Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Diversity within the Genus Pediococcus as Revealed by Randomly Amplified Polymorphic DNA PCR and Pulsed-Field Gel Electrophoresis

ABSTRACT The genomic diversity of 33 previously assigned strains from six species within the genus Pediococcus was assessed by randomly amplified polymorphic DNA (RAPD) PCR and pulsed-field-gel electrophoresis (PFGE). The RAPD PCR patterns produced by two separate random primers, termed P1 (ACGCGCCCT) and P2 (ATGTAACGCC), were compared by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm. Pattern variations between repeat samples set a strain discrimination threshold of less than 70% similarity. P1 and P2 primers alone and in combination produced 14, 21, and 28 distinct patterns, respectively. When each strain was assigned with a type strain with which it shared the highest level of similarity, both primers grouped 17 of the 27 strains to their proposed species. PFGE following genomic digestion with the restriction enzymes ApaI, NotI, and AscI produced 30, 32, and 28 distinct macrorestriction patterns, respectively. Specific DNA fragments within the NotI and AscI macrorestriction patterns for each strain were observed that allowed 27 of the 33 strains to be assigned to their proposed species. For example, following digestion with AscI, all Pediococcus parvulus strains were characterized by two DNA fragments, one of approximately 220 kb and another between 700 and 800 kb. The exceptions correlated with those observed with both RAPD PCR primers and included three P. damnosus and two P. pentosaceus strains that grew at temperatures regarded as nonpermissive for their proposed species but not for those with which they grouped.
Ballistocardiography for nonintrusive sleep structure estimation

Based on the its nonintrusive characteristics, ballistocardiography(BCG) has applied in the estimation of sleep structure without attaching any sensors to the subject's body. Loadcell or polyvinylidenefluoride (PVDF) film sensors are installed on the mattress for the monitoring of BCG. BCG peak was detected and heart rate variability parameters are derived. Parameters representing sleep structure and quality are estimated using these parameters. Sleep efficiency, four stages of sleep structure and sleep onset latency are estimated and results are compared with the results derived from polysomnographic recording.
Benefits of Demand Response on Operation of Distribution Networks: A Case Study

Despite of the great focus of attention dedicated to demand response (DR), the potential benefits of DR on distribution networks have not yet been quantitatively studied. This paper aims to assess DR potential impacts on major attributes of the operation of a residential distribution network. For doing so, grossly metered usage of more than 1600 residential consumers from Kainuu, Finland, is disaggregated to appliance-level load profiles. The flexibility of the load profiles is also estimated from the survey data and questionnaires. The individual profiles are then adjusted within their flexibility such that the most evenly distributed aggregated load profile is realized. Finally, the resulted load profile is applied to a Finnish distribution network, and the impacts of the DR on different aspects of the network operation such as the network losses, voltage profiles, and service reliability are studied. The observations certified significant benefits of the DR potentials for the network operation and reliability. It is also revealed that almost all of the benefits can be achieved by enabling the potential of responsive heating and ventilation systems.
Screening and functional analysis of glioma‑related genes induced by candoxin.

This study aimed to identify time‑specific and common differential genes (CDGs) expressed in glioma cells following exposure to candoxin at three different time‑points. Gene expression data from candoxin‑treated human glioma (Hs 683) cells were downloaded from the Gene Expression Omnibus database (accession number, GSE1682), from a 12‑time‑point set of samples. Differentially expressed genes were screened between control and candoxin‑treated samples at different time‑points, and three time‑specific gene sets and CDGs were identified. All genes were subject to pathway enrichment analysis to gain further insight into gene function. CDGs were clustered based upon their original expression between 0 and 48 h, and, from this subset, feature genes were selected. Small molecules associated with candoxin were identified by comparing the expression pattern of the most valid candidate genes with that of differential genes exposed to small molecules in the Connectivity Map. From the 12‑, 24‑ and 48‑h time‑points, 746, 265 and 539 differentially expressed genes were identified, respectively. A total of 129 genes were differentially expressed and significantly enriched in focal adhesion and gap junction pathways. From these, 11 feature genes and one marker gene (EPS8L1) were identified. Four small molecules that were most relevant to candoxin action were identified. In conclusion, it is hypothesized that candoxin stimulation can cause glial inflammation through mutations in cell adhesion activity. The EPS8L1 gene may be a valid marker for glioma diagnosis, and the four small molecules identified may be relevant for future drug design.
Unique Classes of Mutations in the Saccharomyces cerevisiae G-Protein Translation Elongation Factor 1A Suppress the Requirement for Guanine Nucleotide Exchange

G-proteins play critical roles in many cellular processes and are regulated by accessory proteins that modulate the nucleotide-bound state. Such proteins, including eukaryotic translation elongation factor 1A (eEF1A), are frequently reactivated by guanine nucleotide exchange factors (GEFs). In the yeast Saccharomyces cerevisiae, only the catalytic subunit of the GEF complex, eEF1Bα, is essential for viability. The requirement for the TEF5 gene encoding eEF1Bα can be suppressed by the presence of excess substrate, eEF1A. These cells, however, have defects in growth and translation. Two independent unbiased screens performed to dissect the cause of these phenotypes yielded dominant suppressors that bypass the requirement for extra eEF1A. Surprisingly, all mutations are in the G-protein eEF1A and cluster in its GTP-binding domain. Five mutants were used to construct novel strains expressing only the eEF1A mutant at normal levels. These strains show no growth defects and little to no decreases in total translation, which raises questions as to the evolutionary expression of GEF complexity and other potential functions of this complex. The location of the mutations on the eEF1A-eEF1Bα structure suggests that their mechanism of suppression may depend on effects on the conserved G-protein elements: the P-loop and NKXD nucleotide-binding element.
Tight Control of Platelet-derived Growth Factor B/c-sis Expression by Interplay between the 5′-Untranslated Region Sequence and the Major Upstream Promoter*

The long and GC-rich 5′-untranslated region (5′-UTR) of the known 3.8-kb platelet-derived growth factor B (PDGF-B)/c-sis mRNA is highly conserved and inhibits its own translation. It has been thought that this 5′-UTR functions by regulating translation possibly using an internal ribosome entry site (IRES)-mediated mechanism. However, in the present study we found no evidence that the 5′-UTR sequence of PDGF-B mRNA contains any IRES activity. Instead, we found that the 5′-UTR sequence of PDGF-B functions as a promoter both constitutively and upon induction in a variety of cell lines. The 5′-UTR sequence contains two promoters (termed P1 and P2) when only the 5′-UTR sequence is analyzed. In the presence of the upstream TATA-box-containing promoter (P0), P1 and P0 promoters are integrated into one promoter, whereas the P2 promoter still functions. The full promoter with combined P0, P1, and P2 produced two transcripts, with the major one having the full-length 5′-UTR and the minor one the short 5′-UTR. The integrated P0/P1 promoter and P2 promoter are likely responsible for producing the endogenous 3.8- and 2.8-kb PDGF-B mRNAs that are detected in cultured human renal microvascular endothelial cells, a few tumor cells, and rat brain tissues. Furthermore, we detected the 2.8-kb PDGF-B mRNA in erythroleukemia K562 cells upon 12-O-tetradecanoylphorbol-13-acetate-induced differentiation. Considering that the 5′-UTR in the 3.8-kb mRNA contains no IRES activity and inhibits cap-dependent translation, we believe that the endogenous 2.8-kb mRNA produced from the 5′-UTR promoter is likely the major template responsible for protein production both constitutively and upon induction. We also found that the transcription from the 5′-UTR P2 promoter might be coordinated by the major upstream P0 promoter upon stimulation. Based on these observations, we propose that the TATA-containing P0 promoter and the 5′-UTR promoter work together to tightly control the expression of PDGF-B.
Promoter Hypermethylation: An Important Epigenetic Mechanism for hMLH1 Gene Inactivation in Head and Neck Squamous Cell Carcinoma

OBJECTIVE: The hMLH1 gene is one of the mismatch DNA repair genes. Inactivation of the hMLH1 gene has been implicated in the tumorigenesis of many types of human cancers. In most sporadic forms of human cancers, promoter hypermethylation is responsible for hMLH1 gene inactivation. Lack of hMLH1 protein expression has been found in a subset of head and neck squamous cell carcinomas (HNSCCs). The purpose of this study was to investigate whether promoter hypermethylation causes hMLH1 gene inactivation in HNSCCs. STUDY DESIGN: hMLH1 protein expression was determined by immunohistochemical staining in 62 cases, whereas hMLH1 gene promoter methylation was analyzed by methylation-sensitive restriction enzyme digestion, followed by polymerase chain reaction, in 35 cases of HNSCCs. RESULTS: Sixteen (26%) of 62 cases of HNSCCs showed near-complete loss of hMLH1 protein expression on immunohistochemical staining. Twelve (92%) of 13 cases that were negative for the hMLH1 protein displayed promoter hypermethylation, whereas 17 (77%) of 22 cases positive for the protein were free of promoter methylation. CONCLUSIONS: Promoter hypermethylation may be an important mechanism for hMLH1 gene inactivation in a subset of HNSCCs.
Late reverberation reduction and blind reverberation time measurement for automatic speech recognition

Development of automatic speech recognition (ASR) systems robust to late reverberation action is urgent task. It is well known that a late reverberation reduction algorithm used as ASR pre-processor demands prior estimation of reverberation time. Blind reverberation time measurements are less accurate than ones for known room impulse response (RIR) direct measurements. As result, it is naturally expect that ASR accuracy for blind reverberation time estimation will be lower than one for direct estimation technique. Unfortunately, it is difficult find information on the recognition accuracy loss in literature. In this paper, attempt to eliminate this gap is realized, and conditions of minimizing the loss by it reducing to 3–5% are specified.
Gene position in a long operon governs motility development in Bacillus subtilis

Growing cultures of Bacillus subtilis bifurcate into subpopulations of motile individuals and non‐motile chains of cells that are differentiated at the level of gene expression. The motile cells are ON and the chaining cells are OFF for transcription that depends on RNA polymerase and the alternative sigma factor σD. Here we show that chaining cells were OFF for σD‐dependent gene expression because σD levels fell below a threshold and σD activity was inhibited by the anti‐sigma factor FlgM. The probability that σD exceeded the threshold was governed by the position of the sigD gene. The proportion of ON cells increased when sigD was artificially moved forward in the 27 kb fla/che operon. In addition, we identified a new σD‐dependent promoter that increases sigD expression and may provide positive feedback to stabilize the ON state. Finally, we demonstrate that ON/OFF motility states in B. subtilis are a form of development because mosaics of stable and differentiated epigenotypes were evident when the normally dispersed bacteria were forced to grow in one dimension.
Membrane fusion machines of paramyxoviruses: capture of intermediates of fusion

Peptides derived from heptad repeat regions adjacent to the fusion peptide and transmembrane domains of many viral fusion proteins form stable helical bundles and inhibit fusion specifically. Paramyxovirus SV5 fusion (F) protein‐mediated fusion and its inhibition by the peptides N‐1 and C‐1 were analyzed. The temperature dependence of fusion by F suggests that thermal energy, destabilizing proline residues and receptor binding by the hemagglutinin–neuraminidase (HN) protein collectively contribute to F activation from a metastable native state. F‐mediated fusion was reversibly arrested by low temperature or membrane‐incorporated lipids, and the resulting F intermediates were characterized. N‐1 inhibited an earlier F intermediate than C‐1. Co‐expression of HN with F lowered the temperature required to attain the N‐1‐inhibited intermediate, consistent with HN binding to its receptor stimulating a conformational change in F. C‐1 bound and inhibited an intermediate of F that could be detected until a point directly preceding membrane merger. The data are consistent with C‐1 binding a pre‐hairpin intermediate of F and with helical bundle formation being coupled directly to membrane fusion.
Anogenital bacteriology in non‐abused preschool children: a descriptive study of the aerobic genital flora and the isolation of anogenital Gardnerella vaginalis

The purpose of the study is to describe the genital aerobic bacterial flora including Gardnerella vaginalis in girls and the occurrence of anal G. vaginalis in both genders. From a group of 3773 children, 278 (99 boys and 179 girls) with a mean age of 5.63 y (range: 5.13–6.73) were recruited. Inclusion in the study was based on self‐selection, whereby parents who did not suspect any occurrence of sexual abuse of their child gave informed consent to participate. Several mechanisms were undertaken to exclude abused children. At least one bacterial species was isolated from the genitals of 59 (33.9%) girls. Most isolates (39 out of 99) were bacteria representing skin flora (staphylococci and coryneform organisms), with viridans streptococci and related organisms as the second most common group of isolates (31 out of 99). S. anginosus was the single most frequent bacterial species identified (17 isolates). Streptococcus pyogenes was isolated from the genitals of two girls, Streptococcus pneumoniae from one girl and Haemophilus influenzae from eight girls. G. vaginalis was not isolated from the genitals in any girl, but the organism was isolated from the anal canal in three children.
Increased Dietary Leucine Reduces Doxorubicin-Associated Cardiac Dysfunction in Rats

Cardiotoxicity is one of the most significant adverse effects of the oncologic treatment with doxorubicin, which is responsible for a substantial morbid and mortality. The occurrence of heart failure with ventricular dysfunction may lead to severe cardiomyopathy and ultimately to death. Studies have focused on the effects of leucine supplementation as a strategy to minimize or revert the clinical condition of induced proteolysis by several clinical onsets. However, the impact of leucine supplementation in heart failure induced by doxorubicin is unknown. Therefore, the objective of this work is to evaluate the effects of leucine supplementation on the cardiotoxicity in the heart of rats treated with doxorubicin. Rats treated with a 7.5 mg/kg cumulative dose of doxorubicin for 14 days presented a dilatation of the left ventricle (LV), and a reduction of the ejection fraction (FE). The 5% supplementation of leucine in the rats' food prevented the malfunctioning of the LV when administered with doxorubicin. Some alterations in the extracellular matrix remodeling were confirmed by the increase of collagen fibers in the doxorubicin group, which did not increase when the treatment was associated with leucine supplementation. Leucine attenuates heart failure in this experimental model with doxorubicin. Such protection is followed by the maintenance of interstitial collagen fibers.
Transposon Tn554: complete nucleotide sequence and isolation of transposition‐defective and antibiotic‐sensitive mutants.

The complete nucleotide sequence of the Staphylococcus aureus transposon Tn554, which encodes resistance to erythromycin and spectinomycin, was determined by the dideoxy chain termination method. The transposon was found to be 6691 bp in length and to contain six open reading frames of greater than 125 amino acids. Small insertion and deletion mutations were obtained in each of these by in vitro mutagenesis at restriction endonuclease cleavage sites and the mutants characterized with respect to transposition functions and antibiotic resistance markers. Three of the reading frames, designated tnpA, tnpB and tnpC, encode functions that are required for transposition of Tn554; genetic analysis indicated that these three genes define distinct complementation groups of transposition‐defective mutants. Two of the open reading frames correspond to the resistance determinants spc and ermA, the sixth, designated ORF, has no known function. Tn554‐specific peptides corresponding to tnpA, and spc were identified in a coupled transcription‐translation system in vitro.
Rates, factors, reasons, and economic impact associated with switching in rheumatoid arthritis patients newly initiated on biologic disease modifying anti-rheumatic drugs in an integrated healthcare system

Abstract Objectives To identify how many RA patients newly-initiated on bDMARD therapy switch to another bDMARD during the first year of treatment; to evaluate the factors and reasons associated with bDMARD switching; and to compare the RA-related healthcare resource utilization (HCRU) and costs between switchers vs non-switchers during the post-index period. Methods A retrospective cohort study was conducted in RA patients using the Kaiser Permanente Southern California (KPSC) database with the study time period of January 1, 2007 to December 31, 2012. The index date was defined as the date of the first bDMARD prescription. Patients had to have continuous membership eligibility with drug benefit and no prior history of bDMARD during the 24 months prior to the index date. bDMARD switching was defined as a different bDMARD claim during post-index. A multivariable logistic regression model was used to evaluate factors associated with switchers vs non-switchers. Chart notes were reviewed to evaluate reasons for switching from index bDMARD. RA-related HCRU use and costs were evaluated using a generalized linear model (GLM) with gamma distribution and log link function. Results Two hundred and fifty-one patients (12%) switched from their index bDMARD to a different bDMARD during the post-index period. bDMARD switchers were more likely to be female, of Asian/Pacific race, younger than ≤65 years of age, overweight, CCI score ≤2, initiating etanercept or adalimumab, and have a commercial insurance plan compared to non-switchers. Reasons for switching were related mostly to lack or loss of efficacy (∼51%); bDMARD switchers had overall mean adjusted RA related total costs that were 25% higher (p = 0.04) compared to non-switchers. Conclusion It is important for RA patients to receive appropriate therapy and consider bDMARD with different mechanisms of action to decrease subsequent switching, and decrease overall RA related costs as shown in this study.
Development of e-Government Standard Framework through open innovation strategy

e-Government Standard Framework aims to provide a standardized set of software tools for developing and running e-Government applications in order to improve the efficiency of ICT investment and the quality of e-Government services. It focuses on improving the reusability and interoperability of e-Government applications by setting a standard framework for developing software of e-Government.
Visual attention to motion stimuli and its neural correlates in cannabis users

Attention to motion stimuli and correct motion perception are vital for road safety. Although cannabis use has been associated with increased road crash risks, there is limited research on attentional processing of moving stimuli in cannabis users. This study investigated the neural correlates of the three‐stimulus oddball task in cannabis users (n = 18) and non‐users (n = 23) in response to moving stimuli. Stimulus contrast was under 16% against a low luminance background (M luminance < 16 cd/m2). The two groups did not differ in accuracy or in N2 peak amplitude; however, N2 latency was longer for target and standard stimuli in the cannabis group than in the control group. The cannabis group also showed a significantly reduced P3b amplitude in response to target stimuli. The AUDIT score was added as a random factor to the anova to rule out the effects of uneven alcohol consumption in the two groups. A significant group effect was found for N2 latency in response to target and standard stimuli and a significant interaction between the group, and the AUDIT score was found for the P3b peak amplitude for the distractor and standard stimuli, but not for the target stimuli. The results of this study suggest that cannabis use relates to reduced neural activity underlying attention to motion stimuli. Implications for regular early‐onset cannabis use road safety are discussed.
Further evidence that sperm nuclear proteins are necessary for embryogenesis

We have recently presented evidence that the structural integrity of the mouse sperm nuclear matrix may be necessary for the proper unpackaging of sperm DNA for participation in embryogenesis. It is likely that the sperm nuclear matrix contributes to the organisation of the sperm DNA and its disturbance can seriously damage the paternal genome or its expression. In this work, we confirm our previous data and further suggest that even very subtle changes in the sperm nuclear structure may have a significant impact on embryo development. As reported previously, dithiothreitol (DTT) in the presence of an ionic detergent, ATAB, destabilised the nuclear matrix as measured by the halo assay, and oocytes injected with these nuclei failed to develop. We also discovered that omitting the protease inhibitor PMSF from the buffers used to extract spermatozoa prevented sperm injected into oocytes from participating in development. The organisation of DNA into loop domains by the nuclear matrix in these nuclei appeared normal, as measured by the halo assay. Oocytes injected with sperm nuclei that had been washed with ATAB in the presence of phenylmethylsulphonyl fluoride (PMSF) but in the absence of DTT resulted in live births. Neither DTT treatment nor the absence of PMSF would be expected to disrupt the integrity of the paternal DNA. The data therefore suggest that even very subtle alterations in the structural proteins of the nucleus are enough to deprive sperm DNA of the ability to contribute to embryonic development.