gebhart/patrepeval huggingface dataset:
Fluoroquinolone Action against Clinical Isolates of Mycobacterium tuberculosis : Effects of a C-8 Methoxyl Group on Survival in Liquid Media and in Human Macrophages (1999)

When the lethal action of a C-8 methoxyl fluoroquinolone against clinical isolates of Mycobacterium tuberculosis in liquid medium was measured, the compound was found to be three to four times more effective (as determined by measuring the 90% lethal dose) than a C-8-H control fluoroquinolone or ciprofloxacin against cells having a wild-type gyrA (gyrase) gene. Against ciprofloxacin-resistant strains, the C-8 methoxyl group enhanced lethality when alanine was replaced by valine at position 90 of the GyrA protein or when aspartic acid 94 was replaced by glycine, histidine, or tyrosine. During infection of a human macrophage model by wild-type Mycobacterium bovis BCG, the C-8 methoxyl group lowered survival 20- to 100-fold compared with the same concentration of a C-8-H fluoroquinolone. The C-8 methoxyl fluoroquinolone was also more effective than ciprofloxacin against a gyrA Asn94 mutant of M. bovis BCG. In an M. tuberculosis-macrophage system the C-8 methoxyl group improved fluoroquinolone action against both quinolone-susceptible and quinolone-resistant clinical isolates. Thus, a C-8 methoxyl group enhances the bactericidal activity of quinolones with N1-cyclopropyl substitutions; these data encourage further refinement of fluoroquinolones as antituberculosis agents.
Altered Leukocyte Dynamics by PECAM‐deficient mice during Chemical Contact Hypersensitivity (2008)

We have shown that Platelet Endothelial Cell Adhesion Molecule (PECAM, CD31) deficient mice in the FVB/n background have altered neutrophil and monocyte trafficking. These studies did not look at other leukocyte populations and relied typically on a primary inflammatory response. In this study, we used 2,4 Dinitrofluorobenzene (DNFB) to first sensitize wild type and PECAM deficient mice. Five days later, DNFB was applied to ears, and leukocytes from the ears were collected two days later. Major leukocyte populations were analyzed using six‐color flow‐cytometry. Some leukocyte populations, like dendritic cells and CD8+ T cells were unaffected by PECAM deficiency. Other populations, CD4+ T cells, gamma‐delta T cells, and DX5+, CD3− Natural Killer cells were markedly reduced in PECAM deficient mice. Another marker of inflammation, ear thickness, was unaffected by PECAM deficiency. These studies show that PECAM is differentially by some various leukocyte populations and may explain why some have little or no detectable PECAM expression in humans. This may have significant effects if anti‐PECAM therapies are used to selectively target certain leukocyte subsets.
Supplementary Methods and Materials from HORMAD1 Is a Negative Prognostic Indicator in Lung Adenocarcinoma and Specifies Resistance to Oxidative and Genotoxic Stress (2023)

&lt;p&gt;More detailed methods for the Natural Product Library Generation, Natural Product Cytotoxicity Screens, Purification and Characterization of HORMAD1&lt;/p&gt;
Preparation of Co‐Na Heterobinuclear Polymeric Complex of Salen‐Crown Ether and its Catalytic Activation for Molecular Oxygen (2005)

The Co‐Na heterobinuclear polymer complex based on Salen Schiff base and crown ether have been prepared by a method of interfacial polymerization without the presence of a phase transfer catalyst. The catalytic behavior of the Co‐Na heterobinuclear polymer complex in aerobic oxidation of cyclohexene has been studied.
Twisting the TAPPs: Bay‐Substituted Non‐planar Tetraazapero‐pyrenes and their Reduced Anions (2019)

A new synthesis of tetraazaperopyrenes (TAPPs) starting from a halogenated perylene derivative 3,4,9,10- tetrabromo-1,6,7,12-tetrachloroperylene (1) gave access to bay-substituted TAPPs for the first time. Selective lithiation of the bromine-positions and subsequent addition of tosyl azide led to the formation of the tetraazidotetrachloroperylene (2), which was subsequently reduced by addition of sodium borohydride to the corresponding tetraaminotetrachloroperylene (3). Oxidation to its semiquinoidal form 4 and subsequent cyclization with acid chlorides gave rise to a series of bay-chlorinated TAPPs. Whereas the aromatic core of the previously studied ortho-substituted TAPPs was found to be planar, the steric pressure of the two chlorine substituents on each side leads to the twist of the peropyrene core of approximately 30 degrees, a structural feature also observed in other bay-substituted perylene derivatives. An experimental and computational analysis reveals that introducing chloride substituents at these positions leads to slightly increased electron affinities (EA) enabling the selective generation and characterization of the reduced mono-anionic radicals and closed shell di-anionic species. These anions were isolated and characterized by UV/Vis spectroscopy and EPR or NMR, respectively. Processing of the bay-chlorinated TAPPs in n-channel organic TFTs revealed electron mobilities of 0.001 to 0.003 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup> . These reduced electron mobilities compared to the ortho-halogenated TAPPs are thought to be rooted in the less densely packed solid-state structures.
Isolation and characterization of the genomic human CD7 gene: structural similarity with the murine Thy-1 gene. (1991)

The human CD7 molecule is a 40-kDa member of the immunoglobulin gene superfamily that is expressed on T-lymphoid and myeloid precursors in fetal liver and bone marrow. CD7 is also expressed on T lymphocytes in multiple stages of T-cell development, including a major subset of mature peripheral T cells. In this paper we report the isolation and characterization of the human CD7 gene and 5' flanking region. Sequence analysis revealed that the CD7 gene comprises four exons that span 3.5 kilobases. The 5' flanking region (506 base pairs) has a high G + C content and no "TATA" or "CCAAT" elements. DNase I sensitivity analysis of chromatin from the CD7+ progenitor cell leukemia line, DU528, and the CD7-, CD4+, CD8+, TCR alpha beta + T-cell line, DU980 (where TCR is the T-cell receptor), revealed two distinct hypersensitive sites 5' of the CD7 gene. Hypersensitive site 1, present in the DU980 T-cell line, was located 4.5 kilobases upstream of the presumed CD7 transcription initiation site. Only DNase I hypersensitive site 2, which mapped to the promoter region, was found in the DU528 line. Comparison of the organization of the CD7 gene with that of other members of the immunoglobulin gene superfamily revealed that the human CD7 gene most closely resembles the murine Thy-1 gene. Both CD7 and Thy-1 are encoded by small genes with four exons, contain TATA-less promoters, and have a similar functional organization. These structural similarities suggest that human CD7 and murine Thy-1 may be functional homologues.
Recent Progress of Experiment on DC Superconducting Power Transmission Line in Chubu University (2009)

A test stand of a DC superconducting power transmission cable was finished to construct in October 2006 in Chubu University, Japan, and three cooling cycles were carried out to measure the properties of the cable. Critical current of HTS tapes in the cable was measured at every cooling cycle and shows the similar temperature dependence; conclusively, the HTS tapes suffered no damage after cooling and heating process between the each cycle. Peltier current leads were partly installed in the test stand, and it was measured that the temperatures of the feedthrough near to the liquid nitrogen were decreased in spite of a current feeding.
Using a Policy Spaces Auditor to check for Temporal Inconsistencies in Healthcare Audit Log Files (2013)

The core tenet of the healthcare field is that care delivery comes first and nothing should interfere with it. Consequently, theaccess control mechanisms, used in healthcare to regulate and restrict the disclosure of data, are often bypassed,especially in emergency cases. This concept is called ‘break the glass’ (BtG) and is common in healthcare organizations.Though useful and necessary in emergency situations, from a security perspective, it is an important system flaw. Malicious users can exploit the system by breaking the glass to gain unauthorized privileges and accesses.Also, as the proportion of system accesses that are BtG increases, it becomes easier for an attacker to hide in the crowd of the audit log. In this paper, we build upon existing work that defined policy spaces to help manage the impact of the break the glass phenomenon in healthcare systems. We present a system that enables the inference and discovery of facts that require further scrutiny. This significantly reduces the burden on the person investigating potentially suspicious activity in the audit logs of healthcare information systems.
Effect of sol-gel polymerization of tetraethylorthosilicate on internal aggregate structure in zinc-neutralized ethylene-methacrylic acid ionomers (2000)

Sol-gel reactions of tetraethylorthosilicate have been performed in three different zinc-neutralized ethylene-methacrylic acid copolymer ionomers for the purpose of creating nanostructured organic-inorganic materials with enhanced properties. Extended X-ray absorption fine structure (EXAFS) spectroscopy was used to understand the effect of this in situ reaction on ionic aggregate morphology. EXAFS spectra showed that no large changes occurred in the aggregate structure, indicating that the internal environment of the aggregates did not nucleate the reaction, at least to the extent that the ionic domains were significantly undisrupted. However, small changes in EXAFS patterns were evident. These changes could be a result of nucleation of the reaction at the edges of the aggregates, or aggregate size rearrangement caused by the insertion of inorganic moieties into the polymer. However, the results indicate that the latter cannot include significant amounts of unaggregated zinc ions. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 197–200, 2001
Investigation of Pt-Salt-Doped-Standalone- Multiwall Carbon Nanotubes for On-Chip Interconnect Applications (2019)

In this paper, we investigate, by combining electrical measurements with an atomistic-to-circuit modeling approach, the conductance of doped standalone multiwall carbon nanotubes (CNTs) as a viable candidate for the next generation of back-end-of-line interconnects. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ab initio</i> simulations predict a doping-related shift of the Fermi level, which reduces shell chirality variability and improves electrical resistivity up to 90% by converting semiconducting shells to metallic. Electrical measurements of Pt-salt-doped CNTs provide up to 50% of resistance reduction, which is a milestone result for future CNT interconnect technology. Moreover, we find that defects and contacts introduce additional resistance, which limits the efficiency of doping, and are the primary cause for the mismatch between theoretical predictions and experimental measurements on doped CNTs.
Generalized Collective States and Their Role in a Collective State Atomic Interferometer and Atomic Clock (2014)

We investigate the behavior of an ensemble of N non-interacting, identical atoms, excited by a laser with a wavelength of λ. In general, the i-th atom sees a Rabi frequency Ωi, an initial position dependent laser phase φi, and a motion induced Doppler shift of δi. When Ωi = Ω and δi = δ for all atoms, the system evolves into a superposition of (N + 1) generalized symmetric collective states, independent of the values of φi. If φi = φ for all atoms, these states simplify to the well known Dicke collective states. When Ωi or δi is distinct for each atom, the system evolves into a superposition of symmetric as well as asymmetric collective states. For a large value of N , the number of asymmetric states (2 − (N + 1)) is far greater than that of the symmetric states. For a collective state atomic interferometer (CSAI) and a collective state atomic clock (CSAC) we recently proposed, it is important to understand the behavior of all the collective states under various conditions. In this paper, we show how to formulate the properties of all the collective states under various non-idealities, and use this formulation to understand the dynamics thereof. Specifically, for the case where Ωi = Ω and δi = δ for all atoms, we show how the amplitudes of each of the generalized collective states can be determined explicitly in a simple manner. For the case where Ωi or δi is distinct for each atom, we show how the symmetric and asymmetric collective states can be treated on the same footing. Furthermore, we show that the collective states corresponding to the absorption of a given number of photons can be visualized as an abstract, multi-dimensional rotation in the Hilbert space spanned by the ordered product states of individual atoms. We also consider the effect of treating the center of mass degree of freedom of the atoms quantum mechanically on the description of the collective states. In particular, we show that it is indeed possible to construct a generalized collective state, as needed for the CSAI, when each atom is assumed to be in a localized wave packet. The analysis presented in this paper is crucial to understanding the dynamics of both the CSAI and the CSAC, which in turn represent radically new developments in the area of opto-atomic metrology, with significant improvement in precision over the state of the art. Furthermore, it opens up new avenues for exploring reduction of quantum projection noise via spin squeezing.
Characterization of a soluble, catalytically active form of Escherichia coli leader peptidase: requirement of detergent or phospholipid for optimal activity (1995)

Leader peptidase is a novel serine protease in Escherichia coli, which functions to cleave leader sequences from exported proteins. Its catalytic domain extends into the periplasmic space and is anchored to the membrane by two transmembrane segments located at the N-terminal end of the protein. At present, there is no information on the structure of the catalytic domain. Here, we report on the properties of a soluble form of leader peptidase (delta 2-75), and we compare its properties to those of the wild-type enzyme. We find that the truncated leader peptidase has a kcat of 3.0 S-1 and a Km of 32 microM with a pro-OmpA nuclease A substrate. In contrast to the wild-type enzyme (pI of 6.8), delta 2-75 is water-soluble and has an acidic isoelectric point of 5.6. We also show with delta 2-75 that the replacement of serine 90 and lysine 145 with alanine residues results in a 500-fold reduction in activity, providing further evidence that leader peptidase employs a catalytic serine/lysine dyad. Finally, we find that the catalysis of delta 2-75 is accelerated by the presence of the detergent Triton X-100, regardless if the substrate is pro-OmpA nuclease A or a peptide substrate. Triton X-100 is required for optimal activity of delta 2-75 at a level far below the critical micelle concentration. Moreover, we find that E. coli phospholipids stimulate the activity of delta 2-75, suggesting that phospholipids may play an important physiological role in the catalytic mechanism of leader peptidase.
Xenotransplantation and interspecies organogenesis: current status and issues (2022)

Pancreas (and islet) transplantation is the only curative treatment for type 1 diabetes patients whose β-cell functions have been abolished. However, the lack of donor organs has been the major hurdle to save a large number of patients. Therefore, transplantation of animal organs is expected to be an alternative method to solve the serious shortage of donor organs. More recently, a method to generate organs from pluripotent stem cells inside the body of other species has been developed. This interspecies organ generation using blastocyst complementation (BC) is expected to be the next-generation regenerative medicine. Here, we describe the recent advances and future prospects for these two approaches.
GTC/CanariCam Mid-infrared Polarimetry of Magnetic Fields in Star-forming Region W51 IRS2 (2023)

Abstract We present 0.″4 resolution imaging polarimetry at 8.7, 10.3, and 12.5 μ m, obtained with CanariCam at the Gran Telescopio Canarias, of the central 0.11 pc × 0.28 pc (4.″2 × 10.″8) region of W51 IRS2. The polarization, as high as ∼14%, arises from silicate particles aligned by the interstellar magnetic field ( B -field). We separate, or unfold, the polarization of each sightline into emission and absorption components, from which we infer the morphologies of the corresponding projected B -fields that thread the emitting- and foreground-absorbing regions. We conclude that the projected B -field in the foreground material is part of the larger-scale ambient field. The morphology of the projected B -field in the mid-infrared (mid-IR) emitting region spanning the cometary H ii region W51 IRS2W is similar to that in the absorbing region. Elsewhere, the two B -fields differ significantly with no clear relationship between them. The B -field across the W51 IRS2W cometary core appears to be an integral part of a champagne outflow of gas originating in the core and dominating the energetics there. The bipolar outflow, W51north jet, that appears to originate at or near SMA1/N1 coincides almost exactly with a clearly demarcated north–south swath of lower polarization. While speculative, comparison of mid-IR and submillimeter polarimetry on two different scales may support a picture in which SMA1/N1 plays a major role in the B -field structure across W51 IRS2.
Expanding the stroke team to include interventional cardiology (2020)

Team-based care has been emphasized as a strategy to improve and optimize outcomes for broad groups of patients who have presented with often complex medical conditions including large vessel cerebral occlusion. Although neurointerventionalists from different specialties perform mechanical embolectomy, which has become the standard of care for large vessel cerebral occlusion, these specialties are limited by relatively low numbers typically concentrated in a small number of sites. In this single center experience, approximately 50 patients with large vessel stroke were transferred out of an emergency room to other centers despite the availability of an experienced cardiologist with extensive carotid experience. Such transfer strategies typically result in delays in receiving reperfusion and, therefore, may decrease the success rates and substantial improvement that can be obtained by patients in this setting. Trained interventional cardiologists in centers with limited 24/7/365 coverage could achieve rapid revascularization and reperfusion saving lives. In order to accommodate the need for treating these patients, carotid stent trained cardiologists should enter the arena, learn mechanical embolectomy, and be supported by their colleagues from other disciplines on acute stroke care teams.
Supplementary Table S6 from PROTOCADHERIN 7 Acts through SET and PP2A to Potentiate MAPK Signaling by EGFR and KRAS during Lung Tumorigenesis (2023)

&lt;p&gt;RNA-seq results from HBEC-shp53 and HBEC-shp53-PCDH7 cells&lt;/p&gt;
Neighbourhood disadvantage impacts on pulmonary function in patients with sarcoidosis (2022)

Patients with sarcoidosis living in high disadvantage neighbourhoods experience worse baseline lung function and more rapid lung function decline, highlighting the need for better understanding of how neighbourhood-level factors impact individual patient outcomes.
Stacked Pt/BLT/Pt/IrOx/Ir capacitor for high density feram (2001)

Abstract Pt/BLT/Pt/IrOx/Ir capacitor was successfully integrated on a conventional TiN/TiSi2/poly-Si plug for high density ferroelectric random access memory (FeRAM). Random oriented Bi3.35La0.85Ti3O12 thin (70 nm) film was prepared by optimization of metalorganic decomposition (MOD) and rapid thermal annealing (RTA) processes. After the integration to metal-1 step using a total thermal budget at 650°C for 2 h in O2 for ferroelectric crystallization and recovery, the poly-plug preserved a small contact resistance of 1.5±0.1 kΩ/plug (0.30 μm in diameter). The stacked BLT capacitor showed good electrical properties such as a high switching polarization (P*-P○) of 15±2 μC/cm2 without degradation up to a small capacitor size of 0.7 × 0.7 μm2, a small coercive voltage (2Vc) of 1.3 V, a small leakage current in order of 10−6 A/cm2 and a small polarization loss of 2 μC/cm2 after 1x1011 fatigue cycles.
A large-scale chemical-genetic strategy to design antimicrobial combination chemotherapy for Mycobacterium tuberculosis (2019)

The efficacies of all antibiotics against tuberculosis are eventually eroded by resistance. New strategies to discover drugs or drug combinations with higher barriers to resistance are needed. Previously, we reported the application of a large-scale chemical-genetic interaction screening strategy called PROSPECT to the discovery of new Mycobacterium tuberculosis inhibitors, which resulted in identification of the small molecule BRD-8000, an inhibitor of a novel target, EfpA. Leveraging the chemical genetic interaction profile of BRD-8000, we identified BRD-9327, another, structurally distinct small molecule EfpA inhibitor. We show that the two compounds are synergistic and display collateral sensitivity because of their distinct modes of action and resistance mechanisms. High-level resistance to one increases the sensitivity to and reduces the emergence of resistance to the other. Thus, the combination of BRD-9327 and BRD-8000 represents a proof-of-concept for the novel strategy of leveraging chemical-genetics in the design of antimicrobial combination chemotherapy in which mutual collateral sensitivity is exploited.
Multi-modal program inference: a marriage of pre-trained language models and component-based synthesis (2021)

Multi-modal program synthesis refers to the task of synthesizing programs (code) from their specification given in different forms, such as a combination of natural language and examples. Examples provide a precise but incomplete specification, and natural language provides an ambiguous but more "complete" task description. Machine-learned pre-trained models (PTMs) are adept at handling ambiguous natural language, but struggle with generating syntactically and semantically precise code. Program synthesis techniques can generate correct code, often even from incomplete but precise specifications, such as examples, but they are unable to work with the ambiguity of natural languages. We present an approach that combines PTMs with component-based synthesis (CBS): PTMs are used to generate candidates programs from the natural language description of the task, which are then used to guide the CBS procedure to find the program that matches the precise examples-based specification. We use our combination approach to instantiate multi-modal synthesis systems for two programming domains: the domain of regular expressions and the domain of CSS selectors. Our evaluation demonstrates the effectiveness of our domain-agnostic approach in comparison to a state-of-the-art specialized system, and the generality of our approach in providing multi-modal program synthesis from natural language and examples in different programming domains.
Dispersion compensation in coherence-domain multiplexed systems (1994)

An ultrahigh-bandwidth point-to-point communications system based on white-light sources, pulse shapers, and interferometric receivers is proposed. Dispersion compensation by interferometric receivers is described and demonstrated. Linear dispersion-limited communications bandwidths are shown to scale with the square root of the data packet length.