bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiRiQ Database: A Platform for In Silico Rice Mutant Screening
Authors: Kubo Takahiko , Yamagata Yoshiyuki , Matsusaka Hiroaki , Toyoda Atsushi , Sato Yutaka , Kumamaru Toshihiro 
Published: November 2023

Abstract
Genetic studies using mutant resources have significantly contributed to elucidating plant gene function. Massive mutant libraries sequenced by next-generation sequencing technology facilitate mutant identification and functional analysis of genes of interest. Here, we report the creation and release of an open-access database (https://miriq.agr.kyushu-u.ac.jp/index.php), called Mutation-induced Rice in Kyushu University (MiRiQ), designed for in silico mutant screening based on a whole-genome-sequenced mutant library. This database allows any user to easily find mutants of interest without laborious efforts such as large-scale screening by PCR. The initial version of the MiRiQ database (version 1.0) harbors a total of 1.6 million single-nucleotide variants (SNVs) and InDels of 721 M1 plants that were mutagenized by N-methyl-N-nitrosourea treatment of the rice cultivar Nipponbare (Oryza sativa ssp. japonica). The SNVs were distributed among 87% of all 35,630 annotated protein-coding genes of the Nipponbare genome and were predicted to induce missense and nonsense mutations. The MiRiQ database provides built-in tools, such as a search tool by keywords and JBrowse for mutation searches. Users can request mutant seeds in the M2 or M3 generations from a request form linked to this database. We believe that the availability of a wide range of gene mutations in this database will benefit the plant science community and breeders worldwide by accelerating functional genomic research and crop improvement.
Life-Cycle Multiomics of Rice Shoots Reveals Growth Stage–Specific Effects of Drought Stress and Time–Lag Drought Responses
Authors: Soma Fumiyuki , Kitomi Yuka , Kawakatsu Taiji , Uga Yusaku 
Published: November 2023

Abstract
Field-grown rice plants are exposed to various stresses at different stages of their life cycle, but little is known about the effects of stage-specific stresses on phenomes and transcriptomes. In this study, we performed integrated time-course multiomics on rice at 3-d intervals from seedling to heading stage under six drought conditions in a well-controlled growth chamber. Drought stress at seedling and reproductive stages reduced yield performance by reducing seed number and setting rate, respectively. High temporal resolution analysis revealed that drought response occurred in two steps: a rapid response via the abscisic acid (ABA) signaling pathway and a slightly delayed DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN (DREB) pathway, allowing plants to respond flexibly to deteriorating soil water conditions. Our long-term time-course multiomics showed that temporary drought stress delayed flowering due to prolonged expression of the flowering repressor gene GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (Ghd7) and delayed expression of the florigen genes HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Our life-cycle multiomics dataset on rice shoots under drought conditions provides a valuable resource for further functional genomic studies to improve crop resilience to drought stress.
MdbHLH160 is stabilized via reduced MdBT2-mediated degradation to promote MdSOD1 and MdDREB2A-like expression for apple drought tolerance
Authors: Mao Ke , Yang Jie , Sun Yunxia , Guo Xin , Qiu Lina , Mei Quanlin , Li Na , Ma Fengwang 
Published: November 2023

Abstract
Drought stress is a key environmental factor limiting the productivity, quality, and geographic distribution of crops worldwide. Abscisic acid (ABA) plays an important role in plant drought stress responses, but the molecular mechanisms remain unclear. Here, we report an ABA-responsive bHLH transcription factor, MdbHLH160, which promotes drought tolerance in Arabidopsis (Arabidopsis thaliana) and apple (Malus domestica). Under drought conditions, MdbHLH160 is directly bound to the MdSOD1 (superoxide dismutase 1) promoter and activated its transcription, thereby triggering reactive oxygen species (ROS) scavenging and enhancing apple drought tolerance. MdbHLH160 also promoted MdSOD1 enzyme activity and accumulation in the nucleus through direct protein interactions, thus inhibiting excessive nuclear ROS levels. Moreover, MdbHLH160 directly upregulated the expression of MdDREB2A-like, a DREB (dehydration-responsive element binding factor) family gene that promotes apple drought tolerance. Protein degradation and ubiquitination assays showed that drought and ABA treatment stabilized MdbHLH160. The BTB protein MdBT2 was identified as an MdbHLH160-interacting protein that promoted MdbHLH160 ubiquitination and degradation, and ABA treatment substantially inhibited this process. Overall, our findings provide insights into the molecular mechanisms of ABA-modulated drought tolerance at both the transcriptional and post-translational levels via the ABA–MdBT2–MdbHLH160–MdSOD1/MdDREB2A-like cascade.
What Can Voting Do for Democracy?
Authors: Pottle Justin 
Published: November 2023

Abstract
Empirical political scientists and normative political theorists alike have challenged the grip elections hold on our democratic imagination, albeit for very different reasons. Against both sets of critics, Emilee Booth Chapman’s remarkable and timely new book Election Day: How We Vote and What it Means for Democracy makes a compelling case for the ballot box’s unique place in democratic theory as a site of collective agency among political equals. Chapman offers an invaluable framework for navigating the shifting character of the American voting system and the innumerable proposals for improving it. But at the same time, this essay argues that in face of American democracy’s moral failures, Election Day reveals as much about the limits of well-ordered elections as it does their democratic promise.
Early-life risk factors, accelerated biological aging and the late-life risk of mortality and morbidity
Authors: Gao X , Wang Y , Song Z , Jiang M , Huang T , Baccarelli A A 
Published: November 2023

Summary

Background
Early-life exposure increases health risks throughout an individual’s lifetime. Biological aging is influenced by early-life risks as a key process of disease development, but whether early-life risks could accelerate biological aging and elevate late-life mortality and morbidity risks remains unknown. Knowledge is also limited on the potential moderating role of healthy lifestyle.

Methods
We investigate associations of three early-life risks around birth, breastfeeding, maternal smoking and birth weight, with biological aging of 202 580 UK Biobank participants (54.9 ± 8.1 years old). Biological aging was quantified as KDM-BA, PhenoAge and frailty. Moderate alcohol intake, no current smoking, healthy diet, BMI &lt;30 kg/m2 and regular physical activity were considered as healthy lifestyles. Mortality and morbidity data were retrieved from health records.

Results
Individual early-life risk factors were robustly associated with accelerated biological aging. A one-unit increase in the ‘early-life risk score’ integrating the three factors was associated with 0.060 (SE=0.0019) and 0.036-unit (SE = 0.0027) increase in z-scored KDM-BA acceleration and PhenoAge acceleration, respectively, and with 22.3% higher odds (95% CI: 1.185–1.262) of frailty. Increased chronological age and healthy lifestyles could mitigate the accelerations of KDM-BA and PhenoAge, respectively. Associations of early-life risk score with late-life mortality and morbidity were mediated by biological aging (proportions: 5.66–43.12%). KDM-BA and PhenoAge accelerations could significantly mediate the impact on most outcomes except anxiety, and frailty could not mediate the impact on T2D.

Conclusion
Biological aging could capture and mediate the late-life health risks stemming from the early-life risks, and could be potentially targeted for healthy longevity promotion.
Mapping the contributions of dyadic approaches to couples’ psychosocial adaptation to prostate cancer: a scoping review
Authors: Castro Rita F , Araújo Silvana , Marques Ana , Ferreira Diana , Rocha Hélia , Aguiar Sandra , Pieramico Sonia , Quinta-Gomes Ana , Tavares Inês M , Nobre Pedro J , Carvalho Joana 
Published: November 2023

Abstract

Introduction
Prostate cancer is the second-most prevalent cancer diagnosis worldwide among males. Although prostate cancer affects the physical, sexual, and mental health of patients, the impact of prostate cancer on partners has also been increasingly recognized. Hence, taking a dyadic approach is of relevance. Moreover, there is evidence of the utility of dyadic approaches to the study of relational stress that chronic diseases such as prostate cancer can bring to couples, even though knowledge is sparse about prostate cancer.

Objectives
This scoping review aimed to map existing dyadic studies on the psychosocial adaptation of couples to prostate cancer.

Methods
A systematic search of studies published from 2005 to November 2022 was conducted on electronic databases (PubMed, Cochrane Library, EBSCOHost, Scopus, and Web of Science) following PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-analyses–Extension for Scoping Reviews).

Results
The review included 25 eligible studies from the initial 2514 articles retrieved. Overall, the results emphasized the interdependency between couple members and suggested how partners’ adaptation influences patients’ adaptation to prostate cancer and vice versa, regarding several psychosocial dimensions (eg, intimacy, quality of life).

Conclusions
This work can bring awareness to health care professionals to adopt a couples approach when managing prostate cancer whenever there is a partner, due to these interdependent influences. For researchers and future studies, this work can strengthen the relevance of dyadic approaches on how couples adapt to prostate cancer and explore which other dimensions influence these complex dynamics.
Bark wounding triggers gradual embolism spreading in two diffuse-porous tree species
Authors: Jupa Radek , Pokorná Kamila 
Published: November 2023

Abstract
Xylem transport is essential for the growth, development and survival of vascular plants. Bark wounding may increase the risk of xylem transport failure by tension-driven embolism. However, the consequences of bark wounding for xylem transport are poorly understood. Here, we examined the impacts of the bark wounding on embolism formation, leaf water potential and gas exchange in the terminal branches of two diffuse-porous tree species (Acer platanoides L. and Prunus avium L.). The effects of bark removal were examined on field-grown mature trees exposed to increased evaporative demands on a short-term and longer-term basis (6 h vs 6 days after bark wounding). Bark removal of 30% of branch circumference had a limited effect on the xylem hydraulic conductivity when embolized vessels were typically restricted to the last annual ring near the bark wound. Over the 6-day exposure, the non-conductive xylem area had significantly increased in the xylem tissue underneath the bark wound (from 22–29% to 51–52% of the last annual ring area in the bark wound zone), pointing to gradual yet relatively limited embolism spreading to deeper xylem layers over time. In both species, the bark removal tended to result in a small but non-significant increase in the percent loss of hydraulic conductivity compared with control intact branches 6 days after bark wounding (from 6 to 8–10% in both species). The bark wounding had no significant effects on midday leaf water potential, CO2 assimilation rates, stomatal conductance and water-use efficiency of the leaves of the current-year shoot, possibly due to limited impacts on xylem transport. The results of this study demonstrate that bark wounding induces limited but gradual embolism spreading. However, the impacts of bark wounding may not significantly limit water delivery to distal organs and leaf gas exchange at the scale of several days.
Making Data Count: Estimating a Poverty Trend for Nigeria between 2009 and 2019
Authors: Lain Jonathan , Schoch Marta , Vishwanath Tara 
Published: November 2023

Abstract
Monitoring poverty reduction requires frequent microdata on household welfare that can be compared over time. Such data are unavailable in many countries, given limited statistical capacity, shocks that prevent data collection, and regular improvements to survey methodology. This paper demonstrates how jointly deploying backcasting and survey-to-survey imputations can help to overcome this in a setting where estimating a poverty trend is badly needed, given the scale of the poverty-reduction challenge, but where survey-to-survey imputations are more likely to succeed and can be directly tested. In Nigeria, the most recent official survey that can be used to construct an imputation model was collected through the same methodology and in the same year as the target survey. This data landscape could arise in other settings where the methodology for smaller, interstitial surveys is updated more quickly than for larger, official consumption surveys. Naively comparing Nigeria's last two official consumption surveys would suggest that the poverty rate fell by 17 percentage points between 2009 and 2019. Yet the methods presented in this paper both suggest a much smaller reduction in poverty of between 3 and 7 percentage points, echoing Nigeria's performance on nonmonetary welfare indicators over the same period. The paper therefore provides guidance on when and how backcasting and survey-to-survey imputation techniques can be most valuable for monitoring poverty reduction.
Comparison of midurethral tape with autologous rectus fascial sling surgery for stress urinary incontinence: A systematic review and meta-analysis
Authors: Güler Yavuz 
Published: November 2023

Abstract

Objectives
To compare the success rates of autologous fascial mesh (sling and transobturator tape [TOT]) with midurethral synthetic meshes (tension-free vaginal tape sling [TVT] and TOT) for stress urinary incontinence.

Materials and methods
A literature search for studies published in English was conducted from May 10, 2022, to June 1, 2022. The search included MEDLINE/PubMed, Cochrane Library, Scopus, Web of Science, Google Scholar, and ProQuest, using the terms{“Autologous fascial slings”}OR {“AFS”} AND{“TOT”} OR {“Transobturator tape”} OR{“TVT”} OR{“Transvaginal tape”}. A total of 20 studies, including 10 randomized controlled trials, were selected for the review. RevMan software (version 5.3) was used to calculate the pooled effect estimates for operative and postoperative variables.

Results
In the systemic review, 20 studies, including 10 randomized controlled trials, were assessed. In the TVT versus autologous pubovaginal sling (A-PVS) groups, the effect estimates for the surgical duration, catheter duration, success, and complication rates were more advantageous for TVT. However, in comparison to autologous transobturator tape groups, TOT provided better operative time and a shorter hospital stay. Moreover, in comparison to the A-PVS group, the TOT group was superior in terms of operating time, urethral catheterization, hospital stay, amount of residual urine, and wound complications. The A-PVS group had significantly more groin and thigh pain.

Conclusions
During medium- and long-term follow-ups, the use of autologous rectus fascia grafts using a A-PVS or TOT provided similar complication rates and urinary continence results as using midurethral synthetic meshes (TVT and TOT).
Partial versus radical nephrectomy for T1b renal cell carcinoma: A comparison of efficacy and prognostic factors based on the Surveillance, Epidemiology, and End Results database
Authors: Ren Kong , Wu Fei , Wu Haihu , Ning Hao , Lyu Jiaju 
Published: November 2023

Abstract

Objectives
This study compared the long-term efficacy and prognostic factors of partial nephrectomy (PN) and radical nephrectomy (RN) for T1bN0M0 renal cell carcinoma (RCC) using data from the Surveillance, Epidemiology, and End Results database.

Materials and methods
We retrospectively analyzed the clinical data of 12,471 patients diagnosed with T1bN0M0 RCC from the Surveillance, Epidemiology, and End Results database between 2010 and 2019. Patients were divided into the PN and RN groups, and propensity score matching was conducted to balance the differences between the groups. We compared overall survival (OS), RCC cancer–specific mortality (CSM), and noncancer-specific mortality (NCSM) between the 2 groups. The risk factors for all-cause and RCC-related mortality were analyzed.

Results
After propensity score matching, there were 3817 patients in each group. After matching, OS and NCSM were significantly longer in the PN group (p < 0.001); however, there was no significant between-group difference in the RCC-CSM. The hazard ratio (HR) for all-cause mortality was significantly lower in the PN group (HR, 0.671; 95% confidence interval [CI], 0.579–0.778, p < 0.001), but PN was not associated with lower RCC-related mortality. Subgroup analysis showed that PN reduced the HR of all-cause mortality by 35% (HR, 0.647; 95% CI, 0.536–0.781; p < 0.001) in patients with 4.0- to 5.5-cm tumors compared with RN and by 29% (HR, 0.709; 95% CI, 0.559–0.899; p = 0.004) in those with larger tumors (5.6–7.0 cm). Multifactorial analysis showed that PN was an independent predictor of OS (HR, 0.671; 95% CI, 0.579–0.778; p < 0.001). In addition, multivariate analysis validated that age at diagnosis, sex, pathological grade, and tumor size were associated with outcomes.

Conclusions
In patients with T1b RCC, PN resulted in better OS and NCSM outcomes than RN. The benefit of PN in all-cause mortality was pronounced in patients with 4.0–5.5 cm tumor loads. Therefore, individualized treatment schemes should prioritize PN, when technically feasible.
HMGB2 is a potential diagnostic marker and therapeutic target for liver fibrosis and cirrhosis
Authors: Huang Yi , Liangpunsakul Suthat , Rudraiah Swetha , Ma Jing , Keshipeddy Santosh K. , Wright Dennis , Costa Antonio , Burgess Diane , Zhang Yuxia , Huda Nazmul , Wang Li , Yang Zhihong 
Published: November 2023

Background:
High mobility group proteins 1 and 2 (HMGB1 and HMGB2) are 80% conserved in amino acid sequence. The function of HMGB1 in inflammation and fibrosis has been extensively characterized. However, an unaddressed central question is the role of HMGB2 on liver fibrosis. In this study, we provided convincing evidence that the HMGB2 expression was significantly upregulated in human liver fibrosis and cirrhosis, as well as in several mouse liver fibrosis models.

Methods:
The carbon tetrachloride (CCl4) induced liver fibrosis mouse model was used. AAV8-Hmgb2 was utilized to overexpress Hmgb2 in the liver, while Hmgb2−/−
mice were used for loss of function experiments. The HMGB2 inhibitor inflachromene and liposome-shHMGB2 (lipo-shHMGB2) were employed for therapeutic intervention.

Results:
The serum HMGB2 levels were also markedly elevated in patients with liver fibrosis and cirrhosis. Deletion of Hmgb2 in Hmgb2−/−
mice or inhibition of HMGB2 in mice using a small molecule ICM slowed the progression of CCl4-induced liver fibrosis despite constant HMGB1 expression. In contrast, AAV8-mediated overexpression of Hmgb2 enchanced CCl4-incuded liver fibrosis. Primary hepatic stellate cells (HSCs) isolated from Hmgb2−/−
mice showed significantly impaired transdifferentiation and diminished activation of α-SMA, despite a modest induction of HMGB1 protein. RNA-seq analysis revealed the induction of top 45 CCl4-activated genes in multiple signaling pathways including integrin signaling and inflammation. The activation of these genes by CCl4 were abolished in Hmgb2−/−
mice or in ICM-treated mice. These included C-X3-C motif chemokine receptor 1 (Cx3cr1) associated with inflammation, cyclin B (Ccnb) associated with cell cycle, DNA topoisomerase 2-alpha (Top2a) associated with intracellular component, and fibrillin (Fbn) and fibromodulin (Fmod) associated with extracellular matrix.

Conclusion:
We conclude that HMGB2 is indispensable for stellate cell activation. Therefore, HMGB2 may serve as a potential therapeutic target to prevent HSC activation during chronic liver injury. The blood HMGB2 level may also serve as a potential diagnostic marker to detect early stage of liver fibrosis and cirrhosis in humans.
Relationship Between Sleep Quality and Constipation Severity in Patients With Parkinson Disease: A Cross-sectional Study
Authors: Doi Tomoko , Honda Ikumi , Nakajima Maki , Tamaoki Miharu , Hirayama Masaaki 
Published: November 2023

ABSTRACT

BACKGROUND: Constipation in patients with Parkinson disease (PD) adversely affects motor symptoms, making defecation management critical. Sleep disturbance is another common complaint in patients with PD (PWP). Associations between sleep disturbances and constipation have been reported in recent studies on PD. If improving sleep quality is useful for managing constipation in PWP, it might serve as a new method of constipation management that is less physically and mentally distressing than laxatives. This study aimed to examine the relationship between sleep quality and constipation severity in PWP. METHODS: We administered a questionnaire on sleep and constipation to 1048 PWP. Constipation severity was assessed using Constipation Assessment Scale Japanese version 2 (CAS). General sleep quality was estimated using the Japanese versions of the Pittsburgh Sleep Quality Index (PSQI) and Athens Insomnia Scale. Sleep quality due to PD-specific nighttime problems was estimated using the Parkinson's Disease Sleep Scale-2 Japanese version (PDSS-2). We conducted a multiple regression analysis using the forced entry method to identify the variables that influenced CAS. RESULTS: We analyzed 350 PWP. Overall, 94.9% of PWP had constipation symptoms. The percentages of PWP with poor sleep were as follows: PSQI, 74.7%; Athens Insomnia Scale, 69.8%; and PDSS-2, 73.8%. Furthermore, 17.6% of the patients with constipation and 35.3% with sleep problems did not consult a healthcare provider. Multivariate analysis revealed that CAS was significantly associated only with PDSS-2 (standardized partial regression coefficient, 0.217; 95% confidence interval, 0.030-0.111). CONCLUSION: Poor sleep quality, related to PD-specific nighttime problems, was found be associated with worsening constipation severity. Nursing activities that help PWP with PD-specific nighttime problems have a more comfortable night's sleep would be key to alleviating constipation severity.