Miracle-dz/UniFAR-FTUs huggingface dataset:
The Limits of Refinement by Severe Plastic Deformation

The effect of the different processing parameters on the refinement during severe plastic deformation is evaluated. The attention is focused to very high strains, where saturation in the structural refinement is observed. The single phase metals and alloys show a relatively uniform behaviour, with increasing strain the size of structural elements decreases and reaches saturation between equivalent strains of 5 to 50. The resulting ultra fine or nanostructured granular microstructure contains mainly high angle grain boundaries. Alloying, the temperature, and the strain path are the most important parameters controlling the saturation in the structural refinement. The behavior of the dual and multiphase materials during SPD is more complex, it varies from simple homogenisation of the phase distribution, fragmentation of one phase to disintegration and supersaturation of the phases. Severe plastic deformation of these types of materials offers the potential for the production of new types of materials with a nanocrystalline or a nanocomposite structure for a broad range of industrial applications.
A CD21 low phenotype, with no evidence of autoantibodies to complement proteins, is consistent with a poor prognosis in CLL

B-cell chronic lymphocytic leukemia (CLL) is characterized by differential BCR signaling and autoimmune complications. Complement modulates B-cell function via C3d and CD21 cross-linked to the B-cell receptor (BCR). We hypothesized that CD21 contributes to BCR signaling and participates in the autoimmunity associated with CLL. We analyzed CD21 expression on 106 CLL patient samples and matched serum from 50 patients for the presence of soluble CD21 and autoantibodies to CR2, CR1, MCP and FH. CD21 expression on CLL B-cells was significantly lower than that expressed on B-cells from age-matched controls (P < 0.0001) and was inversely correlated with soluble CD21 (r2 = −0.41). We found no evidence of autoantibody to any complement regulator. Low CD21 expression correlated to prognostic subsets of CLL patients, i.e. cases with unmutated IGHV genes (P = 0.0006), high CD38 (P = 0.02) and high ZAP70 expression (P = 0.0017). Low CD21 expression was inversely correlated to the levels of phosphotyrosine induced in CLL cells following BCR ligation with αIgM (r2=–0.21). Importantly, lower CD21 expression was also predictive for reduced overall survival (P = 0.005; HR = 2.7). In conclusion, we showed that reduced expression of CD21 on CLL B-cells appears functionally relevant and was associated with poor clinical outcomes.
Tetrahymena Metallothioneins Fall into Two Discrete Subfamilies

Background Metallothioneins are ubiquitous small, cysteine-rich, multifunctional proteins which can bind heavy metals. Methodology/Principal Findings We report the results of phylogenetic and gene expression analyses that include two new Tetrahymena thermophila metallothionein genes (MTT3 and MTT5). Sequence alignments of all known Tetrahymena metallothioneins have allowed us to rationalize the structure of these proteins. We now formally subdivide the known metallothioneins from the ciliate genus Tetrahymena into two well defined subfamilies, 7a and 7b, based on phylogenetic analysis, on the pattern of clustering of Cys residues, and on the pattern of inducibility by the heavy metals Cd and Cu. Sequence alignment also reveals a remarkably regular, conserved and hierarchical modular structure of all five subfamily 7a MTs, which include MTT3 and MTT5. The former has three modules, while the latter has only two. Induction levels of the three T. thermophila genes were determined using quantitative real time RT-PCR. Various stressors (including heavy metals) brought about dramatically different fold-inductions for each gene; MTT5 showed the highest fold-induction. Conserved DNA motifs with potential regulatory significance were identified, in an unbiased way, upstream of the start codons of subfamily 7a MTs. EST evidence for alternative splicing in the 3′ UTR of the MTT5 mRNA with potential regulatory activity is reported. Conclusion/Significance The small number and remarkably regular structure of Tetrahymena MTs, coupled with the experimental tractability of this model organism for studies of in vivo function, make it an attractive system for the experimental dissection of the roles, structure/function relationships, regulation of gene expression, and adaptive evolution of these proteins, as well as for the development of biotechnological applications for the environmental monitoring of toxic substances.
Rapid and reliable protein extraction from yeast

The methods currently used for protein extraction from yeast are either laborious or insufficiently reliable. Here I report a method for protein extraction for electrophoretic analysis that is both easy and reliable. In this method, yeast cells are subjected to mild alkali treatment and then boiled in a standard electrophoresis loading buffer. The method was tested for different strains of Saccharomyces cerevisiae and for yeast Hansenula polymorpha DL‐1. It yields virtually complete extraction independently of the strain, growth conditions and protein molecular weight and allows working with small amounts of yeast cells grown on agar plates. Copyright © 2000 John Wiley & Sons, Ltd.
Dealing With Interference in Distributed Large-Scale MIMO Systems: A Statistical Approach

This paper considers the problem of interference control through the use of second-order statistics in massive MIMO multi-cell networks. We consider both the cases of co-located massive arrays and large-scale distributed antenna settings. We are interested in characterizing the low-rankness of users' channel covariance matrices, as such a property can be exploited towards improved channel estimation (so-called pilot decontamination) as well as interference rejection via spatial filtering. In previous work, it was shown that massive MIMO channel covariance matrices exhibit a useful finite-rank property that can be modeled via the angular spread of multipath at a MIMO uniform linear array. This paper extends this result to more general settings including certain non-uniform arrays, and more surprisingly, to two dimensional distributed large-scale arrays. In particular our model exhibits the dependence of the signal subspace's richness on the scattering radius around the user terminal, through a closed-form expression. The applications of the low-rankness covariance property to channel estimation's denoising and low-complexity interference filtering are highlighted.
An Approach to a Comprehensive Test Framework for Analysis and Evaluation of Text Line Segmentation Algorithms

The paper introduces a testing framework for the evaluation and validation of text line segmentation algorithms. Text line segmentation represents the key action for correct optical character recognition. Many of the tests for the evaluation of text line segmentation algorithms deal with text databases as reference templates. Because of the mismatch, the reliable testing framework is required. Hence, a new approach to a comprehensive experimental framework for the evaluation of text line segmentation algorithms is proposed. It consists of synthetic multi-like text samples and real handwritten text as well. Although the tests are mutually independent, the results are cross-linked. The proposed method can be used for different types of scripts and languages. Furthermore, two different procedures for the evaluation of algorithm efficiency based on the obtained error type classification are proposed. The first is based on the segmentation line error description, while the second one incorporates well-known signal detection theory. Each of them has different capabilities and convenience, but they can be used as supplements to make the evaluation process efficient. Overall the proposed procedure based on the segmentation line error description has some advantages, characterized by five measures that describe measurement procedures.
Knock-Down of Both eIF4E1 and eIF4E2 Genes Confers Broad-Spectrum Resistance against Potyviruses in Tomato

Background The eukaryotic translation initiation factor eIF4E plays a key role in plant-potyvirus interactions. eIF4E belongs to a small multigenic family and three genes, eIF4E1, eIF4E2 and eIF(iso)4E, have been identified in tomato. It has been demonstrated that eIF4E-mediated natural recessive resistances against potyviruses result from non-synonymous mutations in an eIF4E protein, which impair its direct interaction with the potyviral protein VPg. In tomato, the role of eIF4E proteins in potyvirus resistance is still unclear because natural or induced mutations in eIF4E1 confer only a narrow resistance spectrum against potyviruses. This contrasts with the broad spectrum resistance identified in the natural diversity of tomato. These results suggest that more than one eIF4E protein form is involved in the observed broad spectrum resistance. Methodology/Principal Findings To gain insight into the respective contribution of each eIF4E protein in tomato-potyvirus interactions, two tomato lines silenced for both eIF4E1 and eIF4E2 (RNAi-4E) and two lines silenced for eIF(iso)4E (RNAi-iso4E) were obtained and characterized. RNAi-4E lines are slightly impaired in their growth and fertility, whereas no obvious growth defects were observed in RNAi-iso4E lines. The F1 hybrid between RNAi-4E and RNAi-iso4E lines presented a pronounced semi-dwarf phenotype. Interestingly, the RNAi-4E lines silenced for both eIF4E1 and eIF4E2 showed broad spectrum resistance to potyviruses while the RNAi-iso4E lines were fully susceptible to potyviruses. Yeast two-hybrid interaction assays between the three eIF4E proteins and a set of viral VPgs identified two types of VPgs: those that interacted only with eIF4E1 and those that interacted with either eIF4E1 or with eIF4E2. Conclusion/Significance These experiments provide evidence for the involvement of both eIF4E1 and eIF4E2 in broad spectrum resistance of tomato against potyviruses and suggest a role for eIF4E2 in tomato-potyvirus interactions.
Anaerobic and aerobic degradation of pyridine by a newly isolated denitrifying bacterium

New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions were isolated from industrial wastewater. The successful enrichment and isolation of these strains required selenite as a trace element. These isolates appeared to be closely related to Azoarcus species according to the results of 16S rRNA sequence analysis. An isolated strain, pF6, metabolized pyridine through the same pathway under both aerobic and anaerobic conditions. Since pyridine induced NAD-linked glutarate-dialdehyde dehydrogenase and isocitratase activities, it is likely that the mechanism of pyridine degradation in strain pF6 involves N-C-2 ring cleavage. Strain pF6 could degrade pyridine in the presence of nitrate, nitrite, and nitrous oxide as electron acceptors. In a batch culture with 6 mM nitrate, degradation of pyridine and denitrification were not sensitively affected by the redox potential, which gradually decreased from 150 to -200 mV. In a batch culture with the nitrate concentration higher than 6 mM, nitrite transiently accumulated during denitrification significantly inhibited cell growth and pyridine degradation. Growth yield on pyridine decreased slightly under denitrifying conditions from that under aerobic conditions. Furthermore, when the pyridine concentration used was above 12 mM, the specific growth rate under denitrifying conditions was higher than that under aerobic conditions. Considering these characteristics, a newly isolated denitrifying bacterium, strain pF6, has advantages over strictly aerobic bacteria in field applications.
MARCHENKO EQUATIONS AND NORMING CONSTANTS OF THE MATRIX ZAKHAROV-SHABAT SYSTEM

In this article we derive the Marchenko integral equations for solving the inverse scattering problem for the matrix Zakharov-Shabat system with a potential without symmetry properties and having L 1 entries under a technical hypothesis preventing the accumulation of discrete eigenvalues onthe continuous spectrum. Wederive additional symmetryproperties in the focusing case. The norming constant matrices appearing as parameter matrices in the Marchenko integral kernels are defined and studied without making any assumptions on the Jordan structure of the matrix Zakharov-Shabat Hamiltonian at the discrete eigenvalues.
Evaluating two sources of dried whey and the effects of replacing the corn and dried whey component with corn gluten meal and lactose in the diets of weanling swine.

Three experiments were conducted to evaluate the efficacy of replacing corn and dried whey with corn gluten meal (CGM) and lactose, and to evaluate two sources of edible-grade dried whey that elicited different postweaning pig growth performances. In Exp. 1, two corn-soybean meal (C-SBM) diets without or with 20% dried whey (C-SBM-DW) were formulated to contain 1.15% lysine. A third diet replaced the corn and dried whey component with CGM and lactose. The experiment used 108 crossbred pigs weaned at 23 +/- 2 d of age weighing 6.25 kg BW and was conducted in six replicates as a randomized complete block design. Pig weight gains when the C-SBM-DW diet was fed were poor in one trial, whereas a second trial resulted in improved (P < .01) performance responses to the inclusion of dried whey. The CGM-SBM-lactose diet resulted in pig gains that equaled the performance responses of the C-SBM-DW diet of Trial 2. A second experiment was subsequently designed to evaluate the effects of adding lactose or lactalbumin to the CGM-SBM-DW diets using the two dried whey sources that had been identified as good or poor quality in Exp. 1. Diets included dried whey at a 25% level and were formulated to a low lysine level (.95%) to assess the nutritional efficacy of the dried whey sources. (ABSTRACT TRUNCATED AT 250 WORDS)
Speeding up slicing

Program slicing is a fundamental operation for many software engineering tools. Currently, the most efficient algorithm for interprocedural slicing is one that uses a program representation called the system dependence graph. This paper defines a new algorithm for slicing with system dependence graphs that is asymptotically faster than the previous one. A preliminary experimental study indicates that the new algorithm is also significantly faster in practice, providing roughly a 6-fold speedup on examples of 348 to 757 lines.
A Systematic Review and Meta-Analysis of Open vs. Laparoscopic Resection of Gastric Gastrointestinal Stromal Tumors

Gastric gastrointestinal stromal tumors (GISTs) are the most common sarcoma of the gastrointestinal tract, and surgical resection is the primary treatment of early disease. Limited data exist concerning laparoscopic resections of these neoplasms. This systematic review was designed to evaluate the literature comparing laparoscopic and open surgical resection of gastric GISTs and to assess the effectiveness and safety of this minimally invasive technique. We performed a systematic search of MEDLINE, the Cochrane Library, PubMed, Embase, Scopus, Web of Science, Google Scholar, the clinical trials database and ProQuest Dissertations and Theses as well as the past 3 years of conference abstracts from the Society of American Gastrointestinal and Endoscopic Surgeons Annual Meetings. Studies comparing the open and the laparoscopic approaches to the resection of gastric GISTs were included in this systematic review. Two reviewers independently performed the screen of titles and abstracts, the full manuscript review, the data extraction and the risk of bias assessment. A quantitative analysis was performed. Of the 189 studies identified, seven studies were included. The laparoscopic approach was associated with a significantly lower length of hospital stay (3.82 days (2.14 - 5.49)). There was no observed difference in operative time, adverse events, estimated blood loss, overall survival and recurrence rates. This study supports that laparoscopic resection is safe and effective for gastric GISTs and is associated with a significantly lower length of hospital stay. Further trials are needed for cost analysis and to rigorously assess oncologic outcomes.
Expression of Trypsinogen-1, Trypsinogen-2, and Tumor-Associated Trypsin Inhibitor in Ovarian Cancer

Purpose: The purpose is to study the prognostic significance of tissue expression of trypsinogen-1, trypsinogen-2, and tumor-associated trypsin inhibitor (TATI) and serum concentration of trypsinogen-2, trypsin-2-API (complex of trypsin-2 with α-1-proteinase inhibitor), and TATI in epithelial ovarian cancer. Experimental Design: Expression of trypsinogen-1, trypsinogen-2, and TATI was determined by immunohistochemistry with monoclonal antibodies in tissue sections of tumors from 119 patients with untreated primary epithelial ovarian cancer. Preoperative serum concentrations of trypsinogen-2, trypsin-2-API and TATI were analyzed using specific immunoassays. Results: Fifty-four percent of the tumors expressed trypsinogen-1, 45% expressed trypsinogen-2, and 30% expressed TATI. In patients with stage III and IV disease, TATI tissue expression (P = 0.002) and elevated TATI concentration in serum (P = 0.048) were associated with adverse cancer-specific and progression-free survival in univariate analysis. In multivariate analysis, TATI tissue expression (P = 0.005), tumor grade (P = 0.0001), histological type (P = 0.02), and stage (P = 0.0005) were independent prognostic factors for adverse cancer-specific survival and TATI tissue expression (P = 0.006) and grade (P = 0.0003) for progression-free survival. In multivariate analysis of all patients and those with advanced disease, serum trypsin-2-API concentration was an adverse prognostic factor for cancer-specific and progression-free survival, and it was independent of stage and histological type of the tumor (P ≤ 0.01). Conclusions: Tissue expression of TATI and an elevated preoperative serum concentration of trypsin-2-API are strong independent prognostic factors in advanced epithelial ovarian cancer. These results suggest that trypsin expression plays a role in the progression of ovarian cancer. TATI and trypsin-2-API are of potential use as an aid for stratification of randomized studies and for selecting treatment strategies.
Generation of bubbles in liquid argon and nitrogen in divergent electric fields

In this paper, we present an experimental study of high field conduction phenomena in liquid argon and liquid nitrogen in a point-plane electrode geometry. These liquids behave qualitatively like saturated hydrocarbons except when they are studied close to their normal boiling point. The generation and dynamics of microscopic bubbles as a function of various parameters (nature of the liquid, injected energy and hydrostatic pressure) are presented and discussed. The possible influence of these phenomena on electrical insulation at cryogenic temperatures is also discussed.
LEVEL SET METHODS FOR FLUID INTERFACES

▪ Abstract We provide an overview of level set methods, introduced by Osher and Sethian, for computing the solution to fluid-interface problems. These are computational techniques that rely on an implicit formulation of the interface, represented through a time-dependent initial-value partial-differential equation. We discuss the essential ideas behind the techniques, the coupling of these techniques to finite-difference methods for incompressible and compressible flow, and a collection of applications including two-phase flow, ship hydrodynamics, and ink-jet-printhead design.
Meropenem-Vaborbactam Resistance Selection, Resistance Prevention, and Molecular Mechanisms in Mutants of KPC-Producing Klebsiella pneumoniae

ABSTRACT Vaborbactam (formerly RPX7009) is a new β-lactamase inhibitor based on a cyclic boronic acid pharmacophore with potent inhibitory activity against Klebsiella pneumoniaecarbapenemases (KPC). It has been developed in combination with meropenem. The objective of these studies was to identify the concentrations of both agents associated with the selection or prevention of single-step mutations leading to reduced sensitivity to the combination and to characterize the selected mutations. Eighteen strains of KPC-producing Klebsiella pneumoniae with various degrees of sensitivity to meropenem (MICs, 8 to 512 μg/ml) and meropenem-vaborbactam (MICs, ≤0.06 to 32 μg/ml) and preexisting resistance mechanisms were selected from a worldwide collection of isolates recovered from surveillance studies, emphasizing strains for which MICs were in the upper range of the meropenem-vaborbactam MIC distribution. Meropenem and vaborbactam at 8 μg/ml each suppressed the drug resistance mutation frequency to <1 × 10−8 in 77.8% (14/18) of strains, and all strains were inhibited when the meropenem concentration was increased to 16 μg/ml. Mutants selected at lower drug concentrations showed phenotypes associated with previously described carbapenem resistance mechanisms, including ompK36 inactivation in mutants selected from OmpK36-proficient strains and an increased blaKPC gene copy number in strains with partially functional ompK36. No mutations in the coding region of blaKPC were identified. These data indicate that the selection of mutants with reduced sensitivity to meropenem-vaborbactam from KPC-producing Klebsiella pneumoniae strains is associated with previously described mechanisms involving porin mutations and the increase in the blaKPC gene copy number and not changes in the KPC enzyme and can be prevented by the drug concentrations achieved with optimal dosing of the combination.
A network model of basal ganglia for understanding the roles of dopamine and serotonin in reward-punishment-risk based decision making

There is significant evidence that in addition to reward-punishment based decision making, the Basal Ganglia (BG) contributes to risk-based decision making (Balasubramani et al., 2014). Despite this evidence, little is known about the computational principles and neural correlates of risk computation in this subcortical system. We have previously proposed a reinforcement learning (RL)-based model of the BG that simulates the interactions between dopamine (DA) and serotonin (5HT) in a diverse set of experimental studies including reward, punishment and risk based decision making (Balasubramani et al., 2014). Starting with the classical idea that the activity of mesencephalic DA represents reward prediction error, the model posits that serotoninergic activity in the striatum controls risk-prediction error. Our prior model of the BG was an abstract model that did not incorporate anatomical and cellular-level data. In this work, we expand the earlier model into a detailed network model of the BG and demonstrate the joint contributions of DA-5HT in risk and reward-punishment sensitivity. At the core of the proposed network model is the following insight regarding cellular correlates of value and risk computation. Just as DA D1 receptor (D1R) expressing medium spiny neurons (MSNs) of the striatum were thought to be the neural substrates for value computation, we propose that DA D1R and D2R co-expressing MSNs are capable of computing risk. Though the existence of MSNs that co-express D1R and D2R are reported by various experimental studies, prior existing computational models did not include them. Ours is the first model that accounts for the computational possibilities of these co-expressing D1R-D2R MSNs, and describes how DA and 5HT mediate activity in these classes of neurons (D1R-, D2R-, D1R-D2R- MSNs). Starting from the assumption that 5HT modulates all MSNs, our study predicts significant modulatory effects of 5HT on D2R and co-expressing D1R-D2R MSNs which in turn explains the multifarious functions of 5HT in the BG. The experiments simulated in the present study relates 5HT to risk sensitivity and reward-punishment learning. Furthermore, our model is shown to capture reward-punishment and risk based decision making impairment in Parkinson's Disease (PD). The model predicts that optimizing 5HT levels along with DA medications might be essential for improving the patients' reward-punishment learning deficits.