gebhart/patrepeval huggingface dataset:
Cover Picture: Structural Basis of Bcl‐xL Recognition by a BH3‐Mimetic α/β‐Peptide Generated by Sequence‐Based Design (ChemBioChem 13/2011) (2011)

The cover picture shows representations of death-inducing BH3 peptides in complex with the anti-apoptotic protein Bcl-xL. Of the four structures, three are naturally occurring BH3 peptides comprising only α-amino acids. However, one of them is a designer α/β-peptide containing β-amino acid residues distributed periodically throughout the sequence. (Question: Can you spot the difference?) Such unnatural backbones are less susceptible to enzymatic degradation than their α-peptide counterparts, thus making them more appealing for use in biological systems. The structure described by S. H. Gellman, W. D. Fairlie et al. on p. 2025 ff. demonstrates that side chains from this α/β-peptide successfully mimic the noncovalent interactions previously identified as critical for binding prosurvival proteins. Further geometric analysis reveals the mechanism by which the α/β-peptide backbone recapitulates the multipoint interaction of the α-helical prototype. Such structural studies provide useful insights into successful α-helix mimicry with sequence-based design strategies. (Answer: The α/β-peptide is in the bottom right panel.)
Cationic Surface Reconstructions on Cerium Oxide Nanocrystals: An Aberration-Corrected HRTEM Study (2011)

Instabilities of nanoscale ceria surface facets are examined on the atomic level. The electron beam and its induced atom migration are proposed as a readily available probe to emulate and quantify functional surface activity, which is crucial for, for example, catalytic performance. In situ phase contrast high-resolution transmission electron microscopy with spherical aberration correction is shown to be the ideal tool to analyze cationic reconstruction. Hydrothermally prepared ceria nanoparticles with particularly enhanced {100} surface exposure are explored. Experimental analysis of cationic reconstruction is supported by molecular dynamics simulations where the Madelung energy is shown to be directly related to the binding energy, which enables one to generate a visual representation of the distribution of "reactive" surface oxygen.
ChemInform Abstract: cis‐ and trans‐3‐Azido‐oxetane‐2‐carboxylate Scaffolds: Hexamers of Oxetane cis‐β‐Amino Acids. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
IoT Applications on Secure Smart Shopping (2016)

We propose to design a smart shopping system based on RFID. The smart carts used in such a system can navigate the customers to the desired products, and they can calculate the billing information as the customer shops. Items that are put in a smart shopping cart can be automatically recognized and billed. In this way, customers can avoid long queuing time at the check-out points. The grocery management also becomes much easier: The sensors on the grocery shelf can keep updating the number of items to the central server so that the server is always aware of the items' status in the store. Furthermore, the inventory management also becomes much easier, because all the items can be automatically read by a RFID reader instead of manually scanned by a laborer. In this paper, we propose a smart shopping cart system with consideration of how this system can work functionally and securely.
Influenza Epidemics (2006)

Abstract Influenza viruses can cause either limited or worldwide epidemics (pandemics), during which acute febrile respiratory disease spreads rapidly among all age groups, accompanied by excess hospitalization and death. Influenza virus replication and adaptation to new hosts account for much of the evolutionary success of these viruses. Several influenza pandemics are described, and clinical features, control and immunity discussed.
Optimal multistream sequential prefetching in a shared cache (2007)

Prefetching is a widely used technique in modern data storage systems. We study the most widely used class of prefetching algorithms known as sequential prefetching . There are two problems that plague the state-of-the-art sequential prefetching algorithms: (i) cache pollution , which occurs when prefetched data replaces more useful prefetched or demand-paged data, and (ii) prefetch wastage , which happens when prefetched data is evicted from the cache before it can be used. A sequential prefetching algorithm can have a fixed or adaptive degree of prefetch and can be either synchronous (when it can prefetch only on a miss) or asynchronous (when it can also prefetch on a hit). To capture these distinctions we define four classes of prefetching algorithms: fixed synchronous (FS), fixed asynchronous (FA), adaptive synchronous (AS), and adaptive asynchronous (AsynchA). We find that the relatively unexplored class of AsynchA algorithms is in fact the most promising for sequential prefetching. We provide a first formal analysis of the criteria necessary for optimal throughput when using an AsynchA algorithm in a cache shared by multiple steady sequential streams. We then provide a simple implementation called AMP (adaptive multistream prefetching) which adapts accordingly, leading to near-optimal performance for any kind of sequential workload and cache size. Our experimental setup consisted of an IBM xSeries 345 dual processor server running Linux using five SCSI disks. We observe that AMP convincingly outperforms all the contending members of the FA, FS, and AS classes for any number of streams and over all cache sizes. As anecdotal evidence, in an experiment with 100 concurrent sequential streams and varying cache sizes, AMP surpasses the FA, FS, and AS algorithms by 29--172%, 12--24%, and 21--210%, respectively, while outperforming OBL by a factor of 8. Even for complex workloads like SPC1-Read, AMP is consistently the best-performing algorithm. For the SPC2 video-on-demand workload, AMP can sustain at least 25% more streams than the next best algorithm. Furthermore, for a workload consisting of short sequences, where optimality is more elusive, AMP is able to outperform all the other contenders in overall performance. Finally, we implemented AMP in the state-of-the-art enterprise storage system, the IBM system storage DS8000 series. We demonstrated that AMP dramatically improves performance for common sequential and batch processing workloads and delivers up to a twofold increase in the sequential read capacity.
Would You Like to Do it Yourself? Service Requests and Their Non-granting Responses (2005)

Many organizations have inherently conflicting goals when it comes to customer service. On the one hand, they must provide their customers with the service they desire to ensure a large, loyal patronage. On the other hand, the cost of providing those services can become very expensive and thus curtail an organization’s profitability. In order to remain solvent, organizations must keep the cost of providing customer service within bounds. Almost inevitably, this will result in a circumscription of services; some customer requests simply cannot be granted.
THERMODYNAMICS OF WETTING (1973)

The thermodynamics of a solid-liquid-vapor system both under chemical equilibrium and non-equilibrium conditions, based on the model of Gibbs, is discussed.Under chemical equilibrium conditions, the degree of wetting or non-wetting of a flat and non-deformable solid by the liquid is defined by Young's equation in terms of the static interfacial tensions.Under chemical non-equilibrium conditions, mass transfer across an interface results in a transient decrease in the corresponding
Phosphoprotein pathway mapping: AKT/mTOR activation is negatively associated with childhood Rhabdomyosarcoma survival (2006)

B72 The elucidation of the kinase-driven signaling pathways within tumors can identify new targets for therapy and provide a means to stratify patients for individualized therapy. Despite advances in combination chemotherapy, the overall survival for childhood rhabdomyosarcoma (RMS) remains approximately 60% . A critical goal is to identify functionally important protein signaling defects associated with treatment failure for the 40% non-responder cohort. Here we show, by phospho-proteomic network analysis of microdissected tumor cells, that inter-linked components of the Akt/mTOR pathway exhibited increased levels of phosphorylation for tumors of patients with short term survival.Frozen tumor specimens (n=59) were obtained from the Children9s Oncology Group Intergroup Rhabdomyosarcoma Study (IRS) IV, D9502 and D9803, with 12 year clinical follow-up. Reverse phase protein microarrays were used to interrogate the in vivo IRS-1/Akt/mTOR phosphoprotein circuits of microdissected childhood Rhabdomyosarcoma samples.High phosphorylation levels were associated with poor overall (OAS) and poor disease-free (DFS) survival (Akt Ser473 (OAS p
Faculty Opinions recommendation of Masking epilepsy by combining two epilepsy genes. (2007)

Inherited errors in ion channel genes comprise the largest subset of monogenic causes of idiopathic epilepsy, and pathogenic variants contribute to genetic risk in the complex inheritance of this common disorder. We generated a digenic mouse model of human idiopathic epilepsy by combining two epilepsy-associated ion channel mutations with mutually opposing excitability defects and overlapping subcellular localization. We found that increasing membrane excitability by removing Shaker-like K(+) channels, which are encoded by the Kcna1 gene, masked the absence epilepsy caused by a P/Q-type Ca(2+) channelopathy due to a missense mutation in the Cacna1a gene. Conversely, decreasing network excitability by impairing Cacna1a Ca(2+)-channel function attenuated limbic seizures and sudden death in Kcna1-null mice. We also identified intermediate excitability phenotypes at the network and axonal levels. Protective interactions between pathogenic ion channel variants may markedly alter the clinical expression of epilepsy, highlighting the need for comprehensive profiling of this candidate gene set to improve the accuracy of genetic risk assessment of this complex disease. PMID: 17982453 Funding information This work was supported by: NINDS NIH HHS, United States Grant ID: NS43124 NINDS NIH HHS, United States Grant ID: NS29709
Thermal properties of cellulose triacetate as prepared from low-grade dissolving pulp (1996)

Because cellulose triacetate is prepared from low-grade dissolving pulp, a considerable amount of the insoluble residue was present in the acetylation medium of the acetic acid/acetic anhydride/sulfuric acid system. To reduce the insoluble residues, a solvent, such as nitromethane, nitroethane, or dichloroacetic acid, added to the acetylation medium was found to be very effective for its reduction. By exploring the optimum conditions for acetylation with these solvents, nitromethane added and dichloroacetic acid added systems with solvent/acetic acid = 3/7 (v/v) were found to have a particularly high transmittance at λ = 670 nm in their acetylation solution with a low insoluble residue. The obtained acetates revealed good thermal properties similar to that from high-grade dissolving pulps. Therefore, a high quality cellulose triacetate can be manufactured from acetylation systems with even low-grade dissolving pulps with an appropriate solvent added. © 1996 John Wiley & Sons, Inc.
Combined Ion Mobility/Time-of-Flight Mass Spectrometry Study of Electrospray-Generated Ions (1997)

A commercially available ion mobility spectrometer was interfaced to a custom-built linear time-of-flight (TOF) mass spectrometer for the purpose of examining electrospray-generated plumes. Ionic species that were separated in the ion mobility spectrometer could be selectively determined with the TOF mass spectrometer. Tetraalkylammonium salts, a peptide, and proteins were examined. Their ion mobility spectra typically comprised a few peaks; some of these mobility-resolved species produced characteristic electrospray ions, while others of lower relative mobility did not. The TOF mass spectra of cytochrome c, injected from the ion mobility spectrometer at an indicated temperature of 90 °C or lower, showed signs that were characteristic of protein-solvent clustering.
Involvement of complement activation in the pulmonary vasoactivity of polystyrene nanoparticles in pigs: unique surface properties underlying alternative pathway activation and instant opsonization (2018)

PS-NPs have extreme surface properties with no relevance to clinically used nanomedicines. They can activate C via the alternative pathway, entailing instantaneous opsonization of NPs in pig serum. Therefore, rather than being solely C-independent reactivity, the mechanism of PS-NP-induced hypersensitivity in pigs may involve C activation. These data are consistent with the "double-hit" concept of nanoparticle-induced hypersensitivity reactions involving both CARPA and C-independent pseudoallergy.
Lack of Glucocorticoids Sustains the Stress-Induced Release of Noradrenaline in the Anterior Hypothalamus (1993)

The release of endogenous noradrenaline in the anterior hypothalamus was studied with microdialysis perfusion in freely moving rats that were subjected to immobilization stress. Experiments were carried out in sham-adrenalectomized and adrenalectomized rats that were first given drinking water containing corticosterone for 5 days following surgery and then switched to a corticosterone-free diet the day before stress application. One group of these adrenalectomized animals was injected with dexamethasone. Basal release of noradrenaline collected in 20-min fractions was similar in the three groups of animals and averaged 24 fmol. The recovery of the probe was about 10%. In sham-adrenalectomized rats application of 20-min immobilization stress increased noradrenaline release to 310% of baseline in the sample collected during stress application. A significant increase (+ 175% of baseline) was still observed in the next 20-min sample. Subsequent values were all identical to baseline. In adrenalectomized rats lacking exogenous corticosterone the stress-induced release of noradrenaline was prolonged with noradrenaline levels remaining elevated for 2 h after the onset of stress. The total noradrenaline release during this entire period was about 2.5 times higher in adrenalectomized than in sham-operated rats. However, the maximal increase during the period of immobilization was not significantly affected. Treatment with dexamethasone prevented the prolonged increase in noradrenaline release but did not affect the increase during the period of stress. While glucocorticoids do not appear to affect the increased release of NA in the anterior hypothalamus during the period of stress, they act to limit the duration of this activation after the application of stress.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis and Biological Activity of a Novel 11a-Homo (Cyclohexyl) Prostaglandin (2000)

The racemic cyclohexane-for-cyclopentane ring substitution analogue of the potent prostaglandin FP agonist cloprostenol (7) was synthesized from cyclohexenediol 11 in 21 steps and 0.07% yield. In a prostaglandin FP receptor-linked second-messenger assay, racemic analogue 7 exhibited an EC(50) value of 319 nM (72% response relative to cloprostenol); the corresponding values for PGF(2)(alpha) and cloprostenol were 23 nM (91% relative response) and 1 nM (defined as 100% response), respectively. Key features of the synthesis were the selective manipulation of four hydroxyl groups to direct independent elaboration of the alpha and omega chains and a new method for synthesis of aryloxy-terminated omega chains involving Horner-Emmons elongation of an aldehyde to a methyl enone, regioselective bromination adjacent to the carbonyl, and phenoxide displacement of bromide.
Supplementary Table S3 from A Dendritic Cell Vaccine Pulsed with Autologous Hypochlorous Acid-Oxidized Ovarian Cancer Lysate Primes Effective Broad Antitumor Immunity: From Bench to Bedside (2023)

&lt;p&gt;Supplementary Table S3 - PDF file 156K, Toxicities observed in ovarian cancer subjects following OCDC administrations&lt;/p&gt;
Trichomes: interaction sites of tomato leaves with biotrophic powdery mildew pathogens (2017)

The present study aimed to explore the possibility of using the type I trichomes of tomato (Solanum lycopersicum) to monitor the infection processes of powdery mildews by microscopy. Individual trichome cells of two tomato genotypes were inoculated with pathogenic and non-pathogenic powdery mildew species, Pseudoidium neolycopersici, Erysiphe trifoliorum and Podosphaera xanthii. On the trichome cells of the tomato cultivar Moneymaker, hyphae of the pathogenic Pseudoidium neolycopersici (isolates KTP-03 and KTP-04) grew vigorously; whereas hyphal growth of the non-pathogenic Erysiphe trifoliorum and Podosphaera xanthii ceased after appressorium formation, which was associated with papilla formation and hypersensitive cell death, respectively. Similar infection processes of the tested powdery mildews were seen in Moneymaker epidermal cells. Therefore, tomato trichomes are suitable for analysing, at individual cell level, the infection processes of different pathotypes of powdery mildews and for observing the cytological responses of plants by non-pathogenic powdery mildews. On the other hand, it was observed that both isolates KTP-03 and KTP-04 failed to produce conidiophores on the hyphae elongating on Moneymaker trichomes. Similarly, no conidiophores were produced on the hyphae elongating on trichomes of Solanum peruvianum LA2172, which is resistant to KTP-03 and susceptible to KTP-04. Interestingly, delayed cell death occurred in LA2172 epidermal cells, which were attacked by KTP-03 hyphae elongating from trichomes and conidiophores were formed on new hyphae growing from the leaf epidermal cells. Thus, leaf trichomes and epidermal cells of the wild tomato species LA2172 reacted differently to the avirulent isolate KTP-03.
Dual-mode Ultra Reliable Low Latency Communications for Industrial Wireless Control (2022)

This paper studies communications service availability for industrial wireless control systems. We consider a motion controller with a continuous closed-loop control link to a group of actuator devices on a factory floor. The goal is to satisfy end-to-end latency for each packet and to guarantee that the communication service will not be un-available for longer than a survival time. We propose to decouple the scheduling operation between the normal and survival modes of operation, enabling a dual-mode ultra-reliable and low-latency communications (URLLC) scheduler. Scheduler strategies for the survival mode are presented, targeting link adaptation and signal to interference and noise ratio (SINR) estimation in presence of temporal and spatial channel correlation. Through numerical examples, we investigate the impact of channel correlation on the schedulers ability to target the required reliability for each mode. We further present our findings on system-level performance evaluation of such scheduling strategies by adopting a realistic system setup and channel model to obtain insights with high level of realism. Extensive simulation results are presented which demonstrate significant reduction in resource utilization with the proposed dual-mode scheduler when compared to single-mode URLLC scheduling. Specifically, our results demonstrate that the scheduler should target moderate packet error rate (PER) for normal mode of operation and very low PER for the survival mode; the latter guarantees service availability while the former saves radio resources.
Hydrogen Storage and Electrode Properties of V-Based Solid Solution Type Alloys Prepared by a Thermic Process (2000)

A vanadium‐based solid‐solution‐type alloy with a large discharge capacity was obtained using a low‐cost precursor of produced by aluminothermic reduction from , , and Ni. The alloy was deoxidized to a low level by adding mischmetal as a reducing agent when the precursor was alloyed with Ti, Co, and Ta. The alloy showed a hydrogen absorption behavior similar to an alloy prepared from high‐purity constituent metals. Moreover, the Mm‐Ni‐O phase was precipitated as spherical particles along the TiNi network phase in the alloy, remarkably improving the electrode rate capability because of enhanced catalytic ability of the network phase. © 2000 The Electrochemical Society. All rights reserved.
Dual Site-Specific Chemoenzymatic Antibody Fragment Conjugation Using CRISPR-Based Hybridoma Engineering (2021)

Functionalized antibodies and antibody fragments have found applications in the fields of biomedical imaging, theranostics, and antibody-drug conjugates (ADC). In addition, therapeutic and theranostic approaches benefit from the possibility to deliver more than one type of cargo to target cells, further challenging stochastic labeling strategies. Thus, bioconjugation methods to reproducibly obtain defined homogeneous conjugates bearing multiple different cargo molecules, without compromising target affinity, are in demand. Here, we describe a straightforward CRISPR/Cas9-based strategy to rapidly engineer hybridoma cells to secrete Fab' fragments bearing two distinct site-specific labeling motifs, which can be separately modified by two different sortase A mutants. We show that sequential genetic editing of the heavy chain (HC) and light chain (LC) loci enables the generation of a stable cell line that secretes a dual tagged Fab' molecule (DTFab'), which can be easily isolated. To demonstrate feasibility, we functionalized the DTFab' with two distinct cargos in a site-specific manner. This technology platform will be valuable in the development of multimodal imaging agents, theranostics, and next-generation ADCs.
Acoustic time reversal in granular media (2016)

In a non-dissipative medium, the wave equation is symmetric in time. Therefore, for every wave diverging from a pulsed source, there exists a wave that retraces all its original paths in a reverse order and converges at the original source. In the early nineties, M. Fink proposed a method for generating such a time-reversed wave. This method was first tested with ultrasound and then successfully extended to other types of waves such as microwaves, water waves, and even in optics. Several studies have shown that time reversal wave focusing is very robust to disorder. Here, we investigate time reversal (TR) of elastic waves propagating in fragile granular media consisting of glass beads under static compression. Pulsed elastic waves transmitted from a compression or a shear wave source are measured, time reversed, and back-propagated. The ability of the time-reversed wave to focus at the initial source is checked as a function of the source amplitude. We find that TR of the ballistic coherent wave is very robust to perturbations but provides poor resolution. By contrast, the short-wavelength scattered waves offer a finer TR focusing but are sensitive to rearrangements induced by the forward propagation wave itself: at large source amplitudes, time reversal focusing is broken, due to sound-induced rearrangements but without visible grain motion. Experimental results are confronted with predictions from a numerical model in which the propagation medium is modelled by a percolating network of masses interacting via linear springs.
A General Method for Simulating the Flow Dependent Nonlinear Vibrations of Compressor Reed Valves (1976)

A mathematical model is developed for the nonlinear vibrations of automatic reed valves in high-speed refrigeration compressors. Specifically considered are a general class of values which wrap about curved backer plates. Two simple experiments are described which allow the nonlinearities of the valve system to be defined by a single nonlinear second order differential equation. Valve oscillation frequencies inside an operating compressor are predicted through a linearization of the valve equation. Comparisons with experiment are included.