gebhart/patrepeval huggingface dataset:
Engineering vaccinia virus as an immunotherapeutic battleship to overcome tumor heterogeneity (2020)

VACV encodes several immunomodulatory genes which aid the virus in overcoming innate and adaptive immune responses. Strategic deletion of these virulence factors will enable an optimal balance between viral persistence and immunogenicity, robust tumor-specific expression of payloads and promotion of a systemic anti-cancer immune response. Rational selection of therapeutic transgenes will maximize the efficacy of OVs and their synergy in combinatorial immunotherapy schemes.
Discovery of Two‐dimensional Hexagonal MBene HfBO and Exploration on its Potential for Lithium‐Ion Storage (2023)

Abstract The practical applications of two‐dimensional (2D) transition‐metal borides (MBenes) have been severely hindered by the lack of accessible MBenes because of the difficulties in the selective etching of traditional ternary MAB phases with orthorhombic symmetry ( ort ‐MAB). Here, we discover a family of ternary hexagonal MAB ( h ‐MAB) phases and 2D hexagonal MBenes ( h ‐MBenes) by ab initio predictions and experiments. Calculations suggest that the ternary h ‐MAB phases are more suitable precursors for MBenes than the ort ‐MAB phases. Based on the prediction, we report the experimental synthesis of h ‐MBene HfBO by selective removal of In from h ‐MAB Hf 2 InB 2 . The synthesized 2D HfBO delivered a specific capacity of 420 mAh g −1 as an anode material in lithium‐ion batteries, demonstrating the potential for energy‐storage applications. The discovery of this h ‐MBene HfBO added a new member to the growing family of 2D materials and provided opportunities for a wide range of novel applications.
SPIRE: A Partial Image Identification Method Based on Sparse Indexing (2005)

tion, 3–1 Morinosato Wakamiya, Atsugi-shi, 243–0198 Japan ∗現在,(株)ぷららネットワークス a) E-mail: akisato@eye.brl.ntt.co.jp (2) VisualSEEK [3]などに代表される,画像内にあ る色領域の大まかな配置を考慮して検索を行う 方法 などが知られている.これらのアプローチは,色情報 あるいはエッジ情報に基づいて画像を分割すること によって,個別物体あるいは特定領域を抽出しようと 試みるものであり,隠れが生じていない物体や色合の はっきりした画像に対しては非常に有効である.しか し,汎用的に十分な精度を与える手法はいまだ確立さ れていない.そのため,これらの手法の多くは,検索 精度を向上させるために,特定の応用に限定したり, 人手による入力を備えるなど,補助的な手段を用いな ければならない.そこで,近年,以下のような方法が 注目されてきている. (3) 画像の部分領域間の類似性に基づいて画像全体の 類似性を判断する手法 [4], [5] このアプローチは region-based approach と呼ばれ, 物体抽出を陽に行わず,画像中の任意の部分領域での 照合結果を統合することによって,画像の類似性を検 出するものであり,前述の二つのアプローチに比べて 適用範囲がより大きく広がると考えられる.しかし, region-based approach では,あらゆる部分領域に対 して問合せが発生する可能性があるため,各画像から
A Bacterial Algorithm for Surface Mapping using a Markov Modulated Markov Chain Model of Bacterial Chemotaxis (2007)

Bacterial chemotaxis refers to the locomotory response of bacteria to chemical stimuli, where the general biological function is to increase exposure to some substances while reducing exposure to others. In this paper, we introduce an algorithm for surface mapping based on a model of the biological signaling network responsible for bacterial chemotaxis. The algorithm tracks the motion of a bacteria-like software agent, referred to as a bacterial agent, on an objective function. Results from simulations using one- and two-dimensional test functions show that the surface mapping algorithm produces an informative estimate of the surface, revealing some of its key characteristics. We also present a modification of the algorithm in which the software agent is given the ability to reduce the value of the surface at locations it visits (analogous to a bacterium consuming a substance as it moves in its environment) and show that it is more effective in reducing the surface integral within a certain period of time than a bacterial agent lacking the ability to sense surface information or respond to it.
<title>Long-wavelength infrared transmitting glasses: new ternary sulfide compositions</title> (1993)

Compositions in the MS-In<SUB>2</SUB>S<SUB>3</SUB> and MS-Y<SUB>2</SUB>S<SUB>3</SUB> systems (M equals Ca or Sr) have been investigated as potential long-wavelength infrared transmitting materials with possible glass-formability. Previous studies of CaY<SUB>2</SUB>S<SUB>4</SUB> and SrY<SUB>2</SUB>S<SUB>4</SUB> single crystals show that these phases have intrinsic infrared cut-offs at longer wavelengths than ZnS, however phases in these systems often exhibit poor crystallinity. Preliminary results indicate that these materials are significantly harder than ZnS, however, they are extremely refractory and therefore difficult to melt by traditional methods.
Data driven semantic integration of translational lung cancer research at MDAnderson Cancer Center. (2008)

The Lung Cancer SPORE at University Texas MDAnderson Cancer Center and Southwestern Medical School requires the integration of heterogeneous multi-institutional sources comprising both molecular and clinical data. In this report we describe a novel method for converging domain specific experimental ontologies that relies on propagating permissions in Resource Description Framework triplets rather than the single access point of conventional relational databases. We address this challenge by combining semantic web data reposition with code distribution.
The use of halothane and succinylcholine to identify broilers prone to developing pale, soft, exudative meat (2004)

Within the last several years, the poultry industry has seen a dramatic increase in the occurrence of pale, soft, and exudative (PSE) meat. This problem is known to be associated with a rapid decline in postmortem (PM) muscle pH, which results in inferior protein functionality similar to that found in PSE pork. Many factors such as seasonal changes have been known to influence the occurrence of PSE meat in poultry and swine. Halothane and succinylcholine have been used within the pork industry to identify animals susceptible to stress and prone to developing PSE meat. The mechanism for the triggering of the PSE gene in poultry has not been fully understood. Therefore, a study was conducted to determine the effectiveness of screening broilers with halothane to identify those prone to developing PSE meat. Succinylcholine was used before slaughter to serve as a triggering agent for the PSE condition. At 4 wk of age, broilers from 4 commercial strains (n = 1,000) were subjected to 3% halothane gas and classified as either halothane positive (HAL+) or negative (HAL-) based on muscle rigidity within the legs. Although halothane sensitivity varied slightly among the strains, approximately 14% of the birds overall were classified as HAL+. All HAL- birds (n = 163) and an equal number of HAL-birds (n = 163) in each strain were grown to market age (7 wk) and were commercially processed. At the time of processing, half of the HAL+ and HAL- birds were injected intravenously with succinylcholine and were slaughtered at 0.25 h postinjection. Pectoralis muscle samples were collected at 0.25, 2, 5, and 24 h PM for the evaluation of rigor development (muscle pH) and meat quality (L* value, moisture, drip loss, and cook loss). Halothane sensitivity had no effect on rigor development, muscle color, or water-holding capacity in the 4 broiler strains. Although birds exhibited reactions to the halothane gas, the halothane sensitivity, along with the use of succinylcholine, was not able to identify birds prone to developing PSE meat.
Western thymomas lack Epstein-Barr virus by Southern blotting analysis and by polymerase chain reaction. (1990)

The authors investigated 16 western thymomas, 9 from the United States and 7 from Europe, for the presence of Epstein-Barr virus (EBV) DNA sequences by both Southern blot hybridization analysis and polymerase chain reaction using EBV-specific DNA probes that detect the long internal repeat and terminal repeat regions and the EBNA-1 gene. None of the 16 thymomas contained evidence of the EBV genome, even though we could detect EBV by Southern blotting when EBV DNA represents less than or equal to 1% of the total DNA and by polymerase chain reaction when a single EBV-positive cell is present among 10(5) EBV-negative cells. These results fail to demonstrate EBV genome in western thymomas and stand in contrast to those of McGuire et al (Am J Pathol 1988, 131:385) who previously reported that the EBV genome is present in thymomas occurring in southern Chinese patients. Therefore EBV does not appear to be implicated in the pathogenesis of all thymomas. The presence of EBV in eastern thymomas, regions where EBV is endemic may be due to epidemiologic factors and/or genetic predispositions.
Simultaneous morphology and molecular imaging of colon cancer (2009)

The objective of this study is to investigate the feasibility of imaging colon cancers using multi-modal optical imaging system combining optical coherence tomography (OCT) and fluorescence molecular imaging (FMI). This system enables simultaneous imaging of tissue morphology and molecular information at high resolution (10-20 mum) over a 3-5 mm field-of-view. OCT reveals the microstructures of normal colon and colon polyps, and the information is confirmed by the corresponding histology. FMI shows uptake of glycoprotein targeting contrast agents. The locations of high fluorescence intensity correspond with the characteristic morphological features of polyps revealed by the co-registered OCT imaging. Our results suggest that multi-modal optical imaging with OCT and fluorescence imaging holds strong potentials for molecular imaging and in situ characterization of colon cancers.
A DC-46Gb/s 2:1 multiplexer and source-series terminated driver in 20nm CMOS technology (2014)

We present a 46Gb/s 2:1 multiplexer and a source series terminated full rate driver for high speed chip-to-chip communications. The multiplexer and the driver are implemented using the pseudo-differential static CMOS circuit. Transmitter driver uses the push-pull structure to produce a VDD peak-to-peak differential voltage swing. The circuit uses no current mode logic gates or large on-chip passive devices aside from series-connected on-chip resistor and the T-coil used to minimize the return loss. We confirmed the total jitter of about 7ps at 46Gb/s and eye opening of 0.605UI up to 50 Gb/s on the test circuit fabricated in 20nm CMOS technology. Measured power consumption is 38.7mW at 46Gb/s (0.84pJ/b power efficiency).
Selective Intratumoral Amplification of an Antiangiogenic Vector by an Oncolytic Virus Produces Enhanced Antivascular and Anti-tumor Efficacy (2006)

The development of effective cancer therapy will require the simultaneous targeting of multiple steps in tumor development. We have previously described an antiangiogenic gene therapy vector, Ad Flk1-Fc, which expresses a soluble VEGF receptor capable of inhibiting tumor angiogenesis and growth. We have also described an oncolytic virus, dl922/947, whose replication and subsequent cytotoxicity are restricted to cancer cells with a loss of the G1-S cell cycle checkpoint. Here we have optimized methods for combining these therapies, yielding significantly greater anti-tumor effects than the respective monotherapies. In cultured tumor lines, co-infection with both Ad Flk1-Fc and dl922/947 allowed replication and repackaging of the replication-deficient Ad Flk1-Fc and enhanced soluble VEGF receptor expression. Similar repackaging and increased gene expression were demonstrated in vivo using bioluminescence imaging studies. Finally, coadministration of these therapeutic viral therapies in vivo produced significantly enhanced anti-tumor effects in colon HCT 116 and prostate PC-3 xenografts in mice. This increased therapeutic benefit correlated with replication of Ad Flk1-Fc viral genomes, increased intratumoral levels of Flk1-Fc protein, and decreased microvessel density, consistent with enhanced antiangiogenic activity.
Beyond von Neumann—logic operations in passive crossbar arrays alongside memory operations (2012)

The realization of logic operations within passive crossbar memory arrays is a promising approach to expand the fields of application of such architectures. Material implication was recently suggested as the basic function of memristive crossbar junctions, and single bipolar resistive switches (BRS) as well as complementary resistive switches (CRS) were shown to be capable of realizing this logical functionality. Based on a systematic analysis of the Boolean functions, we demonstrate here that 14 of 16 Boolean functions can be realized with a single BRS or CRS cell in at most three sequential cycles. Since the read-out step is independent of the logic operation steps, the result of the logic operation is directly stored to memory, making logic-in-memory applications feasible.
Improved Sensitivity for Molecular Detection of Bacterial and Candida Infections in Blood (2014)

The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.
Mono(aryloxido)Titanium(IV) Complexes and Their Application in the Selective Dimerization of Ethylene (2009)

Abstract We report on the synthesis of mono(aryloxido)titanium(IV) complexes of general formula {Ti[O( o ‐R)Ar]X 3 }, with X = O i Pr, ArO = 2‐ tert ‐butyl‐4‐methylphenoxy and R = CMe 3 ( 2a ), CMe 2 Ph ( 2b ) and CH 2 NMe 2 ( 2c ). Attempts to reach pure mono(aryloxido) complexes when R = CH 2 NMe(CH 2 Ph) ( 2d ) or CH 2 N(CH 2 Ph) 2 ( 2e ) were unsuccessful. When R = CH 2 OMe, the analogous mononuclear complex was not obtained, and instead, a dinuclear complex [(2‐ tert ‐butyl‐4‐methyl‐6‐methoxymethylphenoxy) TiCl(O i Pr)(μ 2 ‐O i Pr) 2 TiCl(O i Pr) 2 ] ( 3 ) was formed. Complexes 2b and 3 were characterized by single‐crystal X‐ray diffraction. The former contains a tetrahedrally coordinated Ti IV centre, whereas in the latter the aryloxido ligand behaves as a chelating–bridging ligand between the two, chemically very different metal centres that form two face‐sharing octahedra. Different synthetic approaches starting from [Ti(O i Pr) 4 ] or [TiCl(O i Pr) 3 ] were evaluated and are discussed. The hemilabile behaviour of the aryloxido ligand resulting from reversible coordination of its side arm was studied by variable‐temperature 1 H NMR spectroscopy for 2c (R = CH 2 NMe 2 ). Complexes 2a – d were contacted with ethylene and AlEt 3 as cocatalyst. When activated with AlEt 3 (3 equiv.) at 20 bar and 60 °C, complex 2c exhibits interesting activity (2100 g/gTi/h) for the selective dimerization of ethylene to 1‐butene (92 % C 4 = ; 99 + % C 4 =1 ). Noticeable differences in catalyst activity were observed when the R group was modified. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
IMPLICATIONS OF USING BELBAIS DRAIN WATER FOR IRRIGATION OF WHEAT IN THE NORTH EAST REGION OF EGYPT (2016)

Wastewater may be used for complimentary irrigation of crops in the North East region of Egypt. Implications of using such wastewater on accumulation of heavy metals in soil and plant must be assessed. Water, soil and wheat samples were collected from 10 sites (with 5 km distance between sites) along the drain of Belbais and analyzed for their contents of Pb and Co. Contents of Pb in water were within the permissible levels recommended by FAO; however, there was a significant progressive increase from site 1 to 5 along the drain (North-East direction) beyond which gradual decrease occurred. The Co content in wastewater exceeded the acceptable limits and progressively increased from site 1 to 10. Contents of Pb and Co in soil were higher than the corresponding maximum acceptable levels. Wheat plants were sampled and lead contents in straw and grain were within the permissible level. Cobalt content in wheat straw was higher than the permissible level and exceeded the permissible levels in grains. A positive significant correlation existed between Co content in plant and in water. Using such water for complimentary irrigations may be of potential health hazards.
Induction of Apoptosis in Response to Anhydrobiotic Conditions in Mammalian Cells (2004)

Within many biomedical engineering subspecialties, there is a need for the reversible developmental arrest of cells and tissues in support of global distribution followed by on-demand restoration of cellular function (biopreservation). Recently, the field of anhydrobiotic (dry-state) preservation has emerged as a potential approach to achieve this goal. To date, investigations have focused on different approaches utilizing stabilizing molecules, such as trehalose, to achieve anhydrobiotic preservation, yet there remains a void in the understanding of the molecular-based physiological and biochemical responses of biologics to the desiccation process. Accordingly, we formulated and tested the hypothesis that apoptosis contributes to cell death following anhydrobiotic preservation through the activation of multiple pathways by the complex array of stressors associated with the desiccation process. In addition, we investigated the modulation of cell death following desiccation, hypothesizing that through inhibition of proteolytic caspase activation during the desiccation process, cellular tolerance would be enhanced. Data presented herein demonstrate that: (1) there is an activation of the apoptotic caspase cascade following desiccation, (2) as the extent of cellular desiccation increases so too does the level of apoptotic involvement, and (3) the inhibition of caspases during the process can improve cellular tolerance. Taken together, these data provide early evidence to suggest that the potential for targeted molecular modulation during the anhydrobiotic process may facilitate the successful anhydrobiotic preservation of biological material and its application into biotechnological settings.
Particle Filter Based Tracking of Highly Agile Wireless Agents via Random Input Sampling (2018)

The localization of highly agile targets is complicated by the fact that generic motion models usually cannot capture maneuvers sufficiently. This is particularly the case for aircraft tracking e.g. by means of radar, or in the localization of kinetically passive agents that are subject to unknown external forces. To improve the tracking accuracy in these cases, a novel particle filter scheme with random input sampling is proposed which can be combined with any relevant motion model. Via mimicking the unknown control input or, respectively, the external forces, the introduced sampling from artificial control input densities enables accurate tracking of highly agile agents. The proposed scheme is compared to particle filter based parameter estimation techniques as well as improved versions thereof which are also proposed in this work.
Pharmacological and genetic activation of cAMP synthesis disrupts cholesterol utilization in Mycobacterium tuberculosis (2022)

There is a growing appreciation for the idea that bacterial utilization of host-derived lipids, including cholesterol, supports Mycobacterium tuberculosis (Mtb) pathogenesis. This has generated interest in identifying novel antibiotics that can disrupt cholesterol utilization by Mtb in vivo. Here we identify a novel small molecule agonist (V-59) of the Mtb adenylyl cyclase Rv1625c, which stimulates 3', 5'-cyclic adenosine monophosphate (cAMP) synthesis and inhibits cholesterol utilization by Mtb. Similarly, using a complementary genetic approach that induces bacterial cAMP synthesis independent of Rv1625c, we demonstrate that inducing cAMP synthesis is sufficient to inhibit cholesterol utilization in Mtb. Although the physiological roles of individual adenylyl cyclase enzymes in Mtb are largely unknown, here we demonstrate that the transmembrane region of Rv1625c is required during cholesterol metabolism. Finally, the pharmacokinetic properties of Rv1625c agonists have been optimized, producing an orally-available Rv1625c agonist that impairs Mtb pathogenesis in infected mice. Collectively, this work demonstrates a role for Rv1625c and cAMP signaling in controlling cholesterol metabolism in Mtb and establishes that cAMP signaling can be pharmacologically manipulated for the development of new antibiotic strategies.
Enhanced Patency and Endothelialization of Small-Caliber Vascular Grafts Fabricated by Coimmobilization of Heparin and Cell-Adhesive Peptides (2016)

The clinical utility of a small-caliber vascular graft is still limited, owing to the occlusion of graft by thrombosis and restenosis. A small-caliber vascular graft (diameter, 2.5 mm) fabricated by electrospinning with a polyurethane (PU) elastomer (Pellethane) and biofunctionalized with heparin and two cell-adhesive peptides, GRGDS and YIGSR, was developed for the purpose of preventing the thrombosis and restenosis through antithrombogenic activities and endothelialization. The vascular grafts showed slightly reduced adhesion of platelets and significantly decreased adsorption of fibrinogen. In vitro studies demonstrated that peptide treatment on a vascular graft enhanced the attachment of human umbilical vein endothelial cells (HUVECs), and the presence of heparin and peptides on the graft significantly increased the proliferation of HUVECs. In vivo implantation of heparin/peptides coimmobilized graft (PU-PEG-Hep/G+Y) and PU (control) grafts was performed using an abdominal aorta rabbit model for 60 days followed by angiographic monitoring and explanting for histological analyses. The patency was significantly higher for the modified PU grafts (71.4%) compared to the PU grafts (46.2%) at 9 weeks after implantation. The nontreated PU grafts showed higher levels of α-SMA expression compared to the modified grafts, and for both samples, the proximal and distal regions expressed higher levels compared to the middle region of the grafts. Moreover, immobilization of heparin and peptides and adequate porous structure were found to play important roles in endothelialization and cellular infiltration. Our results strongly encourage that the development of small-caliber vascular grafts is feasible.