Miracle-dz/UniFAR-FTUs huggingface dataset:
A fast H 2 O total column density product from GOME – Validation with in-situ aircraft measurements

Abstract. Atmospheric water vapour is the most important greenhouse gas which is responsible for about 2/3 of the natural greenhouse effect, therefore changes in atmospheric water vapour in a changing climate (the water vapour feedback) is subject to intense debate. H 2 O is also involved in many important reaction cycles of atmospheric chemistry, e.g. in the production of the OH radical. Thus, long time series of global H 2 O data are highly required. Since 1995 the Global Ozone Monitoring Experiment (GOME) continuously observes atmospheric trace gases. In particular it has been demonstrated that GOME as a nadir looking UV/vis-instrument is sensitive to many tropospheric trace gases. Here we present a new, fast H 2 O algorithm for the retrieval of vertical column densities from GOME measurements. In contrast to existing H 2 O retrieval algorithms it does not depend on additional information like e.g. the climatic zone, aerosol content or ground albedo. It includes an internal cloud-, aerosol-, and albedo correction which is based on simultaneous observations of the oxygen dimer O 4 . From sensitivity studies using atmospheric radiative modelling we conclude that our H 2 O retrieval overestimates the true atmospheric H 2 O vertical column density (VCD) by about 4% for clear sky observations in the tropics and sub-tropics, while it can lead to an underestimation of up to -18% in polar regions. For measurements over (partly) cloud covered ground pixels, however, the true atmospheric H 2 O VCD might be in general systematically underestimated. We compared the GOME H 2 O VCDs to ECMWF model data over one whole GOME orbit (extending from the Arctic to the Antarctic) including also totally cloud covered measurements. The correlation of the GOME observations and the model data yield the following results: a slope of 0.96 (r 2 = 0.86) and an average bias of 5%. Even for measurements with large cloud fractions between 50% and 100% an average underestimation of only -18% was found. This high accuracy of our GOME H 2 O data is also confirmed by the excellent agreement with in-situ aircraft measurements during the MINOS campaign in Greece in summer 2001 (slope of 0.97 (r 2 = 0.86), and an average bias of only 0.2%). Our H 2 O algorithm can be directly adapted to the nadir observations of SCIAMACHY (SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY) which was launched on ENVISAT in March 2002. Near real time H 2 O column data from GOME and SCIAMACHY might be of great value for meteorological weather forecast.
Dihydrofolate Reductase/Thymidylate Synthase Fine-Tunes the Folate Status and Controls Redox Homeostasis in Plants

The Arabidopsis DHFR-TS (dihydrofolate reductase-thymidylate synthase) isoform THY3 operates as an inhibitor of its family members, thereby regulating folate and NADPH availability in cells. Folates (B9 vitamins) are essential cofactors in one-carbon metabolism. Since C1 transfer reactions are involved in synthesis of nucleic acids, proteins, lipids, and other biomolecules, as well as in epigenetic control, folates are vital for all living organisms. This work presents a complete study of a plant DHFR-TS (dihydrofolate reductase-thymidylate synthase) gene family that implements the penultimate step in folate biosynthesis. We demonstrate that one of the DHFR-TS isoforms (DHFR-TS3) operates as an inhibitor of its two homologs, thus regulating DHFR and TS activities and, as a consequence, folate abundance. In addition, a novel function of folate metabolism in plants is proposed, i.e., maintenance of the redox balance by contributing to NADPH production through the reaction catalyzed by methylenetetrahydrofolate dehydrogenase, thus allowing plants to cope with oxidative stress.
A case study on testing, commissioning, and operation of very-large-scale software systems

An increasing number of software systems today are very-large-scale software systems (VLSS) with system-of-systems (SoS) architectures. Due to their heterogeneity and complexity VLSS are difficult to understand and analyze, which results in various challenges for development and evolution. Existing software engineering processes, methods, and tools do not sufficiently address the characteristics of VLSS. Also, there are only a few empirical studies on software engineering for VLSS. We report on results of an exploratory case study involving engineers and technical project managers of an industrial automation VLSS for metallurgical plants. The paper provides empirical evidence on how VLSS are tested, commissioned, and operated in practice. The paper discusses practical challenges and reports industrial requirements regarding process and tool support. In particular, software processes and tools need to provide general guidance at the VLSS level as well as specific methods and tools for systems that are part of the VLSS. Processes and tools need to support multi-disciplinary engineering across system boundaries. Furthermore, managing variability and evolution is success-critical in VLSS verification and validation.
Brain regions involved in locomotor steering in a virtual environment

Steering using optic flow allows adapting locomotion to the environment. Persons with brain lesions display difficulty steering and thus, gaining insight into the brain regions involved in steering may shed light on the disturbed mechanisms of visuomotor control. A joystick-based navigation task in a virtual environment was used to explore brain regions involved in steering control while exposed to optic flows of changing directions. Functional magnetic resonance imaging revealed that hMT+, bilateral cerebellum, frontal and supplementary eye fields are specifically involved in steering control and may reflect the pathway in which visual motion information is transformed into goal-directed action.
Educational gradients in psychotropic medication use among older adults in Costa Rica and the United States.

OBJECTIVE The relationship of education, psychiatric diagnoses, and use of psychotropic medication has been explored in the United States, but little is known about this relationship in poorer countries, despite the high burden of mental illness in these countries. This study estimated educational gradients in diagnosis and psychotropic drug use in the United States and Costa Rica, a middle-income country with universal health insurance. METHODS Analyses were conducted by using data of older adults (≥60) from the 2005 U.S. Medical Expenditure Panel Survey (N=4,788) and the 2005 Costa Rican Longevity and Healthy Aging Study (N=2,827). Logistic regressions examined the effect of education level (low, medium, or high) and urban residence on the rates of self-reported mental health diagnoses, screening diagnosis, and psychotropic medication use with and without an associated psychiatric diagnosis. RESULTS Rates of self-reported diagnoses were lower in the United States (12%) than in Costa Rica (20%), possibly reflecting differences in survey wording. In both countries, the odds of having depression were significantly lower among persons with high education. In Costa Rica, use of psychotropic medication among persons with self-reported diagnoses increased by education level. CONCLUSIONS The educational gradients in medication use were different in the United States and Costa Rica, and stigma and access to care in these countries may play an important role in these differences, although type of insurance did not affect educational gradients in the United States. These analyses increase the evidence of the role of education in use of the health care system.
Development of a Behavior-Based Feeding Questionnaire for Infants with Premature History

The long-term feeding problems associated with premature infants must be recognized and managed if outcomes are to be optimized. However, there is no clinical assessment tool currently available to understand preterm infants' feeding behaviors from the perspective of parents/caregivers. In this study, a behavior-based feeding questionnaire was developed for this purpose. This feeding questionnaire demonstrates good face and content validity. It is our hope that clinicians will be able to utilize this questionnaire to systematically obtain feeding-related information from primary caregivers. Future investigations will be focused on establishing this questionnaire as an outcome measure for comparison studies.
Model Formulation: UMLS-based Conceptual Queries to Biomedical Information Databases: An Overview of the Project ARIANE

OBJECTIVE The aim of the project ARIANE is to model and implement seamless, natural, and easy-to-use interfaces with various kinds of heterogeneous biomedical information databases. DESIGN A conceptual model of some of the Unified Medical Language System (UMLS) knowledge sources has been developed to help end users to query information databases. A query is represented by a conceptual graph that translates the deep structure of an end-user's interest in a topic. A computational model exploits this conceptual model to build a query interactively represented as query graph. A query graph is then matched to the data graph built with data issued from each record of a database by means of a pattern-matching (projection) rule that applies to conceptual graphs. RESULTS Prototypes have been implemented to test the feasibility of the model with different kinds of information databases. Three cases are studied: 1) information in records is structured according to the UMLS knowledge sources; 2) information is able to be structured without error in the frame of the UMLS knowledge; 3) information cannot be structured. In each case the pattern-matching is processed by the projection rule according to the structure of information that has been implemented in the databases. CONCLUSION The conceptual graphs theory provides with a homogeneous and powerful formalism able to represent both concepts, instances of concepts in medical contexts, and associations by means of relationships, and to represent data at different levels of details. The conceptual-graphs formalism allows powerful capabilities to operate a semantic integration of information databases using the UMLS knowledge sources.
Prediction of insulin resistance with anthropometric measures: lessons from a large adolescent population

Objective The aim of this study was to describe the minimum number of anthropometric measures that will optimally predict insulin resistance (IR) and to characterize the utility of these measures among obese and nonobese adolescents. Research design and methods Six anthropometric measures (selected from three categories: central adiposity, weight, and body composition) were measured from 1298 adolescents attending two New York City public high schools. Body composition was determined by bioelectric impedance analysis (BIA). The homeostatic model assessment of IR (HOMA-IR), based on fasting glucose and insulin concentrations, was used to estimate IR. Stepwise linear regression analyses were performed to predict HOMA-IR based on the six selected measures, while controlling for age. Results The stepwise regression retained both waist circumference (WC) and percentage of body fat (BF%). Notably, BMI was not retained. WC was a stronger predictor of HOMA-IR than BMI was. A regression model using solely WC performed best among the obese II group, while a model using solely BF% performed best among the lean group. Receiver operator characteristic curves showed the WC and BF% model to be more sensitive in detecting IR than BMI, but with less specificity. Conclusion WC combined with BF% was the best predictor of HOMA-IR. This finding can be attributed partly to the ability of BF% to model HOMA-IR among leaner participants and to the ability of WC to model HOMA-IR among participants who are more obese. BMI was comparatively weak in predicting IR, suggesting that assessments that are more comprehensive and include body composition analysis could increase detection of IR during adolescence, especially among those who are lean, yet insulin-resistant.
Hybrid frequency and phase coding for a high-speed SSVEP-based BCI speller

Steady-state visual evoked potential (SSVEP)-based brain-computer interfaces (BCIs) have potential to realize high-speed communication between the human brain and the external environment. Recently, multiple access (MA) methods in telecommunications have been introduced into the system design of BCIs and showed their potential in improving BCI performance. This study investigated the feasibility of hybrid frequency and phase coding methods in multi-target SSVEP-based BCIs. Specifically, this study compared two hybrid target-coding strategies: (1) mixed frequency and phase coding, and (2) joint frequency and phase coding. In a simulated online BCI experiment using a 40-target BCI speller, BCI performance for both coding approaches were tested with a group of six subjects. At a spelling speed of 40 characters per minute (1.5 seconds per character), both approaches obtained high information transfer rates (ITR) (mixed coding: 172.37±28.67 bits/min, joint coding: 170.94±28.32 bits/min) across subjects. There was no statistically significant difference between the two approaches (p>0.05). These results suggest that the hybrid frequency and phase coding methods are highly efficient for multi-target coding in SSVEP BCIs with a large number of classes, providing a practical solution to implement a high-speed BCI speller.
A Methodology for Exposing Process Risk in Emergent System Properties

Determining whether software and systems achieve desired emergent properties, such as safety, reliability, or security, requires an analysis of the system as a whole. This requires the system to be in the latter stages of development, when changes are difficult and costly to implement. In this paper, we propose the Process Risk Assessment (PRA) methodology for analyzing and evaluating such emergent properties earlier in the development cycle. Properties such as safety and reliability result from one or more development processes put in place to help achieve those properties. The PRA method analyzes artifacts from these processes (e.g., designs pertaining to reliability, or safety analysis reports) to determine: 1) whether the process itself is appropriate for achieving the desired property; and 2) whether the process is being followed appropriately. From PRA analysis, process risk can be quantified to indicate whether the system will have the desired properties. We applied this method to evaluate one emergent property, software safety, during the early stages of the development lifecycle for a network-centric, Department of Defense system-of-systems and several NASA spaceflight projects. We analyzed the safety processes implemented on these projects and their resulting artifacts. The PRA methodology identified potential risks in the software safety process and provided feedback to the projects for reducing these risks.
Alterations in vesicle transport and cell polarity in rat hepatocytes subjected to mechanical or chemical cholestasis.

BACKGROUND & AIMS The molecular mechanisms that contribute to the cholestatic condition in hepatocytes are poorly defined. It has been postulated that a disruption of normal vesicle-based protein trafficking may lead to alterations in hepatocyte polarity. METHODS To determine if vesicle motility is reduced by cholestasis, hepatocytes cultured from livers of bile duct ligation (BDL)- or ethinyl estradiol (EE)-injected rats, were viewed and recorded by high-resolution video microscopy. Cholestatic hepatocytes were analyzed by phalloidin staining and electron microscopy. Functional analysis was done by the sodium fluorescein sequestration assay. RESULTS In cholestatic hepatocytes, there was a significant decrease in the number of motile cytoplasmic vesicles observed compared with control cells. Further examination of cells from BDL- or EE-treated livers revealed the presence of numerous large intracellular lumina. More than 24% of cells in BDL-treated livers and 19% of cells in EE-treated livers displayed these structures, compared with 1.1% found in control hepatocytes. Phalloidin staining of hepatocytes showed a prominent sheath of actin surrounding the lumina, reminiscent of those seen about bile canaliculi. Electron microscopy revealed that these structures were lined by actin-filled microvilli. Further, these pseudocanaliculi perform many of the functions exhibited by bona fide canaliculi, such as sequestering sodium fluorescein. CONCLUSIONS Both mechanically and chemically induced cholestasis have substantial effects on vesicle-based transport, leading to marked disruption of hepatocellular polarity.
Body Mass Index and Breast Cancer Defined by Biological Receptor Status in Pre-Menopausal and Post-Menopausal Women: A Multicenter Study in China

Background Few studies have investigated the association between body mass index (BMI) and breast cancer with consideration to estrogen/progesterone/human epidermal growth factor type 2 receptor status (ER/PR/HER2) in the breast tissue among Chinese pre- and post-menopausal women. Methods Four thousand two hundred and eleven breast cancer patients were selected randomly from seven geographic regions of China from 1999 to 2008. Demographic data, risk factors, pathologic features, and biological receptor status of cases were collected from the medical charts. Chi-square test, fisher exact test, rank-correlation analysis, and multivariate logistic regression model were adopted to explore whether BMI differed according to biological receptor status in pre- and post-menopausal women. Results Three thousand two hundred and eighty one eligible cases with BMI data were included. No statistically significant differences in demographic characteristics were found between the cases with BMI data and those without. In the rank-correlation analysis, the rates of PR+ and HER2+ were positively correlated with increasing BMI among post-menopausal women (rs BMI, PR+ = 0.867, P = 0.001; rs BMI, HER2+ = 0.636, P = 0.048), but the ER+ rates did not vary by increasing BMI. Controlling for confounding factors, multivariate logistic regression models with BMI<24 kg/m2 as the reference group were performed and found that BMI≥24 kg/m2 was only positively correlated with PR+ status among post-menopausal breast cancer cases (adjusted OR = 1.420, 95% CI: 1.116–1.808, Wald = 8.116, P = 0.004). Conclusions Post-menopausal women with high BMI (≥24 kg/m2) have a higher proportion of PR+ breast cancer. In addition to effects mediated via the estrogen metabolism pathway, high BMI might increase the risk of breast cancer by other routes, which should be examined further in future etiological mechanism studies.
Factors Associated with Failed Treatment: an Analysis of 121,744 Women Embarking on Their First IVF Cycles

Background In-vitro fertilization (IVF) is the treatment of choice for unresolved infertility. It comprises a number of key steps, each of which has to be negotiated before the next is attempted, but the factors which are associated with failure at each stage have not been reported. Methods and Findings We analyzed anonymised national data on women undergoing their first fresh autologous IVF and intracytoplasmic sperm injection (ICSI) cycle in the United Kingdom between 2000 and 2007 to predict factors associated with overall lack of livebirth as well as the chance of non-progress at different stages of an IVF cycle. A total of 121,744 women were included in this analysis. Multivariable models underlined the importance of increased female age and duration of infertility, lack of previous pregnancy, and a diagnosis of tubal or male factor infertility in predicting the risk of not having a live birth in an IVF treatment. At each stage, a woman’s chance of proceeding to the next stage of IVF treatment is affected by increased age and duration of infertility. The intention to use intra-cytoplasmic sperm injection (ICSI) is associated with a decreased risk of treatment failure in women starting an IVF cycle (RR 0.93, 99% CI 0.92, 0.94) but this association is reversed at a later stage once fertilisation has been confirmed (RR=1.01, 99%CI 1.00, 1.03). Conclusions Female age is a key predictor of failure to have a livebirth following IVF as well as the risk of poor performance at each stage of treatment. While increased duration of infertility is also associated with worse outcomes at every stage, its impact appears to be less influential. Women embarking on ICSI treatment for male factor infertility have a lower chance of treatment failure but this does not appear to be due to increased chances of implantation of ICSI embryos.
Tumor-induced VEGF-C overexpression in retroperitoneal lymph nodes in VX2 carcinoma-bearing rabbits

Objective To establish the retroperitoneal lymph node (RLN) metastasis model of cervical carcinoma in rabbits and evaluate the relationship of vascular endothelial growth factor-C (VEGF-C) expression and the lymph node status. Methods Forty-eight rabbits were injected with VX2 cells or RPMI solution at muscular mucosae of the myometrium 0.5 cm away from the cervix. Animals were treated with or without cis-diamminedichloroplatinum(II) (cisplatin: DDP) and sacrificed on days 15, 21, and 27 post-VX2 or RPMI injections. Tumor mass and RLNs were examined histopathologically. Quantitative real-time PCR was used to examine the changes in VEGF-C mRNA expression. Levels of VEGF-C protein expression in tissues were determined using immunohistochemistry staining. Results Development of VX2 cervical carcinoma and the RLNs metastasis was confirmed with pathological examination. Significantly increased tumor volume was observed on days 15, 21, and 27 postinjection (P<0.05). The enlargement of RLNs was found on day 21. Expression of VEGF-C was significantly upregulated in peripheral white blood cells, tumor mass, and RLNs in an association with cancer progression. DDP resulted in a suppression of VEGF-C expression, whereas the influences on tumor mass and lymphatic metastasis were insignificant. Conclusion Elevated VEGF-C expressions in peripheral white blood cells and RLNs are associated with tumor progression and lymphatic metastasis. DDP treatment inhibits VEGF-C expression and fails to protect against metastatic cervical cancer.
Cutting Edge: The Conversion of Arginine to Citrulline Allows for a High-Affinity Peptide Interaction with the Rheumatoid Arthritis-Associated HLA-DRB1*0401 MHC Class II Molecule1

Rheumatoid arthritis (RA) is genetically associated with MHC class II molecules that contain the shared epitope. These MHC molecules may participate in disease pathogenesis by selectively binding arthritogenic peptides for presentation to autoreactive CD4+ T cells. The nature of the arthritogenic Ag is not known, but recent work has identified posttranslationally modified proteins containing citrulline (deiminated arginine) as specific targets of the IgG Ab response in RA patients. To understand how citrulline might evoke an autoimmune reaction, we have studied T cell responses to citrulline-containing peptides in HLA-DRB1*0401 transgenic (DR4-IE tg) mice. In this study, we demonstrate that the conversion of arginine to citrulline at the peptide side-chain position interacting with the shared epitope significantly increases peptide-MHC affinity and leads to the activation CD4+ T cells in DR4-IE tg mice. These results reveal how DRB1 alleles with the shared epitope could initiate an autoimmune response to citrullinated self-Ags in RA patients.