gebhart/patrepeval huggingface dataset:
Monte Carlo Simulations for Proteins:  Binding Affinities for Trypsin−Benzamidine Complexes via Free-Energy Perturbations (1997)

Monte Carlo computer simulations have been performed in conjunction with free-energy perturbation calculations to determine the relative binding constants of four benzamidine inhibitors with trypsin. The protein backbone was constrained in the simulations, but sampling of the side chains was allowed. The calculated free energies are very precise and are shown to yield closed thermodynamic cycles. The calculations correctly predict p-aminobenzamidine to be the strongest inhibitor and give relative free energies of binding for p-methyl- and p-chlorobenzamidine in excellent agreement with experiment. The predicted overly weak binding of the parent benzamidine is most likely due to a deficiency in the partial charges. The relative binding affinities are justified in terms of bulk-solvation arguments whereby the more polar inhibitors are preferentially stabilized in water. The calculations demonstrate that Monte Carlo computer simulations can be used to determine accurate and precise relative binding constants for protein systems.
PDE-based analysis and control of the oxygen storage level in three-way catalytic converters (2012)

We develop a model that retains the distributed nature of three-way catalytic converters based on PDE formulation. Based on this model we show that when a square wave air-to-fuel ratio is applied at the inlet of the catalyst, the time-average of the oxygen storage level acquires an equilibrium profile which is asymptotically stable. To suppress various disturbances at the inlet of the catalyst, we design an output feedback control law based on the linearized system around the acquired equilibrium, using the ideal concentration measurements.
Enhanced on-chip SERS based biomolecular detection using electrokinetically active microwells (2008)

Here we present a novel microfluidic technique for on-chip surface enhanced Raman spectroscopy (SERS) based biomolecular detection, exploiting the use of electrokinetically active microwells. Briefly, the chip comprises of a series of microfluidic channels containing embedded microwells that, when electrically actuated, either locally attract or repulse species from solution through a combination of electrokinetic effects. We demonstrate that the approach combines the advantages of existing homogeneous (solution phase) and heterogeneous (surface phase) on-chip techniques by enabling active mixing to enhance the rate of binding between the SERS enhancers and the biomolecular targets as well as rapid concentration of the product for surface phase optical interrogation. This paper describes the chip design and fabrication procedure, experimental results illustrating the optimal conditions for our concentration and mixing processes, and a numerical analysis of the flow pattern. To demonstrate the usefulness of the device we apply it to the quantitative detection of nucleic acid sequences associated with Dengue virus serotype 2. We report a limit of detection for Dengue sequences of 30 pM and show excellent specificity against other serotypes.
Extensive disease among potential candidates for hemi‐ablative focal therapy for prostate cancer (2019)

An important number of patients meeting the focal therapy consensus meeting inclusion criteria can present extensive disease. Further studies using targeted biopsies might provide more accurate information about the selection of focal therapy candidates.
Guarding Machine Learning Hardware Against Physical Side-channel Attacks (2022)

Machine learning (ML) models can be trade secrets due to their development cost. Hence, they need protection against malicious forms of reverse engineering (e.g., in IP piracy). With a growing shift of ML to the edge devices, in part for performance and in part for privacy benefits, the models have become susceptible to the so-called physical side-channel attacks. ML being a relatively new target compared to cryptography poses the problem of side-channel analysis in a context that lacks published literature. The gap between the burgeoning edge-based ML devices and the research on adequate defenses to provide side-channel security for them thus motivates our study. Our work develops and combines different flavors of side-channel defenses for ML models in the hardware blocks. We propose and optimize the first defense based on Boolean masking . We first implement all the masked hardware blocks. We then present an adder optimization to reduce the area and latency overheads. Finally, we couple it with a shuffle-based defense. We quantify that the area-delay overhead of masking ranges from 5.4× to 4.7× depending on the adder topology used and demonstrate a first-order side-channel security of millions of power traces. Additionally, the shuffle countermeasure impedes a straightforward second-order attack on our first-order masked implementation.
Total synthesis of two potent anti-inflammatory macrolactones of the oxacyclododecindione type (2015)

An esterification/Friedel-Crafts-cyclization approach permitted the first successful synthetic entry into the oxacyclododecindione subclass of the dihydroxyphenylacetic acid lactone-type natural products. This route allowed the preparation of two highly active anti-inflammatory fungal secondary metabolites 14-deoxyoxacyclododecindione and 14-deoxy-4-dechlorooxacyclododecindione as well as their 14-desmethyl analogues.
IC‐P‐082: TAU AND ALPHA‐SYNUCLEIN SELECTIVE BINDING COMPOUNDS DERIVED FROM APRINOIA THERAPEUTIC'S PM‐PBB3 BINDING‐SITE FOCUSED COMPOUND COLLECTION (2018)

18F-PM-PBB3 is unique among known Tau imaging agents as it has been shown to be useful for PET imaging of Tau lesions in both AD (3R + 4R) and progressive supranuclear palsy (4R) pathologies. Aprinoia, in collaborating with QST, has initiated global clinical studies with 18F-PM-PBB3 in the US, China, Japan and Taiwan. Aprinoia's development of the next generation PM-PBB3 binding-site focused tracer has led to the generation of a ∼1000 compound CNS-biased collection. This collection has been screened against other protein aggregates and targets to generate selective new leads. Here, we describe the screen of both tau and alpha-synuclein (aSyn) selective binding compounds via in vitro generated aSyn and Tau aggregated proteins. Our goal is to provide a single imaging compound able to image multi-isoforms of Tau across various tauopathies. Additionally, we hope to leverage our compound collection to generate tracers for other protein aggregates such as alpha-synuclein, TDP-43 etc to help facilitate diagnosis, track progression and assist clinical trials.
Homobispiperidinyl Derivatives as Liver X Receptor Beta Agonists, Compositions, and Their Use (2017)

ADVERTISEMENT RETURN TO ISSUEPREVPatent HighlightNEXTHomobispiperidinyl Derivatives as Liver X Receptor Beta Agonists, Compositions, and Their UseBenjamin Blass*View Author Information Temple University School of Pharmacy, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, United States*Tel: 215-707-1085. E-mail: [email protected]Cite this: ACS Med. Chem. Lett. 2017, 8, 8, 783–785Publication Date (Web):July 31, 2017Publication History Received3 July 2017Published online31 July 2017Published inissue 10 August 2017https://pubs.acs.org/doi/10.1021/acsmedchemlett.7b00267https://doi.org/10.1021/acsmedchemlett.7b00267editorialACS PublicationsCopyright © 2017 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views602Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (489 KB) Get e-AlertscloseSUBJECTS:Alkyls,Anatomy,Group 17 compounds,Phenyls,Receptors Get e-Alerts
Photosynthesis of Heteropolycyclic Diquinolones Twofold Photodehydrohalogenation Reaction of Benzo[1,2-b:4,5-b']dithiophene- and Dithieno[3,2-b:2',3'-d]thiophenedicarboxanilides (1995)

Heteropolycyclic diquinolones; benzo[l.Z-b:4>-b']dithieno[2',3'-c':2",3"c"]-5,13-N,N'-dimethyldiquinoline-6,14-dione(9) and dithienoI3.2-b:2',3'd]thienyl[2",3"-c:2",3"-c']-5,lO-N~-dimethyldiquinoline-6,9-dione(17) are prepared by twofold photochemical dehydrohalogenation reaction of corresponding benzodithiophene-and dithienothiophenedicarboxanilides; 3,7dichloro-NR-dimethylbenzo[l ,2-b;4J-b']dithiophene-2,6-dicarboxanilie (8) and 3~-dichloro-N~-dimethyldi~eno[3.Z-b:2',3'-dJthiophene-2,6-dicarboxanilide (16).The products of onefold photochemical dehydrohalogenation reaction, anilidoquinolones; 9-chloro-lO-N'-methylanilidobenzo[l~-b:45-b']dithieno[2,3- el-5-N-methylquinolin-6-one (10) and 10-chloro-9-N'-methy~anilidodithieno[3,2b:2',3'-d]thieny1[2",3"-~']-5-N-methylquinolin-6-one (18) were also isolated to prove the mechanism of the reaction.Recently we reporkdl on the applicability of photochemical dehydrohalogenation reactions of some heteropolycyclic dicarboxanilides in producing anilidoquinolones.Photochemical dehydrogenation reaction of anilidoquinolones to produce multicondensed diquinolones didn't occur.In our previous papers we reported on the usefulness of photochemical dehydrocyclisation reaction for preparing quinolones condensed with heterocyclic nuclei: furoquinolones,2 furo-bis-quinolones,~ benzofurophenanthridones and benwthienophenanthridonesP This reaction was examined and applied to aromatic and heteroarornatic anilides5-9 but the yields of the corresponding heterocyclic quinolons were not high.It was shown that the more applicable reaction to produce heterocyclic quinolones, was photochemical dehydrohalogenation reaction which was first reported by Terashima and coworkers.10The authors examined photochemical dehydrohalogenation reaction on a few different heterocyclic amide systems where the halogen atom was situated in the position 2 of the amino part of heterocyclic nuclei or in the same position of the acidic part of the heterocyclic nuclei.The authors noticed that the reaction of photochemical dehydrohalogenation was facilitated when the halogen atom CHO CH=CHCOOH coa- CHO CH=CHCOOHScheme 1 (to be continued)
Toward Accurate and Efficient Road Extraction by Leveraging the Characteristics of Road Shapes (2023)

Automatically extracting roads from very high resolution (VHR) remote sensing images is of great importance in a wide range of remote sensing applications. However, complex shapes of roads ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i.e</i> ., long, geometrically deformed, and thin) always affected the extraction accuracy, which is one of the challenges of road extraction. Based on the insight into road shape characteristics, we propose a novel road shape aware network (RSANet) to achieve efficient and accurate road extraction. First, we introduce the Efficient Strip Transformer Module (ESTM) to efficiently capture the global context to model the long-distance dependence required by the long roads. Second, we design a Geometric Deformation Estimation Module (GDEM) to adaptively extract the context from the shape deformation caused by shooting roads from different perspectives. Third, we provide a simple but effective Road Edge Focal Loss (REF loss) to make the network focus on optimizing the pixels around the road to alleviate the unbalanced distribution of foreground and background pixels caused by the roads being too thin. Finally, we conduct extensive evaluations on public datasets to verify the effectiveness of RSANet and each of the proposed components. Experiments validate that our RSANet outperforms state-of-the-art methods for road extraction in remote sensing images.
Glenoid loosening and migration in reverse shoulder arthroplasty (2019)

When possible, glenoid loosening after RSA should first be treated conservatively, then by glenosphere revision if necessary, and last by salvage hemiarthroplasty Cite this article: Bone Joint J 2019;101-B:461-469.
Crystal structure of silica-ZSM-12 by the combined use of hgh-resolution solid-state MAS NMR spectroscopy and synchrotron x-ray powder diffraction (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal structure of silica-ZSM-12 by the combined use of hgh-resolution solid-state MAS NMR spectroscopy and synchrotron x-ray powder diffractionC. A. Fyfe, H. Gies, G. T. Kokotailo, B. Marler, and D. E. CoxCite this: J. Phys. Chem. 1990, 94, 9, 3718–3721Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/j100372a066https://doi.org/10.1021/j100372a066research-articleACS PublicationsRequest reuse permissionsArticle Views734Altmetric-Citations117LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Clinically important improvement thresholds for Harris Hip Score and its ability to predict revision risk after primary total hip arthroplasty (2016)

HHS is a valid measure of THA outcomes and is responsive to change. Both absolute HHS postoperative scores and HHS score change postoperatively are predictive of revision risk post-primary THA. We defined MCID and moderate improvement thresholds for HHS in this study.
GREATER SUPERFICIAL PETROSAL NERVE DISSECTION (2009)

The temporal dura can be elevated safely with a front-to-back technique to preserve the GSPN and to help maintain the physiological integrity of the facial nerve.
Catecholaminergic nerve fibres in normal and alkali-burned rabbit cornea. (1998)

Although catecholaminergic nerve fibres were observed in all corneal layers, the pattern of catecholaminergic fibres following the creation of a superficial lesion of the cornea seems to suggest that the superficial and deep nerve fibres may have a different distribution.
Titanium cluster polymers as reactive ion etch barriers (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTitanium cluster polymers as reactive ion etch barriersH. E. Katz, M. L. Schilling, S. M. Stein, F. M. Houlihan, R. S. Hutton, and G. N. TaylorCite this: Chem. Mater. 1995, 7, 8, 1534–1538Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/cm00056a020https://doi.org/10.1021/cm00056a020research-articleACS PublicationsRequest reuse permissionsArticle Views148Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Feedback regulation of the spc operon in Escherichia coli: translational coupling and mRNA processing (1988)

The spc operon of Escherichia coli encodes 10 ribosomal proteins in the order L14, L24, L5, S14, S8, L6, L18, S5, L30, and L15. This operon is feedback regulated by S8, which binds near the translation start site of L5 and inhibits translation of L5 directly and that of the distal genes indirectly. We constructed plasmids carrying a major portion of the spc operon genes under lac transcriptional control. The plasmids carried a point mutation in the S8 target site which abolished regulation and resulted in overproduction of plasmid-encoded ribosomal proteins upon induction. We showed that alteration of the AUG start codon of L5 to UAG decreased the synthesis rates of plasmid-encoded distal proteins, as well as L5, by approximately 20-fold, with a much smaller (if any) effect on mRNA synthesis rates, indicating coupling of the distal cistrons' translation with the translation of L5. This conclusion was also supported by experiments in which S8 was overproduced in trans. In this case, there was a threefold reduction in the synthesis rates of chromosome-encoded L5 and the distal spc operon proteins, but no decrease in the mRNA synthesis rate. These observations also suggest that transcription from ribosomal protein promoters may be special, perhaps able to overcome transcription termination signals. We also analyzed the state of ribosomal protein mRNA after overproduction of S8 in these experiments and found that repression of ribosomal protein synthesis was accompanied by stimulation of processing (and degradation) of spc operon mRNA. The possible role of mRNA degradation in tightening the regulation is discussed.
Renal granulomas in systemic vasculitis. EC/BCR Project for ANCA-Assay Standardization. (1997)

Renal granulomas are a relatively infrequent finding in the kidney biopsy. They have been described in a number of syndromes such as Wegener's granulomatosis, anti-GBM glomerulonephritis, and sarcoidosis, and are commonly believed to be indicative of a fulminant clinical course. In leading textbooks, diverse definitions of renal granulomas are presented, which has led to controversies in identifying them. This, in combination with their rare occurrence, makes it difficult for the general pathologist to identify them. We present the clinical data of 16 patients with renal granulomas, from a total group of 157 patients with systemic vasculitis. Their renal functioning was not significantly different from the other 141 patients in whose renal biopsies renal granulomas were present. Furthermore, we present two practical definitions for the recognition of renal granulomas in the kidney biopsy, and we show a number of examples of their various histopathological shapes.
Arc welding of mild steel in pressurised Ar‐O2atmospheres (1993)

Mild steel was welded in pressurized CO2 atmospheres in the pressure range from 1 to 30 atm using a solid wire of 1.6 mm dia. The effect of ambient pressure on the melting rate of electrode wire, and the geometry, chemical compositions and mechanical properties of weld metals were studied.The results obtained are as follows:1) The melting rate of an electrode wire increases with the increase of ambient pressure up to a certain pressure.2) The bead width decreases with the increase of ambient pressure.3) The penetration depth and fused area of base metals increase with increasing the ambient pressure up to a certain pressure.4) The melting rate of electrode wire and bead geometry appear to be affected with the metal transfer mode of electrode wire in pressurized CO2 atmospheres.5) Oxygen content of weld metals increase with the increase of ambient pressure.6) The charpy impact values of weld metals decrease with increasing the ambient pressure.
Comparative analysis of the expression of the epstein‐barr virus (EBV) anti‐apoptotic gene BHRF1 in nasopharyngeal carcinoma and EBV‐related lymphoid diseases (2001)

Epstein-Barr virus (EBV) has been identified in a wide range of neoplastic and non-neoplastic disorders. The EBV open reading frame BHRF1 encodes a protein with partial sequence and functional homology to the anti-apoptotic onco-protein Bcl-2 and may therefore have a role in the proliferation of EBV positive cells. We have developed a rat monoclonal antibody against pBHRF1, which can detect BHRF1 in paraffin sections. While a number of mutant versions of BHRF1 were recognised, the monoclonal did not detect the BHRF1 homologue encoded by Herpesvirus papio or two mutants with deletions in the BH2 region. This novel rat monoclonal antibody (6A9) was used to examine tissue sections from 39 cases of non-keratinising undifferentiated nasopharyngeal carcinoma (NPC), 6 cases of metastatic NPC, 7 cases of EBV-positive NPC with squamous differentiation from Chinese patients, 15 cases of EBV-positive post-transplant lymphoproliferative disorder (PTLD), 6 EBV-containing lymphoblastoid cell lines, and 2 cases of oral hairy leukoplakia (OHL). In 11 cases of undifferentiated NPC, RT-PCR data were available for comparison with the immunohistochemistry. Both cases of OHL and two cases of LCL were positive for BHRF1 but none of the PTLD showed positive staining. All cases of undifferentiated NPC were positive for Bcl-2 but only one BHRF1 positive cell was identified in 1 of 39 cases of primary undifferentiated NPC. The 6A9 antibody produced less background staining and no nuclear positivity compared with the commercially available mouse monoclonal 5B11. It is concluded that BHRF1 can not be detected by immunohistochemistry in NPC and therefore it appears not to play a significant anti-apoptotic role in the progression of this EBV-associated tumour. The 6A9 monoclonal appears to be superior to 5B11 for the detection of pBHRF1 in tissue sections.