bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of somatic structural variations in 528 Chinese individuals with Esophageal squamous cell carcinoma
Authors: Cui Heyang , Zhou Yong , Wang Fang , Cheng Caixia , Zhang Weimin , Sun Ruifang , Zhang Ling , Bi Yanghui , Guo Min , Zhou Yan , Wang Xinhui , Ren Jiaxin , Bai Ruibing , Ding Ning , Cheng Chen , Wang Longlong , Zhuang Xuehan , Gao Mingwei , Weng Yongjia , Wu Yueguang , Liu Huijuan , Li Shuaicheng , Wang Shubin , Cheng Xiaolong , Cui Yongping , Liu Zhihua , Zhan Qimin 
Published: October 2022

AbstractEsophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations’ mechanisms and biological functions. SVs show multi-mode distributions in size, indicating distinct mutational processes. We develop a tool and define five types of complex rearrangements with templated insertions. We highlight a type of fold-back inversion, which is associated with poor outcomes. Distinct rearrangement signatures demonstrate variable genomic metrics such as replicating time, spatial proximity, and chromatin accessibility. Specifically, fold-back inversion tends to occur near the centrosome; TD-c2 (Tandem duplication-cluster2) is significantly enriched in chromatin-accessibility and early-replication region compared to other signatures. Analyses of TD-c2 signature reveal 9 TD hotspots, of which we identify a hotspot consisting of a super-enhancer of PTHLH. We confirm the oncogenic effect of the PTHLH gene and its interaction with enhancers through functional experiments. Finally, extrachromosomal circular DNAs (ecDNAs) are present in 14% of ESCCs and have strong selective advantages to driver genes.
Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability
Authors: Heskett Michael B. , Vouzas Athanasios E. , Smith Leslie G. , Yates Phillip A. , Boniface Christopher , Bouhassira Eric E. , Spellman Paul T. , Gilbert David M. , Thayer Mathew J. 
Published: October 2022

AbstractASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain “Inactivation/Stability Centers” that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
Construction of conducting bimetallic organic metal chalcogenides via selective metal metathesis and oxidation transformation
Authors: Jin Yigang , Fang Yuhui , Li Ze , Hao Xiang , He Feng , Guan Bo , Wang Dongwei , Wu Sha , Li Yang , Liu Caiming , Dai Xiaojuan , Zou Ye , Sun Yimeng , Xu Wei 
Published: October 2022

AbstractConducting organic metal chalcogenides (OMCs) have attracted considerable interest for their superior electrical properties and fascinating functions. However, the electronic structural and functional regulation of OMCs are typically limited to the combination of monometallic nodes and graphene-like ligands. Here, we report a family of bimetallic OMCs ([CuAgx(C6S6)]n, x = 4 or 2) synthesized via selective metal metathesis and oxidation transformation. Both OMCs have alternatively stacked one-dimensional (1D) copper-dithiolene chains and 2D Ag-S networks, which can synergistically serve as charge transport pathways, rendering these bimetallic materials highly conductive. The incorporation of heterometallic nodes turned nonmagnetic [Ag5(C6S6)]n into paramagnetic metallic [CuAg4(C6S6)]n, which exhibited a coherence-incoherence crossover in magnetic susceptibility measurements and an unusually large Sommerfeld coefficient, reminiscent of the characteristics of Kondo lattice. This work opens up an avenue for tailoring the electronic structures of OMCs and provides a platform for studying the dichotomy between electronic localization and itinerancy.
Ectopic expression of sericin enables efficient production of ancient silk with structural changes in silkworm
Authors: Chen Xuedong , Wang Yongfeng , Wang Yujun , Li Qiuying , Liang Xinyin , Wang Guang , Li Jianglan , Peng Ruji , Sima Yanghu , Xu Shiqing 
Published: October 2022

AbstractBombyx mori silk is a super-long natural protein fiber with a unique structure and excellent performance. Innovative silk structures with high performance are in great demand, thus resulting in an industrial bottleneck. Herein, the outer layer sericin SER3 is ectopically expressed in the posterior silk gland (PSG) in silkworms via a piggyBac-mediated transgenic approach, then secreted into the inner fibroin layer, thus generating a fiber with sericin microsomes dispersed in fibroin fibrils. The water-soluble SER3 protein secreted by PSG causes P25’s detachment from the fibroin unit of the Fib-H/Fib-L/P25 polymer, and accumulation between the fibroin layer and the sericin layer. Consequently, the water solubility and stability of the fibroin-colloid in the silk glandular cavity, and the crystallinity increase, and the mechanical properties of cocoon fibers, moisture absorption and moisture liberation of the silk also improve. Meanwhile, the mutant overcomes the problems of low survival and abnormal silk gland development, thus enabling higher production efficiency of cocoon silk. In summary, we describe a silk gland transgenic target protein selection strategy to alter the silk fiber structure and to innovate its properties. This work provides an efficient and green method to produce silk fibers with new functions.
Co-design, implementation, and evaluation of plain language genomic test reports
Authors: Brett Gemma R. , Ward Aisha , Bouffler Sophie E. , Palmer Elizabeth E. , Boggs Kirsten , Lynch Fiona , Springer Amanda , Nisselle Amy , Stark Zornitza 
Published: October 2022

AbstractUnderstanding and communicating genomic results can be challenging for families and health professionals without genetic specialty training. Unlike modifying existing laboratory reports, plain language genomic test reports provide an opportunity for patient/family-centered approaches. However, emerging examples generally lack co-design and/or evaluation in real-world settings. Through co-design involving patient groups, plain language experts, educators, and genetic health professionals, plain language genomic test report templates were produced for common test outcomes in rare diseases. Eight plain language genomic test report templates were developed. These reports were piloted and evaluated as part of a national pediatric ultra-rapid genomic testing program. Family and genetic health professional experiences with report layout, content, and use were explored using surveys. Of 154 families and 107 genetic health professionals issued with reports, 51 families and 57 clinicians responded (RR = 33% and 53%, respectively). Most families (82%) found their report helpful in understanding the result. Reports were shared by 63% of families, predominantly with family members (72%), or health professionals (68%). Clinicians (15%) adapted the reports for other settings. Through co-design, plain language genomic test reports implemented in a real-world setting can facilitate patient/family and caregiver understanding and communication of genomic test purpose, outcome, and potential clinical implications.
A systematic review of the effects of e-cigarette use on lung function
Authors: Honeycutt Lucy , Huerne Katherine , Miller Alanna , Wennberg Erica , Filion Kristian B. , Grad Roland , Gershon Andrea S. , Ells Carolyn , Gore Genevieve , Benedetti Andrea , Thombs Brett , Eisenberg Mark J. 
Published: October 2022

AbstractGiven the increasing use of e-cigarettes and uncertainty surrounding their safety, we conducted a systematic review to determine the effects of e-cigarettes on measures of lung function. We systematically searched EMBASE, MEDLINE, and PsycINFO databases via Ovid, the Cochrane CENTRAL database, and the Web of Science Core from 2004 until July 2021, identifying 8856 potentially eligible studies. A total of eight studies (seven studying immediate effects and one long-term effects, 273 total participants) were included. The risk of bias was assessed using the Risk of Bias in Non-randomized Studies—of Interventions (ROBINS-I) and Cochrane risk of bias tools. These studies suggest that vaping increases airway resistance but does not appear to impact forced expiratory volume in one second (FEV1), forced vital capacity (FVC), or FEV1/FVC ratio. However, given the limited size and follow-up duration of these studies, larger, long-term studies are required to further determine the effects of e-cigarettes on lung function.
MicroLib: A library of 3D microstructures generated from 2D micrographs using SliceGAN
Authors: Kench Steve , Squires Isaac , Dahari Amir , Cooper Samuel J. 
Published: October 2022

Abstract3D microstructural datasets are commonly used to define the geometrical domains used in finite element modelling. This has proven a useful tool for understanding how complex material systems behave under applied stresses, temperatures and chemical conditions. However, 3D imaging of materials is challenging for a number of reasons, including limited field of view, low resolution and difficult sample preparation. Recently, a machine learning method, SliceGAN, was developed to statistically generate 3D microstructural datasets of arbitrary size using a single 2D input slice as training data. In this paper, we present the results from applying SliceGAN to 87 different microstructures, ranging from biological materials to high-strength steels. To demonstrate the accuracy of the synthetic volumes created by SliceGAN, we compare three microstructural properties between the 2D training data and 3D generations, which show good agreement. This new microstructure library both provides valuable 3D microstructures that can be used in models, and also demonstrates the broad applicability of the SliceGAN algorithm.
A thermoelectric materials database auto-generated from the scientific literature using ChemDataExtractor
Authors: Sierepeklis Odysseas , Cole Jacqueline M. 
Published: October 2022

AbstractAn auto-generated thermoelectric-materials database is presented, containing 22,805 data records, automatically generated from the scientific literature, spanning 10,641 unique extracted chemical names. Each record contains a chemical entity and one of the seminal thermoelectric properties: thermoelectric figure of merit, ZT; thermal conductivity, κ; Seebeck coefficient, S; electrical conductivity, σ; power factor, PF; each linked to their corresponding recorded temperature, T. The database was auto-generated using the automatic sentence-parsing capabilities of the chemistry-aware, natural language processing toolkit, ChemDataExtractor 2.0, adapted for application in the thermoelectric-materials domain, following a rule-based sentence-simplification step. Data were mined from the text of 60,843 scientific papers that were sourced from three scientific publishers: Elsevier, the Royal Society of Chemistry, and Springer. To the best of our knowledge, this is the first automatically-generated database of thermoelectric materials and their properties from existing literature. The database was evaluated to have a precision of 82.25% and has been made publicly available to facilitate the application of data science in the thermoelectric-materials domain, for analysis, design, and prediction.
Understanding the associations between maternal high-risk fertility behaviour and child nutrition levels in India: evidence from the National Family Health Survey 2015–2016
Authors: Das Milan , Jana Arup , Muhammad T. 
Published: October 2022

AbstractAnthropometric markers are the most important aspect of a child’s health assessment. Using large-scale nationally representative data from the National Family Health Survey (NFHS-4), 2015–2016, this study aimed to investigate the relationship between children born to women with high-risk fertility behaviours and children’s health outcomes. The sample consisted of 2,55,726 children of currently married women aged 15–49 years in India. The key explanatory variable, high-risk fertility behaviour was defined by women’s age at birth (below 18 or above 34 years), birth interval (less than 24 months), and higher birth orders (four and above). The key outcome variables for assessing child health outcomes were stunting, wasting, and underweight in children aged 0–59 months. We used descriptive statistics, Pearson’s chi-square test and logistic regression models to analyse the objectives. Approximately 33% of children were born with any single high-risk condition in the last 5 years in India. The bivariate analysis showed that all three components of child health, stunting, wasting, and underweight, were higher among children born to women with high-risk fertility behaviour. The findings from the multivariable analysis suggest that children born with a high risk fertility behaviour were suffering from stunting (AOR = 1.30; 95% CI 1.27–1.33) and underweight (AOR = 1.23; 95% CI 1.20–1.27). In addition, children born to women of multiple high-risk categories had higher odds of stunting (AOR = 1.53; 95% CI 1.46–1.59) and underweight (AOR = 1.38; 95% CI 1.32–1.44) as compared to children born to women with no risk. Our findings highlight an urgent need for effective legislation to prevent child marriage that would be helpful in increasing the maternal age at birth. The government should also focus on the interventions in health education and improvement of reproductive healthcare to promote optimal birth spacing.
Cation hydration by confined water and framework-atoms have crucial role on thermodynamics of clay swell﻿ing
Authors: Adapa Sai , Malani Ateeque 
Published: October 2022

AbstractThe swelling capacity and stability of clay play a crucial role in various areas ranging from cosmetics to oil extraction; hence change in their swelling behaviour after cation exchange with the surrounding medium is important for their efficient utilisation. Here we focus on understanding the role of different hydration properties of cation on the thermodynamics of clay swelling by water adsorption. We have used mica as the reference clay, Na$$^+$$

+

, Li$$^+$$

+

, and H$$^+$$

+

ions as the interstitial cations, and performed grand canonical Monte Carlo simulations of water adsorption in mica pores (of widths $$d = 4-40$$

d
=
4
-
40

Å). The disjoining pressure ($$\Pi$$
Π
), swelling free energy ($$\Delta \Omega ^{ex}$$

Δ

Ω

ex

), and several structural properties of confined water and ions were calculated to perform a thermodynamic analysis of the system. We expected higher water density in H-mica pores ($$\rho_{ \hbox{H}}$$

ρ
H

) due to the smaller size of $$\hbox {H}^+$$

H
+

ions having higher hydration energy. However, the counter-intuitive trend of $$\rho _{\hbox{Li}}> \rho _{\hbox{Na}} > \rho_b$$

ρ
Li

>

ρ
Na

>

ρ
b

(bulk density) $$> \rho_{\hbox{H}}$$

>

ρ
H

was observed due to adsorption energy, where the interaction of water with mica framework atoms was also found to be significant. All three mica systems exhibited oscillatory behaviour in the $$\Pi$$
Π
and $$\Delta \Omega ^{ex}$$

Δ

Ω

ex

profiles, diminishing to zero for $$d \ge 11$$

d
≥
11

Å. The $$\Delta \Omega ^{ex}$$

Δ

Ω

ex

for Na-mica is characterised by global minima at $$d=6 {\hbox {\AA}}$$

d
=
6
Å

corresponding to crystalline swelling with significant and multiple barriers for crystalline swelling to osmotic swelling ($$d > 12$$

d
>
12

Å). A shift in the location of global minima of $$\Delta \Omega ^{ex}$$

Δ

Ω

ex

towards the higher d values and $$\Delta \Omega ^{ex}$$

Δ

Ω

ex

becoming more repulsive is observed in the increasing order of hydration energy of $$\hbox {Na}^+$$

Na
+

, $$\hbox {Li}^+$$

Li
+

, and $$\hbox {H}^+$$

H
+

ions. The $$\Delta \Omega ^{ex} > 0$$

Δ

Ω

ex

>
0

for all d in the H-mica system thus favours osmotic swelling. We found that the Na$$^+$$

+

ions hydrate more surface oxygens, act as anchors, and hold the mica pore together (at smaller d), by sharing hydrating water with ions of the opposite side, forming an electrostatically connected mica-Na-water-Na-mica bridge. The Li$$^+$$

+

ions do hydrate surface oxygen atoms, albeit in lesser numbers, and sharing of hydration shell with nearby Li$$^+$$

+

ions is also minimum. Hydration by surface atoms and water sharing, both, are minimum in the H$$^+$$

+

ion case, as they are mostly present in the center of the pore as diffusive ions, thus exerting a consistent osmotic pressure on the mica frameworks, favouring swelling.
EphrinA4 mimetic peptide impairs fear conditioning memory reconsolidation in lateral amygdala
Authors: Mana Ron , Ilovich Or , Dines Monica , Lamprecht Raphael 
Published: October 2022

AbstractFear memory may undergo a process after memory reactivation called reconsolidation. To examine the roles of ephrinA4 in fear memory reconsolidation an inhibitory ephrinA4 mimetic peptide (pep-ephrinA4), that targets the EphA binding site and inhibits EphA activation, was used. Pep-ephrinA4 was microinjected into the lateral amygdala (LA) of fear-conditioned rats 24 h after training and 30 min before tone CS memory retrieval. Memory retrieval was unaffected by pep-ephrinA4. However, the animals were impaired in fear memory tested 1 h or 24 h afterward when compared to controls. Fear-conditioned animals injected with pep-ephrinA4 into LA immediately after long-term memory retrieval were unaffected when tested 24 h afterward. Microinjection into LA of a peptide originated from an ephrinA4 site that does not interact with EphA did not affect fear memory reconsolidation. Rats that were administrated with pep-ephrinA4 systemically 24 h after fear conditioning and 30 min before CS memory retrieval were impaired in long-term fear conditioning memory tested 24 h afterward when compared to the control peptide. These results show that ephrinA4 binding sites are needed for long-term fear memory reconsolidation in LA and may serve as a target for the treatment of fear-related disorders by blocking reconsolidation.
Lignin, an active component in the corn silk water extract, inhibits glycation
Authors: Sano Aiko , Inoue Yutaka , Suzuki Ryuichiro 
Published: October 2022

AbstractThe formation of advanced glycation end products is associated with aging and diabetic complications such as neuropathy, retinopathy, and nephropathy. Thus, the suppression of AGEs formation could prevent and/or treat their related disorders. Corn silk is used as a traditional medicine for the prevention of diabetic complications and treatment of edema in Japan and China. Previous studies revealed the anti-glycation activity of flavonoids in the methanolic extract of corn silk. The anti-glycation activity of the corn silk water extract was higher than that of the methanolic extract; however, the active components of the water extract remained unidentified. The purpose of this study is to make clear the components showing anti-glycation activity in the corn silk water extract and elucidated their structural characteristics. The evaluation of anti-glycation activity was carried out by enzyme-linked immunosorbent assay to detect glycated bovine serum albumin. Remarkable anti-glycation activity was observed in the > 3 kDa fraction. Reversed-phase HPLC analysis of this fraction showed broad peaks characteristic of high-molecular-weight polyphenols. Decomposition reactions did not provide evidence of condensed or acid-hydrolyzable tannins. Therefore, polyphenols contained in the corn silk water extract were considered to be lignin-carbohydrate complex. The 1H- and 13C-nuclear magnetic resonance (NMR) and Fourier transform infrared (FT-IR) spectroscopy spectra of the > 3 kDa fraction were in agreement with the values reported for lignin. Consequently, we concluded that lignin-carbohydrate complex is one of the active components against glycation in the corn silk water extract.
Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting
Authors: Butler Kimberly S. , Carson Bryan D. , Podlevsky Joshua D. , Mayes Cathryn M. , Rowland Jessica M. , Campbell DeAnna , Ricken J. Bryce , Wudiri George ,   The SNL COVID Dx Assay Team, Cahill Jesse , Hayes Dulce , Hogancamp Tessily N. , Maes Danae M. , Martinez Daniella V. , Peretti Amanda S. , Roberson Stephenie A. , Ruffing Anne M. , Huggins Leslie M. , Settecerri Taylor , Smallwood Chuck R. , Tezak Matthew S. , Winona Linda , Ye Dongmei , Timlin Jerilyn A. 
Published: October 2022

AbstractFor workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24–48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid ‘multiplex-pooled’ strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.