bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Fast-Evolvingphy-2Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa
Authors: Wang Zheng , Li Ning , Li Jigang , Dunlap Jay C. , Trail Frances , Townsend Jeffrey P. 
Published: March 2016

ABSTRACTRapid responses to changes in incident light are critical to the guidance of behavior and development in most species. Phytochrome light receptors in particular play key roles in bacterial physiology and plant development, but their functions and regulation are less well understood in fungi. Nevertheless, genome-wide expression measurements provide key information that can guide experiments that reveal how genes respond to environmental signals and clarify their role in development. We performed functional genomic and phenotypic analyses of the two phytochromes inNeurospora crassa, a fungal model adapted to a postfire environment that experiences dramatically variable light conditions. Expression ofphy-1andphy-2was low in early sexual development and in the case ofphy-2increased in late sexual development. Under light stimulation, strains with the phytochromes deleted exhibited increased expression of sexual development-related genes. Moreover, under red light, thephy-2knockout strain commenced sexual development early. In the evolution of phytochromes within ascomycetes, at least two duplications have occurred, and the faster-evolvingphy-2gene has frequently been lost. Additionally, the three key cysteine sites that are critical for bacterial and plant phytochrome function are not conserved within fungalphy-2homologs. Through the action of phytochromes, transitions between asexual and sexual reproduction are modulated by light level and light quality, presumably as an adaptation for fast asexual growth and initiation of sexual reproduction ofN. crassain exposed postfire ecosystems.IMPORTANCEEnvironmental signals, including light, play critical roles in regulating fungal growth and pathogenicity, and balance of asexual and sexual reproduction is critical in fungal pathogens’ incidence, virulence, and distribution. Red light sensing by phytochromes is well known to play critical roles in bacterial physiology and plant development. Homologs of phytochromes were first discovered in the fungal modelNeurospora crassaand then subsequently in diverse other fungi, including many plant pathogens. Our study investigated the evolution of red light sensors in ascomycetes and confirmed—using the model fungusNeurospora crassa—their roles in modulating the asexual-sexual reproduction balance in fungi. Our findings also provide a key insight into one of the most poorly understood aspects of fungal biology, suggesting that further study of the function of phytochromes in fungi is critical to reveal the genetic basis of the asexual-sexual switch responsible for fungal growth and distribution, including diverse and destructive plant pathogens.
Effect of vitamin D replacement on maternal and neonatal outcomes: a randomised controlled trial in pregnant women with hypovitaminosis D. A protocol
Authors: Chakhtoura M , Nassar A , Arabi A , Cooper C , Harvey N , Mahfoud Z , Nabulsi M , El-Hajj Fuleihan G 
Published: March 2016

IntroductionThe vitamin D recommended doses during pregnancy differ between societies. The WHO guidelines do not recommend routine prenatal supplementation, but they underscore the fact that women with the lowest levels may benefit most. The effects of routine supplementation during pregnancy on maternal and neonatal clinical outcomes have not been investigated in the Middle East, where hypovitaminosis D is prevalent. Our hypothesis is that in Middle Eastern pregnant women, a vitamin D dose of 3000 IU/day is required to reach a desirable maternal 25-hydroxyvitamin D [25(OH)D] level, and to positively impact infant bone mineral content (BMC).Methods and analysisThis is a multicentre blinded randomised controlled trial. Pregnant women presenting to the Obstetrics and Gynaecology clinics will be approached. Eligible women will be randomised to daily equivalent doses of cholecalciferol, 600 IU or 3000 IU, from 15 to 18 weeks gestation until delivery. Maternal 25(OH)D and chemistries will be assessed at study entry, during the third trimester and at delivery. Neonatal anthropometric variables and 25(OH)D level will be measured at birth, and bone and fat mass assessment by dual-energy X-ray absorptiometry scan at 1 month. A sample size of 280 pregnant women is needed to demonstrate a statistically significant difference in the proportion of women reaching a 25(OH)D level ≥50 nmol/L at delivery, and a difference in infant BMC of 6 (10)g, for a 90% power and a 2.5% level of significance. The proportions of women achieving a target 25(OH)D level will be compared between the two arms, using χ2. An independent t test will be used to compare mean infant BMC between the two arms. The primary analysis is an intention-to-treat analysis of unadjusted results.Ethics and disseminationThe protocol has been approved by the Institutional Review Board at the American University of Beirut-Lebanon (IM.GEHF.22). The trial results will be published in peer-reviewed medical journals and presented at scientific conferences.Trial registration numberNCT02434380.
Short-term changes in liver tests predict long-term mortality
Authors: Saffouri Eliana , Lim Eugénie S , Kim Susan W , Hakendorf Paul , Thompson Campbell H 
Published: March 2016

ObjectiveTo determine whether short-term changes in liver tests (bilirubin, albumin, gamma glutamyl transferase, alkaline phosphatase, alanine aminotransferase (ALT) and aspartate aminotransferase) predict 12-month mortality and, if so, which test is most informative.DesignRetrospective review of general medicine inpatients at a tertiary hospital (2005–2012) identified non-elective admissions of minimum 7 days’ duration. Patients with liver disease, malignancy, admission to the intensive care unit or inpatient mortality were excluded. Linear spline modelled the vector of intra-admission change from admission. The association between 12-month mortality and admission and intra-admission changes in liver tests was assessed by logistic regression modelling, adjusted for age, gender, comorbidity index and heart failure.Results12-month mortality was 17% in 4160 patients analysed. 12-month mortality for patients with abnormally low albumin at admission was 5% higher per 1 g/L below 34 g/L (OR 0.95, 95% CI 0.93 to 0.98, p<0.001). Albumin and ALT were the only tests for which an intra-admission change significantly predicted mortality; the predictive effects were additive. 12-month mortality was greater by 4% per 1 g/L intra-admission decrement in albumin (OR 1.04, 95% CI 1.02 to 1.06, p<0.001) and 6% per 100 IU/L intra-admission increment in ALT (OR 1.06, 95% CI 1.02 to 1.1, p=0.005). Intra-admission changes were superior to admission values in predicting mortality.ConclusionsChanges in liver tests predict long-term mortality better than a single value and provide prognostic information more quickly than long-term monitoring. In the absence of known liver disease, albumin predicts long-term mortality better than transaminases. The patient whose albumin decreases in the short term is at high risk of death within 1 year, even from a normal baseline.
Dexmedetomidine versus Magnesium Sulfate as Adjunct during Anesthesia for Laparoscopic Colectomy
Authors: Zarif Pierre , Abdelaal Ahmed Mahmoud Ahmed , Abdelhaq Mohamed Mohamed , Mikhail Hany M. S. , Farag Ahmed 
Published: March 2016

Objectives. To compare dexmedetomidine versus magnesium during laparoscopic colectomy.Patients and Methods. 51 patients were randomly allocated into 3 groups: group C (control) received saline infusion, group D dexmedetomidine 1 g/kg and then 0.4 g/kg/hr, and group M MgSO42 g and then 15 g/kg/min. Intraoperative hemodynamics were measured before and 1 min after intubation (T1 andT2), before and 5 min after peritoneal insufflation (T3 andT4), before and 5 min after 30° Trendelenburg position (T5 andT6), 5 min after resuming flat position (T7), 5 min after peritoneal deflations (T8), after extubation (T9), and at time of admission to PACU (T10). Recovery time and degree of sedation were assessed.Results. HR and MAP were significantly higher inT2,T4, andT6 compared toT1,T3, andT5, respectively, in all groups with lower measurements in groups D and M compared to group C. Mean of collective measurements was significantly higher in group C. Recovery time and sedation score were significantly higher in groups D and M. Time to Aldrete score of ≥9 was significantly longer in groups D and M.Conclusion. Both drugs ameliorate the pressor responses during LC with a nonsignificant difference. This study is registered withPACTR201602001481308.
Homologous Recombination Deficiency (HRD) Score Predicts Response to Platinum-Containing Neoadjuvant Chemotherapy in Patients with Triple-Negative Breast Cancer
Authors: Telli Melinda L. , Timms Kirsten M. , Reid Julia , Hennessy Bryan , Mills Gordon B. , Jensen Kristin C. , Szallasi Zoltan , Barry William T. , Winer Eric P. , Tung Nadine M. , Isakoff Steven J. , Ryan Paula D. , Greene-Colozzi April , Gutin Alexander , Sangale Zaina , Iliev Diana , Neff Chris , Abkevich Victor , Jones Joshua T. , Lanchbury Jerry S. , Hartman Anne-Renee , Garber Judy E. , Ford James M. , Silver Daniel P. , Richardson Andrea L. 
Published: March 2016

AbstractPurpose: BRCA1/2-mutated and some sporadic triple-negative breast cancers (TNBC) have DNA repair defects and are sensitive to DNA-damaging therapeutics. Recently, three independent DNA-based measures of genomic instability were developed on the basis of loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST).Experimental Design: We assessed a combined homologous recombination deficiency (HRD) score, an unweighted sum of LOH, TAI, and LST scores, in three neoadjuvant TNBC trials of platinum-containing therapy. We then tested the association of HR deficiency, defined as HRD score ≥42 or BRCA1/2 mutation, with response to platinum-based therapy.Results: In a trial of neoadjuvant platinum, gemcitabine, and iniparib, HR deficiency predicted residual cancer burden score of 0 or I (RCB 0/I) and pathologic complete response (pCR; OR = 4.96, P = 0.0036; OR = 6.52, P = 0.0058). HR deficiency remained a significant predictor of RCB 0/I when adjusted for clinical variables (OR = 5.86, P = 0.012). In two other trials of neoadjuvant cisplatin therapy, HR deficiency predicted RCB 0/I and pCR (OR = 10.18, P = 0.0011; OR = 17.00, P = 0.0066). In a multivariable model of RCB 0/I, HR deficiency retained significance when clinical variables were included (OR = 12.08, P = 0.0017). When restricted to BRCA1/2 nonmutated tumors, response was higher in patients with high HRD scores: RCB 0/I P = 0.062, pCR P = 0.063 in the neoadjuvant platinum, gemcitabine, and iniparib trial; RCB 0/I P = 0.0039, pCR P = 0.018 in the neoadjuvant cisplatin trials.Conclusions: HR deficiency identifies TNBC tumors, including BRCA1/2 nonmutated tumors more likely to respond to platinum-containing therapy. Clin Cancer Res; 22(15); 3764–73. ©2016 AACR.
The Complex Interplay Between Multisensory Integration and Perceptual Awareness
Authors: Deroy O. , Faivre N. , Lunghi C. , Spence C. , Aller M. , Noppeney U. 
Published: March 2016

The integration of information has been considered a hallmark of human consciousness, as it requires information being globally availableviawidespread neural interactions. Yet the complex interdependencies between multisensory integration and perceptual awareness, or consciousness, remain to be defined. While perceptual awareness has traditionally been studied in a single sense, in recent years we have witnessed a surge of interest in the role of multisensory integration in perceptual awareness. Based on a recent IMRF symposium on multisensory awareness, this review discusses three key questions from conceptual, methodological and experimental perspectives: (1) What do we study when we study multisensory awareness? (2) What is the relationship between multisensory integration and perceptual awareness? (3) Which experimental approaches are most promising to characterize multisensory awareness? We hope that this review paper will provoke lively discussions, novel experiments, and conceptual considerations to advance our understanding of the multifaceted interplay between multisensory integration and consciousness.
Narrowing the Agronomic Yield Gaps of Maize by Improved Soil, Cultivar, and Agricultural Management Practices in Different Climate Zones of Northeast China
Authors: Liu Zhijuan , Yang Xiaoguang , Lin Xiaomao , Hubbard Kenneth G. , Lv Shuo , Wang Jing 
Published: March 2016

Abstract
Northeast China (NEC) is one of the major agricultural production areas in China, producing about 30% of China’s total maize output. In the past five decades, maize yields in NEC increased rapidly. However, farmer yields still have potential to be increased. Therefore, it is important to quantify the impacts of agronomic factors, including soil physical properties, cultivar selections, and management practices on yield gaps of maize under the changing climate in NEC in order to provide reliable recommendations to narrow down the yield gaps. In this study, the Agricultural Production Systems Simulator (APSIM)-Maize model was used to separate the contributions of soil physical properties, cultivar selections, and management practices to maize yield gaps. The results indicate that approximately 5%, 12%, and 18% of potential yield loss of maize is attributable to soil physical properties, cultivar selection, and management practices. Simulation analyses showed that potential ascensions of yield of maize by improving soil physical properties PAYs, changing to cultivar with longer maturity PAYc, and improving management practices PAYm for the entire region were 0.6, 1.5, and 2.2 ton ha−1 or 9%, 23%, and 34% increases, respectively, in NEC. In addition, PAYc and PAYm varied considerably from location to location (0.4 to 2.2 and 0.9 to 4.5 ton ha−1 respectively), which may be associated with the spatial variation of growing season temperature and precipitation among climate zones in NEC. Therefore, changing to cultivars with longer growing season requirement and improving management practices are the top strategies for improving yield of maize in NEC, especially for the north and west areas.
Meridional Rossby Wave Generation and Propagation in the Maintenance of the Wintertime Tropospheric Double Jet
Authors: O’Rourke Amanda K. , Vallis Geoffrey K. 
Published: March 2016

Abstract
The eddy-driven and subtropical jets are two dynamically distinct features of the midlatitude upper-troposphere circulation that are often merged into a single zonal wind maximum. Nonetheless, the potential for a distinct double-jet state in the atmosphere exists, particularly in the winter hemisphere, and presents a unique zonal-mean flow with two waveguides and an interjet region with a weakened potential vorticity gradient upon which Rossby waves may be generated, propagate, reflect, and break.
The authors investigate the interaction of two groups of atmospheric waves—those with wavelengths longer and shorter than the deformation radius—within a double-jet mean flow in an idealized atmospheric model. Patterns of eddy momentum flux convergence for long and short waves differ greatly. Short waves behave following classic baroclinic instability theory such that their eddy momentum flux convergence is centered at the eddy-driven jet core. Long waves, on the other hand, reveal strong eddy momentum flux convergence along the poleward flank of the eddy-driven jet and within the interjet region. This pattern is enhanced when two jets are present in the zonal-mean zonal wind.
Is Anterior Cruciate Ligament Reconstruction Effective in Preventing Secondary Meniscal Tears and Osteoarthritis?
Authors: Sanders Thomas L. , Kremers Hilal Maradit , Bryan Andrew J. , Fruth Kristin M. , Larson Dirk R. , Pareek Ayoosh , Levy Bruce A. , Stuart Michael J. , Dahm Diane L. , Krych Aaron J. 
Published: March 2016

Background: Reconstruction of anterior cruciate ligament (ACL) tears may potentially prevent the development of secondary meniscal injuries and arthritis. Purpose/Hypothesis: The purpose of this study was to (1) evaluate the protective benefit of ACL reconstruction (ACLR) in preventing subsequent meniscal tears or arthritis, (2) determine if earlier ACLR (<1 year after injury) offers greater protective benefits than delayed reconstruction (≥1 year after injury), and (3) evaluate factors predictive of long-term sequelae after ACLR. The hypothesis was that the incidence of secondary meniscal tears, arthritis, and total knee arthroplasty (TKA) would be higher in patients treated nonoperatively after ACL tears than patients treated with surgical reconstruction. Study Design: Cohort study; Level of evidence, 3. Methods: This retrospective study included a population-based incidence cohort of 964 patients with new-onset, isolated ACL tears between 1990 and 2000 as well as an age- and sex-matched cohort of 964 patients without ACL tears. A chart review was performed to collect information related to the initial injury, treatment, and outcomes. A total of 509 patients were treated with early ACLR, 91 with delayed ACLR, and 364 nonoperatively. All patients were retrospectively followed (range, 2 months to 25 years) to determine the development of subsequent meniscal tears, arthritis, or TKA. Results: At a mean follow-up of 13.7 years, patients treated nonoperatively after ACL tears had a significantly higher likelihood of developing a secondary meniscal tear (hazard ratio [HR], 5.4; 95% CI, 3.8-7.6), being diagnosed with arthritis (HR, 6.0; 95% CI, 4.3-8.4), and undergoing TKA (HR, 16.7; 95% CI, 5.0-55.2) compared with patients treated with ACLR. Similarly, patients treated with delayed ACLR had a higher likelihood of developing a secondary meniscal tear (HR, 3.9; 95% CI, 2.2-6.9) and being diagnosed with arthritis (HR, 6.2; 95% CI, 3.4-11.4) compared with patients treated with early ACLR. Age >21 years at the time of injury, articular cartilage damage, and medial/lateral meniscal tears were predictive of arthritis after ACLR. Conclusion: Patients treated with ACLR have a significantly lower risk of secondary meniscal tears, symptomatic arthritis, and TKA when compared with patients treated nonoperatively after ACL tears. Similarly, early ACLR significantly reduces the risk of subsequent meniscal tears and arthritis compared with delayed ACLR.
Laparoscopic Wide Mesocolic Excision and Central Vascular Ligation for Carcinoma of the Colon
Authors: Ehrlich A. , Kairaluoma M. , Böhm J. , Vasala K. , Kautiainen H. , Kellokumpu I. 
Published: March 2016

Background and Aims: The principle of complete mesocolic excision for colon cancer has been introduced to improve oncologic outcome. However, this approach is scantily discussed for laparoscopic surgery and there is a lack of randomized trials. This study examined oncologic and clinical outcome after laparoscopic wide mesocolic excision and central vascular ligation for colon cancer. Material and Methods: This is a review of prospectively gathered data from a single-institution colorectal cancer database. This study was conducted in the Central Hospital of Central Finland. From January 2003 to December 2011, 222 patients underwent laparoscopic colonic resections with wide mesocolic excision and central vascular ligation in the multimodal setting. The main measures of outcome were cancer recurrence and survival, with early recovery, 30d-mortality and morbidity, reoperation, readmission, and late complications as secondary outcomes. Results: The median follow-up was 5.5 (interquartile range (IQR) = 3.7–8.0) years. The 5-year overall survival for all 222 patients was 80.2% and disease-specific survival was 87.5%, and for those 210 R0-patients with stage I–III disease, 83.9% and 91.3%, respectively. The 5-year disease-free survival was 85.8%: stage I was 94.7%, stage II was 90.8%, and stage III was 75.6% ( p = 0.004). Increasing lymph node ratio significantly decreased the 5-year disease-free survival. Conversion rate to open surgery was 12.2%. Thirty-day mortality was 1.3% and morbidity, 19.7%. Median postoperative hospital stay was 5 (IQR = 3–7) days. Conclusion: Laparoscopic wide mesocolic excision and central vascular ligation for colon cancer resulted in good long-term oncologic outcome. Randomized trials are needed to show that laparoscopic complete mesocolic excision technique would become the standard of care for the carcinoma of the colon.
Regulation of transient receptor potential vanilloid 1 expression in trigeminal ganglion neurons via methyl-CpG binding protein 2 signaling contributes tongue heat sensitivity and inflammatory hyperalgesia in mice
Authors: Suzuki Azumi , Shinoda Masamichi , Honda Kuniya , Shirakawa Tetsuro , Iwata Koichi 
Published: March 2016

Background Pain hypoalgesia has been reported in Rett syndrome patients, a severe neurodevelopmental disorder which can be attributed to mutations in the methyl-CpG binding protein 2 (MeCP2). Here, we examined the role of MeCP2 signaling in tongue heat sensitivity in the normal and inflamed state using Mecp2 heterozygous (Mecp2+/−) mice. Results Heat hypoalgesia of the tongue occurred in Mecp2+/− mice and submucosal injection of complete Freund’s adjuvant into the tongue produced a long-lasting heat hyperalgesia at the inflamed site in wild-type mice but not in Mecp2+/− mice. Transient receptor potential vanilloid 1 was expressed in a large number of MeCP2-immunoreactive trigeminal ganglion neurons innervating the tongue in both wild-type and Mecp2+/− mice (70.9% in wild type; 72.1% in Mecp2+/−). The number of transient receptor potential vanilloid 1-immunoreactive trigeminal ganglion neurons innervating the tongue was smaller in Mecp2+/− mice relative to wild-type mice (30.5% in wild type; 20.2% in Mecp2+/−). Following complete Freund’s adjuvant injection, the number of transient receptor potential vanilloid 1- and MeCP2-immunoreactive trigeminal ganglion neurons innervating the tongue, as well as MeCP2 protein expression in trigeminal ganglion, was significantly increased in wild-type mice but not in Mecp2+/− mice. Additionally, tongue heat hyperalgesia following complete Freund’s adjuvant injection was completely suppressed by the administration of SB366791, a transient receptor potential vanilloid 1 antagonist, in the tongue. Conclusions These findings indicate that tongue heat sensitivity and hypersensitivity are dependent on the expression of transient receptor potential vanilloid 1 which is regulated via MeCP2 signaling in trigeminal ganglion neurons innervating the tongue.
Consequential considerations when mapping tRNA fragments
Authors: Telonis Aristeidis G. , Loher Phillipe , Kirino Yohei , Rigoutsos Isidore 
Published: March 2016

AbstractWe examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of currently available knowledge, and discuss their potential impact on the output that the tool generates.
Best approximation and variational inequality problems involving a simulation function
Authors: Tchier Fairouz , Vetro Calogero , Vetro Francesca 
Published: March 2016

AbstractWe prove the existence of a g-best proximity point for a pair of mappings, by using suitable hypotheses on a metric space. Moreover, we establish some convergence results for a variational inequality problem, by using the variational characterization of metric projections in a real Hilbert space. Our results are applicable to classical problems of optimization theory.