bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lurasidone for the treatment of depressive symptoms in schizophrenia: analysis of 4 pooled, 6-week, placebo-controlled studies
Authors: Nasrallah Henry A. , Cucchiaro Josephine B. , Mao Yongcai , Pikalov Andrei A. , Loebel Antony D. 
Published: June 2014

ObjectiveDepressive symptoms are common in schizophrenia and can worsen outcomes and increase suicide risk. Lurasidone is an atypical antipsychotic agent indicated for the treatment of schizophrenia and for the treatment of major depressive episodes associated with bipolar I disorder. This post hoc analysis evaluated the effect of lurasidone on depressive symptoms in patients with schizophrenia.MethodsPatient-level data were pooled from 4 similarly designed, double-blind, placebo-controlled, 6-week registration studies of lurasidone (40–160 mg/d) in adult patients with an acute exacerbation of schizophrenia. Changes in depressive symptoms, measured by the Montgomery–Åsberg Depression Rating Scale (MADRS), were analyzed for the overall sample and for subgroups of patients stratified by baseline MADRS scores.ResultsMADRS assessments at baseline and endpoint (day 42 or last observation carried forward [LOCF]) were available for 1330 patients. Patients receiving lurasidone experienced significantly greater decreases in MADRS score (–2.8, least-squares [LS] mean change, LOCF) compared with patients receiving placebo (–1.4,P< .001, effect size 0.24). Analysis of change in MADRS score (LOCF) by baseline symptom severity (MADRS score of ≥12, ≥14, ≥16, ≥18) showed significantly greater improvement for lurasidone-treated patients across all severity groups; effect sizes ranged from 0.25 to 0.34. Among patients with a baseline MADRS score of ≥12, depressive symptom remission (defined as MADRS score <10 at LOCF endpoint) was attained by 45.0% of lurasidone-treated patients and 36.3% of patients receiving placebo (P< .05).ConclusionsIn a pooled analysis of short-term, placebo-controlled studies, lurasidone significantly improved depressive symptoms in patients with schizophrenia.
Validation of a BMI cut-off point to predict an adverse cardiometabolic profile with adiposity measurements by dual-energy X-ray absorptiometry in Guatemalan children
Authors: Redondo Olga , Villamor Eduardo , Valdés Javiera , Bilal Usama , Caballero Benjamín , Roche Dina , Kroker Fernanda , Ramírez-Zea Manuel , Franco Manuel 
Published: June 2014

AbstractObjectiveTo identify a body fat percentage (%BF) threshold related to an adverse cardiometabolic profile and its surrogate BMI cut-off point.DesignCross-sectional study.SettingTwo public schools in poor urban areas on the outskirts of Guatemala City.SubjectsA convenience sample of ninety-three healthy, prepubertal, Ladino children (aged 7–12 years).ResultsSpearman correlations of cardiometabolic parameters were higher with %BF than with BMI-for-ageZ-score. BMI-for-ageZ-score and %BF were highly correlated (r=0·84). The %BF threshold that maximized sensitivity and specificity for predicting an adverse cardiometabolic profile (elevated homeostasis model assessment–insulin resistance index and/or total cholesterol:HDL-cholesterol ratio) according to receiver operating characteristic curve analysis was 36 %. The BMI-for-ageZ-score cut-off point that maximized the prediction of BF ≥ 36 % by the same procedure was 1·5. The area under the curve (AUC) for %BF and for BMI data showed excellent accuracy to predict an adverse cardiometabolic profile (AUC 0·93 (sd0·04)) and excess adiposity (AUC 0·95 (sd0·02)).ConclusionsSince BMI standards have limitations in screening for adiposity, specific cut-off points based on ethnic-/sex- and age-specific %BF thresholds are needed to better predict an adverse cardiometabolic profile.
TAKING POSTRACIALISM SERIOUSLY
Authors: Taylor Paul C. 
Published: June 2014

AbstractThis essay reconsiders the prospects for postracialist discourse. Critics tend not to take seriously enough the strongest case that can be made for viewing contemporary U.S. racial politics through the postracial lens. As a result, some important criticisms—the ones that survive postracialism’s reformulation in these stronger terms—have yet to be fully developed. It is important to develop a critique of the strongest form of postracialism, because this form of the view shares, or exemplifies, certain problems in garden-variety liberal antiracisms. Clarifying these problems in the more extreme conceptual environment of postracialism may help clarify their implications for the much more widespread commitments of mainstream post-civil rights thinking.
Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats
Authors: Yu Ying , Zhao Chen , Su Zhenqiang , Wang Charles , Fuscoe James C , Tong Weida , Shi Leming 
Published: June 2014

AbstractThe rat is used extensively by the pharmaceutical, regulatory, and academic communities for safety assessment of drugs and chemicals and for studying human diseases; however, its transcriptome has not been well studied. As part of the SEQC (i.e., MAQC-III) consortium efforts, a comprehensive RNA-Seq data set was constructed using 320 RNA samples isolated from 10 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four ages (2-, 6-, 21-, and 104-week-old) with four biological replicates for each of the 80 sample groups (organ-sex-age). With the Ribo-Zero rRNA removal and Illumina RNA-Seq protocols, 41 million 50 bp single-end reads were generated per sample, yielding a total of 13.4 billion reads. This data set could be used to identify and validate new rat genes and transcripts, develop a more comprehensive rat transcriptome annotation system, identify novel gene regulatory networks related to tissue specific gene expression and development, and discover genes responsible for disease and drug toxicity and efficacy.
Tree of Sex: A database of sexual systems
Authors:   The Tree of Sex Consortium, Ashman Tia-Lynn , Bachtrog Doris , Blackmon Heath , Goldberg Emma E , Hahn Matthew W , Kirkpatrick Mark , Kitano Jun , Mank Judith E , Mayrose Itay , Ming Ray , Otto Sarah P , Peichel Catherine L , Pennell Matthew W , Perrin Nicolas , Ross Laura , Valenzuela Nicole , Vamosi Jana C 
Published: June 2014

AbstractThe vast majority of eukaryotic organisms reproduce sexually, yet the nature of the sexual system and the mechanism of sex determination often vary remarkably, even among closely related species. Some species of animals and plants change sex across their lifespan, some contain hermaphrodites as well as males and females, some determine sex with highly differentiated chromosomes, while others determine sex according to their environment. Testing evolutionary hypotheses regarding the causes and consequences of this diversity requires interspecific data placed in a phylogenetic context. Such comparative studies have been hampered by the lack of accessible data listing sexual systems and sex determination mechanisms across the eukaryotic tree of life. Here, we describe a database developed to facilitate access to sexual system and sex chromosome information, with data on sexual systems from 11,038 plant, 705 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian, and 11,556 invertebrate species.
Post-transcriptional regulation of the human reduced folate carrier as a novel adaptive mechanism in response to folate excess or deficiency
Authors: Hou Zhanjun , Orr Steve , Matherly Larry H. 
Published: June 2014

The RFC (reduced folate carrier) is the principal mechanism by which folates and clinically used antifolates are delivered to mammalian cells. hRFC (human RFC) is subject to complex transcriptional controls and exists as homo-oligomer. To explore the post-transcriptional regulation of hRFC by exogenous folates, hRFC-null HeLa cells were stably transfected with hRFC under control of a constitutive promoter. hRFC transcripts and the total membrane protein increased with increasing LCV [(6R,S)5-formyl tetrahydrofolate (leucovorin)] with a maximum at 20 nM LCV, attributable to reduced turnover of hRFC transcripts. hRFC homo-oligomerization was unaffected by increasing LCV. Cell surface hRFC paralleled [3H]methotrexate transport and increased from 0.5 to 2 nM LCV, and then decreased (~2-fold) with increasing LCV up to 20 nM. hRFC was localized to the cell surface at low LCV concentrations (0.5–1.5 nM). However, at higher LCV concentrations, significant intracellular hRFC was localized to the ER (endoplasmic reticulum), such that at 20 nM LCV, intracellular hRFC was predominated. Our results demonstrate a novel post-transcriptional regulation of hRFC involving: (i) increased hRFC transcripts and proteins, accompanying increased extracellular folates, attributable to differences in hRFC transcript stabilities; and (ii) increased retention of hRFC in the ER under conditions of folate excess, because of impaired intracellular trafficking and plasma membrane targeting.
Effects of drying conditions on moisture distribution in rehydrated spaghetti
Authors: Ogawa Takenobu , Adachi Shuji 
Published: June 2014

Abstract
Moisture distributions in spaghettis prepared at a maximum temperature of 50, 70, or 85 °C, designated as LT-, HT-, or VHT-spaghetti, respectively, and cooked to the average moisture content of 1.71 ± 0.01 kg-H2O/kg-d.m., were measured. The moisture contents near the surface and at the center of the LT-spaghetti were lower and higher, respectively, than those of HT- and VHT-spaghetti.
Using Polysome Isolation with Mechanism Alteration to Uncover Transcriptional and Translational Dynamics in Key Genes
Authors: Alicea Bradly , Suhr Steven T. , Cibelli Jose B. 
Published: June 2014

ABSTRACTWhat does it mean when we say a cell’s biochemistry is regulated during changes to the phenotype? While there are a plethora of potential mechanisms and contributions to the final outcome, a more tractable approach is to examine the dynamics of mRNA. This way, we can assess the contributions of both known and unknown decay and aggregation processes for maintaining levels of gene product on a gene-by-gene basis. In this extended protocol, drug treatments that target specific cellular functions (termed mechanism disruption) can be used in tandem with mRNA extraction from the polysome to look at the dynamics of mRNA levels associated with transcription and translation at multiple stages during a physiological perturbation. This is accomplished through validating the polysome isolation method in human cells and comparing fractions of mRNA for each experimental treatment at multiple points in time. First, three different drug treatments corresponding to the arrest of various cellular processes are administered to populations of human cells. For each treatment, the transcriptome and translatome are compared directly at different time points by assaying both cell-type specific and non-specific genes. There are two findings of note. First, extraction of mRNA from the polysome and comparison with the transcriptome can yield interesting information about the regulation of cellular mRNA during a functional challenge to the cell. In addition, the conventional application of such drugs to assess mRNA decay is an incomplete picture of how severely challenged or senescent cells regulate mRNA in response. This extended protocol demonstrates how the gene- and process-variable degradation of mRNA might ultimately require investigations into the course-grained dynamics of cellular mRNA, from transcription to ribosome.
The conservedPFT1tandem repeat is crucial for proper flowering inArabidopsis thaliana
Authors: Rival Pauline , Press Maximilian O. , Bale Jacob , Grancharova Tanya , Undurraga Soledad F. , Queitsch Christine 
Published: June 2014

ABSTRACTIt is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in theArabidopsis thalianagenePFT1(MED25), where it encodes an interrupted polyglutamine tract. Though thePFT1STR is large (∼270 bp), and thus expected to be extremely variable, it shows only minuscule variation acrossA. thalianastrains. We hypothesized that thePFT1STR is under selective constraint, due to previously undescribed roles in PFT1 function. We investigated this hypothesis using plants expressing transgenicPFT1constructs with either an endogenous STR or with synthetic STRs of varying length. Transgenic plants carrying the endogenousPFT1STR generally performed best across adult PFT1-dependent traits, in terms of complementing apft1null mutant. In stark contrast, transgenic plants carrying aPFT1transgene lacking the STR entirely phenocopied apft1loss-of-function mutant for flowering time phenotypes, and were generally hypomorphic for other traits, establishing the functional importance of this domain. Transgenic plants carrying various synthetic constructs occupied the phenotypic space between wild-type andpft1-loss-of-function mutants. By varyingPFT1STR length, we discovered thatPFT1can act as either an activator or repressor of flowering in a photoperiod-dependent manner. We conclude that thePFT1STR is constrained to its approximate wild-type length by its various functional requirements. Our study implies that there is strong selection on STRs not only to generate allelic diversity, but also to maintain certain lengths pursuant to optimal molecular function.
False facts and false views: coalescent analysis of truncated data
Authors: Árnason Einar 
Published: June 2014

AbstractDarwin’s dictum on false facts and false views points the way to opening the road to truth via cogent criticism of the published record. Here I discuss a case in which a truncated dataset (false facts) is used for coalescent analysis of historical demography that reaches a foregone conclusion of a bottleneck of numbers (false views).
Assessing the integrated effects of landscape fragmentation on plants and plant communities: the challenge of multiprocess–multiresponse dynamics
Authors: Ibáñez Inés , Katz Daniel S. W. , Peltier Drew , Wolf Samantha M. , Connor Barrie Benjamin T. 
Published: June 2014

Summary

When human activities change the landscape, several processes affecting remnant vegetation take place simultaneously: there is less suitable habitat, populations become isolated and the environmental conditions of the fragments frequently shift. Such changes affect vegetation in different ways – populations become smaller, the genetic exchanges between populations decline and species interactions are altered. The combination of processes taking place during fragmentation and their subsequent consequences generate a large variety of responses, positive and negative, among plants and plant communities.

To assess the integrated effects of the processes taking place as a result of fragmentation (isolation, edge effects, fragment size and time since fragmentation) on organisms, we conducted a hierarchical meta‐analysis of the studies reporting the effects of landscape fragmentation on plant species and plant communities. Our review included 259 peer‐reviewed journal articles and 990 data entries.

We found the frequency of reports of positive and negative responses to fragmentation were comparable but largely variable. Negative effects of fragmentation due to isolation, edge effects and fragment size were significant; but only edge effects and fragment size had significant positive effects. When looking at specific types of responses to isolation, we found negative effects on density, fecundity, colonization, succession rates and species richness, while positive effects were found on fecundity, herbivory/predation and colonization. Positive responses to edge effects were significant for density, fecundity, survival, growth and richness, and significantly negative for density, survival, colonization and richness. Effects of patch size were mostly significant for both positive and negative responses.

We also assessed the effects of landscape fragmentation for different attributes of the studied system and found no differences among biomes, vegetation types, functional groups or life stages.

Synthesis. Results of this integrated assessment indicate that broad generalizations about the effects of fragmentation on remnant vegetation may not be possible due the large variety of processes and responses associated with fragmentation. Results also identified key knowledge gaps, and areas of research needed to improve assessment and future management of plant species and plant communities in fragmented landscapes (e.g. lag effects, the role of the matrix and the patch quality and integrated effects along life cycles).
Uses and misuses of meta‐analysis in plant ecology
Authors: Koricheva Julia , Gurevitch Jessica 
Published: June 2014

Summary

The number of published meta‐analyses in plant ecology has increased greatly over the last two decades. Meta‐analysis has made a significant contribution to the field, allowing review of evidence for various ecological hypotheses and theories, estimation of effects of major environmental drivers (climate change, habitat fragmentation, invasive species, air pollution), assessment of management and conservation strategies, and comparison of effects across different temporal and spatial scales, taxa and ecosystems, as well as research gap identification.

We identified 322 meta‐analyses published in the field of plant ecology between 1996 and 2013 in 95 different journals and assessed their methodological and reporting quality according to standard criteria. Despite significant recent developments in the methodology of meta‐analysis, the quality of published meta‐analyses was uneven and showed little improvement over time.

We found many cases of imprecise and inaccurate usage of the term ‘meta‐analysis’ in plant ecology, particularly confusion between meta‐analysis and vote counting and incorrect application of statistical techniques designed for primary studies to meta‐analytical data, without recognition of the violation of statistical assumptions of the analyses.

Methodological issues for meta‐analyses in plant ecology include incomplete reporting of search strategy used to retrieve primary studies, failure to test for possible publication bias and to conduct sensitivity analysis to test the robustness of the results, as well as lack of availability of the data set used for the analyses.

The use of meta‐analysis is particularly common in community ecology, ecophysiology and ecosystem ecology, but meta‐analyses in ecophysiology are more likely not to meet standard quality criteria than papers in other subdisciplines. Fewer meta‐analyses have been conducted in plant population ecology.

Synthesis. Over the past two decades, plant ecologists have embraced meta‐analysis as a statistical tool to combine results across studies, and much has been learned as a result. However, as the popularity and usage of meta‐analysis in the field of plant ecology has grown, establishment of quality standards, as has been done in other disciplines, becomes increasingly important. In order to improve the quality of future meta‐analyses in plant ecology, we suggest adoption of a checklist of quality criteria for meta‐analysis for use by research synthesists, peer reviewers and journal editors.
Measuring parents' experiences and satisfaction with care during very preterm birth: a questionnaire development study
Authors: Sawyer A , Rabe H , Abbott J , Gyte G , Duley L , Ayers S ,   ‘The Very Preterm Birth Collaborative Group’
Published: June 2014

ObjectiveTo develop a questionnaire to assess parents' experiences and satisfaction with care during very preterm birth.DesignQuestionnaire development.SettingParents whose babies had been cared for at five tertiary neonatal units in England.PopulationA total of 145 women who gave birth before 32 weeks of gestation, and 85 of their partners.MethodsA 30‐item questionnaire was developed on the basis of qualitative interviews with parents of very preterm babies, a literature review and discussion with relevant experts. The questionnaire was posted to a second group of parents, and its reliability and validity were explored.Main outcome measuresThe Preterm Birth Experience and Satisfaction Scale (P‐BESS) was correlated with two global questions measuring satisfaction with care during the birth. Internal consistency was measured using Cronbach's α.ResultsParents of 458 babies were invited to take part and 147 (32%) responded. Two women and 22 partners were excluded or ineligible, leaving 145 women and 85 partners. Factor analysis produced three clear dimensions: Staff professionalism and empathy, Information and explanations, and Confidence in staff. The total scale and three subscales showed high reliability. Strong positive correlations were found between the questionnaire scales and the two global questions, indicating convergent validity. For women whose partners were present at the birth, a fourth factor was identified ‘Partner Involvement’.ConclusionsThe P‐BESS appears to be a valid measure of satisfaction with care during very preterm birth.
Clinical Effects of Long‐Term (36‐Month) Lanthanum Carbonate Administration in Hemodialysis Patients in Japan
Authors: Kishi Yuichiro , Obara Yoshihiro , Hara Keiko , Yamashiro Hiromitsu , Kurosawa Norio , Takada Daisuke 
Published: June 2014

AbstractIn this study, we investigated the clinical effects of long‐term administration of the phosphorus (P) binder lanthanum carbonate (LC), which was launched in Japan in 2009. The subjects were 58 dialysis patients who began receiving LC, and we evaluated the clinical effects for up to 36 months after treatment initiation. The average serum P concentration remained low during the 36‐month study period, with a significant reduction from 6.25 mg/dL at the start of the study to 4.94 mg/dL after 36 months (P < 0.001). A significant reduction was also observed in the average serum calcium concentration after 36 months (P < 0.05), but not in the serum intact parathyroid hormone concentration. Significant reductions were also observed in the average serum total protein, albumin and potassium concentrations (P < 0.05). The dosages of LC increased by approximately 1.9‐fold after 36 months, in contrast, the dosages of concomitantly used sevelamer hydrochloride and Ca carbonate preparations decreased. These results indicate that LC could be used to treat hyperphosphatemia without causing hypercalcemia, and would be useful for long‐term treatment with hemodialysis patients.
Is Granular Formulation of Lanthanum Carbonate More Effective than Chewable Tablets?
Authors: Okamoto Hidekazu , Haruhara Koutarou , Kamejima Sahoko , Mafune Hana , Manabe Mayumi , Kanzaki Goh , Mashiko Hiroshi , Yokoo Takashi 
Published: June 2014

AbstractMaintenance dialysis patients at our hospital who had been receiving lanthanum carbonate (LC) chewable tablets were switched to the same dosage of the granules, and the differences in serum phosphorus (P) levels were compared, together with stratifying patients at the baseline characteristics. Compared to average serum P level of 5.48 mg/dL for 2 months prior to switching, the average level for 2 months after switching was 4.99 mg/dL (P = 0.049). For patients who were under 60, serum P levels were significantly improved after switching (P = 0.016), and for patients who were concomitantly taking many kinds of medications, a correlation to high reductions of serum P level after switching was shown (R = −0.635, P = 0.015). In order to maximize pharmaceutical potential of LC, we think that it is not only necessary to provide patients with how to take the medication, but it is also important to take into consideration the patients' baseline characteristics.