bluuebunny/crossref_metadata_2025 huggingface dataset:
Operative and Perioperative Durations in O-Arm vs C-Arm Fluoroscopy for Lumbar Instrumentation
Authors: Knafo Steven , Mireau Etienne , Bennis Saad , Baussart Bertrand , Aldea Sorin , Gaillard Stephan
Published: July 2017

BACKGROUND

Intraoperative 3-dimensional fluoroscopy (eg, O-arm) has been shown to improve accuracy of pedicle screw placement over 2-dimensional fluoroscopy (C-arm), but its effect on surgery duration remains unclear.

OBJECTIVE

To compare the durations of operative and perioperative times between O-arm and C-arm procedures for degenerative lumbar disorders.

METHODS

We analyzed 198 patients representing 987 pedicle screws treated in a single center by 4 different surgeons between 2013 and 2015. Accuracy of pedicle screw placement was assessed using the Laine classification on postoperative CT scans. Operative and perioperative durations were prospectively reported on the procedure sheet by anesthesiologists.

RESULTS

As expected, placement of pedicle screws using O-arm navigation was overall more accurate compared to C-arm fluoroscopy (strictly intrapedicular screws: 549/663 = 82.8% vs 239/324 = 73.8%, P = .008). This benefit did not depend on surgeon individual performance (P = .17). Average operative duration per instrumented level was significantly shorter in the O-arm group (57.3 min vs 66.1 min, P = .02) but also depended on the surgeon, indication, and interbody fusion. However, only surgeon individual performance remained significantly associated with surgery duration in multivariate analysis (P < .001). Similarly, the only factor that remained significantly associated with longer perioperative durations in multivariate analysis was the indication of surgery (P < .001).

CONCLUSION

This study shows that O-arm navigation does not independently decrease operative duration, nor increases perioperative time, while improving accuracy of pedicle screw placement.
Cucurbit chlorotic yellows virus: Insights Into Its Natural Host Range, Genetic Variability, and Transmission Parameters
Authors: Orfanidou C. G. , Baltzi A. , Dimou N. A. , Katis N. I. , Maliogka V. I.
Published: July 2017

Cucurbit chlorotic yellows virus (CCYV) (genus Crinivirus, family Closteroviridae) is implicated in cucurbit yellows disease (CYV), causing typical interveinal yellowing symptoms in leaves, and is transmitted by Bemisia tabaci Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1). Due to its recent report in cucurbit crops in Greece, field surveys were conducted during 2011-2016 to determine the presence of the virus in symptomatic cucurbits and alternative hosts among arable weed species. Results indicated the restricted spread of the virus and identified 13 weed species as CCYV hosts for the first time. Sequence analysis of the RNA-dependent RNA polymerase (RNA1) coat and minor coat proteins (RNA2) revealed very low genetic diversity (<0.1%) among the Greek isolates. Transmission experiments were also conducted using B. tabaci MED with retention determined at four days, whereas transmission efficiency was positively correlated with the number of adults used, features linked to the virus semipersistent mode of transmission.
Resistance Genes in Global Crop Breeding Networks
Authors: Garrett K. A. , Andersen K. F. , Asche F. , Bowden R. L. , Forbes G. A. , Kulakow P. A. , Zhou B.
Published: July 2017

Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes.

[Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Fatigue in Residency Education: Understanding the Influence of Work Hours Regulations in Europe
Authors: Taylor Taryn S. , Teunissen Pim W. , Dornan Tim , Lingard Lorelei
Published: July 2017

Purpose

Although one proposed solution to the problem of fatigued medical trainees is the implementation of work hours regulations, concerns about the effectiveness of these regulations are growing. Canada remains one of the few Western jurisdictions without legislated regulation. Recent research suggests that fatigue is a complex social construct, rather than simply a lack of sleep; thus, the authors explored how regulations and fatigue are understood in countries with established work hours frameworks to better inform other jurisdictions looking to address trainee fatigue.

Method

Using constructivist grounded theory methodology, the authors conducted individual, semistructured interviews in 2015–2016 with 13 postgraduate medical trainees from four European countries with established work hours regulations. Data collection and analysis proceeded iteratively, and the authors used a constant comparative approach to analysis.

Results

Trainees reported that they were commonly fatigued and that they violated the work hours restrictions for various reasons, including educational pursuits. Although they understood the regulations were legislated specifically to ensure safe patient care and optimize trainee well-being, they also described implicit meanings (e.g., monitoring for trainee efficiency) and unintended consequences (e.g., losing a sense of vocation).

Conclusions

Work hours regulations carry multiple, conflicting meanings for trainees that are captured by three predominant rhetorics: the rhetoric of patient safety, of well-being, and of efficiency. Tensions within each of those rhetorics reveal that managing fatigue within clinical training environments is complex. These findings suggest that straightforward solutions are unlikely to solve the problem of fatigue, assure patient safety, and improve trainee well-being.
Understanding the Multidimensional Effects of Resident Duty Hours Restrictions: A Thematic Analysis of Published Viewpoints in Surgery
Authors: Devitt Katharine S. , Kim Michael J. , Gotlib Conn Lesley , Wright Frances C. , Moulton Carol-Anne , Keshet Itay , Ahmed Najma
Published: July 2017

Purpose

Individuals representing various surgical disciplines have expressed concerns with the impact of resident duty hours (RDH) restrictions on resident education and patient outcomes. This thematic review of published viewpoints aimed to describe the effects of these restrictions in surgery.

Method

The authors conducted a qualitative systematic review of non-research-based literature published between 2003 and 2015. Articles were included if they focused on the RDH restrictions in surgery and resident wellness, health promotion, resident safety, resident education and/or training, patient safety, medical errors, and/or heterogeneity regarding training or disciplines. A thematic analysis approach guided data extraction. Contextual data were abstracted from the included articles to aid in framing the identified themes.

Results

Of 1,482 identified articles, 214 were included in the review. Most were from authors in the United States (144; 67%) and focused on the 80-hour workweek (164; 77%). The emerging themes were organized into three overarching categories: (1) impact of the RDH restrictions, (2) surgery has its own unique culture, and (3) strategies going forward. Published opinions suggested that RDH restrictions alone are insufficient to achieve the desired outcomes and that careful consideration of the surgical training model is needed to maintain the integrity of educational outcomes.

Conclusions

Opinions from the surgical community highlight the complexity of issues surrounding the RDH restrictions and suggest that recent changes are not achieving all the desired outcomes and have resulted in unintended outcomes. From the perceptions of the various stakeholders in surgical education studied, areas for new policies were identified.
“Anonymous Meltdown”
Authors: Diefenbeck Cynthia A. , Klemm Paula R. , Hayes Evelyn R.
Published: July 2017

By providing care for loved ones in the home, family caregivers save millions of dollars for our overtaxed healthcare system. Support groups can lighten the psychological burden of caregiving. Nonprofessionally facilitated (or peer) online caregiver support groups can help meet a critical need in healthcare as a low-cost resource for caregivers. Online caregiver peer support groups can promote the health and well-being of family caregivers and, by extension, the patients themselves, resulting in cost-savings for society. A better understanding of these types of groups is of critical importance, given the unrelenting pace of demographic shift in the United States. The purpose of this study was to examine content themes emerging from an unstructured, asynchronous online peer support group for family caregivers of people with chronic illness. Qualitative content analysis was used, yielding six themes: “experiencing the emotional toll,” “need for catharsis/venting,” “finding the silver linings,” “seeking specific advice/problem solving,” “realizing home is no longer a haven,” and “adapting to the caregiver role.” The themes reflect what emerged organically in an online support group that was not professionally facilitated or structured in any way. Heterogeneity in the relationship between caregivers and care recipients may negatively affect outcomes and requires further study.
Treatment of Facial Acne Scarring With Fractional Carbon Dioxide Laser in Asians, a Retrospective Analysis of Efficacy and Complications
Authors: Ochi Harumi , Tan Lixian , Tan Wee Ping , Goh Chee Leok
Published: July 2017

BACKGROUND

Fractional carbon dioxide (CO2) laser resurfacing unites the idea of fractional photothermolysis with an ablative 10,600-nm wavelength. This technology permits effective treatment of acne scarring, with shorter recovery and a decreased side effect profile as compared to traditional CO2 laser resurfacing.

OBJECTIVE

The aims of this study were to study the efficacy and safety of fractional CO2 laser for acne scars in Asian patients.

METHODS

This was a retrospective study of all patients treated with the fractional CO2 laser for facial acne scarring between January 2, 2008, and December 31, 2010, at the National Skin Centre, Singapore. Data reviewed included sex, age, and severity of acne, type of scarring, previous treatment history, frequency of treatments, adverse events, and efficacy.

RESULTS

Two hundred and ten fractional CO2 laser treatments for facial acne scars were performed on 107 patients (65 men and 42 women, Fitzpatrick skin Types II to V) during the study period. Sixteen of 107 patients experienced (15.0%) adverse events. The adverse events include hyperpigmentation (6.4%), blistering (4.0%), crusting (2.9%), aggravation of inflammatory acne lesions (1.7%), and scarring (0.6%). There were no reported side effects of hypopigmentation, bacterial or viral infection. Follow-up results after final laser treatment showed that 66.4% of patients reported Grade 1 skin texture improvement, that is, <25% (n = 71); 30.0% had Grade 2 improvement, that is, 25% to 50% improvement (n = 31); 3.7% had Grade 3 improvement, that is, 51% to 75% improvement (n = 4); and 0.9% had Grade 4 improvement, that is, >75% improvement (n = 1).

CONCLUSION

The study demonstrated the efficacy and safety of a fractional CO2 laser in the treatment of acne scars in Asian. Future studies are required to establish optimum treatment parameters and achieve better clinical results.
Reliable and Easy-To-Use Liquid Chromatography–Tandem Mass Spectrometry Method for Simultaneous Analysis of Fluconazole, Isavuconazole, Itraconazole, Hydroxy-Itraconazole, Posaconazole, and Voriconazole in Human Plasma and Serum
Authors: Müller Carsten , Gehlen David , Blaich Cornelia , Prozeller Domenik , Liss Blasius , Streichert Thomas , Wiesen Martin H. J.
Published: July 2017

Background:

A fast and easy-to-use liquid chromatography-tandem mass spectrometry method for the determination and quantification of 6 triazoles [fluconazole (FLZ), isavuconazole (ISZ), itraconazole (ITZ), hydroxy-itraconazole (OH-ITZ), posaconazole (PSZ), and voriconazole (VRZ)] in human plasma and serum was developed and validated for therapeutic drug monitoring.

Methods:

Sample preparation was based on protein precipitation with acetonitrile and subsequent centrifugation. Isotope-labeled analogues for each analyte were used as internal standards. Chromatographic separation was achieved using a 50 × 2.1 mm, 1.9 μm polar Hypersil Gold C18 column and mobile phase consisting of 0.1% formic acid/acetonitrile (45%/55%, vol/vol) at a flow rate of 340 μL/min. The triazoles were simultaneously detected using a triple-stage quadrupole mass spectrometer operated in selected reaction monitoring mode with positive heated electrospray ionization within a single runtime of t = 3.00 minutes.

Results:

Linearity of all azole concentration ranges was verified by the Mandel test and demonstrated for all azoles. All calibration curves were linear and fitted using least squares regression with a weighting factor of the reciprocal concentration. Limits of detection (μg/L/L) were FLZ, 9.3; ISZ, 0.3; ITZ, 0.6; OH-ITZ, 8.6; PSZ, 3.4; and VRZ, 2.1. The lower limits of quantitation (μg/L/liter) were FLZ, 28.3; ISZ, 1.0; ITZ, 1.7; OH-ITZ, 26.2; PSZ, 10.3; and VRZ, 6.3. Intraday and interday precisions ranged from 0.6% to 6.6% for all azoles. Intraday and interday accuracies (%bias) of all analytes were within 10.5%. In addition, we report on a 29-year-old white woman (94 kg body weight) with a history of acute myeloid leukemia who underwent stem cell transplantation. Because of diagnosis of aspergillus pneumonia, antifungal pharmacotherapy was initiated with different application modes and dosages of ISZ, and plasma concentrations were monitored over a time period of 6 months.

Conclusions:

A precise and highly sensitive liquid chromatography-tandem mass spectrometry method was developed that enables quantification of triazoles in plasma and serum matrix across therapeutically relevant concentration ranges. It was successfully implemented in our therapeutic drug monitoring routine service and is suitable for routine monitoring of antifungal therapy and in severely ill patients.
A Retrospective Look at Integrating a Novel Regenerative Medicine Approach in Plastic Limb Reconstruction
Authors: Rodriguez Collazo Edgardo R. , Rathbone Christopher R. , Barnes Brian R.
Published: July 2017

Full-thickness wounds that have rendered patients candidates for amputation may require techniques that may include a combinatorial approach above traditional standard of care. The purpose of this retrospective study was to evaluate the effectiveness of an innovative approach whereby several therapies were combined to avoid amputation. Patients with full-thickness wounds who were previously recommended for amputation and were treated with the combinatorial approach of muscle flap reconstruction and concentrated bone marrow aspirate, platelet-rich plasma, INTEGRA Wound matrix, vacuum-assisted closure, and split-thickness skin grafts were assessed retrospectively. The mean age of the patients identified was 48 years (range, 34–66 years). The average size of the defects was 19.6 cm2. All defects were successfully covered with medial hemisoleus, lateral hemisoleus, or peroneus brevis muscle flaps combined with split-thickness skin grafts, concentrated bone marrow aspirate, and platelet-rich plasma. All flaps healed with an average time to fixator removal of 8.3 weeks; there was 1 above-knee amputation that occurred approximately after successful wound closing and fixator removal. The combinatorial approach described here including several regenerative medicine tools is an effective means of lower limb reconstruction to avoid amputation.
Intimal Surface Suture Line (End-Product) Assessment of End-to-Side Microvascular Anastomosis
Authors: Pafitanis Georgios , Veljanoski Damjan , Ghanem Ali M. , Myers Simon
Published: July 2017

Microsurgery simulation courses increasingly use assessment methodologies to evaluate the quality of microvascular anastomosis and to provide constructive feedback in competency-based training. Assessment tools evaluating the “journey” of skill acquisition in anastomosis have evolved, including global rating scores, hand motion analysis, and evaluation of the final outcome, that is, “end-product” assessment. Anastomotic patency is the gold standard end-product in clinical microvascular surgery, and in vivo end-to-side anastomosis, which can be confirmed using the Acland-test. Microsurgery simulation training is moving to include nonliving models, where possible, according to the principles of the replacement, reduction, and refinement of the use of animals in research. While a standardized end-product assessment tool for nonliving end-to-end anastomosis exists, there is no similar tool for end-to-side anastomosis. Intimal surface suture line assessment is an error list-based tool, which involves exposing the intimal surface of a vessel and analysis of the quality of suture placement. Errors in end-to side anastomosis were classified according to the potential clinical significance (high, medium, or low) perceived by the senior authors. Intimal surface suture line assessment provides constructive feedback during microsurgery training, helping to minimize technical errors, which are likely to impact on the final outcome in a clinical environment. Intimal surface suture line assessment lends itself to nonliving simulation training courses as an end-product self-assessment tool, especially during the early learning curve, to demonstrate progression. It has intraoperative relevance by assessment of the intimal surface suture line as the final sutures are placed in an end-to-side anastomosis to provide objective feedback to trainees in relation to likely physiological anastomotic outcome.
Vitamin D Deficiency, Supplementation, and Cardiovascular Health
Authors: Trehan Naveen , Afonso Luis , Levine Diane L. , Levy Phillip D.
Published: July 2017

Vitamin D has been traditionally recognized as a vitamin quintessential for bone–mineral health. In the past 2 decades, numerous experimental and observational studies have highlighted the role of vitamin D in immunity, metabolic syndrome (obesity and diabetes), cancers, renal disease, memory, and neurological dysfunction. In this article, we review important studies that focused on the impact of vitamin D on blood pressure, myocardial infarction, peripheral arterial disease, heart failure, and statin intolerance. Amidst the current pool of ambiguous evidence, we intend to discuss the role of vitamin D in “high-value cardiovascular health care”.
Trunk Side Strain Has a High Incidence in First-Class Cricket Fast Bowlers in Australia and England
Authors: Nealon Andrew R. , Cook Jill L.
Published: July 2017

Objective:

To investigate the past incidence of side strain injury and its associated factors in first-class cricket fast bowlers in Australia and England.

Design:

Retrospective case series.

Setting:

Professional cricket.

Participants:

Cricket fast bowlers who were professionally contracted full time at first-class level in Australia and England in 2011. All bowlers were male and aged 18 or older. A bowler was defined as a fast bowler if the wicketkeeper would take their stance back from the stumps. There were 207 participants.

Interventions:

Not applicable.

Main Outcome Measures:

The association between bowling arm, player height, active trunk lateral flexion range of motion, side bridge endurance, volume of first-class cricket played, and the history of injury was determined.

Results:

Over half of the bowlers had sustained at least 1 side strain in their career. Seventy-seven percent of primary injuries occurred in bowlers aged 24 or under. A higher proportion of injured bowlers had reached first-class volume in their career. Recurrence occurred in 30% of bowlers, with over 30% of these bowlers sustaining at least 1 further recurrence. Nearly half of all recurrences occurred within 2 years with a further quarter in the next year. The injury was not associated with any measured factors.

Conclusions:

Side strain is a common injury among first-class cricket fast bowlers, especially at younger ages. It was associated with the volume of first-class cricket played. Recurrence was common and occurred most frequently in the first 2 years after primary injury.
Strengths, Limitations, and Geographical Discrepancies in the Eligibility Criteria for Sport Participation in Young Patients With Congenital Heart Disease
Authors: Cantinotti Massimiliano , Giordano Raffaele , Assanta Nadia , Murzi Bruno , Melo Manuel , Franchi Eliana , Crocetti Maura , Iervasi Giorgio , Kutty Shelby
Published: July 2017

Objective:

Benefits of physical activity has been shown in children with congenital heart disease (CHD). In several forms of CHD, the risk of sudden death remains a major concern both for parents and clinicians, who in turn will have to consider the risk–benefit ratio of sport participation versus restriction.

Data source:

A literature search was performed within the National Library of Medicine using the keywords: Sport, CHD, and Eligibility. The search was further refined by adding the keywords: Children, Adult, and Criteria.

Main Results:

Fifteen published studies evaluating sport eligibility criteria in CHD were included. Seven documents from various scientific societies have been published in the past decade but which of them should be adopted remains unclear. Our research highlighted accuracy and consistency of the latest documents; however, differences have emerged between the US and European recommendations. Eligibility criteria were consistent between countries for simple congenital heart defects, whereas there are discrepancies for borderline conditions including moderate valvular lesions and mild or moderate residual defects after CHD repair. Furthermore, some of the more severe defects were not evaluated. Multiple recommendations have been made for the same CHD, and cut-off values used to define disease severity have varied. Published eligibility criteria have mainly focused on competitive sports. Little attention was paid to recreational activities, and the psychosocial consequences of activity restriction were seldom evaluated.

Conclusions:

Comprehensive consensus recommendations for sport eligibility evaluating all CHD types and stages of repair are needed. These should include competitive and recreational activities, use standardized classifications to grade disease severity, and address the consequences of restriction.
Variable-Volume Kinetic Model to Estimate Absolute Blood Volume in Patients on Dialysis Using Dialysate Dilution
Authors: Samandari Hamed , Schneditz Daniel , Germain Michael J. , Horowitz Joseph , Hollot Christopher V. , Chait Yossi
Published: July 2017

Long- and short-term adverse outcomes in hemodialysis (HD) have been associated with intradialytic hypotension, a common HD complication and significant cause of morbidity. It has been suggested that knowledge of absolute blood volume (ABV) could be used to significantly improve treatment outcomes. Different dilution-based protocols have been proposed for estimating ABV, all relying on the classic mono-exponential back-extrapolation algorithm (BEXP). In this paper, we introduce a dialysate dilution protocol and an estimation algorithm based on a variable-volume, two-compartment, intravascular blood water content kinetic model (VVKM). We compare ABV estimates derived using the two algorithms in a dialysate dilution study including three arterio-venous (AV) and three central-venous (CV) access patients, and multiple bolus injection tests (3–5) within each of several (2–6) HD treatments. The distribution of differences between ABV estimated from the two methods showed negligible systematic difference between the mean values of ABVs estimated from the BEXP and VVKM algorithms, however, the VVKM estimates were 53% and 42% more precise for the CV and AV patients, respectively. Good agreement was observed between measured and VVKM-estimated blood water concentration with the root-mean-square error (RMSE) less than 0.02 kg/kg (2%) and 0.03 kg/kg (3%) for AV and CV patients, respectively. The dilution protocol and the new VVKM-based estimation algorithm offer a noninvasive, inexpensive, safe, and practical approach for ABV estimation in routine HD settings.
Reductions in Readmission Rates Are Associated With Modest Improvements in Patient-reported Health Gains Following Hip and Knee Replacement in England
Authors: Friebel Rocco , Dharmarajan Kumar , Krumholz Harlan M. , Steventon Adam
Published: July 2017

Background:

Although many hospital readmission reduction initiatives have been introduced globally, health care systems ultimately aim to improve patients’ health and well-being. We examined whether the hospitals that report greater success in reducing readmissions also see greater improvements in patient-reported outcomes.

Research Design:

We examined hospital groups (Trusts) that provided hip replacement or knee replacement surgery in England between April 2010 and February 2013. For each Trust, we calculated risk-adjusted 30-day readmission rates from administrative datasets. We also obtained changes in patient-reported health between presurgical assessment and 6-month follow-up, using general health EuroQuol five dimensions questionaire (EQ-5D) and EuroQuol visual analogue scales (EQ-VAS) and procedure-specific (Oxford Hip and Knee Scores) measures. Panel models were used to assess whether changes over time in risk-adjusted readmission rates were associated with changes over time in risk-adjusted health gains.

Results:

Each percentage point reduction in the risk-adjusted readmission rate for hip replacement was associated with an additional health gain of 0.004 for EQ-5D [95% confidence interval (CI), 0.002–0.006], 0.39 for EQ-VAS (95% CI, 0.26–0.52), and 0.32 for Oxford Hip Score (95% CI, 0.15–0.27). Corresponding figures for knee replacement were 0.003 for EQ-5D (95% CI, 0.001–0.004), 0.21 for EQ-VAS (95% CI, 0.12–0.30), and 0.14 in the Oxford Knee Score (95% CI, 0.09–0.20).

Conclusions:

Reductions in readmission rates were associated with modest improvements in patients’ sense of their health and well-being at the hospital group level. In particular, fears that efforts to reduce readmission rates have had unintended consequences for patients appear to be unfounded.
Postoperative Delirium as a Target for Surgical Quality Improvement
Authors: Berian Julia R. , Zhou Lynn , Russell Marcia M. , Hornor Melissa A. , Cohen Mark E. , Finlayson Emily , Ko Clifford Y. , Rosenthal Ronnie A. , Robinson Thomas N.
Published: July 2017

Objective:

To explore hospital-level variation in postoperative delirium using a multi-institutional data source.

Background:

Postoperative delirium is closely related to serious morbidity, disability, and death in older adults. Yet, surgeons and hospitals rarely measure delirium rates, which limits quality improvement efforts.

Methods:

The American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) Geriatric Surgery Pilot (2014 to 2015) collects geriatric-specific variables, including postoperative delirium using a standardized definition. Hierarchical logistic regression models, adjusted for case mix [Current Procedural Terminology (CPT) code] and patient risk factors, yielded risk-adjusted and smoothed odds ratios (ORs) for hospital performance. Model performance was assessed with Hosmer-Lemeshow (HL) statistic and c-statistics, and compared across surgical specialties.

Results:

Twenty thousand two hundred twelve older adults (≥65 years) underwent inpatient operations at 30 hospitals. Postoperative delirium occurred in 2427 patients (12.0%) with variation across specialties, from 4.7% in gynecology to 13.7% in cardiothoracic surgery. Hierarchical modeling with 20 risk factors (HL = 9.423, P = 0.31; c-statistic 0.86) identified 13 hospitals as statistical outliers (5 good, 8 poor performers). Per hospital, the median risk-adjusted delirium rate was 10.4% (range 3.2% to 27.5%). Operation-specific risk and preoperative cognitive impairment (OR 2.9, 95% confidence interval 2.5–3.5) were the strongest predictors. The model performed well across surgical specialties (orthopedic, general surgery, and vascular surgery).

Conclusion:

Rates of postoperative delirium varied 8.5-fold across hospitals, and can feasibly be measured in surgical quality datasets. The model performed well with 10 to 12 variables and demonstrated applicability across surgical specialties. Such efforts are critical to better tailor quality improvement to older surgical patients.
Organ Preservation in cT2N0 Rectal Cancer After Neoadjuvant Chemoradiation Therapy
Authors: Habr-Gama Angelita , São Julião Guilherme Pagin , Vailati Bruna Borba , Sabbaga Jorge , Aguilar Patricia Bailão , Fernandez Laura Melina , Araújo Sergio Eduardo Alonso , Perez Rodrigo Oliva
Published: July 2017

Objective:

To demonstrate the difference in organ-preservation rates and avoidance of definitive surgery among cT2N0 rectal cancer patients undergoing 2 different chemoradiation (CRT) regimens.

Background:

Patients with cT2N0 rectal cancer are more likely to develop complete response to neoadjuvant CRT. Organ preservation has been considered an alternative treatment strategy for selected patients. Radiation dose-escalation and consolidation chemotherapy have been associated with increased rates of response and may improve chances of organ preservation among these patients.

Methods:

Patients with distal and nonmetastatic cT2N0 rectal cancer managed by neoadjuvant CRT were retrospectively reviewed. Patients undergoing standard CRT (50.4 Gy and 2 cycles of 5-FU-based chemotherapy) were compared with those undergoing extended CRT (54 Gy and 6 cycles of 5-FU-based chemotherapy). Patients were assessed for tumor response at 8 to 10 weeks. Patients with complete clinical response (cCR) underwent organ-preservation strategy (“Watch and Wait”). Patients were referred to salvage surgery in the event of local recurrence during follow-up.

Results:

Thirty-five patients underwent standard and 46 patients extended CRT. Patients undergoing extended CRT were more likely to undergo organ preservation and avoid definitive surgical resection at 5years (67% vs 30%; P = 0.001). After development of a cCR, surgery-free survival is similar between extended and standard CRT groups at 5 years (78% vs 56%; P = 0.12).

Conclusions:

Dose-escalation and consolidation chemotherapy leads to increased long-term organ-preservation rates among cT2N0 rectal cancer. After achievement of a cCR, the risk for local recurrence and need for salvage surgery is similar, irrespective of the CRT regimen.
On the hydrogen activation by frustrated Lewis pairs in the solid state: benchmark studies and theoretical insights
Authors: Liu Lei , Brandenburg Jan Gerit , Grimme Stefan
Published: July 2017

Recently, the concept of small molecule activation by frustrated Lewis pairs (FLPs) has been expanded to the solid state showing a variety of interesting reactivities. Therefore, there is a need to establish a computational protocol to investigate such systems theoretically. In the present study, we selected several FLPs and applied multiple levels of theory, ranging from a semi-empirical tight-binding Hamiltonian to dispersion corrected hybrid density functionals. Their performance is benchmarked for the computation of crystal geometries, thermostatistical contributions, and reaction energies. We show that the computationally efficient HF-3c method gives accurate crystal structures and is numerically stable and sufficiently fast for routine applications. This method also gives reliable values for the thermostatistical contributions to Gibbs free energies. The meta-generalized gradient approximated TPSS-D3 evaluated in a projector augmented plane wave basis set is able to produce sufficiently accurate reaction electronic energies. The established protocol is intended to support experimental studies and to predict new reactions in the emerging field of solid-state FLPs.

This article is part of the themed issue ‘Frustrated Lewis pair chemistry’.
Design and reactions of a carbon Lewis base/boron Lewis acid frustrated Lewis pair
Authors: Möricke Jennifer , Wibbeling Birgit , Daniliuc Constantin G. , Kehr Gerald , Erker Gerhard
Published: July 2017

The conjugated dienamine
4
selectively adds Piers' borane [HB(C
6
F
5
)
2
] to give the enamine/borane system
5
, which features a boratirane structure by internal enamine carbon Lewis base to boron Lewis acid interaction. Compound
5
behaves as a C/B frustrated Lewis pair and undergoes typical addition reactions to benzaldehyde, several nitriles and to sulfur dioxide.

This article is part of the themed issue ‘Frustrated Lewis pair chemistry’.
Correcting for batch effects in case-control microbiome studies
Authors: Gibbons Sean M. , Duvallet Claire , Alm Eric J.
Published: July 2017

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses.

Author Summary

Batch effects are obstacles to comparing results across studies. Traditional meta-analysis techniques for combining p-values from independent studies, like Fisher’s method, are effective but statistically conservative. If batch-effects can be corrected, then statistical tests can be performed on data pooled across studies, increasing sensitivity to detect differences between treatment groups. Here, we show how a simple, model-free approach corrects for batch effects in case-control microbiome datasets.
Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd
Authors: Tamura Takeyuki
Published: July 2017

Constraint-based metabolic flux analysis of knockout strategies is an efficient method to simulate the production of useful metabolites in microbes. Owing to the recent development of technologies for artificial DNA synthesis, it may become important in the near future to mathematically design minimum metabolic networks to simulate metabolite production. Accordingly, we have developed a computational method where parsimonious metabolic flux distribution is computed for designated constraints on growth and production rates which are represented by grids. When the growth rate of this obtained parsimonious metabolic network is maximized, higher production rates compared to those noted using existing methods are observed for many target metabolites. The set of reactions used in this parsimonious flux distribution consists of reactions included in the original genome scale model iAF1260. The computational experiments show that the grid size affects the obtained production rates. Under the conditions that the growth rate is maximized and the minimum cases of flux variability analysis are considered, the developed method produced more than 90% of metabolites, while the existing methods produced less than 50%. Mathematical explanations using examples are provided to demonstrate potential reasons for the ability of the proposed algorithm to identify design strategies that the existing methods could not identify. The source code is freely available, and is implemented in MATLAB and COBRA toolbox.

Author summary

Metabolic networks represent the relationships between biochemical reactions and compounds in living cells. By computationally modifying a given metabolic network of microbes, we can simulate the effect of knockouts and estimate the production of valuable metabolites. A common mathematical model of metabolic networks is the constraint-based flux model. In constraint-based flux balance analysis, a pseudo-steady state is assumed to predict the metabolic profile where the sum of all incoming fluxes is equal to the sum of all outgoing fluxes for each internal metabolite. Based on these constraints, the biomass objective function, written as a linear combination of fluxes, is maximized. In this study, we developed an efficient method for computing the design of minimum metabolic networks by using constraint-based flux balance analysis to simulate the production of useful metabolites.
Parasite mediated competition facilitates invasion
Authors: Yitbarek Senay , Perfecto Ivette , Vandermeer John H.
Published: July 2017

Parasites play an important role in invasion success with important consequences for biodiversity and community structure. While much research has focused on direct effects of parasites on biological invasions, parasites can also indirectly influence interactions within the invaded community across trophic levels. For instance, parasites can mediate competitive interactions between native and exotic species through trait-mediated indirect effects. We consider the interactions between the parasitoid fly Pseudacteon sp. (Diptera: Phoridae), and its native host ant Linipethema iniquum, and the exotic ant Wasmannia auropunctata in the introduced range of Puerto Rico. We examined the effects of phorid flies on the competitive outcome between the arboreal ants W. auropunctata and native ant L. iniquum. Furthermore, we investigate the searching efficiency of phorid flies in detecting L. iniquum nests. To study the indirect effects on ant competition, we monitored ant recruitment to baits over a 60-min time interval in the presence and absence of phorid fly parasitoids. We then performed field experiments and measured phorid arrival time to arboreal nests of L. iniquum located in both a) W. auropunctata patches and in b) isolated patches dominated by L. iniquum nests. We found that the presence of phorid fly significantly reduced recruitment of L. iniquum workers to baits through induced behavioral changes thereby increasing the ability of W. auropunctata to acquire resources. In addition, we found that phorid arrival time in isolated patches of L. iniquum patches was faster as compared to L. iniquum nests located within W. auropunctata patches. Our results show that phorid fly parasitoids indirectly may influence competitive interactions by attacking the host-ant L. iniquum and consequently providing an advantage to local spread of W. auropuntata populations in Puerto Rico. However, the spatial dynamics of arboreal ants shows that L. iniquum seeks protection from phorid fly parasotoids by moving their nests to W. auropunctata dominated patches.
Estimating Muricid abundances from trapping methods used in Mediterranean Tyrian Purple industry
Authors: Coston-Guarini J , Guarini JM , Boehm Frederike Ricarda , Kerkhove Thomas R. H. , Rivera Frances Camille , Erzini Karim , Charles François , Deprez Tim , Chauvaud Laurent
Published: July 2017

A new statistical method based on a stochastic dynamic model is proposed to assess population abundances of murcid species at scales relevant to both Ancient and Modern artisanal, coastal fisheries. Motivated by the long-term goal of reconstructing the dynamics of exploited murex populations during Antiquity, the objective was to quantify the population density of the banded-dye murex,Hexaplex trunculus(Linnaeus, 1758) from successive captures with baited traps, using a method similar to the technique employed in the Mediterranean purple dye industry. A stochastic model simulating cumulative captures while taking into account high variability was developed and calibrated with data acquired during a field experiment conducted on Crete Island, near Heraklion. Sampling devices were deployed in two shallow water habitats. The traps’ catchability and the Effective Area of Attraction were estimated using the individual speed and behavioural response toward the bait observed during independent laboratory experiments. The average density ofH. trunculuswas estimated at 2.2 ± 1.4 SE individuals per square meter, with no significant differences between seagrass and rocky habitats, respectively. The clearing time (the time to catch all individuals within reach of the trap) of the successive experiments was 84 ± 6 SE hours, on average. This means that clearingca. 0.4 ha of subtidal area would be necessary to produceca. 1.0 g of pure dye pigment. While the method is discussed here with respect to a particular historical context, it is generalizable to making population abundance estimates for other species such as whelks, in modern fisheries.
Best Practice Data Life Cycle Approaches for the Life Sciences
Authors: Griffin Philippa C. , Khadake Jyoti , LeMay Kate S. , Lewis Suzanna E. , Orchard Sandra , Pask Andrew , Pope Bernard , Roessner Ute , Russell Keith , Seemann Torsten , Treloar Andrew , Tyagi Sonika , Christiansen Jeffrey H. , Dayalan Saravanan , Gladman Simon , Hangartner Sandra B. , Hayden Helen L. , Ho William W. H. , Keeble-Gagnère Gabriel , Korhonen Pasi K. , Neish Peter , Prestes Priscilla R. , Richardson Mark F. , Watson-Haigh Nathan S. , Wyres Kelly L. , Young Neil D. , Schneider Maria Victoria
Published: July 2017

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain.

Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
Bayesian inference of transcriptional branching identifies regulators of early germ cell development in humans
Authors: Penfold Christopher A. , Sybirna Anastasiya , Reid John , Venzor Aracely Castillo , Drousioti Elena , Huang Yun , Grant Murray , Wernisch Lorenz , Ghahramani Zoubin , Surani M. Azim
Published: July 2017

During embryonic development, cells undertake a series of fate decisions to form a complete organism comprised of various cell types, epitomising a branching process. A striking example of branching occurs in humans around the time of implantation, when primordial germ cells (PGCs), precursors of sperm and eggs, and somatic lineages are specified. Due to inaccessibility of human embryos at this stage of development, understanding the mechanisms of PGC specification remains difficult. The integrative modelling of single cell transcriptomics data from embryos and appropriatein vitromodels should prove to be a useful resource for investigating this system, provided that the cells can be suitably ordered over a developmental axis. Unfortunately, most methods for inferring cell ordering were not designed with structured (time series) data in mind. Although some probabilistic approaches address these limitations by incorporating prior information about the developmental stage (capture time) of the cell, they do not allow the ordering of cells over processes with more than one terminal cell fate. To investigate the mechanisms of PGC specification, we develop a probabilistic pseudotime approach, branch-recombinant Gaussian process latent variable models (B-RGPLVMs), that use an explicit model of transcriptional branching in individual marker genes, allowing the ordering of cells over developmental trajectories with arbitrary numbers of branches. We use first demonstrate the advantage of our approach over existing pseudotime algorithms and subsequently use it to investigate early human development, as primordial germ cells (PGCs) and somatic cells diverge. We identify known master regulators of human PGCs, and predict roles for a variety of signalling pathways, transcription factors, and epigenetic modifiers. By concentrating on the earliest branched signalling events, we identified an antagonistic role for FGF receptor (FGFR) signalling pathway in the acquisition of competence for human PGC fate, and identify putative roles for PRC1 and PRC2 in PGC specification. We experimentally validate our predictions using pharmacological blocking of FGFR or its downstream effectors (MEK, PI3K and JAK), and demonstrate enhanced competency for PGC fatein vitro, whilst small molecule inhibition of the enzymatic component of PRC1/PRC2 reveals reduced capacity of cells to form PGCsin vitro. Thus, B-RGPLVMs represent a powerful and flexible data-driven approach for dissecting the temporal dynamics of cell fate decisions, providing unique insights into the mechanisms of early embryogenesis. Scripts relating to this analysis are available from:https://github.com/cap76/PGCPseudotime