Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular Proton Concentrations Impacts LN229 Glioblastoma Tumor Cell Fate via Differential Modulation of Surface Lipids

Background Glioblastoma multiforme (GBM) is a highly aggressive form of brain cancer with marginal survival rates. GBM extracellular acidosis can profoundly impact its cell fate heterogeneities and progression. However, the molecules and mechanisms that enable GBM tumor cells acid adaptation and consequent cell fate competencies are weakly understood. Since extracellular proton concentrations (pHe) directly intercept the tumor cell plasma membrane, surface lipids must play a crucial role in pHe-dependent tumor cell fate dynamics. Hence, a more detailed insight into the finely tuned pH-dependent modulation of surface lipids is required to generate strategies that can inhibit or surpass tumor cell acid adaptation, thereby forcing the eradication of heterogeneous oncogenic niches, without affecting the normal cells. Results By using image-based single cell analysis and physicochemical techniques, we made a small-scale survey of the effects of pH ranges (physiological: pHe 7.4, low: 6.2, and very low: 3.4) on LN229 glioblastoma cell line surface remodeling and analyzed the consequent cell fate heterogeneities with relevant molecular targets and behavioral assays. Through this basic study, we uncovered that the extracellular proton concentration (1) modulates surface cholesterol-driven cell fate dynamics and (2) induces ‘differential clustering’ of surface resident GM3 glycosphingolipid which together coordinates the proliferation, migration, survival, and death reprogramming via distinct effects on the tumor cell biomechanical homeostasis. A novel synergy of anti-GM3 antibody and cyclophilin A inhibitor was found to mimic the very low pHe-mediated GM3 supraclustered conformation that elevated the surface rigidity and mechano-remodeled the tumor cell into a differentiated phenotype which eventually succumbed to the anoikis type of cell death, thereby eradicating the tumorigenic niches. Conclusion and significance This work presents an initial insight into the physicochemical capacities of extracellular protons in the generation of glioblastoma tumor cell heterogeneities and cell death via the crucial interplay of surface lipids and their conformational changes. Hence, monitoring of proton–cholesterol–GM3 correlations in vivo through diagnostic imaging and in vitro in clinical samples may assist better tumor staging and prognosis. The emerged insights have further led to the translation of a ‘pH-dependent mechanisms of oncogenesis control’ into the surface targeted anti-GBM therapeutics.
Design of a 60 GHz, 100 kW Cw Gyrotron for Plasma Diagnostics: Gds-V.01 Simulations

In this work, the design studies of a 60GHz, 100kW CW gyrotron have been presented. Mode selection is carefully studied with the aim of minimizing mode competition and to yield a perfect solid beam output through an RF window with a suitable dimpled-wall quasi-optical launcher. Cavity design and interaction computations are then carried out. In addition, preliminary design of the magnetron injection gun, magnetic guidance system, launcher, and RF window are presented. Thus, we present a feasibility study, which indicates that the operation of such a gyrotron is possible and can give a power in excess of 100kW at an e-ciency > 35%. As a part of this work, a complete Graphical User Interface package \GDS V.01" (Gyrotron Design Suit Ver.01) has been developed for the design and conceptualization of speciflc gyrotrons.
Particle filtering by sigmoidal weight update for speech pitch correction

We propose a pitch track correction technique using a sigmoidal objective function in a particle filtering framework. The conventional method for pitch track correction simply considers the peak locations of the autocorrelation functions as the pitch values and depends only on the longest reliable pitch streak. This constraint may induce pitch correction errors. The proposed approach uses particle filtering to further correctly track the pitch values. To apply the particle filtering algorithm to pitch track correction, a method for the importance weight computation using a sigmoidal function on foreground streams is proposed. The similarity between the the estimated pitch values and the subband signals are computed, and a sigmoid transfer function is used to convert it as a probability value. To verify the efficiency of our proposed approach, we carried out speech segregation experiments for mixtures of speech and various noise sources in various mixing signal-to-noise ratios (SNRs). With respect to several performance measures including SNR, energy loss ratio, and noise residue ratio of the segregated speech, the proposed method achieved superior performance compared to the conventional approach.
Prediction of Drug Clearance by Glucuronidation from in Vitro Data: Use of Combined Cytochrome P450 and UDP-Glucuronosyltransferase Cofactors in Alamethicin-Activated Human Liver Microsomes

Glucuronidation via UDP-glucuronosyltransferase (UGT) is an increasingly important clearance pathway. In this study intrinsic clearance (CLint) values for buprenorphine, carvedilol, codeine, diclofenac, gemfibrozil, ketoprofen, midazolam, naloxone, raloxifene, and zidovudine were determined in pooled human liver microsomes using the substrate depletion approach. The in vitro clearance data indicated a varying contribution of glucuronidation to the clearance of the compounds studied, ranging from 6 to 79% for midazolam and gemfibrozil, respectively. The CLint was ob tained using either individual or combined cofactors for cytochrome P450 (P450) and UGT enzymes with alamethicin activation and in the presence and absence of 2% bovine serum albumin (BSA). In the presence of combined P450 and UGT cofactors, CLint ranged from 2.8 to 688 μl/min/mg for zidovudine and buprenorphine, respectively; the clearance was approximately equal to the sum of the CLint values obtained in the presence of individual cofactors. The unbound intrinsic clearance (CLint, u) was scaled to provide an in vivo predicted CLint; the data obtained in the presence of combined cofactors resulted in 5-fold underprediction on average. Addition of 2% BSA to the incubation with both P450 and UGT cofactors reduced the bias in the clearance prediction, with 8 of 10 compounds predicted within 2-fold of in vivo values with the exception of raloxifene and gemfibrozil. The current study indicates the applicability of combined cofactor conditions in the assessment of clearance for compounds with a differential contribution of P450 and UGT enzymes to their elimination. In addition, improved predictability of microsomal data is observed in the presence of BSA, in particular for UGT2B7 substrates.
Cell cycle regulation in Caulobacter: location, location, location

Cellular reproduction in all organisms requires temporal and spatial coordination of crucial events, notably DNA replication, chromosome segregation and cytokinesis. Recent studies on the dimorphic bacterium Caulobacter crescentus (Caulobacter) highlight mechanisms by which positional information is integrated with temporal modes of cell cycle regulation. Caulobacter cell division is inherently asymmetric, yielding progeny with different fates: stalked cells and swarmer cells. Cell type determinants in stalked progeny promote entry into S phase, whereas swarmer progeny remain in G1 phase. Moreover, initiation of DNA replication is allowed only once per cell cycle. This finite window of opportunity is imposed by coordinating spatially constrained proteolysis of CtrA, an inhibitor of DNA replication initiation, with forward progression of the cell cycle. Positional cues are equally important in coordinating movement of the chromosome with cell division site selection in Caulobacter. The chromosome is specifically and dynamically localized over the course of the cell cycle. As the duplicated chromosomes are partitioned, factors that restrict assembly of the cell division protein FtsZ associate with a chromosomal locus near the origin, ensuring that the division site is located towards the middle of the cell.
Providing confidentiality in content-based publish/subscribe systems

Publish/subscribe is a loosely-coupled communication paradigm which allows applications to interact indirectly and asynchronously. Publisher applications generate events that are sent to interested applications through a network of brokers. Subscriber applications express their interests by specifying filters that brokers can use for routing the events. In many cases it is desirable to protect the confidentiality of events and filters from any unauthorised parties, including the brokers themselves. Supporting confidentiality of messages being exchanged is challenging mainly because of the decoupling of publishers and subscribers who should not have to share keys, and because brokers forward messages based on the actual content of the messages that we desire to keep confidential. This paper argues that a complete solution for confidentiality in pub/sub systems should provide: (i) confidentiality of events and filters; (ii) filters that can express very complex constraints on events even if brokers are not able to access any information on both events and filters; (iii) and finally it does not require publishers and subscribers to share keys. We show that current solutions are not able to provide all these properties at the same time and suggest a possible solution based on attribute-based encryption and encrypted search.
Efficient Algorithms for Mining Top-K High Utility Itemsets

High utility itemsets (HUIs) mining is an emerging topic in data mining, which refers to discovering all itemsets having a utility meeting a user-specified minimum utility threshold min_util. However, setting min_util appropriately is a difficult problem for users. Generally speaking, finding an appropriate minimum utility threshold by trial and error is a tedious process for users. If min_util is set too low, too many HUIs will be generated, which may cause the mining process to be very inefficient. On the other hand, if min_util is set too high, it is likely that no HUIs will be found. In this paper, we address the above issues by proposing a new framework for top-k high utility itemset mining, where k is the desired number of HUIs to be mined. Two types of efficient algorithms named TKU (mining Top-K Utility itemsets) and TKO (mining Top-K utility itemsets in One phase) are proposed for mining such itemsets without the need to set min_util. We provide a structural comparison of the two algorithms with discussions on their advantages and limitations. Empirical evaluations on both real and synthetic datasets show that the performance of the proposed algorithms is close to that of the optimal case of state-of-the-art utility mining algorithms.
Capturing a taxonomy of failures during automatic interpretation of questions posed in natural language

An important problem in artificial intelligence is capturing, from natural language, formal representationsallthat can be used by a reasoner to compute an answer. Many researchers have studied this problem by developing algorithms addressing specific phenomena in natural language interpretation, but few have studied (or cataloged) the types of failures associated with this problem. Knowledgeallof these failures can help researchers by providing a roadallmap of open research problems and help practitioners by providing a checklist of issues to address in order to build systems that can achieve good performance on this problem.allIn this paper, we present a study -- conducted in the context of the Halo Project -- cataloging the types of failures that occur when capturing knowledge from naturallanguage. We identified the categories of failures by examining a corpus of questions posed byallnaive usersallto a knowledge based question answering system and empirically demonstrated the generality of ourallcategorizations. We also describe available technologies that can address some of the failures we have identified.
Joint optimization of cloud and edge processing for fog radio access networks

This work studies the joint design of cloud and edge processing for the downlink of a fog radio access network (F-RAN). In an F-RAN, cloud processing is carried out by a baseband processing unit (BBU) that is connected to enhanced remote radio heads (eRRHs) by means of fronthaul links. Edge processing is instead enabled by local caching of popular content at the eRRHs. Focusing on the design of the delivery phase for an arbitrary pre-fetching strategy, a novel superposition coding approach is proposed that is based on the hybrid use of the fronthaul links in both hard-transfer and soft-transfer modes. With the former, non-cached files are communicated over the fronthaul links to a subset of eRRHs, while, with the latter, the fronthaul links are used to convey quantized baseband signals as in a cloud RAN (C-RAN). The problem of maximizing the delivery rate is tackled under fronthaul capacity and per-eRRH power constraints. Numerical results are provided to validate the performance of the proposed hybrid delivery scheme for different baseline pre-fetching strategies.
Structural graph-based representations used for finding hidden patterns

In graph-based data mining (GBDM) tasks, an accurate data representation is fundamental for finding hidden patterns. However, there does not exist a standard representation to describe structural data because of the specific domain characteristics. Then, different graph topologies could be used as data representation, which is a challenge for GBDM tools. In this paper we explore a methodology for discovering hidden patterns in domains where is used a graph based representation. Our methodology is divided in three phases: first, we propose a formal graph notation used to symbolizes our graphs; second, we perform the data mining phase using the SI-COBRA and the SUBDUE tools; finally, we show how could be interpreted the outputs of these tools. We performed a set of experiments in two different domains where our methodology was applied: the web log and the SAT domains. With these examples we show how it is possible to symbolize our graphs with our notation, and also perform the GBDM task with the selected tools.
The Fox-1 Family and SUP-12 Coordinately Regulate Tissue-Specific Alternative Splicing In Vivo

ABSTRACT Many pre-mRNAs are alternatively spliced in a tissue-specific manner in multicellular organisms. The Fox-1 family of RNA-binding proteins regulate alternative splicing by either activating or repressing exon inclusion through specific binding to UGCAUG stretches. However, the precise cellular contexts that determine the action of the Fox-1 family in vivo remain to be elucidated. We have recently demonstrated that ASD-1 and FOX-1, members of the Fox-1 family in Caenorhabditis elegans, regulate tissue-specific alternative splicing of the fibroblast growth factor receptor gene, egl-15, which eventually determines the ligand specificity of the receptor in vivo. Here we report that another RNA-binding protein, SUP-12, coregulates the egl-15 alternative splicing. By screening for mutants defective in the muscle-specific expression of our alternative splicing reporter, we identified the muscle-specific RNA-binding protein SUP-12. We identified juxtaposed conserved stretches as the cis elements responsible for the regulation. The Fox-1 family and the SUP-12 proteins form a stable complex with egl-15 RNA, depending on the cis elements. Furthermore, the asd-1; sup-12 double mutant is defective in sex myoblast migration, phenocopying the isoform-specific egl-15(5A) mutant. These results establish an in vivo model that coordination of the two families of RNA-binding proteins regulates tissue-specific alternative splicing of a specific target gene.
Time Series Prediction as a Problem of Missing Values: Application to ESTSP2007 and NN3 Competition Benchmarks

In this paper, time series prediction is considered as a problem of missing values. A method for the determination of the missing time series values is presented. The method is based on two projection methods: a nonlinear one (Self-Organized Maps) and a linear one (Empirical Orthogonal Functions). The presented global methodology combines the advantages of both methods to get accurate candidates for the prediction values. The methods are applied to two time series competition datasets.
Descemet-stripping Automated Endothelial Keratoplasty: Insertion Using a Novel 40/60 Underfold Technique for Preservation of Donor Endothelium

Purpose: To describe a technique for insertion of an asymmetrically folded donor graft to minimize endothelial damage during Descemet-stripping automated endothelial keratoplasty. Methods: The tissue is folded in a 40/60 underfold rather than the commonly used 60/40 overfold. It is then grasped with the insertion forceps by using a prone hand position. The hand is rotated clockwise until it is supine, bringing the 60% side of the fold anteriorly, and then the tissue is inserted into the anterior chamber. Results: In 112 eyes, conventional 60/40 overfold insertion technique resulted in a 36% loss in endothelial cell density at 6 months. In 36 eyes, the new 40/60 underfold technique results in a 26% cell loss. This difference of 10% was statistically significant (P = 0.001). Conclusions: This simple modification to a commonly used folding technique reduces trauma to the exposed peripheral endothelium in a 60/40 overfolded “taco,” which is due to contact with the donor trephine block or other surface. It is a slight modification to a commonly used technique for graft insertion and can be easily implemented to reduce postoperative endothelial cell loss.
Exploration of de Bruijn Graph Filtering for de novo Assembly Using GraphLab

The emergence of next generation DNA sequencers has raised interest in short read de novo assembly of whole genomes. Though numerous frameworks were developed in the field, the presence of errors in reads as well as the increasing size of datasets call for scalable preprocessing methods for noise filtering. In this paper we present a filtering algorithm that targets determination of valid k-mers in a de Bruijn graph built from short reads. Such preprocessing will help increase accuracy and reduce memory footprint in further assembly procedures by removing erroneous k-mers from the datasets at an early stage. The algorithm leverages GraphLab, a scalable graph processing framework not previously used in traditional assembly toolchains. The accuracy of the algorithm was evaluated with synthetic datasets exhibiting various error rates and proven to be able to determine large parts of de Bruijn graphs on datasets with error level greater than real-life datasets. The implementation is executed on a distributed cluster and a study of its scalability and operating performances is conducted and exhibits interesting scaling properties, hence demonstrating the relevance of GraphLab in such a context.
New species of Ancistrocerus (Vespidae, Eumeninae) from the Neotropics with a checklist and key to all species south of the Rio Grande

Abstract A new species of potter wasp from South America, Ancistrocerus sur sp. n. , is described. A species key and checklist for all described Ancistrocerus that occur south of the Rio Grande are provided. New synonymy includes Odynerus bolivianus Brèthes = Ancistrocerus pilosus (de Saussure), while the subspecies bustamente discopictus Bequaert, lineativentris kamloopsensis Bequaert, lineativentris sinopis Bohart, tuberculocephalussutterianus (de Saussure), and pilosus ecuadorianus Bertoni, are all sunk under their respective nominotypical taxa.
[Incidence of vancomycin-resistant Enterococcus at a university hospital in Brazil].

OBJECTIVE Vancomycin-resistant Enterococcus (VRE) is today one of the principal microorganisms implicated in nosocomial infections. Thus, a study was carried out with the objective of evaluating its epidemiology at a tertiary-level teaching hospital. METHODS This was a three-year retrospective epidemiological study conducted from 2000 to 2002. Samples of VRE-positive clinical cultures at a 660-bed university hospital were analyzed. The incidence of VRE and the main anatomical sites and hospital units from which it was isolated were defined. Differences between the variables over the three years of the study were verified, and these were considered significant when p<0.05. RESULTS There was a progressive increase in the vancomycin resistance in the clinical cultures that were positive for Enterococcus spp. , over the three years of the study. In 2000, 9.5% of the samples were vancomycin-resistant, and this increased to 14.7% in 2001 and 15.8% in 2002. The hospital units with the largest numbers of isolates were, respectively, the emergency ward (19.5%) and the general intensive care unit (15%). The anatomical sites with the highest amounts of isolates included: urine (36%) and blood (20%). CONCLUSIONS With the progressive increase in the incidence of vancomycin resistance and the VRE rate, it is concluded that more effective control measures are needed for deterring the dissemination of VRE.
The introduction of solid food and growth in the first 2 y of life in formula-fed children: analysis of data from a European cohort study.

BACKGROUND Early introduction of solid food has been suspected to induce excessive infant energy intake and weight gain. OBJECTIVE The objective of this study was to test whether introduction of solid foods influences energy intake or growth. DESIGN Healthy, formula-fed infants who were recruited in 5 European countries were eligible for study participation. Anthropometric measurements were taken at recruitment and at 3, 6, 12, and 24 mo. Time of introduction of solid foods and energy intake were determined by questionnaires and 3-d weighed food records at monthly intervals. Age at introduction of solid food was categorized into 4 groups: ≤ 13 wk, 14-17 wk, 18-21 wk, and ≥ 22 wk. RESULTS Of 1090 recruited infants, 830 (76%) had data available for age at first introduction of solid food, and 671 (61%) completed the study until 24 mo of age. The median age at introduction of solid food was 19 wk. The time of introduction of solid foods was associated with country, sex, birth weight, parental education and marital status, and maternal smoking. Energy intake was higher in the first 8 mo of life in children with solid-food intake. Solid-food introduction did not predict anthropometric measures at 24 mo. Growth trajectories differed significantly: children with solid-food introduction in the first 12 wk experienced early catch-up growth, whereas those introduced to solid food at >22 wk of age grew more slowly and stayed on lower trajectories. CONCLUSIONS Solid foods do not simply replace infant formula but increase energy intake. Time of introduction of solid food has little influence on infant growth. This trial was registered at clinicaltrials.gov as NCT00338689.