bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparative study of postnatal anthropometric growth in very preterm infants and intrauterine growth
Authors: Chou Fu-Sheng , Yeh Hung-Wen , Clark Reese H.
Published: September 2023

Most growth references for very preterm infants were developed using measurements taken at birth, and were thought to represent intrauterine growth. However, it remains unclear whether the goal of approximating an intrauterine growth rate as stated by the American Academy of Pediatrics is attainable by very preterm infants. Using real-world measurement data from very preterm infants born between 2010 through 2020, we develop models to characterize the patterns of postnatal growth, and compare them to intrauterine growth. By assessing the weight growth rate, we show three phases of postnatal growth not evident in intrauterine growth. Furthermore, postnatal length and head circumference growth exhibit a slow rate after birth, followed by an acceleration. Collectively, postnatal and intrauterine growth are distinctly different. Although postnatal growth models do not represent optimal growth of very preterm infants, they can serve as a practical tool for clinical assessment of growth and for nutrition research.
Air quality related equity implications of U.S. decarbonization policy
Authors: Picciano Paul , Qiu Minghao , Eastham Sebastian D. , Yuan Mei , Reilly John , Selin Noelle E.
Published: September 2023

Climate policies that target greenhouse gas emissions can improve air quality by reducing co-emitted air pollutant emissions. However, the extent to which climate policy could contribute to the targets of reducing existing pollution disparities across different populations remains largely unknown. We quantify potential air pollution exposure reductions under U.S. federal carbon policy, considering implications of resulting health benefits for exposure disparities across U.S. racial/ethnic groups. We focus on policy cases that achieve reductions of 40-60% in 2030 economy-wide carbon dioxide (CO2) emissions, when compared with 2005 emissions. The 50% CO2 reduction policy case reduces average fine particulate matter (PM2.5) exposure across racial/ethnic groups, with greatest benefit for non-Hispanic Black (−0.44 μg/m3) and white populations (−0.37 μg/m3). The average exposure disparity for racial/ethnic minorities rises from 12.4% to 13.1%. Applying an optimization approach to multiple emissions reduction scenarios, we find that no alternate combination of reductions from different CO2 sources would substantially mitigate exposure disparities. Results suggest that CO2-based strategies for this range of reductions are insufficient for fully mitigating PM2.5 exposure disparities between white and racial/ethnic minority populations; addressing disparities may require larger-scale structural changes.
Evolutionary origin of genomic structural variations in domestic yaks
Authors: Liu Xinfeng , Liu Wenyu , Lenstra Johannes A. , Zheng Zeyu , Wu Xiaoyun , Yang Jiao , Li Bowen , Yang Yongzhi , Qiu Qiang , Liu Hongyu , Li Kexin , Liang Chunnian , Guo Xian , Ma Xiaoming , Abbott Richard J. , Kang Minghui , Yan Ping , Liu Jianquan
Published: September 2023

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.
The isocyanide SN2 reaction
Authors: Patil Pravin , Zheng Qiang , Kurpiewska Katarzyna , Dömling Alexander
Published: September 2023

The SN2 nucleophilic substitution reaction is a vital organic transformation used for drug and natural product synthesis. Nucleophiles like cyanide, oxygen, nitrogen, sulfur, or phosphorous replace halogens or sulfonyl esters, forming new bonds. Isocyanides exhibit unique C-centered lone pair σ and π* orbitals, enabling diverse radical and multicomponent reactions. Despite this, their nucleophilic potential in SN2 reactions remains unexplored. We have uncovered that isocyanides act as versatile nucleophiles in SN2 reactions with alkyl halides. This yields highly substituted secondary amides through in situ nitrilium ion hydrolysis introducing an alternative bond break compared to classical amide synthesis. This novel 3-component process accommodates various isocyanide and electrophile structures, functional groups, scalability, late-stage drug modifications, and complex compound synthesis. This reaction greatly expands chemical diversity, nearly doubling the classical amid coupling’s chemical space. Notably, the isocyanide nucleophile presents an unconventional Umpolung amide carbanion synthon (R-NHC(-) = O), an alternative to classical amide couplings.
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Authors: Nakato Ryuichiro , Sakata Toyonori , Wang Jiankang , Nagai Luis Augusto Eijy , Nagaoka Yuya , Oba Gina Miku , Bando Masashige , Shirahige Katsuhiko
Published: September 2023

Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer–promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.
Dynamically tuning friction at the graphene interface using the field effect
Authors: Greenwood Gus , Kim Jin Myung , Nahid Shahriar Muhammad , Lee Yeageun , Hajarian Amin , Nam SungWoo , Espinosa-Marzal Rosa M.
Published: September 2023

Dynamically controlling friction in micro- and nanoscale devices is possible using applied electrical bias between contacting surfaces, but this can also induce unwanted reactions which can affect device performance. External electric fields provide a way around this limitation by removing the need to apply bias directly between the contacting surfaces. 2D materials are promising candidates for this approach as their properties can be easily tuned by electric fields and they can be straightforwardly used as surface coatings. This work investigates the friction between single layer graphene and an atomic force microscope tip under the influence of external electric fields. While the primary effect in most systems is electrostatically controllable adhesion, graphene in contact with semiconducting tips exhibits a regime of unexpectedly enhanced and highly tunable friction. The origins of this phenomenon are discussed in the context of fundamental frictional dissipation mechanisms considering stick slip behavior, electron-phonon coupling and viscous electronic flow.
Bird clades with less complex appendicular skeletons tend to have higher species richness
Authors: Brinkworth Andrew , Green Emily , Li Yimeng , Oyston Jack , Ruta Marcello , Wills Matthew A.
Published: September 2023

Species richness is strikingly uneven across taxonomic groups at all hierarchical levels, but the reasons for this heterogeneity are poorly understood. It is well established that morphological diversity (disparity) is decoupled from taxonomic diversity, both between clades and across geological time. Morphological complexity has been much less studied, but there is theory linking complexity with differential diversity across groups. Here we devise an index of complexity from the differentiation of the fore and hind limb pairs for a sample of 983 species of extant birds. We test the null hypothesis that this index of morphological complexity is uncorrelated with clade diversity, revealing a significant and negative correlation between the species richness of clades and the mean morphological complexity of those clades. Further, we find that more complex clades tend to occupy a smaller number of dietary and habitat niches, and that this proxy for greater ecological specialisation correlates with lower species richness. Greater morphological complexity in the appendicular skeleton therefore appears to hinder the generation and maintenance of species diversity. This may result from entrenchment into morphologies and ecologies that are less capable of yielding further diversity.
Identification and characterization of endo-α-, exo-α-, and exo-β-d-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria
Authors: Shimokawa Michiko , Ishiwata Akihiro , Kashima Toma , Nakashima Chiho , Li Jiaman , Fukushima Riku , Sawai Naomi , Nakamori Miku , Tanaka Yuuki , Kudo Azusa , Morikami Sae , Iwanaga Nao , Akai Genki , Shimizu Nobutaka , Arakawa Takatoshi , Yamada Chihaya , Kitahara Kanefumi , Tanaka Katsunori , Ito Yukishige , Fushinobu Shinya , Fujita Kiyotaka
Published: September 2023

The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These components are composed of d-arabinose, the enantiomer of the typical l-arabinose found in plants. The unique glycan structures of mycobacteria contribute to their ability to evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-d-arabinanases, GH172 exo-α-d-arabinofuranosidase, and GH116 exo-β-d-arabinofuranosidase) from Microbacterium arabinogalactanolyticum. These enzymes completely degraded the complex d-arabinan core structure of lipoarabinomannan and arabinogalactan in a concerted manner. Furthermore, through biochemical characterization using synthetic substrates and X-ray crystallography, we elucidated the mechanisms of substrate recognition and anomer-retaining hydrolysis for the α- and β-d-arabinofuranosidic bonds in both endo- and exo-mode reactions. The discovery of these d-arabinan-degrading enzymes, along with the understanding of their structural basis for substrate specificity, provides valuable resources for investigating the intricate glycan architecture of mycobacterial cell wall polysaccharides and their contribution to pathogenicity.
Identification of a common ice nucleus on hydrophilic and hydrophobic close-packed metal surfaces
Authors: Chen Pengcheng , Xu Qiuhao , Ding Zijing , Chen Qing , Xu Jiyu , Cheng Zhihai , Qiu Xiaohui , Yuan Bingkai , Meng Sheng , Yao Nan
Published: September 2023

Establishing a general model of heterogeneous ice nucleation has long been challenging because of the surface water structures found on different substrates. Identifying common water clusters, regardless of the underlying substrate, is one of the key steps toward solving this problem. Here, we demonstrate the presence of a common water cluster found on both hydrophilic Pt(111) and hydrophobic Cu(111) surfaces using scanning tunneling microscopy and non-contact atomic force microscopy. Water molecules self-assemble into a structure with a central flat-lying hexagon and three fused pentagonal rings, forming a cluster consisting of 15 individual water molecules. This cluster serves as a critical nucleus during ice nucleation on both surfaces: ice growth beyond this cluster bifurcates to form two-dimensional (three-dimensional) layers on hydrophilic (hydrophobic) surfaces. Our results reveal the inherent similarity and distinction at the initial stage of ice growth on hydrophilic and hydrophobic close-packed metal surfaces; thus, these observations provide initial evidence toward a general model for water-substrate interaction.
A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps
Authors: Forsberg Björn O. , Shah Pranav N. M. , Burt Alister
Published: September 2023

Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great effort to reduce flexibility and heterogeneity to improve the quality of the reconstruction. Clustering algorithms are typically employed to identify populations of data with reduced variability, but lack assessment of remaining heterogeneity. Here we develope a fast and simple algorithm based on spatial filtering to estimate the heterogeneity of a reconstruction. In the absence of flexibility, this estimate approximates macromolecular component occupancy. We show that our implementation can derive reasonable input parameters, that composition heterogeneity can be estimated based on contrast loss, and that the reconstruction can be modified accordingly to emulate altered constituent occupancy. This stands to benefit conventionally employed maximum-likelihood classification methods, whereas we here limit considerations to cryo-EM map interpretation, quantification, and particle-image signal subtraction.
Network controllability of structural connectomes in the neonatal brain
Authors: Sun Huili , Jiang Rongtao , Dai Wei , Dufford Alexander J. , Noble Stephanie , Spann Marisa N. , Gu Shi , Scheinost Dustin
Published: September 2023

White matter connectivity supports diverse cognitive demands by efficiently constraining dynamic brain activity. This efficiency can be inferred from network controllability, which represents the ease with which the brain moves between distinct mental states based on white matter connectivity. However, it remains unclear how brain networks support diverse functions at birth, a time of rapid changes in connectivity. Here, we investigate the development of network controllability during the perinatal period and the effect of preterm birth in 521 neonates. We provide evidence that elements of controllability are exhibited in the infant’s brain as early as the third trimester and develop rapidly across the perinatal period. Preterm birth disrupts the development of brain networks and altered the energy required to drive state transitions at different levels. In addition, controllability at birth is associated with cognitive ability at 18 months. Our results suggest network controllability develops rapidly during the perinatal period to support cognitive demands but could be altered by environmental impacts like preterm birth.
A mechanism that ensures non-selective cytoplasm degradation by autophagy
Authors: Kotani Tetsuya , Sakai Yuji , Kirisako Hiromi , Kakuta Chika , Kakuta Soichiro , Ohsumi Yoshinori , Nakatogawa Hitoshi
Published: September 2023

In autophagy, a membrane cisterna called the isolation membrane expands, bends, becomes spherical, and closes to sequester cytoplasmic constituents into the resulting double-membrane vesicle autophagosome for lysosomal/vacuolar degradation. Here, we discover a mechanism that allows the isolation membrane to expand with a large opening to ensure non-selective cytoplasm sequestration within the autophagosome. A sorting nexin complex that localizes to the opening edge of the isolation membrane plays a critical role in this process. Without the complex, the isolation membrane expands with a small opening that prevents the entry of particles larger than about 25 nm, including ribosomes and proteasomes, although autophagosomes of nearly normal size eventually form. This study sheds light on membrane morphogenesis during autophagosome formation and selectivity in autophagic degradation.
Prosaposin maintains lipid homeostasis in dopamine neurons and counteracts experimental parkinsonism in rodents
Authors: He Yachao , Kaya Ibrahim , Shariatgorji Reza , Lundkvist Johan , Wahlberg Lars U. , Nilsson Anna , Mamula Dejan , Kehr Jan , Zareba-Paslawska Justyna , Biverstål Henrik , Chergui Karima , Zhang Xiaoqun , Andren Per E. , Svenningsson Per
Published: September 2023

Prosaposin (PSAP) modulates glycosphingolipid metabolism and variants have been linked to Parkinson’s disease (PD). Here, we find altered PSAP levels in the plasma, CSF and post-mortem brain of PD patients. Altered plasma and CSF PSAP levels correlate with PD-related motor impairments. Dopaminergic PSAP-deficient (cPSAPDAT) mice display hypolocomotion and depression/anxiety-like symptoms with mildly impaired dopaminergic neurotransmission, while serotonergic PSAP-deficient (cPSAPSERT) mice behave normally. Spatial lipidomics revealed an accumulation of highly unsaturated and shortened lipids and reduction of sphingolipids throughout the brains of cPSAPDAT mice. The overexpression of α-synuclein via AAV lead to more severe dopaminergic degeneration and higher p-Ser129 α-synuclein levels in cPSAPDAT mice compared to WT mice. Overexpression of PSAP via AAV and encapsulated cell biodelivery protected against 6-OHDA and α-synuclein toxicity in wild-type rodents. Thus, these findings suggest PSAP may maintain dopaminergic lipid homeostasis, which is dysregulated in PD, and counteract experimental parkinsonism.
SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
Authors: Dou Yongchao , Liu Yuejia , Yi Xinpei , Olsen Lindsey K. , Zhu Hongwen , Gao Qiang , Zhou Hu , Zhang Bing
Published: September 2023

Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoform-level characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
Histidine modulates amyloid-like assembly of peptide nanomaterials and confers enzyme-like activity
Authors: Yuan Ye , Chen Lei , Kong Lingfei , Qiu Lingling , Fu Zhendong , Sun Minmin , Liu Yuan , Cheng Miaomiao , Ma Saiyu , Wang Xiaonan , Zhao Changhui , Jiang Jing , Zhang Xinzheng , Wang Liping , Gao Lizeng
Published: September 2023

Amyloid-like assembly is not only associated with pathological events, but also leads to the development of novel nanomaterials with unique properties. Herein, using Fmoc diphenylalanine peptide (Fmoc–F–F) as a minimalistic model, we found that histidine can modulate the assembly behavior of Fmoc–F–F and induce enzyme-like catalysis. Specifically, the presence of histidine rearranges the β structure of Fmoc–F–F to assemble nanofilaments, resulting in the formation of active site to mimic peroxidase-like activity that catalyzes ROS generation. A similar catalytic property is also observed in Aβ assembled filaments, which is correlated with the spatial proximity between intermolecular histidine and F-F. Notably, the assembled Aβ filaments are able to induce cellular ROS elevation and damage neuron cells, providing an insight into the pathological relationship between Aβ aggregation and Alzheimer’s disease. These findings highlight the potential of histidine as a modulator in amyloid-like assembly of peptide nanomaterials exerting enzyme-like catalysis.
Clinical blindness in conjunction with childhood bacterial meningitis
Authors: Pelkonen Tuula , Kallio Markku , Latvala Terho , Roine Irmeli , Peltola Heikki
Published: September 2023

Although rarely reported, bilateral loss of vision is a severe complication of childhood bacterial meningitis. We assessed its frequency in five prospective treatment trials performed in Europe, Latin America, and Angola in 1984–2017. Course of illness, follow-up findings, and child’s sight were recorded. Sight was examined at discharge, and conditions permitting, also at 1–3 months post-hospitalization and in Angola on hospital day 7. Experienced pediatricians diagnosed clinical blindness if the child did not make eye contact, did not blink or move the eyes, or remained unresponsive to bright light or movement of large objects before their eyes. Of 1515 patients, 351, 654, and 510 were from Finland, Latin America, and Angola, respectively. At discharge, blindness was observed in 0 (0%), 8 (1.2%), and 51 (10%) children, respectively. In Angola, 64 children appeared to be blind on day 7; 16 of these children died. Blindness found at discharge in Angola was not invariably irreversible; approximately 40% had restored the sight at follow-up visit. Clinical blindness rarely occurred in isolation and was usually associated with young age and poor general condition at hospital arrival. Various other serious sequelae were common among the survivors with clinical blindness.
Screen time and sleep among medical students in Germany
Authors: Liebig Lukas , Bergmann Antje , Voigt Karen , Balogh Erika , Birkas Béla , Faubl Nora , Kraft Theresa , Schöniger Konrad , Riemenschneider Henna
Published: September 2023

Medical students are a vulnerable group for harmful health behaviours due to academic stress. Increased screen time is associated with adverse health behaviour, particularly delayed bedtime, shorter sleep duration and poorer sleep quality. This possible relationship has not yet been examined among medical students in Europe. Medical students at the Technical University of Dresden were invited to participate in an online questionnaire based cross-sectional study. To analyse correlations between screen time and sleep parameters, correlation coefficients, linear regression and mixed-model analysis were calculated. 415 students (average age 24 years, 70% female) were included in the analysis. The students reported an average of 7 h screen time per day and 7.25 h sleep duration per night. Approximately 23% (n = 97) reported sleeping less than 7 h per night and 25% (n = 105) reported fairly to very poor sleep quality. Students who reported more screen time for leisure went to bed significantly later (r = 0.213, p < 0.001). Students who spent more screen time for study/work tended to sleep shorter (r = − 0.108, p < 0.015). There was no significant association between screen time and sleep quality (p = 0.103). The results show a need for educational interventions to promote healthy sleep behaviour and to limit screen time.
Uncertainty analysis of contagion processes based on a functional approach
Authors: López-Pintado Dunia , López-Pintado Sara , García-Milán Iván , Yao Zonghui
Published: September 2023

The spread of a disease, product or idea in a population is often hard to predict. We tend to observe one or few realizations of the contagion process and therefore limited information can be obtained for anticipating future similar events. The stochastic nature of contagion generates unpredictable outcomes throughout the whole course of the dynamics. This might lead to important inaccuracies in the predictions and to the over or under-reaction of policymakers, who tend to anticipate the average behavior. Through an extensive simulation study, we analyze properties of the contagion process, focusing on its unpredictability or uncertainty, and exploiting the functional nature of the data. In particular, we define a novel non-parametric measure of variance based on weighted depth-based central regions. We apply this methodology to the susceptible-infected-susceptible epidemiological model and small-world networks. We find that maximum uncertainty is attained at the epidemic threshold. The density of the network and the contagiousness of the process have a strong and complementary effect on the uncertainty of contagion, whereas only a mild effect of the network’s randomness structure is observed.
Non-thermal plasma disinfecting procedure is harmless to delicate items of everyday use
Authors: Scholtz V. , Jirešová J. , Fišer L. , Obrová K. , Sláma M. , Klenivskyi M. , Khun J. , Vaňková E.
Published: September 2023

Non-thermal plasma (NTP) is a well-known decontamination tool applicable for a wide range of microorganisms and viruses. Since the recent COVID-19 pandemic highlighted the need to decontaminate all daily used items, it is highly desirable to address the applicability of NTP, including its possible harmful effects. To the best of our knowledge, a comprehensive characterization of NTP effects on sensitive materials is still lacking. We investigated the potential damage to common materials of daily use inflicted by air atmospheric NTP generated in Plasmatico v1.0. The materials tested were paper, various metals, and passive and active electronic components modelling sensitive parts of commonly used small electronic devices. The NTP-exposed paper remained fully usable with only slight changes in its properties, such as whitening, pH change, and degree of polymerization. NTP caused mild oxidation of copper, tinned copper, brass, and a very mild oxidation of stainless steel. However, these changes do not affect the normal functionality of these materials. No significant changes were observed for passive electronic components; active components displayed a very slight shift of the measured values observed for the humidity sensor. In conclusion, NTP can be considered a gentle tool suitable for decontamination of various sensitive materials.
Computational redesign of Beta-27 Fab with substantially better predicted binding affinity to the SARS-CoV-2 Omicron variant than human ACE2 receptor
Authors: Treewattanawong Wantanee , Sitthiyotha Thassanai , Chunsrivirot Surasak
Published: September 2023

During the COVID-19 pandemic, SARS-CoV-2 has caused large numbers of morbidity and mortality, and the Omicron variant (B.1.1.529) was an important variant of concern. To enter human cells, the receptor-binding domain (RBD) of the S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) binds to the peptidase domain (PD) of Angiotensin-converting enzyme 2 (ACE2) receptor. Disrupting the binding interactions between SARS-CoV-2-RBD and ACE2-PD using neutralizing antibodies is an effective COVID-19 therapeutic solution. Previous study found that Beta-27 Fab, which was obtained by digesting the full IgG antibodies that were isolated from a patient infected with SARS-CoV-2 Beta variant, can neutralize Victoria, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) variants. This study employed computational protein design and molecular dynamics (MD) to investigate and enhance the binding affinity of Beta-27 Fab to SARS-CoV-2-RBD Omicron variant. MD results show that five best designed Beta-27 Fabs (Beta-27-D01 Fab, Beta-27-D03 Fab, Beta-27-D06 Fab, Beta-27-D09 Fab and Beta-27-D10 Fab) were predicted to bind to Omicron RBD in the area, where ACE2 binds, with significantly better binding affinities than Beta-27 Fab and ACE2. Their enhanced binding affinities are mostly caused by increased binding interactions of CDR L2 and L3. They are promising candidates that could potentially be employed to disrupt the binding between ACE2 and Omicron RBD.
Changes in the negative logarithm of end-tidal hydrogen partial pressure indicate the variation of electrode potential in healthy Japanese subjects
Authors: Kiyama Teruo , Tokunaga Akira , Naji Abumrad , Barbul Adrian
Published: September 2023

Molecular hydrogen (H2) is produced by human colon microbiomes and exhaled. End-tidal H2 sampling is a simple method of measuring alveolar H2. The logarithm of the hydrogen ion (H+)/H2 ratio suggests the electrode potential in the solution according to the Nernst equation. As pH is defined as the negative logarithm of the H+ concentration, pH2 is defined as the negative logarithm of the H2 effective pressure in this study. We investigated whether changes in pH2 indicated the variation of electrode potential in the solution and whether changes in end-tidal pH2 could be measured using a portable breath H2 sensor. Changes in the electrode potential were proportional to ($${\mathrm{pH}}_{2}-2\times \mathrm{pH}$$

pH
2

-
2
×
pH

) in phosphate-buffered solution (pH = 7.1). End-tidal H2 was measured in the morning (baseline) and at noon (after daily activities) in 149 healthy Japanese subjects using a handheld H2 sensor. The median pH2 at the baseline was 4.89, and it increased by 0.15 after daily activities. The variation of electrode potential was obtained by multiplying the pH2 difference, which suggested approximately + 4.6 mV oxidation after daily activities. These data suggested that changes in end-tidal pH2 indicate the variation of electrode potential during daily activities in healthy human subjects.
Prevalence and factors associated with metabolic syndrome in first hospitalization for major depression disorder patients
Authors: Tang Zhongyu , Zhen Yanping , Zhang Lin , Liu Xuebing , Ma Jun
Published: September 2023

Major depressive disorder (MDD) is a common and socially burdensome psychiatric disorder with a causal and complex relationship with metabolic syndrome (MetS), which is often co-morbid. However, the prevalence and risk factors for MetS in patients with MDD are inconclusive. The purpose of this study is to investigate the prevalence and factors influencing MetS in first hospitalization MDD patients. A total of 981 MDD patients were included. Sociodemographic and general clinical data were collected from the patients, while metabolism-related parameters were also measured, and psychological symptoms were assessed. Our study found that the prevalence of MetS in the study population was 9.68%. MDD patients with MetS had higher levels of metabolism-related parameters and more severe psychological symptoms. We identified risk factors for MetS and its severity separately: age of onset of MDD, more severe depressive symptoms, and higher thyroid stimulating hormone (TSH) levels were risk factors for the development of MetS, whereas higher TSH levels were risk factors for the severity of MetS. Our results suggest that MetS is not highly prevalent in MDD patients, but certain risk factors may increase its likelihood and severity, and that these findings could be beneficial for clinical intervention and care of MetS.
The association of arsenic exposure with mortality due to cancer, diabetes, Alzheimer's and congenital anomalies using Poisson regression
Authors: Rahmani Alireza , Khamutian Samira , Doosti-Irani Amin , Shokoohizadeh Mohammad Javad , Shirmohammadi-Khorram Nasrin , Sahraeei Fatemeh , Khodabakhshi Mahdi , Ahangaran Nastaran
Published: September 2023

The present study aims to determine the relationship between the concentration of arsenic in the groundwater of Hamadan province and the mortality rate due to various types of malignancies, congenital anomalies, diabetes mellitus and Alzheimer's. Mortality data due to various causes of death in Hamadan province were collected for five years (2016–2020). Sampling of drinking water was determined in the reference laboratory using polarography method. Poisson regression was used to investigate the relationship between arsenic level and the death rate due to various types of disease, at a significant level (p value < 0.05). According to the results of Poisson regression, among the various causes of death (N = 8042), Alzheimer's 5.94 (3.67–9.61), diabetes mellitus 4.05 (3.5–5.37), congenital malformations 2.98 (1.88–4.72), breast cancer 2.72 (1.56–4.71), leukemia 1.90 (1.24–2.92), stomach cancer 1.64 (1.28–2.10), Liver cancer 1.58 (1.58–2.30), other digestive organs 5.86 (3.38–10.16), meninges and brain cancer 1.57 (1.02–2.41) showed the highest relationship with arsenic contamination. The results of this study could be evidence for a positive and significant relationship between arsenic concentrations and mortality rates due to cancers, diabetes mellitus, Alzheimer disease, and congenital malformations. Therefore, it's necessary to use appropriate water treatment methods to remove arsenic at the source in contaminated areas.
Sand consolidation using enzyme-induced carbonate precipitation: new insights on temperature and particle size effects
Authors: Omarov Kamal , Alarifi Sulaiman A. , Mahmoud Mohamed , Kamal Muhammad Shahzad , Murtaza Mobeen , Humam Abdulmohsen , AlAhmari Manar M.
Published: September 2023

Sand production is a major issue in the oil and gas industry. Unconsolidated sand can be produced with the oil or gas a cause many issues to the production facilities. Enzyme-induced carbonate precipitation (EICP) is a promising method for sand consolidation and is characterized by its environment friendliness. Numerous studies have shown its effectiveness in ambient conditions. However, oil and gas downhole well operations are high pressure and high-temperature conditions. The objective of this study is to investigate effect of high temperature on EICP reaction and its efficiency in terms of uniformity to consolidate different types of sand samples. In this paper, the behavior of EICP solutions is examined in high temperatures from 25 to 90 °C. The study shows that high temperature environment doesn’t handicap efficiency but in contrast it can favor the reaction if optimum concentration of reactants has been selected. The temperature effect is also discussed in terms of controllability of reaction which can favor application of reaction. Qualitive analysis shows when EICP solutions containing more than 50,000 ppm of metal ions and stoichiometrically surplus urea requires exposure to heat for reaction progress. The effect of sand particle size and its implication on the consolidation process was examined. Particle size of fine and medium sand ranged from 125 to 250 µm and 250 to 425 µm respectively while for coarse sand 70% sand particle size was between 425 and 700 µm. Designed EICP solutions achieve 9,000 psi for medium and almost 5,000 psi intrinsic specific energy for coarse sand samples. However, treated samples were subject to non-uniform distribution of strength of which can be up to 8,000 psi difference between top and bottom half of the samples.
Predictive value of ELWI combined with sRAGE/esRAGE levels in the prognosis of critically ill patients with acute respiratory distress syndrome
Authors: Zhang Chengliang , Yin Dekun , Zhu Xi , Zhou Wenshuo , Xu Zhihua , Wu Liuping , Gu Weili
Published: September 2023

Acute respiratory distress syndrome (ARDS) is a life-threatening condition. Accurate judgement of the disease progression is essential for controlling the condition in ARDS patients. We investigated whether changes in the level of serum sRAGE/esRAGE could predict the 28-day mortality of ICU patients with ARDS. A total of 83 ARDS patients in the ICU of the Second Affiliated Hospital of Nantong University from January 2021 to June 2022 were consecutively enrolled in this study. Demographic data, primary diagnosis and comorbidities were obtained. Multiple scoring systems, real-time monitoring systems, and biological indicators were determined within 6 h of admission. The clinical parameters for survival status of the ARDS patients were identified by multivariate logistic regression. Receiver operating characteristic (ROC) curve analysis was employed to verify the accuracy of the prognosis of the related parameters. The admission level of sRAGE was significantly higher in the nonsurvival group than in the survival group (p < 0.05), whereas the serum esRAGE level showed the opposite trend. Multivariate logistic regression analysis showed that sRAGE (AUC 0.673, p < 0.05), esRAGE (AUC 0.704, p < 0.05), and ELWI (extravascular lung water index) (AUC 0.717, p < 0.05) were independent risk factors for the prognosis of ARDS. Model B (ELWI + esRAGE) could not be built as a valid linear regression model (ELWI, p = 0.079 > 0.05). Model C (esRAGE + sRAGE) was proven to have no significance because it had a predictive value similar to that of the serum levels of esRAGE (Z = 0.993, p = 0.351) or sRAGE (Z = 1.116, p = 0.265) alone. Subsequently, Model D (sRAGE + esRAGE + ELWI) showed the best 28-day mortality predictive value with a cut-off value of 0.426 (AUC 0.841; p < 0.001), and Model A (sRAGE + ELWI) had a cut-off value of 0.401 (AUC 0.820; p < 0.001), followed by sRAGE (AUC 0.704, p = 0.004), esRAGE (AUC 0.717, p = 0.002), and ELWI (AUC 0.637, p = 0.028). In addition, there was no statistically significant difference between Model A and Model D (Z = 0.966, p = 0.334). The admission level of sRAGE was higher in the nonsurvival group, while the serum esRAGE level showed the opposite trend. Model A and Model D could be used as reliable combined prediction models for predicting the 28-day mortality of ARDS patients.
Biodistribution and toxicity assessment of methoxyphenyl phosphonium carbosilane dendrimers in 2D and 3D cell cultures of human cancer cells and zebrafish embryos
Authors: Žmudová Zuzana , Šanderová Zuzana , Liegertová Michaela , Vinopal Stanislav , Herma Regina , Sušický Luděk , Müllerová Monika , Strašák Tomáš , Malý Jan
Published: September 2023

The consideration of human and environmental exposure to dendrimers, including cytotoxicity, acute toxicity, and cell and tissue accumulation, is essential due to their significant potential for various biomedical applications. This study aimed to evaluate the biodistribution and toxicity of a novel methoxyphenyl phosphonium carbosilane dendrimer, a potential mitochondria-targeting vector for cancer therapeutics, in 2D and 3D cancer cell cultures and zebrafish embryos. We assessed its cytotoxicity (via MTT, ATP, and Spheroid growth inhibition assays) and cellular biodistribution. The dendrimer cytotoxicity was higher in cancer cells, likely due to its specific targeting to the mitochondrial compartment. In vivo studies using zebrafish demonstrated dendrimer distribution within the vascular and gastrointestinal systems, indicating a biodistribution profile that may be beneficial for systemic therapeutic delivery strategies. The methoxyphenyl phosphonium carbosilane dendrimer shows promise for applications in cancer cell delivery, but additional studies are required to confirm these findings using alternative labelling methods and more physiologically relevant models. Our results contribute to the growing body of evidence supporting the potential of carbosilane dendrimers as vectors for cancer therapeutics.
Enhanced spectroelectrochemistry with lossy-mode resonance optical fiber sensor
Authors: Janik Monika , Lechowicz Katarzyna , Pituła Emil , Warszewski Jakub , Koba Marcin , Śmietana Mateusz
Published: September 2023

Spectroelectrochemical (SEC) measurements play a crucial role in analytical chemistry, utilizing transparent or semitransparent electrodes for optical analysis of electrochemical (EC) processes. The EC readout provides information about the electrode's state, while changes in the transmitted optical spectrum help identify the products of EC reactions. To enhance SEC measurements, this study proposes the addition of optical monitoring of the electrode. The setup involves using a polymer-clad silica multimode fiber core coated with indium tin oxide (ITO), which serves as both the electrode and an optical fiber sensor. The ITO film is specifically tailored to exhibit the lossy-mode resonance (LMR) phenomenon, allowing for simultaneous optical monitoring alongside EC readouts. The LMR response depends on the properties of the ITO and the surrounding medium's optical properties. As a result, the setup offers three types of interrogation readouts: EC measurements, optical spectrum analysis corresponding to the volume of the analyte (similar to standard SEC), and LMR spectrum analysis reflecting the state of the sensor/electrode surface. In each interrogation path, cyclic voltammetry (CV) experiments were conducted individually with two oxidation–reduction reaction (redox) probes: potassium ferricyanide and methylene blue. Subsequently, simultaneous measurements were performed during chronoamperometry (CA) with the sensor, and the cross-correlation between the readouts was examined. Overall, this study presents a novel and enhanced SEC measurement approach that incorporates optical monitoring of the electrode. It provides a comprehensive understanding of EC processes and enables greater insights into the characteristics of the analyte.
Changes in hail hazard across Australia: 1979–2021
Authors: Raupach Timothy H. , Soderholm Joshua S. , Warren Robert A. , Sherwood Steven C.
Published: September 2023

Hail damage is a leading cause of insured losses in Australia, but changes in this hazard have not been robustly quantified. Here, we provide a continental-scale analysis of changes in hail hazard in Australia. A hail proxy applied to reanalysis data shows that from 1979–2021 annual hail-prone days decreased over much of Australia but increased in some heavily populated areas. For example, the annual number of hail-prone days increased by ~40% around Sydney and Perth, the largest cities on Australia’s east and west coasts, respectively. Changes in atmospheric instability have driven the trends. Radar observations, while covering shorter time spans and a more limited area than the reanalysis, corroborate the broad pattern of results. This study shows consistent hail-frequency trends in radar indicators and atmospheric environments and demonstrates substantial increases in hail frequency in major Australian cities where hail impacts are most significant.
Repetitive DNA sequence detection and its role in the human genome
Authors: Liao Xingyu , Zhu Wufei , Zhou Juexiao , Li Haoyang , Xu Xiaopeng , Zhang Bin , Gao Xin
Published: September 2023

Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.
A multimodal sensing ring for quantification of scratch intensity
Authors: Padmanabha Akhil , Choudhary Sonal , Majidi Carmel , Erickson Zackory
Published: September 2023

Background

An objective measurement of chronic itch is necessary for improvements in patient care for numerous medical conditions. While wearables have shown promise for scratch detection, they are currently unable to estimate scratch intensity, preventing a comprehensive understanding of the effect of itch on an individual.

Methods

In this work, we present a framework for the estimation of scratch intensity in addition to the detection of scratch. This is accomplished with a multimodal ring device, consisting of an accelerometer and a contact microphone, a pressure-sensitive tablet for capturing ground truth intensity values, and machine learning algorithms for regression of scratch intensity on a 0–600 milliwatts (mW) power scale that can be mapped to a 0–10 continuous scale.

Results

We evaluate the performance of our algorithms on 20 individuals using leave one subject out cross-validation and using data from 14 additional participants, we show that our algorithms achieve clinically-relevant discrimination of scratching intensity levels. By doing so, our device enables the quantification of the substantial variations in the interpretation of the 0–10 scale frequently utilized in patient self-reported clinical assessments.

Conclusions

This work demonstrates that a finger-worn device can provide multidimensional, objective, real-time measures for the action of scratching.
What's in a word? Student beliefs and understanding about green chemistry
Authors: Armstrong Laura B. , Irie Lauren M. , Chou Kelly , Rivas Mariana , Douskey Michelle C. , Baranger Anne M.
Published: September 2023

For the past decade, the College of Chemistry at UC Berkeley has iteratively redesigned general chemistry laboratory courses to introduce students to green chemistry concepts, while simultaneously using green chemistry as a relevant context to learn chemistry. To investigate the effectiveness of this curriculum we developed approaches to investigate student understanding of green chemistry. We adapted a constructivist educational framework to iteratively design fixed and free response items appropriate for large enrollment courses that probe student knowledge of green chemistry concepts and practices. Two free response items were designed to probe students’ ability to define green chemistry and make green chemistry decisions in the context of a case study. A set of fixed response items were designed to probe particular aspects of green chemistry knowledge that were included in the course. Together, we used these items to characterize (1) changes in student understanding of green chemistry and (2) how prior “green” knowledge impacts student learning of new green chemistry principles in the general chemistry laboratory course. Analysis of student responses indicated that, on average, students demonstrated increased green chemistry understanding after completing this green chemistry aligned laboratory course. Students were able to integrate more normative green chemistry principles in their answers and began to indicate awareness of complex interconnected systems. Because the items focused on assessing student knowledge of green chemistry, rather than their self-assessment of knowledge, they provided valuable insight regarding students’ prior green chemistry knowledge that will be used to develop future versions of the curriculum.
Potassium stearate doped PEDOT:PSS improves the performance of inverted perovskite solar cells
Authors: Li Ying , Yao Yanqing , Yang Yuanlin , Zhao Xusheng , Cheng Wan , Chen Banghui , Chen Lijia , Li Ping , Tang Shuhui
Published: September 2023

This work studied the doping of KSt in the PEDOT:PSS layer of devices ITO/K-PEDOT:PSS/perovskite/PCBM/BCP/Ag. The results showed that the doping of KSt improved the conductivity and charge transfer ability, thereby enhancing the PCE of inverted PSCs.
Local reactivity of metal–insulator–semiconductor photoanodes imaged by photoinduced electrochemiluminescence microscopy
Authors: Descamps Julie , Zhao Yiran , Le-Pouliquen Julie , Goudeau Bertrand , Garrigue Patrick , Tavernier Karine , Léger Yoan , Loget Gabriel , Sojic Neso
Published: September 2023

Photoinduced electrochemiluminescence precisely imaged the hole-driven heterogeneous photoelectrochemical reactivity of n-Si/SiOx photoanodes patterned with Ir microbands.