Miracle-dz/UniFAR-FTUs huggingface dataset:
Biomolecule detection using a silicon nanoribbon: accumulation mode versus inversion mode

Silicon nanoribbons were fabricated using standard optical lithography from silicon on insulator material with top silicon layer thicknesses of 100, 60 and 45 nm. Electrically these work as Schottky-barrier field-effect transistors and, depending on the substrate voltage, electron or hole injection is possible. The current through the nanoribbon is extremely sensitive to charge changes at the oxidized top surface and can be used for biomolecule detection in a liquid. We show that for detection of streptavidin molecules the response is larger in the accumulation mode than in the inversion mode, although not leading to higher detection sensitivity due to increased noise. The effect is attributed to the location in depth of the conducting channel, which for holes is closer to the screened surface charges of the biomolecules. Furthermore, the response increases for decreasing silicon thickness in both the accumulation mode and the inversion mode. The results are verified qualitatively and quantitatively through a two-dimensional simulation model on a cross section along the nanoribbon device.
Differential Sensitivities of the Human ATP-Binding Cassette Transporters ABCG2 and P-Glycoprotein to Cyclosporin A

Several ATP-binding cassette (ABC) transporters can confer multidrug resistance to cancer cells by functioning as energy-dependent efflux pumps. The half-transporter ABCG2 and the widely studied P-glycoprotein (P-gp) are two ABC transporters that, when overexpressed, are capable of extruding a variety of structurally unrelated chemotherapy agents from cells. In this study, we demonstrate that human ABCG2 and P-glycoprotein, despite overlapping substrate specificities, differ in sensitivity to the immunomodulator cyclosporin A. In this study, we used human ABCG2 and human P-gp, each expressed separately in drug-selected MCF-7 sublines and transiently transfected HeLa cells. By flow cytometric analysis using the fluorescent substrates rhodamine 123 and mitoxantrone, we showed that cyclosporin A inhibits P-gp function at low micromolar concentrations, whereas ABCG2 function was unaffected. Furthermore, P-gp, but not ABCG2, was able to transport [3H]cyclosporin A directly in intact cells. We also demonstrated, for the first time, that [125I]iodoarylazidoprazosin, a photoaffinity analog of the substrate prazosin, labels multiple variants of ABCG2 specifically and that this labeling, although competed by some ABCG2 substrates, is unaffected by cyclosporin A. These labeling data also suggest the presence of multiple drug binding sites in ABCG2. In addition, cyclosporin A had no effect on the basal or prazosin-stimulated ATPase activity of ABCG2, whereas both the basal and verapamil-stimulated ATPase activities of P-gp were inhibited markedly. Together, our results suggest that cyclosporin A is neither a substrate nor an inhibitor of the human ABCG2 transporter, under the conditions and concentrations examined.
A top-down design environment for developing pipelined datapaths

This paper presents a design environment for cycle-based systems, such as microprocessors, that permits modeling of these systems at various levels, from the abstract system level, through the detailed RTL level, to an actual implementation. The environment allows the models to be refined to lower levels in a step-wise manner. The environment provides the ability to obtain meaningful metrics from abstract models of a processor's architecture. This capability allows design alternatives to be evaluated earlier in the design cycle, thus eliminating costly redesign and reducing the processor time to market.
Strategic exploration in human adaptive control

How do people explore in order to gain rewards in uncertain dynamical systems? Within a reinforcement learning paradigm, control normally involves trading off between exploration (i.e. trying out actions in order to gain more knowledge about the system) and exploitation (i.e. using current knowledge of the system to maximize reward). We study a novel control task in which participants must steer a boat on a grid, assessing whether participants explore strategically in order to produce higher rewards later on. We find that participants explore strategically yet conservatively, exploring more when mistakes are less costly and practicing actions that will be needed later on.
Quasi-positive realization of externally positive discrete systems

The positive realization of externally positive systems described by their transfer matrix H(z) is a difficult problem whose analysis has been completed only recently on the basis of algebraic and geometric approaches that underline the many constraints that condition the solution of this problem. These constraints concern the minimal order of the obtained models, the minimality of their parameterizations and even their existence; the positive realization becomes, on the contrary, a standard task under simple sufficiency conditions on H(z) that, however, are seldom fulfilled in practical applications. This paper introduces the new category of quasi-positive state-space models that limit the assumptions on the non negativeness of the state-space trajectories to the only trajectories that can be actually generated by the system under nonnegative controls since all other behaviors are of no interest in control problems. It is shown that all externally positive systems admit a quasi-positive minimally parameterized state-space realization whose existence is not conditioned by restrictions on the signs of the coefficients in H(z).
An 8-approximation algorithm for the subset feedback vertex set problem

We present an 8-approximation algorithm for the problem of finding a minimum weight subset feedback vertex set. The input in this problem consists of an undirected graph G=(V,E) with vertex weights w(v) and a subset of vertices S called special vertices. A cycle is called interesting if it contains at least one special vertex. A subset of vertices is called a subset feedback vertex set with respect to S if it intersects every interesting cycle The goal is to find a minimum weight subset feedback vertex set. The best pervious algorithm for the general case provided only a logarithmic approximation factor. The minimum weight subset feedback vertex set problem generalizes two NP-Complete problems: the minimum weight feedback vertex set problem in undirected graphs and the minimum weight multiway vertex cut problem. The main tool that we use in our algorithm and its analysis is a new version of multi-commodity flow which we call relaxed multi-commodity flow. Relaxed multi-commodity flow is a hybrid of multi-commodity flow and multi-terminal flow.
Search on Secondary Attributes in Geo-Distributed Systems

In the age of big data, more and more applications need to query and analyse large volumes of continuously updated data in real-time. In response, cloud-scale storage systems can extend their interface that allows fast lookups on the primary key with the ability to retrieve data based on non-primary attributes. However, the need to ingest content rapidly and make it searchable immediately while supporting low-latency, high-throughput query evaluation, as well as the geo-distributed nature and weak consistency guarantees of modern storage systems pose several challenges to the implementation of indexing and search systems. We present our early-stage work on the design and implementation of an indexing and query processing system that enables realtime queries on secondary attributes of data stored in geo-distributed, weakly consistent storage systems.
Multi-Label Classification with Label Constraints

We extend the multi-label classication setting with constraints on labels. This leads to two new machine learning tasks: First, the label constraints must be properly integrated into the classication process to improve its performance and second, we can try to automatically derive useful constraints from data. In this paper, we experiment with two constraint-based correction approaches as post-processing step within the ranking by pairwise comparison (RPC)-framework. In addition, association rule learning is considered for the task of label constraints learning. We report on the current status of our work, together with evaluations on synthetic datasets and two real-world datasets.
Proof search issues in some non-classical logics

This thesis develops techniques and ideas on proof search. Proof search is used with one of two meanings. Proof search can be thought of either as the search for a yes/no answer to a query (theorem proving), or as the search for all proofs of a formula (proof enumeration). This thesis is an investigation into issues in proof search in both these senses for some non-classical logics. Gentzen systems are well suited for use in proof search in both senses. The rules of Gentzen sequent calculi are such that implementations can be directed by the top level syntax of sequents, unlike other logical calculi such as natural deduction. All the calculi for proof search in this thesis are Gentzen sequent calculi. In Chapter 2, permutation of inference rules for Intuitionistic Linear Logic is studied. A focusing calculus, ILLF, in the style of Andreoli ([And92]) is developed.This calculus allows only one proof in each equivalence class of proofs equivalent up to permutations of inferences. The issue here is both theorem proving and proof enumeration. For certain logics, normal natural deductions provide a proof-theoretic semantics. Proof enumeration is then the enumeration of all these deductions. Herbelin’s cutfree LJT ([Her95], here called MJ) is a Gentzen system for intuitionistic logic allowing derivations that correspond in a 1–1 way to the normal natural deductions of intuitionistic logic. This calculus is therefore well suited to proof enumeration. Such calculi are called ‘permutation-free’ calculi. In Chapter 3, MJ is extended to a calculus for an intuitionistic modal logic (due to Curry) called Lax Logic. We call this calculus PFLAX. The proof theory of MJ is extended to PFLAX. Chapter 4 presents work on theorem proving for propositional logics using a history mechanism for loop-checking. This mechanism is a refinement of one developed by Heuerding et al ([HSZ96]). It is applied to two calculi for intuitionistic logic and also to two modal logics: Lax Logic and intuitionistic S4. The calculi for intuitionistic logic are compared both theoretically and experimentally with other decision procedures for the logic. Chapter 5 is a short investigation of embedding intuitionistic logic in Intuitionistic Linear Logic. A new embedding of intuitionistic logic in Intuitionistic Linear Logic is given. For the hereditary Harrop fragment of intuitionistic logic, this embedding induces the calculus MJ for intuitionistic logic. In Chapter 6 a ‘permutation-free’ calculus is given for Intuitionistic Linear Logic. Again, its proof-theoretic properties are investigated. The calculus is proved to besound and complete with respect to a proof-theoretic semantics and (weak) cutelimination is proved. Logic programming can be thought of as proof enumeration in constructive logics. All the proof enumeration calculi in this thesis have been developed with logic programming in mind. We discuss at the appropriate points the relationship between the calculi developed here and logic programming. Appendix A contains presentations of the logical calculi used and Appendix B contains the sets of benchmark formulae used in Chapter 4
Patient Portal as a Tool for Enhancing Patient Experience and Improving Quality of Care in Primary Care Practices

Introduction: This study assessed whether patient portals influence patients’ ability for self-management, improve their perception of health state, improve their experience with primary care practices, and reduce healthcare utilization. Methods: Patients participating in a nurse-led care coordination program received personalized training to use the portal to communicate with the care team. Data analysis included pre-post comparison of self-efficacy (CDSES), health state (EQVAS), functional status (PROMIS®), experience with the provider/practice (CG-CAHPS), and healthcare utilization (admissions and ED visits). Results: A total of 94 patients were enrolled, and 92 (Intent to Treat) were followed up for 7 months to assess their experience, and for 12 months to assess healthcare utilization. Seventy four (mean age 60+13 years) used the portal (Users). Comparison between baseline and 7-month follow-up showed no statistically significant improvements in self-efficacy, perception of health state or experience with the primary care practice. Only functional status improved significantly. ED visits/1000 patients were reduced by 26% and 21% in the Intent to Treat and Users groups, respectively. Hospital admissions/1000 patients were reduced by 46% in the Intent to Treat group and by 38% in the Users group. Discussion: For patients in care coordination, having access to patient portals may improve access to providers and health data that lead to improvements in patients’ functional status and reduce high-cost healthcare utilization, but it does not seem to improve self-efficacy, perception of health state, or experience with primary care practices. Conclusion: In this study, the use of patient portals improved functional status and reduced high-cost healthcare utilization in patients with chronic conditions.
A Functional Polymorphism in a STAT5B Site of the Human PPAR&ggr;3 Gene Promoter Affects Height and Lipid Metabolism in a French Population

Objective—The peroxisome proliferator-activated receptor-&ggr; (PPAR&ggr;) plays a role in adipocyte differentiation and insulin sensitization. It has been shown that genetic variation in the PPAR&ggr; gene alters body weight control, lipid and insulin homeostasis, and the susceptibility to type 2 diabetes. Four PPAR&ggr; isoforms are generated by alternative splicing and promoter usage. PPAR&ggr;3 is only expressed in adipose tissue, colon, and macrophages and therefore seems to be a good candidate gene for metabolic and cardiovascular-associated diseases. In the present study, we looked for genetic variation in the PPAR&ggr;3 promoter. Methods and Results—The proximal PPAR&ggr;3 promoter was sequenced in 20 individuals. We detected a C/G polymorphism at position −681 from exon A2. Interestingly, it was located in a signal transducer and activator of transcription 5B (STAT5B) binding consensus site. In a French population (n=836), the −681G allele was associated with increased height and plasma low-density lipoprotein cholesterol concentrations. In vitro, we showed that the −681G allele completely abolished the binding of STAT5B to the cognate promoter element as well as the transactivation of the PPAR&ggr;3 promoter by the growth hormone/STAT5B pathway. Conclusions—Our results suggest that PPAR&ggr;3 may regulate the control of height and lipid homeostasis via the STAT5B pathway.
Accuracy of pen injectors versus insulin syringes in children with type 1 diabetes.

OBJECTIVE To compare the accuracy and precision of insulin syringes and pen devices used by children with type 1 diabetes and their parents. RESEARCH DESIGN AND METHODS There were 48 subjects (32 patients, a parent of an additional 16 patients) instructed to measure out morning insulin doses three times from vials and/or cartridges containing saline mixed with small amounts of [14C]glucose (solution used as regular insulin) and [3H]glucose (solution used as NPH insulin) and to dispense the contents into a scintillation vial. Statistical analysis was used to determine the accuracy and precision of both methods of insulin delivery. RESULTS The absolute error in measuring out doses of regular insulin < 5 U was greater with insulin syringes compared with pen injection devices (9.9 +/- 2.4 vs. 4.9 +/- 1.6%, respectively). Both were comparable for regular insulin doses > 5 U (3.2 +/- 0.6 vs. 2.2 +/- 0.4% for syringes and pens, respectively). The accuracy in drawing up NPH doses was similar for low and high insulin doses (mean percent error of 7.5 +/- 1.5 vs. 5.6 +/- 1.1%). CONCLUSIONS Pen devices are more accurate than insulin syringes in measuring out insulin at low insulin doses. The accuracy of insulin syringes improves when higher doses of regular insulin are measured out and becomes comparable to pen devices.
A decision rule for sequential monitoring of clinical trials with a primary and supportive outcome

Background Many clinical trials have multiple outcomes. Formal interim monitoring guidelines that take account of multiple outcomes can be useful to Data Monitoring Committees (DMC). Previous research has focused on marginal criteria that control the overall type I error for bivariate endpoints corresponding to efficacy and safety. Usually, an `or' decision rule is used, that is, the trial is stopped when either the safety or the efficacy endpoint crosses a boundary. Purpose In many trials there is not a clear difference between what is considered a safety and an efficacy endpoint. Likewise, in some studies there is interest in more than one disease outcome and while there may be a primary efficacy endpoint, interim monitoring might also involve a measure of overall health. For these situations, an `and' decision rule might be more appropriate; that is, the trial is stopped only when both endpoints cross a boundary. Formulation of this new decision rule at the design stage would encourage more discussion among trial investigators of monitoring guidelines and would result in improved guidelines for DMCs. Methods In this paper, we propose stopping guidelines for such trials with two major outcomes that control the overall type I error and stop early only if both endpoints indicate superiority for the same treatment. Trials with two treatments are considered and we develop sets of paired two-sided boundaries, permitting one endpoint to be primary and the other supportive, with or without pre-specifying which one is primary. Results The results show that the boundaries depend on the correlation between the two outcomes. The critical values increase as the correlation increases in most cases. For low to moderate correlation and before the last stage, critical values based on the O'Brien Fleming (or Pocock) error spending function that consider the correlation are lower than those which do not. Limitations Investigators might not want to stop a trial early with the small size of the critical values that result from this decision rule for some situations. For a trial in which the treatment effect for one outcome is large, while for the other it is small, the proposed decision rule has low power to accept this treatment for its superiority on both outcomes. Also, we do not provide a separate P-value for each outcome since type I error is not controlled for individual null hypotheses. Conclusions For trials involving two major health outcomes these stopping guidelines may be appropriate for DMCs when the trial investigators and sponsor recommend that early termination not be considered unless the findings are consistent for both outcomes. Clinical Trials 2007; 4: 140—153. http://ctj.sagepub. com
Glucocorticoid-Induced Bone Loss Is Associated with Abnormal Intravertebral Areal Bone Mineral Density Distribution

Individuals with glucocorticoid-induced osteoporosis experience vertebral fractures at an increased rate and at higher vertebral areal bone mineral density (aBMD) than individuals with primary osteoporosis. Standard posteroanterior- (PA-) projection dual energy X-ray absorptiometry (DXA) lacks the diagnostic sensitivity required for reliable estimation of vertebral fracture risk in individuals. Assessment of subregional vertebral aBMD using lateral-projection DXA may improve the predictive value of DXA parameters for fracture. One hundred and four individuals were recruited and grouped for this study: primary osteoporosis with no history of vertebral fracture (n = 43), glucocorticoid-induced bone loss (n = 13), and healthy controls (n = 48). Standard PA-projection and supine-lateral scans were performed, and lateral scans were analysed according to an established protocol to measure aBMD within 6 subregions. Main effects for subregion and group were assessed and observed, by ANCOVA. Ratios were calculated between subregions and compared between groups, to overcome the potentially confounding influence of variability in subregional geometry. Significantly lower values were observed in the glucocorticoid group for the ratios of (i) anterior subregion: whole vertebral body and (ii) posterior: whole vertebral body when compared to the primary osteoporosis and control groups (P < 0.05). Lower anterior subregional aBMD in individuals on glucocorticoid therapy may help to explain the increased vertebral fracture risk in this patient group.
Computing a self-confirming equilibrium in two-player extensive-form games

The Nash equilibrium is the most commonly adopted solution concept for non-cooperative interaction situations. However, it underlays on the assumption of common information that is hardly verified in many practical situations. When information is not common, the appropriate game theoretic solution concept is the self-confirming equilibrium. It requires that every agent plays the best response to her beliefs and that the beliefs are correct on the equilibrium path. We present, to the best of our knowledge, the first study on the computation of a self-confirming equilibrium for two-player extensive-form games. We provide algorithms, we analyze the computational complexity, and we experimentally evaluate the performance of our algorithms in terms of computational time.
[Comparative evaluation of in vitro activities of carbapenems against gram-negative pathogens: Turkish data of COMPACT study].

The aim of this study was to determine the in vitro activities of doripenem, imipenem, and meropenem against clinical gram-negative isolates. A total of 596 clinical isolates were obtained from intensive care unit (ICU) and non-ICU patients in 10 centers over Turkey between September-December 2008. The origin of the isolates was patients with nosocomial pneumonia (42.4%), bloodstream infections (%40.4), and complicated intraabdominal infections (17.1%). Of the isolates, 51.8% were obtained from ICU patients. The study isolates consisted of Pseudomonas spp. in 49.8%, Enterobacteriaceae in 40.3%, and other gram-negative agents in 9.9%. The minimum inhibitory concentrations (MIC) for doripenem, imipenem and meropenem were determined for all isolates in each center using Etest® strips (AB Biodisk, Solna, Sweden). Of the isolates, 188 (31.5%) were resistant to at least one of the carbapenems. MIC50 of doripenem against Pseudomonas spp. Was 1 mg/L which was similar to that of meropenem and two-fold lower than imipenem. Susceptibility to carbapenems in P.aeruginosa was 64% for doripenem at an MIC level of 2 mg/L, 53.9% and 63% for imipenem and meropenem at an MIC level of 4 mg/L, respectively. Doripenem and meropenem showed similar activity with the MIC90 of 0.12 mg/L whereas imipenem was four-fold less active at 0.5 mg/L. Against other gramnegative pathogens, mostly Acinetobacter spp. , MIC50 was 8 mg/L for doripenem and 32 mg/L for other two carbapenems. P.aeruginosa isolates were inhibited 84.2% with doripenem and 72.1% with meropenem at the MIC level of 8 mg/L. Doripenem generally showed similar or slightly better activity than meropenem and better activity than imipenem against pathogens collected in this study. Against Pseudomonas spp. , doripenem was the most active of the three carbapenems. Doripenem and meropenem were equally active against Enterobacteriaceae and at least four-fold more active than imipenem. It was concluded that doripenem seemed to be a promising agent in the treatment of nosocomial pneumonia, blood stream infections and intraabdominal infections particularly in patients who were under risk of developing antimicrobial resistance.