Miracle-dz/UniFAR-FTUs huggingface dataset:
Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics

Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.
Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing

ABSTRACT Restricted availability of cell and animal models is a rate-limiting step for investigation of salivary gland neoplasm pathophysiology and therapeutic response. Conditionally reprogrammed cell (CRC) technology enables establishment of primary epithelial cell cultures from patient material. This study tested a translational workflow for acquisition, expansion and testing of CRC-derived primary cultures of salivary gland neoplasms from patients presenting to an academic surgical practice. Results showed that cultured cells were sufficient for epithelial cell-specific transcriptome characterization to detect candidate therapeutic pathways and fusion genes, and for screening for cancer risk-associated single nucleotide polymorphisms (SNPs) and driver gene mutations through exome sequencing. Focused study of primary cultures of a low-grade mucoepidermoid carcinoma demonstrated amphiregulin-mechanistic target of rapamycin-protein kinase B (AKT; AKT1) pathway activation, identified through bioinformatics and subsequently confirmed as present in primary tissue and preserved through different secondary 2D and 3D culture media and xenografts. Candidate therapeutic testing showed that the allosteric AKT inhibitor MK2206 reproducibly inhibited cell survival across different culture formats. By contrast, the cells appeared resistant to the adenosine triphosphate competitive AKT inhibitor GSK690693. Procedures employed here illustrate an approach for reproducibly obtaining material for pathophysiological studies of salivary gland neoplasms, and other less common epithelial cancer types, that can be executed without compromising pathological examination of patient specimens. The approach permits combined genetic and cell-based physiological and therapeutic investigations in addition to more traditional pathologic studies, and can be used to build sustainable bio-banks for future inquiries. This article has an associated First Person interview with the first author of the paper. Summary: Genetics and therapeutic responses of uncommon neoplasms, including salivary gland cancers, are investigatable through isolation of primary cells from patient material using conditional reprogramming cell technology without compromising pathological diagnosis.
Maximum likelihood estimation of a finite mixture of logistic regression models in a continuous data stream

In marketing we are often confronted with a continuous stream of responses to marketing messages. Such streaming data provide invaluable information regarding message effectiveness and segmentation. However, streaming data are hard to analyze using conventional methods: their high volume and the fact that they are continuously augmented means that it takes considerable time to analyze them. We propose a method for estimating a finite mixture of logistic regression models which can be used to cluster customers based on a continuous stream of responses. This method, which we coin oFMLR, allows segments to be identified in data streams or extremely large static datasets. Contrary to black box algorithms, oFMLR provides model estimates that are directly interpretable. We first introduce oFMLR, explaining in passing general topics such as online estimation and the EM algorithm, making this paper a high level overview of possible methods of dealing with large data streams in marketing practice. Next, we discuss model convergence, identifiability, and relations to alternative, Bayesian, methods; we also identify more general issues that arise from dealing with continuously augmented data sets. Finally, we introduce the oFMLR [R] package and evaluate the method by numerical simulation and by analyzing a large customer clickstream dataset.
Infarct Core Expansion on Computed Tomography before and after Intravenous Thrombolysis

Purpose Infarct core can expand rapidly in acute stroke patients receiving intravenous tissue plasminogen activator (IV t-PA). We investigated changes in the extent of infarct core during IV t-PA treatment, and explored the associative factors of this infarct core expansion in patients with proximal artery occlusion. Materials and Methods We included patients who were considered for sequential intra-arterial therapy (IAT) due to occlusion of intracranial proximal artery after IV t-PA. Patients who had a baseline Alberta Stroke Program Early Computed Tomography (CT) Score (ASPECTS) ≥6 and who underwent two consecutive CT scans before and shortly after IV t-PA infusion were enrolled. Patients were classified into no, moderate, and marked expansion groups based on decreases in ASPECTS (0–1, 2–3, and ≥4, respectively) on follow-up CT. Collateral status was graded using CT angiography. Results Of the 104 patients, 16 (15.4%) patients showed moderate and 13 (12.5%) patients showed marked infarct core expansion on follow-up CT scans obtained at 71.1±19.1 min after baseline CT scan. Sixteen (15.4%) patients had an ASPECTS value <6 on the follow-up CT. None of the patients with marked expansion were independent at 3 months. Univariate analysis and ordinal logistic regression analysis demonstrated that the infarct core expansion was significantly associated with collateral status (p<0.001). Conclusion Among patients who were considered for IAT after IV t-PA treatment, one out of every seven patients exhibited marked expansion of infarct core on follow-up CT before IAT. These patients tend to have poor collaterals and poor outcomes despite rescue IAT.
Predictive validity of the Trauma Screening Questionnaire in detecting post-traumatic stress disorder in patients with psychotic disorders

Background Post-traumatic stress disorder (PTSD) is highly prevalent in patients with a psychotic disorder. Because a PTSD diagnosis is often missed in patients with psychosis in routine care, a valid screening instrument could be helpful. Aims To determine the validity of the Trauma Screening Questionnaire (TSQ) as a screening tool for PTSD among individuals with psychotic disorders. Method Among 2608 patients with a psychotic disorder, the rate of trauma exposure was determined and the TSQ was administered to screen for PTSD. PTSD status was verified in 455 patients using the Clinician-Administered PTSD Scale (trial registration: ISRCTN 79584912). Results Trauma exposure was reported by 78.2% of the 2608 patients. PTSD prevalence was estimated at 16% (95% CI 14.6–17.4%) compared with 0.5% reported in the patients' clinical charts. A TSQ cut-off score of six predicted PTSD with 78.8% sensitivity, 75.6% specificity, 44.5% correct positives and 93.6% correct negatives. Conclusions The TSQ seems to be a valid screening tool for PTSD in patients with a psychotic disorder.
Real-time, high-resolution study of nanocrystallization and fatigue cracking in a cyclically strained metallic glass

Significance The formation of nanocrystals and cracks in metallic glasses subjected to cyclically varying strains in micro- and nanoscale systems is a topic of scientific and technological interest. However, no real-time studies of such phenomena in fatigued metallic glasses have thus far been reported. Here we present unique observations of nanocrystallization and the onset and progression of fatigue failure in a metallic glass through cyclic straining experiments conducted inside a high-resolution transmission electron microscope. Molecular dynamics simulations were also performed to elucidate the underlying mechanisms. We expect that these techniques and results will provide unique fundamental insights into how crystallization occurs in a wide variety of amorphous materials and will help develop strategies for the design and use of metallic glasses. Metallic glasses (MGs) exhibit greater elastic limit and stronger resistance to plastic deformation than their crystalline metal counterparts. Their capacity to withstand plastic straining is further enhanced at submicrometer length scales. For a range of microelectromechanical applications, the resistance of MGs to damage and cracking from thermal and mechanical stress or strain cycling under partial or complete constraint is of considerable scientific and technological interest. However, to our knowledge, no real-time, high-resolution transmission electron microscopy observations are available of crystallization, damage, and failure from the controlled imposition of cyclic strains or displacements in any metallic glass. Here we present the results of a unique in situ study, inside a high-resolution transmission electron microscope, of glass-to-crystal formation and fatigue of an Al-based MG. We demonstrate that cyclic straining progressively leads to nanoscale surface roughening in the highly deformed region of the starter notch, causing crack nucleation and formation of nanocrystals. The growth of these nanograins during cyclic straining impedes subsequent crack growth by bridging the crack. In distinct contrast to this fatigue behavior, only distributed nucleation of smaller nanocrystals is observed with no surface roughening under monotonic deformation. We further show through molecular dynamics simulation that these findings can be rationalized by the accumulation of strain-induced nonaffine atomic rearrangements that effectively enhances diffusion through random walk during repeated strain cycling. The present results thus provide unique insights into fundamental mechanisms of fatigue of MGs that would help shape strategies for material design and engineering applications.
LINERS FOR SHAPED CHARGES

The penetration potential of shaped charges is proportional to the jet length and the square root of the jet density. The bulk-sound velocities of the liner materials define the maximum possible jet tip velocities. The jet tip velocities and breakup, or particulation, times determine the jet length. For shaped-charge optimisations these parameters have to be considered. After a brief discussion of these issues, this paper outlines the potential of a range of materials for use as possible shaped-charge liners. It is further noted that, as well as the selection of optimal materials, a number of other factors have be taken into account, such as quality of the raw material, homogeneity, and grain-size distribution. Finally, the paper describes the different production possibilities for copper liners, identifying the advantages and disadvantages of each. In particular, the flow-turning process is discussed with its potential for spin compensation.
Artificial Basis Functions in Adaptive Control for Transient Performance Improvement

This paper presents a new adaptive control architecture to achieve stabilization and command following of uncertain dynamical systems with improved transient performance. The proposed framework is predicated on a new and novel controller architecture involving an artificial basis function in the update law. Specifically, the proposed artificial basis function allows to shape the system error, which is between the uncertain dynamical system and a reference system capturing a desired closed-loop dynamical system behavior, during the learning phase of an adaptive controller for improving the transient performance. The efficacy of the proposed architecture is illustrated on a numerical example.
KCNE1 and KCNE3 modulate KCNQ1 channels by affecting different gating transitions

Significance Regulatory β-subunits associate with voltage-gated K+ channels to modulate their biophysical properties and physiological roles. KCNE1 and KCNE3 β-subunits turn voltage-dependent KCNQ1 channels into delayed activating KCNQ1/KCNE1 channels and apparent voltage-independent KCNQ1/KCNE3 channels, respectively, which are important for cardiac action potentials and transport of water and salts across epithelial cells. Mutations in KCNQ1/KCNE1 and KCNQ1/KCNE3 channels are associated with diseases, such as cardiac arrhythmias, congenital deafness, secretory diarrhea, and tinnitus. Therefore, KCNQ1, KCNE1, and KCNE3 are potential drug targets. We here propose a model for how KCNE1 and KCNE3 differentially modulate KCNQ1 that will allow for a better understanding of how mutations in KCNQ1, KCNE1, and KCNE3 cause diseases and how to design drugs to treat these diseases. KCNE β-subunits assemble with and modulate the properties of voltage-gated K+ channels. In the heart, KCNE1 associates with the α-subunit KCNQ1 to generate the slowly activating, voltage-dependent potassium current (IKs) in the heart that controls the repolarization phase of cardiac action potentials. By contrast, in epithelial cells from the colon, stomach, and kidney, KCNE3 coassembles with KCNQ1 to form K+ channels that are voltage-independent K+ channels in the physiological voltage range and important for controlling water and salt secretion and absorption. How KCNE1 and KCNE3 subunits modify KCNQ1 channel gating so differently is largely unknown. Here, we use voltage clamp fluorometry to determine how KCNE1 and KCNE3 affect the voltage sensor and the gate of KCNQ1. By separating S4 movement and gate opening by mutations or phosphatidylinositol 4,5-bisphosphate depletion, we show that KCNE1 affects both the S4 movement and the gate, whereas KCNE3 affects the S4 movement and only affects the gate in KCNQ1 if an intact S4-to-gate coupling is present. Further, we show that a triple mutation in the middle of the transmembrane (TM) segment of KCNE3 introduces KCNE1-like effects on the second S4 movement and the gate. In addition, we show that differences in two residues at the external end of the KCNE TM segments underlie differences in the effects of the different KCNEs on the first S4 movement and the voltage sensor-to-gate coupling.
Incidence of local complications in peripheral venous catheters and associated risk factors

DOI http://dx.doi. org/10.1590/19820194201500087 Universidade Federal do Paraná, Curitiba, PR, Brazil. Instituto Federal do Paraná, Curitiba, PR, Brazil. Conflicts of interest: none reported. Abstract Objective: To estimate the incidence of local complications associated with peripheral catheters and identify risk factors for the development of most common complications. Methods: This prospective cohort study included 92 adult inpatients at clinical and surgical units who had peripheral catheterization. By daily observance of the catheters we determined time of permanence and local complications due to the use of a complete safety catheter. All actions began after training of nursing teams. Statistical tests used were the Fisher exact test, G test (Williams), chi-square, Mann-Whitney U test, and relative risk. Results: Local complications occurred in 56.2% of cases. Time of catheter permanence over 72 hours increased the risk for phlebitis development in 2.34% of cases (RR; p=0.0483; CI [0.91; 6.07]). Conclusion: Incidence of local complications was high. Phlebitis was the predominant complication and the time of catheter permanence over 72 hours was a considered risk factor for this complication.
Homological representations of the Iwahori-Hecke algebra

Representations of the Iwahori-Hecke algebra of type An 1 are equivalent to representations of the braid group Bn for which the genera- tors satisfy a certain quadratic relation. We show how to construct such representations from the natural action of Bn on the homology of config- uration spaces of the punctured disk. We conjecture that all irreducible representations of Hn can be obtained in this way, even for non-generic values of q. AMS Classification 20C08; 20F36, 57M07
Study of Mechanical and Thermomechanical Properties of Jute/Epoxy Composite Laminate

This article presents the development and the characterization of composite material (laminate) containing natural jute fiber reinforcement. Thermal characterization of jute fiber reinforcement shows the influence of the temperature on the mechanical behavior of fiber. At 180°C the jute fabric loses 50% of its mechanical characteristics. The laminate obtained by a process known as infusion is polymerized at a temperature lower than that which affects the mechanical properties of dry fabric. The digital image correlation carried out on laminated jute/epoxy (warp and weft direction) under tensile test shows the presence of a considerable gradient of deformation. This gradient is explained by the variability related to the local voluminal change of jute fibers of one place to the other and the nature of the weaving of the jute fiber. The three-point bending tests show a significant dispersion of rupture stress. The thermomechanical tests carried out on samples in the two principal directions, show that the thermal coefficient of expansion in warp direction is 48% larger compared to the weft direction. The thermogravimetric test shows that this laminate absorbs up to 4% water mass after 8 h in a climatic chamber with 70% moisture content.
Diffuse large B-cell lymphoma: 10 years' real-world clinical experience with rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisolone

Treatment with rituximab plus a regimen of cyclophosphamide, doxorubicin, vincristine and prednisolone (CHOP) for patients with diffuse large B-cell lymphoma (DLBCL) has proven efficacy in clinical trials. The present study investigated its application in clinical practice. This single-center, retrospective database analysis included patients with DLBCL treated at the Slovenian Institute of Oncology Ljubljana between 2004 and 2013. Overall survival (OS) and progression-free survival (PFS) were assessed according to International Prognostic Index (IPI) and revised IPI (R-IPI) categories. Overall, 573 patients with DLBCL were included in the study (median follow-up, 45.3 months; range, 0.1–143.0). Patients were categorized as IPI ‘low’ (n=170; 30%), ‘low-intermediate’ (n=134; 23%), ‘high-intermediate’ (n=129; 23%) and ‘high’ (n=140; 24%) risk. R-IPI groups were indicated with ‘very good’ (n=59; 10%), ‘good’ (n=245; 43%) and ‘poor’ (n=269; 47%) prognosis. Ten-year OS and PFS rates were 51 and 72%, respectively; median OS was 124 months and median PFS was not reached. Ten-year OS rates were 80 and 87% in low-risk and ‘very good’ prognosis groups, respectively, and 30 and 37% in high-risk and poor prognosis patients, respectively. This analysis of patients with DLBCL indicated that many patients treated with R-CHOP and R-CHOP-like regimens in the real-world setting have excellent outcomes.
Biophysical processes supporting the diversity of microbial life in soil

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
Linking Democratic Preferences and Political Participation: Evidence from Germany

An extensive body of literature discusses the disaffection of citizens with representative democracy and highlights increasing citizens’ preferences for political decision-makers beyond elected politicians. But so far, little research has been conducted to analyse the relations between citizens’ respective preferences and their political behaviour. To address this void in the literature, our article investigates the extent to which citizens’ preferences for certain political decision-makers (politicians, citizens or expert) have an impact on their retrospective and prospective political participation. Our analysis draws on data from a survey conducted in autumn of 2014 on a probability representative sample in Germany. Results indicate that respondents favouring politicians as decision-makers focus mainly on voting. Those who favour citizens as decision-makers are more willing to get involved in participatory procedures, while those inclined towards expert decision-making show mixed participation.