Host adapted serotypes of <i>Salmonella enterica</i>

Salmonella constitutes a genus of zoonotic bacteria of worldwide economic and health importance. The current view of salmonella taxonomy assigns the members of this genus to two species: S. enterica and S. bongori. S. enterica itself is divided into six subspecies, enterica, salamae, arizonae, diarizonae, indica, and houtenae, also known as subspecies I, II, IIIa, IIIb, IV, and VI, respectively. Members of Salmonella enterica subspecies enterica are mainly associated with warm-blooded vertebrates and are usually transmitted by ingestion of food or water contaminated by infected faeces. The pathogenicity of most of the distinct serotypes remains undefined, and even within the most common serotypes, many questions remain to be answered regarding the interactions between the organism and the infected host. Salmonellosis manifests itself in three major forms: enteritis, septicaemia, and abortion, each of which may be present singly or in combination, depending on both the serotype and the host involved. Although currently over 2300 serovars of Salmonella are recognized, only about 50 serotypes are isolated in any significant numbers as human or animal pathogens and they all belong to subspecies enterica. Of these, most cause acute gastroenteritis characterized by a short incubation period and a severe systemic disease in man or animals, characterized by septicaemia, fever and/or abortion, and such serotypes are often associated with one or few host species. It is the intention of this review to present a summary of current knowledge of these host-adapted serotypes of S. enterica. The taxonomic relationships between the serotypes will be discussed together with a comparison of the pathology and pathogenesis of the disease that they cause in their natural host(s). Since much of our knowledge on salmonellosis is based on the results of work on Typhimurium, this serotype will often be used as the baseline in discussion. It is hoped that an appreciation of the differences that exist in the way these serotypes interact with the host will lead to a greater understanding of the complex host–parasite relationship that characterizes salmonella infections

Contextual modulation involves suppression and facilitation from the center and the surround

In psychophysics, cross-orientation suppression (XOS) and cross-orientation facilitation (XOF) have been measured by investigating mask configuration on the detection threshold of a centrally placed patch of sine-wave grating. Much of the evidence for XOS and XOF comes from studies using low and high spatial frequencies, respectively, where the interactions are thought to arise from within (XOS) and outside (XOF) the footprint of the classical receptive field. We address the relation between these processes here by measuring the effects of various sizes of superimposed and annular cross-oriented masks on detection thresholds at two spatial scales (1 and 7 c/deg) and on contrast increment thresholds at 7 c/deg. A functional model of our results indicates the following (1) XOS and XOF both occur for superimposed and annular masks. (2) XOS declines with spatial frequency but XOF does not. (3) The spatial extent of the interactions does not scale with spatial frequency, meaning that surround-effects are seen primarily at high spatial frequencies. (4) There are two distinct processes involved in XOS: direct divisive suppression and modulation of self-suppression. (5) Whether XOS or XOF wins out depends upon their relative weights and mask contrast. These results prompt enquiry into the effect of spatial frequency at the single-cell level and place new constraints on image-processing models of early visual processing. © ARVO

Complications of tube thoracostomy for chest trauma

Objective. To determine the insertional and positional complications encountered by the placement of intercostal chest drains (ICDs) for trauma and whether further training is warranted in operators inserting intercostal chest drains outside level 1 trauma unit settings. Methods. Over a period of 3 months, all patients with or without an ICD in situ in the front room trauma bay of Tygerberg Hospital were included in the study. Patients admitted directly via the trauma resuscitation unit were excluded. No long-term infective complications were included. A self-reporting system recorded complications, and additional data were obtained by searching the department’s records and monthly statistics. Results. A total of 3 989 patients with trauma injuries were seen in the front room trauma bay during the study period; 273 (6.8%) patients with an ICD in situ or requiring an ICD were assessed in the trauma unit and admitted to the chest drain ward; 24 patients were identified with 26 complications relating to the insertion and positioning of the ICD; 22 (92%) of these had been referred with an ICD in situ. An overall complication rate of 9.5% was seen. Insertional complications numbered 7 (27%), with 19 (73%) positional complications. The most common errors were insertion at the incorrect anatomical site, and extrathoracic and too shallow placement (side portal of the drain lying outside the chest cavity). Conclusion. Operators at the referral hospitals have received insufficient training in the technique for insertion of ICDs for chest trauma and would benefit from more structured instruction and closer supervision of ICD insertion

Guideline for the assessment of trauma centres for South Africa

INTRODUCTION: Trauma is a well-known leading cause of unnatural death and disability in South Africa. Internationally the trend is moving toward systematised care. AIM: To revise the Trauma Centre Criteria of the Trauma Society of South Africa and align these with the terminology and modern scope of emergency care practice, using best-care principles as a prelude to the development of trauma systems in South Africa. METHODOLOGY: Revision of existing documents of the Trauma Society of South Africa, the Emergency Medicine Society of South Africa and the Critical Care Society of Southern Africa, where these are relevant to the care of trauma. The committee attempted to harmonise these criteria with the goals of the World Health Organization essential trauma care guidelines for trauma centres and trauma systems. Wide expert consultation was undertaken to refine the criteria before final compilation. RESULTS AND RECOMMENDATIONS: Four levels of trauma care facility are outlined, with the criteria focusing on the trauma-specific requirements of the facilities and their place in the greater trauma system. Accreditation of hospitals according to the criteria will allow for appropriate transfer and designation of patient destination for trauma patients and will improve the quality of care provided. The criteria address structural, process and human resource requirements and medical aspects for the accreditation of various level of trauma centre. CONCLUSION: There is a great opportunity to apply best practice criteria to improve the care of trauma in South Africa and improve patient outcome

Identification of Salmonella enterica Serovar Dublin-Specific Sequences by Subtractive Hybridization and Analysis of Their Role in Intestinal Colonization and Systemic Translocation in Cattle

Salmonella enterica serovar Dublin is a host-restricted serovar associated with typhoidal disease in cattle. In contrast, the fowl-associated serovar S. enterica serovar Gallinarum is avirulent in calves, yet it invades ileal mucosa and induces enteritis at levels comparable to those induced by S. enterica serovar Dublin. Suppression subtractive hybridization was employed to identify S. enterica serovar Dublin strain SD3246 genes absent from S. enterica serovar Gallinarum strain SG9. Forty-one S. enterica serovar Dublin fragments were cloned and sequenced. Among these, 24 mobile-element-associated genes were identified, and 12 clones exhibited similarity with sequences of known or predicted function in other serovars. Three S. enterica serovar Dublin-specific regions were homologous to regions from the genome of Enterobacter sp. strain 638. Sequencing of fragments adjacent to these three sequences revealed the presence of a 21-kb genomic island, designated S. enterica serovar Dublin island 1 (SDI-1). PCR analysis and Southern blotting showed that SDI-1 is highly conserved within S. enterica serovar Dublin isolates but rarely found in other serovars. To probe the role of genes identified by subtractive hybridization in vivo, 24 signature-tagged S. enterica serovar Dublin SD3246 mutants lacking loci not present in Salmonella serovar Gallinarum SG9 were created and screened by oral challenge of cattle. Though attenuation of tagged SG9 and SD3246 Salmonella pathogenicity island-1 (SPI-1) and SPI-2 mutant strains was detected, no obvious defects of these 24 mutants were detected. Subsequently, a DeltaSDI-1 mutant was found to exhibit weak but significant attenuation compared with the parent strain in coinfection of calves. SDI-1 mutation did not impair invasion, intramacrophage survival, or virulence in mice, implying that SDI-1 does not influence fitness per se and may act in a host-specific manner

Quantifying exposure biases in early instrumental land surface air temperature observations

Exposure biases are a pervasive non-climatic change in land air temperature records which have been introduced as a result of changes in the way thermometers were sheltered from solar radiation and the elements over time. Exposure biases have not been widely accounted for in observational records, due to difficulties detecting/correcting the bias using traditional homogenisation techniques; therefore, exposure biases still contribute significant uncertainty to the early period in global temperature compilations. Here, an empirical approach to address the bias arising from the introduction of Stevenson-type screens from the late-19th century is presented. The approach consists of: (1) an empirical analysis of 54 parallel measurement series to identify the characteristics of the exposure bias in four exposure classes; (2) the development of bias-estimation models based on an analysis of which variables influence the bias; and (3) the application of the models to an extended version of CRUTEM5 (CRUTEM5_ext), based on exposure metadata, to quantify and reduce the bias. Step one identified differences between the temperatures recorded in Stevenson screens and early exposures, which vary seasonally, diurnally, and with location and exposure class. The largest biases (in mean temperatures) were found in freestanding exposures (up to −0.78°C annually) and in summer, while the smallest biases were generally found in wall-mounted exposures (near-0°C annually) and in winter. Significant relationships between the bias and temperature, downward top of atmosphere and/or received shortwave downward solar radiation were found in each exposure class and led to the development of three regression-based bias-estimation models. Application of these models to 1,960 mid-latitude stations in CRUTEM5_ext, resulted in small (≤0.016°C) positive adjustments to the Northern Hemisphere mid-latitude mean before 1880, and larger (≤−0.1°C) negative adjustments to the Northern and Southern Hemisphere mid-latitude means between 1882–1934 and 1856–1900, respectively. Larger adjustments were estimated regionally: up to −0.57°C annually and −0.79°C seasonally in individual grid cells

Perceptions of health providers towards the use of standardised trauma form in managing trauma patients: a qualitative study from Tanzania

Background Trauma registries (TRs) are essential to informing the quality of trauma care within health systems. Lack of standardised trauma documentation is a major cause of inconsistent and poor availability of trauma data in most low- and middle-income countries (LMICs), hindering the development of TRs in these regions. We explored health providers’ perceptions on the use of a standardised trauma form to record trauma patient information in Tanzania. Methods An exploratory qualitative research using a semi-structured interview guide was carried out to purposefully selected key informants comprising of healthcare providers working in Emergency Units and surgical disciplines in five regional hospitals in Tanzania. Data were analysed using a thematic analysis approach to identify key themes surrounding potential implementation of the standardised trauma form. Results Thirty-three healthcare providers participated, the majority of whom had no experience in the use of standardised charting. Only five respondents had prior experience with trauma forms. Responses fell into three themes: perspectives on the concept of a standardised trauma form, potential benefits of a trauma form, and concerns regarding successful and sustainable implementation. Conclusion Findings of this study revealed wide healthcare provider acceptance of moving towards standardised clinical documentation for trauma patients. Successful implementation likely depends on the perceived benefits of using a trauma form as a tool to guide clinical management, standardise care and standardise data reporting; however, it will be important moving forward to factor concerns brought up in this study. Potential barriers to successful and sustainable implementation of the form, including the need for training and tailoring of form to match existing resources and knowledge of providers, must be considered

Trauma care and capture rate of variables of World Health Organisation data set for injury at regional hospitals in Tanzania: first steps to a national trauma registry

Background In Tanzania, there is no national trauma registry. The World Health Organization (WHO) has developed a data set for injury that specifies the variables necessary for documenting the burden of injury and patient-related clinical processes. As a first step in developing and implementing a national Trauma Registry, we determined how well hospitals currently capture the variables that are specified in the WHO injury set. Methods This was a prospective, observational cross-sectional study of all trauma patients conducted in the Emergency Units of five regional referral hospitals in Tanzania from February 2018 to July 2018. Research assistants observed the provision of clinical care in the EU for all patients, and documented performed assessment, clinical interventions and final disposition. Research assistants used a purposefully designed case report form to audit the injury variable capture rate, and to review Ministry of Health (MoH) issued facility Register book recording the documentation of variables. We present descriptive statistics for hospital characteristics, patient volume, facility infrastructure, and capture rate of trauma variables. Results During the study period, 2891 (9.3%) patients presented with trauma-related complaints, 70.7% were male. Overall, the capture rate of all variables was 33.6%. Documentation was most complete for demographics 71.6%, while initial clinical condition, and details of injury were documented in 20.5 and 20.8% respectively. There was no documentation for the care prior to Emergency Unit arrival in all hospitals. 1430 (49.5%) of all trauma-related visits seen were documented in the facility Health Management Information System register submitted to the MoH. Among the cases reported in the register book, the date of EU care was correctly documented in 77% cases, age 43.6%, diagnosis 66.7%, and outcome in 38.9% cases. Among the observed procedures, initial clinical condition (28.7%), interventions at Emergency Unit (52.1%), investigations (49.0%), and disposition (62.9%) were documented in the clinical charts. Conclusions In the regional hospitals of Tanzania, there is inadequate documentation of the minimum trauma variables specified in the WHO injury data set. Reasons for this are unclear, but will need to be addressed in order to improve documentation to inform a national injury registry

BreakTrans: Uncovering the genomic architecture of gene fusions

Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTran

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that large-amplitude RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps.Comment: 55 pages, 10 figure