gebhart/patrepeval huggingface dataset:
Stretchable and Strong Cellulose Nanopaper Structures Based on Polymer-Coated Nanofiber Networks: An Alternative to Nonwoven Porous Membranes from Electrospinning (2012)

Nonwoven membranes based on electrospun fibers are of great interest in applications such as biomedical, filtering, and protective clothing. The poor mechanical performance is a limitation, as is some of the electrospinning solvents. To address these problems, porous nonwoven membranes based on nanofibrillated cellulose (NFC) modified by a hydroxyethyl cellulose (HEC) polymer coating are prepared. NFC/HEC aqueous suspensions are subjected to simple vacuum filtration in a paper-making fashion, followed by supercritical CO(2) drying. These nonwoven nanocomposite membranes are truly nanostructured and exhibit a nanoporous network structure with high specific surface area, as analyzed by nitrogen adsorption and FE-SEM. Mechanical properties evaluated by tensile tests show high strength combined with remarkably high strain to failure of up to 55%. XRD analysis revealed significant fibril realignment during tensile stretching. After postdrawing of the random mats, the modulus and strength are strongly increased. The present preparation route uses components from renewable resources, is environmentally friendly, and results in permeable membranes of exceptional mechanical performance.
“Chiral-at-Metal” Octahedral Ruthenium(II) Complexes with Achiral Ligands:  A New Type of Enantioselective Catalyst (2003)

cis-[Ru(dmp)(2)(CH(3)CN)(2)][PF(6)](2) (dmp = 2,9-dimethyl-1,10-phenanthroline), complex 1[PF(6)](2), exists in two enantiomeric forms, Delta and Lambda. During treatment with the chiral anion tris[tetrachlorobenzene-1,2-bis(olato)]phosphate(V), also named Trisphat, in dichloromethane it has been possible to selectively precipitate each enantiomer, associated with Trisphat in the form of the heterochiral pair. This enantiomerically pure compound has been characterized in solution by UV-visible, CD, ESI-MS, and NMR spectroscopy and by X-ray crystallography in the solid state. Trisphat was also used as an NMR chiral shift reagent to determine the enantiomeric excess of the complex preparations. The "chiral-at-metal" ruthenium complex has been evaluated as a catalyst for the oxidation of sulfides to sulfoxides by hydrogen peroxide. The reactions displayed a low but significant level of enantioselectivity (18% ee in the case of 4-bromophenyl methyl sulfide). Our results thus provide the first demonstration that the chiral information carried by a stereogenic metal center can be catalytically transferred to molecules during stereoselective oxidation.
Les rétrovirus leucémogènes murins : pathogènes, gènes et outils génétiques (2001)

Les retrovirus leucemogenes murins (MLV) existent sous des formes endogenes generalement tres remaniees transmises verticalement dans la lignee germinale, et sous des formes exogenes infectieuses transmises horizontalement. Des retrovirus apparentes aux MLV et infectieux pour leurs hotes sont retrouves dans d'autres especes, y compris oiseaux et primates, temoignant de la possibilite d'une transmission horizontale de ce type de virus entre especes eloignees. Du fait de la diversite des modeles d'infection et de pathogenese in vivo utilisant les MLV, ces virus ont aide a l'approfondissement de nos connaissances sur la regulation de l'expression des genes eucaryotes, la physiopathologie virale et la differenciation cellulaire. De plus, etant donne que la replication du genome ARN retroviral comprend la synthese et l'integration d'un provirus ADN dans le genome cellulaire, les MLV sont devenus des outils precieux aussi bien en embryologie qu'en genetique des populations. Plus recemment, les strategies de transfert de genes, y compris therapeutiques, ont abondamment beneficie des travaux sur les MLV. Dans cette revue, nous avons cherche a fournir un spectre large mais precis d'elements de la connaissance actuelle sur la replication et la pathogenese des MLV, et recense certains aspects de leur utilisation comme vecteurs en therapie genique.
Multi-Task Learning with a Fully Convolutional Network for Rectum and Rectal Cancer Segmentation. (2019)

In a rectal cancer treatment planning, the location of rectum and rectal
cancer plays an important role. The aim of this study is to propose a fully
automatic method to segment both rectum and rectal cancer with axial
T2-weighted magnetic resonance images. We present a fully convolutional network
for multi-task learning to segment both rectum and rectal cancer. Moreover, we
propose an assessment method based on bias-variance decomposition to visualize
and measure the regional model robustness of a segmentation network. In
addition, we suggest a novel augmentation method which can improve the
segmentation performance and reduce the training time. Our proposed method not
only is computationally efficient due to its fully convolutional nature but
also outperforms the current state-of-the-art in rectal cancer segmentation. It
also shows high accuracy in rectum segmentation, for which no previous studies
exist. We conclude that rectum information benefits the training of rectal
cancer segmentation model, especially concerning model variance.
A Design Criterion of Error Correcting Codes for Spectrum-Overlapped Resource Managements (2011)

In this paper, we propose a new criterion for the extrinsic information transfer (EXIT) analysis in the spectrum-overlapped resource management (SORM) for a broadband single carrier transmission. In the SORM technique, each user can ideally obtain a maximum channel gain by allowing overlapped allocation, assuming the soft canceller with minimum mean square error (SC/MMSE) turbo equalization for multi-user detection. When the interference is not completely removed by SC/MMSE turbo equalization, frame error rate (FER) remarkably degrades. To solve this problem, we proposed a new criterion which is used for design of error correcting code in order to improve convergence property of SC/MMSE turbo equalization without large redundancy of channel code. In the proposed criterion, we design the decoder so that the decoder's EXIT property is fitted to the upper bound of equalizer's property and the channel code sharply improves mutual information (MI) in the lower amount of input MI. This paper evaluates FER performance with the irregular low-density parity-check (LDPC) codes designed based on this criterion. As a result, this paper shows that the irregular LDPC code designed based on the proposed criterion for the SORM outperforms conventional codes.
D-penicillamine in the therapy of fibrotic lung diseases. (1986)

We studied 12 patients with pulmonary fibrosis treated with D-Penicillamine in an attempt to regulate the collagen metabolism that is seriously affected in this group of patients. After six years follow-up we found a 33% survival rate compared to a 5% survival rate in patients treated with corticosteroids (p less than 0.01). Functional respiratory tests as well as quality of life were improved in all patients. No side effects attributable to D-Penicillamine were detected probably due to the fact that we used smaller doses than those reported in the treatment of other diseases of the connective tissue. We conclude that D-Penicillamine can be a useful alternative drug in the therapy of patients with pulmonary fibrosis.
Use of a Gene Expression System Based on Potato Virus X to Rapidly Identify and Characterize a Tomato Pto Homolog That Controls Fenthion Sensitivity (1995)

Caius M. T. Rommens, John M. Salmeron, David C. Baulcombe, Brian J. Staskawicz, Use of a Gene Expression System Based on Potato Virus X to Rapidly Identify and Characterize a Tomato Pto Homolog That Controls Fenthion Sensitivity, The Plant Cell, Vol. 7, No. 3 (Mar., 1995), pp. 249-257
DIRECTIONAL DIFFUSION OF K ATOMS ON A GaAs(110) SURFACE (2006)

We performed STM measurements on the K/GaAs (110) surface with high K coverage. The K atoms gradually disappeared while scanning the tip over the surface at negative sample bias voltage. The phenomenon strongly occurred over the scanning area and can be explained by the field-induced surface diffusion from the scanning area to radial direction. Considering the interaction between the dipole moment of the adsorbed K atoms and the electric field, we discuss the relationship between the static and induced dipole moment of K atoms on a GaAs (110) surface.
Autogen (2017)

We present A utogen —an algorithm that for a wide class of dynamic programming (DP) problems automatically discovers highly efficient cache-oblivious parallel recursive divide-and-conquer algorithms from inefficient iterative descriptions of DP recurrences. A utogen analyzes the set of DP table locations accessed by the iterative algorithm when run on a DP table of small size and automatically identifies a recursive access pattern and a corresponding provably correct recursive algorithm for solving the DP recurrence. We use A utogen to autodiscover efficient algorithms for several well-known problems. Our experimental results show that several autodiscovered algorithms significantly outperform parallel looping and tiled loop-based algorithms. Also, these algorithms are less sensitive to fluctuations of memory and bandwidth compared with their looping counterparts, and their running times and energy profiles remain relatively more stable. To the best of our knowledge, A utogen is the first algorithm that can automatically discover new nontrivial divide-and-conquer algorithms.
Brain tumors disrupt the resting-state connectome (2018)

Brain tumor patients often experience functional deficits that extend beyond the tumor site. While resting-state functional MRI (rsfMRI) has been used to map such functional connectivity changes in brain tumor patients, the interplay between abnormal tumor vasculature and the rsfMRI signal is still not well understood. Therefore, there is an exigent need for new tools to elucidate how the blood‑oxygenation-level-dependent (BOLD) rsfMRI signal is modulated in brain cancer. In this initial study, we explore the utility of a preclinical model for quantifying brain tumor-induced changes on the rsfMRI signal and resting-state brain connectivity. We demonstrate that brain tumors induce brain-wide alterations of resting-state networks that extend to the contralateral hemisphere, accompanied by global attenuation of the rsfMRI signal. Preliminary histology suggests that some of these alterations in brain connectivity may be attributable to tumor-related remodeling of the neurovasculature. Moreover, this work recapitulates clinical rsfMRI findings from brain tumor patients in terms of the effects of tumor size on the neurovascular microenvironment. Collectively, these results lay the foundation of a preclinical platform for exploring the usefulness of rsfMRI as a potential new biomarker in patients with brain cancer.
Thermal Modeling for Design Optimization of a Microfluidic Device for Continuous Flow Polymerase Chain Reaction (PCR) (2008)

Polymerase Chain Reaction (PCR) is a molecular biological method for the in vitro amplification of nucleic acid molecules which has wide applications in the area of genetics, medicine and biochemistry. The typical three step PCR cycle consists of heating the sample to 90–94 °C to denature double-stranded DNA, cooling down to 50–54 °C to anneal the specific primers to the single stranded DNA and finally increasing the temperature to 70–75 °C for extension of the primers with thermostable DNA polymerase. The temperature sensitivity of the reaction requires precise temperature control and proper thermal isolation of these three zones. In this paper we present the design of a continuous flow PCR microfluidic device with the channels fabricated in (poly) dimethylsiloxane (PDMS) and thin film Platinum Resistance Temperature Detector (RTD) elements fabricated on glass substrate to define the three different temperature zones. The fluidic arrangement has a water jacket layer to minimize evaporation from the porous PDMS walls. A detailed thermo fluidic model of the device is presented to predict the performance and efficacy of the proposed design. Numerical simulations are carried out to find the temperature distribution and temperature gradients in the device and a parametric study is done by varying flow rate, heat flux and channel dimensions in order to optimize the design for achieving temperature isolation and sharp temperature gradients between different zones.
Exploring the design of accessible goal crossing desktop widgets (2009)

Prior work has shown that goal crossing may be a more accessible interaction technique than conventional pointing-and-clicking for motor-impaired users. Although goal crossing with pen-based input devices has been studied, pen-based designs have limited applicability on the desktop because the pen can "fly in," cross, and "fly out," whereas a persistent mouse cursor cannot. We therefore explore possible designs for accessible mouse-based goal crossing widgets that avoid triggering unwanted goals by using secondary goals, gestures, and corners and edges. We identify four design principles for accessible desktop goal crossing widgets: ease of use for motor-impaired users, safety from false selections, efficiency, and scalability.
Design and testing of fluorescence-guided endoscopic biopsy assessment at the bedside (2021)

Clinical detection of premalignant lesions often requires labeling with molecular probes. In the gastrointestinal tract, most cancers originate in epithelial layers which are interrogated using topically-applied probes with conjugated fluorescence dyes. As part of clinical trials using fluorescence peptide probes, we have developed two different instruments that rapidly image the biopsy at the bedside before fixation. These multimodal images (visible light reflectance and near infrared fluorescence) provide verification that the targeted lesion was sampled, and provide feedback to the clinician at the bedside for any follow-up procedure. Performance of these two prototypes are compared for fluorescence sensitivity and multimodal image quality.
Methods for Evaluating Medical Tests and Biomarkers (2017)

Background: The Test-Treatment Pathway has been proposed as a method to link test accuracy to downstream outcomes. By describing the clinical actions before and after testing, it illustrates how a test is positioned in the pathway, relative to other tests and diagnostics, and how the introduction of a new test may change the current diagnostics pathway. However, there is limited practical guidance on how to model such Test-Treatment Pathways. Methods: We selected the Patient -Index test-Comparator -Outcome (PICO) format, as also used elsewhere in evidence-based medicine, as a starting point for building the Test-Treatment Pathways. From there we developed a structured set of triggering questions. We defined these questions based on several brainstorm sessions and iteratively made changes to this basic structure after three rounds of user testing. During the user testing meetings, a pathway was drawn for each specific application. All sessions were recorded both on audio and video.
Application of a Multiple‐Enzyme System for Chiral Alcohol Production (2010)

This chapter contains sections titled: Introduction Construction of an Enzymatic Reduction System Enzymatic Stereoinversion System References
Thermal Behavior of Free‐Base and Core‐Modified Bicyclo[2.2.2]octadiene‐Fused Porphyrins (2007)

Abstract Multistep thermal fragmentation of quadruply bicyclo[2.2.2]octadiene‐fused porphyrins giving tetrabenzoporphyrins was examined in detail. After the first extrusion of an ethylene molecule from the porphyrin derivative, the opposite bicyclo[2.2.2]octadiene moiety preferentially underwent the second retro‐Diels–Alder reaction to give an opp ‐dibenzoporphyrin derivative rather than an adj ‐dibenzoporphyrin derivative. These two benzoporphyrin derivatives then decomposed to give a tribenzoporphyrin derivative in similar rates. The temperature regions of these fragmentations could not be distinguished by thermogravimetric analysis. In contrast, the third and the fourth fragmentations obviously occurred stepwise. There was a temperature region where the tribenzoporphyrin derivative preferentially existed. In the case of the 21,23‐dithiaporphyrin derivative, opp ‐21,23‐dithiadibenzoporphyrin, possessing benzo moieties fused at the pyrrole parts of the core‐modified porphyrin chromophore was predominantly formed during the fragmentation. In the case of the 21‐thiaporphyrin derivative, an ethylene molecule was extruded selectively from the bicyclo[2.2.2]octadiene moiety adjacent to the thiophene part to give 21‐thiabenzo[ q ]porphyrin and then 21‐thiabenzo[ g , q ]porphyrin derivatives. In these cases, the last ethylene extrusion also occurred very slowly. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
Prevalence, Development, and Molecular Mechanisms of Bacteriocin Resistance in Campylobacter (2011)

Bacteriocins (BCNs) are antimicrobial peptides produced by bacteria with narrow or broad spectra of antimicrobial activity. Recently, several unique anti-Campylobacter BCNs have been identified from commensal bacteria isolated from chicken intestines. These BCNs dramatically reduced C. jejuni colonization in poultry and are being directed toward on-farm control of Campylobacter. However, no information concerning prevalence, development, and mechanisms of BCN resistance in Campylobacter exists. In this study, susceptibilities of 137 C. jejuni isolates and 20 C. coli isolates to the anti-Campylobacter BCNs OR-7 and E-760 were examined. Only one C. coli strain displayed resistance to the BCNs (MIC, 64 μg/ml), while others were susceptible, with MICs ranging from 0.25 to 4 μg/ml. The C. coli mutants resistant to BCN OR-7 also were obtained by in vitro selection, but all displayed only low-level resistance to OR-7 (MIC, 8 to 16 μg/ml). The acquired BCN resistance in C. coli could be transferred at intra- and interspecies levels among Campylobacter strains by biphasic natural transformation. Genomic examination of the OR-7-resistant mutants by using DNA microarray and random transposon mutagenesis revealed that the multidrug efflux pump CmeABC contributes to both intrinsic resistance and acquired resistance to the BCNs. Altogether, this study represents the first report of and a major step forward in understanding BCN resistance in Campylobacter, which will facilitate the development of effective BCN-based strategies to reduce the Campylobacter loads in poultry.
Full-System Simulation of Airborne Capacitive Mems Transducers Operating in the Audible and Ultrasonic Regime (2019)

A compact model of an airborne capacitive acoustic MEMS transducer is generalized to perform predictive full-system simulations in the audible and ultrasonic regime. The model helps to assess and understand the interaction of the device with the surrounding air for frequencies up to 100 kHz while considering acoustic high-frequency effects and sound wave propagation. We successfully simulate transducers with varying design parameters operating under different working scenarios. The predictive power of the model and its potential for full-system design and optimization are highlighted by the very good agreement between simulations and experimental results.
Synthesis of N9- and N7-[2-Hydroxy-3-(phosphonomethoxy)propyl] Derivatives of N6-Substituted Adenines, 2,6-Diaminopurines and Related Compounds (2004)

Base-catalyzed reactions of diethyl [(oxiranylmethoxy)methyl]phosphonate ( 2 ) with purine bases (adenine, 2,6-diaminopurine, 6-chloropurine and 2-amino-6-chloropurine) gave corresponding 9- or 7-[2-hydroxy-3-(phosphonomethoxy)propyl] purines. The adenine and 2,6-diaminopurine derivatives cyclize to cyclic phosphonates 4 and 6 . The 9-[2-hydroxy-3-(phosphonomethoxy)propyl] derivatives of N 6 -substituted adenine and 2,6-diaminopurine ( 15 - 27 ) were prepared by the treatment of diethyl {[3-(6-chloropurin-9-yl)-2-hydroxypropoxy]methyl}phosphonate ( 11 ) or diethyl {[3-(2-amino-6-chloropurin-9-yl)-2-hydroxypropoxy]methyl}phosphonate ( 13 ) with primary or secondary amines. The reaction of 6-chloro- or 2-amino-6-chloropurine derivatives ( 11 , 13 ) with thiourea gave the corresponding diethyl purine-6-thiol or 2-aminopurine-6-thiol phosphonates 47 , 48 . The guanine derivative 49 was prepared by the treatment of compound 13 with 80% acetic acid. All diethyl phosphonates were transformed to free phosphonic acids ( 31 - 43 , 50 - 52 ) by the action of bromotrimethylsilane and subsequent hydrolysis.
Ring closure reactions with nitriles. II. Formation of pyrrolo[1,2‐a] quinazolines and thiazolo[3,2‐a] quinazolines (1968)

Abstract 2‐Quinazolinepropionic acids have been obtained from the reactions of potassium cyanide with o ‐carboxy‐ or o ‐acyl‐3‐chloropropionanilides. Some of these compounds have been cyclized to pyrrolo [1,2‐ a ] quinazolines. The reaction of an o ‐carbethoxy‐2‐chloroacetanilide with potassium thiocyanate formed a 2‐quinazolinylthioacetic acid, which was cyclized to a thiazolo‐[3,2‐ a ]quinazoline. A mechanism is presented for the formation of these compounds.
Self Correspondence Distillation for End-to-End Weakly-Supervised Semantic Segmentation (2023)

Efficiently training accurate deep models for weakly supervised semantic segmentation (WSSS) with image-level labels is challenging and important. Recently, end-to-end WSSS methods have become the focus of research due to their high training efficiency. However, current methods suffer from insufficient extraction of comprehensive semantic information, resulting in low-quality pseudo-labels and sub-optimal solutions for end-to-end WSSS. To this end, we propose a simple and novel Self Correspondence Distillation (SCD) method to refine pseudo-labels without introducing external supervision. Our SCD enables the network to utilize feature correspondence derived from itself as a distillation target, which can enhance the network's feature learning process by complementing semantic information. In addition, to further improve the segmentation accuracy, we design a Variation-aware Refine Module to enhance the local consistency of pseudo-labels by computing pixel-level variation. Finally, we present an efficient end-to-end Transformer-based framework (TSCD) via SCD and Variation-aware Refine Module for the accurate WSSS task. Extensive experiments on the PASCAL VOC 2012 and MS COCO 2014 datasets demonstrate that our method significantly outperforms other state-of-the-art methods. Our code is available at {https://github.com/Rongtao-Xu/RepresentationLearning/tree/main/SCD-AAAI2023}.
Crystal Structures of Tcl1 Family Oncoproteins and Their Conserved Surface Features (2002)

Members of the TCL1 family of oncogenes are abnormally expressed in mature T-cell leukemias and B-cell lymphomas. The proteins are involved in the coactivation of protein kinase B (Akt/PKB), a key intracellular kinase. The sequences and crystal structures of three Tcl1 proteins were analyzed in order to understand their interactions with Akt/PKB and the implications for lymphocyte malignancies. Tcl1 proteins are approximately 15 kD and share 25-80% amino acid sequence identity. The tertiary structures of mouse Tcl1, human Tcl1, and Mtcp1 are very similar. Analysis of the structures revealed conserved semi-planar surfaces that have characteristics of surfaces involved in protein-protein interactions. The Tcl1 proteins show differences in surface charge distribution and oligomeric state suggesting that they do not interact in the same way with Akt/PKB and other cellular protein(s).