bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression Profiling and Structural Characterization of MicroRNAs in Adipose Tissues of Hibernating Ground Squirrels
Authors: Wu Cheng-Wei , Biggar Kyle K. , Storey Kenneth B. 
Published: December 2014

Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 miRNAs in brown (BAT) and white adipose tissue (WAT) during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six miRNAs including let-7a, let-7b, miR-107, miR-150, miR-222 and miR-31 was significantly downregulated in WAT (P  &lt; 0.05), which was 16%–54% of euthermic non-torpid control squirrels, whereas expression of three miRNAs including miR-143, miR-200a and miR-519d was found to be upregulated by 1.32–2.34-fold. Similarly, expression of more miRNAs was downregulated in BAT during torpor. We detected reduced expression of 6 miRNAs including miR-103a, miR-107, miR-125b, miR-21, miR-221 and miR-31 (48%–70% of control), while only expression of miR-138 was significantly upregulated (2.91 ± 0.8-fold of the control, P  &lt; 0.05). Interestingly, miRNAs found to be downregulated in WAT during torpor were similar to those dysregulated in obese humans for increased adipogenesis, whereas miRNAs with altered expression in BAT during torpor were linked to mitochondrial β-oxidation. miRPath target prediction analysis showed that miRNAs downregulated in both WAT and BAT were associated with the regulation of mitogen-activated protein kinase (MAPK) signaling, while the miRNAs upregulated in WAT were linked to transforming growth factor β (TGFβ) signaling. Compared to mouse sequences, no unique nucleotide substitutions within the stem-loop region were discovered for the associated pre-miRNAs for the miRNAs used in this study, suggesting no structure-influenced changes in pre-miRNA processing efficiency in the squirrel. As well, the expression of miRNA processing enzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of miRNA expression in adipose tissues may be linked to distinct biological roles in WAT and BAT during hibernation and may involve the regulation of signaling cascades.
Association Between rs1344706 of ZNF804A and Schizophrenia: A Meta-Analysis
Authors: Zhu Meiyan , Liu Tongyang , Zhang Jihong , Jia Shuting , Tang Wenru , Luo Ying 
Published: December 2014

Abstract
Schizophrenia is one of the most serious mental diseases found in humans. Previous studies indicated that the single nucleotide polymorphism (SNP) rs1344706 in the gene ZNF804A encoding zinc finger protein 804A was associated with schizophrenia in Caucasian population but not in Chinese Han population. However, current results are conflicting in Asian population. In the present study, a meta-analysis was performed to revisit the association between rs1344706 and the risk of schizophrenia in Asian, Caucasian and other populations. Electronic search of PubMed database identified 25 case–control studies with available genotype frequencies of rs1344706 for the meta-analysis, involving a total of 15,788 cases and 22,654 controls. A pooled odds ratio (OR) with 95% confidence interval (CI) was used to assess the association. The current meta-analysis showed an association between rs1344706 and schizophrenia in Caucasian populations (P  = 0.028, OR = 1.138, 95% CI: 1.014–1.278; P  = 0.004 for heterogeneity) and Asian populations (P  = 0.008, OR = 1.092, 95% CI: 1.023–1.165; P  = 0.001 for heterogeneity), but not in other populations (P  = 0.286, OR = 1.209, 95% CI: 0.853–1.714, P  = 0.120 for heterogeneity). Egger’s test (P  &gt;  0.05) and Begg’s test (P  &gt;  0.05) are both suggestive of the lack of publication bias for the included studies. Thus, the absence of association in other populations suggests a genetic heterogeneity in the susceptibility of schizophrenia and demonstrates the difficulties in replicating genome-wide association study findings regarding schizophrenia across different ethnic populations. To validate the association between rs1344706 and schizophrenia, further studies with larger participant populations worldwide are needed.
Dynamics and mass transfer of rising bubbles in a homogenous swarm at large gas volume fraction
Authors: Colombet Damien , Legendre Dominique , Risso Frédéric , Cockx Arnaud , Guiraud Pascal 
Published: December 2014

AbstractThe present work focuses on the collective effect on both bubble dynamics and mass transfer in a dense homogeneous bubble swarm for gas volume fractions${\it\alpha}$up to 30 %. The experimental investigation is carried out with air bubbles rising in a square column filled with water. Bubble size and shape are determined by means of a high-speed camera equipped with a telecentric lens. Gas volume fraction and bubble velocity are measured by using a dual-tip optical probe. The combination of these two techniques allows us to determine the interfacial area between the gas and the liquid. The transfer of oxygen from the bubbles to the water is measured from the time evolution of the concentration of oxygen dissolved in water, which is obtained by means of the gassing-out method. Concerning the bubble dynamics, the average vertical velocity is observed to decrease with${\it\alpha}$in agreement with previous experimental and numerical investigations, while the bubble agitation turns out to be weakly dependent on ${\it\alpha}$. Concerning mass transfer, the Sherwood number is found to be very close to that of a single bubble rising at the same Reynolds number, provided the latter is based on the average vertical bubble velocity, which accounts for the effect of the gas volume fraction on the bubble rise velocity. This conclusion is valid for situations where the diffusion coefficient of the gas in the liquid is very low (high Péclet number) and the dissolved gas is well mixed at the scale of the bubble. It is understood by considering that the transfer occurs at the front part of the bubbles through a diffusion layer which is very thin compared with all flow length scales and where the flow remains similar to that of a single rising bubble.
Biotic and abiotic drivers of dipterocarp seedling survival following mast fruiting in Malaysian Borneo
Authors: Oshima Chiaki , Tokumoto Yuji , Nakagawa Michiko 
Published: December 2014

Abstract:South-East Asian tropical rain forests experience sporadic, but profuse, seed production after general flowering, leading to the synchronous emergence of various seedlings and subsequent seedling dynamics, which play a crucial role in determining species distribution and coexistence. We examined the relative importance of both biotic (initial height, conspecific seedling density) and abiotic (canopy openness, per cent sand, soil water content) drivers using survival data for 1842 seedlings of 12 dipterocarp species for 1.5 y following mast fruiting in an old-growth Bornean tropical rain forest. More than 30% of all dipterocarp seedlings survived 1.5 y after mast fruiting. When all species were analysed together, we found that initial seedling height, canopy openness and conspecific seedling density affected dipterocarp seedling survival. Negative density dependence indicated that predators were not satiated, but dipterocarp seedlings rather suffered from host-specific natural enemies or intraspecific competition. Species-level analyses of seven dipterocarp species showed large variation in response to biotic and abiotic factors. These results suggest that interspecific differences in the relative importance of biotic and abiotic effects on seedling survival might contribute to species coexistence.
An empirical assessment of two-dimensional (2D) Debye–Scherrer-type image-plate X-ray diffraction data collapsed into a 1D diffractogram
Authors: Ross Kirk C. , Petrus Joseph A. , McDonald Andrew M. 
Published: December 2014

X-ray diffraction (XRD) has been routinely employed in the Earth sciences to characterize the crystallography of rocks and minerals. Routine characterization of samples too small for analysis by classic automated powder diffraction methods becomes challenging without access to single crystal or micro-diffraction equipment. Here, we show that a traditional Gandolfi camera lined with an image-plate (IP) as the detection medium can return a fully quantitative diffraction pattern from a sub-milligram single grain specimen in a simple and straightforward manner. Data pertaining to peak positions (d-spacings) were assessed using SRM640c Si powder, while intensity data were compared to the certified values for intensity standard SRM676a alumina powder. The refined unit-cell dimension of Si powder differed from the certified value of 5.4312 Å by no more than 0.0003 Å with a standard deviation (σ) of 0.0002 Å among the three experiments. For intensity, theσand disparity from the certified values of three diffraction experiments on SRM676a were both <2%. The results of a comparative study of the crystallographic parameters determined for a naturally occurring garnet and clinopyroxene given through the refinement of their crystal structure by single-crystal XRD method are presented. These show through Rietveld refinement of X-ray data obtained by the Gandolfi–IP method outlined here that both accurate and precise XRD data can be produced in a timely and cost-effective manner using only an IP, Gandolfi camera, and software freely available on the internet.
Drug-Checking für Drogenkonsumenten – Risiken und Potenziale
Authors: Wiese Salome , Verthein Uwe 
Published: December 2014

Hintergrund: Drug-Checking bezeichnet die chemische Analyse von illegalen Drogen und Substanzen. Die Umsetzung eines wissenschaftlichen Modellprojekts zum „Drug-Checking“ wird aktuell in Deutschland diskutiert. Ziel der vorliegenden Studie ist es, den Wunsch nach einem Drug-Checking-Modellprojekt in der Risikogruppe für Substanzkonsum aus der Techno-Szene zu klären und die bevorzugte Art einer Umsetzung zu erfragen. Methoden: Befragt wurden 433 Personen, von denen sich 338 der Risikogruppe für Substanzkonsum aus der Techno-Szene zugehörig fühlen. Die übrigen 95 Personen ohne Kontakt zu dieser Gruppe dienten als Vergleichsgruppe. Der Onlinefragebogen beinhaltete Fragen zum Drogenkonsum, zu bevorzugten Drug-Checking-Verfahren und Vorgehensweisen und zu Bedenken hinsichtlich solcher Angebote. Ergebnisse: Es zeigt sich, dass ein großer Wunsch nach Drug-Checking-Angeboten besteht (81,7 %) und eine hohe Bereitschaft existiert, für die Angebote zu zahlen (51,1 %) und sich zusätzlich über synthetische Drogen informieren zu lassen (40,9 %). Dabei werden aufwendige, sichere Analyseverfahren wie die Gas-Chromatographie bevorzugt. 30,5 % der befragten Konsumenten würden möglicherweise ihren Konsum illegaler Drogen infolge einer größeren Sicherheit über die Inhaltsstoffe durch Drug-Checking erhöhen. Die Personen der Risikogruppe für Substanzkonsum aus der Techno-Szene wiesen hohe Prävalenzen für den Konsum legaler und illegaler Drogen auf. Die am häufigsten überhaupt konsumierten Substanzen waren Alkohol (97,7 %) und Tabak (90,0 %), gefolgt von Cannabis (89,9 %), MDMA/Ecstasy (70,4 %) und Speed (69,5 %). Weit verbreitet war zudem der Mischkonsum. Die Personen, die sich nicht dieser Gruppe zugehörig fühlten, hatten insbesondere bei den illegalen Substanzen deutlich niedrigere Prävalenzwerte. Schlussfolgerungen: Die mit der Erprobung oder Einführung von Drug-Checking-Verfahren verbundenen möglichen Risiken müssen gegenüber den schadensminimierenden und präventiv nutzbaren Effekten solcher Projekte abgewogen werden.
Transfer of the Brachialis to the Anterior Interosseous Nerve as a Treatment Strategy for Cervical Spinal Cord Injury: Technical Note
Authors: Hawasli Ammar H. , Chang Jodie , Reynolds Matthew R. , Ray Wilson Z. 
Published: December 2014

Study Design Technical report. Objective To provide a technical description of the transfer of the brachialis to the anterior interosseous nerve (AIN) for the treatment of tetraplegia after a cervical spinal cord injury (SCI). Methods In this technical report, the authors present a case illustration of an ideal surgical candidate for a brachialis-to-AIN transfer: a 21-year-old patient with a complete C7 spinal cord injury and failure of any hand motor recovery. The authors provide detailed description including images and video showing how to perform the brachialis-to-AIN transfer. Results The brachialis nerve and AIN fascicles can be successfully isolated using visual inspection and motor mapping. Then, careful dissection and microsurgical coaptation can be used for a successful anterior interosseous reinnervation. Conclusion The nerve transfer techniques for reinnervation have been described predominantly for the treatment of brachial plexus injuries. The majority of the nerve transfer techniques have focused on the upper brachial plexus or distal nerves of the lower brachial plexus. More recently, nerve transfers have reemerged as a potential reinnervation strategy for select patients with cervical SCI. The brachialis-to-AIN transfer technique offers a potential means for restoration of intrinsic hand function in patients with SCI.
Existence of isostatic, maximally random jammed monodisperse hard-disk packings
Authors: Atkinson Steven , Stillinger Frank H. , Torquato Salvatore 
Published: December 2014

Significance
Disordered particle packings are ubiquitous in all areas of science. Although disordered jammed packings of hard spheres are readily observed in 3D, the story is quite different for disks. Most 2D packing protocols tend to produce highly ordered disk arrangements, suggesting that truly disordered jammed disk packings might not exist in 2D. The maximally random jammed (MRJ) configurations we observe have a complete lack of crystallinity and are distinct from the typical jammed configuration that is most probable upon rapid compression. A protocol-independent geometric-structure approach allows us to create, identify, and analyze these previously elusive packings. Our results shed new light on the nature of randomness, which is an issue that arises across the physical, mathematical, and biological sciences.
Conformational activation of ADAMTS13
Authors: South Kieron , Luken Brenda M. , Crawley James T. B. , Phillips Rebecca , Thomas Mari , Collins Richard F. , Deforche Louis , Vanhoorelbeke Karen , Lane David A. 
Published: December 2014

Significance
We show that a CUB–spacer domain interaction impedes exposure of the ADAMTS13 spacer functional exosite, preventing ADAMTS13 from interacting effectively with its complementary binding site in the VWF A2 domain. This CUB–spacer interaction is disrupted by interaction with the C-terminal domains of VWF, leading to conformational activation of ADAMTS13. Our findings also suggest that activation of ADAMTS13 reveals a cryptic epitope in the spacer domain that constitutes the autoantigenic core in patients with acquired TTP. These antibodies inhibit ADAMTS13, causing deposition of VWF and platelet-rich microthrombi in small blood vessels, resulting in organ damage. Thus, this study provides insight into the complexity of both normal haemostatic control and the pathogenesis of autoimmunity.
Allosteric activation of ADAMTS13 by von Willebrand factor
Authors: Muia Joshua , Zhu Jian , Gupta Garima , Haberichter Sandra L. , Friedman Kenneth D. , Feys Hendrik B. , Deforche Louis , Vanhoorelbeke Karen , Westfield Lisa A. , Roth Robyn , Tolia Niraj Harish , Heuser John E. , Sadler J. Evan 
Published: December 2014

Significance
The blood protein von Willebrand factor (VWF) is required for platelets to stop bleeding at sites of injury, and the metalloprotease ADAMTS13 limits platelet adhesion by cleaving VWF only when flowing blood stretches it, especially within a growing thrombus. This feedback inhibition is essential because ADAMTS13 deficiency causes fatal microvascular thrombosis. How ADAMTS13 recognizes VWF so specifically is not understood. We now find that ADAMTS13 is folded roughly in half so that its distal domains inhibit the metalloprotease domain. VWF relieves this autoinhibition and promotes its own destruction by allosterically activating ADAMTS13. Thus, VWF is both a substrate and a cofactor in this critical regulatory process.
Effect of Feed Pellet Characteristics on Growth and Feed Conversion Efficiency of Largemouth Bass Raised in Ponds
Authors: Tidwell James , Coyle Shawn , Bright Leigh Anne 
Published: December 2014

Abstract
We investigated the growth, survival, and feed conversion of Largemouth Bass Micropterus salmoides fed one of two sizes of floating pellets or a sinking pellet for 151 d in 0.04-ha ponds. The floating and sinking pellets were made from almost identical formulas. The fish were fed once daily to apparent satiation based on observed feeding activity. There was no significant difference in survival, growth, or feed conversion of fish fed the larger floating pellet versus those fed the standard-size floating pellet or sinking pellet. Fish fed the sinking pellet were significantly larger at harvest than fish fed either size of floating pellet. The efficiency of feed utilization was not decreased with the sinking pellet. These results indicate the Largemouth Bass accept and utilize sinking pellets well. However, their use on commercial scale farms would probably require some management modifications.
Changing faces of English: why English is not a foreign language in Nepal
Authors: Giri Ram A. 
Published: December 2014

Abstract
The use of English in Nepal was first recorded in the seventeenth century. Officially, however, it was adopted as a foreign language into the formal education system only in the first half of the twentieth century. Despite its “foreign” status until now, users of the language and related studies claim that it is anything but foreign. Its current use in all spheres of life makes the language indispensable and at par with Nepali, the only official language for wider communication. As such, its speakers advocate that English in Nepal deserves more veneration than the term offers. The article provides a socio-linguistic analysis of the English language situation in Nepal, and drawing from research and available literature, it assesses to what extent is such a claim justifiable. In the pretext of its growing popularity and dominance, the article examines its role, status and its position in the national language education policy and points out what implications its changing status has on the national curriculum and pedagogic resources.
Comparison of Toxicity and Treatment Outcomes in HIV-positive Versus HIV-negative Patients With Squamous Cell Carcinoma of the Anal Canal
Authors: White Evan C. , Khodayari Behnood , Erickson Kelly T. , Lien Winston W. , Hwang-Graziano Julie , Rao Aroor R. 
Published: December 2014

Purpose:
To compare the toxicity and treatment outcomes in human immunodeficiency virus (HIV)-positive versus HIV-negative patients with squamous cell carcinoma of the anal canal who underwent definitive concurrent chemoradiation at a single institution.

Materials and Methods:
Fifty-three consecutive HIV-positive patients treated between 1987 and 2013 were compared with 205 consecutive HIV-negative patients treated between 2003 and 2013. All patients received radiotherapy at a single regional facility. The median radiation dose was 54 Gy (range, 28 to 60 Gy). Concurrent chemotherapy consisted of 2 cycles 5-FU with mitomycin-C given on day 1±day 29). After treatment, patients were closely followed with imaging studies, clinical examinations, and rigid proctoscopies. Outcomes assessed were toxicity rates, progression-free survival, colostomy-free survival, cancer-specific survival, and overall survival.

Results:
Median follow-up was 34 months. Compared with HIV-negative patients, HIV-positive patients were younger (median age, 48 vs. 62 y) and predominantly male sex (98% of HIV-positive patients were male vs. 22% of HIV-negative patients). Of the HIV-positive patients, 37 (70%) were on highly active antiretroviral therapy, 26 (65%) had an undetectable viral load at the time of treatment, and 36 (72%) had a CD4 count>200 (mean CD4 count, 455). There were no significant differences in acute or late nonhematologic or hematologic toxicity rates between the 2 groups. At 3 years, there was no significant difference between HIV-positive and HIV-negative patients in regards to progression-free survival (75% vs. 76%), colostomy-free survival (85% vs. 85%), or cancer-specific survival (79% vs. 88%, P=0.36), respectively. On univariate analysis, there was a trend toward worse overall survival in HIV-positive patients (72% vs. 84% at 3 y, P=0.06). For the entire cohort, on multivariate analysis only male sex and stage were predictive of worse survival outcomes. HIV status was not associated with worse outcomes in Cox models.

Conclusions:
In the highly active antiretroviral therapy era, HIV-positive patients with anal cancer treated with standard definitive chemoradiation have equivalent toxicity and cancer-specific survival compared with HIV-negative patients.
Safety and Efficacy of Parenteral Fish Oil–Containing Lipid Emulsions in Premature Neonates
Authors: Zhao Yiyang , Wu Yang , Pei Jiao , Chen Zude , Wang Qi , Xiang Bo 
Published: December 2014

ABSTRACTObjective:The aim of the study was to evaluate the safety and efficacy of fish oil–containing (FO) lipid emulsions that are rich in ω‐3 fatty acids for parenteral nutrition in preterm neonates by using data retrieved from randomized controlled trials.Methods:We performed a meta‐analysis of 8 randomized controlled trials representing 483 premature neonates to compare FO with control (CO) lipid emulsions.Results:This meta‐analysis revealed that the levels of ω‐3 fatty acids in the form of docosahexaenoic acid, eicosapentaenoic acid, and arachidonic acid (% of total fatty acids) in plasma were statistically higher in FO groups (mean difference [MD] −0.7%, 95% confidence interval [CI] −1.05 to −0.36, P < 0.001; MD −1.31%, 95% CI −1.40 to −1.21, P < 0.001). The differences were found in red blood cell (RBC) membranes. The levels of arachidonic acid (% of total fatty acids) as ω‐6 fatty acid in plasma and red blood cell membranes were significantly lower in FO groups (MD 1.27%, 95% CI 1.12–1.42, P < 0.001) (MD 0.92%, 95% CI 0.12–1.72, P = 0.02). The mean body weight, serum level of bilirubin, triglycerides or C‐reactive protein, all‐cause mortality, and rate of lipid emulsion–associated complications were, however, not different between FO and CO groups.Conclusions:The level of docosahexaenoic acid is efficiently improved by FO lipid emulsions. The changes observed in eicosapentaenoic acid and arachidonic acid, and the associated safety issue, however, remain to be clarified. Any clinical benefit or detrimental effect of using FO in premature neonates cannot be demonstrated by the present study.
Biological Organization, Biological Information, and Knowledge
Authors: Kritz Maurício Vieira 
Published: December 2014

AbstractA concept of information designed to handle information conveyed by organizations is introduced. This concept of information may be used at all biological scales: from molecular and intracellular to multi-cellular organisms and human beings, and further on to collectivities, societies and culture. In this short account, two ground concepts necessary for developing the definition will also be introduced: whole-part graphs, a model for biological organization, and synexions, their immersion into space-time. This definition of information formalizes perception, observers and interpretation; allowing for considering information-exchange as a basic form of biological interaction. Some of its elements will be clarified by arguing and explaining why the immersion of whole-part graphs in (the physical) space-time is needed.