bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Experience in a Spanish Pediatric Emergency Department
Authors: Parra Cristina , Carreras Nuria , Vergés Alba , Trenchs Victoria , Luaces Carles
Published: February 2019

Objectives

To study the experience reported by pediatric patients when visiting a pediatric emergency department (PED).

Methods

This was a prospective descriptive study, carried out in November 2014. A 12-question survey was developed, based on the Picker Patient Experience Questionnaire. The aim was to assess patient experience of children between 8 and 18 years old, attended in the PED of a high-complexity pediatric hospital. Questions were about the waiting time and setting, medical staff explanations and actions, treatment, and discharge. The questionnaires were administered and filled in by the children themselves at discharge.

Results

One-hundred seventy questionnaires were completed; 17.1% of respondents had to wait longer than expected, and 44.7% said that there was not enough to do when waiting to be seen. Pain was not correctly treated (3%), there was a lack of privacy (14.7%), and the information provided to the patients during the visit was wanting (10%). However, 80% said that they had been well treated.

Conclusions

The patient experience of children in our PED was positive, although some aspects should be improved such as offering entertainment in the waiting area, increasing privacy during the medical visit, and giving better explanations to the children.
Management of a Pediatric Type 3C Open Femoral Fracture Following a High-Velocity Gunshot Wound at an Adult Level II Trauma Center
Authors: Grisoli Anne , Dynako Joseph , Zimmer David , Zackariya Nuha , Shariff Faadil , Walsh Mark , Mamczak Christiaan N. , Peterson Charles , Boyer Bryan , Hurwich Maurice , Duprat Gerard
Published: February 2019

We present a case of a 10-year-old girl shot in the thigh by a stray bullet who had a favorable outcome when treated with a multidisciplinary approach at the nearest nonpediatric level II trauma center. Point-of-care thromboelastography facilitated effective resuscitation based on her coagulation profile, minimized blood product use, and allowed for damage-control surgery to stabilize and revascularize her complex femur fracture.
Two-Thumb Encircling Technique With a Novel Compression Assist Device Provides Safe and Effective Chest Compressions in Infants
Authors: Lee Se Uk , Kim Do Kyun , Chang Ikwan , Jung Jae Yun , Paek So Hyun , Park Joong Wan , Lee Jin Hee , Kwak Young Ho
Published: February 2019

Objective

Currently, 2-thumb encircling technique is recommended in 2-rescuer infant cardiopulmonary resuscitation (CPR). However, many complications can occur during CPR. Therefore, we developed a novel compression assist device (Reheart) that can reduce chest compression area and determined whether using our device provides better compression quality.

Methods

A novel compression assist device consists of 2 parts. The upper part was designed to put 2 thumbs together in the thumb sleeves, and the lower part was designed based on a circular rubber plate with a 2.0-cm diameter to confine compression area. Infant manikin CPR simulations using the 2-thumb encircling technique with Reheart and without Reheart were sequentially performed by participants in randomized crossover fashion.

Results

A total of 32 health care providers were included. The average age of the participants was 30.2 ± 3.5 years, and 21 participants (65.6%) were male. The accuracy in the Reheart group was better than that in the conventional group (proportion of compression on target area, 52.5% ± 13.2% vs 35.4% ± 17.6%; P < 0.001). The difference in the rates of chest compressions between the 2 groups was not significant (119.6 ± 14.4 vs 120.7 ± 14.0 compressions/min, P = 0.59). The depth of chest compressions was also not significantly different between the 2 groups (34.5 mm [33.6–34.9 mm] vs 34.2 mm [33.0–34.9 mm], P = 0.32).

Conclusions

Our new compression assist device can help provide safe and effective chest compressions during 2-rescuer infant CPR.
Accuracy of Parental-Reported Tetanus Vaccination Status for Children With Lacerations
Authors: Drapkin Zachary , Madsen Troy E. , Weaver Nicholas , Soprano Joyce V.
Published: February 2019

Objectives

The aim of this study was to determine whether emergency department (ED) providers are able to accurately assess whether a child with a laceration needs tetanus prophylaxis.

Methods

We conducted an 8-month prospective cross-sectional study of children presenting with a laceration to a pediatric ED. We asked ED providers whether tetanus prophylaxis was necessary. An ED pharmacist accessed the Utah Statewide Immunization Information System (USIIS), and we assessed the accuracy of the ED provider's determination of necessary tetanus prophylaxis compared with USIIS records.

Results

Among 375 patients aged 5 months to 17 years, ED providers made an inaccurate assessment of necessary tetanus prophylaxis in 33 cases (8.8%; 95% confidence interval [CI], 6.3%–12.1%). Emergency department providers would have inappropriately administered tetanus prophylaxis in 5 cases (1.3%; 95% CI, 0.5%–3.2%) and would have missed the need for tetanus prophylaxis in 28 cases (7.5%; 95% CI, 5.2%–10.6%). Emergency department providers were more likely to provide an inaccurate recommendation in older children (8.3 vs 4.8 years; P < 0.001), in patients with a dirty wound (45.5% vs 11.7%; P < 0.001), and in children who had fewer than 3 vaccines recorded in the USIIS (54.5% vs 1.2%; P < 0.001).

Conclusions

Emergency department providers may inaccurately assess the need for tetanus prophylaxis in children. Special attention should be paid to cases of dirty wounds and cases in which fewer than 3 tetanus-containing vaccines have been given.
The Administration of Postintubation Sedation in the Pediatric Emergency Department
Authors: Berg Kathleen , Gregg Victoria , Cosgrove Peter , Wilkinson Matthew
Published: February 2019

Background

The administration of postintubation sedation (PIS) is an essential component of postintubation care. Recent studies in the adult emergency medicine literature have highlighted both delays in time to administration of PIS and subtherapeutic dosing of sedative agents in the emergency department. We aimed to investigate the administration of PIS in the pediatric population as this has not been adequately reviewed to date.

Objectives

The aim of this study was to determine the percentage of pediatric emergency department patients who received PIS within an adequate time frame. We also investigated the relationship between this primary outcome and the rapid sequence intubation (RSI) agents used, the reason for intubation, and individual patient characteristics.

Methods

This was a retrospective cohort analysis of all pediatric patients who underwent RSI at a tertiary care pediatric emergency department from July 2007 to January 2016. The primary outcome of “sedation in an adequate time frame” was defined as a time to post-RSI sedative administration that was shorter than the duration of action of the RSI sedative agent used. Logistic regression was performed to identify predictors of adequate sedation.

Results

A total of 240 patients were included in the analysis. Of these, 28% (95% confidence interval, 22.7%–34.1%) met the primary outcome of sedation within an adequate time frame; 72.8% (95% confidence interval, 66.8%–78.1%) of patients received some form of PIS during their emergency department stay. Patients receiving long-acting paralytic agents were much less likely to receive PIS with an odds ratio (OR) of 0.16 for meeting the primary outcome (P < 0.001, adjusted OR [AOR] = 0.13, P < 0.001). Children with higher systolic blood pressure were more likely to receive appropriate PIS with an OR of 1.02 for every mm Hg increase in systolic blood pressure (P = 0.006, AOR = 1.02, P = 0.021). Finally, patients who were ultimately admitted to the pediatric intensive care unit (vs the operating room, transfer, or neonatal intensive care unit) were less likely to receive PIS as evidenced by an OR of 0.37 (P = 0.009, AOR = 0.27, P = 0.004).

Conclusions

Most pediatric patients do not receive PIS within an adequate time frame. Patients who receive long-acting paralytic agents are much less likely to be adequately sedated after RSI compared with those receiving succinylcholine.
Differences in Clinical Findings Based on the Duration of Symptoms and Age of Children With Ileocolic Intussusception
Authors: Aoki Yoshihiro , Iguchi Akihiro , Kitazawa Katsuhiko , Kobayashi Hironobu , Senda Masayoshi , Honda Akihito
Published: February 2019

Objectives

The objective of this study was to determine whether the rates of abdominal pain or irritability, vomiting, and hematochezia differ depending on the duration of symptoms and age of the children with ileocolic intussusception.

Methods

We retrospectively investigated the charts of ileocolic intussusception children between January 2008 and December 2017 at a rural general hospital in Japan. Children were separated into 2 groups: the early visiting group, including children examined within 6 hours after onset, and the late visiting group, including children examined more than 6 hours after onset. We further separated them into 2 groups based on age: the infant group (age, <18 months) and the child group (age, ≥18 months). We compared clinical features, such as abdominal pain or irritability, vomiting, and hematochezia, between each group.

Results

Among 105 children with ileocolic intussusception, 51 were in the early visiting group and 49 were in the infant group. Hematochezia less frequently occurred in the early visiting group than in the late visiting group (29% vs 50%, P = 0.046). Furthermore, abdominal pain or irritability occurred less frequently in the infant group than in the child group (79.6% vs 98.2%, P = 0.003). Conversely, vomiting and hematochezia were more frequent in the infant group than in the child group (83.7% vs 51.8%, P < 0.001; 55.1% vs 26.8%, P = 0.005).

Conclusions

Clinical features of pediatric ileocolic intussusception may depend on symptom duration and age.
Japanese cross-cultural validation study of the Pain Stage of Change Questionnaire
Authors: Adachi Tomonori , Sunohara Momoka , Enomoto Kiyoka , Sasaki Keitaro , Sakaue Gaku , Fujita Yoshitsugu , Mizuno Yasuyuki , Okamoto Yoshiaki , Miki Kenji , Yukioka Masao , Nitta Kazuhito , Iwashita Narihito , Kitagawa Hirotoshi , Shibata Masahiko , Sasaki Jun , Jensen Mark P. , Fukui Sei
Published: February 2019

Introduction:

Although evidence supports efficacy of treatments that enhance self-management of chronic pain, the efficacy of these treatments has been hypothesized to be influenced by patient readiness for self-management. The Pain Stage of Change Questionnaire (PSOCQ) is a reliable and valid measure of patient readiness to self-manage pain. However, there is not yet a Japanese version of the PSOCQ (PSOCQ-J), which limits our ability to evaluate the role of readiness for pain self-management in function and treatment response in Japanese patients with chronic pain.

Objective:

Here, we sought to develop the PSOCQ-J and evaluate its psychometric properties.

Methods:

We recruited 201 patients with chronic pain. The study participants were asked to complete the PSOCQ-J and other measures assessing pain severity, pain interference, catastrophizing, self-efficacy, and pain coping strategies.

Results:

The results supported a 4-factor structure of the PSOCQ-J. We also found good to excellent internal consistencies and good test–retest reliabilities for the 4 scales. The Precontemplation scale had weak to moderate positive correlations with measures of pain-related dysfunction and maladaptive coping. The Action and Maintenance scales had weak to moderate positive correlations with measures of self-efficacy and adaptive coping. The Contemplation scale had weak positive correlations with measures of pain interference and both adaptive and maladaptive coping.

Conclusions:

The PSOCQ-J demonstrated adequate psychometric properties in a sample of Japanese patients with chronic pain. This measure can be used to evaluate the role that readiness to self-manage pain may play in adjustment to chronic pain in Japanese pain populations.
Coronary Artery Spasm, Coronary Reactivity, and Their Psychological Context
Authors: Mehta Puja K. , Thobani Aneesha , Vaccarino Viola
Published: February 2019

Symptomatic individuals suspected of having myocardial ischemia often have no obstructive atherosclerotic narrowing of epicardial coronary arteries. Abnormal coronary vascular reactivity and, in particular, coronary artery vasospasm (CAS) may be an explanation in a subset of these patients. Psychological factors play an important role in ischemic heart disease, but their role in CAS is not clear; autonomic dysfunction and increased inflammation are two prevailing pathophysiological mechanisms implicated in abnormal coronary reactivity resulting from mental health conditions. Interrelationships between psychological factors, abnormal coronary reactivity, and sex/gender differences are poorly defined in the etiology of CAS. In this issue of Psychosomatic Medicine (2019;81:237–245), Hung et al. report a frequency of less than 0.1% of new-onset CAS in the Taiwanese population, with higher occurrence in women and younger individuals. Patients with CAS had a higher prevalence of previous anxiety and depression compared with those with coronary artery disease and controls, with no sex differences. In this editorial comment, we discuss the potential reasons for underreporting of CAS and the challenges regarding the use of administrative health records for psychosomatic research. In this editorial, a model is presented to explain the association between emotional stressors and mental health factors with CAS, including the role of sympathetic nervous system activation, inflammation, oxidative stress, endothelial dysfunction, and smooth muscle cell dysregulation.
Patient Safety Incidents Describing Patient Falls in Critical Care in North West England Between 2009 and 2017
Authors: Thomas Antony N. , Balmforth Joanna E.
Published: February 2019

Aim

The aim of the study was to review reported falls in critical care units to see whether the causes and results were different from those described in a general hospital population.

Methods

We reviewed and classified patient safety incidents describing falls from critical care units in the North West of England between 2009 and 2017. The classification reviewed patient and staff factors contributing to the fall, the environment of the fall, and the reported consequences. We then calculated and compared rates of falls in different units.

Results

There were 914 falls reported, representing only 2.0% of all reported incidents. The median (interquartile range) unit rate was 1.0 falls per 1000 (0.5–1.2) days, and falls were unrelated to the number of single rooms and were no more common in specialist units. There were 304 (33%) falls in patients transferring (207 to standing, 8 from standing), and there were 259 (28%) falls from bed. Patient factors included attempting tasks without assistance (323 incidents [35%]) and organic confusion (188 incidents [21%]). Staff factors included being away from the patient (375 incidents [41%]). Harm was described in 201 incidents (22%), including removal of medical devices (40 incidents), injury to staff (10 incidents) subdural hematoma, and possible spinal injury (1 incident each).

Conclusions

There is a low rate of falls and associated harm in critical care units. The variation between units suggests that this rate could be further reduced by the prevention and management of delirium and by educating patients and staff to take care when moving patients to the standing position.
Pursuing Patient Safety at the Intersection of Design, Systems Engineering, and Health Care Delivery Research: An Ongoing Assessment
Authors: Henriksen Kerm , Rodrick David , Grace Erin N. , Shofer Marjorie , Jeffrey Brady P.
Published: February 2019

Objectives

Despite endorsements for greater use of systems approaches and reports from national consensus bodies calling for closer engineering/health care partnerships to improve care delivery, there has been a scarcity of effort of actually engaging the design and engineering disciplines in patient safety projects. The article describes a grant initiative undertaken by the Agency for of Healthcare Research and Quality that brings these disciplines together to test new ideas that could make health care safer.

Methods

Collectively known as patient safety learning laboratories, grantee teams engage in phase-based activities that parallel a systems engineering process—problem analysis, design, development, implementation, and evaluation—to gain an in-depth understanding of related patient safety problems, generate fresh ideas and rapid prototypes, develop the prototypes, ensure that developed components are implemented as an integrated working system, and evaluate the system in a simulated or clinical setting.

Findings

Obstacles are described that can derail the best of intentions in deploying the systems engineering methodology. Based on feedback received from project teams, lessons learned are emerging that find considerable variation among project teams in deploying the methodology and a longer than anticipated amount of time in bringing team members from different disciplines together where they learn to communicate and function as a team.

Conclusions

Three narratives are generated in terms of what success might look like. Much is yet to be learned about the limitations and successes of the ongoing learning laboratory initiative, which should be relevant to the broader scale interest in learning health systems.
Validation of the Casa Colina Fall Risk Assessment Scale in Predicting Falls in Inpatient Rehabilitation Facilities
Authors: Kaplan Stephanie E. , Cournan Michele , Gates Jason , Thorne Melanie , Jones Annette , Ponce Tom , Rosario Emily R.
Published: February 2019

Objective

The aim of this study was to assess the validity, efficacy, and generalizability of a fall risk assessment tool created specifically for inpatient rehabilitation facilities (IRFs).

Design

The Casa Colina Falls Risk Assessment Scale (CCFRAS) was assessed both retrospectively and prospectively on consecutive patients at three IRFs to determine the sensitivity and specificity of this tool in predicting fall risk.

Setting

The setting was in three IRFs.

Participants

Individuals admitted to three IRFs participated in the study.

Main Outcomes Measures

Each IRF quantified the number of falls detected for the patient population under evaluation and determined the site-specific sensitivity and specificity of the CCFRAS.

Results

The sensitivity and specificity of the CCFRAS ranged from 75% to 80% and from 47% to 70%, respectively, for the different IRFs. Using a logistic regression analysis, we identified the optimal CCFRAS cutoff score for identifying high-risk patients at each individual facility, thus improving the specificity to 70%–79%.

Conclusion

Multisite evaluation of this assessment tool indicates that the CCFRAS is effective and broadly generalizable for predicting patients at high risk for falling.
Recombinant Human Bone Morphogenic Protein-2 Combined With Autogenous Bone Graft for Reconstruction of Alveolar Cleft
Authors: Jahanbin Arezoo , Zarch Hossein Hosseini , Irani Sahar , Eslami Neda , Kermani Hamed
Published: February 2019

Recombinant human bone morphogenic proteins (rhBMPs) have been introduced for reconstruction of alveolar defects. The volume of the bone formed at the cleft region may be related to rhBMP-2 dose. Greater side effects have been reported with increased doses of rhBMP-2. The aim of the present study was to assess the bone at the cleft area using low dose of rhBMP-2 combined with autogenous bone graft for reconstruction of the alveolar cleft. Patients with unilateral cleft lip and palate between the 11 to 14 years old were enrolled. After palatal expansion, autogenous graft was placed at the side of cleft in the control group (n = 6). In the BMP group, the rhBMP-2 was injected into the autogenous bone graft at the defect site (n = 5). Cone beam computed tomography (CBCT) images were taken of all patients immediately and 3 months after graft surgery to compare the density, thickness, and height of the bone graft between the 2 groups. Intermolar and interpremolar widths were also measured. The authors found less diminish of density and height of the bone graft 3 months postsurgery in patients with autogenous bone graft combined with rhBMP-2. However, significant difference in the relapse tendency of transverse dimension of the arch or thickness of the bone graft was not observed between the 2 groups. Thus, low dose rhBMP-2 combined with autogenous bone graft can be promising to reach predictable results after alveolar reconstruction in cleft lip and palate patients.
Transient Retinal Artery Occlusion After Uncomplicated Rhinoplasty
Authors: Guler Alis Meryem , Acikalin Banu , Alis Abdulkadir , Ucal Yusuf Orhan
Published: February 2019

Purpose:

Loss of vision is an extremely rare and unexpected complication following a routine uncomplicated nasal surgery. In majority of patients, visual loss has attributed to retinal emboli which occur with retrograde flow of the intra-arterially injected agents into the nasal cavity or direct trauma to the optic nerve. In this report, the authors present a patient with unilateral decreased vision due to branch retinal artery occlusion soon after a routine nasal surgery.

Methods:

Clinical report.

Result:

A 32-year-old female patient admitted to the author’ clinic with the complaints of decreased visual acuity in the left eye. She stated that she had undergone rhinoplasty operation 1 week ago and vision loss started immediately after the surgery.

In the ophthalmological examination, the best corrected visual acuity with Snellen chart was 1.0 in the right eye and 0.3 in the left eye. In the fundoscopic examination of left eye there was a pale area in the inferior part of the macula. Fundus fluorescein angiography showed no evidence of nonperfusion in the right and left eyes and vascular structure was normal. On the optic coherence tomography, hyperreflectivity and increased thickness were observed in the inner retinal layers of the left eye. In the visual field test, there was a loss of the visual field which corresponds to the pale area on the left eye. Hyperbaric oxygen therapy was recommended. The ophthalmologic examination carried out 2 months later revealed a best corrected visual acuity of the left eye 0.9. In the fundoscopy pale area was regressed in the left eye. Fundus fluorescein angiography showed a good perfusion. There was a little progression in the visual field test.

Conclusion:

Direct mechanical trauma and vasoplastic/embolic vascular events are thought to be possible mechanisms. The authors think in this case, there was a retrograde flow of agents used during the surgery through ophthalmic artery to retinal arteries and vasospasm by epinephrin worsened the situation. Although rare retinal artery occlusion may develop after rhinoplasty, vision loss as a result of a surgery, if done for aesthetic purposes is not acceptable.
Assessing the Impact of Suboptimal Donor Characteristics on Mortality After Liver Transplantation: A Time-dependent Analysis Comparing HCC With Non-HCC Patients
Authors: Wallace David , Walker Kate , Charman Susan , Suddle Abid , Gimson Alex , Rowe Ian , Callaghan Chris , Cowling Tom , Heaton Nigel , van der Meulen Jan
Published: February 2019

Background.

Patients who receive a liver transplant for hepatocellular carcinoma (HCC) often receive poorer-quality livers. Tumor recurrence also has a negative effect on posttransplant outcomes. We compared mortality of HCC and non-HCC recipients in different posttransplant time periods (epochs) to separate the impact of these different risk factors on short-term and longer-term posttransplant survival.

Methods.

We identified a population-based cohort of first-time liver transplant recipients (aged ≥16 years) between 2008 and 2016 in the United Kingdom. We used Cox regression to estimate hazard ratios (HRs) comparing posttransplant mortality between HCC and non-HCC patients in 3 posttransplant epochs: 0 to 90 days, 90 days to 2 years, and 2 to 5 years, with adjustment first for recipient and later also for donor characteristics.

Results.

One thousand two hundred seventy HCC and 3657 non-HCC transplant recipients were included. Five-year posttransplant survival was 74.5% (95% confidence interval [CI] 71.2%–77.5%) in HCC patients and 84.6% (83.0%–86.1%) in non-HCC patients. With adjustment for recipient characteristics only, mortality of HCC patients was lower but not statistically significantly different in the first 90 days (HR, 0.76; 95% CI, 0.53–1.09; P = 0.11), but significantly higher thereafter (90 days to 2 years: HR, 1.99; 95% CI, 1.48–2.66; P < 0.001; 2 to 5 years HR, 1.77; 95% CI, 1.30–2.42; P < 0.001). Further adjustment for donor characteristics had little impact on these results.

Conclusions.

HCC recipients have poorer 5-year posttransplant survival than non-HCC recipients, most likely because of tumor recurrence. The more frequent use of poorer-quality donor organs for HCC does not explain this difference.
Brain Death in Asia: Do Public Views Still Influence Organ Donation in the 21st Century?
Authors: Liu Christopher W. , Yeo Charlene , Lu Zhao Boyu , Lai Clin K.Y. , Thankavelautham Suhitharan , Ho Vui Kian , Liu Jean C.J.
Published: February 2019

Background.

Historically, brain death legislation was adopted in Asia at a much later stage than it was in the West, with heated public debates surrounding these laws. In this study, we investigated whether the poor acceptance of brain death continues to the present day, focusing on the following: (1) what the Asian public understands brain death to be; (2) how views toward brain death are compared with those of cardiac death; and (3) the extent to which brain death perception contributes to the low rate of deceased organ donation that has been observed amongst Asians.

Methods.

Using a door-to-door sampling strategy, we recruited 622 residents in Singapore between September 2016 and July 2017.

Results.

Our results suggest that resistance toward brain death persists, with the majority of respondents equating this as a bleak outcome but not as death. Correspondingly, they considered cardiac death a better indicator of death and were more fearful of being alive during organ donation. In turn, these views predicted a decreased willingness to donate either their own or their family members’ organs.

Conclusions.

Taken together, our results suggest that views of brain death continue to hamper organ donation, and are seemingly resistant to both time and legislation.
Outcomes in Older Kidney Transplant Recipients After Prior Nonkidney Transplants
Authors: Haugen Christine E. , Luo Xun , Holscher Courtenay M. , Bowring Mary G. , DiBrito Sandra R. , Garonzik-Wang Jacqueline , McAdams-DeMarco Mara , Segev Dorry L.
Published: February 2019

Background.

Recipients of nonkidney solid organ transplants (nkSOT) are living longer, and 11%–18% will develop end stage renal disease (ESRD). While our general inclination is to treat nkSOT recipients who develop ESRD with a kidney transplant (KT), an increasing number are developing ESRD at an older age where KT may not be the most appropriate treatment. It is possible that the risk of older age and prior nkSOT might synergize to make KT too risky, but this has never been explored.

Methods.

To examine death-censored graft loss and mortality for KT recipients with and without prior nkSOT, we used Scientific Registry of Transplant Recipients data to identify 42 089 older (age ≥65) KT recipients between 1995 and 2016. Additionally, to better understand treatment options for these patients and survival benefit of KT, we identified 5023 older (age ≥65) with prior nkSOT recipients listed for subsequent KT, of whom 863 received transplants.

Results.

Compared with 41 159 older KT recipients without prior nkSOT, death-censored graft loss was similar (adjusted hazard ratio [aHR]: 1.13, 95% CI: 0.93-1.37, P = 0.2), but mortality (aHR: 1.40, 95% CI: 1.28-1.54, P < 0.001) was greater for older KT recipients with prior nkSOT. Nonetheless, in a survival benefit model (survival with versus without the transplant), among older prior nkSOT recipients, KT decreased the risk of mortality by more than half (aHR: 0.47, 95% CI: 0.42-0.54, P < 0.001).

Conclusions.

Older prior nkSOT recipients who subsequently develop ESRD derive survival benefit from KT, but graft longevity is limited by overall survival in this population. These findings can help guide patient counseling for this challenging population.
Impact of Extra-anatomical Hepatic Artery Reconstruction During Living Donor Liver Transplantation on Biliary Complications and Graft and Patient Survival
Authors: Rhu Jinsoo , Kim Jong Man , Choi Gyu-Seong , David Kwon Choon Hyuck , Joh Jae-Won
Published: February 2019

Background.

This study was designed to analyze the feasibility of extra-anatomical hepatic artery (HA) reconstruction in living donor liver transplantation (LT).

Methods.

Patients who underwent their first living donor LT at our center between January 2008 and December 2017 were reviewed. HA reconstruction was classified as anatomical or extra-anatomical reconstruction (EAR). We compared the background characteristics and posttransplantation outcomes, including complications, biliary complications, graft survival, and overall survival. The potential risk factors for bile leakage were analyzed using multivariable logistic regression, while risk factors for biliary stricture-free survival, graft survival, and overall survival were analyzed using multivariable Cox regression.

Results.

Among 800 patients, 35 (4.4%) underwent EAR, of whom 7 (7/35, 20.0%) experienced HA complications after the initial anatomical reconstruction and required EAR during reoperation. Patients who underwent EAR (n = 2/35, 5.7%) had a similar rate of HA complications compared with those who underwent anatomical reconstruction (n = 46/772, 5.9%, P = 0.699). EAR was a significant risk factor for bile leakage (odds ratio [OR], 4.167; 95% confidence interval [CI], 1.928-9.006; P < 0.001) along with multiple bile ducts (OR, 1.606; 95% CI, 1.022-2.526; P = 0.040) and hepaticojejunostomy (OR, 4.108; 95% CI, 2.190-7.707; P < 0.001). However, EAR had no statistical relationship to biliary stricture-free survival (hazard ratio [HR], 1.602; 95% CI, 0.982-2.613; P = 0.059), graft survival (HR, 1.745; 95% CI, 0.741-4.109; P = 0.203), or overall survival (HR, 1.405; 95% CI, 0.786-2.513; P = 0.251). HA complications were associated with poor biliary stricture-free survival (HR, 2.060; 95% CI, 1.329-3.193; P = 0.001), graft survival (HR, 5.549; 95% CI, 2.883-10.681; P < 0.001), and overall survival (HR, 1.958; 95% CI, 1.195-3.206; P = 0.008).

Conclusion.

Extra-anatomical HA reconstruction during living donor LT was not a risk factor for biliary stricture, graft failure, or overall survival.
FL/GCSF/AMD3100-mobilized Hematopoietic Stem Cells Induce Mixed Chimerism With Nonmyeloablative Conditioning and Transplantation Tolerance
Authors: Xu Hong , Zhu Ziqiang , Huang Yiming , Ildstad Suzanne T.
Published: February 2019

Background.

Mobilization of hematopoietic stem cells (HSCs) has become the preferred approach for HSC transplantation. AMD3100, a competitive inhibitor of C-X-C motif chemokine receptor-4, has been found to be a rapid mobilizing agent. The present study evaluated approaches to optimize the product collected.

Methods.

Mobilized peripheral blood mononuclear cells (mPBMCs) from B6 mice were transplanted to recipient BALB/c mice conditioned with ablative or nonmyeloablative approaches.

Results.

The optimal dose of AMD3100 was found to be 5.0 mg/kg. Optimal HSC mobilization was observed when AMD3100 (day 10) was coadministered with Flt3 ligand (FL) (days 1–10) and granulocyte colony-stimulating factor (GCSF) (days 4–10). There was a 228.8-fold increase of HSC with FL/GCSF/AMD3100 compared with AMD3100 treatment alone. When unmodified mPBMCs were transplanted into ablated allogeneic recipients, all recipients expired by day 40 from severe acute graft versus host disease (GVHD). When T cells were depleted from mPBMC, long-term survival and engraftment were achieved in majority of the recipients. When PBMC mobilized by FL/GCSF/AMD3100 were transplanted into recipients conditioned nonmyeloablatively with anti-CD154/rapamycin plus 100, 200, and 300 cGy of total body irradiation, 42.9%, 85.7%, and 100% of mice engrafted, respectively. Donor chimerism was durable, multilineage, and stable. Lymphocytes from mixed chimeras showed no response to host or donor antigens, suggesting functional bidirection T-cell tolerance in vitro. Most importantly, none of the engrafted mice exhibited clinical features of GVHD.

Conclusions.

FL/GCSF/AMD3100 is an efficient treatment to maximally mobilize HSC. Durable engraftment and donor-specific tolerance can be achieved with mPBMC in nonmyeloablative conditioning without GVHD.
CYP1A2 Genetic Polymorphism Is Associated With Treatment Remission to Antidepressant Venlafaxine in Han Chinese Population
Authors: Zhu Yuhao , Zhang Naixing , Ren Decheng , Bi Yan , Xu Fei , Niu Weibo , Sun Qianqian , Guo Zhenming , Yuan Ruixue , Yuan Fan , Wu Xi , Cao Yanfei , Yang Fengping , Wang Lu , Du Li , Li Weidong , Xu Yifeng , Li Xingwang , Zhu Liping , He Lin , Shi Lei , He Guang , Yu Tao
Published: February 2019

Major depressive disorder (MDD) is a common mental disorder. Venlafaxine (VEN) is used to treat patients with MDD as an antidepressant of serotonin-norepinephrine reuptake inhibitor. In addition, current reports reveal that CYP enzymes mediate its metabolism, thereby affecting the treatment efficacy. The aim of this study was to test whether the genetic polymorphisms ofCYP1A2are associated with remission after VEN treatment for MDD. A total of 175 Han Chinese depressed patients have been recruited to accept a 6-week treatment with VEN. Three single-nucleotide polymorphisms ofCYP1A2were selected from dbSNP and previous literature to compare the allele and genotype frequencies between remitters and nonremitters. The A 17-item Hamilton Depression Scale was used to access the improvement of patients' depressive symptoms from the baseline to endpoint. A logistic regression analysis for remission was conducted. Between remitters and nonremitters, the allele and genotype frequencies of single-nucleotide polymorphism rs2470890 demonstrated significant differences. They still had significant differences between remitters and nonremitters after controlling baseline Hamilton Depression Scale scores, sex, and age in logistic regression. Our results suggest that the single-nucleotide polymorphism rs2470890 ofCYP1A2gene might be associated with treatment remission after VEN treatment in patients with MDD.
Bacillus acidinfaciens sp. nov., isolated from farmland soil
Authors: Sun Leni , Chen Yan , Tian Wei , Yao Lunguang , Chen Zhaojin , Ouyang Wenkai
Published: February 2019

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus

Bacillus

and most closely related to

Bacillus fortis

R-6514T (98.9 % similarity),

Bacillus terrae

RA9T (98.0 %) and

Bacillus fordii

R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus

Bacillus

, for which the name

Bacillus
acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).
Sinomicrobium soli sp. nov., isolated from arctic soil
Authors: Liu Xiupian , Lai Qiliang , Du Yaping , Zhang Xiaorong , Zhong Huanzi , Shao Zongze
Published: February 2019

A bacterial strain, designated N-1-3-6T, was isolated from a soil sample collected from the arctic regions. The cells were short rods, Gram-stain-negative, catalase- and oxidase-positive. Growth was observed with 0–12 % (w/v) NaCl, with optimal growth at 0.5–2 %, and at pH 6.0–9.0, with optimum of pH 7.0, and a growth temperature of 10–45 °C, with an optimum of 28–37 °C. Phylogenetic analysis based on the 16S rRNA gene placed N-1-3-6T in the genus

Sinomicrobium

with the closest relative being

Sinomicrobium
pectinilyticum 5DNS001T, exhibiting 95.3 % 16S rRNA pairwise similarity. A polyphasic taxonomic study, including phenotypic, chemotaxonomic and molecular analyses, was performed to clarify its taxonomic position. N-1-3-6T contained MK-6 as the predominant menaquinone. Polar lipids consisted of phosphatidylethanolamine and several unidentified aminolipids, phospholipids and lipids. The principal fatty acids (>10 %) were iso-C15 : 0 (26.9 %), summed feature 3 [C16 : ω7c/ω6c (17.2 %)] and iso-C17 : 0 3-OH (14.7 %). The DNA G+C content of N-1-3-6T was 47.7 mol%. On the basis of its phenotypic and genotypic properties, strain N-1-3-6T should be classified as representing a novel species of the genus

Sinomicrobium

, for which the name

Sinomicrobium
soli sp. nov. is proposed, with the type strain N-1-3-6T (=MCCC 1A06047T=KCTC 52339T).
A general framework for predicting the transcriptomic consequences of non-coding variation
Authors: Abdalla Moustafa , Abdalla Mohamed , McCarthy Mark I. , Holmes Chris C.
Published: February 2019

Genome wide association studies (GWASs) for complex traits have implicated thousands of genetic loci. Most GWAS-nominated variants lie in noncoding regions, complicating the systematic translation of these findings into functional understanding. Here, we leverage convolutional neural networks to assist in this challenge. Our computational framework, peaBrain, models the transcriptional machinery of a tissue as a two-stage process: first, predicting the mean tissue specific abundance of all genes and second, incorporating the transcriptomic consequences of genotype variation to predict individual abundance on a subject-by-subject basis. We demonstrate that peaBrain accounts for the majority (>50%) of variance observed in mean transcript abundance across most tissues and outperforms regularized linear models in predicting the consequences of individual genotype variation. We highlight the validity of the peaBrain model by calculating non-coding impact scores that correlate with nucleotide evolutionary constraint that are also predictive of disease-associated variation and allele-specific transcription factor binding. We further show how these tissue-specific peaBrain scores can be leveraged to pinpoint functional tissues underlying complex traits, outperforming methods that depend on colocalization of eQTL and GWAS signals. We subsequently derive continuous dense embeddings of genes for downstream applications, and identify putatively functional eQTLs that are missed by high-throughput experimental approaches.
A framework for evaluating correspondence between brain images using anatomical fiducials
Authors: Lau Jonathan C. , Parrent Andrew G. , Demarco John , Gupta Geetika , Kai Jason , Stanley Olivia W. , Kuehn Tristan , Park Patrick J. , Ferko Kayla , Khan Ali R. , Peters Terry M.
Published: February 2019

Accurate spatial correspondence between template and subject images is a crucial step in neuroimaging studies and clinical applications like stereotactic neurosurgery. In the absence of a robust quantitative approach, we sought to propose and validate a set of point landmarks, anatomical fiducials (AFIDs), that could be quickly, accurately, and reliably placed on magnetic resonance images of the human brain. Using several publicly available brain templates and individual participant datasets, novice users could be trained to place a set of 32 AFIDs with millimetric accuracy. Furthermore, the utility of the AFIDs protocol is demonstrated for evaluating subject-to-template and template-to-template registration. Specifically, we found that commonly used voxel overlap metrics were relatively insensitive to focal misregistrations compared to AFID point-based measures. Our entire protocol and study framework leverages open resources and tools, and has been developed with full transparency in mind so that others may freely use, adopt, and modify. This protocol holds value for a broad number of applications including alignment of brain images and teaching neuroanatomy.
Multi-phosphorylation reaction and clustering tune Pom1 gradient mid-cell levels according to cell size
Authors: Gerganova Veneta , Floderer Charlotte , Archetti Anna , Michon Laetitia , Carlini Lina , Reichler Thaïs , Manley Suliana , Martin Sophie G
Published: February 2019

Protein concentration gradients convey information at a distance from the source to both pattern developing organisms and organize single cells. In the rod-shaped cells of Schizosaccharomyces pombe, the DYRK-family kinase Pom1 forms concentration gradients with maxima at the cell poles. Pom1 controls the timing of mitotic entry by inhibiting the SAD-family kinase Cdr2, which forms stable membrane-associated nodes at mid-cell. Pom1 gradients rely on membrane association regulated by a phosphorylation-dephosphorylation cycle and lateral diffusion modulated by clustering. Whether the graded pattern directly alters Pom1 medial levels has been controversial. Here, using a combination of quantitative imaging approaches, including single particle tracking PALM and TIRF microscopy, we find that individual Pom1 molecules do not bind the membrane long enough to diffuse from cell pole to cell middle. Instead we propose they exchange within longer-lived clusters that form the functional gradient units. By creating an allelic series progressively blocking auto-phosphorylation, we show that multi-phosphorylation shapes and buffers the gradient to control the cortical mid-cell Pom1 levels, which represent the critical pool regulating Cdr2. Specific imaging of this cortical pool by TIRF microscopy demonstrates that more Pom1 overlaps with Cdr2 nodes in short than long cells, consistent with Pom1 inhibition of Cdr2 decreasing with cell growth. We conclude that Pom1 gradients modulate Pom1 mid-cell levels according to cell size.
Comparative genomics reveals the origin of fungal hyphae and multicellularity
Authors: Kiss Enikő , Hegedüs Botond , Varga Torda , Merényi Zsolt , Kószó Tamás , Bálint Balázs , Prasanna Arun N. , Krizsán Krisztina , Riquelme Meritxell , Takeshita Norio , Nagy László G.
Published: February 2019

Hyphae represent a hallmark structure of multicellular fungi with immense importance in their life cycle, including foraging for nutrients, reproduction, or virulence. Hypha morphogenesis has been the subject to intense interest, yet, the origins and genetic underpinning of the evolution of hyphae are hardly known. Using comparative genomics, we here show that the emergence of hyphae correlates with multiple types of genetic changes, including alterations of gene structure, gene family diversification as well as co-option and exaptation of ancient eukaryotic genes (e.g. phagocytosis-related genes). Half of the gene families involved in hypha morphogenesis have homologs in unicellular fungi and non-fungal eukaryotes and show little or no duplications coincident with the origin of multicellular hyphae. Considerable gene family diversification was observed only in transcriptional regulators and genes related to cell wall synthesis and modification. Despite losing 35-46% of their genes, yeasts retained significantly more multicellularity-related genes than expected by chance. We identified 414 gene families that evolved in a correlated fashion with hyphal multicellularity and may have contributed to its evolution. Contrary to most multicellular lineages, the origin of hyphae did not correlate with the expansion of gene families encoding kinases, receptors or adhesive proteins. Our analyses suggest that fungi took a unique route to multicellularity that involved limited gene family diversification and extensive co-option of ancient eukaryotic genes.
CONSENT: Scalable long read self-correction and assembly polishing with multiple sequence alignment
Authors: Morisse Pierre , Marchet Camille , Limasset Antoine , Lecroq Thierry , Lefebvre Arnaud
Published: February 2019

Motivation

Third-generation sequencing technologies Pacific Biosciences and Oxford Nanopore allow the sequencing of long reads of tens of kbp, that are expected to solve various problems, such as contig and haplotype assembly, scaffolding, and structural variant calling. However, they also display high error rates that can reach 10 to 30%, for basic ONT and non-CCS PacBio reads. As a result, error correction is often the first step of projects dealing with long reads. As first long reads sequencing experiments produced reads displaying error rates higher than 15% on average, most methods relied on the complementary use of short reads data to perform correction, in a hybrid approach. However, these sequencing technologies evolve fast, and the error rate of the long reads now reaches 10 to 12%. As a result, self-correction is now frequently used as the first step of third-generation sequencing data analysis projects. As of today, efficient tools allowing to perform self-correction of the long reads are available, and recent observations suggest that avoiding the use of second-generation sequencing reads could bypass their inherent bias.

Results

We introduce CONSENT, a new method for the self-correction of long reads that combines different strategies from the state-of-the-art. More precisely, we combine a multiple sequence alignment strategy with the use of local de Bruijn graphs. Moreover, the multiple sequence alignment benefits from an efficient segmentation strategy based on k-mer chaining, which allows a considerable speed improvement. Our experiments show that CONSENT compares well to the latest state-of-the-art self-correction methods, and even outperforms them on real Oxford Nanopore datasets. In particular, they show that CONSENT is the only method able to efficiently scale to the correction of Oxford Nanopore ultra-long reads, and is able to process a full human dataset, containing reads reaching lengths up to 1.5 Mbp, in 15 days. Additionally, CONSENT also implements an assembly polishing feature, and is thus able to correct errors directly from raw long read assemblies. Our experiments show that CONSENT outperforms state-of-the-art polishing tools in terms of resource consumption, and provides comparable results. Moreover, we also show that, for a full human dataset, assembling the raw data and polishing the assembly afterwards is less time consuming than assembling the corrected reads, while providing better quality results.

Availability and implementation

CONSENT is implemented in C++, supported on Linux platforms and freely available at https://github.com/morispi/CONSENT.

Contact

pierre.morisse2@univ-rouen.fr