A Comprehensive Review of Performance of Next-Generation Sequencing Platforms.

Background: Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective: The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results: The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion: The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.

Exploring Pakistani Physicians' Knowledge and Practices Regarding High Alert Medications: Findings and Implications.

Introduction: While many low-middle income countries (LMICs), including Pakistan, try and ensure patient safety within available resources, there are considerable concerns with medication use. Unsafe and inappropriate medication use, especially high alert medications (HAMs), is one of the important factors compromising patient safety and quality of care. Besides economic loss, HAMs contribute to greater morbidity, hospitalization, and mortality. Physicians as key members of the provision of healthcare are expected to be well aware of the administration and regulations surrounding HAMs. However, the current status is unknown in Pakistan. Consequently, the objectives of this study were to evaluate the knowledge of Pakistani physicians about the administration, regulation, and practices related to HAMs. This builds on our recently published study with nurses. Methods: An online cross-sectional study design was used, and data were gathered from the physicians throughout Pakistan using previously used self-administered questionnaires during a period of 5 months (January 1 to May 30, 2021). All data were entered and analyzed using SPSS 22 for Windows. Results: Physicians (847) who provided consent were enrolled in the study. Most physicians (62.2%) were male, aged between 25 and 30 years (75.2%) and had 2- to 5-year work experience (50.9%). About 27% were working in the emergency departments. The median (IQR) knowledge score for HAMs administration and regulation was 5 (3) and 5 (2), respectively. About 46.4% of respondents were found to have moderate knowledge about HAMs; increasing age, work experience, and higher qualifications were significantly associated (p < 0.05) with better HAMs knowledge. Around 58% had good practices relating to HAMs during their routine work. Median practice scores increased significantly (p < 0.05) with age, work experience, and postgraduate qualification. Conclusion: Most Pakistani physicians possess moderate knowledge about HAMs administration and regulations. However, their practices relating to the HAMs administration and regulations are typically sub-optimal. Consequently, HAMs awareness needs to be improved by including course content in the current curriculum, provision of hospital-based continuous training programs about patient safety and care, and establishment of multi-disciplinary health care teams, including board-certified pharmacists and specialized nurses, for the effective execution of medication use process in Pakistani hospitals in the future.

Comparing the effects of muscle energy technique and mulligan mobilization with movements on pain, range of motion, and disability in adhesive capsulitis.

OBJECTIVES: To compare the effect of muscle energy technique and Mulligan mobilisation with movement on pain, range of motion and disability in patients of adhesive capsulitis. METHODS: The single-blind, randomised controlled study was conducted at the Physiotherapy Department of Mayo Hospital, Lahore, Pakistan, from July to December, 2018, and comprised patients of either gender aged 30-70 years with adhesive capsulitis stage 2. The subjects were randomised using the lottery method into Mulligan mobilisation with movement group A, and the muscle energy technique grouo B. Conventional treatment, including hot packs and exercises like pulley rope exercise, wall climbing, and shoulder wheel, were part of both the groups. Each technique was applied five times per set, 2 sets per session 3 days a week for three weeks. Baseline and post-intervention readings were recorded for pain, range of motion and disability Using numeric pain rating scale, goniometer, and shoulder pain and disability index. Data was analysed using SPSS 23. RESULTS: Of the 70 individuals assessed, 64(91.4%) were included; 32(50%) in each of the two groups. The mean age in group A was 49.93±6.69 years, while in group B it was 49.17±8.92 years. Group A showed significantly better results compared to group B (p<0.05). CONCLUSIONS: Muscle energy technique and Mulligan mobilisation with movement were both found to be effective, but the latter was significantly better compared to the former. CLINICAL TRIAL NUMBER: IRCT20200611047734N2 (https://www.irct.ir/trial/48851).

Antibiotic use among hospitalized children with lower respiratory tract infections: a multicenter, retrospective study from Punjab, Pakistan.

BACKGROUND: Lower respiratory tract infection (LRTI) is one of the triggering factors toward death in children below the age of five years necessitating appropriate antibiotic selection. This study aimed to evaluate antibiotic use among hospitalized children (≤5 years age) with LRTIs. METHODS: A retrospective study was conducted in seven health facilities of the central region of Punjab province of Pakistan. The medical records of hospitalized children ≤5 years diagnosed with LRTI were thoroughly evaluated to get information on demographics, clinical characteristics, and details of prescribed antibiotics. The appropriateness of antibiotics was assessed according to guidelines of the British National Formulary due to a lack of indigenous standard treatment guidelines. RESULTS: The medical records of 5926 children were searched with the majority (70.9%) diagnosed with community-acquired pneumonia (CAP) followed by acute bronchitis (14.1%). Ceftriaxone plus ampicillin and ceftriaxone plus ampicillin plus amikacin were prescribed to 39% and 11.7% study population, respectively. One-fourth of children were prescribed the wrong dose, and more than half were encountered with the incorrect route of antibiotic administration. Alarmingly, 90.2% of antibiotic prescriptions were inappropriate in our findings. CONCLUSIONS: Current surveillance study revealed a worrying degree of antibiotic misuse among hospitalized LRTI children aged ≤5 years.

Psychopathological symptoms as a common Risk Factor for Tinnitus distress and magnitude: A cross-sectional study.

OBJECTIVE: To examine the association of tinnitus distress, tinnitus magnitude and psychopathological symptoms among patients with ear-related problems. METHODS: The cross-sectional study was conducted from December 1, 2020, to June 30, 2021, at the Hearing and Balance Clinic, Rawalpindi, Pakistan, in collaboration with the National Institute of Psychology, Quaid-i-Azam University, Islamabad, Pakistan, and comprised adult tinnitus patients of either gender. All patients underwent ear examination and audiological evaluations for tinnitus matching. Psychological assessment was done using the Tinnitus Magnitude Index, the Tinnitus Reaction Questionnaire and the Symptoms Check List-90. Data was analysed using SPSS 21. RESULTS: Of the 159 subjects, 97(61%) were male and 62(39%) were females. The overall mean age was 47.94±17.47 years. Patients showed statistically significant tendency to develop psychopathological symptoms, including somatisation, phobic anxiety, depression and paranoid ideation (p<0.05). Additionally, significant gender differences were also observed (p<0.05). CONCLUSIONS: There was a high prevalence of tinnitus distress along with psychopathological symptoms among tinnitus patients.

A cross-sectional study to understand the pervasiveness of psychiatric features among tinnitus and vertigo patients.

OBJECTIVE: To identify the mental health problems among patients having symptoms of tinnitus and vertigo due to vestibulocochlear disturbances. METHODS: The cross-sectional study was conducted from May to September 2019 at the Hearts International Hospital and the Hearing and Balance Clinic, Rawalpindi, in collaboration with the Foundation University, Islamabad, and comprised vestibulocochlear disorder patients of either gender aged >18 years having chief symptoms of vertigo and tinnitus for at least the preceding 3 months. Psychiatric evaluation was conducted using the Tinnitus Handicap Inventory, the Dizziness Handicap Inventory and the Depression, Anxiety, Stress Scale. Audiological evaluations were carried out to gauge the severity of symptoms. Data was analysed using SPSS 20. RESULTS: Of the 202 subjects, 60(30%) were females and 142(70%) were males. Patients experiencing vertigo and tinnitus symptoms had a strong tendency to develop psychiatric problems (p<0.05). Significant differences were noted among male and female patients regarding the representation of psychiatric symptoms (p<0.05). CONCLUSION: Patients experiencing tinnitus and vertigo symptoms tended to have a deviant psychological profile analogous with other chronic diseases.

Long-Term Follow-Up of Autonomic and Enteric Measures in Patients Undergoing Vertical Banded Gastroplasty for Morbid Obesity.

BACKGROUND: A multi-component model of autonomic and enteric factors may correlate with ultimate weight loss or gain after restrictive obesity surgery. This study aimed to determine relevant parameters to predict successful long-term weight loss. METHODS: Thirty-nine patients (four males and 35 females) with a mean age of 37.2 years were followed for over 15 years after vertical banded gastroplasty. Baseline adrenergic: postural adjustment ratio (PAR) and vasoconstriction (VC); cholinergic: electrocardiogram R-to-R interval (RRI) and enteric measure: electrogastrogram (EGG) were utilized by a discriminant function analysis to classify patients as a long-term loser or gainer. Using latest weight compared to baseline, patients were divided as 10 gainers and 29 losers. RESULTS: A discriminate model successfully predicted ultimate weight gain in 8/10 (80%) of patients who subsequently gained weight and weight loss in 24/29 (83%) of patients who lost weight for a total correct classification of 32/39 (82%). The same model with data at 3 months postoperatively predicted weight gain in 9/10 (90%) of patients and weight loss in 24/29 (83%) of patients, for a total correct classification of 34/39 (87%). CONCLUSIONS: A multi-component model at baseline and 3 months postoperative can predict long-term weight outcome from restrictive obesity surgery.

A Comparative Study of Land Cover Classification by Using Multispectral and Texture Data.

The main objective of this study is to find out the importance of machine vision approach for the classification of five types of land cover data such as bare land, desert rangeland, green pasture, fertile cultivated land, and Sutlej river land. A novel spectra-statistical framework is designed to classify the subjective land cover data types accurately. Multispectral data of these land covers were acquired by using a handheld device named multispectral radiometer in the form of five spectral bands (blue, green, red, near infrared, and shortwave infrared) while texture data were acquired with a digital camera by the transformation of acquired images into 229 texture features for each image. The most discriminant 30 features of each image were obtained by integrating the three statistical features selection techniques such as Fisher, Probability of Error plus Average Correlation, and Mutual Information (F + PA + MI). Selected texture data clustering was verified by nonlinear discriminant analysis while linear discriminant analysis approach was applied for multispectral data. For classification, the texture and multispectral data were deployed to artificial neural network (ANN: n-class). By implementing a cross validation method (80-20), we received an accuracy of 91.332% for texture data and 96.40% for multispectral data, respectively.

The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results ofsix most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

Serum catecholamines and dysautonomia in diabetic gastroparesis and liver cirrhosis.

BACKGROUND: Plasma catecholamine influences autonomic function and control, but there are few reports correlating them. In this study, 47 individuals (mean age, 38 years) were studied: 19 diabetes mellitus (DM) patients with gastroparesis, 16 with liver disease and 12 control subjects. METHODS: Noninvasive autonomic function was assessed for sympathetic adrenergic functions as peripheral vasoconstriction in response to cold stress test and postural adjustment ratio (PAR) and cholinergic function as Valsalva ratio, represented by change in R-R intervals. Measurements were compared by analysis of variance and Spearman's correlation, and results were reported as mean ± standard error. RESULTS: Plasma norepinephrine (1902.7 ± 263.3; P = 0.001) and epinephrine (224.5 ± 66.5; P = 0.008) levels, as well as plasma dopamine levels (861.3 ± 381.7), and total plasma catecholamine levels were highest for patients with liver disease, who also had significant negative correlation between norepinephrine level and vasoconstriction (P = 0.01; r = -0.5), PAR1 (P = 0.01; r = -0.5), sympathetic adrenergic functions (P = 0.005; r = -0.6), total autonomic index (P = 0.01-0.5) and total autonomic function (P = 0.01; r = -0.2) and also negative correlation between epinephrine plasma level and total autonomic function (P = 0.04; r = 0.4). DM patients were next highest in norepinephrine level (133.26 ± 7.43), but lowest for plasma catecholamine; a positive correlation between dopamine level and PAR1 (P = 0.008; r = 0.6) was also seen in this group. Plasma dopamine levels and spider score correlated negatively (P = 0.04; r = -0.5) and total plasma catecholamine positively with encephalopathy (P = 0.04; r = 0.5) in patients with liver disease. CONCLUSIONS: Plasma catecholamine levels correlated with adrenergic functions in control subjects and patients with DM and liver disease, with no significant correlation seen for cholinergic function.

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

Autonomic and Enteric Nervous System Dysfunction May Play a Role in Hyperemesis Gravidarum.

BACKGROUND: Nausea and vomiting, seen in 70-85% of all pregnancies, becomes intractable in hyperemesis gravidarum (HG). We aimed to investigate the relationship between HG and autonomic nervous system functioning and gastric electrical activity. METHODS: Twenty-seven pregnant patients, 21 with HG and six normal, were studied with sympathetic adrenergic; percent vasoconstriction (%VC) and postural adjustment ratio (PAR); parasympathetic vagal cholinergic functions by R-to-R intervals (RRIs), a total autonomic score; and enteric nervous system measured by electrogastrography (EGG). RESULTS: Significant differences were found in parasympathetic measures (RRI for HG 29.98 ± 2.95 vs. control 40.91 ± 2.38, P < 0.05); sympathetic PAR was significantly lower in patients (PAR for HG 24.5 ± 5.0 vs. 67.6 ± 11.4 for controls, P < 0.01); mean total autonomic score was significantly lower in HG (131.75 ± 9.61 vs. 196.87 ± 12.8, P < 0.05). EGG results were borderline different (normal < 3.3, HG 3.4 vs. controls 3.0, P = 0.07). CONCLUSION: Autonomic and enteric nervous system dysfunction may play a role in the pathophysiology of HG.

Characteristic symptoms and adaptive behaviors of children with autism.

OBJECTIVE: To determine the characteristic symptoms and adaptive behaviors of children with autism, as well as the distribution of autism severity groups across gender. STUDY DESIGN: Cross-sectional observational study. PLACE AND DURATION OF STUDY: Special Education Schools of Rawalpindi and Islamabad, from September 2011 to January 2012. METHODOLOGY: Thirty nine children of either gender, aged 3 - 16 years and enrolled in special education schools, fulfilled the DSM-IV-TR criteria of autism. Among those, were identified as meeting the criteria of autism. The childhood autism rating scale-2 (CARS-2) was used to study the characteristics and severity of symptoms of autism. Later, adaptive behavior scale (school edition: 2) ABS-S: 2, was administered on children (n=21) to formulate the level of adaptive functioning. RESULTS: There were 15 boys and 8 girls with mean age of 10.6 ± 2.97 years. They showed marked impairment in verbal communication (mean=3.17 ± 0.90) followed by relating to people (mean=2.75 ± 0.83) and general impression (mean=2.73 ± 0.7). Most of the children showed average to below average adaptive behaviors on number and time (n=19, 90.5%), independent functioning (n=17, 81.0%), self direction (n=17, 81.0%), physical development (n=13, 61.9%), responsibility (n=12, 57.1%) and socialization (n=13, 61.9%) as well as poor to very poor adaptive behaviors on prevocational skill (n=15, 71.4%), language development (n=13, 61.9%) and economic development (n=13, 61.9%). The frequency of boys with autism was more towards moderate to severely impaired spectrum, without gender differences in any symptom associated with autism. CONCLUSION: Comprehension of the presentation of characteristic symptoms of children with autism will be helpful in devising the indigenous intervention plans that are congruent with the level of adaptive functioning.

Evaluating the accuracy and efficiency of multiple sequence alignment methods.

A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases.