gebhart/patrepeval huggingface dataset:
Determining the Minimally Effective Dose of a Clinical Candidate Adeno-Associated Virus Vector in a Mouse Model of Hemophilia A (2021)

Hemophilia A, a bleeding disorder, affects 1:5,000 males and is caused by a deficiency of human blood coagulation factor VIII (hFVIII). Studies in mice and macaques identified AAVhu37.E03.TTR.hFVIIIco-SQ.PA75 as a clinical candidate gene therapy vector to treat hemophilia A. In this study, we sought to determine the minimally effective dose (MED) of this vector in a hemophilia A mouse model. Mice received one of four vector doses (3 × 10<sup>11</sup>-1 × 10<sup>13</sup> genome copies [GCs]/kg) via intravenous tail vein injection; one cohort received vehicle as a control. Animals were monitored daily after vector/vehicle administration. Blood samples were collected to evaluate hFVIII activity levels and anti-hFVIII antibodies. Animals were sacrificed and necropsied on days 28 and 56; tissues were harvested for histopathological examination and blood was collected for serum chemistry panel analysis. We found no significant differences in liver transaminase levels in mice administered any vector dose compared to those administered vehicle (except for one group administered 3 × 10<sup>11</sup> GC/kg). Total bilirubin levels were significantly elevated compared to the vehicle group following two vector doses at day 56 (1 × 10<sup>12</sup> and 1 × 10<sup>13</sup> GC/kg). We observed no vector-related gross or histological findings. Most microscopic findings were in the vehicle group and considered secondary to blood loss, an expected phenotype of this mouse model. Since we observed no dose-limiting safety markers, we determined that the maximally tolerated dose was greater than or equal to the highest dose tested (1 × 10<sup>13</sup> GC/kg). Since we detected hFVIII activity in all cohorts administered vector, we conclude that the MED is 3 × 10<sup>11</sup> GC/kg-the lowest dose evaluated in this study.
Nanometer scale patterning of a monolayer Langmuir–Blodgett film with a scanning tunneling microscope in air (1993)

Nanometer scale patterns have been fabricated on a Langmuir–Blodgett deposited monolayer film of stearic acid using a scanning tunneling microscope in air. Carbon deposits build up underneath the tip for tip voltages with absolute value greater than 4 V. Using an atomic force microscope for image, lines 25 nm wide on a 60 nm period have been written. As confirmed with Auger electron spectroscopy, the unexposed film can be removed with a chloroform soak without affecting the existing carbon patterns, and no additional patterns could then be written because of the removal of the monolayer film.
An assessment of a rapid SARS-CoV-2 antigen test in Bangladesh (2021)

Abstract Early detection of SARS-CoV-2 infection is crucial to prevent the spread of the virus. In this study, we evaluated the performance of a commercial rapid antigen detection test, BD Veritor, and compared this (and another rapid test, Standard Q) against a gold-standard of nasopharyngeal (NP) swab tested by reverse transcription-polymerase chain reaction (RT-PCR) in prospectively-recruited adults in Dhaka, Bangladesh. We compared the sensitivity and specificity of the two rapid antigen tests against RT-PCR results in 130 symptomatic and 130 asymptomatic adults. In addition, we evaluated the suitability and ease-of-use of the BD Veritor test in a subsample of study participants (n=42) and implementers (n=5). The sensitivity of the BD Veritor rapid antigen test was 70% in symptomatic (95% confidence interval [CI]: 51-85%) and 87% (95% CI: 69-96%) in asymptomatic individuals with positive SARSCoV-2 RT-PCR, for overall sensitivity of 78% (95% CI: 66-88%). The sensitivity of the Standard Q rapid antigen test was 63% (95% CI: 44-80%) in symptomatic and 73% (95% CI: 54-87%) in asymptomatic individuals. One false positive in BD Veritor test (specificity 99.5) and no false positive in Standard Q tests were observed (specificity 100%). The BD Veritor rapid antigen test was 78% sensitive when compared with RT-PCR irrespective of the cycle threshold (Ct) levels in this evaluation in Bangladesh. The implementation evaluation data showed good acceptability in the field settings. This warrants large field evaluation as well as use of the rapid antigen test for quick assessment of SARS-CoV-2 for containment of epidemics in the country.
A Single-Chip RF Tuner/OFDM Demodulator for Mobile Digital TV Application (2011)

This paper presents a single-chip RF tuner/OFDM demodulator for a mobile digital TV application called “1-segment broadcasting.” To achieve required performances for the single-chip receiver, a tunable technique for a low-noise amplifier (LNA) and spurious suppression techniques are proposed in this paper. Firstly, to receive all channels from 470MHz to 770MHz and to relax distortion characteristics of following circuit blocks such as an RF variable-gain amplifier and a mixer, a tunable technique for the LNA is proposed. Then, to improve the sensitivity, spurious signal suppression techniques are also proposed. The single-chip receiver using the proposed techniques is fabricated in 90nm CMOS technology and total die size is 3.26mm × 3.26mm. Using the tunable LNA and suppressing undesired spurious signals, the sensitivities of less than -98.6dBm are achieved for all the channels.
Femtosecond laser photo-response of Ge_23Sb_7S_70 films (2008)

Ternary chalcogenide glass films from identical parent bulk glasses were prepared by thermal evaporation (TE) and pulsed laser deposition (PLD) and subjected to 810-nm femtosecond laser exposure at both kHz and MHz repetition rates. The exposure-induced modification on the glass film's surface profile, refractive index, and structural properties were shown to be a function of laser irradiance, the number of laser pulses per focal spot, and repetition rate. Film response was shown to be related to deposition technique-related density and the number of glass bonds within the irradiated focal volume. The induced changes resulted from a reduction in glass network connectivity among GeS(4/2), GeS(4), S-S and S(3)Ge-S-GeS(3) units.
Data from A Dose-Escalation and Signal-Generating Study of the Immunocytokine L19-IL2 in Combination with Dacarbazine for the Therapy of Patients with Metastatic Melanoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; L19-IL2 is an immunocytokine composed of an antibody fragment specific to the EDB domain of fibronectin, a tumor angiogenesis marker, and of human interleukin-2 (IL2). L19-IL2 delivers IL2 to the tumor site exploiting the selective expression of EDB on newly formed blood vessels. Previously, the recommended dose of L19-IL2 monotherapy was defined as 22.5 million international units (Mio IU) IL2 equivalents. In this study, safety and clinical activity of L19-IL2 in combination with dacarbazine were assessed in patients with metastatic melanoma.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The first 10 studied patients received escalating doses of L19-IL2 on days 1, 3, and 5 in combination with 1 g/m&lt;sup&gt;2&lt;/sup&gt; of dacarbazine on day 1 of a 3-weekly therapy cycle. Subsequently, 22 patients received L19-IL2 at recommended dose plus dacarbazine. Up to six treatment cycles were given, followed by a maintenance regimen with biweekly L19-IL2.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The recommended dose of L19-IL2 in combination with dacarbazine was defined as 22.5 Mio IU. Toxicity was manageable and reversible, with no treatment-related deaths. Twenty-nine patients were evaluable for efficacy according to Response Evaluation Criteria in Solid Tumors (RECIST). In a centralized radiology analysis, eight of 29 (28%) patients achieved a RECIST-confirmed objective response, including a complete response still ongoing 21 months after treatment beginning. The 12-month survival rate and median overall survival of the recommended dose–treated patients (&lt;i&gt;n&lt;/i&gt; = 26) were 61.5% and 14.1 months, respectively.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The repeated administration of L19-IL2 in combination with dacarbazine is safe and shows encouraging signs of clinical activity in patients with metastatic melanoma. This combination therapy is currently evaluated in a randomized phase II trial with patients with metastatic melanoma. &lt;i&gt;Clin Cancer Res; 17(24); 7732–42. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT (2012)

Diverse bacteria encode RNAs that are not translated into proteins but are instead involved in regulating a wide variety of cellular functions. Computational approaches have proven successful in identifying numerous regulatory RNAs in myriad bacterial species but the difficultly of implementing most of these approaches has limited their accessibility to many researchers. Moreover, few of these approaches provide annotations of predicted loci to guide downstream experimental validation and characterization. Here I describe the implementation of SIPHT, a web-accessible program that enables screens for putative loci encoding regulatory RNAs to be conducted in any of nearly 2,000 sequenced bacterial replicons. SIPHT identifies candidate loci by searching for regions of intergenic sequence conservation upstream of predicted intrinsic transcription terminators. Each locus is then annotated for numerous features that provide clues about its potential function and/or enable the most reliable candidates to be identified.
Streamlined Target Deconvolution Approach Utilizing a Single Photoreactive Chloroalkane Capture Tag (2021)

Identification of physiologically relevant targets for lead compounds emerging from drug discovery screens is often the rate-limiting step toward understanding their mechanism of action and potential for undesired off-target effects. To this end, we developed a streamlined chemical proteomic approach utilizing a single, photoreactive cleavable chloroalkane capture tag, which upon attachment to bioactive compounds facilitates selective isolation of their respective cellular targets for subsequent identification by mass spectrometry. When properly positioned, the tag does not significantly affect compound potency and membrane permeability, allowing for binding interactions with the tethered compound (probe) to be established within intact cells under physiological conditions. Subsequent UV-induced covalent photo-cross-linking "freezes" the interactions between the probe and its cellular targets and prevents their dissociation upon cell lysis. Targets cross-linked to the capture tag are then efficiently enriched through covalent capture onto HaloTag coated beads and subsequent selective chemical release from the solid support. The tag's built-in capability for selective enrichment eliminates the need for ligation of a capture tag, thereby simplifying the workflow and reducing variability introduced through additional operational steps. At the same time, the capacity for adequate cross-linking without structural optimization permits modular assembly of photoreactive chloroalkane probes, which reduces the burden of customized chemistry. Using three model compounds, we demonstrate the capability of this approach to identify known and novel cellular targets, including those with low affinity and/or low abundance as well as membrane targets with several transmembrane domains.
A polarimetrie, low ringing UWB antenna for ground penetrating radar operation (2016)

In this contribution a dual-polarized (DP) UWB antenna for Ground Penetrating Radar (GPR) operation is introduced. Basing upon a Vivaldi structure, the proposed antenna provides high gain, low ringing and polarization purity. The low metal content, as well as the robust housing makes the antenna ideally suited for humanitarian demining field-operation. Measurement results concerning return loss, antenna pattern, and antenna ringing, which prove the antenna's applicability, are shown and discussed in detail.
Mutation Frequency of the Major Frontotemporal Dementia Genes, MAPT, GRN and C9ORF72 in a Turkish Cohort of Dementia Patients (2016)

'Microtubule-associated protein tau' (MAPT), 'granulin' (GRN) and 'chromosome 9 open reading frame72' (C9ORF72) gene mutations are the major known genetic causes of frontotemporal dementia (FTD). Recent studies suggest that mutations in these genes may also be associated with other forms of dementia. Therefore we investigated whether MAPT, GRN and C9ORF72 gene mutations are major contributors to dementia in a random, unselected Turkish cohort of dementia patients. A combination of whole-exome sequencing, Sanger sequencing and fragment analysis/Southern blot was performed in order to identify pathogenic mutations and novel variants in these genes as well as other FTD-related genes such as the 'charged multivesicular body protein 2B' (CHMP2B), the 'FUS RNA binding protein' (FUS), the 'TAR DNA binding protein' (TARDBP), the 'sequestosome1' (SQSTM1), and the 'valosin containing protein' (VCP). We determined one pathogenic MAPT mutation (c.1906C>T, p.P636L) and one novel missense variant (c.38A>G, p.D13G). In GRN we identified a probably pathogenic TGAG deletion in the splice donor site of exon 6. Three patients were found to carry the GGGGCC expansions in the non-coding region of the C9ORF72 gene. In summary, a complete screening for mutations in MAPT, GRN and C9ORF72 genes revealed a frequency of 5.4% of pathogenic mutations in a random cohort of 93 Turkish index patients with dementia.
Construction of Chiral Propeller Architectures from Achiral Molecules (2007)

Classically, chirality is generated bythe incorporation of asymmetric tetrahedral carbons, but self-assembled liquid crystal (LC) materials formed through non-covalent interactions, such as H-bonding, have attracted muchattention, as these materials may also possess chirality inde-pendent of molecular chirality. Amplification processes canenable chirality transfer from the nanometer scale to the mac-roscopic scale, as is often observed in Nature. Here, we showfor the first time that chiral propellers can be constructedfrom achiral molecules (BPCA-C
Soluble Epidermal Growth Factor Receptor Acridinium-Linked Immunosorbent Assay (2006)

This chapter provides basic information for quantifying soluble epidermal growth factor receptor (sEGFR) isoforms in human sera using an acridinium-linked immunosorbent assay (ALISA) developed by Baron and coworkers. This ALISA has been shown to be specific for epidermal growth factor receptor (EGFR) and the isoforms of EGFR encoded by alternate transcripts (i.e., sEGFRs); it, therefore, does not detect other EGFR/ErbB receptor family members, i.e., ErbB2, ErbB3, or ErbB4. In addition, this ALISA recognizes EGFR and sEGFR isoforms that contain subdomains I-IV of the extracellular domain, but it does not recognize EGFR isoforms lacking subdomain IV. The ALISA described here also may be useful for determining EGFR and sEGFR concentrations in lysates of cultured cells, conditioned culture medium, or tissue/tumor specimens, as well as in other human body fluids such as serum, plasma, ascites, urine, saliva, and cystic fluids.
Improved Interfacing of Electrical Machine Models to Electromagnetic Transients Programs (1984)

A new technique is presented for interfacing electrical machine models with electromagnetic transients programs. The machine models with their associated controls, loads or turbines can be assembled as subroutines by the user and interfaced to the electrical network or other machine models directly. The machine models employ the standard state variable equations and may use any integration technique for solution. The technique does not require a Thevenin equivalent circuit of the electrical network.
High-Efficiency circuit at 2.45 GHz for Low-Input Power energy Harvesting 6 Oct. 11 Oct. 2013, Nuremberg, Germany (2013)

International audience
A 25-Gb/s 2.2-W optical transceiver using an analog FE tolerant to power supply noise and redundant data format conversion in 65-nm CMOS (2012)

A one-chip transceiver was developed for optical backplanes by integrating an analog FE with data format conversion in 65-nm CMOS. 10×6.25Gb/s electrical signals were converted to 4×25Gb/s optical signals with 25% redundancy to improve resilience against possible LD failure. To alleviate degradation of the optical link due to power-supply variations, a TIA with a noise canceller and a fully differential LDD are proposed. The noise canceller decreases power-supply variations by 98%. Total power consumption was only 2.2W.
Monitoring Time Series With Missing Values: a Deep Probabilistic Approach (2022)

Systems are commonly monitored for health and security through collection and streaming of multivariate time series. Advances in time series forecasting due to adoption of multilayer recurrent neural network architectures make it possible to forecast in high-dimensional time series, and identify and classify novelties early, based on subtle changes in the trends. However, mainstream approaches to multi-variate time series predictions do not handle well cases when the ongoing forecast must include uncertainty, nor they are robust to missing data. We introduce a new architecture for time series monitoring based on combination of state-of-the-art methods of forecasting in high-dimensional time series with full probabilistic handling of uncertainty. We demonstrate advantage of the architecture for time series forecasting and novelty detection, in particular with partially missing data, and empirically evaluate and compare the architecture to state-of-the-art approaches on a real-world data set.
Benefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses (2021)

Mucin-type O-glycosylation is among the most complex post-translational modifications. Despite mediating many physiological processes, O-glycosylation remains understudied compared to other modifications, simply because the right analytical tools are lacking. In particular, analysis of intact O-glycopeptides by mass spectrometry is challenging for several reasons; O-glycosylation lacks a consensus motif, glycopeptides have low charge density which impairs ETD fragmentation, and the glycan structures modifying the peptides are unpredictable. Recently, we introduced chemically modified monosaccharide analogues that allowed selective tracking and characterization of mucin-type O-glycans after bioorthogonal derivatization with biotin-based enrichment handles. In doing so, we realized that the chemical modifications used in these studies have additional benefits that allow for improved analysis by tandem mass spectrometry. In this work, we built on this discovery by generating a series of new GalNAc analogue glycopeptides. We characterized the mass spectrometric signatures of these modified glycopeptides and their signature residues left by bioorthogonal reporter reagents. Our data indicate that chemical methods for glycopeptide profiling offer opportunities to optimize attributes such as increased charge state, higher charge density, and predictable fragmentation behavior.
Modelling of printed antennas of arbitrary shape with a MultiResolution Method of Moment (2000)

This paper presents the modelling of microstrip antennas of abitrary shape with a two dimensional multiresolution method of moment (MRMoM). A Chui-Haar 2D multiresolution basis is used for the expansion of surface currents and for the testing procedure in the MRMoM. An original technique is proposed to model metallisations of arbitrary shape. The capabilities of the approach are illustrated with the simulation of a circularly polarised patch antenna and a sequentially rotated array.
Direct Hydrocyclization of Biomass‐Derived Levulinic Acid to 2‐Methyltetrahydrofuran over Nanocomposite Copper/Silica Catalysts (2011)

Copper/silica nanocomposite catalysts prove efficient for the direct hydrocyclization of biomass-derived levulinic acid to cyclic 2-methyltetrahydrofuran in the vapor phase, at moderate hydrogen pressures. A nickel-promoted copper/silica catalyst with a high copper loading (72 wt %) is particularly effective for the direct hydrocyclization (89 % selectivity). The catalysts are stable during long-term experiments, showing little sign of leaching or sintering. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mechanical and Biochemical Assessments of Three-Dimensional Poly(1,8-Octanediol- co -Citrate) Scaffold Pore Shape and Permeability Effects on In Vitro Chondrogenesis Using Primary Chondrocytes (2010)

Poly(1,8-octanediol-co-citrate) (POC) is a biocompatible, biodegradable elastomer with potential application for soft tissue applications such as cartilage. For chondrogenesis, permeability is a scaffold design target that may influence cartilage regeneration. Scaffold permeability is determined by many factors such as pore shape, pore size, pore interconnectivity, porosity, and so on. Our focus in this study was to examine the effects of pore shape and permeability of two different POC scaffold designs on matrix production, mRNA gene expression, and differentiation of chondrocytes in vitro and the consequent mechanical property changes of the scaffold/tissue constructs. Since type I collagen gel was used as a cell carrier in the POC scaffolds, we also examined the effects of collagen gel concentration on chondrogenesis. We found that lower collagen I gel concentration provides a favorable microenvironment for chondrocytes promoting better chondrogenic performance of chondrocytes. With regard to scaffold design, low permeability with a spherical pore shape better enhanced the chondrogenic performance of chondrocytes in terms of matrix production, and mRNA gene expressions in vitro compared to the highly permeable scaffold with a cubical pore shape.
GaN light-emitting diodes on glass substrates with enhanced electroluminescence (2012)

We report the enhanced electroluminescence (EL) of GaN light-emitting diodes (LEDs) on glass substrates by controlling GaN crystal morphology, crystallinity, and device fabrication. Depending on the degree of epitaxy, we studied three different GaN morphologies; randomly oriented GaN polycrystals, nearly single-crystalline pyramid arrays, and fully single-crystalline pyramid arrays, which were fabricated by controlling the epitaxial relationship with the substrates. At proper growth temperature, GaN crystallinity was improved with increasing GaN crystal size irrespective of the GaN crystallographic orientation, as determined by spatially resolved cathodoluminescent spectroscopy. All the different GaN morphologies were further fabricated into LEDs to investigate their EL characteristics. The optimized GaN LEDs on glass composed of the nearly single-crystalline GaN pyramid arrays exhibited excellent microscopic EL uniformity and luminance values of about 2700 and 1150 cd m−2 at peak wavelengths of 537 and 480 nm, respectively.