bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple stable states in microbial communities explained by the stable marriage problem
Authors: Goyal Akshit , Dubinkina Veronika , Maslov Sergei 
Published: December 2017

AbstractExperimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in transitions to other states. Can we reliably both predict such stable states as well as direct and control transitions between them? Here we present a new conceptual model — inspired by the stable marriage problem in game theory and economics — in which microbial communities naturally exhibit multiple stable states, each state with a different species’ abundance profile. Our model’s core ingredient is that microbes utilize nutrients one at a time while competing with each other. Using only two ranked tables, one with microbes’ nutrient preferences and one with their competitive abilities, we can determine all possible stable states as well as predict inter-state transitions, triggered by the removal or addition of a specific nutrient or microbe. Further, using an example of 7 Bacteroides species common to the human gut utilizing 9 polysaccharides, we predict that mutual complementarity in nutrient preferences enables these species to coexist at high abundances.
Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-seq
Authors: Cole Michael B. , Risso Davide , Wagner Allon , DeTomaso David , Ngai John , Purdom Elizabeth , Dudoit Sandrine , Yosef Nir 
Published: December 2017

AbstractSystematic measurement biases make data normalization an essential preprocessing step in single-cell RNA sequencing (scRNA-seq) analysis. There may be multiple, competing considerations behind the assessment of normalization performance, some of them study-specific. Because normalization can have a large impact on downstream results (e.g., clustering and differential expression), it is critically important that practitioners assess the performance of competing methods.We have developedscone— a flexible framework for assessing normalization performance based on a comprehensive panel of data-driven metrics. Through graphical summaries and quantitative reports,sconesummarizes performance trade-offs and ranks large numbers of normalization methods by aggregate panel performance. The method is implemented in the open-source Bioconductor R software package scone. We demonstrate the effectiveness ofsconeon a collection of scRNA-seq datasets, generated with different protocols, including Fluidigm C1 and 10x platforms. We show that top-performing normalization methods lead to better agreement with independent validation data.
Does 10-Hz cathodal oscillating current of the parieto-occipital lobe modulate target detection?
Authors: Sheldon Sarah S. , Mathewson Kyle E. 
Published: December 2017

ABSTRACTThe phase of alpha (8-12 Hz) brain oscillations have been associated with moment to moment changes in visual attention and awareness. Previous work has demonstrated that endogenous oscillations and subsequent behavior can be modulated by oscillating transcranial current stimulation (otCS). The purpose of the current study is to establish the efficacy of cathodal otCS for modulation of the ongoing alpha brain oscillations, allowing for modulation of individual’s visual perception. Thirty-six participants performed a target detection with sham and 10-Hz cathodal otCS. Each participant had two practice and two experimental sets composed of three blocks of 128 trials per block. Stimulating electrodes were small square sponges (20 cm2) placed on the participant’s head with the anode electrode at Cz and the cathode electrode at Oz. A 0.5 mA current was applied at the cathode electrode every 100 ms (10 Hz frequency) during the otCS condition. The same current and frequency was applied for the first 10-20 s of the sham condition, after which the current was turned off. Target detection rates were separated into ten 10-ms bins based on the latency between the stimulation/sham pulse and target onset. Target detection rates were then compared between the sham and otCS experimental conditions across the ten bins in order to test for effects of otCS phase on target detection. We found no significant difference in target detection rates between the sham and otCS conditions, and discuss potential reasons for the apparent inability of cathodal otCS to effectively modulate visual perception.
Comparison of video-based and sensor-based head impact exposure
Authors: Kuo Calvin , Wu Lyndia , Loza Jesus , Senif Daniel , Anderson Scott C. , Camarillo David B. 
Published: December 2017

AbstractPrevious research has sought to quantify head impact exposure using wearable kinematic sensors. However, many sensors suffer from poor accuracy in estimating impact kinematics and count, motivating the need for additional independent impact exposure quantification for comparison. Here, we equipped seven collegiate American football players with instrumented mouthguards, and video recorded practices and games to compare video-based and sensor-based exposure rates and impact location distributions. Over 50 player-hours, we identified 271 helmet contact periods in video, while the instrumented mouthguard sensor recorded 2,032 discrete head impacts. Matching video and mouthguard real-time stamps yielded 193 video-identified helmet contact periods and 217 sensor-recorded impacts. To compare impact locations, we binned matched impacts into frontal, rear, side, oblique, and top locations based on video observations and sensor kinematics. While both video-based and sensor-based methods found similar location distributions, our best method utilizing integrated linear and angular position only correctly predicted 81 of 217 impacts. Finally, based on the activity timeline from video assessment, we also developed a new exposure metric unique to American football quantifying number of cross-verified sensor impacts per player-play. We found significantly higher exposure during games (0.35, 95% CI: 0.29-0.42) than practices (0.20, 95% CI: 0.17-0.23) (p<0.05). In the traditional impacts per player-hour metric, we observed higher exposure during practices (4.7) than games (3.7) due to increased player activity in practices. Thus, our exposure metric accounts for variability in on-field participation. While both video-based and sensor-based exposure datasets have limitations, they can complement one another to provide more confidence in exposure statistics.
High throughput single cell RNA-seq of developing mouse kidney and human kidney organoids reveals a roadmap for recreating the kidney
Authors: Combes Alexander N. , Phipson Belinda , Zappia Luke , Lawlor Kynan T. , Er Pei Xuan , Oshlack Alicia , Little Melissa H. 
Published: December 2017

AbstractRecent advances in our capacity to differentiate human pluripotent stem cells to human kidney tissue are moving the field closer to novel approaches for renal replacement. Such protocols have relied upon our current understanding of the molecular basis of mammalian kidney morphogenesis. To date this has depended upon population based-profiling of non-homogenous cellular compartments. In order to improve our resolution of individual cell transcriptional profiles during kidney morphogenesis, we have performed 10x Chromium single cell RNA-seq on over 6000 cells from the E18.5 developing mouse kidney, as well as more than 7000 cells from human iPSC-derived kidney organoids. We identified 16 clusters of cells representing all major cell lineages in the E18.5 mouse kidney. The differentially expressed genes from individual murine clusters were then used to guide the classification of 16 cell clusters within human kidney organoids, revealing the presence of distinguishable stromal, endothelial, nephron, podocyte and nephron progenitor populations. Despite the congruence between developing mouse and human organoid, our analysis suggested limited nephron maturation and the presence of ‘off target’ populations in human kidney organoids, including unidentified stromal populations and evidence of neural clusters. This may reflect unique human kidney populations, mixed cultures or aberrant differentiation in vitro. Analysis of clusters within the mouse data revealed novel insights into progenitor maintenance and cellular maturation in the major renal lineages and will serve as a roadmap to refine directed differentiation approaches in human iPSC-derived kidney organoids.
Complementary studies of lipid membrane dynamics using iSCAT and super-resolved Fluorescence Correlation Spectroscopy
Authors: Reina Francesco , Galiani Silvia , Shrestha Dilip , Sezgin Erdinc , de Wit Gabrielle , Cole Daniel , Lagerholm B. Christoffer , Kukura Philip , Eggeling Christian 
Published: December 2017

AbstractObservation techniques with high spatial and temporal resolution, such as single-particle tracking (SPT) based on interferometric Scattering (iSCAT) microscopy, and fluorescence correlation spectroscopy applied on a super-resolution STED microscope (STED-FCS), have revealed new insights of the molecular organization of membranes. While delivering complementary information, there are still distinct differences between these techniques, most prominently the use of fluorescent dye-tagged probes for STED-FCS and a need for larger scattering gold nanoparticle tags for iSCAT. In this work we have used lipid analogues tagged with a hybrid fluorescent tag – gold nanoparticle construct, to directly compare the results from STED-FCS and iSCAT measurements of phospholipid diffusion on a homogeneous Supported Lipid Bilayer (SLB). These comparative measurements showed that while the mode of diffusion remained free, at least at the spatial (>40 nm) and temporal (50 ≤ t ≤ 100 ms) scales probed, the diffussion coefficient was reduced by 20- to 60-fold when tagging with 20 and 40 nm large gold particles as compared to when using dye-tagged lipid analogues. These FCS measurements of hybrid fluorescent tag – gold nanoparticle labeled lipids also revealed that commercially supplied streptavidin-coated gold nanoparticles contain large quantities of free streptavidin. Finally, the values of apparent diffusion coefficients obtained by STED-FCS and iSCAT differed by a factor of 2-3 across the techniques, while relative differences in mobility between different species of lipid analogues considered were identical in both approaches. In conclusion, our experiments reveal that large and potentially crosslinking scattering tags introduce a significant slow-down in diffusion on SLBs but no additional bias, and our labeling approach creates a new way of exploiting complementary information from STED-FCS and iSCAT measurements.
Sleep spindle refractoriness segregates periods of memory reactivation
Authors: Antony James W. , Piloto Luis , Wang Margaret , Pacheco Paula , Norman Kenneth A. , Paller Ken A. 
Published: December 2017

AbstractThe stability of long-term memories is enhanced by reactivation during sleep. Correlative evidence has linked memory reactivation with thalamocortical sleep spindles, although their functional role is poorly understood. Our initial study replicated this correlation but also demonstrated a novel rhythmicity to spindles, such that spindles are less likely to occur immediately following other spindles. We leveraged this rhythmicity to test the role of spindles in memory by using real-time spindle tracking to present cues inside versus outside the presumptive refractory period; as predicted, cues presented outside the refractory period led to better memory. Our findings reveal a previously undescribed neural mechanism whereby spindles segment sleep into two distinct substates: prime opportunities for reactivation and gaps that segregate reactivation events.One Sentence SummaryThe characteristic timing of sleep spindles regulates when memories can be reactivated during sleep.
S1PR3 mediates itch and pain via distinct TRP channel-dependent pathways
Authors: Hill Rose Z. , Morita Takeshi , Brem Rachel B. , Bautista Diana M. 
Published: December 2017

AbstractSphingosine 1-phosphate (S1P) is a bioactive signaling lipid associated with a variety of chronic pain and itch disorders. S1P signaling has been linked to cutaneous pain, but its role in itch has not yet been studied. Here we find that S1P triggers itch and pain in mice in a concentration-dependent manner, with low levels triggering acute itch alone, and high levels triggering both pain and itch. Calcium imaging and electrophysiological experiments revealed that S1P signals via S1PR3 and TRPA1 in a subset of pruriceptors, and via S1PR3 and TRPV1 in a subset of heat nociceptors. And in behavioral assays, S1P-evoked itch was selectively lost in mice lacking TRPA1, whereas S1P-evoked acute pain and heat hypersensitivity were selectively lost in mice lacking TRPV1. We conclude that S1P acts via different cellular and molecular mechanisms to trigger itch and pain. Our discovery elucidates the diverse roles that S1P signaling plays in somatosensation and provides insight into how itch and pain are discriminated in the periphery.Significance StatementItch and pain are major health problems with few effective treatments. Here, we show that the pro-inflammatory lipid S1P and its receptor S1PR3 trigger itch and pain behaviors via distinct molecular and cellular mechanisms. Our results provide a detailed understanding of the roles that S1P and S1PR3 play in somatosensation, highlighting their potential as targets for analgesics and antipruritics, and provide new insight into the mechanistic underpinnings of itch versus pain discrimination in the periphery.
Mapping mutational effects along the evolutionary landscape of HIV envelope
Authors: Haddox Hugh K. , Dingens Adam S. , Hilton Sarah K. , Overbaugh Julie , Bloom Jesse D. 
Published: December 2017

AbstractThe immediate evolutionary space accessible to HIV is largely determined by how single amino-acid mutations affect fitness. These mutational effects can shift as the virus evolves. However, the prevalence of such shifts in mutational effects remains unclear. Here we quantify the effects on viral growth of all amino-acid mutations to two HIV envelope (Env) proteins that differ at >100 residues. Most mutations similarly affect both Envs, but the amino-acid preferences of a minority of sites have clearly shifted. These shifted sites usually prefer a specific amino acid in one Env, but tolerate many amino acids in the other. Surprisingly, shifts are only slightly enriched at sites that have substituted between the Envs -- and many occur at residues that do not even contact substitutions. Therefore, long-range epistasis can unpredictably shift Env's mutational tolerance during HIV evolution, although the amino-acid preferences of most sites are conserved between moderately diverged viral strains.
Caesarean section wound infection surveillance: Information for action
Authors: Scheck Simon M. , Blackmore Timothy , Maharaj Dushyant , Langdana Fali , Elder Rosalie E. 
Published: December 2017

Surgical site infection (SSI) following caesarean section is common, resulting in significant morbidity. Several factors are known to contribute to wound infection, including maternal, procedural and antibiotic factors. We sought to clarify these issues and sought opportunities to make improvements. A retrospective cohort study was performed assessing all women who underwent caesarean section in 2014 and 2015 at Wellington Hospital. Any women with culture‐positive wound samples within 30 days of surgery were identified, and clinical notes reviewed. Odds ratios (OR) were calculated for available maternal, procedural and antibiotic risk factors. Two simplified surveillance techniques were also tested for their abilities to identify significant trends. The study included 2231 women, of whom 116 (5.2%) were identified as having SSI. Maternal obesity (body mass index (BMI) ≥ 30) was associated with significant SSI risk (OR 4.1, P < 0.001). The pathogen distribution was significantly different between women with BMI < 30 and BMI ≥ 30 (P < 0.001). Increased cefazolin dose based on BMI (3 g dose for BMI ≥ 30) was associated with a significant reduction in SSI (OR 0.309, P < 0.001) and was administered in 74.1% of obese women receiving cefazolin. Māori women had an increased SSI risk (OR 2.1, P = 0.019), as did Samoan women (OR 3.0, P = 0.002). The study reinforces other studies showing that raised BMI is the single biggest risk factor for surgical site infection post‐caesarean section. Surveillance using simplified techniques appears to be adequate to identify trends. We believe that concentrating on appropriate antibiotic dosing and targeting special wound care measures will be pivotal interventions in improving outcomes in high‐risk groups.
Perspectives of patients with non‐insulin‐treated type 2 diabetes on self‐monitoring of blood glucose: A qualitative study
Authors: Chen Chen‐Mei , Hung Li‐Chen , Chen Yang‐Lin , Yeh Mei Chang 
Published: December 2017

Aims and objectivesTo explore experiences of self‐monitoring of blood glucose among patients with non‐insulin‐treated type 2 diabetes.BackgroundSelf‐monitoring of blood glucose is essential to diabetes care and facilitates glycaemic control. Patients’ perspectives of self‐monitoring of blood glucose have seldom been discussed in the literature, and engagement in self‐monitoring of blood glucose is consistently low.DesignThe descriptive phenomenological method was used.MethodsPurposive sampling was conducted to recruit participants from the endocrinology departments of medical institutions in Taiwan based on the following criteria: (i) having a medical diagnosis of type 2 diabetes, (ii) not being treated with insulin, (iii) having engaged in self‐monitoring of blood glucose at least once within the preceding 6 months, (iv) being at least 20 years old and (v) not having any major mental or cognitive disorders. Data were collected in outpatient consultation rooms, the participants’ homes and other settings where the participants felt secure and comfortable. In‐depth interviews were conducted to collect data from 16 patients with diabetes.ResultsThe participants perceived that lifestyle affected blood glucose levels and did not know how to handle high or low blood glucose levels. Their willingness to continue self‐monitoring of blood glucose depended on whether healthcare professionals checked or discussed their blood glucose levels with them.ConclusionsThe patients’ knowledge regarding blood glucose variation and healthcare professionals’ attitudes affected the patients’ self‐monitoring of blood glucose behaviours. The empirical findings illustrated self‐monitoring of blood glucose experiences and recommended that healthcare professionals’ closely attend to patients’ requirements and responses to diabetes and incorporate the self‐monitoring of blood glucose into therapy plans.Relevance to clinical practiceHealthcare professionals should reinforce patients’ knowledge on appropriate responses to high and low blood glucose levels, intervene appropriately, discuss self‐monitoring of blood glucose results with patients and track these results.
Aminoarabinosylation of Lipid A Is Critical for the Development of Colistin Resistance in Pseudomonas aeruginosa
Authors: Lo Sciuto Alessandra , Imperi Francesco 
Published: December 2017

ABSTRACT

Lipid A aminoarabinosylation is invariably associated with colistin resistance in
Pseudomonas aeruginosa
; however, the existence of alternative aminoarabinosylation-independent colistin resistance mechanisms in this bacterium has remained elusive. By combining reverse genetics with experimental evolution assays, we demonstrate that a functional lipid A aminoarabinosylation pathway is critical for the acquisition of colistin resistance in reference and clinical
P. aeruginosa
isolates. This highlights lipid A aminoarabinosylation as a promising target for the design of colistin adjuvants against
P. aeruginosa
.
All-cause mortality in adults with and without type 2 diabetes: findings from the national health monitoring in Germany
Authors: Röckl Susanne , Brinks Ralph , Baumert Jens , Paprott Rebecca , Du Yong , Heidemann Christin , Scheidt-Nave Christa 
Published: December 2017

ObjectiveTo estimate age-specific and sex-specific all-cause mortality among adults with and without type 2 diabetes (T2D) in Germany.Research design and methodsThe German National Health Interview and Examination Survey 1998 (GNHIES98) included a mortality follow-up (median follow-up time 12.0 years) of its nationwide sample representative of the population aged 18–79 years. After exclusion of participants with type 1 diabetes, age- and sex-stratified mortality rates (MR) were calculated for 330 GNHIES98 participants with diagnosed T2D (self-reported diagnosis or antidiabetic medication), 245 with undiagnosed T2D (no diagnosed T2D, glycated hemoglobin A1c ≥6.5% (≥48 mmol/mol)), and 5975 without T2D. Mortality rate ratios (MRR) comparing MR of persons with and without T2D were estimated. Age-/sex-standardized MR and MRR were calculated including persons aged 45 years or older. MRR were used to estimate the number of years of life lost (YLL) due to diagnosed diabetes in 2010.ResultsOver 75 994 person-years, 73 persons with undiagnosed T2D, 103 with diagnosed T2D, and 425 persons without T2D died. MRR were significantly higher in younger age groups, except for analyses limited to women or diagnosed T2D. Age- and sex-standardized MRR (95% CI) among persons aged 45 years or older were 1.96 (1.41 to 2.71) for undiagnosed, 1.68 (1.26 to 2.23) for diagnosed, and 1.82 (1.45 to 2.28) for total (undiagnosed or diagnosed) T2D. Sex-stratified analysis revealed similar age-standardized MRR for undiagnosed (1.56 (0.79 to 3.06)) and diagnosed T2D (1.56 (1.03 to 2.37)) among women, and a higher age-standardized MRR for undiagnosed (2.06 (1.43 to 2.97)) than diagnosed T2D (1.70 (1.10 to 2.63)) among men. YLL due to diagnosed diabetes in Germany in 2010 were 164 600 (35 000 to 279 300) among women and 169 900 (28 300 to 328 300) among men.ConclusionsIn Germany, age- and sex-standardized all-cause mortality is almost twice as high for adults with T2D as for adults without T2D. The T2D-associated excess risk of mortality appears to be most pronounced in younger adults and among men unaware of their T2D.
Confidence in palliative care issues by medical students and internal medicine residents
Authors: Storarri Ana Carolina Montouro , de Castro Giovana Dalmedico , Castiglioni Lilian , Cury Patricia Maluf 
Published: December 2017

BackgroundPalliative care (PC) is a relatively new field in Brazil, but this knowledge is of great importance in medical practice.ObjectiveTo evaluate the degree of confidence among medical students and first-year and second-year internal medicine residents in addressing issues of death and terminal illness with patients and their families.MethodA modified version of the Self-Efficacy in Palliative Care Scale was applied to 293 students in their first year to sixth year at the School of Medicine of São José do Rio Preto and to 43 residents in their first year or second year of medical practice at the same institution in Brazil, in 2015. The questionnaire evaluated students' opinions on the need to include theoretical and practical classes on PC in the medical school.ResultsStudents in their fifth year of medical school were more confident than the students in their first, second, third and fourth years; there were no statistically significant differences between fifth-year students, sixth-year students and the internal medicine residents.ConclusionResidents were more confident than all of the medical school students except those in their fifth year (P<0.05) because they have more contact with terminally ill patients than other students do; fifth-year medical students are likely overestimating their abilities.