bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender and socioeconomic inequalities in the implementation of the Basque programme for multimorbid patients
Authors: Soto-Gordoa Myriam , Arrospide Arantzazu , Millán Eduardo , Calvo Montserrat , Igartua Juan Ignacio , Esnaola Santiago , Ganzarain Jaione , Mar Javier
Published: April 2019

Background

The aim of our study was to increase awareness of the relevance of the implemented programmes to inequity of access and inequality of health by analyzing the impact of a patient-centred strategy for multimorbid patients.

Methods

This retrospective study compared the 2014 multimorbid patient group (intervention group) with its 2012 analogue (control group), before the Department of Health of the Basque Country launched the strategy for managing disease chronicity. Inequalities in healthcare access were represented by differences in the inclusion of patients in the programme and in contacts with primary care (PC) services by gender and socioeconomic status (measured by deprivation index by census track). Likewise, differences in hospital care represented inequalities in health outcomes. Generalized linear models were used to analyze relationships among variables. A propensity score by a genetic matching approach was used to minimize possible selection bias.

Results

At baseline, women had less probability of being eligible for the programme. No clear patterns were seen in resource consumption in PC. The probability of hospitalization was higher for men and increased according to socioeconomic status. The implementation of the programme yielded more contacts with PC services in all groups and a reduction in hospitalizations, especially among men and the most socioeconomically deprived patients.

Conclusion

The patient-centred, integrated-care intervention launched by the Department of Health of the Basque Country might have reduced some gender and socioeconomic inequalities in health outcomes, as it avoided more hospitalizations in subgroups that presented with more episodes of decompensation in the reference year.
Oral anticoagulants usage in Japanese patients aged 18–74 years with non-valvular atrial fibrillation: a retrospective analysis based on insurance claims data
Authors: Ohshima Ayako , Koyama Toshihiro , Ogawa Aiko , Zamami Yoshito , Tanaka Hiroyoshi Y , Kitamura Yoshihisa , Sendo Toshiaki , Hinotsu Shiro , Miller Michael W , Kano Mitsunobu R
Published: April 2019

Background

Oral anticoagulants use has increased rapidly, internationally. Here we look at risks and benefits, based on Japanese data, of therapy with low risk non-valvular atrial fibrillation patients.

Objectives

Using a health insurance claims data set we assessed: (i) oral anticoagulants usage in Japan, and (ii) efficacy and safety of dabigatran compared with warfarin, in Japanese patients with non-valvular atrial fibrillation, aged 18–74 years.

Methods

We identified 4380 non-valvular atrial fibrillation patients treated with anticoagulants between 1 January 2005, and 28 February 2014, and estimated the adjusted hazard ratio for stroke or systemic embolism, and any hemorrhagic event (Cox proportional hazards regression model with stabilized inverse probability treatment weighting).

Results

The data included 101 989 anticoagulant prescriptions for 4380 patients, of which direct oral anticoagulants increased to 40.0% of the total by the end of the study. After applying exclusion criteria, 1536 new non-valvular atrial fibrillation patients were identified, including 1071 treated with warfarin and 465 with dabigatran. Mean ages were 56.11 ± 9.70 years for warfarin, and 55.80 ± 9.65 years for dabigatran. The adjusted hazard ratio (95% confidence interval), comparing dabigatran with warfarin, was 0.48 (0.25–0.91) for stroke or systemic embolism, and 0.91 (0.60–1.39) for any hemorrhage including intracranial and gastrointestinal.

Conclusions

Number of patients prescribed direct oral anticoagulants steadily increased, and incidence of all-cause bleeding related to dabigatran was similar to warfarin, in our study population of younger non-valvular atrial fibrillation patients. Dabigatran, compared with warfarin, generally reduced risk of all-cause stroke and systemic embolism.
TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer
Authors: Carazo Fernando , Campuzano Lucía , Cendoya Xabier , Planes Francisco J , Rubio Angel
Published: April 2019

Background

Aberrant alternative splicing plays a key role in cancer development. In recent years, alternative splicing has been used as a prognosis biomarker, a therapy response biomarker, and even as a therapeutic target. Next-generation RNA sequencing has an unprecedented potential to measure the transcriptome. However, due to the complexity of dealing with isoforms, the scientific community has not sufficiently exploited this valuable resource in precision medicine.

Findings

We present TranscriptAchilles, the first large-scale tool to predict transcript biomarkers associated with gene essentiality in cancer. This application integrates 412 loss-of-function RNA interference screens of >17,000 genes, together with their corresponding whole-transcriptome expression profiling. Using this tool, we have studied which are the cancer subtypes for which alternative splicing plays a significant role to state gene essentiality. In addition, we include a case study of renal cell carcinoma that shows the biological soundness of the results. The databases, the source code, and a guide to build the platform within a Docker container are available at GitLab. The application is also available online.

Conclusions

TranscriptAchilles provides a user-friendly web interface to identify transcript or gene biomarkers of gene essentiality, which could be used as a starting point for a drug development project. This approach opens a wide range of translational applications in cancer.
A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome
Authors: Jiang Justin B , Quattrini Andrea M , Francis Warren R , Ryan Joseph F , Rodríguez Estefanía , McFadden Catherine S
Published: April 2019

Background

More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral “forests,” which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri.

Findings

We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256–448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.

Conclusions

The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.
Risk Factors Associated with the Development of Transaminitis in Oxandrolone-Treated Adult Burn Patients
Authors: Kiracofe Brittany , Zavala Sarah , Gayed Rita M , Foster Charles J , Jones Kendrea M , Oltrogge Pape Kate , Hill David M , Reger Melissa , Porter Kyle , Murphy Claire V
Published: April 2019

Oxandrolone has proven benefits in thermal burn injury and has become a standard of care. Transaminitis is the most frequent side effect of oxandrolone use, although no risk factors have been identified that increase the risk of transaminitis. The objective was to evaluate the frequency of transaminitis while on oxandrolone and to identify risk factors leading to an increased risk of transaminitis in adult burn patients. This multicenter retrospective risk factor analysis compared two patient groups with and without occurrence of transaminitis, which was detected by an aspartate aminotransferase (AST) or alanine aminotransferase (ALT) >100 mg/dL. Secondary outcomes included percentage increase from baseline for AST/ALT, length of stay, and mortality. After univariable analysis, a multivariable logistic regression analysis was performed to detect possible risk factors leading to transaminitis. A total of 309 patients were included, with transaminitis occurring in 128 patients (41.4%) after 13 (interquartile range [IQR] 8–23) days on oxandrolone. After multivariable analysis, age (odds ratio [OR] 0.91; 95% confidence interval [CI] 0.84–0.99 for a 5-year increase in age), intravenous vasopressor use (OR 1.85; 95% CI 1.05–3.27), and amiodarone use (OR 2.51; 95% CI 1.09–5.77) were independent predictors of transaminitis, controlling for TBSA%. Transaminitis was not significantly associated with length of stay or mortality after adjusting for age and TBSA%. We conclude that patients who are younger and have concurrent amiodarone or vasopressor use have the highest risk of developing oxandrolone induced transaminitis and should be monitored closely.
Cold Tolerance of the Tribolium castaneum (Coleoptera: Tenebrionidae), Under Different Thermal Regimes: Impact of Cold Acclimation
Authors: Izadi H , Mohammadzadeh M , Mehrabian M
Published: April 2019

The red flour beetle, Tribolium castaneum (Herbst), is a serious pest of stored product worldwide. Cold tolerance or cold hardiness is an important ecophysiological trait related directly to survival, fitness, and distribution of insects. In this study, the effects of four thermal regimes, i.e., control (C), cold acclimation (CA), rapid cold hardening (RCH), and fluctuating-acclimation (FA), were examined for their effects on cold tolerance, supercooling point (SCP), lower lethal temperature (LLT), and chill-coma recovery time (CCRT) of the red flour beetle. In addition, changes in cryoprotectant (trehalose, sorbitol, and myo-inositol) levels were investigated under each thermal treatment. The results documented a substantial enhancement in the SCP, cold hardiness, and cryoprotectant levels of the adults of T. castaneum under CA regimes. The lowest SCP, highest trehalose and myo-inositol contents, and, subsequently, the greatest survival rate were observed in cold-acclimated beetles. In addition, coordination between cryoprotectant level, SCP, and cold tolerance of the pest was observed. The highest and lowest CCRT were observed at control and CA, respectively. In RCH regime with the highest impact, LLT reached the lowest level of −22°C. As most of the mortality of T. castaneum occurred at a temperature above the SCP, so this pest could be considered as a chill-susceptible insect.
Residual Negative Pressure in Vacuum Blood-Collection Tube and Hemolysis in Pediatric Blood Specimens
Authors: Hu Jing , Zhang Qiao-Xin , Xiao Tong-Tong , Pan Mei-Chen , Cai Ying-Mu
Published: April 2019

Objective

To determine a method to reduce specimen hemolysis rates in pediatric blood specimens.

Methods

A total of 290 blood specimens from pediatric patients were classiﬁed into the capped group or uncapped group. The hemolysis index and levels of lactate dehydrogenase (LDH) were measured using an automated biochemical analyzer. Also, we performed a paired test to measure the concentration of free hemoglobin in specimens from 25 randomly selected healthy adult volunteers, using a direct spectrophotometric technique.

Results

The hemolytic rate of capped specimens was 2-fold higher than that of uncapped specimens. We found significant differences for LDH. Also, there was a significant difference in the concentration of free hemoglobin in the random-volunteers test.

Conclusions

Eliminating the residual negative pressure of vacuum blood-collection tubes was effective at reducing the macrohemolysis and/or microhemolysis rate.
Injury and Illness Surveillance During the 2016 Department of Defense Warrior Games: Review of Methods and Results
Authors: Rogers Amy E , Baker Joshua , Beutler Anthony , Witkop Catherine , Leggit Jeffrey C
Published: April 2019

Introduction

Surveillance systems have become a valuable tool to capture epidemiological data at multi-sport events, with findings serving to predict and prevent injury, reduce illness, and guide efficient utilization of medical resources. In 2016, the first injury and illness surveillance tool for the Department of Defense (DoD) Warrior Games was established to inform the required medical footprint. The purpose of this paper is to describe the methods and findings from the 2016 DoD Warrior Games surveillance system, which included a database of injuries and illness.

Materials and Methods

A total of 245 wounded warrior (WW) athletes were followed over 19 days, to include train-up and competition periods, as they competed for their respective teams of Army, Navy, Air Force, Marines, Special Operations, and United Kingdom. Medical personnel recorded injuries and illnesses treated utilizing a standardized surveillance form and data were entered into a daily tracker to examine patterns or areas for prevention. Reports included sex, age, event discipline, previous injury or illness, reason for presentation, and treatment provided.

Results

From June 3 to June 21, 2016, 114 individual encounters were recorded on the standard form and entered into the surveillance database. Athletes accounted for 67% of all encounters. Illness accounted for 30.7% of all visits, while injuries accounted for 69.2%. The incident proportion of injuries in athletes was 23.3 injuries per 100 athletes (95% CI 17.6, 30.1) and incident rate of 12.2 injuries per 1000 athlete days. Integrative medicine treatments including acupuncture, osteopathic manipulative treatment (OMT), massage therapy, and gua sha accounted for the largest forms of treatment (31%).

Conclusions

From the surveillance data, staff levels and treatment supplies can be adjusted. In addition an improved surveillance tool can be created. Continuous surveillance is required to provide information on trends in injury and illness to support prevention strategies.
Long-term treatment with valganciclovir improves lentiviral suicide gene therapy of glioblastoma
Authors: Hossain Jubayer A , Latif Md A , Ystaas Lars A R , Ninzima Sandra , Riecken Kristoffer , Muller Arnaud , Azuaje Francisco , Joseph Justin V , Talasila Krishna M , Ghimire Jiwan , Fehse Boris , Bjerkvig Rolf , Miletic Hrvoje
Published: April 2019

Background

Suicide gene therapy for malignant gliomas has shown encouraging results in the latest clinical trials. However, prodrug application was most often restricted to short-term treatment (14 days), especially when replication-defective vectors were used. We previously showed that a substantial fraction of herpes simplex virus thymidine kinase (HSV-TK) transduced tumor cells survive ganciclovir (GCV) treatment in an orthotopic glioblastoma (GBM) xenograft model. Here we analyzed whether these TK+ tumor cells are still sensitive to prodrug treatment and whether prolonged prodrug treatment can enhance treatment efficacy.

Methods

Glioma cells positive for TK and green fluorescent protein (GFP) were sorted from xenograft tumors recurring after suicide gene therapy, and their sensitivity to GCV was tested in vitro. GBM xenografts were treated with HSV-TK/GCV, HSV-TK/valganciclovir (valGCV), or HSV-TK/valGCV + erlotinib. Tumor growth was analyzed by MRI, and survival as well as morphological and molecular changes were assessed.

Results

TK-GFP+ tumor cells from recurrent xenograft tumors retained sensitivity to GCV in vitro. Importantly, a prolonged period (3 mo) of prodrug administration with valganciclovir (valGCV) resulted in a significant survival advantage compared with short-term (3 wk) application of GCV. Recurrent tumors from the treatment groups were more invasive and less angiogenic compared with primary tumors and showed significant upregulation of epidermal growth factor receptor (EGFR) expression. However, double treatment with the EGFR inhibitor erlotinib did not increase therapeutic efficacy.

Conclusion

Long-term treatment with valGCV should be considered as a replacement for short-term treatment with GCV in clinical trials of HSV-TK mediated suicide gene therapy.
IDENTIFICATION OF NOVEL BIOMARKERS FOR LUNG CANCER RISK IN HIGH LEVELS OF RADON BY PROTEOMICS: A PILOT STUDY
Authors: Autsavapromporn N , Dukaew N , Wongnoppavich A , Chewaskulyong B , Roytrakul S , Klunklin P , Phantawong K , Chitapanarux I , Sripun P , Kritsananuwat R , Amphol S , Pornnumpa C , Suzuki T , Kudo H , Hosoda M , Tokonami S
Published: April 2019

Radon is the second most important risk factor for lung cancer after tobacco smoking. In Chiang Mai, Thailand, the values of indoor radon activity concentrations are considerably higher than global average values and it is a highest level among East Asian countries. The aim of our study is to identify novel biomarkers for lung cancer risk in high radon areas using a proteomic approach. In our transitional study, a total of 81 participants of non-smokers were examined, consist of 25 lung cancer patients (LC), 16 healthy controls from low levels of natural radiation areas (LLNRA) and 40 healthy controls from high levels of natural radiation areas (HLNRA). The results showed that a total of 799 differentially expressed proteins were identified. Among these, a total of 25 proteins were observed in both LC and HLNRA, but not in LINRA. Owing to the results obtained from this study, we also point out the research direction regarding the validation of some new candidate protein as a biomarker to screen population with high risk for lung cancer in the area with high levels of radon.
A HUMIDITY CONTROL TECHNIQUE BASED ON NAFION MEMBRANE AND ITS APPLICATION ON THE EVALUATION OF HUMIDITY RESPONSE FOR RADON MONITOR
Authors: Mao Yucai , Wang Yunxiang , Zhang Lei , Guo Qiuju
Published: April 2019

Electrostatic collection technique is widely used in various radon monitors. The mechanism of this kind of radon monitor is that the positive Po particles, produced by decay of radon, can be collected on the surface of detector in electric field. Collection efficiency, therefore, could be affected by air humidity. Calibration under different humidity conditions or test of humidity response is necessary consequently. In this study, a humidity control technique based on Nafion membrane tube (NMT) is developed. Under a consistent flowrate with a certain stable level of radon concentration and humidity of main-path inlet, the humidity of outlet sample gas from the main-path can be adjusted and stably controlled at a certain level by changing side-path’s flowrates of NMT. By adjusting main and side-path flowrate, RH of outlet gas of the main-path can be controlled from 5.3 to 80.0%. Theoretical study were also performed. Based on this, humidity influence calibration of an electrostatic radon monitor was performed, and a relationship between the sensitivity of the radon monitor and relative humidity was obtained.
HIGH BACKGROUND AREA FOR RADIATION EDUCATION
Authors: Matsuda N , Fukuda N , Yamauchi M , Tsunoyama Y , Tomita S , Kita M
Published: April 2019

This paper describes our trial experience of the use of high radiation area for radiation education. We used environmental samples collected from the high radiation area in Fukushima prefecture and India, for the practice of radiation measurement and health risk assessment in Nagasaki University Medical School. We also carried out the field monitoring seminar for students in the existing exposure areas in Tottori prefecture and the Yamakiya observatory in Fukushima. Although the evaluation of educational effectiveness is still underway, both types of education appeared attractive for the students mostly due to the exposure from natural environment in our real life which was not achieved by using an artificial radiation source in a classroom.
REDUCTION IN AMBIENT GAMMA DOSE RATE FROM RADIOCESIUM DUE TO SNOW COVER
Authors: Omori Y , Inoue S , Otsuka T , Nagamatsu Y , Sorimachi A , Ishikawa T
Published: April 2019

In the present study, variations in ambient gamma dose rate associated with snow cover were examined in a radioactive-contaminated site in Fukushima Prefecture, Japan. The ambient gamma dose rates decreased with increasing snow depth. The reduction trends were different between fresh snow (0.1–0.2 g/cm3) and granular snow (0.3–0.4 g/cm3) depending on snow density. Snow cover water content (snow water equivalent) calculated from snow depth and density was a key parameter governing the reduction in the ambient gamma dose rate. The ambient gamma dose rates reduced to 0.6 and 0.5 at 4 g/cm2 and 8 g/cm2 of snow water equivalent, respectively. Based on gamma-ray flux density distributions, the ambient gamma dose rates from the primary gamma rays decreased more compared to those from scattered gamma rays due to snow cover.
NATURAL RADIOACTIVITY MEASUREMENT AND DOSE ASSESSMENT OF BEACH PLACER SANDS IN THE COASTAL REGION OF TAMIL NADU (INDIA)
Authors: Veerasamy N , Sahoo S K , Inoue K , Fukushi M , Tsuruoka H , Arae H , Balakrishnan S
Published: April 2019

A preliminary study was carried out to determine the radioactivity concentration of 232Th, 226Ra and 40K in beach placer sands from 13 locations along the coast line of Tamil Nadu state, India. The ambient dose rates varied from 9 to 467 nGy h−1. The activity concentrations of radionuclide 232Th, 226Ra and 40K ranged from 5.2 to 683 Bq kg−1, 13 to 198 Bq kg−1 and 107 to 421 Bq kg−1, respectively. The annual effective dose rate ranges from 27 to 620 μSv y−1 and was higher at seven beaches in comparison to the UNSCEAR annual worldwide average value.
Actimetry in infant sleep research: an approach to facilitate comparability
Authors: Schoch Sarah F , Jenni Oskar G , Kohler Malcolm , Kurth Salome
Published: April 2019

Study Objectives

Only standardized objective assessments reliably capture the large variability of sleep behavior in infancy, which is the most pronounced throughout the human lifespan. This is important for clinical practice as well as basic research. Actimetry is a cost-efficient method to objectively estimate infant sleep/wake behavior from limb movements. Nevertheless, the standardization of actimetry-based sleep/wake measures is limited by two factors: the use of different computational approaches and the bias towards measuring only nighttime sleep—neglecting ~20 % of sleep infants obtain during daytime. Thus, we evaluate the comparability of two commonly used actimetry algorithms in infants and propose adjustments to increase comparability.

Methods

We used actimetry in 50 infants for 10 continuous days at ages 3, 6, and 12 months in a longitudinal approach. We analyzed the infants’ sleep/wake behaviors by applying two algorithms: Sadeh and Oakley/Respironics. We compared minute-by-minute agreement and Kappa between the two algorithms, as well as the algorithms with sleep/wake measures from a comprehensive 24-hour parent-reported diary.

Results

Agreement between uncorrected algorithms was moderate (77%–84%). By introducing a six-step adjustment, we increased agreement between algorithms (96%–97%) and with the diary. This decreased the difference in estimated sleep behaviors, e.g. Total Sleep Duration from 4.5 to 0.2 hours.

Conclusions

These adjustments enhance comparability between infant actimetry studies and the inclusion of parent-reported diaries allows the integration of daytime sleep. Objectively assessed infant sleep that is comparable across different studies supports the establishment of normative developmental trajectories and clinical cutoffs.
Vertical variation in wood CO2 efflux is not uniformly related to height: measurement across various species and sizes of Bornean tropical rainforest trees
Authors: Katayama Ayumi , Kume Tomonori , Ichihashi Ryuji , Nakagawa Michiko
Published: April 2019

Limited knowledge about vertical variation in wood CO2 efflux (Rwood) is still a cause of uncertainty in Rwood estimates at individual and ecosystem scales. Although previous studies found higher Rwood in the canopy, they examined several tree species of similar size. In contrast, in the present study, we measured vertical variation in Rwood for 18 trees including 13 species, using a canopy crane for a more precise determination of the vertical variation in Rwood, for various species and sizes of trees in order to examine the factors affecting vertical variation in Rwood and thus, to better understand the effect of taking into account the vertical and inter-individual variation on estimates of Rwood at the individual scale. We did not find any clear pattern of vertical variation; Rwood increased significantly with measurement height for only one tree, while it decreased for two more trees, and was not significantly related with measurement height in 15 other trees. Canopy to breast height Rwood ratio was not related to diameter at breast height or crown ratio, which supposedly are factors affecting vertical variation in Rwood. On average, Rwood estimates at individual scale, considering inter-individual variation but ignoring vertical variation, were only 6% higher than estimates considering both forms of variation. However, estimates considering vertical variation, while ignoring inter-individual variation, were 13% higher than estimates considering both forms of variation. These results suggest that individual measurements at breast height are more important for estimating Rwood at the individual scale, and that any error in Rwood estimation at this scale, due to the absence of any more measurements along tree height, is really quite negligible. This study measured various species and sizes of trees, which may be attributed to no clear vertical variation because factors causing vertical variation can differ among species and sizes.
Older people living with human immunodeficiency virus/acquired immune deficiency syndrome in Chinese rural areas: perceived stigma and associated factors
Authors: Zhang Qiang , Yang Haixia , Fan Jinyu , Duan Luxi , Chen Dan , Feng Xiangling , Li Xingli
Published: April 2019

Background

Perceived stigma is a common problem among people living with human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) (PLWHA). In recent years, the number of older adults with HIV/AIDS has rapidly increased in China. However, HIV/AIDS-related perceived stigma and associated factors in older PLWHA remain unknown.

Methods

A cross-sectional study was conducted in Yongzhou. Participants were recruited via the Hunan HIV/AIDS Registry system. All participants were ≥50 y of age at the time of their HIV diagnosis. Sowell’s HIV Stigma Scale was used to measure perceived stigma.

Results

A total of 193 participants were interviewed, of which 132 (68.4%) were male. The ages of the participants ranged from 50 to 82 y and the average age was 61.1±5.95 y. Eighteen (9.3%) subjects were ethnic minorities. Older PLWHA reported a relatively high level of perceived stigma, especially individuals of Han ethnicity having high annual incomes. The individuals who had disclosed their HIV-positive status to all their family had higher scores on the dimension related to blame. Regression analysis showed that ethnicity, annual income, living arrangement and disclosure patterns were the main associated factors of perceived stigma.

Conclusions

Perceived stigma is common in older Chinese PLWHA. Individuals of ethnic minorities or with higher economic status have higher levels of stigma. Family relationships have a deep influence on perceived stigma.
A split sex ratio in solitary and social nests of a facultatively social bee
Authors: Smith Adam R. , Kapheim Karen M. , Kingwell Callum J. , Wcislo William T.
Published: April 2019

A classic prediction of kin selection theory is that a mixed population of social and solitary nests of haplodiploid insects should exhibit a split sex ratio among offspring: female biased in social nests, male biased in solitary nests. Here, we provide the first evidence of a solitary–social split sex ratio, using the sweat beeMegalopta genalis(Halictidae). Data from 2502 offspring collected from naturally occurring nests across 6 years spanning the range of theM. genalisreproductive season show that despite significant yearly and seasonal variation, the offspring sex ratio of social nests is consistently more female biased than in solitary nests. This suggests that split sex ratios may facilitate the evolutionary origins of cooperation based on reproductive altruism via kin selection.
Get off my back: vibrational assessment of homeowner strength
Authors: Roberts Louise , Laidre Mark E.
Published: April 2019

Animals may use a variety of sensory modalities to assess ownership and resource-holding potential (RHP). However, few studies have experimentally tested whether animals can assess these key variables through a purely vibrational modality, exclusively involving substrate-borne vibrations. Here we studied social terrestrial hermit crabs (Coenobita compressus), where competitors assess homeowners by climbing on top of a solid external structure—an architecturally remodelled shell home, inside of which the owner then produces vibrations. In the field, we used a miniature vibratory device, hidden within an empty shell, to experimentally simulate a ‘phantom owner’, with variable amplitudes of vibration representing different levels of homeowner strength. We found that assessors could use these vibrations to deduce the owner's RHP: for strong vibrations (indicative of a high RHP owner) assessors were least likely to escalate the conflict; for weak vibrations (indicative of a low RHP owner) assessors showed intermediate escalation; and in the absence of vibration (indicative of an extremely weak or absent owner) assessors were most likely to escalate. These results reveal that animals can assess homeowner strength based solely on substrate vibrations, thereby making important decisions about whether to escalate social conflicts over property.
Facultative oviparity in a viviparous skink (
Saiphos equalis
)
Authors: Laird Melanie K. , Thompson Michael B. , Whittington Camilla M.
Published: April 2019

Facultative changes in parity mode (oviparity to viviparity and vice versa) are rare in vertebrates, yet offer fascinating opportunities to investigate the role of reproductive lability in parity mode evolution. Here, we report apparent facultative oviparity by a viviparous female of the bimodally reproductive skink
Saiphos equalis
—the first report of different parity modes within a vertebrate clutch. Eggs oviposited facultatively possess shell characteristics of both viviparous and oviparous
S. equalis
, demonstrating that egg coverings for viviparous embryos are produced by the same machinery as those for oviparous individuals. Since selection may act in either direction when viviparity has evolved recently, squamate reproductive lability may confer a selective advantage. We suggest that facultative oviparity is a viable reproductive strategy for
S. equalis
and that squamate reproductive lability is more evolutionarily significant than previously acknowledged.
Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data
Authors: Cao Zhixing , Grima Ramon
Published: April 2019

Bayesian and non-Bayesian moment-based inference methods are commonly used to estimate the parameters defining stochastic models of gene regulatory networks from noisy single cell or population snapshot data. However, a systematic investigation of the accuracy of the predictions of these methods remains missing. Here, we present the results of such a study using synthetic noisy data of a negative auto-regulatory transcriptional feedback loop, one of the most common building blocks of complex gene regulatory networks. We study the error in parameter estimation as a function of (i) number of cells in each sample; (ii) the number of time points; (iii) the highest-order moment of protein fluctuations used for inference; (iv) the moment-closure method used for likelihood approximation. We find that for sample sizes typical of flow cytometry experiments, parameter estimation by maximizing the likelihood is as accurate as using Bayesian methods but with a much reduced computational time. We also show that the choice of moment-closure method is the crucial factor determining the maximum achievable accuracy of moment-based inference methods. Common likelihood approximation methods based on the linear noise approximation or the zero cumulants closure perform poorly for feedback loops with large protein–DNA binding rates or large protein bursts; this is exacerbated for highly heterogeneous cell populations. By contrast, approximating the likelihood using the linear-mapping approximation or conditional derivative matching leads to highly accurate parameter estimates for a wide range of conditions.
Formal structure of periodic system of elements
Authors: Leal Wilmer , Restrepo Guillermo
Published: April 2019

For more than 150 years, the structure of the periodic system of the chemical elements has intensively motivated research in different areas of chemistry and physics. However, there is still no unified picture of what a periodic system is. Herein, based on the relations of order and similarity, we report a formal mathematical structure for the periodic system, which corresponds to an ordered hypergraph. It is shown that the current periodic system of chemical elements is an instance of the general structure. The definition is used to devise a tailored periodic system of polarizability of single covalent bonds, where order relationships are quantified within subsets of similar bonds and among these classes. The generalized periodic system allows envisioning periodic systems in other disciplines of science and humanities.
Complexity in phase transforming pin-jointed auxetic lattices
Authors: Hunt G. W. , Dodwell T. J.
Published: April 2019

We demonstrate the complexity that can exist in the modelling of auxetic lattices. By introducing pin-jointed members and large deformations to the analysis of a re-entrant structure, we create a material which has both auxetic and non-auxetic phases. Such lattices exhibit complex equilibrium behaviour during the highly nonlinear transition between these two states. The local response is seen to switch many times between stable and unstable states, exhibiting both positive and negative stiffnesses. However, there is shown to exist an underlying
emergent modulus
over the transitional phase, to describe the average axial stiffness of a system comprising a large number of cells.
Human-induced reductions in fish predator boldness decrease their predation rates in kelp forests
Authors: Rhoades O. Kennedy , Lonhart Steve I. , Stachowicz John J.
Published: April 2019

Humans have restructured food webs and ecosystems by depleting biomass, reducing size structure and altering traits of consumers. However, few studies have examined the ecological impacts of human-induced trait changes across large spatial and temporal scales and species assemblages. We compared behavioural traits and predation rates by predatory fishes on standard squid prey in protected areas of different protection levels and ages, and found that predation rates were 6.5 times greater at old, no-take (greater than 40 years) relative to new, predominantly partial-take areas (approx. 8 years), even accounting for differences in predatory fish abundance, body size and composition across sites. Individual fishes in old protected areas consumed prey at nearly twice the rate of fishes of the same species and size at new protected areas. Predatory fish exhibited on average 50% longer flight initiation distance and lower willingness to forage at new protected areas, which partially explains lower foraging rates at new relative to old protected areas. Our experiments demonstrate that humans can effect changes in functionally important behavioural traits of predator guilds at large (30 km) spatial scales within managed areas, which require protection for multiple generations of predators to recover bold phenotypes and predation rates, even as abundance rebounds.
Processing bias: extending sensory drive to include efficacy and efficiency in information processing
Authors: Renoult Julien P. , Mendelson Tamra C.
Published: April 2019

Communication signals often comprise an array of colours, lines, spots, notes or odours that are arranged in complex patterns, melodies or blends. Receiver perception is assumed to influence preference and thus the evolution of signal design, but evolutionary biologists still struggle to understand how perception, preference and signal design are mechanistically linked. In parallel, the field of empirical aesthetics aims to understand why people like some designs more than others. The model of processing bias discussed here is rooted in empirical aesthetics, which posits that preferences are influenced by the emotional system as it monitors the dynamics of information processing and that attractive signals have effective designs that maximize information transmission, efficient designs that allow information processing at low metabolic cost, or both. We refer to the causal link between preference and the emotionally rewarding experience of effective and efficient information processing as the processing bias, and we apply it to the evolutionary model of sensory drive. A sensory drive model that incorporates processing bias hypothesizes a causal chain of relationships between the environment, perception, pleasure, preference and ultimately the evolution of signal design, both simple and complex.
Task context modulates feature-selective responses in area V4
Authors: Popovkina Dina V. , Pasupathy Anitha
Published: April 2019

Feature selectivity of neuronal responses in primate visual cortex is typically measured while animals fixate a small dot on the screen and a stimulus is presented in the near-periphery. This paradigm allows the efficient exploration of feature space, but it provides only a partial view of selectivity by failing to characterize how cognitive factors influence neuronal tuning. Here we focus on primate area V4, known to be influenced by cognitive processes, and ask how neuronal tuning is modulated by task engagement. We compared the tuning for shape and color in 83 well-isolated V4 neurons measured during passive fixation and during active engagement in a shape discrimination task. In both tasks, animals saw the same set of objects—shape x color combinations—but while neither stimulus feature was relevant during the fixation task, shape identity was relevant for behavior during the discrimination task. Consistent with attentional studies, V4 responses during the discrimination task showed a stimulus-independent gain scaling relative to passive fixation, but this was only in a minority of neurons (21/83). For the rest (62/83), response modulations during discrimination depended on stimulus identity: on stimulus shape in neurons more strongly tuned to shape, and on color in neurons more strongly tuned to color. Overall, this resulted in broader tuning for stimulus color, but not shape, during active task engagement. These results suggest that task context can influence the shape and color selectivity of V4 neurons, and in some neurons this effect is consistent with a change in the width of feature tuning.
libsbmljs — Enabling Web–Based SBML Tools
Authors: Medley J Kyle , Hellerstein Joseph , Sauro Herbert M
Published: April 2019

The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web–capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical capabilities of modern web browsers offer a powerful means for building rich, interactive applications. Also, there is a growing developer population specialized in web technologies that is poised to take advantage of the universality of the web to build the next generation of tools in systems biology and other fields. However, current solutions require server– side processing in order to support existing standards in modeling. We present libsbmljs, a JavaScript / WebAssembly library for Node.js and the Web with full support for all SBML extensions. Our library is an enabling technology for online SBML editors, model–building tools, and web–based simulators, and runs entirely in the browser without the need for any dedicated server resources. We provide NPM packages, an extensive set of examples, JavaScript API documentation, and an online demo that allows users to read and validate the SBML content of any model in the BioModels and BiGG databases. We also provide instructions and scripts to allow users to build a copy of libsbmljs against any libSBML version. Although our library supports all existing SBML extensions, we cover how to add additional extensions to the wrapper, should any arise in the future. To demonstrate the utility of this implementation, we also provide a demo at https://libsbmljsdemo.github.io/ with a proof–of–concept SBML simulator that supports ODE and stochastic simulations for SBML core models. Our project is hosted at https://libsbmljs.github.io/, which contains links to examples, API documentation, and all source code files and build scripts used to create libsbmljs. Our source code is licensed under the Apache 2.0 open source license.
dSreg: A bayesian model to integrate changes in splicing and RNA binding protein activity
Authors: Martí-Gómez Carlos , Lara-Pezzi Enrique , Sánchez-Cabo Fátima
Published: April 2019

Alternative splicing (AS) is an important mechanism in the generation of transcript diversity across mammals. AS patterns are dynamically regulated during development and in response to environmental changes. Defects or perturbations in its regulation may lead to cancer or neurological disorders, among other pathological conditions. The regulatory mechanisms controlling AS in a given biological context are typically inferred using a two step-framework: differential AS analysis followed by enrichment methods. These strategies require setting rather arbitrary thresholds and are prone to error propagation along the analysis. To overcome these limitations, we propose dSreg, a Bayesian model that integrates RNAseq with data from regulatory features, e.g. binding sites of RNA binding proteins (RBPs). dSreg identifies the key underlying regulators controlling AS changes and quantifies their activity while simultaneously estimating the changes in exon inclusion rates. dSreg increased both the sensitivity and the specificity of the identified alternative splicing changes in simulated data, even at low read coverage. dSreg also showed improved performance when analyzing a collection of knock-down RBPs experiments from ENCODE, as opposed to traditional enrichment methods such as Over-representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). dSreg opens the possibility to integrate a large amount of readily available RNA-seq datasets at low coverage for AS analysis and allows more cost-effective RNA-seq experiments. dSreg was implemented in python using stan and is freely available to the community at https://bitbucket.org/cmartiga/dsreg.
Oligotyping and Genome-Resolved Metagenomics Reveal DistinctCandidatusAccumulibacter Communities in Full-Scale Side-Stream versus Conventional Enhanced Biological Phosphorus Removal (EBPR) Configurations
Authors: Srinivasan Varun N. , Li Guangyu , Wang Dongqi , Tooker Nicholas B. , Dai Zihan , Onnis-Hayden Annalisa , Pinto Ameet , Gu April Z.
Published: April 2019

CandidatusAccumulibacter phosphatis (CAP) and its sub-clades-level diversity has been associated and implicated in successful phosphorus removal performance in enhanced biological phosphorus removal (EBPR). Development of high-throughput untargeted methods to characterize clades of CAP in EBPR communities can enable a better understanding of Accumulibacter ecology at a higher-resolution beyond OTU-level in wastewater resource recovery facilities (WRRFs). In this study, for the first time, using integrated 16S rRNA gene sequencing, oligotyping and genome-resolved metagenomics, we were able to reveal clade-level differences in Accumulibacter communities and associate the differences with two different full-scale EBPR configurations. The results led to the identification and characterization of a distinct and dominant Accumulibacter oligotype - Oligotype 2 (belonging to Clade IIC) and its matching MAG (RC14) associated with side-stream EBPR configuration. We are also able to extract MAGs belonging to CAP clades IIB (RCAB4-2) and II (RC18) which did not have representative genomes before. This study demonstrates and validates the use of a high-throughput approach of oligotyping analysis of 16S rRNA gene sequences to elucidate CAP clade-level diversity. We also show the existence of a previously uncharacterized diversity of CAP clades in full-scale EBPR communities through extraction of MAGs, for the first time from full-scale facilities.