gebhart/patrepeval huggingface dataset:
The Effect of Apo‐Transferrin on Bacterial Adhesion to Biomaterials (2002)

Apo-transferrin (apo-Tf), the iron deficient form of Tf, has been identified previously as a potent inhibitor of Staphylococcus epidermidis adhesion to polyurethane surfaces. In this study, the ability of apo-Tf to suppress the adhesion of two other strains of bacteria, namely a Gram-positive Staphylococcus aureus and a Gram-negative Pseudomonas aeruginosa to several biomaterials, including polystyrene, polymethylmethacrylate, and silicone, is documented. The presence of apo-Tf in the medium at 20 microg/ml lowered bacterial adhesion to all tested biomaterials more than fourfold. Moreover, apo-Tf exerted its inhibitory activity even when protein coated surfaces were used as substrates for bacterial adhesion. To emphasize the importance of apo-Tf in the prevention of bacterial adhesion, human serum was depleted of Tf, employing affinity chromatography, and was shown to lose its inhibitory activity toward bacterial adhesion. Upon addition of apo-Tf to Tf-depleted serum, the activity was reestablished, resulting in a marked reduction in the number of bacteria adhered to the surfaces. Following the enzymatic deglycosylation, apo-Tf retained its ability to prevent bacterial adhesion. These results indicate that the carbohydrate moiety does not seem to play a role in this activity. The presented data provide the evidence that the inhibitory activity of apo-Tf is not bacterial strain specific and that the presence of apo-Tf in the medium results in a significant reduction of bacterial adhesion to a variety of neat and/or protein coated surfaces.
ATNT-26PHASE I/II STUDY OF DIANHYDROGALACTITOL IN PATIENTS WITH RECURRENT MALIGNANT GLIOMA (2015)

ATNT-26. PHASE I/II STUDY OF DIANHYDROGALACTITOL IN PATIENTS WITH RECURRENT MALIGNANT GLIOMA Kent Shih1,2, Mahish Patel1,3, Nicholas Butowski4, Jeffrey Bacha5, Dennis Brown5, Anne Steino5, Richard Schwartz5, Sarath Kanekal5, Lorena Lopez5, and Howard Burris1,2; Sarah Cannon Research Institute, Nashville, TN, USA; Tennessee Oncology, Nashville, TN, USA; Florida Cancer Specialists & Research Institute, Florida, USA; University of California San Francisco Division of NeuroOncology, San Francisco, CA, USA; DelMar Pharmaceuticals, Vancouver, BC, Canada Glioblastoma multiforme (GBM) is the most common brain cancer. Front-line systemic therapy with temozolomide is often ineffective due to O-methylguanine-DNA-methyltransferase (MGMT)-mediated resistance. Dianhydrogalactitol (VAL-083) is a bi-functional DNA N cross-linking agent that crosses the blood-brain barrier and demonstrated cytotoxic activity independent of MGMT in vitro. The main goal of this clinical trial was to determine an appropriate dose for Phase II/III trials in refractory GBM. METHODS: Open-label, single-arm Phase I/II dose-escalation study in patients with histologically-confirmed GBM, previously treated with radiation and must have failed both temozolomide and bevacizumab, unless contraindicated. The study utilized 3 + 3 dose-escalation design. Patients received VAL-083 on days 1, 2, 3 of a 21-day cycle. RESULTS: 30 GBM patients were enrolled across 8 dose cohorts ranging from 1.5 to 50mg/m/d. No drug-related severe adverse events were reported, and myelosuppression was mild at doses ≤40mg/m/d. Dose limiting toxicities (DLT) consisting of thrombocytopenia were observed at 50mg/m/d. Platelet nadir occurred around day 20, and DLT-related symptoms resolved rapidlyand spontaneously without concomitant treatment. Pharmacokinetic analyses show dosedependent linear systemic exposure with a short 1-2h plasma terminal halflife; Cmax ranged 739-1130ng/mL (5.1-7.7 mM) at 40mg/m/d resulting in calculated CNS concentrations within the IC50 range observed for multiple GBM cell-lines in vitro. Preliminary analysis shows increasing dose-dependent median survival with median OS 1⁄4 9.0 months at doses ≥30mg/m/d vs. 4.4 months at doses ,10mg/m/d. An expansion cohort of up to 14 patients has been initiatedat40mg/m/d.Asmall cohort (n 1⁄4 3) atan interim 45mg/m/d dose will also be studied, and the expansion cohort may be continued at this higher dose if safety data warrant. CONCLUSIONS: VAL-083 dosing appears limited by myelosuppression; however, 40mg/m/d dose exhibited favorable safety profile, with a trend toward improved survival vs. lower doses. Updated safety and efficacy data from the expansion cohort will be presented. ClinicalTrials.gov Identifier NCT01478178. Neuro-Oncology 17:v10–v17, 2015. doi:10.1093/neuonc/nov205.26 Published by Oxford University Press on behalf of the Society for Neuro-Oncology 2015.
Agile photonic generation of arbitrary RF chirped waveforms based on a single CW laser (2017)

Photonic generation of radio-frequency (RF) chirped signals has proven an attractive solution to overcome the limitations of conventional electronic waveform generators. However most of the designs proposed so far make use of a mode-locked laser as a broadband light source, resulting in high cost and complexity [1, 2]. Here we propose a much simpler concept of photonic generation of arbitrary RF chirped waveforms based on a frequency shifting loop (FSL) seeded with a single CW laser [3]. This simple scheme enables generation of on-demand RF chirps with large bandwidth (> 100 GHz), and fully controllable chirp sign, rate and envelope. The RF chirp duration can be adjusted from a few ns to hundreds of ns, resulting in time-bandwidth products (TBWP) exceeding 1000.
Use of Bidens pilosa L. (Asteraceae) and Curcuma longa L. (Zingiberaceae) to treat intestinal mucositis in mice: Toxico-pharmacological evaluations (2015)

This study showed an interesting potential of the mucoadhesive formulation of BP/CL for the treatment of 5-FU-induced intestinal mucositis. Given the perspectives for the development of a new medicine, clinical studies are in progress to better understand the protective effects of this innovative formulation in treating mucositis.
Catalytic dehydration of lactic acid to acrylic acid using calcium hydroxyapatite catalysts (2013)

A series of calcium hydroxyapatite (HAP) catalysts were synthesised with a Ca/P ratio ranging from 1.3 to 1.89 by a co-precipitation method that involved changing the pH of the calcium and phosphorous precursors. The physicochemical characterization by XRD, SEM, BET surface area and CO2 and NH3-TPD techniques confirmed the hydroxyapatite formation. These HAP catalysts were used for the vapour phase dehydration of lactic acid to acrylic acid. The HAP catalyst with a Ca/P ratio of 1.3 was found to be the most efficient catalyst among the synthesised series, which gave 100% conversion of lactic acid and 60% selectivity towards acrylic acid at 375 °C when a 50% (w/w) aqueous solution of lactic acid was used. The higher selectivity towards acrylic acid has been correlated to the increased acidity and reduced basicity of the HAP catalyst with a Ca/P ratio of 1.3 compared to the other HAP catalysts. The catalyst was found to be very stable and no deactivation was observed even after 300 h of reaction time. In situ FTIR studies were performed for understanding the mechanistic aspects and showed the formation of calcium lactate as an intermediate species during the dehydration of lactic acid to acrylic acid.
Cheese as a delivery vehicle for probiotics and biogenic substances (2006)

Cheese offers an attractive food-based delivery vehicle for probiotic cultures and biogenic substances such as conjugated linoleic acid (CLA) and bioactive peptides. Compared to many other fermented foods it has a relatively high pH and fat content, a solid consistency and a higher buffering capacity. Together these features probably afford improved protection of biological activity during manufacture, storage and gastrointestinal transit. However, it is desirable that probiotics and biogenics are technologically compatible with the cheese manufacturing process. Therefore, some important characteristics of probiotic strains and biogenics need to be assessed when considering cheese as the delivery matrix. Additionally, it is important that the delivery and generation of bioactive materials in cheeses does not disturb the cheese ecosystem by interfering with cheese maturation and/or flavour development. To date, many probiotic cheeses have been made without changing the manufacturing process by using probiotics as adjuncts with the starter cultures. Additionally, spray-dried skim milk powders containing probiotic Lactobacillus cultures have been developed which can be added as direct vat inoculants for cheddar cheese manufacture. Moreover, cheese itself is recognised as a natural source of bioactive peptides which originate from the proteolytic action of lactic acid bacteria (LAB) on milk proteins during cheese manufacture and/or maturation.
Guided test generation for web applications (2013)

We focus on functional testing of enterprise applications with the goal of exercising an application's interesting behaviors by driving it from its user interface. The difficulty in doing this is focusing on the interesting behaviors among an unbounded number of behaviors. We present a new technique for automatically generating tests that drive a web-based application along interesting behaviors, where the interesting behavior is specified in the form of “business rules.” Business rules are a general mechanism for describing business logic, access control, or even navigational properties of an application's GUI. Our technique is black box, in that it does not analyze the application's server-side implementation, but relies on directed crawling via the application's GUI. To handle the unbounded number of GUI states, the technique includes two phases. Phase 1 creates an abstract state-transition diagram using a relaxed notion of equivalence of GUI states without considering rules. Next, Phase 2 identifies rule-relevant abstract paths and refines those paths using a stricter notion of state equivalence. Our technique can be much more effective at covering business rules than an undirected technique, developed as an enhancement of an existing test-generation technique. Our experiments showed that the former was able to cover 92% of the rules, compared to 52% of the rules covered by the latter.
Low‐Voltage Polymer Field‐Effect Transistors Gated via a Proton Conductor (2007)

Low operating voltages for p-channel organic field-effect transistors (OFETs) can be achieved by using an electrolyte as the gate insulator. However, mobile anions in the electrolyte can lead to undesired electrochemistry in the channel. In order to avoid this, a polyanionic electrolyte is used as the gate insulator. The resulting OFET has operating voltages of less than 1 V (see figure) and shows fast switching (less than 0.3 ms) in ambient atmosphere.
Game theoretic power allocation and waveform selection for satellite communications (2015)

Game theory is a useful method to model interactions between agents with conflicting interests. In this paper, we set up a Game Theoretic Model for Satellite Communications (SATCOM) to solve the interaction between the transmission pair (blue side) and the jammer (red side) to reach a Nash Equilibrium (NE). First, the IFT Game Application Model (iGAM) for SATCOM is formulated to improve the utility of the transmission pair while considering the interference from a jammer. Specifically, in our framework, the frame error rate performance of different modulation and coding schemes is used in the game theoretic solution. Next, the game theoretic analysis shows that the transmission pair can choose the optimal waveform and power given the received power from the jammer. We also describe how the jammer chooses the optimal power given the waveform and power allocation from the transmission pair. Finally, simulations are implemented for the iGAM and the simulation results show the effectiveness of the SATCOM power allocation, waveform selection scheme, and jamming mitigation.
Antiagglomerant Hydrate Inhibitors: The Link between Hydrate-Philic Surfactant Behavior and Inhibition Performance (2014)

The application of antiagglomerant hydrate inhibitors (AAs) is becoming more important as advancing technology allows access to petroleum reserves with extreme conditions including high pressures, high temperatures, sour reservoirs, and arctic climates. Application of thermodynamic hydrate inhibitors (THIs) is becoming cumbersome and outdated due to high volumes required, especially in offshore applications. High subcooling scenarios and capital costs preclude the use of kinetic hydrate inhibitors (KHIs) and THIs. Even though AAs are industrially recognized surfactants, they have not been extensively studied with regard to their surfactant properties as related to performance. In this paper, selected AAs have been examined in terms of their surfactant properties. These findings were then related to hydrate inhibition performance in a crude oil system. It is widely known that AAs perform better with increased salinities and decreased water-cuts. This study provides data that shines light on the plausible reasons for these observations.
Discovery and Preclinical Evaluation of BMS-986242, a Potent, Selective Inhibitor of Indoleamine-2,3-dioxygenase 1 (2021)

Indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-containing dioxygenase enzyme implicated in cancer immune response. This account details the discovery of BMS-986242, a novel IDO1 inhibitor designed for the treatment of a variety of cancers including metastatic melanoma and renal cell carcinoma. Given the substantial interest around this target for cancer immunotherapy, we sought to identify a structurally differentiated clinical candidate that performs comparably to linrodostat (BMS-986205) in terms of both <i>in vitro</i> potency and <i>in vivo</i> pharmacodynamic effect in a mouse xenograft model. On the basis of its preclinical profile, BMS-986242 was selected as a candidate for clinical development.
Generalizability of a deep learning airway segmentation algorithm to a blinded low-dose CT dataset (2021)

Chronic obstructive pulmonary disease (COPD) is a common inflammatory disease characterized by restricted lung airflow affecting over 300 million people worldwide. Quantitative computed tomography (CT) has become a benchmark for large multi-center pulmonary research studies for assessment of airway and parenchymal physiology and function towards understanding the occurrence and progression of the disease. Airway tree segmentation is a precursor for such approaches; but current industry-standard methods require manual post-segmentation correction to remove leakages and add missing airway branches. Recently, deep learning (DL) methods have gained popularity in medical image segmentation and outperformed traditional image processing methods due to their data-driven optimization schemes of multi-layered and multi-scale features. Generalizability of DL methods is a lingering concern and essential in multi-site CT-based pulmonary studies due to varying CT imaging settings at different sites. In this paper, we examine the generalizability of a recently developed fully automated DL-based airway segmentation method using low-dose chest CT images from the NELSON lung cancer screening study. The DL method was trained using high-dose chest CT scans from the Iowa cohort of COPDGene study at baseline visits and applied on blinded low-dose images. Results show the recent DL-based method is generalizable to blinded low-dose chest CT imaging, and it achieves branch-level accuracies of 100, 99.6, and 96.0% at segmental, sub-segmental, and sub-sub-segmental branches along the five clinically significant bronchial paths (RB1, RB4, RB10, LB1, and LB10).
Stepwise Differentiation of Retinal Ganglion Cells from Human Pluripotent Stem Cells Enables Analysis of Glaucomatous Neurodegeneration (2016)

Human pluripotent stem cells (hPSCs), including both embryonic and induced pluripotent stem cells, possess the unique ability to readily differentiate into any cell type of the body, including cells of the retina. Although previous studies have demonstrated the ability to differentiate hPSCs to a retinal lineage, the ability to derive retinal ganglion cells (RGCs) from hPSCs has been complicated by the lack of specific markers with which to identify these cells from a pluripotent source. In the current study, the definitive identification of hPSC-derived RGCs was accomplished by their directed, stepwise differentiation through an enriched retinal progenitor intermediary, with resultant RGCs expressing a full complement of associated features and proper functional characteristics. These results served as the basis for the establishment of induced pluripotent stem cells (iPSCs) from a patient with a genetically inherited form of glaucoma, which results in damage and loss of RGCs. Patient-derived RGCs specifically exhibited a dramatic increase in apoptosis, similar to the targeted loss of RGCs in glaucoma, which was significantly rescued by the addition of candidate neuroprotective factors. Thus, the current study serves to establish a method by which to definitively acquire and identify RGCs from hPSCs and demonstrates the ability of hPSCs to serve as an effective in vitro model of disease progression. Moreover, iPSC-derived RGCs can be utilized for future drug screening approaches to identify targets for the treatment of glaucoma and other optic neuropathies. Stem Cells 2016;34:1553-1562.
Effects of the bradykinin antagonist, HOE 140, in experimental acute pancreatitis (1992)

1. The novel bradykinin antagonist, HOE 140, completely blocked the fall in rabbit blood pressure caused, not only by i.v. bradykinin, but also by i.v. kallikrein. This shows that both the effects of exogenously administered bradykinin and those of endogenously released kinins are antagonized by HOE 140. 2. Acute pancreatitis was induced in rats by i.v. infusion of the cholecystokinin analogue, caerulein. This treatment resulted in massive oedema of the pancreas, increased activities of amylase and lipase in serum and a characteristic, biphasic fall in blood pressure. 3. HOE 140 prevented the caerulein-induced pancreatic oedema and the second phase of hypotension whereas NPC 349, a widely used, but short-acting, bradykinin antagonist did not show a significant inhibition. HOE 140, in contrast to its inhibitory effects on caerulein-induced pancreatic oedema and hypotension, significantly augmented the increases in amylase and lipase activities in serum. 4. It is concluded that in this model of acute pancreatitis, the release of kinins induces pancreatic oedema and hypotension. Prevention by HOE 140 of the kinin-induced oedema allows the pancreatic enzymes to leave the tissue without hindrance and thus will diminish subsequent pathological events. It is suggested that the results obtained with the highly potent and long-acting bradykinin antagonist, HOE 140, provide a pharmacological basis for a clinical trial in acute pancreatitis.
A hydrogen-bonded organic nonlinear optical crystal for high-efficiency terahertz generation and detection (2008)

Broadband THz pulses have been generated in 2-[3-(4- hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene]malononitrile (OH1) by optical rectification of sub-picosecond laser pulses. We show that OH1 crystals allow velocity-matched generation and detection of THz frequencies in the whole range between 0.3 and 2.5 THz for a pump laser wavelength range from 1200 to 1460 nm. OH1 crystals show a higher figure of merit for THz generation and detection in the optimized range compared to the benchmark inorganic semiconductor crystals ZnTe and GaAs and the organic ionic salt crystal 4-N,N-dimethylamino-4'-N'-methyl stilbazolium tosylate (DAST). The material shows a low THz absorption coefficient alpha3 in the range between 0.3 and 2.5 THz, reaching values lower than 0.2mm(-1) between 0.7 and 1.0 THz. This is similar as in ZnTe and GaAs, but much lower than in DAST in the respective optimum frequency range. A peak THz electric field of 100 kV/cm and a photon conversion efficiency of 11 percent have been achieved at a pump pulse energy of 45 microJ.
Automatic and efficient heap data management for limited local memory multicore architectures (2013)

Limited Local Memory (LLM) multi-core architectures substitute cache with scratch pad memories (SPM), and therefore have much lower power consumption. As they lack of automatic memory management, programming on such architectures becomes challenging, in the sense that it requires the programmer/compiler to efficiently manage the limited local memory. Managing heap data of the tasks executing in the cores of an LLM multi-core is an important problem. This paper presents a fully automated and efficient scheme for heap data management. Specifically, we propose i) code transformation for automation of heap management, with seamless support for multi-level pointers, and ii) improved data structures to more efficiently manage unlimited heap data. Experimental results on several benchmarks from MiBench demonstrate an average 43% performance improvement over previous approach [1].
Switch Bootstrapping for Precise Sampling Beyond Supply Voltage (2006)

Bootstrapped switches are used in a variety of applications including DC-DC converters, pipelined analog-to-digital converters and high voltage switches and drivers. Current work on highly integrated power management applications often requires the ability to measure voltage quantities that exceed the supply voltage in magnitude. This is primarily due to a basic need to maximize efficiency by running the power management IC on as low supply voltage as possible, while still maintaining the ability to sample and measure quantities from the surroundings that could well exceed the battery voltage. In this paper, a new bootstrapped switch is presented. The switch enables the precise sampling of input signals well greater than the chip supply voltage with no static power consumption, and without activating on-chip parasitic body diodes. The bootstrapped switch, presented here, is designed to sample an input signal with a 0-5.5-V range at a supply voltage of 2.75 V. Measurement data shows functionality for a 0-6-V input signal range with a supply voltage as low as 1.2 V
Large Scale, All-Fiber Optical Cross-Connect Switches for Automated Patch-Panels (2009)

Transparent, all-optical cross-connect switches provide non-blocking, one-to-one reconfigurable interconnections between any of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> input fibers and any of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> output fibers. Cross-connects based on <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">all-fiber</i> rather than free-space interconnections have the potential for low opto-mechanical complexity, miniaturization, high optical power handling and ideal optical performance. In this paper, we propose and analyze novel architectures for large-scale, all-fiber cross-connects based on the application of theory of Knots and Braids to fiber switching and compare them on the basis of scalability, modularity and reconfiguration time. A prototype 140 input by 140 output, automated all-fiber cross-connect is developed to demonstrate these concepts.