bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do patients who read visit notes on the patient portal have a higher rate of “loop closure” on diagnostic tests and referrals in primary care? A retrospective cohort study
Authors: Bell Sigall K , Amat Maelys J , Anderson Timothy S , Aronson Mark D , Benneyan James C , Fernandez Leonor , Ricci Dru A , Salant Talya , Schiff Gordon D , Shafiq Umber , Singer Sara J , Sternberg Scot B , Zhang Cancan , Phillips Russell S 
Published: January 2024

Abstract

Objectives
The 2021 US Cures Act may engage patients to help reduce diagnostic errors/delays. We examined the relationship between patient portal registration with/without note reading and test/referral completion in primary care.

Materials and methods
Retrospective cohort study of patients with visits from January 1, 2018 to December 31, 2021, and order for (1) colonoscopy, (2) dermatology referral for concerning lesions, or (3) cardiac stress test at 2 academic primary care clinics. We examined differences in timely completion (“loop closure”) of tests/referrals for (1) patients who used the portal and read ≥1 note (Portal + Notes); (2) those with a portal account but who did not read notes (Portal Account Only); and (3) those who did not register for the portal (No Portal). We estimated the predictive probability of loop closure in each group after adjusting for socio-demographic and clinical factors using multivariable logistic regression.

Results
Among 12 849 tests/referrals, loop closure was more common among Portal+Note-readers compared to their counterparts for all tests/referrals (54.2% No Portal, 57.4% Portal Account Only, 61.6% Portal+Notes, P &lt; .001). In adjusted analysis, compared to the No Portal group, the odds of loop closure were significantly higher for Portal Account Only (OR 1.2; 95% CI, 1.1-1.4), and Portal+Notes (OR 1.4; 95% CI, 1.3-1.6) groups. Beyond portal registration, note reading was independently associated with loop closure (P = .002).

Discussion and conclusion
Compared to no portal registration, the odds of loop closure were 20% higher in tests/referrals for patients with a portal account, and 40% higher in tests/referrals for note readers, after controlling for sociodemographic and clinical factors. However, important safety gaps from unclosed loops remain, requiring additional engagement strategies.
Utilization of Topical Polysporin and Triamcinolone for the Treatment of Hypergranulation Tissue
Authors: Maynell Kimberly Brown , West William , Marek Jenna , Wright Benjamin , Bodnar Michael , Le Nicole K , Whalen Kristen , Taylor Loryn , Troy Jared , Smith David , Laun Jake 
Published: January 2024

Abstract
Hypergranulation is the abnormal accumulation of granulation tissue in a wound and is commonly seen in burns. It impairs wound healing and can predispose patients to infection. There is no gold standard treatment for hypergranulation tissue, but some options include surgical debridement, chemical cautery with silver nitrate, and topical steroids. Silver nitrate treatment is painful and can lead to scarring, so topical steroid use is on the rise. A retrospective review, between January 1, 2017 and August 30, 2021, at a tertiary burn center was performed to analyze outcomes of hypergranulation tissue after treatment with a topical 50/50 mixture of triamcinolone (Perrigo, Dublin, Ireland) and Polysporin (Johnson & Johnson, New Brunswick, NJ). One hundred and sixteen patients were treated with triamcinolone and Polysporin for hypergranulation tissue, although 24 did not meet inclusion criteria. Eighty-eight out of 92 patients were successfully treated until hypergranulation resolution, while 4/92(4.3%) required silver nitrate or surgery despite the topical cream to achieve resolution. In the 88 patients successfully treated until hypergranulation resolution, 99 areas of hypergranulation were treated. Forty-one of 99 (41.4%) hypergranulation areas resolved within 2 weeks. The average time to hypergranulation resolution was 27.5 ± 2.5 days. We found that a novel 50/50 mixture of triamcinolone and Polysporin topical ointment is an effective and safe treatment for hypergranulation tissue in burn wounds. Further prospective studies are needed to determine its efficacy and safety profile.
LepR-expressing cells are a critical population in periodontal healing post periodontitis
Authors: Xu Chunmei , Xie Xudong , Shi Peilei , Xue Kun , Li Yue , Wu Yafei , Wang Jun 
Published: January 2024

Abstract
Identification of promising seed cells plays a pivotal role in achieving tissue regeneration. This study demonstrated that LepR-expressing cells (LepR+ cells) are required for maintaining periodontal homeostasis at the adult stage. We further investigated how LepR+ cells behave in periodontal healing using a ligature-induced periodontitis (PD) and a self-healing murine model with LepRCre/+; R26RtdTomato/+ mice. Lineage tracing experiments revealed that the largely suppressed osteogenic ability of LepR+ cells results from periodontal inflammation. Periodontal defects were partially recovered when the ligature was removed, in which the osteogenic differentiation of LepR+ cell lineage was promoted and contributed to the newly formed alveolar bone. A cell ablation model established with LepRCre/+; R26RtdTomato/+; R26RDTA/+ mice further proved that LepR+ cells are an important cell source of newly formed alveolar bone. Expressions of β-catenin and LEF1 in LepR+ cells were upregulated when the inflammatory stimuli were removed, which are consistent with the functional changes observed during periodontal healing. Furthermore, the conditional upregulation of WNT signaling or the application of sclerostin neutralized antibody promoted the osteogenic function of LepR+ cells. In contrast, the specific knockdown of β-catenin in LepR+ human periodontal ligament cells with small interfering RNA caused arrested osteogenic function. Our findings identified the LepR+ cell lineage as a critical cell population for endogenous periodontal healing post PD, which is regulated by the WNT signaling pathway, making it a promising seed cell population in periodontal tissue regeneration.
Osteoclast-specific Plastin 3 knockout in mice fail to develop osteoporosis despite dramatic increased osteoclast resorption activity
Authors: Maus Ilka , Dreiner Maren , Zetzsche Sebastian , Metzen Fabian , Ross Bryony C , Mählich Daniela , Koch Manuel , Niehoff Anja , Wirth Brunhilde 
Published: January 2024

Abstract
PLS3 loss-of-function mutations in humans and mice cause X-linked primary osteoporosis. However, it remains largely unknown how PLS3 mutations cause osteoporosis and which function PLS3 plays in bone homeostasis. A recent study showed that ubiquitous Pls3 KO in mice results in osteoporosis. Mainly osteoclasts were impacted in their function However, it has not been proven if osteoclasts are the major cell type affected and responsible for osteoporosis development in ubiquitous Pls3 KO mice. Here, we generated osteoclast-specific Pls3 KO mice. Additionally, we developed a novel polyclonal PLS3 antibody that showed specific PLS3 loss in immunofluorescence staining of osteoclasts in contrast to previously available antibodies against PLS3, which failed to show PLS3 specificity in mouse cells. Moreover, we demonstrate that osteoclast-specific Pls3 KO causes dramatic increase in resorptive activity of osteoclasts in vitro. Despite these findings, osteoclast-specific Pls3 KO in vivo failed to cause any osteoporotic phenotype in mice as proven by micro-CT and three-point bending test. This demonstrates that the pathomechanism of PLS3-associated osteoporosis is highly complex and cannot be reproduced in a system singularly focused on one cell type. Thus, the loss of PLS3 in alternative bone cell types might contributes to the osteoporosis phenotype in ubiquitous Pls3 KO mice.
Grower perceptions and adoption of IPM and non-Bt refuge in field corn: a survey in North and South Carolina
Authors: Bryant Tim B , Greene Jeremy K , Reisig Dominic , Reay-Jones Francis P F 
Published: January 2024

Abstract
Production of field corn in the southeastern United States is often impacted by a number of insect pests. However, surveys to assess stakeholder perception of the relative importance of insect pests and adopted management decisions for these pests have not been extensively reported in the region. A survey was conducted in North and South Carolina to address deficiencies in our knowledge about how corn producers perceive insect pests, implement management and insect resistance strategies, and understand and implement integrated pest management (IPM). The survey indicated that stink bugs (Hemiptera: Pentatomidae) and corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), were the most commonly managed insect pests in field corn. For transgenic corn expressing insecticidal toxins from Bacillus thuringiensis (Bt) (Berliner), the rate of resistance management (i.e., planting of non-Bt corn refuge) implemented (59%) by growers was higher than previously reported. The majority of grower respondents identified ear development as the most critical corn growth stage for managing stink bugs (52%), with the most commonly reported management strategy being applications of insecticide at the economic threshold. Growers also reported understanding the concepts of IPM and implementing it in field corn. Assessing the adoption of preventative approaches, such as Bt corn and insecticide seed treatments, and strategies to manage insect resistance, in the case of Bt corn in particular, is critical for tailoring research and Extension efforts to protect the durability of these management tactics.
Social media as a tool to understand the distribution and ecology of elusive mammals
Authors: Phakoago Makabudi V , Maloney Shane K , Kamerman Peter R , Meyer Leith C R , Weyer Nora M , Fuller Andrea 
Published: January 2024

Abstract
Comparatively little is known about the distribution and ecology of Aardvark (Orycteropus afer) and Temminck’s Ground Pangolin (Smutsia temminckii). Both are elusive species that are normally nocturnal, solitary, and fossorial. Formally collected records have been used to map the distribution of these species, and social media records provide a tool to gather information on their distribution and ecology. We obtained 680 photographs and videos of aardvarks and 790 of ground pangolins in southern Africa from publicly available posts on Facebook and Instagram (2010–2019). The images provide new insights into the distribution, activity, drinking, and predation—and confirm that aardvarks are more diurnally active when they are in poor body condition. Social media can provide useful supplementary information for understanding of elusive mammals. These “soft” data can be applied to other species.
Whole-brain traumatic controlled cortical impact to the left frontal lobe: Magnetic resonance image-based texture analysis
Authors: Alanezi Saleh T , Almutairi Waleed M , Cronin Michelle , Gobbo Oliviero , O’Mara Shane M , Sheppard Declan , O’Connor William T , Gilchrist Michael D , Kleefeld Christoph , Colgan Niall 
Published: January 2024

Abstract
This research assesses the capability of texture analysis (TA) derived from high-resolution (HR) T2-weighted magnetic resonance imaging to identify primary sequelae following 1–5 hours of controlled cortical impact mild or severe traumatic brain injury (TBI) to the left frontal cortex (focal impact) and secondary (diffuse) sequelae in the right frontal cortex, bilateral corpus callosum, and hippocampus in rats. The TA technique comprised first-order (histogram-based) and second-order statistics (including gray-level co-occurrence matrix, gray-level run length matrix, and neighborhood gray-level difference matrix). Edema in the left frontal impact region developed within 1 hour and continued throughout the 5-hour assessments. The TA features from HR images confirmed the focal injury. There was no significant difference among radiomics features between the left and right corpus callosum or hippocampus from 1 to 5 hours following a mild or severe impact. The adjacent corpus callosum region and the distal hippocampus region (s), showed no diffuse injury 1–5 hours after mild or severe TBI. These results suggest that combining HR images with TA may enhance detection of early primary and secondary sequelae following TBI.
Conversion of the CG specific M.MpeI DNA methyltransferase into an enzyme predominantly methylating CCA and CCC sites
Authors: Albert Pál , Varga Bence , Ferenc Györgyi , Kiss Antal 
Published: January 2024

Abstract
We used structure guided mutagenesis and directed enzyme evolution to alter the specificity of the CG specific bacterial DNA (cytosine-5) methyltransferase M.MpeI. Methylation specificity of the M.MpeI variants was characterized by digestions with methylation sensitive restriction enzymes and by measuring incorporation of tritiated methyl groups into double-stranded oligonucleotides containing single CC, CG, CA or CT sites. Site specific mutagenesis steps designed to disrupt the specific contacts between the enzyme and the non-substrate base pair of the target sequence (5′-CG/5′-CG) yielded M.MpeI variants with varying levels of CG specific and increasing levels of CA and CC specific MTase activity. Subsequent random mutagenesis of the target recognizing domain coupled with selection for non-CG specific methylation yielded a variant, which predominantly methylates CC dinucleotides, has very low activity on CG and CA sites, and no activity on CT sites. This M.MpeI variant contains a one amino acid deletion (ΔA323) and three substitutions (N324G, R326G and E305N) in the target recognition domain. The mutant enzyme has very strong preference for A and C in the 3′ flanking position making it a CCA and CCC specific DNA methyltransferase.
Enhancing circuit stability under growth feedback with supplementary repressive regulation
Authors: Stone Austin , Rijal Sadikshya , Zhang Rong , Tian Xiao-Jun 
Published: January 2024

Abstract
The field of synthetic biology and biosystems engineering increasingly acknowledges the need for a holistic design approach that incorporates circuit-host interactions into the design process. Engineered circuits are not isolated entities but inherently entwined with the dynamic host environment. One such circuit-host interaction, ‘growth feedback’, results when modifications in host growth patterns influence the operation of gene circuits. The growth-mediated effects can range from growth-dependent elevation in protein/mRNA dilution rate to changes in resource reallocation within the cell, which can lead to complete functional collapse in complex circuits. To achieve robust circuit performance, synthetic biologists employ a variety of control mechanisms to stabilize and insulate circuit behavior against growth changes. Here we propose a simple strategy by incorporating one repressive edge in a growth-sensitive bistable circuit. Through both simulation and in vitro experimentation, we demonstrate how this additional repressive node stabilizes protein levels and increases the robustness of a bistable circuit in response to growth feedback. We propose the incorporation of repressive links in gene circuits as a control strategy for desensitizing gene circuits against growth fluctuations.
Automated segmentation of ablated lesions using deep convolutional neural networks: A basis for response assessment following laser interstitial thermal therapy
Authors: Haskell-Mendoza Aden P , Reason Ellery H , Gonzalez Ariel T , Jackson Joshua D , Sankey Eric W , Srinivasan Ethan S , Herndon James E , Fecci Peter E , Calabrese Evan 
Published: January 2024

Abstract

Background
Laser interstitial thermal therapy (LITT) of intracranial tumors or radiation necrosis enables tissue diagnosis, cytoreduction, and rapid return to systemic therapies. Ablated tissue remains in situ, resulting in characteristic post-LITT edema associated with transient clinical worsening and complicating post-LITT response assessment.

Methods
All patients receiving LITT at a single center for tumors or radiation necrosis from 2015 to 2023 with ≥9 months of MRI follow-up were included. An nnU-Net segmentation model was trained to automatically segment contrast-enhancing lesion volume (CeLV) of LITT-treated lesions on T1-weighted images. Response assessment was performed using volumetric measurements.

Results
Three hundred and eighty four unique MRI exams of 61 LITT-treated lesions and 6 control cases of medically managed radiation necrosis were analyzed. Automated segmentation was accurate in 367/384 (95.6%) images. CeLV increased to a median of 68.3% (IQR 35.1–109.2%) from baseline at 1–3 months from LITT (P = 0.0012) and returned to baseline thereafter. Overall survival (OS) for LITT-treated patients was 39.1 (9.2–93.4) months. Lesion expansion above 40% from volumetric nadir or baseline was considered volumetric progression. Twenty-one of 56 (37.5%) patients experienced progression for a volumetric progression-free survival of 21.4 (6.0–93.4) months. Patients with volumetric progression had worse OS (17.3 vs 62.1 months, P = 0.0015).

Conclusions
Post-LITT CeLV expansion is quantifiable and resolves within 6 months of LITT. Development of response assessment criteria for LITT-treated lesions is feasible and should be considered for clinical trials. Automated lesion segmentation could speed the adoption of volumetric response criteria in clinical practice.
Should I stay or should I go? Trafficking of plant extra-nuclear transcription factors
Authors: Marathe Sarika , Grotewold Erich , Otegui Marisa S 
Published: January 2024

Abstract
At the heart of all biological processes lies the control of nuclear gene expression, which is primarily achieved through the action of transcription factors (TFs) that generally contain a nuclear localization signal (NLS) to facilitate their transport into the nucleus. However, some TFs reside in the cytoplasm in a transcriptionally inactive state and only enter the nucleus in response to specific signals, which in plants include biotic or abiotic stresses. These extra-nuclear TFs can be found in the cytosol or associated with various membrane systems, including the endoplasmic reticulum and plasma membrane. They may be integral proteins with transmembrane domains or associate peripherally with the lipid bilayer via acylation or membrane-binding domains. Although over 30 plant TFs, most of them involved in stress responses, have been experimentally shown to reside outside the nucleus, computational predictions suggest that this number is much larger. Understanding how extra-nuclear TFs are trafficked into the nucleus is essential for reconstructing transcriptional regulatory networks that govern major cellular pathways in response to biotic and abiotic signals. Here, we provide a perspective on what is known on plant extranuclear-nuclear TF retention, nuclear trafficking, and the post-translational modifications that ultimately enable them to regulate gene expression upon entering the nucleus.
Cytokinin: From autoclaved DNA to two-component signaling
Authors: Argueso Cristiana T , Kieber Joseph J 
Published: January 2024

Abstract
Since its first identification in the 1950s as a regulator of cell division, cytokinin has been linked to many physiological processes in plants, spanning growth and development and various responses to the environment. Studies from the last two and one-half decades have revealed the pathways underlying the biosynthesis and metabolism of cytokinin and have elucidated the mechanisms of its perception and signaling, which reflects an ancient signaling system evolved from two-component elements in bacteria. Mutants in the genes encoding elements involved in these processes have helped refine our understanding of cytokinin functions in plants. Further, recent advances have provided insight into the mechanisms of intracellular and long-distance cytokinin transport and the identification of several proteins that operate downstream of cytokinin signaling. Here, we review these processes through a historical lens, providing an overview of cytokinin metabolism, transport, signaling, and functions in higher plants.
The end game(s) of photosynthetic carbon metabolism
Authors: Sharkey Thomas D 
Published: January 2024

Abstract
The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin–Benson cycle or variants such as the Calvin–Benson–Bassham cycle or Benson–Calvin cycle. However, once the carbon has entered the Calvin–Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin–Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.
A charged existence: A century of transmembrane ion transport in plants
Authors: Blatt Michael R 
Published: January 2024

Abstract
If the past century marked the birth of membrane transport as a focus for research in plants, the past 50 years has seen the field mature from arcane interest to a central pillar of plant physiology. Ion transport across plant membranes accounts for roughly 30% of the metabolic energy consumed by a plant cell, and it underpins virtually every aspect of plant biology, from mineral nutrition, cell expansion, and development to auxin polarity, fertilization, plant pathogen defense, and senescence. The means to quantify ion flux through individual transporters, even single channel proteins, became widely available as voltage clamp methods expanded from giant algal cells to the fungus Neurospora crassa in the 1970s and the cells of angiosperms in the 1980s. Here, I touch briefly on some key aspects of the development of modern electrophysiology with a focus on the guard cells of stomata, now without dispute the premier plant cell model for ion transport and its regulation. Guard cells have proven to be a crucible for many technical and conceptual developments that have since emerged into the mainstream of plant science. Their study continues to provide fundamental insights and carries much importance for the global challenges that face us today.
America's racial framework of superiority and Americanness embedded in natural language
Authors: Lee Messi H J , Montgomery Jacob M , Lai Calvin K 
Published: January 2024

Abstract
America's racial framework can be summarized using two distinct dimensions: superiority/inferiority and Americanness/foreignness. We investigated America's racial framework in a corpus of spoken and written language using word embeddings. Word embeddings place words on a low-dimensional space where words with similar meanings are proximate, allowing researchers to test whether the positions of group and attribute words in a semantic space reflect stereotypes. We trained a word embedding model on the Corpus of Contemporary American English—a corpus of 1 billion words that span 30 years and 8 text categories—and compared the positions of racial/ethnic groups with respect to superiority and Americanness. We found that America's racial framework is embedded in American English. We also captured an additional nuance: Asian people were stereotyped as more American than Hispanic people. These results are empirical evidence that America's racial framework is embedded in American English.