bluuebunny/crossref_metadata_2025_split huggingface dataset:
ascend: R package for analysis of single-cell RNA-seq data
Authors: Senabouth Anne , Lukowski Samuel W , Hernandez Jose Alquicira , Andersen Stacey B , Mei Xin , Nguyen Quan H , Powell Joseph E 
Published: August 2019

Abstract

Background
Recent developments in single-cell RNA sequencing (scRNA-seq) platforms have vastly increased the number of cells typically assayed in an experiment. Analysis of scRNA-seq data is multidisciplinary in nature, requiring careful consideration of the application of statistical methods with respect to the underlying biology. Few analysis packages exist that are at once robust, are computationally fast, and allow flexible integration with other bioinformatics tools and methods.

Findings
ascend is an R package comprising tools designed to simplify and streamline the preliminary analysis of scRNA-seq data, while addressing the statistical challenges of scRNA-seq analysis and enabling flexible integration with genomics packages and native R functions, including fast parallel computation and efficient memory management. The package incorporates both novel and established methods to provide a framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and a wide range of visualization functions.

Conclusions
ascend is designed to work with scRNA-seq data generated by any high-throughput platform and includes functions to convert data objects between software packages. The ascend workflow is simple and interactive, as well as suitable for implementation by a broad range of users, including those with little programming experience.
Computing Euler Obstruction Functions Using Maximum Likelihood Degrees
Authors: Rodriguez Jose Israel , Wang Botong 
Published: August 2019

Abstract
We give a numerical algorithm computing Euler obstruction functions using maximum likelihood degrees. The maximum likelihood degree is a well-studied property of a variety in algebraic statistics and computational algebraic geometry. In this article we use this degree to give a new way to compute Euler obstruction functions. We define the maximum likelihood obstruction function and show how it coincides with the Euler obstruction function. With this insight, we are able to bring new tools of computational algebraic geometry to study Euler obstruction functions.
Characterization of cefotaxime-resistant urinary Escherichia coli from primary care in South-West England 2017–18
Authors: Findlay Jacqueline , Gould Virginia C , North Paul , Bowker Karen E , Williams Martin O , MacGowan Alasdair P , Avison Matthew B 
Published: August 2019

Abstract

Objectives
Third-generation cephalosporin-resistant Escherichia coli from community-acquired urinary tract infections are increasingly reported worldwide. We sought to determine and characterize the mechanisms of cefotaxime resistance employed by urinary E. coli obtained from primary care, over 12 months, in Bristol and surrounding counties in South-West England.

Methods
Cefalexin-resistant E. coli isolates were identified from GP-referred urine samples using disc susceptibility testing. Cefotaxime resistance was determined by subsequent plating onto MIC breakpoint plates. β-Lactamase genes were detected by PCR. WGS was performed on 225 isolates and analyses were performed using the Center for Genomic Epidemiology platform. Patient information provided by the referring general practices was reviewed.

Results
Cefalexin-resistant E. coli (n=900) isolates were obtained from urines from 146 general practices. Following deduplication by patient approximately 69% (576/836) of isolates were cefotaxime resistant. WGS of 225 isolates identified that the most common cefotaxime-resistance mechanism was blaCTX-M carriage (185/225), followed by plasmid-mediated AmpCs (pAmpCs) (17/225), AmpC hyperproduction (13/225), ESBL blaSHV variants (6/225) or a combination of both blaCTX-M and pAmpC (4/225). Forty-four STs were identified, with ST131 representing 101/225 isolates, within which clade C2 was dominant (54/101). Ciprofloxacin resistance was observed in 128/225 (56.9%) of sequenced isolates, predominantly associated with fluoroquinolone-resistant clones ST131 and ST1193.

Conclusions
Most cefalexin-resistant E. coli isolates were cefotaxime resistant, predominantly caused by blaCTX-M carriage. The correlation between cefotaxime resistance and ciprofloxacin resistance was largely attributable to the high-risk pandemic clones ST131 and ST1193. Localized epidemiological data provide greater resolution than regional data and can be valuable for informing treatment choices in the primary care setting.
A Retrospective Review of the Outcomes and Utility of Percutaneous Radiofrequency Rhizotomy for Trigeminal Neuralgia Using Anatomic Landmark Guidance in Asleep Patients
Authors: Stone Lauren E , Falowski Steven M 
Published: August 2019

Abstract

BACKGROUND
Radiofrequency rhizotomy is a percutaneous procedure for trigeminal neuralgia frequently performed with intermittent awakening, although the utility and accuracy of this procedure in continuously sedated patients have not yet been evaluated.

OBJECTIVE
To evaluate pain relief in patients with trigeminal neuralgia undergoing radiofrequency rhizotomy under continuous sedation.

METHODS
Patients from 2012 to 2017 who underwent radiofrequency rhizotomy for trigeminal neuralgia were evaluated retrospectively. Barrow Neurological Institute Pain Intensity scores were assigned to determine relapse at 1 mo, 1 yr, 3 yr, and 5 yr. Descriptive relapse rates for patients with multiple sclerosis and those undergoing repeat procedures are also reported.

RESULTS
A total of 90.8% of procedures reported Barrow Neurological Institute I-III score at 1 mo (P < .0001), 66.3% at 1 yr (P = .0012), and 71.1% at 3 yr (P = .0003). Duration to relapse was 3.0 and 6.0 at 1 and 3 yr, respectively. Procedures in patients with multiple sclerosis reported 100% relief at 1 mo and 87.5% relief at 1 yr (P = .0099). The presence of numbness and postoperative medication changes were not associated with pain relief (P = .0063, P = .1338).

CONCLUSION
The use of continuous sedation in radiofrequency rhizotomy for trigeminal neuralgia provides pain relief comparable to the recorded literature rate for procedures with intermittent awakening.
Dual Microwire Rail Technique to Advance a Microcatheter Past the Ostium of a Dissecting Carotid Artery Aneurysm for Flow Diverter Deployment: 2-Dimensional Operative Video
Authors: Vakharia Kunal , Munich Stephan A , Waqas Muhammad , McPheeters Matthew J , Levy Elad I 
Published: August 2019

Abstract
Flow diversion using a Pipeline embolization device (PED; Medtronic, Dublin, Ireland) is an effective therapy for treating cavernous aneurysms. Currently, flow diverters require a 0.027-inch microcatheter for deployment. To navigate across these aneurysms, a 0.014-inch microwire is used, which often does not offer a sturdy enough rail to advance a 0.027-inch microcatheter past dissecting artery aneurysm ostia. We present a patient with a right cavernous dissecting carotid artery aneurysm. A step off between the 0.027-inch VIA microcatheter (MicroVention Terumo, Tustin, California) and 0.014-inch Synchro 2 microwire (Stryker Neurovascular, Fremont, California) resulted in difficulty with navigation of the microcatheter across the dissected portion of the aneurysm. A dual microwire rail technique involving two 0.014-inch Synchro 2 microwires was used to advance the VIA microcatheter past the dissecting artery aneurysm ostia for PED deployment. The introduction of the second microwire eliminated the step off between the microwire and microcatheter, providing a stronger rail and easier navigation of the microcatheter, without aggressive pushing. Postembolization runs showed optimal wall apposition and contrast stasis within the aneurysm, with successful flow diversion of the aneurysm.
The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary.
Microsurgical Resection of Brain Stem Ependymoma: 2-Dimensional Operative Video
Authors: Pojskić Mirza , Nguyen Vincent , Lakičević Goran , Arnautović Kenan I 
Published: August 2019

Abstract
The brainstem is a less-common location for ependymomas than the spinal cord where they are the most common adult intramedullary tumor.
1-18
In this first video case report in the peer-reviewed literature, we demonstrate microsurgical resection of a medulla oblongata ependymoma.
There are several case reports of medulla oblongata ependymomas
1
,
3
,
5
,
6
,
13
and a few series of spinal cord ependymomas that included cases of ependymomas of the cervicomedullary junction.
9
,
10
The goal of surgery was to stabilize the preoperative neurological function; favorable outcome is achieved in patients with good preoperative statuses and well-defined tumor boundaries.
9
Although gross total resection (GTR) provides the best overall outcome, it is most effective for classic grade II tumors, but not grade I (myxopapillary) and ependymomas, which have a lower GTR rate.
14
,
15

A 55-yr-old patient developed 4-extremity weakness and dysphagia. Pre-/postcontrast magnetic resonance imaging (MRI) revealed centrally located brainstem lesion situated at the lower half of the medulla oblongata. Surgery, performed by the senior author, was performed in the prone position with a small suboccipital craniectomy and C1 posterior arch removal, followed by pia opening and posterior midline myelotomy. Tumor was debulked, dissected from the white matter, and resected. Histology revealed ependymoma (World Health Organization grade II). Postoperative pre-/postcontrast MRI revealed total resection. The patient's neurological deficit completely resolved postoperatively.
Written consent was obtained from the patient.
Manufacturing and quality assessment of allergenic extracts for immunotherapy: state of the art
Authors: Bonertz Andreas , Mahler Vera , Vieths Stefan 
Published: August 2019

Purpose of review
The recent developments in the manufacturing and quality assessment of allergenic extracts in Europe are summarized.

Recent findings
Quality assessment has always been a fundamental part of allergen product evaluation. New analytical methods have been reported that fill currently existing gaps in the characterization of commonly used allergen products. New types of products require innovative considerations and concepts for their assessment. Advanced standardization efforts aim at increasing reliability and comparability of analytical tools applied for allergen product characterization. In consequence, regulatory requirements are updated in line with such developments.

Summary
Current demands on the quality of allergen products ensure production of well characterized products of consistent quality. While experience with manufacturing processes and successful product characterization approaches increase, accompanying and continuous re-evaluation of underlying quality control and assessment concepts is being performed.
Back Pain
Authors: Tailor Yogita , Preston-Hsu Elisabeth 
Published: August 2019

Abstract:
Every age group experiences back pain, a common reason for activity limitation. Management of back pain in a woman is challenging because of physiologic and hormonal changes through the woman’s life cycle. The treatment is dictated by etiology and a woman’s stage of life or reproductive events, such as pregnancy, breastfeeding, and menopause. Most episodes of low back pain are temporary with minimal long-term sequelae, but recurrent and long-lasting episodes require more thorough clinical evaluation. This monograph describes the anatomy of the spine; illustrates a focused, thorough evaluation, including obtaining a medical history and performing a physical examination; discusses warning signs and symptoms of more serious etiologies; provides recommendations for further testing or referral; and offers case vignettes of common causes of low back pain as a woman progresses from young adulthood to advanced age.
RBC Transfusion Strategies in the ICU: A Concise Review
Authors: Cable Casey A. , Razavi Seyed Amirhossein , Roback John D. , Murphy David J. 
Published: August 2019

Objectives:
To critically assess available high-level clinical studies regarding RBC transfusion strategies, with a focus on hemoglobin transfusion thresholds in the ICU.

Data Sources:
Source data were obtained from a PubMed literature review.

Study Selection:
English language studies addressing RBC transfusions in the ICU with a focus on the most recent relevant studies.

Data Extraction:
Relevant studies were reviewed and the following aspects of each study were identified, abstracted, and analyzed: study design, methods, results, and implications for critical care practice.

Data Synthesis:
Approximately 30–50% of ICU patients receive a transfusion during their hospitalization with anemia being the indication for 75% of transfusions. A significant body of clinical research evidence supports using a restrictive transfusion strategy (e.g., hemoglobin threshold < 7 g/dL) compared with a more liberal approach (e.g., hemoglobin threshold < 10 g/dL). A restrictive strategy (hemoglobin < 7 g/dL) is recommended in patients with sepsis and gastrointestinal bleeds. A slightly higher restrictive threshold is recommended in cardiac surgery (hemoglobin < 7.5 g/dL) and stable cardiovascular disease (hemoglobin < 8 g/dL). Although restrictive strategies are generally supported in hematologic malignancies, acute neurologic injury, and burns, more definitive studies are needed, including acute coronary syndrome. Massive transfusion protocols are the mainstay of treatment for hemorrhagic shock; however, the exact RBC to fresh frozen plasma ratio is still unclear. There are also emerging complimentary practices including nontransfusion strategies to avoid and treat anemia and the reemergence of whole blood transfusion.

Conclusions:
The current literature supports the use of restrictive transfusion strategies in the majority of critically ill populations. Continued studies of optimal transfusion strategies in various patient populations, coupled with the integration of novel complementary ICU practices, will continue to enhance our ability to treat critically ill patients.
Emerging mechanistic underpinnings and therapeutic targets for chemotherapy-related cognitive impairment
Authors: Gibson Erin M. , Monje Michelle 
Published: August 2019

Purpose of review
Modern innovations in cancer therapy have dramatically increased the number of cancer survivors. An unfortunately frequent side-effect of cancer treatment is enduring neurological impairment. Persistent deficits in attention, concentration, memory, and speed of information processing afflict a substantial fraction of cancer survivors following completion of these life-saving therapies. Here, we highlight chemotherapy-related cognitive impairment (CRCI) and discuss the current understanding of mechanisms underlying CRCI.

Recent findings
New studies emphasize the deleterious impact of chemotherapeutic agents on glial–glial and neuron–glial interactions that shape the form, function and plasticity of the central nervous system. An emerging theme in cancer therapy-related cognitive impairment is therapy-induced microglial activation and consequent dysfunction of both neural precursor cells and mature neural cell types. Recent work has highlighted the complexity of dysregulated intercellular interactions involving oligodendrocyte lineage cells, microglia, astrocytes, and neurons following exposure to traditional cancer therapies such as methotrexate. This new understanding of the mechanistic underpinnings of CRCI has elucidated potential therapeutic interventions, including colony-stimulating factor 1 receptor inhibition, TrkB agonism, and aerobic exercise.

Summary
Traditional cancer therapies induce lasting alterations to multiple neural cell types. Therapy-induced microglial activation is a critical component of the cause of CRCI, contributing to dysregulation of numerous processes of neural plasticity. Therapeutic targeting of microglial activation or the consequent dysregulation of neural plasticity mechanisms are emerging.
A Tool Kit for Improving Communication in Your Healthcare Organization
Authors: Cunningham Lynne 
Published: August 2019

SUMMARY
Effective leadership starts with communication. The ability to communicate can help healthcare leaders gain the trust and confidence of their entire team, leading to better employee engagement and patient outcomes. As the scope of roles, adoption of technology, and needs of the workforce evolve, it is important for leaders to have a tool kit to help them communicate strategically consistent messages to key stakeholders. This article presents an array of evidence-based tools to strengthen leadership skills and drive better, sustainable results for healthcare organizations.
Neurotransmitter systems involved in placebo and nocebo effects in healthy participants and patients with chronic pain: a systematic review
Authors: Skyt Ina , Lunde Sigrid J. , Baastrup Cathrine , Svensson Peter , Jensen Troels S. , Vase Lene 
Published: August 2019

Abstract
The investigation of neurotransmitter systems in placebo and nocebo effects has improved our understanding of these phenomena. Yet, most studies involve healthy participants. Because the pain modulatory system may differ in healthy participants and patients with chronic pain, it is important to investigate the evidence for neurotransmitter involvement in placebo and nocebo effects in each of these populations. PubMed, Embase, and Scopus databases, and the Cochrane Library were searched for articles investigating the endogenous opioid, endocannabinoid, dopaminergic, oxytocinergic, vasopressinergic, and cholecystokininergic (CCKergic) systems in placebo and nocebo effects in pain. Twenty-eight placebo and 2 nocebo studies were included. Vote counting was used to balance the number of positive vs negative findings. In healthy participants, the endogenous opioid, endocannabinoid, and vasopressinergic systems were involved in placebo effects, whereas findings on the dopaminergic and oxytocinergic systems were mixed. In patients with chronic pain, only 4 studies investigated neurotransmitters showing no involvement of the endogenous opioid system and mixed findings regarding the dopaminergic system. As to nocebo effects, 2 studies suggest that the CCKergic system is involved in nocebo effects in healthy participants. Overall, research has come a long way in specifying the neurotransmitter systems involved in placebo effects in healthy participants. Yet, evidence for the involvement of neurotransmitter systems in placebo effects in patients with chronic pain and in nocebo effects in healthy participants and patients is scarce. Based on the existing evidence, this systematic review suggests that knowledge obtained in healthy participants may not necessarily be transferred to chronic pain.
Differences in Outcomes After Anesthesia-Related Adverse Events in Older and Younger Patients
Authors: Root Christopher W. , Beilin Yaakov , McCormick Patrick J. , Curatolo Christopher J. , Katz Daniel , Hyman Jaime B. 
Published: August 2019

ABSTRACT
Because more older adults undergo surgical procedures, it is incumbent on us to learn how to provide them with the safest possible perioperative care. We conducted a retrospective cohort study at a large tertiary care center to determine whether outcomes after anesthesia-related adverse events differed between patients aged 65 years and older versus patients under age 65. One thousand four hundred twenty-four cases were referred to the Performance Improvement committee of the Department of Anesthesiology from the years 2007–2015. After exclusions of cases that were not anesthesia-related, could not be identified, or were duplicates, 747 cases with anesthesia-related adverse events were included in the study. Two hundred eighty-six were aged 65 years and older and 461 were under age 65. Anesthesia-related adverse events occurred more commonly in the postoperative period in older patients relative to younger patients (37.7% vs. 21.9%, p = .001), and older patients had a greater incidence of mortality compared with a propensity-matched group of younger patients (adjusted odds ratio 1.87 [1.14–3.12], p < .05). We concluded that older patients have a greater likelihood of mortality as a result of suffering an anesthesia-related adverse event and may benefit from increased vigilance in the postoperative period.
Virtual Surgical Planning Assisted Management for Cleft-Related Maxillary Hypoplasia
Authors: Wang Yu , Zhang Zhen , Liu Yao , Ye Bin , Luo En , Li Jihua 
Published: August 2019

Abstract
Maxillary hypoplasia is a common developmental deformity affecting patients with cleft lip and palate. Various surgical techniques including conventional orthognathic surgery, total maxillary distraction osteogenesis, and anterior maxillary segmental distraction have been applied to address the deformity. With the evolution of 3D computed tomography imaging, the visualization of skeletal complexities in different perspectives is greatly enhanced and comprehensive surgical planning is achieved. Intraoperative efficiency is also improved with the fabrication of 3D-printed templates. The study aims to present different surgical techniques with virtual surgical planning (VSP) and 3D-printed surgical templates and the solution of representative cases. From January 2014 to January 2019, VSP was transferred to actual surgery or distraction precisely in 80 adult patients with cleft-related maxillary hypoplasia. The accuracy was analyzed and the relapse was also estimated and observed in 18 patients after 1-year follow-up. Based on our experience, VSP provides a more reliable and effective option to conventional model surgery. It facilitates the preoperative planning and accurately transfers the virtual plan to correct the cleft-related maxillary hypoplasia.
Is Bilateral Sagittal Split Osteotomy of the Mandible With no Step Possible? A Modification in the Technique
Authors: Mont’Alverne Antonio Lopes Filho , Xavier Felipe Gomes , Meneses Anderson Maia , Santos Eliardo Silveira , Franco Jéferson Martins Pereira Lucena 
Published: August 2019

Abstract
The mandibular ramus sagittal osteotomy is a usual procedure used to correct deformities of the lower third of the face. Modifications of the procedure will be presented to avoid the presence of palpable gap at mandibular body, easily seen in greater movements.