bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitrification as an Alternative Approach for Sperm Cryopreservation in Marine Fishes
Authors: Cuevas-Uribe Rafael , Hu E , Daniels Harry , Gill Adriane O , Tiersch Terrence R 
Published: March 2017

Abstract
The Southern Flounder Paralichthys lethostigma is a high-value species and a promising aquaculture candidate. Because sperm volume can be limited in this species (&lt;500 µL), new sperm cryopreservation methods need to be evaluated. Vitrification is an alternative to conventional slow-rate freezing, whereby small volumes are cryopreserved at high cooling rates (&gt;1,000°C/min). The goal of this work was to develop a standardized approach for vitrification of Southern Flounder sperm. The specific objectives were to (1) evaluate thawing methods and vitrification solutions, (2) evaluate the postthaw membrane integrity of sperm vitrified in different cryoprotectant solutions, (3) examine the relationship between membrane integrity and motility, and (4) evaluate the ability of vitrified sperm to fertilize eggs. From the vitrification solutions tested, the highest postthaw motility (28 ± 9% [mean ± SD]) and membrane integrity (11 ± 4%) was observed for 20% ethylene glycol plus 20% glycerol. There was no significant difference in postthaw motility of sperm thawed at 21°C or at 37°C. Fertilization from vitrified sperm in one trial yielded the same fertilization rate (50 ± 20%) as the fresh sperm control, while the sperm from the other two males yielded 3%. This is the first report of fertilization by vitrified sperm in a marine fish. Vitrification can be simple, fast, inexpensive, performed in the field, and, at least for small fishes, offers an alternative to conventional cryopreservation. Because of the minute volumes needed for ultrarapid cooling, vitrification is not presently suited as a production method for large fishes. Vitrification can be used to reconstitute lines from valuable culture species and biomedical models, conserve mutants for development of novel lines for ornamental aquaculture, and transport frozen sperm from the field to the repository to expand genetic resources.
VCNet: vector-based gene co-expression network construction and its application to RNA-seq data
Authors: Wang Zengmiao , Fang Huaying , Tang Nelson Leung-Sang , Deng Minghua 
Published: March 2017

Abstract

Motivation
Building gene co-expression network (GCN) from gene expression data is an important field of bioinformatic research. Nowadays, RNA-seq data provides high dimensional information to quantify gene expressions in term of read counts for individual exons of genes. Such an increase in the dimension of expression data during the transition from microarray to RNA-seq era made many previous co-expression analysis algorithms based on simple univariate correlation no longer applicable. Recently, two vector-based methods, SpliceNet and RNASeqNet, have been proposed to build GCN. However, they failed to work when sample size is less than the number of exons.

Results
We develop an algorithm called VCNet to construct GCN from RNA-seq data to overcome this dimensional problem. VCNet performs a new statistical hypothesis test based on the correlation matrix of a gene–gene pair using the Frobenius norm. The asymptotic distribution of the new test is obtained under the null model. Simulation studies demonstrate that VCNet outperforms SpliceNet and RNASeqNet for detecting edges of GCN. We also apply VCNet to two expression datasets from TCGA database: the normal breast tissue and kidney tumour tissue, and the results show that the GCNs constructed by VCNet contain more biologically meaningful interactions than existing methods.

Conclusion
VCNet is a useful tool to construct co-expression network.

Availability and Implementation
VCNet is open source and freely available from https://github.com/wangzengmiao/VCNet under GNU LGPL v3

Supplementary information
Supplementary data are available at Bioinformatics online.
Subsistence harvesting by a small community does not substantially compromise coral reef fish assemblages
Authors: Martin Tyson S. H. , Connolly Rod M. , Olds Andrew D. , Ceccarelli Daniela M. , Fenner Douglas E. , Schlacher Thomas A. , Beger Maria 
Published: March 2017

AbstractFisheries usually first remove large predators before switching to smaller species, causing lasting changes to fish community structure. Reef fish provide essential protein and income for many people, and the impacts of commercial and high-intensity subsistence fishing on reef fish are well documented. However, how fish communities respond to low levels of subsistence fishing using traditional techniques (fishing for food, few fishers) is less well understood. We use three atolls in the Marshall Islands as a model system to quantify effects of commercial and subsistence fishing on reef fish communities, compared to a near-pristine baseline. Unexpectedly, fish biomass was highest on the commercially-fished atoll where the assemblage was dominated by herbivores (50% higher than other atolls) and contained few top predators (70% lower than other atolls). By contrast, fish biomass and trophic composition did not differ between pristine and subsistence-fished atolls – top predators were abundant on both. We show that in some cases, reefs can support fishing by small communities to provide food but still retain intact fish assemblages. Low-intensity subsistence fishing may not always harm marine food webs, and we suggest that its effects depend on the style and intensity of fishing practised and the type of organisms targeted.
Involvement of reactive oxygen species in ionizing radiation–induced upregulation of cell surface Toll-like receptor 2 and 4 expression in human monocytic cells
Authors: Yoshino Hironori , Kashiwakura Ikuo 
Published: March 2017

AbstractToll-like receptors (TLRs) are pattern recognition receptors that recognize pathogen-associated molecular patterns and are indispensable for antibacterial and antiviral immunity. Our previous report showed that ionizing radiation increases the cell surface expressions of TLR2 and TLR4 and enhances their responses to agonists in human monocytic THP1 cells. The present study investigated how ionizing radiation increases the cell surface expressions of TLR2 and TLR4 in THP1 cells. The THP1 cells treated or not treated with pharmaceutical agents such as cycloheximide and N-acetyl-L-cysteine (NAC) were exposed to X-ray irradiation, following which the expressions of TLRs and mitogen-activated protein kinase were analyzed. X-ray irradiation increased the mRNA expressions of TLR2 and TLR4, and treatment with a protein synthesis inhibitor cycloheximide abolished the radiation-induced upregulation of their cell surface expressions. These results indicate that radiation increased those receptors through de novo protein synthesis. Furthermore, treatment with an antioxidant NAC suppressed not only the radiation-induced upregulation of cell surface expressions of TLR2 and TLR4, but also the radiation-induced activation of the c-Jun N-terminal kinase (JNK) pathway. Since it has been shown that the inhibitor for JNK can suppress the radiation-induced upregulation of TLR expression, the present results suggest that ionizing radiation increased the cell surface expressions of TLR2 and TLR4 through reactive oxygen species–mediated JNK activation.
Past, Present, and Future of Neurosurgery in Uganda
Authors: Haglund Michael M. , Warf Benjamin , Fuller Anthony , Freischlag Kyle , Muhumuza Michael , Ssenyonjo Hussein , Mukasa John , Mugamba John , Kiryabwire Joel 
Published: March 2017

Abstract
Neurosurgery in Uganda was virtually non-existent up until late 1960s. This changed when Dr. Jovan Kiryabwire spearheaded development of a neurosurgical unit at Mulago Hospital in Kampala. His work ethic and vision set the stage for rapid expansion of neurosurgical care in Uganda.
At the beginning of the 2000s, Uganda was a country of nearly 30 million people, but had only 4 neurosurgeons. Neurosurgery's progress was plagued by challenges faced by many developing countries, such as difficulty retaining specialists, lack of modern hospital resources, and scarce training facilities. To combat these challenges 2 distinct programs were launched: 1 by Dr. Benjamin Warf in collaboration with CURE International, and the other by Dr. Michael Haglund from Duke University. Dr. Warf's program focused on establishing a facility for pediatric neurosurgery. Dr. Haglund's program to increase neurosurgical capacity was founded on a “4 T's Paradigm”: Technology, Twinning, Training, and Top-Down. Embedded within this paradigm was the notion that Uganda needed to train its own people to become neurosurgeons, and thus Duke helped establish the country's first neurosurgery residency training program.
Efforts from overseas, including the tireless work of Dr. Benjamin Warf, have saved thousands of children's lives. The influx of the Duke Program caused a dynamic shift at Mulago Hospital with dramatic effects, as evidenced by the substantial increase in neurosurgical capacity. The future looks bright for neurosurgery in Uganda and it all traces back to a rural village where 1 man had a vision to help the people of his country.
Media and Communication
Authors: Briggle Adam , Christians Clifford G. 
Published: March 2017

Abstract“Media and Communication” surveys the historical development and present form of multi-, inter-, and transdisciplinary studies of media and communication. It begins with a brief historical sketch of media and communication in order to indicate the kinds of phenomena motivating the studies. This sketch indicates that the four primary drivers of interdisciplinarity are present in this field. Media and communication are (1) inherently complex, (2) raise questions that are not confined to a single discipline, (3) pose societal problems that transcend the academy, and (4) are tightly linked to new technologies. Indeed, media and communication studies are motivated in large part by the complex questions and social changes brought about by new technologies.
Systems Thinking
Authors: Strijbos Sytse 
Published: March 2017

Abstract
Systems thinking was launched by Ludwig von Bertalanffy and others in the 1950s as an interdisciplinary movement with a broad and bold scientific program. The movement attempts to overcome the dominating mechanistic world picture and related reductionism in the sciences which is regarded as one of the main causes of the problems of the modern world. This chapter discusses the sixty-year history of systems thinking and sketches some main lines of its three domains: systems science, systems approach in technology and management, and systems philosophy. This interdisciplinary movement has stimulated fruitful theory formation in the first mentioned domain, although it has not succeeded in achieving its original far-reaching goals. Furthermore, integrative, interdisciplinary systems approaches in technology and management have become well accepted. Finally, recent developments signal a return to the intellectual-spiritual roots of the systems movement aiming for a renewal of its scientific agenda.
Interdisciplinarity in Research Evaluation
Authors: Huutoniemi Katri , Rafols Ismael 
Published: March 2017

AbstractThe evaluation of interdisciplinary research is complicated by ambiguity about what interdisciplinarity is and what it should be. The question is topical, as evaluation plays an important role in how science is being shaped and changed today. The chapter performs a meta-analysis of the concept of interdisciplinarity in research evaluation, and gives an epistemic account of what would be involved in such evaluations. First, it discusses the various ways interdisciplinarity can add value to the disciplinary organization of academia and their respective implications for research evaluation. Second, it provides tools for mapping and measuring these value-added properties and illustrates what kind of evidence they can convey to research evaluations. The combined examination of values and indicators enables a more differentiated understanding of what exactly to look at when evaluating interdisciplinary research—and more generally, how to design research evaluations from an interdisciplinary point of view.
Doctoral Student and Early Career Academic Perspectives on Interdisciplinarity
Authors: Dooling Sarah , Graybill Jessica K. , Shandas Vivek 
Published: March 2017

Abstract
This chapter focuses on the experiences of graduate students and early career academics who conduct interdisciplinary research and teaching. It offers practical advice to guide multiple participants (individuals, departments, institutions, disciplines) to navigate the benefits and challenges of participating in interdisciplinary research and teaching. The chapter concludes with reflections on the increasing calls for interdisciplinarity in the context of reduced funding for public universities and the rise of interdisciplinary programs at private liberal arts colleges.
The Military-Industrial Route to Interdisciplinarity
Authors: Fuller Steve 
Published: March 2017

Abstract
This chapter considers from both a historical and philosophical standpoint the role of war and commerce in motivating interdisciplinary research, typically against the “normal science” grain of academia. This kind of interdisciplinarity is best described as “use-inspired basic research,” which makes creative use of synergies between relatively uncommunicative academic literatures, or “undiscovered public knowledge.” The Rockefeller Foundation and DARPA are the two major institutional exemplars of this form of interdisciplinarity, which is fairly described as “Mode 2” or “triple-helix” knowledge production. The chapter stresses the adventurous, indeed “creatively destructive” character of this research, which typically leaves a lasting impression on both academia and society as a whole—be it for good or ill. In this context, the career of Fritz Haber—a man steeped in not only philosophy and the physical sciences but also war and commerce—is considered as exemplifying the Janus-faced character of this type of interdisciplinarity.
Vaginal Progesterone as Maintenance Treatment After an Episode of Preterm Labour (PROMISE) Study: A Multicentre, Double-blind, Randomised, Placebo-Controlled Trial
Authors: Palacio Montse , Cobo Teresa , Antolín Eugenia , Ramirez M. , Cabrera Francisco , Mozo de Rosales Francisco , Bartha José Luis , Juan Miquel , Martí Anna , Oros Daniel , Rodríguez A. , Scazzocchio E. , Olivares José María , Varea Sara , Ríos J. , Gratacós Eduard 
Published: March 2017

(Abstracted from BJOG 2016;123:1990–1999)
A large proportion of both short-term neonatal morbidity and mortality and long-term disability is associated with preterm birth. Women with previous preterm delivery, a short cervical length at midgestation, a twin pregnancy, and an episode of preterm labor arrested with tocolytic medication all have an increased risk of preterm delivery.
Regenerating the Anal Sphincter: Cytokines, Stem Cells, or Both?
Authors: Sun Li , Xie Zhuojun , Kuang Mei , Penn Marc , Damaser Margot S. , Zutshi Massarat 
Published: March 2017

BACKGROUND:
Healing of an anal sphincter defect at a time distant from injury is a challenge.

OBJECTIVE:
We aimed to investigate whether re-establishing stem cell homing at the site of an anal sphincter defect when cytokine expression has declined using a plasmid engineered to express stromal derived factor 1 with or without mesenchymal stem cells can improve anatomic and functional outcome.

DESIGN:
This was a randomized animal study.

SETTINGS:
Thirty-two female age- and weight-matched Sprague Dawley rats underwent 50% excision of the anal sphincter complex. Three weeks after injury, 4 interventions were randomly allocated (n = 8), including no intervention, 100-μg plasmid, plasmid and 800,000 cells, and plasmid with a gelatin scaffold mixed with cells.

MAIN OUTCOME MEASURES:
The differences in anal sphincter resting pressures just before and 4 weeks after intervention were used for functional analysis. Histology was analyzed using Masson staining. One-way ANOVA followed by the Tukey post hoc test was used for pressure and histological analysis.

RESULTS:
All 3 of the intervention groups had a significantly greater change in resting pressure (plasmid p = 0.009; plasmid + cells p = 0.047; plasmid + cells in scaffold p = 0.009) compared with the control group. The plasmid-with-cells group showed increased organization of muscle architecture and increased muscle percentage, whereas the control group showed disorganized architecture at the site of the defect. Histological quantification revealed significantly more muscle at the site of defect in the plasmid-plus-cells group compared with the control group, which had the least muscle. Quantification of connective tissue revealed significantly less fibrosis at the site of defect in the plasmid and plasmid-plus-cells groups compared with the control group.

LIMITATIONS:
Midterm evaluation and muscle morphology were not defined.

CONCLUSIONS:
At this midterm follow-up, local delivery of a stromal derived factor 1 plasmid with or without local mesenchymal stem cells enhanced anal sphincter muscle regeneration long after an anal sphincter injury, thereby improving functional outcome. See Video Abstract at http://links.lww.com/DCR/A324.
Systemic Metronidazole May Not Reduce Posthemorrhoidectomy Pain: A Meta-Analysis of Randomized Controlled Trials
Authors: Wanis Kerollos Nashat , Emmerton-Coughlin Heather M. , Coughlin Shaun , Foley Norine , Vinden Christopher 
Published: March 2017

BACKGROUND:
Hemorrhoidectomy is associated with significant postoperative pain. Oral metronidazole has been recommended as an adjunct to improve posthemorrhoidectomy analgesia.

OBJECTIVE:
This study aimed to evaluate the impact of oral metronidazole on patient-reported pain following hemorrhoidectomy.

DATA SOURCES:
We conducted a systematic search in the MEDLINE, EMBASE, ISI Web of Science, and Cochrane Central Register of Controlled Trials databases.

STUDY SELECTION:
Randomized controlled trials examining adults who underwent surgical hemorrhoidectomy were included. Participants in an active intervention group received oral metronidazole postoperatively, and those in a control group received placebo or usual care. Postoperative pain was assessed for at least 3 days postoperatively.

INTERVENTION:
A random-effects model was used.

MAIN OUTCOMES MEASURES:
The primary outcome was pain during the first 2 postoperative weeks, measured on a visual analogue scale. The secondary outcome was time to return to normal activities.

RESULTS:
Patients who received oral metronidazole had significantly lower reported pain scores on postoperative day 1 (standardized mean difference, –0.87 ± 0.44; 95% CI, –1.73 to –0.015; p = 0.046; n = 4) and day 4 (standardized mean difference, –1.43 ± 0.71; 95% CI, –2.83 to –0.037; p = 0.044; n = 3). Metronidazole use was associated with a significantly shorter time to return to normal activities (standardized mean difference, –0.76 ± 0.34; 95% CI, –1.43 to –0.088, p = 0.027). The improvements disappeared in a sensitivity analysis excluding the largest trial with a high risk of bias, and no significance was observed during the remaining postoperative days.

LIMITATIONS:
The meta-analysis was limited by lack of double blinding, absence of a placebo, and unclear or high risk of bias in a proportion of the included trials.

CONCLUSIONS:
Although a favorable adverse effect profile supports consideration of oral metronidazole to reduce posthemorrhoidectomy pain, pooled analysis reveals inconsistent results with no pain reduction on most postoperative days. The current recommendation for routine prescription of oral metronidazole should be reevaluated in the absence of additional well-designed trials.
Preimplantation embryonic mosaicism: origin, consequences and the reliability of comprehensive chromosome screening
Authors: Marin Diego , Scott Richard T. , Treff Nathan R. 
Published: March 2017

Purpose of review
Embryonic mosaicism represents an ongoing challenge for contemporary comprehensive chromosome screening platforms due to the unknown reproductive potential of mosaic embryos and technical difficulties of its detection from a single embryo biopsy.

Recent findings
Mosaicism in preimplantation embryos is a product of mitotic errors arising primarily from anaphase lag and chromosome nondisjunction. To date, there is high variability among estimations of prevalence of mosaicism in blastocysts, the most recent ranging from 3.3 to 83%. It has been reported that alleged mosaic embryos can develop into healthy babies, although the proper study evaluating this question remains to be completed. Technical artefacts from comprehensive chromosome screening platforms may also hinder correct classification of embryos as genuine mosaics.

Summary
Although complex, embryonic mosaicism is a phenomenon that deserves further investigation. Many embryos classified as mosaic may have actual reproductive potential. The predictive value of intermediate chromosome copy number assignments for the remaining embryo and for ongoing reproductive potential needs more careful consideration. In addition, recent advancements in extended embryo culture raise the possibility of investigating whether preferential segregation, selective advantage of normal cells or surveillance of abnormal chromosome numbers occur at postimplantation stages.
CHOROIDAL THICKNESS IN DIABETIC PATIENTS WITHOUT DIABETIC RETINOPATHY
Authors: Tavares Ferreira Joana , Vicente André , Proença Rita , Santos Bruno O. , Cunha João P. , Alves Marta , Papoila Ana L. , Abegão Pinto Luís 
Published: March 2017

Purpose:
To compare choroidal thickness (CT) between diabetic patients without diabetic retinopathy and a nondiabetic group. To explore how CT relates to disease duration, mean arterial pressure, glycemia, glycosylated hemoglobin, intraocular pressure, and ocular pulse amplitude.

Methods:
Choroidal thickness was assessed using a spectral-domain optical coherence tomography and enhanced depth mode at 13 locations (subfoveal and 3 measurements 500 μm apart in 4 directions—nasal, temporal, superior, and inferior). Linear regression models were used.

Results:
One hundred seventy-five patients were recruited (125 diabetic patients without diabetic retinopathy and 50 nondiabetic patients). In diabetic patients, although without statistical significance, CT showed a trend to be thicker in all locations (6.16–24.27 μm). Choroidal thickness was negatively associated with age (P < 0.001) in both groups, but only in the diabetic group, it was positively associated to ocular pulse amplitude (with a mean increase between 8.5 μm and 11.6 μm for each millimeter of mercury increase in ocular pulse amplitude). Diabetic patients' CT seems to stabilize after 150 months of diabetes, increase with higher glycemia levels (>160 mg/dL) while showing no fluctuation with glycosylated hemoglobin and mean arterial pressure.

Conclusion:
There seems to be a thickening of the choroid in diabetic patients without diabetic retinopathy. Moreover, this tissue may be functionally different in diabetes, as the pattern of associations seems to differ between groups.