bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germinants and Their Receptors in Clostridia
Authors: Bhattacharjee Disha , McAllister Kathleen N. , Sorg Joseph A. 
Published: July 2016

ABSTRACTMany anaerobic spore-forming clostridial species are pathogenic, and some are industrially useful. Although many are strict anaerobes, the bacteria persist under aerobic and growth-limiting conditions as multilayered metabolically dormant spores. For many pathogens, the spore form is what most commonly transmits the organism between hosts. After the spores are introduced into the host, certain proteins (germinant receptors) recognize specific signals (germinants), inducing spores to germinate and subsequently grow into metabolically active cells. Upon germination of the spore into the metabolically active vegetative form, the resulting bacteria can colonize the host and cause disease due to the secretion of toxins from the cell. Spores are resistant to many environmental stressors, which make them challenging to remove from clinical environments. Identifying the conditions and the mechanisms of germination in toxin-producing species could help develop affordable remedies for some infections by inhibiting germination of the spore form. Unrelated to infectious disease, spore formation in species used in the industrial production of chemicals hinders the optimum production of the chemicals due to the depletion of the vegetative cells from the population. Understanding spore germination in acetone-butanol-ethanol-producing species can help boost the production of chemicals, leading to cheaper ethanol-based fuels. Until recently, clostridial spore germination is assumed to be similar to that ofBacillus subtilis. However, recent studies inClostridium difficileshed light on a mechanism of spore germination that has not been observed in any endospore-forming organisms to date. In this review, we focus on the germinants and the receptors recognizing these germinants in various clostridial species.
Determinants of regular smoking onset in South Africa using duration analysis
Authors: Vellios Nicole , van Walbeek Corné 
Published: July 2016

ObjectivesSouth Africa has achieved significant success with its tobacco control policy. Between 1994 and 2012, the real price of cigarettes increased by 229%, while regular smoking prevalence decreased from about 31% to 18.2%.MethodsCigarette prices and socioeconomic variables are used to examine the determinants of regular smoking onset. We apply duration analysis techniques to the National Income Dynamics Study, a nationally representative survey of South Africa.ResultsWe find that an increase in cigarette prices significantly reduces regular smoking initiation among males, but not among females. Regular smoking among parents is positively correlated with smoking initiation among children. Children with more educated parents are less likely to initiate regular smoking than those with less educated parents. Africans initiate later and at lower rates than other race groups.ConclusionsAs the tobacco epidemic is shifting towards low-income and middle-income countries, there is an increasing urgency to perform studies in these countries to influence policy. Higher cigarette excise taxes, which lead to higher retail prices, reduce smoking prevalence by encouraging smokers to quit and by discouraging young people from starting smoking.
Recent cohort effects in suicide in Scotland: a legacy of the 1980s?
Authors: Parkinson Jane , Minton Jon , Lewsey James , Bouttell Janet , McCartney Gerry 
Published: July 2016

BackgroundMortality rates are higher in Scotland relative to England and Wales, even after accounting for deprivation. This ‘excess’ mortality is partly due to higher mortality from alcohol-related and drug-related deaths, violence and suicide (particularly in young adults). This study investigated whether cohort effects from exposure to neoliberal politics from the 1980s might explain the recent trends in suicide in Scotland.MethodsWe analysed suicide deaths data from 1974 to 2013 by sex and deprivation using shaded contour plots and intrinsic estimator regression modelling to identify and quantify relative age, period and cohort effects.ResultsSuicide was most common in young adults (aged around 25–40 years) living in deprived areas, with a younger peak in men. The peak age for suicide fell around 1990, especially for men for whom it dropped quickly from around 50 to 30 years. There was evidence of an increased risk of suicide for the cohort born between 1960 and 1980, especially among men living in the most deprived areas (of around 30%). The cohort at highest risk occurred earlier in the most deprived areas, 1965–1969 compared with 1970–1974.ConclusionsThe risk of suicide increased in Scotland for those born between 1960 and 1980, especially for men living in the most deprived areas, which resulted in a rise in age-standardised rates for suicide among young adults during the 1990s. This is consistent with the hypothesis that exposure to neoliberal politics created a delayed negative health impact.
Targeting KIR Blockade in Multiple Myeloma: Trouble in Checkpoint Paradise?
Authors: Felices Martin , Miller Jeffrey S. 
Published: July 2016

Abstract
Findings within the current issue indicate that treatment with IPH2101 when used as a monotherapy in smoldering multiple myeloma, meant to enhance natural killer (NK) cell function through inhibitory KIR blockade, results in a surprising reduction of NK-cell function mediated through monocyte trogocytosis. The significance of these findings is discussed. Clin Cancer Res; 22(21); 5161–3. ©2016 AACR.
See related article by Carlsten et al., p. 5211
Molecular Mechanisms of Resistance to First- and Second-Generation ALK Inhibitors inALK-Rearranged Lung Cancer
Authors: Gainor Justin F. , Dardaei Leila , Yoda Satoshi , Friboulet Luc , Leshchiner Ignaty , Katayama Ryohei , Dagogo-Jack Ibiayi , Gadgeel Shirish , Schultz Katherine , Singh Manrose , Chin Emily , Parks Melissa , Lee Dana , DiCecca Richard H. , Lockerman Elizabeth , Huynh Tiffany , Logan Jennifer , Ritterhouse Lauren L. , Le Long P. , Muniappan Ashok , Digumarthy Subba , Channick Colleen , Keyes Colleen , Getz Gad , Dias-Santagata Dora , Heist Rebecca S. , Lennerz Jochen , Sequist Lecia V. , Benes Cyril H. , Iafrate A. John , Mino-Kenudson Mari , Engelman Jeffrey A. , Shaw Alice T. 
Published: July 2016

AbstractAdvanced, anaplastic lymphoma kinase (ALK)–positive lung cancer is currently treated with the first-generation ALK inhibitor crizotinib followed by more potent, second-generation ALK inhibitors (e.g., ceritinib and alectinib) upon progression. Second-generation inhibitors are generally effective even in the absence of crizotinib-resistant ALK mutations, likely reflecting incomplete inhibition of ALK by crizotinib in many cases. Herein, we analyzed 103 repeat biopsies from ALK-positive patients progressing on various ALK inhibitors. We find that each ALK inhibitor is associated with a distinct spectrum of ALK resistance mutations and that the frequency of one mutation, ALKG1202R, increases significantly after treatment with second-generation agents. To investigate strategies to overcome resistance to second-generation ALK inhibitors, we examine the activity of the third-generation ALK inhibitor lorlatinib in a series of ceritinib-resistant, patient-derived cell lines, and observe that the presence of ALK resistance mutations is highly predictive for sensitivity to lorlatinib, whereas those cell lines without ALK mutations are resistant.Significance: Secondary ALK mutations are a common resistance mechanism to second-generation ALK inhibitors and predict for sensitivity to the third-generation ALK inhibitor lorlatinib. These findings highlight the importance of repeat biopsies and genotyping following disease progression on targeted therapies, particularly second-generation ALK inhibitors. Cancer Discov; 6(10); 1118–33. ©2016 AACR.See related commentary by Qiao and Lovly, p. 1084.This article is highlighted in the In This Issue feature, p. 1069
Ensemble Prediction of Atmospheric Refractivity Conditions for EM Propagation
Authors: Zhao Qingyun , Haack Tracy , McLay Justin , Reynolds Carolyn 
Published: July 2016

AbstractAn ensemble forecast system has been developed at the Naval Research Laboratory to improve the analyses and forecasts of atmospheric refractivity for electromagnetic (EM) propagation with the intention of accounting for uncertainties in model forecast errors. Algorithms for a matrix of ensemble statistics have been developed to analyze the probability, location, intensity, and structure of ducting of various types. Major parameters of ducting layers and their ensemble statistics are calculated from the ensemble forecasts. Their relationships to the large-scale and mesoscale environment are also investigated. The Wallops Island field experiment from late April to early May 2000 is selected to evaluate the system. During the spring season, this coastal region maintains a strong sea surface temperature gradient between cold shelf waters and the warm Gulf Stream, where the boundaries between land, the coastal water, and the Gulf Stream have a strong influence on marine boundary layer structures and the formation of ducting layers. Sounding profiles during the field experiment are used in the study to further understand the structures of the ducting layers and also to validate the ensemble forecast system. While some advantages of the ensemble system over the deterministic forecast for atmospheric refractivity prediction in the boundary layer are studied and demonstrated in this study, the weaknesses of the current ensemble system are revealed for future improvement of the system.
Airborne Radar Observations of Lake-Effect Snowbands over the New York Finger Lakes
Authors: Bergmaier Philip T. , Geerts Bart 
Published: July 2016

AbstractThe vast majority of lake-effect snow research throughout the years has focused on the North American Great Lakes since they are often associated with strong lake-effect events that produce heavy downstream snowfall. This study investigates a lake-effect snow event that instead occurred over two smaller lakes, the New York Finger Lakes, which are just O(5) km wide and O(50) km long. A pair of well-defined snowbands that formed over Seneca and Cayuga Lakes, the two largest of the Finger Lakes, were sampled from above by a vertically pointing Doppler radar and lidar on board the University of Wyoming King Air (UWKA). With typical widths matching the widths of the lakes, and depths of less than 1000 m, the long-lake-axis-parallel bands were actually quite intense for their size. For example, updrafts of 2–3 m s−1 or greater within the band cores were common, and reflectivity occasionally exceeded 5 dBZ. Airborne dual-Doppler data show that both bands were sometimes accompanied by a well-defined thermally driven secondary circulation. Lidar data reveal that the Cayuga Lake band contained significantly more liquid water than the band over Seneca Lake, which was composed mainly of ice. Dissipating lake-effect ice clouds, carried downstream from Lake Ontario toward Seneca Lake, likely seeded the emerging convection over Seneca Lake, resulting in an accelerated depletion of liquid in the Seneca Lake band via more efficient snow growth.
RETRACTED: Effects of Violent Media on Verbal Task Performance in Gifted and General Cohort Children
Authors: Çetin Yakup , Wai Jonathan , Altay Cengiz , Bushman Brad J. 
Published: July 2016

At the request of the Journal Editor(s) and the Publisher and/or the author(s), the following article has been retracted. Çetin, Y., Wai, J., Altay, C., & Bushman B. J. (2016). Effects of violent media on verbal task performance in gifted and general cohort children. Gifted Child Quarterly, 60(4), 279-287. doi: 10.1177/0016986216660382 Joseph Hilgard, postdoctoral fellow at the Annenberg Public Policy Center at the University of Pennsylvania, contacted the journal with questions regarding the pattern of results and conducted reanalyses of the data that called into question the credibility of the data. Unfortunately, the data collection procedures could not be verified because the author who collected the data (Cengiz Altay) could not be contacted following the attempted coup in Turkey. Therefore, as the integrity of the data could not be confirmed, the journal has determined, and the co-authors have agreed, to retract the study.
The association between varicella (chickenpox) and group A streptococcus infections in historical perspective
Authors: Coleman Stephen 
Published: July 2016

Objectives: The aim of the research is to investigate the historical relationship between varicella and Streptococcus pyogenes infections. In the past few decades, varicella has been identified as a risk factor for invasive group A streptococcus infections. The question is whether this relationship also existed between varicella and scarlet fever in the historical era. Methods: The analysis begins with a search of historical medical reports on the relationship between varicella and scarlet fever epidemics in the late 19th and early 20th century, as well as in more recent empirical studies. Correlations and cross-correlations between varicella and scarlet fever are analyzed using weekly public health case reports from 1924 to 1932 for Boston, Chicago, New York City, and Philadelphia. Regression models are used to estimate the relationship between varicella and scarlet fever after controlling for seasonal forcing. Results: Historical records give limited support for a causal relationship between varicella and scarlet fever but indicate that these diseases often occurred close in time to each other. Likewise, statistical analysis shows that varicella and scarlet fever epidemics are closely aligned with each other, and varicella has a strong relationship with scarlet fever. The relationship is stronger than reported in any previous research on the two diseases. Conclusion: The close correspondence of the two diseases likely depends on multiple factors, including seasonal forcing, a causal relationship, and co-infections. The results raise questions about whether this close relationship might have had a synergistic effect or a role in the evolution of S. pyogenes from the virulent, high incidence epidemics of the 19th century to the relatively benign scarlet fever of the 1950s.
Body movement imitation and early language as predictors of later social communication and language outcomes: A longitudinal study
Authors: Dohmen Andrea , Bishop Dorothy VM , Chiat Shula , Roy Penny 
Published: July 2016

Background and aims Over recent decades much research has focused on detecting predictors of different language trajectories in children with early language delay but there has been very little exploration of social communication trajectories in these children. We report a longitudinal study that investigated the predictive value and clinical significance of elicited body movement imitation and language for later social communication and language outcome in Late Talkers. Methods Participants were 29 German-speaking children who were identified with delayed onset and progression of language at two years and followed up at four years. Novel assessments of posture and gesture imitation were administered at Time 1, together with standardised language measures. All body movement imitation items involved self-other mappings, assumed to rely on sociocognitive capacities. At Time 2, children were assessed on standard language tests, together with parental reports of social communication. Results Early language skills at Time 1 were significantly associated with later language outcome and body movement imitation skills at Time 1 with later social communication outcome. Logistic regression analyses revealed that body movement imitation as well as language at Time 1 added significantly to the prediction of language outcome at Time 2, whereas only body movement imitation made a significant contribution to the prediction of social communication outcome at Time 2. Conclusions and implications Theoretically, results highlight the need to account for the heterogeneity of different language and communication trajectories in children with early language delay and point to the importance of sociocognitive difficulties observed in some of these children. Clinically, this study demonstrated that body movement imitation measures have the potential to improve the identification of pre-schoolers who are at risk of later social communication and language problems.
Five-year survival and durability results of brentuximab vedotin in patients with relapsed or refractory Hodgkin lymphoma
Authors: Chen Robert , Gopal Ajay K. , Smith Scott E. , Ansell Stephen M. , Rosenblatt Joseph D. , Savage Kerry J. , Connors Joseph M. , Engert Andreas , Larsen Emily K. , Huebner Dirk , Fong Abraham , Younes Anas 
Published: July 2016

Key PointsA total of 38% of patients who achieved CR (13 of 34) on brentuximab vedotin have remained in remission for >5 years and may be cured. Nine of the 13 patients (9% of all enrolled patients) have remained in long-term remission without a consolidative allogeneic transplant.
Treatment recommendations from the Eighth International Workshop on Waldenström’s Macroglobulinemia
Authors: Leblond Véronique , Kastritis Efstathios , Advani Ranjana , Ansell Stephen M. , Buske Christian , Castillo Jorge J. , García-Sanz Ramón , Gertz Morie , Kimby Eva , Kyriakou Charalampia , Merlini Giampaolo , Minnema Monique C. , Morel Pierre , Morra Enrica , Rummel Mathias , Wechalekar Ashutosh , Patterson Christopher J. , Treon Steven P. , Dimopoulos Meletios A. 
Published: July 2016

Abstract
Waldenström macroglobulinemia (WM) is a distinct B-cell lymphoproliferative disorder for which clearly defined criteria for the diagnosis, initiation of therapy, and treatment strategy have been proposed as part of the consensus panels of the International Workshop on Waldenström’s Macroglobulinemia (IWWM). At IWWM-8, a task force for treatment recommendations was impanelled to review recently published and ongoing clinical trial data as well as the impact of new mutations (MYD88 and CXCR4) on treatment decisions, indications for B-cell receptor and proteasome inhibitors, and future clinical trial initiatives for WM patients. The panel concluded that therapeutic strategies in WM should be based on individual patient and disease characteristics. Chemoimmunotherapy combinations with rituximab and cyclophosphamide-dexamethasone, bendamustine, or bortezomib-dexamethasone provide durable responses and are still indicated in most patients. Approval of the BTK inhibitor ibrutinib in the United States and Europe represents a novel and effective treatment option for both treatment-naive and relapsing patients. Other B-cell receptor inhibitors, second-generation proteasome inhibitors (eg, carfilzomib), and mammalian target of rapamycin inhibitors are promising and may increase future treatment options. Active enrollment in clinical trials whenever possible was endorsed by the panel for most patients with WM.
Application of a library of near isogenic lines to understand context dependent expression of QTL for grain yield and adaptive traits in bread wheat
Authors: Farré Alba , Sayers Liz , Leverington-Waite Michelle , Goram Richard , Orford Simon , Wingen Luzie , Mumford Cathy , Griffiths Simon 
Published: July 2016

AbstractBackgroundPrevious quantitative trait loci (QTLs) studies using the Avalon × Cadenza doubled haploid (DH) population identified eleven QTLs determining plant height, heading date and grain yield. The objectives of this study were: (i) to provide insight into the effects of these QTLs using reciprocal multiple near isogenic lines (NILs) with each pair of alleles compared in both parental backgrounds (Avalon or Cadenza), (ii) quantifying epistasis by looking at the background effects and (iii) predict favourable allelic combinations to develop superior genotypes adapted to a target environment.ResultsTo this aim, a library of 553 BC2NILs and their recurrent parents were tested over two growing seasons (2012/2013 and 2013/2014). The results obtained in the present study validated the plant height, heading date and grain yield QTLs previously identified. Epistatic interactions were detected for the 6B QTL for plant height and heading date, 3A QTL for heading date and grain yield and 2A QTL for grain yield.ConclusionThe marker assisted backcrossing strategy used provided an efficient method of resolving QTL for key agronomic traits in wheat as Mendelian factors determining possible epistatic interactions. The study shows that these QTLs are amenable to marker assisted selection, fine mapping, future positional cloning, and physiological trait dissection.
DNA Mismatch Repair Deficiency in Rectal Cancer: Benchmarking Its Impact on Prognosis, Neoadjuvant Response Prediction, and Clinical Cancer Genetics
Authors: de Rosa Nicole , Rodriguez-Bigas Miguel A. , Chang George J. , Veerapong Jula , Borras Ester , Krishnan Sunil , Bednarski Brian , Messick Craig A. , Skibber John M. , Feig Barry W. , Lynch Patrick M. , Vilar Eduardo , You Y. Nancy 
Published: July 2016

Purpose DNA mismatch repair deficiency (dMMR) hallmarks consensus molecular subtype 1 of colorectal cancer. It is being routinely tested, but little is known about dMMR rectal cancers. The efficacy of novel treatment strategies cannot be established without benchmarking the outcomes of dMMR rectal cancer with current therapy. We aimed to delineate the impact of dMMR on prognosis, the predicted response to fluoropyrimidine-based neoadjuvant therapy, and implications of germline alterations in the MMR genes in rectal cancer. Methods Between 1992 and 2012, 62 patients with dMMR rectal cancers underwent multimodality therapy. Oncologic treatment and outcomes as well as clinical genetics work-up were examined. Overall and rectal cancer–specific survival were calculated by the Kaplan-Meier method. Results The median age at diagnosis was 41 years. MMR deficiency was most commonly due to alterations in MSH2 (53%) or MSH6 (23%). After a median follow-up of 6.8 years, the 5-year rectal cancer–specific survival was 100% for stage I and II, 85.1% for stage III, and 60.0% for stage IV disease. Fluoropyrimidine-based neoadjuvant chemoradiation was associated with a complete pathologic response rate of 27.6%. The extent of surgical resection was influenced by synchronous colonic disease at presentation, tumor height, clinical stage, and pelvic radiation. An informed decision for a limited resection focusing on proctectomy did not compromise overall survival. Five of the 11 (45.5%) deaths during follow-up were due to extracolorectal malignancies. Conclusion dMMR rectal cancer had excellent prognosis and pathologic response with current multimodality therapy including an individualized surgical treatment plan. Identification of a dMMR rectal cancer should trigger germline testing, followed by lifelong surveillance for both colorectal and extracolorectal malignancies. We herein provide genotype-specific outcome benchmarks for comparison with novel interventions.