Miracle-dz/UniFAR-FTUs huggingface dataset:
5‐aminosalicylic acid inhibits colitis‐associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium‐induced colitis

Background: The impact of the antiinflammatory agent 5‐aminosalicylic acid (5‐ASA) on the risk for colitis‐associated colorectal cancer remains controversial. The chemopreventive activity of 5‐ASA was evaluated in the Swiss Webster model of azoxymethane (AOM)/dextran sulfate sodium (DSS)‐induced colitis‐associated neoplasia. Methods: Mice were injected with AOM (7.4 mg/kg i.p.) and randomized to receive either vehicle or 5‐ASA (75, 150, and 225 mg/kg) for the remainder of the study. DSS treatment began at 9 weeks of age and continued for 3 cycles. At the time of sacrifice (18 weeks of age), the entire colon and rectum were processed for histopathologic examination. Results: An inverse trend was observed between dose and multiplicity of colonic dysplasias in all drug‐treated groups (P = 0.03), with animals receiving 75 mg/kg 5‐ASA exhibiting 56% of the number of dysplasias of the AOM/DSS controls (mean ± SEM: 7.6 ± 1.4 and 13.6 ± 2.7, respectively). Administration of 75 mg/kg 5‐ASA decreased both the mean multiplicity of flat dysplasias (1.8 ± 0.4 for drug‐treated versus 5.6 ± 1.2 for AOM/DSS control) and the burden of polypoid dysplasias (tumor burden: 6.7 ± 2.7 for drug‐treated versus 14.9 ± 3.9 units for AOM/DSS controls) significantly (P = 0.002 and 0.04, respectively). Inflammation was least severe in the 75 mg/kg group, which exhibited the fewest number of colorectal tumors. Conclusions: These data suggest that low‐dose 5‐ASA may be efficacious in preventing colitis‐associated dysplasias and provide strong support for optimizing this therapy for the prevention of colonic neoplasms in patients with ulcerative colitis.
Effects of changes in extracellular calcium concentration on the potassium‐induced contracture of frog's skeletal muscle

The exact nature of the process or processes which link the electrical and mechanical events in muscle activity remain unknown. Evidence indicating that calcium ions are in some manner involved in this process has been summarized by Sandow (1952). As a working hypothesis, he suggested that an action potential or depolarization of the muscle fibre surface permits or promotes the entrance of calcium ions into the fibre and that these ions then initiate the mechanical events (Sandow, 1952). The demonstration by Hodgkin & Keynes (1957) that an influx of calcium ions accompanies each action potential in the squid giant axon encouraged investigation of this hypothesis. Recently, a similar influx of calcium into frog's skeletal muscle during activity has been demonstrated by Bianchi & Shanes (1959). In a preliminary note (Frank, 1958), it has been reported that soaking the extensor longus digiti IV muscle of the frog for a few minutes in a calcium-free solution will prevent the development of a potassium-induced contracture in this muscle. Treatment of the muscle with the calciumfree solution did not reduce the depolarization produced by an increased potassium concentration, normally effective in inducing the contracture. Evidence is now presented that the speed with which the potassiuminduced contracture is eliminated is determined by the rate at which calcium ions leave the extracellular spaces of the muscle.
Extraabdominal desmoid tumors.

OBJECT Desmoid tumors are fibrous, slow-growing, nonmalignant tumors with a low potential for metastasis. These lesions show a high propensity for infiltrative growth with local invasion. METHODS The authors undertook a retrospective study of 15 desmoid tumors in 11 women and four men (ranging in age from 32 to 67 years; median 48 years) treated at their institution. This study included further resection for recurrent tumors in nine of 15 patients (60%). RESULTS There were 13 patients (86%) with brachial plexus lesions, one patient (7%) with a lumbar plexus lesion, and one (7%) with a peroneal nerve lesion. There was a female predominance in the study group of 2.75:1. Four patients (27%) reported improvement in pain status, six (40%) reported no change from their preoperative pain levels, and five (33%) reported worsened pain symptoms. There was tumor recurrence in two patients (13%) leading to further surgical intervention. CONCLUSIONS This case series included many recurrent desmoid tumors of the brachial plexus. Most of these lesions were relatively large tumors, predominantly involved with the plexal elements adding to the challenge of the resection. Currently, function-sparing excision is considered the optimal treatment for desmoid tumors arising in extraabdominal sites. Adjunctive radiation or brachytherapy is reserved for a patient with further recurrence in whom resection would be disfiguring or in whom the disease is more refractory.
C to U RNA editing mediated by APOBEC1 requires RNA‐binding protein RBM47

Cytidine (C) to Uridine (U) RNA editing is a post‐transcriptional modification that is accomplished by the deaminase APOBEC1 and its partnership with the RNA‐binding protein A1CF. We identify and characterise here a novel RNA‐binding protein, RBM47, that interacts with APOBEC1 and A1CF and is expressed in tissues where C to U RNA editing occurs. RBM47 can substitute for A1CF and is necessary and sufficient for APOBEC1‐mediated editing in vitro. Editing is further impaired in Rbm47‐deficient mutant mice. These findings suggest that RBM47 and APOBEC1 constitute the basic machinery for C to U RNA editing.
Electrophysiological Observations in Hippocampal Slices from Rats Treated with the Ketogenic Diet

The electrophysiological effects of the high-fat, low-carbohydrate ketogenic diet (KD) were assessed in normal and epileptic [kainic-acid(KA)-treated] adult rats using hippocampal slices. In the first set of experiments, normal rats were fed the KD or a standard control diet for 6–8 weeks (beginning on postnatal day 56, P56), after which they were sacrificed for hippocampal slices. All rats on the KD became ketotic. The baseline effects of the KD were determined by comparing extracellular measures of synaptic transmission and responses to evoked stimulation, and hippocampal excitability was tested in Mg2+-free medium. There were no differences in EPSP slope, input/output relationship, responses to evoked stimulation or Mg2+-free burst frequency between slices from control and KD-fed rats. In another set of experiments, rats were made epileptic by intraperitoneal injection of kainic acid (KA) on P54, which caused status epilepticus followed by the development of spontaneous recurrent seizures (SRS) over the next few weeks. Two days after KA-induced status, rats were divided into a control-fed group and a KD-fed group. Animals on the KD had significantly fewer SRS over the ensuing 8 weeks. In hippocampal slices from KA-treated, KD-fed rats, there were fewer evoked CA1 population spikes than from slices of control-fed rats. These results suggest that the KD does not alter baseline electrophysiological parameters in normal rats. In rats made chronically epileptic by administration of KA, KD treatment was associated with fewer spontaneous seizures and reduced CA1 excitability in vitro. Therefore, at least part of the KD mechanism of action may involve long-term changes in network excitability.
Hooke-Jeeves revisited

The Hooke-Jeeves (HJ) Pattern Search, which seems to be the most popular choice among the local search algorithms, was used as an alternative to the dimensional local search (DLS), which has provided excellent results in previous work. In this paper, the question whether the well-known Hooke-Jeeves pattern search could outperform the DLS algorithm that was devised somewhat ad-hoc, is to be investigated. The Moving Peaks (MP) function is used as a benchmark. In our experiments, the algorithms performed almost identically well on the problem instances used. However, it was observed that the pattern move, an intrinsic part of the HJ algorithm, hardly contributed to the quality of the outcome, in fact less than the number sequence used as step sizes for both local searches. We provide some investigations into why the pattern move is less successful than most authors - including the original inventors of the Hooke-Jeeves search - seem to anticipate.
AN ANALYSIS OF THE SEQUENCES OF THE VARIABLE REGIONS OF BENCE JONES PROTEINS AND MYELOMA LIGHT CHAINS AND THEIR IMPLICATIONS FOR ANTIBODY COMPLEMENTARITY

In an attempt to account for antibody specificity and complementarity in terms of structure, human κ-, human λ-, and mouse κ-Bence Jones proteins and light chains are considered as a single population and the variable and constant regions are compared using the sequence data available. Statistical criteria are used in evaluating each position in the sequence as to whether it is essentially invariant or group-specific, subgroup-specific, species-specific, etc. Examination of the invariant residues of the variable and constant regions confirms the existence of a large number of invariant glycines, no invariant valine, lysine, and histidine, and only one invariant leucine and alanine in the variable region, as compared with the absence of invariant glycines and presence of three each of invariant alanine, leucine, and valine and two each of invariant lysine and histidine in the constant region. The unique role of glycine in the variable region is emphasized. Hydrophobicity of the invariant residues of the two regions is also evaluated. A parameter termed variability is defined and plotted against the position for the 107 residues of the variable region. Three stretches of unusually high variability are noted at residues 24–34, 50–56, and 89–97; variations in length have been found in the first and third of these. It is hypothesized that positions 24–34 and 89–97 contain the complementarity-determining residues of the light chain—those which make contact with the antigenic determinant. The heavy chain also has been reported to have a similar region of very high variability which would also participate in forming the antibody-combining site. It is postulated that the information for site complementarity is contained in some extrachromosomal DNA such as an episome and is incorporated by insertion into the DNA of the structural genes for the variable region of short linear sequences of nucleotides. The advantages and disadvantages of this hypothesis are discussed.
A NOTE ON THE RECOVERY OF MICRO‐ORGANISMS FROM AN OIL‐IN‐WATER CREAM

The isolation of micro‐organisms from the oil‐in‐water Aqueous Cream BP, has been examined using a variety of solvent systems to disperse the cream prior to membrane filtration or direct inoculation. Pour‐plate methods which utilize combinations of either peptone‐water (containing 5% w/v polysorbate 80) or nutrient broth (containing 4% w/v Lubrol W) provided the most efficient recovery of Pseudomonas aeruginosa but still allowed less than 20% recovery. White spirit and isopropyl myristate allowed no recovery when used as dispersants. Recoveries of P. aeruginosa varied according to the source of the cream. A combination of 1% w/v polysorbate 80 in 0.1% w/v peptone‐water and membrane filtration allowed 63.2% w/v and 67.0% w/v recoveries respectively of Aspergillus niger and Candida albicans from unpreserved aqueous cream, but gave unreproducible results for Escherichia coli and P. aeruginosa. Chlorocresol 0.1% w/v) did not meet the British Pharmacopoeial requirements for efficacy of antimicrobial preservatives when tested against C. albicans using membrane filtration to isolate the micro‐organism.
Characterization of the Porcine Carboxypeptidase E cDNA: Comparative Analysis and Investigation of a Non-Synonymous SNP

Carboxypeptidase E (CPE) is an important enzyme responsible for the proteolytic processing of prohormone intermediates. A naturally occurring point mutation, leading to an accumulation of many neuroendocrine peptides has been characterized within exon 5 of the CPE gene in mice. In the present study the sequence of the cDNA for the porcine CPE gene including all the coding region and the 3′-UTR region was generated. Comparisons with bovine, human, mouse, and rat CPE cDNA sequences showed that the coding regions of the gene are highly conserved both at the nucleotide and at the amino acid level. A very low nonsynonymous/synonymous substitution ratios between the proteins was found indicating that purifying selection is acting on the CPE gene. A nonsynonymous SNP identified at position 1272 in the transcript resulting in a codon change from TCA (Serine) to TTA (Leucine) was genotyped in the Danish pig populations. However, the mutated allele was only identified in one particular family. Exon 5 was sequenced in 45 unrelated pigs. No evidence of variation was found in this region. In accordance with previous results and in accordance with comparative mapping information the gene was accurately mapped to porcine chromosome 8 using the ImpRH panel.
Functional Adaptation of BabA, the H. pylori ABO Blood Group Antigen Binding Adhesin

Adherence by Helicobacter pylori increases the risk of gastric disease. Here, we report that more than 95% of strains that bind fucosylated blood group antigen bind A, B, and O antigens (generalists), whereas 60% of adherent South American Amerindian strains bind blood group O antigens best (specialists). This specialization coincides with the unique predominance of blood group O in these Amerindians. Strains differed about 1500-fold in binding affinities, and diversifying selection was evident in babA sequences. We propose that cycles of selection for increased and decreased bacterial adherence contribute to babA diversity and that these cycles have led to gradual replacement of generalist binding by specialist binding in blood group O–dominant human populations.
Hand Posture Recognition Using SURF with Adaptive Boosting

An approach making use of SURF feature and Adaboost for hand posture recognition is proposed. First the SURF key points are extracted to describe the blob or ridge-like structures from grey level images. These are potential points of interest that can be used to match with other images with similar structures. Then the statistic parameters of the tendency of gradient changes within small patches surrounding the points of interest are calculated as feature vectors. With all the points of interest, Adaboost is used to train a strong classifier for each posture by selecting the most efficient features, which largely lowers the computational cost of the classification stage. The proposed method was tested on the Triesch Hand Posture Database which is the benchmark in the field. Experimental results showed that our method outperforms existing methods in terms of better recognition accuracy.
8-CPT-cAMP/all-trans retinoic acid targets t(11;17) acute promyelocytic leukemia through enhanced cell differentiation and PLZF/RARα degradation

The refractoriness of acute promyelocytic leukemia (APL) with t(11;17)(q23;q21) to all-trans retinoic acid (ATRA)-based therapy concerns clinicians and intrigues basic researchers. By using a murine leukemic model carrying both promyelocytic leukemia zinc finger/retinoic acid receptor-α (PLZF/RARα) and RARα/PLZF fusion genes, we discovered that 8-chlorophenylthio adenosine-3′, 5′-cyclic monophosphate (8-CPT-cAMP) enhances cellular differentiation and improves gene trans-activation by ATRA in leukemic blasts. Mechanistically, in combination with ATRA, 8-CPT-cAMP activates PKA, causing phosphorylation of PLZF/RARα at Ser765 and resulting in increased dissociation of the silencing mediator for retinoic acid and thyroid hormone receptors/nuclear receptor corepressor from PLZF/RARα. This process results in changes of local chromatin and transcriptional reactivation of the retinoic acid pathway in leukemic cells. Meanwhile, 8-CPT-cAMP also potentiated ATRA-induced degradation of PLZF/RARα through its Ser765 phosphorylation. In vivo treatment of the t(11;17) APL mouse model demonstrated that 8-CPT-cAMP could significantly improve the therapeutic effect of ATRA by targeting a leukemia-initiating cell activity. This combined therapy, which induces enhanced differentiation and oncoprotein degradation, may benefit t(11;17) APL patients.
N-Terminal Type III Secretion Signal of Enteropathogenic Escherichia coli Translocator Proteins

ABSTRACT We report that the N terminus of the type III secretion system translocator proteins EspB, EspD, and EspA mediate protein secretion and translocation from wild-type enteropathogenic Escherichia coli and hypersecretion from sepL and sepD mutants. EspA containing the translocation signal of Map and Tir containing the secretion signal of EspA are biologically active.
Learning Policies for Data Imputation with Guided Policy Search

We explore the relationship between directed generative models and reinforcement learning by developing a new approach to data imputation that combines ideas from both areas. We address data imputation by defining an MDP for which we construct policies parametrized by (reasonably) large neural networks. We then show how to train these policies using a form of (self) Guided Policy Search (Levine & Koltun, 2013a), which leads to maximizing a variational bound on the quality of the imputations made by our policies. Empirically, our policies perform well over a range of conditions.
Multi-coded variable PPM with level cutting for high data rate visible light communications

In this paper, we propose an improved modulation scheme called multi-coded variable pulse position modulation (MC-VPPM) with level cutting for Visible Light Communications. Similar to conventional MC-VPPM scheme [ 9], two groups of signals (Pulse Width Modulation (PWM) and Pulse Position Modulation (PPM) group) are multi-coded by orthogonal codes for transmitting data simultaneously. Then, multi-coded signals which have larger value than cutting threshold is mapped to small value via level cutting. By limiting the level of multi-coded signals, we can increase the data rate even decreasing the error performance, either. In addition, we can greatly reduce the computational complexity in receiver end by reducing the required correlation metric for demodulation. Through simulation, we confirm that the proposed MC-VPPM with level cutting shows a comparable BER curve and much greater achievable data rate than the conventional variable-pulse position modulation (VPPM) and MC-VPPM scheme under the VLC channel environment.
Correction: sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

The second author's name was entered incorrectly. The correct name is Narmada Sambaturu. The correct citation is: Sridhar J, Sambaturu N, Sabarinathan R, Ou H-Y, Deng Z, et al. (2010) sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes. PLoS ONE 5(8): e11970. doi:10.1371/journal.pone. 0011970
Down-Regulation of the Human CDC16 Gene after Exposure to Ionizing Radiation: A Possible Role in the Radioadaptive Response

Abstract Zhou, P. K. and Rigaud, O. Down-Regulation of the Human CDC16 Gene after Exposure to Ionizing Radiation: A Possible Role in the Radioadaptive Response. We have used the method of differential display of mRNAs to search for changes in gene expression associated with radioadaptation triggered by low doses of ionizing radiation in human lymphoblasts. We isolated a cDNA designated PB13 that was down-regulated as early as 1 h after irradiation with 4 Gy in cells adapted by a pre-exposure to a dose of 2 cGy, compared to 3 h in nonadapted cells (4 Gy alone). Northern analysis confirmed the differential expression of a 2.4-kb transcript that was repressed for at least 10 h after irradiation. The major part of the PB13 cDNA was identical to the human CDC16 mRNA. When using either PB13 or CDC16 cDNA as probes, similar radiation-induced alterations in gene expression were observed. Expression of the CDC16 gene was also repressed after oxidative stress with H2O2. The CDC16 protein belongs to the anaphase-promoting complex (APC) that controls progression through mitosis. The repression of expression of the CDC16 gene by ionizing radiation could result in delayed progression of damaged cells through mitosis. This cycle delay would occur earlier in adapted cells and would allow a more rapid and efficient repair that could contribute to the tolerance to subsequent irradiation.
Extending Statistical Boosting

Summary Background: Boosting algorithms to simultaneously estimate and select predictor effects in statistical models have gained substantial interest during the last decade. Objectives: This review highlights recent methodological developments regarding boosting algorithms for statistical modelling especially focusing on topics relevant for biomedical research. Methods: We suggest a unified framework for gradient boosting and likelihood-based boosting (statistical boosting) which have been addressed separately in the literature up to now. Results: The methodological developments on statistical boosting during the last ten years can be grouped into three different lines of research: i) efforts to ensure variable selection leading to sparser models, ii) developments regarding different types of predictor effects and how to choose them, iii) approaches to extend the statistical boosting framework to new regression settings. Conclusions: Statistical boosting algorithms have been adapted to carry out unbiased variable selection and automated model choice during the fitting process and can nowadays be applied in almost any regression setting in combination with a large amount of different types of predictor effects.
A Self-Splicing Group I Intron in DNA Polymerase Genes of T7-Like Bacteriophages

ABSTRACT Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive bacteria. However, among the phages of enteric and other gram-negative proteobacteria, introns have been encountered only in phage T4 and several of its close relatives. Here we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymerase genes of ΦI and W31, phages that are closely related to T7. The introns belong to subgroup IA2 and both contain an open reading frame, inserted into structural element P6a, encoding a protein belonging to the HNH family of homing endonucleases. The introns splice efficiently in vivo and self-splice in vitro under mild conditions of ionic strength and temperature. We conclude that there is no barrier for maintenance of group I introns in phages of proteobacteria.
The Infra‐Red Absorption Spectrum of Diborane

The infra‐red absorption spectrum of diborane has been examined under high resolution from 3. 7μ to 30μ with automatic recording grating spectrometers. The rotational fine structure in two bands of each of the three types characteristic of asymmetric top molecules has been measured. All results and observations are consistent with the conclusion that diborane has the bridge structure, and belongs to the same symmetry point group, Vh, as ethylene. The observation and structure of the band with center at 368.7 cm−1 provides spectroscopic evidence that the molecule is non‐planar, and makes more definite the assignment of fundamental frequencies. Data on all bands fit quite well the symmetric top approximation, since accidentally two principal moments of inertia are approximately the same, and calculations yield accurate values for certain rotational constants.