Simulating the 21-cm signal from the Epoch of Reionization

In this thesis, the 21-cm signal from the epoch of reionization is simulated using a combination of N-Body techniques and semi-analytical models. Images, line-of-sight spectra and power spectra of the simulated 21-cm signal are presented. The N-Body code, GADGET-2, is used to obtain the distribution of dark matter and a friends-of-friends algorithm is used to identify dark matter halos to construct halo merger trees. We ran seven simulations with periodic boxes of volumes ranging from (10h(^-1)Mpc)(^3) to (140h(^-1)Mpc)(^3), and particle masses ranging from 6.46 x lO(^4)h(^-1)M(_ʘ) to 1.42 X 10(^9) h(^-1)M(_ʘ). These merger trees are used with the GALFORM semi-analytical model of galaxy formation to predict the locations of galaxies and their ionizing luminosities within the halos. We find that halos in a broad range of masses contribute significantly to the total ionizing emissivity of each simulation. The effect of suppressing gas cooling due to reionization in low mass halos in GALFORM was also investigated. For a redshift of reionization, z(_reion) = 15, this significantly reduces the number of ionizing photons produced at z < 15. This results in a prolonged period of reionization as the Universe makes the transition from neutral to fully ionized. Next, the 21-cm signal and ionization state of the hydrogen is calculated for the simulation box with a volume of (20h(^-1)Mpc)(^3) and a particle mass of 5.17 x 10(^5)h(^-1)M(_ʘ). The hydrogen is assumed to follow the dark matter, and the 21-cm differential brightness temperature is calculated from the distribution of neutral hydrogen. High resolution images and spectra of the 21-cm signal are generated from these neutral hydrogen density fields. A toy model is first investigated, randomly distributed ionized spheres of constant radii are generated to investigate the effect ionized regions have on the 21-cm power spectra. We find that this increases power on the scales of the size of the ionized spheres, but decreases power on small scales. The amount of change in power is sensitive to the overall ionized fraction of the simulation box, increasing the ionized fraction increases the power on the scales of the spheres while decreases the power on small scales. Next, the GALFORM model is investigated. The ionizing luminosities of GALFORM galaxies are used to calculate cosmological Strömgren spheres representing ionized regions. These spheres are "painted" around the location of the galaxies on the density field. We find that the power spectra lack any obvious features due to the range of sizes of the GALFORM ionized regions. However, the power spectra is sensitive to the ionized fraction of the simulation box. The slope of the power spectra decreases as ionized fraction increases. Finally, the temperature field is smoothed over a bandwidth of 200 kHz and a 2-D Gaussian beam with a FWHM of 3 arcmin to emulate the LOFAR telescope beam response. We find that only the largest features, such as large ionized regions, are still identifiable after smoothing. LOFAR should be able to detect the early stages of reionization, but may have difficulties during later stages when much of the brightest 21-cm signal is removed by reionization

Management of tracheobronchial obstruction in infants using metallic stents: long-term outcome

© 2015, Springer-Verlag Berlin Heidelberg. Results: Twelve balloon-expandable metallic stents were placed in the trachea (n = 10) and/or bronchi (n = 2) of 5 patients with a median age of 13 months (range 5–30 months). Etiology of the airway obstruction included congenital tracheal stenosis (n = 4), giant cervical and superior mediastinal lymphatic malformation with tracheobronchomalacia (n = 1). Seven complications were reported (3 patients developed granulation tissue, 2 patients had re-stenosis, 1 stent migrated, 1 stent fractured). All patients survived and were in good condition with a median follow-up of 16 years (range 11–18 years). Three patients weaned off ventilator and oxygen. Conclusions: Endoscopic stenting with metallic stent has satisfactory long-term outcome in treating infants with tracheobronchial obstruction. Introduction: Tracheobronchial obstruction, although uncommon in the pediatric age group, remains a challenging problem. We review the long-term outcome of endoscopic metallic stenting in infants with tracheobronchial obstruction. Materials and methods: Medical records of all pediatric surgical patients who underwent tracheobronchial metallic stenting in our center were reviewed retrospectively from 1996 to 2014. Patients’ demographic data, including etiology, associated anomalies and nature of obstruction were reviewed. Outcome measures include complications such as re-stenosis, granulation tissue, stent migration, fractured stent, maximal tracheal diameter achieved, weaning of ventilator and growth at interval follow-up.postprin

Thoracoscopic repair of congenital diaphragmatic hernia: two centres’ experience with 60 patients

© 2014, Springer-Verlag Berlin Heidelberg. Methods: All patients who underwent thoracoscopic repair of congenital diaphragmatic hernia between 2010 and 2013 at the two tertiary referral centres were identified. Medical records were retrospectively reviewed. Data including patients’ demographics, peri-operative outcomes, length of hospitalisation and post-operative complications were extracted and analysed. Introduction: Congenital diaphragmatic hernia is a potentially life-threatening neonatal condition which required surgical intervention. With the advances in endosurgical instruments and techniques, thoracoscopic approach is gaining popularity as a standard procedure in the treatment of this condition. In this study, we reviewed our two centres’ experience with thoracoscopic repair of congenital diaphragmatic hernia in recent years. Conclusion: Thoracoscopic repair of congenital diaphragmatic hernia can be performed safely in specialised centres. The post-operative recovery and cosmesis are excellent. Diaphragmatic hernia with large defect remains a challenge for surgeons. Results: 60 patients were identified over the study period, with 46 males and 14 females. 48 patients received operation within the first 7 days of life. There were seven patients with delayed presentation and were operated after 1 month old. The average body weight was 3.03 kg. Left-sided hernia was more prevalent (n = 50). The mean operative time was 88.5 min (range 31–194 min). No conversion to open thoracotomy or laparotomy was required in any of the patients. All patients except one were intubated and paralysed in neonatal intensive care units for at least 3 days after operation. Average hospital stay was 14.6 days. There was no mortality in this series. There were five recurrences, one being the patient without post-operative paralysis, and the others with deficient posterior muscle rim. No musculoskeletal deformity was noted on follow-up examination.postprin

Early post-operative interleukin-6 and tumor necrosis factor-α levels after single-port laparoscopic varicocelectomy in children

PURPOSE: Laparoendoscopic single-site surgery has recently been described in children and regarded as an improved technology leading to less pain and better cosmetic outcome. Compared to the traditional three-port method, it is not known if the single-port method is less invasive. The aim of this study was thus to investigate the post-operative acute inflammatory response in order to evaluate surgical stress in the two surgical approaches in children. METHODS: A prospective, single blinded, case-control study was carried out. Thirteen male patients who presented with unilateral varicocele were divided into two groups. Six children underwent single-port laparoscopic procedure, while the other seven children underwent three-port laparoscopic procedure. Pre-operative and post-operative blood samples were taken for the measurement of tumor necrosis factor-alpha (TNF-alpha) and interleukin 6 (IL-6) using ELISA. Demographics including the operation time, and complications were recorded. Data between the two groups were analyzed using unpaired t-test and a p value of <0.05 was taken as statistically significant. RESULTS: The mean age of patients was 14.5 years (range 12-19 years). There was no significant difference between the two groups in terms of operative time, nor there was any complication recorded. The change in serum TNF-alpha and IL-6 concentrations pre- and post-operatively between the single-port group and three-port group was not statistically significant. Overall, patients in the two groups showed excellent satisfaction in terms of post-operative cosmesis. CONCLUSION: Single-port laparoscopic varicocelectomy is safe, effective and produces excellent cosmesis with minimal surgical stress.published_or_final_versionSpringer Open Choice, 21 Feb 201

Chinese family with diffuse oesophageal leiomyomatosis: A new COL4A5/COL4A6 deletion and a case of gonosomal mosaicism

© 2015 Liu et al. Background: Diffuse oesophageal leiomyomatosis (DOL) is a rare disorder characterized by tumorous overgrowth of the muscular wall of the oesophagus. DOL is present in 5 % of Alport syndrome (AS) patients. AS is a rare hereditary disease that involves varying degrees of hearing impairment, ocular changes and progressive glomerulonephritis leading to renal failure. In DOL-AS patients, the genetic defect consists of a deletion involving the COL4A5 and COL4A6 genes on the X chromosome. Case presentation: We report a two-generation family (4 individuals; parents and two children, one male and one female) with two members (mother and son) affected with oesophageal leiomyomatosis. Signs of potential renal failure, which characterizes AS, were only apparent in the index patient (son) 2 years and three months after the initial diagnosis of DOL. Blood DNA from the four family members were submitted to exome sequencing and array genotyping to perform a genome wide screening for disease causal single nucleotide (SN) and copy number (CN) variations. Analyses revealed a new 40kb deletion encompassing from intron 2 of COL4A5 to intron 1 of COL4A6 at Xq22.3. The breakpoints were also identified. Possible confounding pathogenic exonic variants in genes known to be involved in other extracellular matrices disorders were also shared by the two affected individuals. Meticulous analysis of the maternal DNA revealed a case of gonosomal mosaicism. Conclusions: This is the first report of gonadosomal mosaicism associated to DOL-AS.published_or_final_versio

The effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review

Background: Administration of convalescent plasma, serum, or hyperimmune immunoglobulin may be of clinical benefit for treatment of severe acute respiratory infections (SARIs) of viral etiology. We conducted a systematic review and exploratory meta-analysis to assess the overall evidence. Methods: Healthcare databases and sources of grey literature were searched in July 2013. All records were screened against the protocol eligibility criteria, using a 3-stage process. Data extraction and risk of bias assessments were undertaken. Results: We identified 32 studies of SARS coronavirus infection and severe influenza. Narrative analyses revealed consistent evidence for a reduction in mortality, especially when convalescent plasma is administered early after symptom onset. Exploratory post hoc meta-analysis showed a statistically significant reduction in the pooled odds of mortality following treatment, compared with placebo or no therapy (odds ratio, 0.25; 95% confidence interval, .14–.45; I(2) = 0%). Studies were commonly of low or very low quality, lacked control groups, and at moderate or high risk of bias. Sources of clinical and methodological heterogeneity were identified. Conclusions: Convalescent plasma may reduce mortality and appears safe. This therapy should be studied within the context of a well-designed clinical trial or other formal evaluation, including for treatment of Middle East respiratory syndrome coronavirus CoV infection

Examining patient-reported late toxicity and its association with quality of life and unmet need for symptom management among nasopharyngeal cancer survivors: a cross-sectional survey

IntroductionAlongside the improved survival of nasopharyngeal cancer (NPC), late radiation toxicities are alarmingly hampering survivors’ quality of life. A patient-reported symptom burden survey is lacking to address the unmet need for symptom management among local NPC survivors.MethodsA single-center cross-sectional survey was conducted on 211 NPC survivors who had completed radiation therapy for three to 120 months. We employed the Chinese version M. D. Anderson Symptom Inventory - Head &amp; Neck Module (MDASI-HN-C), Functional Assessment of Cancer Therapy - Head &amp; Neck (FACT-HN-C), and a question extracted from the Cancer Survivors’ Unmet Needs Measure (CaSUN).ResultsTwo hundred valid responses were collected. Participants suffered from at least four moderate to severe symptoms (mean = 4.84, SD = 4.99). The top five severe symptoms were dry mouth, mucus problems, difficulty swallowing or chewing, teeth or gum problems, and memory problems. MDASI-HN-C subscales were negatively correlated with the physical, emotional, functional, and HN-specific domains of the FACT-HN-C. The unmet need for symptom management was positively associated with symptom burden, either general symptoms (Adjusted odds ratio [ORadj] = 1.566, 95% CI = 1.282 – 1.914, p &lt; 0.001) or top-5 symptoms (ORadj = 1.379, 95% CI = 1.185 – 1.604, p &lt; 0.001), while negatively associated with post-RT time (ORadj = 0.981, 95% CI [0.972, 0.991], p &lt; 0.001).ConclusionVirtually all NPC survivors suffer from late toxicities, which interplay with survivors’ perceptions intricately to affect their unmet needs for symptom management. Personalized supportive care strategies with regular assessments and stratifications are warranted

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment