gebhart/patrepeval huggingface dataset:
Cover Picture: Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines (Chem. Eur. J. 9/2017) (2016)

The amyloidogenic peptide, DFNKF, forms a steric zipper. Iodination of this widely studied sequence facilitated crystallization and allowed its high-resolution single crystal structure determination for the first time. The structure unveils the importance of aromatic–aromatic interactions in stabilizing the amyloid self-assembly. The amino acid side-chains of facing β-strands (shown in red and green, respectively) interdigitate like the teeth of a zipper, similar to that of blue jeans. More information can be found in the Full Paper by P. Metrangolo et al. on page 2051 ff. The amyloidogenic peptide, DFNKF, forms a steric zipper. Iodination of this widely studied sequence facilitated crystallization and allowed its high-resolution single crystal structure determination for the first time. The structure unveils the importance of aromatic–aromatic interactions in stabilizing the amyloid self-assembly. The amino acid side-chains of facing β-strands (shown in red and green, respectively) interdigitate like the teeth of a zipper, similar to that of blue jeans. More information can be found in the Full Paper by P. Metrangolo et al. on page 2051 ff.
Liver and Kidney Growth Hormone (GH) Receptors Are Regulated Differently in Diabetic GH and GH Antagonist Transgenic Mice* (1997)

Elevated GH levels are frequently seen in poorly controlled type I diabetics and have been implicated in diabetic complications. Studies of GH and GH antagonist (GHA) transgenic mice with streptozotocin (STZ)-induced diabetes have revealed that GH has a permissive effect for diabetic nephropathy, and that expression of a GHA gene protected mice against diabetic kidney lesions. To investigate whether kidney GH receptor (GHR) and/or GH-binding protein may play a role in diabetic nephropathy, we evaluated GH-specific binding and messenger RNA levels for GHR/GH-binding protein in mouse livers and kidneys from bovine (b) GH or bGHA transgenic (Tg) mice and their nontransgenic (NTg) littermates with or without STZ-induced diabetes. We found that liver-specific GH binding is significantly higher in both bGH- and bGHA-Tg mice compared to that in their NTg controls. In contrast, kidney GH binding is significantly lower in bGH-Tg mice compared to that in NTg littermates. These results indicate that regulation of mouse GHR expression is tissue specific. STZ-induced diabetes decreased GH-specific binding in both liver and kidney of NTg and GHA-Tg mice, but not in bGH-Tg mice. The lowered GHR binding in diabetic NTg and GHA-Tg mice suggests the involvement of insulin in the regulation of GHR expression. The down-regulation of kidney GHR in GHA-Tg mice in combination with the presence of GHA may partially explain the protective mechanism of GHA against diabetic kidney lesions.
In Memoriam - A Tribute: Prof. Avram Bar-Cohen (2021)

Professor Avram Bar-Cohen (popularly known as Avi), the past President of IEEE Electronics Packaging Society (EPS), and the past Editor-in-Chief of the IEEE TRANSACTIONS ON COMPONENTS AND PACKAGING TECHNOLOGIES, passed away on October 10, 2020. He was a giant in the field of thermal management and made seminal research and professional contributions over a five-decade period. This special issue is dedicated to the memory of Prof. Bar-Cohen and his contributions to the area of liquid cooling of microsystems. Each of us has been profoundly impacted in our research and professional growth through our interactions with Prof. Bar-Cohen. This life achievements are reviewed. This special issue is dedicated to the memory of Prof. Bar-Cohen and his contributions to the area of liquid cooling of microsystems. Each of us has been profoundly impacted in our research and professional growth through our interactions with Prof. Bar-Cohen.
Adaptive Power Shifting for Power-Constrained Heterogeneous Systems (2022)

The number and heterogeneity of compute devices, even within a single compute node, has been steadily on the rise. Since all systems must operate under a power cap, the number of discrete devices that can run simultaneously at their highest frequency is limited by the globally-imposed power cap. Current systems incorporate a centralized power management unit that statically controls the distribution of power among the devices within the node. However, such static distribution policies are unaware of the dynamic utilization profile across the devices, which leads to unfair power allocations that end up degrading system throughput performance. The problem is particularly acute in the presence of heterogeneity since type-specific performance-boost capabilities cannot be leveraged via utilization-agnostic static power allocations. This paper proposes Adaptive Power Shifting for multi-accelerator heterogeneous systems (APS), a technique that leverages system utilization information to dynamically allocate and re-distribute power budgets across multiple discrete devices. Democratizing the power allocation based on dynamic needs results in dramatic speedup over a need-agnostic static allocation. We use APS in a real OpenPOWER compute node with 2 CPUs and 4 GPUs to demonstrate the value of on-demand, equitable power allocations. Overall, the proposed solution increases performance with respect to two state-of-the-art techniques by up to 14.9% and 13.8%.
Molecular electronic structure using auxiliary field Monte Carlo, plane-waves, and pseudopotentials (2000)

Shifted contour auxiliary field Monte Carlo is implemented for molecular electronic structure using a plane-waves basis and norm conserving pseudopotentials. The merits of the method are studied by computing atomization energies of H2, BeH2, and Be2. By comparing with high correlation methods, DFT-based norm conserving pseudopotentials are evaluated for performance in fully correlated molecular computations. Pseudopotentials based on generalized gradient approximation lead to consistently better atomization energies than those based on the local density approximation, and we find there is room for designing pseudopotentials better suited for full valence correlation.
Optimization of Platelet-Derived Growth Factor Receptor (PDGFR) Inhibitors for Duration of Action, as an Inhaled Therapy for Lung Remodeling in Pulmonary Arterial Hypertension (2016)

A series of potent PDGFR inhibitors has been identified. The series was optimized for duration of action in the lung. A novel kinase occupancy assay was used to directly measure target occupancy after i.t. dosing. Compound 25 shows 24 h occupancy of the PDGFR kinase domain, after a single i.t. dose and has efficacy at 0.03 mg/kg, in the rat moncrotaline model of pulmonary arterial hypertension. Examination of PK/PD data from the optimization effort has revealed in vitro:in vivo correlations which link duration of action in vivo with low permeability and high basicity and demonstrate that nonspecific binding to lung tissue increases with lipophilicity.
The rates of growth of the Galton-Watson process in varying environment (1976)

It is shown that a Galton-Watson process in varying environment, unlike a classical Galton-Watson process, can have an infinite (though at most countable) number of distinct rates of growth.
SAR Studies of Piperidine-Based Analogues of Cocaine. 4. Effect of N-Modification and Ester Replacement (2002)

A series of novel N- and 3alpha-modified piperidine-based analogues of cocaine were synthesized and tested for their ability to inhibit reuptake of DA, 5-HT, and NE by the DA, 5-HT, and NE transporters. N-Demethylation of trans-(+)-3alpha-piperidine-based ligands leads to improved activity at the SERT and NET and modest changes at the DAT. Replacement of the N-methyl group in trans-(+)-ester 1a with phenylalkyl groups leads to a modest 2.3-fold improvement in activity at the SERT (K(i) < or = 3.27 microM), insignificant changes at the NET, and a 3.5-fold loss in activity at the DAT (K(i) > or = 810 nM); however, such replacement in cis-(-)-ester 4, the more potent isomer of 1a, leads, in general, to a significant decrease in activity at all monoamine transporters (K(i) > 1 microM). Other N-modified ligands, including the ligands with polar groups incorporated in the N-alkyl substituent (3e-g) and ligands lacking the basic nitrogen (3i and 6d), show decreased activity at all monoamine transporters, though ligands 3e-g are similar in potency at the NET to 1a. N-Norester 2a, a possible metabolite of the lead compound 1a, and alcohol 1c, a compound with a 3alpha-substituent that is more stable to metabolism than 1a, were selected for further behavioral tests in animals. Alcohol 1c and ester 2a are similar in potency at the DAT to cocaine, ester 1a, and oxadiazole 1b, and both fully substitute for cocaine and have potency similar to that of cocaine in drug discrimination tests. Like cocaine, 1c increased locomotor activity (LMA) monotonically with time, whereas 2a produces biphasic effects consisting of initial locomotor depression followed by delayed locomotor stimulation. An interesting difference between cocaine, ester 1a, alcohol 1c, and N-norester 2a is that 1c and 2a are significantly longer acting in LMA tests. Although this result was anticipated for alcohol 1c, it is rather surprising for 2a which has an ester function susceptible to hydrolysis, a pathway of in vivo deactivation of cocaine and its ester analogues. The present results may have important implications for our understanding of the pharmacological mechanisms underlying the behavioral actions of cocaine and of the structural features needed for the design of the new leads in the discovery of a cocaine abuse medication.
A Flexible Sandwich Nanogenerator for Harvesting Piezoelectric Potential from Single Crystalline Zinc Oxide Nanowires (2014)

High-quality single crystalline zinc oxide nanowires were grown on silver and gold coated plastic substrates for the fabrication of a sandwich-like nanogenerator using the aqueous chemical growth method. The applicability of this configuration as a nanogenerator is demonstrated by studying the harvested electrical output under mechanical deformation. Three different configurations were fabricated and utilized for harvesting piezoelectric potential by applying an external force. The maximum resulting output open circuit voltage and short circuit current were 2.4 V and 152.2 μA, respectively. The comparison between the different configurations indicates that more piezoelectric potential can be harvested by using two arrays of ZnO NWs placed face-to-face than by using a single nanowire configuration. In addition, the use of a piezoelectric polymer will enhance the amount of generated piezoelectric potential. The obtained results from different configurations of zinc oxide nanowire nanogenerators offer a cost-effective, flexible, long term stable nanogenerator for promising application. The principle of the sandwich nanogenerator demonstrated a new idea for novel self-powering nanotechnology that harvests electricity from the environment for applications such as portable electronics.
Data from Wide Variability in the Time Required for Immunotoxins to Kill B Lineage Acute Lymphoblastic Leukemia Cells: Implications for Trial Design (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Recombinant immunotoxins (rITs) targeting CD22 are highly active in hairy cell leukemia, but less so in acute lymphoblastic leukemia (ALL). This study aims to understand the variable activity of an rIT against ALL toward improving responses in clinical application.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We determined &lt;i&gt;in vitro&lt;/i&gt; activity of rITs by WST-8 assays and the time needed to kill ALL cell lines and patient-derived ALL blasts by flow cytometry. The findings were translated into two systemic ALL xenograft models. Differences in time needed to kill KOPN-8 cells for distinct rITs were addressed biochemically.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; &lt;i&gt;In vitro&lt;/i&gt; activity (IC&lt;sub&gt;50&lt;/sub&gt;) of anti-CD22 rIT varied 210-fold from 0.02 to 4.6 ng/mL. Activity also varied greatly depending on the time ALL cells were exposed to immunotoxin from &lt; 30 minutes to &gt; 4 days. For KOPN-8, the difference in exposure time was related to intracellular rIT processing. We showed in newly developed ALL xenograft models, where immunotoxins have a short half-life, that the needed exposure time &lt;i&gt;in vitro&lt;/i&gt; predicted the responses &lt;i&gt;in vivo&lt;/i&gt;. By replacing bolus dose with small doses at frequent intervals or with continuous infusion, responses were substantially improved. We confirmed exposure time variability on patient-derived ALL samples and showed a correlation between exposure time needed to reach maximal cytotoxicity &lt;i&gt;in vitro&lt;/i&gt; and their clinical response.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The exposure time needed for rITs targeting CD22 to kill ALL cells varies widely. Our results suggest that ALL patients would have a better response rate to anti-CD22 immunotoxins if treated by continuous infusion rather than by bolus injections. &lt;i&gt;Clin Cancer Res; 22(19); 4913–22. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Schisandrae Fructus Supplementation Ameliorates Sciatic Neurectomy-Induced Muscle Atrophy in Mice (2015)

The objective of this study was to assess the possible beneficial skeletal muscle preserving effects of ethanol extract of Schisandrae Fructus (EESF) on sciatic neurectomy- (NTX-) induced hindlimb muscle atrophy in mice. Here, calf muscle atrophy was induced by unilateral right sciatic NTX. In order to investigate whether administration of EESF prevents or improves sciatic NTX-induced muscle atrophy, EESF was administered orally. Our results indicated that EESF dose-dependently diminished the decreases in markers of muscle mass and activity levels, and the increases in markers of muscle damage and fibrosis, inflammatory cell infiltration, cytokines, and apoptotic events in the gastrocnemius muscle bundles are induced by NTX. Additionally, destruction of gastrocnemius antioxidant defense systems after NTX was dose-dependently protected by treatment with EESF. EESF also upregulated muscle-specific mRNAs involved in muscle protein synthesis but downregulated those involved in protein degradation. The overall effects of 500 mg/kg EESF were similar to those of 50 mg/kg oxymetholone, but it showed more favorable antioxidant effects. The present results suggested that EESF exerts a favorable ameliorating effect on muscle atrophy induced by NTX, through anti-inflammatory and antioxidant effects related to muscle fiber protective effects and via an increase in protein synthesis and a decrease in protein degradation.
The Biocompatibility of Silk Scaffold for Tissue Engineered Ligaments (2007)

The aim of this study was to estimate the mechanical properties and evaluate the biocompatibility of silk and PGA scaffolds as an artificial ligament to an ACL reconstruction. The scaffold for the artificial ligament was braided / knitted silk or PGA thread. The mechanical properties, cell growth, and subcutaneous tissue reactions were determined for both types of scaffolds. The breaking load of the PGA scaffold was double that of the sericin removed silk scaffold (SRSS). However, the initial attachment and growth of human ACL cells on the SRSS was superior to the PGA scaffold. In addition, the immune response was significantly higher on the PGA scaffold after 72 h (p&lt;0.05) compared with the sericin removed silk scaffold by T lymphocyte and mononuclear cells (MNCs) in vitro cultures. In vivo, the ACL scaffold made from silk or PGA were implanted in the subcutaneous layer in rats and harvested 1 week later. A histological evaluation of the scaffolds explants revealed the presence of monocytes in the SRSS, and an absence of giant cells in all cases. An inflammatory tissue reaction was more conspicuous around the silk scaffold containing sericin and even more around the PGA scaffold compared with SRSS. These results support the conclusion that a properly prepared SRSS, aside from providing benefits in terms of biocompatibility both in vitro and in vivo, can provide suitable scaffolds for the support of ACL cell growth. These results suggest that a SRSS for ACL repair can overcome the current limitations with the PGA scaffold. And SRSS is biocompatible, and the in vitro T cell and MNCs culture model showed inflammatory responses that were comparable to those observed in vivo.
Design, Synthesis, and Biological Characterization of Bivalent 1-Methyl-1,2,5,6-tetrahydropyridyl-1,2,5-thiadiazole Derivatives as Selective Muscarinic Agonists (2001)

Selective muscarinic agonists could be useful in the treatment of neurological disorders such as Alzheimer's disease, schizophrenia, and chronic pain. Many muscarinic agonists have been developed, yet most exhibit at best limited functional selectivity for a given receptor subtype perhaps because of the high degree of sequence homology within the putative binding site, which appears to be buried within the transmembrane domains. Bivalent compounds containing essentially two agonist pharmacophores within the same molecule were synthesized and tested for receptor binding affinity and muscarinic agonist activity. A series of bis-1,2,5-thiadiazole derivatives of 1,2,5,6-tetrahydropyridine linked by an alkyloxy moiety exhibited very high affinity (K(i) < 1 nM) and strong agonist activity. The degree of activity depended on the length of the linking alkyl group, which could be replaced by a poly(ethylene glycol) moiety, resulting in improved water solubility, binding affinity, and agonist potency.
High-Performance 50G-PON Burst-Mode Upstream Transmission at 25 Gb/s with DSP-Assisted Fast Burst Synchronization and Recovery (2019)

We experimentally demonstrate high-performance burst-mode upstream transmission at 25 Gb/s for 50G-PON. With a novel DSP-assisted burst-mode receiver, we achieve fast burst synchronization and recovery within ∼200 ns, and a record receiver sensitivity of −29.8 dBm at the SD-LDPC BER threshold of 2×10−2 after 20-km SSMF transmission.
Split-U-Net: Preventing Data Leakage in Split Learning for Collaborative Multi-Modal Brain Tumor Segmentation (2022)

Split learning (SL) has been proposed to train deep learning models in a decentralized manner. For decentralized healthcare applications with vertical data partitioning, SL can be beneficial as it allows institutes with complementary features or images for a shared set of patients to jointly develop more robust and generalizable models. In this work, we propose "Split-U-Net" and successfully apply SL for collaborative biomedical image segmentation. Nonetheless, SL requires the exchanging of intermediate activation maps and gradients to allow training models across different feature spaces, which might leak data and raise privacy concerns. Therefore, we also quantify the amount of data leakage in common SL scenarios for biomedical image segmentation and provide ways to counteract such leakage by applying appropriate defense strategies.
A study of reservation dynamics in integrated services packet networks (2002)

The integrated services packet network (ISPN) architecture proposed within the Internet community incorporates a resource reservation mechanism for those applications requiring quality of service (QoS) guarantees. Resource reservation introduces a new form of resource contention that can lead to reduced network throughput and thrashing. We establish several necessary conditions to induce thrashing. We also look at the effects several different reservation models and user behavior can have on network stability. Our work is unique from previous network resource reservation investigations in that we consider the effects of reservations for multipoint-to-multipoint applications. We conclude with examples of how simple modifications to user behavior can result in significant increases in system stability.
Transcatheter aortic valve implantation (2011)

TAVI outcomes improve with experience and device development. While overall complication rates are low, scope remains to further reduce procedural adverse events.
Beamwidth measurement of single lithotripter shock waves (2008)

New lithotripters with narrower foci and higher peak pressures than the original Dornier HM3 electrohydraulic lithotripter have proven to be less effective and less safe. Hence, accurate measurements of the focal characteristics of lithotripter shock waves are important. The current technique for measuring beamwidth requires collection of single-point measurements over multiple shock waves, thereby introducing error as a result of any shock-to-shock variability. This work reports on the construction of a hydrophone array sensor and on array measurements of individual lithotripter shock waves. Beamwidths for an electrohydraulic lithotripter with a broad-focus, HM3-style reflector and a narrow-focus, modified reflector were measured using both new and worn electrodes as well as two different electrical charging potentials. The array measured the waveform, beamwidth, and focal location of individual shock waves. The HM3-style reflector produced repeatable focal waveforms and beam profiles at an 18-kV charging potential with both new and worn electrodes. Accordingly, these measurements agreed with averaged point measurements acquired under the same conditions. However, a lack of consistency in the measured focal locations and beam profiles at 23 kV underscores the value in obtaining beam profile measurements from individual shock waves. Work supported by Riverside Research Institute, NIH DK43881, and NSBRI SMS00402.
A Soft Preparative Method for Membrane Proteome Analysis Using Frit Inlet Asymmetrical Flow Field-Flow Fractionation: Application in a Prostatic Cancer Cell Line (2009)

Membrane proteins participate in a number of important biological functions such as signal transduction, molecular transport, and cell-cell interactions. However, due to the nature of membrane proteins, the development of a preparative method that produces a sufficient yield of purified membrane proteins from the cell remains a challenge. In the present study, frit inlet asymmetrical flow field-flow fractionation (FI-AFlFFF) was employed to fractionate membrane fragments containing membrane proteins from free cytoplasmic proteins of prostatic cancer cell (DU145 cell) lysates. The isolated membrane proteins were then digested and analyzed by nanoflow liquid chromatography/tandem mass spectrometry (nLC-ESI-MS-MS). Since fractionation of the cell lysate mixtures containing membrane fragments and cytoplasmic proteins could be achieved based on the differences of their sizes in FI-AFlFFF, membrane fragments were partially isolated from the cytoplasmic proteins and collected. The performance of FI-AFlFFF for prefractionation of the membrane proteome was examined by comparing the number of membrane proteins that were identified with the number identified using an ultracentrifugation method. The application of FI-AFlFFF to membrane proteomics produced an increased yield of purified membrane proteins with fewer cytoplasmic proteins compared to a conventional ultracentrifugation method.