bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sex determination in beetles: Production of all male progeny by Parental RNAi knockdown of transformer
Authors: Shukla Jayendra Nath , Palli Subba Reddy 
Published: August 2012

AbstractSex in insects is determined by a cascade of regulators ultimately controlling sex-specific splicing of a transcription factor, Doublesex (Dsx). We recently identified homolog of dsx in the red flour beetle, Tribolium castaneum (Tcdsx). Here, we report on the identification and characterization of a regulator of Tcdsx splicing in T. castaneum. Two male-specific and one female-specific isoforms of T. castaneum transformer (Tctra) were identified. RNA interference-aided knockdown of Tctra in pupa or adults caused a change in sex from females to males by diverting the splicing of Tcdsx pre-mRNA to male-specific isoform. All the pupa and adults developed from Tctra dsRNA injected final instar larvae showed male-specific sexually dimorphic structures. Tctra parental RNAi caused an elimination of females from the progeny resulting in production of all male progeny. Transformer parental RNAi could be used to produce all male population for use in pest control though sterile male release methods.
DNA-dependent Oct4–Sox2 interaction and diffusion properties characteristic of the pluripotent cell state revealed by fluorescence spectroscopy
Authors: Lam Chen Sok , Mistri Tapan Kumar , Foo Yong Hwee , Sudhaharan Thankiah , Gan Hui Theng , Rodda David , Lim Leng Hiong , Chou Chai , Robson Paul , Wohland Thorsten , Ahmed Sohail 
Published: August 2012

Oct4 and Sox2 are two essential transcription factors that co-regulate target genes for the maintenance of pluripotency. However, it is unclear whether they interact prior to DNA binding or how the target sites are accessed in the nucleus. By generating fluorescent protein fusions of Oct4 and Sox2 that are functionally capable of producing iPSCs (induced pluripotent stem cells), we show that their interaction is dependent on the presence of cognate DNA-binding elements, based on diffusion time, complex formation and lifetime measurements. Through fluorescence correlation spectroscopy, the levels of Oct4 and Sox2 in the iPSCs were quantified in live cells and two diffusion coefficients, corresponding to free and loosely bound forms of the protein, were distinguished. Notably, the fraction of slow-diffusing molecules in the iPSCs was found to be elevated, similar to the profile in embryonic stem cells, probably due to a change in the nuclear milieu during reprogramming. Taken together, these findings have defined quantitatively the amount of proteins pertinent to the pluripotent state and revealed increased accessibility to the underlying DNA as a mechanism for Oct4 and Sox2 to find their target binding sites and interact, without prior formation of heterodimer complexes.
Evidence for a link between histone deacetylation and Ca2+ homoeostasis in sphingosine-1-phosphate lyase-deficient fibroblasts
Authors: Ihlefeld Katja , Claas Ralf Frederik , Koch Alexander , Pfeilschifter Josef M. , Meyer zu Heringdorf Dagmar 
Published: August 2012

Embryonic fibroblasts from S1P (sphingosine-1-phosphate) lyase-deficient mice [Sgpl1−/− MEFs (mouse embryonic fibroblasts)] are characterized by intracellular accumulation of S1P, elevated cytosolic [Ca2+]i and enhanced Ca2+ storage. Since S1P, produced by sphingosine kinase 2 in the nucleus of MCF-7 cells, inhibited HDACs (histone deacetylases) [Hait, Allegood, Maceyka, Strub, Harikumar, Singh, Luo, Marmorstein, Kordula, Milstein et al. (2009) Science 325, 1254–1257], in the present study we analysed whether S1P accumulated in the nuclei of S1P lyase-deficient MEFs and caused HDAC inhibition. Interestingly, nuclear concentrations of S1P were disproportionally elevated in Sgpl1−/− MEFs. HDAC activity was reduced, acetylation of histone 3-Lys9 was increased and the HDAC-regulated gene p21 cyclin-dependent kinase inhibitor was up-regulated in these cells. Furthermore, the expression of HDAC1 and HDAC3 was reduced in Sgpl1−/− MEFs. In wild-type MEFs, acetylation of histone 3-Lys9 was increased by the S1P lyase inhibitor 4-deoxypyridoxine. The non-specific HDAC inhibitor trichostatin A elevated basal [Ca2+]i and enhanced Ca2+ storage, whereas the HDAC1/2/3 inhibitor MGCD0103 elevated basal [Ca2+]i without influence on Ca2+ storage in wild-type MEFs. Overexpression of HDAC1 or HDAC2 reduced the elevated basal [Ca2+]i in Sgpl1−/− MEFs. Taken together, S1P lyase-deficiency was associated with elevated nuclear S1P levels, reduced HDAC activity and down-regulation of HDAC isoenzymes. The decreased HDAC activity in turn contributed to the dysregulation of Ca2+ homoeostasis, particularly to the elevated basal [Ca2+]i, in Sgpl1−/− MEFs.
Independence or interdependence
Authors: Luetzelberger Therese 
Published: August 2012

ABSTRACT
This article contributes to understanding the relatively early residential independence of young Northern Europeans, by comparison to their Southern European peers. It explores the norms and underlying meanings that influence the departure from the parental home and the feelings attached to it. Analysing qualitative, biographically oriented interviews with Italian and German university students and their parents (43 participants), two patterns are identified. The first is an ‘independence’ pattern, which prioritizes the importance of leaving home in order to grow up. The second is an ‘interdependence’ pattern which supports the togetherness of the family and sees the family home as the best environment for young adults –i.e., they leave home only for ‘inevitable’ reasons related to work, education, or family formation. Both patterns are handed down over generations and are transmitted in the socialization process.
Improved gap size estimation for scaffolding algorithms
Authors: Sahlin Kristoffer , Street Nathaniel , Lundeberg Joakim , Arvestad Lars 
Published: August 2012

Abstract
Motivation: One of the important steps of genome assembly is scaffolding, in which contigs are linked using information from read-pairs. Scaffolding provides estimates about the order, relative orientation and distance between contigs. We have found that contig distance estimates are generally strongly biased and based on false assumptions. Since erroneous distance estimates can mislead in subsequent analysis, it is important to provide unbiased estimation of contig distance.
Results: In this article, we show that state-of-the-art programs for scaffolding are using an incorrect model of gap size estimation. We discuss why current maximum likelihood estimators are biased and describe what different cases of bias we are facing. Furthermore, we provide a model for the distribution of reads that span a gap and derive the maximum likelihood equation for the gap length. We motivate why this estimate is sound and show empirically that it outperforms gap estimators in popular scaffolding programs. Our results have consequences both for scaffolding software, structural variation detection and for library insert-size estimation as is commonly performed by read aligners.
Availability: A reference implementation is provided at https://github.com/SciLifeLab/gapest
Supplementary information: Supplementary data are availible at Bioinformatics online.
Contact: ksahlin@csc.kth.se
Identification of trans-acting siRNAs and their regulatory cascades in grapevine
Authors: Zhang Changqing , Li Guangping , Wang Jin , Fang Jinggui 
Published: August 2012

Abstract
Motivation: Trans-acting small interfering RNAs (ta-siRNAs) play an essential role in the regulation of plant gene expression, but relevant reports are still limited. Bioinformatic analyses indicate that many ta-siRNA-producing loci (TASs) are present in plants, implying the existence of as yet undiscovered ta-siRNAs and related regulatory pathways. To expand our knowledge of these plant gene regulators, we applied high-throughput computational and experimental methods to grapevine (Vitis vinifera L.).
Results: Based on bioinformatic predictions, we identified 49 TASs from 49 055 small RNA clusters. Using RNA degradome analysis, we experimentally validated 5 TASs, 22 ta-siRNAs and 37 ta-siRNA targets. The cis-activities of ta-siRNAs were also confirmed, which suggested an inactive mechanism of TAS transcription, and a produced mechanism of multiple forms of small RNA from same TAS. We examined the conservation of newly identified ta-siRNA regulatory cascades and found that while the cascade related to vviTAS3 was conserved, cascades related to vviTAS7, vviTAS8, vviTAS9 and vviTAS10 were grape-specific. These results broaden the known scope of ta-siRNA regulation.
Contact:zhang_chq2002@sohu.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Qualimap: evaluating next-generation sequencing alignment data
Authors: García-Alcalde Fernando , Okonechnikov Konstantin , Carbonell José , Cruz Luis M. , Götz Stefan , Tarazona Sonia , Dopazo Joaquín , Meyer Thomas F. , Conesa Ana 
Published: August 2012

Abstract
Motivation: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses.
Results: We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses.
Availability: Qualimap is freely available from http://www.qualimap.org.
Contact: aconesa@cipf.es
Supplementary Information: Supplementary data are available at Bioinformatics online.
Community N2 fixation and Trichodesmium spp. abundance along longitudinal gradients in the eastern subtropical North Atlantic
Authors: Fernández Ana , Graña Rocío , Mouriño-Carballido Beatriz , Bode Antonio , Varela Manuel , Domínguez-Yanes J. Francisco , Escánez José , de Armas Demetrio , Marañón Emilio 
Published: August 2012

AbstractFernández, A., Graña, R., Mouriño-Carballido, B., Bode, A., Varela, M., Domínguez-Yanes, J. F., Escánez, J., de Armas, D., and Marañón, E. 2013. Community N2 fixation and Trichodesmium spp. abundance along longitudinal gradients in the eastern subtropical North Atlantic. – ICES Journal of Marine Science, 70:223–231. We have determined planktonic community N2 fixation, Trichodesmium abundance, the concentration and vertical diffusive flux of phosphate, and satellite-derived estimates of atmospheric concentration of dust along two longitudinal transects in the eastern subtropical North Atlantic during November 2007 and from April–May 2008. Trichodesmium abundance was particularly low (<3 trichome l−1) during the spring 2008 cruise, when low sea surface temperatures were recorded and vertical stratification was less marked. However, community N2 fixation was always measurable, albeit low compared with other regions of the tropical Atlantic. The average, vertically-integrated N2 fixation rate was 1.20 ± 0.48 µmol N m−2 d−1 in autumn 2007 and 8.31 ± 3.31 µmol N m−2 d−1 in spring 2008. The comparison of these rates of diazotrophy with the observed Trichodesmium abundances suggests that other, presumably unicellular, diazotrophs must have contributed significantly to community N2 fixation, at least during the spring 2008 cruise. Satellite data of atmospheric dust concentration suggested similar rates of atmospheric deposition during the two surveys. In contrast, vertical diffusive fluxes of phosphate were 5-fold higher in spring than in autumn (14.2 ± 12.1 µmol P m−2 d−1 and 2.8 ± 2.6 µmol P m−2 d−1, respectively), which may have stimulated N2 fixation. These findings agree with the growing view that N2 fixation is a more widespread process than the distribution of Trichodesmium alone may suggest. Our data also suggest a role for phosphorus supply in controlling the local variability of diazotrophic activity in a region subject to relatively high atmospheric inputs of iron.
Piriformis Syndrome Surgery Causing Severe Sciatic Nerve Injury
Authors: Justice Phillip E. , Katirji Bashar , Preston David C. , Grossman Gerald E. 
Published: August 2012

Abstract
Piriformis syndrome is a controversial entrapment neuropathy in which the sciatic nerve is thought to be compressed by the piriformis muscle. Two patients developed severe left sciatic neuropathy after piriformis muscle release. One had a total sciatic nerve lesion, whereas the second had a predominantly high common peroneal nerve lesion. Follow-up studies showed reinnervation of the hamstrings only. We conclude that piriformis muscle surgery may be hazardous and result in devastating sciatic nerve injury.
Focal Hypokalemic Paralysis
Authors: Negrotto Laura , Barroso Fabio A. 
Published: August 2012

Abstract
Hypokalemia is one of the most frequent electrolytic disturbances encountered in clinical practice. It usually presents with symmetrical generalized muscle weakness and, on occasions, with arrhythmias.
There are scarce reports of cases presenting with asymmetric or focal weakness in the literature and no systematic reviews on the subject. Therefore, our aim is to describe 2 cases of hypokalemic paralysis that presented as monoparesis and to review the literature on focal hypokalemic paralysis.
Hypokalemic paralysis is usually reversible. However, it can be fatal if the diagnosis and treatment are delayed. It is important to take into account this presentation because failure to recognize it could lead to misdiagnosis, delaying the adequate treatment.
Colonoscopic allergen provocation test with rBet v 1 in patients with pollen‐associated food allergy
Authors: Pickert C. N. , Lorentz A. , Manns M. P. , Bischoff S. C. 
Published: August 2012

AbstractBackgroundAfter consumption of fruits, nuts, and vegetables, several patients with pollen allergy experience gastrointestinal (GI) tract symptoms that are possibly caused by pollen‐associated food allergy. The aim of this study was to evaluate the colonoscopic allergen provocation (COLAP) test using the recombinant birch pollen allergen Bet v 1 (rBet v 1) for in vivo diagnosis of pollen‐associated food allergy manifesting in the GI tract.MethodsThirty‐four patients with a history of adverse reactions to food, GI tract symptoms, and birch pollen pollinosis and five healthy controls underwent COLAP test. Twenty minutes after endoscopic challenge of the cecal mucosa with rBet v 1, the mucosal wheal and flare reaction was registered semiquantitatively, and tissue biopsy specimens were examined for eosinophil mucosal activation.ResultsThe mucosal reaction to rBet v 1 was correlated with the presence of pollinosis (P = 0.004), history of adverse reaction to Bet v 1‐associated food allergens (P = 0.001), and tissue eosinophils' activation (P < 0.001). A wheal and flare reaction in the COLAP test was observed in 13 of 16 patients (81%) with a history of GI tract symptoms associated with the ingestion of Bet v 1‐related foods and in four of 18 (22%) patients with a negative history (P < 0.001). The control group did not develop visible mucosal reactions to rBet v 1. Systemic anaphylactic reactions did not occur.ConclusionsThe mucosal administration of rBet v 1 by COLAP test provides a new diagnostic tool that might support the diagnosis of Bet v 1‐associated food allergy manifesting in the GI tract.
Comparative study of one‐step nucleic acid amplification assay, frozen section, and touch imprint cytology for intraoperative assessment of breast sentinel lymph node in Chinese patients
Authors: Wang Yong‐sheng , Ou‐yang Tao , Wu Jiong , Liu Yan‐hui , Cao Xu‐chen , Sun Xiao , Fu Li , Liao Ning , Yang Wen‐tao , Zhong Wei‐xia , Lu Ai‐ping 
Published: August 2012

Conventional procedures for the intraoperative assessment of breast cancer sentinel lymph nodes (SLNs) are frozen section (FS) and touch imprint cytology (TIC). The one‐step nucleic acid amplification (OSNA) assay is a novel molecular technique. The aim of this study was to evaluate the optimal approach by comparing OSNA assay, FS, and TIC. Five hundred and fifty‐two consecutive patients were enroled from five study centers in China. The SLNs were cut into alternating 2 mm blocks. The odd blocks were tested by the OSNA assay intraoperatively, and the even ones were assessed by postoperative histology (four 4‐ to 6‐μm‐thick sections were taken every 200 μm per block). In addition, intraoperative histological assessments were carried out on the even blocks of 211 patients by FS and all blocks of 552 patients by TIC. Overall performance of the assay compared to postoperative histology was: accuracy 91.4%; sensitivity 83.7%; and specificity 92.9%. The sensitivity of the assay was higher than FS (211 patients, 77.6% vs 69.7%; not significant, P = 0.286) and was significantly higher than TIC (552 patients, 83.6% vs 76.2%; P = 0.044). When assessing nodes with micrometastases, the sensitivity of the assay was higher than FS (17 nodes, 47.1% vs 23.5%; not significant, P = 0.289) and was significantly higher than TIC (48 nodes, 62.5% vs 35.4%; P = 0.007). The study indicated that the OSNA assay is an accurate and rapid intraoperative assay for assessing breast SLNs and it can replace FS and TIC for application in general medical practice. The trial was registered as: OSNA assay China Registration Study. Clinical trial registration number: China Breast Cancer Clinical Study Group 001c.
Association of 25‐hydroxyvitamin D with type 2 diabetes among patients undergoing coronary angiography: cross‐sectional findings from the LUdwigshafen Risk and Cardiovascular Health (LURIC) Study
Authors: O'Hartaigh Bríain , Neil Thomas G. , Silbernagel Günther , Bosch Jos A. , Pilz Stefan , Loerbroks Adrian , Kleber Marcus E. , Grammer Tanja B. , Böhm Bernhard O. , März Winfried 
Published: August 2012

SummaryObjectiveEvidence suggests that vitamin D may protect against the onset of diabetes. However, the mechanisms underlying the role of vitamin D on glycaemic status are unclear and warrant further investigation. We sought to determine the relationship between serum 25‐hydroxyvitamin D (25[OH]D) and glycaemic status among intermediate‐to‐high‐risk patients scheduled for coronary angiography.MethodsParticipants were 3316 male and female patients (mean ± SD age, 62·7 ± 10·6 years). Four categories were formed according to serum 25[OH]D levels. The association between serum 25[OH]D and diabetes was assessed using multivariable logistic regression.ResultsFasting and 2 h post‐load glucose, HbA1c and the HOMA‐IR indices diminished with increasing serum 25[OH]D levels (P < 0·001). However, no associations were observed between insulin, pro‐insulin or C‐peptide and serum 25[OH]D concentrations. The pro‐inflammatory markers IL‐6 and hs‐CRP also decreased considerably with higher vitamin D levels (P < 0·001). After full adjustment, those with optimal serum 25[OH]D levels had a reduced odds for fasting diabetes (OR = 0·63; 95% CI, 0·46–0·86; Ptrend = 0·01), 2 h post‐load diabetes (OR = 0·46; 95% CI, 0·29–0·74; Ptrend = 0·004), both fasting/2 h post‐load diabetes (OR = 0·61; 95% CI, 0·42–0·87; Ptrend = 0·001) and all of the combined hyperglycaemic states (OR = 0·68; 95% CI, 0·52–0·80; Ptrend = 0·01).ConclusionsHigher serum 25[OH]D levels were associated with better glycaemic status and lower inflammation. Should these observations be confirmed in future studies, vitamin D supplementation may prove a useful adjunct in attenuating the onset of diabetes.
The relation of vascular endothelial growth factor (VEGF) gene polymorphisms on VEGF levels and the risk of vasoocclusive crisis in sickle cell disease
Authors: Al‐Habboubi Hebah H. , Mahdi Najat , Abu‐Hijleh Tala M. , Abu‐Hijleh Farah M. , Sater Mai S. , Almawi Wassim Y. 
Published: August 2012

AbstractObjectiveThe association of vascular endothelial growth factor (VEGFA) variants and VEGF secretion with sickle cell disease (SCD) vasoocclusive crisis (VOC) was investigated in 210 VOC patients and 114 pain‐free control patients.MethodsVEGFA −2578C/A (rs699947), −460T/C (rs833061), −1154G/A (rs15703060), −634G/C (rs2010963), 398G/A (rs833068), 497G/A (rs833070), −583T/C (rs3025020), and 936C/T (rs3025039) were carried out by real‐time PCR.ResultsHigher frequency of rs2010963 C‐allele, rs833068 A‐allele, and rs3025020 C‐allele and significant differences in rs2010963, rs833068, and rs3025020 genotype distribution were seen in VOC than steady‐state patients. Increased VOC risk was seen with rs2010963 as heterozygous and more as homozygous, and in rs833068 and rs3025020 homozygous carriers. While there were no differences in VEGF levels between VOC and steady‐state controls, there was a progressive decline in serum VEGF in rs2010963 and rs833068 heterozygous and homozygous genotypes, but an opposite trend was seen in VOC patients. Haploview analysis revealed high LD between rs699947, rs833061, rs1570360, rs2010963, rs833068, and rs833070, but weak or no LD between rs3025020 and rs3025039 and other SNPs. Six‐locus (rs699947/rs833061/rs1570360/rs2010963/rs833068/rs833070) VEGFA haplotype analysis identified haplotype 111111 to be negatively (OR = 0.68) and haplotype 111222 to be positively (OR = 1.89) associated with VOC. rs2010963, rs833068, and rs3025020 were correlated with VOC type, while rs3025020 was correlated with hospitalization, VOC treatment, and duration.ConclusionSpecific VEGFA variants contribute to the pathogenesis of SCD VOC.
Exposure to second‐hand smoke damages everyday prospective memory
Authors: Heffernan Thomas M. , O'Neill Terence S. 
Published: August 2012

AbstractAimsProspective memory (PM: remembering future intentions and activities) is critical to everyday remembering. This study compared a group of never‐smokers who reported regular exposure to second‐hand smoke (the SHS group) with a group of current smokers (the CS group) and a group of never‐smokers who reported never having been exposed to SHS (the non‐SHS group) on objective PM.DesignAn existing groups design was employed to compare the SHS, CS and non‐SHS groups.Participants and settingTwenty‐four SHS, 27 CS and 28 non‐SHS were tested on objective PM. All participants were university undergraduates aged between 18–30 years. All participants were tested individually in a laboratory setting.MeasurementsThe Cambridge Prospective Memory Test (CAMPROMPT) was used to assess objective PM. Age, other drug use, mood and IQ were also measured as covariates in the study.FindingsThe non‐SHS group recalled significantly more time‐based PM tasks than the SHS group (means = 16.3 versus 13.7, P < 0.001) and significantly more than the CS group (CS mean = 11.6, P < 0.001); and the SHS group recalled significantly more time‐based tasks than the CS group (P < 0.002). The non‐SHS group recalled significantly more event‐based PM tasks than the CS group (means = 15.2 versus 11.3, P < 0.002) with no significant difference between the non‐SHS group and SHS group (SHS mean = 14.3, P = 0.234); and the SHS group recalled significantly more event‐based tasks than the CS group (P < 0.001).ConclusionNon‐smokers exposed to second‐hand smoke may suffer impairment in time‐based prospective memory.