Master of Science

thesisHIV-1 latently infected cells are the major hurdle impeding viral eradication despite the development of ART (Anti-retroviral therapy), which works by inhibiting various viral proteins necessary for HIV-1 replication. Even after years of daily regimens of ART therapy, HIV-1 reemerges once the ART is discontinued. This is because HIV-1 can go latent or quiescent in resting CD4+ cells. These resting CD4+ cells contain integrated HIV DNA within the genetic material in the host cell, but no viral proteins are produced, and they are thus immune to circulating antiretroviral drugs. For that purpose, it is essential to understand the mechanisms and genes involved in the development, maintenance, and activation of latency. To investigate functions of transcripts and pathways critical for biological processes and disease mechanisms, gene knockout is a very useful technique. We propose to use the CRISPR/ cas9 system to knockout target genes and test if these genes are involved in the development of latency or are involved in the reactivation of latently infected cell

Performance Comparison of Design-Build and Construction Manager/General Contractor Highway Projects

Researchers have conducted numerous studies comparing project performance of design-bid-build (DBB) and design-build (DB) highway projects. However, little research has been done to compare the performance of DB and construction manager/general contractor (CM/GC) highway projects. Therefore, an exploratory study was conducted to compare the performance of 55 DB and 34 CM/GC highway projects from various States Departments of Transportation (DOTs) in terms of cost, change orders, and construction intensity. The results showed that contract award cost growth was significantly lower in DB projects than in CM/GC projects. In contrast to this, the total cost growth of DB projects was higher than that of CM/GC projects. In terms of change order cost factor and construction intensity, DB projects were found to be superior to CM/GC projects. However, no statistical difference was found

Effect of Magnesium Sulphate with Bupivacaine in Ultrasound-guided Transversus Abdominis Plane Block in patients undergoing Total Abdominal Hysterectomy

Background: Transversus abdominis plane block is a valuable component of multimodal analgesia regimen. Magnesium sulphate has been shown to increase the duration of action of different peripheral nerve blocks. We assessed the efficacy of magnesium sulphate as an adjuvant to bupivacaine in transversus abdominis plane block in patients scheduled for total abdominal hysterectomy under general anaesthesia. Methods: Sixty-six patients undergoing total abdominal hysterectomy under general anaesthesia were divided into two groups. Ultrasound-guided bilateral transversus abdominis plane block was performed in both groups before extubation. Bupivacaine alone group received block with 20ml of 0.25% bupivacaine while Bupivacaine with Magnesium group received block with 20ml of 0.25% bupivacaine with 150mg of magnesium sulphate on each side. Pain scores at 0, 2, 4, 6, 12, and 24 hours postoperatively along with time to first request of analgesia, total consumption of fentanyl, and incidence of nausea or vomiting were noted. Results: Group BM showed significantly lower pain scores at 4 and 6 hours (p=0.001 and 0.017 respectively). Time to first request of analgesia was significantly more in Group BM [285 minutes (85, 370) vs. 75 minutes (52.5, 150), (p<0.001)]. Total postoperative fentanyl consumption was significantly less in Group BM (230±59.06 mcg vs. 289.85±69.13 mcg, p<0.001). Conclusions: Bupivacaine with magnesium sulphate in transversus abdominis plane block after total abdominal hysterectomy under general anaesthesia results in lower post-operative pain scores, longer duration of analgesia and less postoperative fentanyl requirement with no difference in the incidence of nausea/vomiting compared with bupivacaine alone

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Synthesis and purification of linkage-specific polyubiquitin chains of distinct length for structural studies

Polyubiquitylation is one of the most versatile post-translational modifications involved in the regulation of numerous intracellular signaling processes. An assembly procedure that is simple, robust, and efficient to synthesize and purify linkage-specific polyubiquitin chains of defined length at a preparative scale is required in biophysical and structural studies. Here, we have optimized known enzymatic procedures in the form of a protocol to obtain multi-milligrams of Lys48-and Lys63-linked polyubiquitin chain types with more than 99% purity. Mass spectrometry (ESI/MS) analysis of K48- and K63-linked diubiquitin confirmed that the enzymes used in the preparation generated homogeneous linkages with no promiscuity

Change Orders and Schedule Performance of Design-Build Infrastructure Projects: Comparison between Highway and Water and Wastewater Projects

According to previous studies, change orders in general lead to delays in design-bid-build (DBB) projects. However, none of the studies have determined such a relationship in design-build (DB) projects. To address this issue, the current paper focuses on change-order- and schedule-related performance differences in highway and water and wastewater projects built using the DB method. To do so, this study collected data from 53 DB highway and 44 DB water and wastewater projects and compared change orders and schedule performance. The average project cost of highway and water and wastewater projects were $128 million and$58 million, respectively, converted to base costs of 2018. In addition, 98% of the highway and 68% of water and wastewater projects used a best value procurement method to select a design-builder and 93% of the projects used a lump sum contract. The t-test results showed that change orders, which are the percentage of extra costs added to the original contract amounts, were significantly higher in DB highway projects (4.5%) than those in DB water and wastewater projects (0.43%). In contrast to this, the construction intensity of DB highway projects was found to be significantly higher than that of water and wastewater projects. The results also showed that the percentage of DB highway projects having positive change orders (76%) was higher than the percentage of DB water and wastewater projects with positive change orders (41%). When the total cost of change orders was calculated, it was found that $123 million of change orders were added in highway projects, whereas in water and wastewater projects only$0.94 million of change orders were added. These findings indicate that DB water and wastewater projects received greater benefits in terms of change orders compared to highway projects. In contrast, DB highway projects were designed and built faster than DB water and wastewater projects. The primary contribution of this study is that in comparison to DB highway projects, DB water and wastewater projects had fewer change orders but lower construction intensity. This finding is opposite to that of DBB projects in the sense that the projects that had fewer change orders had better schedule performance. The authors would recommend conducting similar types of studies with larger sample sizes and with other types of projects, such as residential buildings, commercial buildings, and railroad projects

Autoscopic Hallucination in Alcohol Dependence Syndrome: A Rare or Missed Phenomenon?

Autoscopic phenomenon, a psychic illusionary duplication of one’s own self, has been the subject of interest in the literature and science for years. It has been reported in various diseases of the central nervous system but with an unknown mechanism. Hallucinations are a common presentation in alcohol dependence syndrome during delirium tremens and as induced disorder. However, autoscopic hallucination has been rarely reported in the cases of alcohol dependence. We present a case of a 40-year-old man who experienced autoscopic hallucination during the withdrawal state of alcohol. He was successfully treated with detoxification and an antipsychotic medication and was doing well. The case highlights the need for strong suspicion and exploration of the autoscopic hallucination and autoscopic phenomenon in general in cases of alcohol dependence syndrome

Demographic information.

ObjectiveThis study aimed to translate the DN4 questionnaire into Nepalese version and assess its psychometric properties: diagnostic accuracy, internal consistency, and test-retest reliability.MethodsAn observational study was conducted in a tertiary level teaching hospital of Kathmandu, Nepal. We included 166 patients with chronic pain visiting a pain clinic over a period of one year. The Nepalese version of the DN4 questionnaire was used for detecting signs and symptoms of neuropathic pain. The English version of the questionnaire was translated into Nepali in accordance with the standard guideline with the help of linguistic experts. The patients who met the inclusion criteria were examined and interviewed twice in an interval of two weeks. The association between the index test and the reference test was analyzed using Chi-square test. Diagnostic accuracy was assessed using sensitivity, specificity, Youden’s index, and positive and negative predictive values. We calculated internal consistency using Cronbach’s alpha (∝), and test-retest reliability using Cohen’s kappa and Intra-class correlation coefficient (ICC).ResultsThe study showed a significant association between the result of DN4 questionnaire and the gold standard (physician’s diagnosis) (pConclusionsThe Nepalese version of DN4 questionnaire is a valid and reliable tool for the identification of signs and symptoms of neuropathic pain. This can be used for screening neuropathic pain signs and symptoms in clinical as well as research settings.</div

Test-retest reliability of the pain assessment at baseline and at follow-up using DN4 questionnaire.

Test-retest reliability of the pain assessment at baseline and at follow-up using DN4 questionnaire.</p

Study questionnaire in Nepalese version.

ObjectiveThis study aimed to translate the DN4 questionnaire into Nepalese version and assess its psychometric properties: diagnostic accuracy, internal consistency, and test-retest reliability.MethodsAn observational study was conducted in a tertiary level teaching hospital of Kathmandu, Nepal. We included 166 patients with chronic pain visiting a pain clinic over a period of one year. The Nepalese version of the DN4 questionnaire was used for detecting signs and symptoms of neuropathic pain. The English version of the questionnaire was translated into Nepali in accordance with the standard guideline with the help of linguistic experts. The patients who met the inclusion criteria were examined and interviewed twice in an interval of two weeks. The association between the index test and the reference test was analyzed using Chi-square test. Diagnostic accuracy was assessed using sensitivity, specificity, Youden’s index, and positive and negative predictive values. We calculated internal consistency using Cronbach’s alpha (∝), and test-retest reliability using Cohen’s kappa and Intra-class correlation coefficient (ICC).ResultsThe study showed a significant association between the result of DN4 questionnaire and the gold standard (physician’s diagnosis) (pConclusionsThe Nepalese version of DN4 questionnaire is a valid and reliable tool for the identification of signs and symptoms of neuropathic pain. This can be used for screening neuropathic pain signs and symptoms in clinical as well as research settings.</div