gebhart/patrepeval huggingface dataset:
A hyperfused mitochondrial state achieved at G <sub>1</sub> –S regulates cyclin E buildup and entry into S phase (2009)

Mitochondria undergo fission-fusion events that render these organelles highly dynamic in cells. We report a relationship between mitochondrial form and cell cycle control at the G(1)-S boundary. Mitochondria convert from isolated, fragmented elements into a hyperfused, giant network at G(1)-S transition. The network is electrically continuous and has greater ATP output than mitochondria at any other cell cycle stage. Depolarizing mitochondria at early G(1) to prevent these changes causes cell cycle progression into S phase to be blocked. Inducing mitochondrial hyperfusion by acute inhibition of dynamin-related protein-1 (DRP1) causes quiescent cells maintained without growth factors to begin replicating their DNA and coincides with buildup of cyclin E, the cyclin responsible for G(1)-to-S phase progression. Prolonged or untimely formation of hyperfused mitochondria, through chronic inhibition of DRP1, causes defects in mitotic chromosome alignment and S-phase entry characteristic of cyclin E overexpression. These findings suggest a hyperfused mitochondrial system with specialized properties at G(1)-S is linked to cyclin E buildup for regulation of G(1)-to-S progression.
Using ColE1‐derived RNA I for suppression of a bacterially encoded gene: implication for a novel plasmid addiction system (2006)

The use of plasmid DNA for gene therapeutical purposes is a novel technology with advantages and drawbacks. One of the required improvements is to avoid antibiotic resistance genes or other additional sequences for selection within the plasmid. Here, we describe an alternative approach to equip a ColE1 plasmid with a regulatory function within the cell, which could be used for selection of plasmid carrying cells. No additional sequences are required, since the mechanism is based on RNA/RNA antisense interaction involving the naturally occurring RNA I derived from the plasmid's origin of replication. The plasmid replicational regulatory network was linked to the transcriptional regulatory network of an engineered target gene, present on the bacterial chromosome. Thus, gene suppression of a reporter could be achieved by mere presence of the ColE1-type plasmid pBR322. Proof of this concept was shown in shaker-flask experiments and fed-batch fermentation processes. The strategy of regulating gene expression by plasmid replication implicates a novel strategy for plasmid selection, as the gene to be suppressed could be toxic or growth hampering, providing advantage to plasmid carrying host cells.
A hybrid approach to Chinese-English machine translation (2002)

A hybrid method for Chinese-English machine translation is presented. A rule-based analysis is combined with statistical data. The rule-based lexical analyzer and syntactic analyzer leave some amount of ambiguity that is resolved using a statistical approach. A hidden Markov model (HMM) is used to return a score for each part of speech. An improved probabilistic context free grammar (PCFG) is used for syntactic scoring, and a probabilistic score function is used for the semantic aspect. In addition, parameters are usually estimated poorly when the training data is sparse. Smoothing the parameters is thus important in the estimation process. A back-off procedure is used to smooth the parameters.
PCTR: An improved approach to digitizing well-logging parameter graph (2009)

According to the characteristics of well-logging graphs, we contribute a PCTR (preprocessing, compressing, tracing, and rectifying) approach to digitizing skeleton type of curves. The preprocessing algorithm is based on the biggest variance ratio. We employed line adjacency graph (LAG) data structure to develop the image-compressing algorithm, which compresses image file with great efficiency. The rectifying algorithms based on centimeter grid of coordinates, which perfectly rectify the distortion of parameter graph, are proposed. The experimental results show that the PCTR approach in the system can work effectively.
Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum (2012)

E. coli Dcm methylation decreases transformation efficiency in C. thermocellum DSM1313. The use of properly methylated plasmid DNA should facilitate genetic manipulation of this industrially relevant bacterium.
Sequence-specific binding of single-stranded RNA: is there a code for recognition? (2006)

A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity. Such de novo designed RNA binders could be of extraordinary use in both medical and basic research applications. Furthermore, a code could help to predict the cellular functions of RNA-binding proteins that have not yet been extensively studied. A comparative analysis of Pumilio homology domains, zinc-containing RNA binders, hnRNP K homology domains and RNA recognition motifs is performed in this review. Based on this, a set of binding rules is proposed that hints towards a code for RNA recognition by these domains. Furthermore, we discuss the intermolecular interactions that are important for RNA binding and summarize their importance in providing affinity and specificity.
A ΔclpB Mutant of Francisella tularensis Subspecies holarctica Strain, FSC200, Is a More Effective Live Vaccine than F. tularensis LVS in a Mouse Respiratory Challenge Model of Tularemia (2013)

Francisella tularensis subsp. tularensis is a highly virulent pathogen for humans especially if inhaled. Consequently, it is considered to be a potential biothreat agent. An experimental vaccine, F. tularensis live vaccine strain, derived from the less virulent subsp. holarctica, was developed more than 50 years ago, but remains unlicensed. Previously, we developed a novel live vaccine strain, by deleting the chaperonin clpB gene from F. tularensis subsp. tularensis strain, SCHU S4. SCHU S4ΔclpB was less virulent for mice than LVS and a more effective vaccine against respiratory challenge with wild type SCHU S4. In the current study, we were interested to determine whether a similar mutant on the less virulent subsp. holarctica background would also outperform LVS in terms of safety and efficacy. To this end, clpB was deleted from clinical holarctica strain, FSC200. FSC200ΔclpB had a significantly higher intranasal LD50 than LVS for BALB/c mice, but replicated to higher numbers at foci of infection after dermal inoculation. Moreover, FSC200ΔclpB killed SCID mice more rapidly than LVS. However, dermal vaccination of BALB/c mice with the former versus the latter induced greater protection against respiratory challenge with SCHU S4. This increased efficacy was associated with enhanced production of pulmonary IL-17 after SCHU S4 challenge.
Tetanic force estimation from surface EMG of maximal voluntary eccentric and concentric contractions (2007)

This study aimed to determine whether EMG amplitude from maximum voluntary contractions can be used to estimate the tetanic force -- velocity relationship. Five subjects performed maximal knee extensions over a range of eccentric and concentric velocities on an isovelocity dynamometer and EMG from the quadriceps was recorded. A muscle model of the knee extensions allowed the maximum voluntary (MVC) force -- length -- velocity data to be estimated from the dynamometer data. Normalised root mean square (RMS) amplitude -- length -- velocity data were obtained from the EMG signals. Dividing the MVC forces by these normalised RMS amplitudes generated EMG corrected force -- length -- velocity data. A Hill-type tetanic force function covering eccentric and concentric velocities was fitted to both the MVC and EMG corrected force data. Based on a number of comparative scores, the EMG corrected forces provided a significantly better fit to the tetanic force function compared to the MVC forces (p inline equation 0.05), suggesting that EMG amplitude can be used to estimate tetanic forces from in vivo MVC measurements.
A Single Treatment With a Specific Chymase Inhibitor, TY-51184, Prevents Vascular Proliferation in Canine Grafted Veins (2004)

In this study, we evaluated whether a specific chymase inhibitor, TY-51184 (2-[4-(5-fluoro-3-methylbenzo[b]thiophen-2-yl)sulfonamido-3-methanesulfonylphenyl]oxazole-4-carboxylicacid), prevents the vascular proliferation in canine grafted veins. In the placebo-and chymase inhibitor-treated groups, the external jugular vein was infiltrated with saline and 10 microM TY-51184, respectively, and then it was grafted to the ipsilateral carotid artery. The non-surgical dogs were used as the control group. By 28 days after grafting, the chymase and ACE activities were significantly increased in the injured arteries. TY-51184 significantly reduced the chymase activity in the grafted veins, while it did not affect the ACE activity. The intimal areas in the placebo- and TY-51184-treated groups were 3.32 +/- 0.16 and 1.96 +/- 0.52 mm(2), respectively, and this difference was significant. The ratios of intimal area to medial area in the placebo- and TY-51184-treated groups were 66.8 +/- 3.5% and 34.9 +/- 9.2%, respectively, and this difference was also significant. There was a significant relationship between vascular proliferation and chymase activity, but not ACE activity. In this study, we demonstrated that a single treatment with a specific chymase inhibitor, TY-51184, could prevent the vascular proliferation in canine grafted veins.
Improving Fault Injection in Automotive Model Based Development using Fault Bypass Modeling (2013)

Fault injection is widely used for validating dependability of computer systems. These techniques have been traditionally used for testing dependability of the both hardware and software systems. With widespread use of model based development in automotive software development more sophisticated needs arise for using fault injection techniques at the model level, which can yield significant benefits in combination with model-based testing or model mutation. In this paper, we address challenges with injecting faults into behavioral models in terms of analysis of results and propose a framework for distinguishing between correct and incorrect simulation results. The focus is laid on an important challenge encountered when injecting faults in continuous models - managing systemenvironment interdependencies. We analyze the problem in details and outline an effective approach to deal with this problem.
[18F]FBEM-ZHER2:342-Affibody molecule—a new molecular tracer for in vivo monitoring of HER2 expression by positron emission tomography (2007)

Our results suggest that the [18F]FBEM-Z(HER2:342) radioconjugate can be used to assess HER2 expression in vivo.
Five-year results of brentuximab vedotin in patients with relapsed or refractory systemic anaplastic large cell lymphoma (2017)

This pivotal phase 2 study evaluated the safety and efficacy of brentuximab vedotin in patients with relapsed or refractory (R/R) systemic anaplastic large cell lymphoma (ALCL). After a median observation period of approximately 6 years from first treatment, we examined the durability of remission, progression-free survival (PFS), overall survival (OS), and safety outcomes of patients treated on this trial. Among all enrolled patients (n = 58), no progressions were observed beyond 40 months, and median OS was not reached. Patients with a complete response (CR), as assessed by the investigator (38 of 58, 66%), continued to demonstrate improved outcomes with neither median OS nor PFS reached. Of the 38 CR patients, 16 received a consolidative stem cell transplant (SCT) with median PFS not reached. Among patients who were on-study and in remission at study closure, 16 patients had not received any new treatment after single-agent brentuximab vedotin other than consolidative SCT. Among this subset of 16 patients, 8 received SCT, and the remaining 8 patients (14% of all enrolled patients) remained in sustained remission without consolidative SCT or any new anticancer therapy. Thirty-three patients experienced peripheral neuropathy, among whom, the majority (30 of 33, 91%) had experienced resolution or improvement at their last assessment. These final results, which demonstrated a high rate of peripheral neuropathy resolution, and durable remissions in a subset of patients with relapsed or refractory systemic ALCL, provide evidence that single-agent brentuximab vedotin may be a potentially curative treatment option. This trial was registered at www.clinicaltrials.gov as #NCT00866047.
Novel approaches in pain management in cardiac surgery (2014)

Although published data remain limited, recent evidence indicates that patients may benefit from the addition of a variety of novel pain-management strategies currently under investigation. Selection of a multimodal approach to perioperative pain management is advocated, including selective application of regional analgesia, non-narcotic medications, and complimentary alternative options to improve patient comfort and overall outcome.
Circulating levels of glucagon-like peptide-2 in human subjects with inflammatory bowel disease (2000)

Glucagon-like peptide-2 (GLP-2) is a recently characterized intestine-derived peptide that exerts trophic activity in the small and large intestine. Whether circulating levels of GLP-2 are perturbed in the setting of human inflammatory bowel disease (IBD) remains unknown. The circulating levels of bioactive GLP-2-(1-33) compared with its degradation product GLP-2-(3-33) were assessed using a combination of RIA and HPLC in normal and immunocompromised control human subjects and patients hospitalized for IBD. The activity of the enzyme dipeptidyl peptidase IV (DP IV), a key determinant of GLP-2-(1-33) degradation was also assessed in the plasma of normal controls and subjects with IBD. The circulating levels of bioactive GLP-2-(1-33) were increased in patients with either ulcerative colitis (UC) or Crohn's Disease (CD; to 229 +/- 65 and 317 +/- 89%, P < 0.05, of normal, respectively). Furthermore, the proportion of total immunoreactivity represented by intact GLP-2-(1-33), compared with GLP-2-(3-33), was increased from 43 +/- 3% in normal healthy controls to 61 +/- 6% (P < 0.01) and 59 +/- 2% (P < 0.01) in patients with UC and CD, respectively. The relative activity of plasma DP IV was significantly reduced in subjects with IBD compared with normal subjects (1.4 +/- 0.3 vs. 5.0 +/- 1.1 mU/ml, respectively; P < 0.05). These results suggest that patients with active IBD may undergo an adaptive response to intestinal injury by increasing the circulating levels of bioactive GLP-2-(1-33), facilitating enhanced repair of the intestinal mucosal epithelium in vivo.
Single-Molecule electrophoresis (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSingle-Molecule electrophoresisAlonso. Castro and E. Brooks. SheraCite this: Anal. Chem. 1995, 67, 18, 3181–3186Publication Date (Print):September 15, 1995Publication History Published online1 May 2002Published inissue 15 September 1995https://pubs.acs.org/doi/10.1021/ac00114a013https://doi.org/10.1021/ac00114a013research-articleACS PublicationsRequest reuse permissionsArticle Views314Altmetric-Citations71LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Paclitaxel (Taxol)-induced Gene Expression and Cell Death Are Both Mediated by the Activation of c-Jun NH2-terminal Kinase (JNK/SAPK) (1998)

Paclitaxel (Taxol) is a novel anti-cancer drug that has shown efficacy toward several malignant tumors, particularly ovarian tumors. We reported previously that paclitaxel can induce interleukin (IL)-8 promoter activation in subgroups of ovarian cancer through the activation of both AP-1 and nuclear factor kappaB. Further analysis of paclitaxel analogs indicates that the degree of IL-8 induction by analysis correlates with the extent of cell death; however, IL-8 itself is not the cause of cell death. This suggests that pathways that lead to IL-8 and cell death may overlap, although IL-8 per se does not kill tumor cells. To decipher the upstream signals for paclitaxel-induced transcriptional activation and cell death, we studied the involvement of protein kinases that lead to the activation of AP-1, specifically the c-Jun NH2-terminal kinase (JNK1), p38, and the extracellular signal-regulated kinase 1 (ERK1). The role of IkappaB in paclitaxel-induced cell death was also analyzed. Paclitaxel activated JNK, and to a lesser degree p38, but not ERK1. Paclitaxel-induced IL-8 promoter activation was inhibited by dominant-inhibitory mutants of JNK, p38, and the super-repressor form of IkappaBalpha, but not by dominant-inhibitory forms of ERK1. Dominant-inhibitory mutants of JNK1 also greatly reduced paclitaxel-induced cell death, and the kinetics of JNK induction was closely followed by DNA fragmentation. These results indicate (i) that paclitaxel activates the JNK signaling pathway and (ii) that JNK activation is a common point of paclitaxel-induced gene induction and cell death.
Alternative and aberrant messenger RNA splicing of the mdm2 oncogene in invasive breast cancer. (2001)

mdm2 is part of a complex mechanism that regulates the expression of p53 as well as the function of Rb, p19ARF, and other genes. In humans, mdm2 dysregulation is associated with gene amplification. This study was undertaken to characterize altered mdm2 expression in a cohort of 38 invasive breast cancers and 9 normal breast specimens. Reverse-transcription PCR with primers spanning the entire open reading frame of the mdm2 gene in breast tissue RNA samples generated PCR products of full-length mdm2 (1526 bp) as well as smaller products (653, 281, 254, and 219 bp). Sequence analysis demonstrated that the 653-bp product was an alternatively spliced product (defined as splicing at the exon/intron boundary consensus sites), whereas the 281, 254, and 219 bp mdm2 products were aberrantly spliced products (splicing at sites not considered to be exon/intron boundary sites). Reverse-transcription-PCR with normal breast tissue RNA samples yielded only the 1526-bp product in five samples and the 1526-bp product and the 653-bp product in four samples. The 653-bp alternatively spliced product was expressed in 21% of breast cancers, and the smaller, aberrantly spliced mRNA products (281 bp, 254 bp, and/or 219 bp) were expressed in 16% of breast cancers. The protein products predicted by the alternatively spliced mRNAs and the aberrantly spliced mRNAs lacked either the entire binding domain for p53 or the majority of the binding domain for p53. Immunohistochemical analysis of HER2/neu (c-erbB2), estrogen receptor, progesterone receptor, epidermal growth factor receptor, and p53 protein was performed. p53 sequence alterations were identified by mismatch detection and confirmed by p53 oligonucleotide microarray technology. An association was demonstrated between the expression of aberrantly and/or alternatively spliced mdm2 mRNAs and a lack of progesterone receptor. An association was also demonstrated between mdm2 aberrantly and/or alternatively expression products and the presence of p53 tumor suppressor gene mutations. mdm2 is transcribed from two different promoters: one, p53-dependent, and the other, p53-independent. The 5' untranslated region of the transcripts was evaluated to determine the promoter usage in each breast cancer specimen. No correlation was observed between mdm2 splice products and promoter usage. The presence of aberrant expression products of mdm2 in breast cancer specimens was correlated with a shortened overall patient survival. These observations suggest that mdm2 expression is altered in invasive breast cancer and is associated with more aggressive disease.
Impact of diversity of Mycoplasma hyopneumoniae strains on lung lesions in slaughter pigs (2017)

The importance of diversity of Mycoplasma hyopneumoniae (M. hyopneumoniae) strains is not yet fully known. This study investigated the genetic diversity of M. hyopneumoniae strains in ten pig herds, and assessed associations between the presence of different strains of M. hyopneumoniae and lung lesions at slaughter. Within each herd, three batches of slaughter pigs were investigated. At slaughter, from each batch, 20 post mortem bronchoalveolar lavage fluid samples were collected for multiple locus variable-number tandem repeat analysis (MLVA), and lung lesions (Mycoplasma-like lesions, fissures) were examined. Multivariable analyses including potential risk factors for respiratory disease were performed to assess associations between the number of different strains per batch (three categories: one strain, two-six strains, ≥seven strains), and the lung lesions as outcome variables. In total, 135 different M. hyopneumoniae strains were found. The mean (min.-max.) number of different strains per batch were 7 (1-13). Batches with two-six strains or more than six strains had more severe Mycoplasma-like lesions (P = 0.064 and P = 0.012, respectively), a higher prevalence of pneumonia [odds ratio (OR): 1.30, P = 0.33 and OR: 2.08, P = 0.012, respectively], and fissures (OR = 1.35, P = 0.094 and OR = 1.70, P = 0.007, respectively) compared to batches with only one strain. In conclusion, many different M. hyopneumoniae strains were found, and batches of slaughter pigs with different M. hyopneumoniae strains had a higher prevalence and severity of Mycoplasma-like lung lesions at slaughter, implying that reducing the number of different strains may lead to less lung lesions at slaughter and better respiratory health of the pigs.