gebhart/patrepeval huggingface dataset:
The Rotary Zone Thermal Cycler: A Low-Power System Enabling Automated Rapid PCR (2015)

Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma (2020)

Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq <sup>1</sup> ) to the spike ectodomain (S-ECD <sup>2</sup> ) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing <i>in vitro</i> , we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified <i>in vivo</i> protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å <sup>2</sup> ). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning <sup>3,4</sup> our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.
Aortoiliac Artery Angioplasty and Stenting (1999)

Patients with aortoiliac occlusive disease may be asymptomatic or present with a full range of symptoms from mild claudication to limb-threatening ischemia. The initial assessment should include a physical examination for signs of peripheral ischemia, distal embolization, and the status of the peripheral pulses. Appropriate assessment of these patients includes a complete carotid, abdominal, and lower extremity vascular examination as well as appropriate screening and assessment for coronary artery disease. A complete cardiovascular assessment of the patient with aortoiliac occlusive disease should be performed, given the high incidence of associated atherosclerotic diseases. Since 1980, balloon angioplasty has been used successfully, in the terminal aorta. Stents are an attractive therapeutic option for the management of large artery occlusive disease to maintain or improve the arterial luminal patency after balloon angioplasty. The long-term patency of iliac vessels treated with balloon angioplasty is influenced by both clinical and anatomic variables.
Overexpression of the PDZ1 Domain of PDZK1 Blocks the Activity of Hepatic Scavenger Receptor, Class B, Type I by Altering Its Abundance and Cellular Localization (2008)

PDZK1 is a four-PDZ domain-containing scaffold protein that, via its first PDZ domain (PDZ1), binds to the C terminus of the high density lipoprotein (HDL) receptor scavenger receptor, class B, type I (SR-BI). Abolishing PDZK1 expression in PDZK1 knock-out (KO) mice leads to a post-transcriptional, tissue-specific decrease in SR-BI protein level and an increase in total plasma cholesterol carried in abnormally large HDL particles. Here we show that, although hepatic overexpression of PDZK1 restored normal SR-BI protein abundance and function in PDZK1 KO mice, hepatic overexpression of only the PDZ1 domain was not sufficient to restore normal SR-BI function. In wild-type mice, overexpression of the PDZ1 domain overcame the activity of the endogenous hepatic PDZK1, resulting in a 75% reduction in hepatic SR-BI protein levels and intracellular mislocalization of the remaining SR-BI. As a consequence, the plasma lipoproteins in PDZ1 transgenic mice resembled those in PDZK1 KO mice (hypercholesterolemia due to large HDL). These results indicate that the PDZ1 domain can control the abundance and localization, and therefore the function, of hepatic SR-BI and that structural features of PDZK1 in addition to its SR-BI-binding PDZ1 domain are required for normal hepatic SR-BI regulation.
Reducing DUE-FIT of caches by exploiting acoustic wave detectors for error recovery (2013)

Cosmic radiation induced soft errors have emerged as a key challenge in computer system design. The exponential increase in the transistor count will drive the per chip fault rate sky high. New techniques for detecting errors in the logic and memories that allow meeting the desired failures in-time (FIT) budget in future chip multiprocessors (CMPs) are essential. Among the two major contributors towards soft error rate, silent data corruption (SDC) and detected unrecoverable error (DUE), DUE is the largest. Moreover, processors can experience a super-linear increase in DUE when the size of the write-back cache is doubled. This paper targets the DUE problem in write-back data caches. We analyze the cost of protection against single bit and multi-bit upsets into caches. Our results show that the proposed mechanism can reduce the DUE to “0” with minimum area, power and performance overheads.
Chemically Modifying Viruses for Diverse Applications (2016)

Long fascinating to biologists, viruses offer nanometer-scale benchtops for building molecular-scale devices and materials. Viruses tolerate a wide range of chemical modifications including reaction conditions, pH values, and temperatures. Recent examples of nongenetic manipulation of viral surfaces have extended viruses into applications ranging from biomedical imaging, drug delivery, tissue regeneration, and biosensors to materials for catalysis and energy generation. Chemical reactions on the phage surface include both covalent and noncovalent modifications, including some applied in conjunction with genetic modifications. Here, we survey viruses chemically augmented with capabilities limited only by imagination.
A 920-1650-nm high-current photodiode (1996)

Summary form only given. In this paper we describe an InGaAs-based photodiode, which has demonstrated continuous 140-mA output current at 2-W power dissipation with 0.97-A/W conversion efficiency at 1320 nm.
A 128&#x00D7;128b high-speed wide-and match-line content addressable memory in 32nm CMOS (2011)

A 128-entry × 128b content addressable memory (CAM) design enables 145ps search operation in 1.0V, 32nm high-k metal-gate CMOS technology. A high-speed 16b wide dynamic AND match-line, combined with a fully static search-line and swapped XOR CAM cell simulations show a 49% reduction of search energy at iso-search delay of 145ps over an optimized high-performance conventional NOR-type CAM design, enabling 1.07fJ/bit/search operation. Scaling the supply voltage of the proposed CAM enables 0.3fJ/bit/search with 1.07ns search delay at 0.5V.
Trafficking of ODV-E66 is mediated via a sorting motif and other viral proteins: Facilitated trafficking to the inner nuclear membrane (2004)

The N-terminal 33 aa of the envelope protein ODV-E66 are sufficient to traffic fusion proteins to intranuclear membranes and the ODV envelope during infection with Autographa californica nucleopolyhedrovirus. This sequence has two distinct features: (i) an extremely hydrophobic sequence of 18 aa and (ii) positively charged amino acids close to the C-terminal end of the hydrophobic sequence. In the absence of infection, this sequence is sufficient to promote protein accumulation at the inner nuclear membrane. Covalent cross-linking results show that the lysines of the motif are proximal to FP25K and/or BV/ODV-E26 during transit from the endoplasmic reticulum to the nuclear envelope. We propose that the 33 aa comprise a signature for sorting proteins to the inner nuclear membrane (sorting motif) and that, unlike other resident proteins of the inner nuclear membrane, ODV-E66 and sortingmotif fusions do not randomly diffuse from their site of insertion at the endoplasmic reticulum to the nuclear envelope and viral-induced intranuclear membranes. Rather, during infection, trafficking is mediated by protein-protein interactions.
Endoscopic Optical Coherence Tomography for Evaluation of Success of Tympanoplasty (2020)

Endoscopic OCT is a promising tool for the evaluation of tympanoplasty outcome. It supports established otologic diagnostics and can help differentiating between different causes of conductional hearing loss.
Calibration of Texture-Adjusted Strain-Rate Potential and its Application (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Detitanation of MgCl₂-supported Ziegler-Natta catalysts for the study of active sites organization Part A Polymer chemistry (2008)

Thermal treatments under vacuum of conventional supported Ziegler-Natta precatalysts (MgCl₂/TiCl₄/Dibutylphthalate) were conducted to gradually remove titanium to modify the active sites distribution. Only limited detitanations of precatalysts were achieved paying attention not to chemically alter the internal donor (T < 150 °C). Used in combination with the required cocatalyst and external donor in the propylene slurry polymerization, the modified precatalysts exhibited a drop of activity versus decreasing titanium content but the distributed polymer properties are almost not affected (a slight narrowing of molecular weight distribution was observed). After a titanium chloride secondary impregnation (possibly done in presence of an additional Lewis base), activity resumed but polymer properties are once again unchanged. These findings highlight the difficulty to separate the different families of active sites and lead us to propose a cluster organization of titanium active sites. Active sites are composed of titanium clusters having a size distribution at the precatalyst surface, possessing a critical operating size and operating collectively in polymerization.
A new high intensity focused ultrasound applicator for surgical applications (2001)

Improved high-intensity focused ultrasound (HIFU) surgical applicators are required for use in a surgical environment. We report on the performance and characteristics of a new solid-cone HIFU applicator. Previous HIFU devices used a water-filled stand-off to couple the ultrasonic energy from the transducer to the treatment area. The new applicator uses a spherically-focused element and a solid aluminum cone to guide and couple the ultrasound to the tissue. Compared with the water-filled applicators, this new applicator is simpler to set up and manipulate, cannot leak, prevents the possibility of cavitation within the coupling device, and is much easier to sterilize and maintain during surgery. The design minimizes losses caused by shear wave conversion found in tapered solid acoustic velocity transformers operated at high frequencies. Computer simulations predicted good transfer of longitudinal waves. Impedance measurements, beam plots, Schlieren images, and force balance measurements verified strong focusing and suitable transfer of acoustic energy into water. At the focus, the -3 dB beam dimensions are 1.2 mm (axial) x 0.3 mm (transverse). Radiation force balance measurements indicate a power transfer efficiency of 40%. In vitro and in vivo tissue experiments confirmed the applicator's ability to produce hemostasis.
Processing and cross-presentation of individual HLA-A, -B, or -C epitopes from NY-ESO-1 or an HLA-A epitope for Melan-A differ according to the mode of antigen delivery (2010)

The ability of dendritic cells (DCs) to cross-present protein tumor antigens to cytotoxic T lymphocytes (CTLs) underpins the success of therapeutic cancer vaccines. We studied cross-presentation of the cancer/testis antigen, NY-ESO-1, and the melanoma differentiation antigen, Melan-A by human DC subsets. Monocyte-derived DCs (MoDCs) efficiently cross-presented human leukocyte associated (HLA)-A2-restricted epitopes from either a formulated NY-ESO-1/ISCOMATRIX vaccine or when either antigen was mixed with ISCOMATRIX adjuvant. HLA-A2 epitope generation required endosomal acidification and was proteasome-independent for NY-ESO-1 and proteasome-dependent for Melan-A. Both MoDCs and CD1c(+) blood DCs cross-presented NY-ESO-1-specific HLA-A2(157-165)-, HLA-B7(60-72)-, and HLA-Cw3(92-100)-restricted epitopes when formulated as an NY-ESO-1/ISCOMATRIX vaccine, but this was limited when NY-ESO-1 and ISCOMATRIX adjuvant were added separately to the DC cultures. Finally, cross-presentation of NY-ESO-1(157-165)/HLA-A2, NY-ESO-1(60-72)/HLA-B7, and NY-ESO-1(92-100)/HLA-Cw3 epitopes was proteasome-dependent when formulated as immune complexes (ICs) but only proteasome-dependent for NY-ESO-1(60-72)/HLA-B7-restricted cross-presentation facilitated by ISCOMATRIX adjuvant. We demonstrate, for the first time, proteasome-dependent and independent cross-presentation of HLA-A-, B-, and C-restricted epitopes within the same full-length tumor antigen by human DCs. Our findings identify important differences in the capacities of human DC subsets to cross-present clinically relevant, full-length tumor antigens and how vaccine formulation impacts CTL responses in vivo.
Inhibition of bcr-abl Oncogene Expression by Novel Deoxyribozymes (DNAzymes) (1999)

Deoxyribozymes, or DNA enzymes (DNAzymes), are novel nucleic acids that have the ability to bind to specific sequences of RNA, and to cleave the target site catalytically. DNAzymes are smaller and more efficient enzymatically than ribozymes (RZs), which are catalytic nucleic acids synthesized from ribonucleotides. We have designed three DNAzymes that specifically target the two variants of the p210 bcr-abl gene (splice 1, b3a2; splice 2, b2a2) and the p190 variant (ela2). The cleavage sites for these DNAzymes are located 5 nucleotides (nt) 5' from the fusion site for b3a2, and only 1 nt 5' from the fusion sites for b2a2 and e1a2. We have shown in cell-free in vitro cleavage assays that these DNAzymes efficiently cleave their respective substrates. Mutated DNAzymes, in which only one critical base has been altered, do not cleave these targets. We have used a serum-resistant cytofectin (GS 2888; Gilead) to transfect the DNAzymes into target K562 cells, which express p210bcr-abl. In short-term transfection assays, the DNAzymes specifically inhibited p210bcr-abl protein expression by K562 cells by about 40%, and inhibited cell growth by more than 50% in a 6-day liquid culture assay. We have also transfected freshly isolated CD34+ bone marrow cells from patients with CML with the DNAzymes, which specifically inhibited the growth of bcr-abl-positive CFU-Mix colonies by 53-80%. The potential advantages of anti-bcr-abl DNAzymes over RZs include the following: DNAzymes are much less expensive to synthesize; they are more resistant to serum; and the anti-b2a2 DNAzyme cleaves at a site only 1 nt away from the fusion site, whereas its hammerhead RZ counterpart cleaves this target at a site 8 nt 3' to the fusion site, well within abl exon 2. DNAzymes are novel RNA-cleaving molecules that may significantly improve our ability to inhibit bcr-abl oncogene expression in Ph-positive target cells.
Energy efficient DRAM row buffer management for enterprise workloads (2010)

This paper establishes that adapting the DRAM row buffer policy in accordance with both locality and activity in memory access patterns can lead to significant reductions in DRAM energy. In particular, using two different enterprise workloads, we establish that a spatially and temporally adaptive row buffer timeout policy is more energy-efficient than any static policy. Our results show that energy can be reduced by 6% and 30% for the two enterprise workloads.
CARD9-Dependent Neutrophil Recruitment Protects against Fungal Invasion of the Central Nervous System (2015)

Candida is the most common human fungal pathogen and causes systemic infections that require neutrophils for effective host defense. Humans deficient in the C-type lectin pathway adaptor protein CARD9 develop spontaneous fungal disease that targets the central nervous system (CNS). However, how CARD9 promotes protective antifungal immunity in the CNS remains unclear. Here, we show that a patient with CARD9 deficiency had impaired neutrophil accumulation and induction of neutrophil-recruiting CXC chemokines in the cerebrospinal fluid despite uncontrolled CNS Candida infection. We phenocopied the human susceptibility in Card9-/- mice, which develop uncontrolled brain candidiasis with diminished neutrophil accumulation. The induction of neutrophil-recruiting CXC chemokines is significantly impaired in infected Card9-/- brains, from both myeloid and resident glial cellular sources, whereas cell-intrinsic neutrophil chemotaxis is Card9-independent. Taken together, our data highlight the critical role of CARD9-dependent neutrophil trafficking into the CNS and provide novel insight into the CNS fungal susceptibility of CARD9-deficient humans.
Precision and Safety of the Pulsed Electron Avalanche Knife in Vitreoretinal Surgery (2003)

The PEAK operated well within accept-able safety limits and may greatly facilitate both posterior segment surgeries (eg, membrane dissection and sheathotomy) and anterior segment procedures (eg, capsulotomy, nonpenetrating trabeculectomy, and iridectomy).
Observation of the Bose Peak in NanometerSized Liquid Water Clusters using Terahertz Spectroscopy (2000)

We report the first observation of the disorder-induced Bose peak in nanometersized liquid water pools. The size-dependent properties of the peak permit us to rule out Rayleigh scattering as a possible mechanism for the formation of this ubiquitous feature of amorphous materials.
Lightwave modulation for radio-on-fibre systems (2013)

This paper describes high-speed electro-optic modulation technologies for radio-on-fibre (RoF) systems which can transmit wireless signals with various formats such as 3G mobile, wireless LAN, etc. Precise lightwave modulation is very important to generate radio-wave in accordance with regulations.
Directed Functional Connectivity in Fronto-Centroparietal Circuit Correlates With Motor Adaptation in Gait Training (2016)

Lower-extremity robotic exoskeletons are used in gait rehabilitation to achieve functional motor recovery. To date, little is known about how gait training and post-training are characterized in brain signals and their causal connectivity. In this work, we used time-domain partial Granger causality (PGC) analysis to elucidate the directed functional connectivity of electroencephalogram (EEG) signals of healthy adults in robot-assisted gait training (RAGT). Our results confirm the presence of EEG rhythms and corticomuscular relationships during standing and walking using spectral and coherence analyses. The PGC analysis revealed enhanced connectivity close to sensorimotor areas ( C<sub>3</sub> and CP<sub>3</sub> ) during standing, whereas additional connectivities involve the centroparietal ( CP <sub>z</sub>) and frontal ( F <sub>z</sub> ) areas during walking with respect to standing. In addition, significant fronto-centroparietal causal effects were found during both training and post-training. Strong correlations were also found between kinematic errors and fronto-centroparietal connectivity during training and post-training. This study suggests fronto-centroparietal connectivity as a potential neuromarker for motor learning and adaptation in RAGT.
Bacterial synthesis of C3-C5 diols via extending amino acid catabolism (2020)

Amino acids are naturally occurring and structurally diverse metabolites in biological system, whose potentials for chemical expansion, however, have not been fully explored. Here, we devise a metabolic platform capable of producing industrially important C3-C5 diols from amino acids. The presented platform combines the natural catabolism of charged amino acids with a catalytically efficient and thermodynamically favorable diol formation pathway, created by expanding the substrate scope of the carboxylic acid reductase toward noncognate ω-hydroxylic acids. Using the established platform as gateways, seven different diol-convertible amino acids are converted to diols including 1,3-propanediol, 1,4-butanediol, and 1,5-pentanediol. Particularly, we afford to optimize the production of 1,4-butanediol and demonstrate the de novo production of 1,5-pentanediol from glucose, with titers reaching 1.41 and 0.97 g l<sup>-1</sup>, respectively. Our work presents a metabolic platform that enriches the pathway repertoire for nonnatural diols with feedstock flexibility to both sugar and protein hydrolysates.
Validation of a radioimmunoassay of serum trypsin-like immunoreactivity in ferrets (2018)

Measurement of serum trypsin-like immunoreactivity (TLI) is used to assess exocrine pancreatic function in dogs and cats. Ferrets ( Mustela putorius furo) serve as valuable animal models for human diseases such as cystic fibrosis and other pulmonary diseases, and may be a useful model of other diseases including pancreatitis. We developed and analytically validated a competitive radioimmunoassay (RIA) for measurement of TLI in ferret serum by determination of analytical sensitivity, assay linearity, accuracy of spiking recovery, precision, and reproducibility. Analytical sensitivity of the assay was 0.55 μg/L. Observed-to-expected (O/E) ratio for dilutional parallelism was 90.2-127.9% (mean: 108.1 ± 11.9%). The O/E ratio for spiking recovery was 94.5-113.0% (mean: 103.9 ± 7.2%). The intra- and inter-assay coefficients of variation (CVs) were 2.7-5.7% and 3.5-8.2%, respectively. The reference interval (RI) for serum TLI derived from 31 healthy ferrets was 28-115 μg/L; the 90% confidence interval for the lower and upper limits of the RI were 10.0-32.1 μg/L and 103-126 μg/L, respectively. This TLI RIA is analytically sensitive, sufficiently linear, accurate, precise, and reproducible for the measurement of TLI in ferret serum samples.