bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of RNA–protein interaction networks using PAR‐CLIP
Authors: Ascano Manuel , Hafner Markus , Cekan Pavol , Gerstberger Stefanie , Tuschl Thomas 
Published: December 2011

AbstractAll mRNA molecules are subject to some degree of post‐transcriptional gene regulation (PTGR) involving sequence‐dependent modulation of splicing, cleavage and polyadenylation, editing, transport, stability, and translation. The recent introduction of deep‐sequencing technologies enabled the development of new methods for broadly mapping interaction sites between RNA‐binding proteins (RBPs) and their RNA target sites. In this article, we review crosslinking and immunoprecipitation (CLIP) methods adapted for large‐scale identification of target RNA‐binding sites and the respective RNA recognition elements. CLIP methods have the potential to detect hundreds of thousands of binding sites in single experiments although the separation of signal from noise can be challenging. As a consequence, each CLIP method has developed different strategies to distinguish true targets from background. We focus on photoactivatable ribonucleoside‐enhanced CLIP, which relies on the intracellular incorporation of photoactivatable ribonucleoside analogs into nascent transcripts, and yields characteristic sequence changes upon crosslinking that facilitate the separation of signal from noise. The precise knowledge of the position and distribution of binding sites across mature and primary mRNA transcripts allows critical insights into cellular localization and regulatory function of the examined RBP. When coupled with other systems‐wide approaches measuring transcript and protein abundance, the generation of high‐resolution RBP‐binding site maps across the transcriptome will broaden our understanding of PTGR and thereby lead to new strategies for therapeutic treatment of genetic diseases perturbing these processes. WIREs RNA 2012, 3:159–177. doi: 10.1002/wrna.1103This article is categorized under:

RNA Evolution and Genomics > Computational Analyses of RNA
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition
RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
RNA Methods > RNA Analyses in Cells
Effects of antiviral therapy on long‐term outcome after liver resection for hepatitis B virus‐related hepatocellular carcinoma
Authors: Urata Yorihisa , Kubo Shoji , Takemura Shigekazu , Uenishi Takahiro , Kodai Shintaro , Shinkawa Hiroji , Sakae Masayuki , Kaneda Kazuhisa , Ohata Kazunori , Nozawa Akinori , Suehiro Shigefumi 
Published: December 2011

AbstractBackground/purposeWe investigated the effects of nucleos(t)ide analogues (NAs) on long‐term outcome in patients following curative treatment for hepatitis B virus (HBV)‐related hepatocellular carcinoma (HCC).MethodsThis study involved 70 of the 76 patients who had undergone liver resection for HBV‐related HCC in our department; 6 patients were excluded due to non‐curative resection or advanced cancer. The 70 patients were divided into three groups, as follows: 13 patients with high serum concentration of HBV DNA (⩾4 log10 copies/mL) and no antiviral therapy (high viral group); 46 patients who received antiviral therapy during the serial follow up (antiviral therapy group) because of high viral concentration (⩾4 log10 copies/mL); and 11 patients with low serum concentration of HBV DNA (<4 log10 copies/mL) and no antiviral therapy (low viral group).ResultsTumor‐free survival rate was significantly higher in the low viral group than in the high viral group (P = 0.0058). Multivariate analysis revealed that a high serum concentration of HBV DNA (⩾4 log10 copies/mL) (risk ratio 6.717, 95% confidence interval 1.435–31.434, P = 0.0156) was an independent risk factor for a short tumor‐free survival time. Tumor‐free survival rate was significantly higher in the antiviral therapy group than in the high viral group (P = 0.0478). Multivariate analysis revealed that presence of multiple tumors (risk ratio 2.857, 95% confidence interval 1.403–5.816, P = 0.0038) was an independent risk factor for a short tumor‐free survival time. The cumulative survival rate was significantly higher in the antiviral therapy group than in the high viral group (P = 0.0025). Multivariate analysis revealed that not undergoing antiviral therapy (risk ratio 0.121, 95% confidence interval 0.024–0.608, P = 0.0104) was an independent risk factor for a short survival time.ConclusionsA high serum concentration of HBV DNA (⩾4 log10 copies/mL) was a strong risk factor for HCC recurrence after resection of HBV‐related HCC. Antiviral therapy with NAs improved the long‐term outcome after resection of HBV‐related HCC in patients with high serum concentrations of HBV DNA.
Proposed indications for limited resection of early ampulla of Vater carcinoma: clinico‐histopathological criteria to confirm cure
Authors: Aiura Koichi , Hibi Taizo , Fujisaki Hiroto , Kitago Minoru , Tanabe Minoru , Kawachi Shigeyuki , Itano Osamu , Shinoda Masahiro , Yagi Hiroshi , Masugi Yohei , Sakamoto Michiie , Kitagawa Yuko 
Published: December 2011

AbstractBackgroundLimited resection is reserved for patients with high operative risk or benign adenomas. We aimed to define indications for limited resection of early ampulla of Vater carcinoma with curative intent through detailed preoperative examinations and histopathological evaluations.MethodsWe performed a retrospective cohort study of all consecutive Japanese patients who underwent resection for ampulla of Vater neoplasms at our hospital from 1986 to 2010.ResultsA total of 75 patients were identified. Moderately/poorly differentiated histology, lympho‐vascular/perineural invasion, and duodenal/pancreatic invasion were significant risk factors for lymph node metastases. Macroscopically, non‐exposed protruded‐ or ulcerative‐type disease did not correlate directly with lymph node metastases; however, these tumor types were associated with other invasive features. In a subset of early carcinomas fulfilling the conditions of exposed protruded adenoma or papillary/well‐differentiated adenocarcinoma determined by endoscopic biopsy, negative duodenal invasion determined by endoscopic ultrasonography, no tumor infiltration into the pancreatic duct determined by intraductal ultrasound, and diameter of the pancreatic duct ⩽3 mm determined by endoscopic retrograde cholangiopancreatography (N = 11), the incidence of lymph node metastasis and tumor infiltration into the pancreatic duct was 0%.ConclusionStrictly selected patients with early ampulla of Vater carcinomas may benefit from limited resection if the resected specimen is evaluated to confirm all histopathological criteria.
The Quality of Male Fertility Data in Major U.S. Surveys
Authors: Joyner Kara , Peters H. Elizabeth , Hynes Kathryn , Sikora Asia , Taber Jamie Rubenstein , Rendall Michael S. 
Published: December 2011

Abstract
Researchers continue to question fathers’ willingness to report their biological children in surveys and the ability of surveys to adequately represent fathers. To address these concerns, this study evaluates the quality of men’s fertility data in the 1979 and 1997 cohorts of the National Longitudinal Survey of Youth (NLSY79 and NLSY97) and in the 2002 National Survey of Family Growth (NSFG). Comparing fertility rates in each survey with population rates based on data from Vital Statistics and the U.S. Census Bureau, we document how the incomplete reporting of births in different surveys varies according to men’s characteristics, including their age, race, marital status, and birth cohort. In addition, we use Monte Carlo simulations based on the NSFG data to demonstrate how birth underreporting biases associations between early parenthood and its antecedents. We find that in the NSFG, roughly four out of five early births were reported; but in the NLSY79 and NLSY97, almost nine-tenths of early births were reported. In all three surveys, incomplete reporting was especially pronounced for nonmarital births. Our results suggest that the quality of male fertility data is strongly linked to survey design and that it has implications for models of early male fertility.
Optimal Suturing Technique and Number of Sutures for Surgical Implantation of Acoustic Transmitters in Juvenile Salmonids
Authors: Deters Katherine A. , Brown Richard S. , Boyd James W. , Eppard M. Brad , Seaburg Adam G. 
Published: December 2011

AbstractThe size reduction of acoustic transmitters has led to a reduction in the length of the incision needed to implant a transmitter. Smaller suture knot profiles and fewer sutures may be adequate for closing an incision used to surgically implant an acoustic transmitter. As a result, faster surgery times and reduced tissue trauma could lead to increased survival and decreased infection for implanted fish. The objective of this study was to assess the effects of five suturing techniques on mortality, tag and suture retention, incision openness, ulceration, and redness in juvenile Chinook salmon Oncorhynchus tshawytscha implanted with acoustic transmitters. Suturing was performed by three surgeons, and study fish were held at two water temperatures (12°C and 17°C). Mortality was low and tag retention was high for all treatments on all examination days (7, 14, 21, and 28 d postsurgery). Because there was variation by surgeon in suture retention among treatments, further analyses included only the one surgeon who received feedback training in all suturing techniques. Incision openness and tissue redness did not differ among treatments. The only difference observed among treatments was in tissue ulceration. Incisions closed with a horizontal mattress pattern had more ulcerations than did other treatments among fish held for 28 d at 17°C. Results from this study suggest that one simple interrupted 1 × 1 × 1 × 1 suture is adequate for closing incisions on fish under most circumstances. However, in dynamic environments, two simple interrupted 1 × 1 × 1 × 1 sutures should provide adequate incision closure. Reducing bias in survival and behavior tagging studies is important when making comparisons with the migrating salmon population. Therefore, by minimizing the effects of tagging on juvenile salmon (reduced tissue trauma and reduced surgery time) researchers can more accurately estimate survival and behavior.
Accounting for Tag Loss and Its Uncertainty in a Mark–Recapture Study with a Mixture of Single and Double Tags
Authors: Hyun Saang‐Yoon , Reynolds Joel H. , Galbreath Peter F. 
Published: December 2011

AbstractUnless accounted for in the estimation, tag loss will cause mark–recapture methods to overestimate the true abundance of a closed population and to underestimate the associated uncertainty. Current methods of accounting for tag loss require all marked individuals to be double‐tagged. We present a new model that fully accounts for tag loss and allows for the use of a mixture of single‐ and double‐tagged individuals, thus simplifying implementation in the field. Treating abundance, tag loss rate, and capture probabilities as free parameters, we estimated those parameters and their uncertainty by using maximum likelihood. Whereas existing methods assume that a double‐tagged animal does not lose both tags, the new model allows the animal to lose both tags. The new model's performance was assessed and compared with that of other estimators (modified Petersen and Seber–Felton) via simulation. As expected, estimates from the new model were less biased and more precise than estimates from the other models. The model was used to estimate the abundance of the kokanee Oncorhynchus nerka population in the Metolius River, Oregon, during 2007. Abundance was estimated at 102,970 fish (), tag loss rate was estimated at 0.27 (), the capture probability for the first sample (tagging) was 0.03 (), and the capture probability for the second sample (recovery) was 0.11 (). The new model uses all of the information from single‐ and double‐tag data, provides unbiased abundance estimates in the presence of tag loss for a closed population, and has less‐stringent field requirements that make it easier to employ than other methods.
𝐾-theory of cones of smooth varieties
Authors: Cortiñas G. , Haesemeyer C. , Walker M. , Weibel C. 
Published: December 2011

Let

R
R

be the homogeneous coordinate ring of a smooth projective variety

X
X

over a field

k
k

of characteristic 0. We calculate the

K
K

-theory of

R
R

in terms of the geometry of the projective embedding of

X
X

. In particular, if

X
X

is a curve, then we calculate

K
0

(
R
)

K_0(R)

and

K
1

(
R
)

K_1(R)

, and prove that

K

−
1

(
R
)
=
⨁

H
1

(
C
,

O

(
n
)
)

K_{-1}(R)=\bigoplus H^1(C,\mathcal {O}(n))

. The formula for

K
0

(
R
)

K_0(R)

involves the Zariski cohomology of twisted Kähler differentials on the variety.
Bilateral alterations in somatosensory cortical processing in hemiplegic cerebral palsy
Authors: NEVALAINEN PÄIVI , PIHKO ELINA , MÄENPÄÄ HELENA , VALANNE LEENA , NUMMENMAA LAURI , LAURONEN LEENA 
Published: December 2011

Aim  In individuals with cerebral palsy (CP), cerebral insults during early development may induce profound reorganization of the motor representation. This study determined the extent of alterations in cortical somatosensory functions in adolescents with hemiplegic CP with subcortical brain lesions.Method  We recorded somatosensory evoked magnetic fields in response to hand area stimulation from eight adolescents with hemiplegic CP (five females and three males; mean age 14y 6mo, SD 2y 3mo) and eight age‐ and sex‐matched healthy comparison adolescents (mean age 15y 4mo, SD 2y 4mo). All participants in the CP group had purely subcortical brain lesions in magnetic resonance images.Results  The somatosensory representation of the affected limb was contralateral (i.e. ipsilesional), but detailed inspection of the evoked responses showed alterations bilaterally. In the primary somatosensory cortex, the representation areas of digits II and V were in both hemispheres closer to each other in participants with CP than in comparison participants [ANOVA main effect group F1,14=5.58; p=0.03]. In addition, the morphology of median nerve evoked fields was altered in the participants with CP.Interpretation  In hemiplegic CP, modification of the somatosensory cortical network extends beyond what would be expected based on the unilateral symptoms and the anatomical lesion. Further understanding of the functional alterations in the sensorimotor networks may aid in developing more precisely designed rehabilitation strategies.
Major depression is associated with cardiac autonomic dysregulation
Authors: Chang Hsin-An , Chang Chuan-Chia , Chen Chih-Lun , Kuo Terry B. J. , Lu Ru-Band , Huang San-Yuan 
Published: December 2011

Chang H-A, Chang C-C, Chen C-L, Kuo TBJ, Lu R-B, Huang S-Y. Major depression is associated with cardiac autonomic dysregulation.Objective: Altered cardiac autonomic function has been proposed in patients with major depression (MD), but the results are mixed. Therefore, analyses with larger sample sizes and better methodology are needed.Methods: To examine whether cardiac autonomic dysfunction is associated with MD, 498 unmedicated patients with MD and 462 healthy volunteers, aged 18–65 years, were recruited for a case-control analysis. We used the Hamilton Depression Rating Scale (HAM-D) and the Beck Depression Inventory (BDI) to assess depression severity. Cardiac autonomic function was evaluated by measuring heart rate variability (HRV) parameters. Frequency-domain indices of HRV were obtained.Results: Patients with MD exhibited reduced cardiac vagal control compared to healthy volunteers, and depression severity was negatively correlated with cardiac vagal control. Stratified analyses by suicide ideation revealed more pronounced cardiac vagal withdrawal among MD patients with suicide ideation.Conclusion: This study shows that MD is associated with cardiac autonomic dysregulation, highlighting the importance of assessing HRV in currently depressed patients, given the higher risk for cardiac complications in these individuals. Taking into account that suicidal depressed patients had more adverse patterns of HRV, one might consider the treatment to restore the autonomic function for the patient population having increased susceptibility to autonomic dysregulation.
Reverse‐mode NCX current in mouse airway smooth muscle: Na+ and voltage dependence, contributions to Ca2+ influx and contraction, and altered expression in a model of allergen‐induced hyperresponsiveness
Authors: Rahman M. , Inman M. , Kiss L. , Janssen L. J. 
Published: December 2011

AbstractAim:We examined the electrophysiological properties of reverse‐mode Na+/Ca2+ exchange (NCX) in mouse airway smooth muscle (ASM), assessing its contributions to regulation of [Ca2+], and its expression in acute and chronic airway hyperresponsiveness (AHR).Methods:Membrane currents were studied in single murine ASM cells under voltage clamp at −60 mV using ramp depolarizing commands to +80 mV. Confocal fluorimetric and RT‐PCR techniques were used to monitor changes in cytosolic [Ca2+] and NCX expression, respectively.Results:With standard KCl‐containing electrode, 30 μm KB‐R7943 (an inhibitor of reverse‐mode NCX activity) exhibited variable effects on membrane current, indicating modulation of more than one conductance. KB‐R7943 activated outwardly rectifying current that was inhibited by 100 μm iberiotoxin (blocker of large‐conductance Ca2+‐dependent K+ channels), indicating a direct enhancing effect of KB‐R7943 on those K+ channels. After obviating K+ currents, we found that a current sensitive to 4‐4’‐diisothiocyanostilbene‐2,2’‐disulfonic acid (blocker of Ca2+‐dependent Cl‐ channels) was markedly increased by elevating [Na+] in the electrode solution to 13, 15.5 and 18 mm and suppressed by KB‐R7943, indicating Ca2+ influx via reverse‐mode NCX activity. With conditions preventing Ca2+ influx through voltage‐dependent Ca2+ channels but promoting that through NCX, we found that introduction of Ca2+ led to marked but transient KB‐R7943‐sensitive elevation of [Ca2+]. Additionally, KB‐R7943 suppressed cholinergically evoked Ca2+ waves. Finally, NCX1 expression was not significantly changed in allergen‐induced AHR acute model but increased approx. 2.5‐fold in a chronic model.Conclusion:Reverse‐mode NCX activity leads to a physiologically relevant increase in [Ca2+] even under control conditions, and this may be exaggerated in allergen‐induced AHR and asthma.
Enantiornithine Birds in China
Authors: Xia WANG , Zihui ZHANG 
Published: December 2011

Abstract:A brief introduction to the morphology, flight, size, habits, diet, feathers and systematic paleontology of fossil enantiornithine birds known from the Mesozoic of China is provided. Enantiornithine birds were the dominant land birds of the Mesozoic (245–65 Myr). Although they show great morphological differences from modern birds, their diversification in many respects mimics that of the modern land bird radiation and the reasons for their extinction at the end‐Cretaceous remain a mystery.
Changes of Late Mesozoic Tectonic Regimes around the Ordos Basin (North China) and their Geodynamic Implications
Authors: Yueqiao ZHANG , Wei SHI , Shuwen DONG 
Published: December 2011

Abstract:A synthesis is given in this paper on late Mesozoic deformation pattern in the zones around the Ordos Basin based on lithostratigraphic and structural analyses. A relative chronology of the late Mesozoic tectonic stress evolution was established from the field analyses of fault kinematics and constrained by stratigraphic contact relationships. The results show alternation of tectonic compressional and extensional regimes. The Ordos Basin and its surroundings were in weak N‐S to NNE‐SSW extension during the Early to Middle Jurassic, which reactivated E‐W‐trending basement fractures. The tectonic regime changed to a multi‐directional compressional one during the Late Jurassic, which resulted in crustal shortening deformation along the marginal zones of the Ordos Basin. Then it changed to an extensional one during the Early Cretaceous, which rifted the western, northwestern and southeastern margins of the Ordos Basin. A NW‐SE compression occurred during the Late Cretaceous and caused the termination of sedimentation and uplift of the Ordos Basin. This phased evolution of the late Mesozoic tectonic stress regimes and associated deformation pattern around the Ordos Basin best records the changes in regional geodynamic settings in East Asia, from the Early to Middle Jurassic post‐orogenic extension following the Triassic collision between the North and South China Blocks, to the Late Jurassic multi‐directional compressions produced by synchronous convergence of the three plates (the Siberian Plate to the north, Paleo‐Pacific Plate to the east and Lhasa Block to the west) towards the East Asian continent. Early Cretaceous extension might be the response to collapse and lithospheric thinning of the North China Craton.
Deformation Stages and Ar‐Ar Age Data of the Wan‐Zhe‐Gan Tectonic Zone, Southeast China, and Their Tectonic Significance
Authors: Xinqi YU , De'en WANG , Dazhi JIANG , Laili JIANG , Xiang ZHOU , Chunlin LI 
Published: December 2011

Abstract:The major tectonic zone that passes through the border regions of the Anhui, Zhejiang, and Jiangxi Provinces in southeast China has been commonly referred to as the Wan‐Zhe‐Gan fault zone. Geologically, this zone consists of several regional fault belts of various ages and orientations. We have categorized the faults into four age groups based on field investigations. The Neoproterozoic faults are northeast striking. They start from the northeast Jiangxi Province and extend northeastward to Fuchuan in Anhui Province, the same location of the northeast Jiangxi‐Fuchuan ophiolite belt. The faults probably acted during the Neoproterozoic as a boundary fault zone of a plate or a block suture with mélange along the faults. The nearly east‐west‐ or east‐northeast‐striking faults are of Silurian ages (40Ar/39Ar age 429 Ma). This group includes the Qimen‐Shexian fault and the Jiangwang‐Jiekou ductile shear belt. They represent a major tectonic boundary in the basement because the two sides of the fault have clear dissimilarities. The third group of faults is north‐northeast striking, having formed since the early‐middle Triassic with 40Ar/39Ar ages of 230–254 Ma. They form a fault belt starting from Yiyang in northern Jiangxi and connect with the Wucheng as well as the Ningguo‐Jixi faults. This fault belt is a key fault‐magmatic belt controlling the formation of Jurassic‐Cretaceous red basins, ore distribution, magmatic activity, and mineralization. When it reactivated during the late Cretaceous, the belt behaved as a series of reverse faults from southeast to northwest and composed the fourth fault group. Therefore, classifying the Wan‐Zhe‐Gan fault zone into four fault groups will help in the analysis of the tectonic evolution of the eastern segment of the Jiangnan orogen since the Neoproterozoic era.