bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel screening method for rice allelopathic potential: the inhibitory‐circle method
Authors: Li J Y , Guo X K , Zhang Q , Liu C H , Lin Z H , Yu Z M , Wu H , He H B 
Published: June 2015

SummaryScreening crop accessions for allelopathic activity is of paramount importance for crop allelopathy research. Previous bioassays often did not use a mixed culture of donor and target plants, did not use soil and were not conducted under natural conditions. In this study, we designed an inhibitory‐circle method in which a rice accession (donor plant) and Echinochloa crus‐galli (target plant) were cultured together in paddy soil under natural conditions. First, we determined that the highest allelopathic activity of allelopathic rice accession PI312777 was at the 5‐leaf stage, and the suitable distance of rice seedlings and E. crus‐galli was 12 cm apart. This method was then validated by a field test. A further 40 rice accessions were evaluated for allelopathic activity to E. crus‐galli using this method. Two rice accessions, PI312777 and Taichung Native 1, had highly allelopathic activity to E. crus‐galli (inhibitory rate > 50%), while another accession, Lemont, had non‐allelopathic activity. These experimental results were in accordance with previous studies using direct field experiments. The inhibitory‐circle method integrated three necessary conditions, that is donor and target plants grown together, with soil as the medium and under natural conditions for reliable results. The ‘inhibitory‐circle method’, which combined donor and target plants, soil medium and field conditions, can give reliable results in one step, compared with laboratory screening methods. Also, the ‘inhibitory‐circle method’ gave results in 30‐35 days, thereby substantially reducing the requirements for time, labour and cost.
CLARA: An IT Tool for Detailed Cantilever Design for OCS
Authors: Ramos Rodríguez Joaquín , Garzon Nuñez Jorge , Jorreto Marcos Federico , Collado Carlos , Cara Gilabert Patricia 
Published: June 2015

Highly efficient energy transmission between Overhead Catenary System (OCS) and pantograph is paramount for high speed railway lines. However this is not usually considered relevant for low speed railway lines. But interruptions in mechanical and electrical contact interfaces increase maintenance costs and can lead to EMI problems with its surrounding environment.
In order to avoid this, OCS systems are carefully designed using complex programs for calculation of pantograph/OCS interaction and compared with registered data. This means that it is necessary to invest valuable resources (time and money) to design a proper OCS.
At the end of the day, in order to obtain full benefits of a well designed OCS, both careful calculation and installation of all the elements of the system are a must. If no balance between design, calculation and installation is achieved, the overall procedure can present cost ineffectiveness due to wrong or careless installation.
The first step of a proper OCS installation process is taking into account all the geometrical and mechanical characteristics and restrictions of the system (maximum and minimum span lengths, slopes, cants, etc.) as well as the relative position of masts, portal structures and head spans to the track. The forces applied by the conductors to each mast and cantilever are established bearing all these data into account.
Cantilevers are calculated using these efforts as an input data together with all the geometrical restrictions that the system imposes, thus obtaining their complete geometry and the stresses and strains that they will have to support. These stresses and strains are compared to different standards as well as to rate and calculate masts and foundations. The geometric parameters of the cantilevers are used to prefabricate these elements in order to speed the installation process and to avoid onsite installation errors.
A precise calculation process is needed to assure that the contact wire is in the correct position.
That’s why a proper calculation tool is needed. CLARA, is a tool developed to perform geometrical and mechanical calculations of OCS cantilevers and rate both masts and masts foundations. This tool has been designed in AECOM Madrid Transportation Design Center by the authors. It is an IT tool that performs this calculation in a precise and quick manner, taking into account all the necessary input data and determining output data to the required level of detail as presented in this paper.
This tool provides useful data to design OCS controlling parameters that are of paramount importance for final OCS behavior. Some of these parameters are usually non-controlled due to onsite installation procedures. The authors believe that the use of this tool avoids recalculation, inefficiencies and systematic errors and hence it provides the basis for a more cost efficient design and building process.
The Evolution of Commuter Rail Service in the San Francisco Peninsula
Authors: Tsai N. Tom 
Published: June 2015

Commuting by rail in the San Francisco Peninsula has been a travel option for 150 years. However, only in the past 30 years has commuter rail gained recognition as a mode of public transportation separate and distinct from other intercity railroad services. The development of commuter rail as a mode of public transportation, supported and operated by public entities, was a relative new mode of rail service with new techniques to manage finances, optimize schedules, and market their services. Joint agreements were developed to assign responsibility for costs and liabilities to public entities and set limits on infrastructure usage. The increased responsibility of public entities for commuter rail services has required a public policy permitting subsidy of operations, infrastructure investments, and new governance structures.
This paper traces the evolution of the commuter rail service in the Peninsula between San Francisco and San Jose over the past 150 years and describes the operating practices, agreements, and institutional structures that facilitated its transformation. Ridership and revenue data were compared with other commuter rail operations in the nation. The data also showed that it has responded to the need of this growing community with new technology and practices over the years.
Rail Temperature Approximation and Heat Slow Order Best Practices
Authors: Bruzek Radim , Trosino Michael , Kreisel Leopold , Al-Nazer Leith 
Published: June 2015

The railroad industry uses slow orders, sometimes referred to as speed restrictions, in areas where an elevated rail temperature is expected in order to minimize the risk and consequence of derailment caused by track buckling due to excessive rail temperature. Traditionally, rail temperature has been approximated by adding a constant offset, most often 30°F, to a peak ambient air temperature. When this approximated maximum rail temperature exceeds a given risk threshold, slow orders are usually issued for a predefined period of the day.
This “one size fits all” approach, however, is not effective and suitable in all situations. On very warm days, the difference between rail temperature and ambient air temperature can exceed railroad-employed offsets and remain elevated for extended periods of time. A given temperature offset may be well suited for certain regions and track buckling risk-related rail temperature thresholds but less accurate for others. Almost 160,000 hours of rail temperature measurements collected in 2012 across the eastern United States by two Class I railroads and predicted ambient air temperatures based on the National Weather Service’s National Centers for Environmental Prediction (NCEP) data were analyzed using detection theory in order to establish optimal values of offsets between air and rail temperatures as well as times when slow orders should be in place based on geographical location and the track buckling risk rail temperature threshold. This paper presents the results of the analysis and describes an improved procedure to manage heat-related slow orders based on ambient air temperatures.
ADS-J1 Inhibits Semen-Derived Amyloid Fibril Formation and Blocks Fibril-Mediated Enhancement of HIV-1 Infection
Authors: Xun Tianrong , Li Wenjuan , Chen Jinquan , Yu Fei , Xu Wei , Wang Qian , Yu Ruizhe , Li Xiaojuan , Zhou Xuefeng , Lu Lu , Jiang Shibo , Li Lin , Tan Suiyi , Liu Shuwen 
Published: June 2015

ABSTRACT

Semen-derived enhancer of viral infection (SEVI) is composed of amyloid fibrils that can greatly enhance HIV-1 infectivity. By its cationic property, SEVI promotes viral sexual transmission by facilitating the attachment and internalization of HIV-1 to target cells. Therefore, semen-derived amyloid fibrils are potential targets for microbicide design. ADS-J1 is an anionic HIV-1 entry inhibitor. In this study, we explored an additional function of ADS-J1: inhibition of SEVI fibril formation and blockage of SEVI-mediated enhancement of viral infection. We found that ADS-J1 bound to an amyloidogenic peptide fragment (PAP
248–286
, comprising amino acids 248 to 286 of the enzyme prostatic acid phosphatase), thereby inhibiting peptide assembly into amyloid fibrils. In addition, ADS-J1 binds to mature amyloid fibrils and antagonizes fibril-mediated enhancement of viral infection. Unlike cellulose sulfate, a polyanion that failed in clinical trial to prevent HIV-1 sexual transmission, ADS-J1 shows no ability to facilitate fibril formation. More importantly, the combination of ADS-J1 with several antiretroviral drugs exhibited synergistic effects against HIV-1 infection in semen, with little cytotoxicity to vaginal epithelial cells. Our results suggest that ADS-J1 or a derivative may be incorporated into a combination microbicide for prevention of the sexual transmission of HIV-1.
Insertion Sequence IS
26
Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition
Authors: He Susu , Hickman Alison Burgess , Varani Alessandro M. , Siguier Patricia , Chandler Michael , Dekker John P. , Dyda Fred 
Published: June 2015

ABSTRACT

Carbapenemase-producing
Enterobacteriaceae
(CPE), which are resistant to most or all known antibiotics, constitute a global threat to public health. Transposable elements are often associated with antibiotic resistance determinants, suggesting a role in the emergence of resistance. One insertion sequence, IS
26
, is frequently associated with resistance determinants, but its role remains unclear. We have analyzed the genomic contexts of 70 IS
2
6 copies in several clinical and surveillance CPE isolates from the National Institutes of Health Clinical Center. We used target site duplications and their patterns as guides and found that a large fraction of plasmid reorganizations result from IS
26
replicative transpositions, including replicon fusions, DNA inversions, and deletions. Replicative transposition could also be inferred for transposon Tn
4401
, which harbors the carbapenemase
bla
KPC
gene. Thus, replicative transposition is important in the ongoing reorganization of plasmids carrying multidrug-resistant determinants, an observation that carries substantial clinical and epidemiological implications for understanding how such extreme drug resistance phenotypes evolve.

IMPORTANCE
Although IS
26
is frequently reported to reside in resistance plasmids of clinical isolates, the characteristic hallmark of transposition, target site duplication (TSD), is generally not observed, raising questions about the mode of transposition for IS
26
. The previous observation of cointegrate formation during transposition implies that IS
26
transposes via a replicative mechanism. The other possible outcome of replicative transposition is DNA inversion or deletion, when transposition occurs intramolecularly, and this would also generate a specific TSD pattern that might also serve as supporting evidence for the transposition mechanism. The numerous examples we present here demonstrate that replicative transposition, used by many mobile elements (including IS
26
and Tn
4401
), is prevalent in the plasmids of clinical isolates and results in significant plasmid reorganization. This study also provides a method to trace the evolution of resistance plasmids based on TSD patterns.
Smoking Cessation Interventions in the Cardiology Ward
Authors: Cassar Mark Philip 
Published: June 2015

AbstractHospital admission is a unique opportunity for a smoking cessation attempt; smokers may be more motivated to quit as they are distanced from the usual cues they face associated with nicotine consumption, and the effect of poor lifestyle habits on their health are brought to light. With most hospitals employing smoke-free grounds, patients are further inclined to stop smoking.According to NICE guidance, smoking cessation support should be delivered within 1 working day of admission for inpatients, and NRT products should be recommended and offered to all people who smoke. Despite this, many smokers on the cardiology ward at the John Radcliffe Hospital fail to receive smoking cessation advice, and are unable to benefit from Nicotine Replacement Therapy. This leads to missed opportunities to stop smoking, increased morbidity in patients undergoing cardiovascular procedures, and increased costs for the NHS, with patients who continue smoking being re-admitted with more smoking-related illnesses in the future.
ERG protein expression over time: from diagnostic biopsies to radical prostatectomy specimens in clinically localised prostate cancer
Authors: Berg Kasper Drimer , Brasso Klaus , Thomsen Frederik Birkebæk , Røder M Andreas , Holten-Rossing Henrik , Toft Birgitte Grønkær , Iversen Peter , Vainer Ben 
Published: June 2015

AimsWe evaluated the consistency in ERG protein expression from diagnostic specimens through rebiopsies to radical prostatectomies in patients with clinically localised prostate cancer to investigate the validity of ERG status in biopsies.MethodsERG expression was assessed by immunohistochemistry (IHC) in 625 biopsy sets and 86 radical prostatectomy specimens from 265 patients with prostate cancer managed on active surveillance. For IHC, a rabbit monoclonal primary antibody was used (clone: EPR3864).TMPRSS2-ERGfluorescence in situ hybridisation (FISH) analyses were performed in 74 biopsies using the FISH ZytoLight TriCheck Probe (SPECERG/TMPRSS2). FISH results were correlated with IHC findings.ResultsThe concordance between FISH and IHC was 97.3% and IHC demonstrated a sensitivity and specificity forERGrearrangement of 100% and 95.5%, respectively. Applying IHC, 38.1% of patients were ERG-positive, 53.6% were ERG-negative and 8.3% showed both ERG-positive and negative tumour foci (ERG heterogeneous) at diagnosis. When ERG status was dichotomised (ERG-positive or heterogeneous vs ERG-negative), 95.6%–97.1% of patients did not experience ERG reclassification during the first two rounds of rebiopsies. The concordance in ERG status between biopsies and surgical specimen was 89.5%–94.2% depending on the number of rebiopsies included. Sampling bias was assumed to explain most (81.3%) of the mismatches in ERG status.ConclusionsConsistency in ERG status ranged from 90% to 95% for patients undergoing serial biopsies and radical prostatectomy. This indicates that biopsies can be used reliably to investigate ERG's prognostic and predictive value.
新來港人士的生活滿足感及歸屬感
Authors: 崔 志暉 
Published: June 2015

本研究以抗逆力視野來探討本地新來港人士的生活滿足感及歸屬感等各方面的狀況，並尋找促進新移民正向適應的保護因子及阻礙其發展的危機因子。研究以街頭訪問的方式搜集了1,012位被訪者的資料，當中男性佔35.4%, 女性則有64.3%; 平均年齡為37.7歲。 結果顯示新來港人士比本地出生的居民及非本地出生但居住香港多於七年的居民兩個群組在廣東話的溝通能力、自尊感、社會網絡、社區歸屬感及生活滿足感等5個方面的表現均較差。 結構模式的分析顯示自尊感、社區歸屬感及社會網絡是促進生活滿足感的保護因子； 而溝通能力差是阻礙新移民正向適應的危機因子。 根據研究結果，文中提議一些服務來改善新來港人士的生活滿足感。 This study adopted the resilience perspective to explore the life satisfaction and community attachment of new arrivals in Hong Kong, and to examine the protective factors and risk factors that affecting their well-being. The study used the street interview and the accidental sampling to collect data from 1,012 respondents. The sample comprised 35.4% men and 64.3% women. The mean age of participants was 37.7 years. The results indicated that the new arrivals had lower scores in communication competence, self-esteem, social networks, community attachment and life satisfaction than the local born residents and non-local born residents who have been in Hong Kong for more than 7 years. Moreover, results of the structural equation model confirmed that self-esteem, community attachment and social networks were protective factors of life satisfaction; and poor communication competence was a risk factor that hindered positive adaption. Based on the study results, service recommendation was suggested to improve the life satisfaction and community attachment of the new arrivals.
Correlation between Density of CD8+ T-cell Infiltrate in Microsatellite Unstable Colorectal Cancers and Frameshift Mutations: A Rationale for Personalized Immunotherapy
Authors: Maby Pauline , Tougeron David , Hamieh Mohamad , Mlecnik Bernhard , Kora Hafid , Bindea Gabriela , Angell Helen K. , Fredriksen Tessa , Elie Nicolas , Fauquembergue Emilie , Drouet Aurélie , Leprince Jérôme , Benichou Jacques , Mauillon Jacques , Le Pessot Florence , Sesboüé Richard , Tuech Jean-Jacques , Sabourin Jean-Christophe , Michel Pierre , Frébourg Thierry , Galon Jérôme , Latouche Jean-Baptiste 
Published: June 2015

Abstract
Colorectal cancers with microsatellite instability (MSI) represent 15% of all colorectal cancers, including Lynch syndrome as the most frequent hereditary form of this disease. Notably, MSI colorectal cancers have a higher density of tumor-infiltrating lymphocytes (TIL) than other colorectal cancers. This feature is thought to reflect the accumulation of frameshift mutations in sequences that are repeated within gene coding regions, thereby leading to the synthesis of neoantigens recognized by CD8+ T cells. However, there has yet to be a clear link established between CD8+ TIL density and frameshift mutations in colorectal cancer. In this study, we examined this link in 103 MSI colorectal cancers from two independent cohorts where frameshift mutations in 19 genes were analyzed and CD3+, CD8+, and FOXP3+ TIL densities were quantitated. We found that CD8+ TIL density correlated positively with the total number of frameshift mutations. TIL densities increased when frameshift mutations were present within the ASTE1, HNF1A, or TCF7L2 genes, increasing even further when at least one of these frameshift mutations was present in all tumor cells. Through in vitro assays using engineered antigen-presenting cells, we were able to stimulate peripheral cytotoxic T cells obtained from colorectal cancer patients with peptides derived from frameshift mutations found in their tumors. Taken together, our results highlight the importance of a CD8+ T cell immune response against MSI colorectal cancer–specific neoantigens, establishing a preclinical rationale to target them as a personalized cellular immunotherapy strategy, an especially appealing goal for patients with Lynch syndrome. Cancer Res; 75(17); 3446–55. ©2015 AACR.
Association Between Atrial Fibrillation Symptoms, Quality of Life, and Patient Outcomes
Authors: Freeman James V. , Simon DaJuanicia N. , Go Alan S. , Spertus John , Fonarow Gregg C. , Gersh Bernard J. , Hylek Elaine M. , Kowey Peter R. , Mahaffey Kenneth W. , Thomas Laine E. , Chang Paul , Peterson Eric D. , Piccini Jonathan P. 
Published: June 2015

Background—
Instruments to assess symptom burden and quality of life among patients with atrial fibrillation (AF) have not been well evaluated in community practice or associated with patient outcomes.

Methods and Results—
Using data from 10 087 AF patients in the Outcomes Registry for Better Informed Treatment of AF (ORBIT-AF), symptom severity was evaluated using the European Heart Rhythm Association (EHRA) classification system, and quality of life was assessed using the Atrial Fibrillation Effect on Quality-of-Life (AFEQT) questionnaire. The association between AF-related symptoms, quality of life, and outcomes was assessed using Cox regression. The majority of AF patients (61.8%) were symptomatic (EHRA >2) and 16.5% had severe or disabling symptoms (EHRA 3–4). EHRA symptom class was well correlated with the AFEQT score (Spearman correlation coefficient −0.39). Over 1.8 years of follow-up, AF symptoms were associated with a higher risk of hospitalization (adjusted hazard ratio for EHRA ≥2 versus EHRA 1 1.23, 95% confidence interval, 1.15–1.31) and a borderline higher risk of major bleeding. Lower quality of life was associated with a higher risk of hospitalization (adjusted hazard ratio for lowest quartile of AFEQT versus highest 1.49, 95% confidence interval, 1.2–1.84), but not other major adverse events, including death.

Conclusions—
In a community-based study, most patients with AF were symptomatic and had impaired quality of life. Quality of life measured by the AFEQT correlated closely with symptom severity measured by the EHRA class. AF symptoms and lower quality of life were associated with higher risk of hospitalization but not mortality during follow-up.
Outcomes and Predictors of Perinatal Mortality in Fetuses With Ebstein Anomaly or Tricuspid Valve Dysplasia in the Current Era
Authors: Freud Lindsay R. , Escobar-Diaz Maria C. , Kalish Brian T. , Komarlu Rukmini , Puchalski Michael D. , Jaeggi Edgar T. , Szwast Anita L. , Freire Grace , Levasseur Stéphanie M. , Kavanaugh-McHugh Ann , Michelfelder Erik C. , Moon-Grady Anita J. , Donofrio Mary T. , Howley Lisa W. , Tierney Elif Seda Selamet , Cuneo Bettina F. , Morris Shaine A. , Pruetz Jay D. , van der Velde Mary E. , Kovalchin John P. , Ikemba Catherine M. , Vernon Margaret M. , Samai Cyrus , Satou Gary M. , Gotteiner Nina L. , Phoon Colin K. , Silverman Norman H. , McElhinney Doff B. , Tworetzky Wayne 
Published: June 2015

Background—
Ebstein anomaly and tricuspid valve dysplasia are rare congenital tricuspid valve malformations associated with high perinatal mortality. The literature consists of small, single-center case series spanning several decades. We performed a multicenter study to assess the outcomes and factors associated with mortality after fetal diagnosis in the current era.

Methods and Results—

Fetuses diagnosed with Ebstein anomaly and tricuspid valve dysplasia from 2005 to 2011 were included from 23 centers. The primary outcome was perinatal mortality, defined as fetal demise or death before neonatal discharge. Of 243 fetuses diagnosed at a mean gestational age of 27±6 weeks, there were 11 lost to follow-up (5%), 15 terminations (6%), and 41 demises (17%). In the live-born cohort of 176 live-born patients, 56 (32%) died before discharge, yielding an overall perinatal mortality of 45%. Independent predictors of mortality at the time of diagnosis were gestational age <32 weeks (odds ratio, 8.6; 95% confidence interval, 3.5–21.0;
P
<0.001), tricuspid valve annulus diameter z-score (odds ratio, 1.3; 95% confidence interval, 1.1–1.5;
P
<0.001), pulmonary regurgitation (odds ratio, 2.9; 95% confidence interval, 1.4–6.2;
P
<0.001), and a pericardial effusion (odds ratio, 2.5; 95% confidence interval, 1.1–6.0;
P
=0.04). Nonsurvivors were more likely to have pulmonary regurgitation at any gestational age (61% versus 34%;
P
<0.001), and lower gestational age and weight at birth (35 versus 37 weeks; 2.5 versus 3.0 kg; both
P
<0.001).

Conclusion—
In this large, contemporary series of fetuses with Ebstein anomaly and tricuspid valve dysplasia, perinatal mortality remained high. Fetuses with pulmonary regurgitation, indicating circular shunt physiology, are a high-risk cohort and may benefit from more innovative therapeutic approaches to improve survival.