Notes on the typification of three names in Indian Ranunculus L. (Ranunculaceae)

The erroneous designation of holotype and lectotype of three names in Ranunculus namely R. reniformis Wall. ex Wight & Arn., R. subpinnatus Wight & Arn. and R. wallichianus Wight & Arn. in one of the recent publications is discussed here. This paper also emphasizes the precise application of the phrase typification of the name and also rectifies here the erroneous designation of holotype and lectotype of names in a recent publication

Outcome of substitutional urethroplasty by using dorsal onlay buccal mucosal graft: our experience of 10 years

Background: The term urethral stricture is anterior urethral disease, or a scarring process involving the spongy erectile tissue of the corpus spongiosum. Methods: Total 127 patients were included in the study. Patient selection criteria for urethroplasty by using buccal mucosal graft was length of stricture more than 2 cm, deep spongiofibrosis, failed optical urethrotomy for 3 times, adequate oral hygiene and proper buccal mucosa. Results: Length of stricture varied from 3.2 to 14 cm. In first postoperative week, 20.47% (n=26) patients developed minor wound infection culture negative seroma formation in stitch line in the skin. Donor site complications like eating and drinking difficulty, dysguesia, pain, sensitivity, speaking disorders were not found in any patient while oral tightness was noted in 43.30% (n=55) of patients. On postoperative follow-up mean peak urinary flow rate (Qmax) was 28.0 ml/sec (range 20.0-30.6 ml/sec). After a mean follow-up of 8.8 months range (1 month to 33 months) overall success rate was 90.55% (n=115). Conclusions: Buccal mucosa is an excellent graft material for substitution free graft urethroplasty in case of long anterior urethral stricture with excellent success rate. Success rate of dorsal onlay substitution free buccal mucosal graft urethroplasty is affected by length of stricture and aetiology of strictures. Lichen sclerosus having moderate success rate of urethroplasty and higher rate of complication and failure rate in 1-stage buccal mucosal urethroplasty and can be considered for two stage urethroplasty in case of very long stricture of anterior urethra of lichen sclerosus origin

Comparative evaluation of IS6110 PCR via conventional methods in rapid diagnosis of new and previously treated cases of extrapulmonary tuberculosis

ÖZET Yeni ve önceden tedavi edilmiş ekstrapulmoner tüberkülozlu hastaların hızlı tanısında IS6110 ile konvansiyonel yöntemlerin karşılaştırılmalı değerlendirilmesi Gelişmekte olan ülkelerde ekstrapulmoner tüberküloz (EPTB) tanısı önemli bir problemdir. EPTB'de, az sayıda basil içerme özelliği, yetersiz miktarda örnek gibi birçok sorun bulunmaktadır. Bütün bu kısıtlamalar, konvansiyonel bakteriyolojik tekniklerin EPTB tanısına düşük katkısına neden olmaktadır. Nükleik asit amplifikasyon yöntemleri, mikobakteriyel DNA'nın saptanması amacıyla geliştirilen hızlı ve duyarlı tekniklerdir. Mycobacterium tuberculosis complex'in spesifik genomunda yer alan "insertion sequence" IS6110'a ait 123bp'nin DNA fragmanı, EPTB'nin hızlı tanısı amacıyla polimeraz zincir reaksiyonu (PCR) ile çoğaltıldı. Bu çalışmada, yeni ve önceden tedavi edilmiş EPTB'li hastaların hızlı tanısında IS6110 PCR ile konvansiyonel yöntemler karşılaştırıldı. EPTB şüpheli hastalardan 450 örnek toplandı ve Mycobacteria için Zeihl Neelson (ZN) boyama ve M. tuberculosis için BACTEC kültürü yapıldı. Bütün örnekler ayrıca, M. tuberculosis complex'in insertion element IS6110'un 123bp fragmanını hedefleyen primerlerle PCR amplifikasyonu ile IS6110 için çalışıldı. Testler arasında duyarlılık bakımından anlamlı fark saptandı. Dört yüz elli örnek . Bununla birlikte, testler arasında spesifisite bakımından anlamlı fark yoktu (p> 0.05). IS6110 PCR'nin hem yeni hem de önceden tedavi edilmiş hastalarda, yayma mikroskopi ve BACTEC kültüründen daha duyarlı olduğunu bulduk. IS6110 PCR, yeni ve önceden tedavi edilmiş EPTB'li hastaların tanısında kullanışlı olabilir. Şüpheli EPTB'li hastaların tedavi kararında fayda sağlayabilir. Anahtar Kelimeler: Tüberküloz, ekstrapulmoner tüberküloz, polimeraz zincir reaksiyonu, IS6110. Yazışma Adresi (Address for Correspondence): Dr. Surya KANT, Chhatrapati Shahu Ji Maharaj Medical University UP (Erstwhile King George Medical College), LUCKNOW -INDIA e-mail: [email protected] Tuberculosis (TB) continues to be a major global public health problem. Incidence of extrapulmonary tuberculosis (EPTB) is on increasing worldwide as well as in India (1,2). EPTB compromises 20% of all TB cases in India (3). Diagnosis of EPTB in different clinical presentations has been always as challenge. Smear microscopy and culture lack of sensitivity in EPTB case and culture (solid and liquid media) also takes at least two to four weeks for grow of mycobacteria. A study has reported smear positive is around 10-37% of the patients and mycobacterial culture is positive in variable proportional 12-80% in different biological specimens (3). Studies from many laboratories around the global were using primers most commonly targeting the IS6110 insertion element (4-9). The detection of the IS6110 insertion element present in form of multiple copies to detect of Mycobacterium tuberculosis complex but not other mycobacterial species (9-11). Polymerase chain reaction (PCR) using IS6110 insertion sequences as the target, has potential to conquer limitation of conventional method and to established as rapid, sensitive technique for detecting DNA of M. tuberculosis in different clinical specimens from respiratory and non respiratory sites MATERIALS and METHODS Study Design The study was performed prospectively in a blinded manner. Clinical Specimens and Data Collection 2-5 mL of specimens was collected from 450 specimens, non-repeated specimens from suspected cases of extrapulmonary tuberculosis. The specimens were included as Lymph Node Aspirate and Cold Abscesses, Pleural fluid, C.S.F, Synovial Fluid, Ascetic Fluid, Urine, Gastric Aspirate, Pus, Bone Marrow, Wound and Pus swab and Others specimens (biopsies tissues). All specimens were kept in ice box and transported Mycobacteriology Laboratory, Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India for smear examination by ZN Staining, BACTEC Culture and PCR test. All patients were signed with due informed consent of the patients from indoor and outward wards of Department of Pulmonary Medicine, Chhatrapati Shahuji Maharaj Medical University, Lucknow, India and Mycobacteriology Laboratory, Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India during Jan 2009 to Dec 2010. The clinical history regarding, present and past history of antitubercular treatment (ATT); family history of tuberculosis and any other associated disease were taken in prescribed Performa. Microbiological Analysis of Extra Pulmonary Specimens Specimens was divided in to two part one part was kept at -20 for PCR till processing and another part was processed for mycobacterial smear preparation and BACTEC culture. Smears were stained with Ziehl Neelsen (ZN) method and examined for acid-fast bacilli (AFB) (21). BACTEC vials were incubated and interpreted as per Becton Dickinson (BD, Sparks, MD, USA) manual instructions (22). NAP (p-nitro-α-acetylamino-β-hydroxy propiophenone) (Becton Dickinson, Sparks, MD, USA), identification was done to differentiate M. tuberculosis form non tuberculous mycobacteria (22). A decrease or unchanged growth index (GI) in nap vial indicated presence of M. tuberculosis complex (MTBC), while an increase in GI indicated the presence of Mycobacterium other than tuberculosis (MOTT). Standard H 37 Rv strain of M. tuberculosis complex was used as positive control. Extraction of DNA Extraction of DNA was done by the CTAB (cetyl-trimethyl-ammonium bromide) -phenol chloroform extraction method (23). Specimens were centrifuged at 10.000 rpm for 10 min. The supernatant was discarded and the pellet suspended in 567 µL of TE (Tris EDTA, pH 7.4) buffer, 30 µL 10% SDS (sodium dodecyl sulfate) and 3 µL proteinase K (20 mg/mL), mixed and incubated at 37°C for 1 hour. After incubation, 100 µL of 5 M NaCl and 80 µL of high-salt CTAB buffer (containing 4 M NaCl, 1.8% CTAB was added and mixed followed by incubation at 65°C for 10 min. An approximate equal volume (0.7-0.8 µL) of chloroform-isoamyl alcohol (24.1) was added, mixed thoroughly and centrifuged for 4-5 min in a microcentrifuge at 12.000 rpm. The aqueous viscous supernatant was carefully decanted and transferred to a new tube. An equal volume of phenol: chloroform-isoamyl alcohol (1:1) was added followed by a 5 min spin at 12.000 rpm. The supernatant was separated and then mixed with 0.6 volume of isopropanol to get a precipitate. The precipitated nucleic acids were washed with 75% ethanol, dried and re-suspended in 100 µL of TE buffer. Primer and IS6110 PCR The amplification reaction was performed in a final volume of 20 µL. the reaction mixture contained 10 µL Pyrostart Fast PCR Master Mix 2X (dNTP, Taq polymerase with Mgcl 2 , Fermentas, India), 1 µL (10 pmole) of each primer, 3 µL water (nuclease free) and 5 µL of extracted DNA. The oligonucleotide primers used were IS1 and IS2, are: 5'-CCT GCG AGC GTA GGC GTC GG3' and 5' CTC GTC CAG CGC CGC TTC GG 3' respectively (SBS Gentech Co. Ltd) (24). These primers amplified a target fragment at 123 base pairs (bp) from the insertion, M. tuberculosis sequence element IS6110. The PCR amplification was done in thermal cycler (MJ Research, PTC-100, GMI, Inc, USA), which involved 40 cycles of denaturation at 94°C for 2 minute, annealing of primers at 68°C for 2 minute, and primer extension at 72°C for 1 minute. The amplified products were separated on 2% agarose gels, visualized on a UV-light transilluminator (Bangalore Genei, Bangalore, India). The presence of 123bp fragment indicate as positive test as M. tuberculosis complex. The positive controls included the DNA of H37Rv strain. Negative control included PCR grade water Statistical Analysis Data were analyzed using SPSS 15.0 (Statistical Package for the Social Sciences, Chicago, IL, USA) for Maurya AK, Kant S, Nag VL, Kushwaha RAS, Kumar M, Dhole TN. 215 Tüberküloz ve Toraks Dergisi 2011; 59(3): 213-220 Windows. The significance of difference was taken as significance value (p< 0.05).Sensitivity was calculated as [Tp/(Tp + Fn)] x 100; specificity was calculated as [Tn/(Tn + Fp)] x 100; Tp = total number of positives; Tn = total number of negatives; Fp = total number of false positive, Fn = total number of false negative; respectively. RESULTS Specimen's Characterization of Extrapulmonary Tuberculosis Cases During the two year study period, 470 clinical specimens were strong clinical suspicion of extrapulmonary tuberculosis were subjected from tertiary care hospitals and all mention test were performed. Out of these, 20 specimens found to be contaminated in BACTEC culture. 450 specimens of results were used in the study. Out of 450 specimens, 153 (34%) lymph node aspirate and cold abscesses, 58 (12.8%) pleural fluid, 44 (9.7%) cerebrum spinal fluid (CSF), 48 (10.7%) urine, 31(6.8%) ascetic fluid, 26 (5.8%) pus, 22 (4.9%) wound and pus swab, 16 (3.5%) gastric aspirate, 10 (2.2%) bone marrow, 10 (2.2%) synovial fluid and 30 (6.7%) others specimens (biopsies tissues). Out of 450 patients, 320 (71.1%) patients were males and 130 (28.9%) females. The mean age of all patients was 39.8 ± 16.1 years. Patients 25-44 years of age accounted for 45% of the total cases. Out of 450 cases, 328 (72.8%) were new cases and 122 (22.2%) were previously treated cases of EPTB. Detection Rate of M. tuberculosis by IS6110 PCR, BACTEC Culture and ZN Smear Microscopy According to New Cases and Previously Treated Cases All specimens were colleted from suspected case of extra pulmonary tuberculosis were found to be AFB positive were 60 (13.4%). On the basis of cases, we found that sensitivity of AFB staining on EPTB were 37 (11.2%) in new cases and 23 (18.8%) in previously treated cases. The sensitivity of AFB staining was higher in comparison to previously treated cases. Overall detection rate of M. tuberculosis by AFB Staining was 60 (13.4%). The detection of M. tuberculosis by BACTEC culture was 202 (45%). Results of BACTEC culture according to cases, 151 (46.03%) were in new cases and 51 (41.8%) were in previously treated cases. We found that sensitivity of BACTEC culture was higher in new cases. All culture isolates obtained were confirmed as mycobacteria with biochemical tests mentioned. Using IS 6110 PCR, 283 (61.8%) were positive for IS6110 PCR for M. tuberculosis. 203 (61.8%) were positive in new cases and 80 (65.5%) were positive in previously treated cases. We found that sensitivity of IS6110 PCR was higher in previously treated cases. Overall comparison of tests, IS6110 PCR was found to have much higComparative evaluation of IS6110 PCR via conventional methods in rapid diagnosis of new and previously treated cases of extrapulmonary tuberculosis 216 Tüberküloz ve Toraks Dergisi 2011; 59(3): 213-220 Comparison of Sensitivity of IS6110 PCR Test Via Others Conventional Tests According to New Cases and Previously Treated Cases IS6110 PCR test was found to be much more sensitive than ZN staining and BACTEC culture results individually as well as in combination are shown in 217 Tüberküloz ve Toraks Dergisi 2011; 59(3): 213-220 DISCUSSION Tuberculosis (TB) is a major public health dilemma in India. India is the highest TB burden country accounting for one fifth of the global incidence. Global annual incidence estimate is 9.4 million cases out of which it is estimated that 1.98 million cases are from India (26). In India, EPTB comprises 20% of all TB cases. Its prevalence in the country varies between 8.3-13.1% in different districts according to cohort analysis by Central TB Division, Ministry of Health and Family Welfare in 2002 (27,28). The diagnosis of extrapulmonary tuberculosis is till now challenging for diagnostic routine laborites. Numeric reasons are showing that, lack of adequate specimens amounts or volumes; distribute of the specimens for different diagnostic tests (histology/cytology, biochemical analysis, microbiology, and PCR), non-uniform distribution of microorganisms; paucibacillary nature of the specimens; presence of inhibitors that undermine the performance of nucleic acid amplification-based techniques; and the lack of an efficient sample processing technique universally applicable on all types of extrapulmonary samples (29). The poor performance of conventional M. tuberculosis detection techniques, based on microscopic examination of Ziehl-Neelsen stained and culture of M. tuberculosis (LJ Medium and BACTEC Radiometric culture) are still in widespread use for diagnostic purposes, still though they fail to provide the required sensitivity and specificity. The PCR test would be particularly useful in the diagnosis of EPTB where conventional microbiological techniques for M. tuberculosis are showing poor performance of sensitivity. The specificity, sensitivity and speed of PCR test in diagnosis of M. tuberculosis infection shown in this study should encourage the use of this method in routine diagnosis of EPTB. Previously studies shown the success of microscopy is highly variable from 22% to 96% and most authors rate it at round 60% (30-32). Our results shown that sensitivity of smear microscopy was 13.7% and specificity was 100%. The sensitivity of microscopy depends on the clinical presentation and more than 10.000 bacilli per milliliter are necessary for secure microscopic positivity (33). Our studies shown that conventional bacteriological technique were positive in 202 (45%) specimens, where as IS6110 PCR showed that 283 (63%) specimens were positive for M. tuberculosis. The difference was found that to be statistical significant (p< 0.05). Several studies have been reported on PCR to detect M. tuberculosis (34-39). The detection of the IS6110 insertion element present in multiple copies to detect M. tuberculosis complex, but not other mycobacterial species 218 Tüberküloz ve Toraks Dergisi 2011; 59(3): 213-220 tion and PCR results were positive but BACTEC culture was negative; these could be the presence of nonviable mycobacteria in the sample as patients were receiving antitubercular treatment. IS6110 PCR test is higher sensitivity than microscopy and the culture and could help in therapeutic decision for patients with clinical suspicion of EPTB. CONCLUSION IS6110 PCR test for DNA specific M. tuberculosis may be hopes of a rapid and accurate diagnostic test for EPTB and it will help where conventional diagnosis fails and provisional diagnosis of tuberculosis is made on the basis of clinical presentation and histology/cytology examination without evidence of AFB. IS6110 PCR may be great potential to improve the clinician vision for the early diagnosis, treatment and prevention of EPTB. ACKNOWLEDGEMEN

Nanocolumnar Crystalline Vanadium Oxide-Molybdenum Oxide Antireflective Smart Thin Films with Superior Nanomechanical Properties

Vanadium oxide-molybdenum oxide (VO-MO) thin (21-475 nm) films were grown on quartz and silicon substrates by pulsed RF magnetron sputtering technique by altering the RF power from 100 to 600 W. Crystalline VO-MO thin films showed the mixed phases of vanadium oxides e.g., V2O5, V2O3 and VO2 along with MoO3. Reversible or smart transition was found to occur just above the room temperature i.e., at similar to 45-50 degrees C. The VO-MO films deposited on quartz showed a gradual decrease in transmittance with increase in film thickness. But, the VO-MO films on silicon exhibited reflectance that was significantly lower than that of the substrate. Further, the effect of low temperature (i.e., 100 degrees C) vacuum (10(-5) mbar) annealing on optical properties e.g., solar absorptance, transmittance and reflectance as well as the optical constants e.g., optical band gap, refractive index and extinction coefficient were studied. Sheet resistance, oxidation state and nanomechanical properties e.g., nanohardness and elastic modulus of the VO-MO thin films were also investigated in as-deposited condition as well as after the vacuum annealing treatment. Finally, the combination of the nanoindentation technique and the finite element modeling (FEM) was employed to investigate yield stress and von Mises stress distribution of the VO-MO thin films

Corporate identity, customer orientation and performance of SMEs: Exploring the linkages

This research aims to explore the impact of corporate identity (CI) on performance in B2C small and medium enterprises (SMEs) in food processing, with varying degrees of customer orientation (CO). The research is embedded in the positivistic paradigm. Based on a literature review, a conceptual model (consisting of five hypotheses) has been tested with 102 samples using PLS-SEM tool. This study establishes the mediating role of CO on the CI and performance linkage, it provides empirical evidence to CI and performance linkage, and makes an incremental contribution by extension of theory of CI and CO in the given context

Exploring options for reprocessing of N95 Filtering Facepiece Respirators (N95-FFRs) amidst COVID-19 pandemic: A systematic review.

BackgroundThere is global shortage of Personal Protective Equipment due to COVID-19 pandemic. N95 Filtering Facepiece Respirators (N95-FFRs) provide respiratory protection against respiratory pathogens including SARS-CoV-2. There is scant literature on reprocessing methods which can enable reuse of N95-FFRs.AimWe conducted this study to evaluate research done, prior to COVID-19 pandemic, on various decontamination methods for reprocessing of N95-FFRs.MethodsWe searched 5 electronic databases (Pubmed, Google Scholar, Crossref, Ovid, ScienceDirect) and 1 Grey literature database (OpenGrey). We included original studies, published prior to year 2020, which had evaluated any decontamination method on FFRs. Studies had evaluated a reprocessing method against parameters namely physical changes, user acceptability, respirator fit, filter efficiency, microbicidal efficacy and presence of chemical residues post-reprocessing.Findings and conclusionsOverall, we found 7887 records amongst which 17 original research articles were finally included for qualitative analysis. Overall, 21 different types of decontamination or reprocessing methods for N95-FFRs were evaluated. Most commonly evaluated method for reprocessing of FFRs was Ultraviolet (Type-C) irradiation (UVGI) which was evaluated in 13/17 (76%) studies. We found published literature was scant on this topic despite warning signs of pandemic of a respiratory illness over the years. Promising technologies requiring expeditious evaluation are UVGI, Microwave generated steam (MGS) and based on Hydrogen peroxide vapor. Global presence of technologies, which have been given Emergency use authorisation for N95-FFR reprocessing, is extremely limited. Reprocessing of N95-FFRs by MGS should be considered for emergency implementation in resource limited settings to tackle shortage of N95-FFRs.Systematic review identifierPROSPERO, PROSPERO ID: CRD42020189684, (https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020189684)

An accurate machine learning approach to predict immunogenic peptides in human

Cancer immunotherapy provides durable response to a small subset of treated patients. A variety of approaches are being developed to increase the long term benefit of checkpoint blockade. These include radiation and cytotoxic therapies and use of cancer vaccines among others. Preclinical and clinical studies have demonstrated that cancer vaccines evoke strong anti-tumor immune response by mobilizing CD8+ T-cells. A challenge in the field of cancer vaccines is identifying mutations that are T-cell activating (neoepitopes). Advances in next generation sequencing permit accurate detection of cancer mutations, even when present at a low frequency. However, neoepitope prediction involves a large number of steps many of which cannot be accurately modeled. In humans, class-I peptides, 9-11–mer in length are presented by HLA – A, B and C alleles and activate CD8+ T-cells. Class-II peptides are 14-17-mer, presented by DPA, DPB, DQA, DQB, DRA and DRB alleles and activate CD4+ T-cells.The current method to identify epitopes (peptides) depends primarily on HLA binding prediction algorithm. Our analysis of 9mer peptides from IEDB database showed that there is no difference in binding affinity of peptide that can activate (immunogenic) and that cannot activate (non-immunogenic) the T-cells. The specificity to identify immunogenic peptide using HLA binding based method is only 27.59%. In this study, we present a novel approach using machine learning technique that can predict whether the peptide will be immunogenic or not. We have generated the model using features generated from amino-acid composition, HLA-binding, structural features, peptide processing and peptide transport. Our model achieved an overall accuracy of 77.30% with a specificity of 92.24% on unseen dataset

Nursing students: A vulnerable health-care worker for needlesticks injuries in teaching hospitals

Background: Occupational exposure to bloodborne pathogen is a significant risk to health-care workers. In any teaching hospital apart from regular health-care workers and employees, there are significant population of students and trainee. It is important to assess the health-care worker in hospital which has maximum chances of exposure to these pathogens. The aim of this study is to determine the most susceptible job group for needlestick injury (NSI) reported in a newly established teaching medical institute in the Western part of Rajasthan, India. Methods: This is a retrospective analysis of data of NSI occurred during September 2014 to January 2017. Results: Sixty three NSIs were reported during the study. Nursing students were the most vulnerable group who reported maximum number of NSI. Among the nursing students, 72% were completely vaccinated against hepatitis B virus. Conclusions: Nursing students are at utmost risk for NSIs, the prevention of which requires regular training and education