bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of the Biocontrol and Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens strain UM270
Authors: Hernández-Salmerón Julie E. , Hernández-León Rocio , Orozco-Mosqueda Ma. Del Carmen , Valencia-Cantero Eduardo , Moreno-Hagelsieb Gabriel , Santoyo Gustavo 
Published: January 2016

AbstractThe Pseudomonas fluorescens strain UM270 was isolated form the rhizosphere of wild Medicago spp. A previous work has shown that this pseudomonad isolate was able to produce diverse diffusible and volatile compounds involved in plant protection and growth promotion. Here, we present the draft genome sequence of the rhizobacterium P. fluorescens strain UM270. The sequence covers 6,047,974 bp of a single chromosome, with 62.66 % G + C content and no plasmids. Genome annotations predicted 5,509 genes, 5,396 coding genes, 59 RNA genes and 110 pseudogenes. Genome sequence analysis revealed the presence of genes involved in biological control and plant-growth promoting activities. We anticipate that the P. fluorescens strain UM270 genome will contribute insights about bacterial plant protection and beneficial properties through genomic comparisons among fluorescent pseudomonads.
Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland
Authors: Susanti Dwi , Johnson Eric F. , Lapidus Alla , Han James , Reddy T. B. K. , Pilay Manoj , Ivanova Natalia N. , Markowitz Victor M. , Woyke Tanja , Kyrpides Nikos C. , Mukhopadhyay Biswarup 
Published: January 2016

AbstractThis report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species.
A comparison of burn related injuries following the natural disaster Super Storm Hurricane Sandy to the National Burn Repository of the American Burn Association
Authors: Kalina Michael , Malyutin Grigoriy , Cooper Michael L. 
Published: January 2016

Abstract

Background
Burn related injuries from natural disasters are not well described and natural disasters are not identified as an etiology of burn injury in the National Burn Repository (NBR) of the American Burn Association. The natural disaster Super Storm Hurricane Sandy had devastating effects. Our goal was to detail the burn related injuries following this natural disaster and to compare the data to the NBR.

Methods
This was a retrospective chart review of thirty four patients who sustained burn related injuries following Super Storm Hurricane Sandy (SSHS) and were managed at Staten Island University Hospital Burn Center. Institutional Review Board approval was obtained. Data variables included age, gender, race, past medical history (PMHx), burn type, percentage total body surface area (%TBSA), hospital length of stay (HLOS), and mortality. We compared data from SSHS to the 2003-2013 NBR. Categorical data were summarized using frequency counts, percentages and Clopper-Pearson 95 % confidence interval for proportion. Continuous outcome data were summarized by descriptive statistics. Data analyses performed with SAS® System Version 9.3 (SAS Institute Inc., Cary, NC) and p &lt; 0.05 was significant.

Results
In the SSHS group, average age was 36 + 24 years, range 1-80 years, and 44.1 % were males (15/34, 95 % CI: 27.2 - 62.1). Caucasians comprised 58.8 %, (20/34, 95 % CI: 40.7, 75.4) and 73.5 % had no PMHx (25/34, 95 % CI: 55.6, 87.1). The most common burn type was scald, 55.9 %, (19/34, 95 % CI: 37.9, 72.8) and %TBSA ranged 1 %–47 %, average of 7 % + 12 %. The average HLOS was 13 + 26 days, range of 1–113 days. Mortality was 2.9 % (1/34, 95 % CI: 0.07–15). In comparison, the NBR reported an average age of 32 years and 69 % were males. Caucasians comprised 59.1 %. The most common burn type was flame, 43.2 % and the %TBSA ranged 1 %–9.9 %. HLOS ranged 8.4–10.2 days and mortality was 3.4 %.

Conclusion
We conclude that burn related injuries following a natural disaster differ as compared to those most commonly reported in the NBR.
Integration of controlled-source and radio magnetotellurics, electric resistivity tomography, and reflection seismics to delineate 3D structures of a quick-clay landslide site in southwest of Sweden
Authors: Shan Chunling , Bastani Mehrdad , Malehmir Alireza , Persson Lena , Lundberg Emil 
Published: January 2016

Quick clay, which is the main cause of landslides that occur in the northern countries, liquefies easily, and its presence implies an increased risk of landslide. Geophysical methods have been increasingly used in landslide investigations. Three-dimensional electric resistivity tomography, radio magnetotelluric (RMT), controlled-source RMT (CSRMT), and high-resolution reflection seismic data were acquired at a quick-clay landslide site in the southwest of Sweden. The main objectives were to evaluate the capability of each method in delineating different subsurface geologic structures that controlled a peculiar and hazardous retrogressive-type landslide in the study area. A 3D resistivity model from the inversion of CSRMT data showed the best correlation with the reflection seismic data and borehole information, thanks to the broad frequency range of the data set. It better imaged the resistive crystalline bedrock underlying the marine conductive clays and showed considerable correlations with the 3D reflection seismic data in resolving a coarse-grained layer that was interpreted to act as a conduit directing freshwater into the clays under a confined pressure, leaching their salt and forming quick clays. The 3D CSRMT resistivity model and 3D reflection seismic data showed that the coarse-grained layer has a varying thickness. At some locations, it was too thin to be resolved by the methods used here. Combination of the CSRMT model, reflection seismic data, and the borehole data suggested that a layer with thickness of approximately 5 m and resistivity between [Formula: see text] was potentially quick clay, which probably extended laterally in the entire study area. These observations suggested that future developments should focus on joint inversion of such 3D data sets incorporating sharp boundaries as constraints in the inversion and particularly when quick clays were studied.
ReCAP: Improving the Quality of Radiation Treatment for Patients in Ontario: Increasing Peer Review Activities on a Jurisdictional Level Using a Change Management Approach
Authors: Reddeman Lindsay , Foxcroft Sophie , Gutierrez Eric , Hart Margaret , Lockhart Elizabeth , Mendelsohn Marissa , Ang Michelle , Sharpe Michael , Warde Padraig , Brundage Michael , Reddeman Lindsay , Foxcroft Sophie , Gutierrez Eric , Hart Margaret , Lockhart Elizabeth , Mendelsohn Marissa , Ang Michelle , Sharpe Michael , Warde Padraig , Brundage Michael 
Published: January 2016

QUESTION ASKED: What is the impact of the Cancer Care Ontario (CCO) strategy (designed with guidance from a change management framework) to accelerate the use of peer-review processes in radiation oncology (ie, review of a radiation oncologist’s proposed treatment plan by a second radiation oncologist with or without additional multidisciplinary input) across all of its 14 cancer treatment centers? SUMMARY ANSWER: By following a number of key change management principles for organizational transformation, the proportion of radical-intent radiation therapy courses peer reviewed province-wide increased from 43.5% (April 2013) to 68.0% (March 2015), with some centers reaching over 95%. METHODS: The initiative design was guided by the Kotter eight-step process for organizational transformation, including the creation of a multidisciplinary leadership team, site visits to individual centers, the development of education and implementation processes (done in collaboration with each center), and the creation of new performance metrics for central reporting. Monitoring of these metrics enabled the leadership team to track the percentage of radiation therapy courses peer reviewed and the timing of peer review (before 25% treatment visits complete, after 25% treatment visits complete). Performance targets for the quality measures were arrived at by consensus that included engagement of all center radiation treatment program leaders. BIAS, CONFOUNDING FACTOR(S), DRAWBACKS: Peer review has been shown to increase quality of care. However, it requires that resources be invested, including the time and effort of radiation oncologists, and the programmatic work required to organize, execute, and document peer-review activities. There is currently no way of confirming the quality of peer-review activities. REAL-LIFE IMPLICATIONS: A change management framework can be useful for planning and achieving substantial increases in peer-review activities on a jurisdictional basis. Ongoing work will capitalize on facilitators of peer review and on addressing barriers to its application that were identified as part of the initiative. Guidance for peer-review activities specific to common clinical cases is required and is under development. The principles of peer review could be extended to other oncological disciplines with the goal of improving individual patient care and overall program quality. [Figure: see text]
ReCAP: The ASCO Oncology Composite Provider Utilization File: New Data, New Insights
Authors: Barr Thomas R. , Towle Elaine L. , Barr Thomas R. , Towle Elaine L. 
Published: January 2016

QUESTION ASKED: What can we learn regarding oncology practice economics from the Centers for Medicare & Medicaid Services public use files and other publicly available datasets? SUMMARY ANSWER: By combining and analyzing publicly available datasets, we are able to provide information on the distribution of supply of and demand for oncology services as well as present a clear picture of the financial risks associated with the provision of drug therapies to patients with cancer. METHODS: We combined publicly available datasets into what we call the ASCO Provider Utilization File and used it to calculate the average work performed per physician, observe regional differences in work production, and quantify the downside risk and upside potential associated with the provision of chemotherapy drugs. BIAS, CONFOUNDING FACTOR(S), DRAWBACKS: These data are limited to services provided only to Medicare fee-for-service beneficiaries and are derived from billing data submitted by noninstitutional providers only. Because Medicare data captures only approximately one half of all services provided to patients with cancer, conclusions may reflect age and reimbursement bias. REAL-LIFE IMPLICATIONS: Our analysis demonstrates significant downside financial risk associated with the provision of drug therapy to Medicare beneficiaries. This is of particular concern as it reveals the fragile nature of the complex chemotherapy delivery system that efficiently provides the right drug to the right patient at the right time. The interruption of this system in the absence of an equally effective supply chain would be extremely disruptive. [Table: see text]
Low Oxygen Tension Modulates the Insulin-Like Growth Factor-1 or -2 Signaling via Both Insulin-Like Growth Factor-1 Receptor and Insulin Receptor to Maintain Stem Cell Identity in Placental Mesenchymal Stem Cells
Authors: Youssef Amer , Han Victor K. M. 
Published: January 2016

AbstractPlacental mesenchymal stem cells (PMSCs) are readily available multipotent stem cells for potential use in regenerative therapies. For this purpose, PMSCs must be maintained in culture conditions that mimic the in vivo microenvironment. IGFs (IGF-1 and IGF-2) and oxygen tension are low in the placenta in early gestation and increase as pregnancy progresses. IGFs bind to two receptor tyrosine kinases, the IGF-1 receptor (IGF-1R) and the insulin receptor (IR), and their hybrid receptors. We hypothesized that IGF-1 and IGF-2 signal via distinct signaling pathways under low-oxygen tension to maintain PMSC multipotency. In preterm PMSCs, low-oxygen tension increased the expression of IGF-2 and reduced IGF-1. IGF-1 stimulated higher phosphorylation of IGF-1Rβ, ERK1/2, and AKT, which was maintained at steady lower levels by low oxygen tension. PMSC proliferation was increased by IGF-1 more than IGF-2,and was potentiated by low-oxygen tension. This IGF/low oxygen tension-mediated proliferation was receptor dependent because neutralization of the IGF-1R inhibited PMSC proliferation in the presence of IGF-1 and the IR in presence of IGF-2. These findings suggest that both IGF-1R and the IR can participate in mediating IGF signaling in maintaining PMSCs multipotency. We conclude that low-oxygen tension can modify the IGF-1 or IGF-2 signaling via the IGF-1R and IR in PMSCs.
PROX1 Promotes Secretory Granule Formation in Medullary Thyroid Cancer Cells
Authors: Ishii Jun , Yazawa Takuya , Chiba Tomohiro , Shishido-Hara Yukiko , Arimasu Yuu , Sato Hanako , Kamma Hiroshi 
Published: January 2016

AbstractMechanisms of endocrine secretory granule (SG) formation in thyroid C cells and medullary thyroid cancer (MTC) cells have not been fully elucidated. Here we directly demonstrated that PROX1, a developmental homeobox gene, is transcriptionally involved in SG formation in MTC, which is derived from C cells. Analyses using gene expression databases on web sites revealed that, among thyroid cancer cells, MTC cells specifically and highly express PROX1 as well as several SG-forming molecule genes. Immunohistochemical analyses showed that in vivo MTC and C cells expressed PROX1, although follicular thyroid cancer and papillary thyroid cancer cells, normal follicular cells did not. Knockdown of PROX1 in an MTC cells reduced SGs detected by electron microscopy, and decreased expression of SG-related genes (chromogranin A, chromogranin B, secretogranin II, secretogranin III, synaptophysin, and carboxypeptidase E). Conversely, the introduction of a PROX1 transgene into a papillary thyroid cancer and anaplastic thyroid cancer cells induced the expression of SG-related genes. Reporter assays using the promoter sequence of chromogranin A showed that PROX1 activates the chromogranin A gene in addition to the known regulatory mechanisms, which are mediated via the cAMP response element binding protein and the repressor element 1-silencing transcription factor. Furthermore, chromatin immunoprecipitation-PCR assays demonstrated that PROX1 binds to the transcriptional regulatory element of the chromogranin A gene. In conclusion, PROX1 is an important regulator of endocrine SG formation in MTC cells.
PTSD prevalence among Polish World War II survivors
Authors: Lis-Turlejska Maja , Łuszczyńska Aleksandra , Szumiał Szymon 
Published: January 2016

CelOd kilkunastu lat w różnych krajach Europy prowadzone są badania nad rozpowszechnieniem PTSD wśród osób, przed wszystkim cywilnych, które przeżyły II wojnę światową. Wskaźniki rozpowszechnienia tego zaburzenia wynoszą od 1,9% do 10,8 %. Celem badania był pomiar częstości występowania PTSD wśród polskich ocalałych z II wojny światowej.MetodaPrzebadano 96 osób: 59 kobiet i 37 mężczyzn w wieku 70-96 lat (M=80,94; SD=6,56), urodzonych przed 1945 rokiem. Narzędzia pomiaru (polskie adaptacje): Posttraumatic Diagnostic Scale (PDS), Impact of Event Scale (IES), Beck’s Depression Inventory (BDI) oraz Kwestionariusz odnoszący się do traumatycznych zdarzeń związanych z II wojną światową.WynikiWskaźnik rozpowszechnienia potencjalnego PTSD 32,3% . Zależność pomiędzy doświadczeniem traumy wojennej, a nasileniem objawów PTSD uzasadniającym postawienie diagnozy była istotna statystycznie.WnioskiW porównaniu z danymi z badań związanego w wojną PTSD w innych krajach, uzyskany wskaźnik rozpowszechnienia PTSD jest bardzo wysoki. Poszukiwanie odpowiedzi na pytanie o przyczyny tego stanu rzeczy stanowi istotne wyzwanie.
Comparing treatment programmes for anorexia
Authors: Cotter Lisa J , Lacey Hubert J , Morgan John F , Sly Richard , Ussher Michael H 
Published: January 2016

Objectives: To compare end-of-treatment outcomes for patients receiving either inpatient or day patient specialist treatment for anorexia nervosa. Outcomes included body mass index (BMI), symptom severity (EDE), general psychopathology (CORE), and treatment cost. Methods: A naturalistic study design was used. Participants were asked to complete validated questionnaires at the start and end of treatment, and weight data were also collected at these points. Cost of treatment episode was calculated at the end of treatment. These variables were compared between units. Results: Patients attending the two different treatment modalities had comparable treatment outcomes across weight measures, and global scores on the EDE and CORE questionnaires—all considered key treatment outcome variables. Those attending day patient treatment had treatment costs of on average £17 753 less than those in inpatient treatment. Discussion: Day patient treatment can produce similar treatment outcomes to its more intensive—and expensive—inpatient alternative. This is the first study to examine this in eating disorders, and warrants further examination.
Nestmate Recognition in the Amazonian Myrmecophyte Ant Pseudomyrmex concolor Smith (Hymenoptera, Formicidae)
Authors: Del-Claro Kleber , Pacheco Paulo S.M. 
Published: January 2016

Nestmate recognition is fundamental to colonial cohesion in social insects, since it allows altruistic behavior towards relatives, recognition of intruders, territorial monopoly and resources defense. In ants, olfactory cues is a key factor in this process. Pseudomyrmex concolor is a highly aggressive ant that defends their host plant Tachigali myrmecophila against herbivores. However, this defense depends on the ant ability to discriminate in order to treat differentially between members of their own colony and intruders . In this study we investigated “whether” and “how” P. concolor recognizes nestmates from non-nestmates. We hypothesized that P. concolor is skillful in recognizing nestmates and tested it in field with experiments using nestmates and non-nestmates. Additionally, to test the efficiency of resident ants against intraspecific competition during colony foundation, we simulate the plant occupation by a competitor queen, introducing non-nestmates queens in plants previously occupied by P. concolor. For the issue of the "how", we hypothesized that the main cue used by this ant in nestmate recognition is olfactory signal. Thus, we tested adaptive threshold model, which predicts that, if the individual odor and colony’s internal template are discrepant enough, the resident nestmate will behave aggressively towards incoming individuals. In this case, we confined nestmates with non-nestmates odors, and then, we reintroduced them in its host plants. In each experiment the frequency of aggressive behaviors were recorded and compared. Results showed that P. concolor recognize and discriminate nestmates from non-nestmates workers (biting and stinging them) and exclude potential competitors queens. Workers reintroduced in their own colony after impregnated with non-familiar odor were treated as non-nestmates. The adaptive threshold hypothesis was confirmed, the main cue used by this ant species in nestmate recognition is olfactory signals.
Heterozygous mutations in RelB can be associated with immune dysregulation and lymphoma
Authors: Haynes Alison , Kamra Palinder , Roifman Chaim 
Published: January 2016

Background: The nuclear factor kappa-B (NFκB) family of transcription factors is essential for numerous processes, including the development and function of the innate and adaptive immune response, inflammation and cell growth, differentiation, and survival. Recently, patients with homozygous mutations in the gene for the NFκB transcription factor RelB have been described as presenting with features of combined immunodeficiency such as recurrent infection and failure to thrive as well as reduced response to mitogens and an inability to maintain an adequate antibody response to immunizations. Methods: The immune status and genetics of the parents of patients with homozygous RelB mutations were assessed. In vitro mitogen stimulation, flow cytometry, and cytokine ELISA were used to assess immunological status and signal transduction pathways. Results: Four patients were confirmed to have heterozygous RelB mutations. The majority of patients had evidence of immune dysfunction with impaired in vitro responses to PHA and antigens. One patient developed lymphoma. Conclusion: Heterozygous RelB mutations can be associated with immune dysregulation with impaired mitogen and antigen responses and lymphoma. It is likely that the immune defects apparent in RelB deficient humans are due to a wider effect of RelB on the classical NFκB pathway (involving RelA and c-Rel) through cross-regulation of activation and expression in addition to RelB’s function within the alternate pathway. Statement of novelty: We describe for the first time the immune abnormalities in patients with heterozygous RelB mutations.
Ellipso-Höhentopometrie
Authors: Leonhardt Klaus , Breitmeier Ulrich 
Published: January 2016

Zusammenfassung
Die Ellipso-Höhentopometrie misst zusätzlich
zum topometrischen Höhenprofil die örtliche Verteilung des Materials
an der Oberfläche, so dass eine hochaufgelöste
Materialidentifizierung und Kartierung und eine Korrektur der Messfehler
möglich wird.
Alle kommerziell verfügbaren optischen Profilmessgeräte zeigen
Artefakte an Übergängen verschiedener Materialien einer
Werkstückoberfläche. Beispielsweise wird ein
Ölfilm auf einem Metalluntergrund mit nichtlinear invertierter
Profilamplitude wiedergegeben, so dass er als Vertiefung
anstatt als Erhebung gemessen wird [4,5]. Die Höhe einer Leiterbahn
auf einer mikroelektronischen Struktur wird gleichermaßen falsch
gemessen. Große,
nichtkalibrierbare Fehler können bei Schichtstrukturen
auftreten. Mit einem neuartigen
Ellipso-Höhentopometer können diese Messfehler
und Artefakte durch Korrektur des Phasensprungs bei der Lichtreflexion
für quasiplanare Oberflächen kompensiert werden.
Dazu wird aus denselben Datensätzen, die zur
Berechnung der Höhentopografie H(x, y) aufgenommen
wurden, die lokale Verteilung der Materialien und ihrer
optischen Parameter ermittelt und daraus die Material-
und Schicht-Resonanzphasen zur Korrektur
berechnet.
Die Ellipso-Höhentopometrie kann erstmals
strukturierte Profile im nm-Bereich mit hoher
räumlicher Auflösung optisch richtig messen und zusätzlich
lassen sich Informationen über Materialien,
Schichten und Verschmutzungen auf der Oberfläche
gewinnen.