bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of uniaxial compressive stress with different orientations on the hole mobility of wurtzite GaN heterojunction quantum well
Authors: Liu Yaqun , Li Xiyue , Wang Everett , Zhang Gary , Wang Jing
Published: July 2022

The influence of uniaxial compressive stress with different orientations to the current channel on the physical and transport properties of the wurtzite GaN heterojunction quantum well is investigated in this work. By using the six-band stress-dependent k × p Hamiltonian, accurate two-dimensional physical pictures are given for the quantized valence subband under the uniaxial compressive stress on the (0001) transport plane. The low-field hole mobility is obtained by the Kubo–Greenwood formula, taking the scattering rates for acoustic phonon, polar optical phonon, and surface roughness into account. Using these methods, the microscopic relationship between the orientation of uniaxial compressive stress and low-field hole mobility is obtained according to the variations of valence subband dispersion and hole effective mass. Results show that for temperatures around and above room temperature, the acoustic phonon scattering is predominant. We find that the mobility gain is mostly contributed from effective mass, and there is an increasing trend under uniaxial compressive stress with all orientations due to the effective mass reduction. For the same stress value, the mobility decreases monotonically as the stress orientation changes from 0° to 90° with respect to the current channel. At room temperature, the calculated low-field hole mobility is 182 cm2/V s under 8 GPa uniaxial compressive stress parallel to the current channel, with the hole density of 5.5 × 1013 cm−2 and the effective electric field of 0.93 MV/cm.
Unraveling the mechanisms of aluminum solidification under hyper-gravity condition from molecular dynamics simulations
Authors: Guo Xiaoshuai , Gan Xianglai , Niu Haiyang , Huang Bowen , Hu Wangyu
Published: July 2022

Gradient materials show excellent performance in combining strength, ductility, and fatigue resistance. In the present work, we proposed a novel hyper-gravity loading method and applied it to the solidification of aluminum using molecular dynamics simulation. A gradient structure is obtained after solidification, which is consistent with the experimental studies. The hyper-gravity-induced gradient pressure is identified as the main factor making the melting point, nucleation, and grain growth unevenly in the model, which leads to the decreased grain size along the hyper-gravity direction. Three solidification behaviors are observed in one solidification, i.e., homogenous nucleation initiates first at the bottom of the model, where it undergoes the highest pressure; then heterogeneous solidification combined with homogenous solidification appears in the middle; finally, directional solidification dominates because the insufficient undercooling makes the nucleation difficult. Moreover, the gradient structure and grain refinement are further enhanced with increasing gravity intensity.
Ecological multi-objective joint optimized scheduling of cascade hydropower plants based on improved marine predators algorithm
Authors: Kong Fannie , Zhuo Yiwen , Song Cheng
Published: July 2022

The joint operation of large cascade hydropower plants changes the natural hydrological regime of the river, thereby reducing the stability of the basin ecosystem. To coordinate the power generation of cascade hydropower plants' demand and ecological environment demand, this paper establishes an ecological multi-objective optimized scheduling model (EMOOSM) for cascade hydropower plants, aiming at the maximum power generation of cascade hydropower plants and the minimum inappropriate ecological water volume. To solve the complex EMOOSM, a marine predators algorithm was introduced, which was improved and extended to the multi-objective solution level. Multi-objective improved marine predators algorithm (MOIMPA) based on Cauchy variation preserves non-dominated solutions by adding an external archive set and maintaining them with a crowdedness-based fast sorting strategy. The optimal dispatching results of a cascade hydropower plant in China's Pearl River system show that MOIMPA can effectively deal with conflicting power generation and ecological goals. The recommended scheme determined according to the fuzzy set theory and the principle of maximum satisfaction can adapt to the change law of ecological demand and reasonably adjust the inappropriate ecological water volume in the stage according to the different ecological sensitivity in the dispatching period. The recommended scheme in the normal year reduces the inappropriate ecological water volume caused by the operation of the cascade reservoir by 1.7156 × 105 m3 at the expense of only 1.12% of the power generation, effectively balancing the power generation and ecological benefits of the cascade hydropower plant operation. Compared with the results of other algorithms, the Pareto solution set obtained by MOIMPA has a better diversity metric (DM) indicator, maximum spread (MS) indicator, and hypervolume (HV) indicator. The research results provide a theoretical basis and reference for the ecological operation research of cascade hydropower plants.
Microarrayed human bone marrow organoids for modeling blood stem cell dynamics
Authors: Giger Sonja , Hofer Moritz , Miljkovic-Licina Marijana , Hoehnel Sylke , Brandenberg Nathalie , Guiet Romain , Ehrbar Martin , Kleiner Esther , Gegenschatz-Schmid Katharina , Matthes Thomas , Lutolf Matthias P.
Published: July 2022

In many leukemia patients, a poor prognosis is attributed either to the development of chemotherapy resistance by leukemic stem cells (LSCs) or to the inefficient engraftment of transplanted hematopoietic stem/progenitor cells (HSPCs) into the bone marrow (BM). Here, we build a 3D in vitro model system of bone marrow organoids (BMOs) that recapitulate several structural and cellular components of native BM. These organoids are formed in a high-throughput manner from the aggregation of endothelial and mesenchymal cells within hydrogel microwells. Accordingly, the mesenchymal compartment shows partial maintenance of its self-renewal and multilineage potential, while endothelial cells self-organize into an interconnected vessel-like network. Intriguingly, such an endothelial compartment enhances the recruitment of HSPCs in a chemokine ligand/receptor-dependent manner, reminiscent of HSPC homing behavior in vivo. Additionally, we also model LSC migration and nesting in BMOs, thus highlighting the potential of this system as a well accessible and scalable preclinical model for candidate drug screening and patient-specific assays.
Role of phytoplankton in aquatic mercury speciation and transformations
Authors: Cossart Thibaut , Garcia-Calleja Javier , Santos João P. , Kalahroodi Elaheh Lotfi , Worms Isabelle A. M. , Pedrero Zoyne , Amouroux David , Slaveykova Vera I.
Published: July 2022

Environmental context Understanding mercury transformations in the aquatic environment is of utmost importance for the improvement of mercury biogeochemical modelling and sound environmental risk assessment. In such a context, we discuss critically the advancement in the knowledge on the role of the phytoplankton (algae and cyanobacteria) in mercury cycling and transformations in the aquatic environment. Important research advances revealed that different microalgal species and cyanobacteria contribute: to biotic reduction of inorganic mercury to elemental mercury; to demethylation of methylmercury and transformation of inorganic mercury into metacinnabar; and to production of different biomolecules which can contribute to abiotic mercury reduction. Abstract Phytoplankton may directly influence biogeochemical cycling and transformations of mercury (Hg) through biotic transformations of the accumulated metal via methylation/demethylation and reduction/oxidation, and indirectly, through the excretion of low and high molecular weight ligands, likely triggering or influencing different abiotic transformation pathways as well as the transformations carried out by bacteria. However, unlike the extensive work already done on the role of bacteria in Hg transformations, the current knowledge about the influence of phytoplankton (algae and cyanobacteria) on such processes is still limited. Critical evaluation of the existing advances in the research topic revealed that different microalgal species and cyanobacteria contribute to the biotic reduction of inorganic mercury (iHg or HgII) into elemental Hg (Hg0), monomethylmercury (MeHg) demethylation and transformation of iHg into metacinnabar. The low and high molecular weight biomolecules released by phytoplankton can complex Hg species and contribute to abiotic mercury reduction. Despite these advances, the underlying mechanisms and their importance in the aquatic environment are to be explored and detailed. The development of novel molecular, stable isotope-based and multi-omics approaches would provide further impetus for the understanding of the key interactions between Hg species and phytoplankton. Such understanding will be of utmost importance for the improvement of Hg biogeochemical modelling, mitigation strategies and rational environmental risk assessment in the changing aquatic environment.
Youth perceptions and concerns about sexually transmissible infections versus pregnancy: a qualitative comparative study in California
Authors: Decker Martha J. , Borgen Natasha , Gutmann-Gonzalez Abigail , Brindis Claire D.
Published: July 2022

Background Although rates of adolescent pregnancy have been declining for decades, rates of sexually transmissible infections (STIs) continue to increase among youth. Little is known about youth’s comparative concern regarding pregnancy and STIs, particularly among marginalised populations. Therefore, this study compares concerns toward unplanned pregnancy and STIs and identifies underlying reasons for these differing concerns in youth populations with elevated rates of STIs. Methods Fourteen focus groups were held with 92 youth in two counties in California, USA. Youth were purposefully selected from community-based organisations and schools to represent a variety of backgrounds and populations with elevated rates of pregnancy and STIs. Qualitative coding and analysis were conducted using ATLAS.ti. 7.0. Results Almost all participants were youth of colour (86%), 27% identified as gay, lesbian or bisexual, and 21% had ever experienced homelessness. Although most youth were generally concerned about the consequences of contracting an STI, including the possible stigma associated with it, both males and females were more worried about an unplanned pregnancy. Emergent themes included varying concerns about the lasting consequences of unplanned pregnancies and STIs; greater visibility of pregnancy compared to infection; stigma; and limited STI prevention efforts compared to teen pregnancy prevention. Conclusions By addressing the underlying concerns and varying perceptions that different groups of youth have toward STIs and pregnancy, prevention approaches and messages can be tailored, including by age, gender, sexual orientation, and for those exposed to vulnerable living situations. Additional efforts are needed to address increasing rates of STIs among young people.
An immature, dedifferentiated, and lineage-deconstrained cone precursor origin of N-Myc–initiated retinoblastoma
Authors: Singh Hardeep P. , Shayler Dominic W. H. , Fernandez G. Esteban , Thornton Matthew E. , Craft Cheryl Mae , Grubbs Brendan H. , Cobrinik David
Published: July 2022

Most retinoblastomas develop from maturing cone precursors in response to biallelic
RB1
loss and are dependent on cone maturation-related signaling. Additionally, ∼2% lack
RB1
mutations but have
MYCN
amplification (

MYCN
A

), N-Myc protein overexpression, and more rapid and invasive growth, yet the

MYCN
A

retinoblastoma cell of origin and basis for its responses to deregulated N-Myc are unknown. Here, using explanted cultured retinae, we show that ectopic N-Myc induces cell cycle entry in cells expressing markers of several retinal types yet induces continuous proliferation and tumorigenesis only in cone precursors. Unlike the response to
RB1
loss, both immature cone arrestin-negative (ARR3
–
) and maturing ARR3
+
cone precursors proliferate, and maturing cone precursors rapidly dedifferentiate, losing ARR3 as well as L/M-opsin expression. N-Myc–overexpressing retinal cells also lose cell lineage constraints, occasionally coexpressing the cone-specific RXRγ with the rod-specific NRL or amacrine-specific AP2α and widely coexpressing RXRγ with the progenitor and Müller cell–specific SOX9 and retinal ganglion cell-specific BRN3 and GAP43. Mechanistically, N-Myc induced Cyclin D2 and CDK4 overexpression, pRB phosphorylation, and SOX9-dependent proliferation without a retinoma-like stage that characterizes pRB-deficient retinoblastoma, despite continuous p16
INK4A
expression. Orthotopic xenografts of N-Myc–overexpressing retinal cells formed tumors with retinal cell marker expression similar to those in
MYCN
-transduced retinae and

MYCN
A

retinoblastomas in patients. These findings demonstrate the

MYCN
A

retinoblastoma origin from immature and lineage-deconstrained cone precursors, reveal their opportunistic use of an undifferentiated retinal progenitor cell feature, and illustrate that different cancer-initiating mutations cooperate with distinct developmental stage–specific cell signaling circuitries to drive retinoblastoma tumorigenesis.
Selective targeting of metastatic ovarian cancer using an engineered anthrax prodrug activated by membrane-anchored serine proteases
Authors: Duru Nadire , Pawar Nisha R. , Martin Erik W. , Buzza Marguerite S. , Conway Gregory D. , Lapidus Rena G. , Liu Shihui , Reader Jocelyn , Rao Gautam G. , Roque Dana M. , Leppla Stephen H. , Antalis Toni M.
Published: July 2022

Treatments for advanced and recurrent ovarian cancer remain a challenge due to a lack of potent, selective, and effective therapeutics. Here, we developed the basis for a transformative anticancer strategy based on anthrax toxin that has been engineered to be selectively activated by the catalytic power of zymogen-activating proteases on the surface of malignant tumor cells to induce cell death. Exposure to the engineered toxin is cytotoxic to ovarian tumor cell lines and ovarian tumor spheroids derived from patient ascites. Preclinical studies demonstrate that toxin treatment induces tumor regression in several in vivo ovarian cancer models, including patient-derived xenografts, without adverse side effects, supportive of progression toward clinical evaluation. These data lay the groundwork for developing therapeutics for treating women with late-stage and recurrent ovarian cancers, utilizing a mechanism distinct from current anticancer therapies.
Investigation on high quality ultra-wide band gap β-Ga2O3/AlN heterostructure grown by metal organic chemical vapor deposition
Authors: Li Yifan , Zhang Yachao , Zhang Jincheng , Zhang Tao , Xu Shengrui , Feng Lansheng , Feng Qian , Zhang Chunfu , Hao Yue
Published: July 2022

β-Ga2O3 films were grown on AlN templates by metal organic chemical vapor deposition (MOCVD), and the properties of the β-Ga2O3/AlN heterostructures were investigated in detail. The β-Ga2O3/AlN heterostructure with abrupt interface was observed by the high resolution transmission electron microscope with high angle annular dark field. The refactor of the atoms at the interface is discussed. Moreover, the band structure of the MOCVD β-Ga2O3/AlN heterostructures was investigated by x-ray photoelectron spectroscopy. The conduction band and valence band offsets of β-Ga2O3/AlN heterostructure were calculated to be −1.44 eV ± 0.05 eV and −0.14 eV ± 0.05 eV, respectively.
Effect of kinetic ions on the toroidal double-tearing modes
Authors: Zhang Ruibo , Ye Lei , Chen Yang , Xiang Nong , Yang Xiaoqing
Published: July 2022

We investigate the effects of kinetic ions on double-tearing modes (DTMs) using the gyrokinetic particle-in-cell simulation code GEM with a gyrokinetic ion/fluid electron hybrid model. It is found that the ion kinetic effects can decrease the growth rate of the DTMs. This effect is more significant for stronger coupling of DTMs with smaller distance between the rational surfaces. Kinetic ions can also enhance the coupling effect between the two rational surfaces. Energy transfer analyses between particles and wave fields show that the stabilizing effect of kinetic ions comes mainly from the perpendicular magnetic drift of ions in the coupling region and around the outer rational surface.
Terahertz magnetic resonance in MnCr2O4 under high magnetic field
Authors: Zhang Peng , He Kaibo , Wang Zheng , Zhang Shile , Dai Jianming , Su Fuhai
Published: July 2022

Terahertz (THz) time-domain spectroscopy (THz-TDS) of polycrystalline MnCr2O4 was performed at <9 T and low temperatures. A resonance absorption in the sub-THz range with linear blueshifts was observed as the magnetic field was increased from 4 T to 9 T. These magnetism-driven absorptions originated from a ferromagnetic resonance, which agrees with low-field electron spin resonance measurements and ferromagnetic resonance theory. The low-temperature g-factors of MnCr2O4 were also obtained using THz-TDS. This work provides new insights into the spin dynamics of chromite spinel compounds in the THz region.
Hydrodynamic metamaterials for flow manipulation: Functions and prospects
Authors: Wang Bin , Huang Jiping
Published: July 2022

As an emerging branch in the area of flow control, hydrodynamic metamaterials have received considerable attention because of their novel flow control capabilities. In this review, we present prominent studies on hydrodynamic metamaterials in porous media, non-porous media, creeping flows, and non-creeping flows from several perspectives. In particular, for hydrodynamic cloaking metamaterials, we unify the descriptive form of transformation hydrodynamics for hydrodynamic metamaterials in porous and non-porous media by the hydrodynamic governing equations. Finally, we summarize and outlook the current shortcomings and challenges of current hydrodynamic metamaterials and propose possible future research directions, especially for microfluidics, exotic fluids, hydrodynamic cloaking in high Reynolds numbers, and turbulence.
Determination of the half-life of 184gRe and the isomeric ratio of 184m, gRe induced by D-T neutrons*
Authors: Lan Changlin , Wei Yuting , Wang Jiahao , Yang Xianlin , Jiang Gong , Ge Yujie , Xu Chao , Feng Li , Li Xiaojun
Published: July 2022

The isomeric ratio of 184m, gRe and the half-life of 184gRe were measured in the 185Re (n, 2n) 184Re reaction at 14.8 MeV, and the uncertainty was discussed in detail. The measurements were performed using the activation method implemented for a rhenium sample using the K-400 neutron generator at the Chinese Academy of Engineering Physics (CAEP). Isomeric state and ground state nuclei of 184Re were identified by their γ-ray spectra. To eliminate the effect of the γ-ray emitted from the isomer on the counting of the ground state characteristic peaks, the isomeric ratio of 184m, gRe was calculated to be 0.29 ± 0.11 according to the neutron activation cross-section formula. This result is consistent with previous data within the uncertainty and can be used to determine parameters that characterize the dependence of the level density on the excitation energy and angular momentum. Through exponential function fitting and a detailed discussion of the uncertainty evaluation, the half-life of 184gRe was determined as 35.43 ± 0.16 d, which is consistent with the currently recommended value; however, the uncertainty assessment of the latter was barely documented. In addition, this study indicates that the half-life of the ground state can be obtained by eliminating the contamination of γ-rays emitted from the isomer, which provides the possibility of determining the half-lives of nuclides containing isomers.
Baseline hippocampal beta band power is lower in the presence of movement uncertainty
Authors: Gilbert Zachary D , Martin Del Campo-Vera Roberto , Tang Austin M , Chen Kuang-Hsuan , Sebastian Rinu , Shao Arthur , Tabarsi Emiliano , Chung Ryan S , Leonor Andrea , Sundaram Shivani , Heck Christi , Nune George , Liu Charles Y , Kellis Spencer , Lee Brian
Published: July 2022

Objective. This study aimed to characterize hippocampal neural signatures of uncertainty by measuring beta band power in the period prior to movement cue. Approach. Participants with epilepsy were implanted with hippocampal depth electrodes for stereo electroencephalographic (SEEG) monitoring. Hippocampal beta (13–30 Hz) power changes have been observed during motor tasks such as the direct reach (DR) and Go/No-Go (GNG) tasks. The primary difference between the tasks is the presence of uncertainty about whether movement should be executed. Previous research on cortical responses to uncertainty has found that baseline beta power changes with uncertainty. SEEG data were sampled throughout phases of the DR and GNG tasks. Beta-band power during the fixation phase was compared between the DR and GNG task using a Wilcoxon rank sum test. This unpaired test was also used to analyze response times from cue to task completion between tasks. Main results. Eight patients who performed both reaching tasks were analyzed in this study. Movement response times in the GNG task were on average 210 milliseconds slower than in the DR task. All patients exhibited a significantly increased response latency in the GNG task compared to the DR task (Wilcoxon rank-sum p-value < 0.001). Six out of eight patients demonstrated statistically significant differences in beta power in single hippocampal contacts between the fixation phases of the GNG and DR tasks. At the group level, baseline beta power was significantly lower in the GNG task than in the DR task (Wilcoxon rank-sum p-value < 0.001). Significance. This novel study found that, in the presence of task uncertainty, baseline beta power in the hippocampus is lower than in its absence. This finding implicates movement uncertainty as an important factor in baseline hippocampal beta power during movement preparation.
Fish scale inspired structures—a review of materials, manufacturing and models
Authors: Hossain Md Shahjahan , Ebrahimi Hossein , Ghosh Ranajay
Published: July 2022

Fish scale inspired materials and structures can provide advanced mechanical properties and functionalities. These materials, inspired by fish scales, take the form of either composite materials or multi-material discrete exoskeleton type structures. Over the last decade they have been under intense scrutiny for generating tailorable and tunable stiffness, penetration and fracture resistance, buckling prevention, nonlinear damping, hydrodynamic and camouflaging functions. Such programmable behavior emerges from leveraging their unique morphology and structure–property relationships. Several advanced tools for characterization, manufacturing, modeling and computation have been employed to understand and discover their behavior. With the rapid proliferation of additive manufacturing techniques and advances in modeling and computational methods, this field is seeing renewed efforts to realize even more ambitious designs. In this paper we present a review and recapitulation of the state-of-the art of fish scale inspired materials.
Fluid dynamics, scaling laws and plesiosaur locomotion
Authors: Pourfarzan Ali , Henderson Donald M , Wong Jaime G
Published: July 2022

The evolutionary success of plesiosaurs has led to much attention regarding the dynamics of their locomotion. They exhibit identical tandem flippers, which is unique among all living and extinct species. However, these tandem flippers have been a source of debate regarding plesiosaurs’ locomotion and behavior. Here we propose a new approach to studying plesiosaur locomotion based on universal scaling laws in fluid dynamics, which were used to estimate reduced frequency to characterize unsteadiness of an airfoil. It was found that, while the reduced frequency of plesiosaurs with high-aspect ratio flippers is similar to that of sea turtles, the most commonly used living analog, lower aspect ratio plesiosaurs were more similar in reduced frequency to penguins. This implies that plesiosaurs may have had large variations in agility among themselves, depending in particular on the specimen’s flipper aspect ratio. While our results are consistent with the previous literature indicating a relationship between plesiosaur neck length and agility, our work supports broad and diverse analogies to living animals. Moreover, based on our results, cruising reduced frequency has some predictive value into manoeuvring behavior, rather than simply cruising behavior.
North Eurasian thermal comfort indices dataset (NETCID): new gridded database for the biometeorological studies
Authors: Konstantinov P I , Varentsov M I , Shartova N V
Published: July 2022

Global climate changes give us the important task of obtaining information about the spatial distribution of bioclimatic comfort indicators at the global or continental level. One of the most applicable tools can be based on reanalysis data (meteorological gridded data with global coverage). This issue is fully relevant for the territory of Northern Eurasia with its diverse climates, rapid environmental changes, and often sparse network of in situ observations. In this paper, we present a conceptually new dataset for the most popular thermal comfort indices, namely heat index (HI), humidex (HUM), wind chill temperature, mean radiant temperature, physiologically equivalent temperature (PET) and Universal Thermal Comfort Index (UTCI) derived from ERA-Interim reanalysis hourly data for the territory of Northern Eurasia (the area limited by 40° N–80° N, 10° W–170° W). The dataset has horizontal resolution of 0.75° × 0.75° (up to 79 km), temporal resolution of 3 h, and covers the period from 1979 to 2018 (40 years), which corresponds to the standard of the World Meteorological Organization in determining the parameters of the modern climate. Time series of indices are supplemented with a set of 8092 pre-calculated statistical parameters characterizing climatology of the thermal stress conditions. We further present several examples of the North Eurasian Thermal Comfort Indices Dataset (NETCID) data application, including analysis of the spatial heterogeneity of thermal stress conditions, assessment of their changes and analysis of specific extreme events. Presented examples demonstrate a pronounced difference between considered indices and highlight the need of their accurate selection for applied tasks. In particular, for the whole study areas HI and HUM indices show much smaller thermal stress repeatability and weaker trends of its changes in comparison to PET and UTCI indices. NETCID is available for free download at https://doi.org/10.6084/m9.figshare.12629861.
Electrical, magnetic and microwave absorption properties of multiferroic NiFe2O4-BaTiO3 nanocomposites
Authors: Lam Dao Son , Tung Nguyen Ngoc , Dung Dang Duc , Khuyen Bui Xuan , Lam Vu Dinh , Thanh Tran Dang
Published: July 2022

Multiferroic nanocomposites of xNiFe2O4/(1-x)BaTiO3 (x = 0, 0.1, 0.2, 0.3, and 0.4) (denoted as NFO-BTO) with the particle size about of 70 nm were prepared by the high energy mechanical milling combined with the thermal annealing methods. The x-ray diffraction patterns show a presence of NiFe2O4 (NFO) and BaTiO3 (BTO) phases. The values of the characteristic parameters of nanocomposites such as the coercive field (E
c), the residual polarization (P
r), the remanent magnetization (M
r), the saturation magnetization (M
s), and the coercive force (H
c) increase gradually with an increase in NFO concentration. For an applied electric field below 10 kV cm−1, the values P
r and E
c are found to be 0.004–0.038 μC cm−2 and 0.7–2.0 kV cm−1, corresponding x = 0.1–0.4, respectively. Changes in electrical and magnetic properties of composites depend heavily on the NFO content, which will be studied specifically. Additionally, the ability to absorb microwave at room temperature of a representative sample with x = 0.3 mixed in acrylic paint (denoted as NFO-BTO-AP) in a frequency range of f = 12–18 GHz has also been investigated. It shows a large negative reflection loss (RL) with RL = −39.8 dB occurring at around 16.8 GHz corresponding to the absorptivity of over 99.9% for an absorbing layer with thickness of 5.5 mm. This suggests that NFO-BTO nanocomposites could be considered as a potential material in the field of absorbing and shielding electromagnetic waves.
Inheritance factor on the physical properties in metallic glasses
Authors: Yang Weiming , Li Jiawei , Li Hongyang , Liu Haishun , Mo Jinyong , Lan Si , Li Maozhi , Wang Xun-Li , Eckert Jürgen , Huo Juntao
Published: July 2022

Material genetic engineering can significantly accelerate the development of new materials. As an important topic in material science and condensed matter physics, the development of metallic glasses (MGs) with specific properties has largely been the result of trial and error since their discovery in 1960. Yet, property design based on the physical parameters of constituent elements of MGs remains a huge challenge owing to the lack of an understanding of the property inheritance from constitute elements to the resultant alloys. In this work, we report the inherent relationships of the yield strength σ
y, Young’s modulus E, and shear Modulus G with the valence electron density. More importantly, we reveal that the electronic density of states (EDOSs) at the Fermi surface (E
F) is an inheritance factor for the physical properties of MGs. The physical properties of MGs are inherited from the specific element with the largest coefficient of electronic specific heat (γi
), which dominates the value of the EDOS at E
F. This work not only contributes to the understanding of property inheritances but also guides the design of novel MGs with specific properties based on material genetic engineering.
Insect Floral Visitors of Ptelea trifoliata (Rutaceae) in Iowa, United States
Authors: Talcott Stewart A J , O’Neal M E , Graves W R
Published: July 2022

Ptelea trifoliata L., is a North American tree that supports insect communities through floral rewards. Our objectives were to determine the importance of insects as pollinators of P. trifoliata; describe the community of floral visiting insects of P. trifoliata in Iowa, where no such information was available; and to note insect preferences for male or female flowers. Over two years, inflorescences on 13 trees were covered with mesh bags before blooming and the amount of fruit produced was compared to uncovered inflorescences from the same trees. In one year, insects were collected from male and female trees with an insect vacuum every 3 h between 7 am and 7 pm from four sites in Iowa, USA between 30 May and 16 June 2020. In 2019 and 2020, almost no fruit set occurred from inflorescences covered with mesh bags while an average of 51.2 fruits formed on unbagged inflorescences (P < 0.0001), suggesting insects larger than the 600 μm pore diameters mesh were responsible for pollination of P. trifoliata. Insects from five orders, 49 families, and at least 109 species were collected. Most insects were Hymentoptera (48.3%) or Diptera (28.2%). Male flowers attracted 62.3% of all insects collected. Since most of the insects found visiting P. trifoliata were not bees, the floral rewards of the flowers may be a valuable resource for a wide variety of insects in the central United States.
Whalebone, Hoop Skirts, Corsets, Pants Roles: Women and the Melville Effect in Contemporary Art
Authors: Boone Joseph Allen
Published: July 2022

The past two and a half decades have witnessed an explosion of savvy, edgy, creative work inspired by Melville. This “Melville effect,” occurring across multiple genres and media and often in mixed-media formats, is characterized by an aesthetics of hybridity and pastiche that recalls Melville’s own stylistic and formal innovations. Fascinatingly, many of the most intriguing examples of this effect make the presence of women central to their engagements with the heady “masculinity” associated with Melville’s nearly all-male worlds. Indeed, the material and metaphorical links between whaling as an industry and the female body as a site of consumption—hinging on the historical use of whalebone or baleen in the manufacture of hoop skirts and corsets—form the point of entry for artists T. L. Solien, Ellen Driscoll, and Rinde Eckert, whose bold reenvisionings of Moby-Dick, at once postmodern and feminist, form the subject matter of this essay.Moving the women so often absent in Melville to the forefront is one productive point of entry for such contemporary efforts, and it is an approach that Solien, Driscoll, and Eckert—in their different but complementary ways—exemplify at its best.
Will deeper roots be enough? Engineering drought-resistant crops will entail in-depth understanding of root hydraulic architecture. A Commentary on ‘Root and xylem anatomy varies with root length, root order, soil depth and environment’
Authors: Pierret Alain
Published: July 2022

This article comments on:

Corentin Clément, Hannah M. Schneider, Dorte Bodin Dresbøll, Jonathan P. Lynch and Kristian Thorup-Kristensen, Root and xylem anatomy varies with root length, root order, soil depth and environment in intermediate wheatgrass (Kernza®) and alfalfa, Annals of Botany, Volume 130, Issue 3, 1 September 2022, Pages 367–382 https://doi.org/10.1093/aob/mcac058
PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks
Authors: Guzzi Pietro Hiram , Di Paola Luisa , Giuliani Alessandro , Veltri Pierangelo
Published: July 2022

Motivation

Protein Contact Network (PCN) is a powerful method for analysing the structure and function of proteins, with a specific focus on disclosing the molecular features of allosteric regulation through the discovery of modular substructures. The importance of PCN analysis has been shown in many contexts, such as the analysis of SARS-CoV-2 Spike protein and its complexes with the Angiotensin Converting Enzyme 2 (ACE2) human receptors. Even if there exist many software tools implementing such methods, there is a growing need for the introduction of tools integrating existing approaches.

Results

We present PCN-Miner, a software tool implemented in the Python programming language, able to (i) import protein structures from the Protein Data Bank; (ii) generate the corresponding PCN; (iii) model, analyse and visualize PCNs and related protein structures by using a set of known algorithms and metrics. The PCN-Miner can cover a large set of applications: from clustering to embedding and subsequent analysis.

Availability and implementation

The PCN-Miner tool is freely available at the following GitHub repository: https://github.com/hguzzi/ProteinContactNetworks. It is also available in the Python Package Index (PyPI) repository.
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions
Authors: Liu Quanzhong , Fang Honglin , Wang Xiao , Wang Miao , Li Shuqin , Coin Lachlan J M , Li Fuyi , Song Jiangning
Published: July 2022

Motivation

Accurate annotation of different genomic signals and regions (GSRs) from DNA sequences is fundamentally important for understanding gene structure, regulation and function. Numerous efforts have been made to develop machine learning-based predictors for in silico identification of GSRs. However, it remains a great challenge to identify GSRs as the performance of most existing approaches is unsatisfactory. As such, it is highly desirable to develop more accurate computational methods for GSRs prediction.

Results

In this study, we propose a general deep learning framework termed DeepGenGrep, a general predictor for the systematic identification of multiple different GSRs from genomic DNA sequences. DeepGenGrep leverages the power of hybrid neural networks comprising a three-layer convolutional neural network and a two-layer long short-term memory to effectively learn useful feature representations from sequences. Benchmarking experiments demonstrate that DeepGenGrep outperforms several state-of-the-art approaches on identifying polyadenylation signals, translation initiation sites and splice sites across four eukaryotic species including Homo sapiens, Mus musculus, Bos taurus and Drosophila melanogaster. Overall, DeepGenGrep represents a useful tool for the high-throughput and cost-effective identification of potential GSRs in eukaryotic genomes.

Availability and implementation

The webserver and source code are freely available at http://bigdata.biocie.cn/deepgengrep/home and Github (https://github.com/wx-cie/DeepGenGrep/).

Supplementary information

Supplementary data are available at Bioinformatics online.
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
Authors: Formenti Giulio , Abueg Linelle , Brajuka Angelo , Brajuka Nadolina , Gallardo-Alba Cristóbal , Giani Alice , Fedrigo Olivier , Jarvis Erich D
Published: July 2022

Motivation

With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required.

Results

We sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.

Availability and implementation

Gfastats is implemented in C++. Precompiled releases (Linux, MacOS, Windows) and commented source code for gfastats are available under MIT licence at https://github.com/vgl-hub/gfastats. Examples of how to run gfastats are provided in the GitHub. Gfastats is also available in Bioconda, in Galaxy (https://assembly.usegalaxy.eu) and as a MultiQC module (https://github.com/ewels/MultiQC). An automated test workflow is available to ensure consistency of software updates.

Supplementary information

Supplementary data are available at Bioinformatics online.
Response best-subset selector for multivariate regression with high-dimensional response variables
Authors: Hu Jianhua , Huang Jian , Liu Xiaoqian , Liu Xu
Published: July 2022

This article investigates the statistical problem of response-variable selection with high-dimensional response variables and a diverging number of predictor variables with respect to the sample size in the framework of multivariate linear regression. A response best-subset selection model is proposed by introducing a 0-1 selection indicator for each response variable, and then a response best-subset selector is developed by introducing a separation parameter and a novel penalized least-squares function. The proposed procedure can perform response-variable selection and regression-coefficient estimation simultaneously, and the response best-subset selector has the property of model consistency under mild conditions for both fixed and diverging numbers of predictor variables. Also, consistency and asymptotic normality of regression-coefficient estimators are established for cases with a fixed dimension, and it is found that the Bonferroni test is a special response best-subset selector. Finite-sample simulations show that the response best-subset selector has strong advantages over existing competitors in terms of the Matthews correlation coefficient, a criterion that aims to balance accuracies for both true and false response variables. An analysis of real data demonstrates the effectiveness of the response best-subset selector in an application involving the identification of dosage-sensitive genes.
Hug and hop: a discrete-time, nonreversible Markov chain Monte Carlo algorithm
Authors: Ludkin M , Sherlock C
Published: July 2022

This article introduces the hug and hop Markov chain Monte Carlo algorithm for estimating expectations with respect to an intractable distribution. The algorithm alternates between two kernels, referred to as hug and hop. Hug is a nonreversible kernel that repeatedly applies the bounce mechanism from the recently proposed bouncy particle sampler to produce a proposal point that is far from the current position yet on almost the same contour of the target density, leading to a high acceptance probability. Hug is complemented by hop, which deliberately proposes jumps between contours and has an efficiency that degrades very slowly with increasing dimension. There are many parallels between hug and Hamiltonian Monte Carlo using a leapfrog integrator, including the order of the integration scheme, but hug is also able to make use of local Hessian information without requiring implicit numerical integration steps, and its performance is not terminally affected by unbounded gradients of the log-posterior. We test hug and hop empirically on a variety of toy targets and real statistical models, and find that it can, and often does, outperform Hamiltonian Monte Carlo.
Improved prediction of early cognitive impairment in multiple sclerosis combining blood and imaging biomarkers
Authors: Brummer Tobias , Muthuraman Muthuraman , Steffen Falk , Uphaus Timo , Minch Lena , Person Maren , Zipp Frauke , Groppa Sergiu , Bittner Stefan , Fleischer Vinzenz
Published: July 2022

Disability in multiple sclerosis is generally classified by sensory and motor symptoms, yet cognitive impairment has been identified as a frequent manifestation already in the early disease stages. Imaging- and more recently blood-based biomarkers have become increasingly important for understanding cognitive decline associated with multiple sclerosis. Thus, we sought to determine the prognostic utility of serum neurofilament light chain levels alone and in combination with MRI markers by examining their ability to predict cognitive impairment in early multiple sclerosis. A comprehensive and detailed assessment of 152 early multiple sclerosis patients (Expanded Disability Status Scale: 1.3 ± 1.2, mean age: 33.0 ± 10.0 years) was performed, which included serum neurofilament light chain measurement, MRI markers (i.e. T2-hyperintense lesion volume and grey matter volume) acquisition and completion of a set of cognitive tests (Symbol Digits Modalities Test, Paced Auditory Serial Addition Test, Verbal Learning and Memory Test) and mood questionnaires (Hospital Anxiety and Depression scale, Fatigue Scale for Motor and Cognitive Functions). Support vector regression, a branch of unsupervised machine learning, was applied to test serum neurofilament light chain and combination models of biomarkers for the prediction of neuropsychological test performance. The support vector regression results were validated in a replication cohort of 101 early multiple sclerosis patients (Expanded Disability Status Scale: 1.1 ± 1.2, mean age: 34.4 ± 10.6 years). Higher serum neurofilament light chain levels were associated with worse Symbol Digits Modalities Test scores after adjusting for age, sex Expanded Disability Status Scale, disease duration and disease-modifying therapy (B = −0.561; SE = 0.192; P = 0.004; 95% CI = −0.940 to −0.182). Besides this association, serum neurofilament light chain levels were not linked to any other cognitive or mood measures (all P-values > 0.05). The tripartite combination of serum neurofilament light chain levels, lesion volume and grey matter volume showed a cross-validated accuracy of 88.7% (90.8% in the replication cohort) in predicting Symbol Digits Modalities Test performance in the support vector regression approach, and outperformed each single biomarker (accuracy range: 68.6–75.6% and 68.9–77.8% in the replication cohort), as well as the dual biomarker combinations (accuracy range: 71.8–82.3% and 72.6–85.6% in the replication cohort). Taken together, early neuro-axonal loss reflects worse information processing speed, the key deficit underlying cognitive dysfunction in multiple sclerosis. Our findings demonstrate that combining blood and imaging measures improves the accuracy of predicting cognitive impairment, highlighting the clinical utility of cross-modal biomarkers in multiple sclerosis.
Real-World Effectiveness of Vedolizumab Dose Escalation in Patients With Inflammatory Bowel Disease: A Systematic Literature Review
Authors: Patel Dipen , Martin Stephan , Luo Michelle , Ursos Lyann , Lirio Richard A , Kamble Pravin , Wang Song
Published: July 2022

Background

Vedolizumab is a gut-selective anti-lymphocyte trafficking agent approved for the treatment of moderate to severely active inflammatory bowel disease (IBD: ulcerative colitis [UC] and Crohn’s disease [CD]).

Methods

A systematic literature review (SLR) of real-world studies was conducted to assess the effectiveness of dose escalation of vedolizumab every 8 weeks (Q8W) during maintenance treatment to achieve a response in patients who were either vedolizumab responders experiencing secondary loss of response (SLOR) or non-responders. MEDLINE and EMBASE databases were searched from January 2014 to August 2021.

Results

Screening of SLR outputs identified 72 relevant real-world study publications featuring dose escalation of vedolizumab maintenance therapy. After qualitative review, ten eligible studies (9 articles, 1 abstract) were identified as reporting clinical response and/or clinical remission rates following escalation of intravenous vedolizumab 300 mg Q8W maintenance dosing to every 4 weeks (Q4W) maintenance dosing in adult patients with UC/CD (≥10 patients per study). Overall, 196/395 (49.6%) patients with IBD had a response within 54 weeks of vedolizumab maintenance dose escalation. Although definitions for clinical response/remission varied across the 10 studies, clinical response rates after escalated vedolizumab Q8W maintenance dosing ranged from 40.0% to 73.3% (9 studies) and from 30.0% to 55.8% for remission (4 studies) over a range of 8 to <58 weeks’ follow-up.

Conclusions

This synthesis of real-world effectiveness data in vedolizumab-treated patients with IBD indicates that approximately half were able to achieve or recapture clinical response after escalating vedolizumab maintenance dosing.