bluuebunny/crossref_metadata_2025 huggingface dataset:
Timing is everything, but does it really matter? Impact of 8‐weeks morning versus evening iron supplementation in ballet and contemporary dancers
Authors: Attwell Caitlin , McKay Alannah , Sim Marc , Dugan Cory , Nicholas Joanna , Hopper Luke , Peeling Peter
Published: June 2023

The effectiveness of a morning versus evening oral iron supplement strategy to increase iron stores was explored. Ballet and contemporary dancers with serum ferritin (sFer) < 50μg/L (n = 14), were supplemented daily with 105 mg elemental oral iron in either the morning (FeAM) or evening (FePM) for 8 weeks. A control group (n = 6) with sFer >50μg/L were given no supplement over the same period. Dancers’ sFer were measured at baseline and post‐intervention. Assessment of daily training load, dietary intake, and menstruation were made. A significant interaction (p < 0.001) showed the within group sFer change over the 8‐week intervention in FeAM (+25.9 ± 10.5μg/L) and FePM, (+22.3 ± 13.6μg/L) was significantly different to CON (−30.17 ± 28.7μg/L; both p = 0.001). This change was not different between FeAM and FePM (p = 0.778). sFer levels within FeAM and FePM significantly increased over the 8‐weeks; however, they significantly decreased in the CON group (all p < 0.05). Post‐intervention sFer levels were no longer different between the three groups (p > 0.05). Training load, dietary intake, and number of menstrual cycles incurred were similar between FeAM and FePM (p > 0.05). Oral iron supplementation in either the morning or evening appears equally effective in increasing sFer levels in dancers with sub‐optimal iron status.
Tuning the electrical and cycling performance of nickel manganese oxide hexagonal-shaped particles via preparation routes for lithium-ion batteries
Authors: Jain Anchali , Panwar Amrish K , Tyagi Pawan K
Published: June 2023

In this study, simple and effective solid-state and sol-gel routes are attempted to synthesize nickel manganese oxide, NiMn2O4. Structural, morphological, electrical, and electrochemical properties are investigated with calcination temperatures. X-ray diffraction (XRD) results confirm the highly crystalline cubic spinel structure with zero impurities for all samples, except NMOS_700, which indicates the presence of a slight NiMnO3 phase. Scanning electron microscope (SEM) and transmission electron microscope (TEM) micrographs confirm the formation of hexagonal shape particles of size less than <0.5 μm. At low calcination temperatures, grouped and uneven-shaped particles are observed with increased particle size. Electrical measurements depict the strong dependence of conductivities (σ
ac and σ
dc) on grain size, grain boundary, and operating temperature. All the samples exhibit conductivities between 10−8 and 10−4 S cm−1 with the varied calcination temperature. Electrochemical performances are explored via electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), and galvanostatic charge–discharge (GCD) profiles. Sample NMOB_700 and NMOB_800 exhibit the initial discharging capacity of 1104 mAh g-1 and 1188 mAh g−1 at 100 mA g−1 current density. All the samples exhibit above 98% columbic efficiency after two initial cycles and show the reversible nature of NMO and excellent cyclability. The electrochemical results confirm that preparation methods and calcination temperature have a great impact on the grain properties of materials. Multiple oxidation states of Mn and Ni is also confirmed through the XPS study.
Complex piezoelectric material parameters of hard PZT determined from a single disc transducer
Authors: Kar Bibhu , Basaeri Hamid , Roundy Shad , Wallrabe Ulrike
Published: June 2023

A poled piezoelectric ceramic such as lead zirconate titanate (PZT) belongs to a C

∞

crystal class, with ten independent material constants. If we consider losses, all the material parameters can be represented in complex form as all the ten material parameters also have ten loss components associated with them. Therefore, a total of 20 independent material constants are required to obtain the entire model. In this work, we present a procedure for determining the complete reduced matrix of a piezoelectric ultrasonic disc transducer using one-dimensional resonance analysis in thickness and radial modes and parametric sweep using finite element analysis to numerically calculate the impedance while comparing it with the measured impedance. The objective is to obtain the material parameters that minimize the error between the measured impedance data and the numerical impedance curve without using any optimization techniques. We can follow the standard procedure of resonance analysis for radial and thickness modes and then conduct a sensitivity analysis using parametric sweeps in COMSOL to evaluate the unknown material values. In addition, we present the transform equations in reduced matrix form to evaluate the critically sensitive parameters concerning other consistent evaluated material constant sets. To validate the procedure, we used the impedance responses of two piezoelectric discs with diameter-to-thickness ratios of 25 and 22.5. The comparison between the numerical and experimental results shows an excellent agreement for electrical impedance curves.
Effect of CdSSe nanoparticles on the structural, surface roughness, linear, and nonlinear optical parameters of polyvinyl chloride films for optoelectronic applications
Authors: Soliman T S
Published: June 2023

Polyvinyl chloride (PVC) was used as a host matrix for different CdSSe nanoparticles (NPs) concentrations. PVC-CdSSe films were prepared by the solution-cast method, and CdSSe NPs were prepared by the hot-injection method. A scanning electron microscope attached to an EDX unit was used to identify CdSSe elements. The reinforcement of CdSSe NPs in the PVC matrix exhibits growth in CdSSe particle size due to agglomerations. PVC-CdSSe films were examined via XRD, FT-IR, and a polarized optical microscope. The roughness tester was used to measure the surface roughness parameters of the PVC-CdSSe films, which revealed the growth in film roughness with increasing the CdSSe concentration. The UV-visible spectrophotometer was used to analyze the PVC-CdSSe film’s transmission and absorption. Tauc’s model was used to evaluate the optical bandgap (Eg). The Eg was lessened from 5.45 eV for pure PVC to 4.78 eV for PVC-3wt%CdSSe film, while the Urbach energy was increased upon CdSSe NPs additive to the PVC matrix testifying to the formation of the localized states with high-density. Furthermore, an improvement in nonlinear optical parameters (estimated via the Wemple-DiDomenico model) was observed. The third-order nonlinear optical susceptibility ( χ(3)) enhanced from 4.08 × 10−15 for pure PVC to 1.91 × 10−13 for PVC-3wt%CdSSe, due to the surface plasmon oscillation of CdSSe NPs in the PVC matrix. In view of the improved optical parameters, the as-prepared PVC-CdSSe films make them a possible nominee for nonlinear optical devices.
Tripartite Wigner’s friend scenario and its test
Authors: Ding D , Wang C , He Y Q , Hou T , Gao T , Yan F L
Published: June 2023

Wigner’s friend thought experiment is intended to reveal the inherent tension between unitary evolution and measurement collapse. Inspired by the Wigner’s friend experiment, Brukner derives a no-go theorem for observer-independent facts, focusing on two entangled observers in their respective laboratories. We construct an extended Wigner’s friend scenario, including three laboratories, namely, Alice’s laboratory, Bob’s laboratory and Charlie’s laboratory, where Alice, Bob and Charlie are standing outside the laboratories while their friends are placed inside their own laboratories. To realize this scenario, we create a universal quantum circuit, especially the circuit realization of the state evolution and measurement inside each laboratory, simple but novel. We carry out experiments on the IBM quantum computers to test the primary circuits, i.e. state preparation, state evolution and measurement inside each laboratory. Furthermore, we perform the simulation of the quantum circuit via Q# quantum programming on a classical computer.
Quantum dynamical speedup for correlated initial states
Authors: Gholizadeh Alireza , Hadipour Maryam , Haseli Soroush , Haddadi Saeed , Dolatkhah Hazhir
Published: June 2023

The maximal evolution speed of any quantum system can be expressed by the quantum speed limit time. In this paper, we consider a model in which the system has a correlation with the environment. The influence of the initial correlation between the system and environment on the quantum speed limit is investigated. It is shown that the appearance of non-Markovianity effects causes the speedup of quantum evolution. Moreover, we demonstrate the dependence of quantum dynamical speedup on the quantum coherence of the correlated initial state.
Temporal characteristics of ELMs on the COMPASS divertor
Authors: Adamek J. , Cavalier J. , Tskhakaya D. , Csillag B. , Cinnirella L. , Lips J. , Lopez-Rodriguez D. , Sosa D. , Medina D. , Vondracek P. , Kripner L. , Komm M. , Sos M. , Lindl H.
Published: June 2023

The presented work shows a systematic study of the temporal characteristics of ELM events on the COMPASS divertor obtained with high temporal resolution probe measurements (∼1 μs). The resulting temporal evolution of the total ELM power on the outer target provides the values of rise (τ
rise) and decay (τ
decay) times for each single ELM event. It has been found that τ
rise values are in the range of about 50 μs–100 μs. These values are comparable to the time of the ELM parallel propagation (τ
||) given by the sound speed and the connection length between the outer midplane and the outboard divertor. This comparison indicates that the magnetic field lines in the SOL region are not significantly ergodized during the pedestal crash on COMPASS. It also implies that the peak ELM energy fluence on the outboard divertor is dominated by the ELM parallel transport, which is confirmed by a good agreement with model prediction. In addition, the values of the ratio of τ
decay and τ
rise for each ELM event fit very well to the boundaries 1.5 < τ
decay/τ
rise < 4, as already shown on JET as well as on the HL-2A tokamak, using IR measurements. The ratio does not show any clear dependence on the relative ELM energy or line averaged electron density. It was also found that the ELM energy fluence decay length (λϵ

mid) is clearly linked to this ratio.
Square ice formation in CrOCl and graphene confinement
Authors: Wang Yangjie , Chen Jige
Published: June 2023

The structure and thermodynamic properties of water in nanoscale confinement environment are greatly involved in the research field of material science and nanotechnology. However, a complete picture of the ordered structure formation and thermodynamics behavior of the confined water inside two parallel nanosheets with different surface atomic arrangement is still lacking. In this paper, by using molecular dynamics (MD) simulations, we study the structural variation and thermodynamics behavior for water molecules confined between two parallel CrOCl with a square surface atomic arrangement and two parallel graphene nanosheets with a hexagonal surface atomic arrangement. Square ice, with a lattice constant 2.1 and 2.0 Å, is observed inside the two parallel CrOCl and graphene nanosheets, respectively. By calculating the configuration entropy of the molecular dipoles St
, it is found that, in the CrOCl confinement, St
reaches a peak value and then is greatly reduced due to the square ice formation. On the other hand, in the graphene confinement, St
continues to grow after the square ice formation and is then reduced after reaching its peak value. Interestingly, it is found that the square ice could be stable at a higher entropy state under the external pressure than the bulk water at ambient condition. By calculating the orientational order parameters M, it shows that the conventional tetrahedral geometry of hydrogen bonding between water molecules breaks due to the square ice formation. By analyzing the average number of hydrogen bonds of water molecules Nh
, it is found that the hydrogen bond interaction of the square ice relies on the confinement environment, where Nh
is reduced in the CrOCl confinement and increased in the graphene confinement. Probability distribution functions of the dipole orientation angles between the x- or z-axis and the projection of the oxygen atoms of the water molecules are also calculated. It is observed that the square ice structure is paralleled with the x-axis (unit cell axis) in the CrOCl confinement and tilted with the x-axis (the zigzag direction of graphene) at an angle 30° in the graphene confinement. Furthermore, the square ice formation is found to be insensitive to temperature. Our result reveals the peculiar ordered structure and thermodynamics behavior of water in different nanoscale confinement environments.
Long-time correlations in a binary mixture: analysis of the nonlinearities of fluctuating-hydrodynamic equations
Authors: Bidhoodi Neeta , Das Shankar P
Published: June 2023

The equations of fluctuating nonlinear hydrodynamics (FNH) following the proper conservation laws are considered for a binary mixture. We focus on the density (ρ) correlations’ renormalization due to the FNH equations’ nonlinearities. The consequence of density nonlinearities treated in simplest approximations gives rise to the well-studied form of the mode coupling theory (MCT) for a two-component system. The MCT predicts a sharp ergodicity–nonergodicity transition similar to the one-component fluid in this idealized form. In the first part of the present paper, we compare the predictions of the idealized MCT model with the computer simulation results for a hard sphere mixture. We show that there is clear disagreement in long-time dynamic behaviour. Next, we consider the full set of nonlinearities in the FNH equations using a Martin–Siggia–Rose field theory. From the time reversal properties of the correlation and response function of the associated field theory, a set of fluctuation–dissipation relations (FDR) are obtained. These FDRs impose constraints on the long-time behaviour of the correlation functions. Our non-perturbative analysis considers the viability of freezing the time correlations for the two-component fluid over the longest time scale. Due to the FDR constraints arising from the

1

/

ρ

nonlinearity in the FNH equations, a sharp ergodicity–nonergodicity transition for the binary mixture is not supported. If the

1

/

ρ

are replaced as

1

/

ρ
0

in terms of the average density ρ
0, ad hoc, while the density-nonlinearities in the pressure term of the corresponding FNH equations are kept, the ideal transition model of the simplified MCT is recovered.
Design, modelling, and experimental validation of a self-rotating flapping wing rotorcraft with motor–spring resonance actuation system
Authors: Liu Fangyuan , Li Song , Dong Xin , Wang Ziyu , Xiang Jinwu , Li Daochun , Tu Zhan
Published: June 2023

Compared with traditional flapping motion, the flapping wing rotor (FWR) allows rotating freedom by installing the two wings asymmetrically, which introduces rotary motion characteristics and enables the FWR to have higher lift and aerodynamic efficiency at low Reynolds number. However, most of the proposed FWRs contain linkage mechanical transmission structures, the fixed degrees of freedom of which prohibit the wings from achieving variable flapping trajectories, limiting further optimization and controller design of FWRs. In order to fundamentally address the above challenges of FWRs, this paper presents a new type of FWR with two mechanically decoupled wings, which are directly driven by two independent motor–spring resonance actuation systems. The proposed FWR has 12.4 g of system weight and 165–205 mm wingspan. In addition, a theoretical electromechanical model based on the DC motor model and quasi-steady aerodynamic forces is established, and a series of experiments are conducted in order to determine the ideal working point of the proposed FWR. It is notable that both our theoretical model and experiments exhibit uneven rotation of the FWR during flight, i.e. rotation speed dropping in the downstroke and increasing in the upstroke, which further tests the proposed theoretical model and uncovers the relationship between flapping and passive rotation in the FWR. To further validate the performance of the design, free flight tests are conducted, and the proposed FWR demonstrates stable liftoff at the designed working point.
Efficiency at optimal performance of Brownian heat engines under double tangent constraint
Authors: Streitenberger Peter
Published: June 2023

The efficiency of a steady-state thermochemical Brownian heat engine is considered, where the heat flux from the hot to the cold reservoir drives particles from the lower chemical potential of the hot reservoir to the higher chemical potential of the cold reservoir, converting heat into chemical or potential energy. This model system is used to investigate the optimal performance of a Brownian heat engine under a new constraint based on a double tangent construction between the occupation number distributions of the particles in the two heat reservoirs with temperatures

T
1

>

T
2

and chemical potentials

μ
1

<

μ
2

. This constraint allows an operation mode that forces the heat engine to attain Carnot efficiency

η
C

=
1
−

T
2

/

T
1

at nonvanishing power output when approaching thermal equilibrium. For classical particles, the efficiency at maximum power under double tangent constraint results to

η

m
p
t

=

η
C
2

/

η
C
2

−

1
−

η
C

ln

1
−

η
C

with the asymptotic series expansion

η

m
p
t

=

 

η
C

−

η
C
2

2

+

5

η
C
3

12

+
O

η
C

4

, which shows Carnot behavior for

η
C

toward zero. This efficiency is significantly higher than the corresponding efficiency at unconstrained maximum power

η

m
p

=

η
C
2

/

η
C

−

1
−

η
C

ln

1
−

η
C

derived by Tu (2008 J. Phys. A Math. Theor.
41 312003) for the classical Feynman ratchet and by van den Broeck and Lindenberg (2012 Phys. Rev. E 86 041144) for classical particle transport, which has the expansion

η

m
p

=

1
2

η
C

+

1
8

η
C
2

+

7

96

η
C
3

+
O

η
C

4

showing the Curzon–Ahlborn

η
C

/

2

behavior for

η
C

toward zero. The applicability of the double tangent constraint to other optimization criteria is demonstrated using the ecological criterion as an example. The method can also be applied to quantum distributions, for which, however, only a numerical solution is possible.
Study of Vortex Effect on Vertical Axis Marine Current Turbine Arm
Authors: Amiadji  , Arief I S , Baidowi A
Published: June 2023

The design of a marine current turbine generator specifically in deep water with unequal seabed which requires the designer to develop a floating platform for the turbine. It creates a massive challenge in improving the mechanical system, such as the turbine arm. In order to make the monitoring and maintenance accessible, the generator must be placed on the platform’s deck. A long shaft is required to make the connection between the generator and turbine. The problems occur due to the vibration generated by the vortex around the shaft or the turbine arm. This paper aim is to investigate the vortex effect on the turbine arm and propose an advanced design to reduce its impact. The computational fluid dynamic method is approached to analyse the vortex generated by the turbine arm. The analysis compared the conventional cylindrical and the foil-shaped turbine arm. Moreover, the investigation includes force along the X-axis and Y-axis, flow, drag, lift coefficient, also fatigue lift near the turbine arm. The numerical output illustrates that the foil shaped on the turbine arm provided limited vortex and improved the performance compared to the conventional cylindrical turbine arm.
Fast ship prototype design simulation with fin stabilizer on hydrodynamic characteristics for ship realization planning
Authors: Diatmaja H , Prabowo A R , Muhayat N , Tuswan T , Putranto T
Published: June 2023

This study aims to determine the effect of adding variations of fin stabilizers on the hydrodynamic characteristics of the ship design. It compares the hull without modification with the hull modified by a fin stabilizer on a prototype scale. The results of this study is assessed to obtain the best performance of ships with various models to be used in the design of ship realization. The research method is conducted by numerical approach, including simulation of resistance, stability, and seakeeping. The hull design references chosen are the Fast Police Boat and SMIT Patrol Boat with a Length Overall value of 1 m. The fin stabilizer uses hydrofoil type NACA-0015 with an aspect ratio of 0.7. Then the length variations are 3 cm, 4 cm, and 5 cm, with angle variations being 25°, 30°, and 35°. The results showed that adding a fin stabilizer could increase the ship’s stability. The best fin stabilizers variations are fins with a length of 5 cm and an angle of 30° for the prototype design of the Fast Police Boat hull and fins with a length of 5 cm and an angle of 35° for the prototype design of the SMIT Patrol Boat hull.
Description of Neoseiulus hexaporus sp. nov. and a redescription of Neoseiulus mumai (Acari: Mesostigmata: Phytoseiidae) from Florida citrus groves
Authors: Döker Ismail , Demard Emilie P , Bolton Samuel J , Qureshi Jawwad A
Published: June 2023

Predatory mites are effective natural enemies of small arthropods, including pest mites and insects, which provide biological control of several crop pests worldwide. The family Phytoseiidae (Acari: Mesostigmata) is a diverse group of predators found in cultivated crops and other habitats containing natural vegetation. Although some phytoseiid species are commercialized and widely used in biological control programs, the determination of natural populations and identification of the species is a vital first step in understanding their interactions with the crop, environment, and pests. The citrus crop is a diverse agroecosystem colonized by a variety of pests including mites and warrants an understanding of the complex of predators. We collected predatory mites from multiple citrus groves in Florida, to find and identify species for biological control in citrus crops. The examination of the specimens involved the use of Olympus CX-41 microscope, and drawings were prepared with the help of the attached camera Lucida. Any needed corrections were made using tracing paper, rapidograph pen, and Adobe Photoshop version CS6. Neoseiulus hexaporussp. nov. is described and illustrated as a new species based on its distinct morphology compared with previously described species in paspalivorus group. We also provide a complementary redescription of Neoseiulus mumai (Denmark), including an important diagnostic character of leg chaetotaxy which had led to the description of a new species, Neoseiulus kikuyu Ma, Fan & Zhang. We also provide new illustrations of N. mumai to facilitate its diagnosis.
A dilemma for Nicolausian discounting
Authors: Cibinel Pietro
Published: June 2023

Orthodox decision theory is fanatical in the way it treats small probabilities of enormous value, if unbounded utility functions are allowed. Some have suggested a fix, Nicolausian discounting, according to which outcomes with small enough probabilities should be ignored when making decisions. However, there are lotteries involving only small-probability outcomes, none of which should intuitively be ignored. So the Nicolausian discounter needs a procedure for distinguishing the problematic cases of small-probability outcomes from the unproblematic ones. In this paper, I present a dilemma for Nicolausian discounting: the view must be coupled either with a procedure that delivers fanatical verdicts of its own, as bad as those of orthodox decision theory, or with one that entails intransitive cyclic preferences.
Cognitive Reserve Moderates the Effects of Fatigue and Depressive Symptoms in Multiple Sclerosis
Authors: Bradson Megan L , Cadden Margaret H , Riegler Kaitlin E , Thomas Garrett A , Randolph John J , Arnett Peter A
Published: June 2023

To investigate cognitive reserve as a possible moderator in the relationship between fatigue and depressive symptoms in persons with multiple sclerosis (PwMS). Fifty-three PwMS (37 female; mean age, 52.66; mean education, 14.81) completed comprehensive neuropsychological testing and psychosocial questionnaires assessing the perceived effects of fatigue (Fatigue Impact Scale) and depressive symptoms (Beck Depression Inventory-Fast Screen). Cognitive reserve (CR) was operationalized as Fixed CR and Malleable CR. Fixed CR was quantified as the standardized mean of years of education and a vocabulary-based estimate of premorbid intelligence. Malleable CR was quantified as the standardized mean of cognitive exertion, exercise, and socializing items from the Cognitive Health Questionnaire. Regressions on depressive symptoms examining fatigue, both conceptualizations of CR, and their interactions were explored. A Bonferroni correction was used; results were considered significant at an alpha level of p < .01. The interactions between fatigue and both conceptualizations of CR were significant, p = .005 (Fixed CR); p = .004 (Malleable CR). Simple effects tests revealed that fatigue only predicted depressive symptoms in PwMS with low Fixed CR or low Malleable CR (p’s < .001), and not in those with high Fixed or high Malleable CR (p > .01). Cognitive reserve moderated the relationship between fatigue and depressive symptoms in PwMS. Specifically, fatigue does not appear to influence depression in PwMS with high cognitive reserve. Having higher cognitive reserve (either Fixed or Malleable) may reduce the likelihood that fatigue will lead to depressive symptoms in MS.
Moral Gaslighting
Authors: Manne Kate
Published: June 2023

Philosophers have turned their attention to gaslighting only recently, and have made considerable progress in analysing its characteristic aims and harms. I am less convinced, however, that we have fully understood its nature. I will argue in this paper that philosophers and others interested in the phenomenon have largely overlooked a phenomenon I call moral gaslighting, in which someone is made to feel morally defective—for example, cruelly unforgiving or overly suspicious—for harbouring some mental state to which she is entitled. If I am right about this possibility, and that it deserves to be called gaslighting, then gaslighting is a far more prevalent and everyday phenomenon than has previously been credited. And it can also be a purely structural phenomenon, as well as an interpersonal one, which remains a controversial possibility in the current literature.
Art as a Shelter from Science
Authors: Nguyen C Thi
Published: June 2023

In our life with science, we trust experts; we form judgements by inference from past evidence. We conduct ourselves very differently in the aesthetic domain. We avoid deferring to aesthetic experts. We form our judgements through direct perception of particulars rather than through inference. Why the difference? I suggest that we avoid aesthetic testimony and aesthetic inference, not because they’re unusable, but because we have adopted social norms to avoid them. Aesthetic appreciation turns out to be something like a game. We have laid down certain rules and restrictions in order to shape a kind of activity we cherish. And aesthetic properties turn out to be a kind of social construct. Much like the goal of a game, they are constituted in part by our obedience to certain rules. The norms of aesthetic life are different from those of science because our purposes are different. We engage in science to get the right answers; we engage in aesthetic appreciation to be absorbed in the activity of the sensuous perception of particulars. Our aesthetic practices are a constructed shelter from science; they restore to us a small domain where we may once again engage in our own sensuous perception of particulars.
Family and Marriage: Institutions and the Need for Social Goods
Authors: Munoz-Dardé Véronique , Martin M G F
Published: June 2023

Institutions, if unjust, ought to be reformed or even abolished. This radical Rawlsian thought leads to the question of whether the family ought to be abolished, given its negative impact on the very possibility of delivering equality of life chances. In this article, we address questions regarding the justice of the family, and of marriage, and reflect on rights, equality, and the provision of social goods by institutions. There is a temptation to justify our social institutions in terms which highlight their universal accessibility and benefits. But we may best understand the claim of some of our most important institutions where we recognize that they are forms of social good which may legitimately benefit some without having to benefit all. Their abolition is unjustified where there is sufficient value in them given our collective needs that it is unreasonable for some to refuse the means to maintain and promote these goods.
Attitudes and the Normativity of Fittingness
Authors: McHugh Conor
Published: June 2023

What is the structure of normative reality? According to X First, normativity has a monistic foundationalist structure: there is a unique normatively basic property in terms of which all the other normative properties are analysed. The main aim of this paper is to defend the view that fittingness—the property that an attitude has when it gets things right with respect to its object, as when you admire the admirable or desire the desirable—is first, or perhaps joint first. I will focus in particular on the questions whether and why fittingness is normative.
MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis
Authors: Cai Guoxin , Zhao Wenyi , Zhou Zhan , Gu Xun
Published: June 2023

A phenotype may be associated with multiple genes that interact with each other in the form of a gene module or network. How to identify these relationships is one important aspect of comparative transcriptomics. However, it is still a challenge to align gene modules associated with different phenotypes. Although several studies attempted to address this issue in different aspects, a general framework is still needed. In this study, we introduce Module Alignment of TranscripTomE (MATTE), a novel approach to analyze transcriptomics data and identify differences in a modular manner. MATTE assumes that gene interactions modulate a phenotype and models phenotype differences as gene location changes. Specifically, we first represented genes by a relative differential expression to reduce the influence of noise in omics data. Meanwhile, clustering and aligning are combined to depict gene differences in a modular way robustly. The results show that MATTE outperformed state-of-the-art methods in identifying differentially expressed genes under noise in gene expression. In particular, MATTE could also deal with single-cell ribonucleic acid-seq data to extract the best cell-type marker genes compared to other methods. Additionally, we demonstrate how MATTE supports the discovery of biologically significant genes and modules, and facilitates downstream analyses to gain insight into breast cancer. The source code of MATTE and case analysis are available at https://github.com/zjupgx/MATTE.
A Bayesian approach to estimate MHC-peptide binding threshold
Authors: Liu Ran , Hu Ye-Fan , Huang Jian-Dong , Fan Xiaodan
Published: June 2023

Major histocompatibility complex (MHC)-peptide binding is a critical step in enabling a peptide to serve as an antigen for T-cell recognition. Accurate prediction of this binding can facilitate various applications in immunotherapy. While many existing methods offer good predictive power for the binding affinity of a peptide to a specific MHC, few models attempt to infer the binding threshold that distinguishes binding sequences. These models often rely on experience-based ad hoc criteria, such as 500 or 1000nM. However, different MHCs may have different binding thresholds. As such, there is a need for an automatic, data-driven method to determine an accurate binding threshold. In this study, we proposed a Bayesian model that jointly infers core locations (binding sites), the binding affinity and the binding threshold. Our model provided the posterior distribution of the binding threshold, enabling accurate determination of an appropriate threshold for each MHC. To evaluate the performance of our method under different scenarios, we conducted simulation studies with varying dominant levels of motif distributions and proportions of random sequences. These simulation studies showed desirable estimation accuracy and robustness of our model. Additionally, when applied to real data, our results outperformed commonly used thresholds.
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters
Authors: Zhu Yan , Li Fuyi , Guo Xudong , Wang Xiaoyu , Coin Lachlan J M , Webb Geoffrey I , Song Jiangning , Jia Cangzhi
Published: June 2023

Background

Promoters are DNA regions that initiate the transcription of specific genes near the transcription start sites. In bacteria, promoters are recognized by RNA polymerases and associated sigma factors. Effective promoter recognition is essential for synthesizing the gene-encoded products by bacteria to grow and adapt to different environmental conditions. A variety of machine learning-based predictors for bacterial promoters have been developed; however, most of them were designed specifically for a particular species. To date, only a few predictors are available for identifying general bacterial promoters with limited predictive performance.

Results

In this study, we developed TIMER, a Siamese neural network-based approach for identifying both general and species-specific bacterial promoters. Specifically, TIMER uses DNA sequences as the input and employs three Siamese neural networks with the attention layers to train and optimize the models for a total of 13 species-specific and general bacterial promoters. Extensive 10-fold cross-validation and independent tests demonstrated that TIMER achieves a competitive performance and outperforms several existing methods on both general and species-specific promoter prediction. As an implementation of the proposed method, the web server of TIMER is publicly accessible at http://web.unimelb-bioinfortools.cloud.edu.au/TIMER/.
Machine learning modeling of RNA structures: methods, challenges and future perspectives
Authors: Wu Kevin E , Zou James Y , Chang Howard
Published: June 2023

The three-dimensional structure of RNA molecules plays a critical role in a wide range of cellular processes encompassing functions from riboswitches to epigenetic regulation. These RNA structures are incredibly dynamic and can indeed be described aptly as an ensemble of structures that shifts in distribution depending on different cellular conditions. Thus, the computational prediction of RNA structure poses a unique challenge, even as computational protein folding has seen great advances. In this review, we focus on a variety of machine learning-based methods that have been developed to predict RNA molecules’ secondary structure, as well as more complex tertiary structures. We survey commonly used modeling strategies, and how many are inspired by or incorporate thermodynamic principles. We discuss the shortcomings that various design decisions entail and propose future directions that could build off these methods to yield more robust, accurate RNA structure predictions.
MTM: a multi-task learning framework to predict individualized tissue gene expression profiles
Authors: He Guangyi , Chen Maiyue , Bian Yingnan , Yang Ence
Published: June 2023

Motivation

Transcriptional profiles of diverse tissues provide significant insights in both fundamental and translational researches, while transcriptome information is not always available for tissues that require invasive biopsies. Alternatively, predicting tissue expression profiles from more accessible “surrogate” samples, especially blood transcriptome, has become a promising strategy when invasive procedures are not practical. However, existing approaches ignore tissue-shared intrinsic relevance, inevitably limiting predictive performance.

Results

We propose a unified deep learning-based multi-task learning framework, multi-tissue transcriptome mapping (MTM), enabling the prediction of individualized expression profiles from any available tissue of an individual. By jointly leveraging individualized cross-tissue information from reference samples through multi-task learning, MTM achieves superior sample-level and gene-level performance on unseen individuals. With the high prediction accuracy and the ability to preserve individualized biological variations, MTM could facilitate both fundamental and clinical biomedical research.

Availability and implementation

MTM’s code and documentation are available upon publication on GitHub (https://github.com/yangence/MTM).
Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling
Authors: Jenior Matthew L , Glass Emma M , Papin Jason A
Published: June 2023

Motivation

Genome-scale metabolic network reconstructions (GENREs) are valuable for understanding cellular metabolism in silico. Several tools exist for automatic GENRE generation. However, these tools frequently (i) do not readily integrate with some of the widely-used suites of packaged methods available for network analysis, (ii) lack effective network curation tools, (iii) are not sufficiently user-friendly, and (iv) often produce low-quality draft reconstructions.

Results

Here, we present Reconstructor, a user-friendly, COBRApy-compatible tool that produces high-quality draft reconstructions with reaction and metabolite naming conventions that are consistent with the ModelSEED biochemistry database and includes a gap-filling technique based on the principles of parsimony. Reconstructor can generate SBML GENREs from three input types: annotated protein .fasta sequences (Type 1 input), a BLASTp output (Type 2), or an existing SBML GENRE that can be further gap-filled (Type 3). While Reconstructor can be used to create GENREs of any species, we demonstrate the utility of Reconstructor with bacterial reconstructions. We demonstrate how Reconstructor readily generates high-quality GENRES that capture strain, species, and higher taxonomic differences in functional metabolism of bacteria and are useful for further biological discovery.

Availability and implementation

The Reconstructor Python package is freely available for download. Complete installation and usage instructions and benchmarking data are available at http://github.com/emmamglass/reconstructor.
Generation of a novel Stra8-driven Cre recombinase strain for use in pre-meiotic germ cells in mice
Authors: Ahmed Avery A , Salas Ernesto , Lanza Denise G , Heaney Jason D , Pangas Stephanie A
Published: June 2023

The development of oocytes occurs over a broad time frame, starting at the earliest stages of embryogenesis and continuing into adulthood. Conditional knockout technologies such as the Cre/loxP recombination system are useful for analyzing oocyte development at specific stages, but not every time frame has appropriate Cre drivers, for instance, during oocyte meiotic initiation through early prophase I in the embryo. Here, we generated a novel knockin mouse line that produces a bicistronic transcript from the endogenous Stra8 locus that includes a “self-cleaving” 2A peptide upstream of cre. This allows for high efficiency cleavage and production of both proteins individually and results in expression of cre in both male and female gonads at the biologically relevant stage. Fluorescent reporter analysis confirms that this line recapitulates endogenous Stra8 expression in both sexes and does not affect fertility of heterozygous nor homozygous mice. This line, named Stra8P2Acre, adds to the repertoire of germ-cell specific cre driver lines and, importantly, allows for deletion of target genes during key embryonic oocyte developmental stages, including early events in meiosis.

Summary Sentence Generation of a novel cre recombinase knockin to the Stra8 locus allows production of Stra8 and cre without affecting fertility.
Hyperthermic Intrathoracic Chemotherapy (HITOC) Improves Malignant Pleural Mesothelioma Control Through a Tumor Specific Cytotoxic Immune Response
Authors: Cavin S , Hao Y , Gkasti A , Chriqui L E , Marie D , Abdelnour E , Gonzalez M , Krueger T , Dyson P J , Peters S , Meylan E , Perentes J Y
Published: June 2023

Background

The management of malignant pleural mesothelioma (MPM) remains challenging with poor patient survival. Local therapies such as hyperthermic intrathoracic cisplatin (HITOC) have shown good tumor control in selected patients. HITOC was shown to increase MPM drug exposure while limiting systemic side effects but alternative mechanisms for HITOC are still lacking.

Aims

We hypothesized that HITOC induces an immune response directed against MPM which decreases cancer related mortality.

Methods

A perfusion circuit was downsized to administer cisplatin in the thoracic cavity of MPM bearing mice at normo (37°C, ITOC) or hyperthermic (39°C, HITOC) conditions for 30 minutes. Tumor platinum content and distribution were determined by inductively coupled plasma mass spectrometry (ICP-MS) and by laser ablation ICP-MS respectively. The impact of (H)ITOC on the MPM immune microenvironment was questioned using flow cytometry and immunohistochemistry. Tumor growth and survival was assessed in immunocompetent and T-cell deficient mice. Finally, the combination of HITOC with anti-CTLA-4 and anti-PD-1 antibodies was evaluated in immunocompetent animals.

Results

MPM tumor control and mouse survival were significantly improved by HITOC compared to controls (ITOC, saline 37 and 39°C). This correlated with higher tumor platinum content that was mainly located at the surface of tumors. Furthermore, HITOC enhanced MPM infiltration by cytotoxic T-cells and decreased the level of protumor (M2-like) macrophages at day 7. The beneficial impact of HITOC on tumor control and mice survival was lost in immunocompromised animals. Interestingly, HITOC significantly induced PD-1 and CTLA-4 immune checkpoint molecules expression and administration of dual immune checkpoint blockade after HITOC increased of almost two fold the median survival of the animals.

Conclusions

HITOC improves MPM control through a T lymphocyte immune mediated response. The potentiation of the immune checkpoint blockade response by HITOC opens new perspectives for the combination of immune checkpoint inhibitors with HITOC in clinic.
Maternal Obesity Increases the Risk for Hepatocellular Carcinoma in a Toxic Liver Cancer Model Through the Gut Microbiome
Authors: Moeckli B , Delaune V , Gilbert B , Rodrigues Ribeiro J , Peloso A , Oldani G , El Hajji S , Slits F , Gex Q , Lacotte S , Toso C
Published: June 2023

Background

The obesity pandemic leads to rising obesity rate in women of reproductive age with emerging evidence that maternal obesity has a negative impact on the long-term health of offspring. Additionally, obesity is an independent risk factor for malignancies and particularly hepatocellular carcinoma (HCC).

Aims

The aim of our study is to investigate the impact of maternal obesity on the risk for HCC in the offspring and identify potential mechanisms of transmission.

Methods

Female mice were fed either a high fat (HFD) or a normal diet (ND) before mating. Offspring received ND throughout life. We studied the liver histology and tumor load in a short-term transgenic (12 weeks) or a toxin induced long-term (36 weeks) HCC mouse model. To normalize the gut microbiome, we co-housed offspring of HFD and ND mothers after weaning. The composition of the gut microbiota was assessed through 16S rRNA sequencing.

Results

Maternal obesity induced a distinguishable shift in the microbial composition towards decreased microbial diversity (2.56 vs. 2.92, p=0.0089), increased proportions of Firmicutes and decreased abundance of Bacteroidota. At 40 weeks female HFD offspring developed steatosis (9.43 vs 3.09%, p=0.0023) and a higher number of inflammatory infiltrates (4.8 vs 1.0, p=0.018) compared to ND offspring. A higher proportion of female HFD offspring developed liver tumors after DEN induction (79.8 vs 37.5%, p=0.0084) with a higher total tumor volume at 36 weeks (234 vs 3 µm3, p=0.0041). An effect that we did not observe in the short-term transgenic model. Gut microbiome composition was corrected through co-housing offspring and co-housing normalized the tumor number and volume to the level of ND offspring.

Conclusions

Maternal obesity increases the susceptibility to develop HCC in offspring. The transmission of an altered gut microbiome appears to play an important role in this increased long-term risk profile.
Local Treatment of Neuroendocrine Liver Metastases: How Effective and Safe is Stereotactic Microwave Ablation?
Authors: Hanreich C , Perrodin S F , Candinas D , Lachenmayer A , Kim-Fuchs C
Published: June 2023

Background

The less invasiveness of local ablation techniques such as stereotactic microwave ablation (SMWA) for the treatment of malignant hepatic lesions has made it an attractive alternative to conventional surgical resection.

Aims

The aim of this retrospective study was to assess the successful ablation rate of neuroendocrine tumor liver metastases (NETLM) 3 months after SMWA, the recurrence-free survival time, as well as the rate of peri- and early post interventional complications.

Methods

Retrospective analysis including all patients treated with SMWA for NETLM in our institution between 03/2015 and 07/2022. SMWA was performed as per the decision of the interdisciplinary tumorboard. Patients were included independent of location of primary tumors, disease stage, prior treatments. Patients underwent follow-up imaging (FU) every 1-6 months.

Results

41 metastases were ablated in 21 interventions in 17 patients with a mean age of 63.6±9.7 years. A median of two lesions (range 1-4) were ablated per intervention. Mean time until first FU was 2.8±1.5 months. 39 of 41 (95.1%) lesions were fully ablated at the first FU. The two incompletely ablated lesions were treated using re-ablation and systemic treatment, respectively. A local recurrence occurred in further two ablation zones (4.9%) after 3.6 years in a patient with a progressive disease. Remaining 37 (90.2%) patients had no tumor recurrence in the ablation zone at the latest available FU (mean 24.3±17.3 months). Postinterventional length of hospital stay was a median of 1 [IQR 1;1.5]. No complications higher than Clavien Dindo Grade II occurred.

Conclusions

SMWA is a good minimal invasive intervention for the treatment of NETLM with low morbidity and high local efficacy.