gebhart/patrepeval huggingface dataset:
Identification and characterization of a salt‐stress‐induced plasma membrane H+‐ATPase in tomato (2001)

Abstract Plant plasma membrane H + ‐ATPases (PM H + ‐ATPases) energize the secondary transport of Na + from the cytosol across the plasma membrane and so may play a role in the plant response to salt stress. A PM H + ‐ATPase gene in rice is closely linked to a locus responsible for increased salt resistance. PM H + ‐ATPases are encoded by large gene families, including 10–12 in tomato ( Lycopersicon esculentum ). Salt stress stimulates the accumulation of PM H + ‐ATPase transcripts in a variety of plants but the effect of salt stress on the expression of specific isoforms has not been investigated. We isolated a partial‐length cDNA clone of a novel tomato PM H + ‐ATPase gene from salt‐stressed expanded leaf tissue and characterized its expression in response to salt and osmotic stress. The gene, LHA8 , is a member of the subfamily including AHA1 , AHA2 , AHA3 , AHA4 , AHA9 , LHA4 , PHA2 and PMA4 , and is most closely related to the Nicotiana plumbaginifolia gene PMA6 . LHA8 transcript accumulation is induced by NaCl exposure. LHA8 is not expressed at detectable levels in roots or expanded leaves and is present at very low levels in unexpanded leaves. LHA8 expression is induced in expanded leaves, unexpanded leaves and roots. Induction appears to be specific to the ionic, rather than the osmotic, effects of NaCl because iso‐osmotic levels of polyethylene glycol do not induce message accumulation.
Privacy-preserving publication of provenance workflows (2014)

Provenance workflows capture the data movement and the operations changing the data in complex applications such as scientific computations, document management in large organizations, content generation in social media, etc. Provenance is essential to understand the processes and operations that data undergo, and many research efforts focused on modeling, capturing and analyzing provenance information. Sharing provenance brings numerous benefits, but may also disclose sensitive information, such as secret processes of synthesizing chemical substances, confidential business practices and private details about social media participants' lives. In this paper, we study privacy-preserving provenance workflow publication using differential privacy. We adapt techniques designed for sanitization of multi-dimensional spatial data to the problem of provenance workflows. Experimental results show that such an approach is feasible to protect provenance workflows, while at the same time retaining a significant amount of utility for queries. In addition, we identify influential factors and trade-offs that emerge when sanitizing provenance workflows.
Correlation of the Virus Sequence Content and Biological Properties of Cells Carrying the Herpes Simplex Virus Type 2 Thymidine Kinase Gene (1982)

Seven cell lines, transformed to a thymidine kinase-positive phenotype with herpes simplex virus type 2 (HSV-2) DNA fragments, have been examined to determine their virus-specific DNA sequence content. The results are consistent with the reported map position of the HSV-2 thymidine kinase gene. Different cell lines contained different amounts of non-selected virus-specific sequences and this correlated with the ability of some cell lines to compensate the deficiencies in some temperature-sensitive (ts) mutants of HSV-1 and HSV-2. The cell lines were also examined for their ability to synthesize elevated levels of thymidine kinase in response to infection with a thymidine kinase-negative virus mutant. Of the seven cell lines, two failed to respond to infection in this way and these cell lines lacked sequences on the upstream side of the kinase gene which were present in the remaining cell lines.
Separation of 2(3),9(10),16(17),23(24)-Tetrasubstituted Phthalocyanines with Newly Developed HPLC Phases (1996)

The synthesis of 2(3),9(10),16(17),23(24)-tetrasubstituted phthalocyanines from 1,2-dicyano-4-alkoxybenzenes or the corresponding isoindolines is reported. In each case, four isomers with D2h, C4h, C2v, and Cs symmetry are obtained in the statistical expected yield. The separation of the C4h and the D2h isomers was achieved successfully for the first time from the other two isomers with newly developed HPLC phases based on π−π interactions. In one case, phthalocyanine 12 could be separated into the isomers 12a−d and characterized by UV/vis and 1H-NMR spectroscopy. Due to line broadening at room temperature, T1 and T2 relaxation time measurements of two phthalocyanines (3 and 12) at different temperatures are carried out. Whether the broad peaks are due to aggregation or due to a short relaxation time is explained.
Leaky Lactococcus Cultures That Externalize Enzymes and Antigens Independently of Culture Lysis and Secretion and Export Pathways (2001)

A novel system that leaks beta-galactosidase (beta-gal) without a requirement for secretion or export signals was developed in Lactococcus lactis by controlled expression of integrated phage holin and lysin cassettes. The late promoter of the lytic lactococcal bacteriophage phi31 is an 888-bp fragment (P(15A10)) encoding the transcriptional activator. When a high-copy-number P(15A10)::lacZ.st fusion was introduced into L. lactis strains C10, ML8, NCK203, and R1/r1t, high levels of the resultant beta-gal activity were detected in the supernatant (approximately 85% of the total beta-gal activity for C10, ML8, and NCK203 and 45% for R1/r1t). Studies showed that the phenotype resulted from expression of Tac31A from the P(15A10) fragment, which activated a homologous late promoter in prophages harbored by the lactococcal strains. Despite the high levels of beta-gal obtained in the supernatant, the growth of the strains was not significantly affected, nor was there any evidence of severe membrane damage as determined by using propidium iodide or transmission electron microscopy. Integration of the holin-lysin cassette of phage r1t, under the control of the phage phi31 late promoter, into the host genome of MG1363 yielded a similar "leaky" phenotype, indicating that holin and lysin might play a critical role in the release of beta-gal into the medium. In addition to beta-gal, tetanus toxin fragment C was successfully delivered into the growth medium by this system. Interestingly, the X-prolyl dipeptidyl aminopeptidase PepXP (a dimer with a molecular mass of 176 kDa) was not delivered at significant levels outside the cell. These findings point toward the development of bacterial strains able to efficiently release relevant proteins and enzymes outside the cell in the absence of known secretion and export signals.
GC-MS determination of organic acids with solvent extraction after cation-exchange chromatography (1997)

Abstract We combined column and partition chromatography to isolate, purify, and quantify biological organic acids in urine and cerebrospinal fluid (CSF). Urine and CSF samples were introduced onto a preconditioned cation-exchange column (Dowex 50W × 8 resin) to remove the biological interferences. The effluent with water was extracted with ethyl acetate two times (pH 1 and 3) and the organic acids were quantitatively converted into their trimethylsilyl derivatives for detection by gas chromatography–mass spectrometry. The good quality-control data were obtained through precision and accuracy tests. Inter- and intraassay CVs were 0.01–10.2% and 0.02–12.2%, respectively. Analytical recoveries compared favorably with results from the commonly used solvent extraction method. This method was used for the measurement of the 14 organic acids in the urine and CSF of healthy volunteers. The values obtained were in the range of the published data.
Predictive Factors for Long-term Clinical Outcomes in Patients with Variant Angina (2013)

목적: 한국에서는 혈관 연축에 의하여 발생하는 변이형 협심증이 서양에 비하여 많으며, 이에 대한 국내 환자의 장기적 임상 예후에 관한 보고는 많지 않은 실정이다 방법: 1996년부터 2011년까지 전남대학교 병원 심장센터 심도자실에서 ergonovine 유발검사를 시행하였던 1,162예 중 양성 결과를 보였던 686예를 대상으로 40.2 ± 38.0개월간 추적관찰 기간 중 반복적인 흉통, 재입원, 심근경색증, 심장사, 관상동맥 조영술이 필요하였던 경우를 심장사건으로 정의하고 이가 발생하였던 153예(I군: 52.4 ± 11.0 세, 남:여 = 103:50)와 발생하지 않았던 533예(II군: 51.6 ± 10.7 세, 남:여 = 350:183)로 분류하였다. 양 군 간에 임상적 소견, 검사실 소견, 관상동맥 조영술 등을 비교하였다. ê²°ê³¼: 흡연력은 I군에서 II군보다 높았으며(45.8% vs. 36.3%, p = 0.037), 저밀도 지단백 콜레스테롤(119.4 ± 35.3 vs. 111.1 ± 32.2 mg/dL, p = 0.010) 수치도 I군에서 높았다. Cox 비례 위험 모형을 이용한 분석에서 유의한 심장사건 예측인자는 흡연이었다(HR 1.80, 95% CI 1.036-3.126, p = 0.037). ê²°ë¡ : 한국인 변이형 협심증 환자에서 흡연이 심장사건 발생의 유일한 예측인자이었다. 중심 단어: 흡연; 관상동맥 질환; 이형 협심증
Recalage de modèle vis-à-vis d’une quantité d’intérêt en thermique du bâtiment - Applications dans l’équipement Sense-City (2020)

International audience
Medical Devices Development: The Bottom-Up or The Top-Down Approach? (2018)

Biomedical sensors are often developed under a bottom-up approach, i.e. the researcher point of view or laboratory approach. This is usually the case for microfluidic based integrated systems. The small number of such devices actually translated for use in clinical situations is mostly due to the need of sample pre-treatment by specially trained people and to the fact that industrial transfer had not been taken into account since the very beginning of the development. Conversely, the top-down approach places the end-user at the center of development discussion. In this end-user point of view approach, the participation of industrial, medical and end-users partners more often leads to the design of fully integrated and automated devices which, furthermore, can be manufactured using conventional industrial capabilities. In this opinion communication, we briefly summarize the most common biosensors technologies and we explain how immuno-combined devices may help addressing constraints related to their use in clinical situations in terms of usability by non-trained people, automation and integration..
Compressed video sensing using adaptive sampling rate (2010)

Compressive video sampling is an application of compressed sensing (CS) theory which samples a signal below the Shannon-Nyquist rate. In this paper, we present a compressed video sensing method that samples the blocks with adaptive sampling rate. The edge of the image is exploited to define a deficiency factor for blocks. Considering this factor, we determine sampling rates independently for each block. The simulation results show that the proposed method outperforms the conventional CS in image quality for the same compression ratio.
Structural Evidence That Scytalidolisin (Formerly Scytalidopepsin A) Is a Serine-Carboxyl Peptidase of the Sedolisin Family (2008)

Scytalidopepsin A, a pepstatin-insensitive acid endopeptidase from the fungus Scytalidium lignicolum was found to be a member of the sedolisin family of serine-carboxyl peptidases through analyses of the amino acid sequences of peptides derived from the reduced, pyridylethylated enzyme by enzymatic digestion. Hence it should be renamed scytalidolisin (or Scytalidium sedolisin).
Implication des protéines dérivées de TEL dans l’oncogenèse (1999)

TEL est un gene de la famille ETS qui est frequemment altere dans les leucemies humaines sous forme de translocations chromosomiques specifiques. La proteine TEL se distingue de la plupart des proteines de cette famille par le fait qu’elle est un represseur transcriptionnel dont l’activite depend de sa liaison a des sequences d’ADN specifiques et qu’elle forme des oligomeres homotypiques, une propriete qui est importante pour ses proprietes transrepressives. Les translocations chromosomiques affectant TEL dans les leucemies generent le plus souvent des proteines de fusion. Celles-ci peuvent etre regroupees en deux grandes categories. La premiere comprend des proteines chimeriques dans lesquelles la region amino-terminale de TEL (incluant son domaine d’oligomerisation) est fusionnee au domaine catalytique de differentes proteines tyrosine kinases (PDGFRbeta; ABL ; JAK2 ; TRKC). La seconde inclut des proteines de fusion entre TEL et d’autres regulateurs transcriptionnels (AML1 ; MN1). Ces proteines de fusion peuvent, selon les cas, maintenir (MN1-TEL) ou ne pas maintenir (TEL-AML1) le domaine de liaison a l’ADN de TEL (domaine ETS). Bien qu’affectant des voies intracellulaires de transduction du signal differentes, ces proteines de fusion apparaissent toutes activer leurs proprietes oncogeniques en exploitant et detournant de leur fonction normale plusieurs domaines fonctionnels remarquables de TEL. Le nombre croissant de translocations chromosomiques affectant TEL, le plus souvent dans des leucemies, la diversite des partenaires impliques dans ces translocations et le role presume de la perte de l’allele non rearrange de TEL dans les LAL-B presentant une t(12;21) designent TEL comme une cible importante dans les processus oncogeniques.
Figure S5 from Radiotherapy and Cisplatin Increase Immunotherapy Efficacy by Enabling Local and Systemic Intratumoral T-cell Activity (2023)

&lt;p&gt;Cisplatin modestly reduces the RIT-induced increase in CD8:CD4 T cell ratio and enhances (R)IT-medated control of non-irradiated tumors.&lt;/p&gt;
Nutritional Issues in Pediatric Inflammatory Bowel Disease (1991)

Malnutrition, characterized by weight loss, growth failure and micronutrient depletion, are prominent features of inflammatory bowel disease (IBD) in the pediatric age group. Accurate evaluation of the patient's nutritional status and appropriate nutritional support, whether enteral or parenteral, constitute integral parts of the management of the growing child with IBD. Over the past two decades, a number of studies have supported the potential use of nutritional therapy to induce remission and to control disease activity in symptomatic Crohn's disease. More recently, preliminary studies on the use of dietary supplements of marine-oil-derived omega-3 fatty acids have also indicated a beneficial effect in IBD patients. In parallel with these clinical trials, scientific research has recently focused on the concept that specific dietary alterations can modulate the immune response. Components of the diet that may have particular relevance to mucosal immunity and the pathogenesis of IBD include polyunsaturated fatty acids, nucleotides, and amino acids such as glutamine and arginine. Future research in the interactions between specific nutrients and the immune system will likely increase our understanding of the causes of IBD, as well as enhance the development of novel nutritional therapies for IBD patients.
Structural Analysis and Thermal Behavior of Pore Networks in High-Surface-Area Metal−Organic Framework (2010)

Metal−organic framework-5 (MOF-5) with high surface area was synthesized in this study. The complete picture of pore structure in the crystal from the locally perfect micropore channels to the global mesopore network distributed along the constituent micrograins was revealed by small-angle X-ray scattering (SAXS). The in situ SAXS measurement was conducted to investigate the concurrent evolution of mesopore structure and micrograin boundary during heating and thermal activation at 200 °C. During the pore evacuation and formation of micrograin boundary, the flexible mesopores shrink, swell, and realign, while the micropores remain stably rigid. The result shows the role of the tunable mesopore network in the MOF-5 crystal governing the migration of gas molecules. This new finding will be useful for guiding the rational crystal design and the synthetic modification for improving the crystal quality in potential applications.
A novel approach for modifying tumor cell‐derived plasma membrane vesicles to contain encapsulated IL‐2 and engrafted costimulatory molecules for use in tumor immunotherapy (2001)

The genetic modification of tumor cells and delivery of cytokines have been proposed as useful strategies in the development of anti-tumor vaccines; however, a number of factors limit their use in clinical settings. To facilitate vaccine development, we explored the possibility of modifying plasma membrane vesicles (PMV) by using a novel chelator lipid, nitrilotriacetic acid ditetradecylamine (NTA-DTDA). Our analyses by flow cytometry show that NTA-DTDA can be incorporated into PMV prepared from murine P815 mastocytoma and that the incorporated NTA-DTDA permits anchoring or "engraftment" onto the vesicle surface of hexahistidine-tagged proteins such as recombinant forms of the costimulatory molecules B7.1 and CD40. The engrafted PMV also can incorporate and deliver the immunostimulatory cytokine Interleukin-2 (IL-2). Our results show that modified PMV derived from P815 cells bind the murine T cell clone D10 in a receptor-ligand dependent manner, inducing cell adhesion and promoting cell survival in vitro. The modified PMV can bind syngeneic T cells, stimulating T cell proliferation and cytotoxic T cell responses. Moreover, when used as vaccines in syngeneic animals, the modified vesicles induce significant protection against challenge with the native P815 tumor. The results indicate that PMV modified by engraftment of recombinant forms of B7.1 and CD40 and incorporation of IL-2 can be used to modulate immune responses, which provides a novel approach for the development of anti-tumor vaccines and cancer immunotherapies.
Re‐Expression of locomotion and reflex changes after various types of spinal lesions (2010)

Locomotion of the hindlimbs is a complex motor act involving several levels of control (supraspinal, sensory, neurochemical) of a spinal circuitry called the Central Pattern Generator (CPG) which essentially generates the basic locomotor pattern. The importance of this CPG is quite evident from experiments showing that cats with a complete spinal section at T13 can gradually recover spontaneous hindlimb locomotion on a treadmill with appropriate locomotor training for a few weeks. The key role played by the CPG, and some reflex changes, in the recovery of locomotion after a complete spinal section is thus inescapable. Is the spinal CPG also involved in the re‐expression of locomotion after partial spinal lesions? A dual lesion paradigm was devised to study this question: hemisection at T10‐T11, locomotor training and then complete section at T13. Our main finding was that, within 24 hours (i.e. the first testing session) following the complete spinal section, treadmill‐trained cats walked remarkably well with the hindlimbs on the treadmill. Thus, the present experiments show that there is also a major functional contribution from the CPG in the recovery of locomotion after partial spinal cord lesions. This highlights the importance of fostering such potential spinal neuroplasticity in rehabilitation strategies by reinforcing both voluntary aspects of locomotion and activity in endogenous spinal circuits.
Activation of Orphan Nuclear Constitutive Androstane Receptor Requires Subnuclear Targeting by Peroxisome Proliferator-activated Receptor γ Coactivator-1α (2003)

In contrast to the classical nuclear receptors, the constitutive androstane receptor (CAR) is transcriptionally active in the absence of ligand. In the course of searching for the mediator of CAR activation, we found that ligand-independent activation of CAR was achieved in cooperation with the peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1 alpha). PGC-1 beta, a PGC-1 alpha homologue, also activated CAR to less of an extent than PGC-1 alpha. Coexpression of the ligand-binding domain of a heterodimerization partner, retinoid X receptor alpha, enhanced the PGC-1 alpha-mediated activation of CAR, although it had a weak effect on the basal activity of CAR in the absence of PGC-1 alpha. Both the N-terminal region, with the LXXLL motif, and the C-terminal region, with a serine/arginine-rich domain (RS domain), in PGC-1 alpha were required for full activation of CAR. Pull-down experiments using recombinant proteins revealed that CAR directly interacted with both the LXXLL motif and the RS domain. Furthermore, we demonstrated that the RS domain of PGC-1 alpha was required for CAR localization at nuclear speckles. These results indicate that PGC-1 alpha mediates the ligand-independent activation of CAR by means of subnuclear targeting through the RS domain of PGC-1 alpha.
A study on face milling force model based on complex surface geometry (2009)

Knowing about the face milling force components, their magnitude and directions, are essential for machine-tool construction, workpiece-fixture design and machining distortion analysis etc. Based on a traditional face milling force model, an enhanced model for complex workpiece geometry which more practical has been presented in this paper. The key techniques of the model include the ability to handle complex surface geometry, two-dimensional cutter feed trajectories representation, cutter tooth-workpiece engagement computation. The validity of proposed face milling model has been verified by analysing the simulation results.
Baseline Characteristics of the Median Nerve on Ultrasound Examination (2016)

<b>Background:</b> Previous studies using ultrasound for diagnosis of carpal tunnel syndrome have reported on relatively small series of patients, leading to large standard deviations and/or confidence intervals for the mean cross-sectional area of the median nerve. The purpose of this study is to define the CSA of the median nerve in a large cohort of patients. <b>Methods:</b> Patients (n = 175) without history of carpal tunnel release were recruited. All participants were evaluated using the Carpal Tunnel Syndrome-6 questionnaire, a validated clinical diagnostic tool, with a score of 12 or greater considered positive for CTS. Ultrasound examination was performed on both wrists of all participants using a 13-6 MHz linear array transducer. <b>Results:</b> The mean median nerve CSA was significantly larger (P < .001) for patients with a positive (mean = 11.16, SD = 2.51) versus negative CTS-6 result (mean = 6.91, SD = 2.06). There was a significant correlation (.527, P < .001, n = 349) between CSA and CTS-6 score. Logistic regression analysis determined that a CSA of 10 mm2 optimized sensitivity and specificity at 80% and 88%, respectively. Accuracy was 87.9%. <b>Conclusions:</b> A significant difference in mean CSA was found between patients with and without CTS. Median nerve CSA showed a statistically significant positive correlation with CTS-6. Similar to prior studies, a CSA of 10 mm2 was determined to be the optimal cutoff. In this large series of patients, ultrasound was a sensitive, specific, and accurate test for confirmation of a clinical diagnosis of CTS.