bluuebunny/crossref_metadata_2025 huggingface dataset:
Departures from isotropy: the kinematics of a larval snail in response to food
Authors: DiBenedetto Michelle H. , Meyer-Kaiser Kirstin S. , Torjman Brooke , Wheeler Jeanette D. , Mullineaux Lauren S.
Published: November 2020

The swimming behavior of invertebrate larvae can affect their dispersal, survival, and settlement in the ocean. Modelling this behavior accurately poses unique challenges as behavior is controlled both by physiology and environmental cues. Some larvae use cilia to both swim and create feeding currents, resulting in potential trade-offs between the two functions. Food availability is naturally patchy and often occurs in shallow horizontal layers in the ocean. Also, larval swimming motions generally differ in the horizontal and vertical. In order to investigate behavioral response to food by ciliated larvae, we measure their behavioral anisotropy by quantifying deviations from a model based in isotropic diffusion. We hypothesize that larvae will increase horizontal swimming and decrease vertical swimming after encountering food which could lead to aggregation at food layers. We consider Crepidula fornicata larvae which are specifically of interest as they exhibit unsteady and variable swimming behaviors that are difficult to categorize. We tracked the larvae in still water with and without food, with a portion of the larvae starved beforehand. On average, larvae in the presence of food were observed higher in the water column, with higher swimming speeds and higher horizontal swimming velocities when compared to larvae without food. Starved larvae also exhibited higher vertical velocities in food, suggesting no aggregation behavior. While most treatments showed strong anisotropy in larval behavior, we found that starved larvae without food exhibited approximately isotropic kinematics, indicating that behavioral anisotropy can vary with environmental history and conditions to enhance foraging success or mitigate food-poor environments.
Η ηθική φιλοσοφία του Guillelmus Ockhamiensis
Authors: Θεοδωροπούλου Αθανασία
Published: November 2020

Δεν διατίθεται περίληψη
Jurisprudence, Legal ethics and Virtue
Authors: Franeta Duska
Published: November 2020

Δεν διατίθεται περίληψη
Rescuing Cosmopolitanism: A Marxian Account
Authors: Moschos Giannis
Published: November 2020

Δεν διατίθεται περίληψη
Το παίγνιο της αληθείας και του ψεύδους στην αριστοτελική πραγματεία Περί Ψυχής και η ερμηνεία του Σιμπλικίου
Authors: Ντότσικα Αλεξάνδρα Π.
Published: November 2020

Στο παρόν άρθρο διερευνάται το -πολυσχιδές φιλοσοφικά- παίγνιο της αληθείαςκαι του ψεύδους, όπως αυτό παρουσιάζεται στην πραγματεία Περί Ψυχῆς τουΑριστοτέλους. Στο πρώτο μέρος του άρθρου γίνεται αναφορά στο περιεχόμενοκαι στη δομή του έργου και, εν συνεχεία, στη σχέση του φιλοσοφικού ζητουμένουμε τις αισθήσεις, τη φαντασία και τον νου. Στο δεύτερο μέρος περιγράφεταισυντόμως το υπόμνημα του Σιμπλικίου και αναλύεται διεξοδικότερα η ερμηνείατου υπομνηματιστή για το εν λόγω φιλοσοφικό ερώτημα. Ακολουθεί ο επίλογος,στον οποίο παρατίθενται τα συμπεράσματα. Το πιο σημαντικό που προκύπτει απότην παρούσα μελέτη είναι ότι το αληθές ταυτίζεται στον Σιμπλίκιο με τον ὕπερθεννοῦ, θεωρία οπωσδήποτε πλατωνικής προελεύσεως, ενώ η αλήθεια, κατά τονΑριστοτέλη, σχηματοποιείται εντός της ανθρώπινης νοήσεως και με τη συνδρομήτων αισθήσεων, της φαντασίας και του νου.
Consistency of Pairwise Comparisons and Its Role in Optimal Detection of Customers’ Preferences
Authors: Tošenovský Filip
Published: November 2020

Purpose: This paper analyses a problem that originates in the weighted-average model, a mathematical construct introduced by the theory of multicriteria decision-making that can be used to detect what product a customer desires. The problem occurs because the model needs to know the weight the customer assigns to each product feature, aside from the levels of all the product characteristics, in order to calculate the overall value of the product. And since by one approach the weights can be estimated by optimization, the question arises which optimization criterion to select for the procedure, as different criteria will lead to different weights and thus to different product evaluations. The paper analyses the problem in connection with the so-called consistency of pairwise comparisons, which are utilized in the optimization and describe how much the customer prefers one product feature to another. The analysis shows that the problem of which criterion to use to calculate the weights can be eliminated if the pairwise comparisons are consistent. The analysis is performed within pre-defined criteria and is supplemented with case studies supporting the findings.Methodology/Approach: Linear algebra, optimization techniques, case studies.Findings: The results represent a prescription customers can use if they want to avoid the pitfalls of selecting a specific optimization criterion when informing the product maker about what they want based on the weighted-average model.Research Limitation/Implication: The results are related to a specific decision-making model, although that model is still very general and natural.Originality/Value of paper: The problem of selecting an optimization criterion to determine decision weights is not discussed in the theory.
The Link Between Asset Risk Management and Maintenance Performance: A Study of Industrial Manufacturing Companies
Authors: Maletič Damjan , Pačaiová Hana , Nagyová Anna , Maletič Matjaž
Published: November 2020

Purpose: The purpose of this paper is to examine risk management practices and their impact on performance. Specifically, the study aimed to examine risk management practices as part of physical asset management and their impact on maintenance management and its performance.Methodology/Approach: The empirical data were obtained from 76 manufacturing companies. Partial Least Squares Path Modeling (PLS-PM) was applied to evaluate the measurement and structural model.Findings: The results emphasized the importance of integrating risk management practices into asset management processes in order to improve performance outcomes.Research Limitation/Implication: This study contributes to a better understanding of how companies could achieve higher performance results by implementing risk management practices. The results of this study can help managers identify key asset risk management practices. Despite the important implications that can be derived from this study, further research that would extend the model to include additional performance measures and/or asset management dimensions would be of great importance.Originality/Value of paper: By analyzing the interrelationships between asset risk management practices and their direct and indirect effects on maintenance performance, the study provides important insights for the development of strategies to promote the novel and important discipline of asset management.
Role of Risk Aversion in Price Postponement Under Supply Random Yield
Authors: Kouvelis Panos , Xiao Guang , Yang Nan
Published: November 2020

Price postponement is an effective mechanism to hedge against the adverse effect of supply random yield. However, its effectiveness and the resulting production decisions have not been studied for risk-averse firms. In this paper, we investigate the impact of price postponement and risk aversion under supply yield risk. Specifically, we study a risk-averse monopoly firm’s production and pricing decisions under supply random yield with two distinct pricing schemes: (1) ex ante pricing in which the firm simultaneously makes the sales price and sourcing decisions before production takes place and (2) responsive pricing in which the pricing decision is postponed until after the production yield realization. We adopt conditional value at risk (CVaR) as the risk-aversion measurement and investigate the impact of the firm’s risk-aversion level on its optimal decisions and the corresponding profit. Among other results, we show that, for each pricing scheme, there exists a unique risk-aversion threshold under which the firm chooses not to produce. Interestingly, price postponement has no impact on the risk-aversion threshold as the cutoff values under both pricing schemes are the same. We further show that the value of CVaR improvement from responsive pricing may not be monotonic in the firm’s risk-aversion level. Consequently, our results indicate that, although price postponement induces operational flexibility by better matching demand with available supply, whether the firm should adopt responsive pricing needs to be carefully evaluated as the benefit may not justify the potential fixed cost associated with price postponement, especially for a highly risk-averse firm. In addition, we show that responsive pricing, even with its ex post revenue-maximization behavior, benefits the end-market consumers in equilibrium. Finally, we conduct extensive numerical studies to check and confirm the robustness of our results.

This paper was accepted by Charles Corbett, operations management.
Prevalence of combined abnormalities of tibial and femoral torsion in patients with symptomatic hip dysplasia and femoroacetabular impingement
Authors: Lerch Till D. , Liechti Emanuel F. , Todorski Inga A. S. , Schmaranzer Florian , Steppacher Simon D. , Siebenrock Klaus A. , Tannast Moritz , Klenke Frank M.
Published: November 2020

Aims

The prevalence of combined abnormalities of femoral torsion (FT) and tibial torsion (TT) is unknown in patients with femoroacetabular impingement (FAI) and hip dysplasia. This study aimed to determine the prevalence of combined abnormalities of FT and TT, and which subgroups are associated with combined abnormalities of FT and TT.

Methods

We retrospectively evaluated symptomatic patients with FAI or hip dysplasia with CT scans performed between September 2011 and September 2016. A total of 261 hips (174 patients) had a measurement of FT and TT. Their mean age was 31 years (SD 9), and 63% were female (165 hips). Patients were compared to an asymptomatic control group (48 hips, 27 patients) who had CT scans including femur and tibia available for analysis, which had been acquired for nonorthopaedic reasons. Comparisons were conducted using analysis of variance with Bonferroni correction.

Results

In the overall study group, abnormal FT was present in 62% (163 hips). Abnormal TT was present in 42% (109 hips). Normal FT combined with normal TT was present in 21% (55 hips). The most frequent abnormal combination was increased FT combined with normal TT of 32% (84 hips). In the hip dysplasia group, 21% (11 hips) had increased FT combined with increased TT. The prevalence of abnormal FT varied significantly among the subgroups (p < 0.001). We found a significantly higher mean FT for hip dysplasia (31°; SD 15)° and valgus hips (42° (SD 12°)) compared with the control group (22° (SD 8°)). We found a significantly higher mean TT for hips with cam-type-FAI (34° (SD 6°)) and hip dysplasia (35° (SD 9°)) compared with the control group (28° (SD 8°)) (p < 0.001).

Conclusion

Patients with FAI had a high prevalence of combined abnormalities of FT and TT. For hip dysplasia, we found a significantly higher mean FT and TT, while 21% of patients (11 hips) had combined increased TT and increased FT (combined torsional malalignment). This is important when planning hip preserving surgery such as periacetabular osteomy and femoral derotation osteotomy. Cite this article: Bone Joint J 2020;102-B(12):1636–1645.
Results of a randomized controlled trial with five-year radiostereometric analysis results of vitamin E-infused highly crosslinked versus moderately crosslinked polyethylene in reverse total hip arthroplasty
Authors: Thoen Peder S. , Nordsletten Lars , Pripp Are H. , Röhrl Stephan M.
Published: November 2020

Aims

Vitamin E-infused highly crosslinked polyethylene (VEPE) has been introduced into total hip arthroplasty (THA) with the aim of further improving the wear characteristics of moderately and highly crosslinked polyethylenes (ModXLPE and HXLPE). There are few studies analyzing the outcomes of vitamin E-infused components in cemented arthroplasty, though early acetabular component migration has been reported. The aim of this study was to measure five-year polyethylene wear and acetabular component stability of a cemented VEPE acetabular component compared with a ModXLPE cemented acetabular component.

Methods

In a prospective randomized controlled trial (RCT), we assessed polyethylene wear and acetabular component stability (primary outcome) with radiostereometric analysis (RSA) in 68 patients with reverse hybrid THA at five years follow-up. Patients were randomized to either a VEPE or a ModXLPE cemented acetabular component.

Results

Mean polyethylene wear in the proximal direction was 0.17 mm (SD 0.15) for the VEPE group and 0.20 mm (SD 0.09) for the ModXLPE group (p = 0.005) at five years. Annual proximal wear rates were 0.03 mm/year (VEPE) and 0.04 mm/year (ModXLPE). Total 3D wear was 0.21 mm (SD 0.26) and 0.23 mm (SD 0.10) for the VEPE and ModXLPE groups, respectively (p = 0.009). Total 3D cup translation was 0.72 mm (SD 0.70) (VEPE) and 0.50 mm (SD 0.44) (ModXLPE) (p = 0.409).

Conclusion

At five years, there was less polyethylene wear in the VEPE group than in the ModXLPE group. Both VEPE and ModXLPE cemented components showed low annual wear rates. Component stability was similar in the two groups and remained constant up to five years. Whether these results will equate to a lower long-term revision rate is still unknown. Cite this article: Bone Joint J 2020;102-B(12):1646–1653.
Axial resolution analysis in compressive digital holographic microscopy
Authors: Su Ping , Sun Da , Ma Jianshe , Luo Zhenpeng , Zhang Hua , Feng Shilun , Cao Liangcai
Published: November 2020

Digital holographic microscopy with compressive sensing (CDHM) has
successfully achieved tomography and has been applied in many fields.
However, the enhancement of axial resolution in CDHM remains to be
elucidated. By deducing accurate formulas for the lateral and axial
resolutions without paraxial approximation, we quantized the
elongation effect of a digital holography (DH) system in this study.
Thus, we revealed that the elongation effect, which is affected only
by the system’s numerical aperture (NA), is an inherent
property of DH systems. We present a detailed analysis herein on the
physical significance of the coherence parameter, which is the ratio
of a system’s limit axial resolution to the interlayer spacing
more thoroughly than in previous research. Further, we achieved the
tomography of a fiber by using a DH system with a
10 × microscope, with CS to eliminate the
elongation effect, and experimentally validated our theoretical
results. By applying these theoretical guidelines, we distinguished
crossed fibers at distances of 36.4 μm and
48.5 μm, respectively, using the same experimental
setup. There would be potential applications of this theory in
tomography and observation of microscale objects in the areas of
biological and fluid.
Band-edge mediated frequency down-conversion in a gas-filled anti-resonant hollow-core fiber
Authors: Gavara Trivikramarao , Hasan Md Imran , Abu Hassan Muhammad Rosdi , Deng Ang , Chang Wonkeun
Published: November 2020

We demonstrate frequency down-conversions of femtosecond pulses through dispersive wave generation and degenerate four-wave mixing in a gas-filled anti-resonant hollow-core fiber. These are achieved by exploiting the rapid variation of the dispersion in the fiber’s transmission band edge. In this approach, the wavelength of the down-shifted radiation is governed solely by the thickness of the dielectric wall at the core–cladding interface, while other system parameters are accountable only for inducing sufficient nonlinear phase shifts. With the right choice of cladding wall thickness, the concept can be applied directly for generating high-power mid-infrared femtosecond pulses.
Third-harmonic generation with tailored modes in liquid core fibers with geometric birefringence
Authors: Schaarschmidt Kay , Kobelke Jens , Meyer Tobias , Chemnitz Mario , Schmidt Markus A.
Published: November 2020

Geometrically induced birefringence represents a pathway for precisely engineering the modes in fibers and is particularly relevant for applications that crucially depend on modal dispersion. Here liquid core fibers (LCFs) with elliptical cores are analyzed in view of modal properties and third-harmonic generation (THG) numerically and experimentally. Using finite element modeling, the impact of ellipticity on phase matching, inter-modal coupling, electric field distribution, and birefringence are investigated. Significant THG in practically relevant modes, in accordance with phase-matching calculations, was measured in inorganic solvent-based LCFs.
Impact of gas dynamics on laser filamentation THz sources at high repetition rates
Authors: Koulouklidis Anastasios D. , Lanara Christina , Daskalaki Christina , Fedorov Vladimir Yu. , Tzortzakis Stelios
Published: November 2020

We experimentally demonstrate that the terahertz (THz) emission from two-color laser filaments in gases is strongly affected by the pulse repetition rate of the driving laser. We show that at repetition rates above 100 Hz, propagation of every next laser pulse in the pulse train is altered by gas density depressions produced by the preceding laser pulses. As a result, plasma channels at higher repetition rates become shorter, leading to less efficient THz generation. In particular, we observe a 50% decrease in the emitted THz energy when the repetition rate increases from 6 Hz to 6 kHz.
Mach–Zehnder silicon-photonic switch with low random phase errors
Authors: Song Lijia , Li Huan , Dai Daoxin
Published: November 2020

A Mach–Zehnder silicon photonic switch with low random phase errors is proposed and demonstrated for the first time, to the best of our knowledge, by incorporating judiciously widened and shortened phase shifter waveguides. With a 180 nm complementary metal–oxide–semiconductor (CMOS) foundry process, more than one hundred

2

×

2

thermo-optic Mach–Zehnder switches (MZSs) with varied phase shifter widths have been designed, fabricated, and characterized on 14 silicon chips. The mean and standard deviation of the random phase errors of the MZSs with phase shifters widened to 2 µm are less than a third of those of the conventional design with 0.45-µm-wide single-mode phase shifters. This validates the improved fabrication tolerance and results in considerable reduction of the power consumption for the phase error compensation. Such elegant methodology paves the way to further scaling up

N
×
N

silicon thermo-optic switches and can be generalized for other phase-sensitive integrated photonic devices as well.
Disentangling x-ray dichroism and birefringence via high-purity polarimetry
Authors: Schmitt Annika T. , Joly Yves , Schulze Kai S. , Marx-Glowna Berit , Uschmann Ingo , Grabiger Benjamin , Bernhardt Hendrik , Loetzsch Robert , Juhin Amélie , Debray Jérôme , Wille Hans-Christian , Yavaş Hasan , Paulus Gerhard G. , Röhlsberger Ralf
Published: November 2020

High-brilliance synchrotron radiation sources have opened new avenues for x-ray polarization analysis that go far beyond conventional polarimetry in the optical domain. With linear x-ray polarizers in a crossed setting, polarization extinction ratios down to

10

−
10

can be achieved. This renders the method sensitive to probe the tiniest optical anisotropies that would occur, for example, in strong-field quantum electrodynamics due to vacuum birefringence and dichroism. Here we show that high-purity polarimetry can be employed to reveal electronic anisotropies in condensed matter systems with utmost sensitivity and spectral resolution. Taking CuO and

L
a

2

C
u
O

4

as benchmark systems, we present a full characterization of the polarization changes across the Cu K-absorption edge and their separation into dichroic and birefringent contributions. At diffraction-limited synchrotron radiation sources and x-ray lasers, where polarization extinction ratios of

10

−
12

can be achieved, our method has the potential to assess birefringence and dichroism of the quantum vacuum in extreme electromagnetic fields.
Carrier dynamic process in all-inorganic halide perovskites explored by photoluminescence spectra
Authors: Chen Jing , Zhang Chao , Liu Xiaolin , Peng Lin , Lin Jia , Chen Xianfeng
Published: November 2020

Recently, all-inorganic halide perovskites have received enormous attention because of their excellent optoelectronic properties. Among them, the power conversion efficiency (PCE) of all-inorganic halide perovskite solar cells has made rapid progress in the last few years. However, understanding the intrinsic physical nature of halide perovskites, especially the dynamic process of photo-generated carriers, is a key for improving the PCE. In this review, we introduced and summarized the photoluminescence (PL) technique used to explore the carrier dynamic process in all-inorganic halide perovskites. Several physical models were proposed to investigate the dynamic parameters, i.e., recombination lifetime and diffusion length, by analyzing the steady-state PL as well as the time-resolved PL spectra. We also discussed the distinction of PL spectral behavior between bulk halide perovskite samples and those grown with transport layers due to the participation of different dominant dynamic paths. Finally, we briefly described some other optical techniques reported to study the relevant physical properties of all-inorganic halide perovskites.
EphrinB1 modulates glutamatergic inputs into POMC-expressing progenitors and controls glucose homeostasis
Authors: Gervais Manon , Labouèbe Gwenaël , Picard Alexandre , Thorens Bernard , Croizier Sophie
Published: November 2020

Proopiomelanocortin (POMC) neurons are major regulators of energy balance and glucose homeostasis. In addition to being regulated by hormones and nutrients, POMC neurons are controlled by glutamatergic input originating from multiple brain regions. However, the factors involved in the formation of glutamatergic inputs and how they contribute to bodily functions remain largely unknown. Here, we show that during the development of glutamatergic inputs, POMC neurons exhibit enriched expression of the Efnb1 (EphrinB1) and Efnb2 (EphrinB2) genes, which are known to control excitatory synapse formation. In vivo loss of Efnb1 in POMC-expressing progenitors decreases the amount of glutamatergic inputs, associated with a reduced number of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptor subunits and excitability of these cells. We found that mice lacking Efnb1 in POMC-expressing progenitors display impaired glucose tolerance due to blunted vagus nerve activity and decreased insulin secretion. However, despite reduced excitatory inputs, mice lacking Efnb2 in POMC-expressing progenitors showed no deregulation of insulin secretion and only mild alterations in feeding behavior and gluconeogenesis. Collectively, our data demonstrate the role of ephrins in controlling excitatory input amount into POMC-expressing progenitors and show an isotype-specific role of ephrins on the regulation of glucose homeostasis and feeding.
Generation and validation of versatile inducible CRISPRi embryonic stem cell and mouse model
Authors: Li Rui , Xia Xianyou , Wang Xing , Sun Xiaoyu , Dai Zhongye , Huo Dawei , Zheng Huimin , Xiong Haiqing , He Aibin , Wu Xudong
Published: November 2020

Clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) 9 has been widely used far beyond genome editing. Fusions of deactivated Cas9 (dCas9) to transcription effectors enable interrogation of the epigenome and controlling of gene expression. However, the large transgene size of dCas9-fusion hinders its applications especially in somatic tissues. Here, we develop a robust CRISPR interference (CRISPRi) system by transgenic expression of doxycycline (Dox) inducible dCas9-KRAB in mouse embryonic stem cells (iKRAB ESC). After introduction of specific single-guide RNAs (sgRNAs), the induced dCas9-KRAB efficiently maintains gene inactivation, although it modestly down-regulates the expression of active genes. The proper timing of Dox addition during cell differentiation or reprogramming allows us to study or screen spatiotemporally activated promoters or enhancers and thereby the gene functions. Furthermore, taking the ESC for blastocyst injection, we generate an iKRAB knock-in (KI) mouse model that enables the shutdown of gene expression and loss-of-function (LOF) studies ex vivo and in vivo by a simple transduction of gRNAs. Thus, our inducible CRISPRi ESC line and KI mouse provide versatile and convenient platforms for functional interrogation and high-throughput screens of specific genes and potential regulatory elements in the setting of development or diseases.
Little evidence for an effect of smoking on multiple sclerosis risk: A Mendelian Randomization study
Authors: Mitchell Ruth E. , Bates Kirsty , Wootton Robyn E. , Harroud Adil , Richards J. Brent , Davey Smith George , Munafò Marcus R.
Published: November 2020

The causes of multiple sclerosis (MS) remain unknown. Smoking has been associated with MS in observational studies and is often thought of as an environmental risk factor. We used two-sample Mendelian randomization (MR) to examine whether this association is causal using genetic variants identified in genome-wide association studies (GWASs) as associated with smoking. We assessed both smoking initiation and lifetime smoking behaviour (which captures smoking duration, heaviness, and cessation). There was very limited evidence for a meaningful effect of smoking on MS susceptibility as measured using summary statistics from the International Multiple Sclerosis Genetics Consortium (IMSGC) meta-analysis, including 14,802 cases and 26,703 controls. There was no clear evidence for an effect of smoking on the risk of developing MS (smoking initiation: odds ratio [OR] 1.03, 95% confidence interval [CI] 0.92–1.61; lifetime smoking: OR 1.10, 95% CI 0.87–1.40). These findings suggest that smoking does not have a detrimental consequence on MS susceptibility. Further work is needed to determine the causal effect of smoking on MS progression.
Remote homology search with hidden Potts models
Authors: Wilburn Grey W. , Eddy Sean R.
Published: November 2020

Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations. Recently, statistical physics models called Potts models have been used to infer all-by-all pairwise correlations between sites in deep multiple sequence alignments, and these pairwise couplings have improved 3D structure predictions. Here we extend the use of Potts models from structure prediction to sequence alignment and homology search by developing what we call a hidden Potts model (HPM) that merges a Potts emission process to a generative probability model of insertion and deletion. Because an HPM is incompatible with efficient dynamic programming alignment algorithms, we develop an approximate algorithm based on importance sampling, using simpler probabilistic models as proposal distributions. We test an HPM implementation on RNA structure homology search benchmarks, where we can compare directly to exact alignment methods that capture nested RNA base-pairing correlations (stochastic context-free grammars). HPMs perform promisingly in these proof of principle experiments.
Deconvolution of heterogeneous tumor samples using partial reference signals
Authors: Qin Yufang , Zhang Weiwei , Sun Xiaoqiang , Nan Siwei , Wei Nana , Wu Hua-Jun , Zheng Xiaoqi
Published: November 2020

Deconvolution of heterogeneous bulk tumor samples into distinct cellular populations is an important yet challenging problem, particularly when only partial references are available. A common approach to dealing with this problem is to deconvolve the mixed signals using available references and leverage the remaining signal as a new cell component. However, as indicated in our simulation, such an approach tends to over-estimate the proportions of known cell types and fails to detect novel cell types. Here, we propose PREDE, a partial reference-based deconvolution method using an iterative non-negative matrix factorization algorithm. Our method is verified to be effective in estimating cell proportions and expression profiles of unknown cell types based on simulated datasets at a variety of parameter settings. Applying our method to TCGA tumor samples, we found that proportions of pure cancer cells better indicate different subtypes of tumor samples. We also detected several cell types for each cancer type whose proportions successfully predicted patient survival. Our method makes a significant contribution to deconvolution of heterogeneous tumor samples and could be widely applied to varieties of high throughput bulk data. PREDE is implemented in R and is freely available from GitHub (https://xiaoqizheng.github.io/PREDE).
Immunoreactivity and neutralization study of Chinese Bungarus multicinctus antivenin and lab-prepared anti-bungarotoxin antisera towards purified bungarotoxins and snake venoms
Authors: Lin Bo , Zhang Jia-Rui , Lu Hui-Juan , Zhao Lin , Chen Jing , Zhang Hong-Fei , Wei Xue-Song , Zhang Liang-Yu , Wu Xiao-Bing , Lee Wen-Hui
Published: November 2020

Bungarus multicinctus is the most venomous snake distributed in China and neighboring countries of Myanmar, Laos, north Vietnam and Thailand. The high mortality rate of B. multicinctus envenomation is attributed to the lethal components of α-, β-, γ- and κ- bungarotoxins contained in the venom. Although anti-B. multicinctus sera were produced in Shanghai, Taiwan and Vietnam, the most widely clinic used product was term as B. multicinctus antivenin and manufactured by Shanghai Serum Bio-technology Co. Ltd. In the present investigation, high purity α-, β- and γ-bungarotoxins were separately isolated from B. multicinctus crude venom. Rabbit anti- α-, β- and γ-bungarotoxin antisera were prepared by common methods, respectively. LD50 values of α-, β- and γ-bungarotoxins were systematically determined via three administration pathways (intraperitoneal, intramuscular and intravenous injections) in Kunming mice. LD50 values of β-bungarotoxin were closely related with injection routines but those of both α- and γ-bungarotoxins were not dependent on the injection routines. Commercial B. multicinctus antivenin showed strong immunoreaction with high molecular weight fractions of the B. multicinctus but weakly recognized low molecular weight fractions like α- and γ-bungarotoxins. Although B. multicinctus antivenin showed immunoreaction with high molecular weight fractions of Bungarus fasciatus, Naja atra, Ophiophagus hannah venoms but the antivenin only demonstrated animal protection efficacy against O. hannah venom. These results indicated that the high molecular weight fractions of the O. hannah played an important role in venom lethality but those of B. fasciatus and N. atra did not have such a role.
Disentangling conditional effects of multiple regime shifts on Atlantic cod productivity
Authors: Perälä Tommi , Olsen Esben M. , Hutchings Jeffrey A.
Published: November 2020

Regime shifts are increasingly prevalent in the ecological literature. However, definitions vary and detection methods are still developing. Here, we employ a novel statistical algorithm based on the Bayesian online change-point detection framework to simultaneously identify shifts in the mean and (or) variance of time series data. We detected multiple regime shifts in long-term (59–154 years) patterns of coastal Norwegian Atlantic cod (>70% decline) and putative drivers of cod productivity: North Atlantic Oscillation (NAO); sea-surface temperature; zooplankton abundance; fishing mortality (F). The consequences of an environmental or climate-related regime shift on cod productivity are accentuated when regime shifts coincide, fishing mortality is high, and populations are small. The analyses suggest that increasingFincreasingly sensitized cod in the mid 1970s and late 1990s to regime shifts in NAO, zooplankton abundance, and water temperature. Our work underscores the necessity of accounting for human-induced mortality in regime shift analyses of marine ecosystems.
Cocaine vaccine dAd5GNE protects against moderate daily and high-dose “binge” cocaine use
Authors: Havlicek David F. , Rosenberg Jonathan B. , De Bishnu P. , Hicks Martin J. , Sondhi Dolan , Kaminsky Stephen M. , Crystal Ronald G.
Published: November 2020

The cocaine vaccine dAd5GNE is comprised of a disrupted serotype 5 adenovirus gene therapy vector covalently conjugated to the cocaine analog GNE. The vaccine evokes a high titer of circulating anti-cocaine antibodies that prevent cocaine from reaching its cognate receptors in the central nervous system. Prior studies have demonstrated the efficacy of dAd5GNE in models of occasional, moderate cocaine use. However, previous studies have not sufficiently evaluated the efficacy of dAd5GNE in models of the repetitive and high-dose “binge” use patterns common in human addicts. In the present study, we evaluated the capacity of dAd5GNE vaccination to protect against “binge” cocaine use and circumstances where vaccinated addicts attempt to override the vaccine. We modeled repetitive daily cocaine use in vaccinated Balb/c mice and African green monkeys, and evaluated high-dose “binge” scenarios in Balb/c mice. In each model of daily use the dAd5GNE vaccine prevented cocaine from reaching the central nervous system. In the high-dose “binge” model, vaccination decreased cocaine-induced hyperactivity and reduced the number of cocaine-induced seizures. Based on this data and our prior data in rodents and nonhuman primates, we have initiated a clinical trial evaluating the dAd5GNE anti-cocaine vaccine as a potential therapy for cocaine addicts who wish to stop cocaine use. If dAd5GNE vaccination is safe and produces high anti-cocaine antibody titers in the clinic, we hypothesize that the vaccine will restrict the access of cocaine to the central nervous system and inhibit cocaine-induced “highs” even in the context of moderate daily and high-dose “binge” use that might otherwise cause a drug-induced overdose.
A new approach to estimating the prevalence of hereditary hearing loss: An analysis of the distribution of sign language users based on census data in Russia
Authors: Romanov Georgii P. , Pshennikova Vera G. , Lashin Sergey A. , Solovyev Aisen V. , Teryutin Fedor M. , Cherdonova Aleksandra M. , Borisova Tuyara V. , Sazonov Nikolay N. , Khusnutdinova Elza K. , Posukh Olga L. , Fedorova Sardana A. , Barashkov Nikolay A.
Published: November 2020

The absence of comparable epidemiological data challenges the correct estimation of the prevalence of congenital hearing loss (HL) around the world. Sign language (SL) is known as the main type of communication of deaf people. We suggest that the distribution of SL can be interpreted as an indirect indicator of the prevalence of congenital HL. Since a significant part of congenital HL is due to genetic causes, an assessment of the distribution of SL users can reveal regions with an extensive accumulation of hereditary HL. For the first time, we analyzed the data on the distribution of SL users that became available for the total population of Russia by the 2010 census. Seventy-three out of 85 federal regions of Russia were ranked into three groups by the 25th and 75th percentiles of the proportion of SL users: 14 regions—“low proportion”; 48 regions—“average proportion”; and 11 regions—“high proportion”. We consider that the observed uneven prevalence of SL users can reflect underlying hereditary forms of congenital HL accumulated in certain populations by specific genetic background and population structure. At least, the data from this study indicate that the highest proportions of SL users detected in some Siberian regions are consistent with the reported accumulation of specific hereditary HL forms in indigenous Yakut, Tuvinian and Altaian populations.
Levels of and changes in socioeconomic inequality in delivery care service: A decomposition analysis using Bangladesh Demographic Health Surveys
Authors: Pulok Mohammad Habibullah , Chirwa Gowokani Chijere , Novignon Jacob , Aizawa Toshiaki , Makate Marshall
Published: November 2020

Background

Socioeconomic inequality in maternity care is well-evident in many developing countries including Bangladesh, but there is a paucity of research to examine the determinants of inequality and the changes in the factors of inequality over time. This study examines the factors accounting for the levels of and changes in wealth-related inequality in three outcomes of delivery care service: health facility delivery, skilled birth attendance, and C-section delivery in Bangladesh.

Methods

This study uses from the Bangladesh Demographic and Health Survey of 2011 and 2014. We apply logistic regression models to examine the association between household wealth status and delivery care measures, controlling for a wide range of sociodemographic variables. The Erreygers normalised concentration index is used to measure the level of inequalities and decomposition method is applied to disentangle the determinants contributing to the levels of and changes in the observed inequalities.

Results

We find a substantial inequality in delivery care service utilisation favouring woman from wealthier households. The extent of inequality increased in health facility delivery and C-section delivery in 2014 while increase in skilled birth attendance was not statistically significant. Wealth and education were the main factors explaining both the extent of and the increase in the degree of inequality between 2011 and 2014. Four or more antenatal care (ANC4+) visits accounted for about 8% to 14% of the observed inequality, but the contribution of ANC4+ visits declined in 2014.

Conclusion

This study reveals no progress in equity gain in the use of delivery care services in this decade compared to a declining trend in inequity in the last decade in Bangladesh. Policies need to focus on improving the provision of delivery care services among women from poorer socioeconomic groups. In addition, policy initiatives for promoting the completion of quality education are important to address the stalemate of equity gain in delivery care services in Bangladesh.
Red blood cell homeostasis in children and adults with and without asymptomatic malaria infection in Burkina Faso
Authors: Kaboré Berenger , Post Annelies , Berendsen Mike L. T. , Diallo Salou , Lompo Palpouguini , Derra Karim , Rouamba Eli , Jacobs Jan , Tinto Halidou , de Mast Quirijn , van der Ven Andre J.
Published: November 2020

Asymptomatic malaria infections may affect red blood cell (RBC) homeostasis. Reports indicate a role for chronic hemolysis and splenomegaly, however, the underlying processes are incompletely understood. New hematology analysers provide parameters for a more comprehensive analysis of RBC hemostasis. Complete blood counts were analysed in subjects from all age groups (n = 1118) living in a malaria hyperendemic area and cytokines and iron biomarkers were also measured. Subjects were divided into age groups (<2 years, 2–4, 5–14 and ≥15 years old) and clinical categories (smear-negative healthy subjects, asymptomatic malaria and clinical malaria). We found that hemoglobin levels were similar in smear-negative healthy children and asymptomatic malaria children but significantly lower in clinical malaria with a maximum difference of 2.2 g/dl in children <2 years decreasing to 0.1 g/dl in those aged ≥15 years. Delta-He, presenting different hemoglobinization of reticulocytes and RBC, levels were lower in asymptomatic and clinial malaria, indicating a recent effect of malaria on erythropoiesis. Reticulocyte counts and reticulocyte production index (RPI), indicating the erythropoietic capacity of the bone marrow, were higher in young children with malaria compared to smear-negative subjects. A negative correlation between reticulocyte counts and Hb levels was found in asymptomatic malaria (ρ = -0.32, p<0.001) unlike in clinical malaria (ρ = -0.008, p = 0.92). Free-Hb levels, indicating hemolysis, were only higher in clinical malaria. Phagocytozing monocytes, indicating erythophagocytosis, were highest in clinical malaria, followed by asymptomatic malaria and smear-negative subjects. Circulating cytokines and iron biomarkers (hepcidin, ferritin) showed similar patterns. Pro/anti-inflammatory (IL-6/IL-10) ratio was higher in clinical than asymptomatic malaria. Cytokine production capacity of ex-vivo whole blood stimulation with LPS was lower in children with asymptomatic malaria compared to smear-negative healthy children. Bone marrow response can compensate the increased red blood cell loss in asymptomatic malaria, unlike in clinical malaria, possibly because of limited level and length of inflammation.

Trial registration: Prospective diagnostic study: ClinicalTrials.gov identifier: NCT02669823.

Explorative cross-sectional field study: ClinicalTrials.gov identifier: NCT03176719.
Molecular epidemiology and surveillance of circulating rotavirus among children with gastroenteritis in Bangladesh during 2014–2019
Authors: Dey Shuvra Kanti , Sharif Nadim , Sarkar Omar Sadi , Sarkar Mithun Kumar , Talukder Ali Azam , Phan Tung , Ushijima Hiroshi
Published: November 2020

Acute gastroenteritis is one of the major health problems in children aged <5 years around the world. Rotavirus A (RVA) is an important pathogen of acute gastroenteritis. The burden of rotavirus disease in the pediatric population is still high in Bangladesh. This study investigated the prevalence of group A, B, and C rotavirus (RAV, RBV, RCV), norovirus, adenovirus (AdV) and human bocavirus (HBoV) infections in children with acute gastroenteritis in Bangladesh from February 2014 to January 2019. A total of 574 fecal specimens collected from children with diarrhea in Bangladesh during the period of February 2014-January 2019 were examined for RAV, RBV and RCV by reverse transcriptase- multiplex polymerase chain reaction (RT- multiplex PCR). RAV was further characterized to G-typing and P-typing by RT-multiplex PCR and sequencing method. It was found that 24.4% (140 of 574) fecal specimens were positive for RVA followed by AdV of 4.5%. RBV and RCV could not be detected in this study. Genotype G1P[8] was the most prevalent (43%), followed by G2P[4] (18%), and G9P[8] (3%). Among other genotypes, G9P[4] was most frequent (12%), followed by G1P[6] (11%), G9P[6] (3%), and G11P[25] (3%). We found that 7% RVA were nontypeable. Mutations at antigenic regions of the VP7 gene were detected in G1P[8] and G2P[4] strains. Incidence of rotavirus infection had the highest peak (58.6%) during November to February with diarrhea (90.7%) as the most common symptom. Children aged 4–11 months had the highest rotavirus infection percentage (37.9%). By providing baseline data, this study helps to assess efficacy of currently available RVA vaccine. This study revealed a high RVA detection rate, supporting health authorities in planning strategies such as introduction of RVA vaccine in national immunization program to reduce the disease burden.
Rat donor lung quality deteriorates more after fast than slow brain death induction
Authors: van Zanden Judith E. , Rebolledo Rolando A. , Hoeksma Dane , Bubberman Jeske M. , Burgerhof Johannes G. , Breedijk Annette , Yard Benito A. , Erasmus Michiel E. , Leuvenink Henri G. D. , Hottenrott Maximilia C.
Published: November 2020

Donor brain death (BD) is initiated by an increase in intracranial pressure (ICP), which subsequently damages the donor lung. In this study, we investigated whether the speed of ICP increase affects quality of donor lungs, in a rat model for fastversusslow BD induction. Rats were assigned to 3 groups: 1) control, 2) fast BD induction (ICP increase over 1 min) or 3) slow BD induction (ICP increase over 30 min). BD was induced by epidural inflation of a balloon catheter. Brain-dead rats were sacrificed after 0.5 hours, 1 hour, 2 hours and 4 hours to study time-dependent changes. Hemodynamic stability, histological lung injury and inflammatory status were investigated. We found that fast BD induction compromised hemodynamic stability of rats more than slow BD induction, reflected by higher mean arterial pressures during the BD induction period and an increased need for hemodynamic support during the BD stabilization phase. Furthermore, fast BD induction increased histological lung injury scores and gene expression levels of TNF-α and MCP-1 at 0.5 hours after induction. Yet after donor stabilization, inflammatory status was comparable between the two BD models. This study demonstrates fast BD induction deteriorates quality of donor lungs more on a histological level than slow BD induction.
Significant reductions of host abundance weakly impact infection intensity of Batrachochytrium dendrobatidis
Authors: Bosch Jaime , Carrascal Luis M. , Manica Andrea , Garner Trenton W. J.
Published: November 2020

Infectious diseases are considered major threats to biodiversity, however strategies to mitigate their impacts in the natural world are scarce and largely unsuccessful. Chytridiomycosis is responsible for the decline of hundreds of amphibian species worldwide, but an effective disease management strategy that could be applied across natural habitats is still lacking. In general amphibian larvae can be easily captured, offering opportunities to ascertain the impact of altering the abundance of hosts, considered to be a key parameter affecting the severity of the disease. Here, we report the results of two experiments to investigate how altering host abundance affects infection intensity in amphibian populations of a montane area of Central Spain suffering from lethal amphibian chytridiomycosis. Our laboratory-based experiment supported the conclusion that varying density had a significant effect on infection intensity when salamander larvae were housed at low densities. Our field experiment showed that reducing the abundance of salamander larvae in the field also had a significant, but weak, impact on infection the following year, but only when removals were extreme. While this suggests adjusting host abundance as a mitigation strategy to reduce infection intensity could be useful, our evidence suggests only heavy culling efforts will succeed, which may run contrary to objectives for conservation.