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A middle-aged immigrant male from a region with endemic tuberculosis who had a history of end-stage kidney disease presented to the emergency room for routine hemodialysis and abdominal swelling. He was admitted to the medicine service for suggested daily dialysis to improve his volume overload, which was attributed to nephrogenic ascites. He was found to have several findings concerning for systemic illness, including fevers, night sweats, hypercalcemia, lymphadenopathy, omental thickening, ascitic fluid with a serum ascites albumin gradient of less than 1.1 gm/dL, and exudative pleural effusions. Our suspicion for hematologic malignancy versus disseminated infection was high. During admission, there were many diagnostic challenges in obtaining histologic and bacteriologic confirmation of our leading suspected diagnosis, disseminated tuberculosis. Ultimately, tuberculosis infection was confirmed with histologic evidence of granulomatous inflammation of cervical lymph node and sputum culture positive for Mycobacterium tuberculosis. This case highlights the necessity for every patient presenting with new ascites to undergo diagnostic paracentesis. Nephrogenic ascites is a rare syndrome that is possible in volume overloaded states but is a diagnosis of exclusion that should be supported by an exudative serum ascites albumin gradient and no evidence of an alternate etiology. [ABSTRACT FROM AUTHOR]

Background: Many pancreatic pseudocysts spontaneously resolve, but larger or symptomatic pseudocysts may require procedural management. Though endoscopic ultrasound guided approaches are standard of care and have high success rates, complications can include bleeding, infection, and splenic perforation. This patient case report details an unusual series of complications of endoscopic cystogastrostomy that should encourage clinicians to evaluate for anatomic disruptions caused by mass effects of pancreatic pseudocysts prior to endoscopic pseudocyst drainage.Case Presentation: A 53-year-old African American male with a past medical history notable for alcohol use disorder, chronic pancreatitis, and insulin dependent diabetes presented with a 4-day history of left upper quadrant abdominal pain. Computed tomography imaging with contrast revealed enlargement of a known pancreatic pseudocyst to 15.9 × 10.4 cm. Due to pseudocyst size and the patient's symptoms, endoscopic cystogastrostomy stent placement was performed. However, postprocedurally, he developed leukocytosis to 19,800 cells/m3 (from 14,100 cells/m3 preoperatively) as well as acute hypoxemic respiratory failure with a large left pleural effusion. Postprocedural computed tomography with contrast demonstrated a new large subcapsular splenic hematoma in communication with a new subdiaphragmatic fluid collection. Due to suspicion of endoscopic procedural complication, he underwent open laparotomy which revealed grade 4 splenic laceration, septic splenic hematoma, and a subdiaphragmatic abscess.Conclusions: While endoscopic drainage of pancreatic pseudocyst was technically successful, this case demonstrates complications from mass effect of a large pancreatic pseudocyst which putatively tore the splenorenal ligament, leading to excessive separation of the left kidney and spleen. If anatomic disruptions caused by mass effect from a pancreatic pseudocyst are recognized through preprocedural abdominal imaging, such cases may be considered for early open repair versus cystogastrostomy. [ABSTRACT FROM AUTHOR]

According to contesting theory (Shields & Bredemeier, 2011), people conceptualize competition either through a metaphor of partnership or war. These two alternate metaphors suggest differing sociomoral relationships among the participants. In the current study of intercollegiate athletes (n = 610), we investigated the two approaches to contesting in relation to formalist and consequentialist moral frameworks (Brady & Wheeler, 1996) and individualizing and binding moral foundations (Haidt, 2001). Correlational analysis indicated that the partnership approach correlated significantly with all four moral dimensions, while the war approach correlated with formalist and consequentialist frameworks and binding foundations (i.e., appeals to in-group loyalty, authority, and purity). Multiple regressions demonstrated that the best predictors of a partnership approach were formalist thinking and endorsement of individualizing moral foundations (i.e., appeal to fairness and welfare). Among our primary variables, the best predictors of a war orientation were consequentialist thinking and endorsement of binding foundations. [ABSTRACT FROM AUTHOR]

Researchers have made productive use of Bandura's (1991) construct of moral disengagement (MD) to help explain why sport participants deviate from ethical ideals. In this study of intercollegiate athletes from diverse sports (N = 713), we examined MD in relation to other character-related variables: empathy, moral identity, moral attentiveness, and contesting orientations. We also examined whether moral attentiveness conforms to the pattern of "bracketed morality" found in moral reasoning (Shields & Bredemeier, 1995) and moral behavior (Kavussanu, Boardley, Sagar, & Ring, 2013). Results indicated that MD correlated positively with perceptual moral attentiveness and war contesting orientation; MD correlated negatively with empathy, moral identity, reflective moral attentiveness, and partnership contesting orientation. Results of hierarchical regression demonstrated that gender, contesting orientations, moral identity, and one form of moral attentiveness were significant predictors of MD. Finally, sport participants were found to be less morally attentive in sport than in everyday life. [ABSTRACT FROM AUTHOR]

Grit and self-control are highly desired qualities of character in the sport arena. This two-study investigation used a new theoretical approach, contesting theory, to examine whether contesting orientations could predict these characteristics among intercollegiate athletes. Contesting theory identifies two distinct modes of cognitively processing the meaning and purpose of contesting, one rooted in a contest-is-partnership metaphor and the other a contest-is-war metaphor. Study 1 (N = 799) found that contesting orientations added incremental utility beyond demographic and control variables to the prediction of the two dimensions of grit (perseverance and consistency). Specifically, the partnership orientation positively predicted higher grit scores. Study 2 (N = 1179) replicated the findings of Study 1 with only minor variations and also demonstrated that contesting orientations add to the prediction of self-control. Results are discussed in terms of the practical implications for sport practitioners and, more broadly, the value of contesting theory to positive psychology. [ABSTRACT FROM AUTHOR]

The current study of US intercollegiate athletes (n = 1066) involved in multiple sports investigated relationships among moral (moral reasoning maturity, moral value evaluation [MVE], and moral identity), contesting (partnership and war orientations) and behavioral (prosocial and antisocial) variables in sport. Among other relationships, results demonstrated that prosocial behavior was positively correlated with moral reasoning maturity, higher appreciation of moral values, moral identity and a partnership contesting orientation. In contrast, antisocial behavior was negative correlated with moral reasoning maturity, MVE, moral identity and a partnership orientation. In addition, antisocial behavior was positively correlated with a war contesting orientation. Regression analyses demonstrated that prosocial behavior was best predicted by the partnership contesting orientation and moral identity; antisocial behavior was best predicted by the war orientation followed closely by moral identity. Results are discussed in relation to Kohlbergian moral theory and contesting theory. [ABSTRACT FROM PUBLISHER]

Despite the centrality of competition to sports, little is known about how participants give meaning to their experience of contests. Contesting theory posits that individuals interpret contests through two alternate metaphors. Genuine competition reflects a "contest-is-partnership " metaphor. In contrast, in "decompetition" the contest is interpreted through a "contest-is-war" metaphor. In this two-study investigation, metaphor priming was used to test hypotheses derived from contesting theory. In Study 1, participants (N = 281) were primed with one or the other metaphor and then asked to make moral judgments assessing commitment to integrity in contest situations. In Study 2, following a priming activity, participants (N = 246) were asked to interpret facial expressions of athletes. Both studies provided support for contesting theory. In Study 1, participants primed with the contest-is-war metaphor accepted antisocial behavior to a greater extent than did those primed with the partnership metaphor. In Study 2, those primed with the war metaphor attributed more negative emotion to the portrayed athletes than did those primed with the partnership metaphor. [ABSTRACT FROM AUTHOR]

Objectives This investigation was conducted to determine whether contesting orientations add predictive utility for prosocial behavior, both in and out of sports, beyond other variables related to the component processes of moral action. Design Cross-sectional. Methods Intercollegiate US athletes (n = 2380; 56.4% male), from both individual and team sports, completed measures of contesting orientation, three moral variables (moral attentiveness, moral identity, integrity), three sport-specific variables (athletic identity, goal orientation, and fear of failure), and three outcome variables (sportspersonship, academic honesty, and prosocial helping). Data was analyzed using both correlational and regression analyses. Results Regression analyses demonstrated that contesting orientations were the best predictors of sportspersonship, but were insignificant predictors of nonsport forms of prosocial behavior. Conclusions Consistent with contesting theory, contesting orientation are salient and potent predictors of sportspersonship, but do not predict behavior outside of contest situations. [ABSTRACT FROM AUTHOR]

Objectives To examine the factorial validity of the Contesting Orientations Scale (COS) in a large sample of intercollegiate student-athletes, as well as to extend evidence of the COS’ concurrent validity by examining its relationship to autonomous and controlled motivations in sport. The ability of contesting orientations to predict sportspersonship over and above autonomous and controlled motivations was also examined. Design Cross-sectional and correlational. Methods Five hundred and forty-four intercollegiate US athletes (57.2% male) from individual and team sports completed measures of contesting orientations, autonomous and controlled motivations, and sportspersonship. Results Confirmatory factor analysis (CFA) supported the factorial validity of the COS, while correlational results supported its concurrent construct validity, with autonomous motivation associated with higher levels of partnership orientation and controlled motivation associated with higher levels of war orientation. In addition, sequential regression analyses supported the predictive utility of contesting orientations, with partnership orientation emerging as a significant positive predictor of four – and war orientation a negative predictor of three – dimensions of sportspersonship. Mediation analyses suggested that contesting orientations may partially mediate the relationship between autonomous and controlled motivations for some dimensions of sportspersonship. Conclusions The COS is a valid and reliable measure of contesting orientations. Partnership and war contesting orientations, moreover, add significantly to the prediction of sportspersonship over and above autonomous and controlled motivations. In practice, if the goal is to promote good sportspersonship, coaches and other adults involved in competitive sport should emphasize a partnership contesting orientation in addition to more autonomous forms of motivation. [ABSTRACT FROM AUTHOR]

Background: Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are represented in the ontology and how they are expressed in natural language text. The construction of highly specific GO terms is formulaic, consisting of parts and pieces from more simple terms. Results: We present two different types of manually generated rules to help capture the variation of how GO terms can appear in natural language text. The first set of rules takes into account the compositional nature of GO and recursively decomposes the terms into their smallest constituent parts. The second set of rules generates derivational variations of these smaller terms and compositionally combines all generated variants to form the original term. By applying both types of rules, new synonyms are generated for two-thirds of all GO terms and an increase in F-measure performance for recognition of GO on the CRAFT corpus from 0.498 to 0.636 is observed. Additionally, we evaluated the combination of both types of rules over one million full text documents from Elsevier; manual validation and error analysis show we are able to recognize GO concepts with reasonable accuracy (88%) based on random sampling of annotations. Conclusions: In this work we present a set of simple synonym generation rules that utilize the highly compositional and formulaic nature of the Gene Ontology concepts. We illustrate how the generated synonyms aid in improving recognition of GO concepts on two different biomedical corpora. We discuss other applications of our rules for GO ontology quality assurance, explore the issue of overgeneration, and provide examples of how similar methodologies could be applied to other biomedical terminologies. Additionally, we provide all generated synonyms for use by the text-mining community. [ABSTRACT FROM AUTHOR]

In patent litigation, courts frequently allow patent holders to access an accused infringer's trade secrets and other confidential technology. Those secrets may be relevant to claims of patent infringement. But the confidential access creates a risk that patent holders will misuse those secrets when their attorneys or experts wear two hats-- litigating the patent suit in court and working on patent applications in the same field as the accused infringer's confidential technology. These two hats allow certain attorneys and experts the opportunity to target the accused infringer's secret technology--either inadvertently or deliberately--by patenting it as their client's own intellectual property (IP). Several courts attempt to prevent this potential misuse of IP by imposing a patent prosecution bar, which typically forbids those with access to another party's confidential technology from working at all on patent applications in the same field. But the U.S. Court of Appeals for the Federal Circuit has created a flawed test for determining when a district court may impose prosecution bars. As implemented by most district courts, prosecution bars apply to only those attorneys and experts who are "competitive decisionmakers" and who have a history of working on patent applications. The test is based on a vague and underinclusive term and leaves those without a similar history free of a prosecution bar and positions them to target the other side's trade secrets with new patent claims. This targeted patenting undermines the IP system's channeling between patents and trade secrets. Channeling theory posits that inventors whose inventions are inherently transparent or at risk of being reverse engineered will choose patents and public disclosure over trade secrecy; but inventors whose inventions are inherently opaque may well choose trade secrecy. Both forms of IP promote innovation and deserve protection. Patent prosecution bars protect the integrity and incentives of both forms of IP by ensuring one party does not inadvertently or deliberately misappropriate the other's trade secret and grab a monopoly over technology it did not create. Despite courts and parties routinely struggling to apply the Federal Circuit's test, unfavorable standards of review have deterred appeals and made prosecution bars less visible to scholars. This Article fills a gap in the literature and proposes a new approach to patent prosecution bars that applies to everyone with confidential access. Instead of the current wholesale bars that prohibit any work on patent applications, the proposed model bar would prohibit only specific prosecution activities, such as drafting patent applications and claims, where attorneys or experts risk misusing their access to the other side's secrets. [ABSTRACT FROM AUTHOR]

Background: The recently held Critical Assessment of Function Annotation challenge (CAFA2) required its participants to submit predictions for a large number of target proteins regardless of whether they have previous annotations or not. This is in contrast to the original CAFA challenge in which participants were asked to submit predictions for proteins with no existing annotations. The CAFA2 task is more realistic, in that it more closely mimics the accumulation of annotations over time. In this study we compare these tasks in terms of their difficulty, and determine whether cross-validation provides a good estimate of performance. Results: The CAFA2 task is a combination of two subtasks: making predictions on annotated proteins and making predictions on previously unannotated proteins. In this study we analyze the performance of several function prediction methods in these two scenarios. Our results show that several methods (structured support vector machine, binary support vector machines and guilt-by-association methods) do not usually achieve the same level of accuracy on these two tasks as that achieved by cross-validation, and that predicting novel annotations for previously annotated proteins is a harder problem than predicting annotations for uncharacterized proteins. We also find that different methods have different performance characteristics in these tasks, and that cross-validation is not adequate at estimating performance and ranking methods. Conclusions: These results have implications for the design of computational experiments in the area of automated function prediction and can provide useful insight for the understanding and design of future CAFA competitions. [ABSTRACT FROM AUTHOR]

Objective This three-study investigation was undertaken to develop, validate, and test the Contesting Orientations Scale (COS), a new measure designed to assess individuals' tendencies to use contest-is-partnership and contest-is-war conceptual metaphors (i.e., contesting orientations) when competing (Shields & Bredemeier, 2009, 2011a). Design The research design was correlational. Following preliminary item creation and expert review, survey based studies were conducted to develop theoretically-based, psychometrically sound scales measuring contesting orientations. Method In Study 1, an exploratory factor analysis (EFA) was performed on a preliminary 39-item COS administered to a sample of high school athletes (N = 233). Study 2 used EFA to evaluate a revised 23- item COS with a second sample of high school athletes (N = 92) resulting in a final reduction of the measure to twelve items. Confirmatory factor analysis (CFA) was then conducted on this 12-item COS, which proved an excellent fit to the data. A new sample of college athletes (N = 238) allowed Study 3 to (a) further examine the factorial validity of the COS, including gender invariance testing, (b) assess the concurrent validity of the COS via its correlations with goal orientations, empathy, moral identity, and moral disengagement; and, (c) assess the COS's incremental predictive utility for investigations of sportspersonship. Results and conclusion Results from the sequence of studies demonstrate that the 12-item, two-scale COS has good psychometric properties as assessed through EFA and CFA, good concurrent validity, and adds significantly to existing measures in the prediction of sportspersonship. [ABSTRACT FROM AUTHOR]

Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In this work we evaluate both ontology term co-mention and bag-of-words features mined from the biomedical literature and analyze their impact in the context of a structured output support vector machine model, GOstruct. We find that even simple literature based features are useful for predicting human protein function (F-max: Molecular Function = 0.408, Biological Process = 0.461, Cellular Component = 0.608). One advantage of using literature features is their ability to offer easy verification of automated predictions. We find through manual inspection of misclassifications that some false positive predictions could be biologically valid predictions based upon support extracted from the literature. Additionally, we present a "medium-throughput" pipeline that was used to annotate a large subset of co-mentions; we suggest that this strategy could help to speed up the rate at which proteins are curated. [ABSTRACT FROM AUTHOR]

Background Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed in text. There are many recognizers for specific ontologies, but a general approach for concept recognition is an open problem. Results Three dictionary-based systems (MetaMap, NCBO Annotator, and ConceptMapper) are evaluated on eight biomedical ontologies in the Colorado Richly Annotated Full-Text (CRAFT) Corpus. Over 1,000 parameter combinations are examined, and best-performing parameters for each systemontology pair are presented. Conclusions Baselines for concept recognition by three systems on eight biomedical ontologies are established (Fmeasures range from 0.14-0.83). Out of the three systems we tested, ConceptMapper is generally the best-performing system; it produces the highest F-measure of seven out of eight ontologies. Default parameters are not ideal for most systems on most ontologies; by changing parameters F-measure can be increased by up to 0.4. Not only are best performing parameters presented, but suggestions for choosing the best parameters based on ontology characteristics are presented. [ABSTRACT FROM AUTHOR]

Rainfed agriculture in Sub-Saharan Africa accounts for 95 % of the local cereal production, impacting hundreds of millions of people. Early identification of poor rainfall conditions is a critical indicator of food security. As such, monitoring accumulated seasonal rainfall gives an important mid-season estimate of final accumulated totals. However, characterizing the remaining uncertainty in a season has largely been ignored by the food security community. This paper presents a new technique describing rainfall conditions over the duration of a crop-growing cycle by combining estimated rainfall-to-date with potential scenarios for the remaining season based on available satellite rainfall estimates, the common tool for rainfall analysis in Africa. The limited historical record provided by satellite rainfall estimates using previous seasons provides only a coarse view of likely seasonal totals. To combat this, scenarios developed by bootstrapping dekadal data to create synthetic seasons allow for a finer understanding of potential seasonal accumulations. Updating this throughout the season shows a narrowing envelope of seasonal totals, converging on the final seasonal result. The resulting scenarios inform the expectations for the final seasonal rainfall accumulation, allowing analysts to quantify and visualize the uncertainty in seasonal totals. Giving decision makers a tool for understanding the likelihood of specific rainfall amounts provides additional time to enact and mobilize efforts to reduce the impact of agricultural drought. [ABSTRACT FROM AUTHOR]

Combining heterogeneous sources of data is essential for accurate prediction of protein function. The task is complicated by the fact that while sequence-based features can be readily compared across species, most other data are species-specific. In this paper, we present a multi-view extension to GOstruct, a structured-output framework for function annotation of proteins. The extended framework can learn from disparate data sources, with each data source provided to the framework in the form of a kernel. Our empirical results demonstrate that the multi-view framework is able to utilize all available information, yielding better performance than sequencebased models trained across species and models trained from collections of data within a given species. This version of GOstruct participated in the recent Critical Assessment of Functional Annotations (CAFA) challenge; since then we have significantly improved the natural language processing component of the method, which now provides performance that is on par with that provided by sequence information. The GOstruct framework is available for download at http://strut.sourceforge.net. [ABSTRACT FROM AUTHOR]

Surface temperatures are projected to increase 3-4°C over much of Africa by the end of the 21st century. Precipitation projections are less certain, but the most plausible scenario given by the Intergovernmental Panel on Climate Change (IPCC) is that the Sahel and East Africa will experience modest increases (~5%) in precipitation by the end of the 21st century. Evapotranspiration (E) is an important component of the water, energy, and biogeochemical cycles that impact several climate properties, processes, and feedbacks. The interaction of E with climate change drivers remains relatively unexplored in Africa. In this paper, we examine the trends in E, precipitation (P), daily maximum temperature (T), and daily minimum temperature (T) on a seasonal basis using a 31 year time series of variable infiltration capacity (VIC) land surface model (LSM) E. The VIC model captured the magnitude, variability, and structure of observed runoff better than other LSMs and a hybrid model included in the analysis. In addition, we examine the inter-correlations of E, P, T, and T to determine relationships and potential feedbacks. Unlike many IPCC climate change simulations, the historical analysis reveals substantial drying over much of the Sahel and East Africa during the primary growing season. In the western Sahel, large increases in daily maximum temperature appear linked to E declines, despite modest rainfall recovery. The decline in E and latent heating in this region could lead to increased sensible heating and surface temperature, thus establishing a possible positive feedback between E and surface temperature. [ABSTRACT FROM AUTHOR]

The author advocates a reasonable-child approach to child declarants under the Confrontation Clause. He discusses the case Davis v. Washington, in which the U.S. Supreme Court clarified the definition of a testimonial. The author questions whether a court can consider a child declarant's perspective when deciding whether an out-of court statement is testimonial and if a court can consider subjective factors, such as a child's age and intelligence. The author supports a reasonable-child approach which does consider subjective factors regarding a child's perspective. The article discusses a number of Supreme Court cases related to the issue, including Ohio v. Roberts, Crawford v. Washington, and State v. Siler. A detailed overview of the reasonable-child approach is included.

Shows that clustering can reduce within-class variance and group pixels with similar correlation structures in remote sensing images. Centroid initialization technique introduced to speed up convergence; Matched filtering formulations compared for a variety of of a number of classes and synthetic hyperspectral images; Clustering in conjunction with clutter matched filtering.

Information fusion in networked systems poses challenges with respect to both theory and implementation. Limited available bandwidth can become a bottleneck when high-dimensional estimates and associated error covariance matrices need to be transmitted. Compression of estimates and covariance matrices can endanger desirable properties like unbiasedness and may lead to unreliable fusion results. In this work, quantization methods for estimates and covariance matrices are presented and their usage with the optimal fusion formulas and covariance intersection is demonstrated. The proposed quantization methods significantly reduce the bandwidth required for data transmission while retaining unbiasedness and conservativeness of the considered fusion methods. Their performance is evaluated using simulations, showing their effectiveness even in the case of substantial data reduction. [ABSTRACT FROM AUTHOR]

Due to limitations of neuroimaging, such as the isodense appearance of blood to neuronal tissue in subacute hemorrhagic stroke, a body of studies have been performed to evaluate candidate biomarkers which may aid in accurate determination of cerebrovascular accident type. Beyond aiding in the delineation of stroke cause, biomarkers could also confer useful prognostic information to help clinicians plan use of resources. One of the candidate biomarkers studied for detection of cerebrovascular accident (CVA) includes a class of proteins called galectins. Galectins bind β-galactoside through a highly conserved carbohydrate recognition domain, endowing an ability to interact with carbohydrate moieties on glycoproteins, some of which are relevant to CVA response. Furthermore, galectins-1, -2, -3, -9, and -12 are expressed in tissues relevant to CVA, and some exhibit characteristics (eg, extracellular secretion) that could render feasible their detection in serum. Galectins-1 and -3 appear to have the largest amounts of preclinical evidence, consistently demonstrating increased activity and expression levels during CVA. However, a lack of standardization of biochemical assays across cohort studies limits further translation of these basic science studies. This review aims to increase awareness of the biochemical roles of galectins in CVA, while also highlighting challenges and remaining questions preventing the translation of basic science observations into a clinically useful test. [ABSTRACT FROM AUTHOR]

Clinical trials of chimeric antigen receptor (CAR) T cells in hematologic malignancy associate remissions with two profiles of CAR T cell proliferation kinetics, which differ based upon costimulatory domain. Additional T cell intrinsic factors that influence or predict clinical response remain unclear. To address this gap, we report the case of a 68-year-old woman with refractory/relapsed diffuse large B cell lymphoma (DLBCL), treated with tisagenlecleucel (anti-CD19), with a CD137 costimulatory domain (4-1BB) on an investigational new drug application (#16944). For two months post-infusion, the patient experienced dramatic regression of subcutaneous nodules of DLBCL. Unfortunately, her CAR T exhibited kinetics unassociated with remission, and she died of DLBCL-related sequelae. Serial phenotypic analysis of peripheral blood alongside sequencing of the β-peptide variable region of the T cell receptor (TCRβ) revealed distinct waves of oligoclonal T cell expansion with dynamic expression of immune checkpoint molecules. One week prior to CAR T cell contraction, T cell immunoglobulin mucin domain 3 (Tim-3) and programmed cell death protein 1 (PD-1) exhibited peak expressions on both the CD8 T cell (Tim-3 ≈ 50%; PD-1 ≈ 17%) and CAR T cell subsets (Tim-3 ≈ 78%; PD-1 ≈ 40%). These correlative observations draw attention to Tim-3 and PD-1 signaling pathways in context of CAR T cell exhaustion. [ABSTRACT FROM AUTHOR]

A response by Molly E. Brown, Christopher C. Funk and James Verdin to a letter to the editor about the article "FOOD SECURITY UNDER CLIMATE CHANGE" in the February 1, 2008 issue is presented.

The article focuses on the impact of climate change on agricultural and food systems. It is stated that increasing temperatures and declining precipitation over dry regions could potentially reduce yields for corn, wheat, rice, and other primary crops in the next two decades, affecting the global food security. It has been accounted since 1990s that the rising commodity prices and declining per capita cultivated area have led to decreases in food production, eroding food security in many communities. Information about the climatic change' impact on national revenue is included.

Simple Summary: Galectins are a family of β-galactoside binding proteins whose levels are altered in various stages of different types of cancer. This study provides an analytical comparison of 50 frequently mutated genes in two common cancers and the serum levels of the galectin proteins. The goal is the revelation of potential relationships between the mutation status of these genes and serum levels of galectins. We found that mutations in the KIT gene (which codes for the proto-oncogene c-KIT protein) are associated with increased circulating levels of certain galectins. We also found that patient samples originating from brain tissue have a higher likelihood of having a mutation in the KIT gene. Understanding the relationship between cancer-critical gene mutations and serum galectin levels could provide a feasible and non-invasive avenue to better understand the tumor's unique genetic profile. To investigate a potential role for galectins as biomarkers that enable diagnosis or prognostication of breast or non-small cell lung cancer, the serum levels of galectins -1, -3, -7, -8, and -9 of cancer patients determined by ELISA assays were compared to the mutation status of 50 known cancer-critical genes, which were determined using multiplex PCR in tumors of the same patients. Mutations in the KIT proto-oncogene, which codes for the c-Kit protein, a receptor tyrosine kinase, correlated with higher levels of galectins -1, -3, -8, and -9 in breast cancer patients and galectin-1 in non-small cell lung cancer patients. Mutations in the KIT gene were more likely found in brain metastases from both of these primary cancers. The most common KIT mutation in our panel was p.M541L, a missense mutation in the transmembrane domain of the c-Kit protein. These results demonstrate an association between KIT oncogenic signaling and elevated serum galectins in patients with metastatic disease. Changes in protein trafficking and the glycocalyx composition of cancer cells may explain the observed alterations in galectin expression. This study can be useful for the targeted selection of receptor tyrosine kinase and galectin inhibitor anti-cancer treatments. [ABSTRACT FROM AUTHOR]

The skill of North American multimodel ensemble (NMME) seasonal forecasts in East Africa (EA), which encompasses one of the most food and water insecure areas of the world, is evaluated using deterministic, categorical, and probabilistic evaluation methods. The skill is estimated for all three primary growing seasons: March–May (MAM), July–September (JAS), and October–December (OND). It is found that the precipitation forecast skill in this region is generally limited and statistically significant over only a small part of the domain. In the case of MAM (JAS) [OND] season it exceeds the skill of climatological forecasts in parts of equatorial EA (Northern Ethiopia) [equatorial EA] for up to 2 (5) [5] months lead. Temperature forecast skill is generally much higher than precipitation forecast skill (in terms of deterministic and probabilistic skill scores) and statistically significant over a majority of the region. Over the region as a whole, temperature forecasts also exhibit greater reliability than the precipitation forecasts. The NMME ensemble forecasts are found to be more skillful and reliable than the forecast from any individual model. The results also demonstrate that for some seasons (e.g. JAS), the predictability of precipitation signals varies and is higher during certain climate events (e.g. ENSO). Finally, potential room for improvement in forecast skill is identified in some models by comparing homogeneous predictability in individual NMME models with their respective forecast skill. [ABSTRACT FROM AUTHOR]

Abstract Despite advances in drought early warning systems, forecast information is rarely used for triggering and financing early actions, such as cash transfer. Scaling up cash transfer pay-outs, and overcoming the barriers to actions based on forecasts, requires an understanding of costs resulting from False Alarms, and the potential benefits associated with appropriate early interventions. On this study, we evaluate the potential cost-effectiveness of cash transfer responses, comparing the relative costs of ex-ante cash transfers during the maize growing season to ex-post cash transfers after harvesting in Kenya. For that, we developed a forecast model using Fast-and Frugal Trees that unravels early warning relationships between climate variability, vegetation coverage, and maize yields at multiple lead times. Results indicate that our models correctly forecast low maize yield events 85% of the time across the districts studied, some already six months before harvesting. The models' performance improves towards the end of the growing season driven by a decrease of 29% in the probability of False Alarms. Overall, we show that timely cash transfers ex-ante to a disaster can often be more cost-effective than investing in ex-post expenditures. Our findings suggest that early response can yield significant cost savings, and can potentially increase the effectiveness of existing cash transfer systems. Graphical abstract Unlabelled Image Highlights • Drought early warning systems are rarely used for triggering early actions, such as cash transfer. • We evaluate the cost-effectiveness of cash transfers ex-ante (forecast-based) and ex-post. • We developed a forecast model using Machine Learning named Fast-and-Frugal Trees. • We show that our models predict the majority of the low maize yield events in all districts studied. • Our results indicate that cash transfers ex-ante can often be more cost-effective than ex-post. [ABSTRACT FROM AUTHOR]

Atmospheric methane has been increasing since the beginning of the industrial era due to anthropogenic emissions. Methane has many sources, both natural and anthropogenic, and there continues to be considerable uncertainty regarding the contribution of each source to the total methane budget. Thus, remote sensing techniques for monitoring and measuring methane emissions are of increasing interest. Recently, the Airborne Visible-Infrared Imaging Spectrometer - Next Generation (AVIRIS-NG) has proven to be a valuable instrument for quantitative mapping of methane plumes. Despite this success, uncertainties remain regarding the sensitivity of the retrieval algorithms, including the influence of albedo and the impact of surfaces that may cause spurious signals. To explore these sensitivities, we applied the Iterative Maximum a Posterior Differential Optical Absorption Spectroscopy (IMAP-DOAS) methane retrieval algorithm to synthetic reflected radiances with variable methane concentrations, albedo, surface cover, and aerosols. This allowed for characterizing retrieval performance, including potential sensitivity to variable surfaces, low albedo surfaces, and surfaces known to cause spurious signals. We found that dark surfaces (below 0.10 μWcm −2 nm −1 sr −1 at 2139 nm), such as water and green vegetation, and materials with absorption features in the 2200–2400 nm range caused higher errors in retrieval results. We also found that aerosols have little influence on retrievals in the SWIR. Results from the synthetic scene are consistent with those observed in IMAP-DOAS retrievals for real AVIRIS-NG scenes containing methane plumes from a waste dairy lagoon and coal mine ventilation shafts. Understanding the effect of surface properties on methane retrievals is important given the increased use of AVIRIS-NG to map gas plumes from a diversity of sources over variable landscapes. [ABSTRACT FROM AUTHOR]

Rapidly expanding global trade in the past three decades has lifted millions out of people out of poverty. Trade has also reduced manufacturing wages in high income countries and made entire industries uncompetitive in some communities, giving rise to nationalist politics that seek to stop or reverse further trade expansion in the United States and Europe. Given complex and uncertain political support for trade, how might changes in trade policy affect the global food system’s ability to adapt to climate change? Here we argue that we can best understand food security in a changing climate as a double exposure: the exposure of people and processes to both economic and climate-related shocks and stressors. Trade can help us adapt to climate change, or not. If trade restrictions proliferate, double exposure to both a rapidly changing climate and volatile markets will likely jeopardize the food security of millions. A changing climate will present both opportunities and challenges for the global food system, and adapting to its many impacts will affect food availability, food access, food utilization and food security stability for the poorest people across the world. Global trade can continue to play a central role in assuring that global food system adapts to a changing climate. This potential will only be realized, however, if trade is managed in ways that maximize the benefits of broadened access to new markets while minimizing the risks of increased exposure to international competition and market volatility. For regions like Africa, for example, enhanced transportation networks combined with greater national reserves of cash and enhanced social safety nets could reduce the impact of ‘double exposure’ on food security. [ABSTRACT FROM AUTHOR]

R5238 --> 680.12 --> Fms Related Receptor Tyrosine Kinase 3 (FLT3) is a class III Receptor Tyrosine Kinase (RTK) which binds to the cytokine Flt3 ligand. It acts to promote cell survival, proliferation, and differentiation of hematopoietic stem cells, and is implicated in the development of acute myeloid leukemia. Galectins are a family of β‐galactoside binding proteins which are involved in many cellular pathways including apoptosis and cell migration as well as the innate immune system. Previous studies have shown that galectins are upregulated and aid in cancer pathologies and current clinical trials are underway to use galectin inhibitors in cancer therapy. RTKs are known to have a variety of direct and indirect interactions with galectins. We have found that breast cancer patients with non‐coding mutations of the FLT3 gene have serum concentrations of galectins ‐1 and ‐9 that align with published healthy values, compared to other breast cancer patients without the mutation which had significantly elevated levels of these galectins. Concentrations of galectin‐1 and ‐9 of 40 breast cancer patients were measured by ELISA. Analysis of 2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes from the same patients was conducted using multiplex PCR. Correlations between the galectin serum levels and mutation presence were elucidated by statistical analysis. We found that mean levels of galectin‐1 and ‐9 were at 23.4 ng/mL and 8.4 ng/mL respectively in breast cancer patients. However, patients with a non‐coding FLT3 mutation had levels of galectin‐1 (mean 16.2 ng/mL) and galectin‐9 (mean 5.0 ng/mL) significantly lower than those in cancer patients without the mutation (p‐value, 0.0392 and 0.0266 respectively). Moreover, they were similar to previously published galectin values for healthy controls (18.1 ng/mL and 7.0 ng/mL respectively). While galectins are known to influence spatial organization and trafficking of this class of RTKs, no specific relationship has been elucidated between galectins ‐1 and ‐9 and FLT3. Our results indicate a potential interaction of clinical significance between FLT3 and galectins ‐1 and ‐9, the mechanism of which needs to be investigated further. [ABSTRACT FROM AUTHOR]

Fresh whole blood (FWB) transfusion is an option for providing volume and oxygen carrying capacity to bleeding Special Operations soldiers who are injured in an austere environment and who are far from a regular blood bank. Retrospective data from recent conflicts in Iraq and Afghanistan show an association between the use of FWB and survival. We reviewed the literature to document the issues surrounding FWB transfusion to Special Operations soldiers in the austere environment and surveyed the literature regarding best practice guidelines for and patient outcomes after FWB transfusions. Most literature regarding FWB transfusion is retrospective or historical. There is limited prospective evidence currently to change transfusion practice in tertiary care facilities, but FWB remains an option in the austere setting. [ABSTRACT FROM AUTHOR]

We present an integrative measure of exposure and sensitivity components of vulnerability to climatic and demographic change for the African continent in order to identify 'hot spots' of high potential population vulnerability. Getis-Ord Gi* spatial clustering analyses reveal statistically significant locations of spatio-temporal precipitation decline coinciding with high population density and increase. Statistically significant areas are evident, particularly across central, southern, and eastern Africa. The highly populated Lake Victoria basin emerges as a particularly salient hot spot. People located in the regions highlighted in this analysis suffer exceptionally high exposure to negative climate change impacts (as populations increase on lands with decreasing rainfall). Results may help inform further hot spot mapping and related research on demographic vulnerabilities to climate change. Results may also inform more suitable geographical targeting of policy interventions across the continent. [ABSTRACT FROM AUTHOR]

Abstract: Carbon dioxide is emitted from the combustion of fossil fuels and is an important contributor to anthropogenic climate change. Multiple current and planned satellite missions are designed to quantify atmospheric carbon dioxide concentrations on a global scale, but most of these sensors do not have the spatial resolution necessary to resolve point sources such as fossil fuel power plants. Airborne imaging spectrometer data, such as those from the Airborne Visible InfraRed Imaging Spectrometer (AVIRIS), can have multiple, contiguous bands covering shortwave infrared (SWIR) absorption features produced by carbon dioxide. Therefore, high spatial resolution data from AVIRIS-like sensors may offer a means for detecting plumes and retrieving carbon dioxide concentrations for point source emissions. The objectives of this study include modeling minimum carbon dioxide anomalies detectable in AVIRIS data under different conditions and applying a Cluster-Tuned Matched Filter for detection of carbon dioxide plumes in simulated data and in AVIRIS images acquired over power plants. Radiative transfer simulations were used to model the residual radiance produced by increased absorption by carbon dioxide as concentration was elevated above background levels within a 0–500m layer. Carbon dioxide anomalies, surface reflectance, water vapor concentration, solar zenith angle, sensor height, and aerosol scattering were varied in simulation sets and the resulting residual radiance spectra were compared against noise equivalent delta radiance (NEdL) for the “classic” and “next generation” AVIRIS instruments. Sensitivity to carbon dioxide anomalies improved with increased surface reflectance and declined with increased water vapor concentration, solar zenith angle, sensor height, and aerosol scattering. Zero to 500m concentration anomalies as low as 100 parts per milion by volume (ppm) for AVIRIS C and 25ppm for AVIRIS NG produced residual radiance values that exceeded SWIR NEdL. Carbon dioxide concentrations modeled for a generic power plant emissions scenario using a plume dispersion model were combined with randomly-generated reflectance spectra to create simulated images with varying surface reflectance and NEdL. For these simulated images, true positive and false positive detection rates improved as background reflectance increased and as NEdL decreased. Apparent plumes were detected in all four AVIRIS C images acquired over power plants, although the characteristics of the plumes varied according to solar-plume-sensor geometry. Improvements in modeling may allow retrieval of plume concentration, providing a valuable means for quantifying point source emissions and a basis for comparison with column concentrations retrieved from in situ measurements and coarse resolution satellite data. [Copyright &y& Elsevier]

Abstract: In this study, a Cluster-Tuned Matched Filter (CTMF) technique was applied to data acquired by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over marine and terrestrial locations known to emit methane (CH4). At the Coal Oil Point marine seep field, prominent CH4 anomalies were consistent with advection from known areas of active seepage. For a region with natural CH4 and oil seepage located west of downtown Los Angeles, significant CH4 anomalies were identified for known sources at the La Brea Tar Pits and in close proximity to probable sources, including an office complex documented as venting CH4 continuously and hydrocarbon storage tanks on the Inglewood Oil Field. However, interpretation of anomalies was complicated by noise and false positives for surfaces with strong absorptions at the same wavelengths as CH4 absorption features. Segmentation of results identified 16 distinct locations of contiguous pixels with high CTMF scores and segments were classified into probable CH4 anomalies and confusers based on the spectral properties of the underlying surface over the full spectral range measured by AVIRIS. This technique is particularly well suited for application over large areas to detect CH4 emissions from concentrated point sources and should permit detection of additional trace gasses with distinct absorption features, including carbon dioxide (CO2) and nitrous oxide (N2O). Thus, imaging spectrometry by an AVIRIS-like sensor has the potential to improve high resolution greenhouse gas mapping, better constraining local sources. [Copyright &y& Elsevier]

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. [ABSTRACT FROM AUTHOR]

Background: We introduce the linguistic annotation of a corpus of 97 full-text biomedical publications, known as the Colorado Richly Annotated Full Text (CRAFT) corpus. We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus. Results: Many biomedical natural language processing systems demonstrated large differences between their previously published results and their performance on the CRAFT corpus when tested with the publicly available models or rule sets. Trainable systems differed widely with respect to their ability to build high-performing models based on this data. Conclusions: The finding that some systems were able to train high-performing models based on this corpus is additional evidence, beyond high inter-annotator agreement, that the quality of the CRAFT corpus is high. The overall poor performance of various systems indicates that considerable work needs to be done to enable natural language processing systems to work well when the input is full-text journal articles. The CRAFT corpus provides a valuable resource to the biomedical natural language processing community for evaluation and training of new models for biomedical full text publications. [ABSTRACT FROM AUTHOR]

Simple Summary: Galectins are a family of lectins that function to recognize carbohydrate groups, such as those on glycosylated proteins. Throughout tumor development, changes in the glycosylation patterns of surface proteins occur, often varying as the disease progresses. We show increased circulating levels of certain galectins in a biorepository of samples from patients with breast, colon, and lung cancer. Patterns of overexpression in cancer relative to healthy controls were observed, with galectins-1 and -3 increased in breast, colon, and lung cancer, while the level of galectin-7 was increased in breast and squamous cell lung cancer, and the level of galectin-9 was increased in colon and lung cancer. No noticeable trends in galectin levels were observed between cancer stages. These data suggest that dysregulation of galectins occurs early in oncogenesis. We also identified histologic subsets in lung cancer for which further investigation of galectins may yield useful diagnostic biomarkers. Galectins are proteins with high-affinity β-galactoside-binding sites that function in a variety of signaling pathways through interactions with glycoproteins. The known contributions of galectins-1, -3, -7, -8, and -9 to angiogenesis, metastasis, cell division, and evasion of immune destruction led us to investigate the circulating levels of these galectins in cancer patients. This study compares galectin concentrations by enzyme-linked immunosorbent assay (ELISA) from each stage of breast, lung, and colon cancer. Galectins-1 and -7, which share a prototype structure, were found to have statistically significant increases in breast and lung cancer. Of the tandem-repeat galectins, galectin-8 showed no statistically significant change in these cancer types, but galectin-9 was increased in colon and lung cancer. Galectin-3 is the only chimera-type galectin and was increased in all stages of breast, colon, and lung cancer. In conclusion, there were significant differences in the galectin levels in patients with these cancers compared with healthy controls, and galectin levels did not significantly change from stage to stage. These findings suggest that further research on the roles of galectins early in disease pathogenesis may lead to novel indications for galectin inhibitors. [ABSTRACT FROM AUTHOR]

Fresh whole blood (FWB) transfusion is an option for providing volume and oxygen carrying capacity to bleeding Special Operations soldiers who are injured in an austere environment and who are far from a regular blood bank. Retrospective data from recent conflicts in Iraq and Afghanistan show an association between the use of FWB and survival. We reviewed the literature to document the issues surrounding FWB transfusion to Special Operations soldiers in the austere environment and surveyed the literature regarding best practice guidelines for and patient outcomes after FWB transfusions. Most literature regarding FWB transfusion is retrospective or historical. There is limited prospective evidence currently to change transfusion practice in tertiary care facilities, but FWB remains an option in the austere setting. [ABSTRACT FROM AUTHOR]