bluuebunny/crossref_metadata_2025 huggingface dataset:
Incidence and correlates of HIV and syphilis in a prospective cohort of men who have sex with men in Mianyang, China, over a 36-month period
Authors: Wang Yi , Huang Yuling , Chen Huailiang , Li Liulin , Xu Jie , Li Zhijun , Zhang Guanggui , Fan Jing , Zhao Xihe , Jia Shuguang
Published: August 2015

Background Estimates for the HIV/AIDS epidemic from the China Ministry of Health show that the epidemic is spreading rapidly among men who have sex with men (MSM). Methods: Respondent-driven sampling (RDS) was adapted in 2009 and snowball sampling was adapted to supplement the number of participants in 2010 and 2011. Interviewer-administered questionnaires and blood tests were conducted to confirm enrolment eligibility of participants. Results: A total of 725 HIV-negative participants were included into the cohort study. The cohort had a HIV incidence density of 5.6 (95% CI: 3.9–7.3)/100 person-years (PY) and a syphilis incidence density of 5.6 (95% CI:3.7–7.6)/100 PY. Age ≤20 years (21–25 years, hazard ratio (HR) = 0.32, 95%CI: 0.11–0.95/ ≥ 26 years, HR = 0.17, 95%CI: 0.05–0.66), having not participated in peer education in the past year (HR = 2.96, 95%CI: 1.19–7.35), seeking male sexual partners in a public washroom/park (HR = 3.61, 95%CI: 1.03–12.47), being currently infected with syphilis (HR = 3.21, 95%CI: 1.31–7.91), having sex partners aged ≥30 years (HR = 3.40, 95%CI: 1.11–10.39) and having more than four male sexual partners within the past 6 months (HR = 3.34, 95%CI: 1.24–9.04) were found to be risk factors for HIV seroconversion (each P < 0.05). Being married (HR = 2.38, 95%CI: 1.04–5.46), having not participated in peer education in the past year (HR = 2.28, 95%CI: 1.08–4.82), having limited HIV/AIDS knowledge (HR = 4.28, 95%CI: 1.94–9.43) and having a sexually transmitted disease infection in the past 6 months (HR = 4.74, 95%CI: 1.83–12.30) were identified as factors for syphilis infection (each P < 0.05). Conclusion: The incidence rates of HIV and syphilis in Mianyang City reamained high in the cohort of MSM for 36 months. Increased attention should be given to this serious epidemic, and appropriate interventions should be implemented to address MSM-specific issues in order to prevent HIV and syphilis infection in China.
Fire in arctic tundra of Alaska: past fire activity, future fire potential, and significance for land management and ecology
Authors: French Nancy H. F. , Jenkins Liza K. , Loboda Tatiana V. , Flannigan Michael , Jandt Randi , Bourgeau-Chavez Laura L. , Whitley Matthew
Published: August 2015

A multidecadal analysis of fire in Alaskan Arctic tundra was completed using records from the Alaska Large Fire Database. Tundra vegetation fires are defined by the Circumpolar Arctic Vegetation Map and divided into five tundra ecoregions of Alaska. A detailed review of fire records in these regions is presented, and an analysis of future fire potential was performed based on future climate scenarios. The average size of tundra fire based on the data record is 22 km2 (5454 acres). Fires show a mean size of 10 km2 (2452 acres) and median of 0.064 km2 (16 acres), indicating small fires are common. Although uncommon, 16 fires larger than 300 km2 (74 132 acres) have been recorded across four ecoregions and all five decades. Warmer summers with extended periods of drying are expected to increase fire activity as indicated by fire weather index. The implications of the current fire regime and potential changes in fire regime are discussed in the context of land management and ecosystem services. Current fire management practices and land-use planning in Alaska should be specifically tailored to the tundra region based on the current fire regime and in anticipation of the expected change in fire regime projected with climate change.
Dynamic reconfiguration of frontal brain networks during executive cognition in humans
Authors: Braun Urs , Schäfer Axel , Walter Henrik , Erk Susanne , Romanczuk-Seiferth Nina , Haddad Leila , Schweiger Janina I. , Grimm Oliver , Heinz Andreas , Tost Heike , Meyer-Lindenberg Andreas , Bassett Danielle S.
Published: September 2015

Significance

Cognitive flexibility is hypothesized to require dynamic integration between brain areas. However, the time-dependent nature and distributed complexity of this integration remains poorly understood. Using recent advances in network science, we examine the functional integration between brain areas during a quintessential task that requires executive function. By linking brain regions (nodes) by their interactions (time-dependent edges), we uncover nontrivial modular structure: groups of brain regions cluster together into densely interconnected structures whose interactions change during task execution. Individuals with greater network reconfiguration in frontal cortices show enhanced memory performance, and score higher on neuropsychological tests challenging cognitive flexibility, suggesting that dynamic network reconfiguration forms a fundamental neurophysiological mechanism for executive function.
Parkin loss leads to PARIS-dependent declines in mitochondrial mass and respiration
Authors: Stevens Daniel A. , Lee Yunjong , Kang Ho Chul , Lee Byoung Dae , Lee Yun-Il , Bower Aaron , Jiang Haisong , Kang Sung-Ung , Andrabi Shaida A. , Dawson Valina L. , Shin Joo-Ho , Dawson Ted M.
Published: September 2015

Significance

Mutations or inactivation of parkin causes Parkinson’s disease (PD) in humans. Recent studies have focused on parkin’s role in mitochondrial quality control in the pathogenesis of PD, including defects in mitophagy, mitochondrial fission, fusion, and transport. This study shows that parkin also controls mitochondrial biogenesis and that defects in mitochondrial biogenesis drive the loss of dopamine (DA) neurons due to the absence of parkin. The findings support the role of parkin in regulating multiple arms of mitochondrial quality control and suggest that maintaining mitochondrial biogenesis is critically important in the survival of DA neurons.
Slowing down of North Pacific climate variability and its implications for abrupt ecosystem change
Authors: Boulton Chris A. , Lenton Timothy M.
Published: September 2015

Significance

Sea surface temperature (SST) variations in the North Pacific have triggered past abrupt changes in fisheries and other ecosystems. We have discovered that over the last century, fluctuations of North Pacific SSTs have become less frequent and longer-lived. This “reddening” behavior can also be seen in the dominant pattern of climate variability in the region, known as the Pacific Decadal Oscillation index. This fundamental change in climate variability has important implications for ecosystems in the region. It implies that over the last century, ecosystems have become prone to undergoing larger climate-triggered abrupt shifts. Hence our discovery of changing climate variability could have contributed to the large magnitude of well-known abrupt changes in North Pacific ecosystems in 1977 and 1989.
Natural variation in
ARF18
gene simultaneously affects seed weight and silique length in polyploid rapeseed
Authors: Liu Jing , Hua Wei , Hu Zhiyong , Yang Hongli , Zhang Liang , Li Rongjun , Deng Linbin , Sun Xingchao , Wang Xinfa , Wang Hanzhong
Published: September 2015

Significance

Seed weight is a complex trait controlled by polygenes, and its underlying regulatory mechanisms, especially those involving polyploidy crops, remain elusive.
Brassica napus
L., which is the second leading crop source of vegetable oil around the world, is an important tetraploid (4×) crop. Our results have generated three significant findings. (
i
) By combining the linkage and associated analysis, this study revealed the first (to our knowledge) quantitative trait locus (QTL) in rapeseed, which will provide insights for QTL cloning in polyploidy crops. (
ii
) The functional gene and marker could be useful in rapeseed breeding. (
iii
) We revealed a maternal regulatory pathway affecting seed weight that differs from the mechanisms described in previous reports.
Fluid mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin
Authors: Klein Frieder , Humphris Susan E. , Guo Weifu , Schubotz Florence , Schwarzenbach Esther M. , Orsi William D.
Published: September 2015

Significance

We provide biogeochemical, micropaleontological, and petrological constraints on a subseafloor habitat at the passive Iberia Margin, where mixing of reduced hydrothermal serpentinization fluids with oxic seawater provided the energy and substrates for metabolic reactions. This mixing zone was inhabited by bacteria and archaea and is comparable to the active Lost City hydrothermal field at the Mid-Atlantic Ridge. Our results highlight the potential of magma-poor passive margins to host Lost City-type hydrothermal systems that support microbial activity in subseafloor environments. Because equivalent systems have likely existed throughout most of Earth's history in a wide range of oceanic environments, fluid mixing may have provided the substrates and energy to support a unique subseafloor community of microorganisms over geological timescales.
A phantom road experiment reveals traffic noise is an invisible source of habitat degradation
Authors: Ware Heidi E. , McClure Christopher J. W. , Carlisle Jay D. , Barber Jesse R.
Published: September 2015

Significance

Using landscape-scale traffic noise playbacks to create a “phantom road,” we find that noise, apart from other factors present near roads, degrades the value of habitat for migrating songbirds. We found that nearly one third of the bird community avoided the phantom road. For some bird species that remained despite noise exposure, body condition and stopover efficiency (ability to gain body condition over time) decreased compared with control conditions. These findings have broad implications for the conservation of migratory birds and perhaps for other wildlife, because factors driving foraging behavior are similar across animals. For wildlife that remains in loud areas, noise pollution represents an invisible source of habitat degradation.
Fog and rain in the Amazon
Authors: Anber Usama , Gentine Pierre , Wang Shuguang , Sobel Adam H.
Published: September 2015

Significance

We here demonstrate that we can resolve the seasonality of the hydrologic cycle in the Amazon using an approach, opposite to general circulation models, in which we resolve convection and parameterize large-scale circulation as a function of the resolved convection. The results emphasize the key role of cloud albedo feedback and, in particular, of the morning fog layer in determining the diurnal course of surface heat fluxes and seasonality of the surface and atmospheric heat and water cycles. These results indicate that our understanding of tropical climates over land can be considerably advanced by using coupled land−atmosphere models with explicit convection and parameterized large-scale dynamics.
Evidence integration in model-based tree search
Authors: Solway Alec , Botvinick Matthew M.
Published: September 2015

Significance

Recent behavioral research has made rapid progress toward revealing the processes by which we make choices based on judgments of subjective value. A key insight has been that this process unfolds incrementally over time, as we gradually build up evidence in favor of a particular preference. Although the data for this ‟evidence-integration” model are compelling, they derive almost entirely from single-step choices: Would you like chocolate or vanilla ice cream? Decisions in everyday life are typically more complex. In particular, they generally involve choices between sequences of action, with accompanying series of outcomes. We present here results from two experiments, providing the first evidence to our knowledge that the standard integration model of choice can be directly extended to multistep decision making.
Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble
Authors: Zandarashvili Levani , Esadze Alexandre , Vuzman Dana , Kemme Catherine A. , Levy Yaakov , Iwahara Junji
Published: September 2015

Significance

Many transcription factors and DNA repair/modifying enzymes must first locate the target sites through stochastic scanning of DNA in the vast presence of nonspecific sites. In this work, we demonstrate that target search by these proteins can be accelerated via engineering based on structural dynamic knowledge of the DNA-scanning process. Our biophysical data for the Egr-1 zinc-finger protein and its nuclease derivatives reveal kinetic and thermodynamic roles of the conformational equilibrium between two modes in the DNA-scanning process: one suitable for search and the other for recognition. We found that optimizing the balance between the search and recognition modes improves efficiency in zinc-finger proteins’ target search. This finding can help advance zinc-finger technology for artificial gene regulation and genome editing.
Transport proteins NHA1 and NHA2 are essential for survival, but have distinct transport modalities
Authors: Chintapalli Venkateswara R. , Kato Akira , Henderson Louise , Hirata Taku , Woods Debra J. , Overend Gayle , Davies Shireen A. , Romero Michael F. , Dow Julian A. T.
Published: September 2015

Significance

Cation/proton antiporters (CPAs) are essential to life. The sodium/proton exchanger (NHE) branch of the CPA family has been studied exhaustively and is an important drug target; however, much less is known about the recently discovered NHA branch, represented by two genes in both humans and flies. Here we show that sodium/hydrogen antiporter (NHA) function is essential to life, and that both NHAs protect against salt stress. Their transport mechanisms are radically different, however, suggesting that function cannot be inferred from structural similarity. Although NHA2 was found to be a Na
+
/H
+
exchanger as expected, NHA1 was seen to act as an electroneutral H
+
/Cl
-
cotransporter. This is an important finding for future studies of these transporters.
Precursors to morality in development as a complex interplay between neural, socioenvironmental, and behavioral facets
Authors: Cowell Jason M. , Decety Jean
Published: September 2015

Significance

Research in the past decade indicates that the building blocks of morality are present very early in development. However, little is known about the neural and environmental mechanisms underlying their emergence. Here we show, for the first time, to our knowledge, using multiple levels of analysis, the complex integration of bottom–up and top–down processes in sociomoral evaluation. Brain wave differences elicited by witnessing the prosocial and antisocial behaviors of others predicted infants and toddlers’ subsequent attraction to prosocial others and were associated with parental values of justice and fairness. This developmental social neuroscience perspective provides empirical and theoretical clarity to the biological basis and brain–behavior processes involved in moral sensitivity.
Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centers
Authors: Budeus Bettina , Schweigle de Reynoso Stefanie , Przekopowitz Martina , Hoffmann Daniel , Seifert Marc , Küppers Ralf
Published: September 2015

Significance

The complexity of the human memory B-lymphocyte compartment is a key component to depict and understand adaptive immunity. Despite numerous prior investigations, the generation of certain memory B-cell subsets, the dependency on T-cell help, and the composition, size, and diversity of clonal expansions are either poorly understood or debated. Here we provide an extensive and tightly controlled immunoglobulin heavy chain variable (IGHV) gene repertoire analysis of four main human memory B-cell subpopulations, revealing that an ordered diversification in germinal centers determines a highly versatile memory B-cell compartment in humans with surprisingly many very large B-cell clones.
Targeted delivery of liquid microvolumes into the lung
Authors: Kim Jinho , O’Neill John D. , Dorrello N. Valerio , Bacchetta Matthew , Vunjak-Novakovic Gordana
Published: September 2015

Significance

Systemic drug administrations suffer from inefficient delivery to a specific pathologic region of the lung. Aerosolized drugs, when prepared to display desired transport behavior, can be delivered to selected lung regions by inhalation. We describe an alternative method for delivering drugs directly to a specific lung region in the form of liquid microvolumes based on a mathematical model. Deposition of liquid film on lung epithelium in different target regions of the lung was confirmed in rat lungs using fluorescence imaging. We propose that instilling microvolumes of liquid would enable predictable drug concentrations at the target site, reduce the amount of the drug required for treatment, and minimize systemic side effects for several lung diseases.
miR-15b/16-2 deletion promotes B-cell malignancies
Authors: Lovat Francesca , Fassan Matteo , Gasparini Pierluigi , Rizzotto Lara , Cascione Luciano , Pizzi Marco , Vicentini Caterina , Balatti Veronica , Palmieri Dario , Costinean Stefan , Croce Carlo M.
Published: September 2015

Significance

The role of the microRNA (miR) 15/16 family in oncogenesis and tumor progression has been intensively studied. The miR-15a/16-1 cluster is extensively described in B-cell chronic lymphocytic leukemia, characterized by the deletion of the 13q14 locus. The role of the miR-15b/16-2 cluster on chromosome 3q25 is still far from being elucidated. Because miR-15a is highly similar to miR-15b and miR-16-1 is identical to miR-16-2, we generated miR-15b/16-2 knockout mice to better understand the cluster’s role in vivo. These knockout mice developed B-cell lymphomas by age 15–18 mo, modulating the
CCND2
(Cyclin D2),
CCND1
(Cyclin D1), and
IGF1R
(insulin-like growth factor 1 receptor) genes involved in proliferation and antiapoptotic pathways in mouse B cells. Our results suggest a tumor suppressor role for the miR-15b/16-2 cluster in animal models of B-cell lymphomas.
PopZ identifies the new pole, and PodJ identifies the old pole during polar growth in
Agrobacterium tumefaciens
Authors: Grangeon Romain , Zupan John R. , Anderson-Furgeson James , Zambryski Patricia C.
Published: September 2015

Significance

Rod-shaped bacteria grow and maintain their shape by adding new material to their cell walls. Historically, most studies have focused on bacteria that grow uniformly by interspersed insertion of new material along their entire lengths. Recent work reveals another mechanism of growth from a single pole of the bacterial cell. Notably, many bacteria that use unipolar growth are important pathogens. To understand unipolar growth during the bacterial cell cycle it is critical to identify factors that may determine whether a pole is a growth pole or a non-growing pole. Here, we identify two factors, pole-organizing protein (Pop) PopZ and polar organelle development (Pod) protein PodJ that identify the growth pole and the nongrowing old pole, respectively, in the plant pathogen
Agrobacterium tumefaciens.
Manifestation of axion electrodynamics through magnetic ordering on edges of a topological insulator
Authors: Lee Yea-Lee , Park Hee Chul , Ihm Jisoon , Son Young-Woo
Published: September 2015

Significance

Interactions between two adjacent surfaces of different surface orientations in a single-crystal topological insulator are investigated. We show that the edge between two surfaces can host nontrivial axion electrodynamics with sizeable experimental signals owing to the unique interaction between the two topological surface states. We find that the large work function difference between facets in a topological insulator can generate strong electric fields around the edges and that, in turn, the electric fields give rise to effective magnetic fields for a given broken time-reversal symmetry. Our theoretical work highlights a route to reveal intriguing axion electrodynamics in a real solid and provides methods to exploit macroscopic topological states.
CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells
Authors: Deng Wulan , Shi Xinghua , Tjian Robert , Lionnet Timothée , Singer Robert H.
Published: September 2015

Significance

We have derived a new technology for the detection of genes within undisturbed nuclei of fixed cells and tissues. Previous approaches have used fluorescent DNA probes to hybridize to genes of interest, requiring treatment of heat and disruptive chemicals that distort the natural organization of the nucleus. Instead, we have used a bacterial protein, CRISPR (clustered regularly interspaced short palindromic repeats), combined with an RNA sequence as probes to find the genes of interest in the intact genome. This approach preserves the spatial relationships of the genetic elements, which are important for understanding gene expression, and the process is remarkably rapid (15 min), convenient, and can be used directly on tissues for diagnosis of disease.
ACTN3 R577X genotype and athletic performance in a large cohort of Japanese athletes
Authors: Kikuchi Naoki , Miyamoto‐Mikami Eri , Murakami Haruka , Nakamura Tomohiro , Min Seok‐Ki , Mizuno Masuhiko , Naito Hisashi , Miyachi Motohiko , Nakazato Koichi , Fuku Noriyuki
Published: September 2015

Aim: Recent meta‐analyses of the literature confirmed the association between the RR+RX genotype of the ACTN3 R577X polymorphism and elite sprint/power athletic status in Europeans but not in Asians and Africans, while the association between the R577X genotype and elite endurance athlete status is less convincing. The aim of the present study was to investigate the association between the ACTN3 R577X genotype and elite athlete status in a large Asian (Japanese) cohort of track and field athletes. Methods: One‐thousand fifty‐seven Japanese track and field athletes (627 sprint/power athletes and 430 endurance athletes) and 810 Japanese controls were genotyped for the ACTN3 R577X polymorphism (rs1815739) by using the TaqMan® SNP Genotyping Assay. Results: Elite sprint/power athletes had a higher frequency of the RR+RX genotype than the controls (OR: 1.59, 95% CI: 1.16–2.18; P = .003). A significant linear correlation was found between the RR + RX genotype and athlete status (i.e. regional < national < international) in sprint/power athletes (regional: 71%, national: 81%, international: 84%; P = .001 for trend) and long‐distance runners (regional: 65%, national: 72%, international: 82%; P = .030 for trend). Conclusions: The data obtained for this large Asian (Japanese) cohort of track and field athletes served to confirm the association between the RR + RX genotype of the ACTN3 R577X polymorphism and elite sprint/power athlete status and also the association between the ACTN3 RR + RX genotype and long‐distance running athletic status.
BiopLib and BiopTools—a C programming library and toolset for manipulating protein structure
Authors: Porter Craig T. , Martin Andrew C.R.
Published: September 2015

Summary: We describe BiopLib, a mature C programming library for manipulating protein structure, and BiopTools, a set of command-line tools which exploit BiopLib. The library also provides a small number of functions for handling protein sequence and general purpose programming and mathematics. BiopLib transparently handles PDBML (XML) format and standard PDB files. BiopTools provides facilities ranging from renumbering atoms and residues to calculation of solvent accessibility.

Availability and implementation: BiopLib and BiopTools are implemented in standard ANSI C. The core of the BiopLib library is a reliable PDB parser that handles alternate occupancies and deals with compressed PDB files and PDBML files automatically. The library is designed to be as flexible as possible, allowing users to handle PDB data as a simple list of atoms, or in a structured form using chains, residues and atoms. Many of the BiopTools command-line tools act as filters, taking a PDB (or PDBML) file as input and producing a PDB (or PDBML) file as output. All code is open source and documented using Doxygen. It is provided under the GNU Public Licence and is available from the authors’ web site or from GitHub.

Contact:  andrew@bioinf.org.uk
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets
Authors: Guo Zhengyu , Tzvetkova Boriana , Bassik Jennifer M. , Bodziak Tara , Wojnar Brianna M. , Qiao Wei , Obaida Md A. , Nelson Sacha B. , Hu Bo Hua , Yu Peng
Published: September 2015

Summary: Gene targeting is a protocol for introducing a mutation to a specific gene in an organism. Because of the importance of in vivo assessment of gene function and modeling of human diseases, this technique has been widely adopted to generate a large number of mutant mouse models. Due to the recent breakthroughs in high-throughput sequencing technologies, RNA-Seq experiments have been performed on many of these mouse models, leading to hundreds of publicly available datasets. To facilitate the reuse of these datasets, we collected the associated metadata and organized them in a database called RNASeqMetaDB. The metadata were manually curated to ensure annotation consistency. We developed a web server to allow easy database navigation and data querying. Users can search the database using multiple parameters like genes, diseases, tissue types, keywords and associated publications in order to find datasets that match their interests. Summary statistics of the metadata are also presented on the web server showing interesting global patterns of RNA-Seq studies.

Availability and implementation: Freely available on the web at http://rnaseqmetadb.ece.tamu.edu.

Contact:  pengyu.bio@gmail.com
Plant Disease Detection by Imaging Sensors – Parallels and Specific Demands for Precision Agriculture and Plant Phenotyping
Authors: Mahlein Anne-Katrin
Published: September 2015

Early and accurate detection and diagnosis of plant diseases are key factors in plant production and the reduction of both qualitative and quantitative losses in crop yield. Optical techniques, such as RGB imaging, multi- and hyperspectral sensors, thermography, or chlorophyll fluorescence, have proven their potential in automated, objective, and reproducible detection systems for the identification and quantification of plant diseases at early time points in epidemics. Recently, 3D scanning has also been added as an optical analysis that supplies additional information on crop plant vitality. Different platforms from proximal to remote sensing are available for multiscale monitoring of single crop organs or entire fields. Accurate and reliable detection of diseases is facilitated by highly sophisticated and innovative methods of data analysis that lead to new insights derived from sensor data for complex plant-pathogen systems. Nondestructive, sensor-based methods support and expand upon visual and/or molecular approaches to plant disease assessment. The most relevant areas of application of sensor-based analyses are precision agriculture and plant phenotyping.
Does the P Value Have a Future in Plant Pathology?
Authors: Madden L. V. , Shah D. A. , Esker P. D.
Published: September 2015

The P value (significance level) is possibly the mostly widely used, and also misused, quantity in data analysis. P has been heavily criticized on philosophical and theoretical grounds, especially from a Bayesian perspective. In contrast, a properly interpreted P has been strongly defended as a measure of evidence against the null hypothesis, H0. We discuss the meaning of P and null-hypothesis statistical testing, and present some key arguments concerning their use. P is the probability of observing data as extreme as, or more extreme than, the data actually observed, conditional on H0 being true. However, P is often mistakenly equated with the posterior probability that H0 is true conditional on the data, which can lead to exaggerated claims about the effect of a treatment, experimental factor or interaction. Fortunately, a lower bound for the posterior probability of H0 can be approximated using P and the prior probability that H0 is true. When one is completely uncertain about the truth of H0 before an experiment (i.e., when the prior probability of H0 is 0.5), the posterior probability of H0 is much higher than P, which means that one needs P values lower than typically accepted for statistical significance (e.g., P = 0.05) for strong evidence against H0. When properly interpreted, we support the continued use of P as one component of a data analysis that emphasizes data visualization and estimation of effect sizes (treatment effects).
Cerebral Blood Flow Measurement by Near-Infrared Spectroscopy During Carotid Endarterectomy
Authors: Kato Shinya , Yoshitani Kenji , Ohnishi Yoshihiko
Published: September 2015

Background:

It is crucial to evaluate cerebral blood flow (CBF) during carotid endarterectomy (CEA). However, it is difficult to measure CBF in the operating room. The recent development of high-accuracy near-infrared spectroscopy (NIRS) has enabled the measurement of regional CBF following injection of indocyanine green (ICG). We aimed to measure changes in regional CBF by clamping the carotid artery during CEA and to analyze factors affecting the blood flow index (BFI) in CEA.

Methods:

Patients undergoing elective CEA were enrolled in this study after it was approved by the institutional ethical board. All patients underwent CEA under general anesthesia. Intraoperative blood pressure was controlled about 30% higher than the precarotid cross-clamping during carotid cross-clamping. ICG (0.5 mg/kg) was injected before, during, and after carotid cross-clamping. The kinetics of an intravenous bolus of ICG were monitored by a NIRS oximeter (NIRO200NX) and the BFI was calculated using the slope of the ICG concentration. The impact of carotid cross-clamping on the BFI was evaluated, along with factors influencing changes in the BFI.

Results:

A total of 50 patients were enrolled. The BFI significantly decreased during carotid cross-clamping compared with baseline values (from 0.077±0.019 to 0.0054±0.0019 μmol/L/s) (P<0.01). After unclamping the common carotid artery, the BFI recovered to the preclamping level (0.0073±0.0023 μmol/L/s) (P<0.01). Multiple logistic regression analysis revealed that abnormalities of the circle of Willis correlated significantly with reduced BFI (odds ratio=12.07, P=0.036).

Conclusions:

The BFI was significantly reduced by carotid artery clamping during CEA. Abnormalities of the circle of Willis were a significant factor contributing to reduced BFI.
Is There a Deficit After Nonoperative Versus Operative Treatment of Shortened Midshaft Clavicular Fractures in Adolescents?
Authors: Parry Joshua A. , Van Straaten Meegan , Luo Tianyi D. , Simon Anne-Laure , Ashraf Ali , Kaufman Kenton , Larson A. Noelle , Shaughnessy William J.
Published: September 2015

Background:

Recent clinical studies in adults have reported a higher incidence of symptomatic malunions and functional deficits in nonoperatively treated shortened midshaft clavicular fractures. We sought to determine whether functional or subjective deficits are found in adolescents after operative versus nonoperative treatment of clavicle fractures.

Methods:

Adolescents with displaced midshaft clavicle fractures, >15 mm of shortening, and a minimum of 9 months of follow-up were recruited. Exclusion criteria included concomitant upper extremity injuries or abnormalities that would affect biomechanical strength testing. Sixteen patients, equally divided between nonoperative and operative plate fixation, met inclusion criteria and consented to testing. The average age (±SD) at the time of injury was 14±2 years (range, 10 to 16 y), time from injury was 22±10 months (range, 10 to 41 mo), and shortening was 24±6 mm (range, 16 to 35 mm). Consenting subjects completed a QuickDASH Score, Constant Shoulder Score, and questions regarding satisfaction with treatment. Quantitative isometric strength, range of motion, and abduction fatigue testing was performed on the involved and uninvolved sides for comparison.

Results:

Treatment groups did not differ in age, time from injury, or fracture shortening. QuickDASH and Constant Shoulder Scores were perfect in all but 1 patient in the operative group who actively complained of persistent symptomatic hardware. This patient and one other in the operative group underwent symptomatic hardware removal. There were no cases of symptomatic malunions in the nonoperative group. All patients expressed satisfaction with their treatment. Two in each treatment group were unsatisfied with the appearance of the clavicle. With the exception of a 3% decrease in abduction strength in the operative group (P=0.03) there were no differences in range of motion, isometric strength, or abduction fatigue of the involved shoulder in either treatment group.

Conclusions:

Shortened midshaft clavicular fractures had excellent outcomes after both operative and nonoperative treatments. No subjective or objective differences were observed between treatment groups.

Level of Evidence:

Level III—therapeutic, retrospective comparative study.
Intercondylar Roof Inclination Angle: Is It a Risk Factor for ACL Tears or Tibial Spine Fractures?
Authors: Samora Walter , Beran Matthew C. , Parikh Shital N.
Published: September 2015

Background:

The relationship between the angle of inclination of the intercondylar roof [roof inclination angle (RIA)] and likelihood of knee injury has not been previously investigated in children.

Methods:

Twenty-five skeletally immature patients with a tibial spine fracture were age matched (±1 y) and sex matched with 25 patients with an anterior cruciate ligament (ACL) tear and with 50 control knees (2 for each patient). Demographic and diagnostic information was collected, and radiographic measurements were performed on notch and lateral radiographs of the knee.

Results:

Patients with a tibial spine fracture had an increased RIA compared with controls and patients with an ACL tear. Patients with ACL tears had a steeper notch roof, as indicated by a decreased RIA when compared with controls and patients with tibial spine fractures.

Conclusions:

Our results demonstrated that a decreased RIA was associated with ACL tear and that an increased RIA was associated with tibial spine fracture.

Level of Evidence:

Level III—prognostic.
Changes in the Treatment of Pediatric Femoral Fractures: 15-Year Trends From United States Kids’ Inpatient Database (KID) 1997 to 2012
Authors: Naranje Sameer M. , Stewart Matthew G. , Kelly Derek M. , Jones Tamekia L. , Spence David D. , Warner William C. , Beaty James H. , Sawyer Jeffrey R.
Published: September 2015

Background:

The options for treating femoral fractures in children and adolescents have evolved over the last 2 decades to include a variety of nonoperative and operative methods. The purpose of this study was to identify changes in the types of treatment for pediatric femoral fractures in the United States from 1997 to 2012.

Methods:

From discharge estimates for 1997, 2000, 2003, 2006, 2009, and 2012 in the Kids’ Inpatient Database, data were extracted using the International Classification of Diseases, 9th revision, and Clinical Modification for pediatric femoral fracture treatments. Patients included were 0 to 17 years old and were categorized into 5 age groups: younger than 1, 1 to 4, 5 to 9, 10 to 14, and 15 to 17 years.

Results:

A total of 74,483 estimated discharges were recorded for pediatric patients with femoral fractures in the database for years 1997, 2000, 2003, 2006, 2009, and 2012. A total of 12,986 pediatric femoral fractures were estimated for 1997 and 9813 for 2012, which was statistically different (P<0.0001). Significantly fewer fractures were treated with closed reduction alone in 2012 than in 1997 in age groups 5 to 9, 10 to 14, and 15 to 17 years. Children aged 5 to 9 had more frequent open reduction and internal fixation in 2012 than in 1997, whereas adolescents aged 15 to 17 had less frequent open reduction and internal fixation in 2012 than in 1997.

Conclusions:

Although the number of femoral shaft fractures overall has decreased, the frequency of operative treatment has increased significantly in patients 5 to 9 years of age. Knowledge of these trends can guide educational efforts and resource allocation, but further study is necessary to determine procedure-specific (eg, nailing, plating, external fixation) trends and their clinical and economic impacts.

Level of Evidence:

Level III—case series.
Primary Tumor Thickness is a Prognostic Factor in Stage IV Melanoma
Authors: Luen Stephen , Wong Siew Wei , Mar Victoria , Kelly John W. , McLean Catriona , McArthur Grant A. , Haydon Andrew
Published: September 2015

Introduction:

Stage IV melanoma exhibits a diverse range of tumor biology from indolent to aggressive disease. Many important prognostic factors have already been identified. Despite this, the behavior of metastatic melanoma remains difficult to predict. We sought to determine if any primary tumor characteristics affect survival following the diagnosis of stage IV melanoma.

Methods:

All patients diagnosed with stage IV melanoma between January 2003 and December 2012 were identified from the Victorian Melanoma Service database. Retrospective chart review was performed to collect data on primary tumor characteristics (thickness, ulceration, mitotic rate, melanoma subtype, or occult primary). Known and suspected prognostic factors were additionally collected (time to diagnosis of stage IV disease, age, sex, stage, receipt of chemotherapy, and era of recurrence). The effect of primary tumor characteristics on overall survival from the date of diagnosis of stage IV disease was assessed.

Results:

A total of 227 patients with a median follow-up of 5 years from diagnosis of stage IV disease were identified. Median overall survival of the cohort was 250 days.

Of the primary tumor characteristics assessed, only tumor thickness affected survival from diagnosis of stage IV disease, hazard ratio=1.09 (1.02 to 1.16), P=0.008. This remained significant in multivariate analysis, P=0.007. Other primary tumor characteristics did not significantly influence survival.

Conclusions:

Primary tumor thickness is a significant prognostic factor in stage IV melanoma. Our data suggest that the biology of the primary melanoma may persist to influence the behavior of metastatic disease.
Periocular Melanoma In Situ Treated With Imiquimod
Authors: Elia Maxwell D. , Lally Sara E. , Hanlon Allison M. , Choi Jennifer N. , Servat Juan J. , Shields Jerry A. , Shields Carol L. , Levin Flora
Published: September 2015

Purpose:

To evaluate the efficacy of topical 5% imiquimod cream in the treatment of periocular melanoma in situ (lentigo maligna).

Design:

Retrospective case series.

Subjects:

There were 12 patients in this series, and the mean patient age was 77 years. The anatomical locations were the lower eyelid (n=5), upper and lower eyelid (n=4), lower eyelid including the eyelid margin (n=1), brow (n=1), and the medial canthus (n=1). Topical 5% imiquimod cream was used as a primary treatment (n=6) or as an adjunctive therapy following local excision (n=2), cryotherapy (n=2), or excisional biopsy with cryotherapy (n=2).

Methods:

Twelve patients with periocular melanoma in situ were treated with topical 5% imiquimod cream daily for a mean treatment period of 3.9 months. The clinical features of the patients and the responses to treatment were evaluated in a retrospective case series.

Main Outcome Measures:

Histologic clearance of atypical melanocytes.

Results:

Eleven patients achieved complete histologic clearance of atypical melanocytes on post-treatment biopsy. One patient could not tolerate local irritation from imiquimod and stopped in the first month of therapy with residual disease. The median follow-up time was 1.5 years. Side effects included redness (n=12), discomfort (n=6), swelling (n=4), ectropion (n=1), and conjunctival chemosis (n=1). The patients experienced no systemic side effects from the treatment.

Conclusions:

Topical 5% imiquimod cream is an effective option as primary or adjunct therapy in the treatment of periocular melanoma in situ.
Kamp K'aana, a 2‐Week Residential Weight Management Summer Camp, Shows Long‐Term Improvement in Body Mass Index z Scores
Authors: Farhat Alicia Elena , Sharma Shreela , Abrams Stephanie H. , Wong William W. , Barlow Sarah E.
Published: September 2015

Long‐term effects of Kamp K'aana, a 2‐week residential weight management camp, on body mass index (BMI) measures were evaluated on 71 of 108 (66%) obese youth 10 to 14 years of age. Measures were obtained at 11‐month study follow‐up (n = 38) or extracted from medical record (n = 33). Compared with baseline, BMI increased (P < 0.001), but both BMI percentile and BMI z score decreased (98.7 ± 1.0 to 97.3 ± 6.7 and 2.34 ± 0.30 to 2.23 ± 0.34, P < 0.001). A decrease in BMI z score of ≥0.2 units was seen in 27% of the participants (P < 0.001). The short program has sustained effect.
Small-Scale Purification of Peroxisomes for Analytical Applications
Authors: Cramer Jana , Effelsberg Daniel , Girzalsky Wolfgang , Erdmann Ralf
Published: September 2015

This protocol describes the isolation of peroxisomes from Saccharomyces cerevisiae by density gradient centrifugation using a sucrose, OptiPrep, or OptiPrep/sucrose gradient. Oleic acid–induced cells are first converted to spheroplasts using lyticase for cell wall digestion. Spheroplasts are homogenized, and nuclei and cell debris are removed by low-speed centrifugation to produce a postnuclear supernatant (PNS). Separation of the PNS by density gradient centrifugation is suitable for many analytical applications; however, to increase the yield of peroxisomes, further fractionation of the PNS is possible. Differential centrifugation of the PNS allows removal of the cytosol and other contaminating organelles, resulting in an organellar pellet (OP) enriched in peroxisomes and mitochondria that can be loaded onto the density gradient. Following density gradient centrifugation of the PNS or OP, fractions are collected from the bottom of the centrifuge tube. The distribution of organelles, including peroxisome peak fractions, is characterized by measurement of marker enzyme activity.
Large-Scale Purification of Peroxisomes for Preparative Applications
Authors: Cramer Jana , Effelsberg Daniel , Girzalsky Wolfgang , Erdmann Ralf
Published: September 2015

This protocol is designed for large-scale isolation of highly purified peroxisomes from Saccharomyces cerevisiae using two consecutive density gradient centrifugations. Instructions are provided for harvesting up to 60 g of oleic acid–induced yeast cells for the preparation of spheroplasts and generation of organellar pellets (OPs) enriched in peroxisomes and mitochondria. The OPs are loaded onto eight continuous 36%–68% (w/v) sucrose gradients. After centrifugation, the peak peroxisomal fractions are determined by measurement of catalase activity. These fractions are subsequently pooled and subjected to a second density gradient centrifugation using 20%–40% (w/v) Nycodenz.
Rapid and Efficient Plasmid Construction by Homologous Recombination in Yeast
Authors: van Leeuwen Jolanda , Andrews Brenda , Boone Charles , Tan Guihong
Published: September 2015

The cloning of DNA fragments is a fundamental aspect of molecular biology. Traditional DNA cloning techniques rely on the ligation of an insert and a linearized plasmid that have been digested with restriction enzymes and the subsequent introduction of the ligated DNA into Escherichia coli for propagation. However, this method is limited by the availability of restriction sites, which often becomes problematic when cloning multiple or large DNA fragments. Furthermore, using traditional methods to clone multiple DNA fragments requires experience and multiple laborious steps. In this protocol, we describe a simple and efficient cloning method that relies on homologous recombination in the yeast Saccharomyces cerevisiae to assemble multiple DNA fragments, with 30-bp homology regions between the fragments, into one sophisticated construct. This method can easily be extended to clone plasmids for other organisms, such as bacteria, plants, and mammalian cells.
Analyzing the Colocalization of MAP1LC3 and Lysosomal Markers in Primary Cells
Authors: Phadwal Kanchan
Published: September 2015

This technique evaluates the colocalization of the autophagy protein MAP1LC3 (microtubule-associated proteins 1A/1B light chain 3B, here referred to as LC3) with lysosomes (autolysosomes) in primary cells in a high-throughput manner. It uses an imaging fluorescence-activated cell sorting cytometer called the ImageStream to concomitantly detect surface molecules, making possible the identification of cells in mixed cell populations (e.g., in blood or bone marrow). It can be applied to clinical samples and to rare cell populations because only a few cells are needed for detection.
Detection of Mitochondrial Mass, Damage, and Reactive Oxygen Species by Flow Cytometry
Authors: Puleston Daniel
Published: September 2015

The reagents and procedures highlighted here will give the investigators an indication of the health status and volume of mitochondria in primary cells and cell lines through the use of a number of cell-permeable dyes. Mitochondrial volume can be monitored by using the probe MitoTracker Green FM. This reagent labels mitochondria in a manner that is independent of the membrane potential, therefore providing a readout relating purely to the mitochondrial mass of the cell. In contrast, MitoTracker Red CMXRos, tetramethylrhodamine methyl ester, and 10-N-nonyl acridine orange label mitochondria in a manner dependent on the membrane potential, thus giving an indication of mitochondrial stress. Using MitoSOX Red, it is also possible to analyze the production of the mitochondrial superoxide anion. Like the MitoTracker probes, MitoSOX Red is taken up passively by cells. In the mitochondria, the probe is oxidized by superoxide, resulting in the emission of red fluorescence.
Preparing Cellular DNA from Nuclei or Whole Cells
Authors: Nilsen Timothy W.
Published: September 2015

It is often desirable to have cellular DNA on hand. DNA is stable and can be maintained intact for many years. This protocol describes the preparation of DNA from nuclei after the cytoplasmic extract has been removed. The resulting DNA is suitable for polymerase chain reactions and Southern blots to determine copy number and sites of integration of plasmids in stable cell lines. Quantitation of DNA may not be exact because RNA is not completely removed. The method can also be used on whole cells, but there will be more RNA contamination.
Techniques for the Detection of Autophagy in Primary Mammalian Cells
Authors: Puleston Daniel , Phadwal Kanchan , Watson Alexander Scarth , Soilleux Elizabeth J. , Chittaranjan Suganthi , Bortnik Svetlana , Gorski Sharon M. , Ktistakis Nicholas , Simon Anna Katharina
Published: September 2015

Autophagy is a lysosomal catabolic pathway responsible for the degradation of cytoplasmic constituents. Autophagy is primarily a survival pathway for recycling cellular material in times of nutrient starvation, and in response to hypoxia, endoplasmic reticulum stress, and other stresses, regulated through the mammalian target of rapamycin pathway. The proteasomal pathway is responsible for degradation of proteins, whereas autophagy can degrade cytoplasmic material in bulk, including whole organelles such as mitochondria (mitophagy), bacteria (xenophagy), or lipids (lipophagy). Although signs of autophagy can be present during cell death, it remains controversial whether autophagy can execute cell death in vivo. Here, we will introduce protocols for detecting autophagy in mammalian primary cells by using western blots, immunofluorescence, immunohistochemistry, flow cytometry, and imaging flow cytometry.