gebhart/patrepeval huggingface dataset:
Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals (2008)

With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed.
Tetranuclear copper(i) clusters: impact of bridging carboxylate ligands on solid state structure and photoluminescence (2007)

The X-ray crystallographic characterization and solid state photoluminescence (PL) study of three new tetranuclear copper(I) clusters, [Cu4(O2CR)4], R = (3-F)C6H4 (1), (2,3,4-F)3C6H2 (2), and CF3/C6F5 (3), revealed a dependence of PL on the structural type.
Bioluminescence techniques in metabolic studies in pancreatic islets: Practicalities and pitfalls (1978)

info:eu-repo/semantics/published
Simultaneous in situ conductivity and ESR measurements of electroactive polymers in electrochemical cell (1991)

Experimental aspects of conductivity and spin susceptibility measurements of conducting polymer films as a function of the redox state are discussed. An apparatus for in situ measurements in an electrochemical cell is described. The working electrode consists of two parts separated by an insulating gap which is bridged by the polymer film. Special geometry has been designed to make the cell compatible with utilization inside an ESR microwave cavity. A signal proportional to the film conductivity is recorded continuously as a function of the applied potential. Data obtained on polyaniline are reported. In particular a case of spinless conductivity is evidenced.
Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric‐8 (2009)

Ric-8 is a highly conserved cytosolic protein (MW 63 KDa) initially identified in C. elegans as an essential factor in neurotransmitter release and asymmetric cell division. Two different isoforms have been described in mammals, Ric-8A and Ric-8B; each possess guanine nucleotide exchange activity (GEF) on heterotrimeric G-proteins, but with different Galpha subunits specificities. To gain insight on the mechanisms involved in Ric-8 cellular functions it is essential to obtain some information about its structure. Therefore, the aim of this work was to create a structural model for Ric-8. In this case, it was not possible to construct a model based on comparison with a template structure because Ric-8 does not present sequence similarity with any other protein. Consequently, different bioinformatics approaches that include protein folding and structure prediction were used. The Ric-8 structural model is composed of 10 armadillo folding motifs, organized in a right-twisted alpha-alpha super helix. In order to validate the structural model, a His-tag fusion construct of Ric-8 was expressed in E. coli, purified by affinity and anion exchange chromatography and subjected to circular dichroism analysis (CD) and thermostability studies. Ric-8 is approximately 80% alpha helix, with a Tm of 43.1 degrees C, consistent with an armadillo-type structure such as alpha-importin, a protein composed of 10 armadillo repeats. The proposed structural model for Ric-8 is intriguing because armadillo proteins are known to interact with multiple partners and participate in diverse cellular functions. These results open the possibility of finding new protein partners for Ric-8 with new cellular functions.
HEMOLYTIC DISEASE OF THE FETUS (1999)

Queenan, John T. MD; Eglinton, Gary S. MD; Tomai, Thomas P.; Ural, Serdar H. MD; King, Jeffrey C. MD; Spong, Catherine Y. MD Author Information
Elastic Moduli of Cadmium Telluride (1962)

The elastic moduli of cadmium telluride at 25°C have been determined by measurement of ultrasonic wave velocities in the frequency range 40–300 Mc/sec. Preparation of the crystal specimens is described, and factors affecting the accuracy of results are considered. The question of possible piezoelectric stiffening and its effect on measured wave velocities is also considered. Based on a density of 5.854 g/cm3 as computed from the lattice constant (and taken as exact with respect to uncertainty estimates) the zero field elastic moduli are: ModulusValue d/cm2Uncertainty in %c115.351×10110.15c123.6810.2c441.9940.15
Performance of common density functionals for excited states of tetraphenyldibenzoperiflanthene (2023)

Time-dependent density functional theory is the method of choice to efficiently calculate excitation spectra with the functional and basis set choice allowing to compromise between accuracy and computational cost. In this work the performance of different functionals as well as the second-order approximate coupled cluster singles and doubles model CC2 is evaluated by comparing the results to experimental results of the example molecule tetraphenyldibenzoperiflanthene (DBP). Functional choice has a significant impact on the spectrum of DBP. The performance of a number of different functionals was evaluated, quantified, and, where possible, discussed. The best functional, tuned-CAM-B3LYP, is used to investigate DBP on a surface of hexagonal boron nitride (h-BN). The resulting spectrum shows excellent agreement with experimental results for a monolayer of DBP on h-BN.
Influence of Alkaline Activation over Swelling and Cation Exchange Capacity on Bentonites (2010)

The performance of the alkaline processes on the properties of cation exchange capacity (CEC) and swelling was studied in three different types of bentonite from Brazil, Argentina and Mozambique. Alkaline activations were performed by means of mechanochemical reactions with solutions of NaOH and Na2CO3, to increase the sodium content of bentonite clays and, thus, improve the properties above. Clay samples were characterized by X-ray diffraction, to obtain the constituent phases. Activated samples were evaluated according to their cation exchange capacity – determined by the methylene blue test, and swelling index – measured by the Foster’s method. Results showed that the activation improved the properties of all bentonite types, especially the Brazilian clay, which achieved the most significant raises. There was also an indication that the type of clay affect the processing.
From Outreach to Inreach [President’s Message] (2023)

At my university, University of California, Irvine (UCI), we have started talking about “inreach” as a companion to the established notion of “outreach.” This small change in narrative has led to a surprisingly powerful set of changes in how we operate as an academic unit. As part of this “President’s Message,” I am including a recent article, coauthored with Marvin Maldonado, the director for inreach, equity, and student retention at the Samueli School of Engineering at UCI, to illustrate what this conceptual shift entails on a college campus. The short version is that outreach is focused outside of the organization in order to recruit, inspire, and educate surrounding communities, while inreach focuses on supporting people inside of the organization.
Ten years of feasibility pump, and counting (2018)

The Feasibility Pump (fp) is probably the best-known primal heuristic for mixed-integer programming. The original work by Fischetti et al. (Math Program 104(1):91–104, 2005), which introduced the heuristic for 0–1 mixed-integer linear programs, has been succeeded by more than twenty follow-up publications which improve the performance of the fp and extend it to other problem classes. Year 2015 was the tenth anniversary of the first fp publication. The present paper provides an overview of the diverse Feasibility Pump literature that has been presented over the last decade.
Biomarker analysis from a randomized phase II study of olaparib with or without cediranib in men with metastatic castration-resistant prostate cancer (mCRPC). (2021)

7 Background: We previously reported that cediranib, a vascular endothelial growth factor receptor tyrosine kinase inhibitor, combined with olaparib, a poly (ADP-ribose) polymerase inhibitor, prolonged radiographic progression-free survival (rPFS) compared with olaparib alone in patients with mCRPC. Herein, we present updated clinical data in the overall population and in subgroups by homologous recombination (HR) gene status. Methods: Men with a minimum of one prior line of systemic therapy for mCRPC were randomized 1:1 to receive olaparib 200 mg by mouth twice daily with cediranib 30 mg by mouth daily (C+O) or olaparib 300 mg by mouth twice daily (O). Patients were required to undergo a baseline metastasis biopsy. Next generation sequencing of HR genes was performed on available samples using BROCA-HR assay. HR deficiency (HRD) was defined by presence of homozygous deletions or deleterious mutations in HR genes including BRCA1, BRCA2, ATM, and others. The primary endpoint was rPFS and secondary endpoint was overall survival (OS). Results: Eighty-four patients were included in the analysis of whom 26 patients (31.0%) had HRD mCRPC. The most common HR gene alterations included BRCA2 (n=17, 20%), CDK12 (n=9, 11%), and ATM (n=7, 8%). Consistent with our prior report, in the overall cohort, C+O compared to O resulted in a significant improvement in rPFS (Table). The benefit in rPFS was most pronounced in patients with HRD mCRPC; however, there was no difference between arms in HR proficient (HRP) cancers. Independent of arm allocation, rPFS and OS were numerically longer in patients with HRD mCRPC compared to HRP mCRPC (rPFS: 8.8 versus 4.3 months, p=0.14; OS: 18.6 vs. 12.3 months, p=0.24). Conclusions: C+O improved rPFS in patients with mCPRC compared with O alone. The biomarker analyses revealed that the rPFS benefit of C+O over O is likely driven by patients with HRD mCRPC. Our data warrant validation and support further investigation of the combination of C+O in patients with HRD mCRPC. Clinical trial information: NCT02893917. [Table: see text]
Residual Amputee Limb Segment Lengthening (2022)

Aims: This study aimed to systematically review the indications, techniques, complications, and insights identified for lower extremity residual amputee limb segment lengthening. Methods: Searches in PubMed, Google Scholar, Ovid Medline, Ovid Embase, and the Journal of Limb Lengthening and Reconstruction were performed using terms including “amputee,” “residual limb,” and “stump” combined with “lengthening,” “distraction,” “histogenesis,” “osteogenesis,” and “Callotasis.” Included articles described lengthening amputated tibias or femurs (other segments excluded). The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were utilized. Descriptive statistics were performed. Results: Twenty-two studies reported lengthening 32 femurs and 31 tibias (63 total segments). Fifteen articles described a single segment, five described two to four (15 total segments), and two described five or more (31 total segments). Lengthening was performed to improve prosthesis fit (21/22 studies, 54/63 segments) or to optimize osseointegration (1/22 studies, 9/63 segments) and utilized an external fixator (52/63) or a motorized intramedullary nail (11/63). Femurs were lengthened an average of 7.7 ± 2.5 cm (60% ± 23%) and tibias 5.8 ± 1.8 cm (97% ± 53%) from a starting length of 12.5 ± 4.6 cm for femurs and 6.7 ± 2.3 cm for tibias. The most common minor problem was pin site infection. The most common major problem was over-lengthening bone beyond the soft tissue envelope, requiring flap coverage, bone excision, or knee disarticulation. Conclusions: Amputee lengthening can achieve measurable gains to improve prosthesis use. Over-lengthening can be difficult to manage, if not catastrophic. Osseointegration may be a further rehabilitation solution for amputees struggling with prosthesis problems and willing to consider surgical options.
FPGA adders: performance evaluation and optimal design (1998)

Delay models and cost analyses developed for ASIC technology are not useful in designing and implementing FPGA devices. The authors discuss costs and operational delays of fixed-point adders on Xilinx 4000 series devices and propose timing models and optimization schemes for carry-skip and carry-select adders.
Adaptive Packaging Solution for a Microlens Array Placed over a Micro-UV-LED Array (2007)

A packaging solution has been developed to accurately align a microlens array over a micro-UV-LED array. The novel method provides static as well as dynamic alignment capabilities, the latter allowing the microlens array to be moved in vertical and lateral direction.
DFT Study of 1,4-Diazonium-3,6-diolates: Monocyclic Representatives of Unexplored Semi-Conjugated Heterocyclic Mesomeric Betaines (2023)

Compared to the well-known conjugated (1,3-dipolar) and cross-conjugated (1,4-dipolar) heterocyclic mesomeric betaines (HMBs), semi-conjugated HMBs are unexplored and almost unknown. The three discrete classes of HMB are defined by the connectivity between their ring 2π heteroatoms and the odd-conjugated fragments that complete the ring. A single example of a stable, fully-characterized semi-conjugate HMB has been reported. This study employs the density functional theory (DFT) methodology to investigate the properties of a series of six-membered semi-conjugated HMBs. The electronic character of ring substituents is found to significantly influence the structure and electronic properties of the ring. The aromaticity measured by HOMA and NICS(1)<sub>zz</sub> indices is increased by π-electron-donating substituents whereas π-electron-withdrawing substituents decrease the calculated aromatic character and ultimately lead to non-planar boat or chair structures. A notable property of all derivatives is the small energy gap between their frontier orbitals.
The Onto-Politics of Assemblages (2014)

This chapter explores the problematic politics of assemblage thinking, firstly articulating how assemblage politics challenges constituted power and liberal frameworks of representation and secondly, analysing how this form of onto-political understanding is increasingly dominant in our academic understandings and political practices.
Diverse Functions and Dynamic Expression of Neuronal Sodium Channels (2001)

Nearly a dozen genes encode different Na channels, sharing a common overall motif but with subtly different amino acid sequences. Physiological signatures have now been established for some Na+ channels and it is clear that, from a functional point of view, Na+ channels are not all the same: different channels can have different physiological characteristics, and they can play different roles in the physiology of excitable cells. Moreover, the expression of Na+ channels within neurons is not a static process. Plasticity of Na+ channel gene expression occurs in the normal nervous system, where it accompanies transitions between different physiological states (e.g. low-frequency versus high-frequency firing states) in some types of neurons. Maladaptive changes in Na+ channel gene expression also occur in some pathological neurons. For example, transection of the peripheral axons of spinal sensory neurons triggers downregulation of some Na+ channel genes and up-regulation of others, resulting in changes in Na+ current expression that produce hyperexcitability, thereby contributing to chronic pain. There is also recent evidence for the expression of normally silent Na+ channel genes in Purkinje cells in experimental models of demyelinating diseases and in a human disease, multiple sclerosis; this dysregulation of Na+ channel expression may interfere with neuronal function in these disorders. The diversity and dynamic nature of Na+ channel expression introduce a high degree of complexity into the nervous system and present challenges for neuroscientists. In addition, they may present therapeutic opportunities as selective modulators for various Na+ channel subtypes become available.
Broad‐Spectrum Neutralization of Pore‐Forming Toxins with Human Erythrocyte Membrane‐Coated Nanosponges (2018)

Neutralization of bacterial toxins has become a compelling approach to treating bacterial infections as it may pose less selective pressure for the development of bacterial resistance. Currently, the majority of toxin neutralization platforms act by targeting the molecular structure of the toxin, which requires toxin identification and customized design for different diseases. Therefore, their development has been challenged by the enormous number and complexity of bacterial toxins. Herein, biomimetic toxin nanosponges are formulated by coating membranes of human red blood cells (hRBCs) onto polymeric nanoparticles, which act as a toxin decoy to absorb and neutralize a broad-spectrum of hemolytic toxins regardless of their molecular structure. When tested with model pore-forming toxins, including melittin, α-hemolysin of methicillin-resistant Staphylococcus aureus, listeriolysin O of Listeria monocytogenes, and streptolysin O of Group A Streptococcus, the hRBC nanosponges are able to completely inhibit toxin-induced hemolysis in a concentration-dependent manner. In addition, the nanosponge-detained toxins show no cytotoxicity when tested on human umbilical vein endothelial cells and no lethality when injected into mice, which together indicate effective toxin neutralization. Overall, these results demonstrate the broad applicability and high effectiveness of the hRBC nanosponges as a novel antivirulence platform against hemolytic toxins from various strains of bacteria.
Day‐to‐day reproducibility of anorectal sensorimotor assessments in healthy subjects (2004)

The reproducibility of tests widely utilized to assess anorectal sensorimotor functions is not well established. Our aims were to assess the intra-individual day-to-day reproducibility of these parameters in healthy subjects. Anal sphincter pressures were assessed by perfusion manometry on two separate days in 19 healthy subjects. Rectal pressure-volume (p-v) curves and sensory thresholds were assessed in 12/19 subjects by inflating a highly compliant polyethylene balloon from 0 to 32 mmHg in 4 mmHg steps. Subjects also rated intensity of perception by visual analogue scale (VAS) during phasic distentions 8, 16 and 24 mmHg above operating pressure, in randomized sequence. Resting and squeeze anal pressures and rectal compliance were highly reproducible (r(s) > or = 0.7) in the same subject on separate days. Pressure thresholds for urgency appeared less reproducible than thresholds for initial perception and the desire to defecate. VAS scores were highly reproducible only during the 24-mmHg distention. Thus, anal pressures and rectal compliance are highly reproducible within healthy subjects on separate days, while sensory thresholds are reproducible to a variable degree, dependent on the intensity of stimulation and the perception being assessed.
Noninvasive visualization of the choriocapillaris and its dynamic filling. (1994)

This study clearly documents the segmental nature of the primate choroidal microvasculature. It also illustrates that choroidal angiography by laser-targeted dye delivery provides information useful for studying the response of the choriocapillaris to physiological and pathologic changes.
Effect on cell membrane structural integrity of xylitol‐coated probiotics when stabilised with milk solids – A FTIR study (2020)

Vacuum drying of sorbitol or xylitol‐coated Lactobacillus reuteri LR6 cells and fluidised bed drying with different excipients were compared for the cell viability post‐drying. L. reuteri cells coated with xylitol and desiccated in unsupported form or together with skim milk powder as an excipient were found to be better protected at high drying temperatures. Examination of the protein and polypeptide components of the cell envelopes via Fourier transform infrared spectroscopy revealed different degrees of structural deformation in individual samples, indicating milk solids as supporting excipient and fluidised bed drying helps in retaining high cell viability.
A Dual-Notch +27dBm Tx-Power Electrical-Balance Duplexer (2014)

An electrical-balance duplexer uses series connected step-down transformers to enhance linearity and power handling capability by reducing the voltage swing across nonlinear components. Wideband, dual-notch Tx-to-Rx isolation is demonstrated experimentally with a planar inverted-F antenna. The 0.18μm CMOS prototype achieves >50dB isolation for 220MHz aggregated bandwidth or >40dB dual-notch isolation for 160MHz bandwidth, +49dBm Tx-path IIP3 and -48dBc ACLR1 for +27dBm at the antenna.
Design of a low-noise preamplifier for nerve cuff electrode recording (2003)

This paper discusses certain important issues involved in the design of a nerve signal preamplifier for implantable neuroprostheses. Since the electroneurogram signal measured from cuff electrodes is typically on the order of 1 μV, a very low-noise interface is essential. We present the argument for the use of BiCMOS technology in this application and then describe the design and evaluation of a complete preamplifier fabricated in a 0.8-μm double-metal double-poly process. The preamplifier has a nominal voltage gain of 100, a bandwidth of 15 kHz, and a measured equivalent input-referred noise voltage spectral density of 3.3 nV//spl radic/Hz at 1 kHz. The total input-referred rms noise voltage in a bandwidth 1 Hz-10 kHz is 290 nV, the power consumption is 1.3 mW from ±2.5-V power supplies, and the active area is 0.3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Update to the dataset of cerebral ischemia in juvenile pigs with evoked potentials (2021)

We expand from a spontaneous to an evoked potentials (EP) data set of brain electrical activities as electrocorticogram (ECoG) and electrothalamogram (EThG) in juvenile pig under various sedation, ischemia and recovery states. This EP data set includes three stimulation paradigms: auditory (AEP, 40 and 2000 Hz), sensory (SEP, left and right maxillary nerve) and high-frequency oscillations (HFO) SEP. This permits derivation of electroencephalogram (EEG) biomarkers of corticothalamic communication under these conditions. The data set is presented in full band sampled at 2000 Hz. We provide technical validation of the evoked responses for the states of sedation, ischemia and recovery. This extended data set now permits mutual inferences between spontaneous and evoked activities across the recorded modalities. Future studies on the dataset may contribute to the development of new brain monitoring technologies, which will facilitate the prevention of neurological injuries.