gebhart/patrepeval huggingface dataset:
Fatigue of a Reinforced High Temperature Superconducting Tape (2001)

High-cycle fatigue-life behavior of commercial multifilamentary BSCCO 2223 powder-in-tube tape and reinforced tape was evaluated. Mechanical fatigue at room temperature and 77 K, and the onset of significant superconductivity degradation at 77 K were evaluated under tension perpendicular to the flat faces of the tapes. No fatigue behavior was observed in this transverse configuration for unreinforced tape, but fatigue–life behavior associated with delamination of the reinforcement was found for reinforced tape. Fatigue tolerance of the reinforced tape is very high, about 24 MPa, to at least 100.000 cycles.
Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination (2020)

Developing lymphocytes of jawed vertebrates cleave and combine distinct gene segments to assemble antigen-receptor genes. This process called V(D)J recombination that involves the RAG recombinase binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG-RSS interaction. We employ a single-molecule method known as tethered particle motion to track the formation, lifetime and cleavage of individual RAG-12RSS-23RSS paired complexes (PCs) for numerous synthetic and endogenous 12RSSs. We reveal that single-bp changes, including in the 12RSS spacer, can significantly and selectively alter PC formation or the probability of RAG-mediated cleavage in the PC. We find that some rarely used endogenous gene segments can be mapped directly to poor RAG binding on their adjacent 12RSSs. Finally, we find that while abrogating RSS nicking with Ca2+ leads to substantially shorter PC lifetimes, analysis of the complete lifetime distributions of any 12RSS even on this reduced system reveals that the process of exiting the PC involves unidentified molecular details whose involvement in RAG-RSS dynamics are crucial to quantitatively capture kinetics in V(D)J recombination.
Three-dimensional quantitative structure-activity relationship of human immunodeficiency virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes (1994)

NewPred, a semiautomated procedure to evaluate alternate binding modes and assist three dimensional quantitative structure-activity relationship (3D-QSAR) studies in predictive power evaluation is exemplified with a series of 30 human immunodeficiency virus 1 protease (HIV PR) inhibitors. Five comparative molecular field analysis (CoMFA) models (Waller, C. L.; et al. J. Med. Chem. 1993, 36, 4152-4160) based on 59 HIV-PR inhibitors were tested. The test set included 18 compounds (set A) having a different transition state isostere (TSI), hydroxyethylurea (Getman, D. P.; et al. J. Med. Chem. 1993, 36, 288-291), to investigate the binding mode in P1' and P2'. Twelve dihyroxyethylenes (set B) (Thaisrivongs, S.; et al. J. Med. Chem. 1993, 36, 941-952) were used to investigate binding in P2 and P3 as well as in P2' and P3'. Six other compounds with known or inferred binding structure (set C) were part of the test set, but not investigated with NewPred. Each compound was aligned in accordance to predefined alignment rules for the training set prior to the inclusion in the test set (except for set C). Using NewPred, geometrically different conformers for each compound were generated and individually relaxed in the HIV-PR binding site. Energy comparisons allowed selection of lowest energy structures to be included in the test set. Only in vacuo minimized conformers derived from low-energy complexes were used to determine the predictive power of the five models (predictive r2 varied from 0.1 to 0.7 when two chemical and statistical outliers were excluded). Our models correctly predict the poor inhibitor activity of 1(S)-amino-2(R)-hydroxyindan-containing peptides (set B), which is explained and interpreted from a 3D-QSAR perspective. The use of a new, flexibility-based, semiautomated method to explore alternate binding models for 3D-QSAR models is demonstrated.
Swimming in circles can lead to exotic hyperuniform states of active living matter (2021)

The study of hyperuniform states of matter is an emerging multidisciplinary field, influencing and linking developments across the physical sciences, mathematics, and biology (1, 2). A hyperuniform many-particle system in d-dimensional Euclidean space is characterized by an anomalous suppression of large-scale density fluctuations relative to those in typical disordered systems, such as liquids and amorphous solids. As such, the hyperuniformity concept generalizes the traditional notion of long-range order to include not only all perfect crystals and quasicrystals but also exotic disordered states of matter. Disordered hyperuniform states have attracted great attention across many fields over the last two decades because they can have the character of crystals on large length scales but are isotropic like liquids (2). This hybrid crystal–liquid attribute endows them with unique or nearly optimal, direction-independent physical properties and robustness against defects (3⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓–14). Adding to this flurry of research activity is the finding by Huang et al. (15) that circularly swimming marine algae can robustly self-organize into disordered hyperuniform states through long-range hydrodynamic interactions at air–liquid interfaces.

How is hyperuniformity quantified? Such systems have a structure factor S ( k ) , which can be measured from scattering experiments, that tends to zero as the wavenumber | k | tends to zero (1), where k is the wavevector. Another way to ascertain hyperuniformity is to randomly place many large spherical sampling windows of radius R in the system and count the number of particles within the window. The number of particles registered within the window will fluctuate, enabling one to find the corresponding local number variance σ 2 ( R ) , as shown in Fig. 1. Garden-variety disordered systems, such as typical gases and liquids, are characterized by a variance σ 2 ( R ) … 

[↵][1]1Email: torquato{at}princeton.edu.

 [1]: #xref-corresp-1-1
Unfolding of Hydrated Alkyl Diammonium Cations Revealed by Cryogenic Ion Mobility-Mass Spectrometry (2015)

Hydration of the ammonium ion plays a key role in determining the biomolecular structure as well as local structure of water in aqueous environments. Experimental data obtained by cryogenic ion mobility-mass spectrometry (cryo-IM-MS) show that dehydration of alkyl diammonium cations induces a distinct unfolding transition at a critical number of water molecules, n = 21 to 23, n = 24 to 26, and n = 27 to 29, for 1,7-diaminoheptane, 1,8-diaminooctane, and 1,10-diaminodecane, respectively. Results are also presented that reveal compelling evidence for unique structural transitions of hydrated ammonium ions associated with the development of the hydrogen-bond network around individual charged groups. The ability to track the evolution of structure upon stepwise dehydration provides direct insight into the intricate interplay between solvent-molecule interactions that are responsible for defining conformations. Such insights are potentially valuable in understanding how ammonium ion solvation influences conformation(s) of larger biomolecules.
Electromechanical analysis of an electrodynamic bearing (2017)

As known electrodynamic levitation occurs without active control due to motion induced eddy currents. There are two main drawbacks related to electromagnetic bearings: 1) the presence of losses caused by the eddy currents, and 2) the onset of instability in undamped supercritical rotor systems. Accurate analysis of these devices, especially when the axial symmetry cannot be assumed, can be performed by numerical methods only. This paper presents a comparison between the experimental data taken on a prototype of an electrodynamic bearing and the numerical simulations obtained by a research code. The good agreement envisages the use of this code for the reduction of losses and for a better characterization of the instability conditions.
On Database-Free Authentication of Microelectronic Components (2020)

Counterfeit integrated circuits (ICs) have become a significant security concern in the semiconductor industry as a result of the increasingly complex and distributed nature of the supply chain. These counterfeit chips may result in performance degradation, profit reduction, and reputation risk for the manufacturer. Therefore, developing effective countermeasures against such malpractices is becoming severely crucial. Physical unclonable function (PUF)-based authentication methods have the potential to mitigate these challenges. However, PUF-based solutions are restrained by several factors, such as additional design efforts and significant area/power overhead, struggle to maintain and update challenge-response pairs (CRPs) database, and the vulnerability to machine learning (ML) attacks. In this article, we address these challenges by developing a novel database-free and enrolment-free hardware authentication approaches, i.e., a digital watermark metric for ICs. To enable efficient database-free hardware integrity verification without enrolment, first, we transform the intrinsic variations in circuit parameters, e.g., boundary scan chain (BSC) path delays in the joint test action group (JTAG) chain into robust digital signatures. Then, we perform statistical analysis on a small pilot unit of authentic chips to create a robust watermark for a complete batch of chips, which jointly captures the characteristics of the physical layout, the manufacturing process, and the foundry. The increasing complexity in the current state-of-the-art designs makes it extremely hard for an adversary to perfectly clone such statistical characterization of circuit parameters using counterfeit or compromised hardware. Besides, the proposed approach requires no additional design or hardware overhead in IC design since it utilizes an embedded structure, which inherently exists within the chips. It also obviates the design house from characterizing each manufactured chip instance, reducing overall testing cost. A path-delay measurement method at a high resolution based on clock phase sweep is introduced to measure the delay values effectively. The proposed intrinsic identifier-based authentication approach is validated by performing emulation on FPGAs and also by conducting physical measurements on custom-made printed circuit boards (PCBs). The reliability of the generated watermarks is evaluated with environmental temperature fluctuations and the aging effect.
A band of bound states in the continuum induced by disorder (2018)

Bound states in the continuum usually refer to the phenomenon of a single or a few discrete bound states embedded in a continuous spectrum of extended states. Here we propose a simple mechanism to achieve a band of bound states in the continuum in a class of disordered quasi-1D and quasi-2D systems, where the bound states and extended states overlap completely in a spectral range. The systems are partially disordered in a way that a band of extended states always exists, not affected by the randomness, whereas the states in all other bands become localized and cover the entire spectrum of extended states. We demonstrate such disordered-induced bound states in the continuum in disordered multi-chain and multi-layer systems.
Reflectance of Jezero Crater Floor: 1. Data Processing and Calibration of the Infrared Spectrometer (IRS) on SuperCam (2022)

Abstract The Perseverance rover, Mars 2020 mission, landed on the surface of the Jezero crater, on 18 February 2021. This Martian crater is suspected to have hosted a paleolake as evidenced by the numerous detections of aqueously altered phases and thus is a promising candidate for the search for past Martian life. The SuperCam instrument, a collaboration by a consortium of American and European laboratories, plays a leading role in this investigation, thanks to its highly versatile payload providing rapid, synergistic, fine‐scale mineralogy, chemistry, and color imaging. After its landing, the first measurements of Martian targets with the infrared spectrometer of SuperCam (IRS) showed new instrumental behaviors that had to be characterized and calibrated to derive unbiased science data. The IRS radiometric response has thus been calibrated using periodic observations of the Aluwhite SuperCam Calibration Target (SCCT). Parasitic effects were understood and mitigated, and the instrumental dark and noise are characterized and modeled. The reflectance calibrated data products, provided periodically on the NASA Planetary Data System, are corrected for the main instrumental features. This radiometric calibration allowed us to study the 2.5 μm absorption band, which has been discovered in the Séítah unit and is associated with phyllosilicates‐carbonates mixtures.
Novel Pol II Fusion Promoter Directs Human Immunodeficiency Virus Type 1-Inducible Coexpression of a Short Hairpin RNA and Protein (2006)

We demonstrate a novel approach for coexpression of a short hairpin RNA (shRNA) with an open reading frame which exploits transcriptional read-through of a minimal polyadenylation signal from a Pol II promoter. We first observed efficient inducible expression of enhanced green fluorescent protein along with an anti-rev shRNA. We took advantage of this observation to test coexpression of the transdominant negative mutant (humanized) of human immunodeficiency type 1 (HIV-1) Rev (huRevM10) along with an anti-rev shRNA via an HIV-1-inducible fusion promoter. The coexpression of the shRNA and transdominant protein resulted in potent, long-term inhibition of HIV-1 gene expression and suppression of shRNA-resistant mutants. This dual expression system has broad-based potential for other shRNA applications, such as cases where simultaneous knockdown of mutant and wild-type transcripts must be accompanied by replacement of the wild-type protein.
Motor Impairments, Striatal Degeneration, and Altered Dopamine-Glutamate Interplay in Mice Lacking PSD-95 (2014)

Excessive activation of the N-methyl-d-aspartate (NMDA) receptor and the neurotransmitter dopamine (DA) mediate neurotoxicity and neurodegeneration under many neurological conditions, including Huntington's disease (HD), an autosomal dominant neurodegenerative disease characterized by the preferential loss of medium spiny projection neurons (MSNs) in the striatum. PSD-95 is a major scaffolding protein in the postsynaptic density (PSD) of dendritic spines, where a classical role for PSD-95 is to stabilize glutamate receptors at sites of synaptic transmission. Our recent studies indicate that PSD-95 also interacts with the D1 DA receptor localized in spines and negatively regulates spine D1 signaling. Moreover, PSD-95 forms ternary protein complexes with D1 and NMDA receptors, and plays a role in limiting the reciprocal potentiation between both receptors from being escalated. These studies suggest a neuroprotective role for PSD-95. Here we show that mice lacking PSD-95, resulting from genetic deletion of the GK domain of PSD-95 (PSD-95-ΔGK mice), sporadically develop progressive neurological impairments characterized by hypolocomotion, limb clasping, and loss of DARPP-32-positive MSNs. Electrophysiological experiments indicated that NMDA receptors in mutant MSNs were overactive, suggested by larger, NMDA receptor-mediated miniature excitatory postsynaptic currents (EPSCs) and higher ratios of NMDA- to AMPA-mediated corticostriatal synaptic transmission. In addition, NMDA receptor currents in mutant cortical neurons were more sensitive to potentiation by the D1 receptor agonist SKF81297. Finally, repeated administration of the psychostimulant cocaine at a dose regimen not producing overt toxicity-related phenotypes in normal mice reliably converted asymptomatic mutant mice to clasping symptomatic mice. These results support the hypothesis that deletion of PSD-95 in mutant mice produces concomitant overactivation of both D1 and NMDA receptors that makes neurons more susceptible to NMDA excitotoxicity, causing neuronal damage and neurological impairments. Understanding PSD-95-dependent neuroprotective mechanisms may help elucidate processes underlying neurodegeneration in HD and other neurological disorders.
512 Gbit/s super-channel field trial over a 280 km DWDM terrestrial link in a single 100 GHz slot (2012)

A 512 Gbit/s super-channel has been transmitted in a single 100 GHz ITU-T slot over a terrestrial network segment of 280 km including eight 10.7 Gbit/s OOK channels between Granada and Jaen, Spain.
Monitoring Changes in Mechanical Properties of Rock Bolts Using a Low-Power Coded-Excitation Scheme (2018)

In-situ inspection and quality assessment of rock bolts and other load-bearing structural elements, has received significant attention over the years, but there are still no techniques available capable of monitoring changes over time in mechanical properties of already installed bolts. Since mechanical changes will also affect the propagation of mechanical waves, ultrasound is a strong candidate. In this paper we propose a technique based on Orthogonal Frequency Division Multiplexing (OFDM) for coding the transmitted ultrasound pulse in such a way that the propagation channel (transducer and rock bolt combined) can be estimated. We show that a transmit voltage of 1.1 V r.m.s. is sufficient to obtain reliable channel estimates even in bolts as long as one meter. The channel estimates are then used to predict changes in tensile stress on the bolt, from experiments conducted in a laboratory environment.
Near-infrared–actuated devices for remotely controlled drug delivery (2014)

A reservoir that could be remotely triggered to release a drug would enable the patient or physician to achieve on-demand, reproducible, repeated, and tunable dosing. Such a device would allow precise adjustment of dosage to desired effect, with a consequent minimization of toxicity, and could obviate repeated drug administrations or device implantations, enhancing patient compliance. It should exhibit low off-state leakage to minimize basal effects, and tunable on-state release profiles that could be adjusted from pulsatile to sustained in real time. Despite the clear clinical need for a device that meets these criteria, none has been reported to date to our knowledge. To address this deficiency, we developed an implantable reservoir capped by a nanocomposite membrane whose permeability was modulated by irradiation with a near-infrared laser. Irradiated devices could exhibit sustained on-state drug release for at least 3 h, and could reproducibly deliver short pulses over at least 10 cycles, with an on/off ratio of 30. Devices containing aspart, a fast-acting insulin analog, could achieve glycemic control after s.c. implantation in diabetic rats, with reproducible dosing controlled by the intensity and timing of irradiation over a 2-wk period. These devices can be loaded with a wide range of drug types, and therefore represent a platform technology that might be used to address a wide variety of clinical indications.
Sustainable Synthesis of Bright Fluorescent Nitrogen-Doped Carbon Dots from Terminalia chebula for In Vitro Imaging (2022)

In this study, sustainable, low-cost, and environmentally friendly biomass (<i>Terminalia chebula</i>) was employed as a precursor for the formation of nitrogen-doped carbon dots (N-CDs). The hydrothermally assisted <i>Terminalia chebula</i> fruit-derived N-CDs (TC-CDs) emitted different bright fluorescent colors under various excitation wavelengths. The prepared TC-CDs showed a spherical morphology with a narrow size distribution and excellent water dispensability due to their abundant functionalities, such as oxygen- and nitrogen-bearing molecules on the surfaces of the TC-CDs. Additionally, these TC-CDs exhibited high photostability, good biocompatibility, very low toxicity, and excellent cell permeability against HCT-116 human colon carcinoma cells. The cell viability of HCT-116 human colon carcinoma cells in the presence of TC-CDs aqueous solution was calculated by MTT assay, and cell viability was higher than 95%, even at a higher concentration of 200 μg mL<sup>-1</sup> after 24 h incubation time. Finally, the uptake of TC-CDs by HCT-116 human colon carcinoma cells displayed distinguished blue, green, and red colors during in vitro imaging when excited by three filters with different wavelengths under a laser scanning confocal microscope. Thus, TC-CDs could be used as a potential candidate for various biomedical applications. Moreover, the conversion of low-cost/waste natural biomass into products of value promotes the sustainable development of the economy and human society.
Cervical metastases from small bowel carcinoid tumors (1983)

Small bowel carcinoid tumors usually metastasize to regional lymph nodes and the liver but metastases to the neck are extremely rare. Over a ten-year period 48 cases of small bowel carcinoid were diagnosed at our institution and of these, three cases (6%) were associated with neck metastases--one to the thyroid gland and two to cervical lymph nodes. The former patient and one of the latter patients had symptoms of the carcinoid syndrome. The other patient was asymptomatic and presented with a solitary neck mass. Urine levels of 5-hydroxyindolacetic acid (5-HIAA) were elevated in the two symptomatic patients but were undetectable in the asymptomatic patient. Extirpation of the involved cervical nodes and the primary small bowel lesion was performed in two patients. In addition, both patients have received chemotherapy with 5-fluorouracil. One patient remains asymptomatic four years after diagnosis but the other patient continues to have five to six bowel movements per day nine months after operation. Small bowel resection was performed in the patient with a metastasis to the thyroid. This patient died of sepsis after a second operation for an intraabdominal abscess. The histological patterns of the primary tumor and the metastatic lesions were similar and the cells of the metastases contained argentaffin-positive granules. We conclude that 1) an intraabdominal carcinoid tumor should be considered as the location of the primary tumor in patients who present with a neck mass containing metastatic carcinoid and 2) the prognosis for patients with extraabdominal metastases is similar to that for patients with intraabdominal disease only.