bluuebunny/crossref_metadata_2025 huggingface dataset:
Poor Oral Health Predicts Higher 10-Year Cardiovascular Risk
Authors: Hwang Seon Young , Shim Jae Lan , Kang Dayun , Choi Jungsoon
Published: June 2018

Background:

Although the association between periodontitis and cardiovascular disease (CVD) has been reported, whether periodontitis and poor oral health behavior influence CVD risk remains unclear.

Objective:

The aim of this study was to examine whether periodontal disease and poor oral health behavior predict 10-year general CVD risk using the Framingham Risk Score.

Methods:

Patients older than 30 years with no CVD history (n = 8370) were selected using cross-sectional study data from the Korean National Health and Nutrition Examination Survey in 2013 and 2014. To reduce selection bias in this population-based study, propensity score matching analysis was used with SPSS and R programs to compare CVD risk.

Results:

Overall, 39.2% of the study population (n = 3277) had a global CVD risk of  10% or greater. In the low- and at-risk groups, 20.7% and 45.3% of patients, respectively, were diagnosed with periodontal disease by a dentist. Moreover, 43.2% and 62.8% of the low- and at-risk group patients, respectively, brushed teeth less than 3 times a day. After 1:1 propensity score matching of the low-risk (n = 1135) and at-risk (n = 1135) groups, bivariate analyses showed that a diagnosis of periodontal disease and less frequent toothbrushing were associated with a higher CVD risk (P < .001). Logistic regression analysis also showed that patients having periodontal disease and who brushed teeth less frequently were 1.38 and 1.33 times, respectively, more likely to be at risk of CVD (P < .001).

Conclusion:

Education on periodontitis management and oral hygiene behavior should be included, when strategies for public risk reduction of CVD are developed.
Dating of Traumatic Brain Injury in Forensic Cases Using Immunohistochemical Markers (I)
Authors: Romero Tirado María de los Ángeles , Blanco Pampin José Manuel , Gallego Gómez Rosalía
Published: June 2018

Studies about head trauma are experimental or have a clinical or prognosis purpose. In this study, we used samples from human autopsies to answer common medical-legal questions.

We studied 21 problem cases and 4 controls. Samples were obtained directly from the injured area, fixed in 10% formalin during 24 hours and then preserved in 70% ethanol. This procedure optimizes the immunohistochemical technique.

The neurofilament antibody shows beaded axons since the first moment; over time, they increase their density and diameter as survival time also increases. These changes begin in the gray matter, 2 hours after trauma can be seen around vessels and in hemorrhagic areas. At 24 hours, beaded axons appear in the white mater, which finally loses its structure and cellular density.

On the other hand, the β-amyloid precursor protein marker begins to be weakly seen 2 hours after injury. At 24 hours, a diffuse pattern can appear, suggesting primary traumatic injury. The marker reading keeps increasing until day 26, when a “Z” pattern appears in the white matter, suggesting secondary hypoxic injury.

All these chronologic changes could be useful to approach the date of trauma. They let us to distinguish between long surviving cases from those whose death was immediate (within the first 30 minutes).
Associations Between Race, Perceived Psychological Stress, and the Gut Microbiota in a Sample of Generally Healthy Black and White Women: A Pilot Study on the Role of Race and Perceived Psychological Stress
Authors: Carson Tiffany L. , Wang Fuchenchu , Cui Xiangqin , Jackson Bradford E. , Van Der Pol William J. , Lefkowitz Elliot J. , Morrow Casey , Baskin Monica L.
Published: June 2018

Objective

Racial health disparities persist among black and white women for colorectal cancer. Understanding racial differences in the gut microbiota and related covariates (e.g., stress) may yield new insight into unexplained colorectal cancer disparities.

Methods

Healthy non-Hispanic black or white women (age ≥19 years) provided survey data, anthropometrics, and stool samples. Fecal DNA was collected and isolated from a wipe. Polymerase chain reaction was used to amplify the V4 region of the 16SrRNA gene and 250 bases were sequenced using the MiSeq platform. Microbiome data were analyzed using QIIME. Operational taxonomic unit data were log transformed and normalized. Analyses were conducted using linear models in R Package “limma.”

Results

Fecal samples were analyzed for 80 women (M (SD) age = 39.9 (14.0) years, 47 black, 33 white). Blacks had greater average body mass index (33.3 versus 27.5 kg/m2, p < .01) and waist circumference (98.3 versus 86.6 cm, p = .003) than whites. Whites reported more stressful life events (p = .026) and greater distress (p = .052) than blacks. Final models accounted for these differences. There were no significant differences in dietary variables. Unadjusted comparisons revealed no racial differences in alpha diversity. Racial differences were observed in beta diversity and abundance of top 10 operational taxonomic units. Blacks had higher abundances than whites of Faecalibacterium (p = .034) and Bacteroides (p = .038). Stress was associated with abundances of Bifidobacterium. The association between race and Bacteroides (logFC = 1.72, 0 = 0.020) persisted in fully adjusted models.

Conclusions

Racial differences in the gut microbiota were observed including higher Bacteroides among blacks. Efforts to cultivate an “ideal” gut microbiota may help reduce colorectal cancer risk.
Computed Tomographic Features of Primary Small Cell Neuroendocrine Tumors of the Gallbladder
Authors: Faraoun Sid Ahmed , Guerrache Youcef , Dautry Raphael , Boudiaf Mourad , Dohan Anthony , Barral Matthias , Hoeffel Christine , Rousset Pascal , Fohlen Audrey , Soyer Philippe
Published: June 2018

Purpose

This study aimed to report the computed tomography (CT) imaging features of primary small cell neuroendocrine tumors of the gallbladder (PSCNETGs).

Materials and Methods

The CT examinations of 9 patients (5 women, 4 men; median age, 57 years) with histopathologically proven PSCNETG were reviewed. Computed tomographic images were analyzed with respect to morphologic features of primary tumors and accompanying lymph nodes.

Results

All PSCNETGs were visible on CT, with a median largest axial diameter of 60 mm (Q1, 30 mm; Q3 mm, 82; range, 25–86 mm). These tumors presented with extraluminal growth (8/9; 89%), heterogeneous enhancement (8/9; 89%), gallbladder replacement greater than 50% (5/9; 56%), hepatic metastases (5/9; 56%), and direct liver involvement by tumor (4/9; 44%). Enlarged lymph nodes were present in all patients (9/9; 100%) with a median largest axial diameter of 39 mm (Q1, 23 mm; Q3, 48 mm; range, 12–62 mm). Vessel encasement by lymph nodes was present in 6 (67%) of 9 patients.

Conclusion

Primary small cell neuroendocrine tumors of the gallbladder predominantly presents as a large, heterogeneous gallbladder mass with extraluminal growth in association with large metastatic lymph nodes and intrahepatic metastases.
Accuracy of Automated Liver Contouring, Fat Fraction, and R2* Measurement on Gradient Multiecho Magnetic Resonance Images
Authors: Stocker Daniel , Bashir Mustafa R. , Kannengiesser Stephan A.R. , Reiner Cäcilia S.
Published: June 2018

Objective

This study aimed to evaluate the performance of an automated workflow of volumetric liver proton density fat fraction (PDFFvol) and R2* quantification with automated inline liver volume (LV) segmentation.

Methods

Dual-echo and multiecho Dixon magnetic resonance images were evaluated in 74 consecutive patients (group A, PDFF < 10%; B, PDFF ≥ 10%; C, R2* ≥ 100 s−1; D, post-hemihepatectomy). The values of PDFFvol and R2*vol measurements across the LV were generated on multiecho images in an automated fashion based on inline liver segmentation on dual-echo images. Similar measurements were performed manually.

Results

Using the inline algorithm, the mis-segmented LV was highest in group D (80%). There were no significant differences between automated and manual measurements of PDFFvol. Automated R2*vol was significantly lower than manual R2*vol in group A (P = 0.004).

Conclusions

Inline LV segmentation performed well in patients without and with hepatic steatosis. In cases with iron overload and post-hemihepatectomy, extrahepatic areas were erroneously included to a greater extent, with a tendency toward overestimation of PDFFvol.
Phantom Validation of Spectral Detector Computed Tomography–Derived Virtual Monoenergetic, Virtual Noncontrast, and Iodine Quantification Images
Authors: Ananthakrishnan Lakshmi , Duan Xinhui , Rajiah Prabhakar , Soesbe Todd C. , Lewis Matthew A. , Xi Yin , Fielding Julia R. , Lenkinski Robert E. , Leyendecker John R. , Abbara Suhny
Published: June 2018

Purpose

Spectral detector computed tomography (SDCT) is a new CT technology that uses a dual-layer detector to perform energy separation. We aim to assess 3 clinical concepts using a phantom model: noise profile across the virtual monoenergetic (VME) spectrum, accuracy of iodine quantification, and virtual noncontrast (VNC) reconstructions' ability to remove iodine contribution to attenuation.

Methods

Six vials containing varying concentrations of iodinated contrast (0–6 mg/mL) diluted in water were placed in a water bath and scanned on an SDCT scanner. Virtual monoenergetic (40–200 keV at 10-keV increments), iodine–no-water, and VNC reconstructions were created. Attenuation (in Hounsfield units [HU]), VME noise at each energy level, CT-derived iodine concentration, and VNC attenuation were recorded.

Results

Virtual monoenergetic noise was improved at all energies compared with conventional images (conventional, 9.8–11.2; VME, 7.5–9.5). Noise profile showed a slightly higher image noise at 40 keV, but was otherwise relatively flat across the energy spectrum. On iodine–no-water reconstructions, measured varied from actual iodine concentration by ±0.1 mg/mL (SD, 0.16–0.36). Virtual noncontrast attenuation was within 5 HU of water attenuation at all iodine concentrations.

Conclusion

Reconstructions of SDCT show lower VME image noise, accurate iodine quantification, and VNC attenuation values within 5 HU of expected in a phantom model.
The magic number: Are improved outcomes observed at trauma centers with undertriage rates below 5%?
Authors: Jammula Shreya , Bradburn Eric H. , Gross Brian W. , Cook Alan D. , Reihart Michael J. , Rogers Frederick B.
Published: June 2018

BACKGROUND

The American College of Surgeons Committee on Trauma (ACSCOT) advises trauma centers maintain <5% undertriage rate (UTR), but provides limited rationale for this figure. We sought to determine whether patients managed at Level I/II trauma centers with a UTR less than 5% had improved outcomes compared with centers with greater than 5% UTR. We hypothesized that similar overall adjusted outcomes would be observed at trauma centers in Pennsylvania regardless of their compliance with ACSCOT undertriage recommendation.

METHODS

The Pennsylvania Trauma Outcome Study database was retrospectively queried for all trauma patients managed at accredited adult Level I/II trauma centers (n = 27) from 2003 to 2015. Patients with missing data on Injury Severity Score and/or Trauma Activation Status were excluded from the analysis. Institutional UTR were calculated for all trauma centers based on ACSCOT criteria (Injury Severity Score >15; no trauma activation) and were categorized into less than 5% or greater than 5% subgroups. A multilevel mixed-effects logistic regression model assessed the adjusted impact of management at centers with less than 5% undertriage. Statistical significance was set at p less than 0.05.

RESULTS

A total of 404,315 patients from 27 trauma centers met inclusion criteria. Institutional UTRs ranged from 0% to 20.5%, with 15 centers exhibiting UTR less than 5% and 12 centers with UTR greater than 5%. No clinically meaningful difference in unadjusted mortality rate was observed between subgroups (<5% UTR: 5.19%; >5% UTR: 5.20%; p < 0.001). In adjusted analysis, no difference in mortality was found for patients managed at centers with less than 5% UTR compared to those with greater than 5% UTR (adjusted odds ratio, 1.06; 95% confidence interval, 0.85–1.33; p = 0.608).

CONCLUSION

Achieving ACSCOT less than 5% undertriage standards appears to have limited impact on institutional mortality. Further research should seek to identify new triage criteria that can be uniformly applied to all trauma centers.

LEVEL OF EVIDENCE

Epidemiological study, level III.
Augmentation Effect of Low-Frequency Repetitive Transcranial Magnetic Stimulation Over Presupplementary Motor Area in Obsessive-Compulsive Disorder
Authors: Arumugham Shyam Sundar , VS Subhasini , HN Madhuri , B Vinay , Ravi Malvika , Sharma Eesha , Thirthalli Jagadisha , Reddy YC Janardhan
Published: June 2018

Objective

The current study investigated the efficacy of low-frequency repetitive transcranial magnetic stimulation (rTMS) over bilateral presupplementary motor area (pre-SMA) in patients suffering from obsessive-compulsive disorder (OCD) with partial/poor response to pharmacotherapy, in a double-blinded randomized sham controlled trial.

Method

Forty subjects with OCD, who were on stable medications with partial/poor response to pharmacotherapy were randomly divided into 2 groups (n = 20 in each group), to receive either active or sham low-frequency rTMS over bilateral pre-SMA. Thirty-six patients were eligible for intent-to-treat analysis. There was no significant difference in relevant demographic and clinical variables between the 2 groups at baseline.

Results

There were no statistically significant differences between the 2 groups after 3 weeks of treatment in the Yale-Brown Obsessive Compulsive Scale score (time*group interaction,F2.48,84.16= 0.80,P= 0.40) and other secondary outcome measures including responder rates and depressive and anxiety symptoms.

Conclusions

Low-frequency rTMS over pre-SMA may not be effective as an augmenting agent in partial/poor responders to SRIs. This study underlines the need to explore alternate rTMS protocols in OCD.
Restoration of pyrethroid susceptibility in a highly resistant
Aedes aegypti
population
Authors: Grossman Marissa K. , Uc-Puc Valentin , Rodriguez Julian , Cutler David J. , Morran Levi T. , Manrique-Saide Pablo , Vazquez-Prokopec Gonzalo M.
Published: June 2018

Insecticide resistance has evolved in disease vectors worldwide, creating the urgent need to either develop new control methods or restore insecticide susceptibility to regain use of existing tools. Here we show that phenotypic susceptibility can be restored in a highly resistant field-derived strain of
Aedes aegypti
in only 10 generations through rearing them in the absence of insecticide.
Acid secretion by the boring organ of the burrowing giant clam,
Tridacna crocea
Authors: Hill Richard W. , Armstrong Eric J. , Inaba Kazuo , Morita Masaya , Tresguerres Martin , Stillman Jonathon H. , Roa Jinae N. , Kwan Garfield T.
Published: June 2018

The giant clam
Tridacna crocea
, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However,
T. crocea
's mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of surfaces it contacts by greater than or equal to 2 pH units below seawater pH day and night. Acid secretion is likely mediated by vacuolar-type H
+
-ATPase, which we demonstrate (by immunofluorescence) is abundant in the pedal mantle outer epithelium. Our discovery of acid secretion solves this decades-old mystery and reveals that, during bioerosion,
T. crocea
can liberate reef constituents directly to the soluble phase, rather than producing sediment alone as earlier assumed.
The most effective pollinator principle applies to new invasive pollinators
Authors: Medel Rodrigo , González-Browne Catalina , Salazar Daniela , Ferrer Pedro , Ehrenfeld Mildred
Published: June 2018

G. L. Stebbins’ most effective pollinator principle states that when pollinators are not limiting, plants are expected to specialize and adapt to the most abundant and effective pollinator species available. In this study, we quantify the effectiveness of bees, hummingbirds and hawkmoths in a Chilean population ofErythranthe lutea(Phrymaceae), and examine whether flower traits are subject to pollinator-mediated selection by the most effective pollinator species during two consecutive years. Unlike most species in the pollinator community, the visitation rate of the recently arrivedBombus terrestrisdid not change substantially between years, which together with its high and stable pollen delivery to flower stigmas made this species the most important in the pollinator assemblage, followed by the solitary beeCentris nigerrima. Flower traits were under significant selection in the direction expected for short-tongue bees, suggesting thatE. luteais in the initial steps of adaptation to the highly effective exotic bumblebee.Our results illustrate the applicability of Stebbins' principle for new invasive pollinators, and stress their importance in driving flower adaptation of native plant species, a critical issue in the face of biotic exchange and homogenization.
Dominance structure of assemblages is regulated over a period of rapid environmental change
Authors: Jones Faith A. M. , Magurran Anne E.
Published: June 2018

Ecological assemblages are inherently uneven, with numerically dominant species contributing disproportionately to ecosystem services. Marked biodiversity change due to growing pressures on the world's ecosystems is now well documented. However, the hypothesis that dominant species are becoming relatively more abundant has not been tested. We examined the prediction that the dominance structure of contemporary communities is shifting, using a meta-analysis of 110 assemblage timeseries. Changes in relative and absolute dominance were evaluated with mixed and cyclic-shift permutation models. Our analysis uncovered no evidence of a systematic change in either form of dominance, but established that relative dominance is preserved even when assemblage size (total
N
) changes. This suggests that dominance structure is regulated alongside richness and assemblage size, and highlights the importance of investigating multiple components of assemblage diversity when evaluating ecosystem responses to environmental drivers.
Scalable co-optimization of morphology and control in embodied machines
Authors: Cheney Nick , Bongard Josh , SunSpiral Vytas , Lipson Hod
Published: June 2018

Evolution sculpts both the body plans and nervous systems of agents together over time. By contrast, in artificial intelligence and robotics, a robot's body plan is usually designed by hand, and control policies are then optimized for that fixed design. The task of simultaneously co-optimizing the morphology and controller of an embodied robot has remained a challenge. In psychology, the theory of embodied cognition posits that behaviour arises from a close coupling between body plan and sensorimotor control, which suggests why co-optimizing these two subsystems is so difficult: most evolutionary changes to morphology tend to adversely impact sensorimotor control, leading to an overall decrease in behavioural performance. Here, we further examine this hypothesis and demonstrate a technique for ‘morphological innovation protection’, which temporarily reduces selection pressure on recently morphologically changed individuals, thus enabling evolution some time to ‘readapt’ to the new morphology with subsequent control policy mutations. We show the potential for this method to avoid local optima and converge to similar highly fit morphologies across widely varying initial conditions, while sustaining fitness improvements further into optimization. While this technique is admittedly only the first of many steps that must be taken to achieve scalable optimization of embodied machines, we hope that theoretical insight into the cause of evolutionary stagnation in current methods will help to enable the automation of robot design and behavioural training—while simultaneously providing a test bed to investigate the theory of embodied cognition.
Neutron scanning reveals unexpected complexity in the enamel thickness of an herbivorous Jurassic reptile
Authors: Jones Marc E. H. , Lucas Peter W. , Tucker Abigail S. , Watson Amy P. , Sertich Joseph J. W. , Foster John R. , Williams Ruth , Garbe Ulf , Bevitt Joseph J. , Salvemini Floriana
Published: June 2018

Eilenodontines are one of the oldest radiation of herbivorous lepidosaurs (snakes, lizards and tuatara) characterized by batteries of wide teeth with thick enamel that bear mammal-like wear facets. Unlike most reptiles, eilenodontines have limited tooth replacement, making dental longevity particularly important to them. We use both X-ray and neutron computed tomography to examine a fossil tooth from the eilenodontine
Eilenodon
(Late Jurassic, USA). Of the two approaches, neutron tomography was more successful and facilitated measurements of enamel thickness and distribution. We find the enamel thickness to be regionally variable, thin near the cusp tip (0.10 mm) but thicker around the base (0.15–0.30 mm) and notably greater than that of other rhynchocephalians such as the extant
Sphenodon
(0.08–0.14 mm). The thick enamel in
Eilenodon
would permit greater loading, extend tooth lifespan and facilitate the establishment of wear facets that have sharp edges for orally processing plant material such as horsetails (
Equisetum
). The shape of the enamel dentine junction indicates that tooth development in
Eilenodon
and
Sphenodon
involved similar folding of the epithelium but different ameloblast activity.
Antithetic proportional-integral feedback for reduced variance and improved control performance of stochastic reaction networks
Authors: Briat Corentin , Gupta Ankit , Khammash Mustafa
Published: June 2018

The ability of a cell to regulate and adapt its internal state in response to unpredictable environmental changes is called homeostasis and this ability is crucial for the cell's survival and proper functioning. Understanding how cells can achieve homeostasis, despite the intrinsic noise or randomness in their dynamics, is fundamentally important for both systems and synthetic biology. In this context, a significant development is the proposed antithetic integral feedback (AIF) motif, which is found in natural systems, and is known to ensure robust perfect adaptation for the mean dynamics of a given molecular species involved in a complex stochastic biomolecular reaction network. From the standpoint of applications, one drawback of this motif is that it often leads to an increased cell-to-cell heterogeneity or variance when compared to a constitutive (i.e. open-loop) control strategy. Our goal in this paper is to show that this performance deterioration can be countered by combining the AIF motif and a negative feedback strategy. Using a tailored moment closure method, we derive approximate expressions for the stationary variance for the controlled network that demonstrate that increasing the strength of the negative feedback can indeed decrease the variance, sometimes even below its constitutive level. Numerical results verify the accuracy of these results and we illustrate them by considering three biomolecular networks with two types of negative feedback strategies. Our computational analysis indicates that there is a trade-off between the speed of the settling-time of the mean trajectories and the stationary variance of the controlled species; i.e. smaller variance is associated with larger settling-time.
How ants move: individual and collective scaling properties
Authors: Gallotti Riccardo , Chialvo Dante R.
Published: June 2018

The motion of social insects is often used as a paradigmatic example of complex adaptive dynamics arising from decentralized individual behaviour. In this paper, we revisit the topic of the ruling laws behind the burst of activity in ants. The analysis, done over previously reported data, reconsiders the causation arrows, proposed at individual level, not finding any link between the duration of the ants' activity and their moving speed. Secondly, synthetic trajectories created from steps of different ants demonstrate that a Markov process can explain the previously reported speed shape profile. Finally, we show that as more ants enter the nest, the faster they move, which implies a collective property. Overall, these results provide a mechanistic explanation for the reported behavioural laws, and suggest us a formal way to further study the collective properties in these scenarios.
Forward and inverse problems in the mechanics of soft filaments
Authors: Gazzola M. , Dudte L. H. , McCormick A. G. , Mahadevan L.
Published: June 2018

Soft slender structures are ubiquitous in natural and artificial systems, in active and passive settings and across scales, from polymers and flagella, to snakes and space tethers. In this paper, we demonstrate the use of a simple and practical numerical implementation based on the Cosserat rod model to simulate the dynamics of filaments that can bend, twist, stretch and shear while interacting with complex environments via muscular activity, surface contact, friction and hydrodynamics. We validate our simulations by solving a number of forward problems involving the mechanics of passive filaments and comparing them with known analytical results, and extend them to study instabilities in stretched and twisted filaments that form solenoidal and plectonemic structures. We then study active filaments such as snakes and other slender organisms by solving inverse problems to identify optimal gaits for limbless locomotion on solid surfaces and in bulk liquids.
Analysis of crotonaldehyde puff-by-puff release in mainstream cigarette smoke under various smoking regimens by high-performance liquid chromatography with the modified QuEChERS method
Authors: Li Chao , Li E'xian , Zhang Jian , Tao Ying , Zhang Chengming , Shen Xiaofeng , Liu Ya , Qin Yunhua
Published: June 2018

To study puff-by-puff release characteristics of crotonaldehyde in mainstream cigarette smoke under diverse intensive smoking regimens, we designed an RM20H smoking machine with a puff-by-puff smoke collection unit to automatically trap crotonaldehyde in the mainstream cigarette smoke. Using this process, we trapped, puff-by-puff, crotonaldehyde in mainstream smoke generated by different smoking regimens and quantitatively analysed the levels of crotonaldehyde using high-performance liquid chromatography with a modified QuEChERS sample pretreatment method. On the basis of the crotonaldehyde in each puff, we determined crotonaldehyde's puff-by-puff release characteristics. The results showed that crotonaldehyde's puff-by-puff release remained nearly constant for the International Organization for Standardization mode while increased polynomial trend was seen (
n
 ≥ 6) under the Massachusetts and Health Canada smoking regimens. The equation fit for various regimens was good (
R
2
 > 0.9192). Release characteristics by puff were classified into four categories: (1) first, second and third puffs; (2) fourth and fifth puffs; (3) sixth puff; and (4) seventh and eighth puffs.
Forensic efficiency estimate and phylogenetic analysis for Chinese Kyrgyz ethnic group revealed by a panel of 21 short tandem repeats
Authors: Guo Yuxin , Chen Chong , Xie Tong , Cui Wei , Meng Haotian , Jin Xiaoye , Zhu Bofeng
Published: June 2018

Short tandem repeats (STRs) with a high level of polymorphisms and convenient detection method play an indispensable role in human population and forensic genetics. Recently, we detected the 21 autosomal non-combined DNA index system (non-CODIS) STR loci in a Kyrgyz ethnic group, calculated their forensic parameters and analysed its genetic relationships with reference populations from China. In total, 168 alleles were observed at 21 non-CODIS STRs with corresponding allelic frequencies from 0.0016 to 0.4788. No significant deviations at these STRs were observed from the Hardy–Weinberg equilibrium. The values of cumulative power of discrimination and probability of exclusion for all the 21 non-CODIS STRs were 0.99999999999999999998835 and 0.9999994002, respectively. Furthermore, the analyses of phylogenetic trees, genetic distances and interpopulation differentiations demonstrated that the Kyrgyz group had relatively close genetic relationships with the Uygur and Kazak groups. These 21 non-CODIS STRs were characterized by high genetic diversities in the Kyrgyz group and could be applied as a robust tool for individual identification and kinship testing in forensic sciences.
Novel amphiphilic polyvinylpyrrolidone functionalized silicone particles as carrier for low-cost lipase immobilization
Authors: Zhang Shan , Deng Qianchun , Li Ya , Zheng Mingming , Wan Chuyun , Zheng Chang , Tang Hu , Huang Fenghong , Shi Jie
Published: June 2018

The high catalytic activity, specificity and stability of immobilized lipase have been attracting great interest. How to reduce the cost of support materials has always been a hot topic in this field. Herein, for the development of low-cost immobilized lipase, we demonstrate an amphiphilic polyvinylpyrrolidone (PVP) grafted on silicone particle (SP) surface materials (SP-PVP) with a rational design based on interfacial activation and solution polymerization. Meanwhile, hydrophilic pristine SP and hydrophobic polystyrene-corded silicone particles (SP-Pst) were also prepared for lipase immobilization. SP-PVP was characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy and thermogravimetry. Our results indicated that the lipase loading amount on the SP-PVP composites was about 215 mg of protein per gram. In the activity assay, the immobilized lipase SP-PVP@CRL exhibited higher catalysis activity and better thermostability and reusability than SP@CRL and SP-Pst@CRL. The immobilized lipase retained more than 54% of its initial activity after 10 times of re-use and approximately trended to a steady rate in the following cycles. By introducing the interesting amphiphilic polymer to this cheap and easily obtained SP surface, the relative performance of the immobilized lipase can be significantly improved, facilitating interactions between the low-cost support materials and lipase.
Surface theory in discrete projective differential geometry. I. A canonical frame and an integrable discrete Demoulin system
Authors: Schief W. K. , Szereszewski A.
Published: June 2018

We present the first steps of a procedure which discretizes surface theory in classical projective differential geometry in such a manner that underlying integrable structure is preserved. We propose a canonical frame in terms of which the associated projective Gauss-Weingarten and Gauss-Mainardi-Codazzi equations adopt compact forms. Based on a scaling symmetry which injects a parameter into the linear Gauss-Weingarten equations, we set down an algebraic classification scheme of discrete projective minimal surfaces which turns out to admit a geometric counterpart formulated in terms of discrete notions of Lie quadrics and their envelopes. In the case of discrete Demoulin surfaces, we derive a Bäcklund transformation for the underlying discrete Demoulin system and show how the latter may be formulated as a two-component generalization of the integrable discrete Tzitzéica equation which has originally been derived in a different context. At the geometric level, this connection leads to the retrieval of the standard discretization of affine spheres in affine differential geometry.
Force appropriation of nonlinear structures
Authors: Renson L. , Hill T. L. , Ehrhardt D. A. , Barton D. A. W. , Neild S. A.
Published: June 2018

Nonlinear normal modes (NNMs) are widely used as a tool for developing mathematical models of nonlinear structures and understanding their dynamics. NNMs can be identified experimentally through a phase quadrature condition between the system response and the applied excitation. This paper demonstrates that this commonly used quadrature condition can give results that are significantly different from the true NNM, in particular, when the excitation applied to the system is limited to one input force, as is frequently used in practice. The system studied is a clamped–clamped cross-beam with two closely spaced modes. This paper shows that the regions where the quadrature condition is (in)accurate can be qualitatively captured by analysing transfer of energy between the modes of the system, leading to a discussion of the appropriate number of input forces and their locations across the structure.
An asymptotic higher-order theory for rectangular beams
Authors: Nolde E. , Pichugin A. V. , Kaplunov J.
Published: June 2018

A direct asymptotic integration of the full three-dimensional problem of elasticity is employed to derive a consistent governing equation for a beam with the rectangular cross section. The governing equation is consistent in the sense that it has the same long-wave low-frequency behaviour as the exact solution of the original three-dimensional problem. Performance of the new beam equation is illustrated by comparing its predictions against the results of direct finite-element computations. Limiting behaviours for beams with large (and small) aspect ratios, which can be established using classical plate theories, are recovered from the new governing equation to illustrate its consistency and also to illustrate the importance of using plate theories with the correctly refined boundary conditions. The implications for the correct choice of the shear correction factor in Timoshenko's beam theory are also discussed.
Bumblebees distinguish floral scent patterns, and can transfer these to corresponding visual patterns
Authors: Lawson David A. , Chittka Lars , Whitney Heather M. , Rands Sean A.
Published: June 2018

Flowers act as multisensory billboards to pollinators by using a range of sensory modalities such as visual patterns and scents. Different floral organs release differing compositions and quantities of the volatiles contributing to floral scent, suggesting that scent may be patterned within flowers. Early experiments suggested that pollinators can distinguish between the scents of differing floral regions, but little is known about how these potential scent patterns might influence pollinators. We show that bumblebees can learn different spatial patterns of the same scent, and that they are better at learning to distinguish between flowers when the scent pattern corresponds to a matching visual pattern. Surprisingly, once bees have learnt the spatial arrangement of a scent pattern, they subsequently prefer to visit novel unscented flowers that have an identical arrangement of visual marks, suggesting that multimodal floral signals may exploit the mechanisms by which learnt information is stored by the bee.
Effects of neonicotinoid insecticide exposure and monofloral diet on nest-founding bumblebee queens
Authors: Leza Mar , Watrous Kristal M. , Bratu Jade , Woodard S. Hollis
Published: June 2018

Bumblebees are among the world's most important groups of pollinating insects in natural and agricultural ecosystems. Each spring, queen bumblebees emerge from overwintering and initiate new nests, which ultimately give rise to workers and new reproductives later in the season. Nest initiation and survival are thus key drivers of both bumblebee pollination services and population dynamics. We performed the first laboratory experiment with the model bumblebee species
Bombus impatiens
that explores how early nesting success is impacted by the effects of temporary or more sustained exposure to sublethal levels of a neonicotinoid-type insecticide (imidacloprid at 5 ppb in nectar) and by reliance on a monofloral pollen diet, two factors that have been previously implicated in bumblebee decline. We found that queens exhibited increased mortality and dramatically reduced activity levels when exposed to imidacloprid, as well as delayed nest initiation and lower brood numbers in the nest, but partially recovered from these effects when they only received early, temporary exposure. The effects of pollen diet on individual queen- and colony-level responses were overshadowed by effects of the insecticide, although a monofloral pollen diet alone was sufficient to negatively impact brood production. These findings speak to the sensitivity of queen bumblebees during the nest initiation phase of the colony cycle, with implications for how queens and their young nests are uniquely impacted by exposure to threats such as pesticide exposure and foraging habitat unsuitability.
Nanopore sequencing of Giardia reveals widespread intra-isolate structural variation
Authors: Pollo Stephen M. J. , Reiling Sarah J. , Wit Janneke , Workentine Matthew L. , Guy Rebecca A. , Batoff G. William , Yee Janet , Dixon Brent R. , Wasmuth James D.
Published: June 2018

Background

Genomes of the parasite Giardia duodenalis are relatively small for eukaryotic genomes, yet there are only six publicly available. Difficulties in assembling the tetraploid G. duodenalis genome from short read sequencing data likely contribute to this lack of genomic information. We sequenced three isolates of G. duodenalis (AWB, BGS, and beaver) on the Oxford Nanopore Technologies MinION whose long reads have the potential to address genomic areas that are problematic for short reads.

Results

Using a hybrid approach that combines MinION long reads and Illumina short reads to take advantage of the continuity of the long reads and the accuracy of the short reads we generated reference quality genomes for each isolate. The genomes for two of the isolates were evaluated against the available reference genomes for comparison. The third genome for which there is no previous data was then assembled. The long reads were used to find structural variants in each isolate to examine heterozygosity. Consistent with previous findings based on SNPs, Giardia BGS was found to be considerably more heterozygous than the other isolates that are from Assemblage A. We also find an enrichment of variant-specific surface proteins in some of the structural variant regions.

Conclusions

Our results show that the MinION can be used to generate reference quality genomes in Giardia and further be used to identify structural variant regions that are an important source of genetic variation not previously examined in these parasites.
The relationship between age, neural differentiation, and memory performance
Authors: Koen Joshua D. , Hauck Nedra , Rugg Michael D.
Published: June 2018

Healthy aging is associated with decreased neural selectivity (dedifferentiation) in category-selective cortical regions. This finding has prompted the suggestion that dedifferentiation contributes to age-related cognitive decline. Consistent with this possibility, dedifferentiation has been reported to negatively correlate with fluid intelligence in older adults. Here, we examined whether dedifferentiation is associated with performance in another cognitive domain – episodic memory – that is also highly vulnerable to aging. Given the proposed role of differentiation in age-related cognitive decline, we predicted there would be a stronger link between dedifferentiation and episodic memory performance in older than in younger adults. Young (18-30 yrs) and older (64-75 yrs) male and female humans underwent fMRI scanning while viewing images of objects and scenes prior to a subsequent recognition memory test. We computed a differentiation index in two regions-of-interest (ROIs): parahippocampal place area (PPA) and lateral occipital complex (LOC). This index quantified the selectivity of the BOLD response to an ROI’s preferred versus non-preferred category (scenes for PPA, objects for LOC). The differentiation index in the PPA, but not the LOC, was lower in older than in younger adults. Additionally, the PPA differentiation index predicted recognition memory performance for the studied items. This relationship was independent of and not moderated by age. The PPA differentiation index also predicted performance on a latent ‘fluency’ factor derived from a neuropsychological test battery; this relationship was also age invariant. These findings suggest that two independent factors, one associated with age, and the other with cognitive performance, drive neural differentiation.

Significance Statement

Aging is associated with neural dedifferentiation – reduced neural selectivity in ‘category selective’ cortical brain regions – which has been proposed to mediate cognitive aging. Here, we examined whether neural differentiation is predictive of episodic memory performance, and whether the relationship is moderated by age. A neural differentiation index was estimated for scene-(PPA) and object-(LOC) selective cortical regions while participants studied images for a subsequent memory test. Age related reductions were observed for the PPA, but not the LOC, differentiation index. Importantly, the PPA differentiation index demonstrated age invariant correlations with subsequent memory performance and a fluency factor derived from a neuropsychological battery. Together, these findings suggest that neural differentiation is associated with two independent factors: age and cognitive performance.
Computational investigation of protein surface polarity and pH-dependence: application to antibodies shows that antibody-antigen interfaces tend to be relatively polar
Authors: Hebditch Max , Warwicker Jim
Published: June 2018

Protein instability leads to reversible self-association and irreversible aggregation which is a major concern for developing new biopharmaceutical leads. Protein solution behaviour is dictated by the physicochemical properties of the protein and the solution. Optimising protein solutions through experimental screens and targeted protein engineering can be a difficult and time consuming process. Here, we describe development of the protein-sol web server, which was previously restricted to protein solubility prediction from amino acid sequence. Tools are presented for calculating and mapping patches of hydrophobicity and charge on the protein surface. In addition, predictions of folded state stability and net charge are displayed as a heatmap for a range of pH and ionic strength conditions. Tools are evaluated in the context of antibodies, their fragments and interactions. Surprisingly, antibody-antigen interfaces are, on average, at least as polar as Fab surfaces. This benchmarking process provides the user with thresholds with which to assess non-polar surface patches, and possible solubility implications, in proteins of interest. Stability heatmaps compare favourably with experimental data for CH2 and CH3 domains. Display and quantification of surface polarity and pH / ionic strength dependence will be useful generally for investigation of protein biophysics.
Selective inhibition of CA IX over CA XII in breast cancer cells using benzene sulfonamides: Disconnect between CA activity and growth inhibition
Authors: Mboge Mam Y. , Chen Zhijuan , Wolff Alyssa , Mathias John V. , Tu Chingkuang , Brown Kevin D. , Bozdag Murat , Carta Fabrizio , Supuran Claudiu T. , McKenna Robert , Frost Susan C.
Published: June 2018

Carbonic anhydrases (CAs) have been linked to tumor progression, particularly membrane-bound CA isoform IX (CA IX). The role of CA IX in the context of breast cancer is to regulate the pH of the tumor microenvironment. In contrast to CA IX, expression of CA XII, specifically in breast cancer, is associated with better outcome despite performing the same catalytic function. In this study, we have structurally modeled the orientation of bound ureido-substituted benzene sulfonamides (USBs) within the active site of CA XII, in comparison to CA IX and cytosolic off-target CA II, to understand isoform specific inhibition. This has identified specific residues within the CA active site, which differ between isoforms that are important for inhibitor binding and isoform specificity. The ability of these sulfonamides to block CA IX activity in breast cancer cells is less effective than their ability to block activity of the recombinant protein (by one to two orders of magnitude depending on the inhibitor). The same is true for CA XII activity but now they are two to three orders of magnitude less effective. Thus, there is significantly greater specificity for CA IX activity over CA XII. While the inhibitors block cell growth, without inducing cell death, this again occurs at two orders of magnitude above the Kivalues for inhibition of CA IX and CA XII activity in their respective cell types. Surprisingly, the USBs inhibited cell growth even in cells where CA IX and CA XII expression was ablated. Despite the potential for these sulfonamides as chemotherapeutic agents, these data suggest that we reconsider the role of CA activity on growth potentiation.
The genomic basis of colour pattern polymorphism in the harlequin ladybird
Authors: Gautier Mathieu , Yamaguchi Junichi , Foucaud Julien , Loiseau Anne , Ausset Aurélien , Facon Benoit , Gschloessl Bernhard , Lagnel Jacques , Loire Etienne , Parrinello Hugues , Severac Dany , Lopez-Roques Celine , Donnadieu Cecile , Manno Maxime , Berges Helene , Gharbi Karim , Lawson-Handley Lori , Zang Lian-Sheng , Vogel Heiko , Estoup Arnaud , Prud’homme Benjamin
Published: June 2018

Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research1–6. The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns7,8. In the harlequin ladybirdHarmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus9,10. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the genepanniercontrols melanic pattern polymorphism inH. axyridis. We show thatpannier, which encodes an evolutionary conserved transcription factor, is necessary for the formation of melanic elements on the elytra. Allelic variation inpannierleads to protein expression in distinct domains on the elytra, and thus determines the distinct colour patterns inH. axyridis. Recombination betweenpannieralleles may be reduced by a highly divergent sequence of ca. 170 kb in thecis-regulatory regions ofpannierwith a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations throughcis-regulatory allelic variation of a single gene.