gebhart/patrepeval huggingface dataset:
Corrigendum: Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay (2019)

Dear Editor,If you agree, we would like to raise the possibility that an erratum or corrigendum be added to our recently-published paper by Goux, et al. "Akkermansia muciniphila as a model case for the development of an improved quantitative RPA microbiome assay." Frontiers in cellular and infection microbiology 8 (2018), Manuscript ID: 339908.While the conclusions of the paper are unaffected, the reported relative A. muciniphila abundance measurements failed to take into account that variably-multiple copies of the 16S rRNA gene exist in bacterial genomes. This can introduce an error of about 2-fold in the calculations associated with the final example. The primary methods-development content of the paper is unaffected. We sincerely apologize for our error, and ask for your guidance as to how to proceed. Best regards,Dr. Richard Willson
Robust Synthesis of Methyl 5-Chloro-4-fluoro-1H-indole-2-carboxylate: A Key Intermediate in the Preparation of an HIV NNRTI Candidate (2010)

A synthetic preparation of methyl 5-chloro-4-fluoro-1H-indole-2-carboxylate, a key intermediate towards phosphoindole inhibitors of HIV non-nucleoside reverse transcriptase, is described. The five-step synthesis involved Boc protection of the commercially available 4-chloro-3-fluoroaniline and regioselective iodination at C-2. After facile Boc deprotection, cyclization of the resultant o-iodoaniline gave the corresponding 5-chloro-4-fluoro-indole-2-carboxylic acid which was subsequently esterified to provide the target indole ester in 56% overall yield. Identification of 6-chloro-7-iodo-2(3H)-benzoxazolone as a significant side product in the iodination step led to the development of conditions which eliminated its formation in subsequent batches. Advantages of this alternative approach relative to existing methodologies include (1) potentially hazardous diazonium and azido species were not required, (2) regioisomeric products were not generated, and (3) chromatographic isolations were avoided, as all intermediates were easily crystallized. As a result, the key indole ester was produced rapidly at 100-fold increased scale compared to previous reports with a 10-fold improvement in overall yield.
Vaccination with Designed Neopeptides Induces Intratumoral, Cross-reactive CD4+ T-cell Responses in Glioblastoma (2022)

Turning tumor self-peptides into foreign antigens by introduction of designed mutations is a promising strategy to induce strong intratumoral CD4+ T-cell responses in a cold tumor like glioblastoma.
Multiple Sclerosis Performance Test: Patients Express High Satisfaction with the Application (P3.140) (2014)

OBJECTIVE: To determine patient satisfaction with the Multiple Sclerosis Performance Test (MSPT). BACKGROUND: The MSPT is an iPad-based neuroperformance assessment tool that was designed to simulate the Multiple Sclerosis Functional Composite (MSFC). The MSTP has the potential to provide reliable MS-specific neuroperformance data at lower cost, at more frequent intervals, in the patient’s home environment. Knowledge of patients’ opinions about the usability of the application during in-center testing can provide insight into patients’ acceptance of using this application in the home setting. DESIGN/METHODS: A usability questionnaire regarding the MSPT app was administered to 51 MS patients representing a range of MS severity and 40 age and gender-matched healthy controls (HC) who completed the cross-sectional validation phase of this app’s development. RESULTS: The majority of study participants agreed it was easy to read the applications in the iPad screen (MS=96 % agreed or strongly agreed, HC= 100% agreed or strongly agreed; p=NS). While both groups found the recorded instructions on the MSPT easy to understand, the HC rated this higher (MS= 82.4%strongly agreed, HC= 100% strongly agreed; p=0.02). Both groups reported completing the tests on the touch screen was easy, (MS=98 % agreed/strongly agreed, HC= 95 % agreed/strongly agreed; p=NS). Neither group found it difficult to wear the iPad during the walking and balance tests (MS=90.2 % strongly disagreed/ somewhat disagreed, HC= 97.5 % strongly disagreed/somewhat disagreed; p=NS). While neither group found completing the MSPT fatiguing, HC found it less so (MS=70.6% strongly disagreed/somewhat disagreed, HC= 92.5 % strongly disagreed/somewhat disagreed; p=0.004.) CONCLUSIONS: Participants reported that they found the MSPT to be highly useable. HCs found instructions somewhat easier to understand and less fatiguing than MS patients. These data suggest that the MSPT will be acceptable to patients as a method to quantify MS-related disability.
Anti-LeY monoclonal antibody (mAb) hu3S193 (Rebmab 100) in patients with advanced platinum resistant/refractory (PRR) ovarian cancer (OC), primary peritoneal cancer (PPC), or fallopian tube cancer (FTC). (2011)

5078 Background: Lewis-Y (LeY) antigen is a blood group related antigen expressed in 75% of OC. hu3S193 is a humanized anti-LeY IgG1 mAb with strong complement dependent cytotoxicity and excellent targeting characteristics with a good safety profile in Phase I studies. Methods: This phase II study accrued pts with PRR, OC, PPC or FTC, with LeY expression by IHC, ≤ 1 prior chemotherapy regimens in the PRR state, and a KPS ≥ 70%. Pts received weekly intravenous infusions (1 cycle = 8 weeks) of hu3S193 at 20mg/m2 for up to 3 cycles, until disease progression or unacceptable toxicity. Primary endpoint was clinical benefit rate [objective response (OR) + stable disease (SD) ≥ 24 weeks]. A two-stage design was utilized with H1 set at 15%, requiring at least 1 OR. Secondary objectives were safety, progression-free survival (PFS) and pharmacokinetics (PK). Results: 31 pts were enrolled. Median age: 55 yrs (range 25-78); primary site: OC-29, PPC-1 FTC-1; LeY-positive by IHC (N): 1+ (15), 2+ (5), 3+ (8), 4+ (3). Prior platinum response: refractory 8, primary resistant 8, secondary resistant 14, allergy 1; median KPS: 90% (range 70-100); median CA-125: 257 (range 18-10,041). Number of cycles of hu3S193 delivered: 32 (median 1, range <1-3). Evaluable patients: 26 (5 pts < 4 doses); Responses: OR=0; SD=11 (42%); SD ≥ 24 weeks=6 (23%). No grade 4 toxicities observed. Most frequent toxicities in all pts (N any grade/grade 3): fatigue 4/1, allergy 4/1, tremor 2/1, fever 3/0, nausea 4/0, hypertension 3/0. Median PFS was 10 weeks (95 % CI, 4-15). PK data will be presented. Conclusions: single agent hu3S193 induces disease stabilization in a significant rate in this heavily pretreated population, including long term stabilization. PFS is comparable to historic chemotherapy data with acceptable toxicity. Further studies in combination with chemotherapy are underway.
Long-Range Multichain Adsorption of Polyampholytes on a Charged Surface (1999)

We develop a theory of the adsorption of many polyampholyte chains on a charged surface. The adsorption is due to the polarization of polyampholyte chains in the external electric field created by the charged surface. The equilibrium polymer density profile is determined by balancing the long-range polarization-induced attraction of polyampholytes to the charged surface and the three-body repulsion between monomers in a θ-solvent for the polymer backbone (or the two-body repulsion in a good solvent). We demonstrate that the long-range nature of polyampholyte adsorption can lead to an adsorbed layer much thicker than the size of individual chains. Adsorbed polyampholytes that do not touch the surface form a multibrush of stretched chains. The chains that touch the surface form a self-similar stretched pseudobrush. Polyampholyte chains carrying the net charge of the same sign as that of the surface can also adsorb. In this case, the adsorption stops at that distance from the surface where the electrostatic repulsion between polyampholytes and a similarly charged surface becomes stronger than the polarization-induced attraction. The thickness of the adsorbed layer and the surface coverage decrease with increasing net charge on polyampholytes. The effect of added salt on polyampholyte adsorption is also discussed.
Folding Behaviour of Retro-Rubredoxin (1996)

The hypothesis that retro proteins should adopt conformations similar to that of the parent protein has been tested by preparing the retro derivative of (Ala 31) rubredoxin, a 45 residue polypeptide that is able to adopt stable structures in solution and displaying affinity for bivalent metal ions. Circular dichroism and UV measurements indicated that while the synthetic rubredoxin mutant acquired the typical conformation and iron binding ability in solution, the retro derivative did not show any evidence of structure nor of iron binding activity.
The Chemistry of the 6b-Thioamidopenam 1b-Sulfoxides. The 1,2,4-Dithiazineacetidinones and Thiazolineazetidinones (1990)

6P-Thioamidopenam lg-sulfoxides on thermolysis gave methyl 2-(3-substituted 4,5-dithia-2,7-diazabicyc10[4.2.01oct-2-en-8-0ne-7- y1)-3-methyl-but-3-enoate (1.2.4-dithiazineazetidinonesl.The reac-
Dual-comb Spectroscopy using On-chip Mode-locked Frequency Combs (2017)

We generate broadband soliton mode-locked dual combs on the same chip and demonstrate high SNR (&gt; 40 dB) near-infrared dual-comb spectroscopy of dichloromethane over a 170 nm optical bandwidth with a short acquisition time of 20 µs.
Lockup of a client object cache and how to avoid it (2002)

This paper presents the problem of client object cache lockup in a distributed object-oriented database system where storage is recovered by garbage collection. If garbage collection is augmented with the ability to discard reachable unmodified versions of persistent objects, cache lockup is greatly reduced. This paper outlines some remaining questions about this technique for managing an object cache.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Disappearance of a major cell‐type specific surface glycoprotein antigen (SF) after transformation of fibroblasts by rous sarcoma virus (1974)

Abstract Normal chick fibroblasts are known to contain a tissue‐specific surface component, a major glycoprotein (SF) antigen that is also present in chicken serum. This antigen was greatly reduced in amount or absent in fibroblasts transformed by five different Rous sarcoma virus strains. Fibroblasts infected with virus mutants temperature sensitive for transformation recovered the SF antigen when maintained at the non‐permissive temperature. Productive infection with a non‐transforming avian type‐C virus did not alter the level of SF antigen characteristic of normal fibroblasts. Polyacrylamide gel electrophoresis of total cell extracts indicated that proteins with apparent mol. wt. of 145,000 and mol. wt. 210,000 were greatly decreased following transformation of the fibroblasts. That the ability to synthetize the 145,000 mol. wt. polypeptide was lost upon transformation was implied by pulse labelling experiments, in which normal fibroblasts incorporate [ 35 S] methionine into the above polypeptide whereas transformed cells lose this ability. This polypeptide, unique in its presence in normal but not in transformed cells, appears to have an exceptionally high rate of turnover. Indirect evidence suggests that the 145,000 and 210,000 polypeptides are molecular counterparts of the SF antigen. The transformation‐associated change in the quantity of the SF molecule supports our proposal that tissue‐specific surface glycoproteins, such as the SF antigen, express the stage of differentiation at the membrane of normal cells and may be involved in intercellular control of growth and movement.
Automatic transistor and physical design of FPGA tiles from an architectural specification (2003)

One of the most difficult and time-consuming steps in the creation of an FPGA is its transistor-level design and physical layout. Modern commercial FPGAs typically consume anywhere from 50 to 200 man-years simply in the layout step. To date, automated tools have only been employed in small parts of the periphery and programming circuitry. The core tiles, which are repeated many times, are subject to painstaking manual design and layout. In this paper we present a new system (called GILES, for Good Instant Layout of Erasable Semiconductors) that automatically generates a transistor-level schematic from a high-level architectural specification of an FPGA. It also generates a cell-level netlist that is placed and routed automatically. The architectural specification is the one used as input to the VPR [3] architectural exploration tool. The output is the mask-level layout of a single tile that can be replicated to form an FPGA array. We describe a new placement tool that simultaneously places and compacts the layout to minimize white space and wiring demand, and a special-purpose router built for this task.GILES can place and route a tile consisting of four 4-input LUT logic cells and all of its programmable wires in a 0.18μm CMOS process using 8 layers of metal and 25983μm2 of area. When we generate the layout of an architecture similar to the Xilinx Virtex-E FPGA (built in a 0.18μm process) GILES requires only 47% more area than the original. The layout area of an architecture similar to the Altera Apex 20K400E (also built in a 0.18µm process) constructed by GILES requires 97% more area than the original.
De novo chromosome-length assembly of the mule deer (Odocoileus hemionus) genome (2021)

The mule deer (<i>Odocoileus hemionus</i>) is an ungulate species that is distributed in a range from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can improve our knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. Their large population size, continuous distribution, and diversity of habitat make mule deer excellent candidates for population genomics studies; however, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C technologies. We also provide a genome annotation and compare demographic histories of the mule deer and white-tailed deer using the pairwise sequentially Markovian coalescent model. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.
Defining a Clade by Morphological, Molecular and Toxinological Criteria: Distinctive Forms related to Conus praecellens A. Adams, 1854. (2010)

We carried out a definition of the species group to which Conus praecellens A. Adams 1854 belongs using a combination of comparative morphological data, molecular phylogeny based on standard genetic markers and toxinological markers. Prior to this work, Conus praecellens was generally postulated to belong to a clade of similarly high-spired, smaller Conusspecies such as Conus pagodus Kiener, 1845, Conus memiae (Habe & Kosuge, 1970) and Conus arcuatus Broderip & Sowerby, 1829. The molecular phylogeny and toxinological data demonstrate that these prior hypotheses are incorrect, and that instead, Conus praecellens is in a branch of Conus that includes Conus stupa (Kuroda, 1956), Conus stupella (Kuroda, 1956), Conus acutangulus Lamark, 1810 and surprisingly, some species that are morphologically strikingly different, Conus mitratus Sowerby, 1870 and Conus cylindraceus Broderip & Sowerby, 1830. A more careful analysis of the morphologically diverse forms assigned to Conus praecellens suggests that from the Philippine material alone, there are at least three additional undescribed species, Conus andremenezi, Conus miniexcelsus and Conus rizali. A reevaluation of protoconch/early teleoconch morphology also strongly suggests that Conus excelsus Sowerby III, 1908 is related to these species. Together, the different data suggest a clade including the 10 species above that we designate, the Turriconus (Shikama and Habe, 1968) (clade; there are additional distinctive forms within the clade that may be separable at the species level. The phylogenetic definition using the multidisciplinary approach described herein provides a framework for comprehensively investigating biodiverse lineages of animals, such as the cone snails.
Learning Attributes from the Crowdsourced Relative Labels (2017)

Finding semantic attributes to describe related concepts is typically a hard problem. The commonly used attributes in most fields are designed by domain experts, which is expensive and time-consuming. In this paper we propose an efficient method to learn human comprehensible attributes with crowdsourcing. We first design an analogical interface to collect relative labels from the crowds. Then we propose a hierarchical Bayesian model, as well as an efficient initialization strategy, to aggregate labels and extract concise attributes. Our experimental results demonstrate promise on discovering diverse and convincing attributes, which significantly improve the performance of the challenging zero-shot learning tasks.
Effect of Coating and Lubrication on the Vibration-Induced Loosening of Threaded Fasteners (2006)

This study provides an experimental and theoretical investigation of the effect of the bearing friction coefficient and the thread friction on the self-loosening of threaded fasteners that are subjected to cyclic transverse service loads. Coating and lubrication affect the thread and the underhead friction of the fastener, which affects the loosening rate when it is subjected to transverse loads. A mathematical model was developed to evaluate the self-loosening behavior in threaded fasteners when subjected to cyclic transverse loads. An experimental procedure and test set up are designed in order to collect real-time data on the rate of preload loss per cycle as well as the rotational angle of the bolt head during its gradual loosening. The values of the coefficients of friction under the bolt head and between the threads were changed in the mathematical model to monitor their effect on the loosening rate. Experimentally, the friction coefficients are modified by changing the coating or the lubrication applied to the fasteners. One coating and one solid film lubricant are used, namely, phosphate and oil coating and Olefin and Molydisulfide lubricated bolts. The theoretical and experimental results are presented and discussed.
Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER (2018)

Abstract Probing the molecular organization of tissues requires in situ analysis by microscopy. However current limitations in multiplexing, sensitivity, and throughput collectively constitute a major barrier for comprehensive single-cell profiling of proteins. Here, we report Immunostaining with Signal Amplification By Exchange Reaction (Immuno-SABER), a rapid, highly multiplexed signal amplification method that simultaneously tackles these key challenges. Immuno-SABER utilizes DNA-barcoded antibodies and provides a method for highly multiplexed signal amplification via modular orthogonal DNA concatemers generated by Primer Exchange Reaction. This approach offers the capability to preprogram and control the amplification level independently for multiple targets without in situ enzymatic reactions, and the intrinsic scalability to rapidly amplify and image a large number of protein targets. We validated our approach in diverse sample types including cultured cells, cryosections, FFPE sections, and whole mount tissues. We demonstrated independently tunable 5-180-fold amplification for multiple targets, covering the full signal range conventionally achieved by secondary antibodies to tyramide signal amplification, as well as simultaneous signal amplification for 10 different proteins using standard equipment and workflow. We further combined Immuno-SABER with Expansion Microscopy to enable rapid and highly multiplexed super-resolution tissue imaging. Overall, Immuno-SABER presents an effective and accessible platform for rapid, multiplexed imaging of proteins across scales with high sensitivity.
Correcting the Pspice large-signal model for PWM converters operating in DCM (2000)

It is shown that an incorrect parameter limit in the existing Pspice pulsewidth modulated (PWM) switch model has been detected. The main objective of this work is to alert users of such models to a potential source of simulation error under certain parameter specifications as shown here. Simulation of the boost converter operating in discontinuous conduction mode (DCM) based on the incorrect model results in either convergence problems or wrong results. Correction of the model is provided and its validity is verified using a specific converter example. The results illustrate how the old and corrected models produce different results when the boost converter is subjected to some transients under sudden load variations.
On the stability of glycine-water clusters with excess electron: Implications for photoelectron spectroscopy (2005)

Calculations are presented for the glycine-(H(2)O)(n) (-) (n=0-2) anionic clusters with excess electron, with the glycine core in the canonical or zwitterion form. A variety of conformers are predicted, and their relative energy is examined to estimate thermodynamic stability. The dynamic (proton transfer) pathways between the anionic clusters with the canonical and the zwitterion glycine core are examined. Small barrier heights for isomerization from the zwitterion glycine-(H(2)O)(2) (-) anion to those with canonical glycine core suggest that the former conformers may be kinetically unstable and unfavorable for detection of neutral glycine zwitterion-(H(2)O)(n) (n=1,2) clusters by photodetachment, in accordance with the photoelectron spectroscopic experiments by Bowen and co-workers [Xu et al., J. Chem. Phys. 119, 10696 (2003)]. The calculated stability of the glycine-(H(2)O)(n) (-) anion clusters with canonical glycine core relative to those with zwitterion core indicates that the observation of the anionic conformers with the canonical glycine core would be much more feasible, as revealed by Johnson and co-workers [Diken et al. J. Chem. Phys. 120, 9902 (2004)].
KillerRed and miniSOG as genetically encoded photosensitizers for photodynamic therapy of cancer (2013)

Despite of the success of photodynamic therapy (PDT) in cancer treatment, the problems of low selective accumulation of a photosensitizer in a tumor and skin phototoxicity have not resolved yet. The idea of encoding of a photosensitizer in genome of cancer cells is attractive, particularly because it can provide highly selective light induced cell killing. This work is aimed at the development of new approach to PDT of cancer, namely to using genetically encoded photosensitizers. A phototoxicity of red fluorescent GFP-like protein KillerRed and FMN-binding protein miniSOG was investigated on HeLa tumor xenografts in nude mice. The tumors were generated by subcutaneous injection of HeLa cells stably expressing the phototoxic proteins. The tumors were irradiated with 594 nm or 473 nm laser at 150 mW/cm<sup>2</sup> for 20 or 30 min, repeatedly. Fluorescence intensity of the tumors was measured <i>in vivo</i> before and after each treatment procedure. Detailed pathomorphological analysis was performed 24 h after the therapy. On the epi-fluorescence images <i>in vivo</i> photobleaching of both proteins was observed indicating photodynamic reaction. Substantial pathomorphological abnormalities were found in the treated KillerRed-expressing tumor tissue, such as vacuolization of cytoplasm, cellular and nuclear membrane destruction, activation of apoptosis. In contrast, miniSOG-expressing tumors displayed no reaction to PDT, presumably due to the lack of FMN cofactor needed for fluorescence recovery of the flavoprotein. The results are of interest for photodynamic therapy as a proof of possibility to induce photodamages in cancer cells <i>in vivo</i> using genetically encoded photosensitizers.