A Study about Co-Infection of Fungal Pathogens in Active Tuberculosis Patients

The diagnosis of mycotic lung infection in pulmonary TB patients remains misdiagnosed because of its non-specific clinical manifestations which mimics the symptoms of TB. Physicians have to rely on the investigation but as radiology and pathology cannot probe the appropriate diagnosis, conventional microbiology or PCR testing continue as an essential mode for the diagnosis. In developing country like India PCR is not cost effective. Thus, Direct microscopy by KOH (10%), Gram's staining & Culture remains only option for identification. A three-year cross-sectional study was carried out in the Department of Microbiology, Maharishi Markandeshwar Institute of Medical Science & Research, Mullana, India from August 2015 to August 2018. On 300 LED positive sputum samples collected from previously treated cases of pulmonary TB. Early morning sputum was collected and subjected to KOH 10%, Gram's staining afterwards cultured on Sabouraud Dextrose Agar and species identification was done by LPCB preparation. In 300 LED smear positive samples, the dominant pathogens were C. albicans (43.3%), followed by C. non-albicans (26.7%), A. fumigatus (21.7%) etc. ATT administration for 5-8 months' duration of illness showed highest fungal infection (45%) and maximum growth of fungus was seen in the Autumn season (45%). The co-occurrence of fungi with tubercle bacteria adds fatal consequences thus routine screening is recommended for proper diagnosis and early treatment of mycotic infection in the patients of Pulmonary TB on ATT.

Anharmonic and Anomalous Trends in the High-Pressure Phase Diagram of Silicon

A multifaceted first-principles approach utilizing density functional theory, evolutionary algorithms, and lattice dynamics was used to construct the phase diagram of silicon up to 4 TPa and 26 000  K. These calculations predicted that (i) an anomalous sequence of face-centered cubic to body-centered cubic to simple cubic crystalline phase transitions occur at pressures of 2.87 and 3.89 TPa, respectively, along the cold curve, (ii) the orthorhombic phases of Imma and Cmce-16 appear on the phase diagram only when the anharmonic contribution to the Gibbs free energy is taken into account, and (iii) a substantial change in the slope of the principal Hugoniot is observed if the anharmonic free energy of the cubic diamond phase is considered.

Ethyl Glucuronide as a Long-term Alcohol Biomarker in Fingernail and Hair. Matrix Comparison and Evaluation of Gender Bias

Aims

This work aimed to assess the performance of hair and fingernail ethyl glucuronide (EtG) measurement for use as a biomarker of alcohol consumption in persons with known drinking history across a range of drinking behaviours.

Methods

EtG concentrations were assessed from the hair and fingernails of 50 study participants. Alcohol consumption of the previous 90 days was assessed by participant interview using the alcohol timeline follow-back method. EtG concentration was determined using LC–MS-MS using a method which was validated and accredited to ISO/IEC 17025 standards.

Results

There was significant correlation between alcohol consumption and EtG concentrations found in hair and fingernail samples across the study group (n = 50). From participants testing positive for EtG (male n = 14, female n = 13) no significant difference was found between male and female EtG levels in either hair or fingernails. Across all participants there was no significant difference in hair or fingernail EtG concentration between male (n = 23) and females (n = 27).

Conclusions

Our results support the use of EtG to indicate alcohol consumption over the previous 90 days, or ~3 months as is the normal practice in hair analysis. The results confirm that fingernails can be a useful alternative matrix where hair samples are not available.

Abstract P3-06-05: Whole genome sequence analysis of 77 breast cancer patients reveal increased somatic transposable element insertions responsible for early onset of cancer

More than 50% of the human genome consists of transposable elements (TE). However only certain classes of retrotransposons (ALU, SVA, ERV and L1) are believed to be active. They transpose using an RNA intermediate causing target-site duplications along with a poly-A tail. They can also insert into intronic regions and disrupt normal transcription of protein-coding genes. However, most TEs are repressed using various epigenetic mechanisms such as DNA methylation, histone modifications and RNA silencing. The piRNA pathway also plays an important role in retrotransposon silencing by establishing a repressive chromatin state. In this study, somatic and germline TE insertions in 77 TCGA breast cancer cases were characterized. These studies have revealed that somatic TEs can insert into intronic regions of tumor suppressor genes such as LRP1B, RAD51B and WNK2. Characterization of germline TE insertions, reveal insertions in intronic regions of predisposition genes such as CDH1 and BRCA2. Analysis of germline SNPs in high somatic TE patients reveals the presence of deleterious variants in genes such as NRDE2, RAD51C and DDX3X which are known to regulate TEs using RNA silencing via the piRNA pathway and other DNA-damage response mechanisms. Patients having high somatic TE insertions were found to have lower age of diagnosis suggesting a role in the early onset of cancer (median age of patients with high TE=43.37yrs; low TE=59.77yrs, Wilcoxan p=0.023). Further comparison of somatic TE insertion burden against somatic point-mutation burden revealed an inverse correlation suggesting analysis of TE insertions is indispensable to get the complete mutation profile of breast cancer genomes.

Citation Format: Paul R, Solzak JP, Radovich M. Whole genome sequence analysis of 77 breast cancer patients reveal increased somatic transposable element insertions responsible for early onset of cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-05.

Atomistic analysis of the thermomechanical properties of Sn-Ag-Cu solder materials at the nanoscale with the MEAM potential

Sn-Ag-Cu, commonly known as SAC, is considered to be among the most promising of all lead-free solder alloys. Research aimed at making electronic components smaller has pointed to the possible use of nanosized solder joints in the future. In this study, for the first time, molecular dynamics simulations were used to analyze the thermomechanical properties of SAC solder materials at the nanoscale. The modified embedded-atom method (MEAM) potential was utilized in the simulations of the SAC solder materials. The dimensions of the structures considered were 55 × 55 × 59 Å. Four different SAC solders were studied, with Ag percentages ranging from 1% to 4% (SAC105, SAC205, SAC305, and SAC405). Thus, the effects of the Ag percentage on the thermomechanical properties of the solder at the nanoscale were identified. The impacts of the temperature on the uniaxial tensile properties and coefficient of thermal expansion (CTE) values of the SAC solder materials were investigated by performing simulations of the materials at different temperatures. Results suggest that as the Ag percentage increases, the uniaxial tensile strength and CTE of the solder increase whereas the failure strain and thermal conductivity decrease. The results presented should prove useful in the electronic packaging industry.

Recognition, Diagnostics, and Management of Pediatric Severe Sepsis and Septic Shock in the Emergency Department

Several new studies have emerged in recent years that have attempted to aid emergency department providers in recognizing and treating pediatric patients with severe sepsis and septic shock. National guidelines and supporting literature are unanimous in recommendations that early recognition and timely therapeutics are necessary for improved survival and decreased morbidity. The literature is less concrete in defining how emerging advances in the field can aid in time-sensitive care of these patients. This article summarizes the recent literature as it pertains to the initial presentation of severe sepsis and septic shock in the pediatric patient within the emergency department.

Substrate stiffness and mechanical stress due to intercellular cooperativity guides tissue structure

A key challenge in cell and tissue morphogenesis is to understand how a crucial balance between cell proliferation and apoptosis maintains an evolving tissue structure. These processes are mutually non-exclusive and require stiffness monitoring of the host substrate. Adhered cells actively mechanosense the tension in the extracellular matrix (ECM). They collectively alter self-organization and generate a host of tissue patterns. Using an in silico elastic fiber-network in two dimensions, we simulate cell-ECM composite structures and characterize features of the emerging tissue patterns during successive cell proliferation and apoptosis. Our data reveals that, in general, cell viability is a function of the cell-induced effective ECM stiffness supported by intercellular cooperativity. Translating this into a remodeling tissue, we find that average cell cycle duration in concert with the locally stressed regions of the ECM promote heterogeneous proliferation and apoptosis inducing finger-like protrusions along the tissue periphery - a feature normally observed during tumorigenesis. Further, we find that recovery of a scratch wound is delayed for cells harbored on a compliant or (and) in a highly collagen depleted ECM.

Characterization of the dysplastic Walch type C glenoid

Aims

The Walch Type C dysplastic glenoid is characterized by excessive retroversion. This anatomical study describes its morphology.

Patients and Methods

A total of 29 shoulders with a dysplastic glenoid were analyzed. CT was used to measure retroversion, inclination, height, width, radius-of-curvature, surface area, depth, subluxation of the humeral head and the Goutallier classification of fatty infiltration. The severity of dysplasia and deficiency of the posterior rim of the glenoid were recorded.

Results

A type C glenoid occurred in 1.8% of shoulders referred to our tertiary centres. The mean retroversion, inclination, height, width, radius-of-curvature, surface area, and depth of the glenoid were 37°, 3°, 46 mm, 30 mm, 37°, 1284 mm3, and 16 mm, respectively. The mean posterior subluxation was 90%. The Goutallier class was < 2 in 25 shoulders (86%). Glenoid dysplasia was mild in four, moderate in 14, and severe in 11 shoulders. The typical appearance of the posterior glenoid rim had a rounded or ‘lazy J’ morphology. The glenoid neck was deficient in 18 shoulders (62%).

Conclusion

A dysplastic Type C glenoid characteristically has a uniconcave retroverted morphology, a deficient posteroinferior rim and scapular neck, and a reduced depth. These findings help to define the unique anatomical variations and may aid the planning of surgery and the development of components for these patients. Cite this article: Bone Joint J 2018;100-B:1074–9.

In Vitro Thrombogenicity Testing of Artificial Organs

Thromboembolic complications remain as one of the main problems for blood contacting artificial organs such as heart valves, bloodpumps and others. In vitro evaluation of thrombogenesis in prototypes has not previously been part of the standard evaluation of these devices. In comparison to hemolysis testing, evaluation of the thrombogenic potential is more difficult to perform because of the complexity of the blood coagulation system. We present an in vitro testing procedure that allows the accelerated examination of the thrombogenic potential of different types of blood pumps. Additionally, first results are presented that indicate the reliability of the accelerated clotting test for mechanical heart valves. Results for the centrifugal pump BioMedicus and two microaxial pumps have shown typical thrombus formation at locations such as bearings.

The results indicate that the accelerated clotting test is an excellent addition to the much more expensive animal testing of artificial organs or assist devices. In vitro testing permits studies of thrombus formation to be performed at an early stage and at low costs and also facilitates a more precise investigation of device areas known to be potential hot spots for thrombus formation.

Abstract P3-04-10: Analysis of somatic transposable element insertions in a breast cancer genome

Introduction: More than 50% of the human genome consists of transposable elements (TE). However most TEs are inactive and remain relatively stable among different human populations. However, some classes of retrotransposons consisting of Alu, SVA, ERV and L1s are active and believe to be involved in cancer. Commonly used bioinformatics pipelines of whole genome sequencing (WGS) data do not currently analyze for somatic TE insertions, and maybe missing an important class of somatic mutations. As a proof-of-concept, we analyzed the HCC1143 triple-negative breast cancer cell line along with a matched normal control to analyze for the presence of somatic TEs.

Methods: WGS data of the HCC1143 cell line along with the matched lymphoblastoid control cell line, HCC1143BL, were downloaded from the NCI GDC Commons. We used discordant read-pair (only one paired-end read matches to the reference genome) and split-read (part of a read matches to the reference) analysis to detect novel somatic TE insertion sites in genes known to play important roles in cancer proliferation.

Results: Most TE insertions are heterogenous in nature such that they insert only in a small subset of the cells. Therefore by comparing the number of split reads and discordant reads to the total number of reads the heterogenity of the insertion can be inserted. The discordant and split read analysis revealed about 30 high confidence hits. A subset of the high confidence hits were validated experimentally using PCR amplification and gel electrophoresis. About 85% of the hits were successfully validated. A subset of the validated hits known to be relevant to breast cancer have been shown in Table 1.

Table 1 - Validated somatic TE insertion locations in HCC1143 cell lineGeneFunctionChromosome numberStart positionStop position% heterogeneity in tumor line = (split_reads + discordant_reads)*2 / total_reads% heterogeneity in blood line = (split_reads + discordant_reads)*2 / total_readsPBRM1Chromatin remodeling352662648526635501001.1GLIS3Overexpressed in TNBC/involved in Wnt pathway942369794237291402.5XPR1Receptor of murine leukemia viruses1180857399180857714253.2CSMD1Tumor suppressor gene84452610445304323.520TMEM181Involved in tamoxifen response61590532671590538254.710

Discussion: Using the approach described above, we were able to detect somatic TEs within several genes known to be involved in cancer. PBRM1, a gene involved in chromatin remodeling, was found to have several exons replaced with a TE insert. Other genes such as CSMD1 is a known tumor suppressor gene, and TMEM181 which is involved in tamoxifen response. These results suggest that TE insertions may be involved in cancer biology. Therefore, TE insert prediction can serve as useful biomarkers for early detection and have precision medicine implications in the treatment of breast cancer. Analyses in additional breast cancer patient genomes is currently underway.

Citation Format: Paul R, Solzak JP, Chen Y-H, Hancock BA, Radovich M. Analysis of somatic transposable element insertions in a breast cancer genome [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-10.

Abstract P1-10-03: Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways

Introduction: Triple negative breast cancer (TNBC) accounts for 15% of all breast cancer cases in the United States, and despite its lower incidence, contributes to a disproportionately higher rate of morbidity and mortality compared to other breast cancer subtypes. In an effort to treat TNBC, a cancer that has no targeted therapies, many have chosen to experiment with combinations of drugs that are chosen for their genomic expression or “hard targets”. It has been previously noted however, that single agent therapeutics can change the genomic landscape of both mice and human cells and may be responsible for resistance. Here we show that targeting a compensatory pathway after treatment with a single therapy, results in synergistic combinations and can outperform the choice of hard target therapies.

Methods: Eight TNBC cell lines were chosen based on their abundance of clinically actionable targets. The primary hard target combinations were chosen using data from TCGA and a board consisting of oncologists and researchers at Indiana University School of Medicine. Compensatory therapies were found using RNA sequencing data from untreated versus single therapeutic treated TNBC cell lines. The merged transcript RPKMs were transformed and analyzed for differential expression. Statistically significant genes were imported into Ingenuity Pathway Analysis (IPA) to identify either therapeutics or genomic targets using the Causal network analysis and Upstream regulator functions. All drug combinations were tested in their respective cell lines and cell viability was assessed via Celltiter-Fluor. Synergy of the combinations was calculated using the Chou-Talalay method.

Results: Using genomically chosen hard targets for drug combinations, all eight cell lines displayed additive or antagonistic results except low nanomolar doses for the MDA-MB-231 cell line. Dosing of MDA-MB-231s with Debrafinib and Pazopanib however, turned highly antagonistic as dosing increased. Using next-generation RNA sequencing data of TNBCs, IPA analysis identified several compensatory targets for each cell line when treated with one of the primary genomically driven drug at its IC50. Using dose escalation of the new drugs with a single hard target drug, we found that each compensatory combination displayed a striking increase in synergy across all TNBC cell lines treated when compared to their original hard target combination.

Conclusion: RNA sequencing of TNBC cells lines treated with single therapies chosen by actionable genomic landscape has revealed compensatory pathways, indicating further druggable targets. These compensatory pathways have been observed to more efficacious in treating TNBC cell lines. Using therapeutics that are either FDA approved or in clinical trials we have found that each compensatory combination shows a higher level of synergy across all cell lines. These data show that choosing a secondary therapy based on compensatory pathways may outperform hard target combinations in the clinic.

Citation Format: Solzak J, Hancock B, Paul R, Radovich M. Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-10-03.

Ordering kinetics in the random-bond XY model

We present a comprehensive Monte Carlo study of domain growth in the random-bond XY model with nonconserved kinetics. The presence of quenched disorder slows down domain growth in d=2,3. In d=2, we observe power-law growth with a disorder-dependent exponent on the time scales of our simulation. In d=3, we see the signature of an asymptotically logarithmic growth regime. The scaling functions for the real-space correlation function are seen to be independent of the disorder. However, the same does not apply for the two-time autocorrelation function, demonstrating the breakdown of superuniversality.

Pathogen-specific leptospiral proteins in urine of patients with febrile illness aids in differential diagnosis of leptospirosis from dengue

Leptospirosis and dengue are two commonly seen infectious diseases of the tropics. Differential diagnosis of leptospirosis from dengue fever is often difficult due to overlapping clinical symptoms and lack of economically viable and easy-to-perform laboratory tests. The gold standard for diagnosis is the microscopic agglutination test (MAT). In this study, the diagnostic potential of screening for pathogen-specific leptospiral antigens in urine samples is presented as a non-invasive method of disease diagnosis. In a study group of 40 patients, the serum was tested for anti-leptospiral antibodies by MAT and enzyme-linked immunosorbent assay (ELISA). Urine of these patients was screened for leptospiral antigens by ELISA using specific antibodies against LipL32, LipL41, Fla1, HbpA and sphingomyelinase. Group I patients (n = 23) were classified as leptospirosis-positive based on MAT and high titres of circulating IgM-specific anti-leptospiral antibodies. All of these patients excreted all five leptospiral antigens in the urine. The 17 MAT-negative cases included six patients with pyrexia of unknown origin (PUO; Group II) and 11 confirmed dengue patients (Group III). The latter tested negative for both serum anti-leptospiral antibodies and urinary leptospiral antigens. A salient outcome of this study was highlighting the usefulness of screening for urinary leptospiral antigens in disease diagnosis, as their presence confirmed leptospiral aetiology in two PUO patients. Immunoblots of urinary antigens identified well-defined bands corresponding to LipL32, HbpA and sphingomyelinase; the significance of the 42- and 58-kDa sphingomyelinase bands is discussed.

Non-communicable diseases in the Western Area District, Sierra Leone, before and during the Ebola outbreak

Setting: Twenty-seven peripheral health units, five secondary hospitals and one tertiary hospital, Western Area District, Sierra Leone. Objectives: To describe reporting systems, monthly attendances and facility-based patterns of six non-communicable diseases (NCDs) in the pre-Ebola and Ebola virus disease outbreak periods. Design: A cross-sectional study using programme data. Results: Reporting was 89% complete on the six selected NCDs pre-Ebola and 86% during the Ebola outbreak (P < 0.01). Overall, marked declining trends in NCDs were reported during the Ebola period, with a monthly mean of 342 cases pre-Ebola and 164 during the Ebola outbreak. The monthly mean number of cases per disease in the pre-Ebola and Ebola outbreak periods was respectively 228 vs. 85 for hypertension, 43 vs. 27 for cardiovascular diseases, 36 vs. 18 for diabetes and 25 vs. 29 for peptic ulcer disease; this last condition increased during the outbreak. There were higher proportions of NCDs among females during the Ebola outbreak compared with the pre-Ebola period. Except for peptic ulcer disease, the number of patients with NCDs declined by 25% in peripheral health units, 91% in the secondary hospitals and 70% in the tertiary hospital between the pre-Ebola and the Ebola outbreak periods. Conclusion: Comprehensive reporting of NCDs was suboptimal, and declined during the Ebola epidemic. There were decreases in reported attendances for NCDs between the pre-Ebola and the Ebola outbreak periods, which were even more marked in the hospitals. This study has important policy implications.

Abstract P5-16-12: Pertuzumab and trastuzumab in combination with weekly paclitaxel delivers high pCR rates with favourable toxicity profile in neo-adjuvant treatment of Her-2 positive breast cancer

This abstract was not presented at the symposium.

[Management of anesthesia in endovascular interventions]

Cardiovascular diseases are one of the leading causes of morbidity and mortality in Germany. In these patients, the high-risk profile necessitates an interdisciplinary and multimodal approach to treatment. Endovascular interventions and vascular surgery have become established as an important element of this strategy in the past; however, the different anatomical localizations of pathological vascular alterations make it necessary to use a wide spectrum of procedural options and methods; therefore, the requirements for management of anesthesia are variable and necessitate a differentiated approach. Endovascular procedures can be carried out with the patient under general or regional anesthesia (RA); however, in the currently available literature there is no evidence for an advantage of RA over general anesthesia regarding morbidity and mortality, although a reduction in pulmonary complications could be found for some endovascular interventions. Epidural and spinal RA procedures should be carefully considered with respect to the risk-benefit ratio and consideration of the recent guidelines on anesthesia against the background of the current study situation and the regular use of therapy with anticoagulants. The following article elucidates the specific characteristics of anesthesia management as exemplified by some selected endovascular interventions.