bluuebunny/crossref_metadata_2025 huggingface dataset:
fastp: an ultra-fast all-in-one FASTQ preprocessor
Authors: Chen Shifu , Zhou Yanqing , Chen Yaru , Gu Jia
Published: July 2018

Motivation

Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.

Results

We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.

Availability and implementation

The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences
Authors: Greenside Peyton , Shimko Tyler , Fordyce Polly , Kundaje Anshul
Published: July 2018

Motivation

Transcription factors bind regulatory DNA sequences in a combinatorial manner to modulate gene expression. Deep neural networks (DNNs) can learn the cis-regulatory grammars encoded in regulatory DNA sequences associated with transcription factor binding and chromatin accessibility. Several feature attribution methods have been developed for estimating the predictive importance of individual features (nucleotides or motifs) in any input DNA sequence to its associated output prediction from a DNN model. However, these methods do not reveal higher-order feature interactions encoded by the models.

Results

We present a new method called Deep Feature Interaction Maps (DFIM) to efficiently estimate interactions between all pairs of features in any input DNA sequence. DFIM accurately identifies ground truth motif interactions embedded in simulated regulatory DNA sequences. DFIM identifies synergistic interactions between GATA1 and TAL1 motifs from in vivo TF binding models. DFIM reveals epistatic interactions involving nucleotides flanking the core motif of the Cbf1 TF in yeast from in vitro TF binding models. We also apply DFIM to regulatory sequence models of in vivo chromatin accessibility to reveal interactions between regulatory genetic variants and proximal motifs of target TFs as validated by TF binding quantitative trait loci. Our approach makes significant strides in improving the interpretability of deep learning models for genomics.

Availability and implementation

Code is available at: https://github.com/kundajelab/dfim.

Supplementary information

Supplementary data are available at Bioinformatics online.
Nontraditional Laboratory Animal Species (Cephalopods, Fish, Amphibians, Reptiles, and Birds)
Authors: O’Rourke Dorcas P , Baccanale Cecile L , Stoskopf Michael K
Published: July 2018

Aquatic vertebrates and cephalopods, amphibians, reptiles, and birds offer unique safety and occupational health challenges for laboratory animal personnel. This paper discusses environmental, handling, and zoonotic concerns associated with these species.
Three Infinities in Early Modern Philosophy
Authors: Schechtman Anat
Published: July 2018

Many historical and philosophical studies treat infinity as an exclusively quantitative notion, whose proper domain of application is mathematics and physics. The main aim of this paper is to disentangle, by critically examining, three notions of infinity in the early modern period, and to argue that one—but only one—of them is quantitative. One of these non-quantitative notions concerns being or reality, while the other concerns a particular iterative property of an aggregate. These three notions will emerge through examination of three central figures in the period: Locke (for quantitative infinity), Descartes (ontic infinity), and Leibniz (iterative infinity).
High-throughput screening of biomolecules using cell-free gene expression systems
Authors: Contreras-Llano Luis E , Tan Cheemeng
Published: July 2018

The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
In situ rumen degradation of kernels from short-season corn silage hybrids as affected by processing1,2
Authors: Miorin Renan L , Holtshausen Lucia , Baron Vern , Beauchemin Karen A
Published: July 2018

The objective of this in situ study was to evaluate the rumen degradability of kernels from short-season corn hybrids grown for silage in Western Canada (Lacombe, AB) and determine whether decreasing kernel particle size would enhance ruminal degradability in a similar manner for all hybrids. The study was a completely randomized design with 3 beef cows (replicates) and a 6 (hybrid) × 3 (particle size) factorial arrangement of treatments. Kernels were processed to generate three different particle sizes: large (2.3 mm), medium (1.4 mm), and small (0.7 mm). Processed samples were incubated in the rumen for 0, 3, 6, 12, 24, and 48 h using the in situ method and degradation kinetics of DM and starch were determined. Effective rumen degradability (ED) was estimated using a passage rate of 0.04 (ED4), 0.06 (ED6), and 0.08/h (ED8). Hybrids exhibited a range in whole plant DM content (23.7 to 25.0%), starch content (15.9 to 28.1% DM), kernel hardness (21.9 to 34.4 s/20 g) and density (3.57 to 4.18 g/mL), and prolamin content (8.24 to 11.34 g/100 g starch). Differences in digestion kinetics among hybrids were generally more pronounced for starch than DM. The hybrids differed in starch degradability (P < 0.05), with earlier maturing hybrids having lower A fraction, lower kd, and lower ED, with hybrid effects on ED being accentuated with faster passage rate. Kernel DM content (r = −0.85, −0.87), hardness (r = −0.89, −0.86), and density (r = −0.84, −0.85) were negatively correlated with ED4 and ED8 of starch, respectively, due mainly to decreased kd of fraction B. Reducing the particle size of kernels increased ED of starch due to increased A fraction and kd of the B fraction. A tendency (P = 0.09) for hybrid × processing effects for ED6 and ED8 indicated that processing had greater effects on increasing ED of starch for earlier maturing hybrids. We conclude that short-season hybrids that mature early may have lower ED of DM and starch and would benefit from prolonged ensilage time. Kernel processing during silage making is recommended for short-season corn hybrids as a means of enhancing rumen availability of starch.
Feasibility of a Smartphone-based pilot intervention for Hispanic breast cancer survivors: a brief report
Authors: Buscemi Joanna , Buitrago Diana , Iacobelli Francisco , Penedo Frank , Maciel Crystal , Guitleman Judy , Balakrishnan Aparna , Corden Marya , Adler Rachel F , Bouchard Laura C , Perez-Tamayo Alejandra , Yanez Betina R
Published: July 2018

Hispanic breast cancer survivors (BCS) are at high risk for experiencing poor health-related quality of life (HRQoL) after completion of active breast cancer treatment. Therefore, there is a need to develop culturally tailored interventions for Hispanic BCS. To date, there have been limited interventions that have demonstrated that increasing cancer-related knowledge, self-efficacy in communication, and self-management skills can improve HRQoL among Hispanic BCS. These interventions have been delivered in person or by phone, which may be burdensome for Hispanic BCS. To facilitate intervention delivery, we developed My Guide, a Smartphone application aimed at improving HRQoL among Hispanic BCS. The purpose of the current study is to describe the feasibility results of a 4-week pilot trial testing My Guide among Hispanic BCS. Twenty-five women enrolled in the study (75% recruitment rate) and 22 women were retained (91.6% retention rate). Mean time spent using My Guide across the 4 weeks was 9.25 hr, and mean score on the satisfaction survey was 65.91 (range 42–70), in which higher scores reflect greater satisfaction. Participants’ scores on the Breast Cancer Knowledge Questionnaire significantly improved from study baseline (M = 9.50, SD = 2.92) to the postintervention assessment (M = 11.14, SD = 2.66), d = 0.59. Participants’ HRQoL scores improved over the course of 4 weeks, but these improvements were not statistically significant. Overall, My Guide was feasible and acceptable. Future studies will assess the preliminary efficacy of My Guide in improving HRQoL in a larger, randomized trial of Hispanic BCS.
Ilioinguinal Approach: Indication and Technique
Authors: Fensky Florian , Lehmann Wolfgang , Ruecker Andreas , Rueger Johannes M.
Published: July 2018

This video on the ilioinguinal approach presents its indications and techniques for the operative treatment of acetabular fractures. The principle of the ilioinguinal approach is to work through 3 different windows. The lateral window gives access to the pelvic bone from the sacroiliac joint to the lateral border of the iliopsoas muscle, the middle window accesses the medial border of the iliopsoas muscle to the femoral artery, and the medial window allows for control of the anterior pelvic ring medially from the femoral vein to the symphysis pubis. In this video, we demonstrate anatomical reconstruction of the acetabulum in a patient with an associated both-column fracture using the ilioinguinal approach. Indications are all acetabular fracture types, where in addition to anterior column fracture, a fractured posterior column is reducible through the middle window, that is, there is no involvement of the posterior column or wall that would necessitate a direct posterior approach. The ilioinguinal approach is a standard anatomical approach that gives an excellent visual and palpatory exposure of the anterior column up to the symphysis pubis and of the quadrilateral plate. Indications and techniques, how to develop this approach for the anatomical reduction and fixation of appropriate acetabular fractures, are demonstrated in this video.
Posttraumatic Heterotopic Ossification of the Hip
Authors: Behery Omar A. , Dai Amos Z. , McLaurin Toni M.
Published: July 2018

Introduction:

Posttraumatic heterotopic ossification (HO) of the hip frequently follows acetabular fracture and hip surgery and can become symptomatic, with significant pain and limited range of motion (ROM). Definitive treatment may require surgical excision, which can result in serious complications if not planned and executed appropriately.

Methods:

Surgical excision of posttraumatic hip HO requires appropriate indications, preoperative planning, and intraoperative guidance using fluoroscopy to maximize excision of HO and minimize complications. This video presents a case of severe posttraumatic hip HO, indications and technique of surgical excision using fluoroscopic guidance, postoperative protocol, and the patient's clinical follow-up.

Results:

Surgical excision along with appropriate postoperative HO prophylaxis and immediate mobilization resulted in significant improvement in hip ROM and return to activities of daily living without complications or recurrence. Intraoperative blood loss can be significant and should be appropriately planned for preoperatively.

Conclusions:

Posttraumatic hip HO can cause significantly limited hip ROM and pain with resulting disability. Surgical excision of posttraumatic hip HO in a preserved hip joint can be successful in restoring hip ROM and function. Appropriate postoperative HO prophylaxis can prevent recurrence.
Use of the 95-degree Angled Blade Plate to Treat a Proximal Femur Fracture
Authors: Hartline Braden E. , Achor Timothy S.
Published: July 2018

There are a variety of ways to treat high-energy proximal femur fractures, including intramedullary nails and laterally based plates. Although each have distinct advantages and disadvantages, fracture reduction and avoiding varus alignment are critical. For some fractures, the blade plate is a reliable, straightforward implant to treat these injuries. This article and the accompanying video describe the surgical technique of using a 95-degree angled blade plate to treat an acute high-energy proximal femur fracture.
Ankle Spanning External Fixator Application
Authors: McAndrew Christopher M. , Ricci William M. , Miller Anna N. , Avery Matthew C.
Published: July 2018

A 2-stage approach to treatment of tibia pilon fractures was reported in the 1990s and popularized over the ensuing decade to help avoid catastrophic soft-tissue complications experienced with one-stage open reduction and internal fixation. This approach can be expanded to the treatment of other high-energy injuries of the hind foot, with variation in external fixator application as needed. Key factors to maximize the utility and decrease complications of the external fixation stage include the following: (1) anatomic reduction of the talus under the long axis of the tibia in the coronal and sagittal planes, (2) strategic application of Schantz pins to resist deforming forces resulting from the injury, and (3) external fixation outside the zone of injury and definitive surgical treatment. This video demonstrates concepts and tactics to obtain and maintain fracture reduction with an external fixator with examples of a complex combined plafond and talus injury, as well as a more typical Orthopaedic Trauma Association/Arbeitsgemeinschaft fur Osteosynthesefragen C-type pilon fracture.
Shoulder Arthrodesis
Authors: Legato Joseph M. , O'Connell Megan , Fuller David A.
Published: July 2018

Purpose:

The purpose of this video is to demonstrate the surgical technique of a shoulder arthrodesis for a patient with multidirectional instability and multiple failed previous surgeries.

Methods:

A 25-year-old woman with a long history of left shoulder multidirectional instability in the setting of Ehlers–Danlos syndrome is shown undergoing a shoulder arthrodesis. The video demonstrates intraoperative patient positioning, approach, shoulder osseous and articular preparation, implant placement (narrow 4.5 dynamic compression plate), and wound closure. The video includes a brief case history with preoperative radiographic imaging, indications, and patient outcome with postoperative radiographic imaging.

Results:

The video is 11 minutes, 34 seconds in time.

Conclusion:

This video demonstrates a left shoulder arthrodesis with successful glenohumeral positioning of 30 degrees/30 degrees/30 degrees flexion, abduction, and internal rotation, respectively, and functional ability to reach the mouth and top of the head.
Intraoperative CT and Surgical Navigation for Iliosacral Screws: Technique for Patients With Sacral Dysmorphism
Authors: Khan Jannat M. , Lara Daniel L. , Marquez-Lara Alejandro , Rosas Samuel , Hasty Eddy , Pilson Holly T.
Published: July 2018

Percutaneous iliosacral screw (IS) fixation for pelvic ring injuries with the use of an O-arm imaging system has been associated with decreased procedure time and improved accuracy of IS screw placement compared with the use of fluoroscopic guidance. Specifically, patients with sacral dysmorphism require identification of safe bony sacral corridors, using specific anatomical measurements, to decrease the likelihood of complications such as screw perforation. Intraoperative computed tomography imaging and navigation can aid in safe and accurate IS screw fixation in patients with difficult anatomy.
Open Reduction and Internal Fixation of the Femoral Head via the Smith–Petersen Approach
Authors: Ricci William M. , McAndrew Christopher M. , Miller Anna N. , Avery Matthew C.
Published: July 2018

Pipkin described femoral head fractures in the 1950s, but controversy still exists regarding indications for surgery and approaches for operative treatment of femoral head fractures. Clear indications for operative intervention include inability to reduce the hip with closed methods, a nonconcentric reduction, fracture fragments within the articulating surface of the hip, and associated injuries (acetabulum and femoral neck fractures) with their own indications for surgery. The anterior approach described by Smith–Petersen has been modified (using only the distal portion) and used to visualize, clean, reduce, and fix these fractures with and without anterior dislocation of the hip.
ORIF Pilon via Posteromedial and Anterolateral Approaches
Authors: McAndrew Christopher M. , Ricci William M. , Miller Anna N. , Avery Matthew C.
Published: July 2018

Tibial pilon fractures are complex injuries of soft tissue and bone that challenge patients and surgeons. Outcomes following this injury are guarded, and complications are frequently reported. Soft-tissue compromise at the time of injury is potentially amplified with surgical trauma, necessitating thorough evaluation, preoperative planning, and expertise to minimize complications and maximize outcomes. Understanding angiosome anatomy and typical fracture patterns (and their variations) allows for design of surgical tactics that accomplish these goals.
Range of Motion Improvement Following Surgical Management of Knee Arthrofibrosis in Children and Adolescents
Authors: Fabricant Peter D. , Tepolt Frances A. , Kocher Mininder S.
Published: July 2018

Background:

Arthrofibrosis of the knee is well-described in adults as a potentially debilitating postoperative complication following anterior cruciate ligament reconstruction, total knee arthroplasty, or fracture fixation. Knee arthrofibrosis in children and adolescents, however, has received little attention. The primary purpose of this study was to report improvements in range of motion (ROM) following lysis of adhesions and manipulation under anesthesia (LOA/MUA) in children and adolescents with knee arthrofibrosis, and, secondarily, to evaluate for any effect of preoperative dynamic splinting on ROM outcomes.

Methods:

Ninety patients aged 18 years and below (mean, 14.4±3.5) and 31% male who underwent LOA/MUA at an urban tertiary care hospital following prior knee surgery were evaluated. Demographic, clinical, ROM, and revision data were compiled. Primary outcome was absolute ROM. Secondarily, ROM was analyzed as a categorical variable with “Full ROM” defined to be −5 to 130 degrees or better, “functional” ROM was defined as unable to obtain −5 to 130 degrees but not requiring revision, and “failure” defined as resulting in revision arthrofibrosis surgery. t tests and χ2 analyses were used to compare ROM and count variables between dynamic splinting subgroups.

Results:

Mean time from index surgery to LOA/MUA was 6.0±4.4 months, and follow-up was 42±56 months. Index procedures included anterior cruciate ligament reconstruction (N=33), tibial spine arthroscopic reduction and internal fixation (N=18), fracture fixation (N=17), soft tissue repair (N=17), and multiligament reconstruction (N=5). In total, 68 subjects (76%) had any flexion loss, 57 subjects (63%) had any extension loss, and 40 subjects (44%) had both flexion and extension loss.

Fifty-six subjects (62%) had full ROM at final follow-up, 25 subjects (28%) had functional ROM, and 9 subjects (10%) required revision. No demographic, clinical, or surgical variable was predictive of treatment failure. Patients who underwent dynamic splinting preoperatively (N=46; 51%) had greater preoperative flexion (99±16 vs.77±34 degrees; P=0.001), but no difference in flexion at final follow-up (121±20 vs.128±11 degrees; P=0.08). Failure was not associated with time from index procedure to LOA/MUA, and the proportion who regained full ROM postoperatively was equivalent between those who had dynamic splinting and those who did not (65% vs. 59%; P=0.70).

Conclusions:

LOA/MUA for children with arthrofibrotic knees results in significant improvements in ROM with 90% revision-free success. Preoperative dynamic or static progressive splinting improves preoperative flexion but does not affect postoperative range of motion or failure rate.

Level of Evidence:

Level II.
Population-based Risk Factors for the Development of Degenerative Disk Disease
Authors: Steelman Theodore , Lewandowski Louis , Helgeson Melvin , Wilson Kevin , Olsen Cara , Gwinn David
Published: July 2018

Study Design:

This is a retrospective case control study.

Objective:

Identify risk factors and assess their relative impact on the development of degenerative disk disease (DDD).

Summary of Background Data:

DDD is responsible for widespread disability in the civilian and military population. Despite the impact of low back pain and DDD, its multifactorial etiology is not entirely understood.

Materials and Methods:

The Defense Medical Surveillance System was searched for military members with the diagnosis of DDD as identified with the use of International Classification of Disease, 9th Revision (ICD-9) codes. These patients were compared with an age-matched and sex-matched control of military members without DDD from the Defense Medical Surveillance System. The prevalence of risk factors (obesity, hip, and knee osteoarthritis, tobacco dependence, diabetes, and type of employment) was then determined for both groups. In total, 160,911 patients with DDD were identified compared with 315,225 controls. Multivariate conditional logistical regression analysis was utilized to determine odds ratio (OR) for these groups based on data matched by age and sex and were adjusted for military rank and race/ethnicity.

Results:

Diabetes showed an OR of 1.469 [confidence interval (CI), 1.350–1.598]. Hip and knee arthritis produced an OR of 2.925 (CI, 2.685–3.187) and tobacco dependency showed an OR of 1.799 (CI, 1.762–1.836). The comparison of overweight to normal body mass index produced an OR of 1.334 (CI, 1.307–1.361) and the analysis of obese to normal body mass index had an OR of 1.556 (CI, 1.497–1.618). There failed to be a clinically significant association between military duty assignments and the presence of DDD.

Conclusions:

Our research failed to show a clinical significance association between military duty assignment and DDD. However, we were able to identify a significant association between concomitant hip and knee osteoarthritis, obesity, diabetes, and tobacco dependency with the development of DDD.

Level of Evidence:

Level IV.
Outcomes in Patients With Severe West Nile Neuroinvasive Disease
Authors: Hawkes Maximiliano A. , Carabenciov Ivan D. , Wijdicks Eelco F. M. , Rabinstein Alejandro A.
Published: July 2018

Objective:

To assess the long-term outcomes of patients hospitalized with severe West Nile neuroinvasive disease.

Design:

Retrospective cohort.

Setting:

Patients admitted to a referral center (Saint Mary’s Hospital, Mayo Clinic).

Participants:

Twenty-six patients with West Nile neuroinvasive disease were identified by retrospective search of electronic database of Saint Mary’s Hospital from January 1999 to November 2016.

Interventions:

Retrospective electronic medical records review and prospective telephone follow-up.

Measurements and Main Results:

Functional disability and cognitive outcomes were evaluated with the modified Rankin Scale and the Telephone Interview for Cognitive Status scores. Data on the time that the patient returned home after the hospitalization for West Nile neuroinvasive disease and the time of return to work were also collected. We identified 26 patients (81% males), 59 ± 17 years old. After a median hospital stay of 14.5 days (3–126), four patients died and 90% of survivors had a modified Rankin Scale of 3–5. Two additional patients died, and 80% of survivors had a modified Rankin Scale of 0–2 after a median follow-up of 73 months (1–144). Seven patients had cognitive impairment, which was severe in two of them. The combination of encephalitis and acute flaccid paralysis at presentation was associated with lower likelihood of returning home within 1 month after discharge (p < 0.01). Patients who required mechanical ventilation were more likely to have a modified Rankin Scale of 3–5 at last follow-up (p = 0.03), less likely to return home within 1 month of discharge (p < 0.01), less likely to return to their jobs (p < 0.01), and showed a trend toward having cognitive impairment (p = 0.05).

Conclusions:

Despite having poor outcomes at discharge, most West Nile neuroinvasive disease survivors with severe early disability can recover functional independence in the long term, justifying aggressive support during the acute phase and extensive rehabilitation efforts.
Low Interleukin-7 Receptor Messenger RNA Expression Is Independently Associated With Day 28 Mortality in Septic Shock Patients*
Authors: Delwarde Benjamin , Peronnet Estelle , Venet Fabienne , Cerrato Elisabeth , Meunier Boris , Mouillaux Julie , Lepape Alain , Pachot Alexandre , Rimmelé Thomas , Monneret Guillaume , Textoris Julien
Published: July 2018

Objectives:

Septic shock is the primary cause of death in ICUs. A better comprehension of its pathophysiology, in particular, the immune alteration mechanisms, opened new therapeutic perspectives such as the recombinant interleukin-7. The use of biomarkers could improve the identification of eligible patients for this therapy. The soluble form of the interleukin-7 appears as a promising candidate in this regard since an association between its high plasmatic level and mortality in critically ill patients has been demonstrated. Because there are no data available on the transcriptional regulation of the interleukin-7 receptor in such patients, this study aimed to explore the expression level of different interleukin-7 receptor transcripts after septic shock and evaluate their association with mortality.

Design:

Retrospective discovery cohort (30 patients) and validation cohort (177 patients).

Setting:

Two French ICUs (discovery study) and six French ICUs (validation study).

Patients:

Adult septic shock patients.

Interventions:

None.

Measurements and Main Results:

The quantification of several interleukin-7 receptor transcripts using specific reverse transcription quantitative polymerase chain reaction designs allowed for global evaluation of interleukin-7 receptor gene expression in whole blood. In the discovery cohort, all interleukin-7 receptor transcripts studied were expressed at lower levels in septic shock patients than in healthy volunteers. Interleukin-7 receptor gene expression at day 3 after septic shock diagnosis was associated with day 28 mortality. Patients at a lower risk of death showed higher expression levels. These results were confirmed in the independent validation cohort. Interestingly, using a threshold obtained on the discovery cohort, we observed in the validation cohort a high negative predictive value for day 28 mortality for the transcript encoding the membrane form of interleukin-7 receptor (0.86; 95% CI, 0.79–0.93).

Conclusions:

Interleukin-7 receptor transcripts appear as biomarkers of impaired adaptive immune response in septic shock patients and as a promising tool for patient stratification in clinical trials evaluating immunoadjuvant therapies.
Electronic Charting During Simulation
Authors: Badowski Donna , Horsley Trisha Leann , Rossler Kelly L. , Mariani Bette , Gonzalez Laura
Published: July 2018

Informatics is a core competency for nursing students recognized by several national organizations in healthcare and nursing education. Nurses must be able to use information and technology to communicate and manage knowledge in support of clinical decisions. Many hospitals either limit or deny nursing students’ access to the electronic health record during traditional clinical learning. Simulation-based learning experiences are an alternative to traditional clinical experiences. What remains unclear is how nursing programs are incorporating electronic health record platforms within simulation. This study used a descriptive design to survey nursing programs exploring electronic health record use within simulation-based learning experiences in the classroom, skills laboratory, or simulation laboratory settings. Findings of the survey show that 56.2% of participants used an electronic health record in the classroom, skills laboratory, or simulation laboratory for simulation. Electronic health record use is gaining momentum via simulation-based learning experiences and students are not only documenting but also gathering data and appraising patient data for meaningful use to inform patient care decisions and promote clinical readiness.
Intra-arterial Versus Intravenous Adoptive Cell Therapy in a Mouse Tumor Model
Authors: Visioni Anthony , Kim Minhyung , Wilfong Chandler , Blum Asher , Powers Colin , Fisher Daniel , Gabriel Emmanuel , Skitzki Joseph
Published: July 2018

Adoptive cell transfer therapy for cancer has existed for decades and is experiencing a resurgence in popularity that has been facilitated by improved methods of production, techniques for genetic modification, and host preconditioning. The trafficking of adoptively transferred lymphocytes and infiltration into the tumor microenvironment is sine qua non for successful tumor eradication; however, the paradox of extremely poor trafficking of lymphocytes into the tumor microenvironment raises the issue of how best to deliver these cells to optimize entry into tumor tissue. We examined the route of administration as a potential modifier of both trafficking and antitumor efficacy. Femoral artery cannulation and tail vein injection for the intra-arterial (IA) and IV delivery, respectively, were utilized in the B16-OVA/OT-I mouse model system. Both IV and IA infusions showed decreased tumor growth and prolonged survival. However, although significantly increased T-cell tumor infiltration was observed in IA mice, tumor growth and survival were not improved as compared with IV mice. These studies suggest that IA administration produces increased early lymphocyte trafficking, but a discernable survival benefit was not seen in the murine model examined.
Pathophysiology of Muscle in Pulmonary and Cardiovascular Conditions
Authors: Kasawara Karina Tamy , Castellanos Maria Miñana , Hanada Masatoshi , Reid W Darlene
Published: July 2018

Purpose:

To provide an overview of skeletal muscle pathophysiology in pulmonary and cardiovascular conditions commonly managed by physical therapists.

Summary of Key Points:

This review describes the muscle pathophysiology associated with congestive heart failure, chronic obstructive pulmonary disease, interstitial lung disease, cystic fibrosis, intensive care unit–acquired weakness, immobilization, and aging. Causes of poor muscle performance are multifactorial; disease-specific and generic factors can contribute to the etiology. The time course of deterioration of peripheral and ventilatory muscle may each follow a distinctive course dependent on disease severity, its progression, and other influencing factors. Generic factors that are common in many respiratory and cardiovascular conditions are systemic inflammation and oxidative stress leading to peripheral and ventilatory muscle dysfunction that is accentuated by reduced physical activity. Loss of muscle function associated with aging is also reflected in both peripheral and ventilatory muscles. Evidence of how exercise training can counter the deleterious effects of disease on physical function is outlined.

Statement of Conclusions:

Patients with pulmonary and cardiovascular conditions may experience atrophy and weakness due to macroscopic, cellular, and metabolic alterations. Physical therapy interventions to improve muscle function need to consider the potential reversibility and related time course of the underlying pathophysiology of muscle dysfunction.
0.01% Hypochlorous Acid as an Alternative Skin Antiseptic: An In Vitro Comparison
Authors: Anagnostopoulos Apostolos G. , Rong Andrew , Miller Darlene , Tran Ann Q. , Head Trajen , Lee Michael C. , Lee Wendy W.
Published: July 2018

OBJECTIVE

Compare the in vitro efficacy of hypochlorous acid 0.01% (HA), povidone iodine 5% (PI), chlorhexidine gluconate 4% (CHG), and isopropyl alcohol 70% (IPA) against common skin microorganisms.

MATERIALS AND METHODS

Time-kill studies were conducted against methicillin-susceptible Staphylococcus aureus (MSSA) and Staphylococcus epidermidis (MSSE), methicillin-resistant S. aureus (MRSA) and S. epidermidis (MRSE), Candida albicans, Corynebacterium species (striatum and amycolatum), Propionibacterium acnes, Pseudomonas aeruginosa, Streptococcus pyogenes, Staphylococcus capitis, and Staphylococcus xylosus.

RESULTS

Methicillin-resistant S. aureus: Bactericidal effect was immediate for HA and IPA. For PI and CHG, the effect occurred at 1 and 10 minutes, respectively. Methicillin-resistant S. epidermidis: Hypochlorous acid, IPA, and PI had immediate bactericidal effects, whereas CHG required 1 minute. Methicillin-susceptible Staphylococcus aureus: All agents had bactericidal effects at 1 minute. C. species, S. pyogenes, P. aeruginosa, and P. acnes: All antiseptics demonstrated immediate bactericidal effects. Methicillin-susceptible Staphylococcus epidermidis and S. capitis: Hypochlorous acid and IPA had immediate effect, whereas PI and CHG required 1 minute. C. albicans: Hypochlorous acid, IPA, and PI were immediately bactericidal, whereas CHG required 1 minute. S. xylosus: Hypochlorous acid and CHG were immediately bactericidal, whereas IPA and PI required 1 and 2 minutes, respectively.

CONCLUSION

In vitro studies of HA 0.01% were observed to have equal or more efficacious antiseptic properties compared with IPA, CHG, and PI. Future studies will be needed to investigate its role in periocular use.
Responses to Topical Diphenylcyclopropenone as an Adjunct Treatment for In-Transit Melanoma: A Tertiary Referral Center Experience
Authors: Veverka Kevin K. , Jakub James W. , Baum Christian L.
Published: July 2018

BACKGROUND

In-transit cutaneous metastases occur in 5% to 10% of patients with melanoma. Recently, topical diphenylcyclopropenone (DPCP) has been described as a treatment option.

OBJECTIVE

To evaluate efficacy of DPCP in treatment of in-transit cutaneous melanoma.

METHODS

The authors retrospectively reviewed the records of 13 consecutive patients with in-transit metastases treated with topical DPCP between March 1, 2013, and January 31, 2017. The authors recorded the response of in-transit cutaneous melanoma lesions treated with DPCP measured by clinical examination.

RESULTS

Among the 13 patients, 9 patients completed at least a 1-month course of DPCP treatment. Of these 9 patients, 6 (66.7%) maintained either stable disease or had a partial or complete regression, and 3 (33.3%) had progressive disease. Patients with less burden of disease (e.g., <15 lesions) responded more favorably than those with a greater burden of disease (e.g., >25 lesions or plaques). Both patients who received DPCP alone had progression of their cutaneous lesions. One patient who did not become sensitized to DPCP died within 2 months, and his anergy likely reflecting immense burden of disease.

CONCLUSION

Topical DPCP is a low-cost, patient-applied treatment option for in-transit melanoma, most effective for patients with relatively low tumor burden and localized disease.
Perfluorooctanoate and Perfluorooctanesulfonate plasma concentrations and survival after prostate and bladder cancer in a population-based study
Authors: Roswall Nina , Larsen Signe Benzon , Sørensen Mette , Tjønneland Anne , Raaschou-Nielsen Ole
Published: July 2018

Background:

Perfluorooctanoate (PFOA) and perfluorooctanesulfonate (PFOS) are synthetically produced chemicals, which have been linked to cancer in animal studies, whereas the evidence in humans is merely suggestive. We investigated the association between PFOA and PFOS concentrations in plasma samples and mortality in two survivor cohorts of prostate and bladder cancer patients.

Methods:

We included 688 prostate and 307 bladder cancer cases diagnosed between baseline (1993–97) and July 1, 2006 in the Danish Diet, Cancer and Health cohort. PFOA and PFOS concentrations in plasma samples taken at baseline were measured using high-pressure liquid chromatography. We used Cox proportional hazards models to estimate mortality rate ratios.

Results:

Between diagnosis and February 1, 2016, 356 prostate and 149 bladder cancer cases died. We found no association between PFOA or PFOS concentrations and survival among prostate cancer cases. This was regardless of prognostic factors. For bladder cancer cases, there was an inverse association between PFOA and PFOS and subsequent mortality. Associations were similar for both overall and bladder cancer-specific mortality.

Conclusions:

The results of the present study does not suggest an association between PFOA or PFOS concentrations and survival among prostate cancer patients. In contrast, they may be inversely associated with both overall and bladder cancer–specific mortality in bladder cancer patients. However, this finding requires replication in further studies before firm conclusions can be drawn.
Dofetilide-Associated QT Prolongation: Total Body Weight Versus Adjusted or Ideal Body Weight for Dosing
Authors: Wang Stephen Y. , Welch Terrence D. , Sangha Rajbir S. , Maloney Robert W. , Cui Zhu , Kaplan Aaron V.
Published: July 2018

Dofetilide is an antiarrhythmic drug with dosing based on the Cockcroft–Gault formula using total body weight (TBW). We investigated the impact of calculating dofetilide dose using adjusted body weight (ABW) or ideal body weight (IBW) on subsequent dose reduction or discontinuation. We conducted a retrospective review of 265 patients admitted to an academic medical center for initiation of dofetilide using TBW. Dosing was recalculated using ABW or IBW. Patients who would have received a reduced dose using ABW or IBW (reduced dose group) were compared with patients whose dose would not have changed (same dose group). Manual measurement of QT intervals was performed. We found that Forty-one of 265 patients (15%) would have received a lower initial dose of dofetilide based on ABW. Patients in this reduced dose group had 2.95 times greater odds of drug discontinuations or dose reductions due to QTc prolongation (95% confidence interval, 1.47–5.90; P < 0.01) compared with the same dose group. Seventy-seven of 265 patients (29%) would have received a lower initial dose of dofetilide based on IBW. Patients in this reduced dose group had 1.78 times greater odds of drug discontinuations or dose reductions due to QTc prolongation (95% confidence interval, 0.98–3.21; P = 0.056) compared with the same dose group. These data suggest that caution should be used when dosing dofetilide using TBW, as it may lead to a greater frequency of dose reduction or discontinuation compared with dosing using ABW or IBW.
The Cognitive Impact of Chronic Diseases on Functional Capacity in Community-Dwelling Adults
Authors: KIM JinShil , PARK Eunok , AN Minjeong
Published: July 2018

Background:

People with chronic diseases may experience poor cognitive functioning associated with advanced age, progression of disease, or other comorbid chronic conditions. Empirical evidence of this phenomenon is limited despite the clinical relevance of cognitive decline and associated adverse outcomes such as poor physical functioning.

Purpose:

The purpose of this study was to examine cognitive functioning in the domains of memory, attention, and executive function and its association with functional capacity in a sample of community-dwelling adults with a spectrum of chronic diseases.

Methods:

An exploratory cross-sectional study was conducted in a sample of community-dwelling adults with chronic diseases, including hypertension (58.9%), diabetes mellitus (DM; 20.0%), and dyslipidemia (14.4%). Participants’ mean age was 64.1 ± 11.2 years, and 48.9% were male. Ninety persons completed the face-to-face interviews, which evaluated cognitive functioning in the domains of memory, attention, and executive function using neuropsychological tests and the physical well-being test, which measured functional capacity using the Duke Activity Status Index.

Results:

Compared with those with other chronic diseases, our sample with hypertension and DM had significantly more memory loss and poorer executive function. These significant differences were nullified when adjusting for age, gender, and education. Approximately one third had functional limitations (n = 29, 32.2%), using a cutoff point of 35 or less (Duke Activity Status Index). Memory loss (delayed recall, b = 1.5, p = .016) and poor executive function (Trail Making Test Part A, b = −0.2, p < .001) were predicting factors of functional decline, independent of age, gender, education, and comorbidity.

Conclusions/Implications for Practice:

Cognitive function, particularly memory and executive function, was poorer among chronically ill Korean adults in the community with hypertension or DM than their counterparts. Functional decline was worse in the presence of memory loss and poor executive function. Studies examining the mechanism by which overall functioning is impacted by cognitive decline and its relevance to functional declines in a larger representative sample are warranted.
Psychometric Properties of an Arabic Version of the Patient Satisfaction With Nursing Care Quality Questionnaire
Authors: ALBASHAYREH Alaa , AL-RAWAJFAH Omar M. , AL-AWAISI Huda , KARKADA Suja , AL SABEI Sulaiman D.
Published: July 2018

Background:

Quality measurements are crucial to healthcare quality improvement, and patient satisfaction with nursing care is widely adopted as a key outcome indicator of the overall quality of healthcare. There is a lack of instruments to measure patient satisfaction with nursing care in an Arabic context.

Purpose:

The purpose of this study was to develop and validate an Arabic version of the Patient Satisfaction with Nursing Care Quality Questionnaire and to explore patient satisfaction with nursing care across hospital units.

Methods:

This was a cross-sectional, methodological research study. A forward–backward translation process and face and content validation using a panel of experts and a pilot test were used to produce an Arabic version of the Patient Satisfaction with Nursing Care Quality Questionnaire. A convenience sampling technique was employed to recruit 292 adult patients who were hospitalized for more than 48 hours. Data were collected over the first quarter of 2016 using a secure electronic survey method.

Results:

The item-level content validity index ranged from .83 to 1, and the scale-level content validity index was .94. Evidence of construct validity was obtained. Exploratory factor analysis revealed a two-factor model that explained 69.3% of the total variance. Confirmatory factor analysis showed that the two-factor model fits the observed data. Internal consistency was satisfactory and similar across different hospital units. Cronbach’s alpha estimates for Factors 1 and 2 were .83 and .96, respectively, with an overall Cronbach’s alpha estimate of .96. Level of patient satisfaction with nursing care was quite high (mean = 4.30/5, SD = 0.74).

Conclusions:

This study provides a 17-item, Likert-scaled, self-reporting instrument, which is psychometrically sound for its content, comprehension, readability, and practicality, to measure patient satisfaction with nursing care quality in an Arabic context.
The Effect of Telenursing on Referral Rates of Patients With Head Trauma and Their Family's Satisfaction After Discharge
Authors: Shahrokhi Akram , Azimian Jalil , Amouzegar Atousa , Oveisi Sonia
Published: July 2018

We aimed to assess the effect of telenursing on referral rates of patients with head trauma and their family's satisfaction after discharge. Seventy-two patients with head trauma were randomly allocated to equal intervention and control groups. The caregivers in both groups were provided with 1-hr face-to-face training on patients' home care and educational booklets, 2 days before discharge. The cell phone numbers of the telenurse was given to the caregivers of the intervention group. Then, the patients in the intervention group were followed up every week through phone calls by the telenurse for 12 weeks and the patient status checklists were completed. Caregivers in the intervention group could call the telenurse any time they desired. The health status of the control group was followed once by a phone call after 12 weeks. Data were analyzed using SPSS software, version 19. Ultimately, 33 patients with a mean ± SD age of 31.12 ± 10.83 years were studied in the control group and 35 patients with a mean ± SD age of 34.11 ± 12.34 years were studied in the intervention group (p = .098). The 2 groups differed significantly with respect to referral rates; 39.4% of the participants in the control group referred to physicians whereas only 25.7% of the patients in the intervention group needed to refer to physicians (p = .017). Also, the mean times of referring to a physician differed significantly in both groups. In general, 53.8% of the caregivers were satisfied with the telenursing program. Follow-up programs using telephone calls were effective and would lead to higher caregiver satisfaction.
Change of treatment modalities over the last 10 years in pediatric patients with inflammatory bowel disease in Switzerland
Authors: Guilcher Katharina , Fournier Nicolas , Schoepfer Alain , Schibli Susanne , Spalinger Johannes , Braegger Christian , Nydegger Andreas
Published: July 2018

Background and aim

During the past decade, several new drugs were approved for the treatment of pediatric inflammatory bowel disease (IBD). We aimed to evaluate if and how pharmacologic treatment options for pediatric IBD in Switzerland have changed over time.

Patients and methods

Data from the pediatric Swiss IBD Cohort Study, a national prospective cohort study initiated in 2006, were analyzed. Patients were divided into two groups: patients with IBD diagnosis until 2009 (168 patients) and patients with IBD diagnosis in 2010 and after (210 patients). Both groups were analyzed regarding the past and the current therapies as well as need for surgery.

Results

Overall, 378 pediatric patients with IBD were analyzed, of which 51.9% had Crohn’s disease (CD) and 48.1% had ulcerative colitis/indeterminate colitis. Median age at diagnosis was 12 years. The majority (65.4%) of the patients with ulcerative colitis experienced pancolitis, whereas 45.4% of patients with CD presented with ileocolonic disease at diagnosis. A decreased use of corticosteroids in pediatric patients with CD can be found after 2010 (P=0.041). Use of 5-aminosalicylic acid for patients with CD was dramatically reduced after the year 2010 (33.5 vs. 67.7% after 6 years of disease). A significant shift toward earlier use of biologicals could be shown after 2010 (P<0.001). However, there was no significant decrease of surgery rate after 5 years of disease.

Conclusion

In the past decade, a significant earlier use of anti-tumor necrosis factor-α agents in pediatric patients with IBD was observed with steroid-sparing effect in patients with CD. However, this change was not associated with reduction of surgery.