gebhart/patrepeval huggingface dataset:
Prediction of the Coding Sequences of Unidentified Human Genes. XIV. The Complete Sequences of 100 New cDNA Clones from Brain Which Code for Large Proteins in vitro (1999)

To extend our cDNA project for accumulating basic information on unidentified human genes, we newly determined the sequences of 100 cDNA clones from a set of size-fractionated human adult and fetal brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA1019 to KIAA1118. The sequencing of these clones revealed that the average size of the inserts and corresponding open reading frames were 5.0 kb and 2.6 kb (880 amino acid residues), respectively. Database search of the predicted amino acid sequences classified 58 predicted gene products into the five functional categories, such as cell signaling/communication, cell structure/motility, nucleic acid management, protein management and cell division. It was also found that, for 34 gene products, homologues were detected in the databases, which were similar in sequence through almost the entire regions. The chromosomal locations of the genes were determined by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of all the genes among 10 human tissues, 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substania nigra, subthalamic nucleus, and thalamus), spinal cord, fetal brain and fetal liver were also examined by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
III-nitride photonic crystals (2003)

We report the achievement of nanofabrication and characterization of a triangular lattice array of photonic crystals (PCs) with diameter/periodicity as small as 100/180 nm on an InGaN/GaN multiple quantum well using electron-beam lithography and inductively coupled plasma dry etching. Optical measurements of the PCs performed using near-field scanning optical microscopy showed a 60° periodic variation with the angle between the propagation direction of emission light and the PCs lattice. An unprecedented maximum enhancement factor of 20 was obtained for the emission light intensity at wavelengths as short as 475 nm at room temperature with emission light parallel to the Γ–K direction of the PCs lattice. The implications of these results to nitride-based optoelectronic devices, particularly in improving the light extraction efficiency in light-emitting diodes both for blue/green as well as UV emitters, are discussed.
Spacer DNA sequences upstream of the T-A-T-A-A-A-T-A sequence are essential for promotion of H2A histone gene transcription in vivo. (1980)

The control region of a sea urchin H2A histone gene may be functionally dissected into at least three DNA segments, which we have termed modulator, selector, and initiator elements. While the initiator and in particular the selector containing the T-A-T-A-A-A-T-A sequence are specificity elements that dictate the generation of faithful 5' ends to H2A mRNA, the modulators control the rate at which these specificity elements operate [Grosschedl, R. & Birnstiel, M. L. (1980) Proc. Natl. Acad. Sci. USA 77, 1432-1436]. By functional tests of in vitro mutated histone DNA in the Xenopus oocyte we have now discovered that the segment E of the A+T-rich spacer DNA lying at a considerable distance upstream of the conservative T-A-T-A-A-A-T-A sequence is a strong modulator element of H2A gene transcription. Deletion of this element creates a 15- to 20-fold H2A-specific down mutation. Segment E by itself cannot elicit initiation of transcription except in coordination with the prelude sequence of the H2A gene. The nucleotide sequence of the relevant spacer element showing modulator activity has been determined and found to contain a pattern of T and A runs as well as a series of inverted repeats. Additional pre-H2A spacer mutants, including a spacer inversion mutant, have been constructed in vitro, that, when injected into the oocyte nucleus, modulate the expression of the H2A gene by an overall factor as large as 100. Other factors controlling promoter activity are discussed.
A non-fullerene acceptor with a diagnostic morphological handle for streamlined screening of donor materials in organic solar cells (2017)

Utilizing the <italic>N</italic>-annulated PDI acceptor <bold>PDI–DPP–PDI</bold>, a simple air-processed and air-tested organic photovoltaic device fabrication procedure has been established to streamline the screening of donor materials.
Rad9 Has a Functional Role in Human Prostate Carcinogenesis (2008)

Prostate cancer is currently the most common type of neoplasm found in American men, other than skin cancer, and is the second leading cause of cancer death in males. Because cell cycle checkpoint proteins stabilize the genome, the relationship of one such protein, Rad9, to prostate cancer was investigated. We found that four prostate cancer cell lines (CWR22, DU145, LNCaP, and PC-3), relative to PrEC normal prostate cells, have aberrantly high levels of Rad9 protein. The 3'-end region of intron 2 of Rad9 in DU145 cells is hypermethylated at CpG islands, and treatment with 5'-aza-2'-deoxycytidine restores near-normal levels of methylation and reduces Rad9 protein abundance. Southern blot analyses indicate that PC-3 cells contain an amplified Rad9 copy number. Therefore, we provide evidence that Rad9 levels are high in prostate cancer cells due at least in part to aberrant methylation or gene amplification. The effectiveness of small interfering RNA to lower Rad9 protein levels in CWR22, DU145, and PC-3 cells correlated with reduction of tumorigenicity in nude mice, indicating that Rad9 actively contributes to the disease. Rad9 protein levels were high in 153 of 339 human prostate tumor biopsy samples examined and detectable in only 2 of 52 noncancerous prostate tissues. There was a strong correlation between Rad9 protein abundance and cancer stage. Rad9 protein level can thus provide a biomarker for advanced prostate cancer and is causally related to the disease, suggesting the potential for developing novel diagnostic, prognostic, and therapeutic tools based on detection or manipulation of Rad9 protein abundance.
Are amyotrophic lateral sclerosis patients cognitively normal? (2003)

This study suggests that frontal executive deficits are present in half of ALS patients, many of whom meet strict research criteria for FTLD. Word generation tests are a useful screening tool in this cohort.
Vitamin K and Energy Transduction: A Base Strength Amplification Mechanism (1995)

Energy transfer provides an arrow in the metabolism of living systems. Direct energetic coupling of chemical transformations, such that the free energy generated in one reaction is channeled to another, is the essence of energy transfer, whereas the purpose is the production of high-energy chemical intermediates. Vitamin K provides a particularly instructive example of energy transfer. A key principle at work in the vitamin K system can be termed "base strength amplification." In the base strength amplification sequence, the free energy of oxygenation of vitamin K hydroquinone (vitamin KH2) is used to transform a weak base to a strong base in order to effect proton removal from selected glutamate (Glu) residues in the blood-clotting proteins.
Regnase-1 controls colon epithelial regeneration via regulation of mTOR and purine metabolism (2018)

Damage to intestinal epithelial cell (IEC) layers during intestinal inflammation is associated with inflammatory bowel disease. Here we show that the endoribonuclease Regnase-1 controls colon epithelial regeneration by regulating protein kinase mTOR (the mechanistic target of rapamycin kinase) and purine metabolism. During dextran sulfate sodium-induced intestinal epithelial injury and acute colitis, Regnase-1<sup>∆IEC</sup> mice, which lack Regnase-1 specifically in the intestinal epithelium, were resistant to body weight loss, maintained an intact intestinal barrier, and showed increased cell proliferation and decreased epithelial apoptosis. Chronic colitis and tumor progression were also attenuated in Regnase-1<sup>∆IEC</sup> mice. Regnase-1 predominantly regulates mTORC1 signaling. Metabolic analysis revealed that Regnase-1 participates in purine metabolism and energy metabolism during inflammation. Furthermore, increased expression of ectonucleotidases contributed to the resolution of acute inflammation in Regnase-1<sup>∆IEC</sup> mice. These findings provide evidence that Regnase-1 deficiency has beneficial effects on the prevention and/or blocking of intestinal inflammatory disorders.
Improving the Blood Compatibility of Ion-Selective Electrodes by Employing Poly(MPC-co-BMA), a Copolymer Containing Phosphorylcholine, as a Membrane Coating (2002)

The hydrogelpoly(2-methacryloyloxyethylphosphorylcholine-co-butyl methacrylate), or poly(MPC-co-BMA), was used as a coating for polyurethane- and poly(vinyl chloride)-based membranes to develop ion-selective electrodes (ISEs) with enhanced blood compatibility. Adverse interactions of poly(MPC-co-BMA) with blood were diminished due to the phosphorylcholine functionalities of the hydrogel, which mimic the phospholipid polar groups present on the surface of many cell membranes. As demonstrated by immunostaining, hydrogel-coated PVC membranes soaked in platelet-rich plasma showed less adhesion and activation of platelets than uncoated PVC membranes, indicating an improvement in biocompatibility owing to the hydrogel. Furthermore, little differences in the potentiometric response characteristics, e.g., slope, detection limit, and selectivity, of ISEs employing uncoated and coated membranes were observed.
Viability, Apoptosis, Proliferation, Activation, and Cytokine Secretion of Human Keratoconus Keratocytes after Cross-Linking (2015)

Cross-linking decreases viability, triggers apoptosis, and inhibits proliferation, without an impact on multipotent hematopoietic stem cell transformation and myofibroblastic transformation of KC keratocytes. CXL triggers FGFb secretion of KC keratocytes transiently (5 hours), normalizing after 24 hours.
Quantitative analysis of beam delivery parameters and treatment process time for proton beam therapy (2011)

This analysis shows that the facility has operated at a high performance level and has treated a large number of patients with a variety of diseases. The use factor of beam delivery parameters varies by disease site. Further improvements in efficiency may be realized in the equipment- and patient-related processes of treatment.
Identity of zinc finger nucleases with specificity to herpes simplex virus type II genomic DNA: novel HSV-2 vaccine/therapy precursors (2011)

ZFNs with specificity to HSV-2 genomic DNA that are precursors of novel host-genome expressed HSV-2 gene-therapeutics or vaccines were identified.
Blockade of the B7‐CD28 Pathway by CTLA4–Ig Counteracts Rejection and Prolongs Survival in Small Bowel Transplantation (2000)

Allograft rejection involves T-cell activation, requiring T-cell receptor interactions with major histocompatibility complex (MHC) molecules and costimulatory signals delivered through the B7-CD28 pathway. We evaluated the effect of blocking this pathway on graft rejection and survival, in a rat experimental model of small bowel transplantation. Heterotopic small bowel transplantation was performed between PVG donor rats and DA recipient rats. The recipient animals were treated with CTLA4-Ig or irrelevant immunoglobulin (Ig)G as control and followed for 18, 30 or 90 days. The survival rate and degree of inflammation and accumulation of CD4+ T cells and macrophages were determined in the transplanted bowels. We found that administration of CTLA4-Ig significantly improved the survival rate compared to control rats: after 30 days 73% of the treated rats had survived and at 90 days 5/8 rats were still living, whereas in the control group only 2/8 rats had survived. The grafts showed preserved mucosal structure with only a mild degree of subacute inflammation and the accumulation of CD4+ T cells and macrophages was noticeably reduced in treated animals as compared to control rats. Necrosis was extensive in control rats, whereas CTLA4-Ig treated animals had grafts with at least some preserved villus morphology and no necrotic tissue. Although small bowel transplantation has proven exceptionally difficult, in this study we have shown that CTLA4-Ig treatment may provide a promising strategy to prevent rejection and induce long term tolerance and graft survival.
Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. (1992)

A methodology designed to address the inverse globular protein-folding problem (the identification of which sequences are compatible with a given three-dimensional structure) is described. By using a library of protein finger-prints, defined by the side chain interaction pattern, it is possible to match each structure to its own sequence in an exhaustive data base search. It is shown that this is a permissive requirement for the validation of the methodology. To pass the more rigorous test of identifying proteins that are not close sequence homologs, but that have similar structure, the method has been extended to include insertions and deletions in the sequence, which is compared to the fingerprint. This allows for the identification of sequences having little or no sequence homology to the fingerprint. Examples include plastocyanin/azurin/pseudoazurin, the globin family, different families of proteases and cytochromes, including cytochromes c' and b-562, actinidin/papain, and lysozyme/alpha-lactalbumin. Turning to supersecondary structure prediction, we find that alpha/beta/alpha fragments possess sufficient specificity to identify their own and related sequences. By threading a beta-hairpin through a sequence, it is possible to predict the location of such hairpins and turns with remarkable fidelity. Thus, the method greatly extends existing techniques for the prediction of both global structural homology and local supersecondary structure.
Ester Bonds in Prodrugs (2008)

A recent study challenges the oft-held notion that ester bonds in prodrug molecules are cleaved rapidly and completely inside cells by endogenous, nonspecific esterases. Structure-activity relationship studies on acylated sugars reveal that regioisomeric compounds display disparate biological activity, suggesting that ester bonds can persist in a cellular context.
Comparative studies of CAM 123-6 and carcinoembryonic antigen for the serological detection of pulmonary adenocarcinoma. (1997)

Carcinoembryonic antigen (CEA) has been clinically used as a serum marker for lung cancer, especially for pulmonary adenocarcinoma. Since we had developed a tumor marker against pulmonary adenocarcinoma, CAM 123-6 belonging to KL-6 MUC 1 mucin, we compared its clinical value with that of CEA, in combination with squamous cell carcinoma-related antigen (SCC) and neuron-specific enolase (NSE). The subjects were 30 patients with adenocarcinoma, 23 with squamous cell carcinoma, 16 with small cell carcinoma, and 20 with benign lung disease. For discriminating lung cancer from benign lung disease, the combination of CAM 123-6, SCC, and NSE showed 64% diagnostic accuracy, and the combination of CEA, SCC, and NSE 65%. In differentiating pulmonary adenocarcinoma from other lung cancer, the diagnostic accuracy of CAM 123-6 was 81% and that of CEA was 74%, although there was no significant difference between them. These observations indicate that the diagnostic accuracy of CAM 123-6 is similar to that of CEA. Neither marker is sufficiently specific to differentiate pulmonary adenocarcinoma from other forms of lung cancer.
Combinatorial exploration of rare-earth-free permanent magnets: Magnetic and microstructural properties of Fe-Co-W thin films (2013)

We have investigated the magnetic and structural properties of Fe-Co-W films using a composition spread technique. From the magnetometry measurements, large magnetization (900 emu/cm3) and enhanced perpendicular coercive fields (2–3 kOe) of low W concentration films were observed. The synchrotron diffraction results show a structural transition from a crystalline to an amorphous state and the crystallization onset increases with increasing W concentration. The SEM and TEM characterizations show that the films with low W concentrations have vertically standing platelet-like grain structures which is ascribed to the enhanced coercive fields. Magnetometry studies indicate that as the W concentration increases, microstructural change results in evolution of magnetization reversal mechanism.
Resting and task‐elicited prefrontal EEG alpha asymmetry in depression: Support for the capability model (2014)

The capability model of frontal electroencephalographic (EEG) asymmetry suggests that brain activity during emotional challenge will be a more powerful indicator of predispositions toward psychopathology than activity observed at rest. EEG data were assessed during a resting baseline and a facial emotion task, wherein individuals with (n = 143) and without (n = 163) lifetime major depressive disorder (MDD) made approach (angry and happy) and withdrawal (afraid and sad) facial expressions. EEG asymmetry during emotional challenge was a more powerful indicator of MDD status than resting asymmetry for average, Cz, and linked mastoid references, results in support of the capability model. However, current-source-density (CSD) transformed asymmetry was indicative of lifetime MDD status under resting and task-elicited conditions. Findings suggest that CSD-transformed data may be more robust indicators of trait frontal EEG asymmetry.
E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis (2001)

The retinoblastoma protein (pRB) and its two relatives, p107 and p130, regulate development and cell proliferation in part by inhibiting the activity of E2F-regulated promoters. We have used high-density oligonucleotide arrays to identify genes in which expression changed in response to activation of E2F1, E2F2, and E2F3. We show that the E2Fs control the expression of several genes that are involved in cell proliferation. We also show that the E2Fs regulate a number of genes involved in apoptosis, differentiation, and development. These results provide possible genetic explanations to the variety of phenotypes observed as a consequence of a deregulated pRB/E2F pathway.
Molecular Pathways of Neurodegeneration in Parkinson's Disease (2003)

Parkinson's disease (PD) is a complex disorder with many different causes, yet they may intersect in common pathways, raising the possibility that neuroprotective agents may have broad applicability in the treatment of PD. Current evidence suggests that mitochondrial complex I inhibition may be the central cause of sporadic PD and that derangements in complex I cause α-synuclein aggregation, which contributes to the demise of dopamine neurons. Accumulation and aggregation of α-synuclein may further contribute to the death of dopamine neurons through impairments in protein handling and detoxification. Dysfunction of parkin (a ubiquitin E3 ligase) and DJ-1 could contribute to these deficits. Strategies aimed at restoring complex I activity, reducing oxidative stress and α-synuclein aggregation, and enhancing protein degradation may hold particular promise as powerful neuroprotective agents in the treatment of PD.
Monodisperse w/w/w Double Emulsion Induced by Phase Separation (2012)

We develop an approach to fabricate monodisperse water-in-water-in-water (w/w/w) double emulsion in microfluidic devices. A jet of aqueous solution containing two incompatible solutes, dextran and polyethylene glycol (PEG), is periodically perturbed into water-in-water (w/w) droplets. By extracting water out of the w/w droplet, the solute concentrations in the droplet phase increase; when the concentrations exceed the miscibility limit, the droplet phase separates into two immiscible phases. Consequently, PEG-rich droplets are formed within the single emulsion templates. These PEG-rich droplets subsequently coalesce with each other, resulting in transiently stable w/w/w double emulsions with a high degree of size uniformity. These double emulsions are free of organic solvents and thus are ideal for use as droplet-vessels in protein purification, as microreactors for biochemical reactions, and as templates for fabrication of biomaterials.
Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells (2007)

Embryonic stem (ES) cells are pluripotent cells with the ability to self-renew indefinitely. These unique properties are controlled by genetic factors and chromatin structure. The exit from the self-renewing state is accompanied by changes in epigenetic chromatin modifications such as an induction in the silencing-associated histone H3 Lys 9 dimethylation and trimethylation (H3K9Me2/Me3) marks. Here, we show that the H3K9Me2 and H3K9Me3 demethylase genes, Jmjd1a and Jmjd2c, are positively regulated by the ES cell transcription factor Oct4. Interestingly, Jmjd1a or Jmjd2c depletion leads to ES cell differentiation, which is accompanied by a reduction in the expression of ES cell-specific genes and an induction of lineage marker genes. Jmjd1a demethylates H3K9Me2 at the promoter regions of Tcl1, Tcfcp2l1, and Zfp57 and positively regulates the expression of these pluripotency-associated genes. Jmjd2c acts as a positive regulator for Nanog, which encodes for a key transcription factor for self-renewal in ES cells. We further demonstrate that Jmjd2c is required to reverse the H3K9Me3 marks at the Nanog promoter region and consequently prevents transcriptional repressors HP1 and KAP1 from binding. Our results connect the ES cell transcription circuitry to chromatin modulation through H3K9 demethylation in pluripotent cells.
Lymphokine and nonlymphokine mRNA levels in stimulated human T cells. Kinetics, mitogen requirements, and effects of cyclosporin A. (1986)

Northern and dot blotting with a panel of DNA probes were used to monitor the levels of specific mRNAs in mitogen-stimulated human T cells. The induction of IL-2 and IFN mRNAs required the synergistic action of PMA and either PHA or OKT3 mAb. In contrast, several nonlymphokine genes, the protooncogenes c-fos and c-myc, and the IL-2-R gene, were induced by either PHA or PMA alone. PHA increased the background levels of a 70 kD heat shock protein mRNA, but did not affect the observed background of c-myb mRNA. For all mRNAs that were induced, isolated CD4 and CD8 T cell subsets behaved similarly. Exogenous IL-2 had little (IFN) or no (IL-2) effect on lymphokine mRNAs, but significantly increased c-myc, IL-2-R and heat shock protein mRNAs. Therefore, the stimuli for lymphokine mRNAs differed from those required for several inducible nonlymphokine genes. IL-2 and IFN mRNAs exhibited some important similarities with c-myc, however. The levels of IL-2, IFN, and c-myc mRNA followed similar kinetics, peaking at 3 h in restimulated blasts and at 12 h in unstimulated T cells. The subsequent downregulation of lymphokine and c-myc mRNAs was retarded by cycloheximide. The induction of IL-2, IFN, and c-myc mRNAs was blocked by the immunosuppressive drug CsA, but not by the inactive analog CsH, and this block occurred at the level of nuclear transcription. Since the exogenous stimuli for lymphokine and c-myc gene expression differ, we suggest that intracellular controls must be shared to account for the similarities in their kinetics of expression and CsA sensitivity.