bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses
Authors: Rick Jessica A , Brock Chad D , Lewanski Alexander L , Golcher-Benavides Jimena , Wagner Catherine E 
Published: October 2023

Abstract
Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) &gt;3–4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC &gt;1–2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.
Characterization of a Foxtail Mosaic Virus Vector for Rust Fungus Avirulence Gene Expression in Wheat
Authors: Liu Lu , Montenegro-Alonso Ana Priscilla , Bakkeren Guus 
Published: October 2023

The wheat fungal pathogens Puccinia graminis f. sp. tritici ( Pgt), P. striiformis f. sp. tritici, and P. triticina, causing stem, stripe, and leaf rust, respectively, pose a threat to global wheat production. Genetic resistance in the form of resistance ( R) genes provides the best protection, but rust fungal populations change frequently by mutating avirulence (AVR) effectors matching specific R genes, thereby defeating resistance. Hence, characterization of AVR effectors is needed to understand the evolution of pathogen populations, provide insights for extending the effectiveness of R genes, and yield tools for the identification and isolation of R genes. Functional characterization of Avr genes in rust fungi is challenging in these biotrophic pathogens that lack a reliable and efficient transformation system. Studies indicate that the recently engineered foxtail mosaic virus (FoMV) shows promise as an expression system in cereals. In this study, we utilized two confirmed AVR effectors from Pgt, AVRSr35 and AVRSr50, to assess the applicability of FoMV for investigating rust fungus Avr genes. We showed that vector FoMV PV101 carrying PgtAvrSr35 induced a hypersensitive response (HR) in wheat having the corresponding Sr35 resistance gene. However, when carrying PgtAvrSr50, no HR or even mild viral symptoms were seen in a wheat line having Sr50, as this particular wheat line was not susceptible to FoMV. Several wheat cultivars did not support FoMV replication. The results here show that FoMV PV101 is effective as an expression vector for studying rust fungi AVR effectors, but its applicability relies on the susceptibility of wheat cultivars to FoMV. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Antioxidants restore store‐operated Ca2+entry in patient‐iPSC‐derived myotubes with tubular aggregate myopathy‐associated Ile484ArgfsX21 STIM1 mutation via upregulation of binding immunoglobulin protein
Authors: Sakai‐Takemura Fusako , Saito Fumiaki , Nogami Ken'ichiro , Maruyama Yusuke , Elhussieny Ahmed , Matsumura Kiichiro , Takeda Shin'ichi , Aoki Yoshitsugu , Miyagoe‐Suzuki Yuko 
Published: October 2023

AbstractStore‐operated Ca2+entry (SOCE) is indispensable for intracellular Ca2+homeostasis in skeletal muscle, and constitutive activation of SOCE causes tubular aggregate myopathy (TAM). To understand the pathogenesis of TAM, we induced pluripotent stem cells (iPSCs) from a TAM patient with a rare mutation (c.1450_1451insGA; p. Ile484ArgfsX21) in theSTIM1gene. This frameshift mutation produces a truncated STIM1 with a disrupted C‐terminal inhibitory domain (CTID) and was reported to diminish SOCE. Myotubes induced from the patient's‐iPSCs (TAM myotubes) showed severely impaired SOCE, but antioxidants greatly restored SOCE partly via upregulation of an endoplasmic reticulum (ER) chaperone, BiP (GRP78), in the TAM myotubes. Our observation suggests that antioxidants are promising tools for treatment of TAM caused by reduced SOCE.
Tirzepatide
Authors: Niedbala Christine G. , Sprague Roxanne 
Published: October 2023

ABSTRACT
Obesity affects a large percentage of patients in the United States and is associated with increased mortality and higher healthcare costs. Newer guidelines recommend a minimum of 10% weight loss goal for patients with obesity, and medical management options fall short. Tirzepatide, the first available dual-incretin analog, is a novel treatment for type 2 diabetes that also can induce weight loss. This article discusses tirzepatide as a treatment for obesity.
Managing ascites in patients with cirrhosis
Authors: Jack J. Kyle 
Published: October 2023

ABSTRACT
Patients with cirrhosis have a 50% to 60% chance of developing ascites within 10 years of diagnosis. Once ascites has developed, patients have a predicted 50% mortality within 3 years. This article discusses the pathophysiology of ascites caused by cirrhosis, standards in diagnosing ascites, and the recommendations and guidelines for treating ascites. Properly managing patients with decompensated cirrhosis can improve their quality of life and longevity and minimize additional complications.
Screening for post-traumatic stress disorder among Latinx immigrant children
Authors: Cooper Josseline , Donovan Kelsey , Michel Halee , Peterson Lindsey , Todd-Thompson Megan , Gillette Chris , Hussaini Sobia Shariff 
Published: October 2023

ABSTRACT
Latinx children face psychosocial, linguistic, and economic challenges that put them at an increased risk of developing mental health conditions. Primary care providers should be equipped to recognize the complex mental health needs of this growing population. This article explores some of the barriers to mental health screenings in Latinx children and presents culturally sensitive, validated screening tools for primary care providers.
Traveler's diarrhea
Authors: Gambini Justin M. , Watkins Elyse 
Published: October 2023

ABSTRACT
Traveler's diarrhea (TD) is one of the most common illnesses afflicting the modern traveler. TD refers to a watery diarrhea that varies in severity from tolerable to incapacitating and that develops in individuals during or within 10 days of returning from travel to developing or low-/middle-income countries. Most cases of TD are self-limiting, but in consideration of the ease of international travel, it is important for providers to diagnose and manage TD with the best available evidence.
Military Environmental Exposures
Authors: Miller Cashmere 
Published: October 2023

ABSTRACT
The passage of the PACT Act of 2022 expanded the services veterans receive through the U.S. Department of Veterans Affairs (VA), ensuring they now qualify for benefits if they've been exposed to certain toxins during their military service. This significant expansion of VA benefits also highlights the need for nurses and other health providers working outside the VA system—who care for millions of veterans—to be well-informed about their patients' military experiences and any potential environmental exposures and health impacts. In this article, the author raises awareness of military environmental exposures and offers guidance about exposure-informed care.
A Nursing Research Residency Experience
Authors: Mendoza Rosalina Generoso , Kawar Lina Najib , Rondinelli June L. 
Published: October 2023

ABSTRACT:
Nursing research is essential to improving patient care, yet barriers may hinder bedside nurses from participating in research and evidence-based practice (EBP) activities. This article describes a nursing research residency program that aimed to inspire direct care nurses to participate in research and EBP projects. The program described may be a potential solution to bridge the gap between clinical work and research.
Pernicious anemia
Authors: Underwood Tamara , Le Jenny , Campbell Kim , Smiley Lisa 
Published: October 2023

Abstract:
The symptoms of pernicious anemia might resemble those of other common disorders and can be nonspecific, requiring extensive diagnostic workup. The provider must be aware of the harm pernicious anemia can do if undiagnosed and untreated and must understand that diligence and persistence are crucial for an accurate diagnosis.
Baseline Gastric Volume in Fasting Diabetic Patients Is Not Higher than That in Nondiabetic Patients: A Cross-sectional Noninferiority Study
Authors: Perlas Anahi , Xiao Maggie Z. X. , Tomlinson George , Jacob Binu , Abdullah Sara , Kruisselbrink Richelle , Chan Vincent W. S. 
Published: October 2023

Background
The physiology of diabetes mellitus can increase the risk of perioperative aspiration, but there is limited and contradictory evidence on the incidence of “full stomach” in fasting diabetic patients. The aim of this study is to assess the baseline gastric content (using gastric ultrasound) in diabetic and nondiabetic patients scheduled for elective surgery who have followed standard preoperative fasting instructions.

Methods
This was a prospective, noninferiority study of 180 patients (84 diabetic and 96 nondiabetic patients). Bedside ultrasound was used for qualitative and quantitative assessment of the gastric antrum in the supine and right lateral decubitus positions. Fasting gastric volume was estimated based on the cross-sectional area of the gastric antrum and a validated model. The hypothesis was that diabetic patients would not have a higher baseline fasting gastric volume compared to nondiabetic patients, with a noninferiority margin of 0.4 ml/kg. Secondary aims included the comparison of the incidence of full stomach (solid content or more than 1.5 mL/kg of clear fluid), estimation of the 95th percentile of the gastric volume distribution in both groups, and examination of the association between gastric volume, glycemic control, and diabetic comorbidities.

Results
The baseline gastric volume was not higher in diabetic patients (0.81 ± 0.61 ml/kg) compared to nondiabetic patients (0.87 ± 0.53 ml/kg) with a mean difference of −0.07 ml/kg (95% CI, −0.24 to 0.10 ml/kg). A total of 13 (15.5%) diabetic and 11 (11.5%) nondiabetic patients presented more than 1.5 ml/kg of gastric volume (95% CI for difference, −7.1 to 15.2%). There was little correlation between the gastric volume and either the time since diagnosis or HbA1C.

Conclusions
The data suggest that the baseline gastric volume in diabetic patients who have followed standard fasting instructions is not higher than that in nondiabetic patients.

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DUSP22-IRF4 Rearranged CD30-Positive Primary Cutaneous Lymphoproliferative Disorder With Gamma/Delta Phenotype
Authors: Fattah Yasmin H. , Crasto David , Liu Shuo S. , Linhares Yuliya , Kerdel Franz , Hanly Andrew , Karai Laszlo J. 
Published: October 2023

Abstract:
CD30-positive primary cutaneous lymphoproliferative disorders (CD30+PCLPD) are a heterogeneous group of cutaneous T-cell lymphoma (CTCL) that includes lymphomatoid papulosis (LyP) and primary cutaneous anaplastic large cell lymphoma. They exist as a clinical and pathological spectrum, which display significant overlap and variability. The diagnosis is made based on correlation between clinical and histopathologic findings. LyP with 6p25.3 rearrangement subtype represents <5% of LyP cases and is defined by DUSP22-IRF4 rearrangement on 6p25.3 locus. The reported cases express the alpha/beta T-cell receptor and follow an indolent clinical behavior typical of LyP. The same rearrangement is detected in 28% of anaplastic large cell lymphoma. We hereby present an extraordinary case of CD30+PCLPD with DUSP22-IRF4 rearrangement and novel expression of gamma/delta T-cell immunophenotype in a young patient. Although the gamma/delta T-cell immunophenotype has been described in many other T-cell lymphomas, this is the first reported association with CD30+PCLPD with DUSP22-IRF4 rearrangement.
The Rationale of Coronal Approach to Malar/Zygoma Reduction
Authors: Seol Jae-Yoon , Kim Kenneth K. 
Published: October 2023

Background:
Malar/zygoma reduction is an effective procedure to change a broader, flatter facial appearance to an oval facial shape. Of the intraoral and coronal approaches, the intraoral is the more commonly used technique than the coronal, due to the perception that complications with the coronal approach are significant, and intraoral results are satisfactory. We compared the postoperative effects of both approaches.

Methods:
From 1994 to 1999, we included the 150 intraoral cases that were followed up for 3 years postoperatively. From 2000 to 2018, we changed our technique to the coronal approach and included the 575 cases that were followed up for 3 years postoperatively. We compared the results of our prior intraoral approach with the more recent coronal approach.

Results:
All cases of the intraoral approach resulted in smaller-sized faces horizontally; however, 90 patients (60%) still had resulting flat-shaped faces due to acute angle formation in the resultant zygoma. There were 141 cases (94%) of partial malunion and 138 cases (92%) of midface ptosis. Among the 575 coronal approaches, 518 cases (90%) resulted in an oval facial shape without acute angled zygoma. There were 161 cases (28%) of visible incision scars, 466 cases (81%) of temporary alopecia, 12 cases (2%) of hematoma, and 29 cases (5%) of temporary frontal facial nerve injury.

Conclusions:
The intraoral approach led to flat and acute zygomas. The majority of patients experienced midface soft tissue ptosis. In contrast, the coronal approach led to an oval facial shape. The most notable complications of the coronal approach were visible scars and temporary alopecia.
Preauthorization Inconsistencies Prevail in Reduction Mammaplasty
Authors: Boyd Carter J. , Hemal Kshipra , Cohen Joshua M. , Daar David A. , Gwin John , Zupko Karen , Karp Nolan S. 
Published: October 2023

Background:
Despite evidence documenting the physical and psychological benefits of breast reduction, third-party payer approval remains a cumbersome process. The objective of this study was to assess differences in medical necessity criteria for reduction mammaplasty among US insurance carriers while analyzing trends in claim denials and appeals.

Methods:
The medical necessity criteria for reduction mammaplasty were retrieved from seven large health insurance carriers. Data were extracted from each policy, including claim requirements for approval. Additionally, prospective data on claims and denials submitted from January through August 2022 were collected from The Auctus Group, a medical consulting firm.

Results:
All the policies have been updated since January 2020. Five of the seven policies specifically listed what documentation was required for preauthorization approval, with five third-party payers requiring photograph documentation. Policies required documentation of one to three symptoms lasting from 6 weeks to 1 year. All companies reported a tissue resection estimate threshold, but cutoffs varied. Of 380 reduction mammaplasties performed, 158 (41.6%) received a denial on initial insurance submission. Considering appeals, a total of 216 denials were reviewed with an average of 1.37 denials per patient. Of the 158 initial denials, 104 (65.8%) of these were from claims that received preauthorization. In 12 cases, third-party payers stated that no prior authorization was necessary yet still denied the claim.

Conclusions:
Wide variability exists in medical necessity criteria for reduction mammaplasty policies among major insurance carriers. These nuances introduce inefficiencies for practices contributing to high denial and appeal rates while delaying surgical care for patients.
Intravitreal Melphalan Injection as a Second-line Local Therapy in Vitreoretinal Lymphoma: Case series
Authors: Beser Buse Guneri , Demirci Hakan 
Published: October 2023

Abstract

Purpose:
To evaluate the effectiveness and safety of intravitreal Melphalan(IVM) injection therapy in vitreoretinal lymphoma(VRL).

Methods:
Eight eyes of 5 biopsy-proven VRL patients who were treated with IVM injection as a second-line therapy after intravitreal Methotrexate(IVMTX) and Rituximab(IVR) injections were retrospectively evaluated between January 2011 and March 2023.

Results:
The medical records of five VRL patients (mean age of 62 years at the diagnosis) including four(80%) females and one(20%) male were retrospectively analyzed. Three patients(60%) either had a history of central nervous lymphoma or developed it during the follow-up. Patients were previously treated with a mean of 5 cycles of monthly IVMTX and IVR injections. All eyes showed complete response by the disappearance of vitreal and/or subretinal neoplastic cells within six weeks after IVM injections(range, 1-4 injections/eye). Of 12 IVM injections, three(25%) injections were associated with macular edema diagnosed on optical coherence tomography at one-month follow-up and resolved spontaneously within 5 months. The IVM administration induced new retinal pigment epithelium changes in 3 eyes(37%).

Conclusion:
IVM injection may be effective in the management of VRL as second-line local therapy. Randomized clinical trials with larger numbers of patients are needed to establish the efficacy, treatment protocol, and safety of IVM injection.
Predictive factors associated with the visual prognosis after surgery for idiopathic vitreomacular traction
Authors: Qi Biying , Yang Xiaohan , Yu Yanping , Zhang Ke , Wu Xijin , Wang Xinbo , Jia Qinlang , Feng Xiao , Liu Wu 
Published: October 2023

Abstract

Purpose:
To investigate the predictive factors for post-surgical visual prognosis in vitreomacular traction (VMT) patients.

Methods:
This retrospective study enrolled 31 eyes from 29 patients who underwent vitrectomy for idiopathic VMT with follow-up period ≥ 3 months. The VMT was divided into three grades based on optical coherence tomography images: grade 1 denoted partial vitreomacular separation with foveal attachment; grade 2 exhibited intraretinal cysts or cleft with grade 1 findings; grade 3 was grade 2 plus the subretinal fluid.

Results:
Three eyes developed a full-thickness macular hole after surgery, all of which were grade 3 patients. In the rest 28 eyes, the mean postoperative follow-up period was 23.3 ± 25.8 months. The postoperative central foveal thickness (P=0.001) and final best-corrected visual acuity (BCVA; P<0.001) were both significantly improved from baseline. Fifteen eyes (53.8%) gained ≥ two Snellen lines. Multilinear regression analysis showed that the worse the baseline BCVA (P=0.004), or the more advanced the VMT grade (P=0.049), the worse the final BCVA. Baseline BCVA was negatively associated with the postoperative visual improvement (P<0.001). Those grade 3 patients with baseline Snellen BCVA ≥ 20/40 were more likely to achieve a final Snellen BCVA ≥ 20/25 (P=0.035).

Conclusion:
The VMT grade is an important predictive factor for the post-surgical visual prognosis. Surgical intervention should be performed as early as possible for grade 3 patients to prevent further disease progression and maximize the post-surgical visual benefit.
ANGULAR SIGN OF HENLE FIBER LAYER HYPERREFLECTIVITY IN PURTSCHER AND PURTSCHER-LIKE RETINOPATHY
Authors: Ramanadhane Raghulnadhan , Gupta Shamayita , Bhattacharyya Sampurna , Sen Ahana , Chattree Surabhi , Saurabh Kumar , Roy Rupak 
Published: October 2023

Purpose:
Angular sign of Henle fiber layer hyperreflectivity is a marker of Henle fibre layer ischemia. Our aim is to describe angular sign of Henle fiber layer hyperreflectivity as a novel optical coherence tomography sign in Purtscher and Purtscher-like retinopathy.

Methods:
Here, we present three cases, one classical Purtscher retinopathy and two Purtscher-like retinopathy who had angular sign of Henle fiber layer hyperreflectivity on spectral domain optical coherence tomography imaging.

Results:
Modalities such as color fundus photography, cross-sectional optical coherence tomography, optical coherence tomography angiography, and fluorescein angiography were used.

Conclusion:
Presence of angular sign of Henle fiber layer hyperreflectivity in Purtscher retinopathy and Purtscher-like retinopathy points toward a deep capillary plexus insult and has prognostic implications.
Diabetic myonecrosis: An easily overlooked cause of limb pain in diabetic patients
Authors: Wells Jennifer , Sorsby Stephen C. 
Published: October 2023

ABSTRACT
Diabetic myonecrosis (DMN) is an underdiagnosed cause of spontaneous extremity pain and swelling in patients with diabetes. Failure to consider this diagnosis in patients with recent onset of extremity pain may lead to inappropriate testing and to treatment that worsens symptoms and delays healing. The following is a case report of recurrent diabetic myonecrosis in a 36-year-old woman that highlights several typical features of this uncommon disorder. We discuss the differential diagnosis and how to rapidly identify DMN, as well as best practices for the treatment of the disorder. We approach most types of muscular pain issues with stretching and exercise, but this approach can result in increased pain and delayed resolution in patients with DMN. Nurse practitioners and other providers should consider DMN when faced with a patient with diabetes and spontaneous extremity pain and understand how to efficiently diagnose this disorder and rule out other causes.