bluuebunny/crossref_metadata_2025 huggingface dataset:
MNK2 governs the macrophage antiinflammatory phenotype
Authors: Bartish Margarita , Tong Dongmei , Pan Yangxun , Wallerius Majken , Liu Hui , Ristau Johannes , de Souza Ferreira Sabrina , Wallmann Tatjana , van Hoef Vincent , Masvidal Laia , Kerzel Thomas , Joly Anne-Laure , Goncalves Christophe , Preston Samuel E. J. , Ebrahimian Talin , Seitz Christina , Bergh Jonas , Pietras Kristian , Lehoux Stephanie , Naldini Luigi , Andersson John , Squadrito Mario Leonardo , del Rincón Sonia V. , Larsson Ola , Rolny Charlotte
Published: October 2020

Significance

The tumor-associated macrophage (TAM) phenotype is continuously modulated during tumor progression to facilitate immune escape. Yet, how gene expression programs control TAM phenotypes during this process is largely unknown. Here we show that, during acquisition of a protumor phenotype, gene expression in TAMs is predominantly modulated via selective changes in mRNA translation rather than changes in mRNA abundance. Detailed studies pinpointed augmented activity of MNK2, which phosphorylates eIF4E and thereby modulates mRNA translation, as required for the antiinflammatory macrophage phenotype. Accordingly, suppression of MNK2 reeducated antiinflammatory macrophages toward a proinflammatory phenotype with the ability to activate CD8+T cells.
Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange
Authors: Carrillo Juan D. , Faurby Søren , Silvestro Daniele , Zizka Alexander , Jaramillo Carlos , Bacon Christine D. , Antonelli Alexandre
Published: October 2020

Significance

The biological interchange between North and South America associated with the formation of the Isthmus of Panama is key to defining current gradients of species diversity. A major gap in our understanding of the interchange is its asymmetry, where mammals of North American origin attained higher diversity in South America than vice versa. The prevailing view is that this asymmetry resulted from higher origination of immigrant mammals in South America. In contrast, we find that asymmetry results from high extinction of native mammals in South America, which reduced the diversity of native mammals available to disperse northwards. These results shed light on the legacy of the biotic interchange to understand the current patterns of species diversity across the Americas.
Corpora, Constructions, New Englishes
Authors: Laporte Samantha
Published: October 2020

This book takes an integrated approach to the fields of Corpus Linguistics, Construction Grammar, and World Englishes through a thorough constructional and corpus-based examination of the patterning of the versatile high-frequency verb make in British English and New Englishes. It contributes to Construction Grammar theory by adopting a verb-based, rather than construction-based, perspective on argument structure. This allows the probing of the interface between verb-independent generalizations and item-specificity from an underexplored angle that offers new insights into the shape of the constructicon. From a variationist perspective, it seeks to (i) identify features of New Englishes and gauge whether these features exhibit traces of conventionalization, and (ii) assess whether the degree of institutionalization of the New Englishes correlates with linguistic behavior, both from a social and cognitive perspective, thereby contributing to the budding effort to integrate the cognitive and social dimensions into the modeling of linguistic variation in World Englishes.
Boundary contributions in the causal set action
Authors: Dowker Fay
Published: October 2020

Evidence is provided for a conjecture that, in the continuum limit, the mean of the causal set action of a causal set sprinkled into a globally hyperbolic Lorentzian spacetime,

M

, of finite volume equals the Einstein Hilbert action of

M

plus the volume of the co-dimension 2 intersection of the future boundary with the past boundary. We give the heuristic argument for this conjecture and analyse some examples in 2 dimensions and one example in 4 dimensions.
Joint super-resolution image reconstruction and parameter identification in imaging operator: analysis of bilinear operator equations, numerical solution, and application to magnetic particle imaging
Authors: Kluth Tobias , Bathke Christine , Jiang Ming , Maass Peter
Published: October 2020

One important property of imaging modalities and related applications is the resolution of image reconstructions which relies on various factors such as instrumentation or data processing. Restrictions in resolution can have manifold origins, e.g., limited resolution of available data, noise level in the data, and/or inexact model operators. In this work we investigate a novel data processing approach suited for inexact model operators. Here, two different information sources, high-dimensional model information and high-quality measurement on a lower resolution, are comprised in a hybrid approach. The joint reconstruction of a high resolution image and parameters of the imaging operator are obtained by minimizing a Tikhonov-type functional. The hybrid approach is analyzed for bilinear operator equations with respect to stability, convergence, and convergence rates. We further derive an algorithmic solution exploiting an algebraic reconstruction technique. The study is complemented by numerical results ranging from an academic test case to image reconstruction in magnetic particle imaging.
Dielectrophoretic high-purity isolation of primary T-cells in samples contaminated with leukemia cells, for biomanufacturing of therapeutic CAR T-cells
Authors: Ringwelski Beth , Jayasooriya Vidura , Nawarathna Dharmakeerthi
Published: October 2020

Chimeric antigen receptor (CAR) T-cell therapy is a Food and Drug Administration (FDA)-approved treatment for specific cancers. CAR T-cells are manufactured ex vivo using T-cells derived from patients. Recent clinical trials reported a very high level of efficacy as well as complete remission rates (70%–93%) for acute lymphoblastic leukemia (ALL) patients. However, there have also been reports of significant adverse effects resulting from the contamination of T-cells derived from patients with existing cancer cells during manufacturing. The accidental transfection of cancer cells with CAR genes provides the cancer cells with immunity from CAR T-cells. As a result, genetically modified cancer cells that express the CAR molecules grow into secondary tumors. This significantly undermines the great benefits offered by CAR T-cell therapy. The removal of cancer cells before gene transfer using cell purification methods can address this issue. However, traditional cell purification methods such as fluorescence-activated cell separation and magnetic-activated cell separation have proven to be unsuitable for high-purity T-cell purification. To address this issue, we investigated the utility, in microfluidic channels, of dielectrophoretic cell purification, which is a label-free high-throughput cell purification method. When we conducted the experiments with primary T-cell (CD8+) samples contaminated with cultured acute lymphoblastic leukemia and chronic myelogenous leukemia cells, we found that dielectrophoresis could be used to purify cell samples and achieve 100% purity with high cell viability (greater than 90%).
Negativity artifacts in back-projection based photoacoustic tomography
Authors: Shen Kang , Liu Songde , Feng Ting , Yuan Jie , Zhu Benpeng , Tian Chao
Published: October 2020

Photoacoustic tomography (PAT) has become a fast-evolving biomedical imaging modality in recent years. In PAT, image reconstruction is a critical step to produce high-quality photoacoustic images from raw photoacoustic signals. To date, algorithms based on back projection are the most widely used image reconstruction techniques due to their simplicity and computational efficiency. However, images reconstructed by back projection contain negative values, especially at the edge of photoacoustic sources, which have no physical meaning and are essentially undesired artifacts. In this work, we study the formation mechanism, fundamental causes and removal strategies of the negativity artifacts in back-projection-based PAT. Our results show that limited detector bandwidth and limited view angle are two fundamental causes of negativity artifacts. When the bandwidth of a detector is limited, back-projection signals will be distorted as a result of the loss of frequency contents and negativity artifacts thus appear. When the view angle of the detector is limited, photoacoustic signals propagating in three-dimensional space will be partially lost, resulting in negativity artifacts. Post-processing strategies, such as envelope detection and forced zeroing can be used to remove the negativity artifacts but may cause problems. Since negativity artifacts are a common image quality degradation factor in PAT, understanding their characteristics may expedite the development of novel artifact-removal techniques and artifact-free image reconstruction algorithms, which are of importance to correct image interpretation and quantitative imaging.
Characterization of silicon drift detectors with electrons for the TRISTAN project
Authors: Mertens S , Brunst T , Korzeczek M , Lebert M , Siegmann D , Alborini A , Altenmüller K , Biassoni M , Bombelli L , Carminati M , Descher M , Fink D , Fiorini C , Forstner C , Gugiatti M , Houdy T , Huber A , King P , Lebeda O , Lechner P , Pantuev V S , Parno D S , Pavan M , Pozzi S , Radford D C , Slezák M , Steidl M , Trigilio P , Urban K , Vénos D , Wolf J , Wüstling S , Yen Y-R
Published: October 2020

Sterile neutrinos are a minimal extension of the standard model of particle physics. A promising model-independent way to search for sterile neutrinos is via high-precision β-spectroscopy. The Karlsruhe tritium neutrino (KATRIN) experiment, equipped with a novel multi-pixel silicon drift detector focal plane array and read-out system, named the TRISTAN detector, has the potential to supersede the sensitivity of previous laboratory-based searches. In this work we present the characterization of the first silicon drift detector prototypes with electrons and we investigate the impact of uncertainties of the detector’s response to electrons on the final sterile neutrino sensitivity.
Role of surface termination in forming type-II photocatalyst heterojunctions: the case of TiO2/BiVO4
Authors: Di Liberto Giovanni , Tosoni Sergio , Pacchioni Gianfranco
Published: October 2020

In this work we investigate TiO2 and BiVO4 nanostructures by means of density functional theory (DFT) calculations, to provide an estimate of the band alignment in TiO2/BiVO4 interfaces, highly active in photo-electrochemistry and photocatalytic water splitting. Calculations were carried out with both DFT range separated and self-consistent dielectric dependent hybrid functionals (HSE06 and PBE0DD). The impact of systems’ size has been investigated. The converged electronic levels of TiO2 and BiVO4 surfaces have been used to predict the band alignment in TiO2/BiVO4 heterostructures. Results indicated that when TiO2 (101) surface is matched with BiVO4 (110), a type-II alignment is obtained, where the band edges of BiVO4 are higher in energy that those of TiO2. This picture is favorable for charge-carriers separation upon photoexcitation, where electrons move toward TiO2 and holes toward BiVO4. On the contrary, if TiO2 (101) is interfaced to BiVO4 (010) the offset between the band edges is negligible, thus reducing the driving force toward separation of charge carriers. These results rationalize the dependence on the facet’s exposure of the observed photocatalytic performances of TiO2/BiVO4 composites, where the TiO2 (101)/BiVO4 (110) interface outperforms the TiO2 (101)/BiVO4 (010) one.
Modification of the photoconducting properties of ZnO thin films via low-temperature annealing and air exposure
Authors: Bridoux G , Ruano G D , Ferreyra J M , Villafuerte M
Published: October 2020

A simple thermal annealing at 150 °C followed by exposure to air ambient conditions in epitaxial ZnO thin films produces a photoconductivity enhancement and a reduction of the energy gap. The first effect is related to a release of carriers from bulk traps while the second is caused by a gradual adsorption of species on the film surface which increases the band bending, as x-ray photoemission spectroscopy (XPS) shows. An observed drift of the photoconductivity and the energy gap over the days is connected to this adsorption kinetics. These findings have a potential application in ZnO based optoelectronic devices.
Raman spectrum of layered tilkerodeite (Pd2HgSe3) topological insulator: the palladium analogue of jacutingaite (Pt2HgSe3)
Authors: Longuinhos R , Vymazalová A , Cabral A R , Ribeiro-Soares J
Published: October 2020

The layered mineral tilkerodeite (Pd2HgSe3), the palladium analogue of jacutingaite (Pt2HgSe3), is a promising quantum spin hall insulator for low-power nanospintronics. In this context, a fast and reliable assessment of its structure is key for exploring fundamental properties and architecture of new Pd2HgSe3-based devices. Here, we investigate the first-order Raman spectrum in high-quality, single-crystal bulk tilkerodeite, and analyze the wavenumber relation to its isostructural jacutingaite analogue. By using polarized Raman spectroscopy, symmetry analysis, and first-principles calculations, we assigned all the Raman-active phonons in tilkerodeite, unveiling their wavenumbers, atomic displacement patterns, and symmetries. Our calculations used several exchange–correlation functionals within the density functional perturbation theory framework, reproducing both structure and Raman-active phonon wavenumbers in excellent agreement with experiments. Also, it was found that the influence of the spin–orbit coupling can be neglected in the study of these properties. Finally, we compared the wavenumber and atomic displacement patterns of corresponding Raman-active modes in tilkerodeite and jacutingaite, and found that the effect of the Pd and Pt masses can be neglected on reasoning their wavenumber differences. From this analysis, tilkerodeite is found to be mechanically weaker than jacutingaite against the atomic displacement patterns of these modes. Our findings advance the understanding of the structural properties of a recently discovered layered topological insulator, fundamental to further exploring its electronic, optical, thermal, and mechanical properties, and for device fabrication.
Functionalized carbon microfibers (biomass-derived) ornamented by Bi2S3 nanoparticles: an investigation on their microwave, magnetic, and optical characteristics
Authors: Peymanfar Reza , Moradi Fereshteh
Published: October 2020

The biomass-derived materials emerged as novel, low-cost, green, and light-weight microwave absorbers. On the other hand, the sulfide nanostructures due to narrow band gap demonstrated significant dielectric features. In this research, the pure carbon microfibers were prepared using Erodium cicutarium harvest and they were functionalized by a sonochemistry method. The treated microfibers were coated by Bi2S3 nanoparticles, obtained by a novel modified solvothermal route. X-ray powder diffraction, Fourier transform infrared, diffuse reflection spectroscopy, field emission scanning electron microscopy (FE-SEM), transmission electron microscopy, and vector network analyzer analyses were applied to characterize the features of the prepared structures. The obtained results manifest that the anchoring nanoparticles onto the functionalized microfibers narrowed band gap to 1.35 eV and reinforced polarizability of the nanocomposite, desirable for dielectric attenuation. In this study, the interfacial interactions were modulated using polyacrylonitrile (PAN) and polyvinylidene fluoride. Interestingly, FCMF blended in PAN demonstrated an eye-catching efficient bandwidth as wide as 8.13 GHz (RL > 10 dB) with only 2.00 mm in thickness, whereas it illustrated an outstanding reflection loss of 81.96 at 11.48 GHz with a thickness of 2.50 mm. More significantly, FCMF/Bi2S3/PAN nanocomposite promoted the efficient bandwidth to 3.07 GHz (RL > 20 dB). Noteworthy, all of the samples illustrated total electromagnetic interference shielding effectiveness (SET) more than 15 dB entire the x and ku-band frequency.
Can simultaneous density-determined enhancement of diffusion and cross-diffusion foster boundedness in Keller–Segel type systems involving signal-dependent motilities?
Authors: Winkler Michael
Published: October 2020

The reaction-(cross-)diffusion system

u

t

=
Δ

(

u

m

ϕ

(

v

)

)

,

x
∈
Ω
,

t
>
0
,

v

t

=
Δ
v
−
v
+
u
,

x
∈
Ω
,

t
>
0
,

is considered under no-flux boundary conditions in smoothly bounded convex domains

Ω
⊂

R

n

, where m ⩾ 1 and n ⩾ 2, and where ϕ generalizes the prototype obtained on letting

ϕ

(

v

)

=
a
+
b

(

v
+
d

)

−
α

,
v
>
0
,

with a ⩾ 0, b > 0, d ⩾ 0 and α ⩾ 0. In this framework, it is firstly seen that if

m
>

n

2

,
α
<

n
m
−
2

n
−
2

and

α
<

2

(

m
+
1

)

n
−
2

,

then finite-time blow-up is excluded in the sense that for all suitably regular initial data an associated initial-boundary value problem admits a globally defined weak solution (u, v) with u being locally bounded in

Ω

¯

×

[

0
,
∞

)

. Under the assumption that additionally

α
<

(

n
+
2

)

m
−
n
+
2

2

(

n
−
2

)

,

these solutions are moreover shown to be bounded throughout Ω × (0, ∞) in both components. In view of results known for the case m = 1, this particularly indicates that increasing m in (0.1) goes along with a certain regularizing effect despite the circumstance that thereby both the diffusion and the cross-diffusion mechanisms implicitly contained in (0.1) are simultaneously enhanced.
Exponential law for random maps on compact manifolds*
Authors: Haydn Nicolai T A , Rousseau Jérôme , Yang Fan
Published: October 2020

We consider random dynamical systems on manifolds modelled by a skew product which have certain geometric properties and whose measures satisfy quenched decay of correlations at a sufficient rate. We prove that the limiting distribution for the hitting and return times to geometric balls are both exponential for almost every realisation. We then apply this result to random C
2 maps of the interval, random parabolic maps on the unit interval and random perturbation of partially hyperbolic attractors on a compact Riemannian manifold.
Global dynamics of neoclassical growth model with multiple pairs of variable delays
Authors: Huang Chuangxia , Zhao Xian , Cao Jinde , Alsaadi Fuad E
Published: October 2020

Taking into account the effects of multiple pairs of variable delays, this paper deals with the global dynamics for a class of differential neoclassical growth models. We aim to obtain significant insights into better understanding of how the multiple pairs of variable delays essentially affect the stability and attractiveness of the unique positive equilibrium point. First of all, we prove that every solution of the IVP (initial value problem) with respect to the addressed system exists globally and is positive and bounded above. Secondly, with the help of the methods of fluctuation lemma and analytical techniques, two delay-independent criteria and one delay-dependent criterion on the attractivity of the unique positive equilibrium point are established, which improve and complement some published results. Lastly, two examples with the numerical simulation are arranged to illustrate the effectiveness and feasibility of the obtained theoretical results.
Characterization of noise and background signals in a magnetic particle imaging system
Authors: Paysen Hendrik , Kosch Olaf , Wells James , Loewa Norbert , Wiekhorst Frank
Published: October 2020

Magnetic particle imaging (MPI) is a novel technology, which opens new possibilities for promising biomedical applications. MPI uses magnetic fields to generate a specific response from magnetic nanoparticles (MNPs), to determine their spatial location non-invasively and without using ionizing radiation. One open challenge of MPI is to achieve further improvements in terms of sensitivity to translate the currently preclinical performed research into clinical applications. In this work, we study the noise and background signals of our preclinical MPI system, to identify and characterize disturbing signal contributions. The current limit of detection achieved with our device was determined previously to be

20

ng of iron. Based on the results presented in this work, we describe possible hardware and software improvements and estimate that the limit of detection could be lowered to about 1–2 ng. Additionally, a long-term analysis of the scanner performance over the last 3 years is presented, which proved to be an easy and effective way to monitor possible changes or damage of hardware components. All the presented results were obtained by analysing empty scanner measurements and the presented methodology can easily be adapted for different scanner types, to compare their performances.
Performance comparison of dual-ended readout depth-encoding PET detectors based on BGO and LYSO crystals
Authors: Du Junwei , Ariño-Estrada Gerard , Bai Xiaowei , Cherry Simon R
Published: October 2020

The performance of dual-ended readout depth-encoding positron emission tomography (PET) detectors based on bismuth germanate (BGO) coupled to silicon photomultipliers (SiPM) arrays was measured for the first time and compared to lutetium-yttrium oxyorthosilicate (LYSO)-based detectors using the same readout. The BGO and LYSO crystal arrays all had a crystal pitch of 2.2 mm and were coupled to 8 × 8 SiPM arrays with a matching pitch of 2.2 mm, using a one-to-one coupling configuration. Three types of crystals with Toray reflector were used: polished LYSO, polished BGO, and unpolished BGO, and for two different crystal thicknesses of 20 mm and 30 mm. All the crystal elements in the BGO arrays were clearly resolved in the flood histogram. Better flood histograms were obtained using the LYSO arrays for a selected crystal thickness, and better flood histograms were obtained using the 20 mm thick crystal arrays for a selected crystal type. The average crystal level energy resolution and timing resolution for 20 mm polished LYSO, polished BGO and unpolished BGO crystals at their optimal SiPM bias voltage were 18.6 ± 1.3% and 1.19 ± 0.20 ns, 17.8 ± 0.8% and 4.43 ± 0.47 ns, and 18.0 ± 1.0% and 4.68 ± 1.0 ns, respectively. Depth-of-interaction (DOI) resolution of the 20 mm polished LYSO array was 2.31 ± 0.17 mm and for the 20 mm unpolished BGO array was 3.53 ± 0.25 mm. However, polished BGO arrays with Toray reflector did not provide DOI information. Our key conclusion is that dual-ended readout depth-encoding 20 mm thick unpolished BGO detectors are good candidates for low-activity PET systems with small field-of-view and low timing performance requirements, such as preclinical or compact organ-dedicated PET systems, with the advantage over LYSO of having no background radiation and significantly lower cost.
Runaway electron mitigation with supersonic molecular beam injection (SMBI) in ADITYA-U tokamak
Authors: Banerjee Santanu , Singh K. , Raj H. , Arambhadiya B. , George Siju , Jadeja K.A. , Singh Amit K. , Edappala Praveenlal , Bisai N. , Ghosh J. , Manchanda R. , Chowdhuri M.B. , Tanna R.L. , Raval Jayesh , Nagora U.C. , Paravastu Y. , Raval D. C. , Mishra K. , Chandra D. , Sen A.
Published: October 2020

The generation and subsequent loss of runaway electrons (REs) during the operation sequence in a tokamak is a potent threat to the plasma-facing components and the interface of actively cooled parts. Control and mitigation of REs are of prime importance to the safe operation and machine health of a fusion device. A supersonic molecular beam injection (SMBI) system has been installed in the ADITYA-U tokamak to explore the effects of the high Mach number molecular beam on the REs and ways to mitigate the REs. In the majority of discharges in which SMBI has been injected, a burst in hard x-rays has been observed accompanying the SMBI pulse, indicating significant RE loss. This is followed by a long RE-mitigated phase in the discharge. The most plausible explanation of the mitigation of REs is minor disruption caused by SMBI. This in turn triggers field line stochastization and subsequent rapid RE loss. Finally, this leads to reorganization of the flux surfaces, resulting in bigger islands with the potential of trapping any surviving RE fraction.
Production of magnetite nanoparticles from Ethiopian iron ore using solvent extraction and studying parameters that affect crystallite size
Authors: Sebehanie Kebede Gamo , del Rosario Alberto Velázquez , Ali Abubeker Yimam , Femi Olu Emmanuel
Published: October 2020

Crystallite size is one of the fundamental factors controlling the magnetic property of magnetic nanoparticles. In this study, magnetite nanoparticles were produced from Ethiopian iron ore and the effect of solvent extraction parameters on the crystallite size were investigated by considering classical nucleation theory. First, the iron ore was crushed and unwanted gangues were discarded, then followed by further grinding to get a black powder. Finally, the magnetite nanoparticles were produced using solvent extraction and co-precipitation method. For the solvent extraction, tri-butyl phosphate (TBP) and tri-octyl phosphine oxide (TOPO) was used as an extractant, while 2-ethyl-hexanol, and heptanol were used as a modifier and diluent, respectively. The synthesized nanoparticles was characterized using XRD, SEM (EDS), TGA, and FTIR. The results show that leaching temperature and modifier concentration have a significant effect on the crystallite size of the nanoparticles. Comparison of the crystallite size using the Scherrer equation reveals the mean crystallite size of the sample extracted using TBP is smaller than the sample extracted using TOPO.
Classifying 𝑆𝐿₂-tilings
Authors: Short Ian
Published: October 2020

Recently there has been significant progress in classifying integer friezes and

S
L

2

\mathrm {SL}_2

-tilings. Typically, combinatorial methods are employed, involving triangulations of regions and inventive counting techniques. Here we develop a unified approach to such classifications using the tessellation of the hyperbolic plane by ideal triangles induced by the Farey graph. We demonstrate that the geometric, numeric and combinatorial properties of the Farey graph are perfectly suited to classifying tame

S
L

2

\mathrm {SL}_2

-tilings, positive integer

S
L

2

\mathrm {SL}_2

-tilings, and tame integer friezes – both finite and infinite. In so doing, we obtain geometric analogues of certain known combinatorial models for tilings involving triangulations, and we prove several new results of a similar type too. For instance, we determine those bi-infinite sequences of positive integers that are the quiddity sequence of some positive infinite frieze, and we give a simple combinatorial model for classifying tame integer friezes which generalises the classical construction of Conway and Coxeter for positive integer friezes.
Effect of the Noninvasive Follicular Thyroid Neoplasm With Papillary-Like Nuclear Features (NIFTP) Nomenclature Revision on Indian Thyroid Fine-Needle Aspiration Practice
Authors: Rana Chanchal , Ramakant Pooja , Goel Divya , Singh Akanksha , Singh KulRanjan , Babu Suresh , Mishra Anand
Published: October 2020

Objectives

To analyze risk of malignancy (ROM) in Bethesda categories (BCs) and the impact of noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) reclassification on malignancy risk and surgical outcome.

Methods

In this retrospective study based on fine-needle aspiration samples with histologic follow-up, ROM was analyzed in BCs. Possible cases of NIFTP were reviewed, followed by the analysis of impact of this reclassification on ROM in BCs.

Results

The incidence of NIFTP was 6.9% among excised thyroid nodules and 16.8% among all resected neoplastic lesions. ROM for BCs I to VI was 37.5%, 9.6%, 40.0%, 46.5%, 88.8%, and 96.8%, respectively. Risk of neoplasia was 50.0%, 13.8%, 55.0%, 71.2%, 88.8%, and 96.8% respectively. When NIFTPs were considered nonmalignant lesions, ROM decreased by 6.3%, 4.3%, 20%, 19.1%, 22.5%, and 1.5% in each Bethesda category (I-VI), respectively. Inability to diagnose NIFTP preoperatively led to overtreatment in 16.2%.

Conclusions

Prevalence of NIFTP in Asian countries may be higher than expected. Substantial cases of NIFTP have a benign preoperative cytology; hence, cases of follicular adenoma and adenomatous colloid nodule should be included in the review. NIFTP reclassification has significantly reduced the ROM in indeterminate BCs, suggesting diagnostic lobectomy rather than total thyroidectomy. Countries should establish their own malignancy risk range and parameters.
Against philosophical proofs against common sense
Authors: Doulas Louis , Welchance Evan
Published: October 2020

Many philosophers think that common sense knowledge survives sophisticated philosophical proofs against it. Recently, however, Bryan Frances (‘Philosophical proofs against common sense’ 2021) has advanced a philosophical proof that he thinks common sense cannot survive. Exploiting philosophical paradoxes like the Sorites, Frances attempts to show how common sense leads to paradox and therefore that common sense methodology is unstable. In this paper, we show how Frances’s proof fails and then present Frances with a dilemma.
Daily protein prioritization and long-term nutrient balancing in a dietary generalist, the blue monkey
Authors: Takahashi Maressa Q , Rothman Jessica M , Raubenheimer David , Cords Marina
Published: October 2020

Animals make dietary choices to achieve adequate nutrient intake; however, it is challenging to study such nutritional strategies in wild populations. We explored the nutritional strategy of a generalist social primate, the blue monkey (Cercopithecus mitis). We hypothesized that females balance intake of nutrients, specifically non-protein energy and protein, both on a daily and long-term basis. When balancing was not possible, we expected subjects to prioritize constant protein intake, allowing non-protein energy to vary more. To understand the ecology of nutrient balancing, we examined how habitat use, food availability, diet composition, social dominance rank, and reproductive demand influenced nutrient intake. Over 9 months, we conducted 371 all-day focal follows on 24 subjects in Kakamega Forest, Kenya. Females exhibited short- and long-term nutritional strategies. Daily, they balanced non-protein energy to protein intake but when balancing was impossible, monkeys prioritized protein intake. Longer term, they balanced non-protein energy:protein intake in a 3.8:1 ratio. The ratio related positively to fruit in the diet and negatively to time in near-natural forest, but we found no evidence that it related to food availability, reproductive demand, or dominance rank. Lower-ranked females had broader daily diets, however, which may reflect behavioral feeding strategies to cope with social constraints. Overall, females prioritized daily protein, allowing less variation in protein intake than other aspects such as non-protein energy:protein ratio and non-protein energy intake. The emerging pattern in primates suggests that diverse dietary strategies evolved to allow adherence to a nutrient balance of non-protein energy:protein despite various social and environmental constraints.
Enhancing statistical power in temporal biomarker discovery through representative shapelet mining
Authors: Gumbsch Thomas , Bock Christian , Moor Michael , Rieck Bastian , Borgwardt Karsten
Published: October 2020

Motivation

Temporal biomarker discovery in longitudinal data is based on detecting reoccurring trajectories, the so-called shapelets. The search for shapelets requires considering all subsequences in the data. While the accompanying issue of multiple testing has been mitigated in previous work, the redundancy and overlap of the detected shapelets results in an a priori unbounded number of highly similar and structurally meaningless shapelets. As a consequence, current temporal biomarker discovery methods are impractical and underpowered.

Results

We find that the pre- or post-processing of shapelets does not sufficiently increase the power and practical utility. Consequently, we present a novel method for temporal biomarker discovery: Statistically Significant Submodular Subset Shapelet Mining (S5M) that retrieves short subsequences that are (i) occurring in the data, (ii) are statistically significantly associated with the phenotype and (iii) are of manageable quantity while maximizing structural diversity. Structural diversity is achieved by pruning non-representative shapelets via submodular optimization. This increases the statistical power and utility of S5M compared to state-of-the-art approaches on simulated and real-world datasets. For patients admitted to the intensive care unit (ICU) showing signs of severe organ failure, we find temporal patterns in the sequential organ failure assessment score that are associated with in-ICU mortality.

Availability and implementation

S5M is an option in the python package of S3M: github.com/BorgwardtLab/S3M.
quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Authors: Mallet Vincent , Nilges Michael , Bouvier Guillaume
Published: October 2020

We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations.

Availability and implementation

The method is available on GitHub and distributed as a pip package.
Inselberg floristics exemplify the coast to inland OCBIL transition in a global biodiversity hotspot
Authors: Hopper Stephen D , Fiedler Peggy L , Yates Colin J
Published: October 2020

We examined the floristics of granitoid inselbergs in the hitherto poorly documented south-eastern region of the Southwest Australian Floristic Region (SWAFR) and adjacent Great Western Woodlands, addressing several hypotheses of OCBIL (old, climatically buffered, infertile landscapes) theory. We found exceptional taxon richness (1550 taxa on 89 inselbergs, with 58 well-sampled inselbergs and 1493 taxa chosen for detailed analyses). Granite inselberg endemism declined towards the arid inland, although taxon richness did not. OCBILs are likely to be found up to 500 km inland, not ~300 km as previously hypothesized. Hybrids were extremely rare on the 58 inselbergs analysed, whereas rare species, including singletons, were abundant. Conversely, exotic weeds were less common than in the whole SWAFR flora (8.2% vs 12.8%). Granite plant communities were distributed in bands parallel to the south coast, approximating the general transition from the Esperance and Boylya Floristic Districts across the SWAFR boundary north into the Arid Zone’s Great Western Woodlands. Positive correlations were found between several plant life forms and inselberg area. There was a decrease from the coast inland for most life forms, except for annual and graminoid herbs that increased in taxa inland. Thus, inselberg floristics exemplify the coast-to-inland OCBIL transition in this global biodiversity hotspot.
Modulation of beta bursts in subthalamic sensorimotor circuits predicts improvement in bradykinesia
Authors: Kehnemouyi Yasmine M , Wilkins Kevin B , Anidi Chioma M , Anderson Ross W , Afzal Muhammad Furqan , Bronte-Stewart Helen M
Published: October 2020

No biomarker of Parkinson’s disease exists that allows clinicians to adjust chronic therapy, either medication or deep brain stimulation, with real-time feedback. Consequently, clinicians rely on time-intensive, empirical, and subjective clinical assessments of motor behaviour and adverse events to adjust therapies. Accumulating evidence suggests that hypokinetic aspects of Parkinson’s disease and their improvement with therapy are related to pathological neural activity in the beta band (beta oscillopathy) in the subthalamic nucleus. Additionally, effectiveness of deep brain stimulation may depend on modulation of the dorsolateral sensorimotor region of the subthalamic nucleus, which is the primary site of this beta oscillopathy. Despite the feasibility of utilizing this information to provide integrated, biomarker-driven precise deep brain stimulation, these measures have not been brought together in awake freely moving individuals. We sought to directly test whether stimulation-related improvements in bradykinesia were contingent on reduction of beta power and burst durations, and/or the volume of the sensorimotor subthalamic nucleus that was modulated. We recorded synchronized local field potentials and kinematic data in 16 subthalamic nuclei of individuals with Parkinson’s disease chronically implanted with neurostimulators during a repetitive wrist-flexion extension task, while administering randomized different intensities of high frequency stimulation. Increased intensities of deep brain stimulation improved movement velocity and were associated with an intensity-dependent reduction in beta power and mean burst duration, measured during movement. The degree of reduction in this beta oscillopathy was associated with the improvement in movement velocity. Moreover, the reduction in beta power and beta burst durations was dependent on the theoretical degree of tissue modulated in the sensorimotor region of the subthalamic nucleus. Finally, the degree of attenuation of both beta power and beta burst durations, together with the degree of overlap of stimulation with the sensorimotor subthalamic nucleus significantly explained the stimulation-related improvement in movement velocity. The above results provide direct evidence that subthalamic nucleus deep brain stimulation-related improvements in bradykinesia are related to the reduction in beta oscillopathy within the sensorimotor region. With the advent of sensing neurostimulators, this beta oscillopathy combined with lead location could be used as a marker for real-time feedback to adjust clinical settings or to drive closed-loop deep brain stimulation in freely moving individuals with Parkinson’s disease.
Sex Differences in Anatomical Rich-Club and Structural–Functional Coupling in the Human Brain Network
Authors: Zhao Shuo , Wang Gongshu , Yan Ting , Xiang Jie , Yu Xuexue , Li Hong , Wang Bin
Published: October 2020

Structural and functional differences between the brains of female and male adults have been well documented. However, potential sex differences in the patterns of rich-club organization and the coupling between their structural connectivity (SC) and functional connectivity (FC) remain to be determined. In this study, functional magnetic resonance imaging and diffusion tensor imaging techniques were combined to examine sex differences in rich-club organization. Females had a stronger SC-FC coupling than males. Moreover, stronger SC-FC coupling in the females was primarily located in feeder connections and non–rich-club nodes of the left inferior frontal gyrus and inferior parietal lobe and the right superior frontal gyrus and superior parietal gyrus, whereas higher coupling strength in males was primarily located in rich-club connections and rich-club node of the right insula, and non-rich-club nodes of the left hippocampus and the right parahippocampal gyrus. Sex-specific patterns in correlations were also shown between SC-FC coupling and cognitive function, including working memory and reasoning ability. The topological changes in rich-club organization provide novel insight into sex-specific effects on white matter connections that underlie a potential network mechanism of sex-based differences in cognitive function.
Olfactory Deprivation and Enrichment: An Identity of Opposites?
Authors: Fitzwater Emily , Coppola David M
Published: October 2020

The effects of deprivation and enrichment on the electroolfactogram of mice were studied through the paradigms of unilateral naris occlusion and odor induction, respectively. Deprivation was shown to cause an increase in electroolfactogram amplitudes after 7 days. We also show that unilateral naris occlusion is not detrimental to the gross anatomical appearance or electroolfactogram of either the ipsilateral or contralateral olfactory epithelium even after year-long survival periods, consistent with our previous assumptions. Turning to induction, the increase in olfactory responses after a period of odor enrichment, could not be shown in CD-1 outbred mice for any odorant tried. However, consistent with classical studies, it was evident in C57BL/6J inbred mice, which are initially insensitive to isovaleric acid. As is the case for deprivation, enriching C57BL/6J mice with isovaleric acid causes an increase in their electroolfactogram response to this odorant over time. In several experiments on C57BL/6J mice, the odorant specificity, onset timing, recovery timing, and magnitude of the induction effect were studied. Considered together, the current findings and previous work from the laboratory support the counterintuitive conclusion that both compensatory plasticity in response to deprivation and induction in response to odor enrichment are caused by the same underlying homeostatic mechanism, the purpose of which is to preserve sensory information flow no matter the odorant milieu. This hypothesis, the detailed evidence supporting it, and speculations concerning human odor induction are discussed.
Outcomes of Coronavirus Disease 2019 (COVID-19) Related Hospitalization Among People With Human Immunodeficiency Virus (HIV) in the ISARIC World Health Organization (WHO) Clinical Characterization Protocol (UK): A Prospective Observational Study
Authors: Geretti Anna Maria , Stockdale Alexander J , Kelly Sophie H , Cevik Muge , Collins Simon , Waters Laura , Villa Giovanni , Docherty Annemarie , Harrison Ewen M , Turtle Lance , Openshaw Peter J M , Baillie J Kenneth , Sabin Caroline A , Semple Malcolm G
Published: October 2020

Background

Evidence is conflicting about how human immunodeficiency virus (HIV) modulates coronavirus disease 2019 (COVID-19). We compared the presentation characteristics and outcomes of adults with and without HIV who were hospitalized with COVID-19 at 207 centers across the United Kingdom and whose data were prospectively captured by the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) World Health Organization (WHO) Clinical Characterization Protocol (CCP) study.

Methods

We used Kaplan-Meier methods and Cox regression to describe the association between HIV status and day-28 mortality, after separate adjustment for sex, ethnicity, age, hospital acquisition of COVID-19 (definite hospital acquisition excluded), presentation date, 10 individual comorbidities, and disease severity at presentation (as defined by hypoxia or oxygen therapy).

Results

Among 47 592 patients, 122 (0.26%) had confirmed HIV infection, and 112/122 (91.8%) had a record of antiretroviral therapy. At presentation, HIV-positive people were younger (median 56 vs 74 years; P < .001) and had fewer comorbidities, more systemic symptoms and higher lymphocyte counts and C-reactive protein levels. The cumulative day-28 mortality was similar in the HIV-positive versus HIV-negative groups (26.7% vs. 32.1%; P = .16), but in those under 60 years of age HIV-positive status was associated with increased mortality (21.3% vs. 9.6%; P < .001 [log-rank test]). Mortality was higher among people with HIV after adjusting for age (adjusted hazard ratio [aHR] 1.47, 95% confidence interval [CI] 1.01–2.14; P = .05), and the association persisted after adjusting for the other variables (aHR 1.69; 95% CI 1.15–2.48; P = .008) and when restricting the analysis to people aged <60 years (aHR 2.87; 95% CI 1.70–4.84; P < .001).

Conclusions

HIV-positive status was associated with an increased risk of day-28 mortality among patients hospitalized for COVID-19.
Time-Dependent Displacement of Commensal Skin Microbes by Pathogens at the Site of Colorectal Surgery
Authors: Holder-Murray Jennifer , Yeh Andrew , Rogers Matthew B , Firek Brian , Mahler Brandon , Medich David , Celebrezze James , Morowitz Michael J
Published: October 2020

Background

Although the healthy human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to surgical site infections (SSIs). Our objective in this study was to characterize temporal and spatial variation in the skin microbiota of patients undergoing colorectal surgery and determine if dysbiosis contributes to SSIs.

Methods

Sixty one adults scheduled to undergo elective colon or rectal resection were identified by convenience sampling. By analyzing bacterial 16S rRNA gene sequences isolated from clinical samples, we used a culture-independent strategy to monitor perioperative changes in microbial diversity of fecal samples and the skin.

Results

A total of 990 samples from 61 patients were analyzed. Alpha diversity on the skin decreased after surgery but later recovered at the postoperative clinic visit. In most patients, we observed a transient postoperative loss of skin commensals (Corynebacterium and Propionibacterium) at the surgical site, which were replaced by potential pathogens and intestinal anaerobes (eg, Enterobacteriaceae). These changes were not observed on skin that was uninvolved in the surgical incision (chest wall). One patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was also cultured from wound drainage.

Conclusions

We observed reproducible perioperative changes in the skin microbiome following surgery. The low incidence of SSIs in this cohort precluded analysis of associations between dysbiosis and infection. We postulate that real-time monitoring of the skin microbiome could provide actionable findings about the pathogenesis of SSIs.
The Antigallican Affair: Public and Ministerial Responses to Anglo-Spanish Maritime Conflict in the Seven Years War, 1756–1758
Authors: Brinkman-Schwartz Anna
Published: October 2020

In the first year of the Seven Years War, on 26 December 1756, the British privateer Antigallican captured the French East Indiaman Le Duc de Penthièvre some way off of the Spanish town of Ferrol. In short order the Duc de Penthièvre was given back to the French by Spanish authorities. The actions of the Spanish were a violation of Spain’s stated neutrality in the conflict and led to a protracted diplomatic incident that tested the commitment of Britain’s government to the preservation of Spain’s maritime neutrality, which was key to Britain’s overall wartime maritime strategy. Focusing on the Antigallican affair, this article presents a case-study which affords insight into how ministers dealt with public opinion that was in opposition to strategic needs at a specific political point in time, and over a specific issue. It also suggests that using measures based on the volume and intensity of press coverage as a proxy for public influence on policy making is an uncertain approach. By looking more deeply into the political, personal, and historical contexts of making policy, a micro-history offers a more certain method for understanding the complexity of policy-making and the power of the press at any given time. The point of such a close study is not to generalise about the power of the press to influence policy in the mid-eighteenth century, rather, it is to show that such generalisations are fraught with unanticipated errors and assumptions that gloss over the complexity of interactions between politics and public opinion.