Poliovirus (PV) environmental surveillance (ES) plays an important role in the global eradication program and is crucial for monitoring silent PV circulation especially as clinical cases decrease. This study compared ES results using the novel bag-mediated filtration system (BMFS) with the current two-phase separation method. From February to November 2016, BMFS and two-phase samples were collected concurrently from twelve sites in Pakistan (n = 117). Detection was higher in BMFS than two-phase samples for each Sabin-like (SL) PV serotype (p<0.001) and wild PV type 1 (WPV1) (p = 0.065). Seventeen sampling events were positive for WPV1, with eight discordant in favor of BMFS and two in favor of two-phase. A vaccine-derived PV type 2 was detected in one BMFS sample but not the matched two-phase. After the removal of SL PV type 2 (SL2) from the oral polio vaccine in April 2016, BMFS samples detected SL2 more frequently than two-phase (p = 0.016), with the last detection by either method occurring June 12, 2016. More frequent PV detection in BMFS compared to two-phase samples is likely due to the greater effective volume assayed (1620 mL vs. 150 mL). This study demonstrated that the BMFS achieves enhanced ES for all PV serotypes in an endemic country.

Treatment of real wastewater using co-culture of immobilized Chlorella vulgaris and suspended activated sludge

The use of algal-bacterial symbiotic association establishes a sustainable and cost-effective strategy in wastewater treatment. Using municipal wastewater, the removal performances of inorganic nutrients (nitrogen and phosphorus) and organic pollutants were investigated by the co-culture system having different inoculum ratios (R) of suspended activated sludge to alginate-immobilized microalgae Chlorella vulgaris. The co-culture reactors with lower R ratios obtained more removal of nitrogen than in pure culture of C. vulgaris. The reactor with R = 0.5 (sludge/microalgae) showed the highest performance representing 66% removal after 24 h and 95% removal after 84 h. Phosphorus was completely eliminated (100%) in the co-culture system with inoculum ratios of 0.5 and 1.0 after 24 h and in the pure C. vulgaris culture after 36 h. The COD level was greatly reduced in the activated sludge reactor, while, it was increasing in pure C. vulgaris culture after 24 h of incubation. However, COD was almost stabilized after 24 h in the reactors with high R ratios such as 2.0, 5.0, and 10 due to the higher concentration of activated sludge. The growth of C. vulgaris was promoted from 0.03 g/L/d to 0.05 g/L/d in the co-culture of low inoculum ratios such as R = 0.5, implying that there exist an optimum inoculum ratio in the co-culture system in order to achieve efficient removal of nutrients.

Prediction of cause of death from forensic autopsy reports using text classification techniques: A comparative study

OBJECTIVES

Automatic text classification techniques are useful for classifying plaintext medical documents. This study aims to automatically predict the cause of death from free text forensic autopsy reports by comparing various schemes for feature extraction, term weighing or feature value representation, text classification, and feature reduction.

METHODS

For experiments, the autopsy reports belonging to eight different causes of death were collected, preprocessed and converted into 43 master feature vectors using various schemes for feature extraction, representation, and reduction. The six different text classification techniques were applied on these 43 master feature vectors to construct a classification model that can predict the cause of death. Finally, classification model performance was evaluated using four performance measures i.e. overall accuracy, macro precision, macro-F-measure, and macro recall.

RESULTS

From experiments, it was found that that unigram features obtained the highest performance compared to bigram, trigram, and hybrid-gram features. Furthermore, in feature representation schemes, term frequency, and term frequency with inverse document frequency obtained similar and better results when compared with binary frequency, and normalized term frequency with inverse document frequency. Furthermore, the chi-square feature reduction approach outperformed Pearson correlation, and information gain approaches. Finally, in text classification algorithms, support vector machine classifier outperforms random forest, Naive Bayes, k-nearest neighbor, decision tree, and ensemble-voted classifier.

CONCLUSION

Our results and comparisons hold practical importance and serve as references for future works. Moreover, the comparison outputs will act as state-of-art techniques to compare future proposals with existing automated text classification techniques.

Heavy metals identification and exposure at workplace environment its extent of accumulation in blood of iron and steel recycling foundry workers of Lahore, Pakistan

The determination of heavy metals in blood is an important occupational environmental toxicology screening procedure. The aim of study was to determine the concentrations of Pb, Cd, Cr and Ni in blood samples of iron and steel foundry workplace exposed workers under routine clinical laboratory conditions. The method was employed for the quantitative determination of lead, cadmium, chromium and nickel in workplace environment particulate matter blood samples from iron and steel foundry workers and in unexposed controls. The results indicate that lead, chromium and nickel levels of the exposed workers are significantly higher those of the controls. Nickel Concentration (μg/L) in high P value=0.0306 and Chromium Concentration (μg/L) in P value=0.0295in worker population as compared to controls. Lead showed highest Absorption concentration in serum from particulate matter to Serum 47.3(μg/L). Absorption concentration of nickel in serum 16.5(μg/L) was lower than lead observed in worker's population. Absorption concentration of cadmium and chromium in serum from particulate matter -152(μg/L) observed very low. The results also show the need for immediate improvements in workplace ventilation and industrial hygiene practices.

"Preliminary Seroepidemiological survey of dengue infections in Pakistan, 2009-2014"

Background

Dengue virus is the causative agent of dengue fever, a vector borne infection which causes self-limiting to life threatening disease in humans. A sero-epidemiological study was conducted to understand the current epidemiology of dengue virus in Pakistan which is now known as a dengue endemic country after its first reported outbreak in 1994.

Methods

To investigate the prevalence of dengue virus in Pakistan during 2009-2014, a total of 9,493 blood samples were screened for the detection of anti-dengue IgM antibodies using ELISA. Clinical and demographic features available with hospital records were reviewed to ascertain mortalities related to dengue hemorrhagic shock syndrome.

Results

Out of 9,493 samples tested, 37% (3,504) were found positive for anti-dengue IgM antibodies. Of the seropositive cases, 73.6% (2,578/3,504) were male and 26.4% (926/3,504) were female. The highest number (382/929; 41.1%) of sero-positive cases was observed among the individuals of age group 31-40 years. The highest number of symptomatic cases was reported in October (46%; 4,400/9,493), and the highest number of sero-positive cases among symptomatic cases was observed in November (45.7%; 806/1,764). Mean annual patient incidence (MAPI) during 2009-2014 in Pakistan remained 0.30 with the highest annual patient incidence (11.03) found in Islamabad. According to the available medical case record, 472 dengue related deaths were reported during 2009-2014.

Conclusion

The data from earlier reports in Pakistan described the dengue virus incidence from limited areas of the country. Our findings are important considering the testing of clinical samples at a larger scale covering patients of vast geographical regions and warrants timely implementation of dengue vector surveillance and control programs.

Trial registration number

It is an epidemiological research study, so trial registration is not required.

Electronic supplementary material

The online version of this article (doi:10.1186/s40249-017-0258-6) contains supplementary material, which is available to authorized users.

Automatic ICD-10 multi-class classification of cause of death from plaintext autopsy reports through expert-driven feature selection

OBJECTIVES

Widespread implementation of electronic databases has improved the accessibility of plaintext clinical information for supplementary use. Numerous machine learning techniques, such as supervised machine learning approaches or ontology-based approaches, have been employed to obtain useful information from plaintext clinical data. This study proposes an automatic multi-class classification system to predict accident-related causes of death from plaintext autopsy reports through expert-driven feature selection with supervised automatic text classification decision models.

METHODS

Accident-related autopsy reports were obtained from one of the largest hospital in Kuala Lumpur. These reports belong to nine different accident-related causes of death. Master feature vector was prepared by extracting features from the collected autopsy reports by using unigram with lexical categorization. This master feature vector was used to detect cause of death [according to internal classification of disease version 10 (ICD-10) classification system] through five automated feature selection schemes, proposed expert-driven approach, five subset sizes of features, and five machine learning classifiers. Model performance was evaluated using precisionM, recallM, F-measureM, accuracy, and area under ROC curve. Four baselines were used to compare the results with the proposed system.

RESULTS

Random forest and J48 decision models parameterized using expert-driven feature selection yielded the highest evaluation measure approaching (85% to 90%) for most metrics by using a feature subset size of 30. The proposed system also showed approximately 14% to 16% improvement in the overall accuracy compared with the existing techniques and four baselines.

CONCLUSION

The proposed system is feasible and practical to use for automatic classification of ICD-10-related cause of death from autopsy reports. The proposed system assists pathologists to accurately and rapidly determine underlying cause of death based on autopsy findings. Furthermore, the proposed expert-driven feature selection approach and the findings are generally applicable to other kinds of plaintext clinical reports.

Genetic causes of moderate to severe hearing loss point to modifiers

The genetic underpinnings of recessively inherited moderate to severe sensorineural hearing loss are not well understood, despite its higher prevalence in comparison to profound deafness. We recruited 92 consanguineous families segregating stable or progressive, recessively inherited moderate or severe hearing loss. We utilized homozygosity mapping, Sanger sequencing, targeted capture of known deafness genes with massively parallel sequencing and whole exome sequencing to identify the molecular basis of hearing loss in these families. Variants of the known deafness genes were found in 69% of the participating families with the SLC26A4, GJB2, MYO15A, TMC1, TMPRSS3, OTOF, MYO7A and CLDN14 genes together accounting for hearing loss in 54% of the families. We identified 20 reported and 21 novel variants in 21 known deafness genes; 16 of the 20 reported variants, previously associated with stable, profound deafness were associated with moderate to severe or progressive hearing loss in our families. These data point to a prominent role for genetic background, environmental factors or both as modifiers of human hearing loss severity.

Seroprevalence of Human Cytomegalovirus (HCMV) infection in pregnant women and outcomes of pregnancies with active infection

OBJECTIVE

To determine the prevalence of cytomegalovirus in pregnant women and types of overt congenital infection in neonates.

METHODS

This cross-sectional study was conducted at the Pakistan Institute of Medical Sciences and Federal Government Services Hospital in Islamabad, Pakistan, from March 2010 to June 2011, and comprised blood samples of pregnant women. Seroprevalence of human cytomegalovirus, immunoglobulin G and immunoglobulin M was determined by enzyme-linked immunosorbent assay while its deoxyribonucleic acid was detected by nested polymerase chain reaction.The congenital human cytomegalovirus infection was also identified in newborn babies from actively infected pregnant women. SPSS 18 was used for data analysis.

RESULTS

Of the 409 pregnant women enrolled, 399(97.55%) were seropositive for cytomegalovirus immunoglobulinG and 52(12.71%) for immunoglobulinM, while cytomegalovirus deoxyribonucleic acid was detected in 82(20%). Of the cytomegalovirus immunoglobulinM-positive women, sera of 40(80%) had immunoglobulinG avidity >50%. The remaining 12(23%) sera had avidity assay value <50%. Among the 82(20%) infected pregnant women, 70(85.4%) were successfully followed up. Among them, the virus was isolated from 41(58.5%) newborns babies, of which 15(21%) were symptomatic while 26(47.2%) were asymptomatic. Of the former, 4(26.6%) had hepatosplenomegaly.

CONCLUSIONS

Human cytomegalovirus infection in pregnant women was the main reason of congenital defects among neonates.

Mutations in Human Interferon α2b Gene and Potential as Risk Factor Associated with Female Breast Cancer

The current study explored the potential links between breast cancer and human interferon α-2b (hIFNα-2b) gene mutations. The hIFNα-2b gene was amplified from breast cancer tumor tissue samples (N = 60) by polymerase chain reaction (PCR) and the products were subjected to gene sequencing. A total of 38 (63.3%) samples showed positive PCR amplification results. Several of these also exhibited frequent alterations (mutations) after 400 bp and, in particular, adenine was replaced by other bases. A total of 19 selected mutated amino acids were analyzed for local/general fold pattern changes. Human IFNα-2b receptor (IFNAR): ligand (hIFNα-2b protein) interactions through a Z-DOCK (3.0.2) server were also evaluated to assess the binding patterns of each ligand to receptor to induce Janus-Kinase-signal transducer and activator of transcription antiproliferative signal transduction pathway inside the cancer cells. Certain local structural and conformational changes were predicted to be induced by mutations in the ligand. The variant models of the hIFNα-2b displayed structural and conformational changes that signified that changes to hIFNα-2b may be a risk factor in addition to other known factors associated with onset/progression of female breast carcinoma. It was hoped that others might build upon the research in this study evaluating protein structural models with mutations and their consequent interactions with receptors in the development of potent immune therapeutic drugs for breast cancer that are based on recombinant hIFNα-2b.

Distribution of Cytomegalovirus Genotypes among Neonates Born to Infected Mothers in Islamabad, Pakistan

Background

Congenital cytomegalovirus (cCMV) infection contributes to considerable long-term sequelae in neonates and children all over the world. The association between viral genotypes and severity of clinical cytomegalovirus (CMV) infection is yet to be defined. The objective of this study was to find the impact of active CMV infection during pregnancy and the clinical significance of genotypes in neonates with congenital cytomegalovirus infections in Pakistan.

Methods

A total of 409 blood samples from pregnant women seeking health care services at the two antenatal hospitals of Islamabad during January to December 2012 were tested by ELISA and nested-PCR. Pregnant women with active infection (detected as IgM positive, PCR positive or positive on both assays) were followed until delivery, to detect the outcome of overt cCMV infection in neonates. Genetic characterization of CMV strains was performed by sequence analysis of envelope glycoproteins: gB, gN and gH to detect the contributing CMV genotypes.

Results

The seroprevalence of anti-CMV IgG and IgM was 97.5% (399 out of 409) and 12.7% (52 out of 409), respectively, while 20% (82/409) pregnant women were found positive for CMV DNA by PCR. Logistic regression analysis showed a significant association of active infection with parity [OR = 2.56, 95% CI = 1.82–2.62, p = 0.04], febrile illness [OR = 1.84, 95% CI = 1.76–3.65, p = 0.01] and jaundice [OR = 22.5, 95% CI = 4.53–85.02, p = 0.002]. We were able to isolate virus in 41 out of 70 neonates; 36.6% (15 out of 41) of them were symptomatic at birth while 63.4% (26 out of 41) were asymptomatic. The most prominent clinical feature observed in symptomatic neonates was hepatosplenomegaly (26.6%; 4 out of 15). All three genotypes gB, gN and gH were found with the highest frequency of gB1 genotype, found in 75% infants with hepatic damage. Phylogenetic analysis of Pakistani strains showed 96%-100% homology to their prototype strains.

Conclusions

Active CMV infection during pregnancy is a major cause of congenital CMV infection with comparable distribution of all three genotypes: gB, gN and gH in symptomatic and asymptomatic neonates. Our findings emphasize to conduct a comprehensive large scale survey and introduction of country wide routine screening at maternity clinics for early diagnosis of CMV to reduce its associated devastating outcomes.