bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reassessment of the Fecundity of California Sheephead
Authors: Loke-Smith Kerri A. , Floyd Alyssa J. , Lowe Christopher G. , Hamilton Scott L. , Caselle Jennifer E. , Young Kelly A. 
Published: October 2012

Abstract
Fecundity estimates used in a 2004 stock assessment to evaluate the overall health of the population of California sheephead Semicossyphus pulcher were based primarily on two studies. The first estimated the total fecundity of only nine individuals captured near Santa Catalina Island, California, and the second estimated batch fecundity of individuals taken from only one artificial reef. In order to develop a current and more comprehensive estimate of fecundity, we collected California sheephead from seven locations off southern California throughout the spawning season (July through September). To estimate both total fecundity and batch fecundity, we categorized and counted oocytes from ovarian subsamples of 28 and 24 (respectively) mature females (stage 3, spawning capable; determined by histological analysis). Total and batch fecundity increased with somatic mass, standard length, and ovary mass. We found total fecundity to increase with somatic mass to a power of 5.5, which is considerably greater than the value (2.95) reported previously. Our observations therefore highlight the importance of large females in the reproductive potential of the California sheephead stock. Regression analysis indicates that ovary mass is the most accurate biological indicator of fecundity for California sheephead and should be used for subsequent stock analyses.
Received January 27, 2012; accepted June 19, 2012
Creating reusable tools from scripts: the Galaxy Tool Factory
Authors: Lazarus Ross , Kaspi Antony , Ziemann Mark ,   The Galaxy Team
Published: October 2012

Abstract
Motivation: Galaxy is a software application supporting high-throughput biology analyses and work flows, available as a free on-line service or as source code for local deployment. New tools can be written to extend Galaxy, and these can be shared using public Galaxy Tool Shed (GTS) repositories, but converting even simple scripts into tools requires effort from a skilled developer.
Results: The Tool Factory is a novel Galaxy tool that automates the generation of all code needed to execute user-supplied scripts, and wraps them into new Galaxy tools for upload to a GTS, ready for review and installation through the Galaxy administrative interface.
Availability and implementation: The Galaxy administrative interface supports automated installation from the main GTS. Source code and support are available at the project website, https://bitbucket.org/fubar/galaxytoolfactory. The Tool Factory is implemented as an installable Galaxy tool.
Contact: ross.lazarus@channing.harvard.edu
Stabilization of H
+
–H
2
collision complexes between 11 and 28K
Authors: Plašil Radek , Zymak Illia , Jusko Pavol , Mulin Dmytro , Gerlich Dieter , Glosík Juraj 
Published: October 2012

Formation of

via association of H
+
with H
2
has been studied at low temperatures using a 22-pole radiofrequency trap. Operating at hydrogen number densities from 10
11
to 10
14
cm
−3
, the contributions of radiative,
k
r
, and ternary,
k
3
, association have been extracted from the measured apparent binary rate coefficients,
k
*=
k
r
+
k
3
[H
2
]. Surprisingly,
k
3
is constant between 11 and 22 K, (2.6±0.8)×10
−29
cm
6
s
−1
, while radiative association decreases from
k
r
(11 K)=(1.6±0.3)×10
−16
cm
3
s
−1
to
k
r
(28 K)=(5±2)×10
−17
cm
3
s
−1
. These results are in conflict with simple association models in which formation and stabilization of the complex are treated separately. Tentative explanations are based on the fact that, at low temperatures, only few partial waves contribute to the formation of the collision complex and that ternary association with H
2
may be quite inefficient because of the ‘shared proton’ structure of

.
Molecular events in matrix protein metabolism in the aging kidney
Authors: Sataranatarajan Kavithalakshmi , Feliers Denis , Mariappan Meenalakshmi M. , Lee Hak Joo , Lee Myung Ja , Day Robert T. , Yalamanchili Hima Bindu , Choudhury Goutam G. , Barnes Jeffrey L. , Van Remmen Holly , Richardson Arlan , Kasinath Balakuntalam S. 
Published: October 2012

SummaryWe explored molecular events associated with aging‐induced matrix changes in the kidney. C57BL6 mice were studied in youth, middle age, and old age. Albuminuria and serum cystatin C level (an index of glomerular filtration) increased with aging. Renal hypertrophy was evident in middle‐aged and old mice and was associated with glomerulomegaly and increase in mesangial fraction occupied by extracellular matrix. Content of collagen types I and III and fibronectin was increased with aging; increment in their mRNA varied with the phase of aging. The content of ZEB1 and ZEB2, collagen type I transcription inhibitors, and their binding to the collagen type Iα2 promoter by ChIP assay also showed age‐phase‐specific changes. Lack of increase in mRNA and data from polysome assay suggested decreased degradation as a potential mechanism for kidney collagen type I accumulation in the middle‐aged mice. These changes occurred with increment in TGFβ mRNA and protein and activation of its SMAD3 pathway; SMAD3 binding to the collagen type Iα2 promoter was also increased. TGFβ‐regulated microRNAs (miRs) exhibited selective regulation. The renal cortical content of miR‐21 and miR‐200c, but not miR‐192, miR‐200a, or miR‐200b, was increased with aging. Increased miR‐21 and miR‐200c contents were associated with reduced expression of their targets, Sprouty‐1 and ZEB2, respectively. These data show that aging is associated with complex molecular events in the kidney that are already evident in the middle age and progress to old age. Age‐phase‐specific regulation of matrix protein synthesis occurs and involves matrix protein–specific transcriptional and post‐transcriptional mechanisms.
The CRTH2 antagonist OC000459 reduces nasal and ocular symptoms in allergic subjects exposed to grass pollen, a randomised, placebo‐controlled, double‐blind trial
Authors: Horak F. , Zieglmayer P. , Zieglmayer R. , Lemell P. , Collins L. P. , Hunter M. G. , Steiner J. , Lewis T. , Payton M. A. , Perkins C. M. , Pettipher R. 
Published: October 2012

AbstractBackgroundCRTH2 mediates activation of Th2 cells, eosinophils and basophils in response to prostaglandin D2. The CRTH2 antagonist OC000459 has previously been demonstrated to reduce airway inflammation and improve lung function in moderate persistent asthma. The objective of the present study was to determine the involvement of CRTH2 in promoting nasal and ocular symptoms in allergic subjects exposed to grass pollen.MethodsA single centre, randomised, double‐blind, placebo‐controlled, two‐way crossover study was conducted in 35 male subjects allergic to grass pollen comparing OC000459 200 mg bid with placebo for 8 days. Subjects were exposed to grass pollen (≥1400 grains/m3) for 6 h on the 2nd and 8th days of treatment and assessed for nasal symptoms, ocular symptoms, other symptoms, nasal secretion weight and rhinomanometry over the 6‐h period. After a washout period of 3 weeks, subjects were switched to the alternative treatment for a further 8 days. The trial was registered on the clinical trials.gov database (Identifier NCT01448902).ResultsDuring the first treatment period, treatment with OC000459 significantly reduced both nasal and ocular symptoms in allergic subjects compared with placebo after challenge with grass pollen. A significant effect was observed on the 2nd day of dosing which was increased on the 8th day of dosing. The therapeutic effects of OC000459 persisted into the second treatment period despite a 3‐week washout phase. The safety profile of OC000459 was similar to that of placebo.ConclusionTreatment with OC000459 was well tolerated and led to a significant and persistent reduction in the symptoms of rhinoconjunctivitis.
Short‐interval intracortical inhibition in knee extensors during locomotor cycling
Authors: Sidhu, S. K. , Cresswell A. G. , Carroll T. J. 
Published: October 2012

AbstractAimShort‐interval intracortical inhibition (SICI) can provide information on changes in cortical responsiveness during voluntary contractions. It is, however, unknown whether the magnitude of SICI changes throughout the cycle of rhythmic movements such as leg cycling.MethodsThe effects of four conditioning stimulus (CS) intensities, 70, 80, 90 and 95% of active motor threshold (AMT), on the magnitude of SICI were tested during three conditions: (1) activation phase of the electromyography (EMG) burst, (2) deactivation phase of the EMG burst and (3) static contractions. The three conditions were matched for EMG amplitude and test motor‐evoked potential (MEP) size with reference to the vastus lateralis muscle. Responses were also recorded from rectus femoris and vastus medialis.Resultsshort‐interval cortical inhibition was weak during static knee contractions (15% reduction in control MEP) relative to previous reports during contractions in other muscle groups. SICI was abolished during the activation phase of the knee extensor EMG burst (P > 0.05), but present (approx. 90% of control MEP size) during the deactivation phase of EMG (P < 0.05). Furthermore, inhibition was elicited at a lower CS intensity during the deactivation phase of EMG during cycling than during static contractions (70 AMT vs. 90% AMT).ConclusionThe results suggest that the efficacy of intracortical inhibitory projections to knee extensor corticomotoneurons is particularly weak during muscle activation. A lower threshold of activation for inhibitory cells during deactivation phase of cycling EMG was evident, and there was a phasic modulation of intracortical inhibition affecting corticospinal projections to the working muscles.
Clinical Outcomes After Tricuspid Valve Annuloplasty in Addition to Mitral Valve Surgery
Authors: Koppers Gille , Verhaert David , Verbrugge Frederik H. , Reyskens Rozette , Gutermann Herbert , Van Kerrebroeck Chris , Vandervoort Pieter , Tang W. H. Wilson , Dion Robert , Mullens Wilfried 
Published: October 2012

©2012 Wiley Periodicals, inc.Current guidelines recommend tricuspid valve annuloplasty (TVP) together with mitral valve surgery in cases of tricuspid annulus dilation (≥40 mm) or functional tricuspid valve regurgitation >2/4. Baseline clinical and echocardiographic data of patients undergoing mitral valve surgery in a single tertiary care hospital between 2007 and 2010 were analyzed. Mortality and heart failure hospitalization data were collected and groups with or without TVP were compared. Patients with TVP (n=89) had similar baseline characteristics compared with patients without (n=86), except for lower right ventricular fractional area change and more concomitant aortic valve surgery. Mortality was higher in the TVP group at 30 days (14% vs 5%; P=.04), but the difference was no longer significant at the end of follow‐up. More patients were hospitalized for heart failure in the TVP group (31% vs 17%; hazard ratio, 2.1; 95% confidence interval, 1.1–4.0; P=.05). Right ventricular sphericity index was the only preoperative parameter predicting death or heart failure hospitalizations. In conclusion, patients undergoing TVP in addition to mitral valve surgery are at high risk for early death or subsequent heart failure hospitalizations, which might be partly explained by more complex heart disease. The extent of preoperative right ventricular remodeling may be predictive of adverse outcomes.
Improved method of differentiation, selection and amplification of human melanocytes from the hair follicle cell pool
Authors: Savkovic Vuk , Dieckmann Christina , Milkova Linda , Simon Jan C. 
Published: October 2012

AbstractHair root harbours a complex cell pool with an immense developmental potential. Several lineages, including skin, can be differentiated from the multipotent to pluripotent cells of outer root sheath (ORS) of hair follicle. Outer root sheath presents the most opulent non‐invasively gained adult stem cell source known. For the purposes of cultivating melanocytes designated for graft‐based treatments of depigmentation disorders, we have established an ex vivo/in vitro cultivation method by introducing several methodological improvements to the ORS explant method of Dieckmann. As a result, we gained a higher, purer yield of differentiated melanocytes in half the time (at least 106 of 95% pure cells in 4 weeks). This reliable cultivation procedure begins with the epilation of 60 hairs and yields high numbers of ORS melanocytes that could be used for grafting applications. The procedure not only utilises the developmental potential of hair root cell pool and favors differentiation into melanocytes, but also contributes to the general trend of minimal‐to‐non‐invasive strategies for regenerative medicine.
Insight into the structure–function relationship of the nonheme iron halogenases involved in the biosynthesis of 4‐chlorothreonine – Thr3 from Streptomyces sp. OH‐5093 and SyrB2 from Pseudomonas syringae pv. syringae B301DR
Authors: Fullone Maria Rosaria , Paiardini Alessandro , Miele Rossella , Marsango Sara , Gross Dennis C. , Omura Satoshi , Ros‐Herrera Enric , Bonaccorsi di Patti Maria Carmela , Laganà Aldo , Pascarella Stefano , Grgurina Ingeborg 
Published: October 2012

Molecular cloning of the biosynthetic gene cluster involved in the production of free 4‐chlorothreonine in Streptomyces sp. OH‐5093 showed the presence of six ORFs: thr1, thr2, thr3, orf1, orf2 and thr4. According to bioinformatic analysis, thr1, thr2, thr3 and thr4 encode a free‐standing adenylation domain, a carrier protein, an Fe(II) nonheme α‐ketoglutarate‐dependent halogenase and a thioesterase, respectively, indicating the role of these genes in the activation and halogenation of threonine and the release of 4‐chlorothreonine in a pathway closely reflecting the formation of this amino acid in the biosynthesis of the lipodepsipeptide syringomycin from Pseudomonas syringae pv. syringae B301DR. Orf1 and orf2 show sequence similarity with alanyl/threonyl‐tRNA synthetases editing domains and drug metabolite transporters, respectively. We show that thr3 can replace the halogenase gene syrB2 in the biosynthesis of syringomycin, by functional complementation of the mutant P. s. pv. syringae strain BR135A1 inactivated in syrB2. We also provide an insight into the structure–function relationship of halogenases Thr3 and SyrB2 using homology modelling and site‐directed mutagenesis.DatabaseNucleotide sequence data have been deposited in the ebi.ac.uk/EMBL/GenBank databases under accession numbers: thr1 (gi:378781338|CCF23454); thr2 (gi:378781340|CCF23456); thr3 (gi:378781341|CCF23457); orf1 (gi:378781342|CCF23458); orf2 (gi:378781343|CCF23459); thr4 (gi:378781344|CCF23460)
‘House and garden’: larval galleries enhance resource availability for a sedentary caddisfly
Authors: INGS NICOLA L. , HILDREW ALAN G. , GREY JONATHAN 
Published: October 2012

Summary1. Sedentary grazers can be numerous in fresh waters, despite the constraints on resource availability and the increased predation risk inherent in this lifestyle. The retreats of sedentary grazers have been assumed to provide protection to the resident (a ‘house’), but also may provide additional fertilised food for the grazer (i.e. a ‘garden’). If retreats function as a garden, then they should (i) contain a higher quality and/or quantity of food than the alternative food source. Furthermore, the proportion of retreat‐derived carbon and nitrogen assimilated by the resident should be (ii) related to overall resource availability (more when resources are limited) or (iii) perhaps also to larval density. Alternatively, if retreats provide a less risky food source, then (iv) assimilation of material from the retreat is likely to be greater under conditions in which the risk of emerging from the retreat is high.2. We tested these four hypotheses for the common and widespread gallery‐building grazing caddisfly Tinodes waeneri. Resource availability, larval density and biomass, and exposure were measured for populations from six lakes of differing productivity in August, October and January.3. Galleries always contained more algal food than the surrounding epilithon, suggesting that gardening is effective. Furthermore, gallery chlorophyll a content in August, and the disparity in food quality (assessed from the C : N ratio) between gallery and epilithon (quality higher in the former) in October were positively related to the proportion of larval biomass that was derived from the gallery. Larval density and wave exposure parameters were not related to larval assimilation of gallery material.4. Galleries that are fertilised by the occupant provide more, and sometimes also better quality, food (in terms of the C : N ratio) than is otherwise available. Thus, the gallery plays a substantial role in larval nutrition, and this role is greater at key times of food shortage.
Correlation of metabolic syndrome with urinary stone composition
Authors: Cho Sung Tae , Jung Seung Il , Myung Soon Chul , Kim Tae Hyoung 
Published: October 2012

ObjectiveTo determine the correlation between metabolic syndrome and the distribution of stone components in patients with urolithiasis.MethodsBetween January 2007 and December 2010, renal or ureteral stones were collected from 712 patients (432 males, 280 females) who underwent surgical intervention at three hospitals in South Korea. Metabolic syndrome was defined according to the latest definition of the International Diabetes Federation, using ethnicity‐ and sex‐specific cut‐off values for central obesity. Patients were assessed by factors used in metabolic syndrome. All urinary stones were analyzed using infrared spectrophotometry and categorized according to their main component.ResultsThe patients' mean age was 55.9 years (range 19–93 years). Of the 712 patients, 347 (48.7%; 205 males, 142 females) had a diagnosis of metabolic syndrome. Calcium oxalate (71.5%), uric acid (15.3%), carbonate apatite (8.0%) and struvite (4.1%) calculi were found as the main stone components. Overall, the proportion of uric acid calculi was markedly higher in patients with rather than without metabolic syndrome (19.6 vs 11.2%; P = 0.002). However, the proportion of calcium oxalate, carbonate apatite and struvite calculi did not differ between the two groups. The multivariable‐adjusted odds ratio for uric acid calculi according to the metabolic syndrome components indicated that the presence of metabolic syndrome was associated with a 93% increased odds ratio of uric acid calculi compared with the absence of metabolic syndrome. Impaired fasting glucose and hypertriglyceridemia were independent risk factors for uric acid calculi.ConclusionsMetabolic syndrome is associated with a significantly increased risk of uric acid calculi development, especially those with impaired fasting glucose and hypertriglyceridemia.
Intranasal Oxytocin Blocks Alcohol Withdrawal in Human Subjects
Authors: Pedersen Cort A. , Smedley Kelly L. , Leserman Jane , Jarskog Lars Fredrik , Rau Shane W. , Kampov‐Polevoi Alexei , Casey Robin L. , Fender Trace , Garbutt James C. 
Published: October 2012

BackgroundThe neuropeptide, oxytocin (OT), has been reported to block tolerance formation to alcohol and decrease withdrawal symptoms in alcohol‐dependent rodents. Numerous recent studies in human subjects indicate that OT administered by the intranasal route penetrates into and exerts effects within the brain.MethodsIn a randomized, double‐blind clinical trial, intranasal OT (24 IU/dose, N = 7) or placebo (N = 4) was given twice daily for 3 days in alcohol‐dependent subjects admitted to a research unit for medical detoxification using Clinical Institute Withdrawal Assessment for Alcohol (CIWA) score‐driven PRN administration of lorazepam. Subjects rated themselves on the Alcohol Withdrawal Symptom Checklist (AWSC) each time CIWA scores were obtained. Subjects also completed the Penn Alcohol Craving Scale, an Alcohol Craving Visual Analog Scale (ACVAS) and the Profile of Mood States (POMS) on inpatient days 2 and 3.ResultsAll subjects had drunk heavily each day for at least 2 weeks prior to study and had previously experienced withdrawal upon stopping/decreasing alcohol consumption. OT was superior to placebo in reducing alcohol withdrawal as evidenced by: less total lorazepam required to complete detoxification (3.4 mg [4.7, SD] vs. 16.5 [4.4], p = 0.0015), lower mean CIWA scores on admission day 1 (4.3 [2.3] vs. 11.8 [0.4], p < 0.0001) and day 2 (3.4 [2.2] vs. 11.1 [3.6], p < 0.002), lower AWSC scores on days 1 and 2 (p < 0.02; p = 0.07), and lower ACVAS ratings (p = 0.01) and lower POMS Tension/Anxiety subscale scores on day 2 (p < 0.01).ConclusionsThis is the first demonstration that OT treatment may block alcohol withdrawal in human subjects. Our results are consistent with previous findings in rodents that OT inhibits neuroadaptation to and withdrawal from alcohol. OT could have advantages over benzodiazepines in managing alcohol withdrawal because it may reverse rather than maintain sedative‐hypnotic tolerance. It will be important to test whether OT treatment is effective in reducing drinking in alcohol‐dependent outpatients.
Accommodation of Excess Oxygen in Group II Monoxides
Authors: Middleburgh Simon C. , Lagerlof Karl Peter D. , Grimes Robin W. 
Published: October 2012

Atomic scale simulations are used to predict how excess oxygen is accommodated across the group II monoxides. In all cases, the preference is to form a peroxide ion centered at an oxygen site, rather than a single oxygen species, although the peroxide ionic orientation changes from <100> to <110> to <111> with increasing host cation radius. The enthalpy for accommodation of excess oxygen in BaO is strongly negative, whereas in SrO it is only slightly negative and in CaO and MgO the energy is positive. Interestingly, the increase in material volume due to the accommodation of oxygen (the defect volume) does not vary greatly as a function of cation radius. The vibrational frequency of peroxide ions in the group II monoxides is predicted with the aim to provide test data for future experimental observations of oxygen uptake. Finally, calculations of the dioxide structures have also been carried out. For these materials the oxygen vacancy formation energy is always positive (1.0–1.5 eV per oxygen removed) indicating that they exhibit only small oxygen defect concentrations.