gebhart/patrepeval huggingface dataset:
Lowering P, T boundary for synthesis of pure nano-polycrystalline diamond (2010)

Attempts have been made to synthesize nano-polycrystalline diamond (NPD) from graphite at pressures of 12, 13 and 14 GPa at temperatures 2200-2600 using multi-anvil apparatus. The lower temperature limit for NPD formation increased with decreasing pressure, and we found that pure NPD can be synthesized even at the lowest pressure of 12 GPa, although quite high temperatures of exceeding 2600 are required. This result demonstrates that NPD can be formed at significantly lower pressures than ever synthesized, which should provide an important constraint in synthesizing larger NPD samples under limited press loads.
Nickel‐Promoted Recognition of Long DNA Sites by Designed Peptide Derivatives (2016)

We describe the synthesis of designed peptidic modules that self-assemble in specific DNA sequences of 12 base pairs in the presence of Ni(II) salts. The modules consist of modified fragments of transcription factors that have been appropriately engineered to include metal-chelating His and bipyridine ligands.
Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product (2017)

Farnesyl pyrophosphate synthase (FPPS) is an enzyme of the mevalonate pathway and a well-established therapeutic target. Recent research has focused around a newly identified druggable pocket near the enzyme's active site. Pharmacological exploitation of this pocket is deemed promising; however, its natural biological function, if any, is yet unknown. Here we report that the product of FPPS, farnesyl pyrophosphate (FPP), can bind to this pocket and lock the enzyme in an inactive state. The K<sub>d</sub> for this binding is 5-6 μM, within a catalytically relevant range. These results indicate that FPPS activity is sensitive to the product concentration. Kinetic analysis shows that the enzyme is inhibited through FPP accumulation. Having a specific physiological effector, FPPS is a bona fide allosteric enzyme. This allostery offers an exquisite mechanism for controlling prenyl pyrophosphate levels in vivo and thus contributes an additional layer of regulation to the mevalonate pathway.
Ginseng Berry Extract Prevents Atherogenesis via Anti-Inflammatory Action by Upregulating Phase II Gene Expression (2012)

Ginseng berry possesses higher ginsenoside content than its root, which has been traditionally used in herbal medicine for many human diseases, including atherosclerosis. We here examined the antiatherogenic effects of the Korean ginseng berry extract (KGBE) and investigated its underlying mechanism of action in vitro and in vivo. Administration of KGBE decreased atherosclerotic lesions, which was inversely correlated with the expression levels of phase II genes to include heme oxygenase-1 (HO-1) and glutamine-cysteine ligase (GCL). Furthermore, KGBE administration suppressed NF-κB-mediated expression of atherogenic inflammatory genes (TNF-α, IL-1β, iNOS, COX-2, ICAM-1, and VCAM-1), without altering serum cholesterol levels, in ApoE(-/-) mice fed a high fat-diet. Treatment with KGBE increased phase II gene expression and suppressed lipopolysaccharide-induced reactive oxygen species production, NF-κB activation, and inflammatory gene expression in primary macrophages. Importantly, these cellular events were blocked by selective inhibitors of HO-1 and GCL. In addition, these inhibitors reversed the suppressive effect of KGBE on TNF-α-mediated induction of ICAM-1 and VCAM-1, resulting in decreased interaction between endothelial cells and monocytes. These results suggest that KGBE ameliorates atherosclerosis by inhibiting NF-κB-mediated expression of atherogenic genes via upregulation of phase II enzymes and thus has therapeutic or preventive potential for atherosclerosis.
SupplementaryTable S2 from Paternally Expressed Gene 10 (PEG10) Promotes Growth, Invasion, and Survival of Bladder Cancer (2023)

&lt;p&gt;Probes used in the PCR assays&lt;/p&gt;
New integration schemes for 2,5D interposer (2013)

2,5D interposer are a hot topic at the moment in the packaging world. An interposer allows to inter-chip communication between multiple chips with intra-chip interconnects. This enables unmatched bandwidth, reduced power consumption and very good heat spreading. The 2,5D interposer allows to implement a big part of the promise of 3D ICs without the need to make TSVs into the chips.
Original Article: High sensitivity C-reactive protein levels across spectrum and severity of coronary artery disease (2012)

Background: C-reactive protein (CRP) is an acute-phase reactant protein synthesized by the liver in response to acute stress in a wide range of acute and chronic inflammatory conditions. In healthy subjects and patients presenting with coronary artery disease (CAD), elevated levels of CRP has repeatedly been demonstrated to predict future cardiovascular events. Methods: We measured high sensitivity C-reactive protein (hs-CRP) levels in 382 consecutive patients with CAD and 60 healthy controls by immunoturbidimetry method. Risk factors like hypertension, diabetes mellitus, dyslipidaemia, smoking, obesity and family history of premature CAD were assessed. Results: The mean age of patients with CAD was 53.5±11.8 years (303 males) and that of control group was 50.83±8.07(28 males). The patient group had significant higher concentration of mean hs-CRP levels when compared with the healthy control group (1.8±1.9 mg/L vs 0.35±1.1 mg/L, p<0.001). The mean hs-CRP levels of unstable angina (USA) and myocardial infarction (MI) patients was higher than chronic stable angina (CSA) patients (p<0.05). Based on the disease severity, we found a significantly higher hs-CRP levels in patients of triple vessel disease when compared to patients with single vessel disease (p=0.01).
Simultaneous assessment of cardiac metabolism and perfusion using copolarized [1‐13C]pyruvate and 13C‐urea (2016)

The new pulse sequence was used to obtain maps of metabolism and perfusion in the rodent heart in a single acquisition. This hyperpolarized <sup>13</sup> C imaging test is expected to enable new studies in which the cardiac metabolism/perfusion mismatch can be studied in the acute environment. Magn Reson Med 77:151-158, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.
Transforming Growth Factor-β in Leishmanial Infection: a Parasite Escape Mechanism (1992)

The course of infection with the protozoan parasite Leishmania is determined in part by their early replication in macrophages, the exclusive host cells for these organisms. Although factors contributing to the survival of Leishmania are not well understood, cytokines influence the course of infection. Transforming growth factor-beta (TGF-beta) is a multipotential cytokine with diverse effects on cells of the immune system, including down-regulation of certain macrophage functions. Leishmanial infection induced the production of active TGF-beta, both in vitro and in vivo. TGF-beta was important for determining in vivo susceptibility to experimental leishmanial infection.
A VQ-based blur identification algorithm (2003)

The estimation of the point spread function (PSF) of the degradation system is often a necessary first step in the restoration of blurred images. A novel vector quantization (VQ)-based blur identification algorithm is presented. A number of codebooks are designed corresponding to various versions of the blurring function. Prototype images blurred by each candidate blur are used. Only the non-flat regions for specific frequency bands are represented by the entries in the codebooks. Given a noisy and blurred image, one of the codebooks is chosen based on a similarity measure, therefore providing the identification of the blur. Simulations are performed for various blurring functions and noise levels. The results demonstrate the effectiveness of the proposed algorithms.
Evaluation of the antifactor XA chromogenic assay for measuring rivaroxaban plasma concentrations using calibrators and controls (2012)

<h3>Background</h3> Rivaroxaban is an oral, direct Factor Xa inhibitor approved for clinical use for the prevention and treatment of thromboembolic disorders across several indications. Routine coagulation monitoring is not required, but a quantitative determination of rivaroxaban concentrations might be useful in some clinical circumstances. <h3>Purpose</h3> This multicentre study evaluated the suitability of a modified antifactor Xa chromogenic assay for the measurement of plasma rivaroxaban concentrations (ng/ml) using rivaroxaban calibrators and controls, and to assess the inter-laboratory precision of the measurement. <h3>Materials and methods</h3> Twenty-four centres in Europe and North America were provided with sets of rivaroxaban calibrators (0, 41, 209 and 422 ng/ml) and rivaroxaban pooled human plasma controls (20, 199 and 662 ng/ml; the concentrations were unknown to the participating laboratories). The evaluation was carried out over 10 days by each laboratory using local antifactor Xa reagents as well as a centrally provided, modified STA Rotachrom assay (Diagnostica Stago, Asnières-sur-Seine, France). A calibration curve was produced each day, and day-to-day precision was evaluated by testing three human plasma controls. <h3>Results</h3> When using the local antifactor Xa reagents, the measured rivaroxaban concentrations (mean±SD/actual value) were 17±6.4/20, 205±28.2/199 and 668±94.4 (in diluted samples)/662 ng/ml, and the coefficients of variance (CV) were 37.0%, 13.7% and 14.1%, respectively. When the modified STA Rotachrom method was used, the measured±SD/actual values were 18±3.4/20, 199±21.7/199 and 656±65.8 (in diluted samples)/662 ng/ml and the CV were 19.1%, 10.9% and 10.0%, respectively. Satisfactory inter-laboratory precision was achieved using rivaroxaban calibrators regardless of the type of antifactor Xa reagent and instrument used, except for the lowest concentration tested (20 ng/ml) when using the different local reagent/instrument combinations. <h3>Conclusions</h3> The results indicate that the antifactor Xa chromogenic method is suitable for measuring a wide range of plasma rivaroxaban concentrations (20–660 ng/ml), covering the expected concentrations after therapeutic doses, by using rivaroxaban calibrators and controls.
BYOL for Audio: Exploring Pre-trained General-purpose Audio Representations (2022)

Pre-trained models are essential as feature extractors in modern machine learning systems in various domains. In this study, we hypothesize that representations effective for general audio tasks should provide multiple aspects of robust features of the input sound. For recognizing sounds regardless of perturbations such as varying pitch or timbre, features should be robust to these perturbations. For serving the diverse needs of tasks such as recognition of emotions or music genres, representations should provide multiple aspects of information, such as local and global features. To implement our principle, we propose a self-supervised learning method: Bootstrap Your Own Latent (BYOL) for Audio (BYOL-A, pronounced "viola"). BYOL-A pre-trains representations of the input sound invariant to audio data augmentations, which makes the learned representations robust to the perturbations of sounds. Whereas the BYOL-A encoder combines local and global features and calculates their statistics to make the representation provide multi-aspect information. As a result, the learned representations should provide robust and multi-aspect information to serve various needs of diverse tasks. We evaluated the general audio task performance of BYOL-A compared to previous state-of-the-art methods, and BYOL-A demonstrated generalizability with the best average result of 72.4% and the best VoxCeleb1 result of 57.6%. Extensive ablation experiments revealed that the BYOL-A encoder architecture contributes to most performance, and the final critical portion resorts to the BYOL framework and BYOL-A augmentations. Our code is available online at https://github.com/nttcslab/byol-a for future studies.
Self-Organized Transformation from Hexagonal to Orthorhombic Bronze of Cs–Nb–W–O Mixed Oxides Prepared Hydrothermally (2017)

The thermal transformation of hydrothermally prepared Cs–Nb–W–O mixed oxides has been studied in the 25–1000 °C temperature range. Structural evolution of the prepared solids was monitored by in situ synchrotron X-ray diffraction, absorption spectroscopy techniques, conventional powder X-ray diffraction, thermogravimetric analysis, infrared and Raman spectroscopy, and high resolution transmission electron microscopy (HRTEM and STEM). The as-grown solids show the hexagonal tungsten bronze (HTB) structure, which can be stabilized above 900 °C depending on the chemical composition. From this temperature, solids are selectively transformed into the orthorhombic Cs0.5(Nb2.5W2.5)O14 structure-type. The same results are obtained for Cs0.5(Nb2.5W2.5–xMx)O3, with M = V or Mo (x = 0–1.25). A mechanism for the quantitative transformation at high temperature is proposed in terms of the relative occupancy of the hexagonal channels in the HTB-type phase as well as the Nb/(W + V) ratio.
Deploying Large Scale School Census Hub: An Experience Report (2017)

In this paper, we address the problem of improving data collection of the education system by presenting School Census Hub (SCH). The SCH concept emerged from field studies with stakeholders in Kenya. The goal of these studies were to help unlocking three key high-level requirements for the design of SCH. i) Budget allocation, allocating budget should be based on a verifiable number of active students and teachers, ii) Spending, spending on assets should be transparent and verifiable, iii) and, Improving learning environment, unlocking the limited insight into statistical relationship between school effectiveness and demographic variables. We present the overall architecture and design of SCH based on the findings from the field studies. The first version supporting a core set of capabilities for school data collection has been implemented. To evaluate the system, we conducted a large scale pilot in 97 schools. We report on a usability study of SCH that demonstrates user awareness and support for data acquisition and reporting in education management information system in Sub-Sharan Africa.
Study of signal programming to improve EEPROM cell reliability (2002)

This paper presents a study of EEPROM cell programming in order to increase the reliability of the device. Simulations show that it is possible to decrease the electric field across the tunnel oxide with a new programming signal. We obtain the same injected charge without any change in the device. This study allows us to improve the endurance of the memory cell.
Identification of AML1-ETO modulators by chemical genomics (2009)

Somatic rearrangements of transcription factors are common abnormalities in the acute leukemias. With rare exception, however, the resultant protein products have remained largely intractable as pharmacologic targets. One example is AML1-ETO, the most common translocation reported in acute myeloid leukemia (AML). To identify AML1-ETO modulators, we screened a small molecule library using a chemical genomic approach. Gene expression signatures were used as surrogates for the expression versus loss of the translocation in AML1-ETO-expressing cells. The top classes of compounds that scored in this screen were corticosteroids and dihydrofolate reductase (DHFR) inhibitors. In addition to modulating the AML1-ETO signature, both classes induced evidence of differentiation, dramatically inhibited cell viability, and ultimately induced apoptosis via on-target activity. Furthermore, AML1-ETO-expressing cell lines were exquisitely sensitive to the effects of corticosteroids on cellular viability compared with nonexpressers. The corticosteroids diminished AML1-ETO protein in AML cells in a proteasome- and glucocorticoid receptor-dependent manner. Moreover, these molecule classes demonstrated synergy in combination with standard AML chemotherapy agents and activity in an orthotopic model of AML1-ETO-positive AML. This work suggests a role for DHFR inhibitors and corticosteroids in treating patients with AML1-ETO-positive disease.
Combined Gene Therapy of Cancer Directed at Tumor Stem Cells and Patients Hematopoietic Stem Cells (2016)

The essence of my proposal is to use two known tumor suppressor genes expressed from episomal vectors: one delivered to cancer stem cells to suppress tumor growth, the other delivered to patient’s hematopoietic stem cells to boost the immune system to attack and destroy the tumor.  This cure program applies to all forms of cancer and all patients regardless of their genetic background, gender and age. It totally departs from the prevailing dogma that requires specific therapeutics with “targeted” drugs for each type of cancer, to be tailored to each individual tumor and patient background (“personalized treatment”).
Driver Differentiation With Seat Settings: Part I—Component Selection (2010)

The addition of user-customizable features to automobiles increases the need to differentiate among drivers so that each driver’s custom settings can be automatically applied. This study explored the feasibility of using component adjustment settings (e.g., seat position or steering wheel angle) to differentiate among drivers. The primary consideration in the feasibility assessment is the ratio of the within- and between-driver variance in component adjustments. Differentiation is a function of the stature difference between sharing drivers. Simulation and analysis showed that H-point fore-aft position provides the best single-component differentiation, followed by H-point up-down, steering wheel telescope and steering wheel angle. Seatback angle and seat-cushion angle are less useful in driver differentiation.
A Very low bit-rate speech recognition system (2001)

When using extracted speech feature coefficients for speech synthesis, quantization is considered a lossy compression scheme. The data being compressed cannot be recovered or reconstructed exactly. However, in a speech recognition system for command and control purposes, a certain amount of quantization can be allowed, with comparable results. In some cases, quantization even serves to "close the gaps" between the coefficients of the incoming speech signal and those of the templates. Since the coefficients are not being used to reconstruct the signal, a very coarse quantization can be used, enabling a very low bit-rate transmission with very good recognition results. To reduce the bandwidth further, a binary coding procedure, such as Huffman or Arithmetic Coding, can be applied to the quantized coefficients. Upon receipt of the transmission, the quantized coefficients are decoded and used to perform speech recognition. The sets of coefficients are compared to the templates for each of the commands in the vocabulary. Speech, however, is dynamic in nature and a dynamic recognition procedure is needed to allow for different vocal inflections and durations. A procedure called Dynamic Time Warping is used to "warp" the time axis of the templates to more closely fit the information coming in. By combining all these techniques, a very accurate, very low bit-rate recognizer has been developed and is discussed in this paper.
NanoStringNormCNV: pre-processing of NanoString CNV data (2017)

Supplementary data are available at Bioinformatics online.
Novel Isochoric Cold Storage with Isochoric Impregnation to Improve Postharvest Quality of Sweet Cherry (2022)

Isochoric cold storage with isochoric impregnation is a novel preservation technology that could be used to minimize the quality loss of fresh fruits during postharvest life while increasing its nutrient content. In this study, the effects of isochoric cold storage at −5 °C, with and without isochoric impregnation with sucrose/ascorbic acid solution, on the physicochemical, nutritional, and microbiological qualities of sweet cherry were investigated and compared with refrigeration at 3 °C and isobaric cold storage at −5 °C. Isochoric cold storage better-preserved fruit quality for 30 days when compared with refrigeration and isobaric cold storage. Isochoric stored cherries impregnated with sucrose and ascorbic acid exhibited smaller weight loss (7.1%), lower browning, similar texture, higher anthocyanin retention (74%), 6 times higher ascorbic acid content, and 19% higher antioxidant activity than fresh cherries. In addition, these cherries did not show microbial contamination (total mesophilic aerobic bacteria, yeasts, and molds). The use of subfreezing temperatures during isochoric preservation helped to slow down quality deterioration due to senescence processes and microbial growth, while the absence of ice crystals inside the cellular tissue helped to preserve the integrity of the cherry fruits.
Assessing a novel immuno-oncology-based combination therapy: Ipilimumab plus electrochemotherapy (2015)

Melanoma is responsible for most skin cancer-related deaths and is one of the most common cancers diagnosed in young adults. In melanoma, tumors can become established by activation of the negative regulator of cytotoxic T lymphocytes (CTLs), CTL antigen-4 (CTLA-4). Ipilimumab blocks the interaction of CTLA-4 with CD80/CD86 and augments T-cell activation and proliferation. In electrochemotherapy (ECT), local application of short high-voltage pulses renders cell membranes transiently permeable to chemotherapeutic drugs. The combination of ipilimumab and ECT may be beneficial for the treatment of metastatic melanoma; however, no prospective data are available to date. Here, we report the retrospective analysis of patients treated with ipilimumab in an expanded access program (EAP) who also received ECT. Fifteen patients with previously treated metastatic melanoma who received ipilimumab 3 mg/kg every three weeks for four cycles and underwent ECT for local disease control and/or palliation of cutaneous lesions with bleomycin 15 mg/m<sup>2</sup> after the first ipilimumab infusion were included in the analysis. Over the study period, a local objective response was observed in 67% of patients (27% complete response [CR] and 40% partial response [PR]). According to immune-related response criteria, a systemic response was observed in nine patients (five PR and four stable disease [SD]), resulting in a disease control rate of 60%. Evaluation of circulating T-regulatory (T-reg) cells demonstrated significant differences between responders and non-responders. Overall, treatment was well-tolerated and without notable toxicity. In conclusion, the combination of ipilimumab and ECT appears to be beneficial to patients with advanced melanoma, warranting further investigation in prospective trials.
Thermal management in microfluidics using micro-Peltier junctions (2005)

We report refrigeration and heating of nanoliter fluid volumes with micro-Peltier junctions. The temperature of small liquid reservoirs can be rapidly changed and controlled within a range between −3°C to over 120 °C with good long-term stability. These thermal management systems enable the fabrication of complex chip-based chemical and biochemical reaction systems in which the temperature of many processes can be controlled independently.
Incipient Twinning in Ba2YCu3O7-x Crystals (1987)

Twinning in Ba 2 YCu 3 O 7- x crystals prepared by the standard sintering method was examined by electron optical methods. Under electron beam irradiation in a vacuum in an electron microscope, an orthorhombic crystal transformed irreversibly to a tetragonal form. Prior to the complete transformation, an “incipient” twinning state was observed. The incipient state is considered in terms of domain formation of a tetragonal form.
Macular microcirculation and macular oedema in branch retinal vein occlusion (2009)

A reduction in perifoveal capillary blood-flow velocity may be involved in the development of macular oedema in patients with BRVO.