gebhart/patrepeval huggingface dataset:
Heat shock protein expression as guidance for the therapeutic window of retinal laser therapy (2016)

Unlike conventional photocoagulation, non-damaging retinal laser therapy (NRT) limits laser-induced heating to stay below the retinal damage threshold and therefore requires careful dosimetry. Without the adverse effects associated with photocoagulation, NRT can be applied to critical areas of the retina and repeatedly to manage chronic disorders. Although the clinical benefits of NRT have been demonstrated, the mechanism of therapeutic effect and width of the therapeutic window below damage threshold are not well understood. Here, we measure activation of heat shock response via laser-induced hyperthermia as one indication of cellular response. A 577 nm laser is used with the Endpoint Management (EpM) user interface, a titration algorithm, to set experimental pulse energies relative to a barely visible titration lesion. Live/dead staining and histology show that the retinal damage threshold in rabbits is at 40% of titration energy on EpM scale. Heat shock protein 70 (HSP70) expression in the retinal pigment epithelium (RPE) was detected by whole-mount immunohistochemistry after different levels of laser treatment. We show HSP70 expression in the RPE beginning at 25% of titration energy indicating that there is a window for NRT between 25% and 40% with activation of the heat shock protein expression in response to hyperthermia. HSP70 expression is also seen at the perimeter of damaging lesions, as expected based on a computational model of laser heating. Expression area for each pulse energy setting varied between laser spots due to pigmentation changes, indicating the relatively narrow window of non-damaging activation and highlighting the importance of proper titration.
Emerging clinical importance of the cancer biomarkers kallikrein-related peptidases (KLK) in female and male reproductive organ malignancies (2013)

Most of the information regarding elevated expression of KLKs in tumor-affected organs is available for ovarian cancer; depicting them as valuable biomarkers in the cancerous phenotype. In contrast, for breast cancer, a series of KLKs was found to be downregulated. However, in breast cancer, KLK4 is elevated which is also true for ovarian and prostate cancer. In such cases, selective synthetic KLK inhibitors that aim at blocking the proteolytic activities of certain KLKs may serve as future candidate therapeutic drugs to interfere with tumor progression and metastasis.
Session details: Technical Session 3: Architecture 1 (2015)

No abstract available.
Examination of the solventlike nature of zeolites based on solvatochromic indicator (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExamination of the solventlike nature of zeolites based on solvatochromic indicatorPrabir K. Dutta and Wayne TurbevilleCite this: J. Phys. Chem. 1991, 95, 10, 4087–4092Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://doi.org/10.1021/j100163a036RIGHTS & PERMISSIONSArticle Views123Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (692 KB) Get e-Alerts
Mecamylamine Suppresses Basal and Nicotine-Stimulated Choroidal Neovascularization (2008)

These data suggest that endogenous activation of nAChR promotes CNV and that activation of nAChR by nicotine may contribute to the increased incidence of CNV seen in smokers with age-related macular degeneration (AMD). Topically administered mecamylamine could provide an appealing new treatment approach for CNV.
Fanout of 2 Triangle Shape Spin Wave Logic Gates (2021)

Having multi-output logic gates saves much energy because the same structure can be used to feed multiple inputs of next stage gates simultaneously. This paper proposes novel triangle shape fanout of 2 spin wave Majority and XOR gates; the Majority gate is achieved by phase detection, whereas the XOR gate is achieved by threshold detection. The proposed logic gates are validated by means of micromagnetic simulations. Furthermore, the energy and delay are estimated for the proposed structures and compared with the state-of-the-art spin wave logic gates, and 16nm and 7nm CMOS. The results demonstrate that the proposed structures provide energy reduction of 25%-50% in comparison to the other 2-output spin-wave devices while having the same delay, and energy reduction between 43x and 0.8x when compared to the 16nm and 7nm CMOS while having delay overhead between 11x and 40x.
STRUCTURAL AND SOLVENT EFFECTS IN THE SOLVOLYSES OF SECONDARY BETA-ARYLALKYL ARENESULFONATES (1972)

Abstract not available
Glucocerebrosidase mutations among African-American patients with type 1 Gaucher disease (2001)

While the inherited deficiency of the enzyme glucocerebrosidase (Gaucher disease) is panethnic in its distribution, there have not been studies of the mutations encountered in specific ethnic groups in the United States, other than those on Ashkenazi Jews. We present the clinical descriptions and genotypes of seven patients of African-American ancestry with type 1 Gaucher disease, and summarize the published literature regarding the genotypes encountered in this population. All seven of the patients had moderate-to-severe manifestations of the disease, and all developed symptoms by adolescence. Genotypic analyses revealed that no two probands shared the same genotype. The common mutations N370S, c.84-85insG, IVS2+1 G-->A, and R463C were not seen. Mutation L444P was present on one allele in each of the patients; but the same mutation was encountered as a single point mutation in three of the patients, and as part of a recombinant allele in four of the patients. Southern blot analyses revealed a glucocerebrosidase fusion allele in one patient, and a duplication resulting from recombination in the region downstream from the glucocerebrosidase gene in three of the patients. Five different point mutations (A90T, R48W, N117D, R170C, and V352L), one deletion mutation (c.222-224 delTAC), and one insertion mutation (c.153-154 insTACAGC) were encountered. Our results demonstrate that there is significant genotypic heterogeneity among African-American patients with type 1 Gaucher disease, and that recombinations in the glucocerebrosidase gene locus are particularly common in this patient group. Published 2001 Wiley-Liss, Inc.
LinCE: A Centralized Benchmark for Linguistic Code-switching Evaluation (2020)

Recent trends in NLP research have raised an interest in linguistic code-switching (CS); modern approaches have been proposed to solve a wide range of NLP tasks on multiple language pairs. Unfortunately, these proposed methods are hardly generalizable to different code-switched languages. In addition, it is unclear whether a model architecture is applicable for a different task while still being compatible with the code-switching setting. This is mainly because of the lack of a centralized benchmark and the sparse corpora that researchers employ based on their specific needs and interests. To facilitate research in this direction, we propose a centralized benchmark for Linguistic Code-switching Evaluation (LinCE) that combines ten corpora covering four different code-switched language pairs (i.e., Spanish-English, Nepali-English, Hindi-English, and Modern Standard Arabic-Egyptian Arabic) and four tasks (i.e., language identification, named entity recognition, part-of-speech tagging, and sentiment analysis). As part of the benchmark centralization effort, we provide an online platform at ritual.uh.edu/lince, where researchers can submit their results while comparing with others in real-time. In addition, we provide the scores of different popular models, including LSTM, ELMo, and multilingual BERT so that the NLP community can compare against state-of-the-art systems. LinCE is a continuous effort, and we will expand it with more low-resource languages and tasks.
Self-consistency based control scheme for magnetization dynamics (2001)

A numerical framework is presented for the solution of the Landau–Lifshitz–Gilbert equation of magnetization motion using a semi-implicit Crank–Nicholson integration scheme. Along with the details of both space and time domain discretizations, we report on the development of a physically based self-consistency criterion that allows for a quantitative measurement of error in dynamic micromagnetic simulations. In essence, this criterion relies in recalculating from actual magnetization motion the imposed phenomenological damping constant. Test calculations were performed with special attention paid to the determination of suitable integration time steps.
A Cellularized Biphasic Implant Based on a Bioactive Silk Fibroin Promotes Integration and Tissue Organization during Osteochondral Defect Repair in a Porcine Model (2019)

In cartilage tissue engineering, biphasic scaffolds (BSs) have been designed not only to influence the recapitulation of the osteochondral architecture but also to take advantage of the healing ability of bone, promoting the implant's integration with the surrounding tissue and then bone restoration and cartilage regeneration. This study reports the development and characterization of a BS based on the assembly of a cartilage phase constituted by fibroin biofunctionalyzed with a bovine cartilage matrix, cellularized with differentiated autologous pre-chondrocytes and well attached to a bone phase (decellularized bovine bone) to promote cartilage regeneration in a model of joint damage in pigs. BSs were assembled by fibroin crystallization with methanol, and the mechanical features and histological architectures were evaluated. The scaffolds were cellularized and matured for 12 days, then implanted into an osteochondral defect in a porcine model (<i>n</i> = 4). Three treatments were applied per knee: Group I, monophasic cellular scaffold (single chondral phase); group II (BS), cellularized only in the chondral phase; and in order to study the influence of the cellularization of the bone phase, Group III was cellularized in chondral phases and a bone phase, with autologous osteoblasts being included. After 8 weeks of surgery, the integration and regeneration tissues were analyzed via a histology and immunohistochemistry evaluation. The mechanical assessment showed that the acellular BSs reached a Young's modulus of 805.01 kPa, similar to native cartilage. In vitro biological studies revealed the chondroinductive ability of the BSs, evidenced by an increase in sulfated glycosaminoglycans and type II collagen, both secreted by the chondrocytes cultured on the scaffold during 28 days. No evidence of adverse or inflammatory reactions was observed in the in vivo trial; however, in Group I, the defects were not reconstructed. In Groups II and III, a good integration of the implant with the surrounding tissue was observed. Defects in group II were fulfilled via hyaline cartilage and normal bone. Group III defects showed fibrous repair tissue. In conclusion, our findings demonstrated the efficacy of a biphasic and bioactive scaffold based on silk fibroin and cellularized only in the chondral phase, which entwined chondroinductive features and a biomechanical capability with an appropriate integration with the surrounding tissue, representing a promising alternative for osteochondral tissue-engineering applications.
Investigation on Deep Layer Measurements in the Cerebral Cortex within the Adult Head by near Infrared Spectroscopy Using an Absorbance Difference Technique (2003)

Recent reports on modeled simulation of near infrared photons' paths in the adult head have shown that the cerebrospinal fluid functions as an optical guide, suggesting that non-invasive haemodynamic measurement of the deep layer of the cerebral cortex is difficult. Thus, the authors investigated the volume of the cortex measured by near infrared spectroscopy with the absorbance difference technique. This technique uses two radiation detector probes to yield short and long photon paths in order to realise selective measurement of the cortex by minimising the interference from the superficial layers covering the cortex. The results show that the volume of the cortex measured by this technique is larger in the temporal area than in the frontal area. Therefore, it is concluded that the photons' path in the temporal area reaches the deep layer of the cortex and that it is possible to measure the haemodynamic response of the auditory cortex in the deep temporal area of the adult head to sound stimuli.
Discrete multi-dimensional linear transforms over arbitrarily shaped supports (2002)

In order to apply a multi-dimensional linear transform, over an arbitrarily shaped support, the usual practice is to fill out the support to a hypercube by zero padding. This does not however yield a satisfactory definition for transforms in two or more dimensions. The problem that we tackle is: how do we redefine the transform over an arbitrary shaped region suited to a given application? We present a novel iterative approach to define any multi-dimensional linear transform over an arbitrary shape given that we know its definition over a hypercube. The proposed solution is (1) extensible to all possible shapes of support (whether connected or unconnected) (2) adaptable to the needs of a particular application. We also present results for the Fourier transform, for a specific adaptation of the general definition of the transform which is suitable for compression or segmentation algorithms.
Comparison of tandem mass spectrometry to fluorimetry for newborn screening of LSDs (2017)

Comparison of tandem mass spectrometry to fluorimetry for newborn screening of LSDs Sir -while we have no issues with the data presented in the Letter to the Editor [1], we are compelled to give an alternative conclusion.The majority of newborn labs set their own screen cutoffs, and Illinois uses much higher cutoffs than Missouri.It is only meaningful to compare the number of below-cutoff enzyme activity samples with the use of equivalent cutoffs [2-4].For example, for mucopolysaccharidosis-I, Missouri steadily lowered their cutoff from 20% to 7% of mean iduronidase activity over the past few years [5], whereas Illinois currently uses a much higher cutoff of 14% [6].With a 7% cutoff the number of screen positives per 100,000 newborns by digital microfluidics fluorescence in Missouri was 43 [5], whereas tandem mass spectrometry (MS/MS) gave 9 in Washington [4,6], 12 in Illinois [6], and 16 in New York [6].For Pompe disease with equivalent cutoffs [4,6], Missouri reports 52 screen positives per 100,000 [5], Washington 23 [4,6], Illinois 14 [6], and New York 21 [6]. We hypothesize that the lower number of screen positives with MS/MS is due to the high analytical range (not synonymous with dynamic range) of this method compared to fluorometry [7].Perhaps the clearest evidence that MS/MS performs better than fluorometry comes from a study in Taiwan using an identical set of DBS showing that MS/MS but not fluorometry separates the pseudodeficiency from the Pompe-affected DBS samples (Fig. 1) [8].This shows that variation due to DBS sampling is not a dominant effect and disproves the statement that the "analytical/dynamic range is irrelevant" [1].Additionally, there is no correlation seen in one enzymatic activity compared to another for 111,000 DBS tested for iduronidase, -glucosidase, and -galactosidase [9], showing that variation in white cell count or other DBS quality factors are not dominant effects.
Channel Decoding with Quantum Approximate Optimization Algorithm (2019)

Motivated by the recent advancement of quantum processors, we investigate quantum approximate optimization algorithm (QAOA) to employ quasi-maximum-likelihood (ML) decoding of classical channel codes. QAOA is a hybrid quantum-classical variational algorithm, which is advantageous for the near-term noisy intermediate-scale quantum (NISQ) devices, where the fidelity of quantum gates is limited by noise and de-coherence. We first describe how to construct Ising Hamiltonian model to realize quasi-ML decoding with QAOA. For level-1 QAOA, we derive the systematic way to generate theoretical expressions of cost expectation for arbitrary binary linear codes. Focusing on [7], [4] Hamming code as an example, we analyze the impact of the degree distribution in associated generator matrix on the quantum decoding performance. The excellent performance of higher-level QAOA decoding is verified when Pauli rotation angles are optimized through meta-heuristic variational quantum eigensolver (VQE). Furthermore, we demonstrate the QAOA decoding performance in a real quantum device.
Material Selection for Membrane-Based Gas Separations (1985)

High membrane permselectivity for a gas mixture is well-known to correlate with low permeability of the desired product through the membrane. Exceptions to this rule exist, however, and this suggests the possibility of improved membranes for a number of important applications. This paper suggests possible polymer structural changes which may allow control over the magnitudes of permeabilities and selectivities. These suggestions result from considering the permeability and selectivity in terms of their separate thermodynamic solubility and kinetic mobility contributions. The two contributions vary markedly with changes in the polymer structure and correlate with variations in penetrant and polymer physical properties. The feasibility of developing extremely selective high flux membrane materials is explored in terms of these correlations. The potential for such developments is shown to be fairly high for cases in which the permeant molecule is substantially more compact than the nonpermeant molecule if the resulting mobility advantage is not eliminated by a large solubility advantage favoring the nonpermeant. Several important examples of such systems are discussed including H2/CH4 and CO2/CH4. A short discussion of approaches to assess membrane materials for resistance to attack by components in the process stream is also presented.
Acute pressure changes in the brain are correlated with MR elastography stiffness measurements: initial feasibility in an in vivo large animal model (2017)

In this study, MRE demonstrated the potential for noninvasive measurement of changes in ICP. Magn Reson Med 79:1043-1051, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
Supplementary Text, Figure Legends, Figures S1-S12 from Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma (2023)

&lt;p&gt;Supplemental Figure S1. Integrative Analysis of Functional Genomics and Copy Number Variation in Melanoma Cells and Tissues, Supplemental Figure S2. Elastic Net Derived Biomarker Results for Melanoma Survival Genes and Detection of These Biomarkers in TCGA SKCM, Supplemental Figure S3. The SOX10 Regulatory Network Supporting Cell Autonomous Melanoma Cell Growth and Survival, Supplemental Figure S4. SOX10 Addiction Specifies Sensitivity of BRAF Mutant Melanomas to BRAF and MEK Inhibitors In Vitro, Related to Figure 1, Supplemental Figure S5. SOX10 Addiction Specifies Sensitivity of BRAF Mutant Melanomas to BRAF and MEK Inhibitors In Patients, Related to Figure 2, Supplemental Figure S6. Bicluster of melanoma cell lines and chemical compounds in McDermott/Benes GDSC dataset, Related to Figure 3, Supplemental Figure S7. Nomination of TBK1 as a Therapeutic Target for Drug-Resistant Melanoma, Related to Figure 3, Supplemental Figure S8. TBK1/IKKε-Addiction is Conserved In Vivo, Related to Figure 4, Supplemental Figure S9. TBK1/IKKε-Addiction Corresponds to a Cell Autonomous Innate Immune Melanoma Subtype, Related to Figure 5, Supplemental Figure S10. TBK1/IKKε Activate AKT and YAP to Support Survival of the Cell-autonomous Immune Melanoma Subtype, Related to Figure 6, Supplemental Figure S11. 13C glucose and 13C glutamine metabolism at 30m and 2h, Related to Figure 7 and Supplemental Fig. S7, Supplemental Figure S12. Distinct Epigenetic Cell Fate Programs Specify TBK1/IKKε Addiction, Related to Figure 7.&lt;/p&gt;
Total body 100-mGy X-irradiation does not induce Alzheimer's disease-like pathogenesis or memory impairment in mice (2013)

The cause and progression of Alzheimer's disease (AD) are poorly understood. Possible cognitive and behavioral consequences induced by low-dose radiation are important because humans are exposed to ionizing radiation from various sources. Early transcriptional response in murine brain to low-dose X-rays (100 mGy) has been reported, suggesting alterations of molecular networks and pathways associated with cognitive functions, advanced aging and AD. To investigate acute and late transcriptional, pathological and cognitive consequences of low-dose radiation, we applied an acute dose of 100-mGy total body irradiation (TBI) with X-rays to C57BL/6J Jms mice. We collected hippocampi and analyzed expression of 84 AD-related genes. Mouse learning ability and memory were assessed with the Morris water maze test. We performed in vivo PET scans with (11)C-PIB, a radiolabeled ligand for amyloid imaging, to detect fibrillary amyloid beta peptide (Aβ) accumulation, and examined characteristic AD pathologies with immunohistochemical staining of amyloid precursor protein (APP), Aβ, tau and phosphorylated tau (p-tau). mRNA studies showed significant downregulation of only two of 84 AD-related genes, Apbb1 and Lrp1, at 4 h after irradiation, and of only one gene, Il1α, at 1 year after irradiation. Spatial learning ability and memory were not significantly affected at 1 or 2 years after irradiation. No induction of amyloid fibrillogenesis or changes in APP, Aβ, tau, or p-tau expression was detected at 4 months or 2 years after irradiation. TBI induced early or late transcriptional alteration in only a few AD-related genes but did not significantly affect spatial learning, memory or AD-like pathological change in mice.
Air cooling limits of 3D stacked logic processor and memory dies (2014)

Through-Silicon-Vias (TSVs) enable 3D stack of logic processor and memory dies with significant improvement in latency and energy efficiency of large memory-bound computations. However, additional layers of memory die increase IC package thermal resistance. Thermal management has been identified as a key challenge to achieve high computation power and memory density in the same package. In this paper we present a numerical study on temperature mapping of 3D stacked dies in air-cooled package. We consider DRAM based memory with low power, mid power, and high power logic processors. We study the effect of logic processor power and number of memory dies on the temperature profile. This study provides thermally viable design space of compute-power to memory-size.