bluuebunny/crossref_metadata_2025 huggingface dataset:
Stretching the boundaries
Authors: Pilus Zahariah , Zakaria Nur Shahida , Zakaria Muhamad Khairul , Wahid Ridwan
Published: August 2019

Nowadays, international communication using English as the medium is a common occurrence. To communicate
effectively, English as a second language (ESL) speakers need to possess relevant communicative skills including understanding and
being familiar with inner circle accents. This paper seeks to find out ESL learners’ evaluative reactions to four inner circle
accents, representing British, American, Australian and New Zealand English varieties, through an accent perception and a survey
task conducted on Malaysian undergraduates at a public university in Malaysia. The participants responded to descriptors on
speaker attributes categorized into three dimensions: competence, social appeal and accent
preference while or after listening to a recorded passage read in one of the four accents by male and female
speakers. The learners showed a tendency to prefer certain accents more than others. In general, the best rated accent was the
British accent for the male speakers and the American accent for the female speakers. The New Zealand accent was rated the lowest
among the male speakers and one of the lowest among the female speakers. The study also found that speaker’s competence, speaker’s
social appeal and accent preference were positively correlated. These findings highlight the importance of listening practices and
exposure to various English accents in ESL classrooms to prepare students for international and intercultural communication.
Second order structure functions for higher powers of turbulent velocity
Authors: Paraz F , Bandi M M
Published: August 2019

We experimentally study the temporal second-order structure functions for integer powers of turbulent fluid velocity fluctuations

, in three dimensional (3D) and two dimensional (2D) turbulence. Here

is a composite time-series constructed by averaging the concurrent time-series (

) sampled at N spatially distributed Eulerian points. The N  =  1 case has been extensively studied for velocity fluctuations (m  =  1) and to a lesser extent for m  >  1. The averaging method in case of N  >  1 diverges from the Kolmogorov framework and has not been studied because fluctuations in

are expected to smooth with increasing N leaving behind uninteresting large-scale mean flow information, but we find this is not so. We report the evolution of scaling exponents

for

in going from a single (N  =  1) to a spatial average over several Eulerian points (

). Our 3D experiments in a tank with rotating jets at the floor show

for all m-values in agreement with prior results and evolves to an asymptotic value of

. The evolution of

follows the functional form

, where

points is the only fit parameter representing the convergence rate constant. Results for the 2D experiments conducted in a gravity assisted soap film in the enstrophy cascade regime are in sharp contrast with their 3D counterparts. Firstly

varies polynomially with m and asymptotes to a constant value at m  =  5. Secondly, the evolution of

is logarithmic

, where A and B are fit parameters and eventually deviates at large N and asymptotes to

for all m. The starkly different convergence forms (exponential in 3D versus logarithmic in 2D) may be interpreted as a signature of inter-scale couplings in the respective turbulent flows by decomposing the two-point correlator for

into a self-correlation and cross-correlation term. In addition to aiding in the theoretical development, the results may also have implications for determination of resolution in 2D turbulence experiments and simulations, wind energy and atmospheric boundary layer turbulence.
Supervisor support is key to PhD satisfaction
Authors: Allen Michael
Published: August 2019

Doctoral students are most satisfied in their work when they have a supportive supervisor. That is according to a study of the responses of more than 400 PhD students about how satisfied they were during their studies.
The new race to the Moon
Authors: Dacey James
Published: August 2019

A string of upcoming lunar missions will yield many scientific breakthroughs, as James Dacey discovers
Einstein in Nottingham
Authors: Marshall Rick
Published: August 2019

In response to Andrew Robinson’s feature “Einstein in Oxford” (June pp32–36), which looked at Albert Einstein’s three visits to the city in 1931–1933.
The wood that could cool buildings
Authors: Dumé Belle
Published: August 2019

Everyone loves living at the right temperature, but cooling a building is generally more difficult than heating it.
Polar bears inspire insulating aerogel
Authors: Dumé Belle
Published: August 2019

Polar bears can survive the freezing temperatures of the Arctic Circle in part because of their characteristic white fur.
Quark pioneer Murray Gell-Mann dies
Authors: Banks Michael
Published: August 2019

The US theoretical physicist made a number of breakthroughs in particle physics, including predicting the existence of quarks, as Michael Banks reports
Phenotypic and genetic characterization ofPseudomonas aeruginosaisolate COP2 from the lungs of COPD patients in China
Authors: Zhao Kelei , Yuan Yang , Li Jing , Pan Wenjuan , Yan Chaochao , Fu Huiyao , Lin Jiafu , Yue Bisong , Wang Xinrong , Gou Xiaojun , Chu Yiwen , Zhou Yingshun
Published: August 2019

Pseudomonas aeruginosa is an important opportunistic pathogen normally associated with increasing morbidity and mortality of immunocompromised hosts with respiratory infections. The phenotypic and genetic features of P. aeruginosa from patients with chronic obstructive pulmonary disease (COPD) remain poorly understood. By using the sputum samples of 25 hospitalized COPD patients from the affiliated hospital of Southwest Medical University (China), we identified a P. aeruginosa isolate, COP2, which showed multiple antibiotic resistance and enhanced Pseudomonas quinolone signal (PQS) production but decreased motility, biofilm formation and virulence compared with the model strain PAO1. Importantly, COP2 harbored a substantial amount of mutations that might influence the functions of 1771 genes in the genome and the evolutionary status of this isolate was clearly distinct from the PAO1 lineage. Accordingly, COP2 had a discrepant transcriptional pattern relating to flagellar assembly, antibiotic resistance, biofilm and PQS production, and can increase the capacities of compound degradation in response to resource/space stresses. Therefore, the identification of COP2 in this study provides preliminary information regarding the genetic features and survival strategy of P. aeruginosa in colonizing COPD lungs and lays the foundations for further understanding of the pathogenic mechanisms of pseudomonal infections.
Internet search query data improve forecasts of daily emergency department volume
Authors: Tideman Sam , Santillana Mauricio , Bickel Jonathan , Reis Ben
Published: August 2019

Objective

Emergency departments (EDs) are increasingly overcrowded. Forecasting patient visit volume is challenging. Reliable and accurate forecasting strategies may help improve resource allocation and mitigate the effects of overcrowding. Patterns related to weather, day of the week, season, and holidays have been previously used to forecast ED visits. Internet search activity has proven useful for predicting disease trends and offers a new opportunity to improve ED visit forecasting. This study tests whether Google search data and relevant statistical methods can improve the accuracy of ED volume forecasting compared with traditional data sources.

Materials and Methods

Seven years of historical daily ED arrivals were collected from Boston Children’s Hospital. We used data from the public school calendar, National Oceanic and Atmospheric Administration, and Google Trends. Multiple linear models using LASSO (least absolute shrinkage and selection operator) for variable selection were created. The models were trained on 5 years of data and out-of-sample accuracy was judged using multiple error metrics on the final 2 years.

Results

All data sources added complementary predictive power. Our baseline day-of-the-week model recorded average percent errors of 10.99%. Autoregressive terms, calendar and weather data reduced errors to 7.71%. Search volume data reduced errors to 7.58% theoretically preventing 4 improperly staffed days.

Discussion

The predictive power provided by the search volume data may stem from the ability to capture population-level interaction with events, such as winter storms and infectious diseases, that traditional data sources alone miss.

Conclusions

This study demonstrates that search volume data can meaningfully improve forecasting of ED visit volume and could help improve quality and reduce cost.
Prophylactic Probiotics in Burn Patients: Risk versus Reward
Authors: Fleming Derek , Jiang Yuli , Opoku Kwaku , Alhaj Saleh Adel , Larumbe-Zabala Eneko , Kesey Jennifer E , Griswold John A , Dissanaike Sharmila
Published: August 2019

Probiotics are often used in critically ill patients to prevent antibiotic-associated complications, including Clostridium difficile colitis. However, clinical evidence of their efficacy is lacking. The objective of this study is to assess the impact of prophylactic probiotic administration on bowel function, gut microbial diversity, and nutritional markers in adult burn patients. A retrospective cohort study was done on 108 burn patients aged 18 to 89. Patients were given >1 million colony-forming units per day of Lactobacillus acidophilus and Lactobacillus rhamnosus. Testing for C. difficile was used as a surrogate marker for the presence of diarrhea. Serum C-reactive protein and prealbumin values were measured. Additionally, the gut microbial diversity of eight patients was tracked via 16S quantitative PCR before and throughout the course of a standard probiotic regimen. Patients receiving oral probiotics had more reported diarrhea in the first and second weeks of treatment. In the second week, C-reactive protein levels were increased, while serum prealbumin levels were lower in patients receiving probiotics, suggesting potential malabsorption. Additionally, there was no difference in C. difficile infection, sepsis rates, emesis, or gastric residuals, indicating an absence of therapeutic benefit for probiotic administration in burn patients. Furthermore, it was determined that no discernible benefit to gut microbial diversity was conferred by probiotic therapy. Prophylactic probiotics in burn patients are not associated with improvements in patient outcomes and may in fact be associated with an increased incidence of diarrhea and malabsorption. Additional research is needed before routine use in burn patients.
Chronic Systemic Symptoms in Head and Neck Cancer Patients
Authors: Murphy Barbara A , Wulff-Burchfield Elizabeth , Ghiam Michael , Bond Stewart M , Deng Jie
Published: August 2019

The systemic effects and manifestations of disease and treatment have been of interest for millennium. Until recently, basic and clinical research is just now reaching a watershed. Systemic symptoms usually do not occur in isolation but rather in clusters; however, much of the cutting-edge research pertaining to the etiology, mechanism, manifestations, and moderators of systemic symptoms in humans has been directed at individual symptoms, thus creating silos of knowledge. Breaching these silos and bridging the knowledge from disparate arenas of investigation to build a comprehensive depiction of acute and chronic systemic symptoms has been a challenge. In addition, much of the recent work in systemic symptoms has been conducted in the setting of nonmalignant disease. The degree to which the findings from other chronic disease processes can be translated into the oncologic realm is unknown. This article will explore inflammation as a major contributing factor to systemic symptoms and sickness behavior, discuss the most common manifestations in cancer survivors, and, where available, discuss specific data pertaining to head and neck cancer survivors.
Conversation with Chen-Ning Yang: reminiscence and reflection
Authors: Poo Mu-ming , Chao Alexander Wu
Published: August 2019

Chen-Ning Yang ( ) is the most distinguished Chinese theoretical physicist. In 1954, together with Robert Mills, he formulated the Yang–Mills Gauge Theory, which led to the development of the Standard Model, the leading framework for understanding particle physics. In 1956, Yang and Tsung-Dao Lee ( ) proposed the possibility of parity non-conservation in weak interaction, which won them the Nobel Prize in Physics in 1957. Besides these two major achievements, Yang made many other seminal contributions to particle physics, statistical physics and condensed matter physics.

At the end of 2003, Yang returned to China from the US and established the Institute for Advanced Study at Tsinghua University in Beijing. NSR’s Executive Editor-in-Chief Mu-ming Poo ( ), a neurobiologist, and Alexander Wu Chao ( ), an accelerator physicist at Stanford University, talked with Professor Yang on a variety of topics, ranging from his retrospective view on Yang–Mills theory, on his contemporary physicists, on tastes in scientific research, and on the current and future developments of Chinese science. The following is an excerpt from this conversation that took place on 21 March 2019 at Tsinghua University, Beijing.
Tough Love: The Effects of Debt Contract Design on Firms’ Performance
Authors: Spyridopoulos Ioannis
Published: August 2019

I investigate whether restrictive loan covenants disrupt or improve firms’ operating performance. Using an instrumental variables approach to address the endogenous relationship between covenant strictness and firms’ efficiency, I find that stricter loan covenants lead to an increase in profitability and firm value even when firms do not violate a covenant. Stricter covenants improve performance only in firms with managerial agency conflicts: those without large shareholder ownership, facing softer competition in their product market, or with weaker shareholder rights. The evidence suggests that by designing stringent contracts ex ante, creditors create positive externalities in poorly governed firms through managerial incentives.

Received December 7, 2018; editorial decision May 31, 2019 by Editor Uday Rajan. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Evening intake of alcohol, caffeine, and nicotine: night-to-night associations with sleep duration and continuity among African Americans in the Jackson Heart Sleep Study
Authors: Spadola Christine E , Guo Na , Johnson Dayna A , Sofer Tamar , Bertisch Suzanne M , Jackson Chandra L , Rueschman Michael , Mittleman Murray A , Wilson James G , Redline Susan
Published: August 2019

Study Objectives

We examined the night-to-night associations of evening use of alcohol, caffeine, and nicotine with actigraphically estimated sleep duration, sleep efficiency, and wake after sleep onset (WASO) among a large cohort of African American adults.

Methods

Participants in the Jackson Heart Sleep Study underwent wrist actigraphy for an average of 6.7 nights and completed concurrent daily sleep diary assessments to record any consumption of alcohol, caffeine, and nicotine within 4 hours of bedtime. Linear mixed-effect models were fit and adjusted for age, sex, educational attainment, body mass index, depression, anxiety, stress, and having work/school the next day.

Results

Eligible participants (n = 785) were an average of 63.7 years (SD: 10.6), and were predominantly female (67.9%). There were 5164 days of concurrent actigraphy and sleep diary data. Evening alcohol use was associated with that night’s lower sleep efficiency (−0.98% [95% CI: −1.67% to −0.29%], p = 0.005), but not with WASO or sleep duration. Evening nicotine use was associated with that night’s lower sleep efficiency [1.74% (95% CI: −2.79 to −0.68), p = 0.001] and 6.09 minutes higher WASO ([95% CI: 0.82 to 11.35], p = 0.02), but was not associated with sleep duration. Evening caffeine use was not associated with any of the sleep parameters.

Conclusion

Nicotine and alcohol use within 4 hours of bedtime were associated with increased sleep fragmentation in the associated night, even after controlling for multiple potential confounders. These findings support the importance of sleep health recommendations that promote the restriction of evening alcohol and nicotine use to improve sleep continuity.
The impact of mobile applications on medication adherence: a systematic review
Authors: Ng Ricki , Carter Stephen R , El-Den Sarira
Published: August 2019

In 2008, Apple and Android launched their Application or “App” stores. Since then, there has been a growing interest in using mobile apps for improving medication adherence. However, research on the efficacy of apps, in terms of improved medication adherence and clinical outcome and/or patient-related outcome measures (PROMs) is scarce. The objective of this research was to systematically review the impact of apps on consumers’ medication adherence and to determine the effect on clinical outcome and/or PROM(s). A systematic literature search was conducted to identify publications aimed at improving medication adherence published from January 2008 to April 2018. All studies were assessed for risk of bias using either the Risk Of Bias In Non-randomized Studies-of Interventions or the revised tool for Risk of Bias in randomized trials tool, depending on study design. Eleven randomized controlled trials (RCTs) and 10 non-RCTs were included. All 11 RCTs showed improvements in adherence; however, only seven reported statistically significant improvements in at least one adherence measure. Nine RCTs also demonstrated improvements in clinical outcome/PROM(s), of which five were statistically significant, whereas two RCTs did not report on clinical outcome/PROM(s). Only two studies using non-RCT study designs showed statistically significant improvements in all measures of adherence and clinical outcome/PROM(s). The risk of bias was moderate or serious for all included studies. Even though the use of an app may improve adherence, it is difficult to draw conclusions regarding the impact of apps on medication adherence due to the high degree of heterogeneity across studies, from the methodological design to the features of the app and the measure of adherence.
Comparing the McGrath Mac Video Laryngoscope and Direct Laryngoscopy for Prehospital Emergency Intubation in Air Rescue Patients: A Multicenter, Randomized, Controlled Trial*
Authors: Kreutziger Janett , Hornung Sonja , Harrer Clemens , Urschl Wilhelm , Doppler Reinhard , Voelckel Wolfgang G. , Trimmel Helmut
Published: August 2019

Objectives:

Tracheal intubation in prehospital emergency care is challenging. The McGrath Mac Video Laryngoscope (Medtronic, Minneapolis, MN) has been proven to be a reliable alternative for in-hospital airway management. This trial compared the McGrath Mac Video Laryngoscope and direct laryngoscopy for the prehospital setting.

Design:

Multicenter, prospective, randomized, controlled equivalence trial.

Setting:

Oesterreichischer Automobil- und Touring Club (OEAMTC) Helicopter Emergency Medical Service in Austria, 18-month study period.

Patients:

Five-hundred fourteen adult emergency patients (≥ 18 yr old).

Interventions:

Helicopter Emergency Medical Service physicians followed the institutional algorithm, comprising a maximum of two tracheal intubation attempts with each device, followed by supraglottic, then surgical airway access in case of tracheal intubation failure. No restrictions were given for tracheal intubation indication.

Measurements Main Results:

The Primary outcome was the rate of successful tracheal intubation; equivalence range was ± 6.5% of success rates. Secondary outcomes were the number of attempts to successful tracheal intubation, time to glottis passage and first end-tidal Co
2 measurement, degree of glottis visualization, and number of problems. The success rate for the two devices was equivalent: direct laryngoscopy 98.5% (254/258), McGrath Mac Video Laryngoscope 98.1% (251/256) (difference, 0.4%; 99% CI, –2.58 to 3.39). There was no statistically significant difference with regard to tracheal intubation times, number of attempts or difficulty. The view to the glottis was significantly better, but the number of technical problems was increased with the McGrath Mac Video Laryngoscope. After a failed first tracheal intubation attempt, immediate switching of the device was significantly more successful than after the second attempt (90.5% vs 57.1%; p = 0.0003), regardless of the method.

Conclusions:

Both devices are equivalently well suited for use in prehospital emergency tracheal intubation of adult patients. Switching the device following a failed first tracheal intubation attempt was more successful than a second attempt with the same device.
The “Cough Trick” Reduces Pain During Removal of Closed-suction Drains after Total Knee Arthroplasty: A Randomized Trial
Authors: Yuenyongviwat Varah , Iamthanaporn Khanin , Tuntarattanapong Pakjai , Hongnaparak Theerawit
Published: August 2019

Background

Drain removal after TKA can be painful. Prior research suggests that the “cough trick,” in which a patient coughs at the same time she or he receives an injection, effectively decreases pain. To our knowledge, this intervention has not been evaluated as a way to reduce pain during other brief but painful interventions, such as removal of closed-suction drains after orthopaedic surgery.

Question/purpose

Does the cough trick reduce pain while a surgeon is removing a closed-suction drain after TKA?

Methods

Fifty-six patients with primary osteoarthritis who underwent primary TKA were randomized into two groups: drain removal as the patient coughed (n = 28 patients; three men, 25 women) or drain removal using the usual process, without the cough trick (n = 28 patients; three men, 25 women). The study groups were not different in terms of gender, BMI, surgical time, or other baseline variables, and other than the addition of the cough trick, there were no differences in surgical treatment or other elements of aftercare. Likewise, at baseline, the verbal numeric rating scale (VNRS) score for pain before the drain was removed was not different between the groups (3.1 ± 1.7 versus 3.3 ± 1.3; p = 0.72). The level of pain before and during drain removal was recorded using a VNRS by an orthopaedic surgeon who was not involved in the care of the study patients. We considered the minimum clinically important difference on the 10-point scale to be 2 points, based on prior evidence.

Results

The mean ± SD VNRS for the pain level during drain removal was lower in the cough trick group than that in the control group (1.6 ± 1.0 versus 3.7 ± 1.9, mean difference 2.1; 95% CI, 1.3-2.9; p < 0.001).

Conclusions

The cough trick during removal of a closed-suction drain tube in patients undergoing TKA reduced the level of pain in this small randomized trial. We suggest that surgeons consider this technique when removing drains after TKA because it is a noninvasive technique and it is easy to perform. Because the cough trick has been shown by others to be effective at reducing pain during venipuncture and parenteral injections, and we found it was effective for that purpose during drain removal after TKA, we believe this finding probably generalizes well to most minor procedures that cause transient, sharp pain. We suggest that it could be used to make such procedures more comfortable for patients, as well as for drain removal in other types of surgery where drains still are commonly used (including spine surgery and tumor surgery).

Level of Evidence

Level I, therapeutic study.
Will cell therapies provide the solution for the shortage of transplantable organs?
Authors: Brasile Lauren , Stubenitsky Bart
Published: August 2019

Purpose of review

The potential to regenerate ischemically damaged kidneys while being perfused ex-vivo offers the best near-term solution to increasing kidney allografts for transplantation.

Recent findings

There are a number of stem-cell sources including: stromal mesenchymal cells (MSC), induced adult pluripotent stem cells, fetal stem cells from placenta, membranes, amniotic fluid and umbilical cord and hematopoietic cells. MSC are increasingly the stem cell of choice and studies are primarily focused on novel induction immunosuppression to prevent rejection. Stem-cell therapies appliedin vivomay be of limited benefit because the nonintegrating cells do not remain in the kidney and are not detectable in the body after several days. MSC therapies for transplantation have demonstrated early safety and feasibility. However, efficacy has not been clearly established. A more feasible application of a stem-cell therapy in transplantation is the administration of MSC to treat damaged renal allografts directly while being perfusedex vivo. Initial feasibility has been established demonstrating MSC-treatment results in statistically significant reduction of inflammatory responses, increased ATP and growth factor synthesis and mitosis.

The ability to regenerate renal tissue ex-vivo sufficiently to result in immediate function could revolutionize transplantation by solving the chronic organ shortage.
Assessing the role of urologists and general surgeons in the open repair of bladder injuries: Analysis of a large, statewide trauma database
Authors: Leong Joon Yau , Rshaidat Hamza , Tham Elwin , Mitsuhashi Shuji , Chung Paul H.
Published: August 2019

BACKGROUND

Bladder injuries often occur in the setting of polytrauma, and if severe, may require open surgical repairs. We assess the role of urologists and general surgeons (GS) in the open surgical management of bladder injuries and their outcomes in a traumatic setting.

METHODS

Patients who underwent open bladder injury repair secondary to trauma from 2000 to 2017 by urology or GS were identified in the Pennsylvania Trauma Outcome Study database by International Classification of Diseases—9th Rev.—Clinical Modification procedure codes (57.19–57.93). Patient demographics, initial trauma assessment, length of hospital stay, associated complications, and mortality were evaluated. Urology management of a bladder injury was defined by documentation of a urologist in the operating room or urological consultation during the hospital stay. GS management was defined by documented bladder repair without urology involvement as described previously.

RESULTS

Of 624,504 patients in the database, 701 met inclusion criteria (419 managed by urology, 282 by GS). The most commonly performed procedure was suturing of bladder lacerations (80.5%). On univariate analysis, GS was more likely to manage patients with penetrating injuries and those who required exploratory laparotomy less than 2 hours upon arrival. Urology was more likely to manage patients with concomitant pelvic fractures and higher Injury Severity Score (ISS). On multivariate analysis, higher ISS was predictive of urology management (odds ratio, 1.83; 95% confidence interval, 1.17–2.87, p = 0.008), while patients who required urgent exploratory laparotomy was predictive of GS management (odds ratio, 0.34; 95% confidence interval, 0.21–0.55, p < 0.001). Patients with concomitant pelvic fractures (n = 318) were also more likely to have higher ISS (p < 0.001) and were more likely to be managed by urology (odds ratio, 1.52; 95% confidence interval, 1.01–2.30, p = 0.046). Mortality, length of hospital stay, and complication rates were not significantly different between the two specialties and among individual procedures.

CONCLUSION

Our study describes the landscape of traumatic bladder repairs between urology and GS. GS may maintain similar patient outcomes when managing select cases of traumatic bladder injuries in the absence of urologists.

LEVEL OF EVIDENCE

Therapeutic, level IV.
Bayesian transfer in a complex spatial localisation task
Authors: Kiryakova Reneta , Aston Stacey , Beierholm Ulrik , Nardini Marko
Published: August 2019

Prior knowledge can help observers in various situations. Adults can simultaneously learn two location priors and integrate these with sensory information to locate hidden objects. Importantly, observers weight prior and sensory (likelihood) information differently depending on their respective reliabilities, in line with principles of Bayesian inference. Yet, there is limited evidence that observers actually perform Bayesian inference, rather than a heuristic, such as forming a look-up table. To distinguish these possibilities, we ask whether previously-learnt priors will be immediately integrated with a new, untrained likelihood. If observers use Bayesian principles, they should immediately put less weight on the new, less reliable, likelihood (“Bayesian transfer”). In an initial experiment, observers estimated the position of a hidden target, drawn from one of two distinct distributions, using sensory and prior information. The sensory cue consisted of dots drawn from a Gaussian distribution centred on the true location with either low, medium, or high variance; the latter introduced after block three of five to test for evidence of Bayesian transfer. Observers did not weight the cue (relative to the prior) significantly less in the high compared to medium variance condition, counter to Bayesian predictions. However, when explicitly informed of the different prior variabilities, observers placed less weight on the new high variance likelihood (“Bayesian transfer”), yet substantially diverged from ideal. Much of this divergence can be captured by a model that weights sensory information, according only to internal noise in using the cue. These results emphasise the limits of Bayesian models in complex tasks.
Salivary gland macrophages assist tissue-resident CD8+T cell immune surveillance
Authors: Stolp B. , Thelen F. , Ficht X. , Altenburger L. M. , Ruef N. , Inavalli V. V. G. K. , Germann P. , Page N. , Moalli F. , Raimondi A. , Keyser K. A. , Jafari S. M. Seyed , Barone F. , Dettmer M. S. , Merkler D. , Iannacone M. , Sharpe J. , Schlapbach C. , Fackler O. T. , Nägerl U. V. , Stein J. V.
Published: August 2019

Tissue macrophages and tissue resident memory CD8+T cells (TRM) play important roles for pathogen sensing and rapid protection of barrier tissues. To date, it is incompletely understood how these two cell types cooperate for efficient organ surveillance during homeostasis. Here, we used intravital imaging to show that TRMdynamically crawled along tissue macrophages in murine submandibular salivary glands (SMG) during the memory phase following a viral infection.Ex vivoconfined SMG TRMintegrated an unexpectedly wide range of migration modes: in addition to chemokine-and adhesion receptor-driven motility, SMG TRMdisplayed a remarkable capacity of autonomous motility in the absence of chemoattractants and adhesive ligands. This unique intrinsic SMG TRMmotility was transmitted by friction and adaptation to microenvironmental topography through protrusion insertion into permissive gaps. Analysis of extracellular space in SMG using super-resolution shadow imaging showed discontinuous attachment of tissue macrophages to neighboring epithelial cells, offering paths of least resistance for patrolling TRM. Upon tissue macrophage depletion, intraepithelial SMG TRMshowed decreased motility and reduced epithelial crossing events, and failed to cluster in response to local inflammatory chemokine stimuli. In sum, our data uncover a continuum of SMG TRMmigration modes and identify a new accessory function of tissue macrophages to facilitate TRMpatrolling of the complex exocrine gland architecture.

One sentence summary

Combinedin vitroandin vivoimaging of salivary gland-resident tissue memory CD8+T cells (TRM) uncovers their unique migratory behavior and describes a novel accessory function of tissue macrophages to assist TRMsurveillance.
Construction of two-input logic gates using Transcriptional Interference
Authors: Bordoy Antoni E. , O’Connor Nolan J. , Chatterjee Anushree
Published: August 2019

Transcriptional Interference (TI) has been shown to regulate gene expression at the DNA level via different molecular mechanisms. The obstacles present on the DNA that a transcribing RNA Polymerase might encounter, e.g. a DNA-bound protein or another RNA Polymerase, can result in TI causing termination of transcription, thus reducing gene expression. However, the potential of TI as a new strategy to engineer complex gene expression modules has not been fully explored yet. Here we created a series of two-input devices using the presence of a roadblocking protein using both experimental and mathematical modeling approaches. We explore how multiple characteristics affect the response of genetic devices engineered to act like either AND, OR, or Single Input logic gates. We show that the dissociation constant of the roadblocking protein, inducer activation of promoter and operator sites, and distance between tandem promoters tune gate behavior. This work highlights the potential of rationally creating different types of genetic responses using the same transcription factors in subtly different genetic architectures.
Early transcriptional landscapes ofChlamydia trachomatis-infected epithelial cells at single cell resolution
Authors: Hayward Regan J. , Marsh James W. , Humphrys Michael S. , Huston Wilhelmina M. , Myers Garry S.A.
Published: August 2019

Chlamydiaare Gram-negative obligate intracellular bacterial pathogens responsible for a variety of disease in humans and animals worldwide.C. trachomatiscauses trachoma (infectious blindness) in disadvantaged populations, and is the most common bacterial sexually transmitted infection in humans, causing reproductive tract disease. Antibiotic therapy successfully treats diagnosed chlamydial infections, however asymptomatic infections are common. High-throughput transcriptomic approaches have explored chlamydial gene expression and infected host cell gene expression. However, these were performed on large cell populations, averaging gene expression profiles across all cells sampled and potentially obscuring biologically relevant subsets of cells. We generated a pilot dataset, applying single cell RNA-Seq (scRNA-Seq) toC. trachomatisinfected and mock-infected epithelial cells to assess the utility of single cell approaches to identify early host cell biomarkers of chlamydial infection. 264 time-matchedC. trachomatis-infected and mock-infected HEp-2 cells were collected and subjected to scRNA-Seq. After quality control, 200 cells were retained for analysis. Two distinct clusters distinguished 3-hour cells from 6- and 12-hours. Pseudotime analysis identified a possible infection-specific cellular trajectory forChlamydia-infected cells, while differential expression analyses found temporal expression of metallothioneins and genes involved with cell cycle regulation, innate immune responses, cytoskeletal components, lipid biosynthesis and cellular stress. Changes to the host cell transcriptome at early times ofC. trachomatisinfection are readily discernible by scRNA-Seq, supporting the utility of single cell approaches to identify host cell biomarkers of chlamydial infection, and to further deconvolute the complex host response to infection.
SIRT6 as a transcriptional coactivator of GATA4 prevents doxorubicin cardiotoxicity independently of its deacylase activity
Authors: Qian Minxian , Peng Linyuan , Liu Zuojun , Tang Xiaolong , Wang Zimei , Liu Baohua
Published: August 2019

Activity dependent and independent functions for some enzymes are indispensable as significant biological regulators. Deacylase SIRT6 is well-known to improve stress resistance and promote lifespan extension through enzymatic activity-dependent gene silencing. However, whether and how SIRT6 non-enzymatically actives the transcriptional output hasn’t been characterized. Here, we revealed SIRT6 as a coactivator of GATA4, an essential transcription factor for postnatal cardiomyocyte survival, promoting the expression of anti-apoptotic gene. Chemotherapeutic drug, doxorubicin (DOX), remarkably and rapidly decreased SIRT6 expression, leading to transcriptional repression of GATA4 and cardiomyocyte apoptosis. Interestingly, SIRT6 interacted with GATA4 yet enhanced GATA4 acetylation independent of its deacylase activity, by recruiting the acetyltransferase Tip60 to form a trimeric complex. Nonacyl-mimetic mutation of GATA4 thoroughly blocked its ability against DOX cardiotoxicity. Moreover,Sirt6transgenic mice exhibited preserved cardiac function with attenuated GATA4 activity in response to DOX. Thus, our studies uncover a previously unrecognized role of SIRT6 in cardioprotection independently of deacylase activity, providing the molecular basis to prevent chemotherapeutic side effects.
Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality
Authors: Ramot Michal , Walsh Catherine , Reimann Gabrielle E. , Martin Alex
Published: August 2019

Extensive study of typically developing individuals and those on the autism spectrum has identified a large number of brain regions associated with our ability to navigate the social world. Although it is widely appreciated that this so-called ‘social brain’ is composed of distinct, interacting systems, these component parts have yet to be clearly elucidated. Here we used measures of eye movement and neural typicality – based on the degree to which subjects deviated from the norm – while typically developing (N = 62) and individuals with autism (N = 36) watched a large battery of movies depicting social interactions. Our findings provide clear evidence for distinct, but overlapping, neural systems underpinning two major components of the ‘social brain’, social orienting and inferring the mental state of others.
Accuracy of different modalities of reaction time testing: Implications for online cognitive assessment tools
Authors: Holden Jameson , Francisco Eric , Lensch Rachel , Tommerdahl Anna , Kirsch Bryan , Zai Laila , Dennis Robert , Tommerdahl Mark
Published: August 2019

Reaction time testing is widely used in computerized cognitive assessments, and clinical studies have repeatedly shown it to be a sensitive indicator of cognitive function. Typically, the reaction time test is administered by presenting a subject with a visual stimulus on a computer monitor and prompting the individual to respond (via keypad or computer mouse) as quickly as possible. The individual’s reaction time is calculated as the interval between presentation of the stimulus and the time recorded from the mechanical response. However, there are many inherent latencies and variabilities that may be introduced to the measure by both hardware (computer monitor and mouse) and software (operating system). Because of these delays, we hypothesized that a comparison of hardware protocols (excluding human response) would demonstrate significant differences in the resulting reaction time measures. To simulate the delays of various components of the common systems used to obtain reaction time, we conducted a simple experiment in which either a visual or tactile stimulus evoked a movement from a mechanical transducer to respond to a computer peripheral or a dedicated response device. In the first condition, a simulated visual reaction time test was conducted by flashing a visual stimulus on a computer monitor. The stimulus was detected by a dedicated light sensor, and a linear actuator delivered the mechanical response via computer mouse. The second test condition employed a mobile device as the medium for the visual stimulus, and the mechanical response was delivered to the mobile device’s touchscreen. The third and fourth test conditions simulated tactile reaction time tests in which the stimulus was generated by a dedicated hardware device. The third condition simulated a tactile stimulus, which was detected by a mechanical switch, and again a hardware device delivered the response via computer mouse. The fourth condition also simulated a tactile stimulus, but the response was delivered by a dedicated hardware device designed to store the interval between stimulus delivery and stimulus response. There were significant differences in the range of responses recorded from the four different conditions with the reaction time collected from a visual stimulus on a mobile device being the worst and the device with dedicated hardware designed for the task being the best. The results suggest that some of the commonly used visual tasks on consumer grade computers could be introducing significant errors for reaction time testing and that dedicated hardware designed for the reaction time task is needed to minimize testing errors.
Stimulation-specific information is represented as local activity patterns across the brain
Authors: Sadoun Amirouche , Chauhan Tushar , Mameri Samir , Zhang Yifan , Barone Pascal , Deguine Olivier , Strelnikov Kuzma
Published: August 2019

Modern neuroimaging represents three-dimensional brain activity, which varies across brain regions. It remains unknown whether activity within brain regions is organized in spatial configurations to reflect perceptual and cognitive processes. We developed a rotational cross-correlation method allowing a straightforward analysis of spatial activity patterns for the precise detection of the spatially correlated distributions of brain activity. Using several statistical approaches, we found that the seed patterns in the fusiform face area were robustly correlated to brain regions involved in face-specific representations. These regions differed from the non-specific visual network meaning that activity structure in the brain is locally preserved in stimulation-specific regions. Our findings indicate spatially correlated perceptual representations in cerebral activity and suggest that the 3D coding of the processed information is organized in locally preserved activity patterns. More generally, our results provide the first demonstration that information is represented and transmitted as local spatial configurations of brain activity.
From phages to mammalian viruses: viral receptors play a central role in protein-protein interaction network
Authors: Yu Fen , Zhang Zheng , Zou Yuanqiang , Qiu Ye , Wu Aiping , Jiang Taijiao , Peng Yousong
Published: August 2019

Motivation

Receptors on host cells play a critical role in viral infection. How phages select receptors is still unknown.

Results

Here, we manually curated a high-quality database named phageReceptor, including 355 pairs of phage-host receptor interactions, 280 unique viral species or sub-species and 64 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The protein receptors were highly diverse in their structures, and had little homology with mammalian virus receptors. Further functional characterization of phage protein receptors in Escherichia coli showed that they had larger node degrees and betweennesses in the protein-protein interaction (PPI) network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins, or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors, suggesting that viral protein receptors play a central role in the host’s PPI network. The study deepens our understanding of virus-host interactions.

Availability

The database of phageReceptor is publicly accessible at http://www.computationalbiology.cn/viralRecepetor/index.html.
Fractal-based triangular bandpass filter with a notched band for interference rejection in wideband applications
Authors: S. Karthie , S. Salivahanan
Published: August 2019

Purpose

This paper aims to present the design of a novel triangular-shaped wideband microstrip bandpass filter implemented on a low-cost substrate with a notched band for interference rejection.

Design/methodology/approach

The conventional dual-stub filter is embedded with simple fractal-based triangular-circular geometries through various iterations to reject wireless local area network (WLAN) signals with a notched band at 5.8 GHz.

Findings

The filter covers a wide frequency band from 3.1 to 8.8 GHz and has a fractional bandwidth of 98 per cent with the lower passband of 57.5 per cent and upper passband of 31.6 per cent separated by a notched band at 5.8 GHz. The proposed wideband prototype bandpass filter is fabricated in FR-4 substrate using PCB technology and the simulation results are validated with measurement results which include insertion loss, return loss and group delay. The fabricated filter has a sharp rejection of 28.3 dB at 5.8 GHz. Measured results show good agreement with simulated responses. The performance of the fractal-based wideband filter is compared with other wideband bandpass filters.

Originality/value

In the proposed work, a fractal-based wideband bandpass filter with a notched band is reported. The conventional dual-stub filter is deployed with triangular-circular geometry to design a wideband filter with a notched band to suppress interference signals at WLAN frequency. The proposed wideband filter exhibits smaller size and better interference rejection compared to other wideband bandpass filter designs implemented on low-cost substrate reported in the literature. The aforementioned wideband filter finds application in wideband wireless communication systems.
Lump solutions and interaction phenomena of the (3 + 1)-dimensional nonlinear evolution equations
Authors: Mao Jin-Jin , Tian Shou-Fu , Yan Xing-Jie , Zhang Tian-Tian
Published: August 2019

Purpose

The purpose of this study is to examine the lump solutions of the (3 + 1)-dimensional nonlinear evolution equations by considering a (3 + 1)-dimensional generalized Kadomtsev–Petviashvili (gKP) equation and a (3 + 1)-dimensional variable-coefficient generalized B-type Kadomtsev–Petviashvili (vcgBKP) equation as examples.

Design/methodology/approach

Based on Hirota’s bilinear theory, a direct method is used to examine the lump solutions of these two equations.

Findings

The complete non-elastic interaction solutions between a lump and a stripe are also discussed for the equations, which show that the lump solitons are swallowed by the stripe solitons.

Originality/value

The dynamics of these solutions are analyzed to enrich the diversity of the dynamics of high-dimensional KP-type nonlinear wave equations.
Simulation of nanofluid thermal radiation in Marangoni convection flow of non-Newtonian fluid
Authors: Hayat Tasawar , Ullah Ikram , Waqas Muhammad , Alsaedi Ahmed
Published: August 2019

Purpose

The purpose of this study is to study the impacts of exponential space-dependent heat source (ESHS) and thermal radiation in Marangoni convective flow of Cross fluid. The passively controlled model is developed to exhibit the nanoparticles’ concentration on the surface.

Design/methodology/approach

The resulting problem under consideration is tackled by using the shooting approach.

Findings

Temperature field augments with enhancement of the thermophoretic, exponential-based space heat source (ESHS) and radiation parameters, whereas it decays with the increase of the Marangoni ratio parameter.

Originality/value

To the best of the authors’ knowledge, no such analysis has yet been reported.