gebhart/patrepeval huggingface dataset:
Cabazitaxel, a new taxane with favorable properties (2010)

Cabazitaxel is a new taxane characterized by convenient administration, a favorable pharmacokinetic and safety profile and a decreased propensity for P-glycoprotein (Pgp)-mediated drug resistance. In preclinical studies cabazitaxel inhibited cell growth in a wide range of human cancer cell lines, including tumor models expressing Pgp. Phase I clinical trials established that the cabazitaxel side effect profile is similar to that reported for taxanes, with neutropenia and neuropathy being the most commonly reported toxicities. Further clinical studies have revealed that cabazitaxel is clinically active in women with taxaneresistant metastatic breast cancer and in men with metastatic castration-resistant prostate cancer previously treated with docetaxel. The TROPIC phase III trial concluded that, compared to mitoxantrone/prednisone, the combination cabazitaxel/prednisone conferred a statistically significantly longer overall survival in patients after treatment with a docetaxel-containing regimen, providing the basis for its FDA approval in 2010.
HEAT-ASSISTED TUNNEL BORING MACHINES (1970)

A study was performed to determine: the increase in tunneling machine performance in hard rock resulting from heat weakening of the rock in advance of the tunneling machine, the increase in hourly cost incurred by the heating system, and the net effect of the increased performance and the increased hourly cost on the cost of the finished tunnel. Rock-cutting experiments were performed on Barre granite using a 1-kw CO2-N2-He gas laser for rock heating and disc-type cutters of various diameters. Analytical work included the preparation of specific heat-assisted tunneler designs and their expected performance and economics. An alternative form of using heat for tunneling was also investigated in which slots were melted in the rock instead of merely heating it. The study concludes that the operation of tunneling machines incorporating lasers to provide the heat weakening is technically feasible but economically unattractive. Radiant heaters have insufficient power density to effectively heat the rock, and high-temperature jets create serious environmental problems. However, the test program indicated that a more effective way to assist mechanical cutters would be to use concentrated thermal energy to melt shallow slots in the rock between cutter paths. (DOT)
A 0.13&#x00B5;m CMOS 78dB SNDR 87mW 20MHz BW CT &#x0394;&#x03A3; ADC with VCO-based integrator and quantizer (2009)

In this paper we demonstrate a new technique that eliminates the impact of K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">v</sub> nonlinearity by preserving the integral relationship of the VCO output phase to the input signal. Leveraging the VCO output phase directly precludes the need to span the entire nonlinear K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">v</sub> characteristic since small perturbations (in the range of 10s of mV) at the tuning node are sufficient to shift the VCO phase by a substantial amount. Since an open-loop VCO is sensitive to frequency offsets and drift, and easily saturates its phase detector for large input signals, some form of negative feedback is necessary. Here, a multibit DAC subtracts the previously quantized phase value from the VCO input, creating a residue that is integrated during the next clock cycle. This feedback loop not only allows large signals to drive the VCO without incurring distortion from K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">v</sub> nonlinearity, but also it is a 1s,-order CT DeltaSigma ADC loop, and it therefore 1s,-order shapes quantization noise.
Arabic Handwritten Text Line Extraction by Applying an Adaptive Mask to Morphological Dilation (2012)

This paper presents a robust method for handwritten text line extraction. We use morphological dilation with a dynamic adaptive mask for line extraction. Line separation occurs because of the repulsion and attraction between connected components. The characteristics of the Arabic script are considered to ensure a high performance of the algorithm. Our method is evaluated on the CENPARMI Arabic handwritten documents database which contains multi-skewed and touching lines. With a matching score of 0.95, our method achieved precision and recall rates of 96:3% and 96:7% respectively, which demonstrate the effectiveness of our approach.
The Nuclear Guanine Nucleotide Exchange Factors Ect2 and Net1 Regulate RhoB-Mediated Cell Death after DNA Damage (2011)

Commonly used antitumor treatments, including radiation and chemotherapy, function by damaging the DNA of rapidly proliferating cells. However, resistance to these agents is a predominant clinical problem. A member of the Rho family of small GTPases, RhoB has been shown to be integral in mediating cell death after ionizing radiation (IR) or other DNA damaging agents in Ras-transformed cell lines. In addition, RhoB protein expression increases after genotoxic stress, and loss of RhoB expression causes radio- and chemotherapeutic resistance. However, the signaling pathways that govern RhoB-induced cell death after DNA damage remain enigmatic. Here, we show that RhoB activity increases in human breast and cervical cancer cell lines after treatment with DNA damaging agents. Furthermore, RhoB activity is necessary for DNA damage-induced cell death, as the stable loss of RhoB protein expression using shRNA partially protects cells and prevents the phosphorylation of c-Jun N-terminal kinases (JNKs) and the induction of the pro-apoptotic protein Bim after IR. The increase in RhoB activity after genotoxic stress is associated with increased activity of the nuclear guanine nucleotide exchange factors (GEFs), Ect2 and Net1, but not the cytoplasmic GEFs p115 RhoGEF or Vav2. Importantly, loss of Ect2 and Net1 via siRNA-mediated protein knock-down inhibited IR-induced increases in RhoB activity, reduced apoptotic signaling events, and protected cells from IR-induced cell death. Collectively, these data suggest a mechanism involving the nuclear GEFs Ect2 and Net1 for activating RhoB after genotoxic stress, thereby facilitating cell death after treatment with DNA damaging agents.
Using RNAFOLD to predict the activity of small catalytic RNAs. (1993)

A computer-assisted method for screening the relative activity of small catalytic RNAs is described. A series of four cis-acting variant sequence files are constructed based upon the RNA sequence of a trans-acting catalytic RNA under consideration. These files are individually folded into their lowest energy structure using a standard RNA folding algorithm. The compiled structures are assessed for their ability to form recognizable catalytic RNA secondary structure motifs. We demonstrate here that RNA sequences that do not readily fold into a cis-acting hammerhead ribozyme motif have trans-acting counterparts with reduced in vitro activity. This procedure should be useful in selecting the best candidate sequences in an mRNA to target for catalytic RNA cleavage.
Patterns of brain structural connectivity differentiate normal weight from overweight subjects (2015)

1. An increased BMI (i.e., overweight subjects) is associated with distinct changes in gray-matter and fiber density of the brain. 2. Classification algorithms based on white-matter connectivity involving regions of the reward and associated networks can identify specific targets for mechanistic studies and future drug development aimed at abnormal ingestive behavior and in overweight/obesity.
Collagen density promotes mammary tumor initiation and progression (2008)

This study provides the first data causally linking increased stromal collagen to mammary tumor formation and metastasis, and demonstrates that fundamental differences arise and persist in epithelial tumor cells that progressed within collagen-dense microenvironments. Furthermore, the imaging techniques and signature identified in this work may provide useful diagnostic tools to rapidly assess fresh tissue biopsies.
Ultrafast thermally induced unfolding of RNase A. (1995)

A temperature jump (T-jump) method capable of initiating thermally induced processes on the picosecond time scale in aqueous solutions is introduced. Protein solutions are heated by energy from a laser pulse that is absorbed by homogeneously dispersed molecules of the dye crystal violet. These act as transducers by releasing the energy as heat to cause a T-jump of up to 10 K with a time resolution of 70 ps. The method was applied to the unfolding of RNase A. At pH 5.7 and 59 degrees C, a T-jump of 3-6 K induced unfolding which was detected by picosecond transient infrared spectroscopy of the amide I region between 1600 and 1700 cm-1. The difference spectral profile at 3.5 ns closely resembled that found for the equilibrium (native-unfolded) states. The signal at 1633 cm-1, corresponding to the beta-sheet structure, achieved 15 +/- 2% of the decrease found at equilibrium, within 5.5 ns. However, no decrease in absorbance was detected until 1 ns after the T-ump. The disruption of beta-sheet therefore appears to be subject to a delay of approximately 1 ns. Prior to 1 ns after the T-jump, water might be accessing the intact hydrophobic regions.
Comparison of topographical patterns of ganglion and photoreceptor cell differentiation in the retina of the zebrafish,Danio rerio (1996)

Earlier studies suggested retinal differentiation in the zebrafish commences ventrally rather than centrally as is the case in other vertebrates. Here we describe the topographical spread of cell differentiation for ganglion cells, double cones and rods in the zebrafish retina between 36 and 72 hours postfertilization (hpf), by using immunohistochemical markers in retinal wholemounts. Staining for all three cell types commenced within the ventral retina on the nasal side of the optic nerve and choroid fissure, at 38 hpf for ganglion cells and 50 hpf for double cones and rods. Within 3 to 4 hours, the staining of ganglion cells and double cones spread in a continuous wave-like fashion into the nasal region of the ventral retina. After this time, the staining patterns for ganglion cells and double cones progressed dorsally into the central and temporal retina. Finally, stained somata of ganglion cells were observed within the temporal-ventral region by approximately 48 hpf, more than 8 hours later than the first ganglion cells within the nasal retina. The topographical spread of double cone staining was slightly less orderly. After staining had extended into the nasal retina between 50 and 54 hpf, a small group of stained double cones often appeared at the temporal edge of the choroid fissure by 56 hpf, simultaneously with initial staining observed dorsal and temporal to the optic nerve. The topographical spread of rod staining in the ventral retina was more symmetrical. After rod staining appeared near the nasal edge of the choroid fissure at 50 hpf, rods accumulated within a localized patch nasal to the fissure. Approximately 5 hours after initial rod staining, scattered rod staining appeared on the temporal side of the choroid fissure (approximately 55-57 hpf). Rods increased rapidly within the ventral retina, and a dense symmetrical patch extended out from the choroid fissure into the nasal and temporal regions of the ventral retina by 70 hpf. A scattered pattern of rod staining also occurred within the dorsal retina at this time.
Water soluble poly(histamine acrylamide) with superior buffer capacity mediates efficient and nontoxic in vitro gene transfection (2011)

Abstract Water‐soluble cationic polymers, poly(histamine acrylamide)s (PHAs), with superior buffer capacity at the endosomal pH range were designed, prepared, and investigated for non‐viral gene transfection. PHAs were obtained with molecular weights ranging from 9.2 to 28.7 kDa through controlled radical polymerization of histamine acrylamide (HA). Acid–base titration results displayed that all PHA polymers had a remarkably high buffer capacity of about 70% at pH 5.1–7.2. 12.7–28.7 kDa PHAs were able to effectively condense DNA into nano‐sized (&lt;220 nm) polyplexes with moderate positive surface charges (+13–+19 mV) at N/P ratios ≥10/1. CCK assays indicated that polyplexes of 12.7 and 17.5 kDa PHAs were non‐toxic to COS‐7 cells up to a tested N/P ratio of 20/1. Interestingly, the in vitro transfection using pCMV‐Luc and pEGFP‐C1 plasmid DNA as reporter genes showed that polyplexes of 12.7 kDa PHA formed at an N/P ratio of 20/1 mediated efficient transfection in COS‐7 cells under 10% serum conditions, with transfection efficiencies comparable to that of 25 kDa polyethylenimine control. Their versatile design of structures, controlled synthesis, low cytotoxicity, and high transfection activity render PHA‐based cationic polymers particularly interesting for the development of safe and efficient non‐viral gene delivery systems. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
The contact resistance force relationship of an intrinsically conducting polymer interface (2006)

Investigations on contact connector materials for different applications such as in the automotive industry have focused toward the increasing interest of using conducting polymers, as compared to conventional metallic contacts. The aim is to achieve overall improvements in performance as well as cost effectiveness. Currently, extrinsic conducting polymers (ECPs) are employed as conductive coats or adhesives at contact interfaces. However, frictional abrasion within the metal doped polymer (ECP) causes fretting corrosion, which leads to instability in the contact resistance. To overcome this, intrinsically conducting polymers (ICPs) are explored. Hemispherical contact coatings were fabricated using poly(3,4-ethylenedioxythiopene) (PEDOT) or polyaniline/polyvinylchloride (PANI/PVC) commodity blends. Contact resistances were taken using four-wire resistance measurement techniques. The conductivities of in-house fabricated ICP contacts were found to be in the range of 10/sup -2/ S/spl middot/cm/sup -1/. The response relating the change of contact resistance under varying compression force appeared to be repeatable with minimum deviation of 2%. The surface profiles of the ICP contacts were also recorded by an optical confocal system. The initial investigation results presented in this paper were used to evaluate and validate the hypothesis of employing ICP contacts to eliminate or minimize wearing and fretting effects.
η5-Semiquinone Complexes and the Related η4-Benzoquinone of (Pentamethylcyclopentadienyl)rhodium and -iridium:  Synthesis, Structures, Hydrogen Bonding, and Electrochemical Behavior (2004)

Treatment of hydroquinone with [Cp*M(solvent)3][OTf]2 (M = Rh, Ir) in acetone afforded the π-bonded complexes {[Cp*M(η5-semiquinone)][OTf]}n (M = Rh (1a), M = Ir (1b)) in 95% yield. The 1H NMR spectra of 1a,b recorded in CD3OD indicate strong hydrogen bonding in solution. The crystal structures of 1a and 1b were determined and exhibit strong intermolecular hydrogen bonding, forming organometallic polymers in which the integrity of the system is maintained by hydrogen bonding between metal−semiquinone subunits. Deprotonation of 1a produced the related η4-quinone complex [Cp*Rh(η4-quinone)] (2a), which was fully characterized and its X-ray molecular structure determined. Furthermore, the electrochemical behavior of these η4-quinone π-complexes [Cp*M(η4-quinone)] (M = Rh (2a), M = Ir (2b)) was investigated and compared to that of the well-known couple quinone/hydroquinone. The latter are important species in chemistry and biology; their biological action is often linked to their electron-transfer rates and redox behavior.
Association between Lactobacillus species and bacterial vaginosis-related bacteria, and bacterial vaginosis scores in pregnant Japanese women (2007)

The BV-related bacteria, including BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium, are common in the vagina of pregnant Japanese women with BV. The presence of L. iners may be correlated with vaginal colonization by these BV-related bacteria.
Interferon Alfa Combined with Cytotoxic Chemotherapy for Patients with Non-Hodgkin's Lymphoma (1992)

Interferon alfa, when added to a four-drug doxorubicin-based chemotherapy regimen, is an effective antitumor agent in patients with clinically aggressive low-grade or intermediate-grade non-Hodgkin's lymphoma.
A Selective Retinoid X Receptor Agonist Bexarotene (Targretin) Prevents and Overcomes Acquired Paclitaxel (Taxol) Resistance in Human Non–Small Cell Lung Cancer (2004)

Our results suggest that bexarotene may offer a novel approach to prevent and overcome paclitaxel resistance in patients with NSCLC.
Peptides from conserved regions of paramyxovirus fusion (F) proteins are potent inhibitors of viral fusion. (1996)

The synthetic peptides DP-107 and DP-178 (T-20), derived from separate domains within the human immunodeficiency virus type 1 (HIV-1) transmembrane (TM) protein, gp4l, are stable and potent inhibitors of HIV-1 infection and fusion. Using a computer searching strategy (computerized antiviral searching technology, C.A.S.T.) based on the predicted secondary structure of DP-107 and DP-178 (T-20), we have identified conserved heptad repeat domains analogous to the DP-107 and DP-178 regions of HIV-1 gp41 within the glycoproteins of other fusogenic viruses. Here we report on antiviral peptides derived from three representative paramyxoviruses, respiratory syncytial virus (RSV), human parainfluenza virus type 3 (HPIV-3), and measles virus (MV). We screened crude preparations of synthetic 35-residue peptides, scanning the DP-178-like domains, in antiviral assays. Peptide preparations demonstrating antiviral activity were purified and tested for their ability to block syncytium formation. Representative DP-178-like peptides from each paramyxovirus blocked homologous virus-mediated syncytium formation and exhibited EC50 values in the range 0.015-0.250 microM. Moreover, these peptides were highly selective for the virus of origin. Identification of biologically active peptides derived from domains within paramyxovirus F1 proteins analogous to the DP-178 domain of HIV-1 gp4l is compelling evidence for equivalent structural and functional features between retroviral and paramyxoviral fusion proteins. These antiviral peptides provide a novel approach to the development of targeted therapies for paramyxovirus infections.
In-vivo effect of nicotine on cytokine production by human non-adherent mononuclear cells (1996)

Nicotine in vivo has an inhibitory effect on TH2 cell function as measured by inhibition of IL-10 production, but does not appear to have any effect on TH1 cell function.
Human plasma carboxylesterase 1, a novel serologic biomarker candidate for hepatocellular carcinoma (2009)

To identify and characterize a serologic glycoprotein biomarker for hepatocellular carcinoma (HCC), multi-lectin affinity chromatography was used to isolate intracellular N-linked glycoprotein fractions from five paired non-tumor and tumor tissues. From the series of 2-D DIGE targeted differentially expressed N-linked glycoproteins, we identified human liver carboxylesterase 1 (hCE1), which was remarkably down-regulated in tumor tissues, a finding confirmed by Western blot, a quantitative real-time RT-PCR, and immunohistochemical staining of non-tumor and tumor tissues from total 58 HCC patients. To investigate whether hCE1 is also present in human plasma, we employed a magnetic bead-based immunoprecipitation followed by nano-LC-MS/MS analysis, and we found for the first time that hCE1 is present in human plasma as opposed to that in liver tissues. That is, from normalization of hCE1 signal by the immunoprecipitation and Western blot analysis, hCE1 levels were increased in plasma specimens from HCC patients than in plasma from other disease patient groups (e.g. liver cirrhosis, chronic hepatitis, cholangiocarcinoma, stomach cancer, and pancreatic cancer). From the receiver operating characteristic analysis in HCC, both sensitivity and specificity were shown to be greater than 70.0 and 85.0%, respectively. Thus, the high-resolution proteomic approach demonstrates that hCE1 is a good candidate for further validation as a serologic glycoprotein biomarker for HCC.
A critical reflection on using food as learning materials (2003)

Abstract As early childhood teacher educators, we are thoroughly immersed in conversations about developmentally appropriate practice. Whether teachers should incorporate the use of food as learning materials is a case in point. As with many other concerns we ponder in our field, our task must be to define, clarify, and consider multiple perspectives in the pursuit of a rational justification of our position. In this paper we report the results of our careful review of theory and research that leads us to propose that using food as art material violates principles of best practice for three main reasons, because it: (1) teaches young children that it is acceptable to eat play materials and to play with food, (2) teaches young children that it is acceptable practice to waste limited resources, (3) violates many premises of multicultural education, or teaching children about diverse ethnic groups.
An Optimized, Chemically Regulated Gene Expression System for Chlamydomonas (2008)

We have worked out a chemically regulated gene expression system that can be finely tuned to produce temporally controlled "waves" in gene expression. The use of cassettes containing the CYC6 promoter, and of modified growth media, is a reliable and economically sustainable system for the temporally controlled expression of foreign genes in Chlamydomonas.
Efficient Reduction of Target RNAs by Small Interfering RNA and RNase H-dependent Antisense Agents (2003)

RNA interference can be considered as an antisense mechanism of action that utilizes a double-stranded RNase to promote hydrolysis of the target RNA. We have performed a comparative study of optimized antisense oligonucleotides designed to work by an RNA interference mechanism to oligonucleotides designed to work by an RNase H-dependent mechanism in human cells. The potency, maximal effectiveness, duration of action, and sequence specificity of optimized RNase H-dependent oligonucleotides and small interfering RNA (siRNA) oligonucleotide duplexes were evaluated and found to be comparable. Effects of base mismatches on activity were determined to be position-dependent for both siRNA oligonucleotides and RNase H-dependent oligonucleotides. In addition, we determined that the activity of both siRNA oligonucleotides and RNase H-dependent oligonucleotides is affected by the secondary structure of the target mRNA. To determine whether positions on target RNA identified as being susceptible for RNase H-mediated degradation would be coincident with siRNA target sites, we evaluated the effectiveness of siRNAs designed to bind the same position on the target mRNA as RNase H-dependent oligonucleotides. Examination of 80 siRNA oligonucleotide duplexes designed to bind to RNA from four distinct human genes revealed that, in general, activity correlated with the activity to RNase H-dependent oligonucleotides designed to the same site, although some exceptions were noted. The one major difference between the two strategies is that RNase H-dependent oligonucleotides were determined to be active when directed against targets in the pre-mRNA, whereas siRNAs were not. These results demonstrate that siRNA oligonucleotide- and RNase H-dependent antisense strategies are both valid strategies for evaluating function of genes in cell-based assays.