bluuebunny/crossref_metadata_2025_split huggingface dataset:
It's all about the pentiums: The use, manipulation, and storage of digital microscopy imaging data for the biological sciences
Authors: Hornick Jessica E. , Hinchcliffe Edward H. 
Published: December 2013

SUMMARYDigital microscopy has revolutionized quantitative imaging, with binary‐encoded computer files serving to capture and store imaging data sets for analysis. With the ever‐present use of computers to generate and store imaging data, it becomes increasingly important to understand how these files are created, and how they can be both used and mis‐used. This is a particularly important task for the biologist who may have limited background in computer science. Here we discuss some of the basic aspects of digital data storage and use, including file types, storage media, and the choice between commercial and open‐source software. Often, open‐source software is written by a user or group of users, and then distributed to the scientific community at large. These can be important tools, but there are some hidden costs to this freeware that we will discuss. We will also compare open‐source software to commercial imaging software, which is often written for use by non‐computer scientists. Mol. Reprod. Dev. 82: 508–517, 2015. © 2014 Wiley Periodicals, Inc.
Performance of the timed “up & go” test in spinal muscular atrophy
Authors: Dunaway Sally , Montes Jacqueline , Garber Carol Ewing , Carr Brendan , Kramer Samantha S. , Kamil‐Rosenberg Shirit , Strauss Nancy , Sproule Douglas , De Vivo Darryl C. 
Published: December 2013

ABSTRACTIntroductionThe timed “up & go” (TUG) test is a quick measure of balance and mobility. TUG scores correlate with clinical, functional, and strength assessment and decline linearly over time. Reliability and validity have not been tested in spinal muscular atrophy (SMA). Methods: Fifteen ambulatory SMA participants performed TUG testing and strength, functional, and clinical assessments. Intraclass correlation coefficients quantified test–retest reliability. Convergent validity was determined using Pearson correlation coefficients. Results: Test–retest reliability was excellent for all participants. TUG was associated significantly with total leg and knee flexor strength, as well as the Hammersmith Functional Motor Scale Expanded, the 10‐meter walk/run, and 6‐minute walk tests. TUG findings were not associated with knee extensor strength, pulmonary function, or fatigue. Conclusions: In SMA, the TUG test is easily administered, reliable, and correlates with established outcome measures. TUG testing is a potentially useful outcome measure for clinical trials and a measure of disability in ambulatory patients with SMA. Muscle Nerve 50:273–277, 2014
Treatment of childhood acute lymphoblastic leukemia in central America: A lower‐middle income countries experience
Authors: Navarrete M. , Rossi E. , Brivio E. , Carrillo J.M. , Bonilla M. , Vasquez R. , Peña A. , Fu L. , Martinez R. , Espinoza C.M. Pacheco , Lacayo L.F. Baez , Rodriguez H. , Batista R. , Barr R. , Howard S.C. , Ribeiro R.C. , Masera G. , Biondi A. , Conter V. , Valsecchi M.G. 
Published: December 2013

BackgroundFive Asociación de Hemato‐Oncología de Centroamérica (AHOPCA) countries have used an adapted BFM‐based protocol for childhood acute lymphoblastic leukemia (ALL).ProcedureIn the AHOPCA‐ALL 2008 protocol, patients were stratified by age, white blood cell count, immunophenotype, central nervous system involvement, day 8 prednisone response, and morphologic bone marrow response to induction therapy. Patients at Standard Risk (SR) received a three‐drug induction regimen, a reinduction phase, and maintenance with protracted intrathecal therapy. Those at Intermediate (IR) and High Risk (HR) received, in addition, daunorubicin during induction therapy, a consolidation phase and two or three reinduction phases respectively.ResultsFrom August 2008 through July 2012, 1,313 patients were enrolled: 353 in SR, 548 in IR, 412 in HR. During induction therapy, 3.0% of patients died, 2.7% abandoned treatment, 1.1% had resistant ALL, and 93.2% achieved morphological complete remission (CR). Deaths and abandonment in first CR occurred in 2.7% and in 7.0% of patients, respectively. The relapse rate at a median observation time of 2.1 years was 15.0%. At 3 years, the event‐free survival (EFS) and overall survival (OS), with abandonment considered as an event, were 59.4% (SE 1.7) and 68.2% (SE 1.6). Three‐year EFS was 68.5% (SE 3.0), 62.1% (SE 2.6), and 47.8% (SE 3.2) for SR, IR, and HR groups. Adolescents had a significantly higher relapse rate (P = 0.001).ConclusionsThis experience shows that common international studies are feasible in lower‐middle income countries. Toxic deaths, abandonment of treatment, and relapses remain major obstacles to the successful treatment. Alternative treatment strategies may be beneficial. Pediatr Blood Cancer 2014;61:803–809. © 2013 Wiley Periodicals, Inc.
Flavodiiron Protein Flv2/Flv4-Related Photoprotective Mechanism Dissipates Excitation Pressure of PSII in Cooperation with Phycobilisomes in Cyanobacteria
Authors: Bersanini Luca , Battchikova Natalia , Jokel Martina , Rehman Ateeq , Vass Imre , Allahverdiyeva Yagut , Aro Eva-Mari 
Published: December 2013

Abstract
Oxygenic photosynthesis evolved with cyanobacteria, the ancestors of plant chloroplasts. The highly oxidizing chemistry of water splitting required concomitant evolution of efficient photoprotection mechanisms to safeguard the photosynthetic machinery. The role of flavodiiron proteins (FDPs), originally called A-type flavoproteins or Flvs, in this context has only recently been appreciated. Cyanobacterial FDPs constitute a specific protein group that evolved to protect oxygenic photosynthesis. There are four FDPs in Synechocystis sp. PCC 6803 (Flv1 to Flv4). Two of them, Flv2 and Flv4, are encoded by an operon together with a Sll0218 protein. Their expression, tightly regulated by CO2 levels, is also influenced by changes in light intensity. Here we describe the overexpression of the flv4-2 operon in Synechocystis sp. PCC 6803 and demonstrate that it results in improved photochemistry of PSII. The flv4-2/OE mutant is more resistant to photoinhibition of PSII and exhibits a more oxidized state of the plastoquinone pool and reduced production of singlet oxygen compared with control strains. Results of biophysical measurements indicate that the flv4-2 operon functions in an alternative electron transfer pathway from PSII, and thus alleviates PSII excitation pressure by channeling up to 30% of PSII-originated electrons. Furthermore, intact phycobilisomes are required for stable expression of the flv4-2 operon genes and for the Flv2/Flv4 heterodimer-mediated electron transfer mechanism. The latter operates in photoprotection in a complementary way with the orange carotenoid protein-related nonphotochemical quenching. Expression of the flv4-2 operon and exchange of the D1 forms in PSII centers upon light stress, on the contrary, are mutually exclusive photoprotection strategies among cyanobacteria.
A Nodule-Specific Lipid Transfer Protein AsE246 Participates in Transport of Plant-Synthesized Lipids to Symbiosome Membrane and Is Essential for Nodule Organogenesis in Chinese Milk Vetch
Authors: Lei Lei , Chen Ling , Shi Xiaofeng , Li Yixing , Wang Jianyun , Chen Dasong , Xie Fuli , Li Youguo 
Published: December 2013

Abstract
Rhizobia in legume root nodules fix nitrogen in symbiosomes, organelle-like structures in which a membrane from the host plant surrounds the symbiotic bacteria. However, the components that transport plant-synthesized lipids to the symbiosome membrane remain unknown. This study identified and functionally characterized the Chinese milk vetch (Astragalus sinicus) lipid transfer protein AsE246, which is specifically expressed in nodules. It was found that AsE246 can bind lipids in vitro. More importantly, AsE246 can bind the plant-synthesized membrane lipid digalactosyldiacylglycerol in vivo. Immunofluorescence and immunoelectron microscopy showed that AsE246 and digalactosyldiacylglycerol localize in the symbiosome membrane and are present in infection threads. Overexpression of AsE246 resulted in increased nodule numbers; knockdown of AsE246 resulted in reduced nodule numbers, decreased lipids contents in nodules, diminished nitrogen fixation activity, and abnormal development of symbiosomes. AsE246 knockdown also resulted in fewer infection threads, nodule primordia, and nodules, while AsE246 overexpression resulted in more infection threads and nodule primordia, suggesting that AsE246 affects nodule organogenesis associated with infection thread formation. Taken together, these results indicate that AsE246 contributes to lipids transport to the symbiosome membrane, and this transport is required for effective legume-rhizobium symbiosis.
Expression of a xanthine permease and phosphate transporter in cultures and field populations of the harmful alga Aureococcus anophagefferens: tracking nutritional deficiency during brown tides
Authors: Wurch Louie L. , Gobler Christopher J. , Dyhrman Sonya T. 
Published: December 2013

SummaryTargeted gene expression using quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was employed to track patterns in the expression of genes indicative of nitrogen or phosphorus deficiency in the brown tide‐forming alga Aureococcus anophagefferens. During culture experiments, a xanthine/uracil/vitamin C permease (XUV) was upregulated ∼20‐fold under nitrogen‐deficient conditions relative to a nitrogen‐replete control and rapidly returned to nitrogen‐replete levels after nitrogen‐deficient cells were resupplied with nitrate or ammonium. It was not responsive to phosphorus deficiency. Expression of an inorganic phosphate transporter (PTA3) was enriched ∼10‐fold under phosphorus‐deficient conditions relative to a phosphorus‐replete control, and this signal was rapidly lost upon phosphate resupply. PTA3 was not upregulated by nitrogen deficiency. Natural A. anophagefferens populations from a dense brown tide that occurred in Long Island, NY, in 2009 were assayed for XUV and PTA3 expression and compared with nutrient concentrations over the peak of a bloom. Patterns in XUV expression were consistent with nitrogen‐replete growth, never reaching the values observed in N‐deficient cultures. PTA3 expression was highest prior to peak bloom stages, reaching expression levels within the range of P‐deficient cultures. These data highlight the value of molecular‐level assessments of nutrient deficiency and suggest that phosphorus deficiency could play a role in the dynamics of destructive A. anophagefferens blooms.
Methanogen community composition and rates of methane consumption in Canadian High Arctic permafrost soils
Authors: Allan J. , Ronholm J. , Mykytczuk N. C. S. , Greer C. W. , Onstott T. C. , Whyte L. G. 
Published: December 2013

SummaryIncreasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. In situ CO2 and CH4 flux, measured in 2010 and 2011 from ice‐wedge polygons, indicate that these soil formations are a net source of CO2 emissions, but a CH4 sink. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Gas flux was measured regularly and indicated an increase in CH4 flux after extended incubation. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw. This study provides evidence that although High Arctic ice‐wedge polygons are currently a sink for CH4, higher arctic temperatures and anaerobic conditions, a possible result of climate change, could result in this soil becoming a source for CH4 gas flux.
MicroRNA expression analysis and Multiplex ligation‐dependent probe amplification in metastatic and non‐metastatic uveal melanoma
Authors: Larsen Ann‐Cathrine , Holst Line , Kaczkowski Bogumil , Andersen Morten T. , Manfé Valentina , Siersma Volkert D. , Kolko Miriam , Kiilgaard Jens F. , Winther Ole , Prause Jan U. , Gniadecki Robert , Heegaard Steffen 
Published: December 2013

AbstractPurposeTo determine the association of microRNA expression and chromosomal changes with metastasis and survival in uveal melanoma (UM).MethodsThirty‐six patients with UM were selected based on the metastatic status, and clinicopathological data were collected. Multiplex ligation‐dependent probe amplification (MLPA) was used to identify chromosomal changes. Chromosomal changes and clinicopathological data were correlated with survival and metastasis. The microRNA expression was analysed in 26 of the 36 archived UM samples. Unsupervised analysis, differential expression analysis and Cox regression analysis were performed to determine the association with metastasis and survival.ResultsMetastasis and metastatic death occurred in 20 patients, two patients died of other causes and one patient of unknown causes. A significant association between increasing size category (p = 0.002, log‐rank), extraocular extension (p = 0.001), chromosome 3 loss (p = 0.033) and 1p loss (p = 0.030) and development of metastases was observed. Tumour, node, metastasis (TNM) staging showed a significant association with survival (p < 0.0001, log‐rank). Adjusting for gender and age TNM size category T4 (p = 0.016, Cox regression analysis), mixed (p = 0.029) and epithelioid (p = 0.0058) cell types, chromosome 3 loss (p = 0.014) and 8q gain (p = 0.010) were significant prognosticators for a poor survival.Hierarchical clustering divided the UM into three groups based on microRNA expression. The clusters showed no association with clinical or histopathological features, TNM staging, metastasis or survival. Differential expression analysis did not reveal microRNAs related to metastasis or survival.ConclusionsThe prognostic significance of chromosome 3 loss and 8q gain identified by MLPA analysis was confirmed in archived UM samples. The value of microRNA expression as a predictor of metastasis and survival in UM could not be confirmed.
Kinetics of γ‐cyclodextrin nanoparticle suspension eye drops in tear fluid
Authors: Jóhannesson Gauti , Moya‐Ortega Maria D. , Ásgrímsdóttir Gudrún Marta , Lund Sigrún H. , Thorsteinsdóttir Margrét , Loftsson Thorsteinn , Stefánsson Einar 
Published: December 2013

AbstractPurposeWe have developed nanoparticle γ‐cyclodextrin dexamethasone (DexNP) and dorzolamide (DorzNP) eye drops that provide sustained high drug concentrations on the eye surface. To test these characteristics, we measured dexamethasone and dorzolamide levels in tear fluid in humans following eye drop administration.MethodsConcentration of dexamethasone was measured by mass spectrometry. One drop of DexNP was instilled into one eye. Tear fluid was sampled with microcapillary pipettes at seven time‐points after drop instillation. Control eyes received Maxidex® (dexamethasone). The same procedure was performed for dorzolamide with DorzNP and Trusopt®.ResultsSix subjects were included in each group. The peak concentration (μg/ml ± standard deviation) of dexamethasone for DexNP eye drops (636.6 ± 399.1) was up to 19‐fold higher than with Maxidex® (39.3 ± 18.9) (p < 0.001). At 4 hr, DexNP was still 10 times higher than Maxidex®. In addition, DexNP resulted in about 30‐fold higher concentration of dissolved dexamethasone in the tear fluid of extended time period allowing more drug to partition into the eye tissue. The overall concentration of dorzolamide was about 50% higher for DorzNP (59.5 ± 76.9) than Trusopt® (40.0 ± 76.7) (p < 0.05).ConclusionThe results indicate high and extended concentration of dissolved dexamethasone with DexNP, which can explain the greater and longer lasting effect of dexamethasone in the cyclodextrin nanoparticle drug delivery platform. Dexamethasone seems to fit the cyclodextrin nanoparticle suspension drug delivery platform with longer duration and higher concentrations in tear fluid than available commercial drops, while dorzolamide is less suitable.
Ultrastructure of trichome of old world porcupine of Indian subcontinent
Authors: Raha Paramaa , Ghosh Biswatosh , Bhar Radhaballabh , Das Nilansu , Poddar‐Sarkar Mousumi 
Published: December 2013

AbstractThe present investigation is based on ultrastructural details of different types of quills of two species of old world porcupine (Hystrix indica and Hystrix brachyura) of Indian subcontinent using environmental scanning electron microscopy (ESEM). In H. indica, four types of quills have been detected – bristlelike spines, stilettolike spines, spikes and mane. The quills of H. brachyura are categorized into four types – broad, slender, hollow tail quill and quills of the anogenital region. The ESEM images of surface characteristic of different types of quills of both the species except the hollow tail quill showed usual scaly features without having any differences. The cross‐sectional images of quills of H. indica and H. brachyura show a narrow cortex and a broad medullary region with a network of anastomosing channels. The cortical layer is comparatively thicker in mane hairs of H. indica and in slender quills of H. brachyura. With extensive exploration of the anatomical structures of the quills by ESEM from both the species of Hystrix, we could not find ‘osmetrichia’ in any forms of quill. In contrast, we hypothesized that the channels and network of medulla are serving the purpose for transportation of pheromonal signalling molecules in old world porcupine.
Asymmetric Forecast Information and the Value of Demand Observation in Repeated Procurement
Authors: Shamir Noam 
Published: December 2013

ABSTRACTIn many supply chain relationships that continue over multiple periods, information about the hidden properties of the supply chain partners can be revealed throughout the course of the relationship. This article examines how the availability of such information affects the contracting scheme between a supplier and his manufacturer in a relationship that persists over several selling seasons. At the beginning of the first selling season, the manufacturer observes private information about the demand distribution, whereas the supplier who is less familiar with the market is endowed only with a prior belief about the market condition. When the supplier cannot observe the demand realization during the first selling period, she offers a contract that induces the manufacturer to reveal the market condition in the first selling season. However, the opportunity for the supplier to observe demand realization can result in the supplier offering the manufacturer a simple contract that does not induce the manufacturer to reveal his private information during the first selling season. In the latter case, the supplier observes the demand realization and designs the second period contract based on this information. We show that when the supplier chooses to offer such a contract, the manufacturer becomes worse‐off, and it has an ambiguous effect on the performance of the supply chain.
Tissue Doppler–Derived Strain and Strain Rate during the First 28 Days of Life in Very Low Birth Weight Infants
Authors: Helfer Sven , Schmitz Lothar , Bührer Christoph , Czernik Christoph 
Published: December 2013

BackgroundPreterm infants may have cardiac stress related to patent ductus arteriosus (PDA) or bronchopulmonary dysplasia (BPD). In this study, we examined the development of cardiac function in preterm infants by measuring tissue Doppler–derived peak systolic strain (PSS) and strain rate (PSSR) in the first 28 days of life.MethodsPeak systolic strain and strain rate were measured in series in the free wall of the right (RV) and left (LV) ventricles on days 1, 7, 14, and 28 of life in 119 preterm infants <1500 g birth weight along with weight, heart rate, and presence of hemodynamically significant (hs) PDA or BPD. Both were assigned retrospectively. HsPDA was defined as a PDA requiring intervention whereas BPD was determined based on an infant's need for supplemental oxygen at 36 weeks of gestational age.ResultsPeak systolic strain and strain rate of the RV rose significantly during the first 28 days of life (P < 0.01). Infants who developed BPD had significantly lower RV free wall PSS on days 14 and 28 (P < 0.01 and <0.05). HsPDA resulted in a significantly lower PSS in the LV free wall as of day 14 (P < 0.01). After PDA intervention (day 28), LV PSS remained significantly lower (P < 0.05), but showed a tendency to increase (P = 0.18).ConclusionsPeak systolic strain determined in preterm infants appears to reflect increased afterload (decreased RV PSS in BPD infants) and increased preload (decreased LV PSS in hsPDA infants). The merits of such measurements as a basis for making clinical decisions still need to be explored.
Rationale and Design of a Randomized Trial Comparing Initial Stress Echocardiography versus Coronary CT Angiography in Low‐to‐Intermediate Risk Emergency Department Patients with Chest Pain
Authors: Levsky Jeffrey M. , Haramati Linda B. , Taub Cynthia C. , Spevack Daniel M. , Menegus Mark A. , Travin Mark I. , Vega Shayna , Lerer Rikah , Brown‐Manhertz Durline , Hirschhorn Esther , Tobin Jonathan N. , Garcia Mario J. 
Published: December 2013

BackgroundComparative effectiveness research (CER) has become a major focus of cardiovascular disease investigation to optimize diagnosis and treatment paradigms and decrease healthcare expenditures. Acute chest pain is a highly prevalent reason for evaluation in the Emergency Department (ED) that results in hospital admission for many patients and excess expense. Improvement in noninvasive diagnostic algorithms can potentially reduce unnecessary admissions.ObjectiveTo compare the performance of treadmill stress echocardiography (SE) and coronary computed tomography angiography (CTA) in ED chest pain patients with low‐to‐intermediate risk of significant coronary artery disease.DesignThis is a single‐center, randomized controlled trial (RCT) comparing SE and CTA head‐to‐head as the initial noninvasive imaging modality. The primary outcome measured is the incidence of hospitalization. The study is powered to detect a reduction in admissions from 28% to 15% with a sample size of 400. Secondary outcomes include length of stay in the ED/hospital and estimated cost of care. Safety outcomes include subsequent visits to the ED and hospitalizations, as well as major adverse cardiovascular events at 30 days and 1 year. Patients who do not meet study criteria or do not consent for randomization are offered entry into an observational registry.ConclusionsThis RCT will add to our understanding of the roles of different imaging modalities in triaging patients with suspected angina. It will increase the CER evidence base comparing SE and CTA and provide insight into potential benefits and limitations of appropriate use of treadmill SE in the ED.