Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach.

Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present a modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding rational strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally determined from experiments, augmented with dynamical network computations involving endpoint objective functions, mutual information, change-point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method, based on the strategies described above. The cybernetic-inspired method is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this innovative framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights.

Temporal transcriptional control of neural induction in human induced pluripotent stem cells.

Introduction: Neural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of the temporal and causal relationships that are required for this state transition. Methods: Here, we have carried out a longitudinal analysis of the transcriptome of human iPSCs undergoing neural induction. Using the temporal relationships between the changing profile of key transcription factors and subsequent changes in their target gene expression profiles, we have identified distinct functional modules operative throughout neural induction. Results: In addition to modules that govern loss of pluripotency and gain of neural ectoderm identity, we discover other modules governing cell cycle and metabolism. Strikingly, some of these functional modules are retained throughout neural induction, even though the gene membership of the module changes. Systems analysis identifies other modules associated with cell fate commitment, genome integrity, stress response and lineage specification. We then focussed on OTX2, one of the most precociously activated transcription factors during neural induction. Our temporal analysis of OTX2 target gene expression identified several OTX2 regulated gene modules representing protein remodelling, RNA splicing and RNA processing. Further CRISPRi inhibition of OTX2 prior to neural induction promotes an accelerated loss of pluripotency and a precocious and aberrant neural induction disrupting some of the previously identified modules. Discussion: We infer that OTX2 has a diverse role during neural induction and regulates many of the biological processes that are required for loss of pluripotency and gain of neural identity. This dynamical analysis of transcriptional changes provides a unique perspective of the widespread remodelling of the cell machinery that occurs during neural induction of human iPSCs.

Impact of application of queuing theory on operational efficiency of patient registration.

Background: Hospital administrators are often challenged with overcrowding at hospitals. The study hospital receives referred patients; however, they have to wait in long queues even for getting registered. This was a cause of concern for hospital administrators. The study was undertaken to find an amicable solution to the queues at registration using Queuing Theory. Method: This observational and interventional study was carried out in a tertiary care ophthalmic hospital. In the first phase, data of service time and arrival rate was collected. The queuing model was built using the coefficient of variation (CoV) of the observed times. Server utilization for new patient registration was found to be 1.21 and was 0.63 for revisit patients. Scenario-based simulation carried out using free software for optimal utilization of both types of servers. Recommendations made to combine the registration process and to increase one server were implemented.In the second phase, after one year, patient registration data were collected and compared for the number of patients registered using SPSS 17. Results: Number of patients registered within the registration timings increased whereas the number of patients registered after the registration timings decreased significantly at 95% CI with a p-value of less than 0.001. Queues finished early and more number of patients were registered in the same time. Conclusion: Using queuing theory, the bottleneck of the systems can be identified. Scenario and software-based simulations provide solutions to the problem of queues. The study is an application of Queuing Theory with a focus on efficient resource utilization. It can be replicated in an organization with limited resources facing the challenge of queues.

Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach.

Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present an elegant modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding entirely novel strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally-determined from experiments, augmented with dynamical network computations involving end point objective functions, mutual information, change point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method (CIM), utilizing the strategies described above. The CIM is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this state-of-the-art framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights. STATEMENT OF SIGNIFICANCE: Cellular processes like cell cycle are overly complex, involving multiple players interacting at multiple levels, and explicit modeling of such systems is challenging. The availability of longitudinal RNA measurements provides an opportunity to "reverse-engineer" for novel regulatory models. We develop a novel framework, inspired using goal-oriented cybernetic model, to implicitly model transcriptional regulation by constraining the system using inferred temporal goals. A preliminary causal network based on information-theory is used as a starting point, and our framework is used to distill the network to temporally-based networks containing essential molecular players. The strength of this approach is its ability to dynamically model the RNA temporal measurements. The approach developed paves the way for inferring regulatory processes in many complex cellular processes.

Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2.

Under normal homeostatic conditions, self-double-stranded RNA (self-dsRNA) is modified by adenosine deaminase acting on RNA 1 (ADAR1) to prevent the induction of a type I interferon-mediated inflammatory cascade. Antigen-presenting cells (APCs) sense pathogen-associated molecular patterns, such as dsRNA, to activate the immune response. The impact of ADAR1 on the function of APCs and the consequences to immunity are poorly understood. Here, we show that ADAR1 deletion in CD11c+ APCs leads to (1) a skewed myeloid cell compartment enriched in inflammatory cDC2-like cells, (2) enhanced numbers of activated tissue resident memory T cells in the lung, and (3) the imprinting of a broad antiviral transcriptional signature across both immune and non-immune cells. The resulting changes can be partially reversed by blocking IFNAR1 signaling and promote early resistance against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Our study provides insight into the consequences of self-dsRNA sensing in APCs on the immune system.

SREBP signaling is essential for effective B cell responses.

Our previous study using systems vaccinology identified an association between the sterol regulatory binding protein (SREBP) pathway and humoral immune response to vaccination in humans. To investigate the role of SREBP signaling in modulating immune responses, we generated mice with B cell- or CD11c+ antigen-presenting cell (APC)-specific deletion of SCAP, an essential regulator of SREBP signaling. Ablation of SCAP in CD11c+ APCs had no effect on immune responses. In contrast, SREBP signaling in B cells was critical for antibody responses, as well as the generation of germinal centers,memory B cells and bone marrow plasma cells. SREBP signaling was required for metabolic reprogramming in activated B cells. Upon mitogen stimulation, SCAP-deficient B cells could not proliferate and had decreased lipid rafts. Deletion of SCAP in germinal center B cells using AID-Cre decreased lipid raft content and cell cycle progression. These studies provide mechanistic insights coupling sterol metabolism with the quality and longevity of humoral immunity.

Allocation scheduling leads to optimum utilization of operation theater time.

Background: Cancellation of surgeries is a regular phenomenon in any hospital, and reasons may vary from clinical to managerial ones. The aim of the study is to suggest scheduling to address the problem of time over run related cancellations. This is an observational and descriptive study conducted in a tertiary care hospital with ophthalmology facilities. The sample size is calculated with 95% confidence interval using Epi Info 6 from the total surgeries performed in the last 5 years (n = 380). Simple random sampling technique was used. Methods: Surgical time for all types of ophthalmic surgeries (n = 582) was observed. Allocation of listed cases to the available operating rooms (ORs) was carried out using the observed time using LEKIN software. Results: The time over-run of 2 h and 6 h was noted for two units, whereas idle OR time was observed in other units. An average idle time of 19% was noted on each day. Reallocation of the cases to the ORs was carried out taking all the planned cases (of both the operating units of the day) as the number of jobs and all the available ORs as parallel machines using LEKIN software. All the planned cases could be accommodated; still, an average of 17% of the total available operation theater (OT) time was found idle on each day. Conclusions: Planning of cases using procedure time and scheduling on a daily basis using allocation models with simple algorithms can provide optimal utilization of OTs and can address the time over-run and related cancellations.

Strengthening leadership capacity: an unaddressed issue in Indian healthcare system.

PURPOSE: Leadership skills are vital for efficient delivery of health reforms. India, a low- and middle-income country, is transforming its public health care significantly. The health workforce, particularly doctors, however lacks leadership skills. This study aims to highlight the leadership skills gap and raise concerns about how India might achieve its ambitious health reforms in the lack of formal, prospective leadership training for its workforce. DESIGN/METHODOLOGY/APPROACH: This study conducted nine management development programmes between 2012 and 2020 and collected data from 416 (N = 444, 94% response rate) health-care professionals using a questionnaire. Participants were asked to inform leadership challenges that they perceived critical. A total of 47 unique challenges were identified, which were distributed across five domains of American College of Healthcare Executives Competency Assessment Tool (2020). Relevant information was also obtained from review of secondary sources including journal articles from scientific and grey literature and government websites. FINDINGS: Majority of participants (85.36%) had never attended any management training and were from public sector (56.1%). Mean total experience was 18 years. Top 5 challenges were lack of motivation (54.26%), communication (52.38%), contracts management (48.31%), leadership skills (47.26%) and retention of workforce (45.56%). Maximum challenges (29) were in domain of business skills and knowledge, followed by knowledge of health-care environment (9), leadership, professionalism, and communication and relationship management (3 each). ORIGINALITY/VALUE: In absence of the leadership training, senior health professionals particularly doctors in India, suffer leadership challenges. Efforts should be made to strengthen leadership capacity in Indian health-care system to advance the country's ongoing national health reforms.

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination.

Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.

Adjuvanting a subunit COVID-19 vaccine to induce protective immunity.

The development of a portfolio of COVID-19 vaccines to vaccinate the global population remains an urgent public health imperative1. Here we demonstrate the capacity of a subunit vaccine, comprising the SARS-CoV-2 spike protein receptor-binding domain displayed on an I53-50 protein nanoparticle scaffold (hereafter designated RBD-NP), to stimulate robust and durable neutralizing-antibody responses and protection against SARS-CoV-2 in rhesus macaques. We evaluated five adjuvants including Essai O/W 1849101, a squalene-in-water emulsion; AS03, an α-tocopherol-containing oil-in-water emulsion; AS37, a Toll-like receptor 7 (TLR7) agonist adsorbed to alum; CpG1018-alum, a TLR9 agonist formulated in alum; and alum. RBD-NP immunization with AS03, CpG1018-alum, AS37 or alum induced substantial neutralizing-antibody and CD4 T cell responses, and conferred protection against SARS-CoV-2 infection in the pharynges, nares and bronchoalveolar lavage. The neutralizing-antibody response to live virus was maintained up to 180 days after vaccination with RBD-NP in AS03 (RBD-NP-AS03), and correlated with protection from infection. RBD-NP immunization cross-neutralized the B.1.1.7 SARS-CoV-2 variant efficiently but showed a reduced response against the B.1.351 variant. RBD-NP-AS03 produced a 4.5-fold reduction in neutralization of B.1.351 whereas the group immunized with RBD-NP-AS37 produced a 16-fold reduction in neutralization of B.1.351, suggesting differences in the breadth of the neutralizing-antibody response induced by these adjuvants. Furthermore, RBD-NP-AS03 was as immunogenic as a prefusion-stabilized spike immunogen (HexaPro) with AS03 adjuvant. These data highlight the efficacy of the adjuvanted RBD-NP vaccine in promoting protective immunity against SARS-CoV-2 and have led to phase I/II clinical trials of this vaccine (NCT04742738 and NCT04750343).

A study on economic evaluation of an outreach health-care facility in Jhajjar District of Haryana: Service delivery model for increasing access to health care.

BACKGROUND: An outreach (OR) health-care facility providing broad specialty outpatient services was started by All India Institute of Medical Sciences (AIIMS), New Delhi, in rural area of district Jhajjar, Haryana. OBJECTIVES: This study aimed to ascertain the resource requirement for establishing an OR health-care facility and patient satisfaction with regard to the services being provided. METHODS: A cross-sectional study was conducted in 2017 at an OR Outpatient Department (OPD) of AIIMS, New Delhi, at Jhajjar. Service delivery model adopted for health-care delivery was hub and spoke. Traditional method of costing was used for economic evaluation. Feedback pro forma of 400 patients who attended OPD services was analyzed to measure health service accessibility. RESULTS: Capital expenditure to set up the facility was calculated to be approximately INR 17,57,49,074/- ($ 2,703,832) and operational cost per year was approximately INR 8,73,86,370/- ($ 1,344,406). Approximate per-patient cost for single OPD consultation was calculated to be INR 874 ($13.45) which included medicines and investigations. High scores for all domains of accessibility of health care were observed. CONCLUSION: The study provides a preliminary evidence that OR health-care facilities can be instrumental in increasing access to health-care delivery with lesser capital outlays, however, large-scale multicentric studies are needed to arrive at any conclusion. The services have been very well accepted by the local community members being quality medical care with highly subsidized health-care services.

Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates.

The development of a portfolio of SARS-CoV-2 vaccines to vaccinate the global population remains an urgent public health imperative. Here, we demonstrate the capacity of a subunit vaccine under clinical development, comprising the SARS-CoV-2 Spike protein receptor-binding domain displayed on a two-component protein nanoparticle (RBD-NP), to stimulate robust and durable neutralizing antibody (nAb) responses and protection against SARS-CoV-2 in non-human primates. We evaluated five different adjuvants combined with RBD-NP including Essai O/W 1849101, a squalene-in-water emulsion; AS03, an alpha-tocopherol-containing squalene-based oil-in-water emulsion used in pandemic influenza vaccines; AS37, a TLR-7 agonist adsorbed to Alum; CpG 1018-Alum (CpG-Alum), a TLR-9 agonist formulated in Alum; or Alum, the most widely used adjuvant. All five adjuvants induced substantial nAb and CD4 T cell responses after two consecutive immunizations. Durable nAb responses were evaluated for RBD-NP/AS03 immunization and the live-virus nAb response was durably maintained up to 154 days post-vaccination. AS03, CpG-Alum, AS37 and Alum groups conferred significant protection against SARS-CoV-2 infection in the pharynges, nares and in the bronchoalveolar lavage. The nAb titers were highly correlated with protection against infection. Furthermore, RBD-NP when used in conjunction with AS03 was as potent as the prefusion stabilized Spike immunogen, HexaPro. Taken together, these data highlight the efficacy of the RBD-NP formulated with clinically relevant adjuvants in promoting robust immunity against SARS-CoV-2 in non-human primates.

Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions.

The two main blood flow patterns, namely, pulsatile shear (PS) prevalent in straight segments of arteries and oscillatory shear (OS) observed at branch points, are associated with atheroprotective (healthy) and atheroprone (unhealthy) vascular phenotypes, respectively. The effects of blood flow-induced shear stress on endothelial cells (ECs) and vascular health have generally been studied using human umbilical vein endothelial cells (HUVECs). While there are a few studies comparing the differential roles of PS and OS across different types of ECs at a single time point, there is a paucity of studies comparing the temporal responses between different EC types. In the current study, we measured OS and PS transcriptomic responses in human aortic endothelial cells (HAECs) over 24 h and compared these temporal responses of HAECs with our previous findings on HUVECs. The measurements were made at 1, 4, and 24 h in order to capture the responses at early, mid, and late time points after shearing. The results indicate that the responses of HAECs and HUVECs are qualitatively similar for endothelial function-relevant genes and several important pathways with a few exceptions, thus demonstrating that HUVECs can be used as a model to investigate the effects of shear on arterial ECs, with consideration of the differences. Our findings show that HAECs exhibit an earlier response or faster kinetics as compared to HUVECs. The comparative analysis of HAECs and HUVECs presented here offers insights into the mechanisms of common and disparate shear stress responses across these two major endothelial cell types.

T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers.

Recent efforts toward an HIV vaccine focus on inducing broadly neutralizing antibodies, but eliciting both neutralizing antibodies (nAbs) and cellular responses may be superior. Here, we immunized macaques with an HIV envelope trimer, either alone to induce nAbs, or together with a heterologous viral vector regimen to elicit nAbs and cellular immunity, including CD8+ tissue-resident memory T cells. After ten vaginal challenges with autologous virus, protection was observed in both vaccine groups at 53.3% and 66.7%, respectively. A nAb titer >300 was generally associated with protection but in the heterologous viral vector + nAb group, titers <300 were sufficient. In this group, protection was durable as the animals resisted six more challenges 5 months later. Antigen stimulation of T cells in ex vivo vaginal tissue cultures triggered antiviral responses in myeloid and CD4+ T cells. We propose that cellular immune responses reduce the threshold of nAbs required to confer superior and durable protection.

Outcome of Care Provided in Neonatal Surgery Intensive Care Unit of a Public Sector Tertiary Care Teaching Hospital of India.

AIMS: There is limited literature on the outcome of care in intensive care units (ICUs), especially when it comes to neonatal surgical units. Hence, this study was aimed to observe the outcome of care provided in the neonatal surgery ICU (NSICU) at an apex tertiary care teaching institute of North India. METHODS: A descriptive, observational study was carried out through retrospective medical record analysis of all the patients admitted in NSICU from January to June 2011. RESULTS: In NSICU, from January to June 2011, 85 patients were admitted. More than two-third (69.9%) patients were admitted through the emergency department. Of the total admitted patients, 69.9% were male. Mean and median age of the admitted patients were 6.31 and 2 days (range 0-153 days), respectively. The most common diagnosis was esophageal atresia with tracheoesophageal fistula (36.1%). Within a day of admission at NSICU, 88% patients underwent surgical intervention. Of the total admitted patients, 56.6% required mechanical ventilation with 3.57 days (range 0-31 days) of mean duration of mechanical ventilation. Reintubation rate (within 48 h of extubation) was observed to be 15.7%, and 27.7% (23) of the patients required vasopressor support during their NSICU stay. Patients who developed postoperative complications were 34.25%, with the most common being wound infection/discharge/dehiscence. Two patients were readmitted within 72 h of their discharge/transfer out from the NSICU. CONCLUSION: NSICU survival rate was 85.5% and net death rate was observed to be 14.5%. Sepsis was the major reason for mortality in NSICU.

Low reporting of violence against health-care workers in India in spite of high prevalence.

BACKGROUND: Violence against health-care workers has become a great issue in health-care organizations. This study was conceptualized with the aim to know the prevalence of violence and to identify gap between rate of reporting of an incident of violence at a tertiary care hospital in India. METHODS: The study was descriptive and cross-sectional; a validated questionnaire was used as a tool. Reported incidents of violence against workers were collected. P value <0.05 was considered statistically significant in the analysis. A Z test for proportion at 95% confidence interval was applied to analyze the level of difference between prevalence, rate of reporting, and their level of awareness. RESULTS: Of 394 respondents, 136(34.5%) workers had experienced workplace violence in the last 12 months. It was found that total 32 incidents of workplace violence were reported to the concerned authority. The reporting rate of violence is significantly low (23.5%), in spite of high prevalence (34.5%). Level of awareness regarding the reporting mechanism and regulations for the safeguard of health-care workers against workplace violence is only 24.6 %. CONCLUSION: This study concluded that the prevalence of violence among health-care workers is quite high, but the reporting rate is significantly low. The low rate of reporting is because of lack of awareness about the reporting mechanism of workplace violence. It is recommended that sensitizing workshops should be conducted to increase the level of awareness, which will result in reduction in the prevalence of violence and building a safe and secured workplace for health-care providers.

Medical leadership competencies: A comparative study of physicians in public and private sector hospitals in India.

PURPOSE: Indian health care system comprising of public and private sectors needs enhancement of medical leadership capacity to face the growing challenges. Hence, this study was designed to evaluate medical leadership competencies of public and private sector doctors. FINDINGS: A survey questionnaire was developed to assess "self-assessed proficiency levels" as well as "perceived importance of competency levels," to which 532 doctors responded-290 (54.5%) from private sector and 242 (45.5%) from public sector hospitals. Statistically significant "leadership competency gap" was observed for all 30 leadership competencies in both sectors, more so in public sector. The 10 most deficient competencies were mainly in the NHS-MLCF domains of "working with others," "managing services," and "setting direction." The most low-rated competency among public sector doctors was "knowledge of HR, procurement, financial, and contract management" while "ability to influence key decision makers who determine future government policies" was most deficient among private sector physicians. Further, deficiencies related to "time and stress management" and "conducting need analysis, identifying and prioritizing requirements" were confined to public and private sector doctors, respectively. CONCLUSIONS: This study, first from India, highlights a critical need for medical leadership development programs in both sectors for enhancement of medical leadership capacity in the country.

Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function.

The optimal expression of endothelial nitric oxide synthase (eNOS), the hallmark of endothelial homeostasis, is vital to vascular function. Dynamically regulated by various stimuli, eNOS expression is modulated at transcriptional, post-transcriptional, and post-translational levels. However, epigenetic modulations of eNOS, particularly through long non-coding RNAs (lncRNAs) and chromatin remodeling, remain to be explored. Here we identify an enhancer-associated lncRNA that enhances eNOS expression (LEENE). Combining RNA-sequencing and chromatin conformation capture methods, we demonstrate that LEENE is co-regulated with eNOS and that its enhancer resides in proximity to eNOS promoter in endothelial cells (ECs). Gain- and Loss-of-function of LEENE differentially regulate eNOS expression and EC function. Mechanistically, LEENE facilitates the recruitment of RNA Pol II to the eNOS promoter to enhance eNOS nascent RNA transcription. Our findings unravel a new layer in eNOS regulation and provide novel insights into cardiovascular regulation involving endothelial function.

National survey of infection control programmes in South Asian association for Regional Cooperation countries in the era of patient safety.

BACKGROUND: The implementation of hospital infection prevention and control (IPC) in south Asia is not well described. We aimed to assess IPC programmes in hospitals in this region and explore opportunities for improvement. METHODS: Attendees from hospitals in the South Asian Association for Regional Cooperation (SAARC) region who were at one of four National Initiative for Patient Safety workshops organised by All India Institute of Medical Sciences (New Delhi) from 2009 to 2012 were invited to complete a semi-structured questionnaire. The survey addressed six main components of IPC programmes. RESULTS: We received responses from 306 participants from 82 hospitals. Five key opportunities for improvement emerged: (1) lack of healthcare epidemiologists, (2) relative infrequency of antibiotic guidelines (53%) and prescribing audits (33%) (3) lack of awareness of needle stick injury rates (84%) (4) only 47% of hospitals were prepared for surge capacity for patients with infectious diseases, and (5) limited coordination of hospital infection control personnel with other support services (55%-66%). CONCLUSION: These results outline IPC challenges in the SAARC region and may be useful to guide future quality improvement initiatives.

Systems biology analysis of longitudinal functional response of endothelial cells to shear stress.

Blood flow and vascular shear stress patterns play a significant role in inducing and modulating physiological responses of endothelial cells (ECs). Pulsatile shear (PS) is associated with an atheroprotective endothelial phenotype, while oscillatory shear (OS) is associated with an atheroprone endothelial phenotype. Although mechanisms of endothelial shear response have been extensively studied, most studies focus on characterization of single molecular pathways, mainly at fixed time points after stress application. Here, we carried out a longitudinal time-series study to measure the transcriptome after the application of PS and OS. We performed systems analyses of transcriptional data of cultured human vascular ECs to elucidate the dynamics of endothelial responses in several functional pathways such as cell cycle, oxidative stress, and inflammation. By combining the temporal data on differentially expressed transcription factors and their targets with existing knowledge on relevant functional pathways, we infer the causal relationships between disparate endothelial functions through common transcriptional regulation mechanisms. Our study presents a comprehensive temporally longitudinal experimental study and mechanistic model of shear stress response. By comparing the relative endothelial expressions of genes between OS and PS, we provide insights and an integrated perspective into EC function in response to differential shear. This study has significant implications for the pathogenesis of vascular diseases.