gebhart/patrepeval huggingface dataset:
Excited-State Intramolecular Hydrogen Transfer (ESIHT) of 1,8-Dihydroxy-9,10-anthraquinone (DHAQ) Characterized by Ultrafast Electronic and Vibrational Spectroscopy and Computational Modeling (2014)

We combine ultrafast electronic and vibrational spectroscopy and computational modeling to investigate the photoinduced excited-state intramolecular hydrogen-transfer dynamics in 1,8-dihydroxy-9,10-anthraquinone (DHAQ) in tetrachloroethene, acetonitrile, dimethyl sulfoxide, and methanol. We analyze the electronic excited states of DHAQ with various possible hydrogen-bonding schemes and provide a general description of the electronic excited-state dynamics based on a systematic analysis of femtosecond UV/vis and UV/IR pump-probe spectroscopic data. Upon photoabsorption at 400 nm, the S2 electronic excited state is initially populated, followed by a rapid equilibration within 150 fs through population transfer to the S1 state where DHAQ exhibits ESIHT dynamics. In this equilibration process, the excited-state population is distributed between the 9,10-quinone (S2) and 1,10-quinone (S1) states while undergoing vibrational energy redistribution, vibrational cooling, and solvation dynamics on the 0.1-50 ps time scale. Transient UV/vis pump-probe data in methanol also suggest additional relaxation dynamics on the subnanosecond time scale, which we tentatively ascribe to hydrogen bond dynamics of DHAQ with the protic solvent, affecting the equilibrium population dynamics within the S2 and S1 electronic excited states. Ultimately, the two excited singlet states decay with a solvent-dependent time constant ranging from 139 to 210 ps. The concomitant electronic ground-state recovery is, however, only partial because a large fraction of the population relaxes to the first triplet state. From the similarity of the time scales involved, we conjecture that the solvent plays a crucial role in breaking the intramolecular hydrogen bond of DHAQ during the S2/S1 relaxation to either the ground or triplet state.
Biomechanical and Biochemical Pulping of Sugarcane Bagasse with Ceriporiopsis subvermispora Fungal and Xylanase Pretreatments (2001)

Sugarcane bagasse was pretreated with both the white-rot fungus, Ceriporiopsis subvermispora, and xylanase enzyme for 2 weeks before soda chemithermomechanical (CTMP) and soda chemical (CP) cooking. For fungi-CTMP (BCTMP) and enzyme-fungi-CTMP (EBCTMP), the bagasse, after bio-pretreatment, was cooked with 5% sodium hydroxide, at 130 degrees C for 20 min. For the chemical pulping (CP), after fungi pretreatment (BCP) or after xylanase and fungal pretreatment (EBCP), the bagasse was cooked with 14.5% sodium hydroxide. With the BCTMP, the Klason lignin was reduced, all of the pulp strength properties were increased, and a 28% savings in refining energy consumption was obtained, but the brightness was reduced 5 points compared to the control. With the EBCTMP, the brightness losses were overcome but with a mild reduction in the pulp strength properties compared to the BCTMP. The energy savings were 5% greater than from BCTMP and 33% over the control. The BCP treatment increases somewhat the pulp strength properties, reduces the energy consumption 23%, and reduces the brightness by 9 points compared to the control; however, the kappa no. was 5.5 points higher than the control. EBCP treatment reduces brightness losses and increases the pulp yield 2% compared to the control, but with some reduction in the strength properties compared to BCP.
Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen (2015)

A major goal of HIV-1 vaccine research is the design of immunogens capable of inducing broadly neutralizing antibodies (bnAbs) that bind to the viral envelope glycoprotein (Env). Poor binding of Env to unmutated precursors of bnAbs, including those of the VRC01 class, appears to be a major problem for bnAb induction. We engineered an immunogen that binds to VRC01-class bnAb precursors and immunized knock-in mice expressing germline-reverted VRC01 heavy chains. Induced antibodies showed characteristics of VRC01-class bnAbs, including a short CDRL3 (light-chain complementarity-determining region 3) and mutations that favored binding to near-native HIV-1 gp120 constructs. In contrast, native-like immunogens failed to activate VRC01-class precursors. The results suggest that rational epitope design can prime rare B cell precursors for affinity maturation to desired targets.
A ligand-dependent bipartite nuclear targeting signal in the human androgen receptor. Requirement for the DNA-binding domain and modulation by NH2-terminal and carboxyl-terminal sequences. (1994)

The amino acid sequence requirements for androgen-dependent androgen receptor nuclear import were determined by immunostaining transiently expressed full-length wild type and mutant human androgen receptors (AR) in monkey kidney COS cells and measuring transcriptional activity by cotransfection with a luciferase reporter vector in monkey kidney CV1 cells. Mutagenesis studies revealed a bipartite nuclear targeting sequence in the DNA binding and hinge regions at amino acids 617-633, consisting of two clusters of basic amino acids separated by 10 amino acids, (sequence: see text). In a series of deletion mutants, AR NH2-terminal fragments (residues 1-639 through 1-723) displayed constitutive nuclear import, and transcriptional activity was similar to that of the ligand-activated full-length wild type AR. In contrast, nuclear import and transcriptional activation were inhibited by sequence extensions into the steroid-binding domain (1-771). Constitutive nuclear import was regained in part by NH2-terminal deletions of full-length AR. Expression of AR/pyruvate kinase chimeras defined a sequence required for pre-dominant nuclear localization as residues 580-661, comprised of the second zinc finger region of the DNA-binding domain, the 17-amino-acid putative targeting sequence, and 28 residues of flanking carboxyl-terminal sequence. These studies suggest that the bipartite nuclear targeting sequence of AR includes flanking sequence and is modulated by interactions between the NH2-and carboxyl-terminal regions.
A Short Proof of Representability of Fork Algebras (1995)

In this paper a strong relation is demonstrated between fork algebras and quasi-projective relation algebras. With the help of the representation theorem of quasi-projective relation algebras, a short proof is given for the representation theorem of fork algebras.
Self-Doping Contacts and Associated Silicon Solar Cell Structures (1998)

Presented at the 2nd World Conference on Photovoltaic Solar Energy Conversion; Vienna, Austria; July 6-10, 1998.
The BiBa one-time signature and broadcast authentication protocol (2001)

We introduce the BiBa signature scheme, a new signature construction that uses one-way functions without trapdoors. BiBa features a low verification overhead and a relatively small signature size. In comparison to other one-way function based signature schemes, BiBa has smaller signatures and is at least twice as fast to verify (which probably makes it one of the fastest signature scheme to date for verification). On the downside, the BiBa public key is large, and the signature generation overhead is higher than previous schemes based on one-way functions without trapdoors (although it can be trivially parallelized).One of the main challenges of securing broadcast communication is source authentication, which allows all receivers to verify the origin of the data. An ideal broadcast authentication protocol should be efficient for the sender and the receiver, have a small communication overhead, allow the receiver to authenticate each individual packet, provide perfect robustness to packet loss, scale to large numbers of receivers, and provide instant authentication (no buffering of data at the sender or receiver side). We are not aware of any previous protocol that satisfies all these properties. We present the BiBa broadcast authentication protocol, a new construction based on the BiBa signature, that achieves all our desired properties, with the tradeoff that it requires a moderate computation overhead for the sender to generate the authentication information, and that it requires loose time synchronization between the sender and receivers.
Detection of enterovirus viraemia in blood donors (2001)

The prevalence of enterovirus viraemia detected in this study predicts that at least 1000 enterovirus-contaminated blood components are transfused per year in the UK. The frequency of transmission and clinical outcome after exposure to enterovirus-contaminated blood components in recipients is unknown.
Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery (2010)

Intensive anticancer drug discovery efforts have been made to develop small molecule inhibitors of the p53-MDM2 and p53-MDMX interactions. We present here the structures of the most potent inhibitors bound to MDM2 and MDMX that are based on the new imidazo-indole scaffold. In addition, the structure of the recently reported spiro-oxindole inhibitor bound to MDM2 is described. The structures indicate how the substituents of a small molecule that bind to the three subpockets of the MDM2/X-p53 interaction should be optimized for effective binding to MDM2 and/or MDMX. While the spiro-oxindole inhibitor triggers significant ligand-induced changes in MDM2, the imidazo-indoles share similar binding modes for MDMX and MDM2, but cause only minimal induced-fit changes in the structures of both proteins. Our study includes the first structure of the complex between MDMX and a small molecule and should aid in developing efficient scaffolds for binding to MDMX and/or MDM2.
Neuroanatomy in Rett syndrome (1997)

Rett syndrome (RS), a neurodevelopmental disorder of unknown etiology occurring almost exclusively in females, is characterized by autistic-like behavior, motor dysfunction, loss of language skills, dementia, and microcephaly. This study is a follow-up and extension of a previously reported neuroimaging study of patients with RS. We replicated previously reported findings with a larger patient population, and the volumetric MRI analysis was extended to include an analysis of neuroanatomy of the posterior fossa. Twenty girls with RS were compared with individually age- and gender-matched normal controls. Patients with RS showed global reduction in gray- and white-matter volumes. The prefrontal, posterior-frontal, and anterior-temporal regions showed the largest bilateral decrease in gray-matter volume, whereas white-matter volume was uniformly reduced throughout the brain. We found confirmation for the preferential reduction in caudate nucleus volume. However, we observed no preferential reduction in midbrain volume despite a preferential reduction in the midsagittal area of this region. We also present an individual case comparison between monozygotic twins discordant for RS.
Targeting, dosimetry, and radioimmunotherapy of B-cell lymphomas with iodine-131-labeled LL2 monoclonal antibody. (1991)

Sixteen patients with non-Hodgkin's lymphoma were infused with 6.2 to 58.2 mCi (0.2 to 3.9 mg) doses of radioactive iodine (131I)-labeled LL2 immunoglobulin G (IgG) or F(ab')2, in order to study antibody distribution, pharmacokinetics, dosimetry, toxicity, tumor targeting, and therapy. LL2 is a murine IgG2a monoclonal antibody (MAb) reactive with B cells and non-Hodgkin's B-cell lymphoma. In a series of five assessable therapy patients, doses as small as 30 mCi 131I-LL2 IgG or F(ab')2 resulted in tumor responses (two partial remissions, two mixed and minor responses, and one no response), while one patient receiving diagnostic doses as low as 6.2 mCi showed a partial remission for 1 year and a complete remission after a second low radiation dose. No acute toxicities were noted, and only myelotoxicity accompanied therapeutic doses, with grade IV marrow toxicity seen in three of seven patients receiving total doses of about 50 mCi. Dosimetry calculations showed spleen and tumor dose rules of about 4.6 cGy/mCi, which was three to four times the dose to other organs. Despite the administration of relatively low doses of LL2 (0.2 to 3.9 mg), 82% of 60 known extrasplenic lymphoma sites were imaged. Serum clearance showed an average distribution half-life (T1/2) of 2.1 hours and an elimination T1/2 of 32.0 hours. The average total-body clearance T1/2 was 43 to 45 hours. LL2's antigenic target does not appear to be shed in high amounts into the circulation. Three of eight patients having at least two injections showed a human antimouse antibody response. These patients may have been presensitized to animal protein. An interesting observation in this study was the marked drop in circulating B lymphocytes after the administration of radioiodinated LL2 or anticarcinoembryonic antigen MAbs, suggesting that this is a nonspecific radiation effect and not necessarily related to the binding of MAb to normal B cells.
Magnetic moment and plasma environment of HD 209458b as determined from Lyα observations (2014)

Transit observations of HD 209458b in the stellar Lyman-α(Lyα) line revealed strong absorption in both blue and red wings of the line interpreted as hydrogen atoms escaping from the planet's exosphere at high velocities. The following sources for the absorption were suggested: acceleration by the stellar radiation pressure, natural spectral line broadening, or charge exchange with the stellar wind. We reproduced the observation by means of modeling that includes all aforementioned processes. Our results support a stellar wind with a velocity of ≈400 kilometers per second at the time of the observation and a planetary magnetic moment of ≈1.6 × 10(26) amperes per square meter.
Epinephrine-induced activation of LW-mediated sickle cell adhesion and vaso-occlusion in vivo (2007)

Sickle red cell (SS RBC) adhesion is believed to contribute to the process of vaso-occlusion in sickle cell disease (SCD). We previously found that the LW RBC adhesion receptor can be activated by epinephrine to mediate SS RBC adhesion to endothelial alphavbeta3 integrin. To determine the contribution of LW activation to vaso-occlusive events in vivo, we investigated whether in vitro treatment of SS RBCs by epinephrine resulted in vaso-occlusion in intact microvasculature after RBC infusion into nude mice. Epinephrine enhanced human SS but not normal RBC adhesion to murine endothelial cells in vitro and to endothelium in vivo, promoting vaso-occlusion and RBC organ sequestration. Murine sickle RBCs also responded to epinephrine with increased adhesion to postcapillary endothelium in nude mice. Epinephrine-induced SS RBC adhesion, vaso-occlusion, and RBC organ trapping could be prevented by the beta-adrenergic receptor (beta-AR) antagonist, propranolol. Infusion of soluble recombinant LW also significantly reduced adhesion and vaso-occlusion. In addition, epinephrine-treated SS RBCs induced activation of murine leukocyte adhesion to endothelium as well. We conclude that LW activation by epinephrine via beta-AR stimulation can promote both SS RBC and leukocyte adhesion as well as vaso-occlusion, suggesting that both epinephrine and LW play potentially pathophysiological roles in SCD.
Alternative splicing of fibronectin is temporally and spatially regulated in the chicken embryo (1989)

The primary gene transcript for the adhesive extracellular matrix glycoprotein fibronectin (FN) is alternatively spliced in three regions (EIIIA, EIIIB and V). At least one of these regions (V) has been shown to encode cell-binding sites, suggesting that splicing represents a mechanism to create functionally different forms of FN at different times and places. In order to test this hypothesis, we have examined the extent of alternative splicing of fibronectin during embryonic development. The distribution of the different spliced forms of FN mRNA in developing chicken embryos was determined using probes specific for the spliced regions in ribonuclease protection and in situ hybridization experiments. At embryonic day 2-4 (E2-4), all three spliced regions were included wherever FN mRNA was detected. At E16, however, we found spatially distinct splicing differences within the embryo, with cell-type-specific splicing excluding EIIIA and/or EIIIB in some tissues. In contrast, we did not detect exclusion of the V region. In a more detailed developmental study of the simplest of these tissues, the chorioallantoic membrane, we found that EIIIB was preferentially excluded after the completion of growth. These results suggest that FN splicing is used during development as a mechanism to create different forms of FN within the extracellular matrix by the inclusion or exclusion of specific segments. The data are consistent with an essential role for one of these segments, EIIIB, in the migration and/or proliferation of embryonic cells prior to their terminal differentiation and also suggest possible roles for the EIIIA segment.
Measurement of gut permeability using fluorescent tracer agent technology (2017)

The healthy gut restricts macromolecular and bacterial movement across tight junctions, while increased intestinal permeability accompanies many intestinal disorders. Dual sugar absorption tests, which measure intestinal permeability in humans, present challenges. Therefore, we asked if enterally administered fluorescent tracers could ascertain mucosal integrity, because transcutaneous measurement of differentially absorbed molecules could enable specimen-free evaluation of permeability. We induced small bowel injury in rats using high- (15 mg/kg), intermediate- (10 mg/kg), and low- (5 mg/kg) dose indomethacin. Then, we compared urinary ratios of enterally administered fluorescent tracers MB-402 and MB-301 to urinary ratios of sugar tracers lactulose and rhamnose. We also tested the ability of transcutaneous sensors to measure the ratios of absorbed fluorophores. Urinary fluorophore and sugar ratios reflect gut injury in an indomethacin dose dependent manner. The fluorophores generated smooth curvilinear ratio trajectories with wide dynamic ranges. The more chaotic sugar ratios had narrower dynamic ranges. Fluorophore ratios measured through the skin distinguished indomethacin-challenged from same day control rats. Enterally administered fluorophores can identify intestinal injury in a rat model. Fluorophore ratios are measureable through the skin, obviating drawbacks of dual sugar absorption tests. Pending validation, this technology should be considered for human use.
A Bacillus subtilis gene‐encoding protein homologous to eukaryotic SMC motor protein is necessary for chromosome partition (1998)

We have analysed the function of a gene of Bacillus subtilis, the product of which shows significant homology with eukaryotic SMC proteins essential for chromosome condensation and segregation. Two mutant strains were constructed; in one, the expression was under the control of the inducible spac promoter (conditional null) and, in the other, the gene was disrupted by insertion (disrupted null). Both could form colonies at 23 degree C but not at 37 degree C in the absence of the expression of the Smc protein, indicating that the B. subtilis smc gene was essential for cell growth at higher temperatures. Microscopic examination revealed the formation of anucleate and elongated cells and diffusion of nucleoids within the elongated cells in the disrupted null mutant grown at 23 degree C and in the conditional null mutant grown in low concentrations of IPTG at 37 degree C. In addition, immunofluorescence microscopy showed that subcellular localization of the SpoOJ partition protein was irregular in the smc disrupted null mutant, compared with bipolar localization in wild-type cells. These results indicate that the B. subtilis smc gene is essential for chromosome partition. The role of B. subtilis Smc protein in chromosome partition is discussed.
Electrophysiological examination of the effects of sustained flibanserin administration on serotonin receptors in rat brain (1999)

5-HT1A receptor agonists have proven to be effective antidepressant medications, however they suffer from a significant therapeutic lag before depressive symptoms abate. Flibanserin is a 5-HT1A receptor agonist and 5-HT2A receptor antagonist developed to possibly induce a more rapid onset of antidepressant action through its preferential postsynaptic 5-HT1A receptor agonism. Flibanserin antagonized the effect of microiontophoretically-applied DOI in the medial prefrontal cortex (mPFC) following 2 days of administration, indicating antagonism of postsynaptic 5-HT2A receptors. This reduction in the effect of locally-applied DOI was no longer present following 7-day flibanserin administration. Two-day flibanserin administration only marginally reduced the firing activity of dorsal raphe (DRN) 5-HT neurons. Following 7 days of administration, 5-HT neuronal firing activity had returned to normal and the somatodendritic 5-HT1A autoreceptors were desensitized. The responsiveness of postsynaptic 5-HT1A receptors located on CA3 hippocampus pyramidal neurons and mPFC neurons, examined using microiontophoretically-applied 5-HT and gepirone, was unchanged following a 7-day flibanserin treatment. As demonstrated by the ability of the 5-HT1A receptor antagonist WAY 100635 to selectively increase the firing of hippocampal neurons in 2- and 7-day treated rats, flibanserin enhanced the tonic activation of postsynaptic 5-HT1A receptors in this brain region. The results suggest that flibanserin could be a therapeutically useful compound putatively endowed with a more rapid onset of antidepressant action.
cdc25+ encodes a protein phosphatase that dephosphorylates p34cdc2. (1992)

To determine how the human cdc25 gene product acts to regulate p34cdc2 at the G2 to M transition, we have overproduced the full-length protein (cdc25Hs) as well as several deletion mutants in bacteria as glutathione-S-transferase fusion proteins. The wild-type cdc25Hs gene product was synthesized as an 80-kDa fusion protein (p80GST-cdc25) and was judged to be functional by several criteria: recombinant p80GST-cdc25 induced meiotic maturation of Xenopus oocytes in the presence of cycloheximide; p80GST-cdc25 activated histone H1 kinase activity upon addition to extracts prepared from Xenopus oocytes; p80GST-cdc25 activated p34cdc2/cyclin B complexes (prematuration promoting factor) in immune complex kinase assays performed in vitro; p80GST-cdc25 stimulated the tyrosine dephosphorylation of p34cdc2/cyclin complexes isolated from Xenopus oocyte extracts as well as from overproducing insect cells; and p80GST-cdc25 hydrolyzed p-nitrophenylphosphate. In addition, deletion analysis defined a functional domain residing within the carboxy-terminus of the cdc25Hs protein. Taken together, these results suggest that the cdc25Hs protein is itself a phosphatase and that it may function directly in the tyrosine dephosphorylation and activation of p34cdc2 at the G2 to M transition.
Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients (2019)

T cells, as a crucial compartment of the tumour microenvironment, play vital roles in cancer immunotherapy. However, the basic properties of tumour-infiltrating T cells (TILs) such as the functional state, migratory capability and clonal expansion remain elusive. Here, using Smart-seq2 protocol, we have generated a RNA sequencing dataset of 11,138 T cells isolated from peripheral blood, adjacent normal and tumour tissues of 12 colorectal cancer (CRC) patients, including 4 with microsatellite instability (MSI). The dataset contained an expression profile of 10,805 T cells, as well as the full-length T cell receptor (TCR) sequences of 9,878 cells after quality control. To facilitate data mining of our T cell dataset, we developed a web-based application to deliver systematic interrogations and customizable functionalities ( http://crctcell.cancer-pku.cn/ ). Functioning with our dataset, the web tool enables the characterization of TILs based on both transcriptome and assembled TCR sequences at the single cell level, which will help unleash the potential value of our CRC T cell data resource.