gebhart/patrepeval huggingface dataset:
Monolayer Assemblies Made of Octopusporphyrins with Pyridinium Headgroups:  Electron-Transfer Reactions in Noncovalent Porphyrin−Quinone Platelets in Aqueous Media (1998)

Water-soluble tetraresorcinolporphyrins with eight ω-pyridinium alkyl chains (octopusporphyrins) formed fluorescent and nonfluorescent monolayer assemblies by anion exchange of the headgroups. Electron microscopy of the evaporated solution of the octopusporphyrin having 11-pyridinium-undecanoyl side chains (1) with sodium perchlorate showed planar sheets. The uniform thickness of the layer was 4.0 ± 0.5 nm, corresponding to monomolecular platelets. An exciton calculation on the basis of the red shift of the Soret band (6 nm) is consistent with a two-dimensional arrangement with porphyrin separations of 25.6 and 17.4 Å in the x and y directions, respectively. Organic dianions such as anthraquinone-2,6-disulfonate (AQDS2-) were more effective than perchlorates or iodides for aggregate formation. Arrays of a 1:3 complex of 1/AQDS2- produced a curvature to yield nonfluorescent vesicles. The introduction of dimethyl groups at the bottom of the alkyl chains (octopusporphyrin 2) did not lead to enhanced aggregation, while the octopusporphyrin with long 2,2-dimethyl-C20-pyridinium chains (3) formed fluorescent fibers without assistance of special anions. The electron-transfer reactions of the 1 platelets with perchlorates, in which the relative fluorescence intensity was 30% of the monomer, were investigated. External addition of negatively charged electron acceptors, 1,2-naphthoquinone-4-sulfonate (NQS-) and anthraquinone-2-sulfonate (AQS-), led to partial quenching of the fluorescence of the central porphyrin layer. In both cases, the corresponding Stern−Volmer plots showed plateaus at sufficiently high concentration of the quinones. The results have been evaluated using equations derived for this special case of dynamic quenching by an electrostatically bound quencher. Binding constants of 3.4 × 104 and 1.7 × 105 M-1 and electron-transfer constants of 5 × 109 and 1.3 × 109 s-1 have been calculated for NQS- and AQS-, respectively.
Bright, emission tunable fluorescent dyes based on imidazole and π-expanded imidazole (2012)

A diverse set of imidazole- and π-expanded imidazole derivatives displaying excited state intramolecular proton transfer (ESIPT) was designed and synthesized. The effect of structural variation on photophysical properties was studied in detail for nine dyes. The relationship between the structure and photophysical properties was thoroughly elucidated also by comparing with analogues with blocked ESIPT functionality. All but one of the obtained compounds exhibit ESIPT, as demonstrated by large Stokes shifts (6500–15 600 cm−1). The type of π-expansion strongly influences the overall optical phenomena: while typical π-expansion preserves ESIPT activity, the direct fusion of imidazole with a naphthalene unit at positions 4 and 5 results in dyes which do not exhibit ESIPT. The compound possessing an acidic NH group as part of an intramolecular hydrogen bond system has a much higher fluorescence quantum yield and Stokes shift than its analogue bearing an OH group. The occurrence of ESIPT for tosylamide analogues is less affected by the hydrogen-bonding ability of the solvents compared to the unprotected amines. Two-photon absorption cross-sections of the selected derivatives are in the range of 5–100 GM.
A synthetic distributed genetic multi-bit counter (2021)

Summary A design for genetically-encoded counters is proposed via repressor-based circuits. An N -bit counter reads sequences of input pulses and displays the total number of pulses, modulo 2 N . The design is based on distributed computation, with specialized cell types allocated to specific tasks. This allows scalability and bypasses constraints on the maximal number of circuit genes per cell due to toxicity or failures due to resource limitations. The design starts with a single-bit counter. The N -bit counter is then obtained by interconnecting (using diffusible chemicals) a set of N single-bit counters and connector modules. An optimization framework is used to determine appropriate gate parameters and to compute bounds on admissible pulse widths and relaxation (inter-pulse) times, as well as to guide the construction of novel gates. This work can be viewed as a step toward obtaining circuits that are capable of finite-automaton computation, in analogy to digital central processing units. Graphical Abstract
Clinical management and outcome after laparoscopic surgery in hemophiliacs – a matched pairs analysis (2014)

Aims: Laparoscopic surgery (LS) is worldwide gaining popularity for several striking benefits such as a faster postoperative recovery, earlier hospital discharge and better cosmesis. Rationale, management and outcome of LS in hemophiliacs are thus far poorly defined and therefore issue of our present study.
Reversible Parahydrogen Induced Hyperpolarization of 15N in Unmodified Amino Acids Unraveled at High Magnetic Field (2023)

Amino acids (AAs) and ammonia are metabolic markers essential for nitrogen metabolism and cell regulation in both plants and humans. NMR provides interesting opportunities to investigate these metabolic pathways, yet lacks sensitivity, especially in case of <sup>15</sup> N. In this study, spin order embedded in p-H<sub>2</sub> is used to produce on-demand reversible hyperpolarization in <sup>15</sup> N of pristine alanine and ammonia under ambient protic conditions directly in the NMR spectrometer. This is made possible by designing a mixed-ligand Ir-catalyst, selectively ligating the amino group of AA by exploiting ammonia as a strongly competitive co-ligand and preventing deactivation of Ir by bidentate ligation of AA. The stereoisomerism of the catalyst complexes is determined by hydride fingerprinting using <sup>1</sup> H/D scrambling of the associated N-functional groups on the catalyst (i.e., isotopological fingerprinting), and unravelled by 2D-ZQ-NMR. Monitoring the transfer of spin order from p-H<sub>2</sub> to <sup>15</sup> N nuclei of ligated and free alanine and ammonia targets using SABRE-INEPT with variable exchange delays pinpoints the monodentate elucidated catalyst complexes to be most SABRE active. Also RF-spin locking (SABRE-SLIC) enables transfer of hyperpolarization to <sup>15</sup> N. The presented high-field approach can be a valuable alternative to SABRE-SHEATH techniques since the obtained catalytic insights (stereochemistry and kinetics) will remain valid at ultra-low magnetic fields.
Perturbation of magnetostatic modes observed by ferromagnetic resonance force microscopy (2006)

Magnetostatic modes of yttrium iron garnet (YIG) films are investigated by ferromagnetic resonance force microscopy. A thin-film ``probe'' magnet at the tip of a compliant cantilever introduces a local inhomogeneity in the internal field of the YIG sample. This influences the shape of the sample's magnetostatic modes, thereby measurably perturbing the strength of the force coupled to the cantilever. We present a theoretical model that explains these observations; it shows that the tip-induced variation of the internal field creates either a local ``potential barrier'' or ``potential well'' for the magnetostatic waves. The data and model together indicate that local magnetic imaging of ferromagnets is possible, even in the presence of long-range spin coupling, through the introduction of localized magnetostatic modes predicted to arise from sufficiently strong tip fields.
Demonstration of LWIR channeled spectro-polarimeter (Conference Presentation) (2019)

A compact long wave infrared (LWIR) channeled spectro-polarimeter (IRCSP) has been developed for integration into the ESTO-funded Submm-Wave and LWIR Polarimeters (SWIRP) project to measure the microphysical properties of cloud ice. The IRCSP rotates incident linearly polarized light using the combination of a quarter waveplate with a fast axis at 45◦ and a thick birefringent crystal; the output polarization state’s orientation is then a function of wavelength. To modulate and then measure the rotated light, a subsequent wiregrid linear polarizer tilted at 20◦ generates two output paths with opposite polarities in reflection and transmission to enable joint radiometric and polarimetric measurement and correct for atmospheric attenuation. The two symmetric optical paths following the linear polarizer each consist of a diffraction grating and uncooled microbolometer to simultaneously measure the resulting intensity fringes. Angle and degree of linear polarization (AOLP, DOLP) are retrieved across 8.5-12.5 µm with 1 µm resolution using Fourier decomposition of the modulated spectrum. The IRCSP will not only measure H-V variance but will produce the first full linear Stokes measurements (I, Q, and U) of upper-tropospheric cirrus clouds in the LWIR. Following thermal and polarimetric calibration, the polarimeter is expected to achieve 0.5% DOLP accuracy over 90% of the spectral band.
Synthesis of Planar Compliances With Mechanisms Having Six Compliant Components: Geometric Approach (2019)

Abstract In this paper, the synthesis of any planar compliance with a six-component compliant mechanism is addressed. The mechanisms studied are either serial mechanisms with six elastic joints or parallel mechanisms with six springs. For each type of mechanism, conditions on the mechanism configurations that must be satisfied to realize a given compliance are developed. The geometric significance of each condition is identified and graphically represented. Geometric construction-based synthesis procedures for both types of mechanism are developed. These procedures allow one to select each elastic component from a restricted space based on its geometry.
A novel model of solute transport in a hollow‐fiber bioartificial pancreas based on a finite element method (2002)

Extravascular bioartificial pancreas based on hollow fiber seems to be a promising treatment of diabetes mellitus. However, solutes mass-transport limitations in such a device could explain its lack of success. To determine critical device parameters, we have developed a novel tridimensional model based on finite element method for glucose, insulin, and oxygen diffusion around an islet of Langerhans encapsulated in a hollow-fiber section. A glucose ramp stimulation was applied outside the fiber and diffused to the islet. Concomitantly, a stationary oxygen partial pressure was applied outside the fiber, and determined local oxygen partial pressure on the islet environment. An insulin secretion model stimulated by a glucose concentration ramp and corrected by the local oxygen partial pressure was also implemented. Insulin secretion by the islet was thus computed as a response to glucose signal. The model predictions notably showed that the fiber radius had to be small enough to favor a fast response for insulin secretion and to ensure a maximal oxygen partial pressure in the islet environment. Besides the effect of fiber radius, a better islet oxygenation could be achieved by adjustments on the islet density, i.e., on the fiber length dedicated to a single islet. These hints should allow the future proposal of an optimal design for an implantable bioartificial pancreas.
Apple and strawberry MADS-box genes and their function in plant developmental pathways (2012)

The main role of MADS-box transcription factors in plant developmental processes has been well described in the model plant Arabidopsis thaliana. However, little is known about their function in crops of important agricultural and commercial value. Our study aims to investigate their role in two agronomical relevant Rosaceae crops: apple (Malus x domestica Borkh.) and strawberry (Fragaria vesca).&#13;\nExpression studies using qPCR and RNA seq have identified two apple Dormancy Associated MADS-box (DAM) genes. They group with the StMADS11 clade, and were named MdDAM1 and MdDAM2, the last one discovered ex novo. Real time expression studies in dormant buds collected during the chilling period and chromatin immunoprecipitation (ChIP) analyses confirmed that the genes are downregulated by exposure to cold and MdDAM1 is epigenetically repressed, as it has been demonstrated for Arabidopsis FLC and peach DAM genes.&#13;\nIn parallel we worked on strawberry MADS-box genes of known function involved in flower development. We chose three MADS-box genes that are homologs of Arabidopsis PISTILLATA and AGAMOUS to perform gene expression and functional analysis using a RNA interference approach to obtain post-transcriptional gene silencing. The positive transgenic lines of each transformation were evaluated at the molecular and phenotypic level. Single gene mutants does not show altered flower phenotype, suggesting a different mechanism of flower development in strawberry, probably due to the peculiar flower structure.&#13;\n
Three-Dimensional Quantitative Optical Measurement of Asymmetrically Focused Ultrasound Pressure Field (2012)

High-intensity focused ultrasound (HIFU) is used for the treatment of tumors such as prostate cancer. In the development of this technique, an accurate and fast measurement of the HIFU pressure field is important. A hydrophone is generally used for the measurement, but it might disturb the pressure field and scanning it in the field takes a long time. On the other hand, optical ultrasonic field mapping has the advantages of speed and its nature of not by interfering with the acoustic field. In this study, we reconstructed an asymmetric ultrasound field by optical measurement using a computed tomography (CT) algorithm. The asymmetric field was generated by a focused transducer with four elements. Also, the absolute measurement of ultrasonic pressure was checked by measuring the center of the field of the charge-coupled device (CCD) camera. The results showed overall agreement with those of hydrophone measurement.
NKTR-102, a novel PEGylated irinotecan, results in sustained tumor growth suppression in mouse models of human colorectal and lung tumors that correlates with increased and sustained tumor SN38 exposure (2007)

C157 Purpose NKTR-102, a novel polyethylene glycol (PEG)-irinotecan conjugate, is in Phase I clinical development. During preclinical development, the relationship between drug and metabolite pharmacokinetics and tumor growth was investigated in xenograft mouse models of HT29 human colorectal tumor, which is moderately resistant to irinotecan treatment, and NCI-H460 human lung tumor.  Methods In separate studies, mice implanted subcutaneously with either cell line received 40 mg/kg irinotecan (Irino)-equivalent IV doses of Irino or NKTR-102 every 4 days for 3 doses after measurable tumors had developed. Tumor size was measured and plasma and tumor tissue were sampled serially at planned times for 60 and 30 days in HT-29 and H460 cell lines, respectively. Plasma and tumor samples were assayed for NKTR-102, Irino, and SN38 (the principal active metabolite of Irino) using a sensitive, selective, and validated LC/MS-MS method.  Results NKTR-102 caused marked, statistically significant decreases in both HT-29 and H460 tumor growth, whereas Irino at the same dose and schedule resulted in only modest suppression of tumor growth that was short lived.  Median HT-29 tumor weights (mg) at end of study were 3553 for Irino and 674 for NKTR-102 (p
Microplate-based, label-free detection of biomolecular interactions: applications in proteomics (2006)

This review describes a new type of label-free optical biosensor that is inexpensively manufactured from continuous sheets of plastic film and incorporated into standard format microplates to enable highly sensitive, high-throughput detection of small molecules, proteins and cells. The biosensor and associated detection instrumentation are applied to review two fundamental limiting issues for assays in proteomics research and drug discovery: requirement for quantitative measurement of protein concentration and specific activity, and measurements made with complex systems in highly parallel measurements. SRU BIosystems, Inc.'s BIND label-free detection will address these issues using data examples for hybridoma screening, epitope binning and mapping, small-molecule screening, and cell-based functional assays. The review describes several additional applications that are under development for the system, and the key issues that will drive adoption of the technology over the next 5 years.
Approaching the Hole Mobility Limit of GaSb Nanowires (2015)

In recent years, high-mobility GaSb nanowires have received tremendous attention for high-performance p-type transistors; however, due to the difficulty in achieving thin and uniform nanowires (NWs), there is limited report until now addressing their diameter-dependent properties and their hole mobility limit in this important one-dimensional material system, where all these are essential information for the deployment of GaSb NWs in various applications. Here, by employing the newly developed surfactant-assisted chemical vapor deposition, high-quality and uniform GaSb NWs with controllable diameters, spanning from 16 to 70 nm, are successfully prepared, enabling the direct assessment of their growth orientation and hole mobility as a function of diameter while elucidating the role of sulfur surfactant and the interplay between surface and interface energies of NWs on their electrical properties. The sulfur passivation is found to efficiently stabilize the high-energy NW sidewalls of (111) and (311) in order to yield the thin NWs (i.e., <40 nm in diameters) with the dominant growth orientations of ⟨211⟩ and ⟨110⟩, whereas the thick NWs (i.e., >40 nm in diameters) would grow along the most energy-favorable close-packed planes with the orientation of ⟨111⟩, supported by the approximate atomic models. Importantly, through the reliable control of sulfur passivation, growth orientation and surface roughness, GaSb NWs with the peak hole mobility of ∼400 cm(2)V s(-1) for the diameter of 48 nm, approaching the theoretical limit under the hole concentration of ∼2.2 × 10(18) cm(-3), can be achieved for the first time. All these indicate their promising potency for utilizations in different technological domains.
Feasibility study of SCAAM-type Alt-PSM for 157-nm lithography (2003)

Alternating Phase Shifting Mask (Alt-PSM) technology is one of the most effective Resolution Enhancement Technology (RET). It has been used for current optical lithography and will be used for 157nm lithography also. Considering about topographic structure of Alt-PSM, current etched quartz with undercut structure will be very difficult to be applied for 157nm Alt-PSM because undercut structure limits mechanical durability at narrower chrome width. To solve this problem, Side-wall Chrome Alternating Aperture Mask (SCAAM) is proposed. This structure has the characteristics of “There is no undercut”, “Ideal topographic structure for lithography (All quartz steps are covered by chrome film which means very few refracted light at quartz side-wall will go through chrome film and affect printing results compared with conventional etched quartz type Alt-PSM)”. We fabricated SCAAM type Alt-PSM for 157nm lithography and printed by using 157nm microstepper with a 0.85-NA lens. In this report, we will show preliminary printing results of using SCAAM and which will be compared with the results of using conventional etched quartz type Alt-PSM.
Clonal deletion of V beta 5+ T cells by transgenic I-E restricted to thymic medullary epithelium. (1993)

A variety of cell types expressing MHC class II molecules is known to function as APC in vitro. We employed the Ig kappa gene enhancer and promoter to target the class II E alpha gene, and thereby I-E, exclusively to B cells to address their APC function in vivo. Although transgenic I-E was expressed on B lymphocytes, we unexpectedly obtained I-E on thymic medullary epithelium but not macrophages and at low frequency on dendritic cells. Using these transgenic mice, we constructed bone marrow irradiation chimeras with I-E expressed only on medullary epithelium, in order to determine the role of this cell type in tolerance by clonal deletion in the thymus. Although it is accepted that bm-derived cells play a primary role in deletion, and thymic epithelium can delete clones to a lesser degree, the role of cortical vs medullary thymic epithelium has not been directly dissected. We demonstrate that medullary epithelium alone can tolerize by partial deletion of I-E-reactive V beta 5+ T cells. These results indicate a role for medullary epithelium in deletion during the later stages of thymic development, and support the notion that positive and negative selection of developing T cells can occur in distinct temporal and anatomic compartments.
Supplementary Figures and Tables from A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas (2023)

&lt;p&gt;Supplementary Figure S1 shows the strategy and result of co-essentiality module identificationfrom the DepMap CRISPR screen dataset and further characterization of the BIRC6 module. Supplementary Figure S2 shows the viability effect of BIRC6 depletion in BIRC6-dependent and -nondependent cancer cells lines as well asin nontransformed cells. Supplementary Figure S3 shows in vitro confirmations of the inducible BIRC6 depletion (by RNAi and CRISPR) systems as well as the effect of BIRC6 depletion on metastasis in xenograft models. Supplementary Figure S4 shows detailed results for the allele competition assay to evaluate the role of the BIR and UBC domains of BIRC6 and further evidence for the physical assembly of BIRC6 ubiquitin ligase complex. Supplementary Figure S5 shows evidence for the selective activation of the p-eIF2alpha/ATF4 arm of UPR (or ISR) upon BIRC6 depletion. Supplementary Figure S6 shows evidence supporting the importance of HRI-mediated ISR activation as a mechanism underlying the loss of viability caused by BIRC6 complex suppression. Supplementary Figure S7 shows evidence for the direct regulation of HRI ubiquitination and degradation by the BIRC6 complex Supplementary Figure S8 shows elevated expression of HRI mRNA in the tumor samples compared to the normal samples in large-scale datasets (TCGA, TARGET and GTEx). Supplementary Figure S9 shows the inefficiency of the gene expression and copy number of the functionally related genes in predicting BIRC6 dependency. Supplementary Table S1 lists the top 50 co-essentiality modules identified in the analysis explained in Supplementary Figure S1A. Supplementary Table S2 lists the key DNA and RNA sequences used in this study.&lt;/p&gt;
YfbA, a Yersinia pestis Regulator Required for Colonization and Biofilm Formation in the Gut of Cat Fleas (2014)

For transmission to new hosts, Yersinia pestis, the causative agent of plague, replicates as biofilm in the foregut of fleas that feed on plague-infected animals or humans. Y. pestis biofilm formation has been studied in the rat flea; however, little is known about the cat flea, a species that may bridge zoonotic and anthroponotic plague cycles. Here, we show that Y. pestis infects and replicates as a biofilm in the foregut of cat fleas in a manner requiring hmsFR, two determinants for extracellular biofilm matrix. Examining a library of transposon insertion mutants, we identified the LysR-type transcriptional regulator YfbA, which is essential for Y. pestis colonization and biofilm formation in cat fleas.