Bacteriology of endotracheal tube biofilms and antibiotic resistance: a systematic review

Bacteria commonly adhere to surfaces and produce polymeric material to encase the attached cells to form communities called biofilms. Within these biofilms, bacteria can appear to be many times more resistant to antibiotics or disinfectants. This systematic review explores the prevalence and microbial profile associated with biofilm production of bacteria isolated from endotracheal tubes and its associations with antimicrobial resistance. A comprehensive search was performed on databases PubMed, Embase, and Google Scholar for relevant articles published between 1st January 2000 and 31st December 2022. The relevant articles were exported to Mendeley Desktop 1.19.8 and screened by title and abstract, followed by full text screening based on the eligibility criteria of the study. Quality assessment of the studies was performed using the Newcastle-Ottawa Scale (NOS) customized for cross-sectional studies. Furthermore, the prevalence of antimicrobial resistance in biofilm-producers isolated from endotracheal tube specimens was investigated. Twenty studies encompassing 981 endotracheal tubes met the eligibility criteria. Pseudomonas spp. and Acinetobacter spp. were predominant isolates among the biofilm producers. These biofilms provided strong resistance against commonly used antibiotics. The highest resistance rate observed in Pseudomonas spp. was against fluoroquinolones whereas the least resistance was seen against piperacillin-tazobactam. A similar trend of susceptibility was observed in Acinetobacter spp. with a very high resistance rate against fluoroquinolones, third-generation cephalosporins and carbapenems. In conclusion, endotracheal tubes were associated with colonization by biofilm forming bacteria with varying levels of antimicrobial resistance. Biofilms may promote the occurrence of recalcitrant infections in endotracheal tubes which need to be managed with appropriate protocols and antimicrobial stewardship. Research focus should shift towards meticulous exploration of biofilm-associated infections to improve detection and management.

Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics

Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M₄ muscarinic acetylcholine receptor (M₄ mAChR) is a validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. In this study, we rigorously quantified the affinity, efficacy, and magnitude of modulation of two different positive allosteric modulators, LY2033298 (LY298) and VU0467154 (VU154), combined with the endogenous agonist acetylcholine (ACh) or the high-affinity agonist iperoxo (Ipx), at the human M₄ mAChR. By determining the cryo-electron microscopy structures of the M₄ mAChR, bound to a cognate G_i1 protein and in complex with ACh, Ipx, LY298-Ipx, and VU154-Ipx, and applying molecular dynamics simulations, we determine key molecular mechanisms underlying allosteric pharmacology. In addition to delineating the contribution of spatially distinct binding sites on observed pharmacology, our findings also revealed a vital role for orthosteric and allosteric ligand-receptor-transducer complex stability, mediated by conformational dynamics between these sites, in the ultimate determination of affinity, efficacy, cooperativity, probe dependence, and species variability. There results provide a holistic framework for further GPCR mechanistic studies and can aid in the discovery and design of future allosteric drugs.

Intraglandular Foreign Body - Unusual Aetiology of Submandibular Gland Sialadenitis

Obstructive sialadenitis of submandibular gland is commonly due to sialoliths and strictures in the Wharton's duct. Other endogenous pathologies include mucous plugs and polyps. Foreign bodies of Wharton's duct and submandibular gland are rare. Retrograde migration of foreign bodies via ductal orifice, traversing the ductal system to its final intraglandular location is an even rare entity. These often present with painful swelling of the gland and at times with a purulent sialitis. Diagnostic modalities include plain radiography, ultrasonography, sialography, as well as computed tomography and magnetic resonance imaging. Treatment includes antibiotics, incision and drainage of abscess, and removal of foreign body either surgically (intra-oral approach or sialadenectomy) or more recently via sialoendoscopy. This is a case report of 30 years male with accidental cannulation of Wharton's duct with grass that eventually got lodged in the deep lobe of the gland, and was managed with sialadenectomy.

Critical Non-Covalent Binding Intermediate for an Allosteric Covalent Inhibitor of SUMO E1

Post-translational modifications by small ubiquitin-like modifiers (SUMOs) are dysregulated in many types of cancers. The SUMO E1 enzyme has recently been suggested as a new immuno-oncology target. COH000 was recently identified as a highly specific allosteric covalent inhibitor of SUMO E1. However, a marked discrepancy was found between the X-ray structure of the covalent COH000-bound SUMO E1 complex and the available structure-activity relationship (SAR) data of inhibitor analogues due to unresolved noncovalent protein-ligand interactions. Here, we have investigated noncovalent interactions between COH000 and SUMO E1 during inhibitor dissociation through novel Ligand Gaussian accelerated molecular dynamics (LiGaMD) simulations. Our simulations have identified a critical low-energy non-covalent binding intermediate conformation of COH000 that agreed excellently with published and new SAR data of the COH000 analogues, which were otherwise inconsistent with the X-ray structure. Altogether, our biochemical experiments and LiGaMD simulations have uncovered a critical non-covalent binding intermediate during allosteric inhibition of the SUMO E1 complex.

Effects of presenilin-1 familial Alzheimer's disease mutations on γ-secretase activation for cleavage of amyloid precursor protein

Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer's disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the "Active" state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the "Active" state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.

Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase

The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer's disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and Western blotting were used to quantify the efficiency of tripeptide trimming of wild-type (WT) and familial AD (FAD) mutant Aβ49. In comparison to WT Aβ49, the efficiency of tripeptide trimming was similar for the I45F, A42T, and V46F Aβ49 FAD mutants but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate the tripeptide trimming of Aβ49 by γ-secretase. The starting structure was the active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured the activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai, A., ACS Cent. Sci. 2020, 6, 969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming of Aβ49 by γ-secretase.

A Study of Trauma Patients in the Emergency Department of a Tertiary Care Hospital in Nepal during Lockdown in COVID-19 Pandemic

Background The nationwide lockdown was imposed upon by the Government of Nepal with regards to the COVID-19 pandemic. Even during times of limited mobility and travel, trauma cases were presenting to the hospital. Objective To asses trauma patterns among patients presented to the Emergency department in Dhulikhel hospital during the lockdown period. The assessment of the burden of trauma during the pandemic could aid in planning allocation of resources and improving trauma care. Method A retrospective cross-sectional study design was used to assess all patients with a history of trauma during the period of lockdown announced by the Government of Nepal for COVID-19 from March 24 to June 14, 2020. Result Among 2097 patients that visited the emergency department, 23% were trauma cases. In comparison to the corresponding time-period in 2019, trauma cases reduced by more than half (54.5%). The majority of patients utilized ambulances as a means of transportation; a few patients utilized Dhulikhel emergency medical services. The most common mechanism of injury was fall injury, followed by motor vehicle accident and physical assault. Traumatic brain injury occurred in 30% of patients. Of all patients, 71% were discharged after initial treatment, 26% were admitted to different wards and 3% were referred to other health centres. Conclusion Fall injury is a crucial public health concern followed by motor vehicle accident among trauma patients even during the pandemic condition. Thus, emergency rooms should aid in planning for preparedness, mitigation of trauma during situations like these, in planning the allocation of resources and improving trauma care.

Molecular Simulations and Drug Discovery of Adenosine Receptors

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.

GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling

We introduce a Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and free energy profiling workflow (GLOW) to predict molecular determinants and map free energy landscapes of biomolecules. All-atom GaMD-enhanced sampling simulations are first performed on biomolecules of interest. Structural contact maps are then calculated from GaMD simulation frames and transformed into images for building DL models using a convolutional neural network. Important structural contacts are further determined from DL models of attention maps of the structural contact gradients, which allow us to identify the system reaction coordinates. Finally, free energy profiles are calculated for the selected reaction coordinates through energetic reweighting of the GaMD simulations. We have also successfully demonstrated GLOW for the characterization of activation and allosteric modulation of a G protein-coupled receptor, using the adenosine A₁ receptor (A₁AR) as a model system. GLOW findings are highly consistent with previous experimental and computational studies of the A₁AR, while also providing further mechanistic insights into the receptor function. In summary, GLOW provides a systematic approach to mapping free energy landscapes of biomolecules. The GLOW workflow and its user manual can be downloaded at http://miaolab.org/GLOW.

Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives

Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular dynamics (MD) is a computational approach to analyze these binding processes at an atomistic level, which provides valuable understandings of the mechanisms of biomolecular recognition. However, the rather slow biomolecular binding events often present challenges for conventional MD (cMD), due to limited simulation timescales (typically over hundreds of nanoseconds to tens of microseconds). In this regard, enhanced sampling methods, particularly accelerated MD (aMD), have proven useful to bridge the gap and enable all-atom simulations of biomolecular binding events. Here, we will review the recent method developments of Gaussian aMD (GaMD), ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD), which have greatly expanded our capabilities to simulate biomolecular binding processes. Spontaneous binding of various biomolecules to their receptors has been successfully simulated by GaMD. Microsecond LiGaMD and Pep-GaMD simulations have captured repetitive binding and dissociation of small-molecule ligands and highly flexible peptides, and thus enabled ligand/peptide binding thermodynamics and kinetics calculations. We will also present relevant application studies in simulations of important drug targets and future perspectives for rational computer-aided drug design.

Toothbrush, an Unusual Foreign Body

Accidental consumption of foreign body is a common presenting complain among patients especially in young age group. Majority of patients can be discharged safely after reassurance while a fraction of patient requires observation and further management. Here we report a case of a 35-year-old gentleman who presented to the out-patient department of our hospital in June 2021 for accidental ingestion of toothbrush. After detailed history and physical examination upper gastrointestinal endoscopy was planned for the patient. Failed endoscopic removal was considered the indication for surgery. A supraumbilical midline incision was used to remove the toothbrush. Following the surgical removal, he was managed conservatively and was discharged without significant complications. We describe this case in detail in addition to reviewing the pertinent literature.

Gaussian accelerated molecular dynamics (GaMD): principles and applications

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., "Gaussian approximation"). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica exchange GaMD (rex-GaMD) and replica exchange umbrella sampling GaMD (GaREUS), have also been introduced, further improving sampling and free energy calculations. Recently, new "selective GaMD" algorithms including the ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD) enabled microsecond simulations to capture repetitive dissociation and binding of small-molecule ligands and highly flexible peptides. The simulations then allowed highly efficient quantitative characterization of the ligand/peptide binding thermodynamics and kinetics. Taken together, GaMD and its innovative variants are applicable to simulate a wide variety of biomolecular dynamics, including protein folding, conformational changes and allostery, ligand binding, peptide binding, protein-protein/nucleic acid/carbohydrate interactions, and carbohydrate/nucleic acid interactions. In this review, we present principles of the GaMD algorithms and recent applications in biomolecular simulations and drug design.

Clinical Profile and Diagnosis of Obstructive Sleep Apnea Syndrome using Overnight Polysomnography in a Tertiary Care Hospital

Background Obstructive sleep apnea is a highly prevalent yet largely under-diagnosed disease that poses a significant burden on the healthcare system. Objective To determine the role of predictors for Obstructive sleep apnea syndrome and its severity in Nepalese population. Method Prospective and analytical study conducted in the Department of Otorhinolaryngology and Head and Neck surgery at Kathmandu University Hospital between March 2018 and June 2020. A total of 85 adult patients with Obstructive sleep apnea with an Epworth sleepiness score greater than 10 were included. Overnight polysomnography was done and scoring of sleep associated events were done according to the American Academy of Sleep Medicine criteria. Participants were classified as simple snoring and mild, moderate or severe Obstructive sleep apnea syndrome groups depending on the Apnea Hypopnea Index values. Relationship of Apnea hypopnea index was analyzed with age, neck circumference, body mass index and Epworth Sleepiness score. Result Simple snoring was seen in 18(21.17%) patients, 14(16.47%) had mild Obstructive sleep apnea, 13(15.29%) had moderate Obstructive sleep apnea, whereas the severe group consisted of 40(47.05%) patients. The minimum Epworth Sleepiness Score was 10 and the maximum was 25. The Apnea hypopnea index correlated positively with Body mass index (p=.010) and Epworth sleepiness score (p <.001). However, Apnea hypopnea index had no association with age (p=.437) and neck circumference (p=.118). Conclusion Health professionals need to be extremely vigilant while examining patients presenting with Obstructive Sleep Apnea. Polysomnography is the investigation of choice in the early identification of this treatable disease.

Mechanism of Ligand Recognition by Human ACE2 Receptor

Angiotensin converting enzyme 2 (ACE2) plays a key role in renin-angiotensin system regulation and amino acid homeostasis. Human ACE2 acts as the receptor for severe acute respiratory syndrome coronaviruses SARS-CoV and SARS-CoV-2. ACE2 is also widely expressed in epithelial cells of the lungs, heart, kidney, and pancreas. It is considered an important drug target for treating SARS-CoV-2 as well as pulmonary diseases, heart failure, hypertension, renal diseases, and diabetes. Despite the critical importance, the mechanism of ligand binding to the human ACE2 receptor remains unknown. Here, we have addressed this challenge through all-atom simulations using a novel ligand Gaussian accelerated molecular dynamics (LiGaMD) method. Microsecond time scale LiGaMD simulations have unprecedentedly captured multiple times of spontaneous binding and unbinding of a potent inhibitor MLN-4760 in the ACE2 receptor. With ligand far away in the unbound state, the ACE2 receptor samples distinct Open, Partially Open, Closed, and Fully Closed conformations. Upon ligand binding to the active site, conformational ensemble of the ACE2 receptor is biased toward the Closed state as observed in the X-ray experimental structure. The LiGaMD simulations thus suggest a conformational selection mechanism for ligand recognition by the highly flexible ACE2 receptor, which is expected to facilitate rational drug design targeting human ACE2 against coronaviruses and other related human diseases.

Comparison of Two Entry Methods for Laparoscopic Port Entry

Background The first step in laparoscopic surgery is to establish the pneumoperitoneum for which many approaches have been introduced to minimize the complications. Although controversies exist regarding the most efficient technique, till now the best entry technique is still unsettled. Objective To compare the safety, operating time and outcome of Direct Trocar Insertion with a well-established and widely practised Open Access Technique. Method This is a prospective study at Nobel Medical College Teaching Hospital from November 2019 to February 2021. Patients were grouped into either of the two groups, Group 1 for Direct Trocar Insertion and Group 2 for Open Access Technique. They were later analysed for major and minor complications of the technique and a comparison of either method was done at the end of the study period. Result A total of 823 patients were enrolled in the study. Among the study population, 411 patients had Direct Trocar Insertion while 412 patients had Open Access Technique. The majority of the operation that was done during the study period was laparoscopic cholecystectomy. Patients in the Open Access Technique group experienced more complications compared to Direct Trocar Insertion group. Conclusion Despite the fear of adopting the Direct Trocar Insertion, this is a safe, better and quick technique for laparoscopic port entry. However, any surgeon practising laparoscopic surgery should be competent to adopt either technique to overcome failure in either process during port entry.

Pilonidal sinus of the cheek: an extremely rare clinical entity-case report and brief review of the literature

Background

Pilonidal sinus is commonly seen at the sacrococcygeal region and few other sites, usually located at the midline, at areas where hairs collect or near protuberances or some adjacent rubbing surfaces. Its presence elsewhere is uncommon. We share an interesting case of a recurrent discharging sinus from the cheek bulge of a male which turned out to be a pilonidal sinus containing tuft of hairs on exploration and wide excision.

Case presentation

A 37 years old hirsute male presents to us with a non-healing discharging sinus at the bulge of the cheek. Exploration after a course of antibiotics showed 2 subcutaneous cavities with tuft of hairs. The area was excised along with a margin, thorough irrigation and curettage was done and the wound was closed primarily; a Z-plasty was incorporated in the central part to break the resultant suture line. Histopathological examination was done to confirm the diagnosis and rule out an off-midline dermoid cyst or an underlying/coexisting malignancy. Post-operative course was uneventful. The patient has been recurrence free for 1.5 years and is satisfied with the nature of the scar.

Conclusions

Pilonidal sinus of the cheek bulge is an extremely rare entity. Complete excision and clinical suspicion are important for cure of this nagging ailment, especially at unexpected areas.

Thresholds for Spinal Anaesthesia-induced Hypotension During Caesarean Section

Background Spinal anaesthesia is the current standard for caesarean section. Hypotension, a common complication, potentially results in adverse foetal and maternal outcomes. However, hypotension-defining criteria are varied. Objective To identify the blood pressure thresholds for spinal anaesthesia-induced hypotension during caesarean section. Method This is a retrospective cohort study of spinal anaesthesia-induced hypotension that occurred till baby-delivery during caesarean section. Reports on intraoperative hypotension, collected previously from January to December 2019, were reviewed to identify the hypotension-defining thresholds. The thresholds were categorized into systolic blood pressure (SBP) of 80, 90 or 100 mmHg, mean arterial pressure (MAP) of 60, 65 or 70 mmHg, combinations, and others. Parturient and anaesthesia characteristics, and associated hypotensive symptoms were also recorded for descriptive analysis. Result Spinal anaesthesia-induced hypotension was identified in 129 (11.5%) cases among 1116 caesarean sections. Altogether, 12 hypotension-defining thresholds were employed. Thresholds of SBP 90, MAP 60, and SBP 80 mmHg were used in 53 (41%), 28 (21.7%), and 21 (16.2%) cases respectively. Mean maternal age was 28 (±4.22) years and 87 (67.4%) cases underwent emergency surgery. Median sensory blockade level was T4. Nausea-vomiting, bradycardia, and tachycardia were associated during five (3.8%), six (4.6%), and 15 (11.6%) hypotensive incidents respectively. Two cases had unrecordable blood pressure but there was no maternal mortality. Conclusion Systolic blood pressure of 90 mmHg and mean arterial pressure of 60 mmHg included the most common thresholds for spinal anaesthesia-induced hypotension during caesarean section. Identifying the safe and clinically relevant hypotension-defining criteria needs further investigation.

Mechanism of ligand recognition by human ACE2 receptor

Angiotensin converting enzyme 2 (ACE2) plays a key role in renin-angiotensin system regulation and amino acid homeostasis. Human ACE2 acts as the receptor for severe acute respiratory syndrome coronaviruses SARS-CoV and SARS-CoV-2. ACE2 is also widely expressed in epithelial cells of lungs, heart, kidney and pancreas. It is considered an important drug target for treating SARS-CoV-2, as well as pulmonary diseases, heart failure, hypertension, renal diseases and diabetes. Despite the critical importance, the mechanism of ligand binding to the human ACE2 receptor remains unknown. Here, we address this challenge through all-atom simulations using a novel ligand Gaussian accelerated molecular dynamics (LiGaMD) method. Microsecond LiGaMD simulations have successfully captured both binding and unbinding of the MLN-4760 inhibitor in the ACE2 receptor. In the ligand unbound state, the ACE2 receptor samples distinct Open, Partially Open and Closed conformations. Ligand binding biases the receptor conformational ensemble towards the Closed state. The LiGaMD simulations thus suggest a conformational selection mechanism for ligand recognition by the ACE2 receptor. Our simulation findings are expected to facilitate rational drug design of ACE2 against coronaviruses and other related human diseases.

Higher rates of early initiation of breastfeeding associated with health facility delivery in Nepal

Background

Initiation of breastfeeding within one hour from birth is one of the five key essential newborn care messages, implemented along with birth preparedness package since 2008. This study aimed to determine the trend of early initiation of breastfeeding (EIBF) and to assess the effect of health facility delivery on EIBF in Nepal.

Methods

We analyzed the data from the last four nationally representative Nepal Demographic and Health Surveys (NDHS) conducted in 2001,2006,2011 and 2016. Data on the early initiation of breastfeeding was obtained from the mothers of infants born within 24 months prior to the survey. The explanatory variable was the place of delivery, dichotomized as either the health facility, or home delivery. Survey year had a significant interaction with the place of delivery. Multivariable logistic regression was conducted separately on pooled samples before (NDHS 2001 and 2006) and after (NDHS 2011 and 2016) the program implementation. Adjusted odds ratio (AOR) with 95% confidence interval (CI) for EIBF was calculated after adjusting for predetermined covariates.

Results

The rate of EIBF increased by 26.5% points (from 32.8% in 2001 to 59.3% in 2016) among infants delivered in a health facility, compared to an increase by 17.1% points (from 29.9% to 47.0%) among home born infants. EIBF increased by 32.5% points before, compared to 49.7% points after BPP. Delivery in a health facility was associated with a higher odd of EIBF in later years (AOR2.3, 95% CI 2.0,2.8), but not in earlier years (AOR1.3, 95% CI 0.9,2.0). Delivery by caesarean section, first-born infant, and lack of maternal education were associated with a lower rate of EIBF in both periods.

Conclusions

Higher EIBF was associated with health facility delivery in Nepal, only after programmatic emphasis on essential newborn care messages. This implies the need for explicit focus on EIBF at birth, particularly when mother is less educated, primiparous or undergoing operative delivery.

Key messages

The rate of initiation of breastfeeding within an hour from birth is increasing in Nepal, with higher rates in health facility delivery, as shown by the recent four nationally representative surveys. Programmatic focus on essential newborn care messages may have contributed to significant association of higher rates of early initiation of breastfeeding when delivered in health facility.

Child abuse and all-cause mortality in the Canadian population

Background

A history of child abuse is common and is associated with the later occurrence of risky health behaviors, mental disorders, and chronic conditions, strongly suggesting that child abuse may be associated with elevated mortality. However, most of the literature on child abuse has studied psychosocial/behavioral or medical outcomes and have not addressed mortality directly.

Methods

Data from the 2012 Canadian Community Health Survey, linked to the Canadian Vital Statistics Database, were used in the analysis. The CCHS-2012 interview (n = 19,830) retrospectively assessed childhood physical abuse, sexual abuse, and witnessing intimate partner violence before the age of 16. Each type of abuse was analyzed separately using Cox proportional hazards models for all-cause mortality. Hazard ratios (HR) and associated 95% confidence intervals (CI) were estimated with and without adjustment for covariates.

Results

An effect on mortality was observed among men for witnessing interpersonal violence (age-adjusted HR 2.47, 95% CI 1.48-4.12), and severe physical abuse (age-adjusted HR 2.3, 95% CI 1.21-4.36). In each case, the association was not significant for women; the age-adjusted HRs being 0.93 (95% CI: 0.51-1.70) and 0.59 (95%CI: 0.64-2.60) respectively. The association was seen only among those reporting frequent abuse ( &gt; =10 times) and weakened (became not significant) with adjustment for covariates that may mediate the association such as smoking and chronic conditions.

Conclusions

As predicted by a broader literature on childhood adversity, child abuse increases the risk of mortality. The effect was significant for severe physical abuse in men, but imprecision due to a limited number of deaths may have rendered other associations non-significant. The study provides some degree of confirmation that child abuse contributes to later life mortality. Hence public health strategies that prevent child abuse and mitigate the harms of the mediators might prevent mortality.

Key messages

Witnessing intimate partner violence is just as harmful as actually experiencing physical abuse. Preventing children's exposure to violence in family is valuable in preventing mortality in adulthood. Enhancing child abuse prevention programs and mitigating the harmful effects of the mediators such as smoking, substance use, and chronic conditions is important in reducing mortality in adult life.

Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics

Calculations of ligand binding free energies and kinetic rates are important for drug design. However, such tasks have proven challenging in computational chemistry and biophysics. To address this challenge, we have developed a new computational method, ligand Gaussian accelerated molecular dynamics (LiGaMD), which selectively boosts the ligand nonbonded interaction potential energy based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique. Another boost potential could be applied to the remaining potential energy of the entire system in a dual-boost algorithm (LiGaMD_Dual) to facilitate ligand binding. LiGaMD has been demonstrated on host-guest and protein-ligand binding model systems. Repetitive guest binding and unbinding in the β-cyclodextrin host were observed in hundreds-of-nanosecond LiGaMD_Dual simulations. The calculated guest binding free energies agreed excellently with experimental data with <1.0 kcal/mol errors. Compared with converged microsecond-time scale conventional molecular dynamics simulations, the sampling errors of LiGaMD_Dual simulations were also <1.0 kcal/mol. Accelerations of ligand kinetic rate constants in LiGaMD simulations were properly estimated using Kramers' rate theory. Furthermore, LiGaMD allowed us to capture repetitive dissociation and binding of the benzamidine inhibitor in trypsin within 1 μs simulations. The calculated ligand binding free energy and kinetic rate constants compared well with the experimental data. In summary, LiGaMD provides a powerful enhanced sampling approach for characterizing ligand binding thermodynamics and kinetics simultaneously, which is expected to facilitate computer-aided drug design.

Mechanisms of γ-Secretase Activation and Substrate Processing

Amyloid β-peptide, the principal component of characteristic cerebral plaques of Alzheimer's disease (AD), is produced through intramembrane proteolysis of the amyloid precursor protein (APP) by γ-secretase. Despite the importance in the pathogenesis of AD, the mechanisms of intramembrane proteolysis and substrate processing by γ-secretase remain poorly understood. Here, complementary all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method and biochemical experiments were combined to investigate substrate processing of wildtype and mutant APP by γ-secretase. The GaMD simulations captured spontaneous activation of γ-secretase, with hydrogen bonded catalytic aspartates and water poised for proteolysis of APP at the ε cleavage site. Furthermore, GaMD simulations revealed that familial AD mutations I45F and T48P enhanced the initial ε cleavage between residues Leu49-Val50, while M51F mutation shifted the ε cleavage site to the amide bond between Thr48-Leu49. Detailed analysis of the GaMD simulations allowed us to identify distinct low-energy conformational states of γ-secretase, different secondary structures of the wildtype and mutant APP substrate, and important active-site subpockets for catalytic function of the enzyme. The simulation findings were highly consistent with experimental analyses of APP proteolytic products using mass spectrometry and Western blotting. Taken together, the GaMD simulations and biochemical experiments have enabled us to elucidate the mechanisms of γ-secretase activation and substrate processing, which should facilitate rational computer-aided drug design targeting this functionally important enzyme.

Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor

BACKGROUND

Ensemble docking has proven useful in drug discovery and development. It increases the hit rate by incorporating receptor flexibility into molecular docking as demonstrated on important drug targets including G-protein-coupled receptors (GPCRs). Adenosine A₁ receptor (A₁AR) is a key GPCR that has been targeted for treating cardiac ischemia-reperfusion injuries, neuropathic pain and renal diseases. Development of allosteric modulators, compounds binding to distinct and less conserved GPCR target sites compared with agonists and antagonists, has attracted increasing interest for designing selective drugs of the A₁AR. Despite significant advances, more effective approaches are needed to discover potent and selective allosteric modulators of the A₁AR.

METHODS

Ensemble docking that integrates Gaussian accelerated molecular dynamic (GaMD) simulations and molecular docking using Autodock has been implemented for retrospective docking of known positive allosteric modulators (PAMs) in the A₁AR.

RESULTS

Ensemble docking outperforms docking of the receptor cryo-EM structure. The calculated docking enrichment factors (EFs) and the area under the receiver operating characteristic curves (AUC) are significantly increased.

CONCLUSIONS

Receptor ensembles generated from GaMD simulations are able to increase the success rate of discovering PAMs of A₁AR. It is important to account for receptor flexibility through GaMD simulations and flexible docking.

GENERAL SIGNIFICANCE

Ensemble docking is a promising approach for drug discovery targeting flexible receptors.

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State

G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one-third of currently marketed drugs. In particular, adenosine A1 receptor (A1 AR) is an important therapeutic target for treating cardiac ischemia-reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A1 AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid-protein interactions in order to understand the functional mechanism of GPCRs. Here, all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G-protein bound) A1 AR, which was embedded in a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A1 AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A1 AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.

Solid Variant of Alveolar Rhabdomyosarcoma of Nasal Cavity

Rhabdomyosarcoma comprises about half of the soft tissue tumors. Approximately 40% of the alveolar subtype occur in the head and neck region. Patients present with unilateral nasal mass with/without lymphadenopathy and with/without orbital manifestations. Diagnosis is aided radiologically by CT scan, MRI along with biopsy and is confirmed by immunohistochemistry. Treatment involves surgical resection, chemotherapy, radiotherapy or a combination of these. In spite of treatments, however, the outcome is poor. This is a case report of 14-year-old male who presented with unilateral nasal mass with proptosis of right eye who was eventually diagnosed as a case of alveolar rhabdomyosarcoma of solid variant.

Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor

Despite intense interest in designing positive allosteric modulators (PAMs) as selective drugs of the adenosine A₁ receptor (A₁AR), structural binding modes of the receptor PAMs remain unknown. Using the first X-ray structure of the A₁AR, we have performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) technique to determine binding modes of the A₁AR allosteric drug leads. Two prototypical PAMs, PD81723 and VCP171, were selected. Each PAM was initially placed at least 20 Å away from the receptor. Extensive GaMD simulations using the AMBER and NAMD simulation packages at different acceleration levels captured spontaneous binding of PAMs to the A₁AR. The simulations allowed us to identify low-energy binding modes of the PAMs at an allosteric site formed by the receptor extracellular loop 2 (ECL2), which are highly consistent with mutagenesis experimental data. Furthermore, the PAMs stabilized agonist binding in the receptor. In the absence of PAMs at the ECL2 allosteric site, the agonist sampled a significantly larger conformational space and even dissociated from the A₁AR alone. In summary, the GaMD simulations elucidated structural binding modes of the PAMs and provided important insights into allostery in the A₁AR, which will greatly facilitate the receptor structure-based drug design.

Gaussian accelerated molecular dynamics for elucidation of drug pathways

INTRODUCTION

Understanding pathways and mechanisms of drug binding to receptors is important for rational drug design. Remarkable advances in supercomputing and methodological developments have opened a new era for application of computer simulations in predicting drug-receptor interactions at an atomistic level. Gaussian accelerated molecular dynamics (GaMD) is a computational enhanced sampling technique that works by adding a harmonic boost potential to reduce energy barriers. GaMD enables free energy calculations without the requirement of predefined collective variables. GaMD has proven useful in biomolecular simulations, in particular, the prediction of drug-receptor interactions. Areas covered: Herein, the authors review recent GaMD simulation studies that elucidated pathways of drug binding to proteins including the G-protein-coupled receptors and HIV protease. Expert opinion: GaMD is advantageous for enhanced simulations of, amongst many biological processes, drug binding to target receptors. Compared with conventional molecular dynamics, GaMD speeds up biomolecular simulations by orders of magnitude. GaMD enables routine drug binding simulations using personal computers with GPUs or common computing clusters. GaMD and, more broadly, enhanced sampling simulations are expected to dramatically increase our capabilities to determine the mechanisms of drug binding to a wide range of receptors in the near future. This will greatly facilitate computer-aided drug design.

Obligate Myiasis: A Case Series From Nepal

Although maggots are unanonymously linked to carcass or dead tissues, there are reports of its infestation into living tissues as well. Myiasis denotes maggot infestation in living tissue. There are two forms of myiasis namely obligate and facultative. Obligate myiasis denotes maggots feeding on living tissue whereas facultative myiasis represents the opportunistic behaviour of the fly taking advantage of wound or necrotic tissue, laying by eggs which hatch into maggots. Decreased physical activity and poor hygiene leads to maggot infestation. Maggot invasion of living tissues is undesirable occurrence which can best be avoided by improving hygiene. People with low living standards in the developing nations are the occasional victims for maggot infestations. We present cases of obligate myiasis for their uniqueness and rarity.

Galvanic Skin Response as a Simple Physiology Lab Teaching Tool- An Alternative Indicator of Sympathetic Arousal

Background Sympathetic arousal response due to rewarding emotion may not be considered threat to the well-being but such arousal response evoked by fear or punishment can be stressful. When such changes are recorded in lab as biological signals, induced with appropriate stimulus, the observed response may serve as a good indicator of homeostatic alteration. In this study, skin conductance was utilized to record sympathetic response for cognitive load, by application of simple subtraction task. Objective To detect sympathetic arousal by utilization of galvanic skin response during mental arithmetic task. Method Total of eighty two subjects, forty two female and forty male participated in the study. Twenty two subjects were provided mental task to record skin conductance. In sixty subjects, galvanic skin response, pulse rate, respiratory rate and temperature were recorded by appropriate transducers to obtain baseline and task response to detect differential recordings. Subjects performed the mental exercise of arithmetic task (MAT) with transducer placed in upper limbs. Mean of averages for respective variables were statistically calculated from obtained recordings. Result For measured galvanic skin response, 57 subjects showed increased skin conductance (rise in amplitude) whereas, 25 subjects had no rise in amplitude ("A peak") while performing the mental arithmetic task, when compared to control recording. However, in 20 subjects, pulse rate and respiratory rate showed significant rise though, the change in the skin conductance was not significant. Conclusion Galvanic skin response is useful for demonstration of sympathetic activation induced by simple mental subtraction task, and can be utilized along with vital parameters mentioned in this study to discuss in vivo variation that exist as differential for core and superficial sympathetic outflow among individuals.

Imaging localized electric fields with nanometer precision through tip-enhanced Raman scattering

Tip-enhanced Raman scattering may be used to image various aspects of plasmon-enhanced local electric fields with extremely high spatial resolution.

Management of cysto-biliary communication in hydatid cyst of liver

Introduction: Biliary communication of hepatic hydatosis is one of the important complications. It may be minor or major communication. Minor communication is usually diagnosed during operation by the presence of bile stained hydatid fluid on aspiration or bile leak during surgery. However, in major communication, patients present with obstructive jaundice, abdominal pain and cholangitis. Surgical management of major communication is difficult and is associated with high morbidity and mortality.Methods: This is a retrospective study at Tribhuvan University Teaching Hospital, Kathmandu, Nepal over a period of two year (April 15th 2012 to April 15th 2014) and analyzed the medical records of 30 patients admitted and treated for hydatid cyst of liver in surgical ward during that period. Demography, clinical features, management and outcome were analyzed.Results: Of 30 patients with hepatic hydatid cyst operated over a period of two years, thirteen patients had cystobiliary communication. Amongst them, five minor communications were diagnosed during operation and managed with suture plication and omentopexy. Out of the eight major communications, seven were diagnosed preoperatively and all had cholangitis, and one had hydatid cyst of gallbladder and was diagnosed intraoperatively. Among six cases of major communication, five cases required CBD exploration and bile duct reconstruction while partial cholecystectomy was done for hydatid cyst of gall bladder and one case was managed by ERCP sphincterotomy, evacuation of cyst content and stenting. one case was managed with pigtail drain as the patient had infected hydatid cyst and not fit for surgery.Conclusion: Cystobiliary communication is a common complication of hydatid cyst of liver. Therapeutic options are related to size and location of the cyst and size of communication.Journal of Society of Surgeons of Nepal Vol.17(1) 2014: 31-34

The Effect of Vacuum on Venous Drainage: an Experimental Evaluation on Pediatric Venous Cannulas and Tubing Systems

Introduction: To observe how vacuum assisted venous drainage (VAVD) may influence the flow in a cardiopulmonary bypass circuit with different size of venous lines and cannulas. Methods: The experimental circuit was assembled to represent the cardiopulmonary bypass circuit routinely used during cardiac surgery. Wall suction was applied directly, modulated and measured into the venous reservoir. The blood flow was measured with a flow-meter positioned on the venous line. The circuit prime volume was replaced with group O date expired re-suspended red cells and Plasmalyte 148 to a hematocrit of 28% to 30%. Results: In an open circuit with gravity siphon venous drain, angled cannulae drain more than straight ones regardless the amount of suction applied to the venous line (16 Fr straight cannula (S) drains 90 ml/min less than a 16 Fr angled (A) with a siphon gravity). The same flow can be obtained with lower cannula size and higher suction (i.e. 12 A with and -30 mmHg). Tables have been created to list how the flow varies according to the size of the cannulas, the size of the venous tubes, and the amount of suction applied to the system. Conclusions: Vacuum assisted venous drainage allows the use of smaller cannulae and venous lines to maintain a good venous return, which is very useful during minimally invasive approaches. The present study should be considered as a preliminary attempt to create a scientific-based starting point for a uniform the use of VAVD. Keywords: cardio-pulmonary bypass; experimental study; vacuum assisted drainage.

Effect of Vacuum on Venous Drainage: an Experimental Evaluation on Pediatric Venous Cannulas and Tubing Systems

INTRODUCTION

To observe how vacuum assisted venous drainage (VAVD) may influence the flow in a cardiopulmonary bypass circuit with different size of venous lines and cannulas.

METHODS

The experimental circuit was assembled to represent the cardiopulmonary bypass circuit routinely used during cardiac surgery. Wall suction was applied directly, modulated and measured into the venous reservoir. The blood flow was measured with a flow-meter positioned on the venous line. The circuit prime volume was replaced with group O date expired re-suspended red cells and Plasmalyte 148 to a hematocrit of 28% to 30%.

RESULTS

In an open circuit with gravity siphon venous drain, angled cannulae drain more than straight ones regardless the amount of suction applied to the venous line (16 Fr straight cannula (S) drains 90 ml/min less than a 16 Fr angled (A) with a siphon gravity). The same flow can be obtained with lower cannula size and higher suction (i.e. 12 A with and -30 mmHg). Tables have been created to list how the flow varies according to the size of the cannulas, the size of the venous tubes, and the amount of suction applied to the system.

CONCLUSIONS

Vacuum assisted venous drainage allows the use of smaller cannulae and venous lines to maintain a good venous return, which is very useful during minimally invasive approaches. The present study should be considered as a preliminary attempt to create a scientific-based starting point for a uniform the use of VAVD.

Prevalence of depression among elderly people living in old age home in the capital city Kathmandu

Background: There has been a considerable increase in the numbers of older people in the world population of both developed and developing countries. These populations are thought to be at greater risk for depression. Many researches are conducted on physical wellbeing of elderly but studies regarding depression among elderly, especially in old age home is lesser in the developing countries. Objectives: To assess depression among elderly residing in an old age home in Kathmandu and its association with some of the socio-demographic variables. Methods: One hundred fifty elderly people residing in social welfare centre elderly home, Pashupatinath, Gaushala, Kathmandu, Nepal were selected randomly. Geriatric depression scale (GDS) was applied in all the individuals to assess the prevalence and degree of depression. Results: This study showed that, 47.33% of population had depression. Among the depressed population, 70.42% had mild depression and 29.58% had severe depression. There was significant association between the prevalence of depression and history of physical illness. Conclusion: Depressive disorder is highly prevalent among the elderly population residing in the old age home in Kathmandu with history of physical illness. DOI: http://dx.doi.org/10.3126/hren.v11i3.9634 Health Renaissance 2013;11(3):213-218

Bacteriology and antimicrobial susceptibility of adult chronic dacryocystitis

INTRODUCTION

Chronic dacryocystitis results in chronic infection and inflammation of the lacrimal sac.

OBJECTIVE

To identify the aetiology of chronic dacryocystitis and to determine their antimicrobial susceptibility pattern.

MATERIALS AND METHODS

A cross - sectional study was undertaken including 120 lacrimal swab materials collected from patients aged above 15 years suffering from chronic dacryocystitis.

STATISTICS

Data analysis was done by using software "Win pepi'' ver 7.9.

RESULTS

The bacteria of eight different species were isolated from 76.66 % (92/120) culture positive samples. 85.86 % showed a single and 14.13 % showed a mixed growth pattern. Coagulase negative staphylococci were the most common bacteria (P= 0.018) accounting for 33.96 % followed by Staphylococcus aureus (25.46 %), Streptococcus pneumoniae ( 19.81 % ), Streptococci viridans (5.66 %), Escherichia coli (5.66 %), Haemophilus spp ( 4.71 % ), Streptococcus pyogenes (3.77 %) and Bacillus spp (0.94 % ). Staphylococcus aureus were the most predominant bacteria in mixed growth. Rate of infection was higher in males 81.39 % than in females 74.02 %. Infection was higher in the age group of above 31 years. In the antimicrobial susceptibility test, except staphylococcus aureus, all the Gram positive isolates were 100 % sensitive to chloramphenicol and were least sensitive to tobramycin, but Gram negative isolates were equally sensitive to Chloramphenicol and Nalidixic acid.

CONCLUSION

Coagulase negative staphylococci are the most frequently isolated bacteria. Staphylococcus aureus is predominantly found in mixed growth. Chloramphenicol is the most effective drug of choice for chronic dacryocystitis.