Miracle-dz/UniFAR-FTUs huggingface dataset:
Tower-Based Validation and Improvement of MODIS Gross Primary Production in an Alpine Swamp Meadow on the Tibetan Plateau

Alpine swamp meadow on the Tibetan Plateau is among the most sensitive areas to climate change. Accurate quantification of the GPP in alpine swamp meadow can benefit our understanding of the global carbon cycle. The 8-day MODerate resolution Imaging Spectroradiometer (MODIS) gross primary production (GPP) products (GPP_MOD) provide a pathway to estimate GPP in this remote ecosystem. However, the accuracy of the GPP_MOD estimation in this representative alpine swamp meadow is still unknown. Here five years GPP_MOD was validated using GPP derived from the eddy covariance flux measurements (GPP_EC) from 2009 to 2013. Our results indicated that the GPP_EC was strongly underestimated by GPP_MOD with a daily mean less than 40% of EC measurements. To reduce this error, the ground meteorological and vegetation leaf area index (LAIG) measurements were used to revise the key inputs, the maximum light use efficiency (emax) and the fractional photosynthetically active radiation (FPARM) in the MOD17 algorithm. Using two approaches to determine the site-specific emax value, we suggested that the suitable emax was about 1.61 g C MJ−1 for this alpine swamp meadow which was considerably larger than the default 0.68 g C MJ−1 for grassland. The FPARM underestimated 22.2% of the actual FPAR (FPARG) simulated from the LAIG during the whole study period. Model comparisons showed that the large inaccuracies of GPP_MOD were mainly caused by the underestimation of the emax and followed by that of the undervalued FPAR. However, the DAO meteorology data in the MOD17 algorithm did not exert a significant affection in the MODIS GPP underestimations. Therefore, site-specific optimized parameters inputs, especially the emax and FPARG, are necessary to improve the performance of the MOD17 algorithm in GPP estimation, in which the calibrated MOD17A2 algorithm (GPP_MODR3) could explain 91.6% of GPP_EC variance for the alpine swamp meadow.
Kinetics of retrovirus production and decay.

There has been only limited success in using recombinant retroviruses to transfer genes for the purposes of human gene therapy, in part because the average number of genes delivered to the target cells (transduction efficiency) is often too low to achieve the desired therapeutic effect [Miller, AD. 1990. Blood 76:271-278; Mulligan RC. 1993. Science 260:926-932; Orkin SH, Motulsky AG. 1995. Report and recommendations of the panel to assess the NIH investment in research on gene therapy. Bethesda, MD: National Institutes of Health. ]. One strategy to improve transduction efficiency is to focus on understanding and improving the processes used to produce recombinant retroviruses. In this report, we characterized the dynamics of retrovirus production and decay in batch cultures of virus producer cells using a simple mathematical model, a recombinant retrovirus encoding the Escherichia coli lacZ gene, and quantitative assays for virus activity and number. We found that the rate at which recombinant retroviruses spontaneously lose their activity (decay) is a strong function of temperature, decreasing roughly 2-fold for every 5 degrees C reduction in temperature, whereas the rate at which retroviruses are produced is only weakly affected by temperature, decreasing about 10% for every 5 degrees C reduction in temperature. In addition, we developed a simple mathematical model of virus production and decay that predicted that the virus titer in batch cultures of virus producer cells would reach a maximum steady-state at a rate that is inversely proportional to the virus decay rate and to a level that is proportional to the ratio of the virus production rate to the virus decay rate. Consistent with the model, we observed that the steady-state levels of virus titer increased more than 3-fold when the cell culture temperature was reduced from 37 to 28 degrees C. Despite their higher titers, virus stocks produced at 28 degrees C, when used in undiluted form so as to mimic human gene transfer protocols, did not transduce substantially more cells than virus stocks produced at 37 degrees C. The implications of our findings on the production of retroviruses for use in human gene therapy protocols are discussed.
Estimating familial loading in SLI: a comparison of direct assessment versus parental interview.

PURPOSE Two approaches commonly used for estimating prevalence of language disorders in families were compared. The 1st involved examining a subset of language items from an investigator-based interview used to record parental information on the language and literacy difficulties in relatives. The 2nd was the direct assessment of ability in immediate family using a battery of standardized verbal ability, language, and literacy assessments. METHOD Using these 2 methods, the prevalence of language and literacy disorders was investigated in the immediate family (n=271) of 93 children with a history of SLI (mean age 13;11 years). RESULTS The overall proportion of relatives with reported language or literacy difficulty was similar for both methods (34.5% for reported difficulties compared with 35% on direct assessment). The present study further explored maternal, paternal, and sibling prevalence rates and strength of agreement between parental interview and direct assessment. When a low cutoff score was used, good agreement (of true negatives and true positives) for reading and spelling difficulties and expressive language between the 2 types of case identification method was found. CONCLUSIONS Parents can be effective identifiers when the impairment is severe (below 2 SDs from the population mean). Poor agreement was observed between report and assessment of receptive language difficulties.
The Epstein-Barr Virus Glycoprotein gp150 Forms an Immune-Evasive Glycan Shield at the Surface of Infected Cells

Cell-mediated immunity plays a key role in host control of viral infection. This is exemplified by life-threatening reactivations of e.g. herpesviruses in individuals with impaired T-cell and/or iNKT cell responses. To allow lifelong persistence and virus production in the face of primed immunity, herpesviruses exploit immune evasion strategies. These include a reduction in viral antigen expression during latency and a number of escape mechanisms that target antigen presentation pathways. Given the plethora of foreign antigens expressed in virus-producing cells, herpesviruses are conceivably most vulnerable to elimination by cell-mediated immunity during the replicative phase of infection. Here, we show that a prototypic herpesvirus, Epstein-Barr virus (EBV), encodes a novel, broadly acting immunoevasin, gp150, that is expressed during the late phase of viral replication. In particular, EBV gp150 inhibits antigen presentation by HLA class I, HLA class II, and the non-classical, lipid-presenting CD1d molecules. The mechanism of gp150-mediated T-cell escape does not depend on degradation of the antigen-presenting molecules nor does it require gp150’s cytoplasmic tail. Through its abundant glycosylation, gp150 creates a shield that impedes surface presentation of antigen. This is an unprecedented immune evasion mechanism for herpesviruses. In view of its likely broader target range, gp150 could additionally have an impact beyond escape of T cell activation. Importantly, B cells infected with a gp150-null mutant EBV displayed rescued levels of surface antigen presentation by HLA class I, HLA class II, and CD1d, supporting an important role for iNKT cells next to classical T cells in fighting EBV infection. At the same time, our results indicate that EBV gp150 prolongs the timespan for producing viral offspring at the most vulnerable stage of the viral life cycle.
Implicit and Explicit Motor Learning in Children with and without Down's Syndrome.

This paper reports as tudy investigating the degree of dissociation between performance shown by children with or without Down’ ss yndrome (DS), matched on non-verbal MA-level, following an implicit or explicit learning procedure. Ta skspecific factors wer et ightly controlled using the same task for both modes of learning. The implicit learning task was based on the manipulation of ag raphic production principle . O ur procedur et rained participants to reverse the principle . I nt he explicit task, participants had to learn the tw or ules that account for this reversed principle. Whether they wer et rained implicitly or explicitly ,p articipants then performed the same test in which the impact of their training was assessed. Children with DS performed as wel la sc ontrols in the implicit learning condition. They benefited less from the explicit learning condition than controls. They appeare dt ob e impaire di nt he ability to recollect explicit information about the implicit training situation in comparison with controls. These results ar ed iscussed in the light of the current literatur eo nt he implicit and explicit modes of learning, and hypotheses ar e formulated about specific information processes that ma yb ei mpaired in individuals with DS.
Measles vaccine effectiveness and risk factors for measles in Dhaka, Bangladesh.

OBJECTIVE To evaluate vaccine effectiveness and to assess risk factors for measles in Dhaka, Bangladesh. METHOD A case-control study, involving 198 cases with 783 age-matched neighbourhood controls and 120 measles cases with 365 age-matched hospital controls, was conducted in 1995-96 in three large hospitals in Dhaka. FINDINGS Measles vaccine effectiveness was estimated at 80% (95% confidence interval (CI) = 60-90%) using neighbourhood controls; very similar results were obtained using hospital controls. Visits to a health facility 7-21 days before onset of any symptoms were associated with increased risk of measles compared with neighbourhood (adjusted odds ratio (OR) = 7.0, 95% CI = 4.2-11.6) or hospital (adjusted OR = 1.7, 95% CI = 1.01-2.8) controls. Cases were more likely than controls to come from a household where more than one child lived (adjusted OR = 1.6, 95% CI = 1.1-2.5 versus neighbourhood controls; adjusted OR = 1.8, 95% CI = 1.02-3.0 versus hospital controls). CONCLUSIONS To improve measles control in urban Dhaka missed immunization opportunities must be reduced in all health care facilities by following WHO guidelines. For measles elimination, more than one dose of vaccine would be required.
Monitoring environmental quality at the landscape scale

ver the past century, technological advances have greatly improved the standard of living in the United States. But these same advances have caused sweeping environmental changes, often unforeseen and potentially irreparable. Ethical stewardship of the environment requires that society monitor and assess environmental changes at the national scale with a view toward the conservation and wise management of our natural resources. Some of the most important environmental changes occur a t the spatial scale of landscapes. Obvious examples include clearcutting for lumber, urbanization, the loss of wetlands, and the conversion of forest and prairies into crop and grazing systems. Decisions about how to change land cover may be made by individual landowners, but their im-
New Ways of Generating Large Realistic Benchmarks for Testing Synthesis Tools

In this paper we propose several methods of generating large benchmark circuits for testing logic synthesis tools. The benchmarks are derived from real circuits, so that they are functionally equivalent to their origins. We introduce misleading and/or redundant structures into them, making the benchmark size blow up significantly, with respect to the original circuit. Such benchmarks can be advantageously used for testing logic synthesis tools; the aim is to discover whether particular synthesis processes are sensitive or immune to particular circuit transformations.
The resourcefulness of everyday design

We discuss our study that looks at family members as everyday designers. We explain the design actions of family members to be creative, as evidenced by the resourceful appropriation of artifacts and surroundings, the ongoing adaptation of systems and routines through design-in-use that allows emergent properties to arise and addresses individual needs, and how implicit understanding and explicit tests occur for judging quality. We present a preliminary analysis of design implications in the area of interaction design in the home. Our findings are based on a five-month ethnographic study of three families.
Learning weights for codebook in image classification and retrieval

This paper presents a codebook learning approach for image classification and retrieval. It corresponds to learning a weighted similarity metric to satisfy that the weighted similarity between the same labeled images is larger than that between the differently labeled images with largest margin. We formulate the learning problem as a convex quadratic programming and adopt alternating optimization to solve it efficiently. Experiments on both synthetic and real datasets validate the approach. The codebook learning improves the performance, in particular in the case where the number of training examples is not sufficient for large size codebook.
B Cell–Intrinsic and –Extrinsic Regulation of Antibody Responses by PARP14, an Intracellular (ADP-Ribosyl)Transferase

The capacity to achieve sufficient concentrations of Ag-specific Ab of the appropriate isotypes is a critical component of immunity that requires efficient differentiation and interactions of Ag-specific B and Th cells along with dendritic cells. Numerous bacterial toxins catalyze mono(ADP-ribosyl)ation of mammalian proteins to influence cell physiology and adaptive immunity. However, little is known about biological functions of intracellular mammalian mono(ADP-ribosyl)transferases, such as any ability to regulate Ab responses. poly-(ADP-ribose) polymerase 14 (PARP14), an intracellular protein highly expressed in lymphoid cells, binds to STAT6 and encodes a catalytic domain with mammalian mono(ADP-ribosyl)transferase activity. In this article, we show that recall IgA as well as the STAT6-dependent IgE Ab responses are impaired in PARP14-deficient mice. Whereas PARP14 regulation of IgE involved a B cell–intrinsic process, the predominant impact on IgA was B cell extrinsic. Of note, PARP14 deficiency reduced the levels of Th17 cells and CD103+ DCs, which are implicated in IgA regulation. PARP14 enhanced the expression of RORα, Runx1, and Smad3 after T cell activation, and, importantly, its catalytic activity of PARP14 promoted Th17 differentiation. Collectively, the findings show that PARP14 influences the class distribution, affinity repertoire, and recall capacity of Ab responses in mice, as well as provide direct evidence of the requirement for protein mono-ADP-ribosylation in Th cell differentiation.
Arabidopsis Actin Depolymerizing Factor4 Modulates the Stochastic Dynamic Behavior of Actin Filaments in the Cortical Array of Epidermal Cells[C][W]

Actin filaments in the cortical cytoskeleton of epidermal cells undergo rapid turnover that is based on fast polymerization and prolific severing. Here, advanced imaging techniques and reverse-genetic analyses are used to demonstrate that an actin depolymerizing factor (ADF4) contributes to the disassembly of filaments through its stochastic severing activity. Actin filament arrays are constantly remodeled as the needs of cells change as well as during responses to biotic and abiotic stimuli. Previous studies demonstrate that many single actin filaments in the cortical array of living Arabidopsis thaliana epidermal cells undergo stochastic dynamics, a combination of rapid growth balanced by disassembly from prolific severing activity. Filament turnover and dynamics are well understood from in vitro biochemical analyses and simple reconstituted systems. However, the identification in living cells of the molecular players involved in controlling actin dynamics awaits the use of model systems, especially ones where the power of genetics can be combined with imaging of individual actin filaments at high spatial and temporal resolution. Here, we test the hypothesis that actin depolymerizing factor (ADF)/cofilin contributes to stochastic filament severing and facilitates actin turnover. A knockout mutant for Arabidopsis ADF4 has longer hypocotyls and epidermal cells when compared with wild-type seedlings. This correlates with a change in actin filament architecture; cytoskeletal arrays in adf4 cells are significantly more bundled and less dense than in wild-type cells. Several parameters of single actin filament turnover are also altered. Notably, adf4 mutant cells have a 2.5-fold reduced severing frequency as well as significantly increased actin filament lengths and lifetimes. Thus, we provide evidence that ADF4 contributes to the stochastic dynamic turnover of actin filaments in plant cells.
Research Paper: ALICE: An Algorithm to Extract Abbreviations from MEDLINE

OBJECTIVE To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE (Abbreviation LIfter using Corpus-based Extraction). ALICE aims to extract all types of abbreviations with their expansions from a target paper on the fly. METHODS ALICE extracts an abbreviation and its expansion from the literature by using heuristic pattern-matching rules. This system consists of three phases and potentially identifies valid 320 abbreviation-expansion patterns as combinations of the rules. RESULTS It achieved 95% recall and 97% precision on randomly selected titles and abstracts from the MEDLINE database. CONCLUSION ALICE extracted abbreviations and their expansions from the literature efficiently. The subtly compiled heuristics enabled it to extract abbreviations with high recall without significantly reducing precision. ALICE does not only facilitate recognition of an undefined abbreviation in a paper by constructing an abbreviation database or dictionary, but also makes biomedical literature retrieval more accurate. This system is freely available at http://uvdb3.hgc. jp/ALICE/ALICE_index. html.
LOSSLESS COMPRESSION OF X-RAY CARDIAC IMAGES

Digital medical imaging systems like Picture Archiving and Communication System (PACS) has become a crucial tool supporti ng both decision making and treatment procedures in medical en vironments. Advantages come from reduced storage and management costs associated with image data and increased intra an d interinstitutional portability of data in communication networ ks. One of the most important benefits of the digital medical image is th at it allows the widespread sharing and remote access to medical d at by outside institutions. Mass storage and digital communic ation systems costs are continuously decreasing, but, as individ ual igital medical studies become significantly larger, requirem ents for transmission bandwidth and data storage capacity still exc eed available technologies. Image compression algorithms offer the means to minimize storage cost and to increase transmission speed . This paper provides a comparison about the application of Digita l Im ging and Communication in Medicine (DICOM) lossless compres sion standards on Angiography cine acquisition images. Moreove r, some other state-of-the-art compression schemes are evaluated wh n applied on angiographic images. We also propose new direction s f r the lossless compression of this type of images, based on exp loring a third dimension of the data. Preliminary results are presen ted using some lossless video compression methods.
Is Continuous Positive Airway Pressure an Effective and Practical Antihypertensive Agent?

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