bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography
Authors: Bukhman Yury V , Morin Phillip A , Meyer Susanne , Chu Li-Fang , Jacobsen Jeff K , Antosiewicz-Bourget Jessica , Mamott Daniel , Gonzales Maylie , Argus Cara , Bolin Jennifer , Berres Mark E , Fedrigo Olivier , Steill John , Swanson Scott A , Jiang Peng , Rhie Arang , Formenti Giulio , Phillippy Adam M , Harris Robert S , Wood Jonathan M D , Howe Kerstin , Kirilenko Bogdan M , Munegowda Chetan , Hiller Michael , Jain Aashish , Kihara Daisuke , Johnston J Spencer , Ionkov Alexander , Raja Kalpana , Toh Huishi , Lang Aimee , Wolf Magnus , Jarvis Erich D , Thomson James A , Chaisson Mark J P , Stewart Ron 
Published: February 2024

Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
Maternal nitric oxide homeostasis impacts female gametophyte development under optimal and stress conditions
Authors: Wang Junzhe , Guo Xiaolong , Chen Yijin , Liu Tianxiang , Zhu Jianchu , Xu Shengbao , Vierling Elizabeth 
Published: February 2024

Abstract
In adverse environments, the number of fertilizable female gametophytes (FGs) in plants is reduced, leading to increased survival of the remaining offspring. How the maternal plant perceives internal growth cues and external stress conditions to alter FG development remains largely unknown. We report that homeostasis of the stress signaling molecule nitric oxide (NO) plays a key role in controlling FG development under both optimal and stress conditions. NO homeostasis is precisely regulated by S-nitrosoglutathione reductase (GSNOR). Prior to fertilization, GSNOR protein is exclusively accumulated in sporophytic tissues and indirectly controls FG development in Arabidopsis (Arabidopsis thaliana). In GSNOR null mutants, NO species accumulated in the degenerating sporophytic nucellus, and auxin efflux into the developing FG was restricted, which inhibited FG development, resulting in reduced fertility. Importantly, restoring GSNOR expression in maternal, but not gametophytic tissues, or increasing auxin efflux substrate significantly increased the proportion of normal FGs and fertility. Furthermore, GSNOR overexpression or added auxin efflux substrate increased fertility under drought and salt stress. These data indicate that NO homeostasis is critical to normal auxin transport and maternal control of FG development, which in turn determine seed yield. Understanding this aspect of fertility control could contribute to mediating yield loss under adverse conditions.
Robust Implementation with Costly Information
Authors: Pei Harry , Strulovici Bruno 
Published: February 2024

Abstract
We construct mechanisms that can robustly implement any desired social choice function when (1) agents may incur a cost to learn the state of the world, (2) with small probability, agents’ preferences can be arbitrarily different from some baseline known to the mechanism designer, and (3) the mechanism designer does not know agents’ beliefs and higher-order beliefs about one another’s preferences. The mechanisms we propose have a natural interpretation and do not require the mechanism designer to be able to verify the state ex post. We also establish impossibility results for stronger notions of robust implementation.
HucMSCs Delay Muscle Atrophy After Peripheral Nerve Injury Through Exosomes by Repressing Muscle-Specific Ubiquitin Ligases
Authors: Chen Jian , Zhu Yaqiong , Gao Hui , Chen Xianghui , Yi Dan , Li MoLin , Wang Li , Xing Guanhui , Chen Siming , Tang Jie , Wang Yuexiang 
Published: February 2024

Abstract
Cell therapy based on mesenchymal stem cells (MSCs) alleviate muscle atrophy caused by diabetes and aging; however, the impact of human umbilical cord mesenchymal stem cells on muscle atrophy following nerve injury and the underlying mechanisms remain unclear. In this study, we evaluated the therapeutic efficacy of human umbilical cord MSCs (hucMSCs) and hucMSC-derived exosomes (hucMSC-EXOs) for muscle atrophy following nerve injury and identified the underlying molecular mechanisms. Sciatic nerve crush injury in rats and the induction of myotubes in L6 cells were used to determine the ameliorating effect of hucMSCs and hucMSC-EXOs on muscle atrophy. Q-PCR and Western blot analyses were used to measure the expression of muscle-specific ubiquitin ligases Fbxo32 (Atrogin1, MAFbx) and Trim63 (MuRF-1). Dual-luciferase reporter gene experiments were conducted to validate the direct binding of miRNAs to their target genes. Local injection of hucMSCs and hucMSC-EXOs mitigated atrophy in the rat gastrocnemius muscle following sciatic nerve crush injury. In vitro, hucMSC-EXOs alleviated atrophy in L6 myotubes. Mechanistic analysis indicated the upregulation of miR-23b-3p levels in L6 myotubes following hucMSC-EXOs treatment. MiR-23b-3p significantly inhibited the expression of its target genes, Fbxo32 and Trim63, and suppressed myotube atrophy. Notably, an miR-23b-3p inhibitor reversed the inhibitory effect of miR-23b-3p on myotube atrophy in vitro. These results suggest that hucMSCs and their exosomes alleviate muscle atrophy following nerve injury. MiR-23b-3p in exosomes secreted by hucMSCs contributes to this mechanism by inhibiting the muscle-specific ubiquitination ligases Fbxo32 and Trim63.
Impacts of economic factors influencing net returns of beef feedlot heifers administered two implant programs and fed for differing days-on-feed from pooled randomized controlled trials
Authors: Horton Lucas M , Depenbusch Brandon E , Schroeder Ted C , Pendell Dustin L , Streeter Marshall N , Hutcheson John P , Renter David G 
Published: February 2024

Abstract
The objective of this research was to evaluate the effects of two implant programs and differing days-on-feed (DOF) on net returns of beef feedlot heifers using sensitivity analyses of key economic factors. Crossbred beef heifers [n = 10,583; initial weight 315 kg (± 20.1 SD)] were enrolled across three trials (one Kansas, two Texas feedlot trials). Heifers were blocked by arrival and randomly allocated to one of six pens, resulting in a total of 144 pens and 24 blocks. Pen was randomly assigned to treatment as a 2 × 3 factorial. Implant programs were: IH + 200—Revalor-IH at initial processing, and a terminal implant after approximately 90 DOF (Revalor-200), or, XH—a single implant at initial processing (Revalor-XH). The DOF treatments were: heifers fed to a standard baseline endpoint (BASE) or heifers fed for an additional + 21 or + 42 d beyond BASE. Pen-level partial budgets were used for economic sensitivity analyses, which varied price points of single pricing components with all other components fixed. Variable components were live-fed cattle prices, base carcass prices (i.e., dressed), Choice-Select spread (CS-spread), and feed and yardage prices (FYP). For each, a Low, Mid-Low, Middle, Mid-High, and High price was chosen. Linear mixed models were fit for statistical analyses (α = 0.05). There were no significant two-way interactions (P-values ≥ 0.14). Regardless of the variable component evaluated, XH heifers had poorer net returns than IH + 200 at all prices (P ≤ 0.04). Selling live, the + 21 and (or) + 42 heifers had lower net returns than BASE at every fed cattle price point (P &lt; 0.01). Selling dressed, the + 21 and (or) + 42 heifers had lower returns than BASE at Low, Mid-Low, and Middle fed cattle base prices (P &lt; 0.01); there were no significant DOF differences at Mid-High, or High prices (P ≥ 0.24). Net returns were lower for + 42 than BASE at all CS-spreads (P ≤ 0.03), while BASE and + 21 did not differ significantly. Longer DOF had lower net returns than BASE when selling live at every FYP (P &lt; 0.01) except at the Low price (P = 0.14). Selling dressed, there was no significant effect of DOF at Low or Mid-Low FYP (P ≥ 0.11); conversely, extended DOF had lower net returns than BASE at Middle, Mid-High, and High FYP (P &lt; 0.01). Overall, there was minimal economic evidence to support extending feedlot heifer DOF beyond the BASE endpoint, and when feeding longer, larger reductions in return were observed when marketing live as opposed to dressed.
Parenteral nutrition-associated liver injury: clinical relevance and mechanistic insights
Authors: Mihajlovic Milos , Rosseel Zenzi , De Waele Elisabeth , Vinken Mathieu 
Published: February 2024

Abstract
Intestinal failure-associated liver disease (IFALD) is a relatively common complication in individuals receiving parenteral nutrition (PN). IFALD can be manifested as different types of liver injury, including steatosis, cholestasis, and fibrosis, and could result in liver failure in some cases. The onset and progression of IFALD are highly dependent on various patient and PN-related risk factors. Despite still being under investigation, several mechanisms have been proposed. Liver injury can originate due to caloric overload, nutrient deficiency, and toxicity, as well as phytosterol content, and omega-6 to omega-3 fatty acids ratio contained in lipid emulsions. Additional mechanisms include immature or defective bile acid metabolism, acute heart failure, infections, and sepsis exerting negative effects via Toll-like receptor 4 and nuclear factor κB inflammatory signaling. Furthermore, lack of enteral feeding, gut dysbiosis, and altered enterohepatic circulation that affect the farnesoid x receptor-fibroblast growth factor 19 axis can also contribute to IFALD. Various best practices can be adopted to minimize the risk of developing IFALD, such as prevention and management of central line infections and sepsis, preservation of intestine’s length, a switch to oral and enteral feeding, cyclic PN, avoidance of overfeeding and soybean oil-based lipid formulations, and avoiding hepatotoxic substances. The present review thus provides a comprehensive overview of all relevant aspects inherent to IFALD. Further research focused on clinical observations, translational models, and advanced toxicological knowledge frameworks is needed to gain more insight into the molecular pathogenesis of hepatotoxicity, reduce IFALD incidence, and encourage the safe use of PN.
Comparing Methods for Detection and Quantification of Plasmodesmal Callose in Nicotiana benthamiana Leaves During Defense Responses
Authors: Sankoh Amie F. , Adjei Joseph , Roberts Daniel M. , Burch-Smith Tessa M. 
Published: February 2024

Callose, a β-(1,3)-d-glucan polymer, is essential for regulating intercellular trafficking via plasmodesmata (PD). Pathogens manipulate PD-localized proteins to enable intercellular trafficking by removing callose at PD or, conversely, by increasing callose accumulation at PD to limit intercellular trafficking during infection. Plant defense hormones like salicylic acid regulate PD-localized proteins to control PD and intercellular trafficking during immune defense responses such as systemic acquired resistance. Measuring callose deposition at PD in plants has therefore emerged as a popular parameter for assessing likely intercellular trafficking activity during plant immunity. Despite the popularity of this metric, there is no standard for how these measurements should be made. In this study, three commonly used methods for identifying and quantifying plasmodesmal callose by aniline blue staining were evaluated to determine the most effective in the Nicotiana benthamiana leaf model. The results reveal that the most reliable method used aniline blue staining and fluorescence microscopy to measure callose deposition in fixed tissue. Manual or semiautomated workflows for image analysis were also compared and found to produce similar results, although the semiautomated workflow produced a wider distribution of data points. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
A Colletotrichum tabacum Effector Cte1 Targets and Stabilizes NbCPR1 to Suppress Plant Immunity
Authors: Xue Yuan , Pan Shouhui , Zhang Quan , Dai Fei , Zhang Junxiang 
Published: February 2024

Colletotrichum tabacum, causing anthracnose in tobacco, is a notorious plant pathogen threatening tobacco production globally. The underlying mechanisms of C. tabacum effectors that interfere with plant defense are not well known. Here, we identified a novel effector, Cte1, from C. tabacum, and its expression was upregulated in the biotrophic stage. We found that Cte1 depresses plant cell death initiated by BAX and inhibits reactive oxygen species (ROS) bursts triggered by flg22 and chitin in Nicotiana benthamiana. The CTE1 knockout mutants decrease the virulence of C. tabacum to N. benthamiana, and the Cte1 transgenic N. benthamiana increase susceptibility to C. tabacum, verifying that Cte1 is involved in the pathogenicity of C. tabacum. We demonstrated that Cte1 interacted with NbCPR1, a Constitutive expresser of Plant Resistance (CPR) protein in plants. Silencing of NbCPR1 expression attenuated the infection of C. tabacum, indicating that NbCPR1 negatively regulates plant immune responses. Cte1 stabilizes NbCPR1 in N. benthamiana. Our study shows that Cte1 suppresses plant immunity to facilitate C. tabacum infection by intervening in the native function of NbCPR1. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
Practices of Patient Relatives Aimed at Preventing Pressure Injuries and Their Experiences of Coping with the Burden of Care: A Qualitative Study
Authors: Ulutaşdemir Nilgün , Ay Halil , Göçmen Adalet , Uzun Sevda , Kulakaç Nurşen 
Published: February 2024

ABSTRACT

OBJECTIVE
To determine the practices and coping experiences of the relatives of patients with pressure injuries (PIs).

METHODS
The authors used a qualitative, phenomenologic research design. They interviewed 20 relatives of patients with PIs face-to-face using an in-depth semistructured interview form. The data were analyzed using the Colaizzi phenomenologic method.

RESULTS
Three categories, 8 main themes, and 22 subthemes emerged from the interviews. The category of “the impact of the need for care on the lives of the patient’s relatives” was analyzed according to psychological, social, and physical effects. In the category of “practices to prevent pressure injuries,” two themes emerged: practices toward the patient and the environment. Relatives of individuals with PIs have psychological, physical, and social needs.

CONCLUSIONS
Providing care to a patient with PIs has psychological, social, and physical effects on the patient’s relatives. The care burden mostly affects these caregivers negatively, and they mainly need time for themselves and moral and companion support.
Complication Rates Following Adult Spinal Deformity Surgery
Authors: Lafage Renaud , Bass R. Daniel , Klineberg Eric , Smith Justin S. , Bess Shay , Shaffrey Christopher , Burton Douglas C. , Kim Han Jo , Eastlack Robert , Mundis Gregory , Ames Christopher P. , Passias Peter G. , Gupta Munish , Hostin Richard , Hamilton Kojo , Schwab Frank , Lafage Virginie ,   on behalf of the International Spine Study Group
Published: February 2024

Objective.
Provide benchmarks for the rates of complications by type and timing.

Study Design.
Prospective multicenter database.

Background.
Complication rates following adult spinal deformity (ASD) surgery have been previously reported. However, the interplay between timing and complication type warrants further analysis.

Methods.
The data for this study were sourced from a prospective, multicenter ASD database. The date and type of complication were collected and classified into three severity groups (minor, major, and major leading to reoperation). Only complications occurring before the two-year visit were retained for analysis.

Results.
Of the 1260 patients eligible for two-year follow-up, 997 (79.1%) achieved two-year follow-up. The overall complication rate was 67.4% (N=672). 247 patients (24.8%) experienced at least one complication on the day of surgery (including intraoperatively), 359 (36.0%) between postoperative day 1 and six weeks postoperatively, 271 (27.2%) between six weeks and one-year postoperatively, and finally 162 (16.3%) between one year and two years postoperatively. Using Kaplan-Meier survival analysis, the rate of remaining complication-free was estimated at different time points for different severities and types of complications. Stratification by type of complication demonstrated that most of the medical complications occurred within the first 60 days. Surgical complications presented over two distinct timeframes. Operative complications, incision-related complications, and infections occurred early (within 60 d), while implant-related and radiographic complications occurred at a constant rate over the two-year follow-up period. Neurological complications had the highest occurrence within the first 60 days but continued to increase up to the two-year visit.

Conclusion.
Only one-third of ASD patients remained complication-free by two years, and 2 of 10 patients had a complication requiring a reoperation or revision. An estimation of the timing and type of complications associated with surgical treatment may prove useful for more meaningful patient counseling and aid in assessing the cost-effectiveness of treatment.

Level of Evidence.
3.
Inhaled Volatiles for Status Asthmaticus, Epilepsy, and Difficult Sedation in Adult ICU and PICU: A Systematic Review
Authors: Gorsky Kevin , Cuninghame Sean , Jayaraj Kesikan , Slessarev Marat , Francoeur Conall , Withington Davinia E. , Chen Jennifer , Cuthbertson Brian H. , Martin Claudio , Chapman Martin , Ganesan Saptharishi Lalgudi , McKinnon Nicole , Jerath Angela ,   on behalf of the SAVE-ICU Study Investigators
Published: February 2024

OBJECTIVES:
Inhaled volatile anesthetics support management of status asthmaticus (SA), status epilepticus (SE), and difficult sedation (DS). This study aimed to evaluate the effectiveness, safety, and feasibility of using inhaled anesthetics for SA, SE, and DS in adult ICU and PICU patients.

DATA SOURCES:
MEDLINE, Cochrane Central Register of Controlled Trials, and Embase.

STUDY SELECTION:
Primary literature search that reported the use of inhaled anesthetics in ventilated patients with SA, SE, and DS from 1970 to 2021.

DATA EXTRACTION:
Study data points were extracted by two authors independently. Quality assessment was performed using the Joanna Briggs Institute appraisal tool for case studies/series, Newcastle criteria for cohort/case–control studies, and risk-of-bias framework for clinical trials.

DATA SYNTHESIS:
Primary outcome was volatile efficacy in improving predefined clinical or physiologic endpoints. Secondary outcomes were adverse events and delivery logistics. From 4281 screened studies, the number of included studies/patients across diagnoses and patient groups were: SA (adult: 38/121, pediatric: 28/142), SE (adult: 18/37, pediatric: 5/10), and DS (adult: 21/355, pediatric: 10/90). Quality of evidence was low, consisting mainly of case reports and series. Clinical and physiologic improvement was seen within 1–2 hours of initiating volatiles, with variable efficacy across diagnoses and patient groups: SA (adult: 89–95%, pediatric: 80–97%), SE (adults: 54–100%, pediatric: 60–100%), and DS (adults: 60–90%, pediatric: 62–90%). Most common adverse events were cardiovascular, that is, hypotension and arrhythmias. Inhaled sedatives were commonly delivered using anesthesia machines for SA/SE and miniature vaporizers for DS. Few (10%) of studies reported required non-ICU personnel, and only 16% had ICU volatile delivery protocol.

CONCLUSIONS:
Volatile anesthetics may provide effective treatment in patients with SA, SE, and DS scenarios but the quality of evidence is low. Higher-quality powered prospective studies of the efficacy and safety of using volatile anesthetics to manage SA, SE, and DS patients are required. Education regarding inhaled anesthetics and the protocolization of their use is needed.
Superior Pedicle Inverted T-reduction Mammaplasty with Short Horizontal Scar
Authors: Arbeláez Sergio , Arbeláez Sergio A. , Eslait Rosa C. , Lacouture Carlos J. 
Published: February 2024

Background:
Superior pedicle breast reduction is a very popular technique among plastic surgeons. This technique has had many variations looking for fewer complications and better long-lasting results. The aim of this article is to present a novel technique of breast reduction, making variations in the design of the periareolar incision, using a superior pedicle with a constant vertical incision of 5 cm and a shortened horizontal incision.

Methods:
The superior pedicle inverted T-mammoplasty with a shortened horizontal scar technique was performed in 1200 patients who underwent surgery between 2010 and 2023; follow-up examination was carried out for an average of 1 year (3 months to 3 years). A patient satisfaction survey was conducted.

Results:
Patient satisfaction rate was 99%. There were no cases of total necrosis of the areola–nipple complex, 2.7% of the patients presented partial necrosis of the areola–nipple complex, 1.4% of the patients presented local infection, 1.7% presented dehiscence at some point of the vertical or horizontal suture, 4% of the patients presented a widened scar, 8% of the patients presented alteration in the sensibility of the areola–nipple complex, and 0.6% of the patients presented hematoma. With this technique, a rise of the areola–nipple complex of up to 22cm was achieved.

Conclusions:
The superior pedicle inverted T-mammaplasty with shortened horizontal scar technique showed a lower number of surgical complications compared with other techniques previously used for breast reduction, even when applied in gigantomasty. It provides lasting results and a high rate of patient satisfaction.