bluuebunny/crossref_metadata_2025 huggingface dataset:
Workplace spirituality, mindfulness meditation, and work engagement
Authors: Petchsawang Pawinee , McLean Gary N.
Published: February 2017

Workplace spirituality has received increasing attention during the past few decades, especially their effect on work outcome. The purposes of the research were to: (1) extend the findings of Petchsawang and Duchon (2012) in examining the relationships among mindfulness meditation,
workplace spirituality, and work engagement in an eastern – specifically Thai – context; and (2) compare workplace spirituality and work engagement in organizations that provide mindfulness meditation courses to employees and those that do not. The sample came from four organizations
that offered meditation courses (248 from 300) and four organizations that did not (315 from 400) in Thailand. The level of workplace spirituality and work engagement were found to be higher in organizations that offer meditation courses than in those that do not. Additionally, mindfulness
meditation has a statistically significant relationship with workplace spirituality and work engagement, and workplace spirituality fully meditates the relationship between meditation and work engagement.
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius
Authors: Liu Kai , Xu Dongpo , Li Jia , Bian Chao , Duan Jinrong , Zhou Yanfeng , Zhang Minying , You Xinxin , You Yang , Chen Jieming , Yu Hui , Xu Gangchun , Fang Di-an , Qiang Jun , Jiang Shulun , He Jie , Xu Junmin , Shi Qiong , Zhang Zhiyong , Xu Pao
Published: February 2017

Background

Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to theSinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests.

Findings

A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly.

Conclusion

We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.
GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software
Authors: Mittal Varun , Hung Ling-Hong , Keswani Jayant , Kristiyanto Daniel , Lee Sung Bong , Yeung Ka Yee
Published: February 2017

Background

Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface.

Results

We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud.

Conclusions

As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead.
Phenobook: an open source software for phenotypic data collection
Authors: Crescente Juan M. , Guidobaldi Fabio , Demichelis Melina , Formica Maria B. , Helguera Marcelo , Vanzetti Leonardo S.
Published: February 2017

Background

Research projects often involve observation, registration, and data processing starting from information obtained in field experiments. In many cases, these tasks are carried out by several persons in different places, times, and ways, adding different levels of complexity and error in data collecting. Furthermore, data processing can be time consuming, and input errors may produce unwanted results.

Results

We have developed a novel, open source software called Phenobook, an easy, flexible, and intuitive tool to organize, collect, and save experimental data for further analyses. Phenobook was conceived to collect phenotypic observations in a user-friendly, cost-effective way. It consists of a web-based software for experiment design, data input and visualization, and exportation, combined with a mobile application for remote data collecting. We provide in this article a detailed description of the developed tool.

Conclusion

Phenobook is a software tool that can be easily implemented in collaborative research and development projects involving data collecting and forward analyses. Adopting Phenobook is expected to improve the involved processes by minimizing input errors, resulting in higher quality and reliability of the research outcomes.
The use of Oxford Nanopore native barcoding for complete genome assembly
Authors: Bayliss Sion C , Hunt Vicky L , Yokoyama Maho , Thorpe Harry A , Feil Edward J
Published: February 2017

Background

The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300.

Findings

Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only ~5% to 10% of an average MinION(TM) run (~7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements.

Conclusion

Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.
Developmental coordination disorder in children – experimental work and data annotation
Authors: Vařeka Lukáš , Brůha Petr , Mouček Roman , Mautner Pavel , Čepička Ladislav , Holečková Irena
Published: February 2017

Background

Developmental coordination disorder (DCD) is described as a motor skill disorder characterized by a marked impairment in the development of motor coordination abilities that significantly interferes with performance of daily activities and/or academic achievement. Since some electrophysiological studies suggest differences between children with/without motor development problems, we prepared an experimental protocol and performed electrophysiological experiments with the aim of making a step toward a possible diagnosis of this disorder using the event-related potentials (ERP) technique. The second aim is to properly annotate the obtained raw data with relevant metadata and promote their long-term sustainability.

Results

The data from 32 school children (16 with possible DCD and 16 in the control group) were collected. Each dataset contains raw electroencephalography (EEG) data in the BrainVision format and provides sufficient metadata (such as age, gender, results of the motor test, and hearing thresholds) to allow other researchers to perform analysis. For each experiment, the percentage of ERP trials damaged by blinking artifacts was estimated. Furthermore, ERP trials were averaged across different participants and conditions, and the resulting plots are included in the manuscript. This should help researchers to estimate the usability of individual datasets for analysis.

Conclusions

The aim of the whole project is to find out if it is possible to make any conclusions about DCD from EEG data obtained. For the purpose of further analysis, the data were collected and annotated respecting the current outcomes of the International Neuroinformatics Coordinating Facility Program on Standards for Data Sharing, the Task Force on Electrophysiology, and the group developing the Ontology for Experimental Neurophysiology. The data with metadata are stored in the EEG/ERP Portal.
NanoSim: nanopore sequence read simulator based on statistical characterization
Authors: Yang Chen , Chu Justin , Warren René L , Birol Inanç
Published: February 2017

Background

The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing – valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, the output of which could be used to benchmark analysis tools.

Results

Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim.

Conclusion

In this work, we model the base-calling errors of ONT reads to inform the simulation of sequences with similar characteristics. We showcase the performance of NanoSim on publicly available datasets generated using the R7 and R7.3 chemistries and different sequencing kits and compare the resulting synthetic reads to those of other long-sequence simulators and experimental ONT reads. We expect NanoSim to have an enabling role in the field and benefit the development of scalable next-generation sequencing technologies for the long nanopore reads, including genome assembly, mutation detection, and even metagenomic analysis software.
Paths to Respectability: Consumption and Stigma Management in the Contemporary Black Middle Class
Authors: Crockett David
Published: February 2017

When confronted with racial stigma, how do people manage it? What specific arrangements of objects and tactics do they mobilize to make everyday life more tolerable (if not more equal)? The politics of respectability (respectability) is one such arrangement. Respectability makes life more tolerable by offering a counternarrative that disavows stigma through status-oriented displays. This strategy of action emerged alongside mass consumer culture in the late 19th century, but what relevance does it have to those who are stigmatized in contemporary consumer culture? Based on ethnographic interviews and observations with middle-class African Americans, respectability remains an important strategy that has undergone profound changes since its origins while still operating in similar ways. In the late 20th century it fractured into two related but distinct counternarratives: (1) “discern and avoid,” which seeks distance from whatever is stigmatized, and (2) “destigmatize,” using black culture as a source of high status. Perceptions of how well either counternarrative manages stigma depend on how ideology, strategy, and consumption are connected via specific sociohistorical features of place and individual power resources. I illustrate those connections through four cases that show perceived success and perceived failure for each counternarrative.
Identification of Four ATP-Binding Cassette Transporter Genes in Cnaphalocrocis medinalis and Their Expression in Response to Insecticide Treatment
Authors: Yu Hai-Zhong , Xu Jia-Ping , Wang Xue-Yang , Ma Yan , Yu Dong , Fei Dong-Qiong , Zhang Shang-Zhi , Wang Wan-Ling
Published: February 2017

The ATP-binding cassette (ABC) transporters belong to a superfamily of genes involved in the transport of specific molecules across lipid membranes, as well as insecticide resistance, present in all living organisms. In this study, we combined the Cnaphalocrocis medinals transcriptome database with a bioinformatics approach to identify four C. medinals ABCs (CmABCs), including CmABCG1, CmABCG4, CmABCC2 and CmABCC3. Tissue expression analysis showed that these genes had a tissue-specific expression pattern. CmABCG1 had significantly higher expression in the haemolymph and head compared to the other tissues. The expression of CmABCG4, CmABCC2 and CmABCC3 was highest in the midgut, followed by expression in the fat body. The developmental stage expression analysis showed that CmABCG1, CmABCG4, CmABCC2 and CmABCC3 were mainly expressed in adults. The transcription of CmABCG1, CmABCG4 and CmABCC2 was significantly induced by chlorpyrifos. Taken together, the results of our study provided useful information for understanding of the detoxification system of C. medinalis.
The Advancing Role of Neuromodulation for the Management of Chronic Treatment-Refractory Pain
Authors: Shamji Mohammed F. , De Vos Cecile , Sharan Ashwini
Published: February 2017

Neuropathic pain is a common cause of disability and health care utilization. While judicious pharmacotherapy and management of comorbid psychological distress can provide for improved quality of life, some patients with treatment-refractory disease require more invasive therapies. Spinal cord stimulation can provide for improvement in pain and decrease in medication utilization, with level 1 evidence supporting its use across various pain etiologies including persistent postoperative neuropathic pain, complex regional pain syndrome, chronic inoperable limb ischemia, treatment refractory angina, and painful diabetic neuropathy. These procedures can be done with acceptably low morbidity and provide a cost-effective solution for those patients in whom medical therapies have failed. Technological innovation in lead design, implantable pulse generator capability, and stimulation algorithms and parameters may further enhance the success of this therapy. Neuromodulation of distal targets such as dorsal root ganglion may permit greater anatomic specificity of the therapy, whereas subthreshold stimulation with high-frequency or burst energy delivery may eliminate noxious and off-target paresthesiae. Such new technologies should be subject to rigorous evaluation as their mechanisms of action and long-term outcomes remain hitherto undefined.
Recent and Emerging Advances in Spinal Deformity
Authors: Smith Justin S. , Shaffrey Christopher I. , Bess Shay , Shamji Mohammed F. , Brodke Darrel , Lenke Lawrence G. , Fehlings Michael G. , Lafage Virginie , Schwab Frank , Vaccaro Alexander R. , Ames Christopher P.
Published: February 2017

BACKGROUND: Over the last several decades, significant advances have occurred in the assessment and management of spinal deformity.

OBJECTIVE: The primary focus of this narrative review is on recent advances in adult thoracic, thoracolumbar, and lumbar deformities, with additional discussions of advances in cervical deformity and pediatric deformity.

METHODS: A review of recent literature was conducted.

RESULTS: Advances in adult thoracic, thoracolumbar, and lumbar deformities reviewed include the growing applications of stereoradiography, development of new radiographic measures and improved understanding of radiographic alignment objectives, increasingly sophisticated tools for radiographic analysis, strategies to reduce the occurrence of common complications, and advances in minimally invasive techniques. In addition, discussion is provided on the rapidly advancing applications of predictive analytics and outcomes assessments that are intended to improve the ability to predict risk and outcomes. Advances in the rapidly evolving field of cervical deformity focus on better understanding of how cervical alignment is impacted by thoracolumbar regional alignment and global alignment and how this can affect surgical planning. Discussion is also provided on initial progress toward development of a comprehensive cervical deformity classification system. Pediatric deformity assessment has been substantially improved with low radiation-based 3-D imaging, and promising clinical outcomes data are beginning to emerge on the use of growth-friendly implants.

CONCLUSION: It is ultimately through the reviewed and other recent and ongoing advances that care for patients with spinal deformity will continue to evolve, enabling better informed treatment decisions, more meaningful patient counseling, reduced complications, and achievement of desired clinical outcomes.
Spine Oncology – Primary Spine Tumors
Authors: Dea Nicolas , Gokaslan Ziya , Choi David , Fisher Charles
Published: February 2017

Primary tumors originating from the spine are very complex and challenging entities to treat. Due to their rarity, a multicenter collaborative network is essential to shepherd the best research and contribute to the dissemination of the best evidence possible. Over the last few years, several advances have occurred in many different fields. Surgery is still the cornerstone of treatment in most cases. The occasional suboptimal outcomes and high morbidity of surgical treatment have however encouraged professionals caring for these patients to explore safer treatment options and alternatives or adjuncts to surgical treatment. A number of novel treatment strategies have emerged from the medical, interventional radiology, radiation oncology, and molecular worlds. This has truly positioned primary spine tumors at the forefront of multidisciplinary care. This article discusses these recent advances in detail to equip the oncologic spine surgeon and their team to better counsel and treat these patients. Most of these advances allow for a more tailored, efficient, and, most importantly, less morbid management of primary spine tumors. Some of these advances are still under investigation, however, and evidence-based oncological principles should still be strongly encouraged.
Navigation and Robotics in Spinal Surgery: Where Are We Now?
Authors: Overley Samuel C. , Cho Samuel K. , Mehta Ankit I. , Arnold Paul M.
Published: February 2017

Spine surgery has experienced much technological innovation over the past several decades. The field has seen advancements in operative techniques, implants and biologics, and equipment such as computer-assisted navigation and surgical robotics. With the arrival of real-time image guidance and navigation capabilities along with the computing ability to process and reconstruct these data into an interactive three-dimensional spinal “map”, so too have the applications of surgical robotic technology. While spinal robotics and navigation represent promising potential for improving modern spinal surgery, it remains paramount to demonstrate its superiority as compared to traditional techniques prior to assimilation of its use amongst surgeons.

The applications for intraoperative navigation and image-guided robotics have expanded to surgical resection of spinal column and intradural tumors, revision procedures on arthrodesed spines, and deformity cases with distorted anatomy. Additionally, these platforms may mitigate much of the harmful radiation exposure in minimally invasive surgery to which the patient, surgeon, and ancillary operating room staff are subjected.

Spine surgery relies upon meticulous fine motor skills to manipulate neural elements and a steady hand while doing so, often exploiting small working corridors utilizing exposures that minimize collateral damage. Additionally, the procedures may be long and arduous, predisposing the surgeon to both mental and physical fatigue. In light of these characteristics, spine surgery may actually be an ideal candidate for the integration of navigation and robotic-assisted procedures.

With this paper, we aim to critically evaluate the current literature and explore the options available for intraoperative navigation and robotic-assisted spine surgery.
Intervertebral Disk Degeneration and Repair
Authors: Dowdell James , Erwin Mark , Choma Theodoe , Vaccaro Alexander , Iatridis James , Cho Samuel K
Published: February 2017

Intervertebral disk (IVD) degeneration is a natural progression of the aging process. Degenerative disk disease (DDD) is a pathologic condition associated with IVD that has been associated with chronic back pain. There are a variety of different mechanisms of DDD (genetic, mechanical, exposure). Each of these pathways leads to a final common result of unbalancing the anabolic and catabolic environment of the extracellular matrix in favor of catabolism. Attempts have been made to gain an understanding of the process of IVD degeneration with in Vitro studies. These models help our understanding of the disease process, but are limited as they do not come close to replicating the complexities that exist with an in Vivo model. Animal models have been developed to help us gain further understanding of the degenerative cascade of IVD degeneration In Vivo and test experimental treatment modalities to either prevent or reverse the process of DDD. Many modalities for treatment of DDD have been developed including therapeutic protein injections, stem cell injections, gene therapy, and tissue engineering. These interventions have had promising outcomes in animal models. Several of these modalities have been attempted in human trials, with early outcomes having promising results. Further, increasing our understanding of the degenerative process is essential to the development of new therapeutic interventions and the optimization of existing treatment protocols. Despite limited data, biological therapies are a promising treatment modality for DDD that could impact our future management of low back pain.
Traumatic Spinal Cord Injury—Repair and Regeneration
Authors: Ahuja Christopher S. , Nori Satoshi , Tetreault Lindsay , Wilson Jefferson , Kwon Brian , Harrop James , Choi David , Fehlings Michael G.
Published: February 2017

BACKGROUND: Traumatic spinal cord injuries (SCI) have devastating consequences for the physical, financial, and psychosocial well-being of patients and their caregivers. Expediently delivering interventions during the early postinjury period can have a tremendous impact on long-term functional recovery.

PATHOPHYSIOLOGY: This is largely due to the unique pathophysiology of SCI where the initial traumatic insult (primary injury) is followed by a progressive secondary injury cascade characterized by ischemia, proapoptotic signaling, and peripheral inflammatory cell infiltration. Over the subsequent hours, release of proinflammatory cytokines and cytotoxic debris (DNA, ATP, reactive oxygen species) cyclically adds to the harsh postinjury microenvironment. As the lesions mature into the chronic phase, regeneration is severely impeded by the development of an astroglial-fibrous scar surrounding coalesced cystic cavities. Addressing these challenges forms the basis of current and upcoming treatments for SCI.

MANAGEMENT: This paper discusses the evidence-based management of a patient with SCI while emphasizing the importance of early definitive care. Key neuroprotective therapies are summarized including surgical decompression, methylprednisolone, and blood pressure augmentation. We then review exciting neuroprotective interventions on the cusp of translation such as Riluzole, Minocycline, magnesium, therapeutic hypothermia, and CSF drainage. We also explore the most promising neuroregenerative strategies in trial today including Cethrin™, anti-NOGO antibody, cell-based approaches, and bioengineered biomaterials. Each section provides a working knowledge of the key preclinical and patient trials relevant to clinicians while highlighting the pathophysiologic rationale for the therapies.

CONCLUSION: We conclude with our perspectives on the future of treatment and research in this rapidly evolving field.
Future Advances in Spine Surgery: The AOSpine North America Perspective
Authors: Fehlings Michael G. , Ahuja Christopher S. , Mroz Thomas , Hsu Wellington , Harrop James
Published: February 2017

This focus issue highlights state-of-the-art techniques, equipment, and practices in the modern era of spine surgery while providing a glimpse into the next generation of patient care. A broad range of topics are presented to cover the full spectrum of the field. Degenerative diseases are discussed in a series of 3 articles on (1) pathophysiology, management, and surgical approaches to degenerative cervical myelopathy; (2) novel approaches to degenerative thoracolumbar disease (eg, interspinous process spacers, minimally invasive/endoscopic approaches); and (3) animal models and emerging therapeutics in degenerative disk disease. Also included is a unique study aiming to establish the critically important cost–benefit relationship for spine procedures with perspectives on how value is defined and how to address variability.

Primary and metastatic spine oncology are reviewed with a focus on upcoming targeted biologics, subspecialized radiotherapy (eg, proton-beam, carbon-ion, stereotactic radiosurgery), genetic profiling to stratify risk, and morbidity-reducing surgical approaches (eg, minimally invasive/endoscopic resections, percutaneous instrumentation). Trauma is discussed in 2 high-quality papers on controversies in spinal trauma and neuroprotective/neuroregenerative interventions for traumatic spinal cord injury. A stimulating article on cervical, thoracolumbar, and pediatric deformity highlights the rapid evolution of deformity surgery with a look at innovative tools (eg, high-fidelity 3-dimensional reconstructions, magnetically controlled growing rods) and their impact on quality of life. Additionally, a must-read article on surgical site infections discusses key risk factors and evidence-based preventative techniques to remain aware of. Finally, cutting-edge technologies, including computer-assisted navigation, shared-control robotics, neuromodulation, novel osteobiologics, and biomaterials, are covered in detail in a series of 3 fascinating papers on the next generation of the field.

Each section intends to highlight the salient literature and afford insights from multiple key thought leaders in an effort to minimize bias and provide varied perspectives. Overall, we hope this issue provides high-quality, evidence-based data relevant to trainees and practicing surgeons while also stimulating excitement about the future of spine surgery.
Quality of Life following Stereotactic Radiosurgery for Single and Multiple Brain Metastases
Authors: Miller Jacob A. , Kotecha Rupesh , Barnett Gene H. , Suh John H. , Angelov Lilyana , Murphy Erin S. , Vogelbaum Michael A. , Mohammadi Alireza , Chao Samuel T.
Published: February 2017

BACKGROUND: Given the neurological morbidity and poor prognosis associated with brain metastases, it is critical to deliver appropriate therapy while remaining mindful of patient quality of life (QOL). For many patients, stereotactic radiosurgery (SRS) effectively controls intracranial disease, but QOL outcomes have not been characterized.

OBJECTIVE: To determine the effect of number of brain metastases upon QOL preservation following SRS.

METHODS: The EuroQol 5 Dimensions questionnaire (EQ-5D) and Patient Health Questionnaire 9 instruments were prospectively collected from a cohort of patients undergoing SRS for brain metastasis between 2008 and 2015. These instruments served as measures of overall QOL and depression. QOL deterioration exceeding the minimum clinically important difference was considered failure. Freedom from 12-month EQ-5D index failure was the primary outcome.

RESULTS: One hundred and twenty-two SRS treatments (67 patients, 421 lesions) were eligible for inclusion. Intracranial failure (local or distant) occurred following 61% of treatments. Among 421 lesions, 8% progressed locally. Median follow-up was 12 months.

All subscores of the EQ-5D instrument expectantly worsened at last follow-up; however, the magnitude of this difference (0.079) did not exceed the EQ-5D index minimum clinically important difference (mean 0.752 vs 0.673, P < .01). Twelve-month EQ-5D index QOL preservation was 79%. Patients with more than 3 brain metastases had a greater rate of EQ-5D index deterioration (hazard ratio 4.14, P < .01) than those with a single metastasis.

CONCLUSIONS: Among patients with brain metastasis, QOL preservation must remain paramount as multimodality therapy continues to improve. In the present investigation, 12-month QOL preservation was 79%. However, patients with more than 3 brain metastases were at significantly greater risk for QOL decline.
Mu-ming Poo: China Brain Project and the future of Chinese neuroscience
Authors: Wang Ling
Published: February 2017

Among several major frontier science and technology projects soon to be initiated by the Chinese government, China Brain Project (on ‘Brain Science and Brain-like Intelligence Technology’ (CBP)) has attracted much attention. Mu-ming Poo, Director of the Institute of Neuroscience (ION) and Center for Excellence in Brain Science and Intelligence Technology of Chinese Academy of Sciences (CAS), is currently also the Executive Associate Editor of NSR. He has played a key role in the strategic discussion and planning for CBP. In a recent interview with NSR, Poo discussed his view on the goals and contents of CBP, as well as recent developments and future prospects of neuroscience in general. Throughout his research career that spanned over four decades, Poo has made seminal contributions to several areas in neuroscience. He reminisced during the interview on his own career path, as well as his experience and thoughts on building the research infrastructure for Chinese neuroscience.
Characteristics and Mortality of Pneumocystis Pneumonia in Patients With Cushing’s Syndrome: A Plea for Timely Initiation of Chemoprophylaxis
Authors: van Halem Karlijn , Vrolijk Lucia , Pereira Alberto Martin , de Boer Markus Gerardus Johannes
Published: February 2017

In patients with Cushing’s syndrome, development of Pneumocystis pneumonia (PCP) is associated with extreme cortisol production levels. In this setting, immune reconstitution after abrogation of cortisol excess appears to induce development of symptomatic PCP. The high mortality rate warrants timely initiation of chemoprophylaxis or even preemptive treatment of PCP.
Prescribing of Human Immunodeficiency Virus (HIV) Pre-exposure Prophylaxis by HIV Medical Providers in the United States, 2013–2014
Authors: Weiser John , Garg Shikha , Beer Linda , Skarbinski Jacek
Published: February 2017

Background

Clinical trials have demonstrated the effectiveness of human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) for reducing HIV acquisition. Understanding how HIV care providers are prescribing PrEP is necessary to ensure success of this prevention strategy.

Methods

During 2013–2014, we surveyed US HIV care providers who also provided care to HIV-negative patients. We estimated percentages who had prescribed PrEP and assessed associations between provider characteristics and PrEP prescribing.

Results

An estimated 26% (95% confidence interval [CI], 20–31) had ever prescribed PrEP. Of these, 74% (95% CI, 61–87) prescribed for men who have sex with men (MSM), 30% (95% CI, 21–39) for women who have sex with men, 23% (95% CI, 9–37) for men who have sex with women, 23% (95% CI, 15–30) for uninfected partners in HIV-discordant couples trying to conceive, and 1% (95% CI, 0–2) for persons who inject drugs. The following provider characteristics were significantly associated with having prescribed PrEP: male vs female (32% vs 16%; adjusted prevalence ratio [aPR], 1.5; 95% CI, 1.0–2.2), lesbian/gay/bisexual vs heterosexual orientation (50% vs 21%; aPR, 2.0; 95% CI, 1.3–2.9), and HIV caseload (>200, 51–200, and ≤50 patients, 39%, 29%, and 14%, respectively; >200 vs ≤50 patients, aPR 2.4, 95% CI 1.1–5.2, and 51–200 vs ≤50 patients, aPR 2.2, 95% CI 1.2–4.0).

Conclusions

In 2013–2014, one quarter of HIV care providers reported having prescribed PrEP, most commonly for MSM and rarely for persons who inject drugs. Lesbian/gay/bisexual providers and male providers were more likely than others to have prescribed PrEP. Additional efforts may enable more providers to prescribe PrEP to underserved clients needing the service.
White Blood Cell Counts, Alcoholism, and Cirrhosis in Pneumococcal Pneumonia
Authors: Gardner Julianna G. , Bhamidipati Divya R. , Rueda Adriana M. , Nguyen Duc T. M. , Graviss Edward A. , Musher Daniel M.
Published: February 2017

Background

An elevated white blood cell (WBC) count is a characteristic finding in pneumococcal pneumonia. Very low WBC counts, occurring in some cases, are often associated with overwhelming pneumonia and have been attributed to alcohol-induced suppression of bone marrow. However, a systematic study of neutropenia, leukocytosis, alcohol ingestion, and cirrhosis in pneumococcal pneumonia has not been previously reported.

Methods

Using a database of patients with pneumococcal pneumonia at our medical center, we extracted data on WBC counts at admission, differential counts, alcohol ingestion, and cirrhosis, and we related these to 7-day and 30-day mortality.

Results

White blood cell counts were <6000/mm3 in 49 of 481 patients (10.2%) with pneumococcal pneumonia and >25000/mm3 in 40 (8.3%). Mortality at 7 days was 18.4% and 12.5%, respectively, 5-fold and 3-fold greater in patients with WBC <6000 or >25000 than in those with WBC counts between 6000 and 25000 (P < .001). Increased band forms were not associated with a worse outcome (P = .12). Alcohol use and cirrhosis were not associated with WBC counts <6000 (P = .63 and P = .41, respectively).

Conclusions

In a large series of cases of pneumococcal pneumonia, WBC counts <6000 or >25000 correlated significantly with increased 7-day mortality. More than 10% band forms was not associated with a poor outcome. Alcohol abuse was not associated with low WBC or increased mortality. Our findings suggest that greater consideration be given to more intense care for patients with bacterial pneumonia who have very high or very low WBC counts at the time of hospital admission.
Comparative Sensitivity of Transthoracic and Transesophageal Echocardiography in Diagnosis of Infective Endocarditis Among Veterans With Staphylococcus aureus Bacteremia
Authors: Sekar Poorani , Johnson James R. , Thurn Joseph R. , Drekonja Dimitri M. , Morrison Vicki A. , Chandrashekhar Yellapragada , Adabag Selcuk , Kuskowski Michael A. , Filice Gregory A.
Published: February 2017

Background

Echocardiography is fundamental for diagnosing infective endocarditis (IE) in patients with Staphylococcus aureus bacteremia (SAB), but whether all such patients require transesophageal echocardiography (TEE) is controversial.

Methods

We identified SAB cases between February 2008 and April 2012. We compared sensitivity and specificity of transthoracic echocardiography (TTE) and TEE for evidence of IE, and we determined impacts of IE risk factors and TTE image quality on comparative sensitivities of TTE and TEE and their impact on clinical decision making.

Results

Of 215 evaluable SAB cases, 193 (90%) had TTE and 130 (60%) had TEE. In 119 cases with both tests, IE was diagnosed in 29 (24%), for whom endocardial involvement was evident in 25 (86%) by TEE, vs only 6 (21%) by TTE (P < .001). Transesophageal echocardiography was more sensitive than TTE regardless of risk factors. Even among the 66 cases with adequate or better quality TTE images, sensitivity was only 4 of 17 (24%) for TTE, vs 16 of 17 (94%) for TEE (P < .001). Among 130 patients with TEE, the TEE results, alone or with TTE results, influenced treatment duration in 56 (43%) cases and led to valve surgery in at least 4 (6%). It is notable that, despite vigorous efforts to obtain both tests routinely, TEE was not done in 86 cases (40%) for various reasons, including pathophysiological contraindications (14%), patient refusal or other patient-related factors (16%), and provider declination or system issues (10%).

Conclusions

Patients with SAB should undergo TEE when possible to detect evidence for IE, especially if the results might affect management.
Risk Factors for Surgical Site Infection After Cholecystectomy
Authors: Warren David K. , Nickel Katelin B. , Wallace Anna E. , Mines Daniel , Tian Fang , Symons William J. , Fraser Victoria J. , Olsen Margaret A.
Published: February 2017

Background

There are limited data on risk factors for surgical site infection (SSI) after open or laparoscopic cholecystectomy.

Methods

A retrospective cohort of commercially insured persons aged 18–64 years was assembled using International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) procedure or Current Procedural Terminology, 4th edition codes for cholecystectomy from December 31, 2004 to December 31, 2010. Complex procedures and patients (eg, cancer, end-stage renal disease) and procedures with pre-existing infection were excluded. Surgical site infections within 90 days after cholecystectomy were identified by ICD-9-CM diagnosis codes. A Cox proportional hazards model was used to identify independent risk factors for SSI.

Results

Surgical site infections were identified after 472 of 66566 (0.71%) cholecystectomies; incidence was higher after open (n = 51, 4.93%) versus laparoscopic procedures (n = 421, 0.64%; P < .001). Independent risk factors for SSI included male gender, preoperative chronic anemia, diabetes, drug abuse, malnutrition/weight loss, obesity, smoking-related diseases, previous Staphylococcus aureus infection, laparoscopic approach with acute cholecystitis/obstruction (hazards ratio [HR], 1.58; 95% confidence interval [CI], 1.27–1.96), open approach with (HR, 4.29; 95% CI, 2.45–7.52) or without acute cholecystitis/obstruction (HR, 4.04; 95% CI, 1.96–8.34), conversion to open approach with (HR, 4.71; 95% CI, 2.74–8.10) or without acute cholecystitis/obstruction (HR, 7.11; 95% CI, 3.87–13.08), bile duct exploration, postoperative chronic anemia, and postoperative pneumonia or urinary tract infection.

Conclusions

Acute cholecystitis or obstruction was associated with significantly increased risk of SSI with laparoscopic but not open cholecystectomy. The risk of SSI was similar for planned open and converted procedures. These findings suggest that stratification by operative factors is important when comparing SSI rates between facilities.
Sensitive Molecular Diagnostics for Cutaneous Leishmaniasis
Authors: Sagi Orli , Berkowitz Anat , Codish Shlomi , Novack Victor , Rashti Aviv , Akad Fouad , Shemer-Avni Yonat
Published: February 2017

Background

Rapid diagnosis of cutaneous leishmaniasis (CL) and identification of Leishmania species is highly important for the disease management. In Israel, CL is caused mainly by Leishmania major and Leishmania tropica species.

Methods

We established an easy to handle point of care lesion-swabbing, combined with a highly sensitive multiplex real time PCR (multiplex qPCR) for accurate and rapid diagnosis of Leishmania species.

Results

Using three probes: one general for: Leishmania species, and two specific for L major, and L tropica, we screened 1783 clinical samples collected during two years. Leishmania species was found in 1086 individuals, 1008 L major, and 70 L tropica. Eight samples positive for Leishmania species only, were further tested using a second set of multiplex qPCR developed, and were found positive for Leishmania braziliensis and Leishmania infantum/donovani (2 and 6 samples, concomitantly).

Conclusions

Taken together, the test enabled diagnostics and better treatment of Leishmania infections from the Old World (1078 samples) and the New World (8 samples), and the subtyping of the dominant strains in the region, as well as in returning travelers’.
Infection Rates and Treatment of Low-Velocity Extremity Gunshot Injuries
Authors: Nguyen Mai P. , Savakus Jonathan C. , O'Donnell Jeffrey A. , Prayson Nicholas F. , Reich Michael S. , Golob Joseph F. , McDonald Amy A. , Como John J. , Vallier Heather A.
Published: February 2017

Objectives:

To determine the rates of infection in low-energy gunshot wounds (GSWs) to the extremity.

Design:

Retrospective review.

Setting:

Level I trauma center.

Patients/Participants:

Patients (N = 140) with at least 90-day follow-up for extremity-only low-energy GSW injuries from 2010–2014 were retrospectively reviewed. Treatment was recorded, including type and duration of antibiotics and details of nonoperative and operative managements.

Main Outcome Measures:

The rates of superficial and deep infections.

Results:

The overall infection rate was 15.7% (22 patients), and the deep infection rate was 3.6% (5 patients). Age, sex, and injury location were similar between the groups that did and did not receive antibiotic prophylaxis. Injury Severity Scores were higher in the group that did receive antibiotics. Regarding soft tissue-only injuries, antibiotic prophylaxis trended toward a lower rate of overall infection versus no antibiotic prophylaxis (6.1% vs. 25.9%, respectively, P = 0.07). Multiple doses of antibiotics did not reduce the rate of infection when compared with a single dose (14.6% vs. 12.5%, respectively, P = 1.00). No deep infections occurred in patients with nonoperatively treated fractures, regardless of antibiotic administration. All operatively treated fractures received antibiotic prophylaxis and demonstrated superficial and deep infection rates of 15.1% and 5.7%, respectively.

Conclusions:

Infections after low-energy extremity GSWs are infrequent. For soft tissue injuries without fracture, a single dose of intravenous antibiotics in the emergency department was associated with a lower rate of infection compared with no antibiotics. Operatively treated low-energy GSW fractures should receive standard perioperative antibiotics.

Level of Evidence:

Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
The Anterior Intrapelvic Approach for Acetabular Fractures Using Approach-Specific Instruments and an Anatomical-Preshaped 3-Dimensional Suprapectineal Plate
Authors: Gras Florian , Marintschev Ivan , Grossterlinden Lars , Rossmann Markus , Graul Isabel , Hofmann Gunther O. , Rueger Johannes M. , Lehmann Wolfgang
Published: February 2017

Objectives:

Anatomical acetabular plates the anterior intrapelvic approach (AIP) were recently introduced to fix acetabular fractures through the intrapelvic approach. Therefore, we asked the following: (1) Does the preshaped 3-dimensional suprapectineal plate interfere with or even impair the fracture reduction quality? (2) How often does the AIP approach need to be extended by the first (lateral) window of the ilioinguinal approach?

Design:

Observational case series.

Setting:

Two Level 1 trauma centers.

Patients/Participants:

Patients with unstable acetabular fractures in 2014.

Intervention:

Fracture fixation with anatomical-preshaped, 3-dimensional suprapectineal plates through the AIP approach ± the first window of the ilioinguinal approach.

Outcome Measurements:

Fracture reduction results were measured in computed tomography scans and graded according to the Matta quality of reduction. Intraoperative parameters and perioperative complications were recorded. Radiological results (according to Matta) and functional outcome (modified Merle d'Aubigné score) were evaluated at 1-year follow-up.

Results:

Thirty patients (9 women + 21 men; mean age ± SE: 64 ± 8 years) were included. The intrapelvic approach was solely used in 19 cases, and in 11 cases, an additional extension with the first window of the ilioinguinal approach (preferential for 2-column fractures) was performed. The mean operating time was 202 ± 59 minutes; the fluoroscopic time was 66 ± 48 seconds. Fracture gaps and steps in preoperative versus postoperative computed tomography scans were 12.4 ± 9.8 versus 2.0 ± 1.5 and 6.0 ± 5.5 versus 1.3 ± 1.7 mm, respectively. At 13.4 ± 2.9 months follow-up, the Matta grading was excellent in 50%, good in 25%, fair in 11%, and poor in 14% of cases. The modified Merle d'Aubigné score was excellent in 17%, good in 37%, fair in 33%, and poor in 13% of cases.

Conclusion:

The AIP approach using approach-specific instruments and an anatomical-preshaped, 3-dimensional suprapectineal plate became the standard procedure in our departments. Radiological and functional early results justify joint preserving surgery in most cases.

Level of Evidence:

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.