gebhart/patrepeval huggingface dataset:
An allosteric anti-hepsin antibody derived from a constrained phage display library (2012)

The serine protease hepsin is highly upregulated in prostate cancer and is implicated in tumor progression. Therefore, specific inhibition of hepsin enzymatic activity by an antibody constitutes an attractive therapeutic approach. Here, we report the identification of the anti-hepsin antibody Fab25 by screening of a Fab phage display library with a restricted chemical diversity at the complementary determining regions. Hepsin with its S1 pocket occupied by 3,4-dichloro-isocoumarin was used as the 'bait' for library screening. Fab25 was highly specific and it potently inhibited hepsin activity toward a panel of synthetic and macromolecular substrates. Biochemical and enzymatic studies with synthetic substrates of variable length suggested that Fab25 acts as an allosteric inhibitor based on non-competitive inhibition kinetics. Isothermal titration calorimetric experiments showed that the high-affinity (K(D) 6.1 nM) binding of Fab25 with hepsin is enthalpically driven. Despite an unusually long CDR-H3 loop with several potential hepsin cleavage sites (Lys, Arg residues), Fab25 was not processed by hepsin. Antibody-25 should be valuable for investigating hepsin's role in cancer progression and for potential therapeutic applications. Furthermore, the herein presented phage display strategy using an active site-modified protease should be widely applicable for identifying potential allosteric anti-protease antibodies.
Association of True Positivity with Serum Prostate-Specific Antigen Levels and Other Clinical Factors in Indeterminate PSMA-RADS-3A Lesions Identified on 18F-DCFPyL PET/CT Scans (2022)

The use of prostate-specific membrane antigen targeted PET imaging for the evaluation of prostate cancer has increased significantly in the last couple of decades. When evaluating these imaging findings based on the PSMA reporting and data system version 1.0, which categorize lesions based on their likelihood of prostate cancer involvement, PSMA-RADS-3A lesions are commonly seen, which are indeterminate for the presence of disease. A total of 28 patients with 171 PSMA-RADS-3A lesions on <sup>18</sup>F-DCFPyL PET/CT scans from June 2016 to May 2017 who had follow-up cross-sectional imaging over time were included in this study. The PSA levels of patients with PSMA-RADS-3A lesions were categorized into four groups, 0-0.2, 0.2-1, 1-2, and >2 ng/mL. The pre-operative Gleason score of these patients was categorized into two groups, Gleason score < 7 or ≥7. The median age for these patients was 72.5 years (range 59-81). The median PSA value for patients with positive lesions was significantly higher than those with negative lesions (5.8 ng/mL vs. 0.2 ng/mL, <i>p</i> < 0.0001). The lesion positivity rate was significantly higher in patients with PSA > 1 ng/mL (18.2% vs. 81.9%, <i>p</i> < 0.001). On ROC analysis, the highest classification accuracy was seen at PSA ≥ 0.6 ng/mL of 80.12% (95% CI = 73.69-86.16%), and the area under the curve was 71.32% (95% CI = 61.9-80.7%, <i>p</i> < 0.0001). A total of 96.4% (108/112) of patients with positive lesions and 86.4% (51/59) of patients with negative lesions had a PSMA-RADS-4/5 lymph node on the initial <sup>18</sup>F-DCFPyL PET/CT scan (<i>p</i> = 0.02). In patients with a Gleason score ≥ 7, the presence of positive PSMA-RADS-3A lesions was higher, compared to negative PSMA-RADS-3A lesions (<i>p</i> = 0.049). Higher PSA levels in patients with PSMA-RADS-3A lesions can point towards the presence of true positivity. PSA levels may be considered in deciding whether to call an indeterminate lesion on PSMA PET.
A New Point Mutation (P157S) in the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 Confers Low-Level Resistance to (−)-β-2′,3′-Dideoxy-3′-Thiacytidine (1999)

A P157S mutation in the reverse transcriptase (RT) of human immunodeficiency virus type 1 conferred fivefold resistance to (-)-beta-2',3'-dideoxy-3'-thiacytidine in cell culture. Interestingly, the P157S mutation resulted in increased sensitivity (two- to threefold) to 3'-azido-3'-deoxythymidine (AZT) and to (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA). A similar increase in susceptibility to AZT and to PMPA was also conferred by the M184V mutation in RT.
First Real-Time 100-Gb/s NRZ-OOK Transmission over 2 km with a Silicon Photonic Electro-Absorption Modulator (2017)

We demonstrate the first real-time, serial 100 Gb/s NRZ-OOK transmission with an integrated GeSi EAM implemented on a silicon photonics platform. Transmission over 500m of SSMF and 2 km of dispersion shifted fiber is presented.
Nocturia-Improving Effects of Water Extracts of Cucurbita Pepo seeds (2011)

ペポカボ茶種子水抽出物の夜間頻尿改善作用を検討するため，脱脂ペポカボチャ種子粉末をティーバッグに入れ抽出したお茶を用いてヒト試験を行った．その結果，夜間排尿回数が摂取前期間と比較してペポカボ茶摂取1週目から有意に減少した．摂取前期間で平均2.23±0.77回であったのに対し，ペポカボ茶摂取3週目では1.30±0.51回と有意に減少した．また排尿時の排尿スピード，尿切れ，残尿感についても摂取前期間と比較して改善が認められた．さらに，睡眠についても改善が認められた．以上のことから，ペポカボ茶は夜間頻尿改善作用を有し，睡眠改善作用を持つ可能性が示唆された．我々のこの研究結果は，種子中の脂溶性成分以外の水抽出物に，排尿障害改善作用があることを明らかとした新しい知見である．
Fig S6 from Genetic Disruption of the Multifunctional CD98/LAT1 Complex Demonstrates the Key Role of Essential Amino Acid Transport in the Control of mTORC1 and Tumor Growth (2023)

&lt;p&gt;Figure S6: Tumorigenicity and mTORC1 activity of WT and double CD98KO/ LAT1KO cells.&lt;/p&gt;
Inversion factor based design methodology using the EKV MOS model (2011)

This paper presents a hierarchical design methodology based on the inversion factor (IF) as a key design parameter and the equations of the EKV MOS Model. A structured design approach is used to allow high flexibility. The efficiency of the methodology is demonstrated through the design of a fully differential folded-cascode OTA with gain boosting. Firstly, the partitioning into basic blocks is done. Then, each block is designed independently. The performance of the whole circuit is verified. Â© 2011 Tech Univ of Lodz.
Extracting Spectral Dynamics from Single Chromophores in Solution (2010)

Fluorescence spectroscopy of single chromophores immobilized on a substrate has provided much fundamental insight, yet the spectral line shapes and dynamics of single chromophores freely diffusing in solution have remained difficult or impossible to measure with conventional linear spectroscopies. Here, we demonstrate an interferometric technique for extracting time dependent single chromophore spectral correlations from intensity correlations in the interference pattern of an ensemble fluorescence spectrum. We apply our technique to solutions of colloidal quantum dots and explore the spectrum of single particles on short time scales not feasible with conventional fluorescence measurements.
Recent Progress in Photo-Acid Generators for Advanced Photopolymer Materials (2020)

Photopolymer materials have been widely used in some advanced industries owing to their practicability, low-cost, and ecological advantage. One of the key components of these photopolymer materials is a molecule that releases acidic species upon a photon trigger (known as Photo-acid generators, PAGs). Recently, PAGs have attracted much attention with novel technologies such as near-infrared CTP imaging, 3D printing, and EUV lithography, and are required to have various functions and sophisticated features. This review article summarizes recent advances in the molecular design and function of PAGs, which are required to respond to the increasing applications of the photopolymer materials in advanced industries.
Co-Treatment of Suberoylanilide Hydroxamic Acid and Mitomycin-C Induces the Apoptosis of Rabbit Tenon's Capsule Fibroblast and Improves the Outcome of Glaucoma Filtration Surgery (2008)

This study shows that a co-treatment of SAHA and MMC could improve the outcome of GFS.
Supplementary Table S2 from A Very Long-acting Exatecan and Its Synergism with DNA Damage Response Inhibitors (2023)

&lt;p&gt;Pharmacokinetic parameters of 3A after 40 μmol/kg IP administration in mice.&lt;/p&gt;
Low bit rate image coding over bases (2002)

This paper deals with low bit rate transform coding of images. We point out why the hypotheses used for the characterization of transform coders at high bit rate does not hold at low bit rate, and derive a new analytical formula for the distortion rate function. This formula is tested with JPEG, wavelet and embedded coders.
X-ray Dark-Field CT for Early Detection of Radiation-induced Lung Injury in a Murine Model (2022)

<i>Online supplemental material is available for this article.</i>
Towards assurance case evidence generation through search based testing (2021)

Requirements-driven search-based testing (SBT), also known as falsification, has proven to be a practical and effective method for discovering erroneous behaviors in Cyber-Physical Systems. However, SBT techniques do not provide guarantees on correctness if no falsifying behavior is found within the test budget. Hence, the applicability of SBT methods for evidence generation supporting assurance cases is limited. In this work, we make progress towards developing finite-time guarantees for SBT techniques with associated confidence metrics. We demonstrate the applicability of our approach to the F16 GCAS benchmark challenge.
Comparative UHPLC-HRMS Profiling, Toxicological Assessment, and Protection Against H 2 O 2 -Induced Genotoxicity of Different Parts of Opuntia ficus indica (2019)

<i>Opuntia ficus indica</i> has been an important dietary source and a traditionally used medicinal plant. Given the promising health-promoting properties of this plant, a comparative toxicological assessment and antioxidant bioevaluation of extracts from different parts of the plant were carried out in relation to their chemical profile. Toxicity was examined at multiple endpoints using the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT), Comet and the <i>γ</i>H2AX In-Cell Western Assay, while hyphenated ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) analysis was carried out to identify main constituents. None of the extracts showed any cytotoxic and genotoxic effect on cell lines used, apart from the flower extract in HepG2 cells at the highest concentration tested (2.5 mg/mL). Both fruit flesh and seed extracts demonstrated a prominent protective effect against H<sub>2</sub>O<sub>2</sub>-induced genotoxicity in almost all concentrations tested, while extracts originated from flowers and cladodes were effective only at the low non-cytotoxic (0.312 and 0.625 mg/mL) and high (1.25 and 2.5 mg/mL) concentrations, respectively. In total, 2 phenolic acids, 12 flavonoids, along with 3 feruloyl derivatives and the plant pigment indicaxanthin, were tentatively identified by UHPLC-HRMS analysis. Phenolic acids (compounds <b>1</b> and <b>2</b>) were mainly distributed in cladodes (64.6%), while flavonoids (<b>3-14</b>) in the flowers (81.8%). Overall, the highest amount of total flavonoids (22.76 ± 0.015 mg of quercetin equivalent [QE]/g) and total phenolics (62.80 ± 0.009 mg gallic acid equivalents [GAE]/g) was found in the flower extract. Flavonoid glycosides have not been detected in the seeds and the flesh, while the fruit seed extract contained mainly feruloyl derivatives. Our data provide convincing evidences for the lack of cytotoxic and genotoxic effects of <i>O. ficus indica</i> aqueous extracts and, in parallel, support the potential for further exploitation of this plant in the food supplement or functional food sector.
Peptide-Based Vaccines in Breast Cancer (2004)

Human tumors are immunogenic and tumor-associated proteins that generate immunity in cancer patients have been defined. Many of these proteins are involved in the malignant transformation and play a role in either initiating or maintaining the malignant phenotype. Furthermore, due to technical advances in basic immunology over the last decade we have a better understanding of the immune effector cell phenotypes that are potentially involved in tumor eradication and have developed methods to quantitate and characterize these immune effectors. Breast cancer is an intriguing model tumor to target with active immunization. Dozens of breast cancer antigens have been defined [1]. Although many patients with breast cancer can be rendered free of disease with standard therapy such as surgery, radiation, and chemotherapy, some patients will have their disease recur. However, relapse may not occur for many months to years after definitive treatment giving an extended period of micrometastatic disease that may be amenable to immune eradication or modulation. Peptide based vaccines are one of the most commonly studied vaccine strategies targeting breast cancer.
Tracking and imaging humans on heterogeneous infrared sensor arrays for tactical applications (2002)

We recently implemented a heterogeneous network of infrared motion detectors and an infrared camera for the detection, localization, tracking, and identification of human targets. The network integrates dense deployments of low cost motion sensors for target tracking with sparse deployments of image sensors for target registration. Such networks can be used in tactical applications for local and distributed perimeter and site security. Rapid deployments for crisis management may be of particular interest. This paper focuses particularly on the need for applications that deal with relatively dense and complex source fields such as crowds move through sensor spaces.
Stacking faults in YBa2Cu3O7−x: Measurement using x-ray diffraction and effects on critical current (2006)

The density n of stacking faults (SFs) in epitaxial YBa2Cu3O7−x (Y123) films, consisting of extra CuO planes, is measured by fitting x-ray diffraction patterns using a random stacking model. The SF density is n=0.068nm−1 in films grown by metal-organic deposition on textured templates and optimized for high Ic. The presence of SF is correlated with pinning of magnetic field (H) applied in the Y123 ab plane. SF can be nearly eliminated by a high temperature anneal, or by adding excess Dy, resulting in Ic which is nearly independent of the orientation of H.
ChemInform Abstract: New Antimony Derivatives Isotypic to KTiOPO4. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Performance of co-immobilized yeast and glucoamylase in a fluidized bed reactor for fuel ethanol production (1996)

The performance of co-immobilized Saccharomyces cerevisiae and glucoamylase was evaluated in a fluidized bed reactor. Soluble starch and yeast extract were used as feed stocks. The biocatalyst performed well and demonstrated no significant loss of activity or physical integrity during 10 weeks of continuous operation. The reactor was easily operated and required no pH control. No operational problems were encountered from bacterial contaminants even though the reactor was operated under non-sterile conditions over the entire course of experiments. Productivities ranged between 25 to 44 g ethanol L{sup -1} h{sup -1}. The experiments demonstrated that ethanol inhibition and bed loading had significant effects on bed performance.
Downlink multiuser capacity of interference-limited MIMO systems (2003)

In a paper by Dai and Molisch (see Proc. IEEE VTC 2002 Spring, Birmingham, AL, May 2002), space-time layered architectures (BLAST) and turbo coding/processing techniques, which are effective for single-link transmission, are combined with multiuser detection (MUD) methods for combating intercell interference. It is shown that, depending on the channel configuration, linear MMSE or successive interference cancellation (SIC) can be the preferable MUD method. Based on this fact, an adaptive scheme is developed. T/sup h/e downlink capacity of interference-limited multiple-input multiple-output (MIMO) cellular systems is investigated. It is found that the obtained MUD capacity is excellent in high to medium SIR scenario, but still deteriorates in strong interference environments, leaving ample room for possible improvement through other techniques. The performance of the proposed adaptive MUD scheme in a standard cellular environment, both in the non-line-of-sight (NLOS) and the line-of-sight (LOS) case, is simulated, and the advantages over the standard V-BLAST scheme are quantified.
Supplementary document for Interfacing scalable photonic platforms: solid-state based multi-photon interference in a reconfigurable glass chip - 4105303.pdf (2019)

Supplemental Material
Anode surface modification with activated carbon for improved power generation in urine fed Microbial Fuel Cells (2018)

Microbial Fuel Cells (MFCs) utilise organic feedstocks such as urine as fuel for direct electricity production, by employing anode respiring microbes that convert organic matter into electrons while treating waste. One possible approach to bring this technology into real-world applications, is the multiplication of units connected together as modules (stacks) for usable power levels. The main challenge is therefore to improve the power output of a single MFC, using affordable and simple in preparation materials, which benefit can then be multiplied in a stack. Anode electrode composition and surface morphology are key elements in improving performance and reducing costs, since the electron transfer rate from bacteria towards the electrode surface is one of the critical limiting factors. So far, carbon fibre veil has been successfully used as an anode electrode in numerous practical demonstrations. This work aims to explore simple and inexpensive modifications of this substratum with the addition of microporous activated carbon powder to produce a three-dimensional (3D) structure in order to improve the output of a single MFC unit as a building block for a modular stack.
Potent Inhibitors of Malarial Aspartic Proteases, the Plasmepsins, by Hydroformylation of Substituted 7‐Azanorbornenes (2012)

The increasing prevalence of multidrug-resistant strains of the malarial parasite Plasmodium falciparum requires the urgent development of new therapeutic agents with novel modes of action. The vacuolar malarial aspartic proteases plasmepsin (PM) I, II, and IV are involved in hemoglobin degradation and play a central role in the growth and maturation of the parasite in the human host. We report the structure-based design, synthesis, and in vitro evaluation of a new generation of PM inhibitors featuring a highly decorated 7-azabicyclo[2.2.1]heptane core. While this protonated central core addresses the catalytic Asp dyad, three substituents bind to the flap, the S1/S3, and the S1' pockets of the enzymes. A hydroformylation reaction is the key synthetic step for the introduction of the new vector reaching into the S1' pocket. The configuration of the racemic ligands was confirmed by extensive NMR and X-ray crystallographic analysis. In vitro biological assays revealed high potency of the new inhibitors against the three plasmepsins (IC(50) values down to 6 nM) and good selectivity towards the closely related human cathepsins D and E. The occupancy of the S1' pocket makes an essential contribution to the gain in binding affinity and selectivity, which is particularly large in the case of the PM IV enzyme. Designing non-peptidic ligands for PM II is a valid route to generate compounds that inhibit the entire family of vacuolar plasmepsins.
Laser annealed in-situ P-doped Ge for on-chip laser source applications (Conference Presentation) (2016)

Realization of a monolithically integrated on-chip laser source remains the holy-grail of Silicon Photonics. Germanium (Ge) is a promising semiconductor for lasing applications when highly doped with Phosphorous (P) and or alloyed with Sn [1, 2]. P doping makes Ge a pseudo-direct band gap material and the emitted wavelengths are compatible with fiber-optic communication applications. However, in-situ P doping with Ge2H6 precursor allows a maximum active P concentration of 6×1019 cm-3 [3]. Even with such active P levels, n++ Ge is still an indirect band gap material and could result in very high threshold current densities. In this work, we demonstrate P-doped Ge layers with active n-type doping beyond 1020 cm-3, grown using Ge2H6 and PH3 and subsequently laser annealed, targeting power-efficient on-chip laser sources. The use of Ge2H6 precursors during the growth of P-doped Ge increases the active P concentration level to a record fully activated concentration of 1.3×1020 cm-3 when laser annealed with a fluence of 1.2 J/cm2. The material stack consisted of 200 nm thick P-doped Ge grown on an annealed 1 µm Ge buffer on Si. Ge:P epitaxy was performed with PH3 and Ge2H6 at 320oC. Low temperature growth enable Ge:P epitaxy far from thermodynamic equilibrium, resulting in an enhanced incorporation of P atoms [3]. At such high active P concentration, the n++ Ge layer is expected to be a pseudo-direct band gap material. The photoluminescence (PL) intensities for layers with highest active P concentration show an enhancement of 18× when compared to undoped Ge grown on Si as shown in Fig. 1 and Fig. 2. The layers were optically pumped with a 640 nm laser and an incident intensity of 410 mW/cm2. The PL was measured with a NIR spectrometer with a Hamamatsu R5509-72 NIR photomultiplier tube detector whose detectivity drops at 1620 nm. Due to high active P concentration, we expect band gap narrowing phenomena to push the PL peak to wavelengths beyond the detection limit (1620nm) of the setup. Therefore, the 18× enhancement is a lower limit estimation. In this contribution, an extensive study of laser annealing conditions and their impact on material properties will be discussed. A major concern in using highly doped Ge as an active medium is the increase in free-carrier absorption (FCA). However, results reported in [4] suggest that FCA is significantly dominated by holes due to larger absorption cross-section of holes compared to electrons. The FCA results in [4] and JDOS modeling were used to calculate the gain spectrum for the highest doped Ge samples, including the typical 0.25% biaxial tensile strain of epitaxial Ge on Si. A carrier lifetime of 3 ns is required as shown in Fig. 3 for a target threshold current density of sub-20 kA/cm2 which represents at least tenfold reduction when compared to active P-doping level of 6×1019 cm-3. As a result, laser annealed highly doped Ge layers grown with Ge2H6 precursors are a promising approach for realizing a power efficient on-chip Ge laser source.