gebhart/patrepeval huggingface dataset:
Characterization of the Apoptotic Response Induced by the Cyanine Dye D112: A Potentially Selective Anti-Cancer Compound (2015)

Chemotherapeutic drugs that are used in anti-cancer treatments often cause the death of both cancerous and noncancerous cells. This non-selective toxicity is the root cause of untoward side effects that limits the effectiveness of therapy. In order to improve chemotherapeutic options for cancer patients, there is a need to identify novel compounds with higher discrimination for cancer cells. In the past, methine dyes that increase the sensitivity of photographic emulsions have been investigated for anti-cancer properties. In the 1970's, Kodak Laboratories initiated a screen of approximately 7000 dye structural variants for selective toxicity. Among these, D112 was identified as a promising compound with elevated toxicity against a colon cancer cell line in comparison to a non-transformed cell line. Despite these results changing industry priorities led to a halt in further studies on D112. We decided to revive investigations on D112 and have further characterized D112-induced cellular toxicity. We identified that in response to D112 treatment, the T-cell leukemia cell line Jurkat showed caspase activation, mitochondrial depolarization, and phosphatidylserine externalization, all of which are hallmarks of apoptosis. Chemical inhibition of caspase enzymatic activity and blockade of the mitochondrial pathway through Bcl-2 expression inhibited D112-induced apoptosis. At lower concentrations, D112 induced growth arrest. To gain insight into the molecular mechanism of D112 induced mitochondrial dysfunction, we analyzed the intracellular localization of D112, and found that D112 associated with mitochondria. Interestingly, in the cell lines that we tested, D112 showed increased toxicity toward transformed versus non-transformed cells. Results from this work identify D112 as a potentially interesting molecule warranting further investigation.
Natural strong pinning sites in laser-ablatedYBa2Cu3O7−δthin films (2000)

At low temperatures dislocations are the dominant flux-pinning centers in thin films of ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\ensuremath{-}\ensuremath{\delta}}$ deposited on (100) ${\mathrm{SrTiO}}_{3}$ substrates [B. Dam et al., Nature (London) 399, 439 (1999)]. Using a wet-chemical etching technique in combination with atomic force microscopy, both the length and the lateral dislocation distribution are determined in laser ablated ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\ensuremath{-}\ensuremath{\delta}}$ films. We find that (i) dislocations are induced in the first stages of film growth, i.e., close to the substrate-film interface, and persist all the way up to the film surface parallel to the c axis, resulting in a uniform length distribution, and (ii) the radial dislocation distribution function exhibits a universal behavior: it approaches zero at small distances, indicating short-range ordering of the defects. This self-organization of the growth-induced correlated disorder makes epitaxial films completely different from single crystals with randomly distributed columnar defects created by means of heavy-ion irradiation. Since the substrate temperature can be used to tune the dislocation density ${n}_{\mathrm{disl}}$ over almost two orders of magnitude (\ensuremath{\sim}1--100/\ensuremath{\mu}${\mathrm{m}}^{2}$), the mechanism by which dislocations are induced is closely related to the ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\ensuremath{-}\ensuremath{\delta}}$ nucleation and growth mechanism. We present evidence for preferential precipitation in the first monolayer and precipitate generated dislocations.
The Effect of Defined Lipopolysaccharide Core Defects upon Antibiotic Resistances of Salmonella typhimurium (1977)

Antibiotic resistances of two sets of Salmonella typhimurium rfa transductants (along with those of their smooth pyrE + and cysE + sister transductants) were measured. One set was derived from a pyrE smooth LT2 parent and the other from a cysE smooth LT7 parent. Results showed that strains with defects at the rfa(R-res-2) level and deeper were more susceptible to bacitracin, novobiocin and polymyxin. Those with defects at the rfaG level or deeper were in addition more sensitive to vancomycin, erythromycin, oxacillin and nafcillin. At these levels the presence or absence of galactose I or glucose I from the lipopolysaccharide core made a considerable difference. A heptose-less rfaE mutant was the most sensitive of the strains tested to the above named antibiotics. Strains with rfa lesions at several levels of defect showed slight increases in resistances to tetracycline, cephalothin, ampicillin and penicillin. One would expect strains with galE mutations to be similar to rfa(R-res-2) strains and those with galU mutations to be similar to rfaG strains if the core defects accounted for the differing antibiotic resistances. They proved to be so except that the galE and galU strains in the S. typhimurium FIRN line were as resistant to novobiocin as were smooth strains. The results are interpreted in respect to Nikaido&apos;s hypothesis that hydrophilic antibiotics with molecular weights of less than about 650 can gain access to the periplasmic space through protein-lined, water-filled pores and that hydrophobic ones can gain access in deep rough strains when phospholipid patches appear on the surface due to absence of polysaccharides and proteins.
Thickness dependence of polydopamine thin films on detection sensitivity of surface plasmon-enhanced fluorescence biosensors (2017)

A bioinspired polydopamine (PDA) coating is a good candidate for the rapid and cheap chemical modification of biosensor surfaces. Herein, we report the effect of PDA thickness on the detection sensitivity of a fluorescence biosensor utilizing surface plasmon-enhanced fluorescence. The thickness of PDA films was tuned by the incubation time of the dopamine solution and varied from 1 to 17 nm. The detection sensitivity was evaluated as the limit of detection (LOD) of a fluorescently labelled target analyte by a model immunoassay. The LOD was determined to be 1.6 pM for the thickest PDA film and was improved to 1.0 pM by reducing the thickness to the range from 1 to 5 nm, corresponding to the incubation time of 10 to 60 min. The experimental results indicate that the PDA coating is suitable for the surface functionalization of biosensors in mass production as it does not require precise control of the incubation time.
SIFT-MS Measurement of VOC Distribution Coefficients in Human Blood Constituents and Urine (2003)

The new technique of selected ion flow tube-mass spectrometry (SIFT-MS) has been applied to the measurement of Henry's Law constants for the volatile organic chemicals o-xylene and trichloroethylene that both have low solubility in aqueous solvents. The method is validated by measurements in water at 298 K using the equilibrium partitioning in closed systems (EPICS) methodology in which the equilibrium headspace concentrations for the volatile organic compounds (VOCs) are measured in two sealed bottles containing different liquid volumes of very dilute solutions of the VOC. The range of solvents is then extended to human body fluids at 309 K including urine, saline, whole blood, red cells in saline, and plasma. The dimensionless distribution coefficients for these solvents vary markedly in the different fluids. For o-xylene they range from k(H) = 0.12-0.15 for water, saline, and urine; 0.53 for red cells in saline; 1.9 for whole blood; to 2.4 for plasma. For trichloroethylene the distribution coefficients range from k(H) = 0.070-0.091 for water, saline, and urine; 0.28 for red cells in saline; 0.35 for plasma; to 0.48 in whole blood. The very different solubilities of organic solvents in body fluids influence the uptake of solvents in workers exposed to VOCs. Some implications of these measurements are briefly discussed.
Apolipoprotein deficiency and chronic liver disease. (2001)

Deficiency of apolipoprotein can be of genetic origin or due to diseases like advanced chronic liver disease. Deficiency of apolipoprotein A causes Tangier disease without any major hepatic involvement being reported. Deficiency of apolipoprotein B causes abetalipoproteinemia or familial hypobetalipoproteinemia; with hepatic involvement in the form of raised transaminases, fatty liver and cirrhosis. Advanced chronic liver disease itself can cause reduction of apolipoprotein A and apolipoprotein B levels and acanthocytosis. In patients with chronic liver disease of undetermined etiology, lipid profile and apolipoprotein levels should be obtained routinely. If it suggests apolipoprotein B deficiency, then liver biopsy can be avoided, as the etiology of chronic liver disease is established. Isolated deficiency of either apolipoprotein A or apolipoprotein B suggests etiology of chronic liver disease, while deficiency of both apolipoprotein A and apolipoprotein B is a manifestation of advanced chronic liver disease.
Multiport Diffuser Design for a Negatively Buoyant Discharge (2017)

Wastewater disposal systems are designed to meet minimum dilution requirements within a regulatory mixing zone-a limited region around the discharge structure where initial dilution of the effluent occurs. We present a design case study of a multiport diffuser for a 1 MGD dense discharge into a shallow 60-foot wide river. CORMIX mixing zone modeling software was used to design the diffuser to achieve dilution to meet water quality criteria within a mixing zone for regulatory compliance. An iterative design process was employed using the CORMIX mixing zone model and the CorHyd internal diffuser hydraulics model. CORMIX simulates the multiport diffuser as a line source to predict downstream water column dilution values needed for regulatory compliance. CorHyd is used to (i) calculate port and pipe velocities, (ii) verify uniform discharge distribution from the ports, and (iii) determine the diffuser head requirements. To decrease the diffuser-induced near-field acceleration zone and enhance mixing, a fanned unidirectional multiport diffuser was designed. The diffuser riser lengths vary to conform to the river bathymetry. The riser ports were fitted with duckbill valves to maintain high port velocity over a range of effluent discharge rates. The design was optimized for dilutions at the mixing zone with port geometry, exit velocity, and spacing that allows individual plumes to merge by the end of the near-field and minimizes the potential for scouring the river bed.
Linked Control of Syllable Sequence and Phonology in Birdsong (2010)

The control of sequenced behaviors, including human speech, requires that the brain coordinate the production of discrete motor elements with their concatenation into complex patterns. In birdsong, another sequential vocal behavior, the acoustic structure (phonology) of individual song elements, or "syllables," must be coordinated with the sequencing of syllables into a song. However, it is unknown whether syllable phonology is independent of the sequence in which a syllable is produced. We quantified interactions between phonology and sequence in Bengalese finch song by examining both convergent syllables, which can be preceded by at least two different syllables and divergent syllables, which can be followed by at least two different syllables. Phonology differed significantly based on the identity of the preceding syllable for 97% of convergent syllables and differed significantly with the identity of the upcoming syllable for 92% of divergent syllables. Furthermore, sequence-dependent phonological differences extended at least two syllables away from the convergent or divergent syllable. To determine whether these phenomena reflect differences in central control, we analyzed premotor neural activity in the robust nucleus of the arcopallium (RA). Activity associated with a syllable varied significantly depending on the sequence in which the syllable was produced, suggesting that sequence-dependent variations in premotor activity contribute to sequence-dependent differences in phonology. Moreover, these data indicate that RA activity could contribute to the sequencing of syllables. Together, these results suggest that, rather than being controlled independently, the sequence and phonology of birdsong are intimately related, as is the case for human speech.
Symplekin promotes tumorigenicity by up-regulating claudin-2 expression (2010)

Symplekin is a ubiquitously expressed protein involved in cytoplasmic RNA polyadenylation and transcriptional regulation and is localized at tight junctions (TJs) in epithelial cells. Nuclear symplekin cooperates with the Y-box transcription factor zonula occludens 1-associated nucleic acid-binding protein (ZONAB) to increase the transcription of cell cycle-related genes and also inhibits differentiation of intestinal cells. We detected high levels of nuclear symplekin in 8 of 12 human colorectal cancer (CRC) samples. shRNA-mediated reduction of symplekin expression was sufficient to decrease significantly the anchorage-independent growth and proliferation of HT-29 CRC cells as well as their tumorigenicity when injected into immunodeficient animals. Symplekin down-regulation also was found to alter ion transport through TJs, to promote the localization of ZONAB in the membrane rather than the nucleus, and strongly to enhance cell polarization in a 3D matrix, leading to the formation of spheroids organized around a central lumen. Claudin-2 expression was reduced following symplekin down-regulation, an effect mimicked when ZONAB expression was down-regulated using selective siRNA. Virus-mediated restoration of claudin-2 expression was found to restore nuclear expression of ZONAB in HT29DeltaSym cells and to rescue the phenotypic alterations induced by symplekin down-regulation of cell polarity, paracellular transport, ZONAB localization, cyclin D1 expression, proliferation, and anchorage-independent growth. Finally, siRNA-mediated claudin-2 down-regulation increased the transepithelial resistance and decreased cyclin D1 expression and ZONAB nuclear localization, similar to observations in symplekin-depleted cells. Our results suggest that nuclear overexpression of symplekin promotes tumorigenesis in the human colon and that the regulation of claudin-2 expression is instrumental in this effect.
Prevalence of overweight and obesity among adult Malaysians: an update. (2011)

A total of 4428 adults (>18 years old) from 5 different selected regions in Peninsular and East Malaysia participated in this health survey. Using World Health Organization recommendations for body mass index (BMI), the prevalence of overweight and obesity were found to be 33.6% (95% CI= 32.2, 35.0) and 19.5% (95% CI= 18.3, 20.7) respectively. There were more females who were obese (22.5%, 95% CI=20.9, 24.0) compared to males (14.1%, 95% CI=12.3, 15.9). Highest prevalence of obesity were among the Indians (24.6%, 95% CI=20.3, 29.3), followed closely by the Malays (23.2%, 95% CI=21.6, 24.8%) and lowest prevalence was among the Chinese subjects (8.2%, 95% CI=6.2, 10.6). More than 43% of the 531 younger subjects (<30 years old) were either overweight (20%, 95% CI=16.6, 23.6) or obese (13.9%, 95% CI=11.1, 17.2%). All subjects who claimed to be non-diabetes were required to undergo 75 g glucose tolerance test. Compared to subjects with normal BMI (18.5-24.9 kg/m2), there was a 3- and 2-folds increase in the prevalence of newly diagnosed diabetes and impaired glucose tolerance respectively, among obese subjects (BMI>30 kg/m2) who initially claimed to have no diabetes. This study highlights a need for more active, inter-sectoral participation advocating a health-promoting environment in order to combat obesity in this country.
Effect of Co-medications on Plasma Concentrations of Zonisamide. (1995)

Zonisamide (ZNS), a new antiepileptic drug which features a wide antiepileptic spectrum, is commonly prescribed concomitantly with other drugs. However, there appears to be little data on the drug interaction of ZNS with other coadministered drugs. Concentrations of ZNS and co-medications in plasma were measured simultaneously by HPLC. The ratio of plasma concentration to the administered dose of ZNS in the monotherapy was significantly higher than that in the polytherapy (P>0.05). When co-medications numbered more than two, the ratio was significantly decreased compared with ZNS alone, indicating the possibility that co-medications induce decreases in plasma concentration of ZNS. The present findings provide useful information that the monitoring of plasma concentration of ZNS is needed to adjust dosage regiments of ZNS in the polytherapy.
Archaeology in the World of Display: A Material Study of the Use of History in the Stockholm Exhibition (2011)

History was an important notion in constructing an industrial capitalist society in the nineteenth century. This article deals with the manifest use of history at the Exhibition of 1897. At this exhibition, history was ubiquitous and was most fully expressed in the model of medieval and Renaissance called Stockholm. The history of nineteenth- and twentieth-century exhibitions in general has been thoroughly studied in the field of humanities. However, the specific use of history and space has not attracted much interest. This analysis of the model of Old is of the first archaeological study of remains of the great exhibitions ever to have been done. Even though the Stockholm pavilion was exceedingly popular in the summer of 1897, only very scarce documentation has survived. An archaeological excavation of parts of the temporary historical models, such as the Hospital of the Holy Spirit, showed convincing evidence of the hegemonic position which the use of history enjoyed at the exhibition and in the nineteenth century.
Complete description of fiber strength distribution using lower and upper strength thresholds (1980)

Abstract A common method of predicting the survival of cabled optical fibers under an assumed or calculated stress involves the transformation of strength-dependent and the extrapolation of creep-dependent failure distributions based on a large number of samples of different and preferably long lengths. The use of a complex Weibull distribution of the form has become an accepted practice for describing the failure probability.
Performance of complex Chebyshev approximation in delay-root-Nyquist filter design (2002)

Root-Nyquist filters are crucial components in data communications and recently the ability to attach fractional sample delay attributes to them has become very important. Here we explore the application of Chebyshev approximation to design of such filters. Special attention is paid to the use of the Karam-McClellan algorithm, a fully complex extension of the well-established Parks-McClellan algorithm, which delivers peak error performance improvement in the region of one dB or better.
Randomized phase II study of axitinib versus standard of care in patients with recurrent glioblastoma. (2014)

2018 Background: Vascular endothelial growth factor receptor (VEGFR) signal transduction mediates glioblastoma (GB) associated neo-angiogenesis. Axitinib is an oral small molecule tyrosine kinase inhibitor with high affinity and specificity for the VEGF-receptors, approved for the treatment of metastatic renal cell carcinoma. Methods: Axitinib (5 mg BID starting dose) vs. best alternative choice of therapy was studied in an open label, randomized, phase II clinical trial in patients (pts) with recurrent GB. Six-month progression-free survival (6mPFS) was the primary endpoint. Results: Between Sep 2011 and Oct 2013, 44 pts who failed surgery, RT and temozolomide were randomized 1:1 at 3 sites. Median age 54y (range 20-79), 33M/11F, WHO-PS 0/1/2/3: 6, 26, 11, and 1 pt. In the control arm 20 pts received bevacizumab and 2 pts received lomustine at standard doses. Axitinib (n=22) was generally well tolerated. Most common axitinib related AEs consisted of dysphonia (3x G2), fatigue (6x G2, 2x G3), hypertension (5x G2), oral hyperesthesia (7x G2, 1x G3), diarrhea (2x G2, 2x G3), and hypothyroidism (3x G2). In 4 pts axitinib dosing was interrupted and subsequently dose reduced because of toxicity; in 4 other pts axitinib was dose escalated to 7 or 10 mg BID (2 pts each). Tumor response by RANO criteria was 28% in the axitinib arm vs. 23% in the control arm (Table). All pts had an increased uptake on 18F-FET PET at baseline. A decrease (-26 to -100%) of SUVmax/background was documented in 6/7 pts on axitinib at the time of response on MRI. Corticosteroids could be stopped in 4/12 and tapered in an additional 5/12 pts in the axitinib arm. After a median follow-up of 10.5 mths, the 6mPFS for axitinib was 22% (95% CI 5-40) vs. 19% (95% CI 2-36) for the control arm. Median PFS and OS were respectively 2.9 vs. 2.6 mths, and 10.3 vs. 7.4 mths for pts treated in the axitinib vs. control arm. Conclusions: Axitinib has single-agent activity and manageable toxicity in pts with recurrent GB. The survival on the axitinib arm was comparable to that on the contemporary control arm. Further evaluation of axitinib for recurrent GB is warranted. Clinical trial information: NCT01562197. Axitinib Control BOR Confirmed BOR BOR Confirmed BOR CR 5 2 1 1 PR 6 4 5 4 SD 5 7 PD 5 8 NE 1 1 Abbreviations: BOR, best overall tumor response; NE: not evaluable.
HP/HT Well: Fluid Selection, Planning and Lessons Learned (2010)

As the world’s energy demand increases and drilling technology improves, more and more wells are being drilled in hostile environments such as ultra-deepwater, geothermal zones, high pressure / high temperature (HP/HT) areas, etc. These types of wells present challenges not often encountered in normal drilling situations. Consequently, special considerations in the planning phase can help to mitigate some of the major problems experienced while drilling. A well with a bottomhole static temperature greater than 325uF (190°C) and with hydrostatic pressure greater than 17,500 psi (1,207 bar) is classified as a “critical or challenging well” by many operators and service companies. Critical or challenging wells have additional requirements not only in the drilling phase of the well but also in the extensive planning stage. For an HP/HT well in the Santos basin offshore Brazil, several key aspects were considered to determine the best fluid for the project. Ultimately, a water-based mud was selected as the fluid of choice for this “critical well.” This paper reviews the drilling fluid selection process, the laboratory validation, and the drilling fluid used on this HP/HT well. It also summarizes the lessons learned from the HP/HT section of the well.