bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (Capra species) breeds for the production of dairy, cashmere, and meat
Authors: Zhang Bao , Chang Liao , Lan Xianyong , Asif Nadeem , Guan Fanglin , Fu Dongke , Li Bo , Yan Chunxia , Zhang Hongbo , Zhang Xiaoyan , Huang Yongzhen , Chen Hong , Yu Jun , Li Shengbin
Published: August 2018

Background

The domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection have led to dramatic phenotypic purification and intermediate breeds for the high-quality production of dairy, cashmere wool, and meat. Genomic resequencing provides a powerful means for the direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication.

Results

Here, we report our effort to define such variations based on data from domestic goat breeds (Capra aegagrus hircus; five each) selected for dairy, cashmere, and meat production in reference to their wild ancestors, the Sindh ibex (Capra aegagrus blythi; two) and the Markhor (Capra falconeri; two). Using ~24 million high-quality single nucleotide polymorphisms (SNPs), ~1.9 million insertions/deletions, and 2,317 copy number variations, we define SNP-desert-associated genes (SAGs), domestic-associated genes (DAGs), and trait-associated genes (TAGs) and attempt to associate them with quantitative trait loci (QTL), domestication, and agronomic traits. A greater majority of SAGs shared by all domestic breeds are classified into Gene Ontology categories of metabolism and cell cycle. DAGs, together with some SAGs, are most relevant to behavior, immunity, and trait specificity. Whereas, TAGs such as growth differentiation factor 5 and fibroblast growth factor 5 for bone and hair growth, respectively, appear to be directly involved in growth regulation.

Conclusions

When investigating the divergence of Capra populations, the sequence variations and candidate function-associated genes we have identified provide valuable molecular markers for trait-driven genetic mapping and breeding.
Long-time Behavior of Solutions to Cubic Dirac Equation with Hartree Type Nonlinearity in ℝ1+2
Authors: Tesfahun Achenef
Published: August 2018

In this paper we study the long-time behavior of solutions to the Dirac equation $$\begin{equation*} \big ( -i\gamma^\mu \partial_\mu + m \big) \psi= \left(V \ast ( \overline \psi \psi)\right) \psi \ \ \textrm{in } \ {\mathbb{R}}^{1+2},\end{equation*}$$where $V$ is the Yukawa potential in ${\mathbb{R}}^{2}$. It is proved that if $m>0$ and the initial data is small in $H^s({\mathbb{R}}^2)$ for $s>0$, the corresponding initial value problem is globally well posed and the solution scatters to free waves asymptotically as $t \rightarrow \pm \infty $. The main ingredients in the proof are Strichartz estimates and space-time $L^2$-bilinear null-form estimates for free waves.
Neonatal outcomes among offspring of obese women diagnosed with gestational diabetes mellitus in early versus late pregnancy
Authors: Grotenfelt N E , Rönö K , Eriksson J G , Valkama A , Meinilä J , Kautiainen H , Stach-Lempinen B , Koivusalo S B
Published: August 2018

Background

Maternal metabolic derangements associated with early pregnancy gestational diabetes may affect the fetus differently compared with gestational diabetes diagnosed later in pregnancy. The aim of this observational study was to assess neonatal outcomes according to timing of gestational diabetes diagnosis in obese women.

Methods

Women ≥18 years of age with a pre-pregnancy body mass index ≥30 kg/m2 were grouped according to the results of a 75 g 2-h oral glucose tolerance test performed at 13.1 weeks of gestation and repeated at 23.4 weeks if normal at first testing. The main outcomes were birthweight and large for gestational age.

Results

Out of 361 women, 164 (45.4%) were diagnosed with gestational diabetes, 133 (81.1%) of them in early pregnancy. The mean offspring birthweight was 3673 g (standard deviation (SD) 589 g) in the early and 3710 g (SD 552 g) in the late gestational diabetes group. In a multivariate logit model, the odds ratio for large for gestational age was 2.01 (95% CI: 0.39–10.39) in early compared with late gestational diabetes.

Conclusions

We observed no statistically significant differences in neonatal outcomes according to timing of gestational diabetes diagnosis. In addition to lack of power, early treatment of hyperglycemia may partly explain the results.
RADIATION DOSE DETERMINATION IN ABDOMINAL CT EXAMINATIONS OF CHILDREN AT SUDANESE HOSPITALS USING SIZE-SPECIFIC DOSE ESTIMATES
Authors: Bashier Einas H , Suliman I I
Published: August 2018

In this study, we thought to estimate the radiation exposure of children undergoing multi-detector CT examinations using size-specific dose estimates (SSDE). Console-displayed volume computed tomography dose index (CTDIvol) were recorded for a total of 78 paediatric abdominal CT examinations performed in six hospitals. Measurements of the patient diameters were taken from the mid-slice location on the transverse and scout CT images. Size-specific conversion coefficients were used to translate CTDIvol to the SSDE, according AAPM Report 204. For children aged 0–1 y, CTDIvol, SSDEtrans (from transverse images) and SSDEsco (from scout images) were: 12.80 ± 16.10, 14.43 ± 13.22; and 14.37 ± 13.03 mGy; respectively. For children aged 1–5 y, CTDIvol, SSDEtrans and SSDEsco were: 12.11 ± 14.47, 18.8 ± 18.61 and 16.51 ± 13.55 mGy; respectively. The obtained doses are higher than the corresponding diagnostic reference levels. SSDE increase with patient size as results of tube current modulation and is therefore a valuable tool for dose optimisation.
Afraid to Notice: On Responding to Children with Visible Disabilities
Authors: Gennep Lindsey van
Published: August 2018

Pretending not to see these children can be the cruelest response.
Studies Document Reductions in Murder, Suicide Rates with Certain Gun Laws
Authors: Stockwell Serena
Published: August 2018

Permit-to-purchase and risk-based firearm seizure laws are effective approaches.
Jury Finds in Favor of Nurse Who Sued Brigham and Women's Hospital
Authors: Zolot Joan
Published: August 2018

Lawsuit describes retaliation after she stood up for a colleague.
The WHO Highlights Nurses’ Role in Reducing Noncommunicable Diseases
Authors: Mechcatie Elizabeth
Published: August 2018

Recommendations for ‘mobilizing the nursing workforce’ praised by the ICN.
In Memoriam: Shirley Fondiller
Authors: Kennedy Maureen Shawn
Published: August 2018

Shirley Fondiller
NPs Meet in Denver to ‘Move Mountains’
Authors: Kennedy Maureen Shawn
Published: August 2018

Theme and place come together at the AANP annual conference.
First Drug Approved to Reduce Bleeding Risk During Medical Procedures in Patients with Chronic Liver Disease
Authors: Aschenbrenner Diane S.
Published: August 2018

Avatrombopag (Doptelet) is now approved to treat thrombocytopenia in adults with chronic liver disease who are scheduled for a medical or dental procedure.

The drug has been associated with thrombotic and thromboembolic complications. Nurses should teach patients prescribed avatrombopag how to assess for blood clots.
First Oral Drug for Moderate-To-Severe Ulcerative Colitis
Authors: Aschenbrenner Diane S.
Published: August 2018

Immediate-release tofacitinib (Xeljanz) is now approved to treat moderate-to-severe ulcerative colitis.

Nurses should assess patients for infections prior to the initiation of and throughout tofacitinib treatment.
Failures in Precaution Practices are Common in Hospitals
Authors: Rosenberg Karen
Published: August 2018

According to this study:

Failures in use of standard and transmission-based precautions, which can lead to self-contamination and disease transmission, not only occur frequently during routine hospital care, they happen under a wide variety of circumstances.

A range of strategies is likely needed to address compliance with precautions and reduce transmission risk.
Nursing Simulation and Transfer of Knowledge in Undergraduate Nursing Programs: A Literature Review
Authors: Alt-Gehrman Penny
Published: August 2018

AIM

The purpose of this literature review was to describe what research has been conducted on transfer of knowledge using high-fidelity patient simulation (HFPS) and determine what further research is needed.

BACKGROUND

The use of HFPS has expanded rapidly in recent years. There is research suggesting that HFPS effectively educates nurses for clinical practice.

METHOD

An extensive literature search was conducted and analyzed for themes. Exclusion criteria were studies that focused only on graduate-level nursing education, accelerated programs, medical students, registered nurses, and use of low-fidelity simulation or standardized patients.

RESULTS

Themes that emerged included competence, confidence, safety, timing, method and delivery. Study results varied, with only some showing transfer.

CONCLUSION

More research is needed to determine how HFPS influences knowledge transfer to the clinical setting.
Innovation in Clinical Course Delivery and Impact on Students’ Clinical Decision-Making and Competence
Authors: Woda Aimee , Schnable Theresa , Alt-Gehrman Penny , Bratt Marilyn Meyer , Garnier-Villarreal Mauricio
Published: August 2018

The purpose of this study was to explore the differences in clinical decision-making and clinical competence between two different cohorts of graduating baccalaureate nursing students from a traditional prelicensure program in the United States. A quasi-experimental design was used to compare students who had substituted their traditional medical-surgical clinical experiences with simulation (Cohort 1, n = 35) with students who had supplementary simulation in addition to their traditional clinical experiences (Cohort 2, n = 36). The findings demonstrated that when simulation was used as a supplement to traditional clinical experiences, participants performed better patient assessments.
Predicting Procedure-specific Morphine Consumption of Intravenous Patient-controlled Analgesia With Random-effect Model Approach
Authors: Lin Shih-Pin , Chang Kuang-Yi , Chen Hsiu-Hsi , Tsou Mei-Yung
Published: August 2018

Introduction:

Surgical procedure is an important predictor for analgesic consumptions of intravenous patient-controlled analgesia (IV-PCA) for acute pain.

Objectives:

The aim of this study was to better fit the analgesic consumptions of IV-PCA with regard to the different surgical procedures.

Materials and Methods:

A statistical model (random-effect model) was proposed to develop procedure-specific morphine consumptions for various surgical procedures of IV-PCA. After the model was developed, an independent data set was used for external validation.

Results:

The results showed a significant influence for morphine consumption coming from surgical procedures. Different surgical procedures resulted in a wide range of morphine consumptions. The surgical procedure with the highest morphine consumption was the resection of the pancreas with open approach (76.92 mg), while the lowest one was for the excision of the uterus with open method (34.3 mg). The external validation showed good model performance. The quantitative rank for surgical procedures was also presented.

Discussion:

Adopted IV-PCA regimens for different surgical procedures are therefore strongly recommended and incorporated into postoperative acute pain management.
Improving Neonatal Outcomes Through Global Professional Development
Authors: Riley Cheryl , Spies Lori A. , Prater Lyn , Garner Shelby L.
Published: August 2018

Background:

Globally, stillbirths account for 2.7 million infant deaths each year, with the vast majority occurring in sub-Saharan Africa and South Asia. Approximately 900,000 infants die due to birth asphyxia. The focus of the Helping Babies Breathe (HBB) program is to help the nonbreathing infant to breathe within the first minute of life, termed the “Golden Minute.”

Purpose:

To present a multinational interprofessional development program utilizing the train-the-trainer methodology for HBB to address neonatal morbidity and mortality. Involving nursing students in collaboration with established global partners provided an innovative method of professional development. Lessons learned and challenges will be shared to enhance success of future efforts.

Project Implementation:

HBB train-the-trainer workshops were held to provide professional development for nurses and nursing students in 5 locations in 4 countries including Ethiopia, India, Vietnam, and Zambia. Workshop participants and the trainers participated in discussions and informal conversation to assess impact on professional development.

Results:

HBB training and train-the-trainer workshops were implemented in 4 counties. Equipment and supplies were provided in these countries through several internal university grants. All 145 participants demonstrated increased knowledge and skills at the end of the workshops through the HBB check off. Collaborative teaching and cross-cultural professional skills were enhanced in student and faculty trainers.

Implications for Practice:

Nurses, midwives, and advance practice nurses can engage globally and contribute to closing this gap in knowledge and skills by providing train-the-trainer workshops.

Implications for Research:

Developing systems to integrate the HBB program within each country's existing healthcare infrastructure promotes in-country ownership. Joining the global effort to save the lives of neonates can be a meaningful opportunity for innovative professional development projects. While HBB education has been shown to save lives, a 1-time training is insufficient. Determining how often HBB updates or refreshers are required to maintain skills is an important next step. Another direction for research is to implement this project within prelicensure nursing programs.
Dermatomyositis etiopathogenesis: a rebel soldier in the muscle
Authors: Pinal-Fernandez Iago , Mammen Andrew L.
Published: August 2018

Purpose of review

The purpose of this article is to review the etiopathogenesis of dermatomyositis, including the predisposing factors, triggers, inflammatory cells, pathways and target antigens associated with dermatomyositis.

Recent findings

During the last few years, we have made considerable progress in unveiling the etiopathogenesis of dermatomyositis. In the first place, we have defined genes within the major histocompatibility complex locus as the greatest genetic risk factor for the disease. Second, we have demonstrated that certain environmental factors, as well as tumors, may trigger certain dermatomyositis subtypes. Moreover, we have established the importance of the interferon pathway in dermatomyositis pathogenesis compared with other myositis subtypes. But probably, the most remarkable advance has been the discovery of multiple autoantibodies that define groups of patients with characteristic clinical features, prognosis and response to treatment.

Dermatomyositis cause and pathogenesis have proven to be a complex and fascinating task for the scientific community and the last decade has been full of new findings on how the disease starts and how it causes damage to different organ systems. However, we have still more questions than answers in this topic, answers that will be critical to understanding autoimmunity and finding effective therapies to dermatomyositis.
Attitudes of Spine Surgeons Regarding Management of Preoperative Anxiety
Authors: Musa Arif , Wang Jeffrey C. , Acosta Frank L. , Movahedi Rana , Melkonian Adana , Shahbazi Alan , Safani David , Gucev Gligor
Published: August 2018

Study Design:

This is a cross-sectional study.

Objective:

To investigate spine surgeons’ attitudes regarding preoperative anxiety measurement, management, and responsibility.

Summary of Background Data:

The vast majority of patients scheduled for spine surgery experience preoperative anxiety. However, there are currently no consensus guidelines for measure or management of preoperative anxiety in spinal operations.

Materials and Methods:

An anonymous questionnaire was sent online to spine surgeons of AO Spine North America to capture their views regarding preoperative anxiety.

Results:

Of 69 complete responses, most respondents were male (n=66, 95.7%), orthopedic surgeons (n=52, 75.4%), and practicing at an academic setting (n=39, 56.5%). Most spine surgeons practiced for at least 20 years (n=52, 75.4%), operated on 100–300 patients per year (n=48, 69.6%), and were attending physicians (n=61, 88.4%). Most did not measure preoperative anxiety (n=46, 66.7%) and would not use a rating scale to measure it (n=38, 55.1%). However, most would discuss it if mentioned by the patient (n=40, 58.0%). Other spine surgeons measured anxiety verbally (n=22, 31.9%) or with a rating scale or survey (n=6, 8.7%). Although preferences for preoperative anxiety management varied, most respondents used patient education (n=54, 78.3%) and permitting family members’ presence (n=36, 52.2%) to reduce patient anxieties. Spine surgeons held themselves, anesthesiologists, and patients most responsible to manage preoperative anxiety.

Conclusions:

The majority of spine surgeons surveyed did not regularly measure preoperative anxiety, but would discuss its management if the subject was broached by the patient. Spine surgeons relied on a variety of methods to manage a patient’s anxiety, but most preferred preoperative education and permitting the presence of family members. Responsibility for controlling preoperative anxiety was chiefly allocated to surgeons, anesthesiologists, and patients. Future avenues for research may include developing a preoperative anxiety measurement scale and management protocol specific to spine surgery.

Level of Evidence:

Level IV.
Molecular classification of adult gliomas: recent advances and future perspectives
Authors: Barritault Marc , Meyronet David , Ducray François
Published: August 2018

Purpose of review

This review summarizes recent advances in the molecular classification of adult gliomas.

Recent findings

According to the 2016 WHO classification, five main molecular subgroups of adult diffuse gliomas can be distinguished based on the 1p/19q codeletion, isocitrate dehydrogenase (IDH), and histone H3.3 mutation status. In the future, this classification may be further refined based on the integration of additional biomarkers, in particular CDKN2A/B homozygous deletion in IDH-mutant astrocytomas, TERT promoter mutations, EGFR amplification, chromosome 7 gain and chromosome 10 loss in IDH-wildtype astrocytomas, and FGFR1 mutations in midline gliomas. Histone H3.3 G34R/V defines a distinct subgroup of hemispheric IDH-wildtype high-grade gliomas occurring in young patients and FGFR gene fusions characterize a subgroup of IDH-wildtype glioblastomas that could benefit from specific treatment approaches. RNA sequencing may identify targetable gene fusions in circumscribed gliomas lacking classical BRAF alterations. In chordoid gliomas, recurrent PRKCA mutations could serve as a new diagnostic marker. Among comprehensive molecular analysis methods, DNA methylation profiling appears as a particularly powerful approach to identify new molecular subgroups of gliomas and to classify difficult cases.

The classification of adult gliomas may be improved by the integration of additional biomarkers and/or by comprehensive molecular analysis, in particular DNA methylation profiling. The most relevant approach, however, remains to be established.
Development of AN On-site, Rapid, Environmental Radiation-distribution Monitoring System for Decision Making during a Radiation Emergency
Authors: Lee UkJae , Kim Hee Reyoung
Published: August 2018

An on-site, rapid, measurement-based, radiation-distribution visualization system with radionuclide recognition was developed for quick decision making during a radiation emergency. After scanning of the area was complete, radionuclide-specific radiation-distribution contours were displayed in two and three dimensions on a map of the measurement area, in a few tens of seconds, by clicking once on an execution file, which was programmed using MathWorks’ MATLAB software. The contours were fundamentally verified using 137Cs and 60Co standard sources. Radiation distribution in the measurement area was simultaneously displayed in the main office using code division multiple access. It was demonstrated that rapid decision making for public safety is possible through the prompt display of radiation distribution in a nuclear emergency environment. This can also be applied to establish an environmental restoration plan for decontamination and decommissioning of nuclear power plants.
Optimization of the ICRP 67 and NCRP 156 Transfer Rates Applied to Nonhuman Primates Intramuscularly Injected With 241Am
Authors: Alomairy Nada A. , Brey Richard R. , Guilmette Raymond A.
Published: August 2018

Nonhuman primates intramuscularly injected with 241Am have been investigated using the International Commission on Radiological Protection Report 67 model coupled with National Council on Radiation Protection and Measurements Report 156 model. Default parameters from these models were input into the Integrated Modules for Bioassay Analysis software to predict the intake and skeleton retention in 20 tested nonhuman primates. The predictions generated were compared to the experimental data from the Durbin nonhuman primate studies. A previous study conducted by Alomairy in 2017 indicated that the early behavior of 241Am(NO3)3 in wound cases can be explained using the default transfer rates. However, these transfer rates were not able to predict the intake and skeleton retention at the time of sacrifice after 100 d postintake due to differences in the amount of activity translocated or deposited in liver tissue and nonliver tissues (primarily skeleton). This is likely due to the physiological differences between the nonhuman primate and human. The objective of this study was to develop new transfer rate parameters for wound and systemic models in an effort to improve biokinetic predictions. Estimates of new transfer rates appropriate for nonhuman primate data were estimated by employing a companion software program called Integrated Modules for Bioassay Analysis Uncertainty Analyzer. During validation of the suggested transfer rates, it was observed that the optimized parameters predicted the intake in 66% of the tested animals used in this investigation. The activity retained in the skeleton improved in almost all cases where the differences between predicted and measured activity is less than 20%.
A Holistic Approach to Assessment of Population Exposure to Radiation: Challenges and Initiatives of a Regulatory Authority
Authors: Askounis P. , Boziari A. , Carinou E. , Drikos G. , Economides S. , Hourdakis C.J. , Housiadas C. , Kalathaki M. , Kamenopoulou V. , Karabetsos E. , Kehagia K. , Kolovou M. , Koukorava C. , Lasithiotakis M. , Makridakis T. , Maltezos A. , Mitrakos D. , Nikolaki M. , Nikolaou M. , Nicolaou P. , Petri A. , Potiriadis C. , Raftopoulos S. , Simantirakis G. , Tafili V. , Veltsos C. , Vogiatzi S. , Xarchoulakos D.C. , Zourari K.
Published: August 2018

A regulatory authority for radiation safety should continuously evaluate and improve the national safety framework, in line with current requirements and standards. In this context, the Greek Atomic Energy Commission initiated a series of concerted actions. The radiation dose to the population due to public and medical exposures was assessed. The assessment of dose due to public exposure was based on measurements of radon concentrations in dwellings, radionuclide concentrations in environmental samples, and air dose rates; the assessment of dose due to medical exposure was based on dose measurements for typical examinations or procedures and data on their frequency. The mean effective dose to a member of the population was found to be 4.5 mSv (1.8 mSv and 2.7 mSv from medical and public exposures, respectively). Regarding occupational exposure, aircrew dose assessment, eye lens monitoring, and the national dose registry were significantly improved. With respect to artificial tanning (sun beds), the ultraviolet radiation produced was assessed and the practices followed were observed. Results demonstrated exceedance of the 0.3 W m−2 erythema effective irradiance limit set in European Union standards by 63.5% of the sun beds measured, along with general noncompliance with standards. An overarching activity was the upgrade of the Greek Atomic Energy Commission information system in order to collect and disseminate radiation data electronically, launch a networking strategy for interaction with stakeholders, and facilitate the process of regulatory control. In response to the above findings, regulatory actions have been initiated.
Characterization of Prosthetic Liner Products for People with Transtibial Amputation
Authors: Cagle John C. , Hafner Brian J. , Taflin Nicholas , Sanders Joan E.
Published: August 2018

Introduction

Typical practitioners choose from among only two to three products when selecting liners for their patients. A lack of comparable objective information about similarities and differences among elastomeric liner products may be part of the reason.

Methods

Commonly used, commercially available polyurethane, silicone, and thermoplastic elastomer (TPE) liners were tested for their compressive, shear, tensile, and volumetric elasticities as well as their coefficients of friction (CoFs) and thermal conductivities.

Results

Polyurethane and silicone liners tended to be stiffer in compression and shear than TPE liners. Fabric backings contributed primarily to increased tensile elasticity (and thus reduced pistoning). Polyurethane liners demonstrated relatively low CoFs, whereas silicone and TPE liners had higher CoFs and wider ranges. All materials tested were essentially incompressible. Thermal conductivities of all materials were comparable and similar to that of leather.

Conclusions

Polyurethane liners are softer and less sticky than 16 years ago, and TPE liners have higher tensile stiffness than previously. A stiff fabric backing can increase tensile stiffness by more than 200%. Compressive stiffness may be used to characterize a liner’s ability to flow. Elastomeric liners move heat almost exclusively via conduction.
Can infected pancreatic necrosis really be managed conservatively?
Authors: Al-Sarireh Bilal , Mowbray Nicholas G. , Al-Sarira Ali , Griffith David , Brown Timothy H. , Wells Toby
Published: August 2018

Objectives

Guidelines advocate minimally invasive drainage rather than open surgery for infected pancreatic necrosis (IPN) after acute pancreatitis. We hypothesized that the conservative approach could be extended even further by treating patients using an antibiotics-only protocol.

Patients and methods

Between June 2009 and July 2017, patients with IPN were selectively managed with carbapenem antibiotics for a minimum of 6 weeks. We compared these patients with patients who underwent minimal access retroperitoneal pancreatic necrosectomy (MARPN) for IPN to identify characteristics of this patient group.

Results

Of 33 patients with radiologically proven IPN, 13 patients received antibiotics without any surgical or radiological intervention and resulted in no disease-specific mortality and one case of pancreatic insufficiency. In comparison, 44 patients underwent MARPN with a mortality of 20%, and 81.8% developed pancreatic insufficiency. The modified Glasgow score and computed tomography severity score was less in the antibiotic-only group (P<0.001 and P=0.014, respectively). Patients who underwent MARPN had lower serum haemoglobin and albumin levels (P=0.030 and 0.001, respectively), and a higher C-reactive protein (P=0.027).

Conclusion

Conservative treatment of IPN with antibiotics is a valid management option for haemodynamically stable patients experiencing less severe disease, requiring careful selection by experienced clinicians.
High frequency of secondary, but not primary ocular manifestations of inflammatory bowel disease in patients treated at a tertiary care center
Authors: Walldorf Jens , Twarz Maria , Schober Celestina , Michl Patrick , Hammer Thomas
Published: August 2018

Objective

Ocular manifestations of inflammatory bowel disease (IBD) are relevant complications of IBD. Only a few prospective studies are available on the characteristics of these manifestations. The aim of this study was to characterize the frequency of eye disease in patients with IBD, including primary and secondary ocular manifestations of IBD, and to identify patients who may need specialized ophthalmologic care.

Patients and methods

In a prospective observational study, patients with IBD were examined for ocular symptoms in comparison with control participants without IBD. All patients with IBD underwent a thorough ophthalmologic examination (including slit-lamp, tonometry, tear breakup time, Schirmer’s test, and coherence tomography). The results were analyzed with respect to sociodemographic and disease-related characteristics.

Results

A total of 61 patients (33 women, 39 Crohn’s disease, 22 ulcerative colitis, age 43.3±12.9 years, disease duration 12.4±9.3 years) were included. Ophthalmologic symptoms were reported by 53 patients (86.9%, most frequently deterioration of vision 42.6%, foreign body sensation 36.1%) compared with 60.6% in healthy controls (P=0.001). A clinically relevant, previously undetected ophthalmologic diagnosis was identified in 56 patients (91.8% – dry eye syndrome 75.4%, cataract 67.2%, blepharitis 45.9%, fundus hypertonicus 14.8%, other 16.4%).

Conclusion

Although primary ocular manifestations of IBD are rare in intensively treated patients, the high frequency of unrecognized secondary manifestations should give reason to refer especially patients with longstanding or complicated IBD to an eye specialist – irrespective of ocular symptoms.
Surfactants Improve Live Cell Imaging of Human Pancreatic Islets
Authors: Komatsu Hirotake , Omori Keiko , Kandeel Fouad , Mullen Yoko
Published: August 2018

Objectives

Newport Green is a zinc-specific fluorescent dye developed to monitor cellular zinc transport. In pancreatic islets with zinc-rich β-cells, Newport Green is expected to be useful as an islet-specific indicator for live imaging. However, the low penetration of Newport Green into islets hinders clear detection. The aim of this study was to develop a practical method of live islet imaging by using surfactants to enhance the penetration efficiency.

Methods

Surfactants (F127, Tween 20, and Triton X-100) were co-incubated with Newport Green for fluorescent imaging of live isolated human islet and nonislet tissues. Toxicity, enhancement of Newport Green fluorescence, and effects on specificity to islets were examined.

Results

Newport Green fluorescent intensity was increased after co-incubation with all surfactants tested (0.2–3.2 mM); however, surfactants were toxic to islets at high concentrations. Within the nontoxic range, high specificity to islets was observed when co-incubated with Tween 20 at 0.2–0.4 mM, compared with F127 and Triton X-100. This optimized range successfully distinguished islets from nonislet tissues using statistically calculated cutoff value of Newport Green fluorescent intensity.

Conclusions

Surfactants, particularly Tween 20 in the optimized range, effectively and selectively enhanced Newport Green fluorescence in live islets without increasing islet toxicity.
Resilience and Its Predictors Among Chinese Liver Cancer Patients Undergoing Transarterial Chemoembolization
Authors: Li Caixia , Lu Huijuan , Qin Wei , Li Xiaorong , Yu Jingxian , Fang Fang
Published: August 2018

Background

Although resilience has many positive effects on cancer patients, little is known about the level of resilience and its predictors in Chinese liver cancer patients undergoing transarterial chemoembolization (TACE).

Objective

The aims of this study were to evaluate resilience level and identify its predictors among Chinese liver cancer patients undergoing TACE.

Methods

Two hundred fifty-one patients were recruited from a tertiary hospital in Shanghai, China. According to Kumpfer's resilience framework, participants were assessed with Connor-Davidson Resilience Scale, Demographic and Disease-Related Information, Family Apgar Scale, Social Support Rating Scale, Herth Hope Index, General Self-efficacy Scale, and Simplified Coping Style Questionnaire. Multiple regression analysis was conducted to find predictors of resilience.

Results

The average score for Connor-Davidson Resilience Scale was 70.33 (11.70). Multiple regression identified that educational level, time span since diagnosis, family function, social support, hope, self-efficacy, and positive coping strategies predicted higher resilience, whereas metastasis predicted lower resilience. These predictors accounted for 61.8% of the total variance in resilience.

Conclusions

Resilience in liver cancer patients undergoing TACE needs to be further improved, which was positively predicted by educational level, time span since diagnosis, family function, social support, hope, self-efficacy, and positive coping strategies, but was negatively predicted by metastasis. Hope had the largest influence on resilience.

Implications for Practice

Interventions aimed to improve hope are crucial to patients' resilience. Additional attention should be given to patients who had lower educational level or had metastasis. Family-centered interventions and strategies used to strengthen self-efficacy and positive coping strategies are also important in improving patients' resilience.
Universal Lynch Syndrome Screening Should be Performed in All Upper Tract Urothelial Carcinomas
Authors: Ju Jennifer Y. , Mills Anne M. , Mahadevan Mani S. , Fan Jinbo , Culp Stephen H. , Thomas Martha H. , Cathro Helen P.
Published: August 2018

Lynch syndrome (LS) is defined by germline mutations in DNA mismatch repair (MMR) genes, and affected patients are at high risk for multiple cancers. Reflexive testing for MMR protein loss by immunohistochemistry (IHC) is currently only recommended for colorectal and endometrial cancers, although upper tract urothelial carcinoma (UTUC) is the third-most common malignancy in patients with LS. To study the suitability of universal MMR IHC screening for UTUC, we investigated MMR expression and microsatellite status in UTUC in comparison to bladder UC (BUC), and evaluated the clinicopathologic features of UTUC. We found that 9% of UTUC showed MMR IHC loss (8 MSH6 alone; 1 MSH2 and MSH6; 1 MLH1 and PMS2; n=117) compared with 1% of BUC (1 MSH6 alone; n=160) (P=0.001). Of these, 4/10 (40%) of UTUC (3% overall; 3 MSH6 alone; 1 MLH1 and PMS2) and none (0%) of BUC had high microsatellite instability on molecular testing (P=0.03). The only predictive clinicopathologic feature for MMR loss was a personal history of colorectal cancer (P=0.0003). However, UTUC presents at a similar age to colon carcinoma in LS and thus UTUC may be the sentinel event in some patients. Combining our results with those of other studies suggests that 1% to 3% of all UTUC cases may represent LS-associated carcinoma. LS accounts for 2% to 6% of both colorectal and endometrial cancers. As LS likely accounts for a similar percentage of UTUC, we suggest that reflexive MMR IHC screening followed by microsatellite instability testing be included in diagnostic guidelines for all UTUC.
Pollinator size and its consequences: Predictive allometry for pollinating insects
Authors: Kendall Liam K. , Rader Romina , Gagic Vesna , Cariveau Daniel P. , Albrecht Matthias , Baldock Katherine C. R. , Freitas Breno M. , Hall Mark , Holzschuh Andrea , Molina Francisco P. , Morten Joanne M. , Pereira Janaely S. , Portman Zachary M. , Roberts Stuart P. M. , Rodriguez Juanita , Russo Laura , Sutter Louis , Vereecken Nicolas J. , Bartomeus Ignasi
Published: August 2018

Body size is an integral functional trait that underlies pollination-related ecological processes, yet it is often impractical to measure directly. Allometric scaling laws have been used to overcome this problem. However, most existing models rely upon small sample sizes, geographically restricted sampling and have limited applicability for non-bee taxa. Predictive allometric models that consider biogeography, phylogenetic relatedness and intraspecific variation are urgently required to ensure greater accuracy.

Here, we measured body size, as dry weight, and intertegular distance (ITD) of 391 bee species (4035 specimens) and 103 hoverfly species (399 specimens) across four biogeographic regions: Australia, Europe, North America and South America. We updated existing models within a Bayesian mixed-model framework to test the power of ITD to predict interspecific variation in pollinator dry weight in interaction with different co-variates: phylogeny or taxonomy, sexual dimorphism and biogeographic region. In addition, we used ordinary least squares (OLS) regression to assess intraspecific dry weight – ITD relationships for 10 bee and five hoverfly species.

Including co-variates led to more robust interspecific body size predictions for both bees (BayesianR2: 0.946; ΔR20.047) and hoverflies (BayesianR2: 0.821; ΔR20.058) relative to models with ITD alone. In contrast, at the intraspecific level, our results demonstrate that ITD is an inconsistent predictor of body size for bees (R2: 0.02 – 0.66) and hoverflies (R2: −0.11 – 0.44).

Therefore, predictive allometry is more suitable for interspecific comparative analyses than assessing intraspecific variation. Collectively, these models form the basis of the dynamicRpackage, ‘pollimetry’, which provides a comprehensive resource for allometric research concerning insect pollinators worldwide.
Characterization of emetic and diarrheal Bacillus cereus strains from a 2016 foodborne outbreak using whole-genome sequencing: addressing the microbiological, epidemiological, and bioinformatic challenges
Authors: Carroll Laura M. , Wiedmann Martin , Mukherjee Manjari , Nicholas David C. , Mingle Lisa A. , Dumas Nellie B. , Cole Jocelyn A. , Kovac Jasna
Published: August 2018

The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) has not been routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group strains were obtained from human cases (n =7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (clade III) and B. cereus sensu stricto (clade IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely-related and formed a well-supported clade relative to publicly-available emetic clade III genomes with an identical sequence type (ST 26). When compared to publicly-available emetic clade III ST 26 B. cereus group genomes, the 30 emetic clade III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly-available genomes by a mean of 301.7 to 528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. Based on both WGS and epidemiological data, we hypothesize that the outbreak was a single source outbreak caused by emetic clade III B. cereus belonging to the B. paranthracis species. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.
“Global Transcriptional Response to CRISPR/CAS9-AAV6 Based Genome Editing” Matches Transcriptional Response to Specific Small Molecule Perturbations
Authors: Nordor Akpéli V. , Aryee Martin J. , Siwo Geoffrey H.
Published: August 2018

Cromer et al. [1] recently reported global transcriptional changes occuring in cells in response to CRISPR/Cas9 gene editing. Using a CD34+ hematopoietic and progenitor stem cell model, they observed differentially expressed genes enriched for immune, stress and apoptotic processes following treatment with a CRISPR/Cas9-AAV6 genome-editing system. Following treatment with Cas9’s mRNA they observed transcriptional changes enriched for viral response as well as a downregulation of metabolic and cell cycle processes. Similarly, they observed a downregulation of metabolic processes in response to electroporation. Surprisingly, no enrichment for viral response genes was observed following treatment with AAV6 while minor transcriptional changes enriched for DNA damage signature occurred in response to Cas9/sgRNA ribonucleoprotein.
Structural insights into unique features of the human mitochondrial ribosome recycling
Authors: Koripella Ravi K. , Sharma Manjuli R. , Risteff Paul , Keshavan Pooja , Agrawal Rajendra K.
Published: August 2018

Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation or energy (ATP) generation. Despite their proposed bacterial origin, the composition and structure of the human mitoribosome and its translational factors are dramatically different from their bacterial counterparts. The mammalian mitoribosome recycling factor (RRFmt) carries a mito-specific N-terminus extension (NTE), which is necessary for the function of RRFmt. Here we present a 3.7 Å resolution cryo-EM structure of the human 55S mitoribosome-RRFmt complex, which reveals α-helix and loop structures for a portion of the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNAs segments that constitute the peptidyl transferase center (PTC), those that connect PTC with the GTPase-associated center, and with multiple mitoribosomal proteins. Our structure also reveals novel conformational changes in mitoribosome due to RRFmt binding. Together, these findings help understand the unique features of mitoribosome recycling.
nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data
Authors: Steven Schmid , Timothy R. Julian , Manu Tamminen
Published: August 2018

Advancements in DNA sequencing technologies rapidly change the landscape of modern biology. The novel next-generation sequencing (NGS) applications often have special requirements regarding experimental data processing. Software tools developed and used for novel applications are generally designed for specific use cases and as such may be difficult to adapt to new uses. Simultaneously, software tools designed to be general are often difficult to adapt to special use cases.

Here, we present nsearch, a modern open source C++11 library and command-line tool for biological sequence data processing. nsearch offers commonly used components for handling of biological sequences including paired-end read merging, quality filtering and sequence similarity searching. nsearch can either be embedded natively into other C++ applications or be packaged as a standalone executable.

Functionality and performance of nsearch is shown using benchmark data created using the Rfam 13 database. Benchmarking against common general purpose tools USEARCH and VSEARCH demonstrates that nsearch delivers performance comparable these state-of-the-art tools.

nsearch is available on GitHub under the permissive BSD-3-clause license: https://github.com/stevschmid/nsearch
A simple cloning-free method to efficiently induce gene expression using CRISPR/Cas9
Authors: Fang Lyujie , Hung Sandy S.C. , Yek Jennifer , Nguyen Tu , Khan Shahnaz , Hewitt Alex W , Wong Raymond C.B.
Published: August 2018

Gain-of-function studies often require the tedious cloning of transgene cDNA into vectors for overexpression beyond the physiological expression levels. The rapid development of CRISPR/Cas technology presents promising opportunities to address these issues. Here we report a simple, cloning-free method to induce gene expression at endogenous locus using CRISPR/Cas9 activators. Our strategy utilises synthesized sgRNA expression cassettes to direct a nuclease-null Cas9 complex fused with transcriptional activators (VP64, p65 and Rta) for site-specific induction of endogenous genes. This strategy allows rapid initiation of gain-of-function studies in the same day. Using this cloning-free approach, we tested two CRISPR activation systems, dSpCas9VPR and dSaCas9VPR, for induction of multiple genes in human and rat cells. Our results showed that both CRISPR activators allow efficient induction of six different neural development genes (CRX, RORB, RAX, OTX2, ASCL1 and NEUROD1) in human cells, whereas the rat cells exhibit a more variable and less efficient levels of gene induction, as observed in three different genes (Ascl1, Neurod1, Nrl). Altogether, this study provides a simple method to efficiently activate endogenous gene expression using CRISPR/Cas9 activators, which can be applies as a rapid workflow to initiate gain-of-function studies for a range of molecular and cell biology disciplines.
Influence of crystal structure defects on the small-angle neutron scattering/diffraction patterns of clay-rich porous media
Authors: Ferrage Eric , Hubert Fabien , Baronnet Alain , Grauby Olivier , Tertre Emmanuel , Delville Alfred , Bihannic Isabelle , Prêt Dimitri , Michot Laurent J. , Levitz Pierre
Published: August 2018

Analysing the structure and microstructure of compacted swelling clay minerals is important because of the applications of these minerals in engineering and environmental sciences. Given the typical sub-micrometre size of the particles and pores in clays, small-angle scattering techniques are well suited for such analysis. Interpretation of the intensity patterns, however, remains complex, especially in the intermediate region between the first Bragg peak and the small-angle range. In this study, theoretical small-angle neutron scattering and neutron diffraction patterns are calculated for three-dimensional virtual porous media representative of packed swelling clay particles (i.e. 0.1–0.2 µm size fraction of vermiculite). This packing represents the distribution of the size, shape and particle orientation of a bulk vermiculite sample, for which experimental scattering/diffraction patterns were also collected. It was found that a good fit between the experimental and calculated scattering/diffraction profiles can be obtained only if the presence of crystal-structure defects in the particles is considered. The existence of such defects was supported by transmission electron microscopy analysis. Their influence on power law exponents extracted from intensity profiles is assessed in detail. The analysis is further extended to the influence of mineral dehydration and particle orientation on the intensity profiles. This work shows that using virtual porous media as toy models makes it possible to evaluate the roles of different microstructural parameters in the extent of variation of power law exponents. Such knowledge can be used for better interpretation of small-angle scattering data of natural compacted swelling clay-rich media.