bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing the aggressive intensity of hydrodynamic cavitation through a Venturi tube by increasing the pressure in the region where the bubbles collapse
Authors: Soyama H. , Hoshino J.
Published: April 2016

In this paper, we used a Venturi tube for generating hydrodynamic cavitation, and in order to obtain the optimum conditions for this to be used in chemical processes, the relationship between the aggressive intensity of the cavitation and the downstream pressure where the cavitation bubbles collapse was investigated. The acoustic power and the luminescence induced by the bubbles collapsing were investigated under various cavitating conditions, and the relationships between these and the cavitation number, which depends on the upstream pressure, the downstream pressure at the throat of the tube and the vapor pressure of the test water, was found. It was shown that the optimum downstream pressure, i.e., the pressure in the region where the bubbles collapse, increased the aggressive intensity by a factor of about 100 compared to atmospheric pressure without the need to increase the input power. Although the optimum downstream pressure varied with the upstream pressure, the cavitation number giving the optimum conditions was constant for all upstream pressures.
Temperature-dependent efficiency droop in AlGaN epitaxial layers and quantum wells
Authors: Mickevičius J. , Jurkevičius J. , Kadys A. , Tamulaitis G. , Shur M. , Shatalov M. , Yang J. , Gaska R.
Published: April 2016

Luminescence efficiency droop has been studied in AlGaN epitaxial layers and multiple quantum wells (MQWs) with different strength of carrier localization in a wide range of temperatures. It is shown that the dominant mechanism leading to droop, i.e., the efficiency reduction at high carrier densities, is determined by the carrier thermalization conditions and the ratio between carrier thermal energy and localization depth. The droop mechanisms, such as the occupation-enhanced redistribution of nonthermalized carriers, the enhancement of nonradiative recombination due to carrier delocalization, and excitation-enhanced carrier transport to extended defects or stimulated emission, are discussed.
Urban Australian general practitioners’ perceptions of falls risk screening, falls risk assessment, and referral practices for falls prevention: an exploratory cross-sectional survey study
Authors: Kielich Kajtek , Mackenzie Lynette , Lovarini Meryl , Clemson Lindy
Published: April 2016

Objective The study aimed to explore Australian general practitioners’ (GPs) perceptions of falls risk screening, assessment and their referral practices with older people living in the community, and to identify any barriers or facilitators to implementing evidence-based falls prevention practice. Methods Hardcopy surveys and a link to an online survey were distributed to 508 GPs working at one Medicare Local (now part of a Primary Care Network) located in Sydney, Australia. Data were analysed using descriptive statistics and key themes were identified from open text responses. Results A total of 37 GPs returned the survey. Only 10 (27%) GPs routinely asked older people about falls, and five (13.5%) asked about fear of falls during clinical consultations. Barriers to managing falls risk were identified. GPs estimated that they made few referrals to allied health professionals for falls interventions. Conclusions GPs were knowledgeable about falls risk factors but this did not result in consistent falls risk screening, assessment or referral practices. Due to the small sample, further research is needed with a larger sample to augment these results. What is known about the topic? Falls are a common and serious health issue for older people and fall prevention is vital, especially in the primary care setting. General practitioners (GPs) are key health professionals to identify older people at risk of falls and refer them to appropriate health professionals for intervention. Evidence-based falls prevention interventions exist but are not easily or routinely accessed by older people. What does this paper add? GPs believe that previous falls are an important falls risk factor but they do not routinely ask about falls or fear of falls in clinical practice with older people. GP referral rates to allied health professionals for falls prevention are low, despite evidence-based falls prevention interventions being provided by allied health professionals. There are several barriers to GPs providing falls prevention assessment and intervention referrals, particularly using the current primary health systems. What are the implications for practitioners? GPs need to recognise their potential significant contribution to falls prevention in the community and may require tailored training. Sustainable evidence-based referral pathways need to be developed so that older people can be referred to allied health professionals for falls prevention interventions in the primary care setting, and better local networks need to be developed to allow this to occur. Policy makers may have to address the identified barriers to multidisciplinary practice and funding of services to facilitate effective falls prevention programs in primary care.
Planning and conducting aerial culling operations for feral camels
Authors: Edwards Glenn , Digby Donna , O'Leary Paul , Rafferty Dennis , Jensen Mac , Woolnough Andrew , Secomb Nick , Williams Mark , Schwartzkopff Kym , Bryan Ross
Published: April 2016

This paper describes the application of aerial culling to the management of feral camels during the Australian Feral Camel Management Project. It covers the following: key challenges involved, guiding principles, enabling factors which facilitated the application of aerial culling, the planning and implementation of actual culling operations, feedback loops, and the key operational achievements of the aerial culling program. Animal welfare was a key consideration under the Australian Feral Camel Management Project. Accordingly, aerial culling was applied in accordance with endorsed jurisdictional Standard Operating Procedures and animal welfare outcomes were formally and independently assessed during the project. Aerial culling was undertaken over an area totalling ~685 000 km2 focusing on the environmental assets identified for the project. In total, 57 aerial culling operations were undertaken resulting in the removal of ~136 000 feral camels, which represented nearly 84% of the total number removed during the project.
Canonical NF-κB signaling is uniquely required for the long-term persistence of functional mature B cells
Authors: Derudder Emmanuel , Herzog Sebastian , Labi Verena , Yasuda Tomoharu , Köchert Karl , Janz Martin , Villunger Andreas , Schmidt-Supprian Marc , Rajewsky Klaus
Published: April 2016

Significance

Mature B cells are long-lived cells responsible for the Ab production in the immune system. Canonical NF-κB signaling, one of the two discrete pathways activating transcription factors of the NF-κB family, participates in the generation of a normal mature B-cell compartment. However, the role of these signals specifically in mature B cells is still imperfectly defined. Notably, their role in the persistence of follicular B cells, the main mature B-cell subset, is controversial. Here, we show that canonical NF-κB signaling does not contribute to immediate (short-term) survival of follicular B cells, contrasting with the crucial tonic B-cell antigen receptor survival signals, but is required for their long-term persistence as well as functional fitness.
Language contact and change in the Americas
Authors: Thomason Sarah G.
Published: April 2016

This paper begins by sketching the current state of studies in the history, especially the contact history, of indigenous languages of the Americas. Most of the historical linguistic research to date has focused on North American languages of the United States and Canada: here the membership and development of most language families have received systematic attention, and there is also a large and growing number of investigations of contact phenomena in North American languages. The historical linguistics of the rest of the Americas is less well developed, but rapid progress is now being made, both in genetic classification and in contact phenomena. The second half of the paper places the chapters in this volume in the context of contact and change in the languages of the Americas.
The usual suspects
Authors: Givón T.
Published: April 2016

In the grammaticalization of verbs, a small group of lexical verbs is particularly prominent, invariably found on the short-list of ‘light verbs’ (Wilson 1999) that display peculiar grammatical properties. This chapter describes the behavior of a small group of such verbs in Ute. In addition to the properties noted above, these verbs in Ute display one conspicuous morphotactic irregularity: Unlike most lexical verbs that appear as the first element in the verbal word, these usual suspects can only appear as the second (or last) element in the complex verbal word. That is, in the characteristic position of Ute verbal suffixes.
Discourse pattern replication in South Conchucos Quechua and Andean Spanish
Authors: Hintz Diane M.
Published: April 2016

South Conchucos Quechua (SCQ) and Andean Spanish illustrate how discourse-pragmatic patterns of a model language are replicated in the other language of bilinguals. Specifically, patterns involving two tense forms in SCQ are replicated in the Spanish of bilinguals. The SCQ past -r(q)a is used to introduce and conclude segments of talk and to give explanations, while the past that developed from a present perfect -sha is used with the main events of a narrative and to mark surprise. In Andean Spanish, the preterite and the present perfect are used in the same ways as the SCQ -r(q)a and -sha, respectively. Replication of usage patterns often goes undetected, as these two have been, due to the fact that the substance itself is not copied (Mithun 2012: 13).
Synthesis, characterization and fluorescent properties of water-soluble glycopolymer bearing curcumin pendant residues
Authors: Zhang Haisong , Yu Meng , Zhang Hailei , Bai Libin , Wu Yonggang , Wang Sujuan , Ba Xinwu
Published: April 2016

Curcumin is a potential natural anticancer drug with low oral bioavailability because of poor water solubility. The aqueous solubility of curcumin is enhanced by means of modification with the carbohydrate units. Polymerization of the curcumin-containing monomer with carbohydrate-containing monomer gives the water-soluble glycopolymer bearing curcumin pendant residues. The obtained copolymers (P1 and P2) having desirable water solubility were well-characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), gel permeation chromatography (GPC), UV–Vis absorption spectroscopy, and photoluminescence spectroscopy. The copolymer P2 with a molar ratio of 1:6 (curcumin/carbohydrate) calculated from the proton NMR results exhibits a similar anticancer activity compared to original curcumin, which may serve as a potential chemotherapeutic agent in the field of anticancer medicine.
KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs
Authors: Mangeol Pierre , Prevo Bram , Peterman Erwin J. G.
Published: April 2016

Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way.
Castles in the Air
Authors: Jaffe Audrey
Published: April 2016

This chapter discusses a structure of invitation and prohibition in the fantasies of Orley Farm’s characters and in Trollope’s own writing process, epitomized by the daydreams (“castles in the air”) he described as his own training for the writing of realist fiction. It highlights the question “Why should I not?” which introduces many of these characters’ daydreams, aligning the imagining of real-world prohibitions with the invitation to fantasize or daydream. And it also aligns social prohibitions with the idea of realism as a genre, extending the argument about realism and fantasy to a consideration of genres as ideological formations. Trollope ties his own realist labor to the labor of thinking his characters and, by extension, readers, must undertake as a condition of his own realism.
The mineral clouds on HD 209458b and HD 189733b
Authors: Helling Ch. , Lee E. , Dobbs-Dixon I. , Mayne N. , Amundsen D. S. , Khaimova J. , Unger A. A. , Manners J. , Acreman D. , Smith C.
Published: April 2016

3D atmosphere model results are used to comparatively study the kinetic, non-equilibrium cloud formation in the atmospheres of two example planets guided by the giant gas planets HD 209458b and HD 189733b. Rather independently of hydrodynamic model differences, our cloud modelling suggest that both planets are covered in mineral clouds throughout the entire modelling domain. Both planets harbour chemically complex clouds that are made of mineral particles that have a height-dependent material composition and size. The remaining gas-phase element abundances strongly affect the molecular abundances of the atmosphere in the cloud-forming regions. Hydrocarbon and cyanopolyyne molecules can be rather abundant in the inner, dense part of the atmospheres of HD 189733b and HD 209458b. No one value for metallicity and the C/O ratio can be used to describe an extrasolar planet. Our results concerning the presence and location of water in relation to the clouds explain some of the observed difference between the two planets. In HD 189733b, strong water features have been reported while such features appear less strong for HD 209458b. By considering the location of the clouds in the two atmospheres, we see that obscuring clouds exist high in the atmosphere of HD 209458b, but much deeper in HD 189733b. We further conclude that the (self-imposed) degeneracy of cloud parameters in retrieval methods can only be lifted if the cloud formation processes are accurately modelled in contrast to prescribing them by independent parameters.
Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data
Authors: Wang Yong , Jiang Rui , Wong Wing Hung
Published: April 2016

Cell packs a lot of genetic and regulatory information through a structure known as chromatin, i.e. DNA is wrapped around histone proteins and is tightly packed in a remarkable way. To express a gene in a specific coding region, the chromatin would open up and DNA loop may be formed by interacting enhancers and promoters. Furthermore, the mediator and cohesion complexes, sequence-specific transcription factors, and RNA polymerase II are recruited and work together to elaborately regulate the expression level. It is in pressing need to understand how the information, about when, where, and to what degree genes should be expressed, is embedded into chromatin structure and gene regulatory elements. Thanks to large consortia such as Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomic projects, extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell types. This rich data offer an exciting opportunity to model the causal regulatory relationship. Here, we will review the current experimental approaches, foundational data, computational problems, interpretive frameworks, and integrative models that will enable the accurate interpretation of regulatory landscape. Particularly, we will discuss the efforts to organize, analyze, model, and integrate the DNA accessibility data, transcriptional data, and functional genomic regions together. We believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.
Use of Dexmedetomidine Along With Local Infiltration Versus General Anesthesia for Burr Hole and Evacuation of Chronic Subdural Hematoma (CSDH)
Authors: Surve Rohini M. , Bansal Sonia , Reddy Madhusudan , Philip Mariamma
Published: April 2016

Background:

In neurosurgery, chronic subdural hematoma (CSDH) is a very common clinical entity. Both general anesthesia (GA) and local anesthesia with or without sedation are used for the surgical treatment of CSDH. Sedation with dexmedetomidine has been safely used for various diagnostic and therapeutic procedures. However, its effectiveness against GA has not been evaluated for surgical treatment of CSDH. We tried to compare dexmedetomidine sedation technique with the GA technique for surgical treatment of CSDH.

Materials and Methods:

In this prospective-randomized study, 76 patients undergoing surgery for CSDH were divided into 2 groups using computer-generated randomized tables; Dex group ([n=38]; received IV bolus of dexmedetomidine 1 mcg/kg over 10 min followed by maintenance infusion 0.5 mcg/kg/h) and GA group ([n=38; of which 4 patients were dropped out]; received endotracheal intubation with balanced anesthesia).

Results:

Both anesthesia techniques (Dex group; n=35/38 [92.1%] and GA group; n=34/34 [100%]) were successfully used for surgical treatment of CSDH. Significantly less time for anesthesia onset (14.2±4.2 vs. 20.5±3.4 min, P=0.001), total duration of surgery (77.1±23.9 vs. 102.7± 24.8 min, P=0.001), and recovery from anesthesia (7.4±5.9 vs. 13.2±6.5 min, P=0.004) was observed in the Dex group compared with GA group. Perioperative hemodynamic fluctuations were more common in the GA group as against the Dex group. Postoperative complications (n=2 vs. 9, P=0.021) and length of hospital stay (1.05±0.23 vs. 1.79±2.1 d, P=0.007) were significantly less in the Dex group as against the GA group.

Conclusions:

Dexmedetomidine sedation with local anesthesia is a safe and effective technique for burr hole and evacuation of CSDH. It is associated with significantly shorter operative time, lesser hemodynamic fluctuations, postoperative complications, and length of hospital stay, thus it is a better alternative to GA.
Medial Epicondyle Fractures in the Pediatric Overhead Athlete
Authors: Cruz Aristides I. , Steere Joshua T. , Lawrence J. Todd R.
Published: April 2016

The medial epicondyle serves as the proximal attachment of the medial ulnar collateral ligament and the origin of the flexor pronator musculature and as such it is responsible for resisting the main static and dynamic restraints to valgus force at the elbow. Fractures through the physis in the developing elbow are common and treatment remains controversial. Biomechanical modeling predicts that anterior should be the direction of greatest displacement. Anatomic considerations predict that anterior displacement should have the greatest effect on elbow stability and range of motion making the ulnar collateral ligament too loose in flexion and too tight in extension and potentially leading to valgus laxity in flexion and a block to full extension. In the elite overhead athlete, where elbow stability is critical both for sports performance and the long-term health of the elbow, assessment of anterior displacement is thus theoretically an important consideration. Standard radiographic views cannot adequately assess anterior displacement. Specialized radiographs and 3-dimensional modalities such as computerized tomography and magnetic resonance imaging can adequately assess anterior displacement and in the overhead athlete can sometimes aid in the decision-making process. Here, we present a review of the current literature and the rationale for a treatment algorithm for medial epicondyle fractures in the skeletally immature overhead athlete.
Mean platelet volume and red cell distribution width to platelet ratio for predicting the severity of hepatic fibrosis in patients with chronic hepatitis C
Authors: Karagöz Ergenekon , Tanoğlu Alpaslan , Ülçay Asim , Erdem Hakan , Turhan Vedat , Kara Muammer , Yazgan Yusuf
Published: April 2016

Objective

We designed this study to investigate the relationship between the severity of fibrosis and mean platelet volume (MPV), red cell distribution width, and red cell distribution width to platelet ratio (RPR) in patients with chronic hepatitis C (CHC).

Design

Overall, 98 biopsy-proven naïve CHC cases were enrolled in the study. Complete blood count variables, including white blood cell, hemoglobin, platelet count, MPV, red cell distribution width, platelet distribution width as well as aspartate transaminase, alanine transaminase, total bilirubin, albumin, and other routine biochemical parameters, were tested. Liver biopsy samples were assessed according to the Ishak scoring system. Data analyses were carried out using SPSS-15 software. Statistical significance was set at a P-value of less than 0.05.

Results

Of the 98 cases, 80 (81.6%) were men and 18 (18.4%) were women. Fibrosis scores of 69 cases (70.4%) (group 1) were less than 3, whereas 29 cases had fibrosis scores at least 3 (29.6%) (group 2). Significant differences in MPV and RPR were observed between these two groups (MPV: 8.19±1.002 vs. 8.63±0.67 fl, P<0.05; RPR: 0.0526±0.02 vs. 0.0726±0.02, P=0.001). The areas under the curve of the RPR and MPV for predicting significant fibrosis were 0.705 and 0.670, which was superior to the aspartate transaminase-to-alanine transaminase ratio and aspartate transaminase-to-platelet ratio index scores of the study group. Cut-off values were calculated for diagnostic performance, and the cut-off values for MPV and RPR were 8.5 and 0.07 fl, respectively.

Conclusion

MPV and RPR values were significantly higher in patients with CHC, associated with severity, and can be used to predict advanced histological liver damage. The use of MPV and RPR may reduce the need for liver biopsy. Further studies are required to determine the relationship between these parameters and the severity of fibrosis in hepatitis C patients.
Spiritual Well-being in Patients With Metastatic Colorectal Cancer Receiving Noncurative Chemotherapy
Authors: Rohde Gudrun , Kersten Christian , Vistad Ingvild , Mesel Terje
Published: April 2016

Background:

Spiritual well-being (SWB) is an important quality-of-life dimension for cancer patients in the palliative phase. Therefore, it is important for healthcare professionals to recognize the concept of SWB from the patient’s point of view. A deeper understanding of how patients experience and reflect upon these issues might influence patient care.

Objectives:

The aim of this study was to explore SWB in colorectal cancer patients receiving chemotherapy in the palliative phase.

Methods:

We used a qualitative method of in-depth interviews and a hermeneutic editing approach for the analyses and interpretations.

Results:

Twenty colorectal cancer patients in the palliative phase, aged 34 to 75 years, were included: 12 patients were receiving first-line chemotherapy, and 8 patients were receiving second-line chemotherapy. Through empirical analyses, we identified subthemes according to the SWB dimensions defined by the European Organisation for Research and Treatment of Cancer quality-of-life group. Under the SWB dimension, (i) relationships with self and others, we identified the subthemes: (a) strategies for inner harmony and (b) sharing feelings with significant others. Under the dimension, (ii) existential issues, we identified the subtheme (c) coping with end-of-life thoughts. Under the dimension, (iii) specifically religious and/or spiritual beliefs and practices, we identified the subtheme (d) seeking faith as inner support.

Conclusion:

Knowledge about cancer patients’ use of different strategies to increase their SWB may help healthcare professionals to guide patients through this vulnerable phase.

Implication for Practice:

Healthcare professionals need sufficient courage and willingness to share their patients’ thoughts, beliefs, and grief to be able to guide patients toward improving their SWB.
Severe Acute Kidney Injury Following Stage 1 Norwood Palliation: Effect on Outcomes and Risk of Severe Acute Kidney Injury at Subsequent Surgical Stages*
Authors: Wong Joshua H. , Selewski David T. , Yu Sunkyung , Leopold Kay E. , Roberts Katelyn H. , Donohue Janet E. , Ohye Richard G. , Charpie John R. , Goldberg Caren S. , DeWitt Aaron G.
Published: April 2016

Objectives:

To identify associations of severe acute kidney injury early after stage 1 (Norwood) operation with risk of severe acute kidney injury and comorbidities at subsequent palliative stages in patients with hypoplastic left heart syndrome and other single ventricle lesions with left-sided obstruction.

Design:

Retrospective cohort study. Severe acute kidney injury defined as Kidney Disease Improving Global Outcomes stage 3.

Setting:

Single pediatric cardiac center.

Patients:

Infants less than or equal to 28 days old with single ventricle physiology and left-sided obstruction undergoing stage 1 operation between September 2007 and November 2012 (n = 136).

Interventions:

None.

Measurements and Main Results:

The occurrence rate of severe acute kidney injury was 21% (28/136) following stage 1, 12% (12/98) following stage 2 palliation (superior cavo-pulmonary anastomosis), and 10% (7/73) following stage 3 palliation (total cavo-pulmonary anastomosis). Severe acute kidney injury early after stage 1 operation was significantly associated with continuous intravenous loop diuretic infusion, need for extracorporeal membrane oxygenation, and in-hospital death (all p < 0.05). Gestational age at birth was associated with severe acute kidney injury at stage 2 (p = 0.04) and stage 3 (p = 0.01). Severe acute kidney injury at stage 1 was an independent risk factor for severe acute kidney injury at stage 2 (adjusted odds ratio, 4.3; 95% CI, 1.1–16.9; p = 0.04). Development of severe acute kidney injury after stage 1 was associated with longer mechanical ventilation time after stage 3 (p = 0.047).

Conclusions:

Severe acute kidney injury after stage 1 palliation was an independent risk factor for developing severe acute kidney injury at stage 2, and was associated with prolonged duration of mechanical ventilation following stage 3. Information on the incidence and associated risk factors for postoperative acute kidney injury in hypoplastic left heart syndrome patients from multiple congenital heart centers is a necessary next step to further understand the long-term burden of severe acute kidney injury after staged palliation.
The Phonomotor Approach to Treating Phonological-Based Language Deficits in People With Aphasia
Authors: Kendall Diane L. , Nadeau Stephen E.
Published: April 2016

The phonomotor treatment program for treating word-retrieval deficits among people with aphasia is inspired by a parallel distributed processing model of lexical processing and is focused at the level of individual phonemes and phoneme sequences. Because verbal production of words involves the translation of a lexical-semantic representation into phonological representations, training the repertoire of phonological sequences should enable individuals with anomia to regain the ability to learn words and sequences, generalize to linguistic items not trained, and continue growth following treatment termination. The development and refinement of the phonomotor treatment program, which began in 2000, have followed the 5-phase model for communication disorders and sciences framework outlined by R. Robey (2004). To date, there have been 8 published articles on the phonomotor treatment program. A large-scale randomized trial comparing phonomotor with standard of care for word-retrieval deficits is underway. The goal of this article is to review the theoretical framework, treatment procedures, current evidence, and future directions of the phonomotor protocol.
Script Templates
Authors: Kaye Rosalind C. , Cherney Leora R.
Published: April 2016

Purpose:

Script training for aphasia involves repeated practice of relevant phrases and sentences that, when mastered, can potentially be used in other communicative situations. Although an increasingly popular approach, script development can be time-consuming. We provide a detailed summary of the evidence supporting this approach. We then describe a method in which scripts at various levels of difficulty are created by systematically manipulating readability and grammatical and semantic components. We assess the appropriateness of using these template-based scripts with persons with aphasia of differing severities.

Method:

We evaluated the oral reading performance of 8 individuals with chronic nonfluent aphasia on scripts developed from the templates. Scripts were either of high or low difficulty relative to their aphasia severity and personalized by inserting the participant's town and the name of an acquaintance. Oral reading probes were taken on 3 separate days within a week, and performance within and across participants was examined.

Results:

Regardless of the participant's aphasia severity, scripts in the low-difficulty condition were read with significantly greater accuracy than scripts in the high-difficulty condition.

Discussion:

These findings support the use of graded script templates to ensure that appropriately challenging scripts are delivered to persons with aphasia for both clinical practice and research.
Aphasia Centers and the Life Participation Approach to Aphasia
Authors: Elman Roberta J.
Published: April 2016

The Aphasia Center is a service delivery model that provides an interactive community for persons with aphasia. This model has been increasing in popularity over the last 20 years. Aphasia Centers are consistent with a social model of health care and disability. They offer the potential for linguistic, communicative, and psychosocial benefits. The purpose of this article is to describe the historical context that served as the catalyst for Aphasia Centers as well as to offer a firsthand account of their development. Included is a summary of the research evidence, as well as other factors that support the science underlying aphasia group treatment, Aphasia Centers, and the Life Participation Approach to Aphasia. Finally, examples are provided that show how this service delivery model is being incorporated into clinical guidelines, clinical pathways, and clinical best practices.
A Review of Verb Network Strengthening Treatment
Authors: Edmonds Lisa A.
Published: April 2016

This article examines Verb Network Strengthening Treatment (VNeST), a relatively new treatment approach for anomia in people with aphasia. The VNeST protocol aims to promote generalization to increased lexical retrieval of untrained words across a hierarchy of linguistic tasks, including single-word naming of nouns and verbs, sentence production, and discourse. The concept of the verb network relates to the centrality of the verb to the semantics and syntax of a sentence. The VNeST protocol elicits diverse agents (e.g., musician) and patients (e.g., tambourine) around trained verbs (e.g., shake) to activate a range of semantic concepts and personal responses to potentially facilitate generalization to a multitude of lexical items. The pre- and posttreatment generalization results for the 19 participants reported in English are analyzed. Participants represent a range of aphasia severities and types, including Broca's, transcortical motor, anomic, Wernicke's, and conduction aphasia. A previous study that evaluated 3 monolingual Korean speakers on a modified version of VNeST that accommodated Korean's verb final word order is also summarized. The findings across the 5 English studies and the Korean study revealed increased noun and verb naming and lexical retrieval in sentences and discourse on untrained items and tasks for more than half of the participants, suggesting preliminary efficacy for VNeST. Potential predictors and mechanisms of improvement are explored, and clinical implications, including consideration of goals, outcome measures, dosage, inclusion and evaluation of writing, and verb selection, are discussed.
Who Benefits From an Intensive Comprehensive Aphasia Program?
Authors: Babbitt Edna M. , Worrall Linda , Cherney Leora R.
Published: April 2016

Purpose:

This article summarizes current outcomes from intensive comprehensive aphasia programs (ICAPs) and examines data from one ICAP to identify those who respond and do not respond to treatment.

Methods:

Participants were divided into 2 groups, responders and nonresponders, based on ±5-point change score on the Western Aphasia Battery–Revised Aphasia Quotient. Independent-samples t tests and χ2 tests were performed to identify differences between groups on demographic (age and gender) and aphasia-related factors (months postonset, type of aphasia, aphasia severity, naming, nonverbal cognition measure, and self-rating of communication confidence). Logistic regression determined if factors contributed to a treatment response.

Results:

There were significant differences between the groups on age and months postonset. Gender, type of aphasia, naming, nonverbal cognitive measure, and communication confidence were not significantly different. Logistic regression indicated that age was the only predictive factor contributing to treatment response.

Conclusions:

This study only identified age as a predictor of responders. Future research may need to examine a broader scope of variables that can impact recovery in aphasia.
Preface of the special issue quantum foundations: information approach
Authors: D'Ariano Giacomo Mauro , Khrennikov Andrei
Published: April 2016

This special issue is based on the contributions of a group of top experts in quantum foundations and quantum information and probability. It enlightens a number of interpretational, mathematical and experimental problems of quantum theory.
Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap)
Authors: Hoffberg Sandra L. , Kieran Troy J. , Catchen Julian M. , Devault Alison , Faircloth Brant C. , Mauricio Rodney , Glenn Travis C
Published: April 2016

Molecular ecologists seek to genotype hundreds to thousands of loci from hundreds to thousands of individuals at minimal cost per sample. Current methods such as restriction site associated DNA sequencing (RADseq) and sequence capture are constrained by costs associated with inefficient use of sequencing data and sample preparation, respectively. Here, we demonstrate RADcap, an approach that combines the major benefits of RADseq (low cost with specific start positions) with those of sequence capture (repeatable sequencing of specific loci) to significantly increase efficiency and reduce costs relative to current approaches. The RADcap approach uses a new version of dual-digest RADseq (3RAD) to identify candidate SNP loci for capture bait design, and subsequently uses custom sequence capture baits to consistently enrich candidate SNP loci across many individuals. We combined this approach with a new library preparation method for identifying and removing PCR duplicates from 3RAD libraries, which allows researchers to process RADseq data using traditional pipelines, and we tested the RADcap method by genotyping sets of 96 to 384Wisteriaplants. Our results demonstrate that our RADcap method: 1) can methodologically reduce (to <5%) and computationally remove PCR duplicate reads from data; (2) achieves 80-90% reads-on-target in 11 of 12 enrichments; (3) returns consistent coverage (≥4x) across >90% of individuals at up to 99.9% of the targeted loci; (4) produces consistently high occupancy matrices of genotypes across hundreds of individuals; and (5) is inexpensive, with reagent and sequencing costs totaling <$6/sample and adapter and primer costs of only a few hundred dollars.
Promoter architecture and sex-specific gene expression in the microcrustaceanDaphnia pulexrevealed by large-scale profiling of 5′-mRNA ends
Authors: Raborn R. Taylor , Spitze Ken , Brendel Volker P. , Lynch Michael
Published: April 2016

Large-scale TSS profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize thecis-regulatory landscape of the water fleaDaphnia pulex,an emerging model arthropod that reproduces both asexually (viaparthenogenesis) and sexually (viameiosis). We performed CAGE with RNA isolated fromD. pulexwithin three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a ‘Daphnia Promoter Atlas’-a catalog of active promoters across the surveyed states. We carried outde novomotif discovery using CAGE-defined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements (e.g. TATA, Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable state-specific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. The Daphnia Promoter Atlas presented here provides a valuable resource for comparative study ofcis-regulatory regions in arthropods, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.
Temporal microbiome road-maps guided by perturbations
Authors: García-Jiménez Beatriz , Wilkinson Mark
Published: April 2016

Motivation

There are few tools that allow longitudinal analysis of metagenomic data subjected to distinct perturbations.

Methods

This study examines longitudinal metagenomics data modelled as a Markov Decision Process (MDP). Given an external perturbation, the MDP predicts the next microbiome state in a temporal sequence, selected from a finite set of possible microbiome states.

Results

We examined three distinct datasets to demonstrate this approach. An MDP created for a vaginal microbiome time series generates a variety of behaviour policies. For example, that moving from a state associated with bacterial vaginosis to a healthier one, requires avoiding perturbations such as lubricant, sex toys, tampons and anal sex. The flexibility of our proposal is verified after applying MDPs to human gut and chick gut microbiomes, taking nutritional intakes, or salmonella and probiotic treatments, respectively, as perturbations. In the latter case, MDPs provided a quantitative explanation for why salmonella vaccine accelerates microbiome maturation in chicks. This novel analytical approach has applications in, for example, medicine where the MDP could suggest the sequence of perturbations (e.g. clinical interventions) to apply to follow the best path from any given starting state, to a desired (healthy) state, avoiding strongly negative states.
From Visual Exploration to Storytelling and Back Again
Authors: Gratzl Samuel , Lex Alexander , Gehlenborg Nils , Cosgrove Nicola , Streit Marc
Published: April 2016

A major challenge of data-driven biomedical research lies in the collection and representation of data provenance information to ensure reproducibility of findings. In order to communicate and reproduce multi-step analysis workflows executed on datasets that contain data for dozens or hundreds of samples, it is crucial to be able to visualize the provenance graph at different levels of aggregation. Most existing approaches are based on node-link diagrams, which do not scale to the complexity of typical data provenance graphs. In our proposed approach we reduce the complexity of the graph using hierarchical and motif-based aggregation. Based on user action and graph attributes a modular degree-of-interest (DoI) function is applied to expand parts of the graph that are relevant to the user. This interest-driven adaptive provenance visualization approach allows users to review and communicate complex multi-step analyses, which can be based on hundreds of files that are processed by numerous workflows. We integrate our approach into an analysis platform that captures extensive data provenance information and demonstrate its effectiveness by means of a biomedical usage scenario.
Supramolecular architectures in CoIIand CuIIcomplexes with thiophene-2-carboxylate and 2-amino-4,6-dimethoxypyrimidine ligands
Authors: Karthikeyan Ammasai , Thomas Muthiah Packianathan , Perdih Franc
Published: April 2016

The coordination chemistry of mixed-ligand complexes continues to be an active area of research since these compounds have a wide range of applications. Many coordination polymers and metal–organic framworks are emerging as novel functional materials. Aminopyrimidine and its derivatives are flexible ligands with versatile binding and coordination modes which have been proven to be useful in the construction of organic–inorganic hybrid materials and coordination polymers. Thiophenecarboxylic acid, its derivatives and their complexes exhibit pharmacological properties. Cobalt(II) and copper(II) complexes of thiophenecarboxylate have many biological applications, for example, as antifungal and antitumor agents. Two new cobalt(II) and copper(II) complexes incorporating thiophene-2-carboxylate (2-TPC) and 2-amino-4,6-dimethoxypyrimidine (OMP) ligands have been synthesized and characterized by X-ray diffraction studies, namely (2-amino-4,6-dimethoxypyrimidine-κN)aquachlorido(thiophene-2-carboxylato-κO)cobalt(II) monohydrate, [Co(C5H3O2S)Cl(C6H9N3O2)(H2O)]·H2O, (I), andcatena-poly[copper(II)-tetrakis(μ-thiophene-2-carboxylato-κ2O:O′)-copper(II)-(μ-2-amino-4,6-dimethoxypyrimidine-κ2N1:N3)], [Cu2(C5H3O2S)4(C6H9N3O2)]n, (II). In (I), the CoIIion has a distorted tetrahedral coordination environment involving one O atom from a monodentate 2-TPC ligand, one N atom from an OMP ligand, one chloride ligand and one O atom of a water molecule. An additional water molecule is present in the asymmetric unit. The amino group of the coordinated OMP molecule and the coordinated carboxylate O atom of the 2-TPC ligand form an interligand N—H...O hydrogen bond, generating anS(6) ring motif. The pyrimidine molecules also form a base pair [R22(8) motif]viaa pair of N—H...N hydrogen bonds. These interactions, together with O—H...O and O—H...Cl hydrogen bonds and π–π stacking interactions, generate a three-dimensional supramolecular architecture. The one-dimensional coordination polymer (II) contains the classical paddle-wheel [Cu2(CH3COO)4(H2O)2] unit, where each carboxylate group of four 2-TPC ligands bridges two square-pyramidally coordinated CuIIions and the apically coordinated OMP ligands bridge the dinuclear copper units. Each dinuclear copper unit has a crystallographic inversion centre, whereas the bridging OMP ligand has crystallographic twofold symmetry. The one-dimensional polymeric chains self-assembleviaN—H...O, π–π and C—H...π interactions, generating a three-dimensional supramolecular architecture.
On the group-theoretical approach to the study of interpenetrating nets
Authors: Baburin Igor A.
Published: April 2016

Using group–subgroup and group–supergroup relations, a general theoretical framework is developed to describe and derive interpenetrating 3-periodic nets. The generation of interpenetration patterns is readily accomplished by replicating a single net with a supergroupGof its space groupHunder the condition that site symmetries of vertices and edges are the same in bothHandG. It is shown that interpenetrating nets cannot be mapped onto each other by mirror reflections because otherwise edge crossings would necessarily occur in the embedding. For the same reason any other rotation or roto-inversion axes fromG \ Hare not allowed to intersect vertices or edges of the nets. This property significantly narrows the set of supergroups to be included in the derivation of interpenetrating nets. A procedure is described based on the automorphism group of aHopf ring net[Alexandrovet al.(2012).Acta Cryst.A68, 484–493] to determine maximal symmetries compatible with interpenetration patterns. The proposed approach is illustrated by examples of twofold interpenetratedutp,diaandpcunets, as well as multiple copies of enantiomorphic quartz (qtz) networks. Some applications to polycatenated 2-periodic layers are also discussed.
Vertex-connectivity in periodic graphs and underlying nets of crystal structures
Authors: Eon Jean-Guillaume
Published: April 2016

Periodic nets used to describe the combinatorial topology of crystal structures have been required to be 3-connected by some authors. A graph isn-connected when deletion of less thannvertices does not disconnect it.n-Connected graphs area fortiarin-coordinated but the converse is not true. This article presents an analysis of vertex-connectivity in periodic graphs characterized through their labelled quotient graph (LQG) and applied to a definition of underlying nets of crystal structures. It is shown that LQGs ofp-periodic graphs (p≥ 2) that are 1-connected or 2-connected, but not 3-connected, arecontractiblein the sense that they display, respectively, singletons or pairs of vertices separating dangling or linker components with zero net voltage over every cycle. The contraction operation that substitutes vertices and edges, respectively, for dangling components and linkers yields a 3-connected graph with the same periodicity. 1-Periodic graphs can be analysed in the same way through their LQGs but the result may not be 3-connected. It is claimed that long-range topological properties of periodic graphs are respected by contraction so that contracted graphs can represent topological classes of crystal structures, be they rods, layers or three-dimensional frameworks.
Multidimensional period doubling structures
Authors: Lee Jeong-Yup , Flom Dvir , Ben-Abraham Shelomo I.
Published: April 2016

This paper develops the formalism necessary to generalize the period doubling sequence to arbitrary dimension by straightforward extension of the substitution and recursion rules. It is shown that the period doubling structures of arbitrary dimension are pure point diffractive. The symmetries of the structures are pointed out.