Miracle-dz/UniFAR-FTUs huggingface dataset:
FPBH . jl : A Feasibility Pump Based Heuristic for Multi-objective Mixed Integer Linear Programming in

Feasibility pump is one of the successful heuristic solution approaches developed almost a decade ago for computing high-quality feasible solutions of single-objective integer linear programs, and it is implemented in exact commercial solvers such as CPLEX and Gurobi. In this study, we present the first Feasibility Pump Based Heuristic (FPBH) approach for approximately generating nondominated frontiers of multi-objective mixed integer linear programs with an arbitrary number of objective functions. The proposed algorithm extends our recent study for bi-objective pure integer programs that employs a customized version of several existing algorithms in the literature of both single-objective and multi-objective optimization. The method has two desirable characteristics: (1) There is no parameter to be tuned by users other than the time limit; (2) It can naturally exploit parallelism. An extensive computational study shows the efficacy of the proposed method on some existing standard test instances in which the true frontier is known, and also some randomly generated instances. We also numerically show the importance of parallelization feature of FPBH and illustrate that FPBH outperforms MDLS developed by Tricoire [39] on instances of multi-objective (1-dimensional) knapsack problem. We test the effect of using different commercial and non-commercial linear programming solvers for solving linear programs arising during the course of FPBH, and show that the performance of FPBH is almost the same in all cases. It is worth mentioning that FPBH is available as an open source Julia package, named as ‘FPBH.jl’, in GitHub. The package is compatible with the popular JuMP modeling language (Dunning et al. [16] and Lubin and Dunning [27]), supports input in LP and MPS file formats. The package can plot nondominated frontiers, can compute different quality measures (hypervolume, cardinality, coverage and uniformity), supports execution on multiple processors and can use any linear programming solver supported by MathProgBase.jl (such as CPLEX, Clp, GLPK, etc).
Theory of optical orientation in n -type semiconductors

Time resolved measurements of magnetization in n-GaAs have revealed a rich array of spin decoherence processes, and have shown that fairly long lifetimes (\sim 100 ns) can be achieved under certain circumstances. In time-resolved Faraday rotation and time-resolved Kerr rotation the evolution of the magnetization can be followed as a function of temperature, applied field, doping level and excitation level. We present a theory for the spin relaxation in n-GaAs based on a set of rate equations for two interacting thermalized subsystems of spins: localized states on donor sites and itinerant states in the conduction band. The conduction band spins relax by scattering from defects or phonons through the D'yakonov-Perel' mechanism, while the localized spins relax by interacting with phonons (when in an applied field) or through the Dzyaloshinskii-Moriya interaction. In this model, numerous features of the data, including puzzling temperature and doping dependences of the relaxation time, find an explanation.
The NIN Transcription Factor Coordinates Diverse Nodulation Programs in Different Tissues of the Medicago truncatula Root[OPEN]

The Medicago truncatula transcription factor NIN coordinates diverse processes during nodulation, restricting ENOD11 expression in the root epidermis and promoting CRE1 expression in the root cortex. Biological nitrogen fixation in legumes occurs in nodules that are initiated in the root cortex following Nod factor recognition at the root surface, and this requires coordination of diverse developmental programs in these different tissues. We show that while early Nod factor signaling associated with calcium oscillations is limited to the root surface, the resultant activation of Nodule Inception (NIN) in the root epidermis is sufficient to promote cytokinin signaling and nodule organogenesis in the inner root cortex. NIN or a product of its action must be associated with the transmission of a signal between the root surface and the cortical cells where nodule organogenesis is initiated. NIN appears to have distinct functions in the root epidermis and the root cortex. In the epidermis, NIN restricts the extent of Early Nodulin 11 (ENOD11) expression and does so through competitive inhibition of ERF Required for Nodulation (ERN1). In contrast, NIN is sufficient to promote the expression of the cytokinin receptor Cytokinin Response 1 (CRE1), which is restricted to the root cortex. Our work in Medicago truncatula highlights the complexity of NIN action and places NIN as a central player in the coordination of the symbiotic developmental programs occurring in differing tissues of the root that combined are necessary for a nitrogen-fixing symbiosis.
Skin autofluorescence, a novel marker for glycemic and oxidative stress-derived advanced glycation endproducts: an overview of current clinical studies, evidence, and limitations.

BACKGROUND Advanced glycation endproducts (AGEs) predict long-term complications in agerelated diseases. However, there are no clinically applicable markers for measuring AGEs in vivo. METHODS We have recently introduced the AGE-Reader (DiagnOptics B.V., Groningen, The Netherlands) to noninvasively measure AGE accumulation in the human skin of the forearm, making use of the characteristic autofluorescence (AF) pattern that AGEs encompass. Skin AF is calculated as a ratio of mean intensities detected from the skin between 420-600 nm and 300-420 nm. It correlates with collagen-linked fluorescence and specific skin AGE levels from skin biopsies in diabetes, renal failure, and control subjects. Skin AF levels are increased in patients with diabetes and renal failure and are associated with the presence of vascular complications. Additionally, skin AF is strongly related to the progression of coronary heart disease and mortality, independently of traditional risk factors. Since skin pigmentation might influence skin AF, we have investigated the relation of relative skin reflectance (R%) to skin AF in subjects with varying skin phototypes (SPT). RESULTS The data presented in this article suggest that only in subjects with an SPT of V and VI or R% <12%, no reliable measurement can be performed. Therefore, the current prototype of the AGE-Reader is suitable for subjects with SPT I-IV or R% >12%, and more research is needed for a broader application. CONCLUSION The AGE-Reader is useful as a noninvasive clinical tool for assessment of risk for long-term vascular complications in diabetes and in other conditions associated with AGE accumulation.
Application of frequential properties of power systems to robustness analysis

This paper studies the application of certain frequency domain properties of a class of power systems to the robustness analysis. The small signal models of a significant class of power systems-namely, systems without resistive losses nor excitation control-was recently shown to meet passivity-like, convex conditions in the frequency domain. A classical benchmark is considered and it is shown that the presence of excitation control and resistive elements does not completely destroy the above-mentioned property, which remains valid in the frequency band associated to the electromechanical modes. The example includes a detailed robustness analysis showing the importance of the a priori knowledge of the frequential properties of these models in the frequency band of interest.
Self-Efficacy, Activity Participation, and Physical Fitness of Asthmatic and Nonasthmatic Adolescent Girls

The prevalence of asthma, lung self-efficacy beliefs, physical activities, and physical fitness of adolescent girls were studied in a private inner-city high school serving a multiethnic, middle-class population using a questionnaire, a test of physical fitness, and an activity log. Twenty-two percent of the 1 72 girls were diagnosed with asthma, and an additional 15% of the girls experienced breathing difficulties. It was found that asthmatic girls were less physically fit, reported lower self-efficacy regarding their lung functioning during vigorous activities, and participated less often in those activities than nonasthmatic girls. Perceived lung efficacy was found to predict girls' subsequent participation in physical activities significantly, even when the effects of asthma, smoking, and physical fitness were controlled statistically.
Energy landscape, structure and rate effects on strength properties of alpha-helical proteins

The strength of protein domains is crucial to identify the mechanical role of protein domains in biological processes such as mechanotransduction, tissue mechanics and tissue remodeling. Whereas the concept of strength has been widely investigated for engineered materials, the strength of fundamental protein material building blocks and how it depends on structural parameters such as the chemical bonding, the protein filament length and the timescale of observation or deformation velocity remains poorly understood. Here we report a systematic analysis of the influence of key parameters that define the energy landscape of the strength properties of alpha-helical protein domains, including energy barriers, unfolding and refolding distances, the locations of folded and unfolded states, as well as variations of the length and pulling velocity of alpha-helical protein filaments. The analysis is facilitated by the development of a double-well mesoscale potential formulation, utilized here to carry out a systematic numerical analysis of the behavior of alpha-helices. We compare the results against widely used protein strength models based on the Bell model, one of the simplest models used to characterize the strength of protein filaments. We find that, whereas Bell-type models are a reasonable approximation to describe the rupture of alpha-helical protein domains for a certain range of pulling speeds and values of energy barriers, the model ceases to hold for very large energy barriers and for very small pulling speeds, in agreement with earlier findings. We conclude with an application of our mesoscale model to investigate the effect of the length of alpha-helices on their mechanical strength. We find a weakening effect as the length of alpha-helical proteins increases, followed by an asymptotic regime in which the strength remains constant. We compare strand lengths found in biological proteins with the scaling law of strength versus alpha-helix filament length. The mesoscale model reported here is generally applicable to other protein filaments that feature a serial array of domains that unfold under applied strain, where a similar length-dependent strength could be observed.
Real-Time Imaging of Fluorescent Flagellar Filaments

ABSTRACT Bacteria swim by rotating flagellar filaments that are several micrometers long, but only about 20 nm in diameter. The filaments can exist in different polymorphic forms, having distinct values of curvature and twist. Rotation rates are on the order of 100 Hz. In the past, the motion of individual filaments has been visualized by dark-field or differential-interference-contrast microscopy, methods hampered by intense scattering from the cell body or shallow depth of field, respectively. We have found a simple procedure for fluorescently labeling cells and filaments that allows recording their motion in real time with an inexpensive video camera and an ordinary fluorescence microscope with mercury-arc or strobed laser illumination. We report our initial findings with cells of Escherichia coli. Tumbles (events that enable swimming cells to alter course) are remarkably varied. Not every filament on a cell needs to change its direction of rotation: different filaments can change directions at different times, and a tumble can result from the change in direction of only one. Polymorphic transformations tend to occur in the sequence normal, semicoiled, curly 1, with changes in the direction of movement of the cell body correlated with transformations to the semicoiled form.
Technical overview of a safe, configurable, pressure tolerant, subsea Lithium Ion battery system for oil and gas deep water fields

A growing trend in efforts to build more effective and efficient subsea chokes, completion and work-over control systems, and marine well containment systems in oil and gas deep water fields is to replace hydraulics with electrical drives. Electrical drives have advantages such as faster, smoother, and more precise valve control, including real-time feedback on valve position and performance. However, such electrical driven valves require higher peak electrical power to operate than one can effectively supply via a cable when the valve is thousands of meters below the surface of the sea. Local batteries deployed subsea near the valves and subsea control modules can serve the peak power needs, or even backup power needs. But heretofore the classic sealed lead acid battery technology of 1900 is too heavy, too big, and does not last long enough to make these solutions as practical or efficient as desired. The subsea Oil and Gas deep water field equipment industry needs battery solutions that deliver more electrical capacity at less weight and smaller size than old technology sealed lead acid (“SLA”). They want to tap what battery industry expert Cerina Mikolajczak from Tesla Motors calls the “awesome Lithium-Ion technology” advantage [1], such as four times (4X) the energy density of SLA, yet the batteries need to be safe, reliable, and easy to use in subsea deployment. Also, achieving configurable size and capacity flexibility, long lasting subsea operating life, subsea pressure tolerance, and pre-certified testing for subsea oil and gas standards and international shipping standards are very important. Further, saving project execution time and cost by avoiding custom battery development is preferred. So this is not just an ordinary battery at all.
Negative regulation of immunoglobulin kappa light-chain gene transcription by a short sequence homologous to the murine B1 repetitive element

B-cell-specific expression of the immunoglobulin kappa light-chain (Ig kappa) gene is in part accomplished by negative regulatory influences. Here we describe a new negatively acting element (termed kappa NE) immediately upstream of the NF-kappa B-binding site in the Ig kappa intronic enhancer. The 27-bp kappa NE sequence is conserved in the corresponding positions in the rabbit and human Ig kappa genes, and the human kappa NE homolog was shown to have a similar negative regulatory activity. Data base searches using the mouse kappa NE sequence revealed a striking homology to murine B1 repetitive sequences. A sequence homologous to kappa NE and B1 was also noted in a previously identified silencer element in the murine T-cell receptor alpha locus. The homologous T-cell receptor alpha locus sequence, but notably not a corresponding 27-bp B1 consensus sequence, showed a negative regulatory potential similar to that of kappa NE. The negative effect of kappa NE by itself was not cell type specific but became so when paired with its 5'-flanking sequence in the Ig kappa enhancer. A short (30-bp) fragment upstream of kappa NE (termed kappa BS) was found to be necessary and sufficient for abolishing the negative effect of kappa NE in B cells. Point mutations in a T-rich motif within the kappa BS sequence allowed the transcriptional repression by kappa NE to be evident in B cells as well as other cells. As suggested by this cell-independent negative activity, proteins binding to the mouse and human kappa NE sequences were identified in all cell types tested.
Diagnosis and correction of multiple logic design errors in digital circuits

This paper presents a technique to correct multiple logic design errors in a gate-level netlist. A number of methods have been proposed for correcting single logic design errors. However, the extension of these methods to more than one error is still very limited. We direct our attention to circuits with a low multiplicity of errors. By assuming different error dependency scenarios, multiple errors are corrected by repeatedly applying a single error search and correction algorithm. Experimental results on correcting double-design errors and triple-design errors on ISCAS and MCNC benchmark circuits are included.
Tapered-tip Teflon catheter: another device for sequential dilation in endoscopic ultrasound-guided hepaticogastrostomy

who had previously undergone a gastrojejunostomy due to a perforated gastric ulcer. He developed hilar cholangiocarcinoma and underwent endoscopic retrograde cholangiopancreatography (ERCP), but duodenal intubation failed because of his surgically altered anatomy. He was therefore scheduled to undergo biliary drainage by endoscopic ultrasound (EUS)-guided hepaticogastrostomy using a therapeutic curved linear echo endoscope (GF-UC 140P; Olympus, Tokyo, Japan). The EUS revealed marked dilation of both intrahepatic bile ducts (●" Fig. 1). After the left intrahepatic bile duct was located using the echo endoscope in a short position, the dilated peripheral ductal branch closest to the transducer was punctured transgastrically using a 19-gauge fine needle aspiration (FNA) needle. After bile had been aspirated and contrast had been injected to visualize the duct, a 0.035-inch jag wire was inserted through the FNA needle and positioned deep within the proximal duct. The tract between the stomachand the left intrahepatic bile duct was then sequentially dilated using 7-Fr up to 10-Fr tapered-tip Teflon catheters (●" Figs. 2 and 3). Finally, a fully covered self-expandable metal stent (SEMS; Flare-type, 100mm× 80mm BK1008F, with an 8.5-Fr introducer (TaeWoong Medical, Gyeonggi-do, South Korea) was successfully inserted through the hepaticogastrostomy tract into the intrahepatic bile duct with satisfactory drainage (●" Fig. 4). Themost important step in this procedure was dilation of the tract between the stomach and the intrahepatic bile duct. Most endoscopists use either an ERCP cannula, a 6or 8.5-Fr cystotome, a 6-Fr bougie, or a 4or 6-mm dilating balloon [1–4]. In this case, we planned to place a new flare-type SEMSwith an 8.5-Fr introducer to prevent migration. From our experience, we prefer not to use the dilating balloon because of the possibility of serious complications such as bleeding, bile leakage, or perforation. Therefore, we made three sizes of tapered-tip Teflon catheters (7-, 8.5-, and 10-Fr;●" Fig. 5). This dilation methodwas not difficult, but required good positioning of the tip of the echo endoscope, which allowed for better handling of the scope and catheter. We believe this technique is another good option for dilation of a hepaticogastrostomy tract that is equally successful but possibly has fewer complications.
Cell-invasive activity of epitope-tagged adenylate cyclase of Bordetella pertussis allows in vitro presentation of a foreign epitope to CD8+ cytotoxic T cells

The adenylate cyclase (AC) toxin (CyaA) of Bordetella pertussis has an invasive catalytic domain (AC domain) which penetrates the cytoplasmic membrane of a variety of eukaryotic cells and intoxicates them by unregulated synthesis of cyclic AMP. Previous work led to identification of five permissive sites in the AC domain at which heterologous peptides are accommodated without affecting its enzymatic properties. We have constructed a set of CyaA toxins tagged at these permissive sites by insertion of a CD8+ T-cell epitope, RPQASGVYMGNLTAQ, from the nucleoprotein of lymphocytic choriomeningitis virus. Introduction of the epitope at any of the five sites did not affect the capacity of the toxin to deliver its AC domain into target cells. Moreover, the toxin with the inserted epitope was shown to sensitize target cells for lysis by epitope-specific CD8+ cytotoxic T lymphocytes in vitro, showing that the tagged AC was processed for presentation of the lymphocytic choriomeningitis virus epitope in association with the major histocompatibility complex class I molecules. This finding indicates that by virtue of delivery of foreign epitopes into the antigen-presenting cells, purpose-designed recombinant CyaAs may be useful for induction of specific major histocompatibility complex class I-restricted cell-mediated immunity also in vivo.
Intraspecific Variability of the Terminal Inverted Repeats of the Linear Chromosome of Streptomyces ambofaciens

ABSTRACT The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.
Overexpression of E2F-1 in Lung and Liver Metastases of Human Colon Cancer is Associated with Gene Amplification

We have shown previously that metastatic tumors of human colorectal cancer (CRC) in lung as compared to liver have high levels of thymidylate synthase (TS) mRNA expression correlated with high levels of E2F-1 mRNA expression. We now report that Comparative Genomic Hybridization (CGH) and DNA PCR analyses of lung and liver metastases of human colon cancer show frequent gains in the region of chromosome 20q and have an increase in gene copy number of E2F-1. Six of 48 lung and liver metastases of human CRC (12.5%) had less than or equal to 1.5 fold increase in gene copies while the remainder (87.5%) had greater than 1.5 fold increase. The mean fold increase in E2F-1 gene copy number in the primary CRC samples (2.76, n=9) is lower than that seen in the metastatic CRC tumors (mean value 3.5 fold, n=48). Primary CRC tumors had significantly higher gene copy number for E2F-1 (mean E2F-1 gene copy number was 2.76 fold, n=9) than matched adjacent normal (mean =2.16, n=9, p=0.06 using paired t test). In as much as TS is transcriptionally regulated by E2F-1, these results provide an explanation for the high levels of TS mRNA noted in some tumor samples.