Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of calbindin‐D28K on cyclosporine toxicity in cultured renal proximal tubular cells

Cyclosporine A (CsA) is known to have direct toxicity to renal tubular cells. Its toxicity may be mediated by intracellular calcium because CsA increases intracellular calcium concentration and enhances the activities of calcium‐dependent calpains and caspases. Calbindin‐D28k, a cytosolic calcium binding protein, has been used as an intracellular Ca2+ buffer to reduce calcium‐mediated cytotoxicity in non‐renal cells such as neuronal cells. We investigated the effects of gene transfer of calbindin‐D28k cDNA on CsA cytotoxicity and intracellular calcium concentration ([Ca2+]i) in cultured murine proximal tubular (MCT) cells. A plasmid containing calbindin‐D28k cDNA under the control of CMV promoter was transfected to MCT cells with liposomes. Cytotoxicity was assessed by LDH release and cell viability assay, and [Ca2+]i was measured ratiometrically with fura‐2. Compared with MCT cells, cells transfected with calbindin‐D28k cDNA showed a reduction in LDH release by 27, 30, 32, 33, and 19% (all P < 0.05), respectively, after 24 h exposure to 1, 2.5, 5, 10, and 25 μM CsA. Cell viability after CsA treatment was also significantly higher in CB cells. A mock transfection using plasmid without calbindin‐D28k cDNA insert did not affect the LDH release or cell viability after CsA treatment. CsA treatment did not affect the protein and mRNA abundance of transfected calbindin‐D28k cDNA. The expression of calbindin‐D28k did not affect the baseline [Ca2+]i, but significantly suppressed CsA‐induced elevation in [Ca2+]i. The expression of calbindin‐D28k in renal tubular cells provides cytoprotective effects against CsA toxicity, probably through its buffering effects on [Ca2+]i. © 2004 Wiley‐Liss, Inc.
A DSP for Sensing the Bladder Volume Through Afferent Neural Pathways

In this paper, we present a digital signal processor (DSP) capable of monitoring the urinary bladder volume through afferent neural pathways. The DSP carries out real-time detection and can discriminate extracellular action potentials, also known as on-the-fly spike sorting. Next, the DSP performs a decoding method to estimate either three qualitative levels of fullness or the bladder volume value, depending on the selected output mode. The proposed DSP was tested using both realistic synthetic signals with a known ground-truth, and real signals from bladder afferent nerves recorded during acute experiments with animal models. The spike sorting processing circuit yielded an average accuracy of 92% using signals with highly correlated spike waveforms and low signal-to-noise ratios. The volume estimation circuits, tested with real signals, reproduced accuracies achieved by offline simulations in Matlab, i.e., 94% and 97% for quantitative and qualitative estimations, respectively. To assess feasibility, the DSP was deployed in the Actel FPGA Igloo AGL1000V2, which showed a power consumption of 0.5 mW and a latency of 2.1 ms at a 333 kHz core frequency. These performance results demonstrate that an implantable bladder sensor that perform the detection, discrimination and decoding of afferent neural activity is feasible.
Cutting management and alfalfa stand age effects on organically grown corn grain yield and soil N availability

Abstract Alfalfa is recommended as a rotational crop in corn production, due to its ability to contribute to soil nitrogen (N) and carbon (C) stocks through atmospheric N2 fixation and above- and belowground biomass production. However, there is little information on how alfalfa management practices affect contributions to soil and subsequent corn crop yields, and research has not been targeted to organic systems. A study was conducted to determine the effects of alfalfa stand age, cutting frequency and biomass removal on soil C and N status and corn yields at three organically managed Minnesota locations. In one experiment, five cutting treatments were applied in nine environments: two, three and four cuts with biomass removal; three cuts with biomass remaining in place; and a no-cut control. In the other experiment, corn was planted following 1-, 2-, 3- or 4-year-old alfalfa stands and a no-alfalfa control. Yield was measured in the subsequent corn crop. In the cutting experiment, the two- and three-cut treatments with biomass removal reduced soil mineral N by 12.6 and 11.5%, respectively, compared with the control. Potentially mineralizable N (PMN) was not generally affected by cutting treatments. The three-cut no-removal increased potentially mineralizable C by 17% compared with the other treatments, but lowered soil total C in two environments, suggesting a priming effect in which addition of alfalfa biomass stimulated microbial mineralization of native soil C. Although both yields and soil mineral N tended to be higher in treatments where biomass remained in place, this advantage was small and inconsistent, indicating that farmers need not forgo hay harvest to obtain the rotational benefits of an alfalfa stand. The lack of overall correlation between corn grain yields and mineral and potentially mineralizable N suggests that alfalfa N contribution was not the driver of the yield increase in the no-removal treatments. Alfalfa stand age had inconsistent effects on fall-incorporated N and soil N and C parameters. Beyond the first year, increased alfalfa stand age did not increase soil mineral N or PMN. However, corn yield increased following older stands. Yields were 29, 77 and 90% higher following first-, second- and third-year alfalfa stands than the no-alfalfa control, respectively. This indicates that alfalfa may benefit succeeding corn through mechanisms other than N contribution, potentially including P solubilization and weed suppression. These effects have been less studied than N credits, but are of high value in organic cropping systems.
Compositional GC-FID analysis of the additives to PVC, focusing on the gaskets of lids for glass jars

A gas chromatographic (FID) method is described which aims at the quantitative compositional analysis of the additives in plasticized PVC, particularly the plastisols used as gaskets for lids of glass jars. An extract of the PVC is analysed directly as well as after transesterification to ethyl esters. Transesterification enables the analysis of epoxidized soya bean and linseed oil (ESBO and ELO) as well as polyadipates. For most other additives, the shifts in the chromatogram resulting from transesterification is used to confirm the identifications made by direct analysis. In the gaskets of 69 lids from the European market used for packaging oily foods, a broad variety of plastisol compositions was found, many or possibly all of which do not comply with legal requirements. In 62% of these lids, ESBO was the principal plasticizer, whereas in 25% a phthalate had been used.
Phylogenetic analysis of otospiralin protein

Background: Fibrocyte-specific protein, otospiralin, is a small protein, widely expressed in the central nervous system as neuronal cell bodies and glia. The increased expression of otospiralin in reactive astrocytes implicates its role in signaling pathways and reparative mechanisms subsequent to injury. Indeed, otospiralin is considered to be essential for the survival of fibrocytes of the mesenchymal nonsensory regions of the cochlea. It seems that other functions of this protein are not yet completely understood. Materials and Methods: Amino acid sequences of otospiralin from 12 vertebrates were derived from National Center for Biotechnology Information database. Phylogenetic analysis and phylogeny estimation were performed using MEGA 5.0. 5 program, and neighbor-joining tree was constructed by this software. Results: In this computational study, the phylogenetic tree of otospiralin has been investigated. Therefore, dendrograms of otospiralin were depicted. Alignment performed in MUSCLE method by UPGMB algorithm. Also, entropy plot determined for a better illustration of amino acid variations in this protein. Conclusion: In the present study, we used otospiralin sequence of 12 different species and by constructing phylogenetic tree, we suggested out group for some related species.
revisit: a Workflow Tool for Data Science

In recent years there has been widespread concern in the scientific community over a reproducibility crisis. Among the major causes that have been identified is statistical: In many scientific research the statistical analysis (including data preparation) suffers from a lack of transparency and methodological problems, major obstructions to reproducibility. The revisit package aims toward remedying this problem, by generating a "software paper trail" of the statistical operations applied to a dataset. This record can be "replayed" for verification purposes, as well as be modified to enable alternative analyses. The software also issues warnings of certain kinds of potential errors in statistical methodology, again related to the reproducibility issue.
Covert attention allows for continuous control of brain–computer interfaces

While brain‐computer interfaces (BCIs) can be used for controlling external devices, they also hold the promise of providing a new tool for studying the working brain. In this study we investigated whether modulations of brain activity by changes in covert attention can be used as a continuous control signal for BCI. Covert attention is the act of mentally focusing on a peripheral sensory stimulus without changing gaze direction. The ongoing brain activity was recorded using magnetoencephalography in subjects as they covertly attended to a moving cue while maintaining fixation. Based on posterior alpha power alone, the direction to which subjects were attending could be recovered using circular regression. Results show that the angle of attention could be predicted with a mean absolute deviation of 51° in our best subject. Averaged over subjects, the mean deviation was ∼70°. In terms of information transfer rate, the optimal data length used for recovering the direction of attention was found to be 1700 ms; this resulted in a mean absolute deviation of 60° for the best subject. The results were obtained without any subject‐specific feature selection and did not require prior subject training. Our findings demonstrate that modulations of posterior alpha activity due to the direction of covert attention has potential as a control signal for continuous control in a BCI setting. Our approach will have several applications, including a brain‐controlled computer mouse and improved methods for neuro‐feedback that allow direct training of subjects’ ability to modulate posterior alpha activity.
Studies of the Neutralizing Activity and Avidity of Anti-Human Immunodeficiency Virus Type 1 Env Antibody Elicited by DNA Priming and Protein Boosting

ABSTRACT DNA vaccination is an effective means of eliciting strong antibody responses to a number of viral antigens. However, DNA immunization alone has not generated persistent, high-titer antibody and neutralizing antibody responses to human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env). We have previously reported that DNA-primed anti-Env antibody responses can be augmented by boosting with Env-expressing recombinant vaccinia viruses. We report here that recombinant Env protein provides a more effective boost of DNA-initiated antibody responses. In rabbits primed with Env-expressing plasmids, protein boosting increased titer, persistence, neutralizing activity, and avidity of anti-Env responses. While titers increased rapidly after boosting, avidity and neutralizing activity matured more slowly over a 6-month period following protein boosting. DNA priming and protein immunization with HIV-1 HXB-2 Env elicited neutralizing antibody for T cell line-adapted, but not primary isolate, viruses. The most effective neutralizing antibody responses were observed after priming with plasmids which expressed noninfectious virus-like particles. In contrast to immunizations with HIV-1 Env, DNA immunizations with the influenza virus hemagglutinin glycoprotein did not require a protein boost to achieve high-titer antibody with good avidity and persistence.
Dual task cost of cognition is related to fall risk in patients with multiple sclerosis: a prospective study

Objective: To examine whether change in cognitive performance during dual task condition compared with a task in isolation, known as dual task cost, is related to fall risk of patients with multiple sclerosis. Design: Prospective cohort. During baseline assessment, data about balance, walking and cognitive performance of patients with multiple sclerosis were collected under a single and dual task condition. The dual task cost was calculated as a percentage of change in parameters from single to dual task conditions. Falls were recorded prospectively for six months and participants were classified as none/one time fallers and recurrent fallers (⩾2 falls). The association between dual task costs and fall status was evaluated by logistic regression. Setting: Balance research lab of university hospital. Participants: A total of 60 patients with relapsing-remitting multiple sclerosis. Interventions: Not applicable. Main outcome measures: The dual task cost of the center of pressure sway area, walking velocity and correct response rate were outcome measures for balance, walking and cognitive performance, respectively. Results: A total of 79 falls were reported by 38 of the participants who experienced one or more falls; 26 (43.3%) of them had recurrent falls. Dual tasking resulted in increased sway area and decreased walking velocity and correct response rate during walking (all p values <0.05). Logistic regressions showed that the dual task cost of the correct response rate during walking and walking velocity were associated with increased risk of recurrent falls (P = 0.02, odds ratio = 1.34; confidence interval (CI) 1.04–3.74; P = 0.05, odds ratio = 1.23, CI = 1.02–4.45, respectively). Conclusions: The dual task cost of cognition was related to fall, which should be considered as a target for falls evaluation and prevention strategies.
Comparing Different Systemic Risk Measures for European Banking System

This research examines and compares the performances in terms of systemic risk ranking for three different systemic risk metrics based on daily frequency publicly available data, specifically: Marginal Expected Shortfall (ES), Component Expected Shortfall (CES) and Delta Conditional Value-at-Risk (ΔCoVaR). We compute ΔCoVaR, MES and CES by utilizing EVT principles for modelling marginal distributions and Student’s t copula for describing the dependence structure between every bank and the banking system. Our objective is to attest whether different systemic risk metrics detect the same banks as systemically dangerous institutions with refer to a sample of European banks over the time span 2004-2015. For each bank in the sample we also calculate three traditional market risk measures, like Market VaR, Sharpe’s beta and the correlation between every bank and the banking system (European STOXX 600 Banks Index). Another aim is to explore the existence of a link among systemic risk measures and traditional risk metrics. In addition, the classification results obtained by the different risk metrics are compared with the ranking in terms of systemic riskiness (for European banks) calculated by Financial Stability Board (2015) using end-2014 data and collected in its list of Global Systemically Important Banks (G-SIBs). With refer to the entire sample period, we find a good coherence of ranking results among the three different systemic risk metrics, in particular between CES and ΔCoVaR. Moreover, we find for MES and ΔCoVaR a strong linkage with beta and correlation metrics respectively. Finally, CES metric shows the highest level of concordance with the list of G-SIBs by FSB with refer to European banks.
Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus

The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24–37) was identified as a transient structure (~20–30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.
Change in clinician-assessed measures of multiple sclerosis and subject-reported quality of life: results from the IMPACT study

Background The IMPACT study demonstrated the benefit of interferon beta-1a (IFNβ-1a, Avonex®) two-year change in disability measured by the Multiple Sclerosis Functional Composite (MSFC) in secondary progressive multiple sclerosis (SP-MS) and health-related quality of life (HRQoL) measured by the Multiple Sclerosis Quality of Life Inventory (MSQLI). The IMPACT data permit a detailed assessment of the relation between clinical and self-reported measures. Methods IMPACT was an international randomized, double-blind, placebo-controlled trial of SP-MS patients. As the MSQLI is only in English, this report includes US and Canadian subjects. Subjects were randomized to weekly intramuscular (im) injections of INb-1a (60 mg) or placebo for 24 months. Results At baseline and follow-up, MSQLI correlations were generally stronger with the EDSS than with the MSQLI, MSFC but comparable with MSFC components. Combining the two groups, MSQLI changes for those in the best and worst MSFC change quartiles demonstrated a statistical difference for six of the 11 MSQLI scales. Linear regression demonstrated that EDSS change from baseline to month-24 scores was correlated with change in two MSQLI components. Conclusion These data support the appropriateness of using the MSQLI with individuals who have SP-MS.
Prognosis of advanced hepatocellular carcinoma: comparison of three staging systems in two French clinical trials.

OBJECTIVE The objective of this study was to assess the performance of three staging systems [Okuda, Cancer of the Liver Italian Program (CLIP) and Barcelona Clinic Liver Cancer group (BCLC)], for predicting survival in patients with hepatocellular carcinoma (HCC) and to explore how to improve prognostic classification among French patients with HCC whose main etiology is alcoholic cirrhosis. METHODS We have pooled two randomized clinical trials in palliative condition from the Fédération Francophone de Cancerologie Digestive. They had included 416 and 122 patients. Performances of Okuda, CLIP and BCLC scores have been compared using Akaike information criterion, discriminatory ability (Harrell's C and the Royston's D statistics), monotonicity of gradients and predictive accuracy (Schemper statistics Vs). To explore how to improve classifications, univariate and multivariate Cox model analyses were carried out. RESULTS The pooled database included 538 patients. The median survival was 5.3 months (95% confidence interval 4.6-6.2). For all statistics CLIP staging system had a better prognostic ability. Performances of all staging systems were rather disappointing. World Health Organization performance status (WHO PS) for CLIP or alpha-fetoprotein for BCLC allowed a significant improvement of prognostic information. CONCLUSION Our results indicate that CLIP staging seems to be most adapted to palliative setting and that it could be better by associating WHO PS.
Increased accessibility of the N‐terminus of testis‐specific histone TH2B to antibodies in elongating spermatids

Changes in chromatin structure during spermatogenesis were investigated using a monoclonal antibody that immunoreacts with the N‐terminus of the testis‐specific histone TH2B. This monoclonal antibody, which had been raised against rat tyrosine hydroxylase (TH), cross‐reacted with TH2B because of sequence homology at the N‐termini of TH and TH2B. The epitope was localized to the N‐terminus of TH2B as trypsin‐digested chromatin which lacked the N‐terminal tail did not react with anti‐TH and preincubating anti‐TH with a synthetic peptide made from the homologous sequence between TH2B and TH inhibited its binding to TH and TH2B. In histological sections of rat testis, the primary spermatocytes and round spermatids immunoreacted weakly, whereas elongating spermatids at steps 10–12 immunoreacted intensely with anti‐TH. Increased staining of elongating spermatids was also observed in mouse and hamster by immunohistochemistry. However, immunoblotting proteins extracted from separated rat testis cells showed no increase in the TH2B content of these late steps of spermatids. The apparent increase in the immunohistochemical staining corresponds to increased accessibility of the epitope in the elongating spermatids. This indicated that the N‐terminus of TH2B is less tightly bound to DNA or to other proteins at this time in preparation for the removal of TH2B and other histones. © 1995 wiley‐Liss, Inc.
Modeling of Scattering in Arbitrary-Shape Waveguide Using Broadband Green's Function With Higher Order Low Wavenumber Extractions

The broadband Green's function with low wavenumber extractions (BBGFL) consists of low wavenumber method of moments (MoM) solutions combined with modal expansions. BBGFL is suitable for broadband simulations because the modal functions are independent of frequencies. The modal expansion in this paper has sixth-order convergence. Using wavenumber derivatives of the surface current, it is shown that the higher order extraction requires only a single MoM impedance matrix on the left-hand side. For the same number of modes, the sixth-order convergence has significant improvement in accuracy over the <inline-formula><tex-math notation="LaTeX">${\text{second}}$</tex-math> </inline-formula>- and <inline-formula><tex-math notation="LaTeX">${\text{fourth}}$</tex-math></inline-formula>-order convergence. Scattering in an arbitrary-shape waveguide is modeled by using a surface integral equation formulated with the sixth-order BBGFL. Using BBGFL, the unknowns are only on the surface of the scatterer. Results of simulations are illustrated and the results are in good agreement with those of direct MoM.