bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polygenic scoring accuracy varies across the genetic ancestry continuum
Authors: Ding Yi , Hou Kangcheng , Xu Ziqi , Pimplaskar Aditya , Petter Ella , Boulier Kristin , Privé Florian , Vilhjálmsson Bjarni J. , Olde Loohuis Loes M. , Pasaniuc Bogdan 
Published: May 2023

AbstractPolygenic scores (PGSs) have limited portability across different groupings of individuals (for example, by genetic ancestries and/or social determinants of health), preventing their equitable use1–3. PGS portability has typically been assessed using a single aggregate population-level statistic (for example, R2)4, ignoring inter-individual variation within the population. Here, using a large and diverse Los Angeles biobank5 (ATLAS, n = 36,778) along with the UK Biobank6 (UKBB, n = 487,409), we show that PGS accuracy decreases individual-to-individual along the continuum of genetic ancestries7 in all considered populations, even within traditionally labelled ‘homogeneous’ genetic ancestries. The decreasing trend is well captured by a continuous measure of genetic distance (GD) from the PGS training data: Pearson correlation of −0.95 between GD and PGS accuracy averaged across 84 traits. When applying PGS models trained on individuals labelled as white British in the UKBB to individuals with European ancestries in ATLAS, individuals in the furthest GD decile have 14% lower accuracy relative to the closest decile; notably, the closest GD decile of individuals with Hispanic Latino American ancestries show similar PGS performance to the furthest GD decile of individuals with European ancestries. GD is significantly correlated with PGS estimates themselves for 82 of 84 traits, further emphasizing the importance of incorporating the continuum of genetic ancestries in PGS interpretation. Our results highlight the need to move away from discrete genetic ancestry clusters towards the continuum of genetic ancestries when considering PGSs.
MSHF: A Multi-Source Heterogeneous Fundus (MSHF) Dataset for Image Quality Assessment
Authors: Jin Kai , Gao Zhiyuan , Jiang Xiaoyu , Wang Yaqi , Ma Xiaoyu , Li Yunxiang , Ye Juan 
Published: May 2023

AbstractImage quality assessment (IQA) is significant for current techniques of image-based computer-aided diagnosis, and fundus imaging is the chief modality for screening and diagnosing ophthalmic diseases. However, most of the existing IQA datasets are single-center datasets, disregarding the type of imaging device, eye condition, and imaging environment. In this paper, we collected a multi-source heterogeneous fundus (MSHF) database. The MSHF dataset consisted of 1302 high-resolution normal and pathologic images from color fundus photography (CFP), images of healthy volunteers taken with a portable camera, and ultrawide-field (UWF) images of diabetic retinopathy patients. Dataset diversity was visualized with a spatial scatter plot. Image quality was determined by three ophthalmologists according to its illumination, clarity, contrast and overall quality. To the best of our knowledge, this is one of the largest fundus IQA datasets and we believe this work will be beneficial to the construction of a standardized medical image database.
SIRT6-PAI-1 axis is a promising therapeutic target in aging-related bone metabolic disruption
Authors: Aobulikasimu Alkebaier , Liu Tao , Piao Jinying , Sato Shingo , Ochi Hiroki , Okawa Atsushi , Tsuji Kunikazu , Asou Yoshinori 
Published: May 2023

AbstractThe mechanistic regulation of bone mass in aged animals is poorly understood. In this study, we examined the role of SIRT6, a longevity-associated factor, in osteocytes, using mice lacking Sirt6 in Dmp-1-expressing cells (cKO mice) and the MLO-Y4 osteocyte-like cell line. cKO mice exhibited increased osteocytic expression of Sost, Fgf23 and senescence inducing gene Pai-1 and the senescence markers p16 and Il-6, decreased serum phosphate levels, and low-turnover osteopenia. The cKO phenotype was reversed in mice that were a cross of PAI-1-null mice with cKO mice. Furthermore, senescence induction in MLO-Y4 cells increased the Fgf23 and Sost mRNA expression. Sirt6 knockout and senescence induction increased HIF-1α binding to the Fgf23 enhancer sequence. Bone mass and serum phosphate levels were higher in PAI-1-null aged mice than in wild-type mice. Therefore, SIRT6 agonists or PAI-1 inhibitors may be promising therapeutic options for aging-related bone metabolism disruptions.
Development and validation of a prediction equation for body fat percentage from measured BMI: a supervised machine learning approach
Authors: Xu Shiming , Nianogo Roch A. , Jaga Seema , Arah Onyebuchi A. 
Published: May 2023

AbstractBody mass index is a widely used but poor predictor of adiposity in populations with excessive fat-free mass. Rigorous predictive models validated specifically in a nationally representative sample of the US population and that could be used for calibration purposes are needed. The objective of this study was to develop and validate prediction equations of body fat percentage obtained from Dual Energy X-ray Absorptiometry using body mass index (BMI) and socio-demographics. We used the National Health and Nutrition Examination Survey (NHANES) data from 5931 and 2340 adults aged 20 to 69 in 1999–2002 and 2003–2006, respectively. A supervised machine learning using ordinary least squares and a validation set approach were used to develop and select best models based on R2 and root mean square error. We compared our findings with other published models and utilized our best models to assess the amount of bias in the association between predicted body fat and elevated low-density lipoprotein (LDL). Three models included BMI, BMI2, age, gender, education, income, and interaction terms and produced R-squared values of 0.87 and yielded the smallest standard errors of estimation. The amount of bias in the association between predicted BF% and elevated LDL from our best model was −0.005. Our models provided strong predictive abilities and low bias compared to most published models. Its strengths rely on its simplicity and its ease of use in low-resource settings.
Apoptotic gene loss in Cnidaria is associated with transition to parasitism
Authors: Neverov Alexander M. , Panchin Alexander Y. , Mikhailov Kirill V. , Batueva Marina D. , Aleoshin Vladimir V. , Panchin Yuri V. 
Published: May 2023

AbstractThe phylum Cnidaria consists of several morphologically diverse classes including Anthozoa, Cubozoa, Hydrozoa, Polypodiozoa, Scyphozoa, Staurozoa, and Myxozoa. Myxozoa comprises two subclasses of obligate parasites—Myxosporea and Malacosporea, which demonstrate various degrees of simplification. Myxosporea were previously reported to lack the majority of core protein domains of apoptotic proteins including caspases, Bcl-2, and APAF-1 homologs. Other sequenced Cnidaria, including the parasite Polypodium hydriforme from Polypodiozoa do not share this genetic feature. Whether this loss of core apoptotic proteins is unique to Myxosporea or also present in its sister subclass Malacosporea was not previously investigated. We show that the presence of core apoptotic proteins gradually diminishes from free-living Cnidaria to Polypodium to Malacosporea to Myxosporea. This observation does not favor the hypothesis of catastrophic simplification of Myxosporea at the genetic level, but rather supports a stepwise adaptation to parasitism that likely started from early parasitic ancestors that gave rise to Myxozoa.
Blink-To-Live eye-based communication system for users with speech impairments
Authors: Ezzat Mohamed , Maged Mohamed , Gamal Youssef , Adel Mustafa , Alrahmawy Mohammed , El-Metwally Sara 
Published: May 2023

AbstractEye-based communication languages such as Blink-To-Speak play a key role in expressing the needs and emotions of patients with motor neuron disorders. Most invented eye-based tracking systems are complex and not affordable in low-income countries. Blink-To-Live is an eye-tracking system based on a modified Blink-To-Speak language and computer vision for patients with speech impairments. A mobile phone camera tracks the patient’s eyes by sending real-time video frames to computer vision modules for facial landmarks detection, eye identification and tracking. There are four defined key alphabets in the Blink-To-Live eye-based communication language: Left, Right, Up, and Blink. These eye gestures encode more than 60 daily life commands expressed by a sequence of three eye movement states. Once the eye gestures encoded sentences are generated, the translation module will display the phrases in the patient’s native speech on the phone screen, and the synthesized voice can be heard. A prototype of the Blink-To-Live system is evaluated using normal cases with different demographic characteristics. Unlike the other sensor-based eye-tracking systems, Blink-To-Live is simple, flexible, and cost-efficient, with no dependency on specific software or hardware requirements. The software and its source are available from the GitHub repository (https://github.com/ZW01f/Blink-To-Live).
Wavelet clustering analysis as a tool for characterizing community structure in the human microbiome
Authors: Benincà Elisa , Pinto Susanne , Cazelles Bernard , Fuentes Susana , Shetty Sudarshan , Bogaards Johannes A. 
Published: May 2023

AbstractHuman microbiome research is helped by the characterization of microbial networks, as these may reveal key microbes that can be targeted for beneficial health effects. Prevailing methods of microbial network characterization are based on measures of association, often applied to limited sampling points in time. Here, we demonstrate the potential of wavelet clustering, a technique that clusters time series based on similarities in their spectral characteristics. We illustrate this technique with synthetic time series and apply wavelet clustering to densely sampled human gut microbiome time series. We compare our results with hierarchical clustering based on temporal correlations in abundance, within and across individuals, and show that the cluster trees obtained by using either method are significantly different in terms of elements clustered together, branching structure and total branch length. By capitalizing on the dynamic nature of the human microbiome, wavelet clustering reveals community structures that remain obscured in correlation-based methods.
Detection of dengue virus infection in children presenting with fever in Hawassa, southern Ethiopia
Authors: Shimelis Techalew , Mulu Andargachew , Mengesha Mesfin , Alemu Aynalem , Mihret Adane , Tadesse Birkneh Tilahun , Bartlett Adam W. , Belay Fitsum W/Gebriel , Schierhout Gill , Dittrich Sabine , Crump John A. , Vaz Nery Susana , Kaldor John M. 
Published: May 2023

AbstractDengue fever is a mosquito-borne viral infection, with rising incidence globally. Eastern Ethiopia has had dengue fever outbreaks in recent years. However, the extent to which the infection contributes to hospital presentation among children with fever in southern Ethiopia is unknown. We examined 407 stored plasma samples collected to investigate the aetiology of fever in children aged at least 2 months and under 13 years presenting to the outpatient of the largest tertiary hospital in southern Ethiopia. We analyzed samples for dengue virus non-structural 1 antigen using enzyme-linked immunosorbent assay. The median (interquartile range) age of the 407 children examined was 20 (10–48) months, and 166 (40.8%) of the children were females. Of 407 samples analyzed, 9 (2.2%) were positive for dengue virus non-structural 1 antigen, of whom 2 were initially treated with antimalarial drugs despite having negative malaria microscopy, and 1 of the 8 patients had a persistent fever at the seventh day of follow-up time. The presence of active dengue virus infection in the study area highlights the need for studies at the community level as well as the integration of dengue diagnostics into fever-management strategies. Further research to characterize circulating strains is warranted.
Antimicrobial activity of Limosilactobacillus fermentum strains isolated from the human oral cavity against Streptococcus mutans
Authors: Park Do-Young , Hwang Jiyoung , Kim Yunji , Lee Dahye , Kim Young-Youn , Kim Hye-Sung , Hwang Inseong 
Published: May 2023

AbstractOral probiotics have been recently gaining much attention owing to their potential to inhibit the progression of dental caries by controlling the cariogenic effects of Streptococcus mutans. We isolated and genotypically identified 77 lactic acid bacteria including 12 Limosilactobacillus fermentum probiotic candidates from the oral cavity of healthy volunteers. Among the 12 L. fermentum isolates, nine isolates effectively inhibited the growth of S. mutans via hydrogen peroxide (H2O2) production. The others neither suppressed the growth of S. mutans nor produced H2O2. Eight out of the nine H2O2-producing L. fermentum isolates exhibited strong adherence to oral epithelial KB cells while inhibiting the adherence of S. mutans to KB cells. The eight H2O2-producing isolates were neither haemolytic based on a blood-agar test, cytotoxic according to lactate dehydrogenase assay, nor resistant to eight antibiotics represented by the European Food Safety Authority guideline, indicating that the isolates have potential to suppress the cariogenesis driven by S. mutans while providing general probiotic benefits.
A multi-analytical approach to studying the chemical composition of typical carbon sink samples
Authors: Astolfi Maria Luisa , Massimi Lorenzo , Rapa Mattia , Plà Rita Rosa , Jasan Raquel Clara , Tudino Mabel Beatriz , Canepari Silvia , Conti Marcelo Enrique 
Published: May 2023

AbstractPeatlands in southern South America (Tierra del Fuego region, TdF) play a key role in the ecological dynamics of Patagonia. It is, therefore, necessary to increase our knowledge and awareness of their scientific and ecological value to ensure their conservation. This study aimed to assess the differences in the distribution and accumulation of elements in peat deposits and Sphagnum moss from the TdF. Chemical and morphological characterization of the samples was carried out using various analytical techniques, and total levels of 53 elements were determined. Furthermore, a chemometric differentiation based on the elemental content of peat and moss samples was performed. Some elements (Cs, Hf, K, Li, Mn, Na, Pb, Rb, Si, Sn, Ti and Zn) showed significantly higher contents in moss samples than in peat samples. In contrast, only Mo, S and Zr were significantly higher in peat samples than in moss samples. The results obtained highlight the ability of moss to accumulate elements and to act as a means to facilitate the entry of elements into peat samples. The valuable data obtained in this multi-methodological baseline survey can be used for more effective conservation of biodiversity and preservation of the ecosystem services of the TdF.
Functional and structural responses of plankton communities toward consecutive experimental heatwaves in Mediterranean coastal waters
Authors: Soulié Tanguy , Vidussi Francesca , Mas Sébastien , Mostajir Behzad 
Published: May 2023

AbstractThe frequency of marine heatwaves (HWs) is projected to increase in the Mediterranean Sea over the next decades. An in situ mesocosm experiment was performed in a Mediterranean lagoon for 33 days. Three mesocosms were used as controls following the natural temperature of the lagoon. In three others, two HWs of + 5 °C compared to the controls were applied from experimental day (d) 1 to d5 (HW1) and from d11 to d15 (HW2). High-frequency data of oxygen, chlorophyll-a (chl-a), temperature, salinity and light from sensors immersed in all mesocosms were used to calculate gross primary production (GPP), respiration (R) and phytoplankton growth (µ) and loss (L) rates. Nutrients and phytoplankton community structure from pigments were also analyzed. HW1 significantly increased GPP, R, chl-a, µ and L by 7 to 38%. HW2 shifted the system toward heterotrophy by only enhancing R. Thus, the effects of the first HW resulted in the attenuation of those of a second HW on phytoplankton processes, but not on community respiration, which was strongly regulated by temperature. In addition, natural phytoplankton succession from diatoms to haptophytes was altered by both HWs as cyanobacteria and chlorophytes were favored at the expense of haptophytes. These results indicate that HWs have pronounced effects on Mediterranean plankton communities.
Semantic Context Can Mask Intelligibility Declines at Above-Conversational Speech Levels in Normal-Hearing Listeners
Authors: Fereczkowski Michal , Neher Tobias 
Published: May 2023

Purpose:
While speech audibility generally improves with increasing level, declines in intelligibility are inconsistently observed at above-conversational levels, even in listeners with normal audiograms (NAs). The inconsistent findings could be due to different types of speech materials, ranging from monosyllabic words to everyday sentences, used across studies. Here, we hypothesized that semantic context can “mask” intelligibility declines at high levels by constraining plausible response options.

Method:
Intelligibility was assessed in speech-shaped noise with monosyllabic words, sentences without semantic context, and sentences with semantic context. Two presentation levels were used: 80 and 95 dB SPL broadband. Bandpass filtering was applied to minimize upward spread of masking. Twenty-two young adults with NAs were tested.

Results:
Poorer performance at the higher level was found with the monosyllabic words and context-free sentences but not with the context-rich sentences. The scores obtained at the higher level with the two context-free materials were strongly correlated. The correlation was independent of the lower-level scores, suggesting that the high-level performance declines reflect “normal” auditory functioning.

Conclusions:
Young adults with NAs show intelligibility decreases at above-conversational levels when tested with speech materials without semantic context. Top-down processing as facilitated by context information can mask such declines.
Inhibition of pulmonary artery smooth muscle cells via the delivery of curcuminoid WZ35 by Cu‐based metal organic frameworks
Authors: Hua Zhidan , Han Mingming , Song Lanlan , Yan Yongle , Chen Honglang , Wang Jilong , Li Chao , Chen Yanfan , Yan Hanhan , Chen Mayun 
Published: May 2023

AbstractHypoxic pulmonary hypertension (HPH) is a life‐threatening disease that occurs due to a lack of oxygen in the lungs, leading to an increase in pulmonary vascular resistance, right ventricular failure, and ultimately death. HPH is a multifactorial disorder that involves multiple molecular pathways, making it a challenge for clinicians to identify effective therapies. Pulmonary artery smooth muscle cells (PASMCs) play a crucial role in HPH pathogenesis by proliferating, resisting apoptosis, and promoting vascular remodelling. Curcumin, a natural polyphenolic compound, has shown potential as a therapeutic agent for HPH by reducing pulmonary vascular resistance, inhibiting vascular remodelling, and promoting apoptosis of PASMCs. Regulation of PASMCs could significantly inhibits HPH. However, curcumin has the disadvantages of poor solubility and low bioavailability, and its derivative WZ35 has better biosafety. Here, Cu‐based metal organic frameworks (MOFCu) was fabricated to encapsulate the curcumin analogue WZ35 (MOFCu@WZ35) for the inhibition of PASMCs proliferation. The authors found that the MOFCu@WZ35 could promote the death of PASMCs. Furthermore, the authors believed that this drug delivery system will effectively alleviate the HPH.
3D physico-chemical model of a pre-stellar core
Authors: Jensen S. S. , Spezzano S. , Caselli P. , Grassi T. , Haugbølle T. 
Published: May 2023

Context. Pre-stellar cores represent the earliest stage of the formation process of stars and planets. By characterizing the physical and chemical structure of these cores, we can establish the initial conditions for star and planet formation and determine to what degree the chemical composition of pre-stellar cores is inherited by the later stages.
Aims. We aim to determine the underlying causes of spatial chemical segregation observed in pre-stellar cores and study the effects of the core structure and external environment on the chemical structure of pre-stellar cores.
Methods. A three-dimensional (3D) magnetohydrodynamic model of a pre-stellar core embedded in a dynamic star-forming cloud was post-processed with a sequentially continuum radiative transfer, a gas-grain chemical model, and a line-radiative transfer model. The results were analyzed and compared to observations of CH3OH and c-C3H2 in L1544. We compared nine different chemical models to the observations to determine which initial conditions are compatible with the observed chemical segregation in the prototypical pre-stellar core L1544.
Results. The model is able to reproduce several aspects of the observed chemical differentiation in L1544. Extended methanol emission is shifted towards colder and more shielded regions of the core envelope, while c-C3H2 emission overlaps with the dust continuum, which is consistent with the observed chemical structure. Furthermore, these results are consistent across a broad spectrum of chemical models. Increasing the strength of the interstellar radiation field or the cosmic-ray ionization rate with respect to the typical values assumed in nearby star-forming regions leads to synthetic maps that are inconsistent with the observed chemical structure.
Conclusions. Our model shows that the observed chemical dichotomy in L1544 can arise as a result of uneven illumination due to the asymmetrical structure of the 3D core and the environment within which the core has formed. This highlights the importance of the 3D structure at the core-cloud transition on the chemistry of pre-stellar cores. The reported effect is likely to affect later stages of the formation process of stars and planets through chemical inheritance.