bluuebunny/crossref_metadata_2025_split huggingface dataset:
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase–substrate interactions in eukaryotic species
Authors: Wang Xun , Li Yang , He Mengqi , Kong Xiangren , Jiang Peng , Liu Xi , Diao Lihong , Zhang Xinlei , Li Honglei , Ling Xinping , Xia Simin , Liu Zhongyang , Liu Yuan , Cui Chun-Ping , Wang Yan , Tang Liujun , Zhang Lingqiang , He Fuchu , Li Dong 
Published: October 2021

Abstract
As an important post-translational modification, ubiquitination mediates ∼80% of protein degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the delicate balance between specific ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase-mediated deubiquitination. In 2017, we developed UbiBrowser 1.0, which is an integrated database for predicted human proteome-wide E3–substrate interactions. Here, to meet the urgent requirement of proteome-wide E3/deubiquitinase–substrate interactions (ESIs/DSIs) in multiple organisms, we updated UbiBrowser to version 2.0 (http://ubibrowser.ncpsb.org.cn). Using an improved protocol, we collected 4068/967 known ESIs/DSIs by manual curation, and we predicted about 2.2 million highly confident ESIs/DSIs in 39 organisms, with &gt;210-fold increase in total data volume. In addition, we made several new features in the updated version: (i) it allows exploring proteins’ upstream E3 ligases and deubiquitinases simultaneously; (ii) it has significantly increased species coverage; (iii) it presents a uniform confidence scoring system to rank predicted ESIs/DSIs. To facilitate the usage of UbiBrowser 2.0, we also redesigned the web interface for exploring these known and predicted ESIs/DSIs, and added functions of ‘Browse’, ‘Download’ and ‘Application Programming Interface’. We believe that UbiBrowser 2.0, as a discovery tool, will contribute to the study of protein ubiquitination and the development of drug targets for complex diseases.
ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition
Authors: Bakr Ali , Hey Joschka , Sigismondo Gianluca , Liu Chun-Shan , Sadik Ahmed , Goyal Ashish , Cross Alice , Iyer Ramya Lakshmana , Müller Patrick , Trauernicht Max , Breuer Kersten , Lutsik Pavlo , Opitz Christiane A , Krijgsveld Jeroen , Weichenhan Dieter , Plass Christoph , Popanda Odilia , Schmezer Peter 
Published: October 2021

AbstractThe inhibitor of DNA-binding 3 (ID3) is a transcriptional regulator that limits interaction of basic helix-loop-helix transcription factors with their target DNA sequences. We previously reported that ID3 loss is associated with mutational signatures linked to DNA repair defects. Here we demonstrate that ID3 exhibits a dual role to promote DNA double-strand break (DSB) repair, particularly homologous recombination (HR). ID3 interacts with the MRN complex and RECQL helicase to activate DSB repair and it facilitates RAD51 loading and downstream steps of HR. In addition, ID3 promotes the expression of HR genes in response to ionizing radiation by regulating both chromatin accessibility and activity of the transcription factor E2F1. Consistently, analyses of TCGA cancer patient data demonstrate that low ID3 expression is associated with impaired HR. The loss of ID3 leads to sensitivity of tumor cells to PARP inhibition, offering new therapeutic opportunities in ID3-deficient tumors.
Novel biomarkers of inflammation, kidney function and chronic kidney disease in the general population
Authors: Nano Jana , Schöttker Ben , Lin Jie-sheng , Huth Cornelia , Ghanbari Mohsen , Garcia Pamela Matias , Maalmi Haifa , Karrasch Stefan , Koenig Wolfgang , Rothenbacher Dietrich , Roden Michael , Meisinger Christa , Peters Annette , Brenner Hermann , Herder Christian , Thorand Barbara 
Published: October 2021

ABSTRACTBackgroundInflammatory processes have been implicated in the development of chronic kidney disease (CKD). We investigated the association of a large panel of inflammatory biomarkers reflecting aspects of immunity with kidney function and CKD incidence.MethodsWe used data from two independent population-based studies, KORA F4 (discovery, n = 1110, mean age 70.3 years, 48.7% male) and ESTHER (replication, n = 1672, mean age 61.9 years, 43.6% male). Serum levels of biomarkers were measured using proximity extension assay technology. The association of biomarkers with estimated glomerular filtration rate (eGFR) at baseline and with incident CKD was investigated using linear and logistic regression models adjusted for cardiorenal risk factors. Independent results from prospective analyses of both studies were pooled. The significance level was corrected for multiple testing by false-discovery rate (PFDR &lt; 0.05).ResultsIn the KORA F4 discovery study, 52 of 71 inflammatory biomarkers were inversely associated with eGFR based on serum creatinine. Top biomarkers included CD40, TNFRSF9 and IL10RB. Forty-two of these 52 biomarkers were replicated in the ESTHER study. Nine of the 42 biomarkers were associated with incident CKD independent of cardiorenal risk factors in the meta-analysis of the KORA (n = 142, mean follow-up 6.5 years) and ESTHER (n = 103, mean follow-up 8 years) studies. Pathway analysis revealed the involvement of inflammatory and immunomodulatory processes reflecting cross-communication of innate and adaptive immune cells.ConclusionsNovel and known biomarkers of inflammation were reproducibly associated with kidney function. Future studies should investigate their clinical utility and underlying molecular mechanisms in independent cohorts.
Trend and Predictors of Short-term Mortality of Adult Bacteremia at Emergency Departments: A 14-Year Cohort Study of 14 625 Patients
Authors: Chiang Hsiu-Yin , Chen Tsung-Chia , Lin Che-Chen , Ho Lu-Ching , Kuo Chin-Chi , Chi Chih-Yu 
Published: October 2021

Abstract

Background
Bacteremia is a life-threatening condition with a high mortality rate in critical care and emergency settings. The current study investigated the trend of mortality and developed predictive models of mortality for adults with bacteremia at emergency departments (EDs).

Methods
We conducted a retrospective cohort study of adults with bacteremia at the ED of China Medical University Hospital. Patient data were obtained from the Clinical Research Data Repository, and mortality information was obtained from the National Death Registry. We developed a new model to predict 7-day mortality in the derivation population and compared the model performance of the new model with Pitt Bacteremia Score (PBS) and Bloodstream Infection Mortality Risk Score (BSIMRS) in the validation population.

Results
We identified 14625 adult patients with first-time bacteremia at the ED, of whom 8.4% died within 7 days. From 2003 to 2016, both the cumulative incidence and 7-day mortality rate of bacteremia decreased significantly. The ED bacteremia mortality (ED-BM) model included PBS parameters, age, infection source, baseline steroid use, and biochemical profiles (estimated glomerular filtration rate, platelet, blood urea nitrogen, potassium, and hemoglobin) for predicting 7-day mortality. The discrimination performance of the ED-BM model (area under curve [AUC], 0.903) was significantly better than that of PBS (AUC, 0.848) or BSIMRS (AUC, 0.885).

Conclusions
Although the cumulative incidence and mortality of ED bacteremia decreased, its mortality burden remains critical. The proposed ED-BM model had significantly better model performance than other scoring systems in predicting short-term mortality for adult patients with bacteremia at EDs.
The Relationship Between Strength of the Affected Leg and Walking Speed After Stroke Varies According to the Level of Walking Disability: A Systematic Review
Authors: Dorsch Simone , Ada Louise , Sorial Tiffany , Fanayan Emma 
Published: October 2021

ABSTRACT

Objective
The objectives of this review were to determine the relationship between muscle strength of the affected leg and walking speed after stroke and whether this relationship varied according to muscle group or level of walking disability.

Methods
This systematic review with meta-analysis focused on observational studies of adult survivors of stroke. Muscle strength had to be measured as maximum voluntary force production during an isometric contraction of the affected leg. Walking had to be measured as walking speed. Studies had to report correlations between muscle strength and walking speed.

Results
Thirty studies involving 1001 participants were included. Pooled mean correlations between muscle strength of the affected leg and walking speed was 0.51 (95% CI = 0.45 to 0.57). Pooled correlations between the strength of individual muscle groups and walking speed ranged from 0.42 (for the hip abductors) to 0.57 (for the ankle dorsiflexors). The correlation between level of walking disability and the mean correlation between muscle strength and walking speed was −0.70 (95% CI = −0.42 to −0.86).

Conclusion
After stroke, there is a strong relationship between strength of the affected leg and walking speed, with little variability across individual muscle groups. However, the level of walking disability of people with stroke does make a difference such that the more disabled people are, the stronger the relationship is between strength of the affected leg and walking speed.

Impact
This study suggests that the strength of all muscles of the affected leg is important for walking after stroke. It appears that increasing strength in the affected leg could be most important in people who are more disabled.

Lay Summary
After stroke, the speed at which a person can walk is highly associated with the muscle strength of their affected leg. In people whose walking speed is severely affected, this association is stronger, and the physical therapist might focus on strengthening that leg so the individual can walk faster.
PAs' attitudes about adolescent suicide screening: The Theory of Planned Behavior
Authors: Gillette Chris , Bodner Gayle , Grant Jill , Aldrich Rosalie , Mospan Cortney , Ip Edward Hak-Sing , Daniel Stephanie , Crandall Sonia 
Published: October 2021

ABSTRACT

Objective:
Suicide is an increasing public health problem for adolescents and young adults. The purpose of this study was to identify the frequency of physician assistants' (PAs') self-reported adolescent suicide risk assessments and to elicit salient beliefs regarding behavioral attitudes, norm referents, control factors, and intention to conduct suicide risk assessment with adolescents.

Methods:
A convenience sample of PAs completed an anonymous cross-sectional questionnaire. Relationships were assessed using bivariate analyses and qualitative theme analysis.

Results:
Forty-three PAs completed the questionnaire. Many PAs supported suicide risk assessment screening as a strategy to identify adolescents who are suicidal at an earlier stage of their illness; lack of time during the visit and problematic parental involvement were identified as barriers.

Conclusions:
PAs recognized that screening adolescents for suicide ideation may help prevent suicides. Their practice behaviors, however, did not correspond to this belief.
Caring for the psychosocial needs of the acutely traumatized patient
Authors: Powell C. Chloe 
Published: October 2021

ABSTRACT
Support for a patient in the aftermath of a potentially traumatic event is enhanced when clinicians understand the normal reactions that may occur during the traumatization process. This article discusses recommendations from international and national guidelines as well as best practices from the medical and psychiatric literature to help guide clinicians providing care for acutely traumatized patients.
Relative Efficacy and Safety of Tanezumab for Osteoarthritis
Authors: Zhang Bocheng , Tian Xiaoyuan , Qu Zhenan , Liu Jiaming , Yang Liang 
Published: October 2021

Objectives:
The aim of this meta-analysis was to evaluate the efficacy and safety of tanezumab for the treatment of patients with knee or hip osteoarthritis (OA).

Methods:
PubMed, Embase, Cochrane Central Register of Controlled Trials, and Web of Science were searched from inception to July 2020. Randomized-controlled trials comparing tanezumab with placebo or nonsteroidal anti-inflammatory drugs in patients with OA. Two investigators identified studies and independently extracted data, and conventional meta-analyses were conducted with Review Manager 5.3. The outcomes were pain relief, functional improvement, and risk of adverse events (AEs).

Results:
A total of 8 articles, comprising 9 randomized-controlled trials, were included. Overall, tanezumab was superior to placebo for relieving pain and improving function, as well as in the patient’s global assessment. Tanezumab also had significant advantages over nonsteroidal anti-inflammatory drugs for relieving pain and improving function, as well as in the patient’s global assessment. Significantly more patients discontinued treatment because of AEs after treatment with tanezumab. However, the differences in serious AEs and total joint replacement were not significant. Moreover, tanezumab-treated patients experienced significantly more rapid progression of osteoarthritis.

Discussion:
Tanezumab can alleviate pain and improve function for patients with OA of the hip or knee. Although tanezumab does not cause serious AEs, rapid progression of OA occurred in a small number of participants, so more clinical trials are needed to explore its safety.
Clinical Outcomes of Surgical Correction and Fusion for Postlaminectomy Kyphosis Following Spinal Tumor Resection in Adolescent Patients
Authors: Pan Wei , Li Jie , Qiu Yong , Zhu Zezhang , Zhu Weiguo , Liu Zhen 
Published: October 2021

Background:
Progressive spinal deformity following laminectomy and resection surgery of spinal tumor has been well-documented. However, the postlaminectomy deformity in adolescent patients often bring challenge to clinical treatment, which may be subjected to rapid progression of kyphosis during the growth spurt. The aim of this study is to investigate the clinical outcome of long fusion correction surgery for thoracic or thoracolumbar kyphotic deformity secondary to laminectomy and tumor resection in adolescent patients.

Methods:
Records of 12 cases underwent correction surgery of postlaminectomy thoracic (n=6) or thoracolumbar (n=6) kyphotic deformity were reviewed. The Cobb angle of sagittal and coronal curve before surgery, immediately after surgery, and at the final follow-up were measured to evaluate the correction of deformity and loss of correction. Neurological function was evaluated using the Frankel grading system. Back pain was assessed by using the visual analog score (VAS). Disability status was evaluated by the Oswestry Disability Index (ODI). Patients’ satisfaction to surgery was assessed by the patient satisfactory index.

Results:
The mean kyphosis angle reduced from 76±20 degrees before surgery to 34±18 degrees immediately after surgery and remained at 39±17 degrees at the final follow-up with the average correction rate of 58.6% and 51.0%, respectively. For 7 patients with concomitant scoliosis, the Cobb angle of major curve reduced from 52±21 degrees before surgery to 16±9 degrees immediately after surgery and 20±9 degrees at the final follow-up. The average corrective rate was 69.5% and 62.4%, respectively. The mean ODI score improved from 19.9±7.5 to 10.8±8.0, whereas the mean VAS score improved from 5.3±2.0 to 1.5±1.4. The sagittal and coronal balance of the spine, Frankel grading, ODI, and VAS were improved, and the patient satisfactory index was 100%. One patient had inferior paraplegia recovered to Frankel grade E after treatment.

Conclusions:
Satisfactory clinical outcomes can be achieved after long fusion surgery for thoracic or thoracolumbar kyphotic deformity secondary to laminectomy for spinal tumor. Due to the high risk of secondary kyphotic deformity in adolescent patients, internal fixation should be performed simultaneously with the resection of spinal tumor, especially for the cases in the thoracic or thoracolumbar region.

Level of Evidence:
Level III.
Quality of Surgery and Patient Selection Are Keys to Success in Hip Stabilization Surgery in Cerebral Palsy
Authors: Wong Janus S.H. , Kuong Evelyn E. , So Noah L.W. , Ali Abbas , To Michael K.T. , Chow Wang 
Published: October 2021

Background:
Cerebral palsy patients are at risk of hip instability, to which various soft tissue and bony surgeries are performed should conservative management fail. We aim to identify factors associated with treatment failure to guide surgical management.

Methods:
Cerebral palsy patients treated at 2 university-affiliated tertiary pediatric orthopaedic referral centers with hip stabilization surgery performed for subluxation in 1998 to 2015 with minimum of 5 years follow-up were reviewed. Failure was defined as reoperation to the same hip because of recurrent subluxation. Age, sex, Gross Motor Function Classification System level, tone abnormality, operation type, Reimer’s migration index (RMI), and acetabular index (AI) were assessed. Cut-off values were identified through Youden index on receiver operating characteristic curve.

Results:
Eighty-nine hips from 55 patients with mean follow-up of 12.4 years were analyzed. Revision surgery was performed in 14 hips. Postoperative hip subluxation (P<0.001) and acetabular dysplasia (P=0.001) were predictive of failure, with postoperative RMI conferring an adjusted hazard ratio of 1.13 (95% confidence interval: 1.08-1.19, P<0.001) on multivariable survival analysis. Achieving a postoperative RMI of <27.5% predicts success with 92.9% sensitivity and 72% specificity with area under curve of 0.916 (P<0.001), while postoperative AI of <23.1 degrees predicts success with 92.3% sensitivity and 62.2% specificity with area under curve of 0.796 (P=0.001). In subgroup analysis of soft-tissue-only procedures, RMI >44% preoperative and >32% postoperative were associated with reoperation. In femur-only osteotomies, preoperative RMI >48% and postoperative RMI >28% were associated with failure. In pelvic and combined osteotomies, postoperative RMI >32% and AI >30 degrees were associated with failure. Other factors analyzed were not associated with reoperation.

Conclusions:
Patient selection and quality of surgery in terms of residual postoperative hip subluxation and acetabular dysplasia are associated with need for remedial surgery. Soft-tissue-only procedures should aim to correct RMI to <32%. Bony surgery should be considered when preoperative RMI >44%, and pelvic osteotomies if RMI >48%. Pelvic osteotomies should target postoperative RMI <32% and AI <30 degrees.

Level of Evidence:
Level II—prognostic study.
Toward Useful Interventions for Burnout in Academic Medical Faculty: The Case for Unit-Specific Approaches
Authors: McKinley Tara 
Published: October 2021

Introduction:
Despite a plethora of research on the topic of physician burnout, drivers and interventions are poorly understood. This study aimed to create a holistic picture of burnout drivers in academic medical faculty within a single department of a large, research university to better inform organization-sponsored interventions.

Methods:
The author used interpretive phenomenological analysis and the Job Demands-Resources model in this qualitative study. Full-time academic medical faculty completed two semistructured interviews approximately 6 months apart. Transcripts were coded using deductive and inductive coding.

Results:
Twenty-two faculty members participated in both interviews. Factors affecting burnout depended on individual and unit-level context, but interpersonal factors such as relationships with colleagues and interaction with learners created meaning for faculty or drove intention to leave the university. All participants reported personal coping mechanisms, and none participated in organization-sponsored, individual-level interventions.

Discussion:
In striving for meaningful burnout interventions, organizations should promote interpersonal factors (relationships with colleagues and meaningful interaction with learners) and provide protected time for faculty for their own personal coping. Research has suggested moving toward a universal burnout driver and intervention plan, but these data point toward the need for unit-specific study and interventions.
The Burnout Dyad: A Collaborative Approach for Including Patients in a Model of Provider Burnout
Authors: Martinez-Hollingsworth Adrienne , Hicks Melissa , Dobrota Sylvie , Chu Larry F. 
Published: October 2021

Abstract
Both patients and providers in the United States (US) suffer from burnout, which can impact the clinical relationship and quality of care. Among providers, burnout is a state of exhaustion including heightened depersonalization; among patients, burnout can negatively affect clinical outcomes. More than half of clinical providers in the United States suffer from burnout; less is known about the magnitude and prevalence among patients. Understanding patient burnout will improve our recognition of treatment barriers, understanding of patient-provider communication, and perceived quality of care. The purpose of the 2019 Stanford University MedicineX Burnout Workgroup was to use a collaborative approach to expand on the National Academy of Medicine (NAM) Wellness and Resilience Model, which does not currently include the patient as an influential member of the care team potentially experiencing burnout. This collaboration among patients, physicians, students, caregivers, technologists, and researchers used a convenience sample of conference attendees, broken into three focus groups to (1) provide an expanded definition of burnout that includes patients' perspectives, (2) analyze the NAM burnout model for inclusion of the patient experience, and (3) define a care experience that includes both patients and providers. The design of this workgroup was informed by Everyone Included, a model that recognizes and rejects hierarchical traditions in clinical practice. This approach allowed for the creation of a safe space for the exchange of knowledge between the various stakeholders. The resulting inclusive conceptual model, The Burnout Dyad, describes a cocreated care experience informed by both patient and provider characteristics.
Promoting Transfer of Learning to Practice in Online Continuing Professional Development
Authors: Luhanga Ulemu , Chen Weichao , Minor Suzanne , Drowos Joanna , Berry Andrea , Rudd Mariah , Gupta Shanu , Bailey Jean M. 
Published: October 2021

Abstract:
Leveraging online learning tools and encouraging transfer of learning to practice remains a critical challenge to successful continuing professional development (CPD) offerings. Four sets of factors are essential to the transfer of learning from CPD into practice: learner characteristics, instructional design, content, and environment. Through incorporating elements of educational theories/frameworks into the planning of online CPD activities, educators can maximize opportunities for learning transfer. In this article, we highlight four educational theories/frameworks that provide useful insight to tackle these interrelated factors in online CPD: Self-Determination Theory considers the intrinsic and extrinsic motivation of participants, which can be encouraged through flexibility, customization, and choices available in online formats. Practical Inquiry Model encourages intentionally planning and embedding opportunities for reflection and dialogue in online activities to enhance knowledge application. Virtual Communities of Practice can be used to transcend spatial and temporal boundaries, promoting interactions and relationships where participants learn from peers. Finally, Professional Learning Networks can be fostered through developing interpersonal connections and sharing resources for informal and flexible learning. Online CPD is likely to increase in the future, and educators should consider elements of these educational theories/frameworks in the design and delivery of CPD to support participants' application of newly acquired knowledge.