bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward data-driven, dynamical complex systems approaches to disaster resilience
Authors: Yabe Takahiro , Rao P. Suresh C. , Ukkusuri Satish V. , Cutter Susan L.
Published: February 2022

With rapid urbanization and increasing climate risks, enhancing the resilience of urban systems has never been more important. Despite the availability of massive datasets of human behavior (e.g., mobile phone data, satellite imagery), studies on disaster resilience have been limited to using static measures as proxies for resilience. However, static metrics have significant drawbacks such as their inability to capture the effects of compounding and accumulating disaster shocks; dynamic interdependencies of social, economic, and infrastructure systems; and critical transitions and regime shifts, which are essential components of the complex disaster resilience process. In this article, we argue that the disaster resilience literature needs to take the opportunities of big data and move toward a different research direction, which is to develop data-driven, dynamical complex systems models of disaster resilience. Data-driven complex systems modeling approaches could overcome the drawbacks of static measures and allow us to quantitatively model the dynamic recovery trajectories and intrinsic resilience characteristics of communities in a generic manner by leveraging large-scale and granular observations. This approach brings a paradigm shift in modeling the disaster resilience process and its linkage with the recovery process, paving the way to answering important questions for policy applications via counterfactual analysis and simulations.
Enhancing computational enzyme design by a maximum entropy strategy
Authors: Xie Wen Jun , Asadi Mojgan , Warshel Arieh
Published: February 2022

Significance

Designing efficient enzymes could contribute to a sustainable future. Current computational approaches, including physics-based and machine learning–based design, have not led to a robust enzyme design. Predicting enzyme catalytic power is the crucial step for enzyme design. Here, we found that the properties of enzymes are correlated in a nontrivial way with their evolutionary information. For the active site region and the more distant region, the statistical energy obtained from the maximum entropy model for enzyme homologs is strongly correlated with enzyme catalytic power and stability, respectively. The findings here could be used to understand enzyme catalysis and evolution. Combining the present approach with physics-based computer modeling can provide a potent tool for enzyme design.
Anomalous magnetic interference of cross-type Josephson junctions exposed to oblique magnetic fields
Authors: Mawatari Yasunori
Published: February 2022

Gauge-invariant phase difference and critical currents of cross-type Josephson junctions with thin and narrow superconducting strips exposed to three-dimensional magnetic fields are theoretically investigated. When a sandwich-type Josephson junction in the xy plane is exposed to parallel magnetic fields H

x
and H

y
, the phase difference linearly depends on the spatial coordinates, x and y, and the critical currents exhibit the standard Fraunhofer-type magnetic interference. The perpendicular field H

z
, on the other hand, nonlinearly modulates the distribution of the phase difference and the critical currents as the functions of the oblique field exhibit anomalous magnetic interference. We obtain simple analytical expressions for critical currents of small cross-type junctions by neglecting the effects of self-field and trapped vortices. The resulting dc critical currents show anomalous and diverse interference patterns depending on the parallel and perpendicular magnetic fields.
Indirect excitation and luminescence activation of Tb doped indium tin oxide and its impact on the host’s optical and electrical properties
Authors: Llontop P , Torres C E , Piñeiro M , Conde L , Tejada A , Töfflinger J A , Rumiche F , Aragón F F H , Pacheco-Salazar D G , Grieseler R , Korte L , Guerra J A
Published: February 2022

The effect of adding terbium to indium tin oxide (ITO) thin films on the electrical, optical and light emission properties was investigated. The films were prepared by radio frequency dual magnetron sputtering, maintaining a high optical transmittance in the ultraviolet and visible spectral regions, and a low electrical resistivity ranging from

5
×

10

−
3

 
Ω
⋅

cm

to

0.3

 
Ω
⋅

cm

. Terbium-related luminescence is achieved after annealing at 470 ∘C in air at atmospheric pressure. Electrical resistivity and optical transmittance were measured after each annealing step to evaluate the compromise between the achieved light emission intensity, electrical and optical properties. Additionally, temperature dependence of Tb-related luminescence quenching was assessed by temperature-dependent photoluminescence measurements, from 83 to 533 K, under non-resonant excitation. Thermal quenching activation energies suggest an effective energy transfer mechanism from the ITO host to the rare-earth (RE) ions. This indirect excitation mechanism was modeled using a spherical potential-well and a tight-binding one-band approximation approaches, describing a short-range charge trapping process and subsequent formation of bound excitons to RE ion clusters.
Spin-valley-coupled quantum spin Hall insulator with topological Rashba-splitting edge states in Janus monolayer CSb1.5Bi1.5
Authors: Guo San-Dong , Zhu Yu-Tong
Published: February 2022

Achieving combination of spin and valley polarized states with topological insulating phase is pregnant to promote the fantastic integration of topological physics, spintronics and valleytronics. In this work, a spin-valley-coupled quantum spin Hall insulator (svc-QSHI) is predicted in Janus monolayer CSb1.5Bi1.5 with dynamic, mechanical and thermal stabilities. Calculated results show that the CSb1.5Bi1.5 is a direct band gap semiconductor with and without spin–orbit coupling, and the conduction-band minimum and valence-band maximum are at valley point. The inequivalent valleys have opposite Berry curvature and spin moment, which can produce a spin-valley Hall effect. In the center of Brillouin zone, a Rashba-type spin splitting can be observed due to missing horizontal mirror symmetry. The topological characteristic of CSb1.5Bi1.5 is confirmed by the Z
2 invariant and topological protected conducting helical edge states. Moreover, the CSb1.5Bi1.5 shows unique Rashba-splitting edge states. Both energy band gap and spin-splitting at the valley point are larger than the thermal energy of room temperature (25 meV) with generalized gradient approximation level, which is very important at room temperature for device applications. It is proved that the spin-valley-coupling and nontrivial quantum spin Hall state are robust again biaxial strain. Our work may provide a new platform to achieve integration of topological physics, spintronics and valleytronics.
Slot-die processed perovskite solar cells: effects of solvent and temperature on device performances
Authors: Lee Hyun-Jung , Seo Yu-Hyun , Kim Seok-Soon , Na Seok-In
Published: February 2022

We studied the effects of perovskite precursor solvents and deposition temperatures on perovskite-layer formation for slot-die coating based solar cell fabrication. To select better solvent and temperature conditions, various representative polar solvents (dimethyl sulfoxide (DMSO), N-methyl-2-pyrrolidone, N,N-dimethylformamide (DMF), γ-butyrolactone) and various deposition temperatures (70 °C–150 °C), well-known as key conditions in conventional spin-coating systems, were studied and compared. Comparative studies revealed the DMSO:DMF (5:5) solvents and the 130 °C can provide better solar-cell performances with cell-efficiency up to 15.40% in slot-die based planar perovskite devices, demonstrating an advanced step for better-efficiency slot-die-coating based perovskite solar cells.
Self-organized neuronal subpopulations and network morphology underlying superbursts
Authors: Kim Byoungsoo , Lee Kyoung J
Published: February 2022

Neural bursts are an important phenomenon that needs to be understood for their relevance to many different neurological diseases as well as neural computations. While there are different types of neuronal bursts, in this study we investigate the nature of population (as opposed to intrinsic cell-level) bursts, in particular, superbursts (SBs) that are a small (∼100 ms) packet of several population bursts (PBs). It has been suggested that neuronal PBs occur when there exists a delicate balance of system-wide excitation and inhibition and when recurrent excitation loops exist in the network. However, there has been no rigorous investigation on the relation between network morphology and (super)burst dynamics. Here we investigate the important issue based on a well-established Izhikevich network model of integrate-fire neurons. We have employed the overall conduction delay as our control parameter for tuning network morphology as well as its matching burst dynamics. Interestingly, we found that initially identical neurons self-organize to develop several distinct neuronal subpopulations, which are characterized by different spike firing patterns as well as local network properties. Moreover, a few different motifs of SB emerge according to a distinct mixture of neuronal subpopulations that, on average, fire at slightly different phases. Our analyses suggest that recurring motifs of different SBs reflect complex yet organized modular structures of different subpopulations.
Glycine based auto-combustion synthesis of ZnO nanoparticles as electrode material for supercapacitor
Authors: AlFawaz Amal , Ahmad Ashfaq , Ahmad Naushad , Alharthi Fahad A
Published: February 2022

In this work, ZnO is prepared using glycine based auto-combustion synthesis with advantages of nanoparticles with mesoporosity. x-ray diffraction and Fourier-transform infrared spectroscopy were used to investigate the structural and bond formation of ZnO. Brunauer–Emmett–Teller method was employed to calculate the surface area of ZnO nanoparticles. The surface area was determined to be 6.098 m2 g−1 having pore width lying of 121.389 Å. Chemical bonding of ZnO nanoparticles was studied using x-ray photoelectron spectroscopy and results revealed successful formation of Zn-O bond. The morphology was investigated using scanning electron microscopy and the particles were noticed in 100–500 nm with cylindrical, spherical, and random shaped sharp-edged particles. The electrochemical properties of ZnO were investigated as anode for supercapacitor. ZnO electrode exhibits capacitance of 209.8 F g−1, 186.2 F g−1, 170.6 F g−1, and 167 F g−1 at current densities of 0.25 A g−1, 0.5 A g−1, 1 A g−1, and 2 A g−1, respectively.
Upper bound efficiency for several configurations of work extractors receiving and releasing statistically deformed heat and radiation fluxes
Authors: Badescu Viorel
Published: February 2022

A unified work extractor model is proposed, covering the four possible combinations of heat and radiation reservoirs. In case of heat driven work extractors the upper bounds of the conversion efficiency derived here have the Chambadal-Novikov-Curzon-Ahlborn efficiency as special case and the Carnot efficiency as a particular, ultimate upper bound limit. In case of radiation driven work extractors the upper bounds efficiency covers as a particular case the Petela-Landsberg-Press efficiency, which only applies to fully concentrated radiation. Depending on the value of the geometric factor of the radiation source, the upper bound efficiency ranges between the Petela-Landsberg-Press efficiency and the Carnot efficiency. The upper bound efficiency obtained for the four combinations of heat and radiation reservoirs correctly estimate that work is not generated in some particular cases when both Petela-Landsberg-Press efficiency and Carnot efficiency wrongly estimate that work is generated.
Characterizing Crosstalk within the Pan-STARRS GPC1 Camera
Authors: de Boer T. J. L. , Huber M. E. , Magnier E. A. , Onaka P. M. , Chambers K. C. , Lin C.-C. , Gao H. , Fairlamb J. , Wainscoat R. J.
Published: February 2022

Using data from a year-long dedicated campaign to observe bright stars, we study the crosstalk channels present in the GPC1 camera. By analyzing these data, we construct a data set that checks source stars on almost every CCD of every chip within the camera against all possible crosstalk destinations. We use a clustering algorithm to find potential crosstalk occurrences, and then also check all possible combinations (driven by the hardware layout) by eye. This results in a total of 640 rules, with a flux attenuation factor ranging from 2.5 × 102 for the bright end to 2.5 × 104 at the faint end. The average value of m
cross–m
src ≈ −10.25 corresponds to an attenuating factor of 1.25 × 104, which produces crosstalk ghosts with an average signal-to-noise ratio of 0.64 ± 0.1 on the bright images. We find no evidence of crosstalk signals between CCDs not connected in the hardware setup. The distribution of attenuation factors is also found to be dependent on crosstalk movement. A clear dependence on cell column offsets is found, consistent with the idea that the source star charge is progressively attenuated during the traversal of cell readout lines. While we can see the trends, the uncertainties on aperture magnitude measurements are large at this stage.
Bidirectional bionic limbs: a perspective bridging technology and physiology
Authors: Pasluosta C , Kiele P , Čvančara P , Micera S , Aszmann O C , Stieglitz T
Published: February 2022

Precise control of bionic limbs relies on robust decoding of motor commands from nerves or muscles signals and sensory feedback from artificial limbs to the nervous system by interfacing the afferent nerve pathways. Implantable devices for bidirectional communication with bionic limbs have been developed in parallel with research on physiological alterations caused by an amputation. In this perspective article, we question whether increasing our effort on bridging these technologies with a deeper understanding of amputation pathophysiology and human motor control may help to overcome pressing stalls in the next generation of bionic limbs.
Generalized hydrodynamics in the one-dimensional Bose gas: theory and experiments
Authors: Bouchoule Isabelle , Dubail Jérôme
Published: February 2022

We review the recent theoretical and experimental progress regarding the generalized hydrodynamics (GHD) behavior of the one-dimensional (1D) Bose gas with contact repulsive interactions, also known as the Lieb–Liniger gas. In the first section, we review the theory of the Lieb–Liniger gas, introducing the key notions of the rapidities and of the rapidity distribution. The latter characterizes the Lieb–Liniger gas after relaxation and is at the heart of GHD. We also present the asymptotic regimes of the Lieb–Liniger gas with their dedicated approximate descriptions. In the second section we enter the core of the subject and review the theoretical results of GHD in 1D Bose gases. The third and fourth sections are dedicated to experimental results obtained in cold atom experiments: the experimental realization of the Lieb–Liniger model is presented in section 3, with a selection of key results for systems at equilibrium, and section 4 presents the experimental tests of the GHD theory. In section 5 we review the effects of atom losses, which, assuming slow loss processes, can be described within the GHD framework. We conclude with a few open questions.
Molecular sexing in Bos taurus using quantitative polymerase chain reaction (qPCR) method
Authors: Fathurrahman I , Kusumawati A , Rahman A , Ulviani Y , Prihantoko K D , Unsunnidhal L
Published: February 2022

Cattle are animals that are widely found all over the world which is the domestication of bulls. In Indonesia, domesticated cattle are used as livestock, could be meat cattle or dairy cattle. The sex of the cattle is very influential in terms of selling, especially the type of bull. Calf bull is a product of the process of artificial insemination with spermatozoa resulting in sexing. Mammals have X and Y chromosomes to distinguish their sex. Each chromosome has a special gene such as the SRY gene on the Y chromosome and the PLP gene on the X chromosome. Molecular methods are effective methods of determining the chromosomes carried by spermatozoa. Both special genes are found in the home box (GADPH) of mammals. Primer is made from the mRNA SRY (sex-determining region Y) sequence from Bos taurus with a size above 200bp (SRY B) and below 200bp (SRY A) so that optimal results are obtained between the two. The type of sample that has been used in this research was sexing semen from limousin bulls that are treated from 4 pairs of primers each. The results of the qPCR from both primers are viewed from the melt-peak graph and comparison analysis. The differences between SRY A and SRY-B primer indicates that SRY-A produces a more stable melt-peak graph than SRY B. This indicates that the SRY A primer is more stable when used for molecular verification processes using qPCR.
The important value of mangrove crabs based on sediment conditions at the Asam-Asam river estuary of Tanah Laut regency
Authors: Halang B , Suhaili A , Hani R , Arianto  , Haekal A F , Akbar Z , Isnaeni R
Published: February 2022

Mangrove scabs (Scylla) are organisms that have very high commodity values and are satisfied by many communities in Indonesia, including communities at the Estuary of Asam-Asam River. This research aimed to analyze the important value index of mangrove crabs based on sediment conditions at the Estuary of Asam-Asam River in Tanah Laut Regency. The method of this research was the descriptive method with the direct observation to the field for defining the five sampling points. We took mangrove crab samples three times at each sampling point with distinct periods. The three sampling points lay at the river estuaries and two sample points lay at the non-river estuaries (about 100 meters to 200 meters from the estuary). The results showed that two species of mangrove crabs were found at the region of the river estuaries were Scylla serrata with the Important Value was 133,33 dan Scylla paramamosain which the Important Value was 66,67. Important Value Indexes of these mangroves were high and indicated that these mangrove crabs could play large important ecologic roles in their communities. The mangrove crabs which be found were very little because the condition of the texture of sediments were clays and the contents of air hardness of water were high (smallest 50,8 mg/l) as well as Total Suspended Solid (smallest 55 mg/l) were a high concentration
Predation ability Toxorhynchites splendens larvae from Banjarbaru
Authors: Muhamat  , Hadisusanto S , Umniyati S R , Soesilohadi R C H
Published: February 2022

The population of Toxorhynchites splendens in the rural area of the administrative city of Banjarbaru is quite abundant. This can be developed as part of the control management of Aedes sp. and Culex sp. as disease vectors. The purpose of this study was to test the predation ability of Tx. splendens against larvae of Ae. aegypti and Cx. quinquefasciatus and larval development time of Tx. splendens fed with larvae of Ae. aegypti and Cx. quinquefasciatus. The study used a completely randomized design with 10 replications. The results obtained were the predation ability of Tx. splendens larvae from instar 2 to pupae against larvae of Ae. aegypti and Cx. quinquefasciatus were 5.5 larvae/day and 6 larvae/day, respectively. The average length of the developmental phase of Tx. splendens larvae fed with Ae. aegypti and Cx. quinquefasciatus was 14.55 days and 12 days. The conclusion of this research is Tx. splendens originating from the city of Banjarbaru has the power of predation against Ae. aegypti and Cx. quinquefasciatus.
Molecular fish sexing on Kohaku Koi (Cyprinus carpio) based on ArS.9-15 gene amplification by PCR method
Authors: ‘Aysi N R , Santi M D , Andrian K N , Haryanto A
Published: February 2022

This study aims to sex determine on Kohaku Koi fish rapidly, precisely, accurately, and as early as possible based on the amplification of the ArS.9-15 gene using the PCR method. This study began with the maintenance of 10 Kohaku Koi fish, obtained from Koi fish farmers in the Sleman area in Yogyakarta. The 10 Kohaku Koi were adapted in a filtered aquarium with O2 aeration and fed ad libitum by fish pellets for 1-3 days. Then, a collection of 0.5 ml peripheral blood samples per fish from the caudalis vein was performed under anesthesia conditions using special anesthetic preparation for Koi fish, namely Koi Anesthesia mixed with fresh water. Those samples were then collected in tubes containing the Ca-EDTA anticoagulant. The DNA then was extracted from peripheral blood samples and used as a template for PCR amplification by specific oligonucleotide primer pairs to amplify the ArS.9-15 gene. PCR products in the form of DNA fragments were visualized with 1.5% agarose gel electrophoresis and SybrSafe staining using Transilluminator-UV in a dark room. The DNA fragments were analyzed descriptively to sex determination between male and female Kohaku Koi. Electrophoresis results of PCR products showed two DNA bands of 850 bp and 1,100 bp in male Kohaku Koi, while in female Kohaku Koi showed only a band DNA in size of 850 bp. The results of the molecular fish sexing of the 10 Kohaku Koi showed that 70% are female and 30% are male.
Interactive governance framework and its potential for governing protected area landscape
Authors: Santosa E B
Published: February 2022

One of the recurring problems in the protected area management in Indonesia is the lack of collaboration between various actors who influence and were affected by the existence of these areas. One causes of existing conflicts are the diverse actor’s perceptions regarding the needs, interests, and priorities that will be considered in the region’s policymaking, relating to the management and use of natural resources. Biodiversity conservation versus physical-economic development is one among them. Instruments to tackle this problem are urgently needed, and interactive governance is one prospective alternative. Its various components, including the division of sub-system elements, properties, orders, and styles of interactive governance, can be used to strengthen the governability of a protected area. Enhancing governability can solve societal problems or develop opportunities in protected areas as the ultimate goal. This article is a literature review that explores the potential of an interactive governance framework as a solution to the lack of dialogue between actors in the protected area’s landscape. The study was conducted by exploring the understanding and history of theoretical development, followed by previous studies using this framework, and discussing the application possibilities in the protected area landscape’s management, especially in Indonesia. The study results show that this framework is remarkably feasible to be applied in Indonesia, primarily supported by the perspective of land ownership aspect, traditional community participation, the collaboration between actors and sectors, and the democratic maturation in Indonesia.
Institutional network of the peat ecosystem restoration plan in Riau Province: Hierarchy and classification approaches
Authors: Sukwika T , Febrina L , Mulyawati I
Published: February 2022

Government institutions, both central and local, have issued many policies and regulatory products related to tropical peatland management. Still, peatland degradation and conversion and even land fires continue to occur in Riau. The role of an effective and synergistic institutional network is essential and strategic for its existence. This paper analyzes the dominant role of key institutions in the arena of action for the peat ecosystem restoration plan and formulates a model of the institutional network. The method used is applying systematic and iterative graphic theory with institutional analysis tools, namely ISM or Interpretative Structure Modeling. The study results obtained three classifications of peat ecosystem restoration institutional networks based on critical institutions’ main tasks and functions: institutional coordination, cooperation, and assistance/guidance programs. The conclusion drawn is that based on the institutional network model, it is known that cooperative institutions facilitate the maturation of the concept of peat restoration against the jointly planned program. The policy implication is strengthening the synergy of multi-stakeholder institutions formed as a critical factor in the management of sustainable peat restoration.
Reduction in carbon dioxide and methane production of tropical peatlands due to coal fly-ash application
Authors: Saidy A R , Priatmadi B J , Septiana M
Published: February 2022

Tropical peatlands with very high organic carbon (C) contents have the potential to be a source of carbon dioxide (CO2) and methane (CH4) production. Therefore, the management of tropical peatlands is essential to prevent peat decomposition and to reduce the production of CO2 and CH4. We added different amounts of coal fly-ash (CFA) (0, 25, 50, 75, 100 and 125 Mg ha−1) to tropical peats in a laboratory study to quantify changes in CO2 and CH4 production in response to the application of CFA. The amounts of CO2 and CH4 produced by the mixtures of peats and CFA over 90 days were monitored on weekly basis. Peat pH, concentrations of hot-water soluble C, calcium and iron were also measured at the end of incubation period. Results of study revealed that the application of CFA up to 50 Mg ha−1 did not change the production of CO2 and CH4, while the application of CFA by 50–125 Mg ha−1 reduced 12–24% of CO2 and 9–15% of CH4. The decrease in the production of CO2 and CH4 due to the relatively high amount of CFA application was related to the decrease in the amount of hot soluble organic C and the increase in the concentrations of Ca and Fe. This study demonstrates the potential of CFA as waste materials from coal processing of power plants in reducing CO2 and CH4 emissions of tropical peatlands.
Involvement and roles of stakeholders in Mahakam delta management to support mitigation and adaptation effort of climate change in East Kalimantan
Authors: Wahyuni T , Karmilasanti  , Indriyanti S Y , Abdurachman
Published: February 2022

East Kalimantan provincial government supports Nationally Determined Contribution (NDC) commitment by developing Green Growth Compact (GGC) initiative. This initiative emphasizes participatory and collaborative efforts among stakeholders at different levels and roles in forest management. One of the prototype initiatives currently under development is the management of mangrove forest areas in Mahakam delta. This paper aims to provide information on the process of involving the parties by identifying more details about the role, importance and influence of stakeholders on the Mahakam delta area in order to support the initiative. Data collected through interviews, observation, documents study and using stakeholder analysis. The analysis showed that stakeholders concerned have a direct and influential role can be broadly divided into three main sub-groups: those who provide services needed for the sustainable use and management of these resources (mainly government, NGOs); KPHP (Production Forest Management Unit/FMU) Mahakam delta, Mangrove Lestari Foundation, and Planete Urgence/Bioma Foundation; those who are directly involved in production and trade of oil and gas: Pertamina Hulu Mahakam Company, Pertaminan Hulu Sanga-Sanga Company and Chevron Indonesia; those who are directly involved in production and trade of marine products: Conventional Shrimp Farmers Group and Sustainable Shrimp Farmers Group. Also, there are several parties or stakeholders are classified in the secondary and key stakeholders. This paper supports and provides information and inputs for such initiatives and better management efforts of FMU Mahakam delta.
Absorption of dyes from mixed fungi by cotton fabric with distinct mordants and dyeing pH
Authors: Suciatmih
Published: February 2022

Cotton fabrics processed in dyes with different mordants and staining pH might alter colors variation and dye absorption. A recent study showed a mixture of Aspergillus and Paecilomyces can be used to dye cotton fabric using five different mordant chemicals, CuSO4.5H2O, FeSO4.7H2O, KAl (SO4)2.12H2O, K2Cr2O7, and MnSO4.H2O, and three distinctive dyeing pH (3, 7, and 11). Both fungi were collectively cultured on mineral salt glucose medium to a stationary stage in dark conditions for four weeks. The RHS color chart was used to determine the color of the filtrate and the spectrum of colors created on dyed materials. The results suggested that the color development and dye absorption of the fabrics were greatly affected by chemical compounds of mordant and the acidity degree of the dyeing process. The pH of the dyeing process has a greater impact on the absorption of fungal dyes by cloth than the mordant. Colors formed on cotton fabric can add colors variation to textile dyeing.
Changes of stomatal distribution and leaf thickness in response to transpiration rate in six dicot plant species
Authors: Daningsih E , Mardiyyanigsih A N , Costa Y O Da , Primawati R , Karlina S
Published: February 2022

Changes in leaf anatomy can be influenced by the surrounding environment and several other factors. Shade plants or ornamental plants themselves also have their characteristics in responding to surrounding conditions through transpiration. This study aimed to measure the rate of transpiration related to changes in the distribution of stomata and leaf thickness of six types of dicot ornamental plants and to describe the leaf anatomy of each type. The experiment used Completely Randomized Design (CRD) with six types of plants as treatment with three replications. Transpiration rate was measured by modified lysimeter method, stomatal distribution was calculated from the ratio of the number of stomata to epidermal cells and leaf anatomy was observed using preserved slide made from paraffin method. Data were analyzed by SAS with CRD model and correlation was performed between transpiration rate and leaf thickness. The results showed that the transpiration rate, leaf thickness, and stomatal distribution were significantly different atα= 0.05 amongst plants. The transpiration rate was inversely proportional to leaf thickness with various correlation coefficients. The leaf anatomy of six plant species showed various thicknesses between tissues. Further research needs to be done to explain the rate of transpiration with changes in leaf anatomy.
Notes on leaf anatomy: Additional information for Indonesian Pandanus spp. (Pandanaceae)
Authors: Tihurua E F , Widoyanti  , Rustiami H , Megawati
Published: February 2022

In Indonesia, Pandanus spp. were distributed from Sumatra to Papua. These Pandanus species has broader variation of anatomical leaf characters whether epidermis or transversal section traits. This study was conducted to obtain an information of anatomical characters of Pandanus leaf and supporting character on Pandanus identification. Pandanus collections of Herbarium Bogoriense were used for this study, and some of Pandanus species from Papua New Guinea and Malay Peninsula were added as well. Paraffin method and simple peeling of the leaf surface were used to get leaf transversal sections and epidermis characters. In general, anatomical characters of examined species in this study relatively similar to other Pandanus species which were studied by former researchers. Pandanus has broad range of stomata types on the lower leaf surface, from simple stomata to the most specialized stomata. The upper leaf surface of Pandanus spp. has similar stomata type, viz. class 1 (simple). Zonation always presents on all species, except on P. atropurpureus, P. conoideus and P. nitidus. Mostly, crystals CaCO3 were found in three forms, namely rectangular and needle-like shape in idioblast cells, while prism-shape is scattered in the mesophyll area. These crystal shapes absent in P. odorifer and there is one additional crystal shape, drusse which present in P. conoideus. Silica bodies located in the upper and lower hypodermis of leaf. Bundle sheath extension was seen in all species except P. beguinii, P. conoideus, and P. fusinus.
Optimal pulse configuration for peripheral inductive nerve stimulation
Authors: Rapp J , Braun P , Hemmert W , Gleich B
Published: February 2022

Peripheral magnetic stimulation is a promising technique for several applications like rehabilitation or diagnose of neuronal pathways. However, most available magnetic stimulation devices are designed for transcranial stimulation and require high-power, expensive hardware. Modern technology such as rectangular pulses allows to adapt parameters like pulse shape and duration in order to reduce the required energy. Nevertheless, the effect of different temporal electromagnetic field shapes on neuronal structures is not yet fully understood. We created a simulation environment to find out how peripheral nerves are affected by induced magnetic fields and what pulse shapes have the lowest energy requirements. Using the electric field distribution of a figure-of-8 coil together with an axon model in saline solution, we calculated the potential along the axon and determined the required threshold current to elicit an action potential. Further, for the purpose of selective stimulation, we investigated different axon diameters. Our results show that rectangular pulses have the lowest thresholds at a pulse duration of 20 μs. For sinusoidal coil currents, the optimal pulse duration was found to be 40 μs. Most importantly, with an asymmetric rectangular pulse, the coil current could be reduced from 2.3 kA (cosine shaped pulse) to 600 A. In summary, our results indicate that for magnetic nerve stimulation the use of rectangular pulse shapes holds the potential to reduce the required coil current by a factor of 4, which would be a massive improvement.
CPU-GPU coupling independent reaction times method in NASIC and application in water radiolysis by FLASH irradiation
Authors: Hu Ankang , Qiu Rui , Wu Zhen , Zhang Hui , Li Junli
Published: February 2022

The mechanism of the FLASH effect remains unclear and could be revealed by studying chemical reactions during irradiation. Monte Carlo simulation of the radiolytic species is an effective tool to analyze chemical reactions, but the simulation is limited by computing costs of the step-by-step simulation of radiolytic species, especially when considering beam with complex time structure. The complexity of the time structure of beams from accelerators in FLASH radiotherapy requires a high-performance Monte Carlo code. In this work, we develop a CPU-GPU coupling accelerating code with the independent reaction times (IRT) method to extend the chemical module of our nanodosimetry Monte Carlo code NASIC. Every chemical molecule in the microenvironment contains time information to consider the reactions from different tracks and simulate beams with complex time structures. Performance test shows that our code significantly improved the computing efficiency of the chemical module by four orders of magnitude. Then the code is used to study the oxygen depletion hypothesis in FLASH radiotherapy for different conditions by setting different parameters. The transient oxygen consumption rate values in the water are calculated when the pulses width ranges from 2 ps to 2 μs, the total dose ranges from 0.5 Gy to 100 Gy and the initial oxygen concentration ranges from 0.1% to 21%. The time evolution curves are simulated to study the effect of the time structure of an electron linear accelerator. Results show that the total dose in several microseconds is a better indicator reflecting the radiolytic oxygen consumption rate than the dose rate. The initial oxygen greatly affects the oxygen consumption rate because of the reaction competition. The diffusion of oxygen determined by the physiological parameters is the key factor affecting oxygen depletion during the radiation using electron linear accelerators. Our code provides an efficient tool for simulating water radiolysis in different conditions.
Positive scores on the 4AT delirium assessment tool at hospital admission are linked to mortality, length of stay and home time: two-centre study of 82,770 emergency admissions
Authors: Anand Atul , Cheng Michael , Ibitoye Temi , Maclullich Alasdair M J , Vardy Emma R L C
Published: February 2022

Background

Studies investigating outcomes of delirium using large-scale routine data are rare. We performed a two-centre study using the 4 ‘A’s Test (4AT) delirium detection tool to analyse relationships between delirium and 30-day mortality, length of stay and home time (days at home in the year following admission).

Methods

The 4AT was performed as part of usual care. Data from emergency admissions in patients ≥65 years in Lothian, UK (n = 43,946) and Salford, UK (n = 38,824) over a period of $\sim$3 years were analysed using logistic regression models adjusted for age and sex.

Results

4AT completion rates were 77% in Lothian and 49% in Salford. 4AT scores indicating delirium (≥4/12) were present in 18% of patients in Lothian, and 25% of patients in Salford. Thirty-day mortality with 4AT ≥4 was 5.5-fold greater than the 4AT 0/12 group in Lothian (adjusted odds ratio (aOR) 5.53, 95% confidence interval [CI] 4.99–6.13) and 3.4-fold greater in Salford (aOR 3.39, 95% CI 2.98–3.87). Length of stay was more than double in patients with 4AT scores of 1–3/12 (indicating cognitive impairment) or ≥ 4/12 compared with 4AT 0/12. Median home time at 1 year was reduced by 112 days (Lothian) and 61 days (Salford) in the 4AT ≥4 group (P < 0.001).

Conclusions

Scores on the 4AT used at scale in practice are strongly linked with 30-day mortality, length of hospital stay and home time. The findings highlight the need for better understanding of why delirium is linked with poor outcomes and also the need to improve delirium detection and treatment.
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification
Authors: Moon Sehwan , Lee Hyunju
Published: February 2022

Motivation

Accurate diagnostic classification and biological interpretation are important in biology and medicine, which are data-rich sciences. Thus, integration of different data types is necessary for the high predictive accuracy of clinical phenotypes, and more comprehensive analyses for predicting the prognosis of complex diseases are required.

Results

Here, we propose a novel multi-task attention learning algorithm for multi-omics data, termed MOMA, which captures important biological processes for high diagnostic performance and interpretability. MOMA vectorizes features and modules using a geometric approach and focuses on important modules in multi-omics data via an attention mechanism. Experiments using public data on Alzheimer’s disease and cancer with various classification tasks demonstrated the superior performance of this approach. The utility of MOMA was also verified using a comparison experiment with an attention mechanism that was turned on or off and biological analysis.

Availability and implementation

The source codes are available at https://github.com/dmcb-gist/MOMA.

Supplementary information

Supplementary materials are available at Bioinformatics online.
Optimal transport improves cell–cell similarity inference in single-cell omics data
Authors: Huizing Geert-Jan , Peyré Gabriel , Cantini Laura
Published: February 2022

Motivation

High-throughput single-cell molecular profiling is revolutionizing biology and medicine by unveiling the diversity of cell types and states contributing to development and disease. The identification and characterization of cellular heterogeneity are typically achieved through unsupervised clustering, which crucially relies on a similarity metric.

Results

We here propose the use of Optimal Transport (OT) as a cell–cell similarity metric for single-cell omics data. OT defines distances to compare high-dimensional data represented as probability distributions. To speed up computations and cope with the high dimensionality of single-cell data, we consider the entropic regularization of the classical OT distance. We then extensively benchmark OT against state-of-the-art metrics over 13 independent datasets, including simulated, scRNA-seq, scATAC-seq and single-cell DNA methylation data. First, we test the ability of the metrics to detect the similarity between cells belonging to the same groups (e.g. cell types, cell lines of origin). Then, we apply unsupervised clustering and test the quality of the resulting clusters. OT is found to improve cell–cell similarity inference and cell clustering in all simulated and real scRNA-seq data, as well as in scATAC-seq and single-cell DNA methylation data.

Availability and implementation

All our analyses are reproducible through the OT-scOmics Jupyter notebook available at https://github.com/ComputationalSystemsBiology/OT-scOmics.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors
Authors: Wagner Naama , Avram Oren , Gold-Binshtok Dafna , Zerah Ben , Teper Doron , Pupko Tal
Published: February 2022

Motivation

Type-III secretion systems are utilized by many Gram-negative bacteria to inject type-3 effectors (T3Es) to eukaryotic cells. These effectors manipulate host processes for the benefit of the bacteria and thus promote disease. They can also function as host-specificity determinants through their recognition as avirulence proteins that elicit immune response. Identifying the full effector repertoire within a set of bacterial genomes is of great importance to develop appropriate treatments against the associated pathogens.

Results

We present Effectidor, a user-friendly web server that harnesses several machine-learning techniques to predict T3Es within bacterial genomes. We compared the performance of Effectidor to other available tools for the same task on three pathogenic bacteria. Effectidor outperformed these tools in terms of classification accuracy (area under the precision–recall curve above 0.98 in all cases).

Availability and implementation

Effectidor is available at: https://effectidor.tau.ac.il, and the source code is available at: https://github.com/naamawagner/Effectidor.

Supplementary information

Supplementary data are available at Bioinformatics online.
Reconstructing viral haplotypes using long reads
Authors: Cai Dehan , Sun Yanni
Published: February 2022

Motivation

Most RNA viruses lack strict proofreading during replication. Coupled with a high replication rate, some RNA viruses can form a virus population containing a group of genetically related but different haplotypes. Characterizing the haplotype composition in a virus population is thus important to understand viruses’ evolution. Many attempts have been made to reconstruct viral haplotypes using next-generation sequencing (NGS) reads. However, the short length of NGS reads cannot cover distant single-nucleotide variants, making it difficult to reconstruct complete or near-complete haplotypes. Given the fast developments of third-generation sequencing technologies, a new opportunity has arisen for reconstructing full-length haplotypes with long reads.

Results

In this work, we developed a new tool, RVHaplo to reconstruct haplotypes for known viruses from long reads. We tested it rigorously on both simulated and real viral sequencing data and compared it against other popular haplotype reconstruction tools. The results demonstrated that RVHaplo outperforms the state-of-the-art tools for viral haplotype reconstruction from long reads. Especially, RVHaplo can reconstruct the rare (1% abundance) haplotypes that other tools usually missed.

Availability and implementation

The source code and the documentation of RVHaplo are available at https://github.com/dhcai21/RVHaplo.

Supplementary information

Supplementary data are available at Bioinformatics online.
HIV-1 drug resistance profiling using amino acid sequence space cartography
Authors: Pikalyova Karina , Orlov Alexey , Lin Arkadii , Tarasova Olga , Marcou MarcouGilles , Horvath Dragos , Poroikov Vladimir , Varnek Alexandre
Published: February 2022

Motivation

Human immunodeficiency virus (HIV) drug resistance is a global healthcare issue. The emergence of drug resistance influenced the efficacy of treatment regimens, thus stressing the importance of treatment adaptation. Computational methods predicting the drug resistance profile from genomic data of HIV isolates are advantageous for monitoring drug resistance in patients. However, existing computational methods for drug resistance prediction are either not suitable for emerging HIV strains with complex mutational patterns or lack interpretability, which is of paramount importance in clinical practice. The approach reported here overcomes these limitations and combines high accuracy of predictions and interpretability of the models.

Results

In this work, a new methodology based on generative topographic mapping (GTM) for biological sequence space representation and quantitative genotype–phenotype relationships prediction purposes was introduced. The GTM-based resistance landscapes allowed us to predict the resistance of HIV strains based on sequencing and drug resistance data for three viral proteins [integrase (IN), protease (PR) and reverse transcriptase (RT)] from Stanford HIV drug resistance database. The average balanced accuracy for PR inhibitors was 0.89 ± 0.01, for IN inhibitors 0.85 ± 0.01, for non-nucleoside RT inhibitors 0.73 ± 0.01 and for nucleoside RT inhibitors 0.84 ± 0.01. We have demonstrated in several case studies that GTM-based resistance landscapes are useful for visualization and analysis of sequence space as well as for treatment optimization purposes. Here, GTMs were applied for the in-depth analysis of the relationships between mutation pattern and drug resistance using mutation landscapes. This allowed us to predict retrospectively the importance of the presence of particular mutations (e.g. V32I, L10F and L33F in HIV PR) for the resistance development. This study highlights some perspectives of GTM applications in clinical informatics and particularly in the field of sequence space exploration.

Availability and implementation

https://github.com/karinapikalyova/ISIDASeq.

Supplementary information

Supplementary data are available at Bioinformatics online.
Aberrant motor contagion of emotions in psychopathy and high-functioning autism
Authors: Sun Lihua , Lukkarinen Lasse , Noppari Tuomo , Nazari-Farsani Sanaz , Putkinen Vesa , Seppälä Kerttu , Hudson Matthew , Tani Pekka , Lindberg Nina , Karlsson Henry K , Hirvonen Jussi , Salomaa Marja , Venetjoki Niina , Lauerma Hannu , Tiihonen Jari , Nummenmaa Lauri
Published: February 2022

Psychopathy and autism are both associated with aberrant social skills and empathy, yet only psychopaths are markedly antisocial and violent. Here, we compared the functional neural alterations underlying these two groups that both have aberrant empathetic abilities but distinct behavioral phenotypes. We studied 19 incarcerated male offenders with high psychopathic traits, 20 males with high-functioning autism, and 19 age-matched healthy controls. All groups underwent functional magnetic resonance imaging while they viewed dynamic happy, angry, and disgusted faces or listened to laughter and crying sounds. Psychopathy was associated with reduced somatomotor responses to almost all expressions, while participants with autism demonstrated less marked and emotion-specific alterations in the somatomotor area. These data suggest that psychopathy and autism involve both common and distinct functional alterations in the brain networks involved in the socioemotional processing. The alterations are more profound in psychopathy, possibly reflecting the more severely disturbed socioemotional brain networks in this population.