gebhart/patrepeval huggingface dataset:
LINKER: a web server to generate peptide sequences with extended conformation (2004)

LINKER was developed as an online server to assist biomedical researchers to design linker sequences for constructing functional fusion proteins. The program automatically generates a set of peptide sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. In addition to the desired linker sequence length, the web interface provides a number of optional input parameters so that the users may enhance sequence selection based on the requirements of specific applications. The output of LINKER includes a list of peptide sequences with specified length and sequence characteristics. A graphical subroutine was implemented to highlight the chemical features of every linker sequence by hydrophobicity plots. LINKER can be accessed at http://astro.temple.edu/~feng/Servers/BioinformaticServers.htm.
Localization and tracking in known large environments using portable real-time 3D sensors (2016)

Ego-motion estimation and localization in large environments are key components in any assistive technology for real-time user orientation and navigation. We consider the case where a large known environment is explored without a priori assumptions on the initial location. In particular we propose a framework that uses a single portable 3D sensor to solve the place recognition problem and continuously tracks its position even when leaving the known area or when significant changes occur in the observed environment. We cast the place recognition step as a classification problem and propose an efficient search space reduction considering only navigable areas where the user can be localized. Classification hypotheses are then discarded exploiting temporal consistency w.r.t. a relative tracker that exploits only the sensor input data. The solution uses a compact classifier whose representation scales well with the map size. After being localized, the user is continuously tracked exploiting the known environment using an efficient data structure that provides constant access time for nearest neighbor searches and that can be streamed to keep only the local region close to the last known position in memory. Robust results are achieved by performing a geometrically stable selection of points, efficiently filtering outliers and integrating the relative tracker based on previous observations. We experimentally show that such a framework provides good localization results and that it scales well with the environment map size yielding real-time performance for both place recognition and tracking.
Verification of the IDI-MRSA Assay for Detecting Methicillin-Resistant Staphylococcus aureus in Diverse Specimen Types in a Core Clinical Laboratory Setting (2006)

The IDI-MRSA assay has a sensitivity of 96% and a specificity of 96% when used to screen patients at extranasal sites. This verification study used previously unverified swabs and was undertaken in a core medical laboratory using nonmicrobiology technologists trained in sample processing, molecular laboratory work flow, and PCR practice.
Defensins promote fusion and lysis of negatively charged membranes (1993)

Defensins, a family of cationic peptides isolated from mammalian granulocytes and believed to permeabilize membranes, were tested for their ability to cause fusion and lysis of liposomes. Unlike alpha-helical peptides whose lytic effects have been extensively studied, the defensins consist primarily of beta-sheet. Defensins fuse and lyse negatively charged liposomes but display reduced activity with neutral liposomes. These and other experiments suggest that fusion and lysis is mediated primarily by electrostatic forces and to a lesser extent, by hydrophobic interactions. Circular dichroism and fluorescence spectroscopy of native defensins indicate that the amphiphilic beta-sheet structure is maintained throughout the fusion process. Taken together, these results support the idea that protein-mediated membrane fusion depends not only on hydrophobic and electrostatic forces but also on the spatial arrangement of the amino acid residues to form a three-dimensional amphiphilic structure, which promotes the efficient mixing of the lipids between membranes. A molecular model for membrane fusion by defensins is presented, which takes into account the contributions of electrostatic forces, hydrophobic interactions, and structural amphiphilicity.
Purification of the Escherichia coli type 1 pilin and minor pilus proteins and partial characterization of the adhesin protein (1988)

Type 1 pili of Escherichia coli contain three integral minor proteins with apparent molecular weights (Mr) of 28,000 (28K protein), 16,500, and 14,500 attached to rods composed of Mr-17,000 pilin subunits (Hanson and Brinton, Nature [London] 322:265-268). We describe here an improvement on our earlier method of pilus purification, which gives higher yields and higher purity. Also reported are methods allowing fractionation of intact type 1 pili into rods of pure pilin and free minor proteins, as well as fractionation of the 28K tip adhesion protein from the 16.5K and 14.5K proteins. We have determined the amino acid composition and amino-terminal sequence of the adhesion protein. This sequence shows limited homology with the amino-terminal sequences of several E. coli pilins, including type 1.
Preparation and reactions of functionalized benzylic organometallics of zinc and copper (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and reactions of functionalized benzylic organometallics of zinc and copperScott C. Berk, Ming Chang P. Yeh, Nakcheol Jeong, and Paul KnochelCite this: Organometallics 1990, 9, 12, 3053–3064Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/om00162a016https://doi.org/10.1021/om00162a016research-articleACS PublicationsRequest reuse permissionsArticle Views2972Altmetric-Citations93LEARN 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
Bioengineered non-coding RNA agent (BERA) in action (2016)

Non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are important players in the control of gene regulation and represent novel promising therapeutic targets or agents for the treatment of various diseases. While synthetic ncRNAs are predominately utilized, the effects of excessive artificial modifications on higher-order structures, activities and toxicities of ncRNAs remain uncertain. Inspired by recombinant protein technology allowing large-scale bioengineering of proteins for research and therapy, efforts have been made to develop practical and effective means to bioengineer ncRNA agents. The fermentation-based approaches shall offer biological ncRNA agents with natural modifications and proper folding critical for ncRNA structure, function and safety. In this article, we will summarize current recombinant RNA platforms to the production of ncRNA agents including siRNAs and miRNAs. The applications of bioengineered ncRNA agents for basic research and potential therapeutics are also discussed.
Test Exclusions Develop into Test Scandal (2005)

Many states used test results to hold schools accountable, with the stakes for children, teachers and administrators becoming higher. High school principal Kimberly Reeves had to show substantial progress in raising achievement scores to keep her school off the state's low-performing list and to help the district maintain positive community relations. Reeves declined to test several high school students who were failing core courses and would be required to retake them the following year. The principal had not considered this a form of cheating, even though it ran counter to the spirit of the state testing guidelines. Her decision could have unintended consequences for the district and the local economy.
Lack of an effect of nephron-specific deletion of adenylyl cyclase 3 on renal sodium and water excretion or arterial pressure (2015)

Adenylyl cyclase (AC)-stimulated cAMP plays a key role in modulating transport and channel activity along the nephron. However, the role of individual adenylyl cyclase isoforms in such regulation is largely unknown. Since adenylyl cyclase 3 (AC3) is expressed throughout nephron, we investigated its role in the physiologic regulation of renal Na(+) and water transport. Mice were generated with inducible nephron knockout of AC3 (AC3 KO) by breeding mice with loxP-flanked critical exons in the Adcy3 gene with mice expressing Pax8-rtTA and LC-1 transgenes. After doxycycline treatment at 1 month of age, nephron AC3 KO mice had 100% Adcy3 gene recombination in all renal tubule segments, but not in glomeruli. Sodium intake, urinary Na(+) excretion, glomerular filtration rate, and blood pressure were similar between nephron KO mice and the controls during normal, high, and low Na(+) diets. Plasma renin concentration was not different between the two groups during varied Na(+) intake. Moreover, there were no differences in urine volume and urine osmolality between the two genotypes during normal or restricted water intake. In conclusion, these data suggested that AC3 is not involved in the physiological regulation of nephron Na(+) and water handling.
A Convenient Synthesis of 4-Aminomethyl-L-Phenylalanine (1991)

Abstract N-Boc-4-Aminomethyl-L-phenylalanine is prepared from N-Boc-4-Iodophenylalanine in 78% yield over three steps. The method features an efficient Pd-catalyzed carbonylation, oxime formation, and subsequent catalytic reduction employing an ethanol/water/acetic acid solvent system which is crucial to successful reaction.
Effect of Molecular Conformations on the Adsorption Behavior of Gold-Binding Peptides (2008)

Despite extensive recent reports on combinatorially selected inorganic-binding peptides and their bionanotechnological utility as synthesizers and molecular linkers, there is still only limited knowledge about the molecular mechanisms of peptide binding to solid surfaces. There is, therefore, much work that needs to be carried out in terms of both the fundamentals of solid-binding kinetics of peptides and the effects of peptide primary and secondary structures on their recognition and binding to solid materials. Here we discuss the effects of constraints imposed on FliTrx-selected gold-binding peptide molecular structures upon their quantitative gold-binding affinity. We first selected two novel gold-binding peptide (AuBP) sequences using a FliTrx random peptide display library. These were, then, synthesized in two different forms: cyclic (c), reproducing the original FliTrx gold-binding sequence as displayed on bacterial cells, and linear (l) dodecapeptide gold-binding sequences. All four gold-binding peptides were then analyzed for their adsorption behavior using surface plasmon resonance spectroscopy. The peptides exhibit a range of binding affinities to and adsorption kinetics on gold surfaces, with the equilibrium constant, Keq, varying from 2.5x10(6) to 13.5x10(6) M(-1). Both circular dichroism and molecular mechanics/energy minimization studies reveal that each of the four peptides has various degrees of random coil and polyproline type II molecular conformations in solution. We found that AuBP1 retained its molecular conformation in both the c- and l-forms, and this is reflected in having similar adsorption behavior. On the other hand, the c- and l-forms of AuBP2 have different molecular structures, leading to differences in their gold-binding affinities.
Sex bias occurrence of hepatocellular carcinoma in Poly7 molecular subclass is associated with EGFR (2012)

Sex bias occurrence of HCC associated with EGFR was confirmed in experimental animals using the SB transposon system in a reverse genetic approach. This study provides evidence for the role of EGFR in sex bias occurrences of liver cancer and as the driver mutational gene in the Poly7 molecular subclass of human HCC.
Tris(chalkogeno)carbenium‐Ionen [C(XR)3]+(X = O, S, Se, Te): ein experimenteller und quantenchemischer Vergleich (1996)

[C(OR) 3 ]+‐Ionen werden anders stabilisiert als [C(XR) 3 ] + ‐lonen (X = S, Se, Te) . Während bei RO‐substituierten Carbenium‐Ionen hauptsächlich die Polarität der C δ+ ‐O δ− ‐Bindung die Stabilität bestimmt, ist die C‐X‐Bindung in den homologen S‐, Se‐ und Te‐haltigen Ionen umgepolt, und die Stabilisierung erfolgt durch den σ‐ und π‐dativen Einfluß der Chalkogenzentren. Dies folgt aus ab‐initio‐Rechnungen an [C(XH) 3 ] + ‐Ionen und experimentellen Untersuchungen an den neuen Verbindungen [C(XR) 3 ][PF 6 ] (X  S, Se, Te; R  2,4,6‐ i Pr 3 C 6 H 2 ).
Reduced Oxidative Pentose Phosphate Pathway Flux in Recombinant Xylose-Utilizing Saccharomyces cerevisiae Strains Improves the Ethanol Yield from Xylose (2002)

In recombinant, xylose-fermenting Saccharomyces cerevisiae, about 30% of the consumed xylose is converted to xylitol. Xylitol production results from a cofactor imbalance, since xylose reductase uses both NADPH and NADH, while xylitol dehydrogenase uses only NAD(+). In this study we increased the ethanol yield and decreased the xylitol yield by lowering the flux through the NADPH-producing pentose phosphate pathway. The pentose phosphate pathway was blocked either by disruption of the GND1 gene, one of the isogenes of 6-phosphogluconate dehydrogenase, or by disruption of the ZWF1 gene, which encodes glucose 6-phosphate dehydrogenase. Decreasing the phosphoglucose isomerase activity by 90% also lowered the pentose phosphate pathway flux. These modifications all resulted in lower xylitol yield and higher ethanol yield than in the control strains. TMB3255, carrying a disruption of ZWF1, gave the highest ethanol yield (0.41 g g(-1)) and the lowest xylitol yield (0.05 g g(-1)) reported for a xylose-fermenting recombinant S. cerevisiae strain, but also an 84% lower xylose consumption rate. The low xylose fermentation rate is probably due to limited NADPH-mediated xylose reduction. Metabolic flux modeling of TMB3255 confirmed that the NADPH-producing pentose phosphate pathway was blocked and that xylose reduction was mediated only by NADH, leading to a lower rate of xylose consumption. These results indicate that xylitol production is strongly connected to the flux through the oxidative part of the pentose phosphate pathway.
Actively mode-locked GaInAsP laser with subpicosecond output (1988)

Mode-locked semiconductor lasers are needed for fiber-optic communication systems using external modulation and for time division multiplexing. Active mode locking of semiconductor lasers has produced pulses as short as 4.6 ps.1,2 Previous to the work reported here, shorter pulses have only been demonstrated with additional pulse shaping mechanisms such as saturable absorbers made from damaged or multiple-quantum-well material.3,4 With a combination of active and passive mode-locking schemes, trains of pulses as short as 0.65 ps have been obtained,3 and external pulse compression of passively mode-locked lasers has yielded pulses as short as 0.83 ps.4
Efficacy and safety of patisiran for familial amyloidotic polyneuropathy: a phase II multi-dose study (2015)

NCT01617967 .
Morphological assessment of neuronal aggregates in the striatum of the rat (1991)

Regional variations in cell-packing density, culminating in the formation of cell clusters, is now a recognized morphological characteristic of the striatum that has been correlated, in some instances, with either regional histochemical variations or the distribution pattern of afferent fiber systems, or both. Within these cluster regions a further level of organization exists, in the form of discrete neuronal aggregates. The light microscopic morphology of these neurons and the nature of their intercellular contacts at the electron microscope level form the focus of this report. The neurons composing such aggregates are characterized by contiguous soma-somatic or soma-dendritic contact with extended regions of junctionlike symmetrical and consistent contacts where the distance between the cytoplasmic membranes of apposing neurons narrows to as close as 7 nm. Coated vesicles close to the contact areas are common. Three-dimensional computer reconstructions of serial 1 micron sections through aggregates in either the caudatoputamen or nucleus accumbens reveal "chains" of contiguous cells that frequently involve as many as 60 neurons. These contiguous cell aggregates are discrete entities within the larger clusters or islands. It is postulated that the cellular aggregates may represent the fundamental level of striatal organization and may be local modules for intrinsic information processing, modifying extrinsic data processed through the biochemical compartmentalization of the striatum imparted by striosomes, neuropeptides, and dopaminergic, thalamic and cortical afferents.
Privacy-preserving computation of disease risk by using genomic, clinical, and environmental data (2013)

Abstract—According to many scientists and clinicians, genomics is the “next big thing ” in the field of medicine. On one hand, decreasing costs in genome sequencing has been paving the way to better preventive and personalized medicine. On the other hand, genomic data also raises serious privacy concerns, as it is the ultimate identifier of an individual and it contains privacy-sensitive data (e.g., disease predispositions, ancestry information). Thus, it is necessary to find ways of using genomic data without abusing the genomic privacy of individuals. To get a more comprehensive medical assessment, genomic information must be combined with other clinical and environmental data (such as demographic information, family history, disease history, laboratory test results, etc.) that are also privacy-sensitive (e.g., HIV status of an individual) and need to be treated as such. Focusing on disease risk tests, in this paper, we propose a privacy-preserving system for storing and processing genomic, clinical, and environmental data by using homomorphic encryption and privacy-preserving integer comparison. We implement the proposed system using real patient data and reliable disease risk factors. In particular, we use 23 genetic and 14 clinical and environmental risk factors to compute the risk of coronary artery disease in a privacypreserving way. Finally, we show the practicality of the proposed system via a complexity evaluation. I.
RECENT ADVANCES IN THE DEVELOPMENT OF PROCESSABLE HIGH-TEMPERATURE POLYMERS (1998)

▪ Abstract High-temperature polymers have found widespread use in aerospace and electronics applications. This review deals with recent developments in the chemistry of these materials that have led to improvements in processability and high-temperature stability.
Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis (2000)

Flowering time mutants represent genetic functions in control of the floral transition, an important developmental phase switch in the life cycle of higher plants. Many such mutants have been identified and characterized, particular in Arabidopsis. Here we describe the identification and initial characterization of a new early flowering mutant of Arabidopsis. The corresponding gene, SVP (SHORT VEGETATIVE PHASE), was cloned through transposon tagging and represents a new member of the MADS-box gene family of transcription factors. Analysis of its transcriptional activity revealed the presence of differently sized transcripts that were confined to vegetative tissues and floral primordia and absent from developed flowers and siliques. The function of SVP as a repressor of the floral transition is discussed.
Expression of heteromeric amino acid transporters along the murine intestine (2004)

Members of the new heterodimeric amino acid transporter family are composed of two subunits, a catalytic multitransmembrane spanning protein (light chain) and a type II glycoprotein (heavy chain). These transporters function as exchangers and thereby extend the transmembrane amino acid transport selectivity to specific amino acids. The heavy chain rBAT associates with the light chain b degrees (,+)AT to form a cystine and cationic amino acid transporter. The other heavy chain, 4F2hc, can interact with seven different light chains to form various transporters corresponding to systems L, y(+)L, asc or x(-)(c). The importance of some of these transporters in intestinal and renal (re)absorption of amino acids is highlighted by the fact that mutations in either the rBAT or b degrees (,+)AT subunit result in cystinuria whereas a defect in the y(+)-LAT1 light chain causes lysinuric protein intolerance. Here we investigated the localization of these transporters in intestine since both diseases are also characterized by altered intestinal amino acid absorption. Real time PCR showed organ-specific expression patterns for all transporter subunit mRNAs along the intestine and Western blotting confirmed these findings on the protein level. Immunohistochemistry demonstrated basolateral coexpression of 4F2hc, LAT2 and y(+)-LAT1 in stomach and small intestine, whereas rBAT and b degrees (,+)AT were found colocalizing on the apical side of small intestine epithelium. In stomach, 4F2hc and LAT2 were localized in H(+)/K(+)-ATPase-expressing parietal cells. The abundant expression of several members of the heterodimeric transporter family along the murine small intestine suggests their involvement in amino acids absorption. Furthermore, strong expression of rBAT, b degrees (,+)AT and y(+)-LAT1 in the small intestine explains the reduced intestinal absorption of some amino acid in patients with cystinuria or lysinuric protein intolerance.
Size Distributions of Maternal and Fetal DNA in Maternal Plasma (2004)

Abstract Background: The discovery of fetal DNA in maternal plasma has opened up an approach for noninvasive prenatal diagnosis. Despite the rapid expansion in clinical applications, the molecular characteristics of plasma DNA in pregnant women remain unclear. Methods: We investigated the size distribution of plasma DNA in 34 nonpregnant women and 31 pregnant women, using a panel of quantitative PCR assays with different amplicon sizes targeting the leptin gene. We also determined the size distribution of fetal DNA in maternal plasma by targeting the SRY gene. Results: The median percentages of plasma DNA with size &amp;gt;201 bp were 57% and 14% for pregnant and nonpregnant women, respectively (P &amp;lt;0.001, Mann–Whitney test). The median percentages of fetal-derived DNA with sizes &amp;gt;193 bp and &amp;gt;313 bp were 20% and 0%, respectively, in maternal plasma. Conclusion: Plasma DNA molecules are mainly short DNA fragments. The DNA fragments in the plasma of pregnant women are significantly longer than those in the plasma of nonpregnant women, and the maternal-derived DNA molecules are longer than the fetal-derived ones.