bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-generation libraries for robust RNA interference-based genome-wide screens
Authors: Kampmann Martin , Horlbeck Max A. , Chen Yuwen , Tsai Jordan C. , Bassik Michael C. , Gilbert Luke A. , Villalta Jacqueline E. , Kwon S. Chul , Chang Hyeshik , Kim V. Narry , Weissman Jonathan S. 
Published: June 2015

Significance
Genetic screening is a classic approach to identify genes acting in a biological process of interest. In mammalian cells, screens are commonly based on RNA interference (RNAi), in which a short interfering RNA (siRNA) or short-hairpin RNA (shRNA) triggers degradation of cellular messenger RNAs. RNAi approaches are prone to false-positive results because of siRNA/shRNA off-target effects and false-negative results because of siRNAs/shRNAs lacking activity. We previously established that these problems can be minimized with ultracomplex shRNA libraries. Here, we present next-generation shRNA libraries targeting the human and mouse genomes, for which we improved several features to increase shRNA activity. In a pilot screen, the new library yields complementary results to clustered regularly interspaced short palindromic repeats interference (CRISPRi), an orthogonal approach we developed recently.
Inflammation induces dermal Vγ4
+
γδT17 memory-like cells that travel to distant skin and accelerate secondary IL-17–driven responses
Authors: Ramírez-Valle Francisco , Gray Elizabeth E. , Cyster Jason G. 
Published: June 2015

Significance
An attribute of adaptive immunity is the generation of memory cells that mount enhanced responses after rechallenge. While memory is best understood for αβT cell receptor-bearing lymphocytes, the properties of γδT cells in the context of a secondary challenge have been less examined. After murine skin inflammation with imiquimod, IL-17–secreting γδT cells expand in lymph nodes and traffic to skin where they persist as memory-like cells capable of rapid activation upon rechallenge. This enhanced secondary response is in part mediated by increased IL-1R1 expression. Expansion of potentially pathogenic memory cells in lymph nodes and redistribution throughout normal and inflamed skin may help explain the generalized worsening of psoriasis reported in patients undergoing localized skin treatment with imiquimod.
Osborne Reynolds pipe flow: Direct simulation from laminar through gradual transition to fully developed turbulence
Authors: Wu Xiaohua , Moin Parviz , Adrian Ronald J. , Baltzer Jon R. 
Published: June 2015

Significance
The precise dynamics of disturbance energy growth and breakdown in pipe transition is a century-old unresolved problem in fluid mechanics. In this paper, we demonstrate that the mystery attributed to the breakdown process of the Osborne Reynolds pipe transition can be partially resolved with a direct, spatially evolving simulation that carries weakly but finitely perturbed laminar inflow through gradual rather than abrupt transition arriving at the fully developed turbulent state. Some of the previously attributed abruptness and mysteriousness was perhaps due to the inability to study the process accurately with very fine spatial and temporal resolution. The energy norm was found to grow exponentially rather than algebraically. The sensitivity of the transition process to pipe entrance conditions is demonstrated.
Diel Resource Partitioning among Juvenile Atlantic Salmon, Brown Trout, and Rainbow Trout during Summer
Authors: Johnson James H. , McKenna James E. 
Published: June 2015

Abstract
Interspecific partitioning of food and habitat resources has been widely studied in stream salmonids. Most studies have examined resource partitioning between two native species or between a native species and one that has been introduced. In this study we examine the diel feeding ecology and habitat use of three species of juvenile salmonids (i.e., Atlantic Salmon Salmo salar, Brown Trout Salmo trutta, and Rainbow Trout Oncorhynchus mykiss) in a tributary of Skaneateles Lake, New York. Subyearling Brown Trout and Rainbow Trout fed more heavily from the drift than the benthos, whereas subyearling Atlantic Salmon fed more from the benthos than either species of trout. Feeding activity of Atlantic Salmon and Rainbow Trout was similar, with both species increasing feeding at dusk, whereas Brown Trout had no discernable feeding peak or trough. Habitat availability was important in determining site-specific habitat use by juvenile salmonids. Habitat selection was greater during the day than at night. The intrastream, diel, intraspecific, and interspecific variation we observed in salmonid habitat use in Grout Brook illustrates the difficulty of acquiring habitat use information for widespread management applications.
Received June 13, 2014; accepted January 28, 2015
Selection and evaluation of reference genes for expression analysis of Cassi
Authors: Liu Zubi , Zhu Qiankun , Li Juanjuan , Yu Jihua , Li Yangyang , Huang Xinhe , Wang Wanjun , Tan Rui , Zhou Jiayu , Liao Hai 
Published: June 2015

Abstract
Cassia obtusifolia, belonging to legume family, is important in many fields with high pharmaceutical, economic, and ecological values. These interests of C. obtusifolia triggered in-depth and fundamental genetic and molecular research. Therefore, the stable reference gene is necessary for normalization of the gene expression studies. In this study, 10 candidate reference genes were subjected to expression analysis in 12 different tissues and under different stresses by qRT-PCR. The expression stability was evaluated using geNorm, NormFinder, and BestKeeper software. In conclusion, different suitable reference genes were selected in different tissues and under different stress. CYP1, EF1α2, ACT2, UBQ1 were the most stable reference genes in all samples. The relative expression levels of WRKY gene were detected to confirm the reliability of the selected reference genes. These results provided suitable reference genes that could be used for normalization in C. obtusifolia tissues and under different stress.
MetaPathways v2.5: quantitative functional, taxonomic and usability improvements
Authors: Konwar Kishori M. , Hanson Niels W. , Bhatia Maya P. , Kim Dongjae , Wu Shang-Ju , Hahn Aria S. , Morgan-Lang Connor , Cheung Hiu Kan , Hallam Steven J. 
Published: June 2015

Abstract
Summary: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.
Availability and implementation: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2.
Contact: shallam@mail.ubc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
REDEMPTION: reduced dimension ensemble modeling and parameter estimation
Authors: Liu Yang , Manesso Erica , Gunawan Rudiyanto 
Published: June 2015

Abstract
Summary: Here, we present REDEMPTION (Reduced Dimension Ensemble Modeling and Parameter estimation), a toolbox for parameter estimation and ensemble modeling of ordinary differential equations (ODEs) using time-series data. For models with more reactions than measured species, a common scenario in biological modeling, the parameter estimation is formulated as a nested optimization problem based on incremental parameter estimation strategy. REDEMPTION also includes a tool for the identification of an ensemble of parameter combinations that provide satisfactory goodness-of-fit to the data. The functionalities of REDEMPTION are accessible through a MATLAB user interface (UI), as well as through programming script. For computational speed-up, REDEMPTION provides a numerical parallelization option using MATLAB Parallel Computing toolbox.
Availability and implementation: REDEMPTION can be downloaded from http://www.cabsel.ethz.ch/tools/redemption.
Contact: rudi.gunawan@chem.ethz.ch
An algorithm to identify medication nonpersistence using electronic pharmacy databases
Authors: Parker Melissa M , Moffet Howard H , Adams Alyce , Karter Andrew J 
Published: June 2015

Abstract
Objective Identifying patients who are medication nonpersistent (fail to refill in a timely manner) is important for healthcare operations and research. However, consistent methods to detect nonpersistence using electronic pharmacy records are presently lacking. We developed and validated a nonpersistence algorithm for chronically used medications.
Materials and Methods Refill patterns of adult diabetes patients (n = 14,349) prescribed cardiometabolic therapies were studied. We evaluated various grace periods (30-300 days) to identify medication nonpersistence, which is defined as a gap between refills that exceeds a threshold equal to the last days’ supply dispensed plus a grace period plus days of stockpiled medication. Since data on medication stockpiles are typically unavailable for ongoing users, we compared nonpersistence to rates calculated using algorithms that ignored stockpiles.
Results When using grace periods equal to or greater than the number of days’ supply dispensed (i.e., at least 100 days), this novel algorithm for medication nonpersistence gave consistent results whether or not it accounted for days of stockpiled medication. The agreement (Kappa coefficients) between nonpersistence rates using algorithms with versus without stockpiling improved with longer grace periods and ranged from 0.63 (for 30 days) to 0.98 (for a 300-day grace period).
Conclusions Our method has utility for health care operations and research in prevalent (ongoing) and new user cohorts. The algorithm detects a subset of patients with inadequate medication-taking behavior not identified as primary nonadherent or secondary nonadherent. Healthcare systems can most comprehensively identify patients with short- or long-term medication underutilization by identifying primary nonadherence, secondary nonadherence, and nonpersistence.
The effect of tablet computers with a mobile patient portal application on hospitalized patients’ knowledge and activation
Authors: O’Leary Kevin J , Lohman Mary E , Culver Eckford , Killarney Audrey , Randy Smith G , Liebovitz David M 
Published: June 2015

AbstractObjective To assess the effect of tablet computers with a mobile patient portal application on hospitalized patients’ knowledge and activation.Methods We developed a mobile patient portal application including pictures, names, and role descriptions of team members, scheduled tests and procedures, and a list of active medications. We evaluated the effect of the application using a controlled trial involving 2 similar units in a large teaching hospital. Patients on the intervention unit were offered use of tablet computers with the portal application during their hospitalization. We assessed patients’ ability to correctly name their nurse, primary service physicians, physician roles, planned tests and procedures, medications started, and medications stopped since admission. We also administered the Short Form of the Patient Activation Measure.Results Overall, 100 intervention- and 102 control-unit patients participated. A higher percentage of intervention-unit patients correctly named ≥1 physician (56% vs 29.4%; P &lt; .001) and ≥1 physician role (47% vs 15.7%; P &lt; .001). Knowledge of nurses’ names, planned tests, planned procedures, and medication changes was generally low and not significantly different between the study units. The Short Form of the Patient Activation Measure mean (SD) score was also not significantly different at 64.1 (13.4) vs 62.7 (12.8); P = .46.Conclusions Additional research is needed to identify optimal methods to engage and inform patients during their hospitalization, which will improve preparation for self- management after discharge.
Mycobacterium avium Complex Osteomyelitis in Persons With Human Immunodeficiency Virus: Case Series and Literature Review
Authors: Wood Brian R. , Buitrago Martha O. , Patel Sugat , Hachey David H. , Haneuse Sebastien , Harrington Robert D. 
Published: June 2015

Abstract
In persons with advanced immunosuppression, Mycobacterium avium complex (MAC) typically causes disseminated disease with systemic symptoms. We report 2 cases in which MAC caused localized osteomyelitis in human immunodeficiency virus (HIV)-infected individuals on antiretroviral therapy with rising CD4 counts. We summarize 17 additional cases of HIV-associated MAC osteomyelitis from the literature and compare CD4 count at presentation for vertebral cases versus nonvertebral cases, which reveals a significantly higher CD4 at presentation for vertebral cases (median 251 cells/µL vs 50 cells/µL; P = .043; Mann–Whitney U test). The literature review demonstrates that the majority of cases of MAC osteomyelitis, especially vertebral, occurs in individuals with CD4 counts that have increased to above 100 cells/µL on antiretroviral therapy. Among HIV-infected individuals with osteomyelitis, MAC should be considered a possible etiology, particularly in the setting of immune reconstitution.
Revisiting the Role of the Myofibroblast in Socket Surgery: An Immunohistochemical Study
Authors: Tawfik Hatem A. , Abdulhafez Mohamed H. , Fouad Yousef A. , Rashed Hazem O. , Osman Wesam M. 
Published: June 2015

Purpose:
To determine the impact of a single injection of various anti-inflammatory, antimitotic, and antiangiogenic agents on the cell count of myofibroblasts in an eviscerated socket.

Methods:
One eye from 15 skeletally mature New Zealand white rabbits was eviscerated, and the rabbits were divided into 5 groups. Each group of 3 rabbits received a 0.1 ml subconjunctival injection of a different agent. Group I received bevacizumab 25 mg/ml, group II received triamcinolone 40 mg/ml, group III received 5-fluorouracil 50 mg/ml, group IV received mitomycin-C 0.4 mg/ml, while group V was the control group and received no injections. The animals were euthanized 19 days after evisceration and conjunctival samples were submitted for histopathological examination. Monoclonal α-smooth muscle actin antibody was applied, and the mean of 5 readings of the number of myofibroblasts was recorded in each slide.

Results:
The mean count of myofibroblasts was highest for the control group and all groups achieved a statistically significant reduction in myofibroblast count compared with the control group. Sorting the means showed that Group IV (mitomycin-C) achieved the lowest mean value (p = 0.000006) followed by triamcinolone (p = 0.00048), while group I (bevacizumab) achieved the least reduction in myofibroblast count (p = 0.00148).

Conclusion:
Until newer antimyofibroblast medications and antibodies are commercially available, a single injection of mitomycin-C or triamcinolone during surgery achieves the highest mean reduction of myofibroblast count.
Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing
Authors: Ando Hiroki , Lemire Sebastien , Pires Diana P. , Lu Timothy K. 
Published: June 2015

SUMMARYBacteria are central to human health and disease, but the tools available for modulating and editing bacterial communities are limited. New technologies for tuning microbial populations would facilitate the targeted manipulation of the human microbiome and treatment of bacterial infections. For example, antibiotics are often broad spectrum in nature and cannot be used to accurately manipulate bacterial communities. Bacteriophages can provide highly specific targeting of bacteria, but relying solely on natural phage isolation strategies to assemble well-defined and uniform phage cocktails that are amenable to engineering can be a time-consuming and labor-intensive process. Here, we present a synthetic-biology strategy to modulate phage host ranges by manipulating phage genomes inSaccharomyces cerevisiae. We used this technology to swap multiple modular phage tail components and demonstrated thatEscherichia coliphage scaffolds can be redirected to target pathogenicYersiniaandKlebsiellabacteria, and conversely,Klebsiellaphage scaffolds can be redirected to targetE. coli. The synthetic phages achieved multiple orders-of-magnitude killing of their new target bacteria and were used to selectively remove specific bacteria from multi-species bacterial communities. We envision that this approach will accelerate the study of phage biology, facilitate the tuning of phage host ranges, and enable new tools for microbiome engineering and the treatment of infectious diseases.
Americana Group: KFC in Mecca
Authors: Balakrishnan Melodena Stephens 
Published: June 2015

Subject area
Marketing, Strategy, International Business.

Study level/applicability
Post-Graduates' classes.

Case overview
This case focuses on the particularities of the Kentucky Fried Chicken (KFC) restaurant run by the Americana Group in Mecca, in the Kingdom of Saudi Arabia. It allows students in the service industry, and especially those interested in the quick service industry to understand some of the challenges of operating in a market with high volume and other specific local market conditions. Perhaps, it will also allow those organizations wishing to enter into emerging markets to realize that globalization does not mean standardization of all practices but rather values.

Expected learning outcomes
On completion of utilizing the case study as an exercise, students should be able to develop: Case-specific skills: critically examine the importance of the international business and marketing strategy in the Middle East and demonstrate this by analyzing real regional/ world examples using complex theoretical frameworks; identify examples of best practice and explain the dynamics toward international business and marketing strategy with reference to a range of theoretical models; and apply these in a meaningful way to the Middle East North Africa region. Discipline-specific skills: synthesize and critically evaluate a corpus of academic literature and government reports on international business and marketing strategy; and link international business and marketing strategy concepts and theories to real regional/world examples. Personal and key skills: reflect on the process of learning and undertake independen/self-directed learning (including time management) to achieve consistent, proficient and sustained attainment. Work as either a participant or a leader of a group and contribute effectively to the achievement of objectives in the field of international business and marketing strategy.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
GEA Group – doing business in the Middle East
Authors: Michael Ian , Balakrishnan Melodena Stephens , Khan Zeenath 
Published: June 2015

Subject area
Management, Strategy, International business.

Study level/applicability
Undergraduate or Graduates.

Case overview
This case is suitable for students of international business and strategy at the advanced undergraduate-level or introductory masters-level courses. It can be used for organizational design, brand management and business-to-business management classes. It may be of interest to practitioners in the Middle East and North African (MENA) markets looking at managing cross-functional teams.

Expected learning outcomes
On completion of utilizing the case study as an exercise, students should be able to develop the following. Case-specific skills: Critically examine the importance of the international business and strategy in the Middle East and demonstrate this by analyzing real-regional/-examples using complex theoretical frameworks; identify examples of best practice and explain the dynamics toward international business and strategy with reference to a range of theoretical models and apply these in a meaningful way to the MENA region. Discipline-specific skills: Synthesize and critically evaluate a corpus of academic literature and government reports on international business and strategy; link international business and strategy concepts and theories to real-regional/world examples. Personal and key skills: Reflect on the process of learning and undertake independent/self-directed learning (including time management) to achieve consistent, proficient and sustained attainment; work as a participant or leader of a group and contribute effectively to the achievement of objectives in the field of international business and strategy.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.