bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering spatiotemporal patterns: information encoding, processing, and controllability in oscillator ensembles
Authors: Bomela Walter , Singhal Bharat , Li Jr-Shin 
Published: June 2023

Abstract
The ability to finely manipulate spatiotemporal patterns displayed in neuronal populations is critical for understanding and influencing brain functions, sleep cycles, and neurological pathologies. However, such control tasks are challenged not only by the immense scale but also by the lack of real-time state measurements of neurons in the population, which deteriorates the control performance. In this paper, we formulate the control of dynamic structures in an ensemble of neuron oscillators as a tracking problem and propose a principled control technique for designing optimal stimuli that produce desired spatiotemporal patterns in a network of interacting neurons without requiring feedback information. We further reveal an interesting presentation of information encoding and processing in a neuron ensemble in terms of its controllability property. The performance of the presented technique in creating complex spatiotemporal spiking patterns is demonstrated on neural populations described by mathematically ideal and biophysical models, including the Kuramoto and Hodgkin-Huxley models, as well as real-time experiments on Wein bridge oscillators.
Study on lubrication characteristics of rotary combination seals under stress relaxation
Authors: Zhang Yi , Zhong Sipeng , Xiong Siyang , Xiong Zijie 
Published: June 2023

Abstract
Temperatures in the drilling environment can reach 150 °C and pressures up to 30 MPa, all of which can cause oil film rupture and even seal failure. In addition, under high pressure, viscosity changes can lead to stress relaxation, which may eventually cause seal failure as well. In order to study the influence of high temperature and high pressure conditions on seal performance during stress relaxation, the pressure permeation loading method on both sides is used in the finite element model to simulate the fluid pressure on both sides of the seal interface, and the TEHL (thermo-elastohydrodynamic lubrication) model of the rotary combination seal is also established. On this basis, the TEHL characteristics of the rotary combination seal under different working conditions were analyzed. The results show that: Firstly, the contact pressure and von Mises stress of the seal tend to increase at high temperature, and the higher the temperature, the faster the growth rate, while the increase of the seal area temperature leads to the thinning of the oil film thickness and the high oil film pressure. Secondly, at high fluid pressure, the contact pressure of the rotary combination seal gradually increases, and its peak is close to the peak oil-side contact pressure. Thirdly, with the increase of the linear speed (or rotational speed), the oil film pressure and thickness increase. Fourthly, the larger the rotational speed, the larger the volume leakage and friction, and the larger the compression ratio, the larger the contact pressure.
Structural design and analytical study of a new polysilicon tunable microactuator for measurement of different resonance frequencies
Authors: Taherian Sina , Gholinataj-Jelodar Ehsan 
Published: June 2023

Abstract
This paper presents a novel MEMS tunable resonator that draws inspiration from the folded beam structure in its comb drive resonator design. Conventional electrostatic comb-drive resonators commonly employ folded-beam suspensions to achieve linearity and reduce system stiffness. The proposed design incorporates eight zigzag-shaped meander springs to support the comb finger structure, featuring two central anchors. The objective of this design is to introduce zigzag-shaped nested-folded beam suspensions to the comb parts, thereby reducing the tuning voltage and sensor size. The governing equations are provided to calculate the support springs’ stiffness, and a comparative analysis is conducted to evaluate the stiffness of the proposed design against other parameters. The mathematical analysis demonstrates that Zigzag Nested-Folded beams result in a decreased resonance frequency and a softened electrostatic spring under applied DC voltage. The integration of zigzag-shaped nested-folded beam flexures enables MEMS resonator devices to exhibit reduced stiffness, leading to a lower pull-in voltage. The resonator design and simulation are performed using Intellisuite and SolidWorks software. Results indicate that the resonant frequency of the proposed tunable comb-drive resonator, equipped with 26 finger pairs and a movable part displacement of 21 μm, is reduced by 66% from the original frequency of 2.420 kHz when a tuning voltage of 59 V is applied. Simultaneously, the corresponding effective stiffness decreases by 66% from the initial value of 0.72 N m−1. This compact resonator occupies an area of approximately 1.058×278 (μm)2, demonstrating a smaller size compared to previous works.
Effects of epigallocatechin gallate, caffeine, and their combination on fat accumulation in high-glucose diet-fed Caenorhabditis elegans
Authors: Guo Cheng , Shen Wangyang , Jin Weiping , Jia Xiwu , Ji Zhili , Jinling Li , Bin Li 
Published: June 2023

ABSTRACT
Epigallocatechin gallate (EGCG) and caffeine are inevitable to be ingested together in the process of drinking green tea. This study used Caenorhabditis elegans as an organism model to examine whether the binding of EGCG and caffeine could influence the fat-reduction effect. The results revealed that EGCG significantly reduced the Nile Red fluorescence intensity and the triglyceride/protein ratio of the C. elegans obesity model by 14.7% and 16.5%, respectively, while the effect of caffeine was not significant. Moreover, the degree of reduction in fluorescence intensity and triglyceride/protein ratio by EGCG + caffeine was comparable to that of EGCG. In the exploration of underlying mechanism, we found that EGCG and EGCG + caffeine treatments had no influence on food intake and energy expenditure of C. elegans. Their fat-reduction effects were dependent on the regulation of lipogenesis, as shown by the decreased expression of the sbp-1, fat-7, and daf-16 genes.
Network integration and protein structural binding analysis of neurodegeneration-related interactome
Authors: Chen Hongjun , Zhou Yekai , Liu Yongjing , Zhang Peijing , Chen Ming 
Published: June 2023

Abstract
Neurodegenerative diseases (NDs) usually connect with aggregation and molecular interactions of pathological proteins. The integration of accumulative data from clinical and biomedical research will allow for the excavation of pathological proteins and related interactors. It is also important to systematically study their interacting proteins in order to find more related proteins and potential therapeutic targets. Understanding binding regions in protein interactions will help functional proteomics and provide an alternative method for predicting novel interactions. This study integrated data from biomedical research to achieve systematic mining and analysis of pathogenic proteins and their interaction network.
A workflow has been built as a solution for the collective information of proteins involved in NDs, related protein–protein interactions (PPIs) and interactive visualizations. It also included protein isoforms and mapped them in a disease-related PPI network to illuminate the impact of alternative splicing on protein binding. The interacting proteins enriched by diseases and biological processes (BPs) revealed possible regulatory modules. A high-resolution network with structural affinity information was generated. Finally, Neurodegenerative Disease Atlas (NDAtlas) was constructed with an interactive and intuitive view of protein docking with 3D molecular graphics beyond the traditional 2D network. NDAtlas is available at http://bis.zju.edu.cn/ndatlas.
JTK: targeted diploid genome assembler
Authors: Masutani Bansho , Suzuki Yoshihiko , Suzuki Yuta , Morishita Shinichi 
Published: June 2023

Abstract

Motivation
Diploid assembly, or determining sequences of homologous chromosomes separately, is essential to elucidate genetic differences between haplotypes. One approach is to call and phase single nucleotide variants (SNVs) on a reference sequence. However, this approach becomes unstable on large segmental duplications (SDs) or structural variations (SVs) because the alignments of reads deriving from these regions tend to be unreliable. Another approach is to use highly accurate PacBio HiFi reads to output diploid assembly directly. Nonetheless, HiFi reads cannot phase homozygous regions longer than their length and require oxford nanopore technology (ONT) reads or Hi-C to produce a fully phased assembly. Is a single long-read sequencing technology sufficient to create an accurate diploid assembly?

Results
Here, we present JTK, a megabase-scale diploid genome assembler. It first randomly samples kilobase-scale sequences (called ‘chunks’) from the long reads, phases variants found on them, and produces two haplotypes. The novel idea of JTK is to utilize chunks to capture SNVs and SVs simultaneously. From 60-fold ONT reads on the HG002 and a Japanese sample, it fully assembled two haplotypes with approximately 99.9% accuracy on the histocompatibility complex (MHC) and the leukocyte receptor complex (LRC) regions, which was impossible by the reference-based approach. In addition, in the LRC region on a Japanese sample, JTK output an assembly of better contiguity than those built from high-coverage HiFi+Hi-C. In the coming age of pan-genomics, JTK would complement the reference-based phasing method to assemble the difficult-to-assemble but medically important regions.

Availability and implementation
JTK is available at https://github.com/ban-m/jtk, and the datasets are available at https://doi.org/10.5281/zenodo.7790310 or JGAS000580 in DDBJ.
Large-scale rare variant burden testing in Parkinson's disease
Authors: Makarious Mary B , Lake Julie , Pitz Vanessa , Ye Fu Allen , Guidubaldi Joseph L , Solsberg Caroline Warly , Bandres-Ciga Sara , Leonard Hampton L , Kim Jonggeol Jeffrey , Billingsley Kimberley J , Grenn Francis P , Jerez Pilar Alvarez , Alvarado Chelsea X , Iwaki Hirotaka , Ta Michael , Vitale Dan , Hernandez Dena , Torkamani Ali , Ryten Mina , Hardy John ,   UK Brain Expression Consortium (UKBEC),, Scholz Sonja W , Traynor Bryan J , Dalgard Clifton L , Ehrlich Debra J , Tanaka Toshiko , Ferrucci Luigi , Beach Thomas G , Serrano Geidy E , Real Raquel , Morris Huw R , Ding Jinhui , Gibbs J Raphael , Singleton Andrew B , Nalls Mike A , Bhangale Tushar , Blauwendraat Cornelis 
Published: June 2023

Abstract
Parkinson’s disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson’s disease.
To address this gap, we investigated the rare genetic component of Parkinson’s disease at minor allele frequencies &lt;1%, using whole genome and whole exome sequencing data from 7184 Parkinson’s disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact.
Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson’s disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson’s disease. To date, this is the largest analysis of rare genetic variants in Parkinson’s disease.
Albuminuria and the risk of cancer: the Stockholm CREAtinine Measurements (SCREAM) project
Authors: Luo Li , Yang Yuanhang , Kieneker Lyanne M , Janse Roemer J , Bosi Alessandro , Mazhar Faizan , de Boer Rudolf A , de Bock Geertruida H , Gansevoort Ron T , Carrero Juan-Jesus 
Published: June 2023

ABSTRACT

Background
Studies investigating the association of chronic kidney disease and cancer have focused on estimated glomerular filtration (eGFR) rather than on albuminuria. This study aimed to examine whether albuminuria is associated with cancer incidence, and whether this association is independent of eGFR.

Methods
We included subjects of the Stockholm Creatinine Measurements (SCREAM) project without a history of cancer—250 768 subjects with at least one urine albumin–creatinine ratio (ACR) test (primary cohort) and 433 850 subjects with at least one dipstick albuminuria test (secondary cohort). Albuminuria was quantified as KDIGO albuminuria stages. The primary outcome was overall cancer incidence. Secondary outcomes were site-specific cancer incidence rates. Multivariable Cox proportional hazards regression models adjusted for confounders including eGFR to calculate hazard ratios and 95% confidence intervals (HRs, 95% CIs).

Results
During a median follow-up of 4.3 (interquartile range 2.0–8.2) years, 21 901 subjects of the ACR cohort developed de novo cancer. In multivariable analyses, adjusting among others for eGFR, subjects with an ACR of 30–299 mg/g or ≥300 mg/g had a 23% (HR 1.23; 95% CI 1.19–1.28) and 40% (HR 1.40; 95% CI 1.31–1.50) higher risk of developing cancer, respectively, when compared with subjects with an ACR &lt;30 mg/g. This graded, independent association was also observed for urinary tract, gastrointestinal tract, lung and hematological cancer incidence (all P &lt; .05). Results were similar in the dipstick albuminuria cohort.

Conclusions
Albuminuria was associated with the risk of cancer independent of eGFR. This association was primarily driven by a higher risk of urinary tract, gastrointestinal tract, lung and hematological cancers.
T-next: a new custom-made Thoraflex graft to simplify proximal and distal aortic reinterventions
Authors: Di Eusanio Marco , Gatta Emanuele 
Published: June 2023

Abstract
Secondary root and distal thoraco-abdominal endovascular aortic re-interventions can be challenging after frozen elephant trunk. We obtained from the TERUMO Aortic custom-made platform a Thoraflex graft with a modified disposition of the arch branches that facilitate secondary proximal and distal reinterventions. Here we describe the graft and our first implant.
Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade
Authors: Marr R Alexander , Moore Jackson , Formby Sean , Martiniuk Jonathan T , Hamilton Jonah , Ralli Sneha , Konwar Kishori , Rajasundaram Nisha , Hahn Aria , Measday Vivien 
Published: June 2023

Abstract
Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The “wine circle/Region B”, a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.
Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants
Authors: Einson Jonah , Glinos Dafni , Boerwinkle Eric , Castaldi Peter , Darbar Dawood , de Andrade Mariza , Ellinor Patrick , Fornage Myriam , Gabriel Stacey , Germer Soren , Gibbs Richard , Hersh Craig P , Johnsen Jill , Kaplan Robert , Konkle Barbara A , Kooperberg Charles , Nassir Rami , Loos Ruth J F , Meyers Deborah A , Mitchell Braxton D , Psaty Bruce , Vasan Ramachandran S , Rich Stephen S , Rienstra Michael , Rotter Jerome I , Saferali Aabida , Shoemaker Moore Benjamin , Silverman Edwin , Smith Albert Vernon ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi Pejman , Castel Stephane E , Iossifov Ivan , Lappalainen Tuuli 
Published: June 2023

Abstract
Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-sequencing data in GTEx V8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased whole genome sequencing data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
A Randomized Clinical Trial of Online Social Intelligence Training With Custodial Grandmothers
Authors: Smith Gregory C , Infurna Frank J , Dolbin-MacNab Megan , Webster Britney , Castro Saul , Crowley Daniel M , Musil Carol , Hu Luxin , Hancock Gregory R 
Published: June 2023

Abstract

Background and Objectives
In this study, we investigated the efficacy of a self-administered, online Social Intelligence Training (SIT) program aimed at enhancing psychological and relational well-being among a nationwide U.S. sample of custodial grandmothers.

Research Design and Methods
A two-arm randomized clinical trial (RCT) was conducted, where 349 grandmothers raising grandchildren aged 11–18 years were assigned to either SIT or an attention control condition (ACC). Participants self-completed online surveys at baseline and immediately postintervention, in addition to follow-ups at 3-, 6-, and 9-month postintervention. First-order latent difference score models were used to compare SIT to ACC, across all times of measurement, along key indicators of psychological and relational well-being on an intent-to-treat basis.

Results
Although SIT was largely superior to ACC at yielding positive results, it appears that it attenuated longitudinal declines that occurred among ACC participants. SIT also exerted stronger effects on relational than psychological outcomes, with perceived relations with grandchildren being the most positively affected.

Discussion and Implications
Given that the historical time of this RCT unpredictably corresponded with the coronavirus disease 2019 pandemic, we suspect that SIT helped offset declines in psychological and relational well-being that are widely documented to have resulted from the pandemic. Our overall positive findings support future use of the inexpensive and easily delivered SIT program under normal environmental conditions, with the vulnerable and geographically disperse population of custodial grandmothers.

Clinical Trials Registration Number
NCT03239977
Comparing the peri-implantation endometrial T-bet/GATA3 ratio between control fertile women and patients with recurrent miscarriage: establishment and application of a reference range
Authors: Yu Shuyi , Diao Lianghui , Lian Ruochun , Chen Cong , Huang Chunyu , Li Xinyuan , Li Yuye , Zeng Yong 
Published: June 2023

Abstract

STUDY QUESTION
Is the ratio of endometrial T-box expressed in T cell (T-bet) and GATA-binding protein 3 (GATA3) changed in patients with recurrent miscarriage (RM) compared to fertile controls?

SUMMARY ANSWER
Our study showed a significantly higher T-bet/GATA3 ratio in patients with RM compared with fertile controls.

WHAT IS KNOWN ALREADY
The endometrial T-bet (Th1 lineage-committed transcription factor)/GATA3 (Th2 lineage-committed transcription factor) ratio could represent the Th1/Th2 balance, which is particularly important for healthy pregnancy. However, a reliable reference range for the T-bet/GATA3 ratio during the peri-implantation period has not yet been established for use in clinical practice.

STUDY DESIGN, SIZE, DURATION
This was a retrospective study carried out in a private fertility center. The control group included 120 women in couples undergoing IVF treatment for male infertility, who had experienced a live-birth baby following the first IVF cycle. The study group included 93 women diagnosed with RM that experienced at least two consecutive clinically spontaneous miscarriages before gestational week 12. The ratio of T-bet/GATA3 was calculated in the control group and RM group.

PARTICIPANTS/MATERIALS, SETTING, METHODS
Endometrium samples were collected at mid-luteal phase of the menstrual cycle prior to IVF treatment or pregnancy. The percentage of T-bet+ and GATA3+ cells in total endometrial cells was analyzed using immunohistochemical staining and quantitative analysis.

MAIN RESULTS AND THE ROLE OF CHANCE
Using the 95th percentile to define the upper limits of the endometrial T-bet/GATA3 ratio during the mid-luteal phase, the reference range of control fertile women was ≤0.22. Compared with the control group, the RM group exhibited a significantly higher T-bet/GATA3 ratio (P = 0.02), and 19.4% (18/93) women with RM exhibited a T-bet/GATA3 ratio above the reference range in the mid-luteal phase.

LIMITATIONS, REASONS FOR CAUTION
All patients were recruited from a single center. The stability and clinical value of the endometrial T-bet/GATA3 ratio require further investigation.

WIDER IMPLICATIONS OF THE FINDINGS
The present study suggests that an abnormal endometrial T-bet/GATA3 ratio may be one of the risk factors of RM. Further studies are needed to follow up the pregnancy outcomes in patients with RM with normal and abnormal endometrial T-bet/GATA3 ratio according to the reference range.

STUDY FUNDING/COMPETING INTEREST(S)
This work was supported by Shenzhen Fundamental Research Program (JCYJ20180228164631121, JCYJ20190813161203606, JCYJ20220530172817039). There are no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER
N/A.