gebhart/patrepeval huggingface dataset:
<i>Agrobacterium</i> -mediated transformation of indica rice cultivars using binary and superbinary vectors (1999)

The Agrobacterium -mediated transformation system was extended to two indica cultivars: a widely cultivated breeding line IR-64 and an elite basmati cultivar Karnal Local. Root tips and shoot tips of seedlings, and scutellar-calli derived from mature seeds showed high-efficiency Agrobacterium tumefaciens infection and stable transformation. In addition to the superbinary vector pTOK233 in Agrobacterium strain LBA4404, almost equally high levels of transformation were achieved with a relatively much smaller (13.1 kb) binary vector (pCAMBIA1301) in a supervirulent host strain AGL1. In both cases, as well as in both cultivars, while 60–90% of the infected explants produced calli resistant to the selectable agent hygromycin, 59–75% of such calli tested positive for GUS. A high level (400 µM) of acetosyringone in the preinduction medium for Agrobacterium and a higher level (500 µM) in the cocultivation medium was necessary for an enhancement in transformation frequency of the binary vector to levels comparable to a superbinary. Hygromycin-resistant calli could be produced from all the explants used. Transformants could be regenerated for both cultivars using the superbinary and binary vector, but only for calli of scutellar origin. In addition to the molecular confirmation of hpt and gus gene transfer and transcription, absence of gene sequences outside the transferred DNA (T-DNA) region confirmed absence of any long T-DNA transfer.
Prospective randomized trial of high-dose cisplatin and fluorouracil infusion with or without sodium diethyldithiocarbamate in recurrent and/or metastatic squamous cell carcinoma of the head and neck. (1988)

Previous studies have indicated that sodium diethyldithiocarbamate (DDTC) can reduce cisplatin's (CP) toxic effects without altering the antitumor activity. DDTC has also been shown to have immunostimulative properties. Sixty patients with objectively measurable recurrent and/or metastatic squamous cell carcinoma (SCC) of the head and neck were randomized to receive either (A) CP at 120 mg/m2 over one hour on day 1, plus fluorouracil (5-FU) at 1,000 mg/m2 over 24 hours as a continuous infusion on days 1 through 5, or (B) CP/5-FU as in A, plus DDTC at 600 mg/m2 over 30 minutes administered intravenously (IV) exactly 30 minutes after CP infusion. Group B also received DDTC at 200 mg/m2 administered IV over 30 minutes on days 8 and 15. Each cycle was repeated at 3-week intervals. Objective responses were achieved in 41% of the CP/5-FU group and in 29% of the CP/5-FU with DDTC group (P = .26). Median survival was 9 months in group A and 10 months in group B. CP-related toxicity between the groups was equivalent with respect to nausea and vomiting, renal impairment, neurotoxicity, ototoxicity, and hematologic toxicity. The pharmacokinetics of reactive platinum species in plasma ultrafiltrate and urine samples obtained from both groups were comparable. The immune status of 48 patients was evaluated before and after completion of therapy. There were no significant differences in mean pretreatment and posttreatment values within or between groups A or B, except for absolute pretreatment OKT4 values (P = .02). We conclude that (1) the present dose and infusion schedule of DDTC did not significantly reduce CP-mediated toxic effects, (2) DDTC did not alter the disposition of ultrafilterable platinum species, (3) DDTC did not affect immune responses, and (4) the addition of DDTC improved neither the clinical response nor the survival of patients with recurrent SCC of the head and neck.
Noncovalent Interactions in Peri-Substituted Chalconium Acenaphthene and Naphthalene Salts: A Combined Experimental, Crystallographic, Computational, and Solid-State NMR Study (2012)

Twelve related monocation chalconium salts [{Nap(EPh)(E'Ph)Me}(+){CF(3)SO(3)}(-)] 2-4, [{Acenap(Br)(EPh)Me}{CF(3)SO(3)}(-)] 5-7, and [{Acenap(EPh)(E'Ph)Me}(+){CF(3)SO(3)}(-)] 8-13 have been prepared and structurally characterized. For their synthesis naphthalene compounds [Nap(EPh)(E'Ph)] (Nap = naphthalene-1,8-diyl; E/E' = S, Se, Te) N2-N4 and associated acenaphthene derivatives [Acenap(X)(EPh)]/[Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te; X = Br) A5-A13 were independently treated with a single molar equivalent of methyl trifluoromethanesulfonate (MeOTf). In addition, reaction of bis-tellurium compound A10 with 2 equiv of MeOTf afforded the doubly methylated dication salt [{Acenap(TePhMe)(2)}(2+){(CF(3)SO(3))(2)}(2-)}] 14. The distortion of the rigid naphthalene and acenaphthene backbone away from ideal was investigated in each case and correlated in general with the steric bulk of the interacting atoms located at the proximal peri positions. Naturally, introduction of the ethane linker in acenaphthene compounds increased the splay of the bay region compared with equivalent naphthalene derivatives resulting in greater peri distances. The conformation of the aromatic rings and subsequent location of p-type lone pairs has a significant impact on the geometry of the peri region, with anomalies in peri separations correlated to the ability of the frontier orbitals to take part in attractive or repulsive interactions. In all but one of the monocations a quasi-linear three-body C(Me)-E···Z (E = Te, Se, S; Z = Br/E) fragment provides an attractive component for the E···Z interaction. Density functional studies confirmed these interactions and suggested the onset of formation of three-center, four-electron bonding under appropriate geometric conditions, becoming more prevalent as heavier congeners are introduced along the series. The increasingly large J values for Se-Se, Te-Se, and Te-Te coupling observed in the (77)Se and (125)Te NMR spectra for 1, 3, 4, 9, 10, and 13 give further evidence for the existence of a weakly attractive through-space interaction.
Centrosomes and cancer (1999)

The centrosome functions as the major microtubule organizing center (MTOC) of the cell and as such it determines the number, polarity, and organization of interphase and mitotic microtubules. Cytoplasmic organization, cell polarity and the equal partition of chromosomes into daughter cells at the time of cell division are all dependent on the normal function of the centrosome and on its orderly duplication, once and only once, in each cell cycle. Malignant tumor cells show characteristic defects in cell and tissue architecture and in chromosome number that can be attributed to inappropriate centrosome behavior during tumor progression. In this review, we will summarize recent observations linking centrosome defects to disruption of normal cell and tissue organization and to chromosomal instability found in malignant tumors.
Yb-doped amplifier fiber with distributed filtering by resonant core-ring coupling (2006)

An Yb-doped amplifier fiber with distributed gain filtering along its length was fabricated. Measured amplified spontaneous emission confirms gain suppression at wavelengths relevant to important laser noise components. Pump efficiency improvement was observed.
Design and Implementation of the MIMO–COOK Scheme Using an Image Sensor for Long-Range Communication (2020)

Radio-frequency technologies are widely applied in many fields such as mobile systems, healthcare systems, television and radio broadcasting, and satellite communications. However, one major problem in wireless communication based on radio frequencies is its impact on human health. High frequencies adversely impact human health more than low frequencies if the signal power transgresses the permissible threshold. Therefore, researchers are investigating the use of visible light waves (instead of the radio-frequency band) for data transmission in three major areas: visible light communication, light fidelity, and optical camera communication. In this paper, we propose a scheme that upgrades the camera on-off keying (COOK) scheme by using it with the multiple-input multiple-output (MIMO) scheme; COOK has been recommended by the IEEE 802.15.7-2018 standard. By applying technologies, such as matched filter, region of interest, and MIMO, our proposed scheme promises to improve the performance of the conventional scheme by improving the data rate, communication distance, and bit error rate. By controlling the exposure time, the focal length in a single camera and using channel coding, our proposed scheme can achieve the communication distance of up to 20 m, with a low error rate.
Information processing in marine archaeology (2002)

At the Oceans'95 conference the authors presented a paper entitled "Applications of remotely controlled equipment in Norwegian marine archaeology". That paper discussed the use of remotely controlled equipment in Norwegian marine archaeology, and more specifically a project that studies the wreck of a Russian navy ship which sank in 1760 off the coast of mid-Norway. This wreck, located in 280 meters water depth, has been examined by ROVs (remotely operated vehicles) for the last couple of years. The project came along as a result of a Norwegian oil company's plan to lay a pipeline from one of its platforms to the shore. According to Norwegian law, a survey of the pipeline route had to be carried out, and this revealed the wreck of the Russian ship called the Unicorn. This paper will discuss the latest results of the project. However, the focus will primarily be on the information processing aspects of the project. Having a number of sensors mounted on the remotely controlled vehicle, considerable amounts of information have to be stored, processed and interpreted. The aim of the paper is to explain how this task was solved. The information processing sub-project was initiated with an analysis of the general activities in marine archaeology: Surveying, localisation, documentation and identification. Information needs were specified for each of these activities and an information processing model was defined. This served as a basis for the definition of requirements for the information system. The computer based information processing system developed by Fjellanger Wideroe AS and the project team at the Norwegian University of Science and Technology is then presented. This system utilises digital maps, offers real-time tracking capability of both the ship and the ROV, and has a link to a database which stores information about objects found etc. The advantages and limitations of such an automated information processing system in underwater work and the possibilities it offers to increase the effectiveness of marine archaeology are discussed.
The high versatility of silicon based micro-optical modulators (2009)

"One product, one process": This MEMS law is true for micro-optical modulators, too and thus puts a high load on every product and technology development team. On the other hand the law expresses nothing but the high versatility of the underlying usually silicon based technology. A huge variety of applications where an electromagnetic wave experiences a spatial-temporal modulation makes use of this technology: High resolution as well as ultra-compact displays, optical switches in telecommunication as well as data storage devices, spectrometers e. g. for quality control, as well as adaptive optics and pattern generation to mention only a few. The applications completely differ with regard to the requirements in almost all aspects. The most important drivers to use silicon based micro-optical modulators are high accuracy, high bandwidth and high miniaturization. A continuous further development of the technology can be reported. Novel optical, mechanical and electrical working principles are investigated to meet future requirements. After a short overview of the most typical applications of silicon based micro-optical modulators the high versatility of this technology is detailed by means of selected devices and applications. Single 1D and 2D micro mirrors with diameters of up to 4 mm e. g. for projection, imaging and spectroscopy are as well presented and discussed as micro mirror arrays comprising up to 1 million analog deflectable mirrors for image generation and phase modulation in microlithography and adaptive optics.
Nickel Superoxide Dismutase Structure and Mechanism (2004)

The 1.30 A resolution crystal structure of nickel superoxide dismutase (NiSOD) identifies a novel SOD fold, assembly, and Ni active site. NiSOD is a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with N-terminal hooks chelating the active site Ni ions. This newly identified nine-residue Ni-hook structural motif (His-Cys-X-X-Pro-Cys-Gly-X-Tyr) provides almost all interactions critical for metal binding and catalysis, and thus will likely be diagnostic of NiSODs. Conserved lysine residues are positioned for electrostatic guidance of the superoxide anion to the narrow active site channel. Apo structures show that the Ni-hook motif is unfolded prior to metal binding. The active site Ni geometry cycles from square planar Ni(II), with thiolate (Cys2 and Cys6) and backbone nitrogen (His1 and Cys2) ligands, to square pyramidal Ni(III) with an added axial His1 side chain ligand, consistent with electron paramagentic resonance spectroscopy. Analyses of the three NiSOD structures and comparisons to the Cu,Zn and Mn/Fe SODs support specific molecular mechanisms for NiSOD maturation and catalysis, and identify important structure-function relationships conserved among SODs.
Time and antenna diversity in wireless sensor and actuator networks (2009)

In this paper we focus on increasing error resilience in sensor networks by means of antenna diversity techniques. The potential of antenna diversity in wireless sensor networks is not fully exploited. Therefore in our study, we compare pure time diversity, time diversity with antenna switching and receiver selection diversity with CC2431 radio modules. We analyze our results for two types of data links i.e. with and without feedback channel and discuss options to increase bandwidth efficiency with current diversity techniques. The introduced schemes can be implemented with any commercially available IEEE 802.15.4 radios without any changes to the baseband processing. We present our experimental results for an indoor measurement setup and show that even when operating at a low signal to noise ratio, antenna diversity effect can significantly improve performance of the system.
Blockade of CTLA-4 and PD-1 Enhances Adoptive T-cell Therapy Efficacy in an ICOS-Mediated Manner (2019)

Adoptive transfer of tumor-reactive T cells (ACT) has led to modest clinical benefit in the treatment of solid tumors. Failures with this therapy are primarily due to inadequate infiltration and poor function of adoptively transferred cells in the tumor microenvironment. To improve the efficacy of ACT, we combined ACT with dual blockade of CTLA-4 and PD-1. Treatment with anti-CTLA-4 plus anti-PD-1 compared with monotherapy resulted in durable antitumor responses, enhanced effector function of ACT, utilizing PMEL-1 transgenic (Tg<sup>+</sup>) CD8<sup>+</sup> T cells, and improved survival. Using PMEL-1ICOS<sup>-/-</sup> mice, we showed that deletion of the inducible T-cell costimulator (ICOS) receptor abolished the therapeutic benefits, with selective downregulation of Eomesodermin (Eomes), interferon gamma (IFNγ), and perforin. Higher expression of IFNγ and Eomes was noted in human ICOS<sup>hi</sup> CD8<sup>+</sup> T cells compared with ICOS<sup>low</sup> counterparts. Together, our data provide direct evidence that ACT combined with immune-checkpoint therapy confers durable antitumor responses, which largely depended on CD8<sup>+</sup> T-cell-intrinsic expression of ICOS. Our study provides a foundation of testing combinatorial therapy of ACT of CD8 T cells and dual blocking of CTLA-4 and PD-1 in patients with melanoma.
The clinical relevance of maintaining the functional integrity of the stratum corneum in both healthy and disease-affected skin. (2011)

It has been recognized for approximately 50 years that the stratum corneum exhibits biological properties that contribute directly to maintaining and sustaining healthy skin. Continued basic science and clinical research coupled with keen clinical observation has led to more recent recognition and general acceptance that the stratum corneum completes many vital "barrier" tasks, including but not limited to regulating epidermal water content and the magnitude of water loss; mitigating exogenous oxidants that can damage components of skin via an innate antioxidant system; preventing or limiting cutaneous infection via multiple antimicrobial peptides; responding via innate immune mechanisms to "cutaneous invaders" of many origins, including microbes, true allergens, and other antigens; and protecting its neighboring cutaneous cells and structures that lie beneath from damaging effects of ultraviolet radiation. Additionally, specific abnormalities of the stratum corneum are associated with the clinical expression of certain disease states. This article provides a thorough "primer" for the clinician, reviewing the multiple normal homeostatic functions of the stratum corneum and the cutaneous challenges that arise when individual functions of this thin yet very active epidermal layer are compromised by exogenous and/or endogenous factors.
CA-RAM: A High-Performance Memory Substrate for Search-Intensive Applications (2007)

This paper proposes a specialized memory structure called CA-RAM (content addressable random access memory) to accelerate search operations present in many important real-world applications. Search operations can occupy a significant portion of total execution time and energy consumption, while posing a difficult performance problem to tackle using traditional memory hierarchy concepts. In essence, CA-RAM is a direct hardware implementation of the well-known hashing technique. Searchable records are stored in CA-RAM at a location determined by a hash function, defined on their search key. After a database has been built, looking up a record in CA-RAM typically involves a single memory access followed by a parallel key matching operation. Compared with a conventional CAM (content addressable memory) solution, CA-RAM capitalizes on dense SRAM and DRAM designs, and achieves comparable search performance while occupying much smaller area and consuming significantly less power. This paper presents detailed design aspects of CA-RAM, to be integrated in future general-purpose and application-specific processors and systems. To further motivate and justify our approach, we present two real examples of using CA-RAM to build a high-performance search accelerator targeting: IP address lookup in core routers and trigram lookup in a large speech recognition system
Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance (2012)

A series of cyclic peptides were designed and prepared to investigate the physicochemical properties that affect oral bioavailabilty of this chemotype in rats. In particular, the ionization state of the peptide was examined by the incorporation of naturally occurring amino acid residues that are charged in differing regions of the gut. In addition, data was generated in a variety of in vitro assays and the usefulness of this data in predicting the subsequent oral bioavailability observed in the rat is discussed.
Vaginal microflora in postmenopausal women on hormone replacement therapy. (2006)

To study the spectrum of vaginal microflora in postmenopausal women on hormone replacement therapy (HRT) and to compare the efficacy of Papanicolaou (Pap) smears with other methods for their detection. Eighty postmenopausal women were recruited for the study. These included 40 women who had attained spontaneous and were on HRT (User 1); 20 hysterectomised women on only estrogen therapy (User 2) and 20 controls (Non users). Their clinical data was recorded and specimens were collected for vaginal cultures (for aerobic bacteria and fungi), vaginal pH, Gram stain and Pap stain on cervical-vaginal smears and toluidine blue on wet smears. Vaginal pH was significantly lower in Users as compared to Non users. Lactobacilli and Gardnerella were more frequently isolated from Users while Bacteroides and E. coli were more common in Non users. Cultures were significantly more sensitive than Gram stained direct vaginal smears in detection of aerobic bacteria; however, Candida could be detected on Gram stain alone in all the cases. Frequency of detection of organisms significantly improved by application of Gram stain to the cervico-vaginal smears. However, clinically relevant organisms like Candida, Gardnerella and Mobiluncus could be identified on Pap smears alone in >50% cases. Lactobacilli could be readily identified in Pap smears in 98% cases. Wet mounts could detect cocci more easily as compared to Pap smears. Altered vaginal microbial profile in post menopausal women receiving HRT may cause bacterial and fungal vaginitis. Although culture studies remain the gold standard to detect these microorganisms, Pap and Gram stains and wet smears provide useful supplements and may be used as alternative procedures especially in resource limited settings lacking adequate culture facilities.
The NS3 proteinase domain of hepatitis C virus is a zinc-containing enzyme (1997)

NS3 proteinase of hepatitis C virus (HCV), contained within the N-terminal domain of the NS3 protein, is a chymotrypsin-like serine proteinase responsible for processing of the nonstructural region of the HCV polyprotein. In this study, we examined the sensitivity of the NS3 proteinase to divalent metal ions, which is unusual behavior for this proteinase class. By using a cell-free coupled transcription-translation system, we found that HCV polyprotein processing can be activated by Zn2+ (and, to a lesser degree, by Cd2+, Pb2+, and Co2+) and inhibited by Cu2+ and Hg2+ ions. Elemental analysis of the purified NS3 proteinase domain revealed the presence of zinc in an equimolar ratio. The zinc content was unchanged in a mutated NS3 proteinase in which active-site residues His-57 and Ser-139 were replaced with Ala, suggesting that the zinc atom is not directly involved in catalysis but rather may have a structural role. Based on data from site-directed mutagenesis combined with zinc content determination, we propose that Cys-97, Cys-99, Cys-145, and His-149 coordinate the structural zinc in the HCV NS3 proteinase. A similar metal binding motif is found in 2A proteinases of enteroviruses and rhinoviruses, suggesting that these 2A proteinases and HCV NS3 proteinase are structurally related.
Enriching CRISPR-Cas9 targeted cells by co-targeting the HPRT gene (2015)

The CRISPR-Cas9 system uses guide RNAs to direct the Cas9 endonuclease to cleave target sequences. It can, in theory, target essentially any sequence in a genome, but the efficiency of the predicted guide RNAs varies dramatically. If no targeted cells are obtained, it is also difficult to know why the experiment fails. We have developed a transient transfection based method to enrich successfully targeted cells by co-targeting the hypoxanthine phosphoribosyltransferase (HPRT) gene. Cells are transfected with two guide RNAs that target respectively HPRT and the gene of interest. HPRT targeted cells are selected by resistance to 6-thioguanine (6-TG) and then examined for potential alterations to the gene targeted by the co-transfected guide RNA. Alterations of many genes, such as AAVS1, Exo1 and Trex1, are highly enriched in the 6-TG resistant cells. This method works in both HCT116 cells and U2OS cells and can easily be scaled up to process multiple guide RNAs. When co-targeting fails, it is straightforward to determine whether the target gene is essential or the guide RNA is ineffective. HPRT co-targeting thus provides a simple, efficient and scalable way to enrich gene targeting events and to identify the cause of failure.