bluuebunny/crossref_metadata_2025 huggingface dataset:
Robotic Nipple-sparing Mastectomy and Immediate Breast Reconstruction with Gel Implant
Authors: Lai Hung-Wen , Lin Shih-Lung , Chen Shou-Tung , Chen Shu-Ling , Lin Ya-Ling , Chen Dar-Ren , Kuo Shou-Jen
Published: June 2018

Background:

The experience of application of robotic surgery platform in the management of breast cancer was limited. The preliminary experience and results of robotic nipple-sparing mastectomy (R-NSM) and immediate breast reconstruction (IBR) with Gel implant was reported.

Methods:

The medical records of patients who underwent R-NSM and IBR with Gel implant for breast cancer during the period March 2017 to October 2017 were collected from single institution. Data on clinicopathologic characteristics, type of surgery, method of breast reconstruction, complications, and recurrence were analyzed to determine the effectiveness and oncologic safety of R-NSM. Patients’ oriented cosmetic outcome report was also obtained.

Results:

A total of 15 patients was analyzed, and the mean age of them was 46.5 ± 10.0 years. The pathologic stage was 30.8% ductal carcinoma in situ, 30.8% stage I, 30.8% stage II, and 7.7% stage III. The mean operation time was 282.8 ± 70.4 minutes, and mean hospital stay was 6.7 ± 1.2 days. The positive surgical margin rate was 0%. One patient suffered from delayed axillary wound healing. Two patients (13.3%) with transit nipple ischemia change, but no total nipple areolar complex necrosis case was observed. No local recurrence, distant metastasis, or case mortality was found during mean 6.3 ± 2.1 months follow-up. All 15 patients were satisfied with the postoperative aesthetic outcome.

Conclusion:

From our preliminary experience, R-NSM and IBR with Gel implant is a safe procedure, with good cosmetic results, and could be a promising new technique for breast cancer patients indicated for mastectomy.
Going Forward Lightening the Shadow of Cancer
Authors: Hassankhani Hadi , Eghtedar Samereh , Rahmani Azad , Ebrahimi Hossein
Published: June 2018

This qualitative study was conducted to explore the empowerment experiences of family caregivers of patients with cancer. Empowerment consisted of 3 main categories: (1) seeking tranquility with the help of religious beliefs, (2) developing a positive attitude, and (3) restoring control over the situation. Results may help nurses for planning spiritual and supportive care.
Living With Diabetes in Appalachia
Authors: Carpenter Roger , Smith Mary Jane
Published: June 2018

This article presents an innovative holistic practice application based on evidence from a focus group study on managing diabetes. The purpose of this study addressed the research question: How do persons with type 2 diabetes describe ways of managing the challenge of living with diabetes? A second purpose was to link the findings on ways to manage diabetes to holistic nursing practice through story theory. Nine adults with type 2 diabetes living in rural West Virginia participated in 3 focus groups. Using content analysis, the study findings integrated themes with core qualities, and are as follows: living life as an evolving process is awakening to the present and doing it your way, being on guard is a vigilant ongoing responsibility, attending to bodily experience is awareness of body and facing life stress, and knowing the consequences is awareness of potential problems and taking charge. Merging the study findings with the concepts of story theory led to the development of an innovative practice application for managing diabetes. Managing diabetes in this practice application goes beyond problem-centeredness to a patient-centered approach, offering attention to individual preferences. Since managing diabetes is a major problem in Appalachia, there a need for innovative approaches. This study adds to the body of knowledge on how persons from Appalachia manage diabetes. In addition, it offers a story practice approach for managing diabetes—replacing a problem focus to a more holistic approach to practice leading to more meaningful and fulfilling outcomes.
Risk Factors for Loss of Lung Sliding in a Medical Intensive Care Population With Acute Respiratory Failure
Authors: Mallow Christopher , Isakow Warren
Published: June 2018

Background:

Point of care bedside ultrasound is widely utilized as a rapid technique to evaluate patients with acute pulmonary emergencies, including acute pneumothorax. The presence of a pneumothorax is a known cause of loss of lung sliding by ultrasound examination, but no other risk factors have been clearly identified. We attempted to identify demographic and patient characteristics that are risk factors for loss of ultrasonographic lung sliding in the absence of a pneumothorax.

Methods:

Data were collected on 159 patients admitted to the medical intensive care unit with acute respiratory failure, undergoing routine admission lung ultrasound. The lung ultrasound examination consisted of 3 views of each hemithorax using a phased array abdominal probe.

Results:

There were 4 confirmed pneumothoraces out of 20 patients with loss of lung sliding at ≥1 ultrasound interrogation points on either hemithorax. Hypercarbic respiratory failure [odds ratio (OR), 5.59] and low body mass index (OR, 0.88) were statistically significant risk factors for the loss of lung sliding in the absence of pneumothorax. There was a trend toward significance in patients with a known history of a decreased forced expiratory volume 1/forced vital capacity ratio (OR, 0.02), COPD/asthma exacerbation as the cause of their respiratory failure (OR, 4.52) and previous pneumothorax (OR, 11.53).

Conclusion:

Common diagnoses and comorbidities are associated with the loss of ultrasonographic lung sliding, in the absence of pneumothorax.
Postdischarge Feeding of Very‐low‐birth‐weight Infants
Authors: Francis Jane , Unger Sharon , Bando Nicole , Vance Ashleigh , Gibbins Sharyn , Kiss Alex , Church Paige , Sellen Daniel , O'Connor Deborah L. ,   GTA‐DoMINO Feeding Group
Published: June 2018

Objectives:

Infant feeding guidelines are important public health strategies to promote optimal growth, development, and chronic disease prevention, but their effectiveness is contingent upon families’ ability to adhere to them. Little is known of adherence to guidelines among nutritionally vulnerable infants, specifically those born very‐low‐birth‐weight (VLBW) (<1500 g). This study investigated whether postdischarge feeding practices for VLBW infants align with current recommendations and explored parental and infant baseline sociodemographics related to these practices.

Methods:

Prospectively collected data from families of 300 VLBW infants participating in a randomized clinical trial (ISRCTN35317141) were used. Baseline demographics were obtained at enrollment and postdischarge feeding practices via monthly telephone questionnaires to 6 months corrected age (CA).

Results:

At discharge, 4 and 6 months CA, 72%, 39%, and 29% of infants received any amount of mother's milk, respectively; exclusive breast‐feeding rates were 49%, 20%, and 6%, respectively. Among infants receiving mother's milk, rates of vitamin D supplementation were ≥83%. Recommendations for introducing solids between 4 and 6 months CA were followed by 71% of the cohort and for iron supplementation by 58%. Overall, 12% of infants adhered to all aforementioned recommendations. Mothers with university degrees were more likely to provide mother's milk, whereas mothers of Middle Eastern/South Asian ethnicity were less likely to provide mother's milk.

Conclusions:

Low rates of partial and exclusive breast‐feeding of VLBW infants to 6 months CA were reported. Overall adherence to iron supplementation was low. Strategies to provide increased support for mothers identified as at‐risk should be developed.
Will the Real Coeliac Disease Please Stand Up? Coeliac Disease Prevalence in the German LIFE Child Study
Authors: Händel Norman , Mothes Thomas , Petroff David , Baber Ronny , Jurkutat Anne , Flemming Gunter , Kiess Wieland , Hiemisch Andreas , Körner Antje , Schlumberger Wolfgang , Thiery Joachim , Wolf Johannes
Published: June 2018

Objectives:

Assessing the seroprevalence and the prevalence of definite coeliac disease (CD) in the German LIFE Child Health study cohort including immunoglobulin A (IgA) antibodies against tissue transglutaminase (IgA‐TTG) in addition to IgG antibodies against deamidated gliadin peptides (IgG‐DGP) and human leukocyte antigen (HLA)‐DQ2/8 genotyping.

Methods:

Samples from children and adolescents were first screened for IgA‐TTG and IgG‐DGP. If IgA‐TTG was above 0.5 times the upper limit of normal and/or IgG‐DGP was positive, IgA antibodies against endomysium (IgA‐EmA) were measured, and HLA was genotyped. In patients with only IgG‐DGP positivity, total IgA was assayed. Subjects with suspicious results were followed up serologically and, in case of repeatedly positive antibody results, invited for a personal interview. Further diagnostic data were obtained independent from our study.

Results:

We screened 2363 children's blood samples collected from 2011 to 2015. The seroprevalence, that is, IgA‐TTG and/or IgA‐EmA positivity or IgG‐DGP positivity with IgA <0.05 g/L, was 1.57% (95% confidence interval [CI95%] 1.14–2.15). The prevalence of suspected CD, that is, seroprevalence and compatible HLA genotype with hitherto unknown mucosal damage, was 1.35% (CI95% 0.96–1.91). Definite CD, that is, seropositivity accompanied by positive intestinal biopsy or IgA‐TTG ≥ 10 × upper limit of normal, was found in 0.42% (CI95% 0.22–0.80). Seven children claimed to have CD. The HLA haplotype, however, matched in only 4 of them resulting in an overall CD prevalence of at least 0.59% (CI95% 0.34–1.02). Thirteen unclear cases remained; therefore, the prevalence may even be higher.

Conclusions:

The prevalence of definite CD in a population‐representative German cohort is higher than previously described. HLA‐DQ typing is helpful to identify false‐positive IgA‐TTG patients negative for IgA‐EmA and/or IgG‐DGP under screening conditions and unmasks possible misdiagnoses of CD.
Low Insulin‐like Growth Factor‐1 Influences Fatigue and Quality of Life in Children With Inflammatory Bowel Disease
Authors: Lucia Casadonte Chantal J. , Brown Jeffrey , Strople Jennifer , Neighbors Katie , Fei Lin , Alonso Estella M.
Published: June 2018

Objective:

Fatigue is common among patients with inflammatory bowel disease (IBD). Proinflammatory cytokines are elevated in chronic inflammation and can induce “sickness behaviors,” such as fatigue. Chronic inflammatory states also lead to growth hormone resistance, demonstrated by low levels of insulin‐like growth factor (IGF‐1) and elevated growth hormone. This study evaluated the relationship between IGF‐1, proinflammatory cytokine levels, and fatigue in patients with IBD.

Methods:

In this prospective study children with IBD, ages 10 to 16 years, were recruited from a subspecialty ambulatory clinic. Participants and their parents completed age‐appropriate generic and disease‐specific health‐related quality of life (HRQOL) instruments. Serum samples obtained at the same encounter were analyzed for Th17 cytokine and IGF‐1 levels. HRQOL scores were compared to a healthy sample and HRQOL scores and cytokine levels were compared by IGF‐1 z score quartiles.

Results:

A total of 67 patients with IBD were recruited, median age of 13.7 years (interquartile range, 11.7–15.3). Forty‐eight (72%) had inactive disease based on Physician Global Assessment. Patients with IBD reported lower generic HRQOL (P = 0.0006) and more fatigue (P = 0.0004) than a healthy sample. Patients with IGF‐1 z scores in the lowest quartile had significantly lower disease‐specific HRQOL (P = 0.01) and more fatigue (P = 0.02) than the remainder of the cohort. Serum interleukin (IL)‐10, IL‐17A, IL‐6, and interferon‐γ were significantly higher in patients with IBD with IGF‐1 z scores in the lowest quartile (P < 0.05).

Conclusions:

Children with subclinical IBD experience more fatigue and lower generic HRQOL than healthy children. Lower IGF‐1 z scores are associated with more fatigue, and this relationship may be mediated through proinflammatory cytokines.
Serum Prolactin Contributes to Enhancing Prolactin Receptor and pJAK2 in Type I Endometrial Cancer Cells in Young Women Without Insulin Resistance
Authors: Erdenebaatar Chimeddulam , Yamaguchi Munekage , Monsur Mahina , Saito Fumitaka , Honda Ritsuo , Tashiro Hironori , Ohba Takashi , Iyama Ken-ichi , Katabuchi Hidetaka
Published: June 2018

Elevated levels of serum prolactin and a high expression of prolactin receptor (PRLR) in cancer cells was recently identified in patients with endometrial cancer (EC). However, the impact of prolactin on EC remains unknown. The aim of this study was to elucidate the clinical and immunohistochemical characteristics of hyperprolactinemic patients with EC according to the pathogenetic types, type I and type II. EC patients were retrospectively divided into a high prolactin (HP) group and a low prolactin (LP) group by a serum prolactin level of 20 ng/mL and were compared between 2 groups. The expression of PRLR, phosphorylated Janus-kinase 2 (pJAK2), estrogen receptor-α, progesterone receptor, and PTEN in cancer tissue were evaluated by immunohistochemistry. Ninety-nine patients were identified. In the type I group, HP group was significantly younger (45.2 vs. 52.2, P=0.028) and their insulin resistance was significantly lower (1.6 vs. 2.5, P=0.033) than those in LP group, and the expression of PRLR and pJAK2 in the HP group was significantly higher than that in the LP group (immunoreactive score: 6.8 vs. 3.9, P=0.003; 5.7 vs. 2.6, P<0.001, respectively). In the type 2 group, there were no differences between all the term. In the type I group, the rate of loss of PTEN in the HP group was significantly lower than the LP group (25.0% vs. 60.7%, P=0.024). Prolactin-PRLR signaling may play a crucial role for the progression of type I EC without involving the PTEN mutation in young hyperprolactinemic women without insulin resistance.
Expression of Markers of Müllerian Clear Cell Carcinoma in Primary Cervical and Vaginal Gastric-type Adenocarcinomas
Authors: Talia Karen L. , Wong Richard Wing-Cheuk , McCluggage W. Glenn
Published: June 2018

The incidence of cervical adenocarcinoma, both absolute and relative to squamous cell carcinoma, is increasing. Most cervical adenocarcinomas are human papillomavirus associated, although non–human papillomavirus-associated neoplasms exist; the latter include gastric-type adenocarcinoma (GAS) and clear cell carcinoma (CCC). Histologically, these 2 tumors may superficially resemble one other and although morphologic evaluation usually permits a correct diagnosis, immunohistochemistry may be required to resolve diagnostic uncertainty, especially in a small biopsy specimen. Markers of CCC include hepatocyte nuclear factor 1 beta (HNF1β) and Napsin A. In order to explore the utility of these markers in distinguishing between GAS and CCC, we stained 24 cases of GAS (19 cervical, 5 vaginal), 3 of cervical gastric-type adenocarcinoma in situ (gAIS) and 14 CCCs (13 cervical, 1 vaginal) with these antibodies. We found HNF1β expression in 21 of 23 cases of GAS (91.3%; there was no material available for staining in 1 case), 3/3 cases of gAIS (100%) and 10 of 14 (71.4%) CCCs. Napsin A was expressed in 4 of 24 (16.7%) cases of GAS, 0 of 3 (0%) gAIS, and 11 of 14 (78.6%) CCC. On the basis of these findings, Napsin A is of value in resolving diagnostic confusion between GAS and CCC, whereas HNF1β lacks specificity and its use in this setting is discouraged.
Diffuse 18F-FDG Avidity in Liver Associated With X-Linked Protoporphyria on PET/CT
Authors: Fu Zhanli , Liu Meng , Chen Xueqi , Yang Xing , Li Qian
Published: June 2018

An 18F-FDG PET/CT was performed on a 43-year-old woman with photosensitive skin rash, abnormal liver function, and pancytopenia, which demonstrated prominent hepatomegaly, splenomegaly, and diffuse liver 18F-FDG avidity. The liver biopsy revealed intrahepatic cholestasis with biliary fibrosis resulting from the deposition of protoporphyrin. X-linked erythroid-specific 5-aminolevulinate synthase gene analysis proved the diagnosis of X-linked protoporphyria.
Evidence of Prostate-Specific Membrane Antigen Expression in Metastatic Differentiated Thyroid Cancer Using 68Ga-PSMA-HBED-CC PET/CT
Authors: Verma Priyanka , Malhotra Gaurav , Agrawal Ritesh , Sonavane Sunita , Meshram Vilas , Asopa Ramesh V.
Published: June 2018

Purpose of the Report

Prostate-specific membrane antigen (PSMA) overexpression is not restricted to prostate cancer, but it has also been demonstrated in gliomas, lung cancer, and in tumor neovasculature. Systematic studies exploring PSMA uptake in thyroid tumors are lacking. The aim of this pilot study was to assess PSMA expression in patients with metastatic differentiated thyroid cancer (mDTC).

Materials and Methods

Ten patients of mDTC harboring 32 lesions (5 men; age range, 38–65 years; mean age, 50 years) underwent prospective evaluation with radioiodine (131I), 18F-FDG PET, and 68Ga-PSMA-HBED-CC PET scans as per the institution protocol. PSMA expression (SUVmax) was compared with 18F-FDG and 131I scan findings in all patients.

Results

Lesions were radioiodine avid in 8 patients, whereas 2 were classified as thyroglobulin elevation with negative iodide scintigraphy (TENIS) patients. All patients with iodine-avid metastatic disease showed substantial PSMA uptake. PSMA PET detected 30/32 total lesions (93.75%; SUVmax ranging from 4.86 to 101.81 with median SUVmax of 31.35), whereas FDG PET/CT was positive in 23/32 lesions (81.85%). Twenty-one (70%) of 30 lesions that showed PSMA expression were localized to the bones. PSMA localized a lesion in each of the 2 TENIS patients similar to FDG PET scan.

Conclusions

68Ga-PSMA-HBED-CC PET/CT is a potentially useful imaging modality in patients of mDTC with most (70%) of PSMA expressing metastasis being localized to the bones. PSMA PET/CT could be useful for identifying patients with limited therapeutic options (eg, TENIS) who might benefit from PSMA-targeted radionuclide therapy.
Persistent Vaginal Leakage in the Setting of an Apical Vaginal Sinus Tract: A Case Report
Authors: Bastawros Dina , Beano Hamza , Kennelly Michael J. , Stepp Kevin J.E.
Published: June 2018

Fistulas are defined as abnormal connections between 2 organ, vessels, or structures. They can often present in the genitourinary tract as a result of iatrogenic injury during pelvic surgery. A 46-year-old female presents many years after a hysterectomy for persistent vaginal leakage with concern for a vesicovaginal fistula. Computed tomography urogram, intravenous retrograde pyelogram, and cystoscopy were negative for vesicovaginal fistula; however, a vaginal sinus tract was noted and further explored. This case report will describe the use of both laparoscopy and concomitant vaginoscopy to diagnose and, ultimately, surgically excise a salpingovaginal fistula.
Deep clustering of protein folding simulations
Authors: Bhowmik Debsindhu , Gao Shang , Young Michael T , Ramanathan Arvind
Published: June 2018

We examine the problem of clustering biomolecular simulations using deep learning techniques. Since biomolecular simulation datasets are inherently high dimensional, it is often necessary to build low dimensional representations that can be used to extract quantitative insights into the atomistic mechanisms that underlie complex biological processes. In this paper, we use a convolutional variational autoencoder (CVAE) to learn low dimensional, biophysically relevant latent features from long time-scale protein folding simulations in an unsupervised manner. We demonstrate our approach on three model protein folding systems, namely the Fs-peptide (14μs aggregate sampling), villin head piece (single trajectory of 125μs) and the mixedβ-β-α(BBA) protein (223 + 102μs sampling across two independent trajectories). In these systems, we show that the CVAE latent features learned correspond to distinct conformational substates along the protein folding pathways. The CVAE model predicts nearly 89% of all contacts within the folding trajectories correctly, while being able to extract folded, unfolded and potentially misfolded states in an unsupervised manner. Further, the CVAE model can be used to learn latent features of protein folding that can be applied to other independent trajectories, making it particularly attractive for identifying intrinsic features that correspond to conformational substates that share similar structural features. Together, we show that the CVAE model can quantitatively describe complex biophysical processes such as protein folding.
Quantifying Platelet Margination in Diabetic Blood Flow
Authors: Chang H.-Y. , Yazdani A. , Li X.J. , Douglas K. A. A. , Mantzoros C. S. , Karniadakis G. E.
Published: June 2018

Patients with type 2 diabetes mellitus (T2DM) develop thrombotic abnormalities strongly associated with cardiovascular diseases. In addition to the changes of numerous coagulation factors such as elevated levels of thrombin and fibrinogen, the abnormal rheological effects of red blood cells (RBCs) and platelets flowing in blood are crucial in platelet adhesion and thrombus formation in T2DM. An important process contributing to the latter is the platelet margination. We employ the dissipative particle dynamics method to seamlessly model cells, plasma, and vessel walls. We perform a systematic study on the RBC and platelet transport in cylindrical vessels by considering different cell shapes, sizes and RBC deformabilities in healthy and T2DM blood, as well as variable flowrates and hematocrit. In particular, we use cellular-level RBC and platelet models with parameters derived from patient-specific data and present a sensitivity study. We find T2DM RBCs, which are less deformable compared to normal RBCs, lower the transport of platelets toward the vessel walls whereas platelets with higher mean volume (often observed in T2DM) lead to enhanced margination. Furthermore, increasing the flowrate or hematocrit enhances platelet margination. We also investigated the effect of platelet shape and observed a non-monotonic variation with the highest near-wall concentration corresponding to platelets with moderate aspect ratio of 0.38. We examine the role of white blood cells (WBCs), whose count is increased notably in T2DM patients. We find that WBC rolling or WBC adhesion tend to decrease platelet margination due to hydrodynamic effects. To the best of our knowledge, such simulations of blood including all blood cells have not been performed before, and our quantitative findings can help separate the effects of hydrodynamic interactions from adhesive interactions, and potentially shed light on the associated pathological processes in T2DM such as increased inflammatory response, platelet activation and adhesion, and ultimately thrombus formation.
Engineered resistance to Zika virus in transgenicAe. aegyptiexpressing a polycistronic cluster of synthetic miRNAs
Authors: Buchman Anna , Gamez Stephanie , Li Ming , Antoshechkin Igor , Lee Shin-Hang , Wang Shin-Wei , Chen Chun-Hong , Klein Melissa J. , Duchemin Jean-Bernard , Paradkar Prasad N. , Akbari Omar S.
Published: June 2018

Recent Zika virus (ZIKV) outbreaks have highlighted the necessity for development of novel vector control strategies to combat arboviral transmission, including genetic versions of the sterile insect technique, artificial infection withWolbachiato reduce population size and/or vectoring competency, and gene drive based methods. Here, we describe the development of mosquitoes synthetically engineered to impede vector competence to ZIKV. We demonstrate that a polycistronic cluster of engineered microRNAs (miRNAs) targeting ZIKV is expressed and fully processed following a blood meal inAe. aegypti, ensuring the formation of mature synthetic miRNAs in the midgut where ZIKV resides in the early stages of infection. Critically, we demonstrate that engineeredAe. aegyptimosquitoes harboring the anti-ZIKV transgene have significantly reduced viral infection, dissemination, and transmission rates of ZIKV. Taken together, these compelling results provide a promising path forward for development of effective genetic-based ZIKV control strategies, which could potentially be extended to curtail other arboviruses.

One Sentence Summary

Here we describe the generation ofAe. aegyptimosquitoes that are engineered to confer reduced vector competence to Zika virus (ZIKV) and we discuss how such engineering approach can be used to combat the major health burden of ZIKV and potentially other arboviruses in the future.
Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating inDrosophila
Authors: Combs Peter A. , Krupp Joshua J. , Khosla Neil M. , Bua Dennis , Petrov Dmitri A. , Levine Joel D. , Fraser Hunter B.
Published: June 2018

Pheromones known as cuticular hydrocarbons are a major component of reproductive isolation inDrosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister speciesD. simulansandD. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongaseeloF, broadly affects both the complement of hydrocarbons present onD. sechelliafemales and the propensity ofD. simulansmales to mate with those females. In addition, knockdown ofeloFin the more distantly relatedD. melanogasterled to a similar shift in hydrocarbons as well as lower interspecific mate discrimination byD. simulansmales. Thus, cis-regulatory changes ineloFappear to be a major driver in the sexual isolation ofD. simulansfrom multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.
Developing a modern data workflow for evolving data
Authors: Yenni Glenda M. , Christensen Erica M. , Bledsoe Ellen K. , Supp Sarah R. , Diaz Renata M. , White Ethan P. , Ernest S.K. Morgan
Published: June 2018

Data management and publication are core components of the research process. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. “Evolving data” present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a evolving data workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to: 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow uses two tools from software development, version control and continuous integration, to create a modern data management system that automates the pipeline.
Synergistic Recruitment of UbcH7~Ub and Phosphorylated Ubl Domain Triggers Parkin Activation
Authors: Condos Tara E.C. , Dunkerley Karen M. , Aisha Freeman E. , Barber Kathryn R. , Aguirre Jacob D. , Chaugule Viduth K. , Xiao Yiming , Konermann Lars , Walden Helen , Shaw Gary S.
Published: June 2018

The mechanism of activation and ubiquitin conjugation by the E3 ligase parkin is pivotal to understand the molecular pathology of early-onset Parkinson’s disease. Parkin is normally autoinhibited but is activated by the kinase PINK1 that phosphorylates parkin’s N-terminal ubiquitin-like (pUbl) domain and ubiquitin. How these alter the structure of parkin to allow recruitment of an E2~Ub conjugate to enhance ubiquitination is an unresolved question. We present the structure of an incoming E2~Ub conjugate with the phospho-ubiquitin bound C-terminus of parkin (R0RBR). We show the UbcH7~Ub conjugate is recruited by R0RBR parkin in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR experiments indicate there is re-modelling near the RING0/RING2 interface remote from the E2-binding site. This, and parkin phosphorylation lead to rapid reactivity of the RING2(Rcat) catalytic cysteine in parkin, needed for ubiquitin transfer. Parkin phosphorylation also leads to relocation and weak interaction of the pUbl domain with the RING0 domain that is enhanced upon E2~Ub recruitment indicating these events act synergistically to drive parkin activity.
An introduced crop plant is driving diversification of the virulent bacterial pathogenErwinia tracheiphila
Authors: Shapiro Lori R. , Paulson Joseph N. , Arnold Brian J. , Scully Erin D. , Zhaxybayeva Olga , Pierce Naomi , Rocha J. , Klepac-Ceraj Vanja , Holton Kristina , Kolter Roberto
Published: June 2018

Erwinia tracheiphilais the causal agent of bacterial wilt of cucurbits, an economically important phytopathogen affecting few cultivated Cucurbitaceae host plant species in temperate Eastern North America. However, essentially nothing is known aboutE. tracheiphilapopulation structure or genetic diversity. To address this shortcoming, a representative collection of 88E. tracheiphilaisolates was gathered from throughout its geographic range, and their genomes were sequenced. Phylogenomic analysis revealed three genetic clusters with distincthrpT3SS virulence gene repertoires, host plant association patterns, and geographic distributions. The low genetic variation within each cluster suggests a recent population bottleneck followed by population expansion. We showed that in the field and greenhouse, cucumber (Cucumis sativus), which was introduced to North America by early Spanish conquistadors, is the most susceptible host plant species, and the only species susceptible to isolates from all three lineages. The establishment of large agricultural populations of highly susceptibleC. sativusin temperate Eastern North America may have facilitated the original emergence ofE. tracheiphilainto cucurbit agro-ecosystems, and this introduced plant species may now be acting as a highly susceptible reservoir host. Our findings have broad implications for agricultural sustainability by drawing attention to how worldwide crop plant movement, agricultural intensification and locally unique environments may affect the emergence, evolution, and epidemic persistence of virulent microbial pathogens.

Importance

Erwinia tracheiphilais a virulent phytopathogen that infects two genera of cucurbit crop plants,Cucurbitaspp. (pumpkin and squash) andCucumisspp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate Eastern North America. Here, we complete the first large-scale sequencing of anE. tracheiphilaisolate collection. From phylogenomic, comparative genomic, and empirical analyses, we find that introducedCucumisspp. crop plants are driving the diversification ofE. tracheiphilainto multiple, closely related lineages. Together, the results from this study show that locally unique biotic (plant population) and abiotic (climate) conditions can drive the evolutionary trajectories of locally endemic pathogens in unexpected ways.
Long-read viral metagenomics enables capture of abundant and microdiverse viral populations and their niche-defining genomic islands
Authors: Warwick-Dugdale Joanna , Solonenko Natalie , Moore Karen , Chittick Lauren , Gregory Ann C. , Allen Michael J. , Sullivan Matthew B. , Temperton Ben
Published: June 2018

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a ‘universal’ gene to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution. However, short-read assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Assembly across genomic islands which likely contain niche-defining genes that drive ecological speciation is also challenging. While such populations and features are successfully captured by single-virus genomics and fosmid-based approaches, both techniques require considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative method for improving assembly of viral metagenomics using long read technology. Named ‘VirION’ (Viral, long-read metagenomics via MinION sequencing), our sequencing approach and complementary bioinformatics pipeline (i) increased number and completeness of assembled viral genomes compared to short-read sequencing methods; (ii) captured populations of abundant viruses with high microdiversity missed by short-read methods and (iii) captured more and longer genomic islands than short-read methods. Thus, VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.
Linkage disequilibrium connects genetic records of relatives typed with disjoint genomic marker sets
Authors: Kim Jaehee , Edge Michael D. , Algee-Hewitt Bridget F. B. , Li Jun Z. , Rosenberg Noah A.
Published: June 2018

In familial searching in forensic genetics, a query DNA profile is tested against a database to determine whether it represents a relative of a database entrant. We examine the potential for using linkage disequilibrium to identify pairs of profiles as belonging to relatives when the query and database rely on nonoverlapping genetic markers. Considering data on individuals genotyped with both microsatellites used in forensic applications and genome-wide SNPs, we find that ~30-32% of parent–offspring pairs and ~35-36% of sib pairs can be identified from the SNPs of one member of the pair and the microsatellites of the other. The method suggests the possibility of performing familial searches of microsatellite databases using query SNP profiles, or vice versa. It also reveals that privacy concerns arising from computations across multiple databases that share no genetic markers in common entail risks not only for database entrants, but for their close relatives as well.
Motor learning shapes temporal activity in human sensorimotor cortex
Authors: Zich Catharina , Woolrich Mark W , Becker Robert , Vidaurre Diego , Scholl Jacqueline , Hinson Emily L , Josephs Laurie , Braeutigam Sven , Quinn Andrew J , Stagg Charlotte J
Published: June 2018

Although neuroimaging techniques have provided vital insights into the anatomical regions involved in motor learning, the underlying changes in temporal dynamics are not well understood. Using magnetoencephalography and Hidden Markov Modelling to model the dynamics of neural oscillations on data-adaptive time-scales, we detected specific changes in movement-related sensorimotor β-activity during practice of a self-paced sequential visuo-motor task. The behaviourally-relevant neural signature generalised to another motor task, emphasising the centrality of β-activity in motor plasticity.
Crystal growth and characterization of second- and third-order nonlinear optical chalcone derivative: (2E)-3-(5-bromo-2-thienyl)-1-(4-nitrophenyl)prop-2-en-1-one
Authors: Patil Parutagouda Shankaragouda , Maidur Shivaraj R. , Shkir Mohd , AlFaify S. , Ganesh V. , Krishnakanth Katturi Naga , Rao S. Venugopal
Published: June 2018

Experimental and computational studies of linear and nonlinear optical (NLO) properties of (2E)-3-(5-bromo-2-thienyl)-1-(4-nitrophenyl)prop-2-en-1-one (5B2SNC) single crystals are reported. Good-quality and large-sized single crystals of 5B2SNC were successfully grown and characterized by powder X-ray diffraction and high-resolution X-ray diffractometry techniques. 5B2SNC was found to crystallize in the monoclinic noncentrosymmetric space group Cc and possesses moderately good crystalline perfection. The linear optical properties were investigated using the absorption spectrum, which reveals a direct optical band gap of 3.1 eV. The thermal stability was studied with thermogravimetric analysis/differential thermal analysis. The powder second harmonic generation efficiency was evaluated by the Kurtz and Perry method, and 5B2SNC was found to be 26 times more efficient than urea standard. Third-order NLO properties were studied by the z-scan technique with a femtosecond laser. The second hyperpolarizability was obtained to be ∼1.45 × 10−31 e.s.u. The molecule reveals a strong reverse saturation absorption and negative nonlinear refraction. The molecule exhibited good optical limiting properties, and its limiting threshold was measured to be ∼3.2 mJ cm−2. In addition, static electric dipole moments, linear polarizabilities, and first- and second-order hyperpolarizabilities were calculated by density functional theory (DFT). Highest occupied molecular orbital/lowest unoccupied molecular orbital band gaps were also evaluated by DFT calculations. The experimental and theoretical results showed that 5B2SNC exhibits excellent second- and third-order nonlinear optical properties.
Structural defects in ZnGeP2single crystals revealed by X-ray topography
Authors: Lei Zuotao , Kolesnikov Aleksei , Vasilenko Anton , Zhu Chongqiang , Verozubova Galina , Yang Chunhui
Published: June 2018

The results of X-ray transmission topography and diffraction analysis of a ZnGeP2single crystal grown by the vertical Bridgman method in the [001] direction are presented and discussed. The FWHM of rocking curves over a large area of a (100) longitudinal slice is about 12′′, which is indicative of the high quality of the examined sample. Glow discharge mass spectrometry does not show significant content of foreign chemical elements. X-ray topography reveals growth striations and dislocations. The predominant defects are single dislocations and their pile-ups. Near to the growth-axis region, curved dislocation bundles passing through the entire crystal are observed, on which precipitates are formed. In the initial part of the crystal, dislocations are located chaotically, while towards the middle of the sample they are aligned along the growth striae. In the final part of the crystal, the dislocation density increases.
Single engine turboprop aeroplane class in small air transport
Authors: Bakunowicz Jerzy
Published: June 2018

Purpose

This paper aims to present the analysis of introduction of single engine turbo-prop aeroplane class in terms of certification specifications and flight crew licensing regulations.

Design/methodology/approach

Following the results of flight testing and additional performance and sizing calculations, the proposed class was placed among the existing aeroplane taxonomy in terms of performance, flight loads, mass penalty, fuel economy and several other factors. Concerning small air transport initiative, the new class was tried to be placed as a starting point in commercial pilot career.

Findings

The paper points the potential market for single engine turbopropeller aeroplanes and lists today obstacles in wider introduction. Therefore, remarks about required change of regulations and requirements for design process, as well as for crew licensing, are underlined.

Practical implications

The results of the study would be helpful in preliminary design of a new low-power turboprop aeroplane, as well as during tailoring the certification specifications.

Originality/value

The approach presented in this paper is a detailed extension of an original idea presented by author for the first time during Clean Sky/small air transport workshop.
Lean production practices and bundles: a comparative analysis
Authors: Sahoo Saumyaranjan , Yadav Sudhir
Published: June 2018

Purpose

Total productive maintenance and total quality management are two lean manufacturing initiatives that are used by manufacturing plant managers to improve operations capabilities. The purpose of this paper is to investigate the effects of standalone lean practices and lean bundles on manufacturing business performance.

Design/methodology/approach

A quantitative approach was used. The survey data were drawn from 160 manufacturing organizations in India. The respondent companies were grouped on the basis of the duration of lean production in operation and then classified based on the profile of their operations strategy. The approach, based on comparative assessment between standalone lean practices and lean bundles, has been directed toward justification of lean bundles for its support to competitive manufacturing in the context of the Indian manufacturing sector.

Findings

The paper establishes the long-term effects of lean bundles in significantly improving manufacturing business performance as compared to standalone lean practices. Further findings of the study revealed the significance of the duration of lean production in operation in achieving higher levels of manufacturing business performance.

Research limitations/implications

The study is cross-sectional in nature. It would be interesting to test the analytical framework adopted for this study for more industries and in different countries. The use of subjective measures in survey questionnaire is also another limitation of the study.

Practical implications

This study offers clear implications for practitioners, proving that they should give higher emphasis on the implementation of lean bundles using total productive maintenance and total quality management practices together, to prioritize their product, production and business strategies, to achieve sustainable competitive advantage.

Originality/value

This paper empirically examines and evaluates the effect of lean practices and bundles in the context of medium- and large-sized manufacturing industries in India. Besides, there are very few studies that comparatively assess the differences in performance contribution of various lean operational strategies considering duration of implementation of lean. Also, the theoretical contribution of the study establishes the essence of integrating total productive management and total quality management for attaining world class manufacturing is of high value.
Manipulator residual estimation and its application in collision detection
Authors: Guo Mingming , Zhang Hua , Feng Chuncheng , Liu Manlu , Huo Jianwen
Published: June 2018

Purpose

This paper aims to present a method to improve the sensitive and low probabilities of false alarm of a manipulator in a human–robot interaction environment, which can improve the performance of the system owing to non-linear uncertainty in the model of the robot controller.

Design/methodology/approach

A novel collision detection method based on adaptive residual estimation is proposed, promoting the detection accuracy of the collision of the manipulator during operation. First, a general momentum residual estimator is designed to incorporate the non-linear factors of the manipulator (e.g. joint friction, speed and acceleration) into the residual-related uncertainty of the model. Second, model parameters are estimated through gradient correction. The residual filter is used to determine the dynamic threshold, resulting in higher detection accuracy. Finally, the performance of the residual estimation scheme is evaluated by comparing the dynamic threshold with residual in real-time experiments where a single Universal Robot 5 robot end–effector collides with the obstacle.

Findings

Experimental results demonstrate that the collision detection system can improve sensitivity and lead to low probabilities of false alarm of non-linear uncertainty in the model.

Practical implications

The method proposed in this article can be applied to industry and human–robot interaction area.

Originality/value

An adaptive collision detection method is proposed in this paper to address non-linear uncertainties of the model in industrial application.
Participatory place management in the age of shrinkage
Authors: Capitanio Marco
Published: June 2018

Purpose

This paper aims to focus on citizen participation as a crucial place management factor in Tokyo’s shrinking suburbs as a way to facilitate the goal of retaining and attracting population and improving townscape quality. This research qualitatively examines participatory practices in place management and place branding strategies in one case study.

Design/methodology/approach

A historical overview of participatory place management in Japan introduces the case study of Kunitachi City, in the western periphery of Tokyo, chosen because of its peculiar development tied to bottom-up practices, high-quality built environment and strong identity. Analysis was carried out by means of literature review in Japanese and English, interviews and extensive fieldwork between 2015 and 2017.

Findings

A certain degree of conflict between progressive and reactionary participatory practices can be beneficial to place management, and local governments should seek ways to actively support and grant legal status to civic involvement. Moreover, high-quality unique built space, achieved through participatory actions, is a prime tool to brand peripheral areas and foster the pride of residents.

Originality/value

In a context where municipalities need to devolve more and more responsibilities to their inhabitants, Kunitachi has emerged as a best practice thanks to a high degree of civic capital. While there is no ready-made recipe to be replicated, other areas should closely examine the efforts by this municipality to sustain bottom-up involvement, yielding the benefits of an attractive city image created by its own residents.