Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Quantification of Recombinant Protein Inclusion Bodies within Intact Cells by FT‐IR Spectroscopy

The accomplishment of the quantification of the recombinant protein content of whole bacterial cells by FT‐IR spectroscopy by application of chemometrics is shown. Recombinant Escherichia coli cells expressing an inclusion body forming fusion protein were dried on a 96‐well silicon plate for the analysis in a high‐throughput FT‐IR spectrometer. Acquired spectra of additionally conventionally quantified samples were used to establish a multivariate calibration. The obtained method was tested by predicting inclusion body contents of samples not used for the multivariate model. Results from FT‐IR spectra coincided well with the data of universalized electrophoresis analysis. Hence FT‐IR spectroscopy could prove as a fast and simple alternative to conventional quantification methods.
Perioperative Mortality in Patients with Pulmonary Hypertension Undergoing Major Joint Replacement

BACKGROUND: There is a paucity of perioperative outcomes data for patients with chronic pulmonary hypertension (PHTN) undergoing noncardiac surgery. Clinicians, therefore, have little information on which to evaluate the risk for morbidity and mortality in this patient population. In this study, we evaluated the incidence and risks of perioperative morbidity and mortality in patients with PHTN undergoing primary total hip arthroplasty (THA) and total knee arthroplasty (TKA). METHODS: Using the largest inpatient database in the United States (National Inpatient Sample), we identified entries for THA and TKA between the years of 1998 and 2006. Patients with the diagnosis of PHTN were identified and matched to those without the disease based on health-related demographic variables. Perioperative mortality was considered the primary outcome. Multivariate logistic regression models were fitted to assess the impact of PHTN on in-hospital mortality. RESULTS: We identified 670,516 entries for TKA and 360,119 for THA. Of those patients, 2184 (0.3%) and 1359 (0.4%), respectively, had the diagnosis of PHTN (average annual rate of 1180 for TKA [range, 507–2073] and 739 for THA [range, 467–1054]). Patients with PHTN undergoing THA experienced an approximately 4-fold increased adjusted risk of mortality (2.4% vs 0.6%), and those undergoing TKA a 4.5-fold increased adjusted risk of mortality (0.9% vs 0.2%) compared with patients without PHTN in the matched sample (P < 0.001 for each comparison). Patients with primary PHTN undergoing THA experienced the highest mortality rate (5% [95% CI, 2.3%–7.7%]). CONCLUSIONS: This analysis demonstrates that patients with PHTN are at increased risk for perioperative mortality after THA and TKA.
Solar System Abundances and Condensation Temperatures of the Elements

Solar photospheric and meteoritic CI chondrite abundance determinations for all elements are summarized and the best currently available photospheric abundances are selected. The meteoritic and solar abundances of a few elements (e.g., noble gases, beryllium, boron, phosphorous, sulfur) are discussed in detail. The photospheric abundances give mass fractions of hydrogen (X = 0.7491), helium (Y = 0.2377), and heavy elements (Z = 0.0133), leading to Z/X = 0.0177, which is lower than the widely used Z/X = 0.0245 from previous compilations. Recent results from standard solar models considering helium and heavy-element settling imply that photospheric abundances and mass fractions are not equal to protosolar abundances (representative of solar system abundances). Protosolar elemental and isotopic abundances are derived from photospheric abundances by considering settling effects. Derived protosolar mass fractions are X0 = 0.7110, Y0 = 0.2741, and Z0 = 0.0149. The solar system and photospheric abundance tables are used to compute self-consistent sets of condensation temperatures for all elements.
Group VII ethylene response factor diversification and regulation in four species from flood-prone environments.

Flooding events negatively affect plant performance and survival. Flooding gradients thereby determine the dynamics in vegetation composition and species abundance. In adaptation to flooding, the group VII Ethylene Response Factor genes (ERF-VIIs) play pivotal roles in rice and Arabidopsis through regulation of anaerobic gene expression and antithetical survival strategies. We investigated if ERF-VIIs have a similar role in mediating survival strategies in eudicot species from flood-prone environments. Here, we studied the evolutionary origin and regulation of ERF-VII transcript abundance and the physiological responses in species from two genera of divergent taxonomic lineages (Rumex and Rorippa). Synteny analysis revealed that angiosperm ERF-VIIs arose from two ancestral loci and that subsequent diversification and duplication led to the present ERF-VII variation. We propose that subtle variation in the regulation of ERF-VII transcript abundance could explain variation in tolerance among Rorippa species. In Rumex, the main difference in flood tolerance correlated with the genetic variation in ERF-VII genes. Large transcriptional differences were found by comparing the two genera: darkness and dark submergence-induced Rumex ERF-VIIs, whereas HRE2 expression was increased in submerged Rorippa roots. We conclude that the involvement of ERF-VIIs in flooding tolerance developed in a phylogenetic-dependent manner, with subtle variations within taxonomic clades.
Floral biology and pollination requirements of sesame (Sesamum indicum L.)

This study aimed to investigate the floral biology and pollination requirements of sesame (Sesamum indicum L.), cultivar CNPA G2. The study was carried out at Barbalha, State of Ceara, and consisted of two phases: floral biology and pollination requirements. Flowers were observed as for time of anthesis, lifespan and stigma receptivity, and were applied the following pollination treatments: open pollination, hand cross-pollination, hand self-pollination, pollination restricted with tulle bags and pollination restricted with paper bags. Significant differences (p < 0.05) were detected between treatments for the number of fruits harvested 30 days after pollination. It was shown that the sesame plant presents a mixed-pollination system, because it can produce fruit whatever the type of pollination tested. Flowers are able to autopollinate and do not depend on external agents. Pollinations restricted with paper and tulle bags produced fruit with greater number of heavier seeds. It is concluded that sesame crop is able to autopollinate and benefit from both self-pollination and cross-pollination.
Transplantation of Alginate Microcapsules with Proliferating Cells in Mice

Abstract: Alginate microcapsules may be used to encapsulate therapeutic cells and, thereby, to protect them from the host immune system. Both the biomaterial, as well as the therapeutic cells, may give rise to immunological reactions. We have developed methods that are useful in the study of capsule biocompatibility, as well as reactions against the grafts. These imply investigation of the survival of the encapsulated cells as well as fibrotic reactions against the microcapsules. Studies were performed in Balb/c mice with empty alginate‐PLL‐alginate microcapsules as well as microcapsules containing cells of human or mouse origin. Confocal laser scanning microscopy (CLSM) was used to visualize live and dead cells within the microcapsules and to define some of the cells involved in the fibrotic reaction against the microcapsules. In both grafts, live cells were detected seven days after transplantation. Minor fibrotic reactions were found against empty alginate‐PLL‐alginate microcapsules and to microcapsules containing mouse cells. An extensive fibrotic reaction was found one week after transplantation against microcapsules containing human cells, and the secretion of therapeutic protein endostatin had ceased. Fibroblasts and macrophages were involved in the fibrotic reaction against the xenograft.
Brooks' Vertex-Colouring Theorem in Linear Time

Brooks' Theorem [R. L. Brooks, On Colouring the Nodes of a Network, Proc. Cambridge Philos. Soc. } 37:194-197, 1941] states that every graph $G$ with maximum degree $\Delta$, has a vertex-colouring with $\Delta$ colours, unless $G$ is a complete graph or an odd cycle, in which case $\Delta+1$ colours are required. Lov\'asz [L. Lov\'asz, Three short proofs in graph theory, J. Combin. Theory Ser. 19:269-271, 1975] gives an algorithmic proof of Brooks' Theorem. Unfortunately this proof is missing important details and it is thus unclear whether it leads to a linear time algorithm. In this paper we give a complete description of the proof of Lov\'asz, and we derive a linear time algorithm for determining the vertex-colouring guaranteed by Brooks' Theorem.
Finding genes underlying human disease

With the surge in genome‐wide association studies (GWAS), many have asked the question ‘Are linkage studies dead? ’ In this article, we survey the approaches used in mapping human disease genes, reviewing the analysis strategies that preceded and laid the groundwork for GWAS. We note that earlier approaches are still useful and the development of new methodology is warranted.
PTF11iqb: cool supergiant mass-loss that bridges the gap between Type IIn and normal supernovae

The supernova (SN) PTF11iqb was initially classified as a Type IIn event caught very early after explosion. It showed narrow Wolf–Rayet (WR) spectral features on day 2 (as in SN 1998S and SN 2013cu), but the narrow emission weakened quickly and the spectrum morphed to resemble Types II-L and II-P. At late times, Hα exhibited a complex, multipeaked profile reminiscent of SN 1998S. In terms of spectroscopic evolution, we find that PTF11iqb was a near twin of SN 1998S, although with somewhat weaker interaction with circumstellar material (CSM) at early times, and stronger interaction at late times. We interpret the spectral changes as caused by early interaction with asymmetric CSM that is quickly (by day 20) enveloped by the expanding SN ejecta photosphere, but then revealed again after the end of the plateau when the photosphere recedes. The light curve can be matched with a simple model for CSM interaction (with a mass-loss rate of roughly 10^(−4) M_⊙ yr^(−1)) added to the light curve of a normal SN II-P. The underlying plateau requires a progenitor with an extended hydrogen envelope like a red supergiant at the moment of explosion, consistent with the slow wind speed (<80 km s^(−1)) inferred from narrow Hα emission. The cool supergiant progenitor is significant because PTF11iqb showed WR features in its early spectrum – meaning that the presence of such WR features does not necessarily indicate a WR-like progenitor. Overall, PTF11iqb bridges SNe IIn with weaker pre-SN mass-loss seen in SNe II-L and II-P, implying a continuum between these types.
Prediction of the Evolution of Ceftazidime Resistance in Extended-Spectrum β-Lactamase CTX-M-9

ABSTRACT A random mutagenesis technique was used to predict the evolutionary potential of β-lactamase CTX-M-9 toward the acquisition of improved catalytic activity against ceftazidime. Thirty CTX-M mutants were obtained during three rounds of mutagenesis. These mutants conferred 1- to 128-fold-higher MICs of ceftazidime than the parental enzyme CTX-M-9. The CTX-M mutants contained one to six amino acid substitutions. Mutants harbored the substitutions Asp240Gly and Pro167Ser, which were previously observed in clinical CTX-M enzymes. Additional substitutions, notably Arg164His, Asp179Gly, and Arg276Ser, were observed near the active site. The kinetic constants of the three most active mutants revealed two distinct ways of improving catalytic efficiency against ceftazidime. One enzyme had a 17-fold-higher kcat value than CTX-M-9 against ceftazidime. The other two had 75- to 300-fold-lower Km values than CTX-M-9 against ceftazidime. The current emergence of CTX-M β-lactamases with improved activity against ceftazidime may therefore be the beginning of an evolutionary process which might subsequently generate a great diversity of CTX-M-type ceftazidimases.
Comparison of the aPTT with alternative tests for monitoring direct thrombin inhibitors in patient samples.

OBJECTIVES The activated partial thromboplastin time (aPTT) test has been used for years to monitor parenteral direct thrombin inhibitors (DTIs) and unfractionated heparin. Because the aPTT correlates poorly with unfractionated heparin levels, we hypothesized that the aPTT may not be the best test for monitoring parenteral DTIs. METHODS Using 235 excess plasma specimens from 82 adult patients receiving treatment with DTIs (argatroban, bivalirudin, or dabigatran), we compared the aPTT with the ecarin chromogenic assay (ECA), the dilute thrombin time (dTT) test, and the prothrombinase-induced clotting time (PiCT) test. RESULTS The aPTT correlated poorly with each of the other tests in both bivalirudin- and argatroban-containing samples (r(2) = 0.04-0.23). The ECA and dTT exhibited the best correlations (r(2) = 0.66-0.93). Intermediate correlations were seen when the results of the PiCT were plotted against the dTT or ECA (r(2) = 0.46-0.58). Nineteen specimens obtained from six patients receiving dabigatran showed a good correlation between the dTT and the ECA (r(2) = 0.92). CONCLUSIONS The aPTT does not correlate well with other tests that might be used to monitor parental DTI administration. Further studies are needed to evaluate the clinical usefulness of alternative tests and their correlation with clinical outcomes.
Syllable structure effects turn out to be word length effects: Comment on Santiago et al. (2000)

Santiago, MacKay, Palma, and Rho (2000) report two picture naming experiments examining the role of syllable onset complexity and number of syllables in spoken word production. Experiment 1 showed that naming latencies are longer for words with two syllables (e.g., demon) than one syllable (e.g., duck), and longer for words beginning with a consonant cluster (e.g., drill) than a single consonant (e.g., duck). Experiment 2 replicated these findings and showed that the complexity of the syllable nucleus and coda has no effect. These results are taken to support MacKay's (1987) Node Structure theory and to refute models such as WEAVER++ (Roelofs, 1997a) that predict effects of word length but not of onset complexity and number of syllables per se. In this comment, I show that a re-analysis of the data of Santiago et al. that takes word length into account leads to the opposite conclusion. The observed effects of onset complexity and number of syllables appear to be length effects, supporting WEAVER++ and contradicting the Node Structure theory.
Role of Angiotensin-(1-7) in Rostral Ventrolateral Medulla in Blood Pressure Regulation via Sympathetic Nerve Activity in Wistar-Kyoto and Spontaneous Hypertensive Rats

Abstract Angiotensin (Ang)-(1-7) Ang-(1-7) is formed from angiotensin II by angiotensin-converting enzyme 2 (ACE2) and modulates the renin-angiotensin system. We evaluated whether the Ang-(1-7)-Mas axis in the rostral ventrolateral medulla (RVLM) contributes to neural mechanisms of blood pressure (BP) regulation. We microinjected Ang-(1-7), Ang-(1-7)-Mas receptor antagonist A-779, and ACE2 inhibitor DX600 into the RVLM of anesthetized Wistar-Kyoto rats (WKY) and spontaneously hypertensive rats (SHRs). Unilateral Ang-(1-7) microinjection induced a significantly greater increase in AP (arterial blood pressure) in SHR than in WKY. Bilateral A-779 microinjection induced a significantly greater decrease in AP and renal sympathetic nerve activity in SHR than in WKY. Bilateral DX600 microinjection induced a significantly greater decrease in AP in SHR than in WKY. Our results suggest that endogenous Ang-(1-7) in the RVLM contributes to maintain AP and renal sympathetic nerve activity both in SHR and WKY and that its activity might be enhanced in SHR.
Human serum antibodies to varicella-zoster virus thymidine kinase

The conditions required for the production of varicella-zoster virus (VSV)-induced deoxythymidine kinase (dTk) have been studied. Extracts from Vero cells harvested 62 h after VZV infection were found to contain VZV-induced dTk activity, with a minimal contribution from the cellular dTk activity. VZV dTK was shown to have a broad substrate specificity phosphorylating both deoxythymidine, deoxycytidine, and iododeoxyuridine. Deoxythymidine triphosphate inhibition studies revealed an intermediate deoxythymidine triphosphate sensitivity when compared with that of the cellular cytosolar enzyme and the deoxythymidine triphosphate-insensitive herpes simplex virus dTk. An assay for VZV dTk-blocking antibodies was developed, with [125I]iododeoxyuridine as a substrate in the presence of a deoxythymidine triphosphate concentration which selectively blocked the dTK of host cell origin. A total of 79 serum samples were studied; these included serum pairs from patients with varicella or herpes zoster and single sera from immune and nonimmune adults. VZV dTk blocking antibodies were detected exclusively in sera from patients with herpes zoster. All serum pairs showing VZV dTK seroconversion also showed a parallel conversion of complement fixation titers. The VZV dTk antibodies were found to be of the immunoglobulin G class. The immunological specificity of VZV dTK was investigated, and no cross-reactivity with herpes simplex virus type 1 or 2 dTk was found.
Observer-based compensator design for networked control systems with long time delays

Network-induced delays in the networked control systems (NCS) are inevitable and have a significant effect on system performance. In this paper, time-varying delays are regarded as the sum of the mean delays and uncertain delays. Furthermore, NCS with long time delays is modelled as a discrete-time model with structural uncertainty for its time-varying network-induced delays. Based on the model, a new control law via an iterative linear matrix inequality (LMI) approach is presented which can stabilize the closed-loop system. Theoretical analysis and simulation results compared to some existing schemes show that the control strategy presented in this paper is effective and feasible.
Forecasting Distribution of Body Mass Index in the United States: Is There More Room for Growth?

Background. Much of the literature on obesity has consistently documented the unprecedented rise in body weight over the past 2 decades. Less attention is paid to future projections of the population distribution of body mass index (BMI). Objective. To forecast the distribution of BMI in children (6—17 years) and adults (>17 years) in the United States (US) by age group, sex, and race over the period 2004—2014. Methods. Analysis of Medical Expenditure Panel Survey data (2001—2002 and 2004— 2005) to estimate and compare the 1-year transitions across BMI categories for children and adults. Forecasting distributions of obesity over 2004—2014 using a probabilistic population-level simulation model and validating it with prevalence data from 2005—2006 National Health and Nutrition Examination Survey. Results. During 2004— 2005, a majority of adults in each BMI category remained in the same category after 1 year, these estimates being not significantly different than the corresponding estimates in 2001—2002. Among children, stabilities within BMI categories are low during 2004—2005, and compared with 2001—2002, transition probabilities into overweight class 2 from other BMI categories increase substantially. Forecasts reveal significant increases in the risk of overweight category among children 6 to 9 years old (5% to 14% in 5 years), with a greater increase anticipated in males, and increases in the overweight category for many years to come for adults, although the adult obesity prevalence remains at the current levels. Conclusions. Although the absolute levels of obesity remain high among US adults, the growth in obesity appears to have stagnated. On the contrary, continued growth in the prevalence of the highest BMI category for children is anticipated.
Phosphorothioate Nucleotides and Oligonucleotides – Recent Progress in Synthesis and Application

We dedicate this work to Prof. Fritz Eckstein (MPI, Gçttingen) and Prof. Wojciech J. Stec (CMMS PAS, Łódź), who invented the phosphorothioate modification of nucleic acids, envisioned its many important applications, carefully elucidated its biochemical and stereochemical aspects, and fostered PS-Oligos over decades. We are very grateful to have had the honor and pleasure to develop our understanding of PS-Oligos through guidance by their papers and lectures, and through stimulating scientific discussions with these two great scientists.
Mechanistic and Kinetic Aspects of Photosensitization in the Presence of Oxygen†,§

Abstract Determining whether the first step of photooxygenation is Type I or Type II is a necessary prerequisite in order to establish the mechanism of photodynamic action. But this distinction is not sufficient, because other processes, both consecutive and competitive, commonly participate in the overall mechanism. Thus, in both Type I and Type II reactions, the initial products are often peroxides that can break down and induce free radical reactions. These aspects of photosensitization are discussed and illustrated by sensitizer/substrate systems involving (1) only radical reactions (decatungstate/alkane) and (2) reactions of singlet oxygen occurring in competitive and consecutive processes and possibly followed by radical reactions (methylene blue/2′-deoxyguanosine). Two other previously investigated systems involving, respectively, a Type II interaction followed by radical processes (methylene blue/alkene) and Type II reactions, some of which being competitive or consecutive (rose bengal/alkene), are briefly reconsidered.
High-Throughput Multi-Rate Decoding of Structured Low-Density Parity-Check Codes

As an enhancement of the state-of-the-art solutions, a high-throughput architecture of a decoder for structured LDPC codes is presented in this paper. Thanks to the peculiar code definition and to the envisaged architecture featuring memory paging, the decoder is very flexible, and the support of different code rates is achieved with no significant hardware overhead. A top-down design flow of a real decoder is reported, starting from the analysis of the system performance in finite-precision arithmetic, up to the VLSI implementation details of the elementary modules. The synthesis of the whole decoder on 0.18 μm standard cells CMOS technology showed remarkable performances: small implementation loss (0.2 dB down to BER = 10-8), low latency (less than 6.0 μs), high useful throughput (up to 940 Mbps) and low complexity (about 375 Kgates).
Unique Boron Carbide Nanoparticle Nanobio Interface: Effects on Protein-RNA Interactions and 3-D Spheroid Metastatic Phenotype.

AIM The effect of boron carbide (B4C) nanoparticles (NP) on protein-RNA complexes and metastatic phenotype of 3-D tumor spheroids was investigated. MATERIALS AND METHODS Characterization was performed by transmission electron microscopy (TEM), zeta potential (ZP), 2-dimensional fluorescence difference spectroscopy (2-D FDS), gel electrophoresis, MTT, haemolysis and 3-D tumor spheroid assays. RESULTS TEM showed NP were homogenous (≤50 nm) and spherical in shape. Zeta potential (ζ) of NP (-43.3) shifted upon protein:RNA interaction (+26.9). Protein:RNA complex interaction with NP was confirmed by 2-D FDS, demonstrating excitation/emission blue shift and lowered fluorescence intensity, and electrophoretic mobility shift assay (EMSA), where presence of B4C ablated visualization of the complex. B4C NP cytotoxicity was less than zinc oxide by MTT assay, protected haemolysis and effected 3-D tumor spheroid metastatic phenotype. CONCLUSION Nanobio interface of B4C nanoparticles is unique and its anticancer potential may be mediated by altering protein and RNA interactions.