gebhart/patrepeval huggingface dataset:
SMS MUSSELS: A navigator‐free reconstruction for simultaneous multi‐slice‐accelerated multi‐shot diffusion weighted imaging (2019)

For the slice accelerations considered in this study, the proposed method can successfully recover DWIs from SMS-accelerated ms-DWI acquisitions.
The Realizable Space of Spatial Stiffnesses Achieved With a Parallel Connection of Simple Springs (1997)

Abstract In this paper, we identify the space of spatial compliant behavior that can be achieved through the use of simple springs connected in parallel to a single rigid body. Here, the expression “simple spring” refers to the set of compliant relations associated with purely translational springs and purely rotational springs. We show that, regardless of the number of springs used, there exists a subspace within the 21 dimensional symmetric spatial stiffness matrix space that cannot be reached by a parallel simple spring system. The subspace of “realizable” spatial stiffness matrices achieved with parallel simple springs is 20 dimensional and is defined by a linear necessary and sufficient condition on the positive semidefinite stiffness matrix. We show that any full-rank spatial stiffness matrix satisfying the condition can be realized using only line springs.
Long-Term SMN- and Ncald-ASO Combinatorial Therapy in SMA Mice and NCALD-ASO Treatment in hiPSC-Derived Motor Neurons Show Protective Effects (2023)

For SMA patients with only two <i>SMN2</i> copies, available therapies might be insufficient to counteract lifelong motor neuron (MN) dysfunction. Therefore, additional SMN-independent compounds, supporting SMN-dependent therapies, might be beneficial. Neurocalcin delta (NCALD) reduction, an SMA protective genetic modifier, ameliorates SMA across species. In a low-dose <i>SMN</i>-ASO-treated severe SMA mouse model, presymptomatic intracerebroventricular (i.c.v.) injection of <i>Ncald</i>-ASO at postnatal day 2 (PND2) significantly ameliorates histological and electrophysiological SMA hallmarks at PND21. However, contrary to <i>SMN</i>-ASOs, <i>Ncald</i>-ASOs show a shorter duration of action limiting a long-term benefit. Here, we investigated the longer-term effect of <i>Ncald</i>-ASOs by additional i.c.v. bolus injection at PND28. Two weeks after injection of 500 µg <i>Ncald</i>-ASO in wild-type mice, NCALD was significantly reduced in the brain and spinal cord and well tolerated. Next, we performed a double-blinded preclinical study combining low-dose <i>SMN</i>-ASO (PND1) with 2× i.c.v. <i>Ncald</i>-ASO or CTRL-ASO (100 µg at PND2, 500 µg at PND28). <i>Ncald</i>-ASO re-injection significantly ameliorated electrophysiological defects and NMJ denervation at 2 months. Moreover, we developed and identified a non-toxic and highly efficient human <i>NCALD</i>-ASO that significantly reduced NCALD in hiPSC-derived MNs. This improved both neuronal activity and growth cone maturation of SMA MNs, emphasizing the additional protective effect of <i>NCALD</i>-ASO treatment.
Increased Risk of Aging-Related Neurodegenerative Disease after Traumatic Brain Injury (2023)

Traumatic brain injury (TBI) survivors frequently suffer from chronically progressive complications, including significantly increased risk of developing aging-related neurodegenerative disease. As advances in neurocritical care increase the number of TBI survivors, the impact and awareness of this problem are growing. The mechanisms by which TBI increases the risk of developing aging-related neurodegenerative disease, however, are not completely understood. As a result, there are no protective treatments for patients. Here, we review the current literature surrounding the epidemiology and potential mechanistic relationships between brain injury and aging-related neurodegenerative disease. In addition to increasing the risk for developing all forms of dementia, the most prominent aging-related neurodegenerative conditions that are accelerated by TBI are amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Parkinson's disease (PD), and Alzheimer's disease (AD), with ALS and FTD being the least well-established. Mechanistic links between TBI and all forms of dementia that are reviewed include oxidative stress, dysregulated proteostasis, and neuroinflammation. Disease-specific mechanistic links with TBI that are reviewed include TAR DNA binding protein 43 and motor cortex lesions in ALS and FTD; alpha-synuclein, dopaminergic cell death, and synergistic toxin exposure in PD; and brain insulin resistance, amyloid beta pathology, and tau pathology in AD. While compelling mechanistic links have been identified, significantly expanded investigation in the field is needed to develop therapies to protect TBI survivors from the increased risk of aging-related neurodegenerative disease.
In Vivo Functional Characterization of the Aldolase B Gene Enhancer (2002)

A 400-bp intronic enhancer fragment in conjunction with the proximal promoter of the aldolase B gene provided correct tissue-specific expression in transgenic mice together with hormonal regulation in the liver. We investigated in vivo and in cultured cells the contribution of the intronic regulatory sequences and their interaction with the promoter elements in controlling aldolase B gene expression. Transgene activity was completely abolished by disruption of the two hepatocyte nuclear factor 1 (HNF1) binding sites in the enhancer, whereas mutation of one HNF1 site had no effect in the liver but strongly decreased activity in the kidney. Our data show that the HNF1 binding site(s) in the enhancer were key regulators of aldolase B transgene expression both in the liver and kidney. Deletion of the CCAAT/enhancer-binding protein site in the promoter completely abolished the enhancer function in HepG2 cells. These results suggest that expression of the aldolase B gene in the liver requires cooperative interactions between CCAAT/enhancer-binding protein and HNF1. Deletion of the HNF4 binding site in the enhancer suppressed expression in both liver and kidney in half of the transgenic lines, suggesting that this element might play a role in chromatin opening at the insertion site. We firmly establish that the endogenous aldolase B gene's first response to glucagon or cyclic AMP exposure was a transient increase in the expression in the liver, followed by a secondary decline in the transcription, as previously reported. This response was reproduced by all transgenes studied, indicating that neither HNF1 nor HNF4 binding sites in the enhancer were involved in this biphasic cyclic AMP response.
The Design of a new Persistent Object Store for PJama (2007)

This paper presents the design of a new store layer for PJama. PJama is a platform that provides orthogonal persistence for Java. Based on experience with a prototype, PJama0, a new architecture has been devised to permit incremental store management and to allow a number of object management regimes to co-exist in one store. It uses a plug-in model for composing a Java Virtual Machine (JVM) with the persistent store and a descriptor abstraction to limit the impact of changes in JVMs on store management. Its anticipated advantages over the current scheme include flexibility, adaptability, scalability, and maintainability.
Effect of influent carbon fractionation and reactor configuration on mainstream nitrogen removal and NOB out-selection (2019)

The magnitude of A-stage effluent particulate COD correlated negatively with B-stage NOB rate during fully intermittent aeration. This was likely due to heterotrophic competition for nitrite during intermittent aeration.
Carrier Gas Dependence at Initial Processes for a-Plane AlN Growth on r-Plane Sapphire Substrates by Hydride Vapor Phase Epitaxy (2011)

The influence of the carrier gas used during the thermal cleaning of r -plane sapphire substrates and the subsequent first AlN layer growth at 1050 °C on two-step growth of a -plane AlN layers by hydride vapor phase epitaxy (HVPE) was investigated. When hydrogen (H 2 ) was used as the carrier gas, the decomposition of r -plane sapphire occurred during the thermal cleaning, and unintentional nitridation of the sapphire surface occurred at the beginning of the growth of the first AlN layer, which resulted in the occurrence of misoriented AlN grains in the second AlN layer grown at 1450 °C. When a mixture of H 2 and nitrogen (N 2 ) was used as the carrier gas, nitridation of the sapphire surface occurred during the thermal cleaning, which also resulted in the occurrence of misoriented AlN grains. A single-crystalline a -plane AlN layer free of misoriented grains could be obtained by using only N 2 as the carrier gas during the thermal cleaning and the growth of the first AlN layer to prevent nitridation of the sapphire surface.
Data from Cancer Immunotherapy Targeting the High Molecular Weight Melanoma-Associated Antigen Protein Results in a Broad Antitumor Response and Reduction of Pericytes in the Tumor Vasculature (2023)

&lt;div&gt;Abstract&lt;p&gt;The high molecular weight melanoma-associated antigen (HMW-MAA), also known as melanoma chondroitin sulfate proteoglycan, has been used as a target for the immunotherapy of melanoma. This antigen is expressed on the cell surface and has a restricted distribution in normal tissues. Besides its expression in a broad range of transformed cells, this antigen is also found in pericytes, which are important for tumor angiogenesis. We generated a recombinant &lt;i&gt;Listeria monocytogenes&lt;/i&gt; (&lt;i&gt;Lm&lt;/i&gt;-LLO-HMW-MAA-C) that expresses and secretes a fragment of HMW-MAA (residues 2,160–2,258) fused to the first 441 residues of the listeriolysin O (LLO) protein. Immunization with &lt;i&gt;Lm&lt;/i&gt;-LLO-HMW-MAA-C was able to impede the tumor growth of early established B16F10-HMW-MAA tumors in mice and both CD4&lt;sup&gt;+&lt;/sup&gt; and CD8&lt;sup&gt;+&lt;/sup&gt; T cells were required for therapeutic efficacy. Immune responses to a known HLA-A2 epitope present in the HMW-MAA&lt;sub&gt;2160-2258&lt;/sub&gt; fragment was detected in the HLA-A2/K&lt;sup&gt;b&lt;/sup&gt; transgenic mice immunized with &lt;i&gt;Lm&lt;/i&gt;-LLO-HMW-MAA-C. Surprisingly, this vaccine also significantly impaired the &lt;i&gt;in vivo&lt;/i&gt; growth of other tumorigenic cell lines, such as melanoma, renal carcinoma, and breast tumors, which were not engineered to express HMW-MAA. One hypothesis is that the vaccine could be targeting pericytes, which are important for tumor angiogenesis. In a breast tumor model, immunization with &lt;i&gt;Lm&lt;/i&gt;-LLO-HMW-MAA-C caused CD8&lt;sup&gt;+&lt;/sup&gt; T-cell infiltration in the tumor stroma and a significant decrease in the number of pericytes in the tumor blood vessels. In conclusion, a &lt;i&gt;Lm&lt;/i&gt;-based vaccine against HMW-MAA can trigger cell-mediated immune responses to this antigen that can target not only tumor cells but also pericytes in the tumor vasculature. [Cancer Res 2008;68(19):8066–75]&lt;/p&gt;&lt;/div&gt;
Brain Iron Deposition in Aging and Disease: Role of HO-1 (2009)

• Mechanisms responsible for the pathological deposition of redox-active iron in the aging and degenerating human brain remain incompletely understood. • Heme oxygenase-1 (HO-1) is a 32-kDa stress protein that degrades heme to biliverdin, free iron, and carbon monoxide. • Brain HO-1 expression increases with advancing age, and the enzyme is further induced in CNS tissues affected by Alzheimer’s disease, Parkinson’s disease, and other neurodegenerative and neuroinflammatory conditions. • Upregulation of HO-1 in astrocytes exacerbates intracellular oxidative stress and promotes sequestration of non-transferrin-derived iron by the mitochondrial compartment. • The glial mitochondrial iron catalyzes the bio-activation of protoxins (e.g., catechols, MPTP) to potent neurotoxins (o-semiquinones, MPP+) and may further facilitate neural injury by attenuating glutathione biosynthesis and other ATP-dependent processes. • Suppression of glial HO-1 induction or activity may constitute a rational therapeutic approach to curtail pathological iron deposition and mitochondrial insufficiency in disorders of the aging human CNS.
Supplementary Figure 2 from <i>TMPRSS2-ERG</i> Status Is Not Prognostic Following Prostate Cancer Radiotherapy: Implications for Fusion Status and DSB Repair (2023)

&lt;p&gt;Supplementary Figure 2 - PDF file 71K, Construction of biopsy TMA blocks. Four millimeter length of the needle biopsy core (previously delimited by pathologist) is cut out from the original formalin fixed paraffin embedded tissue block. A scalpel blade is used to cut the exceeding wax on the opposite side of the biopsy tissue (opposite side marked in green) in order to reach a final 4 mm x 2 mm x 2 mm checker. These checkers are flipped 90 degrees (long axis of the prostate needle biopsy turns vertical) and placed within a stainless steel mold as a TMA template. The TMA block is completed by re-embedding the checkers by pouring hot wax into the mold. Last step on the right side shows an Hematoxylin and Eosin (H-E)-stained section from a biopsy TMA block (low power)&lt;/p&gt;
Generating Negative Samples for Sequential Recommendation (2022)

To make Sequential Recommendation (SR) successful, recent works focus on designing effective sequential encoders, fusing side information, and mining extra positive self-supervision signals. The strategy of sampling negative items at each time step is less explored. Due to the dynamics of users' interests and model updates during training, considering randomly sampled items from a user's non-interacted item set as negatives can be uninformative. As a result, the model will inaccurately learn user preferences toward items. Identifying informative negatives is challenging because informative negative items are tied with both dynamically changed interests and model parameters (and sampling process should also be efficient). To this end, we propose to Generate Negative Samples (items) for SR (GenNi). A negative item is sampled at each time step based on the current SR model's learned user preferences toward items. An efficient implementation is proposed to further accelerate the generation process, making it scalable to large-scale recommendation tasks. Extensive experiments on four public datasets verify the importance of providing high-quality negative samples for SR and demonstrate the effectiveness and efficiency of GenNi.
MSK1 is required for CREB phosphorylation in response to mitogens in mouse embryonic stem cells (2000)

Mouse embryonic stem (ES) cells homozygous for disruption of the MSK1 gene had no detectable MSK1 activity. However, their activators (extracellular signal related kinase (ERK)1/ERK2) were stimulated normally in mitogen- and stress-activated protein kinase (MSK)1-/- and wild type cells in response to tetradecanoylphorbol acetate (TPA) and epidermal growth factor (EGF). TPA and EGF induced the phosphorylation of cyclic AMP-responsive element binding protein (CREB) at Ser-133 and ATF1 at Ser-63 in wild type cells and this was abolished by inhibition of the mitogen-activated protein kinase cascade. In contrast, the TPA- and EGF-induced phosphorylation of CREB/ATF1 was barely detectable in MSK1-/- cells. However, basal and forskolin-induced phosphorylation was similar, indicating that the MSK1 'knockout' did not prevent CREB phosphorylation by cyclic AMP-dependent protein kinase. Thus MSK1 is required for CREB and ATF1 phosphorylation after mitogenic stimulation of ES cells.
Rapid and Highly Selective Cleavage of Ribonucleoside 2′,3′‐Cyclic Monophosphates by Dinuclear CuII Complexes (1997)

Two characteristics that never before appeared together are combined in complexes 1 and 2, which show high activity and high selectivity in the hydrolysis of cyclic nucleoside 2′,3′-monophosphates as model compounds for RNA. In the case of 1 the regioselectivity is exceptional, and, in the case of 2, the base selectivity.
Substrate and epitaxial issues for SiC power devices (2002)

Realization of the full potential of semiconductor SiC for electronic and optical applications is critically dependent on the production of large diameter SiC single-crystals of high crystalline quality and controlled impurity content as well as high quality uniform epitaxial layers. In this paper, current substrate and epitaxial issues are presented in the light of recent results. Progress in monocrystalline SiC bulk crystal growth is characterized by the attainment of substrate diameters up to 100-mm; residual impurities in the 10/sup 15/ cm/sup -3/ range; and micropipe densities as low as 1.1 cm/sup -2/ over an entire 50-mm diameter 4H-SiC wafer. Epitaxial growth progress is highlighted by growth rates as high as 50 /spl mu/m/h, residual impurities of 10/sup 14/ cm/sup -3/, and doping uniformities of less than 4.7% in commercial multiwafer reactors. Current materials challenges are the reduction of micropipes, dislocations and dislocation related defects.
Bounds for the On-line Multicast Problem in Directed Graphs. (1997)

On-line multicasting has received a lot of attention lately, because of its great practical importance. However, most research assumes undirected graphs, which fail to model the directivity of real networks. In this paper, we fill this gap by offering upper and lower bounds for the on-line directed multicast problem in a worst case analysis. We examine two types of on-line problems: the join-only problem where destinations join arbitrarily but stay till the end of the session, and the join-leave problem, where destinations can join and leave arbitrarily. We define the asymmetry of a graph to be the maximum ratio of opposite directed edges between a pair of nodes for all node-pairs. For the join-only on-line problem, we prove that a greedy on-line algorithm is log(A + 1)-competitive compared to any on-line algorithm. For the join-leave problem on both undirected and directed graphs, we prove a new lower bound, which is exponential in the previous undirected bound (the number o...
Thick Printed Copper as Highly Reliable Substrate Technology for Power Electronics (2015)

Up to now Direct Bonded Copper (DBC) is the standard substrate technology for most power electronics applications. This paper presents Thick Printed Copper (TPC) as an alternative technology for applications with highest reliability requirements in power electronics and high brightness LEDs with a high freedom in design. The drawbacks of DBC are the relatively low reliability under thermo-mechanical stress, a low spatial resolution and a low freedom of design in regards of layer thickness. The outstanding high reliability of Thick Printed Copper is demonstrated in this paper by passive thermal shock tests in direct comparison to DBC. In the second part, the high spatial resolution possible with copper paste technology is described. Furthermore, the work shows that TPC can be applied to a wide range of relevant ceramic substrate materials including alumina, aluminum nitride and zirconia toughened alumina. Finally, a detailed review is given discussing the different copper layer to substrate bonding mechanisms, which prevent void formation and are responsible for the excellent thermo-mechanical reliability.
Molecular Design for Moisture Insensitivity of Compositionally Graded Hybrid Films (2015)

Effective bonding of organic/inorganic interfaces especially in high humidity environments is paramount to the structural reliability of modern multilayer device technologies, such as flexible electronics, photovoltaics, microelectronic devices, and fiber-metal laminates used in aerospace applications. We demonstrate the ability to design compositionally graded hybrid organic/inorganic films with an inorganic zirconium network capable of forming a moisture-insensitive bond at the interface between an oxide and organic material. By controlling the chemistry of the deposited films and utilizing time-dependent debonding studies, we were able to correlate the behavior of the hybrid films at high humidity to their underlying molecular structure. As a result, an outstanding threefold improvement in adhesion of silicon/epoxy interfaces can be obtained with the introduction of these films even in high humidity environments.
Optimized Periodic ΣΔ Bitstreams for DC Signal Generation Used in Dynamic Calibration Applications (2020)

Settling time is an important performance metric in digital-to-analog converters (DACs) that are used for dynamic calibration applications. To obtain an area efficient DAC design, periodic sequences are generated from sigma-delta modulators (ΣΔMs) using software, stores the sequence in memory and then passes it to a low-pass filter (LPF). In this brief, the sigma-delta (ΣΔ) bitstream generated in software will be optimized such that it yields a system that settles faster and is more area efficient. Two optimization routines are used, namely, serial method and random method algorithms. The random method is chosen to optimize the ΣΔ bitstreams for its computational simplicity. It will be shown, that using the random method routine provides at least 46% improvement in settling time performance of a 12-bit DAC, used in the paper as a design example. Moreover, it offers silicon area savings by at least 10% for resistor components and 35% for capacitor components. Similar results were obtained for 8 to 11 bits of resolution.
Distinctive ionic transport of freshly excised human epileptogenic brain tissue (2021)

Epileptogenic lesions have higher concentrations of sodium than does normal brain tissue. Such lesions are palpably recognized by a surgeon and then excised in order to eliminate epileptic seizures with their associated abnormal electrical behavior. Here, we study the frequency-dependent electrical conductivities of lesion-laden tissues excised from the brains of epilepsy patients. The low-frequency (<1000 Hz) conductivity of biological tissue primarily probes extracellular solvated sodium-cations traveling parallel to membranes within regions bounded by blockages. This conductivity rises monotonically toward saturation as the frequency surpasses the rate with which diffusing solvated sodium cations encounter blockages. We find that saturation occurs at dramatically higher frequencies in excised brain tissue containing epileptogenic lesions than it does in normal brain tissue. By contrast, such an effect is not reported for tumors embedded in other excised biological tissue. All told, epileptogenic lesions generate frequency-dependent conductivities that differ qualitatively from those of both normal brain tissues and tumors.
Copper‐dependent regulation of NMDA receptors by cellular prion protein: implications for neurodegenerative disorders (2012)

N-Methyl-D-aspartate (NMDA) receptors mediate a wide range of important nervous system functions. Conversely, excessive NMDA receptor activity leads to cytotoxic calcium overload and neuronal damage in a wide variety of CNS disorders. It is well established that NMDA receptors are tightly regulated by a number of cell signalling pathways. Recently, it has been shown that NMDA receptor activity is modulated by cellular prion protein (PrP(C)) in a copper-dependent manner. Here we give an overview of the current state of knowledge concerning the novel concept of potent modulation of this receptor's kinetics by copper ions, and the interplay between NMDA receptors and PrP(C) in the context of neurological diseases such as Alzheimer's disease, epilepsy, pain and depression.
Supplementary Figure S8 from Preclinical Activity of SAR408701: A Novel Anti-CEACAM5–maytansinoid Antibody–drug Conjugate for the Treatment of CEACAM5-positive Epithelial Tumors (2023)

&lt;p&gt;Supplementary Figure S8&lt;/p&gt;