Data Analysis and Visualization with Google Data Studio

As part of an Information Systems course a project was created to illustrate how Google Data Studio can play a role in improving the analysis and visualization of data. Often practitioners interact with data from already existing databases or datasets and need to make sense of them before analyzing, visualizing and gleaning insights from them. The dataset used in this case is retrieved from the w3schools learn SQL online course. A query is written to extract the data, and the data is imported to Google Sheets for visualization with Google Data studio. The process enables the identification of data anomalies, the analysis of trends, visualization of outliers and creation of additional data to gain further insights. This process reduces the time of analysis and provides students with insights on the life cycle of data analysis from business understanding, to data understanding and back to business understanding. Further, results that may be expected such as performance of employees, products or vendors is reviewed in more detail to gain further insights

Laboratory Water Distiller project

Abstract The goal of the water distiller project is to provide purified water to all hospitals and laboratories for daily use. As per WHO standards, purified water is a great necessity in these facilities for DNA sequencing, protein research, among others. Available water is not always clean because it is transported through pipes and can get into contact with organisms thereby causing the spread of waterborne diseases. Water distillation processes remove 99.9% of contaminants and water chemicals like fluorine and calcium to produce pure water. For every use, the distiller mechanism uses an electric current as the source of energy which is run into a heating element located in the contaminated water (in the boiler) through transferring heat, causing it to boil to steam. The evaporated water (steam) leaves behind 99.9% of the contaminants in the boiler producing mostly uncontaminated vapor. The steam created then enters into the condensing coil where heat transfer takes place and the result is purified water which is directed to the storage container. To construct the distiller unit, individual parts components are first developed in Solid Works drawings and then assembled based on design calculations and dimensions. Purchased and manufactured parts are then assembled to a complete distiller unit. The system is designed to efficiently transmit heat to the water, heating it to steam thereby providing 1 pint of purified water per hour. All components of the unit are cost efficient making it affordable to everyone. The machine is easy to operate and requires minimal maintenance

Characterization of the Hsp40 partner proteins of Plasmodium falciparum Hsp70

Human malaria is an economically important disease caused by single-celled parasites of the Plasmodium genus whose biology displays great evolutionary adaptation to both its mammalian host and transmitting vectors. This thesis details the 70 kDa heat shock protein (Hsp70) and J protein chaperone complements in malaria parasites affecting humans, primates and rodents. Heat shock proteins comprise a family of evolutionary conserved and structurally related proteins that play a crucial role in maintaining the structural integrity of proteins during normal and stress conditions. They are considered future therapeutic targets in various cellular systems including Plasmodium falciparum. J proteins (Hsp40) canonically partner with Hsp70s during protein synthesis and folding, trafficking or targeting of proteins for degradation. However, in P. falciparum, these classes of proteins have also been implicated in aiding the active transport of parasite proteins to the erythrocyte cytosol following erythrocyte entry by the parasite. This host-parasite “cross-talk” results in tremendous modifications of the infected erythrocyte, imparting properties that allow it to adhere to the endothelium, preventing splenic clearance. The genome of P. falciparum encodes six Hsp70 homologues and a large number of J proteins that localize to the various intracellular compartments or are exported to the infected erythrocyte cytosol. Understanding the Hsp70-J protein interactions and/or partnerships is an essential step for drug target validation and illumination of parasite biology. A review of these chaperone complements across the Plasmodium species shows that P. falciparum possesses an expanded Hsp70-J protein complement compared to the rodent and primate infecting species. It further highlights how unique the P. falciparum chaperone complement is compared to the other Plasmodium species included in the analysis. In silico analysis showed that the genome of P. falciparum encodes approximately 49 J proteins, 19 of which contain a PEXEL motif that has been implicated in routing proteins to the infected erythrocyte. Most of these PEXEL containing J proteins are unique with no homologues in the human system and are considered as attractive drug targets. Very few of the predicted J proteins in P. falciparum have been experimentally characterized. To this end, cell biological and biochemical approaches were employed to characterize PFB0595w and PFD0462w (Pfj1) J proteins. The uniqueness of Pfj1 and the controversy in literature regarding its localization formed the basis for the experimental work. This is the first study showing that Pfj1 localizes to the mitochondrion in the intraerythrocytic stage of development of P. falciparum and has further proposed PfHsp70-3 as a potential Hsp70 partner. Indeed, attempts to heterologously express and purify Pfj1 for its characterization are described. It is also the first study that details the successful expression and purification of PfHsp70-3. Further, research findings have described for the first time the expression and localization of PFB0595w in the intraerythrocytic stages of P. falciparum development. Based on the cytosolic localization of both PFB0595w and PfHsp70-1, a chaperone – cochaperone partnership was proposed that formed the basis for the in vitro experiments. PFB0595w was shown for the first time to stimulate the ATPase activity of PfHsp70-1 pointing to a functional interaction. Preliminary surface plasmon spectroscopy analysis has revealed a potential interaction between PFB0595w and PfHsp70-1 but highlights the need for further related experiments to support the findings. Gel filtration analysis showed that PFB0595w exists as a dimer thereby confirming in silico predictions. Based on these observations, we conclude that PFB0595w may regulate the chaperone activity of PfHsp70-1 in the cytosol while Pfj1 may play a co-chaperoning role for PfHsp70-3 in the mitochondrion. Overall, this data is expected to increase the knowledge of the Hsp70-J protein partnerships in the erythrocytic stage of P. falciparum development, thereby enhancing the understanding of parasite biology

Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics

The upper airway – which consists mainly of the naso- and oro-pharynx - is the first point of contact between the respiratory system and microbial organisms that are ubiquitous in the environment. It has evolved highly specialised functions to address these constant threats whilst facilitating seamless respiratory exchange with the lower respiratory tract. Dysregulation of its critical homeostatic and defence functions can lead to ingress of pathogens into the lower respiratory tract, potentially leading to serious illness. Systems-wide proteomic tools may facilitate a better understanding of mechanisms in the upper airways in health and disease. In this study, we aimed to develop a mass spectrometry based proteomics method for characterizing the upper airways proteome. Naso- and oropharyngeal swab samples used in all our experiments had been eluted in the Universal Transport Media (UTM) containing significantly high levels of bovine serum albumin. Our proteomic experiments tested the optimal approach to characterize airway proteome on swab samples eluted in UTM based on the number of proteins identified without BSA depletion (Total proteome: Protocol A) and with its depletion using a commercial kit; Allprep, Qiagen (cellular proteome: Protocol B, Ci, and Cii). Observations and lessons drawn from protocol A, fed into the design and implementation of protocol B, and from B to protocol Ci and finally Cii. Label free proteome quantification was used in Protocol A (n = 6) and B (n = 4) while commercial TMT 10plex reagents were used for protocols Ci and ii (n = 83). Protocols Ci and ii were carried out under similar conditions except for the elution gradient: 3 h and 6 h respectively. Swab samples tested in this study were from infants and children with and without upper respiratory tract infections from Kilifi County Hospital on the Kenyan Coast. Protocol A had the least number of proteins identified (215) while B produced the highest number of protein identifications (2396). When Protocol B was modified through sample multiplexing with TMT to enable higher throughput (Protocol Ci), the number of protein identified reduced to 1432. Modification of protocol Ci by increasing the peptide elution time generated Protocol Cii that substantially increased the number of proteins identified to 1875. The coefficient of variation among the TMT runs in Protocol Cii was <20%. There was substantial overlap in the identity of proteins using the four protocols. Our method was were able to identify marker proteins characteristically expressed in the upper airway. We found high expression levels of signature nasopharyngeal and oral proteins, including BPIFA1/2 and AMY1A, as well as a high abundance of proteins related to innate and adaptive immune function in the upper airway. We have developed a sensitive systems-level proteomic assay for the systematic quantification of naso-oro-pharyngeal proteins. The assay will advance mechanistic studies of respiratory pathology, by providing an untargeted and hypothesis-free approach of examining the airway proteome

Oral contraceptives and intrauterine devices as risk factors for breast and cervical cancers: a systematic review

Breast and cervical cancers have commandingly become major public health threats across the world. While studies have reported on the nexus between the use of oral contraceptives (OCs) and intrauterine devices (IUDs) as risk factors for breast and cervical cancers, there exists a paucity of explicit data on the nature of the association. Authors report the effect of oral contraceptives and the use of IUDs on the development of breast and cervical cancers. Several databases (Cochrane Library, Google Scholar and PubMed) were searched using well-specified criteria and a total of 15 papers selected. Meta-analyses, systematic reviews and studies that used cross-sectional designs were excluded from the review. Three and twelve cohort and case-control studies were reviewed respectively. Four of these studies reported an increased association between oral contraceptives and the risk of cervical cancer while nine showed positive correlation between oral contraceptives and risk of breast cancer. One study showed association between levonogestrel IUDs and risk of breast cancer while the other study did not show association between both levonogestrel and copper IUDs with risk of breast cancer. Use of copper IUDs was associated with diminishing risk of cervical cancer. Overall, use of oral contraceptives upsurges risk of breast and cervical cancers especially when used for longer periods of time. Further studies should therefore be done to understand the mechanisms of action of oral contraceptives and IUDs on the development of both cancers

Phenotype is sustained during hospital readmissions following treatment for complicated severe malnutrition among Kenyan children : a retrospective cohort study

Hospital readmission is common among children with complicated severe acute malnutrition (cSAM) but not well-characterised. Two distinct cSAM phenotypes, marasmus and kwashiorkor, exist, but their pathophysiology and whether the same phenotype persists at relapse are unclear. We aimed to test the association between cSAM phenotype at index admission and readmission following recovery. We performed secondary data analysis from a multicentre randomised trial in Kenya with 1-year active follow-up. The main outcome was cSAM phenotype upon hospital readmission. Among 1,704 HIV-negative children with cSAM discharged in the trial, 177 children contributed a total of 246 readmissions with cSAM. cSAM readmission was associated with age<12 months (p = .005), but not site, sex, season, nor cSAM phenotype. Of these, 42 children contributed 44 readmissions with cSAM that occurred after a monthly visit when SAM was confirmed absent (cSAM relapse). cSAM phenotype was sustained during cSAM relapse. The adjusted odds ratio for presenting with kwashiorkor during readmission after kwashiorkor at index admission was 39.3 [95% confidence interval (95% CI) [2.69, 1,326]; p = .01); and for presenting with marasmus during readmission after kwashiorkor at index admission was 0.02 (95% CI [0.001, 0.037]; p = .01). To validate this finding, we examined readmissions to Kilifi County Hospital, Kenya occurring at least 2 months after an admission with cSAM. Among 2,412 children with cSAM discharged alive, there were 206 readmissions with cSAM. Their phenotype at readmission was significantly influenced by their phenotype at index admission (p < .001). This is the first report describing the phenotype and rate of cSAM recurrence

Biomarkers of post-discharge mortality among children with complicated severe acute malnutrition

High mortality after discharge from hospital following acute illness has been observed among children with Severe Acute Malnutrition (SAM). However, mechanisms that may be amenable to intervention to reduce risk are unknown. We performed a nested case-control study among HIV-uninfected children aged 2-59 months treated for complicated SAM according to WHO recommendations at four Kenyan hospitals. Blood was drawn from 1778 children when clinically judged stable before discharge from hospital. Cases were children who died within 60 days. Controls were randomly selected children who survived for one year without readmission to hospital. Untargeted proteomics, total protein, cytokines and chemokines, and leptin were assayed in plasma and corresponding biological processes determined. Among 121 cases and 120 controls, increased levels of calprotectin, von Willebrand factor, angiotensinogen, IL8, IL15, IP10, TNF alpha, and decreased levels of leptin, heparin cofactor 2, and serum paraoxonase were associated with mortality after adjusting for possible confounders. Acute phase responses, cellular responses to lipopolysaccharide, neutrophil responses to bacteria, and endothelial responses were enriched among cases. Among apparently clinically stable children with SAM, a sepsis-like profile is associated with subsequent death. This may be due to ongoing bacterial infection, translocated bacterial products or deranged immune response during nutritional recovery

トピックス 5号 2001年8月号

Background Few hospitals in high malaria endemic countries in Africa have the diagnostic capacity for clinically distinguishing acute bacterial meningitis (ABM) from cerebral malaria (CM). As a result, empirical use of antibiotics is necessary. A biochemical marker of ABM would facilitate precise clinical diagnosis and management of these infections and enable rational use of antibiotics. Methods We used label-free protein quantification by mass spectrometry to identify cerebrospinal fluid (CSF) markers that distinguish ABM (n=37) from CM (n=22) in Kenyan children. Fold change (FC) and false discovery rates (FDR) were used to identify differentially expressed proteins. Subsequently, potential biomarkers were assessed for their ability to discriminate between ABM and CM using receiver operating characteristic (ROC) curves. Results The host CSF proteome response to ABM (Haemophilus influenza and Streptococcus pneumoniae) is significantly different to CM. Fifty two proteins were differentially expressed (FDR&lt;0.01, Log FC≥2), of which 83% (43/52) were upregulated in ABM compared to CM. Myeloperoxidase and lactotransferrin were present in 37 (100%) and 36 (97%) of ABM cases, respectively, but absent in CM (n=22). Area under the ROC curve (AUC), sensitivity, and specificity were assessed for myeloperoxidase (1, 1, and 1; 95% CI, 1-1) and lactotransferrin (0.98, 0.97, and 1; 95% CI, 0.96-1). Conclusion Myeloperoxidase and lactotransferrin have a high potential to distinguish ABM from CM and thereby improve clinical management. Their validation requires a larger cohort of samples that includes other bacterial aetiologies of ABM.</p

The disruptive impact of COVID-19 on the utilization of cancer chemotherapy-related healthcare assistance at the principal nationwide referral hospital In Kenya

Background: Lockdown measures to reduce the outbreak of COVID-19 negatively impacted the administration of cancer chemotherapy globally; however, data from Kenya are limited. Researchers strove to address this information gap and assess chemotherapy trends before and during the pandemic at Kenyatta National Hospital (KNH), the most wide-ranging referral infirmary in Kenya, along with associated factors to provide future guidance. Methods: Time series analyses and patient interviews were undertaken at the KNH Cancer Treatment Centre. Patient data were analyzed descriptively and inferentially. The average quarterly scores of chemotherapy-related patients from January 2019 to December 2020 were computed for the time series analysis. Results: A total of 241 participants were recruited. Of the participants, 164 (68%) were female, and the mean age was 55. Breast cancer was the most typical cancer type. Independent risk factors for missed chemotherapy sessions were a considerable increase in travel costs, rescheduled appointments alongside difficulties in securing an appointment, comorbidities, and marital status. There was a decline in chemotherapy utilization before COVID-19, with a sharp drop at the pandemic's peak. Conclusion: COVID-19 and associated measures did appreciably affect the treatment of cancer patients with chemotherapy in this developing country, with several factors contributing to this. Efforts should be geared toward continuity of services during future pandemics in developing countries to improve patient outcomes