Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining Human Pathways of Drug Metabolism In Vivo through the Development of a Multiple Humanized Mouse Model

Variability in drug pharmacokinetics is a major factor in defining drug efficacy and side effects. There remains an urgent need, particularly with the growing use of polypharmacy, to obtain more informative experimental data predicting clinical outcomes. Major species differences in multiplicity, substrate specificity, and regulation of enzymes from the cytochrome P450–dependent mono-oxygenase system play a critical role in drug metabolism. To develop an in vivo model for predicting human responses to drugs, we generated a mouse, where 31 P450 genes from the Cyp2c, Cyp2d, and Cyp3a gene families were exchanged for their relevant human counterparts. The model has been improved through additional humanization for the nuclear receptors constitutive androgen receptor and pregnane X receptor that control the expression of key drug metabolizing enzymes and transporters. In this most complex humanized mouse model reported to date, the cytochromes P450 function as predicted and we illustrate how these mice can be applied to predict drug-drug interactions in humans.
Inoculum effect of new beta-lactam antibiotics on Pseudomonas aeruginosa

The degree of the inoculum effect shown by the new beta-lactam antibiotics with Pseudomonas aeruginosa was investigated, and the antibiotics were divided into three groups based upon the observations. The group 1 antibiotics (cefotaxime, moxalactam, cefoperazone, azlocillin, piperacillin, and aztreonam) demonstrated a large inoculum effect, were poorly bactericidal, produced aberrant, elongated bacilli, and did not inhibit the increase in turbidity of high inocula during an 18-h incubation. The group 2 antibiotics (ceftazidime and ticarcillin) were slowly bactericidal, caused minimal formation of aberrant, elongated bacilli, and slowly decreased the turbidity of high inocula. The group 3 antibiotics (imipenem and gentamicin) were bactericidal, did not cause the formation of elongated bacilli, and decreased the turbidity of high inocula rapidly. Data are presented which suggest that the inoculum effect seen with the group 1 beta-lactam antibiotics is related to (i) the poor intrinsic antibactericidal activity of these antibiotics for P. aeruginosa at the inocula tested and (ii) failure of these antibiotics to inhibit the formation of aberrant and filamentous bacilli, which can result in increased bacterial mass and turbidity.
Indonesia sea surface temperature from TRMM Microwave Imaging (TMI) sensor

We analysis the Tropical Rainfall Measuring Mission's (TRMM) Microwave Imager (TMI) data to monitor the sea surface temperature (SST) of Indonesia waters for a decade of 2005-2014. The TMI SST data shows the seasonal and interannual SST in Indonesian waters. In general, the SST average was highest in March-May period with SST average was 29.4°C, and the lowest was in June – August period with the SST average was 28.5°C. The monthly SST average fluctuation of Indonesian waters for 10 years tends to increase. The lowest SST average of Indonesia occurred in August 2006 with the SST average was 27.6° C, while the maximum occurred in May 2014 with the monthly SST average temperature was 29.9 ° C.
The Relation of Intraseasonal Variations With Local Onset and Demise of the Indian Summer Monsoon

Two of the most important hydroclimatic features of the Indian summer monsoon (ISM) rainfall are its onset/demise and intraseasonal oscillations (ISOs) manifested by the active‐break cycles. In this study, we aim to understand the quantitative association between these two phenomena. An objective definition of local onset/demise of the ISM based on more than a century‐long India Meteorological Department rain gauge observation is taken into consideration. Using multichannel singular spectrum analysis we isolate northward‐propagating low‐frequency (20–60 days; LF‐ISO) and northwestward propagating high‐frequency (10–20 days; HF‐ISO) ISOs from the daily ISM rainfall. Our results suggest that a large number of local onset (59%) and demise (62%) events occur during positive developing phases and positive decaying phases of two ISOs, respectively, with phase locking between LF‐ISO and HF‐ISO being particularly important. Local onset is largely associated with favorable phases of ISOs across India except for LF‐ISO over eastern India and HF‐ISO over western Ghats and central India (CI). We find that local demise is more coherent with the ISO phases, especially with HF‐ISO across the domain. We performed a case study to understand large‐scale association with the onset of the ISM over CI. In 44 of total 58 cases (1948–2005), when CI onset occurred during favorable LF‐ISO or HF‐ISO phase, they are either linked with a northward propagation of convection from the equator in LF‐ISO time scale (28 cases) or westward propagating structures from the western Pacific in HF‐ISO time scale (27 cases).
A Magnetic Post Approach for Measuring the Viscoelasticity of Biomaterials

A wide variety of tools are used in studying the viscoelasticity of materials. Devices used range from microbeads dispersed in a fluid to standard cone-and-plate rheometers. In order to further the techniques for in situ testing of materials, we have developed a new microdevice for measuring viscoelasticity. The device uses a polydimethylsiloxane post filled with magnetic microparticles. The force on the post is controlled with oscillating magnetic fields in order to measure properties of a fluid or gel. The device was calibrated with mixtures of glycerol and then used to observe the gelation process for collagen gels. The results from using the new device had good agreement with previous experimental results.
Concurrency Control in Database Systems

Concurrency control mechanisms including the wait, time-stamp and rollback mechanisms have been briefly discussed. The concepts of validation in optimistic approach are summarized in a detailed view. Various algorithms have been discussed regarding the degree of concurrency and classes of serializability. Practical questions relating arrival rate of transactions have been presented. Performance evaluation of concurrency control algorithms including degree of concurrency and system behavior have been briefly conceptualized. At last, ideas like multidimensional timestamps, relaxation of two-phase locking, system defined prewrites, flexible transactions and adaptability for increasing concurrency have been summarized.
Structural and Biochemical Dissection of Photorespiration in Hybrids Differing in Genome Constitution between Diplotaxis tenuifolia (C 3 -C 4 ) and Radish (C 3 ) 1

We compared the structural, biochemical, and physiological characteristics involved in photorespiration of intergeneric hybrids differing in genome constitution (DtDtR, DtDtRR, and DtRR) between the C 3 -C 4 intermediate species Diplotaxis tenuifolia (DtDt) and the C 3 species radish ( Raphanus sativus ; RR). The bundle sheath (BS) cells in D . tenuifolia included many centripetally located chloroplasts and mitochondria, but those of radish had only a few chloroplasts and mitochondria. In the hybrids, the numbers of chloroplasts and mitochondria, the ratio of centripetally located organelles to total organelles, and the mitochondrial size in the BS cells increased with an increase in the constitution ratio of the Dt:R genome. The P-protein of glycine decarboxylase (GDC) was confined to the BS mitochondria in D . tenuifolia , whereas in radish, it accumulated more densely in the mesophyll than in the BS mitochondria. In the hybrids, more intense accumulation of GDC in the BS relative to the mesophyll mitochondria occurred with an increase in the Dt:R ratio. These structural and biochemical features in the hybrids were reflected in the gas exchange characteristics of leaves, such as the CO 2 compen- sation point. Our data indicate that the leaf structure, the intercellular pattern of GDC expression, and the gas exchange characteristics of C 3 -C 4 intermediate photosynthesis are inherited in the hybrids depending on the constitution ratio of the parent genomes. Our findings also demonstrate that the apparent reduced photorespiration in C 3 -C 4 intermediate plants is mainly due to the structural differentiation of mitochondria and chloroplasts in the BS cells combined with the BS-dominant expression of GDC.
Contraceptive failure, method-related discontinuation and resumption of use: results from the 1995 National Survey of Family Growth.

CONTEXT Half of all pregnancies in the United States are unintended. Of these, half occur to women who were practicing contraception in the month they conceived, and others occur when couples stop use because they find their method difficult or inconvenient to use. METHODS Data from the 1995 National Survey of Family Growth were used to compute life-table probabilities of contraceptive failure for reversible methods of contraception, discontinuation of use for a method-related reason and resumption of contraceptive use. RESULTS Within one year of starting to use a reversible method of contraception, 9% of women experience a contraceptive failure--7% of those using the pill, 9% of those relying on the male condom and 19% of those practicing withdrawal. During a lifetime of use of reversible methods, the typical woman will experience 1.8 contraceptive failures. Overall, 31% of women discontinue use of a reversible contraceptive for a method-related reason within six months of starting use, and 44% do so within 12 months; however, 68% resume use of a method within one month and 76% do so within three months. Multivariate analyses show that the risk of contraceptive failure is elevated among low-income women and Hispanic women. Low-income women are also less likely than other women to resume contraceptive use after discontinuation. CONCLUSIONS The risks of pregnancy during typical use of reversible methods of contraception are considerably higher than risks of failure during clinical trials, reflecting imperfect use of these methods rather than lack of inherent efficacy. High rates of method-related discontinuation probably reflect dissatisfaction with available methods.
Multipath Routing Scheme in Solar Powered Wireless Sensor Networks

Constant growth in the wireless sensor network (WSN) needs routing protocol which can cater for renewable energy sources as compared to conventionally used nonrenewable energy sources in sensor nodes. In this paper, adaptive topological knowledge (ATK) algorithm is used to periodically and locally determine the topological knowledge range (KR) of each solar-powered node, based on an estimated energy budget for the following period. Energy budget includes current energy, the predicted energy consumption and the energy expected from the solar cell. Multipath routing scheme (MRS) is used for route selection based on round-robin model. Thus energy optimization is attained during real-time route discovery and packet forwarding by reducing congestion in the network.
High quality machine translation using a machine-learned sentence realization component

We describe the implementation of two new language pairs (English-French and English-German) which use machine-learned sentence realization components instead of hand-written generation components. The resulting systems are evaluated by human evaluators, and in the technical domain, are equal to the quality of highly respected commercial systems. We comment on the difficulties that are encountered when using machine-learned sentence realization in the context of MT.
Extracellular vesicles derived from Staphylococcus aureus induce atopic dermatitis-like skin inflammation

To cite this article: Hong S‐W, Kim M‐R, Lee E‐Y, Kim JH, Kim Y‐S, Jeon SG, Yang J‐M, Lee B‐J, Pyun B‐Y, Gho YS, Kim Y‐K. Extracellular vesicles derived from Staphylococcus aureus induce atopic dermatitis‐like skin inflammation. Allergy 2011; 66: 351–359.
Bitwidth-aware scheduling and binding in high-level synthesis

Many high-level description languages, such as C/C++ or Java, lack the capability to specify the bitwidth information for variables and operations. Synthesis from these specifications without bitwidth analysis may introduce wasted resources. Furthermore, conventional high-level synthesis techniques usually focus on uniform-width resources, thus they cannot obtain the full resource savings even with bitwidth information. This work develops a bitwidth-aware synthesis flow, including bitwidth analysis, scheduling and binding, and register allocation and binding, to exploit the multi-bitwidth nature of operations and variables for area-efficient designs. We also develop lower bound estimation to evaluate the efficiency of our proposed solutions for register allocation and binding. The flow is implemented in the MCAS synthesis system (Cong et al., 2004). Experimental results show that our proposed bitwidth-aware synthesis flow reduces area by 36% and wire-length by 52% on average compared to the uniform-width MCAS flow, while achieving the same performance.
Understanding systematic and collaborative code changes by mining evolutionary trajectory patterns

The life cycle of a large‐scale software system can undergo many releases. Each release often involves hundreds or thousands of revisions committed by many developers over time. Many code changes are made in a systematic and collaborative way. However, such systematic and collaborative code changes are often undocumented and hidden in the evolution history of a software system. It is desirable to recover commonalities and associations among dispersed code changes in the evolutionary trajectory of a software system. In this paper, we present Summarizing Evolutionary Trajectory by Grouping and Aggregation (SETGA), an approach to summarizing historical commit records as trajectory patterns by grouping and aggregating relevant code changes committed over time. The SETGA extracts change operations from a series of commit records from version control systems. It then groups extracted change operations by their common properties from different dimensions such as change operation types, developers, and change locations. After that, SETGA aggregates relevant change operation groups by mining various associations among them. We implement SETGA and conduct an empirical study with 3 open‐source systems. We investigate underlying evolution rules and problems that can be revealed by the identified patterns and analyze the evolution of trajectory patterns in different periods. The results show that SETGA can identify various types of trajectory patterns that are useful for software evolution management and quality assurance.
Evolving migration

Mass migrations of wildebeest, caribou, song birds, sting rays, and monarch butterflies are among the wonders of the natural world (Fig. 1). At a very different scale, the coordinated migration of cells within the body is central to embryological development, immune responses, and wound healing. Although the scale, functions, and mechanisms may differ, these examples share one key feature: they are the product of local interactions among individual agents (wildebeest, butterflies, or cells). The proximate mechanisms where collective behavior arises from local interactions between individuals have become a fertile area of research, founded on models from statistical physics in which interacting agents are modeled as self-propelled particles (1–4). Guttal and Couzin (5) take such analyses to the next level and ask how and under what ecological circumstances might collective migration have evolved.
Long-Term Evaluation of the Risk of Recurrence After Cerebral Sinus-Venous Thrombosis

Background— The clinical course of cerebral sinus-venous thrombosis (CSVT) is largely unknown because prospective studies with a long follow-up and with the goal to assess thrombosis recurrence rate and predisposing factors for recurrence are lacking. Methods and Results— One hundred forty-five patients with a first CSVT were followed up for a median of 6 years after discontinuation of anticoagulant treatment. End points were recurrent CSVT or other clinical manifestations of venous thromboembolism. CSVT recurred in 5 patients (3%) and other manifestations of venous thromboembolism (deep vein thrombosis of the lower limbs or pulmonary embolism) were seen in 10 additional patients (7%), for a recurrence rate of 2.03 per 100 person-years (95% confidence interval, 1.16 to 3.14) for all manifestations of venous thromboembolism and 0.53 per 100 person-years (95% confidence interval, 0.16 to 1.10) for CSVT. Nearly half of the recurrences occurred within the first year after discontinuation of anticoagulant therapy. Risk factors for recurrent venous thrombosis were male sex (adjusted hazard ratio, 9.66; 95% confidence interval, 2.86 to 32.7) and, for thromboses other than CSVT, severe thrombophilia resulting from antithrombin, protein C, protein S deficiency, anti-phospholipid antibodies, or combined abnormalities (adjusted hazard ratio, 4.71; 95% confidence interval, 1.34 to 16.5). Conclusions— The risk of recurrent CSVT is low and is higher in the first year after discontinuation of anticoagulant treatment and among men. Mild thrombophilia abnormalities are not associated with recurrent CSVT, but severe thrombophilia entails an increased risk of deep vein thrombosis of the lower limbs or pulmonary embolism.
Ume6 Is Required for the MATa/MATα Cellular Identity and Transcriptional Silencing in Kluyveromyces lactis

To explore the similarities and differences of regulatory circuits among budding yeasts, we characterized the role of the unscheduled meiotic gene expression 6 (UME6) gene in Kluyveromyces lactis. We found that Ume6 was required for transcriptional silencing of the cryptic mating-type loci HMLα and HMRa. Chromatin immunoprecipitation (ChIP) suggested that Ume6 acted directly by binding the cis-regulatory silencers of these loci. Unexpectedly, a MATa ume6 strain was mating proficient, whereas a MATα ume6 strain was sterile. This observation was explained by the fact that ume6 derepressed HMLα2 only weakly, but derepressed HMRa1 strongly. Consistently, two a/α-repressed genes (MTS1 and STE4) were repressed in the MATα ume6 strain, but were expressed in the MATa ume6 strain. Surprisingly, ume6 partially suppressed the mating defect of a MATa sir2 strain. MTS1 and STE4 were repressed in the MATa sir2 ume6 double-mutant strain, indicating that the suppression acted downstream of the a1/α2-repressor. We show that both STE12 and the MATa2/HMRa2 genes were overexpressed in the MATa sir2 ume6 strain. Consistent with the idea that this deregulation suppressed the mating defect, ectopic overexpression of Ste12 and a2 in a MATa sir2 strain resulted in efficient mating. In addition, Ume6 served as a block to polyploidy, since ume6/ume6 diploids mated as pseudo a-strains. Finally, Ume6 was required for repression of three meiotic genes, independently of the Rpd3 and Sin3 corepressors.
Comparing Nonlinear Regression and Markov Chain Monte Carlo Methods for Assessment of Prediction Uncertainty in Vadose Zone Modeling

In vadose zone modeling, parameter estimates and model predictions are inherently uncertain, regardless of quality and quantity of data used in model‐data fusion. Accurate quantification of the uncertainty is necessary to design future data collection for improving the predictive capability of models. This study is focused on evaluating predictive performance of two commonly used methods of uncertainty quantification: nonlinear regression and Bayesian methods. The former quantifies predictive uncertainty using the regression confidence interval (RCI), whereas the latter uses the Bayesian credible interval (BCI); neither RCI nor BCI includes measurement errors. When measurement errors are considered, the counterparts of RCI and BCI are regression prediction interval (RPI) and Bayesian prediction interval (BPI), respectively. The predictive performance is examined through a cross‐validation study of two‐phase flow modeling, and predictive logscore is used as the performance measure. The linear and nonlinear RCI and RPI are evaluated using UCODE_2005. The nonlinear RCI performs better than the linear RCI, and the nonlinear RPI outperforms the linear RPI. The Bayesian intervals are calculated using Markov Chain Monte Carlo (MCMC) techniques implemented with the differential evolution adaptive metropolis (DREAM) algorithm. The BCI/BPI obtained from DREAM has better predictive performance than the linear and nonlinear RCI/RPI. Different from observations in other studies, it is found that estimating nonlinear RCI/RPI is not computationally more efficient than estimating BCI/BPI in this case with low‐dimensional parameter space and a large number of predictions. MCMC methods are thus more appealing than nonlinear regression methods for uncertainty quantification in vadose zone modeling.
Minimizing User Annotations in the Generation of Layout Ground-Truthed Data

This paper describes the adaptation of a previously developed document recognition framework called PLANET (Physical Layout Analysis of complex structured Arabic documents using artificial neural NETs) into a ground truthing system for complex Arabic document images [8]. PLANET is a layout analysis tool for Arabic documents with complex structures allowing incremental learning in an interactive environment. Artificial neural nets drive the classification of homogeneous text blocks. We have observed that when users use PLANET for ground truthing, the number of interactive corrections is quite large. In order to reduce user intervention and to make use of PLANET as a ground truthing system we have adapted its architecture.
Arsenic Mobility and Groundwater Extraction in Bangladesh

High levels of arsenic in well water are causing widespread poisoning in Bangladesh. In a typical aquifer in southern Bangladesh, chemical data imply that arsenic mobilization is associated with recent inflow of carbon. High concentrations of radiocarbon-young methane indicate that young carbon has driven recent biogeochemical processes, and irrigation pumping is sufficient to have drawn water to the depth where dissolved arsenic is at a maximum. The results of field injection of molasses, nitrate, and low-arsenic water show that organic carbon or its degradation products may quickly mobilize arsenic, oxidants may lower arsenic concentrations, and sorption of arsenic is limited by saturation of aquifer materials.