bluuebunny/crossref_metadata_2025_split huggingface dataset:
NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes
Authors: Salimullah Md , Mizuho Sakai , Plessy Charles , Carninci Piero 
Published: January 2011

INTRODUCTIONCap analysis gene expression (CAGE) is a method to identify the 5′ ends of transcripts, allowing the discovery of new promoters and the quantification of gene activity. Combining promoter location and their expression levels, CAGE data are essential for annotation-agnostic studies of regulatory gene networks. However, CAGE requires large amounts of input RNA, which usually are not obtainable from highly refined samples such as tissue microdissections or subcellular fractions. The nanoCAGE method can capture the 5′ ends of transcripts from as little as 10 ng of total RNA and takes advantage of the capacity of current sequencers to produce longer (50-100 bp) reads. The method prepares cap-selected cDNAs ready for direct sequencing of their 5′ ends (optionally mate-paired with the 3′ end) that can provide information about downstream sequences. This protocol describes how to prepare nanoCAGE libraries from as little as 50 ng of total RNA within two working days. The libraries can be sequenced using an Illumina Gene AmplifierIIx with a level of sensitivity 1000 times higher than CAGE.
Multiple Testing and Power Calculations in Genetic Association Studies
Authors: So Hon-Cheong , Sham Pak C. 
Published: January 2011

INTRODUCTIONModern genetic association studies typically involve multiple single-nucleotide polymorphisms (SNPs) and/or multiple genes. With the development of high-throughput genotyping technologies and the reduction in genotyping cost, investigators can now assay up to a million SNPs for direct or indirect association with disease phenotypes. In addition, some studies involve multiple disease or related phenotypes and use multiple methods of statistical analysis. The combination of multiple genetic loci, multiple phenotypes, and multiple methods of evaluating associations between genotype and phenotype means that modern genetic studies often involve the testing of an enormous number of hypotheses. When multiple hypothesis tests are performed in a study, there is a risk of inflation of the type I error rate (i.e., the chance of falsely claiming an association when there is none). Several methods for multiple-testing correction are in popular use, and they all have strengths and weaknesses. Because no single method is universally adopted or always appropriate, it is important to understand the principles, strengths, and weaknesses of the methods so that they can be applied appropriately in practice. In this article, we review the three principle methods for multiple-testing correction and provide guidance for calculating statistical power.
Hypomorphic Alleles RevealFCA-Independent Roles forFYin the Regulation ofFLOWERING LOCUS C
Authors: Feng Wei , Jacob Yannick , Veley Kira M. , Ding Lei , Yu Xuhong , Choe Goh , Michaels Scott D. 
Published: January 2011

AbstractThe autonomous floral promotion pathway plays a key role in the regulation of flowering in rapid-cycling Arabidopsis (Arabidopsis thaliana) by providing constitutive repression of the floral inhibitor FLOWERING LOCUS C (FLC). As a result, autonomous pathway mutants contain elevated levels of FLC and are late flowering. Winter annual Arabidopsis, in contrast, contain functional alleles of FRIGIDA (FRI), which acts epistatically to the autonomous pathway to up-regulate FLC and delay flowering. To further explore the relationship between FRI and the autonomous pathway, we placed autonomous pathway mutants in a FRI-containing background. Unexpectedly, we found that a hypomorphic allele of the autonomous pathway gene fy (fy null alleles are embryo lethal) displayed background-specific effects on FLC expression and flowering time; in a rapid-cycling background fy mutants contained elevated levels of FLC and were late flowering, whereas in a winter annual background fy decreased FLC levels and partially suppressed the late-flowering phenotype conferred by FRI. Because FY has been shown to have homology to polyadenylation factors, we examined polyadenylation site selection in FLC transcripts. In wild type, two polyadenylation sites were detected and used at similar levels. In fy mutant backgrounds, however, the ratio of products was shifted to favor the distally polyadenylated form. FY has previously been shown to physically interact with another member of the autonomous pathway, FCA. Interestingly, we found that fy can partially suppress FLC expression in an fca null background and promote proximal polyadenylation site selection usage in the absence of FCA. Taken together, these results indicate novel and FCA-independent roles for FY in the regulation of FLC.
Inactivation of Snt2, a BAH/PHD‐containing transcription factor, impairs pathogenicity and increases autophagosome abundance in Fusarium oxysporum
Authors: DENISOV YOULIA , FREEMAN STANLEY , YARDEN ODED 
Published: January 2011

SUMMARYThe soil‐borne, asexual fungus Fusarium oxysporum f.sp. melonis (FOM) is a causal agent of muskmelon wilt disease. The current study focused on the most virulent race of FOM—race 1,2. The tagged mutant D122, generated by Agrobacterium tumefaciens‐mediated transformation, caused the delayed appearance of initial wilt disease symptoms, as well as a 75% reduction in pathogenicity. D122 was impaired in the gene product homologous to the Snt2‐like transcription factor of Schizosaccharomyces pombe. Involvement of snt2 in the early stage of FOM pathogenesis and its requirement for host colonization were confirmed by targeted disruption followed by quantitative reverse transcription‐polymerase chain reaction analysis of snt2 expression in planta. Δsnt2 mutants of FOM and Neurospora crassa exhibited similar morphological abnormalities, including a reduction in conidia production and biomass accumulation, slower vegetative growth and frequent hyphal septation. In N. crassa, snt‐2 is required for sexual development, as Δsnt‐2 mutants were unable to produce mature perithecia. Suppressive subtraction hybridization analysis of the D122 mutant versus wild‐type isolate detected four genes (idi4, pdc, msf1, eEF1G) that were found previously in association with the target of rapamycin (TOR) kinase pathway. Expression of the autophagy‐related idi4 and pdc genes was found to be up‐regulated in the Δsnt2 FOM mutant. In N. crassa, disruption of snt‐2 also conferred a significant over‐expression of idi4.
The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites
Authors: Dian Cyril , Vitale Sylvia , Leonard Gordon A. , Bahlawane Christelle , Fauquant Caroline , Leduc Damien , Muller Cécile , de Reuse Hilde , Michaud‐Soret Isabelle , Terradot Laurent 
Published: January 2011

SummaryFur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for binding to specific DNA sequences named Fur boxes. In Helicobacter pylori, HpFur is involved in acid response and is important for gastric colonization in model animals. Here we present the crystal structure of a functionally active HpFur mutant (HpFur2M; C78S‐C150S) bound to zinc. Although its fold is similar to that of other Fur and Fur‐like proteins, the crystal structure of HpFur reveals a unique structured N‐terminal extension and an unusual C‐terminal helix. The structure also shows three metal binding sites: S1 the structural ZnS4 site previously characterized biochemically in HpFur and the two zinc sites identified in other Fur proteins. Site‐directed mutagenesis and spectroscopy analyses of purified wild‐type HpFur and various mutants show that the two metal binding sites common to other Fur proteins can be also metallated by cobalt. DNA protection and circular dichroism experiments demonstrate that, while these two sites influence the affinity of HpFur for DNA, only one is absolutely required for DNA binding and could be responsible for the conformational changes of Fur upon metal binding while the other is a secondary site.
Integration of sedimentology and ground‐penetrating radar for high‐resolution imaging of a carbonate platform
Authors: JORRY STÉPHAN J. , BIÉVRE GRÉGORY 
Published: January 2011

AbstractGround‐penetrating radar has not been applied widely to the recognition of ancient carbonate platform geometries. This article reports the results of an integrated study performed on an Upper Jurassic outcrop from the south‐east Paris basin, where coral bioherms laterally change into prograding depositional sequences. Ground‐penetrating radar profiles illustrate the different bedding planes and major erosional unconformities visible at outcrop. A ground‐penetrating radar profile conducted at the base of the cliff displays a palaeotopographic surface on which the outcropping bioherms settled. The excellent penetration depths of the ground‐penetrating radar (20 m with a monostatic 200 MHz antenna) images the carbonate platform geometries, ranging between outcrop workscale (a few metres) and seismic scale (several hundreds of metres). This study supports recent evidence of icehouse conditions and induced sea‐level fluctuations controlling the Upper Jurassic carbonate production.
Presynaptic facilitatory adenosine A2A receptors mediate fade induced by neuromuscular relaxants that exhibit anticholinesterase activity
Authors: Bornia Elaine CS , Correia‐de‐Sá Paulo , Alves‐Do‐Prado Wilson 
Published: January 2011

Summary1. Pancuronium, cisatracurium and vecuronium are antinicotinic agents that, in contrast with d‐tubocurarine and hexamethonium, exhibit anticholinesterase activity. Pancuronium‐, cisatracurium‐ and vecuronium‐induced fade results from blockade of facilitatory nicotinic receptors on motor nerves, but fade produced by such agents also depends on the presynaptic activation of inhibitory muscarinic M2 receptors by acetylcholine released from motor nerve terminals and activation of inhibitory adenosine A1 receptors by adenosine released from motor nerves and muscles. The participation of presynaptic facilitatory A2A receptors in fade caused by pancuronium, cisatracurium and vecuronium has not yet been investigated. In the present study, we determined the effects of ZM 241385, an antagonist of presynaptic facilitatory A2A receptors, on fade produced by these neuromuscular relaxants in the rat phrenic nerve–diaphragm (PND) preparation.2. The muscles were stimulated indirectly at 75 ± 3 Hz to induce a sustained tetanizing muscular contraction. The lowest concentration at which each antinicotinic agent produced fade without modifying initial tetanic tension (presynaptic action) was determined.3. d‐Tubocurarine‐induced fade occurred only at 55 nmol/L, a concentration that also reduced maximal tetanic tension (post‐synaptic action). At 10 nmol/L, ZM 241385 alone did not produce fade, but it did attenuate pancuronium (0.32 μmol/L)‐, cisatracurium (0.32 μmol/L)‐ and vecuronium (0.36 μmol/L)‐induced fade.4. The fade induced by the ‘pure’ antinicotinic agents d‐tubocurarine (55 nmol/L) and hexamethonium (413 μmol/L) was not altered by 10 nmol/L ZM 241385, indicating that presynaptic adenosine A2A receptors play a significant role in the fade produced by antinicotinic agents when such agents have anticholinesterase activity.
Clinicopathological staging of colorectal cancer: Evolution and consensus—an Australian perspective
Authors: Chapuis Pierre H , Chan Charles , Dent Owen F 
Published: January 2011

AbstractIn 1991 this journal published the report of an international working party to the World Congress of Gastroenterology regarding the clinicopathological staging of colorectal cancer. Since that time staging has continued to evolve as further prognostic factors in colorectal cancer have been elucidated in studies of increasingly large databases in several countries. This review summarizes several of the key issues that have arisen during this evolutionary process and raises matters which still remain controversial in staging at the present time.
Nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in Japan
Authors: Okanoue Takeshi , Umemura Atsushi , Yasui Kohichiroh , Itoh Yoshito 
Published: January 2011

AbstractDuring the past 20 to 30 years, the frequency of patients presenting with nonalcoholic fatty liver diseases (NAFLD) has increased gradually in Japan in proportion to the increase in the population with life‐style related diseases. We describe here the current status of the clinical and basic aspects of research into NAFLD in Japan.The increase in the incidence of life‐style‐related diseases has resulted in an increase in NAFLD throughout the past 20 to 30 years. The rate of obesity in the population is not high compared to western countries but the incidence of NAFLD is similar to those countries. In 2008 we started a nationwide study of NAFLD which has been supported by the Ministry of Labor and Welfare Japan. In this project, we planned to investigate the epidemiology, genetic backgrounds and biochemical markers, and liver injury in patients with diabetes mellitus (DM) and hepatocellular carcinoma in NASH, and treatment of NASH. Approximately 20 to 25% of DM patients showed NAFLD in which the prevalence of NASH might be more than 30 to 40%. Fortunately, we have been able to obtain very interesting results from our group studies, including single necleotide polymorphisms (SNPs) which will be published in the near future.
Changing etiologies and outcomes of acute liver failure: A perspective from Japan
Authors: Oketani Makoto , Ido Akio , Tsubouchi Hirohito 
Published: January 2011

AbstractAcute liver failure in Japan usually consists of fulminant hepatitis (FH) due to viral infection, autoimmune hepatitis and drug‐allergy‐induced liver injury. The annual incidence of FH was estimated at 429 cases in 2004. FH is classified into acute or subacute type, and the prognosis of the latter is poor. Hepatitis B virus (HBV) is the most frequently identifiable agent that causes FH in Japan. Transient HBV infection is more prevalent in the acute than subacute type, whereas the frequency of HBV carriers is greater in the subacute type. FH due to HBV reactivation from resolved hepatitis B has been increasingly observed in patients with malignant lymphoma treated with rituximab and corticosteroid combination therapy. The prognosis is poor in HBV carriers with acute exacerbation, especially in patients with HBV reactivation from resolved hepatitis B. Despite careful investigation, the etiology is still unknown in 16% and 39% of the acute and subacute type of FH, respectively. Autoimmune hepatitis and drug‐allergy‐induced liver injury are found in 7% and 10%, respectively, and are more frequently observed in the subacute type of FH. Living donor liver transplantation is now the standard care for individuals with poor prognosis. Artificial liver support with plasmapheresis and hemodiafiltration plays a central role while waiting for a donor liver or for the native liver to regenerate. Further research is necessary to identify the causes of unknown origin. In addition, to improve the prognosis of FH, it is necessary to establish treatment modalities that are effective for liver regeneration.
Terlipressin in hepatorenal syndrome: Evidence for present indications
Authors: Rajekar Harshal , Chawla Yogesh 
Published: January 2011

AbstractHepatorenal syndrome (HRS) is the most frequent life threatening complication of advanced liver failure and cirrhosis. HRS results from a functional renal dysfunction due to circulatory disturbances in patients with advanced liver disease and portal hypertension. Reduction in the effective circulating blood volume and hence hypoperfusion of the kidney is the basic underlying common pathogenetic mechanism for the development of hepatorenal syndrome. The prognosis for HRS remains very poor with types 1 and 2—both having an expected survival time of 2 weeks and 6 months, respectively.Although the available data are derived from studies including a limited number of patients mainly affected by type 1 HRS, vasoconstrictor drugs, in particular the vasopressin analog Terlipressin, seem to be the most effective approach for the management of HRS. Associated with albumin infusion, these drugs have been shown to lead to reduced mortality and improved renal function in HRS. Terlipressin administration significantly increases mean arterial pressure and systemic vascular resistance; while the heart rate, cardiac output, HVPG and portal venous blood flow decrease significantly. This decrease correlates well with the decrease in plasma renin activity. Thus the vasoconstrictor effect of Terlipressin reverses the basic pathology of HRS by reducing the plasma renin activity. The improvement in hemodynamics with Terlipressin is associated with an increase in glomerular filtration rate and deactivation of the vasoconstrictor and sodium‐conserving hormones with reduced activity of the RAAS resulting in increased natriuresis.Terlipressin thus reverses HRS and is useful in bridging the patient to liver transplantation and may hence indirectly improve survival. Patients with HRS who show an improvement in renal function with Terlipressin and albumin seem to have an excellent post‐transplantation outcome similar to that of patients without HRS. Thus, the use of Terlipressin has been shown to be safe, with minimal side effects that usually disappear after dose reduction, and results in an improved outcome in patients with HRS.
Helicobacter pylori and gastritis: Untangling a complex relationship 27 years on
Authors: Tan Victoria P Y , Wong Benjamin C Y 
Published: January 2011

AbstractSince its' introduction by Warren and Marshall 27 years ago, Helicobacter pylori (HP) has become the linchpin in our understanding of important gastric conditions including gastritis, intestinal metaplasia (IM), gastric/duodenal ulcers (GU/DU), Mucosal Associated Lymphoid Tumour (MALToma) and gastric cancer. Initially named Campylobacter pyloridis, it was re‐named HP when biochemical and genetic characterization of the organism showed that it was not a member of the Campylobacter genus. The finding in 1983 was seminal. It is now recognized that HP is the most common chronic human bacterial infection and it is the most common cause of gastritis. It is strongly implicated in the development of peptic ulcer disease and gastric neoplasms. In the years since its' discovery, much headway has been made in the understanding of this ubiquitous organism that had remained elusive, with much work focused on eradication, in part driven by pharmaceutical research and development. Standard triple therapy emerged to eradicate HP. However, with the emergence of HP resistance, newer regimes have been put forth that include quadruple therapy, sequential therapy and a dizzying array of other combinations bent on eradicating HP. Much less is known about the natural history of HP, the different faces of HP internationally, HP eradication and its effect on gastritis, IM, GU/DU and gastric cancer. This review will address the changing face of HP in 2011.
Elcatonin is effective for lower back pain and the symptoms of gastroesophageal reflux disease in elderly osteoporotic patients with kyphosis
Authors: Yamane Yuko , Yamaguchi Toru , Tsumori Michihiro , Yamauchi Mika , Yano Shozo , Yamamoto Masahiro , Honda Chie , Kinoshita Yoshikazu , Sugimoto Toshitsugu 
Published: January 2011

Aim:  Elderly osteoporotic patients with kyphosis tend to be frequently accompanied by the symptoms of gastroesophageal reflux disease (GERD) such as heartburn and acid reflux. Elcatonin, which is effective for lower back pain of osteoporosis, has a physiological action of reducing gastric acid. We examine whether or not this drug would alleviate GERD symptoms as well as lower back pain in patients with osteoporosis.Methods:  Elcatonin was administrated at a dose of 20 units once weekly for 3 months. The visual analog scale (VAS) and the frequency scale for the symptoms of GERD (FSSG) were used to evaluate lower back pain and GERD symptoms, respectively.Results:  Both VAS and FSSG scores significantly decreased after 1, 2 and 3 months of elcatonin administration (at least P < 0.001). Even after the cessation of elcatonin, both scores remained significantly low for an extra 1 and 3 months, respectively. These beneficial effects were also observed in non‐steroidal anti‐inflammatory drug (NSAID) or GERD drug users.Conclusion:  The present findings suggest that elcatonin could improve the symptoms of GERD as well as osteoporosis‐invoked back pain in elderly patients with kyphosis, and that these effects are long‐lasting and independent of NSAID or GERD drugs. Geriatr Gerontol Int 2011; 11: 215–220.
The prevalence of menstrual pain and associated risk factors among Iranian women
Authors: Tavallaee Mahkam , Joffres Michel R. , Corber Stephen J. , Bayanzadeh Mana , Rad Mahnaz Mahmoudi 
Published: January 2011

AbstractAim:  To estimate the prevalence of dysmenorrhea in Iranian women and investigate associated risk factors.Material & Methods:  In a cross‐sectional study in Tehran, Iran in 2007, 381 women (81% response rate, age 16–56 years) were selected through a stratified random sample of 22 different districts and completed a questionnaire about dysmenorrhea. Descriptive statistics, spearman rank correlation statistic, and ordinal logistic regression models were used. Confounding and effect‐modification were explored for each association.Results:  The prevalence of no, mild, moderate, and severe menstrual pain was 10%, 41%, 28%, and 22%, respectively. Older age and high intake of fruits and vegetables were protective factors for menstrual pain while women with family history of dysmenorrhea, higher stress and depression tended to have more severe pain. Body mass index, parity, smoking, and physical activity were not significantly associated with dysmenorrhea after controlling for potential confounding factors and effect modifiers.Conclusion:  Menstrual pain is a common complaint in Iranian women. The inverse association between fruit and vegetable intake and dysmenorrhea, and reduction of stress and depression need to be further explored and considered in terms of recommendation to reduce dysmenorrhea.
Management of retained products of conception with marked vascularity
Authors: Kitahara Tomoko , Sato Yukiyasu , Kakui Kazuyo , Tatsumi Keiji , Fujiwara Hiroshi , Konishi Ikuo 
Published: January 2011

AbstractCases of retained products of conception (RPOC) with marked vascularity present a clinical challenge because simple dilation and curettage (D&C) can lead to life‐threatening hemorrhage. We describe here two cases of hypervascular RPOC that were successfully managed with two different approaches. Case 1: A 26‐year‐old woman with history of 3 D&Cs was transported to the emergency room for heavy vaginal bleeding 45 days after a spontaneous abortion. Diagnosis of RPOC with aneurysm‐like structure was considered and uterine artery embolization was performed. Four days after the uterine artery embolization, reduction of the vascularity of RPOC was confirmed on color Doppler ultrasonography and D&C was successfully carried out. Case 2: A 37‐year‐old woman with history of one cesarean section became pregnant after the regular menses. She underwent D&C for missed abortion at 8 weeks' gestation. Seven days after the D&C, sonographically heterogenous mass emerged in the vicinity of the previous cesarean scar. Thereafter, the mass gradually grew larger and diagnosis of hypervascular placental polyp was considered. As the amount of vaginal bleeding was small, expectant management was instituted. Sixty‐one days after the first D&C, reduction of the vascularity of RPOC was confirmed on color Doppler ultrasonography and D&C was successfully completed.