bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution and transport of holes in the p-GaN/AlGaN/GaN heterostructure
Authors: Ng Yat Hon , Zheng Zheyang , Zhang Li , Liu Ruizi , Chen Tao , Feng Sirui , Shao Qiming , Chen Kevin J.
Published: October 2023

The p-GaN/AlGaN/GaN heterostructure, predominantly epitaxially grown on large-scale silicon wafers, has been widely used for producing consumer power switching devices and recently manifested favorable for developing GaN-based complementary devices and circuits. This work investigates the hole distribution and transport in this structure based on wide-temperature-range (20–600 K) Hall measurements and TCAD simulations. It is revealed that the p-channel thereof is composed of the bulk holes in the p-GaN and the two-dimensional hole gas (2DHG) at the p-GaN/AlGaN interface, and both substantially contribute to the lateral p-type conduction at room temperature. Their complementary temperature responses lead to conductivity enhancement at both high- and low-temperature regimes. The high-density (1.2 × 1013 cm−2) 2DHG is formed owing to the polarization-induced potential well and the ionization of the Mg acceptors that thermally diffused into the barrier during the epi-growth. Such ionized Mg acceptors would partially deplete the two-dimensional electron gas (2DEG) at the access region in the n-channel side where the p-GaN is removed and result in a trade-off between the carrier density of 2DHG and 2DEG.
The future of photonic crystal surface-emitting lasers
Authors: Zhou Weidong , Pan Mingsen
Published: October 2023

Semiconductor lasers are the heart for the development of technologies in many fields. In recent decades, a new type of large-area surface-emitting lasers based on the in-plane photonic crystal modulation and feedback have emerged to show superior advantages of high output power, low-divergence, high beam quality and brightness, and compact and monolithic structure. In this paper, we review the design and development of photonic crystal surface-emitting laser and discuss the future investigation and improvements.
The femtosecond structure of extreme contrast, multi-terawatt second-harmonic laser pulses at 400 nm
Authors: Aparajit C. , Dulat Ankit , Choudhary Anandam , Lad Amit D. , Ved Yash M. , Couairon Arnaud , Kumar G. Ravindra
Published: October 2023

Ultrahigh intensity contrast and short pulse laser–solid interactions offer an attractive platform for investigating high-energy-density matter, particularly in the context of structured and ultra-thin targets that form hot, dense plasma conditions. Harmonic generation can improve the contrast of laser pulses by several orders of magnitude. In this study, we present the characterization of extreme contrast, relativistic intensity second-harmonic pulses at 400 nm, using the self-diffraction frequency-resolved optical gating technique. The 400 nm pulses were generated at various input intensities using potassium dihydrogen phosphate and lithium triborate crystals. Our observations reveal the presence of spectral broadening, pulse compression, and complex structures at higher input intensities. We see that extreme contrast, few tens of femtosecond pulses can have multiple “prepulses” at the 100s femtosecond scale as large as ten percent of the peak value. These can preionize a solid significantly and may influence the interaction. Simulations based on nonlinear pulse propagation equations reinforce our findings.
Dynamic extracellular vestibule of human SERT: Unveiling druggable potential with high-affinity allosteric inhibitors
Authors: Salomon Kristine , Abramyan Ara M. , Plenge Per , Wang Lingle , Bundgaard Christoffer , Bang-Andersen Benny , Loland Claus J. , Shi Lei
Published: October 2023

The serotonin transporter (SERT) tightly regulates synaptic serotonin levels and has been the primary target of antidepressants. Binding of inhibitors to the allosteric site of human SERT (hSERT) impedes the dissociation of antidepressants bound at the central site and may enhance the efficacy of such antidepressants to potentially reduce their dosage and side effects. Here, we report the identification of a series of high-affinity allosteric inhibitors of hSERT in a unique scaffold, with the lead compound, Lu AF88273 (3-(1-(2-(1
H
-indol-3-yl)ethyl)piperidin-4-yl)-6-chloro-1
H
-indole), having 2.1 nM allosteric potency in inhibiting imipramine dissociation. In addition, we find that Lu AF88273 also inhibits serotonin transport in a noncompetitive manner. The binding pose of Lu AF88273 in the allosteric site of hSERT is determined with extensive molecular dynamics simulations and rigorous absolute binding free energy perturbation (FEP) calculations, which show that a part of the compound occupies a dynamically formed small cavity. The predicted binding location and pose are validated by site-directed mutagenesis and can explain much of the structure–activity relationship of these inhibitors using the relative binding FEP calculations. Together, our findings provide a promising lead compound and the structural basis for the development of allosteric drugs targeting hSERT. Further, they demonstrate that the divergent allosteric sites of neurotransmitter transporters can be selectively targeted.
Molecular basis of signal transduction mediated by the human GIPR splice variants
Authors: Zhao Fenghui , Hang Kaini , Zhou Qingtong , Shao Lijun , Li Hao , Li Wenzhuo , Lin Shi , Dai Antao , Cai Xiaoqing , Liu Yanyun , Xu Yingna , Feng Wenbo , Yang Dehua , Wang Ming-Wei
Published: October 2023

Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a potential drug target for metabolic disorders. It works with glucagon-like peptide-1 receptor and glucagon receptor in humans to maintain glucose homeostasis. Unlike the other two receptors, GIPR has at least 13 reported splice variants (SVs), more than half of which have sequence variations at either C or N terminus. To explore their roles in endogenous peptide-mediated GIPR signaling, we determined the cryoelectron microscopy (cryo-EM) structures of the two N terminus–altered SVs (referred as GIPR-202 and GIPR-209 in the Ensembl database, SV1 and SV2 here, respectively) and investigated the outcome of coexpressing each of them in question with GIPR in HEK293T cells with respect to ligand binding, receptor expression, cAMP (adenosine 3,5-cyclic monophosphate) accumulation, β-arrestin recruitment, and cell surface localization. It was found that while both N terminus–altered SVs of GIPR neither bound to the hormone nor elicited signal transduction per se, they suppressed ligand binding and cAMP accumulation of GIPR. Meanwhile, SV1 reduced GIPR-mediated β-arrestin 2 responses. The cryo-EM structures of SV1 and SV2 showed that they reorganized the extracellular halves of transmembrane helices 1, 6, and 7 and extracellular loops 2 and 3 to adopt a ligand-binding pocket-occupied conformation, thereby losing binding ability to the peptide. The results suggest a form of signal bias that is constitutive and ligand-independent, thus expanding our knowledge of biased signaling beyond pharmacological manipulation (i.e., ligand specific) as well as constitutive and ligand-independent (e.g., SV1 of the growth hormone-releasing hormone receptor).
Actuation-enhanced multifunctional sensing and information recognition by magnetic artificial cilia arrays
Authors: Han Jie , Dong Xiaoguang , Yin Zhen , Zhang Shuaizhong , Li Meng , Zheng Zhiqiang , Ugurlu Musab Cagri , Jiang Weitao , Liu Hongzhong , Sitti Metin
Published: October 2023

Artificial cilia integrating both actuation and sensing functions allow simultaneously sensing environmental properties and manipulating fluids in situ, which are promising for environment monitoring and fluidic applications. However, existing artificial cilia have limited ability to sense environmental cues in fluid flows that have versatile information encoded. This limits their potential to work in complex and dynamic fluid-filled environments. Here, we propose a generic actuation-enhanced sensing mechanism to sense complex environmental cues through the active interaction between artificial cilia and the surrounding fluidic environments. The proposed mechanism is based on fluid–cilia interaction by integrating soft robotic artificial cilia with flexible sensors. With a machine learning-based approach, complex environmental cues such as liquid viscosity, environment boundaries, and distributed fluid flows of a wide range of velocities can be sensed, which is beyond the capability of existing artificial cilia. As a proof of concept, we implement this mechanism on magnetically actuated cilia with integrated laser-induced graphene-based sensors and demonstrate sensing fluid apparent viscosity, environment boundaries, and fluid flow speed with a reconfigurable sensitivity and range. The same principle could be potentially applied to other soft robotic systems integrating other actuation and sensing modalities for diverse environmental and fluidic applications.
How free is the position of German object pronouns?
Authors: Bader Markus
Published: October 2023

Corpus studies show that weak object pronouns in German directly precede or follow the subject, depending on properties of the subject, including weight, animacy and thematic role. Whether the same factors also affect the acceptability of sentences with object pronouns was investigated in three magnitude-estimation experiments. The results show that both orders (object pronoun before/after subject) are highly acceptable, with some small acceptability differences depending on weight, animacy and thematic roles. Based on these results, the hypothesis is advanced that the position of weak object pronouns in German relative to the subject is an instance of free variation within the grammar but choosing a specific order during language production follows general production preferences and is thus not random.
Non-verbal plural number agreement. Between the distributive plural and singular
Authors: Rudnicka Karolina , Klégr Aleš
Published: October 2023

Unlike Slavic languages, such as Polish and Czech, English is assumed to prefer distributive plural agreement between the plural subject and the noun in the predicate part of the sentence. The aim of this paper is to verify this claim and (since this preference is apparently not without exceptions) provide an overview of scenarios in which the tendency for the distributive plural is overruled. We start with a classification of factors blocking the use of the plural and enabling the use of distributive singular. The preference is tested by reviewing the occurrences of two constructions, lose one’s life and lose one’s job,1 in the BNC2 and COCA,3 In view of the distributive singular cases in the dataset, the chapter investigates the possibility of the distributive plural and singular cases being in a free variation and proposes a new condition for them to be seen as such: they need to have a similar distribution across different genres.
Variation and change in the Aanaar Saami conditional perfect
Authors: Niinemägi Merit
Published: October 2023

The present study captures a case of language variation in the verbal system of Aanaar (Inari) Saami, namely that of the conditional perfect, which can be expressed by two periphrastic constructions. The aim of this paper is twofold: (1) to give a diachronic description of the Aanaar Saami conditional perfect and (2) to investigate whether its variation can be considered to be ‘free’ or whether it is explainable by intra- and extralinguistic determinants. The data consists of language samples gathered in 1887 and 1952, the Aanaar Saami text corpus and a survey carried out in 2020. The diachronic comparison indicates changes in the variation which are, among others, discussed in the light of linguistic interference and Aanaar Saami’s recent revitalisation.
Syntactic priming and individual preferences
Authors: Rosemeyer Malte
Published: October 2023

This paper analyses the relation between syntactic priming/persistence and individual preferences in the variation between the two forms of the Spanish past subjunctive (-ra vs -se). The analysis finds that the probability of repetition of one of these variants is governed by an interaction between individual preferences and the difference between self- and other-priming. Previous use of a variant by another speaker is more likely to lead to persistence than previous use by the current speaker in the case that the current speaker does not usually prefer usage of the variant in question. However, if the current speaker prefers usage of the variant in question, this situation is inverted. These findings suggest that for speakers who prefer usage of the primed variant, self-priming in corpus data might actually be more adequately explained as an effect of individual preferences.
Optionality, variation and categorial properties
Authors: Yu Yidong
Published: October 2023

In this paper, I propose a semantic account of the optionality of plural marking in Yucatec Maya (Mayan; Mexico) which pins the variation in plural marking on the variation in noun denotations (Chierchia 1998; Borer 2005; Deal 2017; Moroney 2021). I argue that this optionality is not a free variation. I further argue that the noun denotations vary between apportionable and generic, which is manifested in the option of a pseudopartitive operation (Selkirk 1977; Higginbotham 1994) available at the final stage of the interpretation of the nouns in the semantics. The fact that, by this account, the computation of Yucatec constructions that involve counting yields correct results provides further supporting evidence for the proposed analysis.
Animal Rescue Tourism: Supporting the Welfare and Rights of Domesticated Street Animals in the Age of Social Media
Authors: Blaer Madelene
Published: October 2023

This case focuses on domesticated animals in tourism and explores how animal rescue organisations can engage voluntourism to promote animal welfare and rights in the digital age. A key issue addressed is how social media can be both harmful and beneficial for animals in tourism. In terms of the latter, the case shows how an animal rescue organisation in India has leveraged social media to heighten awareness and engagement in animal welfare and rights through tourism. Rather than partake in harmful wildlife selfies or unwittingly support cruel industry practices, voluntourists actively help to rescue and rehabilitate injured and ill street animals and further promote the cause by sharing their experiences online. Through detailing a real-world example of an organisation that promotes animal rights while simultaneously providing voluntourists with meaningful experiences, this case study encourages reader reflection on animal ethics in tourism. Interested stakeholders, including other animal rescue organisations, can use and adopt the lessons learnt to achieve similar positive outcomes.

Information

© The Author 2023
Effect of SeO2 on corrosion resistance of micro-arc oxidation
Authors: Zhang D.F. , Zheng R. , Chen X.W. , Zhang G.H.
Published: October 2023

In order to make titanium alloy implants have better corrosion resistance in the human body, selenium-containing coating was added to the surface of Ti6Al7Nb through micro-arc oxidation. The results indicate that the coating has a higher thickness and lower roughness after the addition of selenium element. XRD, SEM, and XPS analysis showed that selenium element was successfully added into the coating. Then the dynamic polarization curve and EIS indicate that the prepared samples have better corrosion resistance in SBF solution compared to the unadded samples, (i corr) and (E corr) are 2.695 × 10−8 A·cm−2 and 0.101 V, respectively. The addition of selenium helps to improve the biological corrosion resistance of the sample in body fluids.
The ‘thin lens’ in the light of idealisations
Authors: Winkelmann Jan , Römer Daniel
Published: October 2023

This paper argues that the simplifying idealisations assumed in making complex science tractable should be identified and discussed before model-building. It is suggested that alternative conceptions can persist, and learning difficulties arise for students when they do not adequately understand these idealisations. We argue that explicitly addressing idealisations for a particular physical phenomenon can ease students’ conceptual understanding. A theoretical framework for identifying and reflecting idealisations is introduced based on epistemological considerations from science philosophy. The thin lens approximation of geometric optics, a common topic taught in the introductory classroom, is used as an archetypal illustration.
Analysis of intracranial pressure pulse waveform in studies on cerebrospinal compliance: a narrative review
Authors: Kazimierska Agnieszka , Manet Romain , Vallet Alexandra , Schmidt Eric , Czosnyka Zofia , Czosnyka Marek , Kasprowicz Magdalena
Published: October 2023

Continuous monitoring of mean intracranial pressure (ICP) has been an essential part of neurocritical care for more than half a century. Cerebrospinal pressure–volume compensation, i.e. the ability of the cerebrospinal system to buffer changes in volume without substantial increases in ICP, is considered an important factor in preventing adverse effects on the patient’s condition that are associated with ICP elevation. However, existing assessment methods are poorly suited to the management of brain injured patients as they require external manipulation of intracranial volume. In the 1980s, studies suggested that spontaneous short-term variations in the ICP signal over a single cardiac cycle, called the ICP pulse waveform, may provide information on cerebrospinal compensatory reserve. In this review we discuss the approaches that have been proposed so far to derive this information, from pulse amplitude estimation and spectral techniques to most recent advances in morphological analysis based on artificial intelligence solutions. Each method is presented with focus on its clinical significance and the potential for application in standard clinical practice. Finally, we highlight the missing links that need to be addressed in future studies in order for ICP pulse waveform analysis to achieve widespread use in the neurocritical care setting.
Numerical calculation for instability criterion of tearing modes influenced by energetic ions
Authors: Ma Yuehao , Zhang Runzhe , Cai Huishan
Published: October 2023

The instability criterion of tearing modes, including the effects of circulating energetic ions (CEIs), is numerically solved through an iterative method and fast Fourier transform algorithm. The influence of beta (the ratio of pressure to the magnetic pressure) profile of CEIs and magnetic shear on instability criterion of the tearing modes are investigated systematically. CEIs impact the tearing modes through altering the total perturbed parallel current density, and the gradient of their beta profile at the rational surface (the location of tearing mode) plays an important role. The effect of CEIs on tearing modes depends on the deposition position and the toroidal circulating direction of CEIs. Specifically, the on-axis peaked co-CEIs have a stabilizing effect on tearing modes. For off-axis peaked co-CEIs, in order to stabilize the tearing modes, the deposition position of co-CEIs should be located between the magnetic axis and rational surface, and there is an optimal peak width and deposition location where the stabilizing effect is strongest. For counter-CEIs, they would destabilize the tearing modes when the deposition position is located between the magnetic axis and rational surface. However, if the deposition position is located near the outside rational surface, counter-CEIs have a stabilizing effect on tearing modes. Furthermore, there exists a critical deposition position for CEIs. Whether CEIs plays a stable role or an unstable role depends on the deposition position within or outside the critical deposition position. The critical deposition position is related to the orbital width of CEIs. Finally, the magnetic shear can stabilize the tearing modes, but the effect of co-CEIs on tearing modes is weakened as the magnetic shear increases.
Water Quality Assessment of Lake Maninjau After the Mass Fish Kill Event
Authors: Jasalesmana Taofik , Putri Mutiara Rachmat , Abdurrachman Mirzam , Henny Cynthia , Nomosatryo Sulung , Akhdiana Ira
Published: October 2023

A mass fish kill is often occurring in Lake Maninjau. A lack of oxygen has reportedly resulted in numerous fish kills, including the recent lake Maninjau condition. Deoxygenation of lake water is a natural phenomenon that often occurs after heavy rain events and low sunlight intensity. Additionally, during the strong wind for a long period, the decrease in oxygen could be chemically triggered by the diffusion of sulfide from the bottom layer of the water column. Furthermore, this study examines water quality parameters after the mass fish mortality occurred across locations in Lake Maninjau. Field surveys were conducted by measuring physiochemical parameters and total sulfide at the Fifteen sampling points (five points in the middle and ten points around the lake) from November 26 to December 2, 2022. They were measured directly using the Horriba©U 52 water quality checker (WQC), DO meter YSI ProDO© International and the HACH spectrophotometer DR3900 method. The results show that the average DO levels at each observation point were close to 0 mg/L while the average sulfide level on the surface was 9.5 micro g/L. The average Oxidation Reduction Potential (ORP) of -79.26 mV indicates that the lake is in a reduced state and signifies that much of the dead and decaying material in the water would be slowly broken down and decomposed. Low ORP values indicate that the compound in the water is available in reduced form, which is more toxic. Our diel DO measurement show that sunlight intensity was effective in increasing oxygen concentration in the lake.
Fragmentation Evaluation of Some Selected Mudrock Indiced by Physical and Mineralogical Properties
Authors: Misbahudin  , Perdana P R D , Fatimah D Y , Amanda F F , Kusumastuti D P , Wicaksono B , Chairat A S N
Published: October 2023

Not many mudrock in Indonesia have been evaluated for slaking characteristics. Mudrock disintegrates rapidly when interacting with the atmosphere and hydrosphere. This research investigates the fragmentation of slaked claystone from the Kerek Formation. These formations are known for causing road, slope, and land-strengthening engineering problems along Jalan Semarang-Bawen, Middle Java, Indonesia. In this research, the method includes quantitative analysis of rock slaking level, which collides with the physical and mineralogical properties of the rocks. The slaking test with natural exposure for four cycles was carried out on as many as five samples. It is found the durability parameter value for all samples generally shows a slight difference. The durability index and Fragment Size Distribution Ratio in the 4-month cycle may be considered to evaluate the degree of fragmentation of material mudrock. RGL.0708.10 have an average DIR of 11.81%, and RGI.0908.1 is 2.18%. The value of FSDRatio
for RGI.0908.2, RGL.0908.1, RGI.0908.1, and RGI.0708.3 is 1.00, whereas RGI.0708.10 is 0.9997. The indices in this research can be projected and considered to be used in another formation sample with engineering problems. The mineralogical composition of smectite minerals does not show a significant relationship to affect the fragmentation of mudrock with R2 .0.268 in month-4 for the DIR
and 0.1322 for the FSDRatio
. On the microscopic texture of the sample, there is the presence of calcite minerals, and a modest relationship exists between calcite content and its effect on the fragmentation of mudrock with R2 for DR
and FSDRatio
, respectively 0.6797 and 0.4732. In addition, physical properties such as natural water content highly influence mudrock’s durability with R2 for DIR
and FSDRatio
, respectively 0.8321 and 0.9023.
Rain Scanner Radar and Optical Flow Combination For Early Identification of The Incoming Bow Echo Heavy Precipitation
Authors: Nugroho G A , Syahrul  , Maryadi E , Rahmawati A , Sinatra T , Indrawati A , Cholianawati N , Awaludin A
Published: October 2023

In this study, heavy precipitation in the form of bow echo is observed, identified, and tracked using a rain scanner and optical flow method. Two case studies of bow echoes with a range of properties from 15 to 33 km were observed in the afternoon on 1st February and 4th February 2021. The rain scanner developed based on X-band radar could obtain the first detection of the bow echo shape. The difference between these two bow echoes events is from their initiation. The first bow echo cases are initiated from weakly organized cells. Meanwhile, the second case of bow echo is initiated from a squall line event. Bow echo is initially observed in the western part of Bandung city. Approximately twenty minutes after the first detection, the bow echo passed the center of Bandung city. Image processing using edge detection could track the bow echo from the radar data. Applied Lucas-Kanade optical flow was then used to retrieve the bow echo movement. Vector flow from optical flow showed the dominant movement toward the east direction in both case studies. A simple method to predict the incoming time of the bow echo using the estimated speed from vector flow and the image translation is also presented.
Evaluation of coastal erosion by using Landsat data in Ca Mau Cape, Ngoc Hien District, Ca Mau Province
Authors: Huan V D , Dinh P T
Published: October 2023

Coastal erosion as well as loss of aquaculture, cultivated and residential lands are of great concern in the Mekong Delta, especially in the Ca Mau Cape region. Historical map data and remote sensing images such as Landsat data combined with GPS field surveys are the optimal methods for assessing shoreline changes including coastal erosion and sedimentation. The 57-year coastline change during the period from 1965 to 2022 has been described through the processing of topographic map data published in 1965 and a series of Landsat-1 to Landsat-8 images collected in 1973, 1993, 2003, and 2022. The study found that the northeast of the study area in Cho Thu hamlet, Tam Giang Tay commune was the place where the largest erosion reached an annual average of 42.4 m/year. Due to the development program of afforestation, largest sediment reaches an annual average of 88.7 m/year in Ca Mau Cape National Park in Lach Vam hamlet, Dat Mui commune. However, during the 57-year period, coastal erosion has caused a loss of 1,714 hectares of land or 2.60% of the total area. Results from this work also suggest that the accuracy of the shoreline studies should be improved by using higher satellite data spatial resolution and the GPS system with dual frequencies for Real-time Kinematics (RTK) for coordinate positioning measurement.
Assessment of livelihood vulnerability to climate change in Phu Hoa district, Phu Yen Province, Vietnam
Authors: Nguyen A T T , Nguyen Q N T , Au N H
Published: October 2023

This study aims to assess the livelihood vulnerability in Phu Hoa district, Phu Yen Province, which is located in Vietnam’s southern middle coastal areas. Climate change has strongly impacted coastal areas and threatened the living conditions there. Using the Livelihood Vulnerability Index (LVI), 200 local households were surveyed to determine the level of livelihood vulnerability in Phu Hoa district. In the results, LVI increased from 0 to 0.4. The values indicated that household characteristics are the least vulnerable of the choosing factors (0.114), followed in ascending order by water source (0.230), food (0.237), social network (0.238), health (0.271), livelihood strategies (0.370), natural disasters and climate change (0.399). The overall LVI in Phu Hoa district reached a moderate level of 0.270. It is expected that the study will serve as a reference document that provides administrators and the community with information to proactively adapt and develop policies and strategies to support and mitigate the effects of natural disasters.
Surface chemistry analysis of acidified and nickel impregnated carbon for desulfurization of fuels
Authors: Bhattacharjee T S , Ghadge S , Khilari R , Ingole T N , Janrao G S , Godage P S , Gole S P , Hussian M M
Published: October 2023

Emission norms tend to reduce sulfur content in transport fuels to 10ppm. Considering this new method like adsorptive desulfurization are widely researched. The main motive in adsorptive desulfurization is to selectively adsorb Dibenzothiophene (DBT) and 4,6-DimethylDBT. Considering this adsorbent with nickel impregnation and acidic surface functionalities were developed. Topographical and surface chemical features were studied of developed carbon adsorbents. Presence of carboxylic surface functionalities and reduced solid nickel was confirmed on adsorbents surfaces. In addition to this formation of nickel complexes due to neutralization of nickel ion and carboxylic groups was confirmed. This type of adsorbents can act as potential adsorbents for adsorption of DBT and 4,6-dimethyl DBT.
Bulk metallic glass Al2Ca from a biomedical application viewpoint: A molecular dynamics study
Authors: Shankar A. , Bhatt N. K.
Published: October 2023

Molecular dynamics simulations were performed to investigate the glass transition temperature (Tg) and mechanical properties of Al–Ca-based bulk metallic glass (BMG), Al2Ca. The second-neighbour modified embedded atom method potential was used to simulate the system. We estimate the Tg between 600 to 660 K. To ensure the glassy state of the studied material, the total radial distribution function (RDF) has been calculated from 300 to 1500 K. Partial RDF for Al, Ca, and Al–Ca subsystems are also calculated. Elastic properties including bulk modulus, compressibility, Young’s modulus, shear modulus, tensile yield strength and Poisson ratio are calculated. From the obtained data of elastic constants, it is concluded that Al2Ca BMG can be the potential material to be used in the biomedical field.
Experimental Investigation of SPIF Process for Conical Frustum
Authors: Patel Hiteshkumar , Surani Kapil
Published: October 2023

In sheet metal industries, single point incremental forming (SPIF) is a popular technology for quick prototyping and small series manufacturing techniques. In producing specific components with complicated geometries, the technique has become known for its flexibility, effectiveness, and simplicity of usage. The objective of this research work is to carry out the numerical investigation of the SPIF process to study the effect of different parameters on the formability for truncated cone. Al 1060 grade of aluminium is used for this study which is commonly used for kitchenware, reflectors, electronic components etc; where strength is not a major concern. Three dimensional models were developed for different set of parameters using commercial finite element software ABAQUS 6.13 with Dynamic/Explicit solver using solid mechanics model. Taguchi analysis has been carried out to find the effect of parameters (Tool rotational speed, Feed, Step size, Tool diameter and Wall angle) on thickness reduction. Each parameter was varied for three levels and L9 orthogonal array was used. The ANOVA tool has been used to summarize the contribution of each variable. Results have been compared with reported experimental results for validation. The process modelling is concluded with a brief overview of approaches for improving part quality.
Sublattice imbalance of states in graphene nanoflakes
Authors: Yorikawa H
Published: October 2023

The energy states of π-electrons in a graphene nanoflake obtained from graphene, a well-known bipartite lattice or honeycomb lattice of carbon atoms, are studied using the tight-binding method. It is reported that the sublattice imbalance ΔN of the entire graphene nanoflake including vacancy clusters, which characterizes the electronic states, consists of those of the outer and inner edges. In nonzero-energy states, the electrons are evenly distributed between the sublattices A and B, regardless of the value of ΔN. In contrast, zero-energy states are ∣ΔN∣-fold degenerate states where the electrons are unevenly distributed on either sublattice A or sublattice B. Occasionally, large or specific graphene nanoflakes have substantial zero-energy states, which are mixed states of the nonzero-energy states and zero-energy states.
Evaluating optimal cultivation sites for microalgae as a sustainable biofuel energy resource
Authors: Arsalan Syed , Iqbal Muhammad Jawed
Published: October 2023

Microalgae are promising candidates for the production of sustainable biofuels due to their high productivity, ability to grow in diverse environments, and carbon capture potential. However, the selection of suitable cultivation sites is crucial to achieve efficient and sustainable microalgae cultivation for biofuel production. This study discusses the evaluation of optimal cultivation sites for microalgae as a sustainable biofuel energy resource, with a focus on the naturally favorable conditions for microalgae cultivation in district Gwadar, Pakistan. The global demand for renewable energy sources has increased due to the rising energy crisis, and microalgae has emerged as an efficient source of biofuel on a large scale. The study utilizes geographic information systems to highlight suitable microalgae cultivation areas in district Gwadar. The results indicate that district Gwadar has the potential to overcome the energy crisis by cultivating microalgae as a biofuel energy source. The research provides a promising idea for designing a master plan to install a microalgae cultivation system in the highlighted sites for the concerned authorities.
Geometric local systems on very general curves and isomonodromy
Authors: Landesman Aaron , Litt Daniel
Published: October 2023

We show that the minimum rank of a non-isotrivial local system of geometric origin on a suitably general

n
n

-pointed curve of genus

g
g

is at least

2

g
+
1

2\sqrt {g+1}

. We apply this result to resolve conjectures of Esnault-Kerz and Budur-Wang. The main input is an analysis of stability properties of flat vector bundles under isomonodromic deformations, which additionally answers questions of Biswas, Heu, and Hurtubise.
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease
Authors: Velissari Rania , Ilieva Mirolyuba , Dao James , Miller Henry E , Madsen Jens Hedelund , Gorodkin Jan , Aikawa Masanori , Ishii Hideshi , Uchida Shizuka
Published: October 2023

The cases of inflammatory bowel disease (IBD) are increasing rapidly around the world. Due to the multifactorial causes of IBD, there is an urgent need to understand the pathogenesis of IBD. As such, the usage of high-throughput techniques to profile genetic mutations, microbiome environments, transcriptome and proteome (e.g. lipidome) is increasing to understand the molecular changes associated with IBD, including two major etiologies of IBD: Crohn disease (CD) and ulcerative colitis (UC). In the case of transcriptome data, RNA sequencing (RNA-seq) technique is used frequently. However, only protein-coding genes are analyzed, leaving behind all other RNAs, including non-coding RNAs (ncRNAs) to be unexplored. Among these ncRNAs, long non-coding RNAs (lncRNAs) may hold keys to understand the pathogenesis of IBD as lncRNAs are expressed in a cell/tissue-specific manner and dysregulated in a disease, such as IBD. However, it is rare that RNA-seq data are analyzed for lncRNAs. To fill this gap in knowledge, we re-analyzed RNA-seq data of CD and UC patients compared with the healthy donors to dissect the expression profiles of lncRNA genes. As inflammation plays key roles in the pathogenesis of IBD, we conducted loss-of-function experiments to provide functional data of IBD-specific lncRNA, lung cancer associated transcript 1 (LUCAT1), in an in vitro model of macrophage polarization. To further facilitate the lncRNA research in IBD, we built a web database, IBDB (https://ibd-db.shinyapps.io/IBDB/), to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in IBD patients compared with healthy donors.
G2GSnake: a Snakemake workflow for host–pathogen genomic association studies
Authors: Xu Zhi Ming , Naret Olivier , Oumelloul Mariam Ait , Fellay Jacques
Published: October 2023

Joint analyses of paired host and pathogen genome sequences have the potential to enhance our understanding of host–pathogen interactions. A systematic approach to conduct such a joint analysis is through a “genome-to-genome” (G2G) association study, which involves testing for associations between all host and pathogen genetic variants. Significant associations reveal host genetic factors that might drive pathogen variation, highlighting biological mechanisms likely to be involved in host control and pathogen escape. Here, we present a Snakemake workflow that allows researchers to conduct G2G studies in a reproducible and scalable manner. In addition, we have developed an intuitive R Shiny application that generates custom summaries of the results, enabling users to derive relevant insights.

Availability and implementation

G2GSnake is freely available at: https://github.com/zmx21/G2GSnake under the MIT license.
UDock2: interactive real-time multi-body protein–protein docking software
Authors: Plateau-Holleville Cyprien , Guionnière Simon , Boyer Benjamin , Jiménez-Garcia Brian , Levieux Guillaume , Mérillou Stéphane , Maria Maxime , Montes Matthieu
Published: October 2023

Motivation

Protein–protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software.

Results

This article presents an interactive multi-body protein–protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties.

Availability and implementation

UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.
Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces
Authors: Jang Hyojung , Park Solha , Koh Hyunwook
Published: October 2023

It is a central goal of human microbiome studies to see the roles of the microbiome as a mediator that transmits environmental, behavioral, or medical exposures to health or disease outcomes. Yet, mediation analysis is not used as much as it should be. One reason is because of the lack of carefully planned routines, compilers, and automated computing systems for microbiome mediation analysis (MiMed) to perform a series of data processing, diversity calculation, data normalization, downstream data analysis, and visualizations. Many researchers in various disciplines (e.g. clinicians, public health practitioners, and biologists) are not also familiar with related statistical methods and programming languages on command-line interfaces. Thus, in this article, we introduce a web cloud computing platform, named as MiMed, that enables comprehensive MiMed on user-friendly web interfaces. The main features of MiMed are as follows. First, MiMed can survey the microbiome in various spheres (i) as a whole microbial ecosystem using different ecological measures (e.g. alpha- and beta-diversity indices) or (ii) as individual microbial taxa (e.g. phyla, classes, orders, families, genera, and species) using different data normalization methods. Second, MiMed enables covariate-adjusted analysis to control for potential confounding factors (e.g. age and gender), which is essential to enhance the causality of the results, especially for observational studies. Third, MiMed enables a breadth of statistical inferences in both mediation effect estimation and significance testing. Fourth, MiMed provides flexible and easy-to-use data processing and analytic modules and creates nice graphical representations. Finally, MiMed employs ChatGPT to search for what has been known about the microbial taxa that are found significantly as mediators using artificial intelligence technologies. For demonstration purposes, we applied MiMed to the study on the mediating roles of oral microbiome in subgingival niches between e-cigarette smoking and gingival inflammation. MiMed is freely available on our web server (http://mimed.micloud.kr).
Harmonization of outcomes in epidermolysis bullosa: report of the Core Outcome Sets for Epidermolysis Bullosa (COSEB) kick-off meeting
Authors: Korte Eva W H , Spuls Phyllis I , van den Akker Peter C , Kiritsi Dimitra , Laimer Martin , Pasmooij Anna M G , Riedl Rainer , Vroom Elizabeth , Wally Verena , Welponer Tobias , Bolling Maria C
Published: October 2023

The COSEB kick-off meeting was organized in April 2023, and highlighted the stakeholder perspectives on the unmet and urgent need to work towards reasonable harmonization of outcome measurement in epidermolysis bullosa (EB) by developing core outcome sets for the different EB types. Standardized and uniform outcome assessment holds great promise to reduce selective reporting, improve the comparability and pooling of treatment outcomes, and enhance the efficacy of future research in EB.
Emerging evidence on the role of breast microbiota on the development of breast cancer in high-risk patients
Authors: Actis Silvia , Cazzaniga Massimiliano , Bounous Valentina Elisabetta , D’Alonzo Marta , Rosso Roberta , Accomasso Francesca , Minella Carola , Biglia Nicoletta
Published: October 2023

Cancer is a multi-factorial disease, and the etiology of breast cancer (BC) is due to a combination of both genetic and environmental factors. Breast tissue shows a unique microbiota, Proteobacteria and Firmicutes are the most abundant bacteria in breast tissue, and several studies have shown that the microbiota of healthy breast differs from that of BC. Breast microbiota appears to be correlated with different characteristics of the tumor, and prognostic clinicopathologic features. It also appears that there are subtle differences between the microbial profiles of the healthy control and high-risk patients. Genetic predisposition is an extremely important risk factor for BC. BRCA1/2 germline mutations and Li-Fraumeni syndrome are DNA repair deficiency syndromes inherited as autosomal dominant characters that substantially increase the risk of BC. These syndromes exhibit incomplete penetrance of BC expression in carrier subjects. The action of breast microbiota on carcinogenesis might explain why women with a mutation develop cancer and others do not. Among the potential biological pathways through which the breast microbiota may affect tumorigenesis, the most relevant appear to be DNA damage caused by colibactin and other bacterial-derived genotoxins, β-glucuronidase-mediated estrogen deconjugation and reactivation, and HPV-mediated cancer susceptibility. In conclusion, in patients with a genetic predisposition, an unfavorable breast microbiota may be co-responsible for the onset of BC. Prospectively, the ability to modulate the microbiota may have an impact on disease onset and progression in patients at high risk for BC.
Diagnostic miRNA Signatures in Paired Tumor, Plasma, and Urine Specimens From Renal Cell Carcinoma Patients
Authors: Bustos Matias A , Gottlieb Josh , Choe Jane , Suyeon Ryu , Lin Selena Y , Allen Warren M , Krasne David L , Wilson Timothy G , Hoon Dave S B , Linehan Jennifer A
Published: October 2023

Background

The incidence of patients diagnosed with renal cell carcinoma (RCC) is increasing. There are no approved biofluid biomarkers for routine diagnosis of RCC patients. This retrospective study aims to identify cell-free microRNA (cfmiR) signatures in urine samples that can be utilized as biomarkers for early diagnosis of sporadic RCC patients.

Methods

Tissue, plasma, and urine samples (n = 221) from 56 sporadic RCC patients and respective normal healthy donors were profiled for 2083 microRNAs (miRs) using the next-generation sequencing-based HTG EdgeSeq miR Whole Transcriptome Assay. DESeq2 (FC |1.2|, false discovery rate <0.05) was performed to identify differentially expressed miRs. Data from RCC tissue samples of The Cancer Genome Atlas database were used for miR validation.

Results

We found a 10-miR signature that distinguished RCC tissues from remote normal kidney tissue or benign kidney lesion samples. Additionally, we identified subtype-specific miRs (miR-122-5p, miR-210-3p, and miR-21-3p) and miRs specific for all RCC subtypes (miR-106b-3p, miR-629-5p, and miR-885-5p). We observed that miR-155-5p was associated with tumor size. Using The Cancer Genome Atlas data sets, we validated the miRs found in RCC tissue samples. In plasma or urine analysis, we found cfmiRs that were consistently and significantly upregulated in RCC tissue samples. A 15-cfmiR signature was proposed in urine samples of RCC patients, of which miR-1275 was consistently upregulated in tissue, plasma, and urine samples.

Conclusions

This integrative study found diagnostic miRs/cfmiRs for RCC patients, which were validated using The Cancer Genome Atlas data sets. Distinctive cfmiR signatures found in urine may have clinical utility for the diagnosis of RCC.
Extraintestinal Manifestations of Inflammatory Bowel Disease Are Associated With Increased Biologic Cycling
Authors: Alizadeh Madeline , Ali Osman , Cross Raymond K
Published: October 2023

Background

Extraintestinal manifestations (EIMs) of inflammatory bowel disease (IBD) are a common, frequently debilitating complication of the disease. Biologics are indicated and often required in patients with EIMs to control disease; however, little is known about whether patients with EIMs cycle through more therapies than their counterparts without EIMs.

Methods

To address this question, we performed a retrospective analysis of patients enrolled in the Study of Prospective Adult Research Cohort with IBD registry seen at our University Medical Center, on data from December 2016 to January 2021. Four hundred fifty-six participants with information on EIMs and biologic use available were included, and demographic and clinical characteristics were analyzed.

Results

Three hundred thirty-eight and 118 participants without and with EIMs were identified, respectively. Those with EIMs were likelier to have biologic exposure, and cycle through more biologics, both in univariate and multivariate analyses controlling for age, disease duration, sex, corticosteroid use, and IBD type (P-value = .006). In a subanalysis of patients with Crohn’s disease (CD), EIMs were associated with increased biologic cycling in ileocolonic disease (P-value = .050).

Conclusions

To our knowledge, this is the first study assessing biologic cycling in patients with EIMs. Our findings that patients with EIMs are likelier to cycle through biologics, particularly CD patients with ileocolonic disease, highlights the need for more research on which biologics may be most effective for specific subsets of IBD patients, including those with concurrent EIMs. The presence of EIMs is a marker of harder-to-treat IBD and may indicate earlier initiation of advanced therapies.