gebhart/patrepeval huggingface dataset:
Metabolic bioengineering: glycans and glycoconjugates (2018)

The application of metabolic engineering to the production of glycans and glycoconjugates is the subject of this of Emerging Topics in Life Science. The lack of availability of these complex carbohydrate or saccharide structures has severely limited the development of the field of glycobiology. This issue contains eight articles from respected scientists in the field that cover this new and emerging field.
APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa (2018)

Recessive dystrophic epidermolysis bullosa (RDEB) is a rare inherited skin and mucous membrane fragility disorder complicated by early-onset, highly malignant cutaneous squamous cell carcinomas (SCCs). The molecular etiology of RDEB SCC, which arises at sites of sustained tissue damage, is unknown. We performed detailed molecular analysis using whole-exome, whole-genome, and RNA sequencing of 27 RDEB SCC tumors, including multiple tumors from the same patient and multiple regions from five individual tumors. We report that driver mutations were shared with spontaneous, ultraviolet (UV) light-induced cutaneous SCC (UV SCC) and head and neck SCC (HNSCC) and did not explain the early presentation or aggressive nature of RDEB SCC. Instead, endogenous mutation processes associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) deaminases dominated RDEB SCC. APOBEC mutation signatures were enhanced throughout RDEB SCC tumor evolution, relative to spontaneous UV SCC and HNSCC mutation profiles. Sixty-seven percent of RDEB SCC driver mutations was found to emerge as a result of APOBEC and other endogenous mutational processes previously associated with age, potentially explaining a >1000-fold increased incidence and the early onset of these SCCs. Human papillomavirus-negative basal and mesenchymal subtypes of HNSCC harbored enhanced APOBEC mutational signatures and transcriptomes similar to those of RDEB SCC, suggesting that APOBEC deaminases drive other subtypes of SCC. Collectively, these data establish specific mutagenic mechanisms associated with chronic tissue damage. Our findings reveal a cause for cancers arising at sites of persistent inflammation and identify potential therapeutic avenues to treat RDEB SCC.
Synthesis of 2‐substituted 4‐quinazolone‐5‐carboxylic acids as inhibitors of DNA‐gyrase (1997)

Abstract A series of 4‐quinazolone‐5‐carboxylic acids were designed as bacterial DNA gyrase inhibitors. The syntheses of the target compounds were accomplished by reacting 3‐aminophthalimide with aroyl chlorides followed by rearrangement of the resulting 3‐acylaminophthalimides under basic conditions. The designed compounds showed moderate DNA gyrase inhibitory activity.
Phase transition in amphiphilic poly(N-isopropylacrylamide): controlled gelation (2018)

Thermally reversible gelation of polymers is of converging interest in both the fundamental research and practical biomedical or pharmaceutical applications. While the block structure is widely reported to favor gelation, there are few studies regarding the behavior of amphiphilic random copolymers. Herein, hydrophobically modified poly(N-isopropylacrylamide) (pNIPAM) polymers were designed and synthesized by reversible addition-fragmentation chain transfer (RAFT) copolymerization of NIPAM and butyl acrylate (BA). A library of polymer systems was created by varying the BA : NIPAM ratio, molecular weight (Mw) and concentrations. While a coil-to-globule transition induced microphase separation occurred in the dilute solution, diverse phase behaviors were observed by phase diagram study. A transparent gel phase was identified in p(NIPAM-co-BA) systems, which was missing in its block counterpart pNIPAM-b-pBA, and existed over a wider temperature range with increased BA content, Mw and concentrations. A dynamic rheological analysis revealed that the gel properties were strongly dependent on temperature, which regulated the interchain hydrophobic association, and the gel proved to be highly elastic, stable, reversible and self-healable under the optimized conditions. The p(NIPAM-co-BA) system will be highly desirable for injectable in situ forming hydrogel materials, and the study demonstrated here can be potentially extended to other amphiphilic pNIPAM copolymers.
Design method for assembly-insensitive freeform reflective optical systems (2018)

The sensitivity of an optical system to assembly errors can greatly affect the actual image quality. The system design must be changed if its tolerance for assembly errors is too tight. In this paper, we present an automated design method for initial systems of freeform reflective optical systems that are insensitive to assembly errors. By this method, an assembly-insensitive initial system comprised of surfaces with different types (sphere, aspheric, freeform) can be obtained directly without human interaction. To illustrate the design process, an assembly-insensitive off-axis optical system that has two freeform surfaces and one spherical surface is designed, which shows the effectiveness of the proposed method.
Comprehensive backscattering characteristics analysis for quantitative ultrasound with an annular array: a basic study on homogeneous scattering phantom (2019)

High-frequency ultrasound (HFU, >20 MHz) and quantitative ultrasound (QUS) methods permit a means to understand the relationship between anatomical and acoustic characteristics. In our previous research, we showed that analyzing the acoustic scattering with HFU was an effective method for noninvasive diagnosis. However, the depth of field (DOF) of HFU transducers was limited, which constrains the range of QUS analysis. In this study, we seek to improve the accuracy of HFU, QUS-based parameters on the envelope statistics and frequency-based analysis by using an annular array that allows for an extended DOF. A 20-MHz annular-array transducer with five elements was employed to obtain signals which were beamformed in post-processing. Two kinds of low concentration scattering phantoms were scanned with 30-<i>μ</i>m step size. Two QUS analysis techniques were employed: the Nakagami distribution and the reflector method. The results demonstrated that the annular array provides a stable analysis over an extended axial range.
Program Synthesis using Natural Language (2015)

Interacting with computers is a ubiquitous activity for millions of people. Repetitive or specialized tasks often require creation of small, often one-off, programs. End-users struggle with learning and using the myriad of domain-specific languages (DSLs) to effectively accomplish these tasks. We present a general framework for constructing program synthesizers that take natural language (NL) inputs and produce expressions in a target DSL. The framework takes as input a DSL definition and training data consisting of NL/DSL pairs. From these it constructs a synthesizer by learning optimal weights and classifiers (using NLP features) that rank the outputs of a keyword-programming based translation. We applied our framework to three domains: repetitive text editing, an intelligent tutoring system, and flight information queries. On 1200+ English descriptions, the respective synthesizers rank the desired program as the top-1 and top-3 for 80% and 90% descriptions respectively.
Prediciting Cone Quantum Catches Under Illumination Change (2003)

Given LMS cone quantum catches from a surface under a first illuminant what is the best method of predicting what the corresponding quantum catches will be for the same surface under a second illuminant given only the quantum catches of a white surface under both illuminants? The von Kries rule is one well known method. In this paper, two new prediction methods along with a variation on an existing third method are introduced and then compared experimentally. In contrast to the von Kries rule which is equivalent to a diagonal transformation, all three methods estimate a full 3-by-3 linear transformation mapping LMS values between illuminants. All the new methods perform better than the von Kries rule.
COLLAGENOUS COLITIS, BUT NOT LYMPHOCYTIC COLITIS, IS ASSOCIATED WITH CIGARETTE SMOKING (2004)

Purpose: Crohn's disease is associated with cigarette smoking whereas ulcerative colitis is associated with non-smoking. It is unknown if any association exists between microscopic colitis (MC) and smoking. We studied the association between smoking status and the diagnosis of MC in a population-based cohort. Methods: The Rochester Epidemiology Project, a unique medical records linkage system providing data on all health care for a defined population in Olmsted County, MN was used to identify all county residents with a diagnosis of MC between 1/1/85-12/31/01. These biopsies were reviewed by an expert GI pathologist for confirmation. In addition, all colon biopsies for evaluation of diarrhea in county residents over the same time period were reviewed be sure that cases were not missed. Smoking status was determined by review of the medical record at the time that MC was diagnosed. The smoking status of an age-, gender-, and calendar year-matched control group of county residents without MC was assessed for comparison using hazard ratios. Results: 135 cases were identified (89 lymphocytic colitis [LC] and 46 collagenous colitis [CC]). Median age was 68 (23–96); 69% were women. The hazard ratios for current or former smoking in cases compared to controls are listed in Table 1. For LC, there was no significant association with smoking status. For CC, the association with current smoking was significant (p = 0.04).Table: Hazard Ratios and 95% confidence intervals CurrentConclusions: In this population-based cohort, the diagnosis of CC was associated with current but not former cigarette smoking. In LC, there was no association with smoking status. In these very similar clinicopathologic entities, cigarette smoking may be one factor that favors the deposition of subepithelial collagen.
Effects of experimental pseudorabies virus infection on vaccinated pregnant sows. (1987)

In regard to field problems, a study was done to determine the effects of an infection with virulent Pseudorabies virus (PRV) on pregnant sows vaccinated with an inactivated virus vaccine. Three routes of viral inoculation have been tested: intranasal, intra-uterine and intra-fetal. The nasal infection did not allow to induce pregnancy disorders observed on the field on pregnant sows. After insemination with semen mixed with PRV, abortion was observed on one of the two immune sows. In this one, viral antigen has been identified on vagina, sacral and trigeminal ganglia. The second sow, slaughtered 2 months after infection presented a normal pregnancy. The results of intra-fetal inoculations showed that the vaccination does not prevent the spread of the virus from fetus to fetus and the pregnancy failure. These trials allowed to study the spread and repartition of the virus in the genital tract. PRV antibodies have been detected in the vaginal and uterine washing fluids as well as the follicular fluids of infected animals, vaccinated or not.
How to Hide Circuits in MPC: An Efficient Framework for Private Function Evaluation. (2013)

We revisit the problem of general-purpose private function evaluation (PFE) wherein a single party P1 holds a circuit C, while each Pi for 1 ≤ i ≤ n holds a private input xi, and the goal is for a subset (or all) of the parties to learn C(x1,..., xn) but nothing else. We put forth a general framework for designing PFE where the task of hiding the circuit and securely evaluating its gates are addressed independently: First, we reduce the task of hiding the circuit topology to oblivious evaluation of a mapping that encodes the topology of the circuit, which we refer to as oblivious extended permutation (OEP) since the mapping is a generalization of the permutation mapping. Second, we design a subprotocol for private evaluation of a single gate (PFE for one gate), which we refer to as private gate evaluation (PGE). Finally, we show how to naturally combine the two components to obtain efficient and secure PFE. We apply our framework to several well-known general-purpose MPC constructions, in each case, obtaining the most efficient PFE construction to date, for the considered setting. Similar to the previous work we only consider semi-honest adversaries in this paper. • In the multiparty case with dishonest majority, we apply our techniques to the seminal GMW protocol [GMW87] and obtain the first general-purpose PFE with linear complexity in the circuit
Marine Indole Alkaloids: Potential New Drug Leads for the Control of Depression and Anxiety (2010)

ADVERTISEMENT RETURN TO ISSUEReviewNEXTMarine Indole Alkaloids: Potential New Drug Leads for the Control of Depression and AnxietyAnna J. Kochanowska-Karamyan and Mark T. Hamann*View Author Information Departments of Pharmacognosy, Pharmacology, Chemistry & Biochemistry, and the Research Institute of Pharmaceutical Sciences, School of Pharmacy, the University of Mississippi, University, Mississippi 38677* To whom correspondence should be addressed. E-mail: [email protected]Cite this: Chem. Rev. 2010, 110, 8, 4489–4497Publication Date (Web):April 9, 2010Publication History Received3 June 2009Published online9 April 2010Published inissue 11 August 2010https://pubs.acs.org/doi/10.1021/cr900211phttps://doi.org/10.1021/cr900211preview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views18350Altmetric-Citations1668LEARN 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 SUBJECTS:Molecules,Neurophysiology,Organic compounds,Reaction products,Receptors Get e-Alerts
ChemInform Abstract: Aromatic Versions of Claisen Rearrangement of Lactonic Silyl Enolates. (1986)

Abstract Aus dem Cyclohexanon‐Derivat (I) werden mit den Furyl‐lithium‐Derivaten (II) die Lactone (III) hergestellt, aus denen durch Silylierung die Ketenacetale (IV) erhalten werden.
Femtosecond laser-induced formation of submicrometer spikes on a semiconductor substrate (2023)

The present invention generally provides semiconductor substrates having submicron-sized surface features generated by irradiating the surface with ultra short laser pulses. In one aspect a method of processing a semiconductor substrate is disclosed that includes placing at least a portion of a surface of the substrate in contact with a fluid, and exposing that surface portion to one or more femtosecond pulses so as to modify the topography of that portion. The modification can include, e.g., generating a plurality of submicron-sized spikes in an upper layer of the surface.
The beneficial effect of alpha-blockers for ureteral stent-related discomfort: systematic review and network meta-analysis for alfuzosin versus tamsulosin versus placebo (2015)

This study was carried out a network meta-analysis of evidence from randomized controlled trials (RCTs) to evaluate stent-related discomfort in patients with alfuzosin or tamsulosin versus placebo. Relevant RCTs were identified from electronic databases. The proceedings of appropriate meetings were also searched. Seven articles on the basis of RCTs were included in our meta-analysis. Using pairwise and network meta-analyses, comparisons were made by qualitative and quantitative syntheses. Evaluation was performed with the Ureteric Stent Symptoms Questionnaire to assess the urinary symptom score (USS) and body pain score (BPS). One of the seven RCTs was at moderate risk of bias for all quality criteria; two studies had a high risk of bias. In the network meta-analysis, both alfuzosin (mean difference [MD];−4.85, 95 % confidence interval [CI];−8.53–−1.33) and tamsulosin (MD;−8.84, 95 % CI;−13.08–−4.31) showed lower scores compared with placebo; however, the difference in USS for alfuzosin versus tamsulosin was not significant (MD; 3.99, 95 % CI;−1.23–9.04). Alfuzosin (MD;−5.71, 95 % CI;−11.32–−0.52) and tamsulosin (MD;−7.77, 95 % CI;−13.68–−2.14) showed lower scores for BPS compared with placebo; however, the MD between alfuzosin and tamsulosin was not significant (MD; 2.12, 95 % CI;−4.62–8.72). In the rank-probability test, tamsulosin ranked highest for USS and BPS, and alfuzosin was second. The alpha-blockers significantly decreased USS and BPS in comparison with placebo. Tamsulosin might be more effective than alfuzosin.
Performance-optimized optical bidirectional backplane bus for multiprocessor systems (1996)

We review the recent results on the design and implementation of the performance-optimized bidirectional optical backplane bus aimed at high speed multiprocessor systems. It employs an array of multiplexed holograms, in conjunction with a waveguiding plate within which cascaded fanouts are generated. Data transfer rate of 1.2 Gbit/sec at 1300 nm is demonstrated with a single bus line for a system composed of nine boards. Packaging-related issues and misalignment effects are addressed. Theoretical treatment to minimize fluctuations among the received powers at each board was carried out and the overall performance was optimized. We also introduce a hybrid optical backplane with multiple bus lines. The hybrid backplane maintains the same waveguiding structure, and exploits optoelectronic array devices. A new demonstration system is being implemented. The optical backplane that we developed is transparent to higher level bus protocols, thus can support standard backplane buses such as Futurebus+, Multibus II, and VMEbus.
Synthesis, Potency, and In Vivo Profiles of Quinoline Containing Histamine H3Receptor Inverse Agonists (2007)

A new structural series of histamine H3 receptor antagonist was developed. The new compounds are based on a quinoline core, appended with a required basic aminoethyl moiety, and with potency- and property-modulating heterocyclic substituents. The analogs have nanomolar and subnanomolar potency for the rat and human H3R in various in vitro assays, including radioligand competition binding as well as functional tests of H3 receptor-mediated calcium mobilization and GTPgammaS binding. The compounds possessed favorable drug-like properties, such as good PK, CNS penetration, and moderate protein binding across species. Several compounds were found to be efficacious in animal behavioral models of cognition and attention. Further studies on the pharmaceutic properties of this series of quinolines discovered a potential problem with photochemical instability, an issue which contributed to the discontinuation of this series from further development.
ChemInform Abstract: Very High Density Sensing Arrays (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Inflammatory Bowel Disease in the Setting of Autoimmune Pancreatitis (2007)

Purpose: Though there have been scattered case reports of inflammatory bowel disease (IBD) occurring in patients with autoimmune pancreatitis (AIP), the prevalence of IBD in patients with AIP is unknown. We sought to better characterize the putative association between the conditions. Methods: Medical records of 71 patients with AIP meeting the HISORt criteria (Clin Gastroenterol Hepatol 2006;4:1010–1016) were reviewed to identify patients with endoscopic and biopsy evidence of IBD. Clinical features and outcomes were described. Colon samples were immunostained to identify IgG4 positive cells. Results: 4 patients with AIP (5.6%) had a diagnosis of IBD; 3 had ulcerative colitis (UC) and 1 had Crohns disease (CD). Diagnosis of IBD preceded that of AIP in 3 patients, and was simultaneous in 1. Serum IgG4 was elevated in 1 of 2 patients with AIP and IBD, compared to 31 of 44 in those with AIP alone. Only 1 of 4 patients with AIP and IBD had a positive p-ANCA. Primary sclerosing cholangitis-like intra-hepatic biliary strictures were seen in 1 of 4 patients with AIP and IBD. 2 patients treated for AIP with a standard prednisone taper had recurrence of AIP, with 1 requiring 6-mercaptopurine for long-term steroid-sparing treatment. The other 2 patients underwent Whipple procedures, with 1 recurrence of AIP. All 3 UC patients presented with extensive colitis, with total colectomy for refractory colitis necessary in 2 of 3 patients. Colon samples from 1 patient with UC and 1 patient with CD were available for review. 10 IgG4 positive cells/high power field were noted on the colon sample from the patient with UC; none were seen on the CD sample. Conclusion: As recognition of AIP increases, several important clinical associations become apparent, including the relationship between AIP and IBD. Almost 6% of patients in our cohort of 71 patients with proven AIP had a diagnosis of IBD, compared to a prevalence of approximately 0.4 – 0.5% in the general population, potentially implying a 12-fold to 15-fold increase in risk. Interestingly, all 3 UC-AIP patients presented with extensive colitis; two with refractory colitis requiring total colectomy. The finding of IgG4 positive cells on colon biopsy suggests that IBD may represent an extra pancreatic manifestation of AIP. Further studies are needed to determine if IBD is an extra-pancreatic manifestation of AIP or an associated disease.
Synthesis of Fluorene-Based Semiconducting Copolymers for Organic Solar Cells (2012)

Semiconducting polymers composed of 2,2'-(9,9-dioctyl-9H-fluorene-2,7-diyl)dithiophenes (F8T2s) and (2E,2'E)-3,3'-(2,5-bis(octyloxy)-1,4-phenylene) bis(2-(5-bromothiophene-2-yl)acrylonitrile)s (OPTANs) have been synthesized through Pd(O)-catalyzed Suzuki coupling polymerization by controlling the monomer ratio. The synthesized polymers were confirmed to exhibit good solubility in common solvents, simple processability, and thermal stability up to 350 degrees C. The highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs), and optical band-gap energies were determined using cyclic voltammetry (CV) and UV-visible spectrometry. The synthesized polymers showed their maximum absorption and edge at around 520 and 650 nm, respectively. The optical band-gap energies of the polymers were determined to be 1.89 eV. Bulk heterojunction organic solar cells were fabricated using the conjugated polymer as the electron donor, and 6,6-phenyl C61-butyric acid methylester (PC61BM) or 6,6-phenyl C71-butyric acid methylester (PC71BM) as the electron acceptor. The power conversion efficiencies (PCEs) of the solar cells based on polymer:PC71BM (1:1) and polymer:PC71BM (1:2) were 0.68% and 1.22%, respectively, under air mass 1.5 global (AM 1.5 G) illumination at 100 mW/cm2.