Simulation of the Performance of the IISc Chemical Kinetics Shock Tube

This report presents the results of an investigation of the performance of the Chemical Kinetics Shock tube at the Indian Institute of Science. The one-dimensional Lagrangian code L1d of Jacobs (1998) has been used to simulate the tube at several operating conditions. The conditions have different shock tube filling pressures, resulting in different shock speeds and different tube lengths, resulting in different dwell times. The simulations have been performed both with and without viscous effects simulated in the tubes. At the lowest shock tube filling pressure condition, the shock tube operates in an overtailored mode and it is undertailored at the higher filling pressure conditions. The results show that viscous effects, which lead to attenuation of the primary shock and heat loss from the test gas to the tube walls, result in an increasing p5 pressure during the test time. The viscous effects are more dominant at the condition with the lowest filling pressure (highest primary shock speed). A simulation run for 50 ms after diaphragm rupture or the configuration with a long driver tube shows that the test gas is periodically re-compressed by reflections of waves along the driver and shock tubes. The recompressions become sequentially weaker and thus the test gas temperature and pressure are never raised to as high levels as for the primary compression

Pulsed nozzle Fourier transform microwave spectrometer: an ideal spectrometer to define hydrogen bond radius

A pulsed nozzle Fourier transform microwave (PNFTMW) spectrometer has been recently fabricated at the Indian Institute of Science. The basic design is the same as that of Balle and Flygare. However, recent advances in microwave and computer technologies have helped in designing a state-of-the-art PNFTMW spectrometer. The range of the spectrometer is from 2 to 26.5 GHz. Strong signals from OCS and several of its low abundant isotopes as well as weakly bound complexes such as Ar-(H2O), Ar-H2S and Ar3-H2S have been obtained. For the OCS parent isotopomer, the observed line width is only 2.8 kHz, indicating the high resolution of the spectrometer. Small hyperfine splittings could also be observed from the 13C spin-rotation interaction (4.9 kHz) in OCS and the I=1 state of H2O (10 kHz) in Ar-H2O complex. This article gives the details of the newly fabricated PNFTMW spectrometer. By analysing the structural data available in the literature, most of it using PNFTMW spectrometer, we had recently defined a 'hydrogen bond radius' for all the hydrogen halides. This approach is extended to acetylene and water in this article, as models for the OH and CH groups involved in H bonding in biological systems. The H bond radius for H2O is 0.78 ± 0.07 Å and that of C2H2 is 1.09 ± 0.05 Å

Laboratory investigation of shock-induced dissociation of buckminsterfullerene and astrophysical insights

Fullerene C60 is one of the most iconic forms of carbon found in the interstellar medium (ISM). The interstellar chemistry of carbon-rich components, including fullerenes, is driven by a variety of energetic processes including UV and X-ray irradiation, cosmic-ray (CR) bombardment, electron impact, and shock waves. These violent events strongly alter the particle phase and lead to the release of new molecular species in the gas phase. Only a few experimental studies on the shock processing of cosmic analogs have been conducted so far. We explored in the laboratory the destruction of buckminsterfullerene C60 using a pressure-driven shock tube coupled with optical diagnostics. Our efforts were first devoted to probing in situ the shock-induced processing of C60 at high temperatures (≤4500 K) by optical emission spectroscopy. The analysis of the spectra points to the massive production of C2 units. A broad underlying continuum was observed as well and was attributed to the collective visible emission of carbon clusters, generated similarly in large amounts. This proposed assignment was performed with the help of calculated emission spectra of various carbon clusters. The competition between dissociation and radiative relaxation, determined by statistical analysis, alludes to a predominance of clusters with less than 40 carbon atoms. Our laboratory experiments, supported by molecular dynamics simulations performed in the canonical ensemble, suggest that C60 is very stable, and that high-energy input is required to process it under interstellar low-density conditions and to produce C2 units and an abundance of intermediate-sized carbon clusters. These results provide some insights into the life cycle of carbon in space. Our findings hint that only J-type shocks with velocities above ∼100 km s−1 or C-type shocks with velocities above 9 km s−1 can lead to the destruction of fullerenes. Observational tracers of this process remain elusive, however. Our work confirms the potential of shock tubes for laboratory astrophysics

Quantum mechanical studies of lincosamides

Lincosamides are a class of antibiotics used both in clinical and veterinary practice for a wide range of pathogens. This group of drugs inhibits the activity of the bacterial ribosome by binding to the 23S RNA of the large ribosomal subunit and blocking protein synthesis. Currently, three X-ray structures of the ribosome in complex with clindamycin are available in the Protein Data Bank, which reveal that there are two distinct conformations of the pyrrolidinyl propyl group of the bound clindamycin. In this work, we used quantum mechanical methods to investigate the probable conformations of clindamycin in order to explain the two binding modes in the ribosomal 23S RNA. We studied three lincosamide antibiotics: clindamycin, lincomycin, and pirlimycin at the B3LYP level with the 6-31G** basis set. The focus of our work was to connect the conformational landscape and electron densities of the two clindamycin conformers found experimentally with their physicochemical properties. For both functional conformers, we applied natural bond orbital (NBO) analysis and the atoms in molecules (AIM) theory, and calculated the NMR parameters. Based on the results obtained, we were able to show that the structure with the intramolecular hydrogen bond C=O…H–O is the most stable conformer of clindamycin. The charge transfer between the pyrrolidine-derivative ring and the six-atom sugar (methylthiolincosamide), which are linked via an amide bond, was found to be the dominant factor influencing the high stability of this conformer

Primary prevention of variceal bleeding in people with oesophageal varices due to liver cirrhosis: a network meta-analysis

BACKGROUND: Approximately 40% to 95% of people with cirrhosis have oesophageal varices. About 15% to 20% of oesophageal varices bleed in about one to three years. There are several different treatments to prevent bleeding, including: beta-blockers, endoscopic sclerotherapy, and variceal band ligation. However, there is uncertainty surrounding their individual and relative benefits and harms. OBJECTIVES: To compare the benefits and harms of different treatments for prevention of first variceal bleeding from oesophageal varices in adults with liver cirrhosis through a network meta-analysis and to generate rankings of the different treatments for prevention of first variceal bleeding from oesophageal varices according to their safety and efficacy. SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase, Science Citation Index Expanded, World Health Organization International Clinical Trials Registry Platform, and trials registers to December 2019 to identify randomised clinical trials in people with cirrhosis and oesophageal varices with no history of bleeding. SELECTION CRITERIA: We included only randomised clinical trials (irrespective of language, blinding, or status) in adults with cirrhosis and oesophageal varices with no history of bleeding. We excluded randomised clinical trials in which participants had previous bleeding from oesophageal varices and those who had previously undergone liver transplantation or previously received prophylactic treatment for oesophageal varices. DATA COLLECTION AND ANALYSIS: We performed a network meta-analysis with OpenBUGS using Bayesian methods and calculated the differences in treatments using hazard ratios (HR), odds ratios (OR), and rate ratios with 95% credible intervals (CrI) based on an available-case analysis, according to National Institute for Health and Care Excellence Decision Support Unit guidance. We performed the direct comparisons from randomised clinical trials using the same codes and the same technical details. MAIN RESULTS: We included 66 randomised clinical trials (6653 participants) in the review. Sixty trials (6212 participants) provided data for one or more comparisons in the review. The trials that provided the information included people with cirrhosis due to varied aetiologies and those at high risk of bleeding from oesophageal varices. The follow-up in the trials that reported outcomes ranged from 6 months to 60 months. All but one of the trials were at high risk of bias. The interventions compared included beta-blockers, no active intervention, variceal band ligation, sclerotherapy, beta-blockers plus variceal band ligation, beta-blockers plus nitrates, nitrates, beta-blockers plus sclerotherapy, and portocaval shunt. Overall, 21.2% of participants who received non-selective beta-blockers ('beta-blockers') - the reference treatment (chosen because this was the most common treatment compared in the trials) - died during 8-month to 60-month follow-up. Based on low-certainty evidence, beta-blockers, variceal band ligation, sclerotherapy, and beta-blockers plus nitrates all had lower mortality versus no active intervention (beta-blockers: HR 0.49, 95% CrI 0.36 to 0.67; direct comparison HR: 0.59, 95% CrI 0.42 to 0.83; 10 trials, 1200 participants; variceal band ligation: HR 0.51, 95% CrI 0.35 to 0.74; direct comparison HR 0.49, 95% CrI 0.12 to 2.14; 3 trials, 355 participants; sclerotherapy: HR 0.66, 95% CrI 0.51 to 0.85; direct comparison HR 0.61, 95% CrI 0.41 to 0.90; 18 trials, 1666 participants; beta-blockers plus nitrates: HR 0.41, 95% CrI 0.20 to 0.85; no direct comparison). No trials reported health-related quality of life. Based on low-certainty evidence, variceal band ligation had a higher number of serious adverse events (number of events) than beta-blockers (rate ratio 10.49, 95% CrI 2.83 to 60.64; 1 trial, 168 participants). Based on low-certainty evidence, beta-blockers plus nitrates had a higher number of 'any adverse events (number of participants)' than beta-blockers alone (OR 3.41, 95% CrI 1.11 to 11.28; 1 trial, 57 participants). Based on low-certainty evidence, adverse events (number of events) were higher in sclerotherapy than in beta-blockers (rate ratio 2.49, 95% CrI 1.53 to 4.22; direct comparison rate ratio 2.47, 95% CrI 1.27 to 5.06; 2 trials, 90 participants), and in beta-blockers plus variceal band ligation than in beta-blockers (direct comparison rate ratio 1.72, 95% CrI 1.08 to 2.76; 1 trial, 140 participants). Based on low-certainty evidence, any variceal bleed was lower in beta-blockers plus variceal band ligation than in beta-blockers (direct comparison HR 0.21, 95% CrI 0.04 to 0.71; 1 trial, 173 participants). Based on low-certainty evidence, any variceal bleed was higher in nitrates than beta-blockers (direct comparison HR 6.40, 95% CrI 1.58 to 47.42; 1 trial, 52 participants). The evidence indicates considerable uncertainty about the effect of the interventions in the remaining comparisons. AUTHORS' CONCLUSIONS: Based on low-certainty evidence, beta-blockers, variceal band ligation, sclerotherapy, and beta-blockers plus nitrates may decrease mortality compared to no intervention in people with high-risk oesophageal varices in people with cirrhosis and no previous history of bleeding. Based on low-certainty evidence, variceal band ligation may result in a higher number of serious adverse events than beta-blockers. The evidence indicates considerable uncertainty about the effect of beta-blockers versus variceal band ligation on variceal bleeding. The evidence also indicates considerable uncertainty about the effect of the interventions in most of the remaining comparisons

Switch-peptides: design and characterization of controllable super-amyloid-forming host-guest peptides as tools for identifying anti-amyloid agents

Several amyloid-forming proteins are characterized by the presence of hydrophobic and highly amyloidogenic core sequences that play critical roles in the initiation and progression of amyloid fibril formation. Therefore targeting these sequences represents a viable strategy for identifying candidate molecules that could interfere with amyloid formation and toxicity of the parent proteins. However, the highly amyloidogenic and insoluble nature of these sequences has hampered efforts to develop high-throughput fibrillization assays. Here we describe the design and characterization of host-guest switch peptides that can be used for in vitro mechanistic and screening studies that are aimed at discovering aggregation inhibitors that target highly amyloidogenic sequences. These model systems are based on a host-guest system where the amyloidogenic sequence (guest peptide) is flanked by two beta-sheet-promoting (Leu-Ser)(n) oligomers as host sequences. Two host-guest peptides were prepared by using the hydrophobic core of Abeta comprising residues 14-24 (HQKLVFFAEDV) as the guest peptide with switch elements inserted within (peptide 1) or at the N and C termini of the guest peptide (peptide 2). Both model peptides can be triggered to undergo rapid self-assembly and amyloid formation in a highly controllable manner and their fibrillization kinetics is tuneable by manipulating solution conditions (for example, peptide concentration and pH). The fibrillization of both peptides reproduces many features of the full-length Abeta peptides and can be inhibited by known inhibitors of Abeta fibril formation. Our results suggest that this approach can be extended to other amyloid proteins and should facilitate the discovery of small-molecule aggregation inhibitors and the development of more efficacious anti-amyloid agents to treat and/or reverse the pathogenesis of neurodegenerative and systemic amyloid diseases

Secondary prevention of variceal bleeding in adults with previous oesophageal variceal bleeding due to decompensated liver cirrhosis: a network meta-analysis

BACKGROUND: Approximately 40% to 95% of people with cirrhosis have oesophageal varices. About 15% to 20% of oesophageal varices bleed in about one to three years of diagnosis. Several different treatments are available, which include endoscopic sclerotherapy, variceal band ligation, beta-blockers, transjugular intrahepatic portosystemic shunt (TIPS), and surgical portocaval shunts, among others. However, there is uncertainty surrounding their individual and relative benefits and harms. OBJECTIVES: To compare the benefits and harms of different initial treatments for secondary prevention of variceal bleeding in adults with previous oesophageal variceal bleeding due to decompensated liver cirrhosis through a network meta-analysis and to generate rankings of the different treatments for secondary prevention according to their safety and efficacy. SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase, Science Citation Index Expanded, World Health Organization International Clinical Trials Registry Platform, and trials registers until December 2019 to identify randomised clinical trials in people with cirrhosis and a previous history of bleeding from oesophageal varices. SELECTION CRITERIA: We included only randomised clinical trials (irrespective of language, blinding, or status) in adults with cirrhosis and previous history of bleeding from oesophageal varices. We excluded randomised clinical trials in which participants had no previous history of bleeding from oesophageal varices, previous history of bleeding only from gastric varices, those who failed previous treatment (refractory bleeding), those who had acute bleeding at the time of treatment, and those who had previously undergone liver transplantation. DATA COLLECTION AND ANALYSIS: We performed a network meta-analysis with OpenBUGS using Bayesian methods and calculated the differences in treatments using hazard ratios (HR), odds ratios (OR) and rate ratios with 95% credible intervals (CrI) based on an available-case analysis, according to National Institute of Health and Care Excellence Decision Support Unit guidance. MAIN RESULTS: We included a total of 48 randomised clinical trials (3526 participants) in the review. Forty-six trials (3442 participants) were included in one or more comparisons. The trials that provided the information included people with cirrhosis due to varied aetiologies. The follow-up ranged from two months to 61 months. All the trials were at high risk of bias. A total of 12 interventions were compared in these trials (sclerotherapy, beta-blockers, variceal band ligation, beta-blockers plus sclerotherapy, no active intervention, TIPS (transjugular intrahepatic portosystemic shunt), beta-blockers plus nitrates, portocaval shunt, sclerotherapy plus variceal band ligation, beta-blockers plus nitrates plus variceal band ligation, beta-blockers plus variceal band ligation, sclerotherapy plus nitrates). Overall, 22.5% of the trial participants who received the reference treatment (chosen because this was the commonest treatment compared in the trials) of sclerotherapy died during the follow-up period ranging from two months to 61 months. There was considerable uncertainty in the effects of interventions on mortality. Accordingly, none of the interventions showed superiority over another. None of the trials reported health-related quality of life. Based on low-certainty evidence, variceal band ligation may result in fewer serious adverse events (number of people) than sclerotherapy (OR 0.19; 95% CrI 0.06 to 0.54; 1 trial; 100 participants). Based on low or very low-certainty evidence, the adverse events (number of participants) and adverse events (number of events) may be different across many comparisons; however, these differences are due to very small trials at high risk of bias showing large differences in some comparisons leading to many differences despite absence of direct evidence. Based on low-certainty evidence, TIPS may result in large decrease in symptomatic rebleed than variceal band ligation (HR 0.12; 95% CrI 0.03 to 0.41; 1 trial; 58 participants). Based on moderate-certainty evidence, any variceal rebleed was probably lower in sclerotherapy than in no active intervention (HR 0.62; 95% CrI 0.35 to 0.99, direct comparison HR 0.66; 95% CrI 0.11 to 3.13; 3 trials; 296 participants), beta-blockers plus sclerotherapy than sclerotherapy alone (HR 0.60; 95% CrI 0.37 to 0.95; direct comparison HR 0.50; 95% CrI 0.07 to 2.96; 4 trials; 231 participants); TIPS than sclerotherapy (HR 0.18; 95% CrI 0.08 to 0.38; direct comparison HR 0.22; 95% CrI 0.01 to 7.51; 2 trials; 109 participants), and in portocaval shunt than sclerotherapy (HR 0.21; 95% CrI 0.05 to 0.77; no direct comparison) groups. Based on low-certainty evidence, beta-blockers alone and TIPS might result in more, other compensation, events than sclerotherapy (rate ratio 2.37; 95% CrI 1.35 to 4.67; 1 trial; 65 participants and rate ratio 2.30; 95% CrI 1.20 to 4.65; 2 trials; 109 participants; low-certainty evidence). The evidence indicates considerable uncertainty about the effect of the interventions including those related to beta-blockers plus variceal band ligation in the remaining comparisons. AUTHORS' CONCLUSIONS: The evidence indicates considerable uncertainty about the effect of the interventions on mortality. Variceal band ligation might result in fewer serious adverse events than sclerotherapy. TIPS might result in a large decrease in symptomatic rebleed than variceal band ligation. Sclerotherapy probably results in fewer 'any' variceal rebleeding than no active intervention. Beta-blockers plus sclerotherapy and TIPS probably result in fewer 'any' variceal rebleeding than sclerotherapy. Beta-blockers alone and TIPS might result in more other compensation events than sclerotherapy. The evidence indicates considerable uncertainty about the effect of the interventions in the remaining comparisons. Accordingly, high-quality randomised comparative clinical trials are needed

Urinary incontinence and use of incontinence surgery after radical prostatectomy: a national study using patient-reported outcomes.

OBJECTIVES: To investigate whether patient-reported urinary incontinence (UI) and bother scores after radical prostatectomy (RP) result in subsequent intervention with UI surgery. PATIENTS AND METHODS: Men diagnosed with prostate cancer in the English National Health Service between April 2014 and January 2016 were identified. Administrative data were used to identify men who had undergone a RP and those who subsequently underwent a UI procedure. The National Prostate Cancer Audit database was used to identify men who had also completed a post-treatment survey. These surveys included the Expanded Prostate Cancer Composite Index (EPIC-26). The frequency of subsequent UI procedures, within 6 months of the survey, was explored according to EPIC-26 UI scores. The relationship between 'good' (≥75) or 'bad' (≤25) EPIC-26 UI scores and perceptions of urinary bother was also explored (responses ranging from 'no problem' to 'big problem' with respect to their urinary function). RESULTS: We identified 11 290 men who had undergone a RP. The 3-year cumulative incidence of UI surgery was 2.5%. After exclusions, we identified 5165 men who had also completed a post-treatment survey after a median time of 19 months (response rate 74%). A total of 481 men (9.3%) reported a 'bad' UI score and 207 men (4.0%) also reported that they had a big problem with their urinary function. In all, 47 men went on to have UI surgery within 6 months of survey completion (0.9%), of whom 93.6% had a bad UI score. Of the 71 men with the worst UI score (zero), only 11 men (15.5%) subsequently had UI surgery. CONCLUSION: In England, there is a significant number of men living with severe, bothersome UI after RP, and an unmet clinical need for UI surgery. The systematic collection of patient-reported outcomes could be used to identify men who may benefit from UI surgery