gebhart/patrepeval huggingface dataset:
Significantly shorter telomeres in T‐cells of patients with ZAP‐70+/CD38+ chronic lymphocytic leukaemia (2008)

In contrast to other B-cell neoplasias, chronic lymphocytic leukaemia (CLL) is characterized by increased non-leukaemic T-cells. In order to assess their replicative history, telomere length was analyzed in subsets of leucocytes from CLL patients. Naive and memory T-cells from ZAP-70(+)/CD38(+) patients exhibited significantly shorter average telomere lengths than ZAP-70(-)/CD38(-) patients. Compared to the age-related percentiles of telomere length values from healthy individuals practically all values of the naive and memory T-cells from the ZAP-70(+)/CD38(+) CLL patients fell below the 50th percentile. This indicated an extensive expansion and a role for T-cells in ZAP-70(+)/CD38(+) CLL patients.
Structural Basis for Double-Stranded RNA Processing by Dicer (2006)

The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.
Electrochemical Conversion of Carbon Dioxide to Formate in Alkaline Polymer Electrolyte Membrane Cells (2010)

This paper is about the continuous electrochemical conversion of carbon dioxide to formate in a polymer electrolyte membrane cell using an alkaline ion-exchange membrane sandwiched between two catalyzed electrodes. This type of cell configuration allows carbon dioxide conversion to occur at high efficiencies and is particularly attractive for large-scale implementation. Formate was produced at high efficiency, and hydrogen evolution was suppressed with lead and indium as catalysts. The production of formate was monitored by UV–visible spectroscopy. During short experimental runs, the faradaic efficiency of formate production was as high as 80%. The faradaic efficiency was strongly dependent on the concentrations of carbon dioxide, bicarbonate, and carbonate at the surface of the electrodes. Low concentrations of carbon dioxide in the reactant feed led to the mass transport limitations and hence low faradaic efficiencies. The results show that mass transport limitations can be mitigated and high efficiencies can be realized by conducting the electrolysis in a pulsed mode. An alkaline membrane-based flow cell that ensures abundant availability of carbon dioxide to the electrodes can be a cost-effective and efficient approach for the continuous production of fuels from sunlight, storing of renewable energy, and lowering carbon dioxide levels in the atmosphere.
Transient Liquid Phase Bonding (1992)

Advances in machine learning have impacted myriad areas of materials science, such as the discovery of novel materials and the improvement of molecular simulations, with likely many more important developments to come. Given the rapid changes in this ...Read More
Synthesis of Barnase Site-Specifically Labelled with Two 13C Atoms Using Partially Protected Peptide Thioester Building Blocks (1993)

Abstract Barnase, site-specifically labelled with two 13C atoms, was synthesized using partially protected peptide thioesters as building blocks. Four partially protected peptide segments (Boc–[Lys(Boc)19,27]–barnase(1—34)–SC(CH3)2CH2CO–Nle–NH2, iNoc–[Lys(Boc)39,49]–barnase(35—52)–SC(CH3)2CH2CO–Nle–NH2, iNoc–[Lys(Boc)62,66]–barnase(53—81)–SC(CH3)2CH2CO–Nle–NH2, [Lys(Boc)98,108]–barnase(82—110)) were successively condensed in the presence of silver ions and N-hydroxysuccinimide (HONSu). Finally, barnase with full ribonuclease activity was obtained in a yield of 11% based on the carboxyl terminal peptide segment.
Dynamic proportional-integral-differential controller for high-speed atomic force microscopy (2006)

In tapping mode atomic force microscopy, the cantilever tip intermittently taps the sample as the tip scans over the surface. This mode is suitable for imaging fragile samples such as biological macromolecules, because vertical oscillation of the cantilever reduces lateral forces between the tip and sample. However, the tapping force (vertical force) is not necessarily weak enough for delicate samples, particularly for biomolecular systems containing weak inter- or intramolecular interactions. Light tapping requires an amplitude set point (i.e., a constant cantilever amplitude to be maintained during scanning) to be set very close to its free oscillation amplitude. However, this requirement does not reconcile with fast scans, because, with such a set point, the tip may easily be removed from the surface completely. This article presents two devices to overcome this difficulty; a new feedback controller (named as “dynamic proportional-integral-differential controller”) and a compensator for drift in the cantilever-excitation efficiency. Together with other devices optimized for fast scan, these devices enable high-speed imaging of fragile samples.
Similar proportions of immunoglobulin A1 (IgA1) protease-producing streptococci in initial dental plaque of selectively IgA-deficient and normal individuals (1993)

By comparing the initial colonization of cleaned teeth in immunoglobulin A (IgA)-deficient, IgM-compensating individuals with that in normal individuals, no significant difference in the proportion of IgA1 protease-producing streptococci was found. Thus, as one of several bacterial means of immune evasion, the ability to cleave secretory IgA1 does not appear essential to the successful adherence of oral streptococci.
Activation of JAK-STAT and MAP Kinases by Leukemia Inhibitory Factor Through gp130 in Cardiac Myocytes (1996)

These results demonstrate for the first time that a JAK-STAT pathway and a MAPK pathway are present down-stream of gp130 in cardiac myocytes and are rapidly activated by LIF both in vitro and in vivo. Activation of gp130 constitutes a novel signaling pathway in cardiac myocytes.
Shotgun proteomics identifies proteins specific for acute renal transplant rejection (2010)

This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of UP for serial, non-invasive clinical monitoring for graft rejection after kidney transplantation.
High-level expression of a 56-kilodalton protein gene (bor56) of Rickettsia tsutsugamushi Boryong and its application to enzyme-linked immunosorbent assays (1993)

The 56-kDa protein of Rickettsia tsutsugamushi, which is located on the rickettsial surface, has been shown to be an immunodominant antigen. The gene that encodes the 56-kDa protein of R. tsutsugamushi Boryong (bor56) was cloned. Sequencing revealed an open reading frame of 1,602 bp encoding 534 amino acids with a molecular weight of 56,803. The 56-kDa protein of R. tsutsugamushi Boryong (Bor56) was expressed as a fusion protein with the maltose-binding protein of Escherichia coli by deleting 252 bp from the 5' end of the open reading frame and subcloning it into the StuI site of pIH821. The recombinant fusion protein was purified by amylose column chromatography for application in an enzyme-linked immunosorbent assay to evaluate the ability of the method to detect the antibody to R. tsutsugamushi in human patient sera. By using sera from 100 patients with scrub typhus and 70 patients with other febrile diseases, a high diagnostic sensitivity (95%) and a high diagnostic specificity (100%) were demonstrated, suggesting the suitability of the recombinant antigen for use as an immunodiagnostic tool.
A compact and highly fluorescent orange-emitting polymer dot for specific subcellular imaging (2011)

We demonstrate a new compact CN-PPV dot, which emits in the orange wavelength range with high brightness. The small particle size, high brightness, and the ability to highly specifically target subcellular structures make the CN-PPV dots promising probes for biological imaging and bioanalytical applications.
The effect of using prebiotic and probiotic products on intestinal micro-flora of the honeybee (Apis mellifera carpatica) (2012)

Maintaining bee colonies in a healthy state throughout the year is one of the main concerns of apiculture researchers. The phenomenon of disappearance of bee colonies is determined by several factors, one of which is bee disease. Due to the organizational structure of the bee colony, disease transmission is rapid, especially through infected food or via the nurse worker bees that feed the brood bees of the colony concerned. The practice of stimulating the bee colonies in spring using sugar syrup feeds with added prebiotic products (lactic acid or acetic acid) and probiotics (Lactobacillus acidophilus LA-14 and Bifidobacterium lactis BI-04) by using an Enterobiotic product (Lactobacillus casei), marketed as Enterolactis Plus, for three weeks, resulted in a significant reduction of the total number of bacteria in the digestive tracts of the bees, compared with the control group. By contrast, intestinal colonization with beneficial bacteria contained in probiotics products administered to the bees was observed. This resulted in an improved health status and bio productive index of the bee colonies studied.
Structure and expression of the herpes simplex virus type 2 glycoprotein gB gene (1987)

The gene for glycoprotein gB2 of herpes simplex virus type 2 strain 333 was cloned, sequenced, and expressed in mammalian cells. The gB2 protein had an overall nucleotide and amino acid sequence homology of 86% with the cognate gB1 protein. However, of the 125 amino acid substitutions or deletions, only 12.5% were conservative replacements. These differences were clustered within an NH2-terminal region, a central region, and a COOH-terminal region, resulting in domains of near identity broken by small regions of marked divergence. Regions of greatest homology included a 90-amino-acid stretch starting at residue 484 and 39 amino acids spanning residues 835 to 873, which cover a rate-of-entry locus mapped to Ala-552 and a syn locus mapped to Arg-857, respectively, in gB1 by Bzik et al. (D. J. Bzik, B. A. Fox, N. A. DeLuca, and S. Person, Virology 133:301-314, 1984). Pellett et al. (P. E. Pellett, K. G. Kousoulas, L. Pereira, and B. Roizman, J. Virol. 53:243-253, 1985) mapped the mutations in three monoclonal antibody-resistant gB1 mutants between amino acids 273 and 443. These epitopes are included in a region of 98 residues identical between gB1 and gB2. The identity of this protein was verified by placing a truncated gene lacking the 303 carboxyl-terminal amino acids of gB2 into mammalian COS and CHO cells. Expression was demonstrated by immunofluorescence and radioimmunoprecipitation. This protein will be purified from the stable CHO cell lines and compared with gB1 for immunogenicity and protective efficacy in animal challenge models.
Dialkyl Ether Formation by Nickel‐Catalyzed Cross‐Coupling of Acetals and Aryl Iodides (2015)

Abstract A new substrate class for nickel‐catalyzed C(sp 3 ) cross‐coupling reactions is reported. α‐Oxy radicals generated from benzylic acetals, TMSCl, and a mild reductant can participate in chemoselective cross‐coupling with aryl iodides using a 2,6‐bis( N ‐pyrazolyl)pyridine (bpp)/Ni catalyst. The mild, base‐free conditions are tolerant of a variety of functional groups on both partners, thus representing an attractive CC bond‐forming approach to dialkyl ether synthesis. Characterization of a [(bpp)NiCl] complex relevant to the proposed catalytic cycle is also described.
Subdecoherent information encoding in a quantum-dot array (1999)

A potential implementation of quantum-information schemes in semiconductor nanostructures is studied. To this end, the formal theory of quantum encoding for avoiding errors is recalled and the existence of noiseless states for model systems is discussed. Based on this theoretical framework, we analyze the possibility of designing noiseless quantum codes in realistic semiconductor structures. In the specific implementation considered, information is encoded in the lowest energy sector of charge excitations of a linear array of quantum dots. The decoherence channel considered is electron-phonon coupling We show that besides the well-known phonon bottleneck, reducing single-qubit decoherence, suitable many-qubit initial preparation, as well as register design may enhance the decoherence time by several orders of magnitude. This behavior stems from the effective one-dimensional character of the phononic environment in the relevant region of physical parameters.
Cyclic Amplification and Selection of Targets (CASTing) for the Myogenin Consensus Binding Site (1991)

The consensus binding site for the muscle regulatory factor myogenin was determined from an unbiased set of degenerate oligonucleotides using CASTing (cyclic amplification and selection of targets). Stretches of totally random sequence flanked by polymerase chain reaction priming sequences were mixed with purified myogenin or myotube nuclear extracts, DNA-protein complexes were immunoprecipitated with an antimyogenin antibody, and the DNA was amplified by polymerase chain reaction. Specific binding was obtained after four to six cycles of CASTing. The population of selected binding sites was then cloned, and a consensus was determined from sequencing individual isolates. Starting from a pool with 14 random bases, purified myogenin yielded a consensus binding site of AACAG[T/C]TGTT, while nuclear extracts retrieved the sequence TTGCACCTGTTNNTT from a pool containing 35 random bases. The latter sequence is consistent with that predicted from combining an E12/E47 half-site (N[not T]CAC) with the purified myogenin half-site ([T/C] TGTT). The presence of paired E boxes in many of the sequences isolated following CASTing with nuclear extracts proves that myogenin can bind cooperatively with other E-box-binding factors.
Inhibition of antibody formation by receptor cross‐linking: the molecular characteristics of inhibitory haptenated polymers (1990)

Previous studies from this laboratory have reported on the characteristics of a molecule which make it inhibitory. These findings were based on studies using the T cell-independent haptenated polymer, 2,4-dinitrophenyl-polyacrylamide (DNP-PA). The present study was undertaken to determine whether the same molecular properties which defined the inhibitory potentials of DNP-PA were characteristic of other haptenated polymers as well. The molecules studied here consisted of a series of five diverse fluoresceinated polymers with varying molecular mass and hapten valence. In agreement with the previous findings on DNP-PA, definable molecular forms of fluoresceinated dextrans. Ficolls, polyacrylamides, carboxymethyl celluloses and polyvinyl alcohols were each found to be capable of inhibiting the anti-fluorescein response to immunogenic forms of haptenated polymers of either the same or different carrier chemistry. This inhibitory ability was relatively independent of the chemical composition and conformation of the carrier polymer. These studies allow some logical generalizations to be made as to which quantitative molecular properties of haptenated type 2 T cell-independent antigens determine whether they will be stimulatory or inhibitory of an anti-hapten immune response.
A High-Performance Keyboard Neural Prosthesis Enabled by Task Optimization (2014)

Communication neural prostheses are an emerging class of medical devices that aim to restore efficient communication to people suffering from paralysis. These systems rely on an interface with the user, either via the use of a continuously moving cursor (e.g., mouse) or the discrete selection of symbols (e.g., keyboard). In developing these interfaces, many design choices have a significant impact on the performance of the system. The objective of this study was to explore the design choices of a continuously moving cursor neural prosthesis and optimize the interface to maximize information theoretic performance. We swept interface parameters of two keyboard-like tasks to find task and subject-specific optimal parameters as measured by achieved bitrate using two rhesus macaques implanted with multielectrode arrays. In this paper, we present the highest performing free-paced neural prosthesis under any recording modality with sustainable communication rates of up to 3.5 bits/s. These findings demonstrate that meaningful high performance can be achieved using an intracortical neural prosthesis, and that, when optimized, these systems may be appropriate for use as communication devices for those with physical disabilities.
Tweets from Justin Bieber's heart (2011)

Little research exists on one of the most common, oldest, and most utilized forms of online social geographic information: the 'location' field found in most virtual community user profiles. We performed the first in-depth study of user behavior with regard to the location field in Twitter user profiles. We found that 34% of users did not provide real location information, frequently incorporating fake locations or sarcastic comments that can fool traditional geographic information tools. When users did input their location, they almost never specified it at a scale any more detailed than their city. In order to determine whether or not natural user behaviors have a real effect on the 'locatability' of users, we performed a simple machine learning experiment to determine whether we can identify a user's location by only looking at what that user tweets. We found that a user's country and state can in fact be determined easily with decent accuracy, indicating that users implicitly reveal location information, with or without realizing it. Implications for location-based services and privacy are discussed.
(R.) Jenkins. An introduction to X-ray spectrometry. London and Rheine (Heyden & Son, Ltd.), 1974. xi + 163 pp., 87 figs. Price £5.00. (1975)

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Measurement of the axial wavefront aberration of the human eye (1985)

Abstract— An objective variation of Howland and Howland's subjective crossed-cylinder aberroscope method of estimating ocular aberration is described. An ophthalmoscopic arrangement allows the distorted retinal image of the aberroscope grid to be directly photographed for later analysis. Results for 10 subjects show that the ocular wavefront aberration near the visual axis is rarely symmetrical about the pupil centre and that, as a result, the phase transfer function is generally non-zero. Calculated modulation transfer functions at various pupil diameters broadly agree with those of earlier authors but suggest that marked differences occur between individual eyes when the pupil diameter exceeds about 3 mm.
Improving Editing Efficiency for the Sequences with NGH PAM Using xCas9-Derived Base Editors (2019)

The development of CRISPR/Cas9-mediated base editors (BEs) provided a versatile tool for precise genome editing. The recently developed xCas9-derived base editors (xBEs) that recognize the NG PAM substantially expand the targeting scope in the genome, while their editing efficiency needs to be improved. Here, we described an improved version of xBEs by fusing the BPNLS and Gam to the N terminus of xBEs (BPNLS-Gam-xBE3 and BPNLS-xABE), and this version of base editor displayed higher targeting efficiency for the majority of detected sites. By using this improved version of xBEs, we successfully created and corrected pathogenic mutations at genomic sites with the NGN protospacer-adjacent motif in human cells. Lastly, we used BPNLS-Gam-xBE3 to model pathogenic mutations in discarded human tripronuclear (3PN) zygotes, and no obvious off-targets and indels were detected. Taken together, the data in our study offer an efficient tool for precise genome editing and, thus, an enriched base editing toolkit.
Iron-Responsive Gene Regulation in a Campylobacter jejuni fur Mutant (1998)

The expression of iron-regulated systems in gram-negative bacteria is generally controlled by the Fur protein, which represses the transcription of iron-regulated promoters by using Fe2+ as a cofactor. Mutational analysis of the Campylobacter jejuni fur gene was carried out by generation of a set of mutant copies of fur which had a kanamycin or chloramphenicol resistance gene introduced into the regions encoding the N and C termini of the Fur protein. The mutated genes were recombined into the C. jejuni NCTC 11168 chromosome, and putative mutants were confirmed by Southern hybridization. C. jejuni mutants were obtained only when the resistance genes were transcribed in the same orientation as the fur gene. The C. jejuni fur mutant grew slower than the parental strain. Comparison of protein profiles of fractionated C. jejuni cells grown in low- or high-iron medium indicated derepressed expression of three iron-regulated outer membrane proteins with molecular masses of 70, 75, and 80 kDa. Characterization by N-terminal amino acid sequencing showed the 75-kDa protein to be identical to CfrA, a Campylobacter coli siderophore receptor homologue, whereas the 70-kDa protein was identified as a new siderophore receptor homologue. Periplasmic fractions contained four derepressed proteins with molecular masses of 19, 29, 32, and 36 kDa. The 19-kDa protein has been previously identified, but its function is unknown. The cytoplasmic fraction contained two iron-repressed and two iron-induced proteins with molecular masses of 26, 55, 31, and 40 kDa, respectively. The two iron-repressed proteins have been previously identified as the oxidative stress defense proteins catalase (KatA) and alkyl hydroperoxide reductase (AhpC). AhpC and KatA were still iron regulated in the fur mutant, suggesting the presence of Fur-independent iron regulation. Further analysis of the C. jejuni iron and Fur regulons by using two-dimensional gel electrophoresis demonstrated the total number of iron- and Fur-regulated proteins to be lower than for other bacterial pathogens.
Dynamics of taut DNA chains (1999)

We discuss the dynamics of stretched DNA chains, subjected to a tension force f, in a "taut" regime where φ = flp0/kBT > 1 (lp0 being the unperturbed persistence length). We deal with two variables: the local transverse displacements u, and the longitudinal position of a monomer u∥. The variables u and u∥ follow two distinct Rouse equations, with diffusion coefficients D⊥ = f/η (where η is the solvent viscosity) and D∥ = 4φ1/2D⊥. We apply these ideas to a discussion of various transient regimes.