bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metatranscriptomic Characterization of Coronavirus Disease 2019 Identified a Host Transcriptional Classifier Associated With Immune Signaling
Authors: Zhang Haocheng , Ai Jing-Wen , Yang Wenjiao , Zhou Xian , He Fusheng , Xie Shumei , Zeng Weiqi , Li Yang , Yu Yiqi , Gou Xuejing , Li Yongjun , Wang Xiaorui , Su Hang , Zhu Zhaoqin , Xu Teng , Zhang Wenhong 
Published: May 2020

Abstract

Background
The recent identification of a novel coronavirus, also known as severe acute respiratory syndrome coronavirus 2, has caused a global outbreak of respiratory illnesses. The rapidly developing pandemic has posed great challenges to diagnosis of this novel infection. However, little is known about the metatranscriptomic characteristics of patients with coronavirus disease 2019 (COVID-19).

Methods
We analyzed metatranscriptomics in 187 patients (62 cases with COVID-19 and 125 with non–COVID-19 pneumonia). Transcriptional aspects of 3 core elements, pathogens, the microbiome, and host responses, were evaluated. Based on the host transcriptional signature, we built a host gene classifier and examined its potential for diagnosing COVID-19 and indicating disease severity.

Results
The airway microbiome in COVID-19 patients had reduced alpha diversity, with 18 taxa of differential abundance. Potentially pathogenic microbes were also detected in 47% of the COVID-19 cases, 58% of which were respiratory viruses. Host gene analysis revealed a transcriptional signature of 36 differentially expressed genes significantly associated with immune pathways, such as cytokine signaling. The host gene classifier built on such a signature exhibited the potential for diagnosing COVID-19 (area under the curve of 0.75–0.89) and indicating disease severity.

Conclusions
Compared with those with non–COVID-19 pneumonias, COVID-19 patients appeared to have a more disrupted airway microbiome with frequent potential concurrent infections and a special trigger host immune response in certain pathways, such as interferon-gamma signaling. The immune-associated host transcriptional signatures of COVID-19 hold promise as a tool for improving COVID-19 diagnosis and indicating disease severity.
LSTUR regression theory and the instability of the sample correlation coefficient between financial return indices
Authors: Ginker Tim , Lieberman Offer 
Published: May 2020

SummaryIt is well known that the sample correlation coefficient between many financial return indices exhibits substantial variation on any reasonable sampling window. This stylised fact contradicts a unit root model for the underlying processes in levels, as the statistic converges in probability to a constant under this modeling scheme. In this paper, we establish asymptotic theory for regression in local stochastic unit root (LSTUR) variables. An empirical application reveals that the new theory explains very well the instability, in both sign and scale, of the sample correlation coefficient between gold, oil, and stock return price indices. In addition, we establish spurious regression theory for LSTUR variables, which generalises the results known hitherto, as well as a theory for balanced regression in this setting.
Whole-exome sequencing of a large Chinese azoospermia and severe oligospermia cohort identifies novel infertility causative variants and genes
Authors: Chen Shitao , Wang Guishuan , Zheng Xiaoguo , Ge Shunna , Dai Yubing , Ping Ping , Chen Xiangfeng , Liu Guihua , Zhang Jing , Yang Yang , Zhang Xinzong , Zhong An , Zhu Yongtong , Chu Qingjun , Huang Yonghan , Zhang Yong , Shen Changli , Yuan Yiming , Yuan Qilong , Pei Xiuying , Cheng C Yan , Sun Fei 
Published: May 2020

AbstractRare coding variants have been proven to be one of the significant factors contributing to spermatogenic failure in patients with non-obstructive azoospermia (NOA) and severe oligospermia (SO). To delineate the molecular characteristics of idiopathic NOA and SO, we performed whole-exome sequencing of 314 unrelated patients of Chinese Han origin and verified our findings by comparing to 400 fertile controls. We detected six pathogenic/likely pathogenic variants and four variants of unknown significance, in genes known to cause NOA/SO, and 9 of which had not been earlier reported. Additionally, we identified 20 novel NOA candidate genes affecting 25 patients. Among them, five (BRDT, CHD5, MCM9, MLH3 and ZFX) were considered as strong candidates based on the evidence obtained from murine functional studies and human single-cell (sc)RNA-sequencing data. These genetic findings provide insight into the aetiology of human NOA/SO and pave the way for further functional analysis and molecular diagnosis of male infertility.
Resilience of clinical text de-identified with “hiding in plain sight” to hostile reidentification attacks by human readers
Authors: Carrell David S , Malin Bradley A , Cronkite David J , Aberdeen John S , Clark Cheryl , Li Muqun (Rachel) , Bastakoty Dikshya , Nyemba Steve , Hirschman Lynette 
Published: May 2020

Abstract

Objective
Effective, scalable de-identification of personally identifying information (PII) for information-rich clinical text is critical to support secondary use, but no method is 100% effective. The hiding-in-plain-sight (HIPS) approach attempts to solve this “residual PII problem.” HIPS replaces PII tagged by a de-identification system with realistic but fictitious (resynthesized) content, making it harder to detect remaining unredacted PII.

Materials and Methods
Using 2000 representative clinical documents from 2 healthcare settings (4000 total), we used a novel method to generate 2 de-identified 100-document corpora (200 documents total) in which PII tagged by a typical automated machine-learned tagger was replaced by HIPS-resynthesized content. Four readers conducted aggressive reidentification attacks to isolate leaked PII: 2 readers from within the originating institution and 2 external readers.

Results
Overall, mean recall of leaked PII was 26.8% and mean precision was 37.2%. Mean recall was 9% (mean precision = 37%) for patient ages, 32% (mean precision = 26%) for dates, 25% (mean precision = 37%) for doctor names, 45% (mean precision = 55%) for organization names, and 23% (mean precision = 57%) for patient names. Recall was 32% (precision = 40%) for internal and 22% (precision =33%) for external readers.

Discussion and Conclusions
Approximately 70% of leaked PII “hiding” in a corpus de-identified with HIPS resynthesis is resilient to detection by human readers in a realistic, aggressive reidentification attack scenario—more than double the rate reported in previous studies but less than the rate reported for an attack assisted by machine learning methods.
Siliplant1 protein precipitates silica in sorghum silica cells
Authors: Kumar Santosh , Adiram-Filiba Nurit , Blum Shula , Sanchez-Lopez Javier Arturo , Tzfadia Oren , Omid Ayelet , Volpin Hanne , Heifetz Yael , Goobes Gil , Elbaum Rivka 
Published: May 2020

AbstractSilicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume using an unknown biological factor. Using bioinformatics tools, we identified a previously uncharacterized protein in Sorghum bicolor, which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell types. Our results show that Slp1 precipitates silica in sorghum silica cells.
TFII-I-mediated polymerase pausing antagonizes GLI2 induction by TGFβ
Authors: McCleary-Wheeler Angela L , Paradise Brooke D , Almada Luciana L , Carlson Annika J , Marks David L , Vrabel Anne , Vera Renzo E , Sigafoos Ashley N , Olson Rachel L , Fernandez-Zapico Martin E 
Published: May 2020

AbstractThe modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GLI2 expression. Mapping experiments suggest that the INR region of the GLI2 promoter is necessary for GLI2 repression. ChIP studies showed that TFII-I binds to this INR. TFII-I knockdown decreased the binding of NELF-A, a component of the promoter–proximal pausing complex at this site, and enriched phosphorylated RNAPII serine 2 in the GLI2 gene body. Immunoprecipitation studies demonstrate TFII-I interaction with SPT5, another pausing complex component. TFII-I overexpression antagonized GLI2 induction by TGFβ, a known activator of GLI2 in cancer cells. TGFβ reduced endogenous TFII-I binding to the INR and increased RNAPII SerP2 in the gene body. We demonstrate that this regulatory mechanism is not exclusive of GLI2. TGFβ-induced genes CCR7, TGFβ1 and EGR3 showed similar decreased TFII-I and NELF-A INR binding and increased RNAPII SerP2 in the gene body post-TGFβ treatment. Together these results identify TFII-I as a novel repressor of a subset of TGFβ-responsive genes through the regulation of RNAPII pausing.
Postoperative hemorrhage secondary to acquired hemophilia A
Authors: Asher Zachary P. , Buckner Tyler W. , McIntyre Robert C. 
Published: May 2020

ABSTRACT
Acquired hemophilia A in postoperative patients can cause major bleeding and an accurate diagnosis is required for effective treatment. Standard treatment is costly, difficult to obtain, and takes 4 to 6 weeks to be effective. This article describes a patient successfully treated with recombinant factor VIIa, porcine factor VIII, plasmapheresis, rituximab, and high-dose corticosteroids.
Amyotrophic lateral sclerosis
Authors: Vacca Vincent M. 
Published: May 2020

Abstract:
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disease that is always fatal, although treatment can help slow disease progression. This article discusses the etiology and pathophysiology, signs and symptoms, diagnosis, and clinical management of ALS, with special nursing considerations to help patients at the end of life.
Empowering nurses to activate the rapid response team
Authors: Granitto Margaret , Linenfelser Paula , Hursey Ryan , Parsons Megan , Norton Colleen 
Published: May 2020

Abstract:
All clinical nurses need to be prepared to recognize deterioration in a patient's clinical status and activate the rapid response team when appropriate. This article explores the clinical nurse's role in recognizing and responding to deterioration in a patient's condition with a focus on hospital-based nurses practicing on a medical-surgical unit.
Relationship Between Alcohol-related Family Adversity, Alcohol Use Across Adolescence, and Mental States Recognition in Young Adulthood
Authors: Kopera Maciej , Trucco Elisa M. , Jakubczyk Andrzej , Suszek Hubert , Kobyliński Paweł , Wojnar Marcin , Zucker Robert A. 
Published: May 2020

Objectives:
Although a theoretical link between childhood adversity and mental states recognition has been established, empirical findings are mixed. Some prior work indicates that childhood adversity might enhance, preserve, or reduce mentalization skills in selected at-risk populations. In the current study, we examine whether the presence of risky alcohol use during adolescence moderates the association between childhood alcohol-related family adversity and mental states recognition in young adulthood.

Methods:
Secondary data analysis was conducted on 266 young adults who participated in the Michigan Longitudinal Study—a multiwave prospective study on at-risk youth. Children were assessed after initial recruitment (wave 1, target child age range 3–5 years), with assessments repeated every 3 years using parallel measures. The current study focuses on data spanning wave 2 (age range 7–9 years) through wave 6 (target child age range 18–21 years). A family adversity index was derived reflecting exposure to a maladaptive family environment during childhood as assessed at wave 1. An alcohol use risk factor was established reflecting early problem alcohol use during adolescence (target child age range 12–17 years). Mental states recognition was measured with a computerized version of the Reading the Mind in the Eyes Task (RMET) at wave 6. Information about demographics, psychopathological symptoms, and IQ was obtained. The alcohol use risk factor was tested as a potential moderator of the association between childhood family adversity on RMET performance during young adulthood.

Results:
Alcohol use risk moderated the relationship between childhood alcohol-related family adversity, and negative and neutral mental states recognition. Specifically, childhood family adversity was positively associated with neutral mental states recognition among participants high in alcohol risk (P = 0.03) and positively associated with negative mental states recognition among participants at average (P = 0.02) and high (P = 0.002) levels of alcohol risk.

Conclusions:
Findings indicate that history of childhood adversity may actually improve young adult negative and neutral mental states recognition among those demonstrating high levels of risky alcohol use, as substance use may serve as an external self-regulatory tool. Clinical interventions that target enhancing metacognitive competence and emotion regulation could ultimately help to break the cycle of alcohol-related family adversity.
Appropriate Use Criteria for Treatment of Pediatric Supracondylar Humerus Fractures With Vascular Injury: Do Our Hospital Practice Patterns Agree With Current Recommendations?
Authors: Brandt Aaron M. , Wally Meghan K. , Casey Virginia F. , Clark Christian C. , Paloski Michael D. , Scannell Brian P. , Brighton Brian K. 
Published: May 2020

Background:
Managing the pulseless pediatric supracondylar humerus fracture (PSHF) remains a significant clinical decision-making challenge for the treating surgeon. The purpose of the study is to determine frequency of the treatments according to the American Academy of Orthopaedic Surgeons (AAOS) Appropriate Use Criteria (AUC) for the PSHF with vascular injury and evaluate the appropriateness of these interventions.

Methods:
We identified all PSHF with concern for vascular injury at one high volume, level 1 trauma center managed by 6 fellowship-trained pediatric orthopaedic surgeons over 4.5 years. Demographic information and other injury and treatment variables were obtained. Each patient was classified as 1 of the 6 patient scenarios specified by the AAOS AUC. Each of the 18 interventions identified in the AUC were documented, including the level of “appropriateness” as specified by AAOS AUC.

Results:
A total of 638 PSHF were managed identified; of these, 52 were pink, pulseless, or dysvascular (8.2%). Only 7 of the 18 treatment options suggested by the AUC were used in this cohort. Across all 7 interventions used in this cohort, 20.2% (17/84) of interventions were “appropriate,” 52.4% (44/84) were “maybe appropriate,” 22.6% (19/84) were “rarely appropriate,” and 4.8% (4/84) were not listed in treatment options.

Conclusions:
Supracondylar fractures are the most common injury to the elbow seen in children and are variable in presentation and management. The pink, pulseless fracture continues to be a major topic for research and discussion due to the morbidity if not treated “appropriately.” The AUC were created to help guide practitioners when strong evidence is lacking. In this study at a single, pediatric hospital, there was variation and disagreement with “appropriateness” of treatments that were performed but this discrepancy did not result in any poor outcomes. Although the AUC do offer valuable guidance, our findings highlight a need for continued research in this area to help validate the AUC and help strengthen the recommendations moving forward.

Level of Evidence:
Level III—retrospective.
Trends in Reoperation for Surgical Site Infection After Spinal Surgery With Instrumentation in a Multicenter Study
Authors: Kobayashi Kazuyoshi , Imagama Shiro , Ando Kei , Nakashima Hiroaki , Kato Fumihiko , Sato Koji , Kanemura Tokumi , Matsubara Yuji , Yoshihara Hisatake , Hirasawa Atsuhiko , Deguchi Masao , Shinjo Ryuichi , Sakai Yoshihito , Inoue Hidenori , Ishiguro Naoki 
Published: May 2020

Study Design.
A multicenter retrospective analysis of a prospectively maintained database.

Objective.
To examine the characteristics of reoperation for surgical site infection (SSI) after spinal instrumentation surgery, including the efficacy of treatment for SSI and instrumentation retention.

Summary of Background Data.
Aging of the population and advances in surgical techniques have increased the demand for spinal surgery in elderly patients. Treatment of SSI after this surgery has the main goals of eliminating infection and retaining instrumentation.

Methods.
The subjects were 16,707 patients who underwent spine surgery with instrumentation in 11 hospitals affiliated with the Nagoya Spine Group from 2004 to 2015. Details of those requiring reoperations for SSI were obtained from surgical records at each hospital.

Results.
There were significant increases in the mean age at the time of surgery (54.6–63.7 years) and the number of instrumentation surgeries (726–1977) from 2004 to 2015. The incidence of reoperation for SSI varied from 0.9% to 1.8%, with a decreasing trend over time. Reoperation for SSI was performed in 206 cases (115 men, 91 women; mean age 63.2 years). The average number of reoperations (1.4 vs. 2.3, P < 0.05), time from SSI to first reoperation (4.3 vs. 9.5 days, P < 0.05), and the methicillin-resistant Staphylococcus identification rate (20% vs. 37%, P < 0.01) were all significantly lower in cases with instrumentation retention (n = 145) compared to those with instrumentation removal (n = 61).

Conclusion.
There were marked trends of aging of patients and an increase in operations over the study period; however, the incidences of reoperation and instrumentation removal due to SSI significantly decreased over the same period. Rapid debridement after SSI diagnosis may have contributed to instrumentation retention. These results can serve as a guide for developing strategies for SSI treatment and for improved planning of spine surgery in an aging society.

Level of Evidence: 3
Prevalence of Occult Infections in Posterior Instrumented Spinal Fusion
Authors: Callanan Tucker C. , Abjornson Celeste , DiCarlo Edward , Henry Michael , Sama Andrew A. , Girardi Federico P. , Schroeder Josh , Kiely Paul , Lebl Darren R. , Cammisa Frank P. 
Published: May 2020

Study Design:
This is a prospective observational study.

Objective:
The aim of this study is to determine the rate of occult infection after instrumented spine surgery in presumed aseptic patients.

Summary of Background Data:
The reported incidence rate of delayed/occult infection determined by positive culture swabs after instrumented spine surgery in prospective studies is 0.2%–6.9%. However, this rate may be higher as delayed infections are challenging to diagnose. Fever can be absent and inflammatory markers are often normal. If indolent organisms exist in low concentrations surrounding the instrumentation, these organisms can possibly avoid detection and disrupt bone formation leading to instrumentation loosening, pain generation, and/or failure of a solid fusion.

Materials and Methods:
This study included 50 consecutive presumed aseptic patients undergoing a posterior revision requiring removal of instrumentation at least 6 months following their index procedure. Common markers of infection were examined preoperatively. Multiple culture swabs were taken directly from the removed instrumentation and cultured for 14 days.

Results:
Of the 50 patients, 19 (38%) were culture-positive (CP) for bacteria upon removal of their instrumentation, with 14 patients (28%) having ≥2 positive specimens of the same organism. The average length of time between the index procedure and the revision surgery was 4.55 years (range: 0.53–21 y). Polymicrobial infections were found in 26% (5/19) of CP patients. The most prevalent microorganism found was Propionibacterium acnes, in 63% (12/19) of CP patients. There was no significant difference between CP and culture-negative patients regarding preoperative markers for infection, age, or length between index and revision procedures.

Conclusions:
The results of this study indicate a positive culture rate of 38% in presumed aseptic patients who had previously undergone instrumented spine surgery. These results are consistent with other retrospective studies and are >6 times greater than any previous prospective study utilizing culture swabs.

Level of Evidence:
Level-III.
Transpsoas Lumbar Interbody Fusion Without Psoas Stimulated Electromyography
Authors: Patel Shyam A. , Goyal Dhruv K.C. , Reid Daniel , Patel Ram , Babu Jacob , Fereydonyan Naderafshar , Anderson David Greg 
Published: May 2020

Study Design:
This is a retrospective case review.

Objective:
The objective of this study was to present an anatomic approach to transpsoas interbody fusion without psoas stimulated electromyography (sEMG) and to evaluate the rate of neurological and approach-related complications.

Background:
The transpsoas approaches have become commonly utilized for lumbar interbody fusion and may have certain advantages compared with other methods of interbody stabilization. Traditionally, transpsoas approaches have been performed utilizing sEMG as it has been purported to reduce the risk of injury to the lumbar plexus; however, an anatomic approach to transpsoas surgery is also possible as cadaveric studies have demonstrated the anatomy of the psoas muscle and lumbar plexus.

Methods:
Patients who underwent transpsoas interbody fusion using an anatomic approach without psoas sEMG between 2005 and 2018 were enrolled in this study. The preoperative and postoperative medical records for this cohort were carefully reviewed to identify any new or persistent radicular symptoms, neurological deficits or approach-related complications.

Results:
A total of 133 patients (48 males, 85 females) underwent transpsoas interbody fusion at 222 levels in this cohort—which had a mean age of 63 (61, 65) years and body mass index of 28.8 (27.8, 29.9). New neurological complications were seen in 5 patients (3.8%) and 5 patients (3.8%) were found to have new postoperative radicular pain, up to 3 months postoperatively. The total number of perioperative, approach-related complications was 7 (5.3%) for the entire cohort.

Conclusion:
An anatomic transpsoas approach to the interbody space without psoas sEMG demonstrated a rate of neurological and approach-related complications that was comparable or superior to the rate of complications reported using the traditional transpsoas approach with sEMG.