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Tick-borne spotted fever rickettsioses (SFRs) continue to cause severe illness and death in otherwise-healthy individuals due to lack of a timely and reliable diagnostic laboratory test. We recently identified a diagnostic biomarker for SFRs, the putative N-acetylmuramoyl-l-alanine amidase RC0497. Here, we developed a prototype laboratory test that targets RC0497 for diagnosis of SFRs. The concentrations of RC0497 in sera of Rickettsia rickettsii-infected guinea pigs and R. conorii-infected mice were determined by stable isotope dilution–parallel reaction monitoring mass spectrometry (SID-PRM-MS), ranging from 0.1 to 1.1 ng/ml. Using europium chelate nanoparticle reporters, we developed a lateral flow assay (LFA) and evaluated the test with a panel of serum samples of mock and experimentally infected animals. Interestingly, 21 of 22 (95.5%) serum samples from R. rickettsii-infected guinea pigs and R. conorii-infected mice yielded positive results with a ratio of test line / control line greater than the cutoff value determined for non-infected animals. All uninfected samples were in agreement with the intended results, suggesting that the initially assessed specificity of the test is 100%, among these samples. Mice infected with a lethal dose of R. conorii and treated with doxycycline on day 3 post-infection (p.i.), upon RC0497 detection by LFA, displayed significantly decreased rickettsial loads, comparable to the sublethal infection group on day 5 p.i.. A panel of human serum samples spiked with various concentrations of recombinant RC0497 were analyzed by LFA, suggesting that the limit of detection of the LFA was 0.64 ng/mL. These findings suggest that the timely detection of RC0497 by a europium LFA offers guidance for treatment, leading to a significant improvement in infection outcomes. This work, for the first time, shows significant promise for a rapid and easy-to-use platform offering a timely diagnostic assay for severe SFRs. [ABSTRACT FROM AUTHOR]

Performance variability is present in a series of competition results in athletics. Some of the variability is random and some can be attributed to factors such as the environment and changes in the level of physical, mental, and technical states of the athlete. Changes in the state of the athlete may be due to the competition schedule. It has been shown that there is periodicity in performance aligned with the seasonal competition schedule in athletics and with the Olympic cycle in pooled athletics data dating from 1896 to 2008. We investigated whether Olympic cycle periodicity was present in modern era long and triple jumping in elite men and women. Top 50 performances per year in the horizontal jumps in men and women from 1996 to 2019 were used. Each performance was normalized to the best result from the previous Olympic year. Two-way ANOVAs revealed significantly lower mean normalized performances in top ten women compared to top ten men (p < 0.001) in both jumps. In both jumps, ten top-performing women also showed decreases between the Olympic year mean normalized performances and the 1st year following (Long Jump: p = 0.022, Triple Jump: p = 0.008). In triple jump, the decrease in performance was also found in the second year following the Olympics. Performances deciles ranked from 11th to 50th place showed a similar pattern in women’s triple jump but only for ranks 11 to 20 in the women’s long jump. The findings suggest that periodicity driven by the Olympic cycle exists in women’s long and triple jump at the elite level.

The management of cancer patients has markedly improved with the advent of personalised medicine where treatments are given based on tumour antigen expression amongst other. Within this remit, liquid biopsies will no doubt improve this personalised cancer management. Identifying circulating tumour cells in blood allows a better assessment for tumour screening, staging, response to treatment and follow up. However, methods to identify/capture these circulating tumour cells using cancer cells’ antigen expression or their physical properties are not robust enough. Thus, a methodology that can identify these circulating tumour cells in blood regardless of the type of tumour is highly needed. Fourier Transform Infrared (FTIR) microspectroscopy, which can separate cells based on their biochemical composition, could be such technique. In this feasibility study, we studied lung cancer cells (squamous cell carcinoma and adenocarcinoma) mixed with peripheral blood mononuclear cells (PBMC). The data obtained shows, for the first time, that FTIR microspectroscopy together with Random Forest classifier is able to identify a single lung cancer cell in blood. This separation was easier when the region of the IR spectra containing lipids and the amide A (2700 to 3500 cm-1) was used. Furthermore, this work was carried out using glass coverslips as substrates that are widely used in pathology departments. This allows further histopathological cell analysis (staining, immunohistochemistry, …) after FTIR spectra are obtained. Hence, although further work is needed using blood samples from patients with cancer, FTIR microspectroscopy could become another tool to be used in liquid biopsies for the identification of circulating tumour cells, and in the personalised management of cancer.

[This corrects the article DOI: 10.1371/journal.pone.0089754.].

Background The increasing number of physicians leaving practice, especially hospitalists, has been well-documented. The most commonly examined factor associated with this exodus has been burnout. The COVID-19 pandemic has put a unique and unprecedented stress on hospitalists who have been at the front lines of patient care. Therefore, the investigation of burnout and its related factors in hospitalists is essential to preventing future physician shortages. Objective This study examined the relationship between burnout, second victim, and moral injury experiences before and during the COVID-19 pandemic among hospitalists. Methods Two anonymous cross-sectional surveys of hospitalists from a community hospital in the metropolitan Washington, DC area were conducted. One was conducted pre-COVID-19 (September-November 2019) and one was conducted during COVID-19 (July-August 2020). The surveys were sent to all full-time hospitalists via an online survey platform. A variety of areas were assessed including demographic (e.g., age, gender), work information (e.g., hours per week, years of experience), burnout, second victim experiences, well-being, and moral injury. Results Burnout rates among providers during these two time periods were similar. Second victim experiences remained prevalent in those who experienced burnout both pre and during COVID-19, but interestingly the prevalence increased in those without burnout during COVID-19. Moral injury was predictive of burnout during COVID-19. Conclusion While there were some factors that predicted burnout that were similar both pre- and during-pandemic, moral injury was unique to predicting burnout during COVID-19. With burnout as a contributing factor to future physician shortages, it is imperative that predictive factors in a variety of different environments are well understood to prevent future shortages. Hospitalists may be an excellent barometer of these factors given their presence on the front line during the pandemic, and their experiences need to be further explored so that targeted interventions aimed at addressing those factors may be created.

Schizophrenia patients exhibit well-documented visual processing deficits. One area of disruption is visual integration, the ability to form global objects from local elements. However, most studies of visual integration in schizophrenia have been conducted in the context of an active attention task, which may influence the findings. In this study we examined visual integration using electroencephalography (EEG) in a passive task to elucidate neural mechanisms associated with poor visual integration. Forty-six schizophrenia patients and 30 healthy controls had EEG recorded while passively viewing figures comprised of real, illusory, or no contours. We examined visual P100, N100, and P200 event-related potential (ERP) components, as well as neural synchronization in the gamma (30-60 Hz) band assessed by the EEG phase locking factor (PLF). The N100 was significantly larger to illusory vs. no contour, and illusory vs. real contour stimuli while the P200 was larger only to real vs. illusory stimuli; there were no significant interactions with group. Compared to controls, patients failed to show increased phase locking to illusory versus no contours between 40-60 Hz. Also, controls, but not patients, had larger PLF between 30-40 Hz when viewing real vs. illusory contours. Finally, the positive symptom factor of the BPRS was negatively correlated with PLF values between 40-60 Hz to illusory stimuli, and with PLF between 30-40 Hz to real contour stimuli. These results suggest that the pattern of results across visual processing conditions is similar in patients and controls. However, patients have deficits in neural synchronization in the gamma range during basic processing of illusory contours when attentional demand is limited.

Schizophrenia patients exhibit well-documented visual processing deficits. One area of disruption is visual integration, the ability to form global objects from local elements. However, most studies of visual integration in schizophrenia have been conducted in the context of an active attention task, which may influence the findings. In this study we examined visual integration using electroencephalography (EEG) in a passive task to elucidate neural mechanisms associated with poor visual integration. Forty-six schizophrenia patients and 30 healthy controls had EEG recorded while passively viewing figures comprised of real, illusory, or no contours. We examined visual P100, N100, and P200 event-related potential (ERP) components, as well as neural synchronization in the gamma (30-60 Hz) band assessed by the EEG phase locking factor (PLF). The N100 was significantly larger to illusory vs. no contour, and illusory vs. real contour stimuli while the P200 was larger only to real vs. illusory stimuli; there were no significant interactions with group. Compared to controls, patients failed to show increased phase locking to illusory versus no contours between 40-60 Hz. Also, controls, but not patients, had larger PLF between 30-40 Hz when viewing real vs. illusory contours. Finally, the positive symptom factor of the BPRS was negatively correlated with PLF values between 40-60 Hz to illusory stimuli, and with PLF between 30-40 Hz to real contour stimuli. These results suggest that the pattern of results across visual processing conditions is similar in patients and controls. However, patients have deficits in neural synchronization in the gamma range during basic processing of illusory contours when attentional demand is limited.

Background and purposeBladder radiotherapy is a management option for carefully selected patients with muscle-invasive bladder cancer. However, the inability to visualize the tumor site during treatment and normal bladder movement limits targeting accuracy and increases collateral radiation. A means to accurately and reliably target the bladder during radiotherapy is needed.Materials and methodsEighteen consecutive patients with muscle-invasive bladder cancer (T1-T4) elected bladder-preserving treatment with maximal transurethral resection (TUR), radiation and concurrent chemotherapy. All underwent endoscopic placement of 24-K gold fiducial markers modified with micro-tines (70 [2.9×0.9 mm.]; 19 [2.1×0.7 mm.) into healthy submucosa 5-10 mm. from the resection margin, using custom-made coaxial needles. Marker migration was assessed for with intra-op bladder-filling cystogram and measurement of distance between markers. Set-up error and marker retention through completion of radiotherapy was confirmed by on-table portal imaging.ResultsBetween 1/2007 and 7/2012, a total of 89 markers (3-5 per tumor site) were placed into 18 patients of mean age 73.6 years. Two patients elected cystectomy before starting treatment; 16/18 completed chemo-radiotherapy. All (100%) markers were visible with all on-table (portal, cone-beam CT), fluoroscopy, plain-film, and CT-scan imaging. In two patients, 1 of 4 markers placed at the tumor site fell-out (voided) during the second half of radiotherapy. All other markers (80/82, 98%) were present through the end of radio-therapy. No intraoperative (e.g. uncontrolled bleeding, collateral injury) or post-operative complications (e.g. stone formation, urinary tract infection, post-TUR hematuria >48 hours) occurred. Use of micro-tined fiducial tumor-site markers afforded a 2 to 6-fold reduction in bladder-area targeted with high-dose radiation.DiscussionPlacement of the micro-tined fiducial markers into the bladder was feasible and associated with excellent retention-rate and no complications. All markers were well-visualized during radiotherapy with all imaging modalities. Bladder fiducial markers improve targeting accuracy, and may increase treatment efficacy and reduce morbidity from collateral radiation.

Background: Idiopathic pulmonary fibrosis (IPF) is a common, progressive and invariably lethal interstitial lung disease with no effective therapy. We hypothesised that KCa3.1 K+ channel-dependent cell processes contribute to IPF pathophysiology. Methods: KCa3.1 expression in primary human lung myofibroblasts was examined using RT-PCR, western blot, immunofluorescence and patch-clamp electrophysiology. The role of KCa3.1 channels in myofibroblast proliferation, wound healing, collagen secretion and contraction was examined using two specific and distinct KCa3.1 blockers (TRAM-34 and ICA-17043 [Senicapoc]). Results: Both healthy non fibrotic control and IPF-derived human lung myofibroblasts expressed KCa3.1 channel mRNA and protein. KCa3.1 ion currents were elicited more frequently and were larger in IPF-derived myofibroblasts compared to controls. KCa3.1 currents were increased in myofibroblasts by TGFβ1 and basic FGF. KCa3.1 was expressed strongly in IPF tissue. KCa3.1 pharmacological blockade attenuated human myofibroblast proliferation, wound healing, collagen secretion and contractility in vitro, and this was associated with inhibition of TGFβ1-dependent increases in intracellular free Ca2+. Conclusions: KCa3.1 activity promotes pro-fibrotic human lung myofibroblast function. Blocking KCa3.1 may offer a novel approach to treating IPF with the potential for rapid translation to the clinic. © 2013 Roach et al.

Nurses and surgeons must identify and handle specialized instruments with high temporal and spatial precision. It is crucial that they are trained effectively. Traditional training methods include supervised practices and text-based study, which may expose patients to undue risk during practice procedures and lack motor/haptic training respectively. Tablet-based simulations have been proposed to mediate some of these limitations. We implemented a learning task that simulates surgical instrumentation nomenclature encountered by novice perioperative nurses. Learning was assessed following training in three distinct conditions: tablet-based simulations, text-based study, and real-world practice. Immediately following a 30-minute training period, instrument identification was performed with comparable accuracy and response times following tablet-based versus text-based training, with both being inferior to real-world practice. Following a week without practice, response times were equivalent between real-world and tablet-based practice. While tablet-based training does not achieve equivalent results in instrument identification accuracy as real-world practice, more practice repetitions in simulated environments may help reduce performance decline. This project has established a technological framework to assess how we can implement simulated educational environments in a maximally beneficial manner.

In dynamic multisensory environments, the perceptual system corrects for discrepancies arising between modalities. For instance, in the ventriloquism aftereffect (VAE), spatial disparities introduced between visual and auditory stimuli lead to a perceptual recalibration of auditory space. Previous research has shown that the VAE is underpinned by multiple recalibration mechanisms tuned to different timescales, however it remains unclear whether these mechanisms use common or distinct spatial reference frames. Here we asked whether the VAE operates in eye- or head-centred reference frames across a range of adaptation timescales, from a few seconds to a few minutes. We developed a novel paradigm for selectively manipulating the contribution of eye- versus head-centred visual signals to the VAE by manipulating auditory locations relative to either the head orientation or the point of fixation. Consistent with previous research, we found both eye- and head-centred frames contributed to the VAE across all timescales. However, we found no evidence for an interaction between spatial reference frames and adaptation duration. Our results indicate that the VAE is underpinned by multiple spatial reference frames that are similarly leveraged by the underlying time-sensitive mechanisms.

BackgroundEarly life exposure to adverse environments, and maternal stress in particular, has been shown to increase risk for metabolic diseases and neurobehavioral disorders. While many studies have examined the hypothalamic-pituitary-adrenal axis (HPA axis) as the primary mechanism behind these relationships, emerging research on the brain-gut axis suggests that the microbiome may play a role. In this study, we tested the relationships among maternal precarity and HPA axis dysregulation during the peripartum period, infant gut microbiome composition, and infant HPA axis functioning.MethodsData come from 25 mother-infant dyads in the Galápagos, Ecuador. Women completed surveys on precarity measures (food insecurity, low social support, depression, and stress) and gave salivary cortisol samples during and after pregnancy. Infant salivary cortisol and stool were collected in the postpartum. Statistical significance of differences in microbial diversity and relative abundance were assessed with respect to adjusted linear regression models.ResultsMaternal precarity was associated with lower diversity and higher relative abundance of Enterobacteriaceae and Streptococcaceae and a lower relative abundance of Bifidobacterium and Lachnospiraceae. These patterns of colonization for Enterobacteriaceae and Bifidobacterium mirrored those found in infants with HPA axis dysregulation. Maternal HPA axis dysregulation during pregnancy was also associated with a greater relative abundance of Veillonella.ConclusionsOverall, exposures to precarity and HPA axis dysregulation were associated with an increase in groups that include potentially pathogenic bacteria, including Enterobacteriaceae, Streptococcaceae, and Veillonella, and a decrease in potentially protective bacteria, including Bifidobacterium and Lachnospiraceae, as well as a decrease in overall diversity.

COVID-19, the disease caused by the SARS-CoV-2 virus, can cause shortness of breath, lung damage, and impaired respiratory function. Containing the virus has proven difficult, in large part due to its high transmissibility during the pre-symptomatic incubation. The study's aim was to determine if changes in respiratory rate could serve as a leading indicator of SARS-CoV-2 infections. A total of 271 individuals (age = 37.3 ± 9.5, 190 male, 81 female) who experienced symptoms consistent with COVID-19 were included- 81 tested positive for SARS-CoV-2 and 190 tested negative; these 271 individuals collectively contributed 2672 samples (days) of data (1856 healthy days, 231 while infected with COVID-19 and 585 while negative for COVID-19 but experiencing symptoms). To train a novel algorithm, individuals were segmented as follows; (1) a training dataset of individuals who tested positive for COVID-19 (n = 57 people, 537 samples); (2) a validation dataset of individuals who tested positive for COVID-19 (n = 24 people, 320 samples); (3) a validation dataset of individuals who tested negative for COVID-19 (n = 190 people, 1815 samples). All data was extracted from the WHOOP system, which uses data from a wrist-worn strap to produce validated estimates of respiratory rate and other physiological measures. Using the training dataset, a model was developed to estimate the probability of SARS-CoV-2 infection based on changes in respiratory rate during night-time sleep. The model's ability to identify COVID-positive individuals not used in training and robustness against COVID-negative individuals with similar symptoms were examined for a critical six-day period spanning the onset of symptoms. The model identified 20% of COVID-19 positive individuals in the validation dataset in the two days prior to symptom onset, and 80% of COVID-19 positive cases by the third day of symptoms.

The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms–both pathogenic and beneficial–have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.

PurposeFrequencies of single nucleotide polymorphisms (SNPs) from pain related candidate genes are available for individuals with sickle cell disease (SCD). One of those genes, the arginine vasopressin receptor 1A gene (AVPR1A) and one of its SNPs, rs10877969, has been associated with pain and disability in other pain populations. In patients with SCD, clinical factors such as pain and stress have been associated with increased health care utilization, but it is not known if the presence of the AVPR1A SNP plays a role in this observation. The study purpose was to explore the relationships between rs10877969 and self-reported pain, stress, and acute care utilization events among individuals with SCD.MethodsIn a cross-sectional investigation of outpatients with SCD, participants completed PAINReportIt®, a computerized pain measure, to describe their pain experience and contributed blood or saliva samples for genetic analysis. We extracted emergency department and acute care utilization from medical records.ResultsThe SNP genotype frequencies (%) for this sample were CC 30 (28%), CT 44 (41%), TT 33 (31%). Acute care utilization and stress as an aggravator of pain were significantly associated with the rs10877969 genotype (p = .02 and p = .002, respectively). The CT genotype had the highest mean utilization and CC genotype was associated with not citing stress as a pain aggravator. Chronic pain was not associated with rs10877969 (p = .41).ConclusionThis study shows that rs10877969 is related to indicators of stress and acute pain. Further research is recommended with other measures of stress and acute pain.

[This corrects the article DOI: 10.1371/journal.pone.0202858.].

The purpose of this study was to assess the prevalence of psychological distress in employees in the metalliferous mining industry in Australia, and to examine associated demographic, health, and workplace characteristics. A cross sectional survey was conducted among 1,799 participants from four metalliferous mines. Psychological distress was measured by the Kessler Psychological Distress Scale (K10), alongside other measures of personal demographics, health history, health behaviour, and workplace characteristics. Univariate and multivariate statistical methods were used to examine associations between psychological distress and personal and workplace characteristics. Levels of moderate to very high psychological distress were significantly higher in this sample (44.4%) compared to the general population (27.2%). Moderate to very high psychological distress was significantly associated with younger age; individual health factors (a prior history of depression, anxiety, or drug/alcohol problems); health behaviours (using illicit drugs in the last month); and a range of workplace factors (concern about losing their job; lower satisfaction with work; working shifts of over 12 hours duration; working in mining for financial reasons and social factors (poorer social networks). The identification of a number of social, personal and workplace factors associated with high psychological distress present useful targets to inform the development of tailored workplace interventions to reduce distress in metalliferous mine employees.

We are colonized by a vast population of genetically diverse microbes, the majority of which are unculturable bacteria that reside within the gastrointestinal tract. As affordable, advanced next-generation sequencing technologies become more widely available, important discoveries about the composition and function of these microbes become increasingly possible. In addition to rapid advancement in sequencing technologies, automated systems have been developed for nucleic acid extraction; however, these methods have yet to be widely used for the isolation of bacterial DNA from fecal samples. Here, we adapted Promega's Maxwell® RSC PureFood GMO and Authentication kit for use with fecal samples and compared it to the commonly used Qiagen QIAamp® PowerFecal® kit. Results showed that the two approaches yielded similar measures of DNA purity and successful next-generation sequencing amplification and produced comparable composition of microbial communities. However, DNA extraction with the Maxwell® RSC kit produced higher concentrations with a lower fecal sample input weight and took a fraction of the time compared to the QIAamp® PowerFecal® protocol. The results of this study demonstrate that the Promega Maxwell® RSC system can be used for medium-throughput DNA extraction in a time-efficient manner without compromising the quality of the downstream sequencing.

Performance variability is present in a series of competition results in athletics. Some of the variability is random and some can be attributed to factors such as the environment and changes in the level of physical, mental, and technical states of the athlete. Changes in the state of the athlete may be due to the competition schedule. It has been shown that there is periodicity in performance aligned with the seasonal competition schedule in athletics and with the Olympic cycle in pooled athletics data dating from 1896 to 2008. We investigated whether Olympic cycle periodicity was present in modern era long and triple jumping in elite men and women. Top 50 performances per year in the horizontal jumps in men and women from 1996 to 2019 were used. Each performance was normalized to the best result from the previous Olympic year. Two-way ANOVAs revealed significantly lower mean normalized performances in top ten women compared to top ten men (p < 0.001) in both jumps. In both jumps, ten top-performing women also showed decreases between the Olympic year mean normalized performances and the 1st year following (Long Jump: p = 0.022, Triple Jump: p = 0.008). In triple jump, the decrease in performance was also found in the second year following the Olympics. Performances deciles ranked from 11th to 50th place showed a similar pattern in women's triple jump but only for ranks 11 to 20 in the women's long jump. The findings suggest that periodicity driven by the Olympic cycle exists in women's long and triple jump at the elite level. [ABSTRACT FROM AUTHOR]

There is increasing evidence that science & engineering PhD students lose interest in an academic career over the course of graduate training. It is not clear, however, whether this decline reflects students being discouraged from pursuing an academic career by the challenges of obtaining a faculty job or whether it reflects more fundamental changes in students' career goals for reasons other than the academic labor market. We examine this question using a longitudinal survey that follows a cohort of PhD students from 39 U.S. research universities over the course of graduate training to document changes in career preferences and to explore potential drivers of such changes. We report two main results. First, although the vast majority of students start the PhD interested in an academic research career, over time 55% of all students remain interested while 25% lose interest entirely. In addition, 15% of all students were never interested in an academic career during their PhD program, while 5% become more interested. Thus, the declining interest in an academic career is not a general phenomenon across all PhD students, but rather reflects a divergence between those students who remain highly interested in an academic career and other students who are no longer interested in one. Second, we show that the decline we observe is not driven by expectations of academic job availability, nor by related factors such as postdoctoral requirements or the availability of research funding. Instead, the decline appears partly due to the misalignment between students' changing preferences for specific job attributes on the one hand, and the nature of the academic research career itself on the other. Changes in students' perceptions of their own research ability also play a role, while publications do not. We discuss implications for scientific labor markets, PhD career development programs, and science policy.

This paper investigates how the encouragement of entrepreneurship within university research labs relates with research activities, research outputs, and early doctorate careers. Utilizing a panel survey of 6,840 science & engineering doctoral students at 39 R1 research universities, this study shows that entrepreneurship is widely encouraged across university research labs, ranging from 54% in biomedical engineering to 18% in particle physics, while only a small share of labs openly discourage entrepreneurship, from approximately 3% in engineering to approximately 12% in the life sciences. Within fields, there is no difference between labs that encourage entrepreneurship and those that do not with respect to basic research activity and the number of publications. At the same time, labs that encourage entrepreneurship are significantly more likely to report invention disclosures, particularly in engineering where such labs are 41% more likely to disclose inventions. With respect to career pathways, PhDs students in labs that encourage entrepreneurship do not differ from other PhDs in their interest in academic careers, but they are 87% more likely to be interested in careers in entrepreneurship and 44% more likely to work in a startup after graduation. These results persist even when accounting for individuals' pre-PhD interest in entrepreneurship and the encouragement of other non-academic industry careers.

[This corrects the article DOI: 10.1371/journal.pone.0123282.].

[This corrects the article DOI: 10.1371/journal.pone.0089754.].

To present en face optical coherence tomography (OCT) images generated by graph-search theory algorithm-based custom software and examine correlation with other imaging modalities.En face OCT images derived from high density OCT volumetric scans of 3 healthy subjects and 4 patients using a custom algorithm (graph-search theory) and commercial software (Heidelberg Eye Explorer software (Heidelberg Engineering)) were compared and correlated with near infrared reflectance, fundus autofluorescence, adaptive optics flood-illumination ophthalmoscopy (AO-FIO) and microperimetry.Commercial software was unable to generate accurate en face OCT images in eyes with retinal pigment epithelium (RPE) pathology due to segmentation error at the level of Bruch's membrane (BM). Accurate segmentation of the basal RPE and BM was achieved using custom software. The en face OCT images from eyes with isolated interdigitation or ellipsoid zone pathology were of similar quality between custom software and Heidelberg Eye Explorer software in the absence of any other significant outer retinal pathology. En face OCT images demonstrated angioid streaks, lesions of acute macular neuroretinopathy, hydroxychloroquine toxicity and Bietti crystalline deposits that correlated with other imaging modalities.Graph-search theory algorithm helps to overcome the limitations of outer retinal segmentation inaccuracies in commercial software. En face OCT images can provide detailed topography of the reflectivity within a specific layer of the retina which correlates with other forms of fundus imaging. Our results highlight the need for standardization of image reflectivity to facilitate quantification of en face OCT images and longitudinal analysis.

Schizophrenia patients exhibit well-documented visual processing deficits. One area of disruption is visual integration, the ability to form global objects from local elements. However, most studies of visual integration in schizophrenia have been conducted in the context of an active attention task, which may influence the findings. In this study we examined visual integration using electroencephalography (EEG) in a passive task to elucidate neural mechanisms associated with poor visual integration. Forty-six schizophrenia patients and 30 healthy controls had EEG recorded while passively viewing figures comprised of real, illusory, or no contours. We examined visual P100, N100, and P200 event-related potential (ERP) components, as well as neural synchronization in the gamma (30-60 Hz) band assessed by the EEG phase locking factor (PLF). The N100 was significantly larger to illusory vs. no contour, and illusory vs. real contour stimuli while the P200 was larger only to real vs. illusory stimuli; there were no significant interactions with group. Compared to controls, patients failed to show increased phase locking to illusory versus no contours between 40-60 Hz. Also, controls, but not patients, had larger PLF between 30-40 Hz when viewing real vs. illusory contours. Finally, the positive symptom factor of the BPRS was negatively correlated with PLF values between 40-60 Hz to illusory stimuli, and with PLF between 30-40 Hz to real contour stimuli. These results suggest that the pattern of results across visual processing conditions is similar in patients and controls. However, patients have deficits in neural synchronization in the gamma range during basic processing of illusory contours when attentional demand is limited.

The KCa3.1 K+ channel has been proposed as a novel target for pulmonary diseases such as asthma and pulmonary fibrosis. It is expressed in epithelia but its expression and function in primary human bronchial epithelial cells (HBECs) has not been described. Due to its proposed roles in the regulation of cell proliferation, migration, and epithelial fluid secretion, inhibiting this channel might have either beneficial or adverse effects on HBEC function. The aim of this study was to assess whether primary HBECs express the KCa3.1 channel and its role in HBEC function. Primary HBECs from the airways of healthy and asthmatic subjects, SV-transformed BEAS-2B cells and the neoplastic H292 epithelial cell line were studied. Primary HBECs, BEAS-2B and H292 cells expressed KCa3.1 mRNA and protein, and robust KCa3.1 ion currents. KCa3.1 protein expression was increased in asthmatic compared to healthy airway epithelium in situ, and KCa3.1 currents were larger in asthmatic compared to healthy HBECs cultured in vitro. Selective KCa3.1 blockers (TRAM-34, ICA-17043) had no effect on epithelial cell proliferation, wound closure, ciliary beat frequency, or mucus secretion. However, several features of TGFβ1-dependent epithelial-mesenchymal transition (EMT) were inhibited by KCa3.1 blockade. Treatment with KCa3.1 blockers is likely to be safe with respect to airway epithelial biology, and may potentially inhibit airway remodelling through the inhibition of EMT.

Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clusteredin exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K(26%) and 11 had G947R (8%) mutations [corrected].Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

Interferons (IFNs) have been shown to inhibit influenza A virus (IAV) replication and play an essential role in controlling viral infection. Here we studied the kinetics and magnitude of induction of type I and type III IFN transcripts by primary porcine airway epithelial cells (pAECs) in response to swine and human origin IAV. We observed that swine influenza viruses (SIV) replicate more efficiently than the human pandemic influenza A/California/2009 (pH1N1 CA/09) in pAECs. Interestingly, we also found significant difference in kinetics of IFN-β, IFN-λ1 and IFN-λ3 gene expression by these viruses. While there was delay of up to 12 hours post infection (h p.i.) in induction of IFN genes in pAECs infected with swine IAV A/Sw/Illinois/2008 (H1N1 IL/08), human pH1N1 CA/09 rapidly induced IFN-β, IFN-λ1 and IFN-λ3 gene expression as early as 4 h p.i. However, the magnitude of IFN-β and IFN-λ3 induction at 24 h p.i. was not significantly different between the viral strains tested. Additionally, we found that swine H1N1 IL/08 was less sensitive to dsRNA induced antiviral response compared to human pH1N1 CA/09. Our data suggest that the human and swine IAVs differ in their ability to induce and respond to type I and type III interferons in swine cells. Swine origin IAV may have adapted to the pig host by subverting innate antiviral responses to viral infection.

Pig hepatocytes are an important investigational tool for optimizing hepatocyte transplantation schemes in both allogeneic and xenogeneic transplant scenarios. MRI can be used to serially monitor the transplanted cells, but only if the hepatocytes can be labeled with a magnetic particle. In this work, we describe culture conditions for magnetic cell labeling of cells from two different pig hepatocyte cell sources; primary pig hepatocytes (ppHEP) and stem cell-derived hepatocytes (PICM-19FF). The magnetic particle is a micron-sized iron oxide particle (MPIO) that has been extensively studied for magnetic cell labeling for MRI-based cell tracking. ppHEP could endocytose MPIO with labeling percentages as high as 70%, achieving iron content as high as ~55 pg/cell, with >75% viability. PICM-19FF had labeling >97%, achieving iron content ~38 pg/cell, with viability >99%. Extensive morphological and functional assays indicated that magnetic cell labeling was benign to the cells. The results encourage the use of MRI-based cell tracking for the development and clinical use of hepatocyte transplantation methodologies. Further, these results generally highlight the importance of functional cell assays in the evaluation of contrast agent biocompatibility.

Supercentenarians (110 years or older) are the world's oldest people. Seventy four are alive worldwide, with twenty two in the United States. We performed whole-genome sequencing on 17 supercentenarians to explore the genetic basis underlying extreme human longevity. We found no significant evidence of enrichment for a single rare protein-altering variant or for a gene harboring different rare protein altering variants in supercentenarian compared to control genomes. We followed up on the gene most enriched for rare protein-altering variants in our cohort of supercentenarians, TSHZ3, by sequencing it in a second cohort of 99 long-lived individuals but did not find a significant enrichment. The genome of one supercentenarian had a pathogenic mutation in DSC2, known to predispose to arrhythmogenic right ventricular cardiomyopathy, which is recommended to be reported to this individual as an incidental finding according to a recent position statement by the American College of Medical Genetics and Genomics. Even with this pathogenic mutation, the proband lived to over 110 years. The entire list of rare protein-altering variants and DNA sequence of all 17 supercentenarian genomes is available as a resource to assist the discovery of the genetic basis of extreme longevity in future studies.

Bladder radiotherapy is a management option for carefully selected patients with muscle-invasive bladder cancer. However, the inability to visualize the tumor site during treatment and normal bladder movement limits targeting accuracy and increases collateral radiation. A means to accurately and reliably target the bladder during radiotherapy is needed.Eighteen consecutive patients with muscle-invasive bladder cancer (T1-T4) elected bladder-preserving treatment with maximal transurethral resection (TUR), radiation and concurrent chemotherapy. All underwent endoscopic placement of 24-K gold fiducial markers modified with micro-tines (70 [2.9×0.9 mm.]; 19 [2.1×0.7 mm.) into healthy submucosa 5-10 mm. from the resection margin, using custom-made coaxial needles. Marker migration was assessed for with intra-op bladder-filling cystogram and measurement of distance between markers. Set-up error and marker retention through completion of radiotherapy was confirmed by on-table portal imaging.Between 1/2007 and 7/2012, a total of 89 markers (3-5 per tumor site) were placed into 18 patients of mean age 73.6 years. Two patients elected cystectomy before starting treatment; 16/18 completed chemo-radiotherapy. All (100%) markers were visible with all on-table (portal, cone-beam CT), fluoroscopy, plain-film, and CT-scan imaging. In two patients, 1 of 4 markers placed at the tumor site fell-out (voided) during the second half of radiotherapy. All other markers (80/82, 98%) were present through the end of radio-therapy. No intraoperative (e.g. uncontrolled bleeding, collateral injury) or post-operative complications (e.g. stone formation, urinary tract infection, post-TUR hematuria >48 hours) occurred. Use of micro-tined fiducial tumor-site markers afforded a 2 to 6-fold reduction in bladder-area targeted with high-dose radiation.Placement of the micro-tined fiducial markers into the bladder was feasible and associated with excellent retention-rate and no complications. All markers were well-visualized during radiotherapy with all imaging modalities. Bladder fiducial markers improve targeting accuracy, and may increase treatment efficacy and reduce morbidity from collateral radiation.

An understanding of human responses to hypoxia is important for the health of millions of people worldwide who visit, live, or work in the hypoxic environment encountered at high altitudes. In spite of dozens of studies over the last 100 years, the basic mechanisms controlling acclimatization to hypoxia remain largely unknown. The AltitudeOmics project aimed to bridge this gap. Our goals were 1) to describe a phenotype for successful acclimatization and assess its retention and 2) use these findings as a foundation for companion mechanistic studies. Our approach was to characterize acclimatization by measuring changes in arterial oxygenation and hemoglobin concentration [Hb], acute mountain sickness (AMS), cognitive function, and exercise performance in 21 subjects as they acclimatized to 5260 m over 16 days. We then focused on the retention of acclimatization by having subjects reascend to 5260 m after either 7 (n = 14) or 21 (n = 7) days at 1525 m. At 16 days at 5260 m we observed: 1) increases in arterial oxygenation and [Hb] (compared to acute hypoxia: PaO2 rose 9±4 mmHg to 45±4 while PaCO2 dropped a further 6±3 mmHg to 21±3, and [Hb] rose 1.8±0.7 g/dL to 16±2 g/dL; 2) no AMS; 3) improved cognitive function; and 4) improved exercise performance by 8±8% (all changes p

It is classically thought that increases in hemoglobin mass (Hbmass) take several weeks to develop upon ascent to high altitude and are lost gradually following descent. However, the early time course of these erythropoietic adaptations has not been thoroughly investigated and data are lacking at elevations greater than 5000 m, where the hypoxic stimulus is dramatically increased. As part of the AltitudeOmics project, we examined Hbmass in healthy men and women at sea level (SL) and 5260 m following 1, 7, and 16 days of high altitude exposure (ALT1/ALT7/ALT16). Subjects were also studied upon return to 5260 m following descent to 1525 m for either 7 or 21 days. Compared to SL, absolute Hbmass was not different at ALT1 but increased by 3.7 ± 5.8% (mean ± SD; n = 20; p

Computing the genetic relationship between two humans is important to studies in genetics, genomics, genealogy, and forensics. Relationship algorithms may be sensitive to noise, such as that arising from sequencing errors or imperfect reference genomes. We developed an algorithm for estimation of genetic relationship by averaged blocks (GRAB) that is designed for whole-genome sequencing (WGS) data. GRAB segments the genome into blocks, calculates the fraction of blocks sharing identity, and then uses a classification tree to infer 1st- to 5th- degree relationships and unrelated individuals. We evaluated GRAB on simulated and real sequenced families, and compared it with other software. GRAB achieves similar performance, and does not require knowledge of population background or phasing. GRAB can be used in workflows for identifying unreported relationships, validating reported relationships in family-based studies, and detection of sample-tracking errors or duplicate inclusion. The software is available at familygenomics.systemsbiology.net/grab.

Idiopathic pulmonary fibrosis (IPF) is a common, progressive and invariably lethal interstitial lung disease with no effective therapy. We hypothesised that K(Ca)3.1 K(+) channel-dependent cell processes contribute to IPF pathophysiology.K(Ca)3.1 expression in primary human lung myofibroblasts was examined using RT-PCR, western blot, immunofluorescence and patch-clamp electrophysiology. The role of K(Ca)3.1 channels in myofibroblast proliferation, wound healing, collagen secretion and contraction was examined using two specific and distinct K(Ca)3.1 blockers (TRAM-34 and ICA-17043 [Senicapoc]).Both healthy non fibrotic control and IPF-derived human lung myofibroblasts expressed K(Ca)3.1 channel mRNA and protein. K(Ca)3.1 ion currents were elicited more frequently and were larger in IPF-derived myofibroblasts compared to controls. K(Ca)3.1 currents were increased in myofibroblasts by TGFβ1 and basic FGF. K(Ca)3.1 was expressed strongly in IPF tissue. K(Ca)3.1 pharmacological blockade attenuated human myofibroblast proliferation, wound healing, collagen secretion and contractility in vitro, and this was associated with inhibition of TGFβ1-dependent increases in intracellular free Ca(2+).K(Ca)3.1 activity promotes pro-fibrotic human lung myofibroblast function. Blocking K(Ca)3.1 may offer a novel approach to treating IPF with the potential for rapid translation to the clinic.

Persistent immune activation and microbial translocation associated with HIV infection likely place HIV-infected aging women at high risk of developing chronic age-related diseases. We investigated immune activation and microbial translocation in HIV-infected aging women in the post-menopausal ages.Twenty-seven post-menopausal women with HIV infection receiving antiretroviral treatment with documented viral suppression and 15 HIV-negative age-matched controls were enrolled. Levels of immune activation markers (T cell immune phenotype, sCD25, sCD14, sCD163), microbial translocation (LPS) and biomarkers of cardiovascular disease and impaired cognitive function (sVCAM-1, sICAM-1 and CXCL10) were evaluated.T cell activation and exhaustion, monocyte/macrophage activation, and microbial translocation were significantly higher in HIV-infected women when compared to uninfected controls. Microbial translocation correlated with T cell and monocyte/macrophage activation. Biomarkers of cardiovascular disease and impaired cognition were elevated in women with HIV infection and correlated with immune activation.HIV-infected antiretroviral-treated aging women who achieved viral suppression are in a generalized status of immune activation and therefore are at an increased risk of age-associated end-organ diseases compared to uninfected age-matched controls.

Epigenetic modifications are heritable changes in gene expression without changes in DNA sequence. DNA methylation has been implicated in the control of several cellular processes including differentiation, gene regulation, development, genomic imprinting and X-chromosome inactivation. Methylated cytosine residues at CpG dinucleotides are commonly associated with gene repression; conversely, strategic loss of methylation during development could lead to activation of lineage-specific genes. Evidence is emerging that bone development and growth are programmed; although, interestingly, bone is constantly remodelled throughout life. Using human embryonic stem cells, human fetal bone cells (HFBCs), adult chondrocytes and STRO-1(+) marrow stromal cells from human bone marrow, we have examined a spectrum of developmental stages of femur development and the role of DNA methylation therein. Using pyrosequencing methodology we analysed the status of methylation of genes implicated in bone biology; furthermore, we correlated these methylation levels with gene expression levels using qRT-PCR and protein distribution during fetal development evaluated using immunohistochemistry. We found that during fetal femur development DNA methylation inversely correlates with expression of genes including iNOS (NOS2) and COL9A1, but not catabolic genes including MMP13 and IL1B. Furthermore, significant demethylation was evident in the osteocalcin promoter between the fetal and adult developmental stages. Increased TET1 expression and decreased expression of DNA (cytosine-5-)-methyltransferase 1 (DNMT1) in adult chondrocytes compared to HFBCs could contribute to the loss of methylation observed during fetal development. HFBC multipotency confirms these cells to be an ideal developmental system for investigation of DNA methylation regulation. In conclusion, these findings demonstrate the role of epigenetic regulation, specifically DNA methylation, in bone development, informing and opening new possibilities in development of strategies for bone repair/tissue engineering.

Pocillopora damicornis (Linnaeus, 1758; Scleractinia, Pocilloporidae) has recently been found to comprise at least five distinct genetic lineages in Eastern Australia, some of which likely represent cryptic species. Due to similar and plastic gross morphology of these lineages, field identification is often difficult. Here we present a quick, cost effective genetic assay as well as three novel microsatellite markers that distinguish the two most common lineages found on the Great Barrier Reef. The assay is based on PCR amplification of two regions within the mitochondrial putative control region, which show consistent and easily identifiable fragment size differences for the two genetic lineages after Alu1 restriction enzyme digestion of the amplicons.