bluuebunny/crossref_metadata_2025 huggingface dataset:
Consensus of second‐order multi‐agents with actuator saturation and asynchronous time‐delays
Authors: Yanumula Venkata Karteek , Kar Indrani , Majhi Somanath
Published: September 2017

This study presents the consensus of a saturated second‐order multi‐agent system with non‐switching dynamics that can be represented by a directed graph. The system is affected by data processing (input delay) and communication time‐delays that are assumed to be asynchronous. The agents have saturation non‐linearities, each of them is approximated into separate linear and non‐linear elements. Non‐linear elements are represented by describing functions. Describing functions and stability of linear elements are used to estimate the existence of limit cycles in the system with multiple control laws. Stability analysis of the linear element is performed using Lyapunov–Krasovskii functions and frequency domain analysis. A comparison of pros and cons of both the analyses with respect to time‐delay ranges, applicability and computation complexity is presented. Simulation and corresponding hardware implementation results are demonstrated to support theoretical results.
Dynamic behaviours of constant on‐time one‐cycle controlled boost converter
Authors: Hu Wei , Zhang Bo , Yang Ru , Qiu Dongyuan
Published: September 2017

In this study, the discrete‐time model is used to analyse a constant on‐time one‐cycle controlled boost converter operating in continuous conduction mode. Then, it derives the critical boundary between continuous conduction mode and discontinuous conduction mode. In terms of Newton–Raphson methodology, the numerical solutions of fixed points are obtained. Thereafter, the stability of closed‐loop boost converter is analysed based on its Jacobian matrix. It remarks that a couple of conjugate multipliers of Jacobian matrix of the system cross the unit circle gradually with constant on‐time value increasing, while the step‐up power stage moves from period‐1 state into Neimark–Sacker bifurcation. Based on the stability analysis, an additional current loop is developed to improve the control for extending the stable region. Finally, simulation and experimental results well validate the theoretical analysis.
Review of recent advancements of direct torque control in induction motor drives – a decade of progress
Authors: Kumar Ravi Hemantha , Iqbal Atif , Lenin Natesan Chokkalingam
Published: September 2017

Since the invention of direct torque control (DTC) in later 1980s for alternating current (AC) motor drives, it has undergone many modifications to improve the control strategy. This study provides a comprehensive review of recent advancements of DTC of induction motor (IM) for the past one decade. Strategies adopted to improve the performance of DTC based on switching table, constant switching frequency operation, intelligent control, sensorless control and predictive control are extensively discussed with its key results and algorithms.
Krankenhausfinanzierung: Es ist an der Zeit, zu handeln
Authors: Penter Volker
Published: September 2017

Seit Jahren kommen die Länder ihren Investitionsverpflichtungen nicht nach – und das hat langfristig eine verheerende Wirkung: Die Verschuldung der Krankenhäuser steigt und somit auch der Druck auf die Produktivität, eine 2-Klassen-Medizin wird gefördert und Kapazitäten werden aufgebaut statt abgebaut. Hier muss sich etwas ändern!
Lean Management bei der Kliniken Südostbayern AG: Auf dem Weg zu einem schlanken und effizienten Entlassmanagement
Authors: Frank Reinhold , Möhlenkamp Evelyn , Paech Stefan
Published: September 2017

Die Kliniken Südostbayern AG hat Methoden des Lean Managements an allen 6 Klinikstandorten etabliert, um Patientenorientierung, Prozessqualität und Wirtschaftlichkeit nachhaltig zu verbessern. Besonders im Fokus standen die Stationsorganisation und -ablaufsteuerung sowie die Prozesse in der Notaufnahme. Welche Schritte auf dem Weg bis zur erfolgreichen Implementierung erforderlich sind und welche Aspekte man dabei beachten sollte, beleuchtet der folgende Beitrag.

Von Reinhold Frank, Evelyn Möhlenkamp, Dr. Stefan Paech
Interview mit Carla Kriwet: Reagieren, bevor die Lage eskaliert
Authors: Mau Jens
Published: September 2017

Philips hat sich zum Gesundheitskonzern transformiert, und macht die Vernetzung von Patientendaten zu einem Schlüsselthema. Im kma-Interview erklärt Carla Kriwet, Vorstand bei Philips, unter anderem welche Rolle medizinische Frühwarnsysteme in Zukunft spielen werden.
BuFaTa 2017: Austausch bringt Fortschritt
Authors: Thalmayr Maria
Published: September 2017

Einen gelungenen Mix aus technischen und übergeordneten gesundheitswirtschaftlichen Themen bot die FKT-Bundesfachtagung Ende Juni auf der 2. Fachmesse Krankenhaus Technologie in Gelsenkirchen. Die Berufsgruppen und Stakeholder im Gesundheitswesen brauchen mehr Austausch. Diese zentrale Erkenntnis zog sich als roter Faden durch die Veranstaltung.
Neuroradiological Features of Six Patients with Propionic Acidemia
Authors: Víllora-Morcillo Nuria , Quijada-Fraile Pilar , Martín-Hernández Elena , Camacho-Salas Ana , García-Silva Maria Teresa , Martinez De Aragón Ana , Berenguer-Potenciano Maria
Published: September 2017

Propionic acidemia (PA) is a rare autosomal recessive neurometabolic disorder caused by propionyl-CoA carboxylase deficiency. Diffuse brain atrophy, myelination delay, and basal ganglia abnormalities, either chronic or transient, have been previously reported in brain magnetic resonance imaging (MRI) of patients with PA. Clinical manifestations are heterogeneous and long-term outcome of affected individuals is unpredictable.

Neuroradiological studies and clinical symptoms of six patients diagnosed with PA were reported in our center between 1999 and 2015. Brain MRI was performed in all patients (sagittal T1-weighted images, axial T2-weighted images, coronal FLAIR images, and axial diffusion-weighted images) and magnetic resonance spectroscopy (MRS) in four of them. Follow-up MRI abnormalities are heterogeneous and highly variable over time, in some cases even reversible. New neuroradiological findings are for the first time reported here as cerebellum signal changes, posterior brain stem diffusion restriction, and cortical development malformations. We suggest including serial MRI in follow-up programs as a monitoring tool in assessing intracerebral changes in PA, but more data are required to evaluate the benefits of serial MRI in PA patients.
Meniscal Ramp Lesion Repair Using the FasT-Fix Technique: Evaluating Healing and Patient Outcomes with Second-Look Arthroscopy
Authors: Chen Zhong , Li Wei-Ping , Yang Rui , Song Bin , Jiang Chuan , Hou Jing-Yi , Luo Huan , Zhou Yun-Feng
Published: September 2017

Although the suture-hook technique remains popular for meniscal ramp lesions, which frequently occur after anterior cruciate ligament (ACL) injury, it is unclear whether the all-inside FasT-Fix technique (Smith & Nephew, Andover, MA) is appropriate for the repair of ramp lesions. This study evaluated results of arthroscopic FasT-Fix meniscal ramp lesion repair using second-look arthroscopy. From August 2010 to December 2014, 46 knees diagnosed with combined ACL injury and ramp lesion underwent ACL reconstruction with meniscal repair using the FasT-Fix technique. We classified ramp lesions into three types according to tear pattern: meniscotibial ligament tear, meniscocapsular tear, and combined meniscotibial/meniscocapsular tear. Second-look arthroscopy was performed postoperatively. The healing capacity of the ramp lesion was evaluated retrospectively. At the final follow-up (mean = 32 months), the Lysholm knee score and the International Knee Documentation Committee (IKDC) objective score were compared with preoperative scores. All patients (n = 46) underwent a second-look arthroscopy, with 45 (97.8%) exhibiting complete or partial healing after the FasT-Fix technique was used in conjunction with ACL reconstruction. The Lysholm knee score and IKDC objective score were significantly better than preoperative scores at final follow-up. The FasT-Fix technique for meniscal ramp lesion repair—when performed with concomitant ACL reconstruction—exhibits excellent healing results.
Defektdeckung an der Hand mit einer seltenen siamesischen Lappenkombination
Authors: Pasternak Itai , Hug Urs , Rüegg Eva , Fritsche Elmar
Published: September 2017

Wir berichten über 2 Fälle mit ausgedehnten Weichteildefekten, gleichzeitig den Handrücken und die Handinnenfläche betreffend. Die Defektdeckung erfolgte jeweils mit einer siamesischen Lappenkombination aus einem freien, mikrovaskulär angeschlossenem, weit nach distal gezogenem Oberarmlappen und einer distal gestielten A. interossea posterior Lappenplastik. Wir diskutieren die möglichen Indikationen, Präparationstechnik sowie Vor- und Nachteile dieser selten verwendeten Lappenkombination.
Assessment of quality indicators among nurse practitioners performing upper endoscopy
Authors: Baumgardner Jeffrey , Sewell Justin , Day Lukejohn
Published: September 2017

Background and study aims Limited international data have shown that non-physicians can safely perform upper endoscopy, but no such study has been performed in the United States. Our aim was to assess the quality of outpatient upper endoscopies performed by nurse practitioners (NPs).

Patients and methods Retrospective chart review of upper endoscopies performed by 3 NPs between 2010 and 2013 was performed. Comparisons among all NPs performing upper endoscopy and assessment of individual NP performance over time with respect to quality indicators were performed.

Results Three NPs performed 333 upper endoscopies (distribution of 166, 44, and 123, respectively). Of the cases, 98.2 %s were successfully completed to the second portion of the duodenum. In most cases, photo-documentation of required anatomical landmarks was performed: GE junction (84.2 %), GE junction in retroflexed view (84.2 %), antrum (82.1 %) and duodenum (80.9 %). Photo-documentation improved with increasing experience. NPs appropriately performed biopsies for specific medical conditions: 10/11 (90.9 %) gastric ulcers were biopsied and 63/66 (95.5) of patients with iron deficiency had duodenal biopsies performed for celiac disease. A physician endoscopist was required during the procedure 22.5 % of the time. Important parameters such as documenting informed consent (100 %) and documenting a discharge plan (99.4 %) in the procedure reports were overwhelming present. There was a single adverse event during the study period.

Conclusion In the first US study of NPs performing upper endoscopy, they were able to perform high-quality and safe upper endoscopies. These findings support incorporation of non-physicians alongside physicians to help meet the growing demand for endoscopic services across the United States.
Naturheilverfahren bei Herzinsuffizienz: Hydro-Thermo-Therapie
Authors: Brenke Rainer
Published: September 2017

Durch Naturheilverfahren kann die Therapie der Herzinsuffizienz in vielen Fällen in optimaler Weise ergänzt werden. Im vorliegenden Beitrag
wird der Schwerpunkt auf die heute oft vernachlässigte Hydrotherapie gelegt, denn neue Erkenntnisse, insbesondere zur Sauna und anderen
Maßnahmen der milden Hyperthermie, scheinen ein immenses, therapeutisch noch viel zu wenig genutztes Potenzial zur flankierenden Behandlung
von Herzinsuffizienz zu haben.
Trainingstherapie bei Herzinsuffizienz – Forschungsstand 2017
Authors: Edel Klaus
Published: September 2017

Körperliches Training ist in den aktuellen Leitlinien ein fester Bestandteil der Therapie bei stabiler chronischer Herzinsuffizienz
(Klasse-IA-Indikation) sowohl bei reduzierter als auch bei erhaltener linksventrikulärer Pumpfunktion. Belastung, Symptomatik und
Lebensqualität können durch körperliches Training signifikant verbessert werden. Epidemiologische Daten und verschiedene Studien zeigen,
dass ein aktiver Lebensstil im Alter vor der Entwicklung einer Herzinsuffizienz schützt und ein regelmäßiges körperliches Training das
Risiko einer Herzinsuffizienz reduziert. Die Wirksamkeit ist sowohl dosis- als auch adhärenzabhängig. Empfohlen wird ein Ausdauertraining in
Form eines moderaten, aeroben Trainings („moderate continuous training", MCT), das idealerweise durch ein Krafttraining ergänzt werden
sollte.
Tunable fractional-order capacitor using layered ferroelectric polymers
Authors: Agambayev Agamyrat , Patole Shashikant , Bagci Hakan , Salama Khaled N.
Published: September 2017

Pairs of various Polyvinylidene fluoride P(VDF)-based polymers are used for fabricating bilayer fractional order capacitors (FOCs). The polymer layers are constructed using a simple drop casting approach. The resulting FOC has two advantages: It can be easily integrated with printed circuit boards, and its constant phase angle (CPA) can be tuned by changing the thickness ratio of the layers. Indeed, our experiments show that the CPA of the fabricated FOCs can be tuned within the range from -83° to -65° in the frequency band changing from 150 kHz to 10 MHz. Additionally, we provide an empirical formula describing the relationship between the thickness ratio and the CPA, which is highly useful for designing FOCs with the desired CPA.
Study of the synergistic effect in dielectric breakdown property of CO2–O2 mixtures
Authors: Zhao Hu , Deng Yunkun , Lin Hui
Published: September 2017

Sulfur hexafluoride, SF6, is a common dielectric medium for high-voltage electrical equipment, but because it is a potent greenhouse gas, it is important to find less environmentally harmful alternatives. In this paper we explore the use of CO2 and O2 as one alternative. We studied the synergistic effect in a mixture of CO2 and O2 from both macroscopic and microscopic perspectives. The effect leads to a dielectric strength of the mixture being greater than the linear interpolation of the dielectric strengths of the two isolated gases. We analyzed the critical reduced electric field strength, (E/N)cr, the breakdown gas pressure reduced electric field, E/p, and the breakdown electron temperature, Tb, and their synergistic effect coefficients for various CO2 concentrations and various products of the gas pressure times the gap distance (pd). A gas discharge and breakdown mechanism in a homogenous electric field is known to be controlled by the generation and disappearance of free electrons, which strongly depend on the electron temperature. The results indicate that adding a small amount of O2 to CO2 can effectively improve the value of (E/N)cr and bring a clear synergistic effect. In addition, significantly different variation trends of the synergistic effect in the E/p and Tb of CO2-O2 mixtures at various CO2 concentrations and pd values were also observed.
Aging in Australia: country of birth and language preferences of residents in aged care facilities
Authors: Petrov Ljubica , Joyce Catherine , Gucciardo-Masci Tonina
Published: September 2017

Objective
There is a need to better understand the use of aged care services by people from culturally and linguistically diverse backgrounds. The aim of the present study was to describe the prevalence of people living in residential aged care facilities (RACFs) who were born in non-English-speaking countries and/or have a preferred language other than English and to describe service utilisation rates.

Methods
The present study consisted of a secondary analysis of data from the Australian Institute of Health and Welfare National Aged Care Data Clearinghouse. Data were analysed by country of birth, preferred language, state or territory and Aged Care Planning Regions within Victoria.

Results
Nationally, over 30000 (18.3%) RACF residents were born in a non-English-speaking country. In Victoria, almost one in four RACF residents (23.9%) was born in a non-English-speaking country, and approximately one in eight (13.1%) has a preferred language other than English. Most Victorian RACFs (72.4%) have at least one resident with a preferred language other than English. Approximately one in four residents (26.1%) with a preferred language other than English are the sole speaker of the language in their facility.

Conclusion
All RACFs need to effectively address the needs and preferences of their residents, including those who were born in a non-English-speaking country or prefer to speak a language other than English.

What is known about the topic?
The number of older people from a non-English-speaking background continues to increase, but little is known about the prevalence of this cohort living in RACFs and how aged care providers are responding to their needs and preferences.

What does this paper add?
The present study provides detailed, service- and policy-relevant information, demonstrating a substantial degree of diversity among people living in RACFs, with wide distribution across facilities and regions. The findings confirm the need for a systematic, sector-wide approach to addressing linguistic diversity and developing inclusive practices.

What are the implications for practitioners?
All RACFs are required to develop policies and procedures in order to cater to the needs and preferences of residents who were born in non-English-speaking countries and/or who prefer to speak a language other than English.
Quality characteristics of meat from triceps brachii muscle from steers and heifers finished on high-concentrate diets containing increasing concentrations of linseed oil
Authors: Oliveira E. A. , Sampaio A. A. M. , Rosa B. L. , Henrique W. , Pivaro T. M. , Carvalho V. G. , Cirne L. G. A. , Duckett S. K.
Published: September 2017

The aim of the present study was to assess the qualitative and chemical characteristics of a shoulder muscle (triceps brachii muscle, medial head (TBm)) of 15 Nellore × Canchim steers and 14 heifers of the same cross fed diets containing 80% concentrate on a dry-matter (DM) basis and increasing concentrations of linseed oil (1%, 3.8% and 5.2% of DM). A randomised incomplete-block design, divided on the basis of initial bodyweight, in a 3 × 2 factorial scheme (oil concentration and animal sex) was used. Oil concentrations were evaluated by linear and quadratic regression. The finishing period lasted for 96, 110 or 138 days, until the average weight of each block reached 500 kg. At 24 h postmortem, TBm samples were taken to evaluate quality traits and chemical composition. Meat from steers was significantly (P < 0.05) brighter than was heifer meat (brightness (L*) = 39.55 vs 36.28). The addition of linseed oil up to 5.2% improved the pH value of TBm in heifers (6.07, 6.22 and 5.77). No significant (P > 0.05) influence was observed for linseed oil addition up to 5.2% of DM or animal sex on the chemical characteristics of TBm, estimated activity of Δ9-desaturase and elongase, and atherogenic and thrombogenic indices. However, the increasing inclusion of linseed oil in the diet of crossbred cattle increased (P < 0.05) conjugated linoleic acid (0.46, 0.66 and 0.73 g/100 g total fatty acids), α-linolenic acid (0.39, 0.69 and 1.31 g/100 g total fatty acids for steers; 0.36, 0.79 and 0.76 g/100 g total fatty acids for heifers), γ-linolenic acid (0.07, 0.10 and 0.24 g/100 g total fatty acids), and the sum of n-3 fatty acids. The increasing inclusion of linseed oil also increased the ratio of polyunsaturated fatty acids to saturated fatty acids and decreased the ratio of n-6:n-3 fatty acids (11.68, 6.43 and 5.26 for steers; 10.69, 6.93 and 6.03 for heifers). Supplementation of finishing cattle with linseed oil is an effective means to increase n-3 fatty acid concentration in forequarter muscle.
Effect of freezing on the quality of meat from broilers raised in different rearing systems
Authors: Giampietro-Ganeco A. , Mello J. L. M. , Souza R. A. , Ferrari F. B. , Machado B. M. , Souza P. A. , Borba H.
Published: September 2017

We evaluated the effect of freezing (−18°C) for 12 months on the qualitative characteristics of breast, thigh and drumstick meat. Samples from male Cobb 500 broilers raised in antibiotic-free (n = 125), conventional (n = 125) and organic (n = 125) rearing systems and samples from male Hubbard ISA broilers raised in a free-range (n = 125) rearing system were used. Among the studied systems, up to the ninth month of freezing, the organic chicken breast meat showed lower (P < 0.001) water activity (aw) (0.966, on average). After 12 months of freezing, samples of antibiotic-free and organic poultry showed a pH value similar to that of fresh meat (5.94 and 5.86, respectively). Freezing for 12 months preserved the redness of drumstick meat from conventional broilers (a* = 4.86, on average) and the rearing system did not influence the aw of drumstick meat during the entire experimental period. Freezing preserved the aw of conventional and organic chicken meat samples until the ninth month of evaluation (0.978 and 0.974, respectively). Lipid oxidation in the breast, thigh and drumstick samples from the four rearing systems increased (P < 0.001) from the third month of freezing onwards. There were variations in colour, pH, aw and lipid oxidation of chicken meat among birds raised in different rearing systems. Freezing chicken meat did not prevent colour and pH changes or occurrence of lipid oxidation and did not promote a reduction of aw to levels unfavourable to microbiological development.
Transgender women and HIV-related health disparities: falling off the HIV treatment cascade
Authors: Kalichman Seth C. , Hernandez Dominica , Finneran Stephanie , Price Devon , Driver Redd
Published: September 2017

Background
Transgender women living with HIV infection experience poorer health outcomes across the HIV continuum of care. While disparities are well established, their underlying mechanisms are not well understood. This study examined the HIV continuum of care (also known as the HIV treatment cascade), including linkage and engagement in care and health status among transgender women and cisgender women and cisgender men living with HIV. Method: Case-control matching was applied to a cohort of 1101 people living with HIV; 70 transgender women living with HIV were matched on years since testing HIV positive with cisgender women and cisgender men. Participants provided measures indicative of the HIV treatment cascade that included linkage and engagement in care, receiving and adhering to antiretroviral therapy (ART), and HIV viral suppression. Common correlates of HIV-related health status: depression symptoms, HIV-related stress, alcohol and drug use, healthcare conspiracy beliefs, medical mistrust, emotional social support and tangible social support, were also assessed. Results: Transgender women were significantly less likely to receive ART, were less adherent to ART and had poorer HIV viral suppression than cisgender persons. Multivariable models demonstrated that health disparities were predicted by transgender women having poorer tangible social support over and above the other correlates of health outcomes. Conclusion: Tangible support is amenable by interventions such as building and strengthening supportive networks and paraprofessional services. Socially supportive interventions should be considered critical in efforts to decrease HIV health disparities among transgender women.
Suzaku observations of the outskirts of the galaxy cluster Abell 3395, including a filament toward Abell 3391
Authors: Sugawara Yuuki , Takizawa Motokazu , Itahana Madoka , Akamatsu Hiroki , Fujita Yutaka , Ohashi Takaya , Ishisaki Yoshitaka
Published: September 2017

The results of Suzaku observations of the outskirts of Abell 3395, including a large-scale structure filament toward Abell 3391, are presented. We measured temperature and abundance distributions from the southern outskirt of A 3395 to the north at the virial radius, where a filament structure has been found in the former X-ray and Sunyaev–Zel’dovich (SZ) effect observations between A 3391 and A 3395. The overall temperature structure is consistent with the universal profile proposed by Okabe, N., et al. 2014, PASJ, 66, 99 for relaxed clusters, except for the filament region. A hint of intracluster medium heating is found between the two clusters, which might be due to their interaction in the early phase of a cluster merger. Although we obtained a relatively low metal abundance of $Z=0.169^{+0.164+0.009+0.018 }_{-0.150-0.004-0.015 }$ solar, where the first, second, and third errors are statistical, cosmic X-ray background systematic, and non-X-ray background systematic, respectively, at the virial radius in the filament, our results are still consistent with previous results for other clusters (Z ∼ 0.3 solar) within errors. Therefore, our results are also consistent with the early enrichment scenario. We estimated Compton y parameters only from X-ray results in the region between A 3391 and A 3395 assuming a simple geometry. They are smaller than the previous SZ results with the Planck satellite. The difference could be attributed to a more elaborate geometry such as a filament inclined to the line-of-sight direction, or underestimation of the X-ray temperature because of the unresolved multi-temperature structures or undetected hot X-ray emission of the shock-heated gas.
Comparison of Solubility of Corn Proteins in Propanol, Ethanol, and tert‐Butyl Alcohol Solutions on the Tortilla Process Samples
Authors: Chaidez‐Laguna Leslie D. , Torres‐Chávez Patricia I. , Ramirez‐Wong Benjamin , Medina‐Rodríguez Concepción L. , Carvajal‐Millán Elizabeth
Published: September 2017

To find the best solvent of those reported and to study changes in protein aggregation during corn processing to obtain tortillas, extractability of corn proteins with three alcoholic solutions (70% ethanol, 50% propanol, and 60% tert‐butyl alcohol) was compared in corn, nixtamal, masa, and tortillas. Relative solubility was assessed through size‐exclusion chromatography, SDS‐PAGE, and insoluble polymeric protein determination using the Dumas procedure. Differences in the behavior of solvents in the samples indicate that different protein interactions are promoted during each of the processing steps. All the three alcoholic solutions can be used to study changes in corn proteins, but the best solvent was 50% propanol. Ethanol (70%) extracted the lowest amounts of corn proteins in tortilla process samples.
Development of a Simple Hydroponic Assay to Study Vertical and Horizontal Resistance of Soybean and Pathotypes of Phytophthora sojae
Authors: Lebreton A. , Labbé C. , De Ronne M. , Xue A. G. , Marchand G. , Bélanger R. R.
Published: September 2017

Phytophthora root rot, caused by Phytophthora sojae, is one of the most damaging diseases of soybean and the introgression of Rps (Resistance to P. sojae) genes into elite soybean lines is arguably the best way to manage this disease. Current bioassays to phenotype the gene-for-gene relationship are hampered with respect to reproducibility and long-term stability of isolates, and do not accurately predict horizontal resistance individually. The aim of our study was to investigate a new way of phenotyping P. sojae isolates and vertical and horizontal resistance in soybean that relies on zoospores inoculated directly into a hydroponic system. Inoculation of P. sojae isolates against a set of eight differentials accurately and reproducibly identified pathotypes over a period of two years. When applied to test vertical resistance of soybean lines with known and unknown Rps genes, the bioassay relied on plant dry weight to correctly identify all genes. In addition, simultaneous inoculations of three P. sojae isolates, collectively carrying eight major virulence factors against 64 soybean lines with known and unknown levels of horizontal resistance, separated the plants into five distinct groups of root rot, allowing the discrimination of lines with various degrees of partial resistance. Based on those results, this bioassay offers several advantages in facilitating efforts in breeding soybean for P. sojae resistance and in identifying virulence factors in P. sojae.
Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana
Authors: Oest Hansen Bjoern , Meyer Etienne H. , Ferrari Camilla , Vaid Neha , Movahedi Sara , Vandepoele Klaas , Nikoloski Zoran , Mutwil Marek
Published: September 2017

Despite increasing availability of sequenced genomes, accurate characterization of gene functions is needed to close the genotype-phenotype gap. Recent advances in gene function prediction rely on ensemble approaches that integrate the results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We present Neighbor Counting Ensemble, a gene function prediction method which integrates eleven gene co-function networks for Arabidopsis thaliana, and produces more accurate gene function predictions for a larger fraction of genes with unknown function. We used these predictions to identify genes involved in mitochondrial complex I formation, and for five of them we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet, available at http://www.gene2function.de/ensemblenet.html.
Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network
Authors: Yamada Kazunori D
Published: September 2017

A profile comparison method with position-specific scoring matrix (PSSM) is one of the most accurate alignment methods. Currently, cosine similarity and correlation coefficient are used as scoring functions of dynamic programming to calculate similarity between PSSMs. However, it is unclear that these functions are optimal for profile alignment methods. At least, by definition, these functions cannot capture non-linear relationships between profiles. Therefore, in this study, we attempted to discover a novel scoring function, which was more suitable for the profile comparison method than the existing ones. Firstly we implemented a new derivative free neural network by combining the conventional neural network with evolutionary strategy optimization method. Next, using the framework, the scoring function was optimized for aligning remote sequence pairs. Nepal, the pairwise profile aligner with the novel scoring function significantly improved both alignment sensitivity and precision, compared to aligners with the existing functions. Nepal improved alignment quality because of adaptation to remote sequence alignment and increasing the expressive power of similarity score. The novel scoring function can be realized using a simple matrix operation and easily incorporated into other aligners. With our scoring function, the performance of homology detection and/or multiple sequence alignment for remote homologous sequences would be further improved.
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data
Authors: Rashid Sabrina , Shah Sohrab , Bar-Joseph Ziv , Pandya Ravi
Published: September 2017

Motivation

Intra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers, and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for unmasking the underlying tumor heterogeneity. However, extracting features from single cell genomic data in order to infer their evolutionary trajectory remains computationally challenging due to the extremely noisy and sparse nature of the data.

Results

Here we describe ‘Dhaka’, a variational autoencoder method which transforms single cell genomic data to a reduced dimension feature space that is more efficient in differentiating between (hidden) tumor subpopulations. Our method is general and can be applied to several different types of genomic data including copy number variation from scDNA-Seq and gene expression from scRNA-Seq experiments. We tested the method on synthetic and 6 single cell cancer datasets where the number of cells ranges from 250 to 6000 for each sample. Analysis of the resulting feature space revealed subpopulations of cells and their marker genes. The features are also able to infer the lineage and/or differentiation trajectory between cells greatly improving upon prior methods suggested for feature extraction and dimensionality reduction of such data.

Availability and Implementation

All the datasets used in the paper are publicly available and developed software package is available on Githubhttps://github.com/MicrosoftGenomics/Dhaka.

Supporting info and Software:https://github.com/MicrosoftGenomics/Dhaka
Evaluating Antioxidant Capacity of Different Propolis Samples from Konya, Turkey and Their Inhibitory Effect on Head and Neck Cancer Cells
Authors: Ciftci-Yilmaz Sultan , Azman Zeynep N. , Kosem Kubra , Gunduz Esra , Grenman Reidar
Published: September 2017

Propolis is a resinous mixture collected and used by the honey bees to construct and repair their hives. The component of propolis varies depend on the type of the plants collected. Propolis and its constituents have been subjected to many studies and are known for their antioxidant, antimicrobial and anticarcinogenic properties. In our study, antioxidant and antitumor capacity of propolis from Konya Sakyatan and Kiziloren regions were investigated. According to our result, Kızıloren propolis sample possesses higher antioxidant component and antioxidant capacity than Sakyatan sample. Accordingly, Kiziloren sample showed antiproliferative effect at much lower doses compared to the Sakyatan sample. Both samples effectively inhibited the migration of cancer cells at their determined IC50dosages. Obtained data indicates that constituents of propolis can greatly vary from one sample to another even in the same region and propolis selections for cancer prevention and treatment studies should be carefully considered.
Sporosarcina pasteuriican form nanoscale crystals on cell surface
Authors: Bhaduri Swayamdipta , Ghosh Tanushree , Montemagno Carlo , Kumar Aloke
Published: September 2017

Using a semi-solid 0.5% agar column, we study the phenomenon of microbially induced mineral (calcium carbonate) by the bacteriaSporosarcina pasteurii. Our platform allows forin-situvisualization of the phenomena, and we found clear evidence of bacterial cell surface facilitating formation of nanoscale crystals. Moreover, in the bulk agar we found the presence of microspheres, which seem to arise from an aggregation of nanoscale crystals with needle like morphology. Extensive chemical characterization confirmed that the crystals to be calcium carbonate, and two different polymorphs (calcite and vaterite) were identified.
Dissemination ofCryptococcus neoformansvia localised proliferation and blockage of blood vessels
Authors: Gibson Josie F , Evans Robert J , Bojarczuk Aleksandra , Hotham Richard , Lagendijk Anne K , Hogan Benjamin M , Ingham Philip W , Renshaw Stephen A , Johnston Simon A
Published: September 2017

Cryptococcus neoformansis an opportunistic fungal pathogen that can cause life-threatening cryptoccocal meningitis, predominantly within immunocompromised individuals. Cortical infarcts are observed in as many as 30% of cryptococcal meningitis cases, being particularly common in severe infection. Limited clinical case studies suggest infarcts are secondary to vasculitis and blood vessel damage caused by cryptococcal infection. However, the cause of infarcts in cryptococcal infection has not been determined. To examine potential causes of vascular damage and cryptococcal dissemination in cryptococcal infection, the zebrafishC. neoformansinfection model was used. We demonstrate that spread of cryptococci from the vasculature occurs at sites where cryptococci grow within the blood vessels, originating from a single or small number of cryptococci. We find that cryptococcal cells become trapped within the vasculature and can proliferate there resulting in vasodilation. Localised cryptococcal growth in the vasculature is also associated with sites of dissemination – in some cases simultaneously with a loss of blood vessel integrity. Using a cell-cell junction protein reporter (VE-cadherin) we identified sites dissemination associated with both intact blood vessels and where vessel rupture occurred. Thus, we have identified a mechanism for blood vessel damage during cryptococcal infection that may represent a cause of the vascular damage and cortical infarction observed in cryptococcal meningitis.

Author summary

Human infection by the fungal pathogen,Cryptococcus neoformans, can lead to life-threatening cryptococcal meningitis. In severe cases of cryptococcal meningitis, a lack of blood supply can cause tissue death and a resulting area of dead tissue (infarct) in the brain. Although vasculature inflammation in known to occur in cryptococcal meningitis, the cause of infarcts in unknown. Using a zebrafish model of cryptococcal infection, the growth and dissemination of fungal cells was observed over time. We show that cryptococcal cells become trapped and proliferate in the vasculature, resulting in cryptococcoma that damage the blood vessels. We propose that vessel damage results from increased blood pressure caused by cryptococci blocking blood vessels suggesting that the vascular damage that ensues on cryptococcoma formation may in turn be a cause of infarct formation seen in cryptococcal meningitis.
Specialized plant biochemistry drives gene clustering in fungi
Authors: Gluck-Thaler Emile , Slot Jason C.
Published: September 2017

The fitness and evolution of both prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of functionally related genes can facilitate coordinated gene expression and can prevent the breakup of co-adapted alleles in recombining populations. While clustering may thus result from selection for phenotype optimization and persistence, the extent to which eukaryotic gene organization in particular is driven by specific environmental selection pressures has rarely been systematically explored. Here, we investigated the genetic architecture of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified over one thousand gene clusters, as well as many conserved combinations of clusters, in a phylogenetically and ecologically diverse set of fungal genomes. We demonstrate that congruence in gene organization over small spatial scales in fungal genomes is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules in a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between gene organization and ecological evolution in this ancient eukaryotic lineage.
Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation
Authors: Joo Yoo Jin , Ficarro Scott B. , Soares Luis M. , Chun Yujin , Marto Jarrod A. , Buratowski Stephen
Published: September 2017

TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. Although the TATA-Binding Protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-Associated Factor (TAF) subunits recognize downstream promoter elements, act as co-activators, and interact with nucleosomes. Here we show that transcription induces stable TAF binding to downstream promoter DNA, independent of upstream contacts, TBP, or other basal transcription factors. This transcription-dependent TAF complex promotes subsequent activator-independent transcription, and promoter response to TAF mutations in vivo correlates with the level of downstream, rather than overall, Taf1 crosslinking. We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations.
Systemic evidence of acute seizure-associated neuronal injury in patients with temporal lobe epilepsy
Authors: Kunda Shailaja , LaFrance-Corey Reghann G , Khadjevand Fatemeh , Worrell Gregory A , Howe Charles L
Published: September 2017

Patients with drug refractory temporal lobe epilepsy frequently accumulate cognitive impairment over time, suggesting neuronal loss induced by seizures. We measured serum levels of neuron-specific enolase (NSE), a neuronal injury marker, relative to levels of S100β, a marker of glial injury, at 6 AM, 9 AM, noon, 3 PM, and 6 PM over the course of several days in 7 epilepsy patients and 4 healthy controls. All epilepsy patients exhibited significant deviations in NSE levels through time, and 4 of the epilepsy patients exhibited large sample entropy values and large signal variation metrics for NSE relative to S100β. Controls did not exhibit such changes. Correlation analysis revealed that NSE levels were significantly elevated after clinical seizure events. There was also a highly significant relationship between increased EEG spike frequency and an increase in serum NSE levels measured 24 hours later. The detection of large but transient post-ictal increases in NSE suggests that even self-limited seizures may cause an injury to neurons that underlies cognitive decline in some patients. Post-ictal assessment of serum NSE may serve as a biomarker for measuring the efficacy of future acute neuroprotective strategies in epilepsy patients.
Floral herbivory does not reduce pollination-mediated fitness in shelter rewarding Royal Irises
Authors: Ghara Mahua , Ewerhardy Christina , Yardeni Gil , Matzliach Mor , Sapir Yuval
Published: September 2017

Florivory, the damage to flowers by herbivores can affect fitness both directly and indirectly. Flowers consumed by florivores may fail to produce fruit or produce lower seed set because of direct damage to reproductive organs. In addition, eaten flowers are less attractive to pollinators because of reduced or modified advertisement, which reduces pollination services. While observational data are abundant, experimental evidence is scarce and results are contrasting. We tested experimentally the effect of florivory on both pollinator visitation and reproductive success in three species of the Royal Irises, which have large flowers that are attractive to pollinators, and potentially also for florivores. We hypothesized that florivory will reduce pollen deposition due to reduced attractiveness to pollinators, while fruit set and seed set will depend on the extent of florivory. We performed artificial florivory in two experiments over two years. In the first experiment, each of the three floral units of a singleIrisflower was subject to either low or high artificial florivory, or left un-touched as control. We counted the number of pollen grains deposited on each of the three stigmas as a measure of pollinator visitation. In the second experiment, three flowers of the same plant received low, high, or no artificial florivory and were further recorded for fruit and seed production. In 2016, high artificial florivory revealed lower number of pollen grains on stigmas ofIris atropurpurea, but in 2017 there was no difference. Similarly, number of pollen grains in high artificial was lower than low florivory in 2017 inI. petrana. No significant effect of florivory was found on pollen grain deposition, fruit set or seed set. The results remained consistent across species and across years. The results undermine the assumption that flower herbivory is necessarily antagonistic interaction and suggests that florivores may not be strong selection agents on floral reproductive biology in theOncocyclusirises.
G-quadruplex secondary structure from circular dichroism spectroscopy
Authors: del Villar-Guerra Rafael , Trent John O. , Chaires Jonathan B.
Published: September 2017

A curated library of circular dichroism spectra of 23 G-quadruplexes of known structure was built and analyzed. The goal of this study was to use this reference library to develop an algorithm to derive quantitative estimates of the secondary structure content of quadruplexes from their experimental CD spectra. Principle component analysis and singular value decomposition were used to characterize the reference spectral library. CD spectra were successfully fit to obtain estimates of the amounts of base steps inanti-anti, syn-antioranti-synconformations, in diagonal or lateral loops or in other conformations. The results show that CD spectra of nucleic acids can be analyzed to obtain quantitative structural information about secondary structure content in an analogous way to methods used to analyze protein CD spectra.
A “molecular guillotine” reveals an interphase function of Kinesin-5
Authors: Lv Zhiyi , Rosenbaum Jan , Aspelmeier Timo , Großhans Jörg
Published: September 2017

Motor proteins are important for transport and force generation in a variety of cellular processes and morphogenesis. Here we design a general strategy for conditional motor mutants by inserting a protease cleavage site at the “neck” between the head domain and the stalk of the motor protein, making the protein susceptible to proteolytic cleavage at the neck by the corresponding protease. To demonstrate the feasibility of this approach, we inserted the cleavage site of TEV protease into the neck of the tetrameric motor Kinesin-5. Application of TEV protease led to a specific depletion and functional loss of Kinesin-5 in Drosophila embryos. By this, we revealed that Kinesin-5 stabilized the microtubule network during interphase in syncytial embryos. The “molecular guillotine” can potentially be applied to many motor proteins due to the conserved structures of kinesin, dynein and myosin with accessible necks.

Author summary

We design a general strategy for conditional motor mutants by inserting a protease cleavage site between head and stalk domain of the motor protein, making it susceptible to specific proteolytic cleavage. We demonstrate the feasibility of the approach with the motor Kinesin-5 and the protease TEV in Drosophila embryos. This approach can potentially be applied to motor proteins kinesin, dynein and myosin due to the conserved structures.
Return to Chittagong: ten years since the “postcard”
Authors: Cairns George M.
Published: September 2017

Purpose

This paper aims to revisit the author’s 2007 “Postcard from Chittagong” to reprise the past decade of activity related to the ship breaking industry of Bangladesh.

Design/methodology/approach

The study is based on content analysis of global and local source documentation. This includes academic works, research reports from non-governmental organizations and general and specialist media reports.

Findings

Over the past decade, there have been a number of international initiatives that seek to control the disposal and dismantling of redundant ships. However, based on evidence of ongoing environmental and health impacts in Bangladesh, the effectiveness of these is questioned.

Research limitations/implications

The paper is intended to prompt debate on the ship breaking industry in Bangladesh and on the nature of global supply chains and logistics in the consumption society.

Originality/value

The paper revisits and updates a 2007 study that has been referred to and cited in a range of outlets. It is intended to continue and enhance discussion.