Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of novel hypoxia-responsive factors in deep-water rice conferring tolerance to flood during germination

Flood in rice fields at the time of seed sowing and early seedling establishment causes extensive crop loss due to the inability of the seeds to tolerate and overcome submergence. In the present study, rice genotypes from Assam, India tolerant to hypoxia during germination were identified through systematic screening of deep-water rice genotype collection from flood-prone ecosystem of Brahmaputra river valley. The difference in tolerance to hypoxia during germination within the species provides scope for identification of novel hypoxia-responsive factors involved in tolerance as mechanism of tolerance may not be conserved across tolerant germplasms. Tolerant genotypes were further subjected to physiological and molecular characterization. Growth rate kinetics in tolerant genotypes new Rangdhakekua bao (RKB) and cultivar Khao Hlan On (KHO) from International Rice Research Institute (IRRI) used as positive control exhibited stronger escape strategy under hypoxic condition compared to sensitive genotype IR-64 (negative control). Activities of α-amylase and pyruvate decarboxylase were significantly higher in RKB and KHO than in IR-64, while no significant difference was observed in the alcohol dehydrogenase activity. Reverse transcription quantitative PCR confirmed increased amounts of transcripts of sucrose nonfermenting 1 related protein kinase, myeloblastosis-related protein S1, rice amylase 3D, and trehalose phosphate phosphatase 7 genes, which are known to be involved in hypoxia signaling cascade. Besides, transcription factors (TFs) like ethylene responce factors 71 and 63, ethylene insensitive 3-like 1a and proteins like expansins A7 and A2, which are involved in cell elongation had also significantly higher amounts in RKB compared to IR-64. Additional factors that include TFs like ERF71 and ERF63 that shows perturbation at transcription even within tolerant genotypes might constitute the genotype-specific regulation, evolved as a part of its adaptive mechanism to survive under submerged conditions.
The MRZ-Reaction and Specific Autoantibody Detection for Differentiation of ANA-Positive Multiple Sclerosis From Rheumatic Diseases With Cerebral Involvement

Objective: Rheumatic diseases with involvement of the central nervous system (RDwCNS) may mimic multiple sclerosis (MS). Inversely, up to 60% of MS-patients have antinuclear autoantibodies (ANAs) and may be misdiagnosed as RDwCNS. The detection of antibodies against extractable nuclear antigens (ENA) and oligoclonal bands (OCB) are established valuable diagnostic tools in the differential diagnosis of RDwCNS and MS. The MRZ-reaction (MRZR) is defined by three antibody indices (AIs) against neurotropic viruses and is frequently positive in MS. To investigate the added value of MRZR combined with testing for antibodies against ENAs and OCB detection to distinguish RDwCNS from ANA positive MS. Methods: MRZR was evaluated in RDwCNS (n = 40) and 68 ANA positive MS-patients. Two stringency levels, MRZR-1 and MRZR-2 (at least one respectively two of three AIs positive) were applied. Autoantibody testing included ANA plus ENA and anti-dsDNA antibodies, antiphospholipid antibodies, and anti-neutrophil cytoplasmic antibodies. Results: Most of the RDwCNS patients (n = 32; 80%) suffered from systemic lupus erythematosus. Within the RDwCNS group 20% had a positive MRZR-1 and 8.5% a positive MRZR-2 compared to 80.9 and 60%, respectively within the MS-group (p < 0.0001 for both comparisons). Oligoclonal bands were found in 28.6% of the RDwCNS patients and 94.3% of the MS-patients (p < 0.0001). Conversely, autoantibodies to specific nuclear antigens or phospholipids were found more frequently in RDwCNS. A positive MRZR in conjunction with the absence of ENA autoantibodies distinguished MS from RDwCNS with high specificity (97.5%). Conclusions: We suggest combining MRZR, OCBs, and specific autoantibody diagnostics to differentiate RDwCNS from MS.
The Shadow Economy, Human Development and Foreign Direct Investment Inflows

During the past few decades, competition between countries has intensified. Every country seeks to become an essential player in international economic relations and take a prominent place in the world market. In this context, foreign direct investment inflows are accepted as a source of competitiveness through knowledge, know-how and technology transfer, but competitiveness is also accepted as a significant determinant of foreign direct investment attraction. Therefore, the specification of foreign direct investment inflow determinants is also important to improve competitiveness. In this research article, we aim to evaluate the impact of shadow economies and human development on foreign direct investment inflows as a possible determinant of competitiveness in 11 post-transition EU members over 1995-2015 period. The methodology employed in the applied section includes comparative and systematic literature analysis as well as second generation panel cointegration and causality analyses regarding both cross-sectional dependence and heterogeneity. The empirical analyses revealed that both the shadow economy and human development are significant determinants of foreign direct investment inflows. The causality analysis revealed a mutual interaction between foreign direct investment inflows and human development for all the countries in the sample, but a two-way causality between the foreign direct investment inflows and shadow economies only for Bulgaria, Croatia, and Romania and a one-way causality from shadow economies to the foreign direct investment inflows in the Czech Republic, Estonia, Hungary, Latvia, Lithuania, Poland, Slovakia, and Slovenia. The long-run analysis revealed that shadow economies negatively affected foreign direct investment inflows, while human development positively affected foreign direct investment inflows.
Adverse event profiles of solvent-based and nanoparticle albumin-bound paclitaxel formulations using the Food and Drug Administration Adverse Event Reporting System

Objectives: Paclitaxel is a highly effective antitumor agent with notable adverse events, including hypersensitivity reactions, peripheral neuropathy, arthralgia, myalgias, and neutropenia. Solvent-based paclitaxel causes severe allergic, hypersensitivity, and anaphylactic reactions. Nanoparticle albumin-bound paclitaxel was recently developed and provides an advantage over solvent-based paclitaxel in avoiding solvent/surfactant-related adverse events. The aim of this study was to assess the adverse event profiles of solvent-based paclitaxel and nanoparticle albumin-bound paclitaxel formulations using data from the spontaneous adverse event reporting system of the US Food and Drug Administration Adverse Event Reporting System database. Methods: This study relied on Medical Dictionary for Regulatory Activities preferred terms and standardized queries, and calculated the reporting ratio and reporting odds ratios of paclitaxel formulations. Results: Of 8,867,135 reports recorded in the US Food and Drug Administration Adverse Event Reporting System database from January 2004 to December 2016, 3469 and 4447 adverse events corresponded to solvent-based paclitaxel and nanoparticle albumin-bound paclitaxel, respectively. Reporting odds ratios (95% confidence interval) for anaphylactic reaction (standardized MedDRA query code: 20000021) associated with the use of solvent-based paclitaxel and nanoparticle albumin-bound paclitaxel were 1.69 (1.56–1.84) and 0.75 (0.68–0.83), respectively. Reporting odds ratio signal for anaphylactic reaction was not detected for nanoparticle albumin-bound paclitaxel. Reporting odds ratios (95% confidence interval) for acute renal failure (standardized MedDRA query code: 20000003) associated with the use of solvent-based paclitaxel and nanoparticle albumin-bound paclitaxel were 0.75 (0.58–0.98) and 1.60 (1.37–1.89), respectively. Conclusion: This is the first study to evaluate the adverse event profile of nanoparticle albumin-bound paclitaxel using US Food and Drug Administration Adverse Event Reporting System data. Considering that the US Food and Drug Administration Adverse Event Reporting System database does not allow to infer causality or risk ranking, the different reporting frequencies of anaphylactic reaction and acute renal failure between solvent-based paclitaxel and nanoparticle albumin-bound paclitaxel must be further investigated via analytical observational research.
Woody plant distributions along an Amazon-to-Andes elevation gradient: evolutionary trends and tendencies

With high taxonomic turnover and exceptional levels of endemism, tropical montane forests are one of the most biodiverse ecosystems on the planet. The taxa within these forests frequently occupy narrow elevational ranges, and display upslope migration rates insufficient to track predicted temperature increases. Consequently, tropical montane forests and the diversity within them are expected to be susceptible to declines in abundance and potential extinction under ongoing environmental change. Substantial changes to biodiversity patterns across elevation may have significant consequences for the carbon and nutrient cycles as well as the regulation of hydrological processes provided by these forests. In this thesis I examine the diversity and distribution trends of woody plants across a tropical montane forest elevation gradient on the Amazonian flank of the Peruvian Andes, stretching from 425 to 3625 m asl. I consider the influence of the major environmental changes which occur over elevation, such as decreasing temperature. A particular focus is on the transitions which occur at the cloud-base ecotone, above which forests are defined by frequent and prolonged cloud immersion. I apply an evolutionary perspective, using phylogenetic approaches throughout this research. Closely related evolutionary lineages are frequently similar in terms of their ecology and functional characteristics, yet the influence of this tendency on the elevational distribution pattern of woody plants within tropical montane forest has received limited attention Using census data from a network of one-hectare plots, in combination with phylogenetic information, covering a breadth of vascular plant diversity, from angiosperms and gymnosperms to pteridophyte tree ferns, I investigate the influence of evolutionary heritage on elevational distribution trends at the genus level. I further employ these plot data to reflect on the differences between taxonomic and phylogenetic richness patterns across elevation. A deeper consideration of the way variation in the evolutionary age structure of communities can influence diversity trends is also undertaken. In order to test the consistency of elevational patterns between genus and species scales,
Effect of Dynamic Versus Stylet-Guided Intubation on First-Attempt Success in Difficult Airways Undergoing Glidescope Laryngoscopy: A Randomized Controlled Trial.

BACKGROUND Tracheal intubation failure in patients with difficult airway is still not uncommon. While videolaryngoscopes such as the Glidescope offer better glottic vision due to an acute-angled blade, this advantage does not always lead to an increased success rate because successful insertion of the tube through the vocal cords may be the limiting factor. We hypothesize that combined use of Glidescope and fiberscope used only as a dynamic guide facilitates tracheal intubation compared to a conventional Glidescope technique with a preshaped nondynamic stylet. METHODS One hundred sixty adult patients with predicted difficult airway were randomly assigned to a conventional Glidescope (standard Glidescope group) or a combined Glidescope + fiberscope group intubation. In the Glidescope + fiberscope group under direct vision from the Glidescope, tracheal intubation was performed using the fiberscope as a guide without using fiberoptic vision, while in the standard Glidescope group, a conventional stylet-guided intubation technique was performed. We evaluated the rate of tracheal intubation success at first attempt as the primary end point (Fisher exact test). The difference between groups in airway injury, time to successful intubation, and the need for an alternative technique was also evaluated. RESULTS First-attempt intubation success was higher in the Glidescope + fiberscope group than in the standard Glidescope group (91% vs 67%; P = .0012; fragility index, 8; absolute risk reduction, 24% [95% CI, 12%-36%]). Median time to successful tracheal intubation was shorter in the Glidescope + fiberscope group (50 vs 64 seconds; P = .035). Airway injury rate was lower in the Glidescope + fiberscope group than in the standard Glidescope group (1% vs 11%; P = .035; fragility index, 1; absolute risk reduction, 10% [95% CI, 3%-18%]). Alternative rescue technique requirements to achieve tracheal intubation were higher in the standard Glidescope group (24% vs 4%; P < .001; fragility index, 7). CONCLUSIONS The use of a dynamic, flexible guide during a Glidescope laryngoscopy in patients with a predicted difficult airway compared to a standard intubation technique improves first-attempt intubation success, decreases the incidence of airway injury and time to successful intubation, as well as the need of an alternative technique to succeed.
Randomized Trial of an Innovative Electronic Screening and Brief Intervention for Reducing Drinking Among Women of Childbearing Age.

OBJECTIVES To evaluate the efficacy of an innovative, self-administered, electronic Screening and Brief Intervention (e-SBI) in English and Spanish, "DrinkWise," for reducing drinking among nonpregnant women of childbearing age. METHODS A parallel design, phase 1 trial included 185 nonpregnant women reporting risky drinking (8 or more drinks in a week or 3 or more drinks in a day) who were recruited from 2 publicly funded Nutritional Assistance for Women, Infants and Children (WIC) program sites in the United States from 2016 to 2017. Participants were 18 to 44 years in age, 75% of Hispanic ethnicity, 44% Spanish speakers, 30% had not completed high school, and 15% were currently breastfeeding. Participants were randomized to receive (intervention condition, n = 99) or not receive (control condition, no intervention, n = 86) DrinkWise and followed at 3 and 6 months. RESULTS Women receiving DrinkWise had greater reductions in the odds of self-reported weekly alcohol use (odds ratio [OR] = 0.22, SE = 0.12, P < 0.01) and heavy alcohol use (OR = 0.23, SE = 0.14, P < 0.05) at 6-month follow-up than controls, with no group differences at 3-month follow-up. Compared with heavy drinking controls, heavy drinkers receiving DrinkWise showed a trend (P = 0.06) for greater reductions in drink (pour) size from 3- to 6-month follow-up. CONCLUSIONS DrinkWise may be efficacious in reducing drinking among low-income women of childbearing age and provides a low-cost tool for increasing access to recommended SBI among childbearing-age women. Studies should continue to build DrinkWise's evidence base. TRIAL REGISTRATION: ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/NCT02337361.
Direct Saliva Real Time Polymerase Chain Reaction Assay Shows Low Birth Prevalence of Congenital CMV Infection in Urban Western India.

BACKGROUND Congenital cytomegalovirus infection is the leading infectious cause of mental retardation, developmental delay and sensorineural deafness. Non primary infection plays a major role in transmission of this infection in countries with high maternal seroprevalence. Non invasive sampling and testing is a useful alternative to traditional methods of laboratory detection of congenital CMV infection. The present study was conducted to understand birth prevalence of congenital cytomegalovirus (cCMV) infection using molecular techniques, in an urban setting of a developing country with evidence of high maternal seroprevalence. METHODS Universal newborn screening for cCMV was performed for 750 infants born at a tertiary care centre in Western India. Real-time PCR was directly carried out on saliva samples. Follow up laboratory testing of saliva, urine and blood was performed for neonates identified as positive. Sequential clinical follow up was offered to the affected infants. RESULTS A birth prevalence of 0.4% (95% CI 0.13-1.2) was observed with 3 of 750 babies confirmed to be positive for cCMV infection. All three babies were born to seropositive mothers (anti CMV IgG positive). One of the babies detected was symptomatic with sepsis like features. All of them survived and did not develop any sequelae upto one year of age. CONCLUSION The use of direct real-time PCR of saliva samples can be considered as a feasible option for newborn screening of congenital CMV infection in developing countries. Relatively low birth prevalence of cCMV infection was observed in our study, which needs to be corroborated through further studies.
Can Vegetation Removal Successfully Restore Coastal Dune Biodiversity?

Coastal dune habitats have been declining globally over the last several decades due to rapid urbanization. Within remaining dune systems, dune fixation has resulted in further losses of mobile dunes with negative impacts on their associated species. Some studies suggest vegetation removal can initially promote habitat heterogeneity, and increase availability of suitable habitats for psammophile, xeric and endemic mobile dune species, but longer-term responses are generally unknown. We investigated the temporal trends of four taxonomic groups to determine the effect of vegetation removal on dune assemblages over a 12-year period at an LTER site. Three different forms of removal are investigated here—removal in a grid form on fixed dunes, removal of the wind-facing slope vegetation on semi-fixed dunes and opportunistic off-road driving on disturbed dunes. Results were varied across taxa, highlighting the need for multi-taxa monitoring in conservation and restoration management. Overall, fixed dune treatment had very little effect, while a stronger response was found in semi-fixed treatments in particular for mobile dune indicator species, which showed evidence of recolonization within a few years following treatment. Disturbed dunes were most similar to mobile dunes for animal taxa indicating that pulse removal may not be as effective as continuous press disturbance. Nevertheless, a less destructive form of disturbance such as re-introduction of grazing might be preferable and requires further investigation.
Quantification of Three Dimensional Characteristics of Macrofauna Macropores and Their Effects on Soil Hydraulic Conductivity in Northern Vietnam

Soil bioturbation is associated with the production of soil macropores that influence numerous ecological functions such as those associated with water infiltration and the generation of runoff water. This impact is especially important on sloping lands in the tropics that are highly susceptible to erosion. In this study, we questioned the influence of soil biodiversity on soil macropore properties (> 20 mm3) and saturated hydraulic conductivity (Ksat) on sloping land in northern Vietnam. Biostructures found at the soil surface (casts, sheetings and soil excavated on the ground) were used to identify areas colonized either by earthworms, termites or dung beetles, respectively. The influence of soil macrofauna on Ksat was measured in situ using the Beerkan method below bioturbated zones and compared to the surrounding soil without visible biostructures at the soil surface. Undisturbed soil columns were afterwards sampled and scanned by X-ray computed tomography (X-CT). Properties of macropores below each biostructure depicted a large variability, revealing the complexity of the macropore network. Further, galleries made by termites, dung beetles and earthworms were manually isolated from the rest of macroporosity. Galleries made by beetles, termites and earthworms were clearly differentiated on the basis of their diameter, verticality, sphericity, tortuosity, length and number of branches and the fraction of galleries in the top part of the column and. Ksat was most increased by dung beetles (45-fold), then by termites (30-fold) and to a lesser extent by earthworms (16-fold). Relationships between total macropore properties and Ksat showed that the most important properties explaining Ksat were (i) the volume of percolating macropores, (ii) the diameter, (iii) the critical macropore diameter and (iv) the number of macropores. In conclusion, this study confirmed not only the interest in using X-CT for the quantification of macroporosity but also the absence of a clear relationship between aboveground biostructures and macropore properties and functional impacts.
Toward a Variable Stiffness Surgical Manipulator Based on Fiber Jamming Transition

Soft robots have proved to represent a new frontier for the development of intelligent machines able to show new capabilities that can complement those currently performed by robots based on rigid materials. One of the main application areas where this shift is promising an impact is minimally invasive surgery. In previous works, the STFF-FLOP soft manipulator has been introduced as a new concept of using soft materials to develop endoscopic tools. In this paper, we present a novel kind of stiffening system based on fiber jamming transition that can be embedded in the manipulator to widen its applicability by increasing its stability and with the possibility to produce and transmit higher forces. The STIFF-FLOP original module has been re-designed in two new versions to incorporate the variable stiffness mechanism. The two designs have been evaluated in terms of dexterity and variable stiffness capability and, despite a general optimization rule did not clearly emerge, the study confirmed that fiber jamming transition can be considered an effective technological approach for obtaining variable stiffness in slender soft structures.
What You Say and How You Say it: Joint Modeling of Topics and Discourse in Microblog Conversations

This paper presents an unsupervised framework for jointly modeling topic content and discourse behavior in microblog conversations. Concretely, we propose a neural model to discover word clusters indicating what a conversation concerns (i.e., topics) and those reflecting how participants voice their opinions (i.e., discourse). 1 Extensive experiments show that our model can yield both coherent topics and meaningful discourse behavior. Further study shows that our topic and discourse representations can benefit the classification of microblog messages, especially when they are jointly trained with the classifier.Our data sets and code are available at: http://github.com/zengjichuan/Topic_Disc.
Deep Gaussian Processes for Multi-fidelity Modeling

Multi-fidelity methods are prominently used when cheaply-obtained, but possibly biased and noisy, observations must be effectively combined with limited or expensive true data in order to construct reliable models. This arises in both fundamental machine learning procedures such as Bayesian optimization, as well as more practical science and engineering applications. In this paper we develop a novel multi-fidelity model which treats layers of a deep Gaussian process as fidelity levels, and uses a variational inference scheme to propagate uncertainty across them. This allows for capturing nonlinear correlations between fidelities with lower risk of overfitting than existing methods exploiting compositional structure, which are conversely burdened by structural assumptions and constraints. We show that the proposed approach makes substantial improvements in quantifying and propagating uncertainty in multi-fidelity set-ups, which in turn improves their effectiveness in decision making pipelines.