bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Personalized Music Intervention in Mechanically Ventilated Children in the PICU: A Pilot Study*
Authors: Liu Mei-hua , Zhu Li-hui , Peng Jian-xiong , Zhang Xin-ping , Xiao Zheng-hui , Liu Qiong-jie , Qiu Jun , Latour Jos M.
Published: October 2019

Objectives:

To determine the feasibility of a personalized music intervention with mechanically ventilated patients in the PICU.

Design:

Pilot study with a quasi-experimental design.

Setting:

Tertiary children’s hospital in China with a 40-bed PICU.

Patients:

Children, 1 month to 7 years, with mechanical ventilation were recruited and assigned to music group (n = 25) and control group (n = 25).

Interventions:

Children in the music group received their own favorite music and listened for 60 minutes three times a day. The control group receive routine care without music.

Measurements and Main Results:

Primary outcome measure was comfort measured with the COMFORT Behavior scale 5 minutes before and after the music. Secondary outcome measures were physiologic variables; heart rate, respiration, blood pressure, oxygen saturation. Mechanical ventilation time, length of stay, and sedation medication were also collected. Qualitative analysis revealed that nurses had a positive attitude in delivering the interventions and identified improvements for the main trial. Children in the music group had lower COMFORT Behavior scores (15.7 vs 17.6; p = 0.011). Children in the music group had better physiologic outcomes; heart rate (140 vs 144; p = 0.039), respiration rate (40 vs 43; p = 0.036), systolic blood pressure (93 vs 95 mm Hg; p = 0.031), oxygen saturation (96% vs 95%; p < 0.001), diastolic blood pressure was not significantly (52 vs 53 mm Hg; p = 0.11). Children in the music group had a shorter ventilation time (148.7 vs 187.6; p = 0.044) and a shorter length of stay, but not significant (11.2 vs 13.8; p = 0.071). Children in the control group had higher total amount of on-demand midazolam (29 vs 33 mg; p = 0.040).

Conclusions:

Our pilot study indicates that personalized music intervention is feasible and might improve the comfort of children with mechanical ventilation. Further studies are needed to provide conclusive evidence in confirming the effectiveness of music interventions comforting critically ill children in PICUs.
Predictors of Viremia in Postpartum Women on Antiretroviral Therapy
Authors: Hoffman Risa M. , Warshaw Meredith G. , Amico K. Rivet , Pilotto Jose , Masheto Gaerolwe , Achalapong Jullapong , Machado Elizabeth , Chokephaibulkit Kulkanya , Duarte Geraldo , João Esau , Graham Kathleen K. , Knapp Katherine M. , Stek Alice M. , Scott Gwendolyn B. , Coletti Anne , Loftis Amy J. , Chakhtoura Nahida , Currier Judith S. ,   for the PROMISE 1077HS Team
Published: October 2019

Background:

HIV-infected, postpartum women on antiretroviral therapy (ART) have high rates of viremia. We examined predictors of postpartum viremia in the PROMISE study.

Methods:

Women with pre-ART CD4+ T-cell counts ≥400 cells/mm3 who started ART during pregnancy were randomized postpartum to continue ART (CTART) or discontinue ART (DCART). Viral load and self-reported adherence were collected every 12 weeks, up to 144 weeks. Women in DCART reinitiated therapy when clinically indicated. Viremia was defined as 2 consecutive viral loads >1000 copies/mL after 24 weeks on ART. Adherence was dichotomized as missing versus not missing ART doses in the past 4 weeks. Predictors of viremia were examined using Cox proportional hazards regression with adherence as a time-varying covariate.

Results:

Among 802 women in the CTART arm, median age at entry was 27 years and median CD4+ T-cell count 696 cells/mm3. Of 175 women in CTART with viremia (22%), 141 had resistance data, and 12% had resistance to their current regimen. There was an estimated 0.12 probability of viremia by week 48 and 0.25 by week 144. Predictors of viremia included missed ART doses within the past 4 weeks, younger age, shorter duration of pre-entry ART, and being from the South American/Caribbean region. Of 137 women in DCART who reinitiated therapy, probability of viremia was similar to CTART (0.24 by week 96; 0.27 by week 144).

Conclusions:

Rates of postpartum viremia are high and viremia is more likely in younger postpartum women who start ART later in pregnancy. Interventions should target these higher-risk women.
Asymptomatic Metastasis to Thyroid Cartilage Detected by 18F-Choline and 64Cu-PSMA PET/CT as a Single Site of Disease Relapse in a Patient With Castration-Resistant Prostate Carcinoma
Authors: Annovazzi Alessio , Faiella Adriana , Pescarmona Edoardo , Sanguineti Giuseppe , Sciuto Rosa
Published: October 2019

Metastatic involvement of the larynx is rare due to the absence of vessels within the cartilaginous tissue. The probability of metastatic spread increases with aging as a result of larynx ossification. The secondary involvement of larynx is more frequently associated with melanoma and renal cell carcinoma. Few observations have been reported also in prostate cancer patients, usually associated with advanced disease and diffuse metastatic bone involvement. We report a case of an 83-year-old man with castration-resistant prostate cancer in whom a metastasis to the thyroid cartilage was the only site of relapse.
Simultaneous Correction of Complex Secondary Deformities of Cleft Lip Using Autogenous Costal Cartilage Combined With Rib Grafts
Authors: Zhang Lu , Wei Shuqiang , Qi Lin , Huang Weilong , Yu Chunbo , Cheng Liying , Jin Rong , Zhang Ying , Sun Xiaoming , Zhang Yuguang
Published: October 2019

Objective:

Complex secondary deformities of cleft lip include nasal and labial deformities, alveolar cleft, oronasal fistula, and so on. In this report, the authors present a method to simultaneously repair the above complex deformities with autogenous costal cartilage and rib grafts.

Methods:

The surgical procedure of simultaneous correction includes

Results:

Satisfactory outcomes were achieved in all 22 patients. Fifteen patients were followed up for 6 to 24 months and exhibited good nasal shape, repaired alveolar cleft, improved labial shape, and closed oronasal fistula. Three patients presented with red nasal tips. One patient had local infection, which was cured by antibiotics.

Conclusion:

This method

As this method has led to positive outcomes, it has the potential to be widely used in clinical practice.
Treatment of Intraosseous Hemangioma With Embolization in Mandible
Authors: Yalcin Mustafa , Ozer Nedim
Published: October 2019

The authors report a rare case of intraosseous hemangioma of the mandible in a 14-year-old male. Surgical intervention with embolization is as important as histological and radiological examination to reduce the bleeding complication. Magnetic resonance angiography is paramount of importance in these lesions to detect the supplier arteries.
The Effect of Burn Resuscitation Volumes on the Gut Microbiome in a Swine Model
Authors: McIntyre Matthew K. , Winkler Charlotte J. , Gómez Belinda I. , Lapierre Jean-Paul , Little Joshua S. , Dubick Michael A. , Nicholson Susannah E. , Burmeister David M.
Published: October 2019

Introduction:

While recent reports underscore the significance of the gut microbiome (GM) in health and disease, its importance in burn outcomes remains unclear. Moreover, aggressive intravenous (IV) fluid resuscitation of patients may alter intestinal flora. Herein, we describe GM changes following a large burn in swine randomized to different volumes of IV Lactated Ringers’ (LR).

Methods:

Anesthetized Yorkshire swine sustained 40% total body surface area full-thickness burns and were randomized to different volumes of IV LR: none (n = 5), 15 mL/kg/d (low; n = 6), or 80 mL/kg/d (high; n = 6). At baseline and days 1 and 2, fecal swabs were collected for 16s rDNA sequencing. Proximal jejunum was collected immediately after euthanasia (day 2) for western blot, histopathology, and cytokine analyses.

Results:

Burns produced significant shifts in β-diversity and non-significant reductions in α-diversity that did not recover regardless of treatment group. Burn-induced increases in Proteobacteria and decreases in Firmicutes were attenuated by IV fluids in a dose-dependent manner, and also correlated with α-diversity. IV fluids caused a dose-dependent increase in Bacteroides and prevented a transient increase in the opportunistic pathogen Haemophilus parainfluenzae. While high volumes of IV fluids increased intestinal Hsp70 levels (P = 0.0464), they reduced SGLT1 (P = 0.0213) and caspase3 (P = 0.0139) levels. IV fluids elicited a non-specific cytokine response; however, Bacteroidetes levels correlated with intestinal IL18 levels (P = 0.0166, R2 = 0.4201).

Conclusions:

We present the first report on the gut microbiome in a porcine burn model, and present data to suggest that IV fluids may influence GM and gut functional proteins following a burn. Overall, burn-induced GM diversity shifts may expose diagnostic and/or therapeutic targets to improve outcomes.
Medical Student Skill Retention After Cardiopulmonary Resuscitation Training
Authors: Saad Rafael , Sampaio Favarato Maria Helena , Ferreira de Paiva Edison , do Patrocinio Tenorio Nunes Maria
Published: October 2019

Introduction

The retention of cardiopulmonary resuscitation skills and the ideal frequency of retraining remain unanswered. This study investigated the retention of cardiopulmonary resuscitation skills by medical students for up to 42 months after training.

Methods

In a cross-sectional study, 205 medical students received 10 hours of training in basic life support in 3 practical classes, during their first semester at school. Then, they were divided into 4 groups, according to the time elapsed since the training: 73 after 1 month, 55 after 18 months, 41 after 30 months, and 36 after 42 months. Nineteen cardiopulmonary resuscitation skills and 8 potential technical errors were evaluated by mannequin-based simulation and reviewed using filming.

Results

The mean retention of the skills was 90% after 1 month, 74% after 18 months, 62% after 30 months, and 61% after 42 months (P < 0.001). The depth of chest compressions had the greatest retention over time (87.8%), with no significant differences among groups. Compressions performed greater than 120 per minute were less likely to be done with adequate depth. Ventilation showed a progressive decrease in retention from 93% (n = 68) after 1 month to 19% (n = 7) after 42 months (P < 0.001). All 205 students were able to turn the automated external defibrillator on and deliver the shock.

Conclusions

The depth of chest compressions and the use of an automated external defibrillator were the skills with the highest retention over time. Based on a skills retention prediction curve, we suggest that 18 to 24 months as the minimum retraining interval to maintain at least 70% of skills.
Aging Adults' Preferences for Wellness Program Activities and Delivery Characteristics
Authors: Talley Kristine M. C. , Cheung Corjena , Mathiason Michelle A. , Schorr Erica , McMahon Siobhan , Wyman Jean F.
Published: October 2019

Background:

Lifestyle wellness programs help prevent and manage chronic diseases, yet few are designed for aging adults.

Purpose:

Identify characteristics associated with aging adults' preferences for wellness program activities and delivery characteristics.

Subjects/Methods:

Cross-sectional, self-administered survey of a convenience sample of 386 adults aged 55 years and older. Logistic regression models identified characteristics influencing preferences.

Results:

Current healthy behaviors, gender, and age influenced many preferences, while body mass index, multiple chronic conditions, self-rated general health status, and quality of life did not.

Discussion:

Incorporating aging adults' preferences for wellness programs will help design appealing and engaging programs.
Outcomes of Patients Suspended From the National Kidney Transplant Waiting List in the United Kingdom Between 2000 and 2010
Authors: Wallace David , Robb Matthew , Hughes Winter , Johnson Rachel , Ploeg Rutger , Neuberger James , Forsythe John , Cacciola Roberto
Published: October 2019

Background.

In the United Kingdom, 1 in 3 patients on the National Kidney Transplant Waiting List (NKTWL) is suspended from the list at least once during their wait. The mortality of this large cohort of patients remains underreported and poorly described.

Methods.

We linked patient records from the UK transplant registry to mortality data from the Office of National Statistics and evaluated the impact of a clinically induced suspension event by estimating hazard ratios (HRs) that compared mortality and graft survival between those who had experienced a suspension event and those who had not.

Results.

Between January 1, 2000, and December 31, 2010, 16.7% (2221/13 322) of all patients registered on the NKTWL were suspended. Forty-eight percent (588/1225) of those who were suspended and who were never transplanted died, most often from cardiothoracic causes. A suspension event was associated with increased mortality from the time of listing (adjusted HR [aHR], 1.79; 1.64-1.95) and from the time of transplantation (aHR, 1.20; 1.06-1.37; P = 0.005). Graft survival was also poorer in those who had been suspended (aHR, 1.13; 1.01-1.28; P = 0.04).

Conclusions.

Patients suspended on the NKTWL have a significantly higher rate of mortality both on the waiting list and following transplantation. Earlier prioritization of patients at risk of experiencing a suspension event may improve their outcomes.
Delayed Implantation of Pumped Kidneys Decreases Renal Allograft Futility in Combined Liver–Kidney Transplantation
Authors: Lunsford Keri E. , Agopian Vatche G. , Yi Stephanie G. , Nguyen Duc T.M. , Graviss Edward A. , Harlander-Locke Michael P. , Saharia Ashish , Kaldas Fady M. , Mobley Constance M. , Zarrinpar Ali , Hobeika Mark J. , Veale Jeffrey L. , Podder Hemangshu , Farmer Douglas G. , Knight Richard J. , Danovitch Gabriel M. , Gritsch H. Albin , Li Xian C. , Ghobrial R. Mark , Busuttil Ronald W. , Gaber A. Osama
Published: October 2019

Background.

Combined liver–kidney transplantation (CLKT) improves survival for liver transplant recipients with renal dysfunction; however, the tenuous perioperative hemodynamic and metabolic milieu in high-acuity CLKT recipients increases delayed graft function and kidney allograft failure. We sought to analyze whether delayed KT through pumping would improve kidney outcomes following CLKT.

Methods.

A retrospective analysis (University of California Los Angeles [n = 145], Houston Methodist Hospital [n = 79]) was performed in all adults receiving CLKT at 2 high-volume transplant centers from February 2004 to January 2017, and recipients were analyzed for patient and allograft survival as well as renal outcomes following CLKT.

Results.

A total of 63 patients (28.1%) underwent delayed implantation of pumped kidneys during CLKT (dCLKT) and 161 patients (71.9%) received early implantation of nonpumped kidneys during CLKT (eCLKT). Most recipients were high-acuity with median biologic model of end-stage liver disease (MELD) score of, 35 for dCLKT and 34 for eCLKT (P = ns). Pretransplant, dCLKT had longer intensive care unit stay, were more often intubated, and had greater vasopressor use. Despite this, dCLKT exhibited improved 1-, 3-, and 5-year patient and kidney survival (P = 0.02) and decreased length of stay (P = 0.001), kidney allograft failure (P = 0.012), and dialysis duration (P = 0.031). This reduced kidney allograft futility (death or continued need for hemodialysis within 3 mo posttransplant) for dCLKT (6.3%) compared with eCLKT (19.9%) (P = 0.013).

Conclusions.

Delayed implantation of pumped kidneys is associated with improved patient and renal allograft survival and decreased hospital length of stay despite longer kidney cold ischemia. These data should inform the ethical debate as to the futility of performing CLKT in high-acuity recipients.
Case Study on Management of Postsurgical Pyoderma Gangrenosum After Spinal Surgery
Authors: Ratliff Catherine R.
Published: October 2019

BACKGROUND:

Postsurgical pyoderma gangrenosum (PSPG) is a rare autoimmune, neutrophilic dermatosis that results with the occurrence of pyoderma gangrenosum (PG) within surgical incisions. Presenting symptoms include erythema and pain at the surgical incision with wound dehiscence. The clinical appearance of the PSPG wound (similar to PG) shows raised with dusky red or violaceous (violet-colored) wound edges and undermining with little or no evidence of granulation tissue. “Pathergy” is the term used to describe worsening of the wound in response to trauma such as debridement. Postsurgical pyoderma gangrenosum should be suspected in postoperative wounds, which continue to become progressively worse despite broad-spectrum antibiotics, good wound care, and surgical debridement.

CASE:

A clinical case study of a patient with PSPG from spine surgery is described.

CONCLUSION:

Postsurgical pyoderma gangrenosum should be suspected in postoperative wounds, which continue to become progressively worse despite broad-spectrum antibiotics, good wound care, and surgical debridement.
An evaluation of a training intervention to support the use of evidence in healthcare commissioning in England
Authors: Sabey Abigail
Published: October 2019

Aim:

Clinical commissioning groups (CCGs) in England are responsible for the health of their populations through the services they provide, yet we know that the use of evidence to inform commissioning decisions is low. A programme of training in seven CCGs in England was instigated in a joint piece of work by the National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care and Academic Health Science Network in the West of England, to help build an evidence informed culture in commissioning.

Methods:

Evidence workshops were delivered in each of the seven CCGs in the West of England by an experienced senior lecturer (the author) and local healthcare librarians. The workshop was developed by the author and an information scientist and included guidance and demonstration of a systematic evidence search covering both traditional and grey literature, and a brief look at quality of evidence including a critical appraisal activity. Participants were asked to evaluate the workshop on the day and to indicate an intended action they would take as a result of the workshop; a short follow-up interview was carried out with a sample of participants between 3 and 6 months later, to identify any longer term impact of the training.

Results:

A total of 63 staff in a variety of commissioning-related roles attended the workshops between March and September 2016. 95% rated the workshop overall as either ‘excellent’ or ‘good’. Of particular value was the involvement of the local healthcare librarian, helping to promote their expertise and services; and the discussion of grey literature as a valuable source of evidence. A variety of intended actions as a result of the training included initiating a thorough search for evidence for new projects, use of bibliographic databases, and making use of local library services for evidence searching. Follow-up interviews with nine staff revealed a positive impact in the longer-term. This ranged from simply triggering an interest in using evidence, boosting motivation and sharing information with colleagues; to changes in processes such as broadening the responsibility for finding and filtering evidence for business cases; to one clear case of financial savings resulting from a search for evidence by a senior commissioning manager.

Conclusion:

Offering short, interactive training workshops is valued by healthcare commissioners and can make a difference to their approach to and use of evidence in decision-making. There is a need for a flexible approach to the concept of evidence in healthcare commissioning, which includes the use of grey literature, and training can encourage and support the systematic search for an appraisal of this type of evidence. Tools for improving and sustaining this aspect of evidence use by commissioners are included here.
Digital morphometry of tumor nuclei correlates to BAP-1 status, monosomy 3, gene expression class and survival in uveal melanoma
Authors: Herrspiegel Christina , O. See Thonnie Rose , Mendoza Pia R. , Grossniklaus Hans E. , Stålhammar Gustav
Published: October 2019

Cytologic features such as the shape and size of tumor cells can predict metastatic death in uveal melanoma and other cancers but suffer from poor reproducibility. In this study, we investigate the interobserver concordance of digital morphometry, and correlate the results with BRCA associated protein-1 (BAP-1) expression and BAP-1 gene mutation status, monosomy 3, gene expression classifications and patient survival in uveal melanoma. The average number of cells analyzed in each of 107 tumors, was 1957 (SD 349). Mean time consumption was less than 2.5 minutes per tumor. Identical morphometric classification was obtained for ≥ 85 % of tumors in all twelve evaluated morphometric variables (κ 0.70–0.93). The mean nucleus area, nucleus perimeter, nucleus max caliper and nucleus to cell area ratio were significantly greater in tumors with low BAP-1 expression and gene expression class 2. Patients had significantly shorter survival if their tumors had low BAP-1 (Log-Rank p=0.002), gene expression class 2 (p=0.004), long nucleus perimeters (p=0.031), long nucleus max calipers (p=0.029) and high mean nucleus to cell area ratios (p=0.041) as defined in a training cohort and then tested in a validation cohort. In the validation cohort, long nucleus perimeters and long nucleus max calipers correlated with monosomy 3 (Pearson Chi-Square p=0.006 and p=0.009, respectively). Long nucleus perimeters also correlated with BAP-1 mutation (p=0.017). We conclude that digital morphometry can be fast and highly reproducible, that for the first time, morphometry parameters can be objectively quantitated in thousands of cells at a time in sub-μm resolutions, and that variables describing the shape and size tumor nuclei correlate to BAP-1 status, monosomy 3, gene expression class as well as patient survival.
Brain derived neurotrophic factor (BDNF) Val66Met polymorphism is not risk factor for bipolar disorder
Authors: Rai Vandana , Jamal Farhin , Kumar Pradeep
Published: October 2019

Bipolar disorder (BPD) is a psychiatric disease, characterized by the cycles of mania and depression. Several genetic studies investigated BDNF gene Val66Met polymorphism as risk factor for BPD, but results were inconclusive. Therefore, present meta-analysis was performed to reevaluate the BDNF Val66Met polymorphism and BPD association. Four databases (Pubmed, Springer Link, Science Direct and Google Scholar) were searched for eligible studies up to March 31,2018. Pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated to estimate the strength of the association. All statistical analyses were done by MetaAnalyst and Mix program. Forty studies with a total of 28,787 subjects (10,085 cases and 18,702 controls) were included in this meta-analysis. Overall, pooled analysis indicated that there was no significant association between BDNF Val66Met polymorphism and BPD risk under all five genetic models (ORA vs.G =0.99, 95%CI= 0.94-1.03, p=0.49; ORAG vs. GG= 0.1.02, 95%CI= 0.95-1.07, p= 0.57; ORAA vs. GG = 0.98, 95%CI=0.89-1.08, p=0.75; ORAA+AG vs. GG= 1.0, 95%CI= 0.94-1.06, p= 0.89;ORAA vs. AG+GG= 0.96, 95%CI= 0.89-1.05, p= 0.47). Similarly, no significant association was observed in ethnicity based subgroup analysis in both Asian and Caucasian population. However, significant association was found in subtype analysis between BDNF Val66Met and BPDII (ORAA+AG vs. GG= 1.21, 95%CI= 1.06-1.37, p= 0.003) but not with BPDI. These findings suggested that the BDNF Val66Met polymorphism confer no genetic susceptibility to BPD I but risk for BPDII.
Phylogenomic approaches reveal how a climatic inversion and glacial refugia shape patterns of diversity in an African rain forest tree species
Authors: Helmstetter Andrew J. , Amoussou Biowa E. N. , Bethune Kevin , Kandem Narcisse G. , Kakaï Romain Glèlè , Sonké Bonaventure , Couvreur Thomas L. P.
Published: October 2019

Abstract

The world’s second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity close to the equator at the level of a climatic inversion. Here, we take a phylogeographic approach using 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree speciesAnnickia affinis(Annonaceae). We show for the first time that the North-South divide is the result of a single major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggest that differences in ecological niche of populations distributed either side of this inversion may have contributed to this phylogenetic discontinuity. We find evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.
Reversed Signaling Flow of a Bacterial Pseudokinase
Authors: Kowallis Kimberly A. , Silfani Elayna M. , Kasumu Amanda P. , Rong Grace , So Victor , Childers W. Seth
Published: October 2019

Bacteria respond to environmental and cellular cues both through isolated signaling events between one sensor histidine kinase and its response regulator, and through more interconnected arrays.Caulobacter crescentusachieves asymmetric division through a network of histidine kinases, and here we interrogate a novel DivL pseudokinase reverse signaling mechanism that enables productive cross-talk across the network. A leucine zipper fusion method was used to synthetically stimulate reverse signaling between the sensor and kinase domains and directly test if reverse signaling could modulate the signaling networkin vivo. Stimulation of sensor-kinase helix conformational changes resulted in changes inC. crescentusmotility and DivL accumulation at the cell poles. The repurposed roles of the sensor domain in these processes were evaluated. We demonstrate that a domain of unknown function that binds to two scaffolding proteins, and two conserved signaling domains are employed as modulators of an active kinase. We propose that reversed signaling may be widely used across signaling enzymes.
Promises and pitfalls ofin vivoevolution to improve phage therapy
Authors: Bull James J , Levin Bruce R. , Molineux Ian J.
Published: October 2019

(Background) Phage therapy is the use of bacterial viruses (phages) to treat bacterial infections. Phages lack the broad host ranges of antibiotics, so individual phages are often used with no prior history of use in treatment. Therapeutic phages are thus often chosen based on limited criteria, sometimes merely an ability to plate on the pathogenic bacterium. It is possible that better treatment outcomes might be obtained from an informed choice of phages. Here we consider whether phages used to treat the bacterial infection in a patient might specifically evolve to improve treatment. Phages recovered from the patient could then serve as a source of improved phages or cocktails for use on subsequent patients. (Methods) With the aid of mathematical and computational models, we explore this possibility for four phage properties expected to promote therapeutic success:in vivogrowth, phage decay rate, overcoming resistant bacteria, and enzyme activity to degrade protective bacterial layers. (Results) Phage evolution only sometimes works in favor of treatment, and even in those cases, intrinsic phage dynamics in the patient are usually not ideal. An informed use of phages is invariably superior to reliance on within-host evolution and dynamics, although the extent of this benefit varies with the application.
The effect of individual learning on collective foraging in honey bees in complex environments
Authors: Lemanski Natalie J. , Cook Chelsea N. , Ozturk Cahit , Smith Brian H. , Pinter-Wollman Noa
Published: October 2019

The trade-off between exploiting known resources and exploring for new ones is a complex decision-making challenge, particularly when resource patches are variable in quality and heterogeneously distributed in the landscape. Social insect colonies navigate this challenge, in the absence of centralized control, by allocating different individuals to each of these tasks based on variation in individual behavior. To investigate how heritable differences in individual learning affect a colony’s collective ability to locate and choose among different quality food resources, we develop an agent based model and test its predictions using two genetic lines of honey bees, selected for differences in their learning behavior. Here we show that, paradoxically, colonies containing individuals that are better at learning to ignore unrewarding stimuli are worse at choosing the highest quality resource at the collective level. This work highlights the importance of individual variation within groups on the emergence of collective behavior.
Climatic niche predicts the landscape structure of locally adaptive standing genetic variation
Authors: Chhatre Vikram E. , Fetter Karl C. , Gougherty Andrew V. , Fitzpatrick Matthew C. , Soolanayakanahally Raju Y. , Zalesny Ronald S. , Keller Stephen R.
Published: October 2019

Within a species’ range, intraspecific diversity in the form of adaptive standing genetic variation (SGV) may be non-randomly clustered into different geographic regions, reflecting the combined effects of historical range movements and spatially-varying natural selection. As a consequence of a patchy distribution of adaptive SGV, populations in different parts of the range are likely to vary in their capacity to respond to changing selection pressures, especially long-lived sessile organisms like forest trees. However, the spatial distribution of adaptive SGV across the landscape is rarely considered when predicting species responses to environmental change. Here, we use a landscape genomics approach to estimate the distribution of adaptive SGV along spatial gradients reflecting the expansion history and contemporary climatic niche of balsam poplar,Populus balsamifera(Salicaceae), a widely distributed forest tree with a transcontinental distribution in North America. By scanning the genome for signatures of spatially varying local adaptation, we estimated how adaptive SGV has been shaped by geographic distance from the rear range edge (expansion history) versus proximity to the current center of the climatic niche (environmental selection). We found that adaptive SGV was strongly structured by the current climatic niche, with surprisingly little importance attributable to historical effects such as migration out of southern refugia. As expected, the effect of the climatic niche on SGV was strong for genes whose expression is responsive to abiotic stress (drought), although genes upregulated under biotic (wounding) stress also contained SGV that followed climatic and latitudinal gradients. The latter result could reflect parallel selection pressures, or co-regulation of functional pathways involved in both abiotic and biotic stress responses. Our study in balsam poplar suggests that clustering of locally adaptive SGV within ranges primarily reflects spatial proximity within the contemporary climatic niche – an important consideration for the design of effective strategies for biodiversity conservation and avoidance of maladaptation under climate change.
DeepSeqPanII: an interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction
Authors: Liu Zhonghao , Jin Jing , Cui Yuxin , Xiong Zheng , Nasiri Alireza , Zhao Yong , Hu Jianjun
Published: October 2019

Human leukocyte antigen (HLA) complex molecules play an essential role in immune interactions by presenting peptides on the cell surface to T cells. With significant progress in deep learning, a series of neural network based models have been proposed and demonstrated with their good performances for peptide-HLA class I binding prediction. However, there still lack effective binding prediction models for HLA class II protein binding with peptides due to its inherent challenges. In this work, we present a novel sequence-based pan-specific neural network structure, DeepSeaPanII, for peptide-HLA class II binding prediction. Compared with existing pan-specific models, our model is an end-to-end neural network model without the need for pre- or post-processing on input samples. Besides state-of-the-art peformance in binding affinity prediction, DeepSeqPanII can also extract biological insight on the binding mechanism over the peptide and HLA sequences by its attention mechanism based binding core prediction capability. The leave-one-allele-out cross validation and benchmark evaluation results show that our proposed network model achieved state-of-the-art performance in HLA-II peptide binding. The source code and trained models are freely available at https://github.com/pcpLiu/DeepSeqPanII.
A chromosome-scale genome assembly of European Hazel (Corylus avellana L.) reveals targets for crop improvement
Authors: Lucas Stuart J. , Kahraman Kadriye , Avşar Bihter , Buggs Richard J.A. , Bilge Ipek
Published: October 2019

European hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially to northern Turkey, where the majority of production takes place. Hazelnut production is currently challenged by environmental stresses such as a recent outbreak of severe powdery mildew disease; furthermore, allergy to hazelnuts is an increasing health concern in some regions.

In order to provide a foundation for utilizing the available hazelnut genetic resources for crop improvement, we produced the first fully assembled genome sequence and annotation for a hazelnut species, from Corylus avellana cv. ‘Tombul’, one of the most important Turkish varieties. A hybrid sequencing strategy combining short reads, long reads and proximity ligation methods enabled us to resolve heterozygous regions and produce a high-quality 370 Mb assembly that agrees closely with cytogenetic studies and genetic maps of the 11 C. avellana chromosomes, and covers 97.8% of the estimated genome size. The genome includes 28,409 high-confidence protein-coding genes, over 20,000 of which were functionally annotated based on homology to known plant proteins. We focused particularly on gene families encoding hazelnut allergens, and the MLO proteins that are an important susceptibility factor for powdery mildew. The complete assembly enabled us to differentiate between members of these families and identify novel homologs that may be important in mildew disease and hazelnut allergy. These findings provide examples of how the genome can be used to guide research and develop effective strategies for crop improvement in C. avellana.
Finding genetic variants in plants without complete genomes
Authors: Voichek Yoav , Weigel Detlef
Published: October 2019

Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the genetic variants detected in GWAS to include major deletions, insertions, and rearrangements. We first use raw sequencing data directly to derive short sequences,k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then linkk-mers associated with phenotypes to specific genomic regions. Using this approach, we re-analyzed 2,000 traits measured inArabidopsis thaliana, tomato, and maize populations. Associations identified withk-mers recapitulate those found with single-nucleotide polymorphisms (SNPs), however, with stronger statistical support. Moreover, we identified new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allow detection of a wider range of genetic variants responsible for phenotypic variation.
Metabarcoding a Metacommunity: detecting change in a wetland wilderness
Authors: Bush A. , Monk W.A. , Compson Z.G. , Peters D.L. , Porter T.M. , Shokralla S. , Wright M.T.G. , Hajibabaei M. , Baird D.J.
Published: October 2019

The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large-scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed, and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification, and DNA metabarcoding. Using multi-species occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification, and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera, and for the first time, quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were near random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales, but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.
Asymmetric molecular architecture of the human γ-tubulin ring complex
Authors: Wieczorek Michal , Urnavicius Linas , Ti Shih-Chieh , Molloy Kelly R. , Chait Brian T. , Kapoor Tarun M.
Published: October 2019

The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation 1–4. Metazoan γ-TuRCs isolate as ∼2 MDa complexes containing the conserved proteins γ-tubulin, GCP2 and GCP3, as well as the expanded subunits GCP4, GCP5, and GCP6 3,5,6. However, in current structural models, γ-TuRCs assemble solely from subcomplexes of γ-tubulin, GCP2 and GCP3 7. The role of the metazoan-specific subunits in γ-TuRC assembly and architecture are not currently known, due to a lack of high resolution structural data for the native complex. Here, we present a cryo-EM structure of the native human γ-TuRC at 3.8Å resolution. Our reconstruction reveals an asymmetric, single helical-turn and cone-shaped structure built from at least 34 polypeptides. Pseudo-atomic models indicate that GCP4, GCP5 and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes and are distal to the γ-TuRC “seam”. Evolutionary expansion in metazoan-specific subunits diversifies the γ-TuRC by introducing large (>100,000 Å2) surfaces that could interact with different regulatory factors. We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric composition and architecture, the human γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g. within biological condensates 8 or alongside existing filaments 9.
The persuasive effects of emotional green packaging claims
Authors: Aagerup Ulf , Frank Anna-Sofia , Hultqvist Evelina
Published: October 2019

Purpose

The purpose of this paper is to investigate the effects of rational green packaging claims vs emotional green packaging claims on consumers’ purchase propensity for organic coffee.

Design/methodology/approach

Three within-subjects experiment were carried out (N=87, N=245, N=60). The experimental design encompasses packaging with rational green claims, emotional green claims, as well as a neutral (control) claim. Measured variables are introduced to assess participants’ environmental commitment and information processing ability. A manipulated between-subjects variable is introduced to test how distraction interacts with preference for the claims.

Findings

Overall, consumers prefer products with green claims over those with neutral (control) claims, and products with emotional green claims to those with rational green claims. The studies also reveal that this effect is moderated by participants’ environmental commitment, information processing ability and by distraction. The findings were statistically significant (p<0.05).

Research limitations/implications

As a lab experiment, the study provides limited generalizability and external validity.

Practical implications

For most organic FMCG products, it is advisable to employ emotional packaging claims.

Social implications

The presented findings provide marketers with tools to influence consumer behavior toward sustainable choices.

Originality/value

The paper validates previous contributions on the effects of product claim types, and extends them by introducing comprehensive empirical data on all the Elaboration Likelihood Model’s criteria for rational decision-making; motivation, opportunity and ability.
Investigation on human rights ethics in artificial intelligence researches with library literature analysis method
Authors: Miao Zeyi
Published: October 2019

Purpose

The purpose of this paper was to identify whether artificial intelligence (AI) products can possess human rights, how to define their rights and obligations and what ethical standards they should follow. In this study, the human rights ethical dilemma encountered in the application and development of AI technology has been focused on and analyzed in detail in the light of the existing research status of AI ethics.

Design/methodology/approach

In this study, first of all, the development and application of AI technology, as well as the concept and characteristics of human rights ethics, are introduced. Second, the human rights ethics of AI technology are introduced in detail, including the human rights endowment of AI machines, the fault liability of AI machines and the moral orientation of AI machines. Finally, the approaches to human rights ethics are proposed to ensure that AI technology serves human beings. Every link of its research, production and application should be strictly managed and supervised.

Findings

The results show that the research in this study can provide help for the related problems encountered in AI practice. Intelligent library integrates human rights protection organically so that readers or users can experience more intimate service in this system. It is a kind of library operation mode with more efficient and convenient characteristics, which is based on digital, networked and intelligent information science. It aims at using the greenest way and digital means to realize the reading and research of human rights protection literature in the literature analysis method.

Originality/value

Intelligent library is the future development mode of new libraries, which can realize broad interconnection and sharing. It is people-oriented and can make intelligent management and service and establish the importance of the principle of human rights protection and the specific idea of the principle. The development of science and technology brings not only convenience to people's social life but also questions to be thought. People should reduce its potential harm, so as to make AI technology continue to benefit humankind.
Empowerment, passion and job performance: implications from Ghana
Authors: Appienti William Ansah , Chen Lu
Published: October 2019

Purpose

Drawing upon the “too-much-of-a-good-thing (TMGT)” effect and conservation of resources (COR) theory, the purpose of this paper is to examine the mediation mechanism between empowering leadership and employee job performance. Specifically, the authors propose a curvilinear relationship between empowering leadership and job performance, and also suggest that employee harmonious and obsessive work passions mediate the curvilinear relationship between empowering leadership and job performance. Further the moderation role of collectivism orientation (CO) in the relationship between empowering leadership and job performance is also examined.

Design/methodology/approach

Questionnaires are used to obtain survey data from 256 supervisor–subordinate dyads in three companies in the communication sector of Ghana. A follow-up interview was also conducted to enhance explanation of research findings. Hierarchical regression analysis is used to analyze the associations among the variables.

Findings

The results revealed that the significant inverted U-shaped relationship between empowering leadership and subordinate job performance is mediated by both harmonious and obsessive passion for work. A significant moderation effect of CO in the empowering leadership–job performance relationship could not be established.

Originality/value

This study adapts the “TMGT” effect and COR theory in the explanation of an integrated model including empowering leadership, job performance, employee passion for work, and CO in the Ghanaian context.
Exploring blockchain implementation in the supply chain
Authors: van Hoek Remko
Published: October 2019

Purpose

There is great interest in blockchain in the supply chain yet there is little empirical research to support the consideration of the technology. Ferdows (2018) calls for research aimed at learning from pioneers in the field and Gartner points out that the interest in blockchain holds similarities to the interest surrounding RFID 15 years ago. As a result, there may be opportunities to leverage insights from RFID research to inform the consideration of blockchain. The purpose of this paper is to explore how the Reyeset al.(2016) framework for the implementation of RFID may inform the consideration of blockchain in the supply chain.

Design/methodology/approach

A two-stage approach is used to explore RFID implementation considerations from the Reyeset al.(2016) RFID implementation framework, using an initial exploration of managers interested in blockchain using a focus group and a survey and to more in depth explore three case companies pioneering blockchain.

Findings

Several RFID implementation considerations can inform the consideration of blockchain but there are also differences in considering blockchain. A framework is developed that details considerations found to be relevant by implementation stage.

Originality/value

This paper adds to the limited amount of empirical research on blockchain in the supply chain and advances research beyond the consideration of use cases into the exploration of actual implementation of blockchain in the supply chain. The decision framework developed both leverages and nuances findings from RFID research and can inform managerial decision making. It also adds to research a multi-stage approach to implementation and uncovers rich opportunity to further learn from pioneers.