gebhart/patrepeval huggingface dataset:
Photoaffinity Isolation and Identification of Proteins in Cancer Cell Extracts that Bind to Platinum‐Modified DNA (2008)

The activity of the anticancer drug cisplatin is a consequence of its ability to bind DNA. Platinum adducts bend and unwind the DNA duplex, creating recognition sites for nuclear proteins. Following DNA damage recognition, the lesions will either be repaired, facilitating cell viability, or if repair is unsuccessful and the Pt adduct interrupts vital cellular functions, apoptosis will follow. With the use of the benzophenone-modified cisplatin analogue Pt-BP6, 25 bp DNA duplexes containing either a 1,2-d(G*pG*) intrastrand or a 1,3-d(G*pTpG*) intrastrand crosslink were synthesized, where the asterisks designate platinated nucleobases. Proteins having affinity for these platinated DNAs were photocrosslinked and identified in cervical, testicular, pancreatic and bone cancer-cell nuclear extracts. Proteins identified in this manner include the DNA repair factors RPA1, Ku70, Ku80, Msh2, DNA ligase III, PARP-1, and DNA-PKcs, as well as HMG-domain proteins HMGB1, HMGB2, HMGB3, and UBF1. The latter strongly associate with the 1,2-d(G*pG*) adduct and weakly or not at all with the 1,3-d(G*pTpG*) adduct. The nucleotide excision repair protein RPA1 was photocrosslinked only by the probe containing a 1,3-d(G*pTpG*) intrastrand crosslink. The affinity of PARP-1 for platinum-modified DNA was established using this type of probe for the first time. To ensure that the proteins were not photocrosslinked because of an affinity for DNA ends, a 90-base dumbbell probe modified with Pt-BP6 was investigated. Photocrosslinking experiments with this longer probe revealed the same proteins, as well as some additional proteins involved in chromatin remodeling, transcription, or repair. These findings reveal a more complete list of proteins involved in the early steps of the mechanism of action of the cisplatin and its close analogue carboplatin than previously was available.
Heat Intolerance in Patients With Chronic Schizophrenia Maintained With Antipsychotic Drugs (2000)

Schizophrenic patients maintained on antipsychotic drugs exhibit impaired heat tolerance. Possible explanations are a reduced ability to convey heat from the body's core to the periphery with or without excessive heat production. The hyperthermic response to the heat tolerance test may reflect a dysfunction associated with schizophrenia, a neuroleptic-induced side effect, or both.
Hypervalent Iodine(III) Reagents as Safe Alternatives to α-Nitro-α-diazocarbonyls (2003)

A cyclopropanation reaction involving iodonium ylides generated in situ allows for efficient preparation of substituted 1-nitro-1-carbonyl cyclopropanes. This robust cyclopropanation reaction can be performed in organic solvents, biphasic aqueous media, or under solvent-free conditions with alkene substrates. The iodonium ylides generated in situ display some surprising differences in reactivity when compared to alpha-nitro-alpha-diazocarbonyl compounds. They do not undergo O-H insertion reactions and exhibit reduced reactivity with certain alkenes. [reaction: see text]
Supplementary Figures from CD137/OX40 Bispecific Antibody Induces Potent Antitumor Activity that Is Dependent on Target Coengagement (2023)

&lt;p&gt;Supplementary Figures 1-10&lt;/p&gt;
Pretrain Knowledge-Aware Language Models (2021)

How much knowledge do pretrained language models hold? Recent research observed that pretrained transformers are adept at modeling semantics but it is unclear to what degree they grasp human knowledge, or how to ensure they do so. In this paper we incorporate knowledge-awareness in language model pretraining without changing the transformer architecture, inserting explicit knowledge layers, or adding external storage of semantic information. Rather, we simply signal the existence of entities to the input of the transformer in pretraining, with an entity-extended tokenizer; and at the output, with an additional entity prediction task. Our experiments show that solely by adding these entity signals in pretraining, significantly more knowledge is packed into the transformer parameters: we observe improved language modeling accuracy, factual correctness in LAMA knowledge probing tasks, and semantics in the hidden representations through edge probing. We also show that our knowledge-aware language model (\kalm{}) can serve as a drop-in replacement for GPT-2 models, significantly improving downstream tasks like zero-shot question-answering with no task-related training.
Time-Interleaved Carrier-Suppressed Return-to-Zero QPSK for Filter-less Dual-Carrier Transmission (2014)

We demonstrate time-interleaved carrier-suppressed return-to-zero (TI-CSRZ) signaling, aiming for high-spectral-efficiency dual-carrier transmission. Optical filter-less modulation and demodulation schemes are proposed, achieving 40-Gb/s TI-CSRZ-QPSK.
Developmental photochemistry. Norrish Type II reaction (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDevelopmental photochemistry. Norrish Type II reactionDouglas C. Neckers, Richard M. Kellogg, W. L. Prins, and B. SchoustraCite this: J. Org. Chem. 1971, 36, 13, 1838–1840Publication Date (Print):July 1, 1971Publication History Published online1 May 2002Published inissue 1 July 1971https://pubs.acs.org/doi/10.1021/jo00812a028https://doi.org/10.1021/jo00812a028research-articleACS PublicationsRequest reuse permissionsArticle Views408Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
New Variotin Analogues from Aspergillus viridi-nutans (2000)

Besides the antifungal agents variotin (1), wasabidienone B(0) (4), and phomaligin A (5), two new but inactive metabolites, viriditin (2) and O-methylviriditin (3), were isolated from extracts of the culture filtrate of liquid cultures of a strain of Aspergillus viridi-nutans. In addition, wasabidienone B(1) (6) was isolated and characterized by spectroscopy.
Dynamical Heterogeneity in the Thermodynamically Miscible Polymer Blend of Poly(vinyl ethyl ether) and Styrene-co-p-hydroxystyrene Copolymer (2003)

The dynamic heterogeneity of the thermodynamically miscible blend of poly(vinyl ethyl ether) and styrene-co-p-hydroxystyrene (PVEE/SHS) has been investigated using broadband dielectric spectroscopy (DRS) and other experimental probes. In our previous study of PVEE/poly(p-hydroxystyrene) blends, we found that the segmental relaxations of the component polymers can be coupled if there is sufficient intermolecular hydrogen bonding. For SHS/PVEE blends, however, two segmental relaxations are observed in the DRS spectra, even for blends with a fraction of intermolecular hydrogen bonds as large as that in the PVPh/PVEE blend, in which a single segmental relaxation was found as a result of the coupling effect from the hydrogen bonds. This behavior is explained by the existence of unfavorable interactions between PVEE and the styrene units in SHS, which is supported by the immiscibility between PS and PVEE. The repulsive force endows the non-hydrogen-bonded PVEE segments with more freedom to relax, so that they can be distinguished from the relaxation of intermolecularly hydrogen-bonded PVEE−SHS segments. This indicates more significant dynamic heterogeneity in SHS/PVEE than in PVEE/poly(p-hydroxystyrene) blends.
In situ small angle x-ray studies of coal gasification (1983)

This report summarizes the progress made the first 12 months of a planned 36 month project on small angle x-ray studies of coal and char pore structure. Model carbon studies have been employed to demonstrate the usefulness of small angle x-ray scattering (SAXS) in monitoring the structural changes in porous carbonaceous materials during gasification. Scattering data from particles gasified to varying levels of conversion show increases in the micropore sizes with conversion. This is also supported by surface area measurements by SAXS showing a maximum at intermediate conversion in agreements with previous studies by conventional means. The application of SAXS to PSOC coal samples is also demonstrated. Existing models for the porous structure have been reviewed and percolation theory has been selected as a consistent framework for both the modelling and the data analysis. This theory will make it possible to describe the porous structure in terms of its geometry and connectivity, rather than being limited to a fixed geometry as in conventional approaches. Two graduate students and the PI have been trained in SAXS and the associated theory. Results from the model carbon studies have been published. 18 references, 9 figures, 2 tables.
A novel concept for mains voltage proportional input current shaping of a VIENNA rectifier eliminating controller multipliers. II. Operation for heavily unbalanced mains phase voltages and in wide input voltage range (2002)

For pt. I see ibid., p.582-6 (2001). Part II shows the operation of a three phase PWM (VIENNA) rectifier operating with symmetric and heavily unbalanced mains voltage for application of a conventional phase current control and for the novel multiplier free current control concept. Taking into consideration the additional parts which are required in equal form for both concepts (input current measurement, output voltage measurement and control, supervisory functions and microcontroller), the saving in board space will be, however, only in the range of about 10%. A further advantage of the multiplier free control concept is that no information about the sign or magnitude of the input phase voltages is required for performing the control function. Furthermore, in contrast to the conventional control concept there is no requirement of an adjustment of the amplitude of the triangular shaped carrier signal and of the amplitude of rectangular shaped pre-control signal to the rectifier voltage transfer ratio. This would be especially advantageous for applications where the output voltage level is considered as a degree of freedom for maximizing the efficiency of the rectifier in combination with a DC-to-DC converter connected in series at the output. A drawback of the multiplier free control concept is the requirement of generating two unipolar triangular shaped carrier signals with adjustable amplitude and high accuracy.
Haematological disorders in adult patients with congenital heart disease (2002)

s: European Association of Cardiothoracic Anaesthesiologists; 17th Annual Meeting; Dublin, Ireland; June 12-15, 2002: Coagulation and Transfusion
A Yaw Rate Based Stability Control for Under-Actuated Vehicles (2020)

Full electric vehicles (FEVs) are becoming more and more common. For these vehicles, a widely adopted driveline configuration consists in all-wheel drive (AWD) technology realized by independently drive front and rear axles. In this paper, we investigate the possibility of implementing an electronic stability control (ESC) exploiting only front and rear motor torques. The proposed control is robust with respect to friction variation and easily tunable thanks to a control allocation that permits single-input single-output formulation. The allocator is based on a multi-dimensional linearized tire model that accounts for longitudinal and lateral slip. Despite being an under-actuated configuration, incapable of generating arbitrary yaw moments, experimental tests show that this configuration still passes the EU homologation tests for ESC.
Mesenchymal condensation‐dependent accumulation of collagen VI stabilizes organ‐specific cell fates during embryonic tooth formation (2015)

These findings suggest that the odontogenic differentiation process that is induced by cell compaction during mesenchymal condensation is stabilized and sustained through mechanically regulated production of collagen VI within the mesenchymal ECM.
Synthesis and regulation of the two human complement C4 genes in stable transfected mouse fibroblasts. (1987)

The major histocompatibility complex-linked human complement C4 genes are highly homologous in primary structure but give rise to products which differ in complement-activating function. In order to examine the synthesis, function, and regulation of these two genes independently, cloned C4A and C4B genes were transfected into mouse fibroblast L-cells. In the stable transfected cell lines, C4A and C4B are synthesized, undergo a complex series of post-translational modifications, and each functions appropriately in activation of the classical complement pathway. A marked difference in the kinetics of complement component C1-mediated cleavage of the C4A- and C4B-alpha chains was demonstrated in the transfectants and may contribute to the differences in the intrinsic functional activity of the two C4 isotypes. In contrast to the expression of other complement genes which are affected during the hepatic acute phase response (factor B, C3), the expression of C4 was not regulated by interleukin-1 or tumor necrosis factor. Interferon-gamma, however, mediated a dose- and time-dependent increase in the expression of the C4 genes. Moreover, interferon had a significantly greater and longer-lasting effect on the synthesis of C4A than that of C4B. Differences in the expression and regulation of these two genes provide insight into the control of complement activation during inflammation.
Guidelines for Evaluation of Error Structure for Impedance Response of Polymer Electrolyte Membrane (PEM) Fuel Cells (2008)

Impedance spectroscopy provides the opportunity for in-situ identification and quantification of physical processes in any electrochemical system. However, the impedance response is influenced by instrumental artifacts and non-stationary behavior. General guidelines, based on use of a measurement model, are outlined for estimation of an error structure of impedance measurements. The methodology is applied to estimate error in the impedance response of a Polymer Electrolyte Membrane (PEM) fuel cell. The analysis was used to show that low-frequency inductive loops in impedance response of the fuel cell were, in some cases, fully self consistent, and could therefore be attributed to processes occurring in the fuel cell. The error analysis was also used to improve the sensitivity of the impedance to onset of flooding in the fuel cell.
Biomechanical Analysis of the Ross Procedure in an Ex Vivo Left Heart Simulator (2022)

Neo-aortic pulmonary roots demonstrated equivalence in valve function and distensibility but did experience changes in biomechanical properties and morphology. These changes may contribute to long-term complications associated with the Ross procedure.
Enhanced polarization of embryonic hippocampal neurons on micron scale electrospun fibers (2009)

Electrospun fibers have been fabricated for wide use as artificial tissue engineering scaffolds. In particular, fibers smaller than a cell body have been extensively employed to mimic natural extracellular matrix (ECM) and to explore specific responses by various cell types. We investigated the effects of various poly(lactic acid-co-glycolic acid) (PLGA) fiber features on embryonic hippocampal neurons in the early developmental stages in terms of initial axon formation (i.e., polarization) and axon orientation. We produced PLGA fibers that have average diameters ranging from 0.44 microm to 2.2 microm and different degrees of fiber alignment (16-58 degrees in angular standard deviation). After 22 h in culture, embryonic hippocampal neurons grown on PLGA fibers exhibited more axon formation with a 30-50% increase over those on spin-coated smooth PLGA films. This improvement was independent of fiber diameter and alignment; however, slightly more polarization was observed on the smaller fibers and the more aligned fibers. In addition, average axon length of the polarized embryonic hippocampal neurons was not significantly different among the PLGA fibers when compared with cells grown on spin-coated PLGA films. These findings suggest that fibers of subcellular diameters stimulate initial axon establishment and guide the direction of axonal extension; however, these fibers do not appear to affect the overall axon length. This information will be valuable in understanding the roles of subcellular features on neuron development and for the design of biomaterials for neural tissue interfacing.
Real-Time Embedded Models for Simulation and Control of Clean and Fuel-Efficient Heavy-Duty Diesel Engines (2020)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper presents a framework for modeling a modern diesel engine and its aftertreatment system which are intended to be used for real-time implementation as a virtual engine and in a model-based control architecture to predict critical variables such as fuel consumption and tailpipe emissions. The models are specifically able to capture the impact of critical control variables such as the Exhaust Gas Recirculation (EGR) valve position and fuel injection timing, as well as operating conditions of speed and torque, on the engine airpath variables and emissions during transient driving conditions. To enable real-time computation of the models, a minimal realization of the nonlinear airpath model is presented and it is coupled with a cycle averaged NOx emissions predictor to estimate feed gas NOx emissions. Then, the feedgas enthalpy is used to calculate the thermal behavior of the aftertreatment system required for prediction of tailpipe emissions. The complete engine and aftertreatment system models were implemented on a rapid prototyping controller and experimentally validated over steady state and transient test cycles. Results show the performance of the reduced order model was comparable to that of the full state model in predicting the transient behavior of engine airpath dynamics and NO&lt;sub&gt;X&lt;/sub&gt; emissions. With an integrated torque controller equipped with a Smith predictor that cancels communication delays, the developed models present a complete setup which can be used both as a virtual engine setup or serve in engine simulation environment or in a mode-based controller design.&lt;/div&gt;&lt;/div&gt;
Native Disulfide Bonds in Plasma Retinol-Binding Protein Are Not Essential for All-trans-Retinol-Binding Activity (2003)

A human plasma retinol-binding protein (RBP) mutant, named RBP-S, has been designed and produced in which the six native cysteine residues, involved in the formation of three disulfide bonds, have been replaced with serine. A hexa-histidine tag was also added to the C-terminus of RBP for ease of purification. The removal of the disulfide bonds led to a decrease in the affinity of RBP for all trans-retinol. Data indicates all-trans-retinol binds RBP and RBP-S with Kd = 4 x 10(-8) M and 1 x 10(-7) M, respectively, at approximately 20 degrees C. RBP-S has reduced stability as compared to natural RBP below pH 8.0 and at room temperature. Circular dichroism in the far-UV shows that there is a relaxation of the RBP structure upon the removal of its disulfide bonds. Circular dichroism in the near-UV shows that in the absence of the disulfide bonds, the optical activity of RBP is higher in the 310-330 nm than in the 280-290 nm range. This work suggests that the three native disulfide bonds aid in the folding of RBP but are not essential to produce a soluble, active protein.
2-Aminophenols Containing Electron-Withdrawing Groups from N-Aryl Hydroxylamines (2010)

Reaction of substituted N-aryl hydroxylamines with methanesulfonyl chloride, p-toluenesulfonyl chloride, or trifluoromethanesulfonic anhydride under basic conditions leads to the rearranged 2-aminophenols (45-94%). The overall reaction sequence can be performed using polymer-supported sulfonyl chloride resin allowing for the effective conversion of N-aryl hydroxylamines to the 2-aminophenols without the need for chromatography.
An Essential Role of the Mitochondrial Electron Transport Chain in Cell Proliferation Is to Enable Aspartate Synthesis (2015)

The mitochondrial electron transport chain (ETC) enables many metabolic processes, but why its inhibition suppresses cell proliferation is unclear. It is also not well understood why pyruvate supplementation allows cells lacking ETC function to proliferate. We used a CRISPR-based genetic screen to identify genes whose loss sensitizes human cells to phenformin, a complex I inhibitor. The screen yielded GOT1, the cytosolic aspartate aminotransferase, loss of which kills cells upon ETC inhibition. GOT1 normally consumes aspartate to transfer electrons into mitochondria, but, upon ETC inhibition, it reverses to generate aspartate in the cytosol, which partially compensates for the loss of mitochondrial aspartate synthesis. Pyruvate stimulates aspartate synthesis in a GOT1-dependent fashion, which is required for pyruvate to rescue proliferation of cells with ETC dysfunction. Aspartate supplementation or overexpression of an aspartate transporter allows cells without ETC activity to proliferate. Thus, enabling aspartate synthesis is an essential role of the ETC in cell proliferation.
Protective Role of Limitrin in Experimental Autoimmune Optic Neuritis (2021)

Limitrin deficiency induced severe neuroinflammation and reactive gliosis in the optic nerve after EAON induction. Our results imply that astrocyte-derived limitrin may protect against neuroinflammation by decreasing immune cell infiltration into the optic nerve. The plasma limitrin level may reflect the extent of blood-brain barrier disruption and provide a valuable biomarker reflecting the severity of optic neuritis.
A high-throughput deterministic lateral displacement device for rapid and sensitive field-diagnosis of sleeping sickness (2012)

We present a simple and rapid microfluidic device capable of extracting and concentrating the parasite causing the fatal disease sleeping sickness (SS) from blood. The device is based on deterministic lateral displacement (DLD) and constructed with a single inlet with flow induced by an ordinary syringe. The simplicity is crucial as the device is intended for use in the resource depraved areas where the disease is endemic. With only one inlet an intricate design with multiple depths has been utilized to create a cell free stream from the blood plasma into which the parasites are forced and subsequently collected in a detection region. In order to maximize the sample volume up to 10 device layers were stacked on top of each other which resulted in a throughput of ∼10 μL/min. This allowed for an approximate time per test of below 15 min.
Effect of Aerosol Devices and Administration Techniques on Drug Delivery in a Simulated Spontaneously Breathing Pediatric Tracheostomy Model (2015)

In this in vitro pediatric breathing model with a TT, the pMDI delivered the highest IM%, whereas the vibrating mesh nebulizer delivered the highest IM. The jet nebulizer was the least efficient device. Delivery efficiency was similar with unassisted and assisted administration techniques.