gebhart/patrepeval huggingface dataset:
Transcriptional regulation of immunoglobulin expression in a chronic lymphocytic leukemia cell line (1989)

A cell line derived from a B-type chronic lymphocytic leukemia, Corinna II, was found to down-regulate its steady-state level of IgM mRNA after treatment with phorbol 12-myristate 13-acetate while the proliferative capacity of the cell line was unaffected. No changes in the splicing pattern of the IgM transcript could be observed after treatment. The down-regulatory effect on IgM RNA expression was found to be inhibited by cycloheximide, suggesting that functional protein synthesis was needed for the effect. Transfection experiments showed that the down-regulatory effect of phorbol myristate acetate was exerted at the level of transcriptional initiation. The DNA element mediating the down-regulatory effect was found to be present within 140 bp 5' of the mRNA cap site in an immunoglobulin promoter.
Morphology and mechanical properties of layered silicate reinforced natural and polyurethane rubber blends produced by latex compounding (2004)

Abstract Natural rubber (NR), polyurethane rubber (PUR), and NR/PUR‐based nanocomposites were produced from the related latices by adding a pristine synthetic layered silicate (LS; sodium fluorohectorite) in 10 parts per hundred parts rubber (phr). The dispersion of the LS latices in the composite was studied by X‐ray diffraction (XRD) and transmission electron microscopy (TEM). Further information on the rubber/LS interaction was received from Fourier transform infrared spectroscopy (FTIR) and dynamic mechanical thermal analysis (DMTA). Tensile and tear tests were used to characterize the performance of the rubber nanocomposites. It was found that LS is more compatible and thus better intercalated by PUR than by NR. Further, LS was preferably located in the PUR phase in the blends, which exhibited excellent mechanical properties despite the incompatibility between NR and PUR. Nano‐reinforcement was best reflected in stiffness‐ and strength‐related properties of the rubber composites. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 543–551, 2004
Amino acid residues of bitter taste receptor TAS2R16 that determine sensitivity in primates to β-glycosides (2016)

In mammals, bitter taste is mediated by TAS2Rs, which belong to the family of seven transmembrane G protein-coupled receptors. Since TAS2Rs are directly involved in the interaction between mammals and their dietary sources, it is likely that these genes evolved to reflect species-specific diets during mammalian evolution. Here, we analyzed the amino acids responsible for the difference in sensitivities of TAS2R16s of various primates using a cultured cell expression system. We found that the sensitivity of TAS2R16 varied due to several amino acid residues. Mutation of amino acid residues at E86T, L247M, and V260F in human and langur TAS2R16 for mimicking the macaque TAS2R16 decreased the sensitivity of the receptor in an additive manner, which suggests its contribution to the potency of salicin, possibly via direct interaction. However, mutation of amino acid residues 125 and 133 in human TAS2R16, which are situated in helix 4, to the macaque sequence increased the sensitivity of the receptor. These results suggest the possibility that bitter taste sensitivities evolved independently by replacing specific amino acid residues of TAS2Rs in different primate species to adapt to species-specific food.
Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid (2015)

Polyketides have enormous structural diversity, yet polyketide synthases (PKSs) have thus far been engineered to produce only drug candidates or derivatives thereof. Thousands of other molecules, including commodity and specialty chemicals, could be synthesized using PKSs if composing hybrid PKSs from well-characterized parts derived from natural PKSs was more efficient. Here, using modern mass spectrometry techniques as an essential part of the design-build-test cycle, we engineered a chimeric PKS to enable production one of the most widely used commodity chemicals, adipic acid. To accomplish this, we introduced heterologous reductive domains from various PKS clusters into the borrelidin PKS' first extension module, which we previously showed produces a 3-hydroxy-adipoyl intermediate when coincubated with the loading module and a succinyl-CoA starter unit. Acyl-ACP intermediate analysis revealed an unexpected bottleneck at the dehydration step, which was overcome by introduction of a carboxyacyl-processing dehydratase domain. Appending a thioesterase to the hybrid PKS enabled the production of free adipic acid. Using acyl-intermediate based techniques to "debug" PKSs as described here, it should one day be possible to engineer chimeric PKSs to produce a variety of existing commodity and specialty chemicals, as well as thousands of chemicals that are difficult to produce from petroleum feedstocks using traditional synthetic chemistry.
Human Papillomavirus Type-16 Virus-Like Particles Activate Complementary Defense Responses in Key Dendritic Cell Subpopulations (2004)

Human papillomavirus type-16 (HPV16) L1 virus-like particles (VLPs) activate dendritic cells (DCs) and induce protective immunity. In this study, we demonstrate, using global gene expression analysis, that HPV16 VLPs produce quite distinct innate responses in murine splenic DC subpopulations. While HPV16 VLPs increase transcription of IFN-gamma and numerous Th1-related cytokines and chemokines in CD8alpha(+)CD11c(+) DCs, CD4(+)CD11c(+) DCs up-regulate only type I IFN and a different set of Th2-associated cytokines and chemokines. Type I IFN, but not IFN-gamma, potentiates humoral immunity, notably production of VLP-specific IgG2a. However, HPV16 VLP-stimulated IL-12 production by CD8alpha(+)CD11c(+) DCs is augmented by autocrine IFN-gamma signaling. Thus, before adaptive immunity, HPV16 VLPs signal complementary defense responses in key DC subpopulations, indicating specialized DC lineages with predetermined polarization.
The Impact of Hybrid PET-CT Scan on Overall Oncologic Management, with a Focus on Radiotherapy Planning: A Prospective, Blinded Study (2009)

Functional imaging using fluorodeoxyglucose positron-emission tomography (FDG-PET) has been increasing incorporated into radiotherapy planning in conjunction with computed tomography (CT). Hybrid FDG-PET/CT scanners allow these images to be obtained in very close temporal proximity without the need for repositioning patients, thereby minimizing imprecision when overlying these images. To prospectively examine the impact of hybrid PET/CT imaging on overall oncologic impact, with a focus on radiotherapy planning, we performed a prospective, blinded trial in 111 patients. Patients with lung cancer (n=38), head-and-neck squamous cell carcinoma (n=23), breast (n=8), cervix (n=15), esophageal (n=9), and lymphoma (n=18) underwent hybrid PET/CT imaging at the time of radiation therapy planning. A physician blinded to the PET dataset designed a treatment plan using all clinical information and the CT dataset. The treating physician subsequently designed a second treatment plan using the hybrid PET/CT dataset. The two treatment plans were compared to determine if a major alteration in overall oncologic management occured. In patients receiving potentially curative radiotherapy the concordance between CT-based and PET/CT-based GTVs was quantified using an index of conformality (CI). In 76/111 (68%) of patients, the PET/CT data resulted in a change in one or more of the following: GTV volume, regional/local extension, prescribed dose, or treatment modality selection. In 35 of these 76 cases (46%; 31.5% of the entire cohort) the change resulted in a major alteration in the oncologic management (dose, field design, or modality change). Thus, nearly a third of all cases had a major alteration in oncologic management as a result of the PET/CT data, and 29 of 105 patients (27.6%) who underwent potentially curative radiotherapy had major alterations in either dose or field design. Hybrid PET/CT imaging at the time of treatment planning may be highly informative and an economical manner in which to obtain PET imaging, with the dual goals of staging and treatment planning.
Reconstructing metastatic seeding patterns of human cancers (2017)

Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15-95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods.
Design and Performance of an Automatic Control System for Fastener Tightening (1977)

Methods of controlling the tightness of bolted assemblies by presetting the torque or bolt rotation are reviewed. It is shown that these produce either inaccurate clamp loads or excessive elongation of the fastener. As a result the tightening operation is often the weakest link in obtaining a reliable assembly. The development of a system of tightening control that overcomes these problems is described. It operates by sensing the gradient of the torque-rotation characteristic, thus detecting the yield point of the fastener. In principle it requires no preset control torques or rotation angles. Comparative results show that the system increases bolt clamp loads and reduces their scatter very significantly.
The relationship of body mass index, belt placement, and abdominopelvic injuries in motor vehicle crashes: A Crash Injury Research and Engineering Network (CIREN) study (2021)

Utilizing CT scans to confirm ASBS and lap belt placement relative to the ASIS, superior belt placement above the ASIS was associated with elevated BMI and a trend of increasing incidence of internal abdominopelvic organ injury.
Synthesis and Polymerization of Liquid Crystalline Donor−Acceptor Monomers (1996)

The synthesis and polymerization of the following liquid crystalline monomers (containing both a vinyl ether group (electron donor) and a maleimide group (electron acceptor) within the same molecule) are described: 4-[(4-maleimidobenzoyl)oxy]phenyl 4-[[4-(vinyloxy)butyl]oxy]benzoate (1), 4-[[11-[(4-maleimidobenzoyl)oxy]undecyl]oxy]phenyl 4-[[4-(vinyloxy)butyl]oxy]benzoate (2), and 4-[[6-[(4-maleimidobenzoyl)oxy]hexyl]oxy]phenyl 4-[[4-(vinyloxy)butyl]oxy]benzoate (3). In the absence of photoinitiators, direct photolysis of a mixture of monomers 2 and 3, oriented in the nematic phase, led to initiation of polymerization and the formation of an ordered nematic LC polymer network. The use of a nonliquid crystalline model substance, N-[4-[[[4-(vinyloxy)butyl]oxy]carbonyl]phenyl]maleimide (4), showed that irradiation with a high-power microwave lamp, without the presence of photoinitiators, resulted in fast and efficient polymerization.
Design, Synthesis, and Progress toward Optimization of Potent Small Molecule Antagonists of CC Chemokine Receptor 8 (CCR8) (2006)

Activation of CCR8 by its ligand CCL1 may play an important role in diseases such as asthma, multiple sclerosis, and cancer. The study of small molecule CCR8 antagonists will help establish the validation of these hypotheses. We report the design, synthesis, and progress toward optimization of potent small molecule CCR8 antagonists identified from a high-throughput screen. These analogues exhibit good potency in binding and chemotaxis assays, show good selectivity versus the hERG channel, and have good eADME (early absorption, distribution, metabolism, and excretion) profiles.
Influence of "selective" antimuscarinic agents on gastric acid secretion and motility. (1985)

The effects of antimuscarinic agents, claimed as acting selectively on gastric acid secretion (pirenzepine) or gut motility (secoverine) or lacking selectivity (atropine and ipratropium bromide), were assayed on both functions by means of two simple experimental models: the gastric acid secretion induced by pylorus ligation and the gastric emptying of a high viscosity meal in the conscious rat. When the same experimental conditions were used in the two tests (i.v. route; duration of the test: 1 hr) we found that pirenzepine was not more selective than atropine on either function while ipratropium bromide was 16 times more selective for gastric secretion and secoverine 2.6 times more selective for gastric motility. Even if routes of administration and times of duration were different between the two tests, similar results were obtained. It was concluded that, when compared to atropine, in our in vivo experimental conditions pirenzepine and secoverine show a scant if any selectivity for either function, while, paradoxically, a sharp selectivity for gastric secretion is shown by the bronchodilator ipratropium bromide.
Effects of hand postures on voice directivity (2022)

While speaking, hand postures, such as holding a hand in front of the mouth or cupping the hands around the mouth, influence human voice directivity. This study presents and analyzes spherical voice directivity datasets of an articulated [a] with and without hand postures. The datasets were determined from measurements with 13 subjects in a surrounding spherical microphone array with 32 microphones and then upsampled to a higher spatial resolution. The results show that hand postures strongly impact voice directivity and affect the directivity index by up to 6 dB, which is more than variances caused by phoneme-dependent differences.
Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency (2012)

Background: Lignocellulosic biorefineries must be able to efficiently process the regional feedstocks that are available at cost-competitive prices year round. These feedstocks typically have low energy densities and vary significantly in composition. One potential solution to these issues is blending and/or densifying the feedstocks in order to create a uniform feedstock. Results & discussion: We have mixed four feedstocks – switchgrass, lodgepole pine, corn stover and eucalyptus – in flour and pellet form, and processed them using the ionic liquid 1-ethyl-3-methylimidazolium acetate. Sugar yields from both the mixed flour and pelletized feedstocks reach 90% within 24 h of saccharification. Conclusion: Mixed feedstocks, in either flour or pellet form, are efficiently processed using this pretreatment process, and demonstrate that this approach has significant potential.
ChemInform Abstract: Synthesis of Dictyopterene B (Hormosirene) and Its Enantiomer via Asymmetric SN Reactions. (1985)

Abstract Mit Hilfe der von (+)‐Campher abgeleiteten optisch aktiven Hilfs‐Alkohole (I) und (IV) werden mit hoher Selektivität die optisch aktiven trans‐Cyclopropancarbonsäureester (III) bzw. (V) erhalten, aus denen in drei Stufen mit hoher Selektivität Dictyopteren B (VII) bzw. sein Enantiomeres (VIII) hergestellt werden.
The Prion Protein Modulates A-type K+ Currents Mediated by Kv4.2 Complexes through Dipeptidyl Aminopeptidase-like Protein 6 (2013)

Widely expressed in the adult central nervous system, the cellular prion protein (PrP(C)) is implicated in a variety of processes, including neuronal excitability. Dipeptidyl aminopeptidase-like protein 6 (DPP6) was first identified as a PrP(C) interactor using in vivo formaldehyde cross-linking of wild type (WT) mouse brain. This finding was confirmed in three cell lines and, because DPP6 directs the functional assembly of K(+) channels, we assessed the impact of WT and mutant PrP(C) upon Kv4.2-based cell surface macromolecular complexes. Whereas a Gerstmann-Sträussler-Scheinker disease version of PrP with eight extra octarepeats was a loss of function both for complex formation and for modulation of Kv4.2 channels, WT PrP(C), in a DPP6-dependent manner, modulated Kv4.2 channel properties, causing an increase in peak amplitude, a rightward shift of the voltage-dependent steady-state inactivation curve, a slower inactivation, and a faster recovery from steady-state inactivation. Thus, the net impact of wt PrP(C) was one of enhancement, which plays a critical role in the down-regulation of neuronal membrane excitability and is associated with a decreased susceptibility to seizures. Insofar as previous work has established a requirement for WT PrP(C) in the Aβ-dependent modulation of excitability in cholinergic basal forebrain neurons, our findings implicate PrP(C) regulation of Kv4.2 channels as a mechanism contributing to the effects of oligomeric Aβ upon neuronal excitability and viability.
Striatal and extrastriatal dopamine D 2 receptor occupancy by the partial agonist antipsychotic drug aripiprazole in the human brain: a positron emission tomography study (2012)

Rationale Second-generation antipsychotics demonstrate clinical efficacy with fewer extrapyramidal side effects compared with first-generation antipsychotics. One of the proposed explanations is the hypothesis of preferential extrastriatal dopamine D2 receptor occupancy (limbic selectivity) by antipsychotics. In the present study, we focused on aripiprazole, which has a unique pharmacological profile with partialagonismatdopamineD2receptorsandtheminimalrisk of extrapyramidal side effects. Previous positron emission tomography (PET) studies using high-affinity radioligands for dopamine D2 receptors have reported inconsistent results regarding regional differences of dopamine D2 receptor occupancy by aripiprazole.
A Simplified Structure for FIR Filters with an Adjustable Fractional Delay (2007)

This paper introduces an efficient filter structure for implementing finite-impulse response (FIR) filters with an adjustable fractional delay. In this structure the first two subfilters are the same as in the modified Farrow structure, whereas the remaining ones are generated by properly combining these two subfilters with some additional very short filters, pure delay terms, adders, and multipliers. For significantly reducing the number of multipliers, the three-step synthesis scheme proposed by Yli-Kaakinen and Saramaki in the case of the modified Farrow structure is followed. First, the number of subfilters and their orders are determined such that the given criteria are sufficiently exceeded. Second, an initial filter is determined using a simple design scheme. This filter serves as a start-up solution for further optimization being performed using a constrained nonlinear optimization algorithm. Third, those coefficient values of the subfilters having a negligible effect on the overall system performance are fixed to be zero-valued. Both the performance and complexity of the proposed adjustable digital filters are compared with those of some existing adjustable FIR filters proposed in the literature. This comparison shows that, in the case of stringent amplitude and phase delay specifications, the number of multipliers for the proposed filters is less than 80 percent when compared with the corresponding optimized modified Farrow structure.
1200V SC(Schottky controlled injection)-diode, an advanced fast recovery concept with high carrier lifetime (2013)

In this paper, a 1200V novel PiN-diode concept realizing low forward voltage drop (VF), low reverse recovery loss and low leakage current at high temperature over 175°C has been proposed. To realize these above-mentioned characteristics, this concept of 1200V diode design adopts a combination of flat and linear distribution of carrier concentration from anode side to cathode side and reducing injection efficiency at both sides at forward bias condition. This carrier profile can also realize reduction of voltage ringing effectively at reverse condition. Furthermore, we have successfully obtained high reverse recovery ruggedness combining a new edge termination design with Schottky contact.
Hemorrhagic Enteritis in Turkeys: Purification and Quantification of the Virus (1983)

Two methods for purifying the virus of hemorrhagic enteritis from infected turkey spleens are described. One procedure utilized precipitation with polyethylene glycol, and the other consisted of trichlorotrifluoroethane extraction. Both procedures included sucrose-cesium chloride gradient centrifugation in the final purification step. The buoyant density of the viral fraction was 1.34 g/cm3, typical for adenoviral particles, and the size and morphologic characteristics of the virions observed by transmission electron microscopy suggested that the purified virus belongs to the family Adenoviridae. The biologic activity of the purified virus was titrated by inoculating 10-fold dilutions of the viral suspension into turkey poults. Mortality and hemorrhagic diarrhea proved to be inconsistent parameters of infection, and the degree of splenomegaly was proportional to the virus dose. The body/spleen ratio was the parameter selected for measuring viral activity, and the body/spleen ratio 50% was adopted as the unit for the titration of the virus. By using the same system it was demonstrated that the infectivity of the virus could be neutralized with antiserum produced in turkeys.
Comparing the effectiveness of peer instruction to individual learning during a chromatography course (2015)

Abstract Peer instruction has been recognized as an instructional method having a positive impact on learning compared to traditional lectures in science. This method has been widely supported by the socio‐constructivist approach to learning giving a positive role to interaction between peers in the construction of knowledge. As far as we know, no study has been conducted from the socio‐cognitive approach which suggests that individuals working alone perform better than those interacting with others in groups. Thus, the aim of the present study was to examine whether peer instruction improves learning when compared with an individual learning method that does not require any interaction with peers. After being randomly divided into either a peer instruction or an individual learning condition in a chromatography course, students had to answer to a series of multiple‐choice questions using clickers at the beginning (pre‐test) and end of (post‐test) the session. Results revealed that the percentage of correct answers increased similarly from the pre‐ to the post‐test in both conditions. Nevertheless, students perceived the peer instruction method as being more satisfying, engaging and useful than the individual learning method. The findings revealed that peer instruction provides subjective benefits, but failed to demonstrate a greater learning gain.
Characterizing Microblogs with Topic Models (2010)

As microblogging grows in popularity, services like Twitter are coming to support information gathering needs above and beyond their traditional roles as social networks. But most users’ interaction with Twitter is still primarily focused on their social graphs, forcing the often inappropriate conflation of “people I follow” with “stuff I want to read.” We characterize some information needs that the current Twitter interface fails to support, and argue for better representations of content for solving these challenges. We present a scalable implementation of a partially supervised learning model (Labeled LDA) that maps the content of the Twitter feed into dimensions. These dimensions correspond roughly to substance, style, status, and social characteristics of posts. We characterize users and tweets using this model, and present results on two information consumption oriented tasks.