gebhart/patrepeval huggingface dataset:
Site-directed mutagenesis of β-lactamase I: role of Glu-166 (1994)

Two Glu-166 mutants of beta-lactamase I from Bacillus cereus 569/H were constructed: one with a lengthened side chain (E166Cmc, the S-carboxymethylcysteine mutant) and the other with the side chain shortened and made non-polar (E166A). Their kinetic properties were studied and compared with those of the wild-type and the E166D mutant (with a shortened side chain) previously made by Gibson, Christensen and Waley (1990) (Biochem. J. 272, 613-619). Surprisingly, with good penicillin substrates, Km, kcat. and kcat./Km of the two conservative mutants (E166Cmc and E166D) are similar to those of the non-conservative mutant E166A. Their kcat. values are 3000-fold lower than that of the wild-type enzyme, showing that Glu-166 is a very important residue. The acylenzyme intermediate of E166A and a good substrate, penicillin V, was trapped by acid-quench and observed by electrospray ionization mass spectrometry, suggesting that Glu-166 is more important in catalysing the deacylation step than the acylation step. The beta-lactamase I E166A mutant is about 200-fold more active than the Bacillus licheniformis E166A mutant with nitrocefin or 6 beta-furylacryloyl-amidopenicillanic acid as substrate. This suggested that other groups in the active site of the beta-lactamase I mutant may activate the catalytic water molecule for deacylation.
Harnessing the protective potential of HIV-1 neutralizing antibodies (2016)

Recent biological, structural, and technical advances are converging within the HIV-1 vaccine field to harness the power of antibodies for prevention and therapy. Numerous monoclonal antibodies with broad neutralizing activity against diverse HIV-1 isolates have now been identified, revealing at least five sites of vulnerability on the envelope (Env) glycoproteins. While there are practical and technological barriers blocking a clear path from broadly neutralizing antibodies (bNAb) to a protective vaccine, this is not a dead end. Scientists are revisiting old approaches with new technology, cutting new trails through unexplored territory, and paving new roads in the hopes of preventing HIV-1 infection. Other promising avenues to capitalize on the power of bNAbs are also being pursued, such as passive antibody immunotherapy and gene therapy approaches. Moreover, non-neutralizing antibodies have inhibitory activities that could have protective potential, alone or in combination with bNAbs. With a new generation of bNAbs, and a clinical trial that associated antibodies with reduced acquisition, the field is closer than ever to developing strategies to use antibodies against HIV-1.
Applications of "Wired" Peroxidase Electrodes for Peroxide Determination in Liquid Chromatography Coupled to Oxidase Immobilized Enzyme Reactors (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplications of "Wired" Peroxidase Electrodes for Peroxide Determination in Liquid Chromatography Coupled to Oxidase Immobilized Enzyme ReactorsLiu. Yang, Elsa. Janle, Tiehua. Huang, James. Gitzen, Peter T. Kissinger, Mark. Vreeke, and Adam. HellerCite this: Anal. Chem. 1995, 67, 8, 1326–1331Publication Date (Print):April 15, 1995Publication History Published online1 May 2002Published inissue 15 April 1995https://pubs.acs.org/doi/10.1021/ac00104a005https://doi.org/10.1021/ac00104a005research-articleACS PublicationsRequest reuse permissionsArticle Views293Altmetric-Citations78LEARN 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
Counterfactuals and Causal Inference (2014)

In this second edition of Counterfactuals and Causal Inference, completely revised and expanded, the essential features of the counterfactual approach to observational data analysis are presented with examples from the social, demographic, and health sciences. Alternative estimation techniques are first introduced using both the potential outcome model and causal graphs; after which, conditioning techniques, such as matching and regression, are presented from a potential outcomes perspective. For research scenarios in which important determinants of causal exposure are unobserved, alternative techniques, such as instrumental variable estimators, longitudinal methods, and estimation via causal mechanisms, are then presented. The importance of causal effect heterogeneity is stressed throughout the book, and the need for deep causal explanation via mechanisms is discussed.
Mechanisms, Capabilities, and Applications of High‐Resolution Electrohydrodynamic Jet Printing (2015)

This review gives an overview of techniques used for high-resolution jet printing that rely on electrohydrodynamically induced flows. Such methods enable the direct, additive patterning of materials with a resolution that can extend below 100 nm to provide unique opportunities not only in scientific studies but also in a range of applications that includes printed electronics, tissue engineering, and photonic and plasmonic devices. Following a brief historical perspective, this review presents descriptions of the underlying processes involved in the formation of liquid cones and jets to establish critical factors in the printing process. Different printing systems that share similar principles are then described, along with key advances that have been made in the last decade. Capabilities in terms of printable materials and levels of resolution are reviewed, with a strong emphasis on areas of potential application.
Symptom Dimensions in Chinese Patients with Obsessive‐Compulsive Disorder (2009)

To study the symptom dimensions of Chinese patients with obsessive-compulsive disorder (OCD), the symptom checklist of the Dimensional Yale-Brown Obsessive-Compulsive Scale (DY-BOCS) was used to assess the symptom dimensions of 139 OCD patients at a mental health center in Shanghai. The most common symptom dimensions were symmetry (67.6%), contamination (43.2%), and aggression (31.7%). The frequency of patients with the miscellaneous, sexual/religious, and hoarding symptom dimensions was 25.9%, 10.8%, and 8.6%, respectively. The frequency of male patients with symmetry concerns was higher than that of the female patients, and the frequency of female patients with contamination concerns was higher than that of male patients. OCD symptom dimensions can be identified in the Chinese context but there is a low frequency of endorsement of certain dimensions: sexual/religious, aggression, and hoarding concerns. Future studies need to further investigate the sociocultural and gender factors that may result in these findings: low numbers of people in China with a religious affiliation and the Chinese emphasis on Confucian harmony philosophy, thrift, and saving.
Applications and Systematics of Bacillus and Relatives (2002)

List of Contributors. Foreword. 1. Whither Bacillus? (Berkeley). 2. From Phylogeny To Systematics: Dissection Of The Genus Bacillus (Stackebrandt & Swiderski). 3. Longstanding Taxonomic Enigmas Within The a Bacillus Cereus Groupa Are On The Verge Of Being Resolved By Far--Reaching Molecular Developments: Forecasts On The Possible Outcome By An Ad Hoc Team. (Turnbull, Jackson, Hill, Keim, Kolsto & Beecher). 4. Bacillus Cereus And Food Poisoning (Granum). 5. Thermophilic Bacillus Isolates From Antarctic Environments (Nicolaus, Lama & Gambacorta). 6. Bacilli Associated With Spoilage In Dairy Products And Other Foods (Heyndrickx & Scheldeman). 7. Moderately Halophilic And Halotolerant Species Of Bacillus And Related Genera (Arahal & Ventosa). 8. Bacillus Identification -- Traditional Approaches (Fritze). 9. Modern Methods For Identification (Logan). 10. Nucleic Acid Analysis And SDS--PAGE Of Whole--Cell Proteins In Bacillus Taxonomy (De Vos). 11. Bacillus Thuringiensis Insecticides (Bishop). 12. Bt Crops: A Novel Insect Control Tool (Van Rie). 13. Bacillus Sphaericus And Its Insecticidal Toxins (Priest). 14. The Importance Of Bacillus Species In The Production Of Industrial Enzymes (Outtrop & Jorgensen). 15. Plant Growth Promotion By Bacillus And Relatives (Chanway). 16. Insertion Sequence Elements And Transposons In Bacillus (Mahillon). 17. Fingerprint Spectrometry Methods In Bacillus Systematics (Magee & Goodacre). 18. Whole--Cell Fatty Acid Analysis In The Systematics Of Bacillus And Related Genera (Kampfer). 19. Some Concluding Observations (Norris). Index
Using Three-Phase Flow of Immiscible Liquids To Prevent Coalescence of Droplets in Microfluidic Channels:  Criteria To Identify the Third Liquid and Validation with Protein Crystallization (2007)

This manuscript describes the effect of interfacial tensions on three-phase liquid-liquid-liquid flow in microfluidic channels and the use of this flow to prevent microfluidic plugs from coalescing. One problem in using microfluidic plugs as microreactors is the coalescence of adjacent plugs caused by the relative motion of plugs during flow. Here, coalescence of reagent plugs was eliminated by using plugs of a third immiscible liquid as spacers to separate adjacent reagent plugs. This work tested the requirements of interfacial tensions for plugs of a third liquid to be effective spacers. Two candidates satisfying the requirements were identified, and one of these liquids was used in the crystallization of protein human Tdp1 to demonstrate its compatibility with protein crystallization in plugs. This method for identifying immiscible liquids for use as a spacer will also be useful for applications involving manipulation of large arrays of droplets in microfluidic channels.
Hormonal antagonistic properties of chemically deglycosylated human choriogonadotropin. (1983)

The biological properties of chemically deglycosylated human choriogonadotropin (DG-hCG) preparations were examined in collagenase-dispersed rat interstitial cells in vitro. Despite effective receptor binding activity in membrane preparations, DG-hCG failed to induce cyclic AMP accumulation in the cells when incubated in the presence or absence of a phosphodiesterase inhibitor. The steroidogenic ability as assessed by testosterone accumulation in the medium was less than 0.5% of the native hormone with a failure to attain maximal steroid production. Time course experiments have revealed that altered kinetics could not be responsible for the loss of hormone response. Consistent with its property of good receptor binding and poor cell activation, DG-hCG antagonized the action of native hCG. When added to the cells at the same time, DG-hCG inhibited the action of a maximal stimulatory dose of hCG in a dose-dependent manner. Inhibition of cyclic AMP accumulation was complete whereas inhibition of steroidogenesis was about 75%. DG-hCG had no effect on the stimulatory action of cholera toxin in interstitial cells or that of follitropin in rat seminiferous tubular preparations. The data suggest that DG-hCG has a conformation conductive for effective interaction with the receptor, but its ability to activate the adenylate cyclase is either lost or weakly expressed.
Regioselective Preparation of Saturated Spirocyclic and Ring-Expanded Fused Pyrazoles (2014)

Saturated bicyclic pyrazoles represent an important class of biologically active molecules, but their preparation can be hampered by labor-intensive synthesis of required starting materials. A convenient one- or two-step procedure for the synthesis of saturated spirocyclic and fused pyrazoles is reported. The synthesis benefits from the use of readily available alkynes and bench-stable tosylhydrazones, which are easily prepared from their parent ketones. Sigmatropic rearrangement of spirocyclic pyrazoles to fused analogues occurs with concomitant one-carbon expansion of the saturated ring, allowing rapid access to a range of pharmaceutically and agrochemically relevant polycyclic structures featuring a broad scope of saturated ring sizes.
Lanthanide porphyrin complexes. Evaluation of nuclear magnetic resonance dipolar probe and shift reagent capabilities (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLanthanide porphyrin complexes. Evaluation of nuclear magnetic resonance dipolar probe and shift reagent capabilitiesWilliam D. Horrocks Jr. and Ching-Ping WongCite this: J. Am. Chem. Soc. 1976, 98, 23, 7157–7162Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://doi.org/10.1021/ja00439a007Request reuse permissionsArticle Views689Altmetric-Citations91LEARN 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 InReddit PDF (794 KB) Get e-Alertsclose Get e-Alerts
Genomic Fingerprinting by Arbitrarily Primed Polymerase Chain Reaction Resolves Borrelia burgdorferi into Three Distinct Phyletic Groups (1992)

The causative agent of Lyme disease, Borrelia burgdorferi, was first identified by Burgdorfer et al. in 1982 (W. Burgdorfer, A. G. Barbour, S. F. Hayes, J. L. Benach, E. Grunwaldt, and J. P. Davis, Science 216:1317-1319, 1982) and was isolated by Barbour et al. in 1983 (A. G. Barbour, W. Burgdorfer, S. E. Hayes, O. Peter, and A. Aeschlimann, Curr. Microbiol. 8:123-126, 1983). Since then, a large number of isolates have been collected, and there have been questions regarding the relationships among the various strains. Using genomic fingerprinting by an arbitrarily primed polymerase chain reaction, we resolved into three groups a collection of Eurasian and North American isolates of spirochetes that are generally categorized as B. burgdorferi. Group I strains have been identified in both North America and Eurasia, while strains belonging to Borrelia groups II and III have been found only in Eurasia. These same three groups have also been delineated by Baranton et al. (G. Baranton, D. Postic, I. Saint Girons, P. Boerlin, J.-C. Piffaretti, M. Assous, and P. A. D. Grimont, Int. J. Syst. Bacteriol. 42:370-375, 1992) by independent methods. Two isolates are distinct from all of the other strains in our collection but are clearly members of the genus Borrelia.
Heart Rate Changes and ECG Abnormalities During Epileptic Seizures: Prevalence and Definition of an Objective Clinical Sign (2002)

Heart rate changes occur frequently and occur around the time or even before the earliest electrographic or clinical change. The change can clarify the timing of seizure onset and the specific rate pattern may be useful for seizure diagnosis and for automatic seizure detection. ECG abnormalities occur often and repeatedly in several seizures of the same patient.
Passive Immunization with Melanin-Binding Monoclonal Antibodies Prolongs Survival of Mice with Lethal Cryptococcus neoformans Infection (2001)

Passive immunization with monoclonal antibodies (MAbs) to melanin prolonged the survival of and reduced the fungal burden in Cryptococcus neoformans-infected mice in comparison to controls. MAbs to melanin reduced the growth rate of in vitro-melanized C. neoformans cells, suggesting a new mechanism of antibody-mediated protection.
ENCYCLOPEDIA OF Surface and Colloid Science (2021)

This comprehensive reference collects fundamental theories and recent research from a wide range of fields including biology, biochemistry, physics, applied mathematics, and computer, materials, surface, and colloid science-providing key references, tools, and analytical techniques for practical applications in industrial, agricultural, and forensic processes, as well as in the production of natural and synthetic compounds such as foods, minerals, paints, proteins, pharmaceuticals, polymers, and soaps.
Intramuscular Dexmedetomidine Sedation for Pediatric MRI and CT (2011)

The intramuscular route is an alternative approach to dexmedetomidine delivery for pediatric sedation. Larger studies are warranted to evaluate the efficacy, safety, and hemodynamic outcome associated with the intramuscular use of dexmedetomidine in the care of children.
Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88 (2011)

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
Removal of the skin blood flow artifact in functional near-infrared spectroscopic imaging data through independent component analysis (2007)

We investigate whether the functional near-infrared spectroscopic (fNIRS) signal includes a signal from the changing skin blood flow. During a locomotor task on a treadmill, changes in the hemodynamic response in the front-parietal area of healthy human subjects are simultaneously recorded using an fNIRS imaging system and a laser Doppler tissue blood flow meter. Independent component analysis (ICA) for fNIRS signals is performed. The skin blood flow changes during locomotor tasks on a treadmill. The activated spatial distribution of one of the components separated by ICA reveals an overall increase in fNIRS channels. To evaluate the uniformity of the activated spatial distribution, we define a new statistical value-the coefficient of spatial uniformity (CSU). The CSU value is a highly discriminating value (e.g., 2.82) compared with values of other components (e.g., 1.41, 1.10, 0.96, 0.61, and 0.58). In addition, the independent component signal corresponding to the activated spatial distribution is similar to changes in skin blood flow measured with the laser Doppler tissue blood flow meter. The coefficient of correlation indicates strong correlation. Localized activation areas around the premotor and medial somatosensory cortices are shown more clearly by eliminating the extracted component.
Design and fabrication of binary slanted surface-relief gratings for a planar optical interconnection (1997)

We propose the use of binary slanted surface-relief gratings with parallel-groove walls as input and output couplers in a planar optical interconnect. Parametric optimization of cascaded output couplers is employed to design an interconnect consisting of N output couplers producing a uniform intensity distribution with a high efficiency that may be realized in one lithographic etching step. The sensitivity of a N = 4 interconnect to various fabrication errors is analyzed. We demonstrate the operation of a slanted surface-relief grating manufactured with electron-beam lithography and reactive-ion etching for an operating wavelength of lambda = 0.633 mum.
Health Outcomes Associated With Various Antihypertensive Therapies Used as First-Line Agents (2003)

Low-dose diuretics are the most effective first-line treatment for preventing the occurrence of cardiovascular disease morbidity and mortality. Clinical practice and treatment guidelines should reflect this evidence, and future trials should use low-dose diuretics as the standard for clinically useful comparisons.
High thermal stability is essential for tumor targeting of antibody fragments: engineering of a humanized anti-epithelial glycoprotein-2 (epithelial cell adhesion molecule) single-chain Fv fragment. (1999)

The epithelial glycoprotein-2 is abundantly expressed on many solid tumors and is a suitable target for antibody-based therapy. In the present study, an antiepithelial glycoprotein-2 single-chain Fv (scFv) was derived from the hybridoma MOC31 by phage display. Despite its high affinity (KD = 3.9 x 10(-9) M), however, this antibody fragment failed to significantly enrich at lung tumor xenografts in mice, mostly because of its insufficient thermal stability. To overcome this limitation, the antigen-binding residues of the MOC31 scFv fragment were grafted onto the framework of the highly stable and well-folding anti-c-erbB2 scFv 4D5. Further modification of the resulting 4D5 MOC-A, which was performed by transferring eight additional residues of the heavy chain variable domain core of the parent MOC31 antibody, produced 4D5 MOC-B, resulting in increased serum stability at 37 degrees C and also significantly improved expression behavior while retaining the antigen specificity and affinity of the parent MOC31 scFv. In mice, the scFv 4D5 MOC-B, which was radiolabeled with 99mtechnetium using a new histidine-tag specific labeling method (Waibel et al., Nature Biotechnol., 17: 897-901, 1999), showed favorable blood clearance and efficient enriches at lung tumor xenografts, with a tumor:blood ratio of 5.25 and a total dose of 1.47% injected dose per gram after 24 h. Biophysical properties such as high thermal stability are thus decisive for whether these molecules are useful in vivo, and our approach may provide a general strategy to solve this problem. This is also the first report of using a humanized anti-EGP-2 scFv in vivo for targeting solid tumors, which is a promising targeting moiety for the diagnostics and therapy of EGP-2-positive tumors in patients.