bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ade novotranscriptome assembly ofLucilia sericata(Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates
Authors: Sze S‐H. , Dunham J. P. , Carey B. , Chang P. L. , Li F. , Edman R. M. , Fjeldsted C. , Scott M. J. , Nuzhdin S. V. , Tarone A. M. 
Published: January 2012

AbstractThe blow flyLucilia sericata(Diptera: Calliphoridae) (Meigen) is a nonmodel organism with no reference genome that is associated with numerous areas of research spanning the ecological, evolutionary, medical, veterinary and forensic sciences. To facilitate scientific discovery in this species, the transcriptome was assembled from more than six billion bases of Illumina and twenty‐one million bases of 454 sequence derived from embryonic, larval, pupal, adult and larval salivary gland libraries. The assembly was carried out in a manner that enabled identification of putative single nucleotide polymorphisms (SNPs) and alternative splices, and that provided expression estimates for various life history stages and for salivary tissue. The assembled transcriptome was also used to identify transcribed transposable elements inL. sericata. The results of this study will enable blow fly biologists, dipterists and comparative genomicists to more rapidly develop and test molecular and genetic hypotheses, especially those regarding blow fly development and salivary gland biology.
The impact of hepatitis C virus donor and recipient status on long‐term kidney transplant outcomes: University of Wisconsin experience
Authors: Singh Neeraj , Neidlinger Nikole , Djamali Arjang , Leverson Glen , Voss Barbara , Sollinger Hans W. , Pirsch John D. 
Published: January 2012

Singh N, Neidlinger N, Djamali A, Leverson G, Voss B, Sollinger HW, Pirsch JD. The impact of hepatitis C virus donor and recipient status on long‐term kidney transplant outcomes: University of Wisconsin experience.Abstract:  The survival benefit of transplanting hepatitis C (HCV)‐positive donor kidneys into HCV‐positive recipients remains uncertain. The purpose of this study was to assess the effect of HCV‐status of the donor (D) kidney on the long‐term outcomes in kidney transplant recipients (R). We evaluated 2169 consecutive recipients of deceased‐donor kidney transplants performed between 1991 and 2007. The following HCV cohorts were identified: D−/R− (n = 1897), D−/R+ (n = 59), D+/R− (n = 118), and D+/R+ (n = 95). Patients were followed for a mean of 6.02 (standard deviation = 4.26) yr. In a mulitvariable Cox‐proportional hazards model, D+/R+ cohort had significantly lower patient survival (adjusted‐hazard ratio [HR] 2.1, 95% CI [1.4–2.9]) with respect to the reference D−/R− group, whereas mortality was not increased in D−/R+ group. The rate of graft loss was increased in both D+/R+ and D−/R+ but was comparable with each other (adjusted‐HR 1.8, 95% CI [1.4–2.5]) vs. adjusted‐HR 2.0, 95% CI [1.4–2.8], respectively). D−/R+ cohort experienced significantly higher rate of rejection (adjusted‐HR 1.7, 95% CI [1.2–2.5]) and chronic allograft nephropathy (adjusted‐HR 2.1, 95% CI [1.2–3.7]). Neither donor nor recipient HCV‐status impacted the risk of recurrent or de novo GN. Transplanting HCV‐positive kidneys as opposed to HCV‐negative kidneys into HCV‐positive recipients provided similar graft survival but compromised patient survival in the long term.
Peritransplant kidney biopsies: comparison of pathologic interpretations and practice patterns of organ procurement organizations
Authors: Singh Pooja , Farber John L. , Doria Cataldo , Francos George C. , Gulati Rakesh , Ramirez Carlo B. , Maley Warren R. , Frank Adam M. 
Published: January 2012

Singh P, Farber JL, Doria C, Francos GC, Gulati R, Ramirez CB, Maley WR, Frank AM. Peritransplant kidney biopsies: comparison of pathologic interpretations and practice patterns of organ procurement organizations.  Clin Transplant 2012 DOI: 10.1111/j.1399‐0012.2011.01584.x.  © 2012 John Wiley & Sons A/S.Abstract:  The preimplantation kidney biopsy affects utilization by diagnosing glomerulosclerosis, interstitial fibrosis (IF), arteriosclerosis, and arteriolar hyalinosis. Organ procurement organizations (OPOs) determine whether a donor warrants this biopsy and the donor hospital pathologists (DHPs) report on an OPO‐specific pathology interpretation form. Biopsy slides from 40 deceased donor kidneys transplanted at our institution were used to compare interpretations between our transplant pathologist and the DHPs. Thirty‐three of these kidneys also had post‐perfusion biopsies (PPB). All 58 OPOs were queried for criteria used to request a preimplantation biopsy, and their pathology interpretation forms were also analyzed. The transplant and DHPs had substantial agreement for percent glomerulosclerosis with 75% of biopsies being interpreted within five percentage points. Concordance for IF was poor. The DHP rarely reported arterial pathology. Seventy percent of preimplantation and PPB were read similarly for glomerulosclerosis; concordance for other lesions was weaker. There were no cues for arterial disease on our OPO’s pathology interpretation form. Criteria for obtaining a preimplantation biopsy lacked uniformity for the 21 OPOs with a self‐generated policy. The pathology interpretation forms varied widely among the OPOs. Current OPO practices with regard to the preimplantation biopsy should be improved.
Rapidly progressive fatal hemorrhagic pneumonia caused by Stenotrophomonas maltophilia in hematologic malignancy
Authors: Araoka H. , Fujii T. , Izutsu K. , Kimura M. , Nishida A. , Ishiwata K. , Nakano N. , Tsuji M. , Yamamoto H. , Asano‐Mori Y. , Uchida N. , Wake A. , Taniguchi S. , Yoneyama A. 
Published: January 2012

Abstract:BackgroundPneumonia caused by Stenotrophomonas maltophilia is rare, but can be lethal in severely immunocompromised patients. However, its clinical course remains unclear.Patients and methodsPatients with pneumonia caused by S. maltophilia in Toranomon Hospital (890 beds, Tokyo, Japan) were reviewed retrospectively between April 2006 and March 2010.ResultsDuring the study period, 10 cases of S. maltophilia pneumonia were identified. Seven patients had acute myeloid leukemia, 2 had myelodysplastic syndrome, and 1 had malignant lymphoma. All patients developed symptoms after allogeneic hematopoietic stem cell transplantation (HSCT). Five patients received first cord blood transplantation (CBT), 4 patients received second CBT, and 1 patient received first peripheral blood stem cell transplantation (PBSCT). The overall incidence of S. maltophilia pneumonia among 508 patients who received HSCT during the period was 2.0%. The incidence was 0% (0/95) in patients after bone marrow transplantation, 0.8% (1/133) after PBSCT, and 3.2% (9/279) after CBT. Pneumonia developed a median of 13.5 days (range, 6–40) after transplantation. At onset, the median white blood cell count was 10/μL (range, 10–1900), and the median neutrophil count was 0/μL (range, 0–1720). In all patients, S. maltophilia bacteremia developed with bloody sputum or hemoptysis. The 28‐day mortality rate was 100%; the median survival after onset of pneumonia was 2 days (range, 1–10).ConclusionsHemorrhagic S. maltophilia pneumonia rapidly progresses and is fatal in patients with hematologic malignancy. Attention should be particularly paid to the neutropenic phase early after HSCT or prolonged neutropenia due to engraftment failure. A prompt trimethoprim‐sulfamethoxazole‐based multidrug combination regimen should be considered to rescue suspected cases of S. maltophilia pneumonia in these severely immunosuppressed patients.
Pollination mutualism between Alocasia macrorrhizos (Araceae) and two taxonomically undescribed Colocasiomyia species (Diptera: Drosophilidae) in Sabah, Borneo
Authors: Takano K. Takenaka , Repin R. , Mohamed M. B. , Toda M. J. 
Published: January 2012

AbstractTwo taxonomically undescribed Colocasiomyia species were discovered from inflorescences of Alocasia macrorrhizos in Kota Kinabalu City, Sabah, Borneo, Malaysia. The aims of this study were to investigate the reproductive ecology of the flies and the plant, ascertain the importance of the flies as pollinators and examine the intimate association between flowering events and life history of the flies. We conducted sampling, observations and field pollination experiments. The flies were attracted by the odour of female‐phase inflorescences in the early morning on the first day of anthesis. They fed, mated and oviposited in the inflorescences for 1 day. On the second day, the flies, covered with pollen grains, left the male‐phase inflorescences for the next female‐phase inflorescences. The immature forms of both fly species hatched, developed and pupated within the infructescences without damaging the fruits, and developed adults emerged when the mature infructescences dehisced. The flowering events and fly behaviours were well synchronized. In field pollination experiments, inflorescences bagged with a fine mesh (insect exclusion) produced almost no fruits, whereas those bagged with a coarse mesh (bee exclusion) produced as many fruits as the open‐pollinated controls. These results indicate that these flies are the most efficient and specialised pollinators for their host, A. macrorrhizos. These flies, in return, depend on A. macrorrhizos for food and habitat through most of their life cycle. This study provides a deeper insight into the less recognised, highly intimate pollination mutualism between Araceae plants and Colocasiomyia flies.
Flow experience and health‐related quality of life in community dwelling elderly Japanese
Authors: Hirao Kazuki , Kobayashi Ryuji , Okishima Kyota , Tomokuni Yumiko 
Published: January 2012

AbstractThis study was performed to investigate the relationship between mental state (especially flow experience [Flow Experience Checklist of Ishimura]) health‐related quality of life (Medical Outcome Study 8‐Item Short‐Form Health Survey), and stress (salivary amylase concentrations). The subjects were 119 healthy elderly persons living in rural areas who participated in a “meeting for the elderly” at a nursing home in Kagawa Prefecture, Japan. The subjects were classified into apathetic, anxious, relaxed, and flow groups. It was found that physical health was significantly better when performing important daily activities in the group who experienced flow and the relaxed group than in the group that was in an apathetic state. However, no significant relationship was observed between the degree of flow experience and stress. The present findings suggested that interventions which make the activities of daily life either “high‐challenge, high‐skill” situations or “low‐challenge, high‐skill” situations could have a positive influence on the physical health of community‐living elderly Japanese. A longitudinal study should be performed in the future.
Sipunculan phylogeny based on six genes, with a new classification and the descriptions of two new families
Authors: Kawauchi Gisele Y. , Sharma Prashant P. , Giribet Gonzalo 
Published: January 2012

Kawauchi, G. Y., Sharma, P. P. & Giribet, G. (2012). Sipunculan phylogeny based on six genes, with a new classification and the descriptions of two new families. —Zoologica Scripta, 41, 186–210.The internal phylogeny of Sipuncula has proven elusive, with the monophyly of multiple traditional groups in question. Repeated attempts to infer sipunculan relationships have attained discordant results, possibly owing to fragmentary molecular sequence data sets. We reassessed the phylogeny of Sipuncula using a six‐gene data set and with larger target amplicons of certain loci. We additionally dated the molecular phylogeny employing recently discovered fossil taxa to constrain node ages. Our multilocus data set recovers six major clades of Sipuncula across multiple analytical treatments. Some groups considered suspect in previous studies are vindicated (e.g. Aspidosiphonidae), but most traditional sipunculan families were recovered as para‐ or polyphyletic groups, especially Sipunculidae, whose members appear in three distinct clades. To redress the dissonance between the current classification and the phylogeny of Sipuncula, we provide a new classification of the group, wherein (i) we erect two new families, Siphonosomatidae fam. nov. and Antillesomatidae fam. nov.; (ii) Phascolionidae and Themistidae are synonymized with Golfingiidae, new synonymies (iii) Phascolopsis is transferred to Golfingiidae, new familial assignment; and (iv) Lithacrosiphon is synonymized with Aspidosiphon, new synonymy. We observe that the origins of all families recognized are ancient, dating at least to the Mesozoic.
Effects on bladder function of combining elocalcitol and tolterodine in rats with outflow obstruction
Authors: Streng Tomi , Andersson Karl‐Erik , Hedlund Petter , Gratzke Christian , Baroni Enrico , D'Ambrosio Daniele , Benigni Fabio 
Published: January 2012

What's known on the subject? and What does the study add?It has previously been shown that elocalcitol might protect bladder contractile function in experimental models and that elocalcitol has beneficial effects in patients with LUTS. In humans, elocalcitol was demonstrated with a very good safety profile but only exhibited limited efficacy on LUTS in patients with BPH and overactive bladder (OAB). Recent reports show that therapies with antimuscarinics, when combined with other drugs in clinical use, might perform better than a monotherapy in managing LUTS. It is not known how a combination of elocalcitol and an antimuscarinic performs on bladder dysfunction.The present study suggests that concomitant use of secosteroids and antimuscarinics has additive beneficial effects on obstruction‐related functional changes in an experimental model. If confirmed also in a clinical setting, this could allow for individual dose adjustments to improve efficacy in obstruction‐related LUTS, and possibly reduce unwanted adverse activities by antimuscarinic therapy.OBJECTIVE
To evaluate the effects of tolterodine on urodynamics in elocalcitol‐ or vehicle‐treated rats with partial urethral obstruction (PUO).
MATERIALS AND METHODS
After ethical approval, 20 female Sprague–Dawley rats were subjected to PUO and treated (gavage) for 14 days (once daily) with elocalcitol (75 µg/kg) or vehicle.
Cystometries were performed on day 15 in awake rats before and after i.v. administration of tolterodine (1, 10 and 100 µg/kg).
RESULTS
No differences in bladder weights or body/bladder weight ratios were noted between groups. Tolterodine dose‐dependently increased micturition intervals and volumes and bladder capacity in both elocalcitol‐ (n= 11) and vehicle‐treated rats (n= 9).
In elocalcitol‐treated rats, flow pressure (FP) was dose‐dependently reduced (12–20%) by tolterodine, whereas no effect on FP was noted in vehicle‐treated animals (P < 0.05).
Flow compliance (FC) was increased by tolterodine by 21–54% in vehicle‐treated rats, and by 47–131% (P < 0.05 vs vehicle) in elocalcitol‐treated animals. Maximal tension vs bladder weight was improved in elocalcitol‐treated rats in comparison to vehicle (P < 0.05).
The area under the curve (AUC) was reduced by tolterodine with 11–16% in vehicle‐treated rats and 26–30% in elocalcitol ‐treated rats (P < 0.05).
CONCLUSIONS
Elocalcitol‐treatment improved the effects of tolterodine on bladder compliance at the start of flow.
The effects of tolterodine on AUC suggest that elocalcitol exerts additional beneficial actions on PUO‐induced functional changes during the filling phase of micturition.
The reduction of FP and increase in FC by elocalcitol and tolterodine could have translational value and, if valid in humans, support combined therapy in benign prostatic obstruction (BPO)‐related lower urinary tract symptoms (LUTS).
A systematic review and mixed treatment comparison of pharmacological interventions for the treatment of obesity
Authors: Gray L. J. , Cooper N. , Dunkley A. , Warren F. C. , Ara R. , Abrams K. , Davies M. J. , Khunti K. , Sutton A. 
Published: January 2012

SummaryThe study aims to compare anti‐obesity interventions in a single evidence synthesis framework. Electronic databases were searched for randomized controlled trials of orlistat, rimonabant or sibutramine reporting weight or body mass index (BMI) change from baseline at 3, 6 or 12 months. A mixed treatment comparison was used to combine direct and indirect trial evidence. Ninety‐four studies involving 24,808 individuals were included; 83 trials included data on weight change and 41 on BMI change. All results are in comparison with placebo. The active drugs were all effective at reducing weight and BMI. At 3 months, orlistat reduced weight by −2.65 kg (95% credibility interval −4.00 kg, −1.31 kg). For sibutramine, 15 mg gave a greater reduction than 10 mg at 12 months, −6.35 kg versus −5.42 kg, respectively. Rimonabant reduced weight by −11.23 kg at 3 months and −4.55 kg at 12 months. Lifestyle advice alone also reduced weight at 6 and 12 months, but was less effective than the pharmacological interventions. In conclusion, modest weight reductions were seen for all pharmacological interventions. Those interventions which have now been withdrawn from use (sibutramine and rimonabant) seem to be the most effective, implying that there may be a place in clinical practice for similar drugs if side effects could be avoided.
MEANINGFUL LIVES?
Authors: Vitrano Christine 
Published: January 2012

AbstractContemporary ethical theorists have sought criteria to identify meaningful lives. A central issue that divides accounts is whether the concept of meaningfulness rests on objective values. My own view is that each side in the controversy is partially right and partially wrong. I believe objective values are needed for the concept of a meaningful life but that no successful account of such values has yet been offered. Lacking such an account, the concept of a meaningful life should be replaced by more useful terminology. I shall contrast my view with that of Susan Wolf though my goal is not primarily critical but, instead, the development of a different and, I believe, more useful approach.
Spatiotemporal Quantile Regression for Detecting Distributional Changes in Environmental Processes
Authors: Reich Brian J. 
Published: January 2012

SummaryClimate change may lead to changes in several aspects of the distribution of climate variables, including changes in the mean, increased variability and severity of extreme events. We propose the use of spatiotemporal quantile regression as a flexible and interpretable method for simultaneously detecting changes in several features of the distribution of climate variables. The spatiotemporal quantile regression model assumes that each quantile level changes linearly in time, permitting straightforward inference on the time trend for each quantile level. Unlike classical quantile regression which uses model-free methods to analyse a single quantile or several quantiles separately, we take a model-based approach which jointly models all quantiles, and thus the entire response distribution. In the spatiotemporal quantile regression model, each spatial location has its own quantile function that evolves over time, and the quantile functions are smoothed spatially by using Gaussian process priors. We propose a basis expansion for the quantile function that permits a closed form for the likelihood and allows for residual correlation modelling via a Gaussian spatial copula. We illustrate the methods by using temperature data for the south-east USA from the years 1931–2009. For these data, borrowing information across space identifies more significant time trends than classical non-spatial quantile regression. We find a decreasing time trend for much of the spatial domain for monthly mean and maximum temperatures. For the lower quantiles of monthly minimum temperature, we find a decrease in Georgia and Florida, and an increase in Virginia and the Carolinas.
Automated Feature Extraction from Profiles with Application to a Batch Fermentation Process
Authors: Andersen Stina W. , Runger George C. 
Published: January 2012

SummaryAn automated approach to extract interpretable features of univariate or multivariate profiles (functional data) is proposed. A landmark alignment algorithm is modified and the alignment is combined with piecewise linear approximations. Least absolute shrinkage and selection operator (lasso) regression is used for selecting the most important intercepts and slopes and yields an alternative to partial least squares to model a response associated with the profiles. Latent variables can be difficult to interpret but our extracted features simply correspond to slopes and intercepts of particular parts of the profiles. Also, features that relate to the degree of warping between a given profile and a reference can be extracted as predictors. Selection criteria for the number of knots and common knot locations between profiles are developed. We apply our proposed method to batch fermentation data where the profiles consist of on-line measurements of process variables and the corresponding yield of the process. The extracted features have good interpretability (with large dimensional reduction) and in combination with the lasso have prediction accuracy which is comparable with that of partial least squares applied to the original profiles. Also our proposed feature extraction method is applied to publicly available data where near infrared spectra define the profiles and the prediction accuracy of our feature lasso method is comparable with those of more complicated alternatives.
Functional assessment of high‐grade ICA stenosis with duplex ultrasound and transcranial Doppler
Authors: Zachrisson Helene , Fouladiun Marita , Blomstrand Christian , Holm Jan , Volkmann Reinhard 
Published: January 2012

SummaryBackground:  Duplex ultrasound (DUS) has shown a >90% accuracy compared to angiography, concerning the degree of internal carotid artery (ICA) stenosis. However, uncertainty may occur in a severe stenosis, in which peak systolic velocity (PSV) may decrease owing to high flow resistance or high backward pressure. We investigated intracranial collateral flows using transcranial Doppler (TCD) to further evaluate the hemodynamic significance of high‐grade ICA stenosis.Methods:  In this retrospective study, 320 consecutive symptomatic patients were examined. The degree of ICA stenosis and collateral capacity in the circle of Willis was investigated by DUS and TCD. In addition, magnetic resonance angiography (MRA) was added in a subgroup of 204 patients. The criterion for hemodynamic significant ICA stenosis was established collateral flow.Results:  In 91% of all symptomatic vessels (291 vessels), an ICA stenosis of ≥70% was found. Established collateral flow always indicated precerebral carotid artery disease of ≥70%. Furthermore, in 11% of the whole study material, collateral reserve capacity was found despite high‐grade (≥70%) ICA stenosis. PSV in ICA <2·5 m s−1 was combined with established collateral flow and MRA stenosis of ≥70% in 9% (19 arterial systems). In 4%, doubt existed concerning the degree of stenosis after DUS.Conclusion:  Transcranial Doppler helps to determine whether an ICA stenosis is of hemodynamic significance and to assess collateral patterns. Established collateral blood flow will help to identify patients with ≥70% (ECST) carotid artery disease. TCD might be of value when flow velocity criteria combined with plaque assessment by DUS are inclusive. Other diagnostic methods may also be considered.