bluuebunny/crossref_metadata_2025 huggingface dataset:
Policymakers’ perception regarding tin mining impacts on local varieties as intellectual property (case study in the Bangka Belitung islands)
Authors: Darwance D , Haryadi D
Published: July 2024

In addition to being one of the world’s leading producers of white pepper, the Bangka Belitung Islands Province, Indonesia, is also known for its abundant tin production. This implies the existence of rigorous mining activities in the region. Prior to unrestricted mining, tin could only be mined by specific companies authorized by the government. At that time, a majority of the population still worked as farmers. Moreover, mining, which was limited to specific areas, did not have a significant impact on the environmental conditions, including the various types of local varieties in this region. Besides extensive marine mining, unregulated mining has already been carried out on land, including in forests, plantations, and backyard gardens containing local plants. This research employs a juridical-empirical method, examining the interrelation between tin mining and the existence of local varieties as intellectual property, while also assessing the policymakers’ perception of the ongoing situation. The study findings indicate that a majority of policymakers acknowledge that the extensive tin mining actually impacts the existence of local varieties that have existed, both registered and unregistered.
Investigation of ballistic performance on metal-coir fiber composite laminate with variation of fiber volume fraction: Experimental and simulation
Authors: Bakri B , Naharuddin  , Mustafa  , Anwar K , Fadly M S , Wahyudi K
Published: July 2024

This paper aims to investigate the ballistic performance of metal-coir fiber composite laminate with the variation of fiber volume fraction. the experimental and simulation methode was used to analysis the ballistic performance. The variation of fiber volume fraction in coir fiber composite are 17%, 22%, and 27%. Composite laminate was produced by 3 layers including metal plate on the outer layer and coir fiber composite on the middle layer (core), and metal (steel) plate on the back. The experimental and numerical simulation results show that the fiber volume fraction of coir fiber composite in composite laminate causes unequal impact yield characteristics. The bullet projectile pushes and forms a crater in the first layer steel plate as a result of plastic deformation. The coir fiber composite in the second layer experienced delamination with the failure in the matrix, as a result of bullet impact and damage to the composite surface. The metal plate on the third layer of the laminate is pushed in the direction of the bullet producing a bulge. The effect of the volume fraction of the coir fiber composite as a layer for energy absorption is very effective so that the stress distribution is not directly transmitted to the third layer steel plate. The results of experimental tests and numerical simulations of steel plate-coir fiber composite laminate with a volume fraction of 27% which is influenced by bullet speed are able to stop bullets faster at 5.75×10−5 s with an energy absorption of 435.6 Joule. The failure mechanism that occurs from the results of experimental testing and numerical simulations is the formation of a crater in the first steel plate with the presence of petals formed around the crater and the occurrence of intralaminar failure in the composite and the formation of bulges in the third layer of metal plate due to ballistic deformation.
2D modelling of wave propagation at the Palu estuary after the 2018 tsunami
Authors: Hendra  , Tunas I G
Published: July 2024

In September 2018, the powerful and shallow earthquake with a magnitude of 7.4 rattled Sulawesi Island. This earthquake triggered a tsunami disaster in Palu Bay which caused changes in the morphology of the Palu Bay coastline. The coast along Palu Bay underwent significant changes due to the impact of the tsunami waves. Changes in the morphology of the beach also affect the characteristics and current waves that enter the mouth of the Palu River. This study aims to analyse the propagation and transformation of waves entering the Palu River estuary. Wave analysis and simulation was performed using the Surface-water modelling system (SMS) package generated from the Meteorological, Climatological, and Geophysical Agency (BMKG) wind data. Statistical analysis of wind data was carried out using Windrose Software and the Shore Protection Manual method to predict deep sea waves. This forecasting method is employed in a hybrid manner with the Weibull method to determine extreme wave heights for 50-year return periods. The simulation results using the CGWAVE model show that the maximum wave height coming from north direction approaching the mouth of the Palu River is 1.3 m. Furthermore, the wave height coming from the northwest approaching the Palu River estuary is 0.8 m.
Biodiversity based on ecosystem services in Morowali
Authors: Suleman S M , Edy N , Isrun  , Sabran M
Published: July 2024

Central Sulawesi is included in the Wallacean biogeographic region, which has a tropical climate and is an area that has a high diversity of organisms. The high level of unique and specific biodiversity is a wealth of natural resources that need to be preserved because it has various functions, including as a food source and life support system. One indicator that can be used to assess the status of biodiversity values is based on the value of ecosystem services. The higher the biodiversity character, the higher the ecosystem’s support function for life. This study aims to analyze the condition of biodiversity ecosystem services. The results of the analysis show that the status of ecosystem services supporting habitat and biodiversity in Morowali Regency is still high status, with a coverage area of 81% of the total area of Morowali Regency. The results of this research contribute to recommendations for restoration or conservation needed regarding the condition of biodiversity ecosystem services in Morowali Regency.
Estimation of bed load sediment rate at sabo dam 2 bangga river
Authors: Rustiati NB , Lipu S , Andiese VM , Kaseng W
Published: July 2024

The flood that occurred on November 2018 was a sediment disaster in the upstream of the Bangga River which resulted in the entire village being buried by sediment. The current research will estimate the volume of bed sediment transport at Sabo Dam. Measurements of the width of the riverbed were carried out on the specified river section. Measurements were carried out along 300 m and divided by 50 m per segment. Data obtained from primary data and secondary data are processed to obtain parameters that will be used when calculating the distribution of sediment. So, it can be seen that the characteristics of sediment grains in the 18 samples have grain sizes that are not much different. Based on the average data, segment 1, 2 and 3 can be classified as having poor gradation gravel, sand from gravel fragments, little/no fine grains. From the results of sieve analysis testing, it can be seen that the characteristics of sediments are dominated by sand and gravel. The bed sediment has a size of d50 0.2 mm - 12 mm and d90 0.44 mm - 50 mm. which is spread along the Bangga River Sabo Dam.
Infiltration rate in various land covers in Beka Village, Sigi Regency
Authors: Andiese V W , Tunas I G
Published: July 2024

Changes in Land Use that result in increased direct surface runoff due to reduced places for rainwater absorption. The amount of water absorption into the soil or infiltration can be included in the flood calculations to design and plan water structures. Beka Village is in Sigi Regency, Central Sulawesi Province. This research aims to determine the magnitude of the infiltration rate that occurs in Beka Village and examine the soil’s physical properties that are related to the infiltration rate. This research was carried out on three types of land cover, namely mixed field land, forest, and settlement areas, each taken under two conditions, namely dry conditions and conditions after rain. Infiltration measurements were carried out using a Double Ring Infiltrometer measuring instrument and analyzed using the Horton equation. Undisturbed soil samples were taken at each land cover and condition using paralon pipes to determine the physical properties of the soil. The rate of infiltration in the three land covers with each condition is that for dry soil conditions on forest land, it is in the relatively fast category (6.3 - 12.7 cm/hour); in the mixed field and settlement areas it is in the medium category (2 - 6.3 cm/hour). Meanwhile, wet soil conditions in forest land and mixed field fall into the medium criteria (2 - 6.3 cm/hour), and in settlement areas fall into the slow criteria (0.5 - 2 cm/hour).
Effects of date fruit consumption and vitamin D against increased hb levels of pregnant women
Authors: Sumarni  , Muthiah A , Oktaviani D
Published: July 2024

One of the health problems in pregnant women is anemia. Anemia in pregnant women can harm the mother and fetus conceived. In pregnant women, anemia can cause abortion, premature birth, antepartum hemorrhage, and low fetal birth weight. This study aims to determine the effect of dates and vitamin D consumption on increasing hemoglobin levels in pregnant women. This research was carried out in the working area of the Pantoloan Health Center in Palu City. The research method used is quasi-experimental with the group pre-test-post-test method. The research results from 20 respondents generally showed increased hemoglobin levels in pregnant women. This study concludes that there is an effect of the consumption of dates and vitamin D on increasing Hb levels of pregnant women.
Potential flooding in the APT Pranoto Samarinda Airport area as a result of the airport runway extension
Authors: Eko W , Pitojo T J , Suhartanto E , Sholichin M , Limantara L M , Sutapa I W
Published: July 2024

Samarinda City has the Aji Pangeran Tumenggung (APT) International Airport Pranoto in the Karangmumus watershed prone to flooding. The planned extension of the runway for approximately 1 km will cross over the Karangmumus River. This study aims to determine the potential for flooding in the APT Pranoto Airport area and to determine the planned utilization of the Karangmumus Hulu Dam. The methodology used includes design rain analysis. Rain data is sourced from the BMKG Temindung Station, Samarinda City (1978-2021). The flood discharge design was analyzed using the Limantara method. Flood tracking was carried out on the Upper Karangmumus River channel and its tributaries, as well as on the planned Upper Karangmumus Dam, using HEC-RAS 6.1 software. Flood exposure map analysis is based on LiDAR maps. The results showed that 2 hours after the rain, floods had entered the airport area, both from the Karangmumus River and its tributaries. The development of the dam in the Upper Karangmumus can reduce flooding that enters the airport area. The research recommendations are in the form: that it is necessary to build flood control upstream of the Karangmumus watershed and to normalize and arrange the Karangmumus River channel in the APT Pranoto Airport area.
Identification of The Need For Construction Expert In Donggala Regency
Authors: Labombang M. , Mangitung D.M. , Fahruddin F.
Published: July 2024

Construction Experts are one of the important elements that affect the continuity and smoothness of a construction project. Along with the increasing growth in construction services in Central Sulawesi Province, especially in Donggala Regency, the need for workers has also increased, mainly competent construction experts. However, the current conditions are relatively not ideal due to the lack of experts and skilled workers to support the rapid growth of construction services. So this research was conducted with the aim of identifying the need for construction experts in Donggala Regency in the next 5 years. The data collection method used in this study was a research questionnaire given to contractors who had worked on work packages in Donggala Regency in the last 3 years. Furthermore, the data obtained was processed using descriptive statistical methods and regression linear simple with help software SPSS. The results of the research based on calculations and analysis of the estimated need for construction experts in Donggala Regency in 2022-2027, it can be concluded that the relationship between the need for experts and the availability of experts has a perfect level and not influenced by other variables. With the regression method linear simple processed using software SPSS version 24 assuming an increase in the need for experts each year by 15%, the need for construction experts in Donggala Regency in 2027 is 44 people. This number can still be fulfilled based on the results of research through questionnaires to determine the availability of construction experts in Donggala Regency. The number of available construction experts in Donggala Regency in 2027 is 165 people.
Slope stability analysis at Layana view residence with finite element method
Authors: Irvan A , Tawil S , Rahayu A
Published: July 2024

The Palu City area, especially Layana Village, is characterized by hilly topography with poor soil conditions, especially during the rainy season, so that the slopes in this area become unstable due to the shear stress of the soil mass which is unable to carry the load and water pressure. Alternatives for strengthening slopes include creating water channels, planting vegetation and repairing slopes. Building water channels and planting vegetation can reduce the hydrostatic pressure of soil shear strength, while slope improvements are carried out by reducing the driving force that causes landslides. So that a stable slope safety factor value is obtained. Accurate results for slope stability continue to be developed. In this research, field testing took the form of geoelectric investigations to determine soil resistivity values. The calculation of slope safety factors was analyzed using the Geostudio application, Slope/W sub program by entering soil property index data (water content, soil volume weight)), and soil shear strength parameters (cohesion value, soil friction angle) obtained from laboratory test results.
Redesign of the electrical power and lighting network at ice cream parlor located in the city of Quito
Authors: Zurita Kevin , Segura Juan , Topón-Visarrea Blanca , Barriga Bryan , Ahmed Gutiérrez Edgar
Published: July 2024

This article proposes the redesign of the electrical power and lighting network in an Ice Cream Parlor located in the city of Quito to ensure continuity in the electrical service and a luminous level according to the UNE 12464.1 Standard, established in the country. For this purpose, a survey of all the electrical load installed in the organization was carried out, where the nominal parameters of each equipment were identified with the help of the nameplate of each one of them. Using the specifications of the Ecuadorian Construction Standard (NEC) and the data obtained from the electrical load survey, five (5) circuits for outlets were proposed, considering a possible expansion of small equipment and the ten (10) maximum outlets established by the aforementioned standard. Additionally, four (4) circuits were proposed to feed the power load. With respect to the lighting network, the DIAlux software is used to determine the number of lamps, luminaires and their location to comply with the luminous level indicated. Therefore, it was necessary to propose six (6) circuits in order not to exceed the fifteen (15) lighting points established by the NEC. For each circuit, the following was calculated: conductor cross section, overcurrent protection, type of insulation and the diameter of the corresponding conduit to protect the conductors. Finally, quotations were made for the materials required for the implementation of the project. From these, an organization is selected, based on the availability of the necessary materials, their cost and accessibility, compared to other suppliers. The total amount of the proposal is US$2,518.24.
Feasibility analysis of charging stations for electric vehicles. Case study route E35, Loja-Cuenca in Ecuador
Authors: Méndez-Jaramillo Edgar , Coronel-Villavicencio Iván , Paccha-Herrera Edwin , Briceño-Martínez Bryan , Tapia-Viñan Erik , Camacho-Muñoz Jefferson
Published: July 2024

This paper analyzes a methodology to identify suitable charging stations for electric vehicles (EV) and locate them on the E35 Pan-American Highway, between the cities of Loja and Cuenca, in Ecuador, to promote the use of EVs and reduce dependence on fossil fuels. The study employs several selection criteria, such as government and international regulations, to determine the best type of charging station for the route. The literature review reveals that international standards shape the infrastructure of charging stations in Ecuador, and a fast-charging station with an-output power of 50 kW in mode 4, this concept refers to the arrangement in which the transformer is stationary at the charging point, and the connection is made exclusively on the vehicle’s charging side; furthermore, it involves the use of significantly high charging capacities. The station satisfies international standard connectors for charging most EVs in use in Ecuador. In addition, the methodology analyzes several factors related to the environment, economy, society, electricity, geography, and road quality to identify the most suitable locations for charging stations. The analysis concludes that only four of the fourteen locations analyzed meet the requirements for suitable areas. It also highlights that the three-phase electric grid shared by two electric companies (EERSSA and CENTROSUR) meets the quality standards. EERSSA only has a three-phase network in Carigán and Saraguro, which are the two cities with the highest population or energy use.
Analysis and study of the factors involved in the accident rate of vehicles, during the period 2017-2022 in the province of Pichincha, Ecuador.
Authors: Caizaluisa David , Dávila Joel , Molina Paúl , Rivera Néstor
Published: July 2024

In this work, the factors involved in the incidence of vehicular accidents during the period 2017-2022 in the province of Pichincha, Ecuador, were studied with the purpose of identifying the most influential variables in traffic accidents. From the methodological point of view, an analytical and descriptive research approach was adopted. The methodological process started with an exploratory study based on data provided by the National Traffic Agency (ANT), which records the accidents that occurred from January 2017, to December 2022. For the statistical analysis of the data, a free software tool was used. After carrying out an exhaustive analysis, it was concluded that there is no significant variation by month or by time slot in the incidence of accidents. The primary cause identified was speeding, followed by disregarding traffic signals, with the third cause being picking up and dropping off passengers in unauthorized areas. Additionally, it was observed that the canton of Quito had a higher implication in terms of accident frequency. Throughout the study period, a decrease in the incidence of accidents was noted until 2020. However, an upturn in the trend was observed in 2021, although 14 fewer accidents were recorded in 2022 compared to 2021. The completion of this study is crucial as understanding the causes of accidents enables the implementation of measures to enhance road safety, thereby reducing the likelihood of accidents and safeguarding lives. Identifying the underlying causes of accidents can contribute significantly to preventing injuries and fatalities.
Thermal instability in an inclined fluid layer subjected to Couette–Poiseuille flow
Authors: Batra Akshita , Kaur Gurpreet , Bajaj Renu
Published: July 2024

The present work deals with the onset of thermal instability in an inclined fluid layer subjected to Couette–Poiseuille flow. We consider the configuration in which one boundary is maintained at a constant temperature and the other boundary is imposed with a constant heat flux. The collocation method, based on Chebyshev polynomials, is used to discuss the instability of the flow with respect to the thermal Rayleigh number. It is found that there exists a value of the angle of inclination below which the instability sets in as longitudinal rolls, and the critical value of the Rayleigh number remains unaffected by superimposed Couette–Poiseuille flow. However, for angles of inclination greater than this threshold value, the critical mode of instability is transverse mode, and the critical value of the Rayleigh number is significantly affected by the superposition of Couette–Poiseuille flow. Further, the onset of instability also depends upon the Prandtl number of the fluid.
Datacube segmentation via deep spectral clustering
Authors: Bombini Alessandro , García-Avello Bofías Fernando , Bracci Caterina , Ginolfi Michele , Ruberto Chiara
Published: July 2024

Extended vision techniques are ubiquitous in physics. However, the data cubes steaming from such analysis often pose a challenge in their interpretation, due to the intrinsic difficulty in discerning the relevant information from the spectra composing the data cube. Furthermore, the huge dimensionality of data cube spectra poses a complex task in its statistical interpretation; nevertheless, this complexity contains a massive amount of statistical information that can be exploited in an unsupervised manner to outline some essential properties of the case study at hand, e.g. it is possible to obtain an image segmentation via (deep) clustering of data-cube’s spectra, performed in a suitably defined low-dimensional embedding space. To tackle this topic, we explore the possibility of applying unsupervised clustering methods in encoded space, i.e. perform deep clustering on the spectral properties of datacube pixels. A statistical dimensional reduction is performed by an ad hoc trained (variational) AutoEncoder, in charge of mapping spectra into lower dimensional metric spaces, while the clustering process is performed by a (learnable) iterative K-means clustering algorithm. We apply this technique to two different use cases, of different physical origins: a set of macro mapping x-ray fluorescence (MA-XRF) synthetic data on pictorial artworks, and a dataset of simulated astrophysical observations.
Systematic review of climate change induced health impacts facing Malaysia: gaps in research
Authors: Pandya-Wood Raksha , Azhari Azliyana , Johar Hamimatunnisa , Johns-Putra Adeline , Muhamad Nurfashareena , Su Tin Tin
Published: July 2024

In Malaysia, climate change typically manifests as frequent and extreme weather events. The effects on human health of such meteorological and ecological imbalances are multiple and diverse. Urgent attention is needed to address the health-related threats facing Malaysia as a result of climate change. This systematic review (SR) of available evidence adopted Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and identified and assessed a broad range of English language empirical, published research and excluded grey literature. Bias and quality of articles was assessed using Mixed Methods Assessment Tool. Using the search engines Scopus, PubMed, Ovid EMBASE, Web of Science, and EBSCO Host Medline, n = 374 results were yielded. Of these, after checking, n = 23 studies were examined. The studies can be grouped into three climatic themes
Exposure
,
Outcomes
and
Planning
. Our review confirms that urgent funding and investment is needed for larger-scale intervention studies on each of these themes. We observed a scarcity of high-quality empirical research, a preponderance of modelling studies to project and simulate scenarios, and a limited number of qualitative studies. Particular gaps in knowledge exist on climate change impacts on health in population groups in terms of demographic intersections to support these epidemiological data and simulation pathways. Furthermore, there was an absence of data on various topics concerning the effects of climate change on, for example, mental health, women, older people and/or the effects of displacement. The limitations of this work include accepting only English language publications and presenting only empirical studies. The study was not funded but was managed by the Monash Climate Change Communication Research node. This SR was registered on PROSPERO ID: CRD42023431868.
On Singularity Properties of Word Maps and Applications to Probabilistic Waring Type Problems
Authors: Glazer Itay , Hendel Yotam
Published: July 2024

We study singularity properties of word maps on semisimple Lie algebras, semisimple algebraic groups and matrix algebras and obtain various applications to random walks induced by word measures on compact

p
p

-adic groups.

Given a word

w
w

in a free Lie algebra

L

r

\mathcal {L}_{r}

, it induces a word map

φ

w

:

g

r

→

g

\varphi _{w}:\mathfrak {g}^{r}\rightarrow \mathfrak {g}

for every semisimple Lie algebra

g

\mathfrak {g}

. Given two words

w

1

∈

L

r

1

w_{1}\in \mathcal {L}_{r_{1}}

and

w

2

∈

L

r

2

w_{2}\in \mathcal {L}_{r_{2}}

, we define and study the convolution of the corresponding word maps

φ

w

1

∗

φ

w

2

≔

φ

w

1

+

φ

w

2

:

g

r

1

+

r

2

→

g

\varphi _{w_{1}}*\varphi _{w_{2}}≔\varphi _{w_{1}}+\varphi _{w_{2}}:\mathfrak {g}^{r_{1}+r_{2}}\rightarrow \mathfrak {g}

.

By introducing new degeneration techniques, we show that for any word

w
∈

L

r

w\in \mathcal {L}_{r}

of degree

d
d

, and any simple Lie algebra

g

\mathfrak {g}

with

φ

w

(

g

r

)
≠
0

\varphi _{w}(\mathfrak {g}^{r})\neq 0

, one obtains a flat morphism with reduced fibers of rational singularities (abbreviated an (FRS) morphism) after taking

O
(

d

4

)

O(d^{4})

self-convolutions of

φ

w

\varphi _{w}

. Similar results are obtained for matrix word maps. We deduce that a group word map of length

ℓ
\ell

becomes (FRS), locally around identity, after

O
(

ℓ

4

)

O(\ell ^{4})

self-convolutions, for every semisimple algebraic group

G
_

\underline {G}

. We furthermore provide uniform lower bounds on the log canonical threshold of the fibers of Lie algebra, matrix and group word maps. For the commutator word

w

0

=
[
X
,
Y
]

w_{0}=[X,Y]

, we show that

φ

w

0

∗
4

\varphi _{w_{0}}^{*4}

is (FRS) for any semisimple Lie algebra, improving a result of Aizenbud-Avni, and obtaining applications in representation growth of compact

p
p

-adic and arithmetic groups.

The singularity properties we consider, such as the (FRS) property, are intimately connected to the point count of fibers over finite rings of the form

Z

/

p

k

Z

\mathbb {Z}/p^{k}\mathbb {Z}

. This allows us to relate them to properties of some natural families of random walks on finite and compact

p
p

-adic groups. We explore these connections, characterizing some of the singularity properties discussed in probabilistic terms, and provide applications to

p
p

-adic probabilistic Waring type problems.
Accent Bias in Professional Evaluations: A Conceptual Replication Study in Brazil
Authors: Teló Cesar , Silveira Rosane , Marcelino Ana Flávia Boeing , O’Brien Mary G
Published: July 2024

Evidence from Canada suggests that accent bias can be moderated by speakers’ demonstrated job-relevant performance and the prestige level of their occupation (Teló et al. 2022). In this study, we replicated Teló et al.’s (2022) work in Brazil. First language (L1) Brazilian Portuguese-speaking listeners rated audio recordings of L1 Brazilian Portuguese and L1 Spanish speakers along continua capturing one professional (competence), one experiential (treatment preference), and one linguistic (comprehensibility) dimension. Our findings challenge the notion of consistent bias, as listeners did not uniformly perceive L1 Brazilian Portuguese speakers as more competent and comprehensible than L1 Spanish speakers, and, in fact, generally preferred treatment provided by L1 Spanish speakers. Complex interactions provided a nuanced account of listeners’ evaluations, revealing, among other patterns, that demonstrated performance level and job prestige affected the evaluated dimensions differently depending on the speaker’s L1. This replication further expands the initial study by examining the role of four listener variables as predictors of speaker ratings. Greater listener familiarity with the context depicted in the script was associated with the assignment of higher ratings overall.
GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach
Authors: Zhu Cheng , Zhang Chengyun , Shang Tianfeng , Zhang Chenhao , Zhai Silong , Cao Lujing , Xu Zhenyu , Su Zhihao , Song Ying , Su An , Li Chengxi , Duan Hongliang
Published: July 2024

Protein–peptide interactions (PPepIs) are vital to understanding cellular functions, which can facilitate the design of novel drugs. As an essential component in forming a PPepI, protein–peptide binding sites are the basis for understanding the mechanisms involved in PPepIs. Therefore, accurately identifying protein–peptide binding sites becomes a critical task. The traditional experimental methods for researching these binding sites are labor-intensive and time-consuming, and some computational tools have been invented to supplement it. However, these computational tools have limitations in generality or accuracy due to the need for ligand information, complex feature construction, or their reliance on modeling based on amino acid residues. To deal with the drawbacks of these computational algorithms, we describe a geometric attention-based network for peptide binding site identification (GAPS) in this work. The proposed model utilizes geometric feature engineering to construct atom representations and incorporates multiple attention mechanisms to update relevant biological features. In addition, the transfer learning strategy is implemented for leveraging the protein–protein binding sites information to enhance the protein–peptide binding sites recognition capability, taking into account the common structure and biological bias between proteins and peptides. Consequently, GAPS demonstrates the state-of-the-art performance and excellent robustness in this task. Moreover, our model exhibits exceptional performance across several extended experiments including predicting the apo protein–peptide, protein–cyclic peptide and the AlphaFold-predicted protein–peptide binding sites. These results confirm that the GAPS model is a powerful, versatile, stable method suitable for diverse binding site predictions.
Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining
Authors: Xiang Wenkai , Zhong Feisheng , Ni Lin , Zheng Mingyue , Li Xutong , Shi Qian , Wang Dingyan
Published: July 2024

Accurate prediction of molecular properties is fundamental in drug discovery and development, providing crucial guidance for effective drug design. A critical factor in achieving accurate molecular property prediction lies in the appropriate representation of molecular structures. Presently, prevalent deep learning–based molecular representations rely on 2D structure information as the primary molecular representation, often overlooking essential three-dimensional (3D) conformational information due to the inherent limitations of 2D structures in conveying atomic spatial relationships. In this study, we propose employing the Gram matrix as a condensed representation of 3D molecular structures and for efficient pretraining objectives. Subsequently, we leverage this matrix to construct a novel molecular representation model, Pre-GTM, which inherently encapsulates 3D information. The model accurately predicts the 3D structure of a molecule by estimating the Gram matrix. Our findings demonstrate that Pre-GTM model outperforms the baseline Graphormer model and other pretrained models in the QM9 and MoleculeNet quantitative property prediction task. The integration of the Gram matrix as a condensed representation of 3D molecular structure, incorporated into the Pre-GTM model, opens up promising avenues for its potential application across various domains of molecular research, including drug design, materials science, and chemical engineering.
Atypical intrinsic neural timescale in the left angular gyrus in Alzheimer’s disease
Authors: Murai Shota A , Mano Tatsuo , Sanes Jerome N , Watanabe Takamitsu
Published: July 2024

Alzheimer’s disease is characterized by cognitive impairment and progressive brain atrophy. Recent human neuroimaging studies reported atypical anatomical and functional changes in some regions in the default mode network in patients with Alzheimer’s disease, but which brain area of the default mode network is the key region whose atrophy disturbs the entire network activity and consequently contributes to the symptoms of the disease remains unidentified. Here, in this case–control study, we aimed to identify crucial neural regions that mediated the phenotype of Alzheimer’s disease, and as such, we examined the intrinsic neural timescales—a functional metric to evaluate the capacity to integrate diverse neural information—and grey matter volume of the regions in the default mode network using resting-state functional MRI images and structural MRI data obtained from individuals with Alzheimer’s disease and cognitively typical people. After confirming the atypically short neural timescale of the entire default mode network in Alzheimer’s disease and its link with the symptoms of the disease, we found that the shortened neural timescale of the default mode network was associated with the aberrantly short neural timescale of the left angular gyrus. Moreover, we revealed that the shortened neural timescale of the angular gyrus was correlated with the atypically reduced grey matter volume of this parietal region. Furthermore, we identified an association between the neural structure, brain function and symptoms and proposed a model in which the reduced grey matter volume of the left angular gyrus shortened the intrinsic neural time of the region, which then destabilized the entire neural timescale of the default mode network and resultantly contributed to cognitive decline in Alzheimer’s disease. These findings highlight the key role of the left angular gyrus in the anatomical and functional aetiology of Alzheimer’s disease.
Challenges for Novel Antiretroviral Development in an Era of Widespread tenofovir-disoproxil/lamivudine (or emtricitabine)/dolutegravir availability (TLD) Availability
Authors: Fairhead Cassandra , Levi Jacob , Hill Andrew
Published: July 2024

More than 80% of people with human immunodeficiency virus (HIV) in low- and middle-income countries (LMICs) take first-line tenofovir-disoproxil/lamivudine (or emtricitabine)/dolutegravir (TLD). Due to hard-fought activism, TLD now costs <$45 per person per year in more than 100 LMICs under Voluntary License. With final dolutegravir (DTG) patents expiring by 2029, generic TLD will soon be available globally. Here, we identify seven critical benchmarks that underpin TLDs' success which novel antiretroviral therapy (ART) should now meet, and an eighth benchmark for which novel ART should aim. These benchmarks are superior efficacy; high genetic barrier to resistance; safety in hepatitis B coinfection; favourable drug interaction profiles; HIV2 efficacy; safety in pregnancy, long-acting formulation availability and affordable pricing. We compare the generic TLD availability timeline with development timelines for two case-study novel ART combinations: islatravir/doravirine and cabotegravir/rilpivirine. We demonstrate that currently these regimens and trial programs will not meet key benchmarks required to compete with TLD.
Long-term atrial arrhythmia characterization and treatment efficacy evaluation using non-invasive echocardiography-based electromechanical cycle length mapping: a case series
Authors: Tourni Melina , Weber Rachel , Biviano Angelo , Konofagou Elisa
Published: July 2024

Background

Atrial fibrillation (AF) is a prevalent cardiac condition characterized by irregular heart rhythm. Conventional non-invasive diagnostic techniques, while useful, have limitations in providing comprehensive information for treatment planning. To address this gap, electromechanical cycle length mapping (ECLM), a non-invasive echocardiography-based technique, has emerged as a promising approach. Electromechanical cycle length mapping offers quantitative and spatially specific insights into atrial electromechanical activation rate mapping, thereby enhancing our understanding of arrhythmia disease progression in AF patients.

Case summary

In this case series, we present two patient cases demonstrating the potential utility of ECLM in monitoring and evaluating treatment responses in atrial arrhythmia. The 1st case involved a 61-year-old male with persistent AF who underwent multiple procedures, including direct current cardioversion (DCCV) and radiofrequency ablation. Over three different DCCV encounters, pre- and post-procedure ECLM scans were performed, and the results showed the localization and incomplete elimination of arrhythmic triggers post-DCCV, which were used as early indicators of AF recurrence. The 2nd case involved a 71-year-old male with paroxysmal AF who also underwent cardioversion and ablation procedures. Electromechanical cycle length mapping imaging demonstrated a progressive reduction and elimination of arrhythmia triggers after each encounter, resulting in long-term maintenance of sinus rhythm.

Discussion

The findings from this case series highlight the potential of ECLM as a non-invasive imaging tool for long-term monitoring and evaluating immediate and long-term treatment responses in AF patients. The integration of ECLM with standard echocardiograms holds promise in guiding clinical decisions and improving patient outcomes in managing atrial fibrillation.
Goldfish phenomics reveals commonalities and a lack of universality in the domestication process for ornamentation
Authors: Le Verger Kévin , Küng Laurelle C , Fabre Anne-Claire , Schmelzle Thomas , Wegmann Alexandra , Sánchez-Villagra Marcelo R
Published: July 2024

Domestication process effects are manifold, affecting genotype and phenotype, and assumed to be universal in animals by part of the scientific community. While mammals and birds have been thoroughly investigated, from taming to intensive selective breeding, fish domestication remains comparatively unstudied. The most widely bred and traded ornamental fish species worldwide, the goldfish, underwent the effect of long-term artificial selection on differing skeletal and soft tissue modules through ornamental domestication. Here, we provide a global morphological analysis in this emblematic ornamental domesticated fish. We demonstrate that goldfish exhibit unique morphological innovations in whole-body, cranial, and sensory (Weberian ossicles and brain) anatomy compared to their evolutionary clade, highlighting a remarkable morphological disparity within a single species comparable to that of a macroevolutionary radiation. In goldfish, as in the case of dogs and pigeons in their respective evolutionary contexts, the most ornamented varieties are extremes in the occupied morphological space, emphasizing the power of artificial selection for nonadaptive traits. Using 21st century tools on a dataset comprising the 16 main goldfish breeds, 23 wild close relatives, and 39 cypriniform species, we show that Charles Darwin’s expressed wonder at the goldfish is justified. There is a commonality of overall pattern in the morphological differentiation of domesticated forms selected for ornamental purposes, but the singularity of goldfish occupation and extension within (phylo)morphospaces, speaks against a universality in the domestication process.
Non-ribosomal peptide synthase profiles remain structurally similar despite minimally shared features across fungus-farming termite microbiomes
Authors: Murphy Robert , Strube Mikael Lenz , Schmidt Suzanne , Silué Kolotchèlèma Simon , Koné N’golo Abdoulaye , Rosendahl Søren , Poulsen Michael
Published: July 2024

Fungus-farming termites (Macrotermitinae) engage in an obligate mutualism with members of the fungal genus Termitomyces, which they maintain as a monoculture on specialized comb structures. Both these comb structures and the guts of the termites host diverse bacterial communities that are believed to assist in sustaining monoculture farming through antagonist suppression. Among candidate bacteria-derived compounds serving this function are non-ribosomal peptides (NRPs), which are a highly bioactive class of specialized metabolites, frequently produced by symbionts within eukaryotic hosts. However, our understanding of specialized metabolites in termite-associated microbiomes is limited. Here we use amplicon sequencing to characterize both bacterial composition and NRP potential. We show that bacterial and NRP diversity are correlated and that the former varies more than the latter across termite host and gut and comb samples. Compositions of the two are governed by host species and sample type, with topological similarity indicating a diverse set of biosynthetic potential that is consistent with the long evolutionary history of the Macrotermitinae. The structure of both bacterial and NRP compositional networks varied similarly between guts and combs across the Macrotermitinae albeit with auxiliary termite genus-specific patterns. We observed minimal termite species-specific cores, with essentially no Macrotermitinae-wide core and an abundance of putatively novel biosynthetic gene clusters, suggesting that there is likely no single solution to antagonist suppression via specialized NRP metabolites. Our findings contribute to an improved understanding of the distribution of NRP potential in the farming termite symbiosis and will help guide targeted exploration of specialized metabolite production.
Following hip fracture, hospital organizational factors associated with prescription of anti-osteoporosis medication on discharge, to address imminent refracture risk: a record-linkage study
Authors: Patel Rita , Judge Andrew , Johansen Antony , Javaid Muhammad K , Griffin Xavier L , Chesser Tim , Griffin Jill , Marques Elsa M R ,   REDUCE Study Group, Gregson Celia L , Johansen Antony , Chesser Tim , Javaid Muhammad K , Griffin Xavier L , Griffin Jill , Marques Elsa M R , Ben-Shlomo Yoav , Drew Sarah , Judge Andrew , Patel Rita , Whale Katie , Ben-Shlomo Yoav , Gregson Celia L
Published: July 2024

Patients who sustain a hip fracture are known to be at imminent refracture risk. Their complex multidisciplinary rehabilitation needs to include falls prevention and anti-osteoporosis medication (AOM) to prevent such fractures. This study aimed to determine which hospital-level organizational factors predict prescription of post-hip fracture AOM and refracture risk. A cohort of 178 757 patients aged ≥60 yr who sustained a hip fracture in England and Wales (2016-2019) was examined and followed for 1 yr. Patient-level hospital admission datasets from 172 hospitals, the National Hip Fracture Database, and mortality data were linked to 71 metrics extracted from 18 hospital-level organizational reports. Multilevel models determined organizational factors, independent of patient case-mix, associated with (1) AOM prescription and (2) refracture (by ICD10 coding). Patients were mean (SD) 82.7 (8.6) yr old, 71% female, with 18% admitted from care homes. Overall, 101 735 (57%) were prescribed AOM during admission, while 50 354 (28%) died during 1-yr follow-up, 12 240 (7%) refractured. Twelve organizational factors were associated with AOM prescription, for example, orthogeriatrician-led care compared to traditional care models (odds ratio [OR] 4.65 [95% CI, 2.25–9.59]); AOM was 9% (95% CI, 6%–13%) more likely to be prescribed in hospitals providing routine bone health assessment to all patients. Refracture occurred at median 126 d (IQR 59–234). Eight organizational factors were associated with refracture risk; hospitals providing orthogeriatrician assessment to all patients within 72 h of admission had an 18% (95% CI, 2%–31%) lower refracture risk, weekend physiotherapy provision had an 8% (95% CI, 3%–14%) lower risk, and where occupational therapists attended clinical governance meetings, a 7% (95% CI, 2%–12%) lower risk. Delays initiating post-discharge community rehabilitation were associated with a 15% (95% CI, 3%–29%) greater refracture risk. These novel, national findings highlight the importance of orthogeriatrician, physiotherapist, and occupational therapist involvement in secondary fracture prevention post hip fracture; notably, fracture risk reductions were seen within 12 mo of hip fracture.
Osteoclast-derived coupling factors: origins and state-of-play Louis V Avioli lecture, ASBMR 2023
Authors: Sims Natalie A
Published: July 2024

Coupling, the mechanism that controls the sequence of events in bone remodeling, is a fundamental theory for understanding the way the skeleton changes throughout life. This review is an adapted version of the Louis V Avioli lecture, delivered at the Annual Scientific Meeting of the American Society of Bone and Mineral Research in 2023. It outlines the history of the coupling concept, details how coupling is thought to occur within trabecular and cortical bone, and describes its multiple contexts and the many mechanisms suggested to couple bone-forming osteoblasts to the prior action of osteoclasts on the same bone surface. These mechanisms include signals produced at each stage of the remodeling sequence (resorption, reversal, and formation), such as factors released by osteoclasts through their resorptive action and through protein synthesis, molecules deposited in the cement line during the reversal phase, and potential signals from osteocytes within the local bone environment. The review highlights two examples of coupling factors (Cardiotrophin 1 and EphrinB2:EphB4) to illustrate the limited data available, the need to integrate the many functions of these factors within the basic multicellular unit (BMU), and the multiple origins of these factors, including the other cell types present during the remodeling sequence (such as osteocytes, macrophages, endothelial cells, and T-cells).
Molecular analyses of the Kalotermes dispar-complex (Blattodea: Kalotermitidae) from the Canary Islands reveal cryptic intraspecific divergence and a connection to a lone Nearctic congener
Authors: Hernández-Teixidor David , Cussigh Alex , Suárez Daniel , García Javier , Scheffrahn Rudolf H , Luchetti Andrea
Published: July 2024

The Canary Islands is a Macaronesian volcanic archipelago with a depauperate community of three species of Kalotermitidae, including Kalotermes dispar. A total of 54 Kalotermes colonies were collected from Gran Canaria, Tenerife, La Gomera, La Palma, and El Hierro islands. Soldiers and imagos were morphologically examined and sequenced for four mitochondrial markers. Although morphological differences could not be detected, phylogenetic analysis of both cox1/tRNA/cox2 and rrnL markers revealed two distinct clades of K. dispar, suggesting cryptic diversity. The diversification within the Canary Kalotermes lineage most likely occurred around 7.5 Mya, while the divergence within the two clades was reconstructed at about 3.6 Mya and 1.9 Mya. Kalotermes approximatus from the southeastern Nearctic constitutes a sister to the Canary Kalotermes, while the Palearctic K. flavicollis, K. italicus, and K. phoenicae form a separate clade. It is hypothesized that a faunal exchange of Kalotermes from the Nearctic to the Canary Islands occurred via transoceanic rafting during the mid-Miocene.