gebhart/patrepeval huggingface dataset:
Destabilizing loop swaps in the CDRs of an immunoglobulin VL domain (1995)

It is generally believed that loop regions in globular proteins, and particularly hypervariable loops in immunoglobulins, can accommodate a wide variety of sequence changes without jeopardizing protein structure or stability. We show here, however, that novel sequences introduced within complementarity determining regions (CDRs) 1 and 3 of the immunoglobulin variable domain REI VL can significantly diminish the stability of the native state of this protein. Besides their implications for the general role of loops in the stability of globular proteins, these results suggest previously unrecognized stability constraints on the variability of CDRs that may impact efforts to engineer new and improved activities into antibodies.
HIV with Multiple Gene Deletions as a Live Attenuated Vaccine for AIDS (1992)

Most viral vaccines currently in use in humans are live attenuated strains of virus that lack pathogenic potential. In general, such live attenuated vaccines induce the strongest longest-lasting immunity. Live attenuated strains of human immunodeficiency virus type 1 (HIV-1) have not been previously considered as vaccines for acquired immunodeficiency syndrome (AIDS) because of an inability to envision how their safety could be adequately assured. This report describes a means for making live, nonpathogenic strains of SIVmac and HIV-1 that cannot revert to a virulent form and a stepwise scheme for demonstrating their safety. Replication-competent, multiply deleted derivatives that are currently being tested are missing combinations of auxiliary genes (nef, vpr, vif, vpx, vpu) and certain control elements in the negative regulatory element (NRE) of the long terminal repeat (LTR). Since these genomic regions are in large part conserved among the SIVs and HIVs, they are likely to be important for the virus life cycle in vivo. Consistent with this line of reasoning, a replication-competent nef deletion mutant of SIVmac apparently has lost most or all of its pathogenic potential, yet it still induces strong immune responses. Multiply deleted derivatives of SIVmac and HIV-1 will have to be extensively tested in animal models prior to moving a promising HIV-1 candidate to initial trials in high-risk human volunteers. Definitive evidence for safety and general acceptance for this approach can only evolve gradually over a prolonged period of time.
Thalamocortical Oscillations in the Sleeping and Aroused Brain (1993)

Sleep is characterized by synchronized events in billions of synaptically coupled neurons in thalamocortical systems. The activation of a series of neuromodulatory transmitter systems during awakening blocks low-frequency oscillations, induces fast rhythms, and allows the brain to recover full responsiveness. Analysis of cortical and thalamic networks at many levels, from molecules to single neurons to large neuronal assemblies, with a variety of techniques, ranging from intracellular recordings in vivo and in vitro to computer simulations, is beginning to yield insights into the mechanisms of the generation, modulation, and function of brain oscillations.
P3‐196: A genome‐wide association study for late‐onset Alzheimer's disease using DNA pooling (2008)

Late-onset Alzheimer's disease (LOAD) is an age related neurodegenerative disease with a high prevalence consequently placing major demands on healthcare resources in societies with increasingly aged populations. The only extensively replicable genetic risk factor for LOAD is the apolipoprotein E gene. In order to identify additional genetic risk loci we have conducted a genome-wide association (GWA) study in a large LOAD case – control sample, reducing costs by using DNA pooling. DNA samples were collected from 1,082 individuals with LOAD and 1,239 control subjects. Age at onset ranged from 60 to 95 and Controls were matched for age (mean = 76.53 years, SD = 6.33), gender and ethnicity. Equimolar amounts of each DNA sample were added to either a case or control pool. The pools were genotyped using Illumina HumanHap300 and Illumina Sentrix HumanHap240S arrays testing over 550,000 SNPs. 114 of our best hit SNPs from the pooling data were identified and then individually genotyped in the case – control sample used to construct the pools. Highly significant association with LOAD was observed at the APOE locus (p=9.0 × 10–5 to 3.6 × 10–22)confirming the validity of the pooled genotyping approach. For 109 SNPs outside the APOE locus, we obtained uncorrected p-values ≤ 0.05 for 74 after individual genotyping. To further test these associations, we added control data from 1400 subjects from the 1958 Birth Cohort with the evidence for association increasing to 3.4x10–6 for our strongest finding, rs727153. rs727153 lies 13kb from the start of transcription of lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase, LRAT). Five of seven tag SNPs chosen to cover LRAT showed significant association with LOAD with a SNP in intron 2 of LRAT, showing greatest evidence of association (rs201825, p-value = 6.1 × 10–7). We have validated the pooling method for GWA studies by both identifying the APOE locus and by observing a strong enrichment for significantly associated SNPs. We provide evidence for LRAT as a novel candidate gene for LOAD. LRAT plays a prominent role in the Vitamin A cascade a system that has been previously implicated in LOAD.
C−H Bond Amination from a Ferrous Dipyrromethene Complex (2009)

In this Communication, we report an intramolecular C-H bond amination reaction of a dipyrromethene ferrous complex with organic azides. Monitoring of the spectral changes (variable-temperature NMR and UV-vis) of the Fe(II) complex reveals no buildup of an intermediate during conversion of the starting material into the nitrene-inserted product. The rate-determining step appears to be azide addition to the 14-electron Fe(II) complex, hinting at the potential that these and related platforms may have to effect atom- and group-transfer processes.
Nucleotide sequence of a cDNA encoding the human muscle-specific enolase (MSE) (1990)

Journal Article Nucleotide sequence of a cDNA encoding the human muscle-specific enolase (MSE) Get access Larissa Cali, Larissa Cali 1Dipartimento di Biologia Cellulare e dello SviluppoVia Archirafi 20–22, 90123 Palermo, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Salvatore Feo, Salvatore Feo Search for other works by this author on: Oxford Academic PubMed Google Scholar Daniele Oliva, Daniele Oliva 1Dipartimento di Biologia Cellulare e dello SviluppoVia Archirafi 20–22, 90123 Palermo, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Agata Giallongo Agata Giallongo Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 7, 11 April 1990, Page 1893, https://doi.org/10.1093/nar/18.7.1893 Published: 11 April 1990 Article history Accepted: 06 March 1990 Published: 11 April 1990
Sequential O-glycosylation of nuclear pore complex protein gp62 in vitro. (1993)

Gp62 is a nuclear pore complex glycoprotein of vertebrates containing multiple O-linked N-acetylglucosamine monosaccharides. We have recently shown (Cordes et al., Eur. J. Cell Biol. 55, 31-47 (1991)) that gp62 of mouse and Xenopus laevis is predominantly glycosylated in the amino-terminal half of the molecule. Here we describe in vitro glycosylation in rabbit reticulocyte lysate of gp62 and of individual segments of this protein expressed as recombinant polypeptides in E. coli. Competition experiments between purified polypeptides revealed that gp62 exhibits in vitro at least two types of binding sites for a cytosolic N-acetylglucosaminyltransferase resulting in a sequential glycosylation of the protein. High affinity binding sites for this glycosyltransferase were located in the amino-terminal domain between amino acids 248-341 of mouse gp62, whereas low affinity binding sites were scattered in the entire amino-terminal half. The segment containing amino acids 248-341 was able to compete with in vitro O-glycosylation of gp62 subdomains containing low affinity binding sites. This gp62 segment was also able to compete with O-glycosylation of other unrelated cellular proteins in vitro.
[The effects of interleukin-10 and -8 in chronic prostatitis]. (2004)

IL-10 and IL-8 had a very important role in etiology of CP, and could be detected in VB3 as well as in routine semen and EPS.
Enhancing Both Efficiency and Representational Capability of Isomap by Extensive Landmark Selection (2015)

The problems of improving computational efficiency and extending representational capability are the two hottest topics in approaches of global manifold learning. In this paper, a new method called extensive landmark Isomap (EL-Isomap) is presented, addressing both topics simultaneously. On one hand, originated from landmark Isomap (L-Isomap), which is known for its high computational efficiency property, EL-Isomap also possesses high computational efficiency through utilizing a small set of landmarks to embed all data points. On the other hand, EL-Isomap significantly extends the representational capability of L-Isomap and other global manifold learning approaches by utilizing only an available subset from the whole landmark set instead of all to embed each point. Particularly, compared with other manifold learning approaches, the data manifolds with intrinsic low-dimensional concave topologies and essential loops can be unwrapped by the new method more successfully, which are shown by simulation results on a series of synthetic and real-world data sets. Moreover, the accuracy, robustness, and computational complexity of EL-Isomap are analyzed in this paper, and the relation between EL-Isomap and L-Isomap is also discussed theoretically.
Synthesis and Crystal Structure of Mono-Substituted Ferrocene-Containing Liquid Crystals (2001)

Abstract Ten mono-substituted ferrocene-containing liquid crystals, which containing Schiff base or ester group, were prepared and their mesogenic behaviors were investigated. Two molecular structures were analyzed by X-ray. 4-ferrocenylphenyl 3′-chloro-4′-(2-methylbutyloxy)-benzoate, triclinic crystal system, P1 space group, a=12.035(2)Å, b=14.402(3)Å, c=15.137(3)Å, α =103.07(3)Å, ß = 102.01(3)Å, γ = 96.70(3)Å, Z=4, 8141 independent reflections, R=0.0528, Rw=0.1724. 4-ferrocenylphenyl 3′-chloro-4′-decanyloxybenzoate, triclinic crystal system, P1 space group, a= 11.663(2)Å, b= 11.729(2)Å, c=22.005(4)Å, α=76.10(3)Å, ß =87.56(3)Å, γ = 77.89(3)Å, Z=4, 7935 independent reflections, R=0.0784, Rw=0.2265.
A RAKE receiver with intracell interference cancellation for a DS-CDMA synchronous downlink with orthogonal codes (2002)

The conventional receiver for DS-CDMA communications is the RAKE receiver. The RAKE receiver is a matched filter, matched to the operations of spreading, pulse shape filtering and channel filtering. Such a matched filter maximizes the signal-to-interference-plus-noise ratio (SINR) at its output if the interference-plus-noise is white. This may be approximately the case if user-dependent scrambling (aperiodic spreading) is used. This is one option for the uplink in 3rd generation systems. However, this is not the case in the synchronous downlink with cell-dependent scrambling, orthogonal codes and a common channel. We propose a restricted class of linear receivers for the downlink, exhibiting a limited or no complexity increase with respect to the RAKE receiver. The linear receivers in this class have the same structure as a RAKE receiver, but the channel matched filter gets replaced by an equalizer filter that is designed to maximize the SINR at the output of the receiver. The complexity of the equalizer filter is variable and can possibly be taken to be as low as in the RAKE receiver (same structure as the channel matched filter), while its adaptation guarantees improved performance with respect to (w.r.t.) the RAKE receiver. Various adaptation strategies are considered and compared in simulations.
The Current Status of Child Health and Our Task (2009)

The purpose of this study was to examine the realities of physical health conditions of children aged from 0 to 11 for the last decade. On the basis of the analyzed results, the pragmatic and policy issues are as follows : First, in the perspective of child development, studies of physical health are needed for the benefit of integrative development of children. Second, appropriate health education programs suitable for ages of children need to be developed and made compulsory for them. Third, the prohibition of adopting the ranking evaluation in physical education is to be required at the policy level. Forth, for sustainment of the health-related activities for children, the space or facilities specifically prepared for families to exercise and rest are needed. Lastly, new regulations and management systems are needed in order to resolve the safety problems with food for children.
Genetic engineering including superseding microinjection: new ways to make GM pigs (2010)

Recent improvements in several fields of cell and molecular biology offer new promises and opportunities toward an easier, cost-effective and efficient generation of transgenic pigs.
Ultralow Fouling and Functionalizable Surface Chemistry Based on a Zwitterionic Polymer Enabling Sensitive and Specific Protein Detection in Undiluted Blood Plasma (2008)

A crucial step in the development of implanted medical devices, in vivo diagnostics, and microarrays is the effective prevention of nonspecific protein adsorption from real-world complex media such as blood plasma or serum. In this work, a zwitterionic poly(carboxybetaine acrylamide) (polyCBAA) biomimetic material was employed to create a unique biorecognition coating with an ultralow fouling background, enabling the sensitive and specific detection of proteins in blood plasma. Conditions for surface activation, protein immobilization, and surface deactivation of the carboxylate groups in the polyCBAA coating were determined. An antibody-functionalized polyCBAA surface platform was used to detect a target protein in blood plasma using a sensitive surface plasmon resonance (SPR) sensor. A selective protein was directly detected from 100% human blood plasma with extraordinary specificity and sensitivity. The total nonspecific protein adsorption on the functionalized polyCBAA surface was very low (<3 ng/cm (2) for undiluted blood plasma). Because of the significant reduction of nonspecific protein adsorption, it was possible to monitor the kinetics of antigen-antibody interactions in undiluted blood plasma. The functionalization effectiveness and detection characteristics using a cancer protein marker candidate of polyCBAA were compared with those of the conventional nonfouling oligo(ethylene glycol)-based surface chemistry.
LONG-TERM OUTCOME FOR MEN WITH ANDROGEN INDEPENDENT PROSTATE CANCER TREATED WITH KETOCONAZOLE AND HYDROCORTISONE (2005)

Ketoconazole can induce prolonged responses, occasionally lasting for years. Long responses are more likely to occur in men initiating HDK earlier in the course of disease before the cancer burden becomes excessive.
Long-Term Miglustat Therapy in Children With Niemann-Pick Disease Type C (2009)

Niemann-Pick disease type C is a rare, genetic disease associated with impaired intracellular lipid trafficking and progressive neurological symptoms. Miglustat slowed disease progression in a 12-month randomized trial in juveniles and adults with Niemann-Pick disease type C, and in a parallel, noncontrolled study in affected children. Here, the authors report the open-label extension to the pediatric study. Patients aged 4 to 12 years received open-label miglustat (dose adjusted for body surface area) for an initial 12 months, during a further 12-month extension, and a long-term, continued extension phase. Efficacy assessments included horizontal saccadic eye movement, swallowing, and ambulation. Ten children completed 24 months' treatment. Horizontal saccadic eye movement, ambulation, and swallowing were stabilized at 24 months. Analysis of key parameters of disease progression showed disease stability in 8 of 10 patients (80%). Miglustat stabilized neurological disease progression in pediatric patients with Niemann-Pick disease type C, with comparable safety and tolerability to that observed in adults and juveniles.
CHRONIC KIDNEY DISEASE—MINERAL AND BONE DISORDER (CKD‐MBD): A NEW TERM FOR A COMPLEX APPROACH (2009)

The global widespread of the chronic kidney disease (CKD) is a worldwide health problem. Its increasing incidence and prevalence and adverse outcomes (including decreased quality of life, increased morbidity and mortality) represents a huge challenge for all recent health are systems. Reflecting this situation, the new, global initiative (KDIGO) was established to enhance communication and clinical decision-making, promote the use of evidence based medicine and facilitate clinical research. The new definition, evaluation and classification of "renal osteodystrophy"; has been one of the first outcome of this initiative, suggesting the topic of chronic kidney disease--mineral and bone disorder (CKD-MBD) to be a hot problem of recent nephrology. The new terminology is consistent with a recent view on this topic and describes CKD-MBD as a complex syndrome, including abnormal mineral and PTH metabolism, altered bone structure as far as extra-skeletal calcifications.
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. (1994)

An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner, oligomers bind up to 1000-fold more tightly adjacent to the hairpin stem than predicted for binding to a free tetramer at 37 degrees C. For the interface (/) in [formula: see text] additional free energy change, delta delta G 37 degrees, for binding is roughly the nearest-neighbor delta G 37 degrees for propagation of an uninterrupted helix of equivalent sequence, CGGC. When X and Z are omitted, the delta delta 37 degrees is even more favorable by approximately 1 kcal/mol (1 cal = 4.184J). On average, predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.
A Novel Solid-Phase Synthesis of Highly Diverse Guanidines:  Reactions of Primary Amines Attached to the T2* Linker (2000)

The reaction of primary amines with the T2 diazonium resin generates polymer-bound triazenes, which can in turn be acylated by the addition of isothiocyanate. The formed thioureas are readily transformed into the corresponding guanidines by the reaction with amines in the presence of mercury(II) oxide, tosyl chloride, or silver nitrate. This reaction sequence furnishes trisubstituted guanidines that are potentially useful pharmacophores.
PCR Cloning of Human Immunoglobulin Genes (2004)

One of the first steps in an antibody-engineering project is the isolation of the immunoglobulin heavy (VH)- and light (VL)-chain variable-region genes that encode the binding domains of an antibody. This is best accomplished using the polymerase chain reaction (PCR). Before PCR, cloning antibody genes was a laborious process, requiring the creation and screening of genomic or cDNA libraries. PCR has streamlined the process considerably, simplifying tasks such as the isolation of VH and VL genes from hybridomas, and allowing entirely new approaches such as generation of large antibody fragment gene repertoires from immunized or naïve hosts that can be displayed on filamentous phage (antibody phage display; see Chapter 8 ) (1) or in other display technologies (e.g., ribosome display; see Chapter 9 ).
Overexpressing Centriole-Replication Proteins In Vivo Induces Centriole Overduplication and De Novo Formation (2007)

Our data suggest that the levels of centriolar DSas-6 determine the number of daughter centrioles formed during centriole replication. Overexpression of either DSas-6 or Sak can induce the formation of extra centrioles in some tissues but not others, suggesting that centriole replication is regulated differently in different tissues. The finding that the overexpression of DSas-4, DSas-6, or Sak can rapidly induce the de novo formation of centriole-like structures in Drosophila eggs suggests that this process results from the stabilization of centriole-precursors that are normally present in the egg.
Visual memory and motor planning in a natural task (2003)

This paper investigates the temporal dependencies of natural vision by measuring eye and hand movements while subjects made a sandwich. The phenomenon of change blindness suggests these temporal dependencies might be limited. Our observations are largely consistent with this, suggesting that much natural vision can be accomplished with "just-in-time" representations. However, we also observe several aspects of performance that point to the need for some representation of the spatial structure of the scene that is built up over different fixations. Patterns of eye-hand coordination and fixation sequences suggest the need for planning and coordinating movements over a period of a few seconds. This planning must be in a coordinate frame that is independent of eye position, and thus requires a representation of the spatial structure in a scene that is built up over different fixations.
AN OPTIMAL CONTROL MODEL FOR ANALYSIS OF TIMBER RESOURCE UTILIZATION IN SOUTHEAST ASIA (1987)

A discrete time optimal forestry model is built and a shooting method solution algorithm identified. The applicability of the model and algorithm to public policies that affect forestry resources is demonstrated in an application of the model to examine the development of wood processing capacity in Southeast Asia. The necessary conditions of the optimal control model are manipulated to identify a difference equation problem with initial and terminal conditions. The solution to this boundary value problem is identified using a search routine that repetitively, numerically evaluates (shoots) the difference equations. The solution is the trajectory that satisfies the initial and terminal conditions.
Effects of Postproduction Treatment on Plastic Solar Cells (2003)

Abstract Efficiencies of organic solar cells based on an interpenetrating network of a conjugated polymer and a fullerene as donor and acceptor materials still need to be improved for commercial use. We have developed a postproduction treatment that improves the performance of solar cells based on poly(3‐hexylthiophene) (P3HT) and [6,6]‐phenyl C 61 ‐butyric acid methyl ester (PCBM) by means of a tempering cycle at elevated temperatures in which an external voltage is simultaneously applied, resulting in a significant increase of the short‐circuit current. Using this postproduction treatment, an enhancement of the short‐circuit current density, I sc , to 8.5 mA cm –2 under illumination with white light at an illumination intensity of 800 W m –2 and an increase in external quantum efficiency (IPCE, incident photon to collected electron efficiency) to 70 % are demonstrated.
Novel cytotoxic compounds from the ascidian Lissoclinum bistratum (1989)

The isolation and structures of two new cyclic hexapeptides and two new macrocyclic ethers from the aplousobranch ascidian Lissoclinum bistratum are described. Their structures were determined by two-dimensional NMR techniques. The hexapeptides, named bistratamide A and bistratamide B, differ only by the presence or absence of one double bond. They were tested for cytotoxicity toward human fibroblast and tumor cell lines and displayed similar toxicities to the octapeptides called patellamides from Lissoclinum patella. The peptides are found within the obligate algal symbiont Prochloron but clearly differ from peptides isolated from the same Prochloron of L. patella. The macrocyclic ethers isolated from L. bistratum are exceedingly potent in cytotoxicity. They have been named bistratenes A and B, and structures for these compounds are proposed.