gebhart/patrepeval huggingface dataset:
The traE Gene of Plasmid RP4 Encodes a Homologue of Escherichia coli DNA Topoisomerase III (1997)

The polypeptide encoded by the plasmid RP4 traE gene shows extensive protein sequence similarity to Escherichia coli topB, the gene encoding DNA topoisomerase III (Topo III). The traE gene product has been cloned into a bacteriophage T7-based transient expression system, and the polypeptide has been expressed and purified. The TraE protein exhibits topoisomerase activity similar to that of Topo III. Relaxation is stimulated by high temperature and low concentrations of Mg2+. In addition, similar to E. coli Topo III, the TraE protein is a potent decatenase and can substitute for Topo III activity in vivo. The biochemical properties of the TraE protein in vitro suggest that the protein may be involved in the resolution of plasmid DNA replication intermediates either during vegetative replication or in conjugative DNA transfer. Putative homologues of Topo III have been found to be encoded by other broad host range, conjugative plasmids isolated from both Gram-negative and Gram-positive organisms, suggesting that Topo III-like polypeptides may have an essential role in the propagation of many promiscuous plasmids.
Cutinase structure, function and biocatalytic applications (1998)

This review analyses the role of cutinases in nature and their potential biotechnological applications. The cloning and expression of a fungal cutinase from Fusarium solani f. pisi, in Escherichia coli and Saccharomyces cerevisiae hosts are described. The three dimensional structure of this cutinase is also analysed and its function as a lipase discussed and compared with other lipases. The biocatalytic applications of cutinase are described taking into account the preparation of different cutinase forms and the media where the different types of enzymatic reactions have been performed, namely hydrolysis, esterification, transesterification and resolution of racemic mixtures. The stability of cutinase preparations is discussed, particularly in anionic reversed micelles considering the role of hexanol as substrate, co-surfactant and stabilizer. Process development based on the operation of cutinase reactors is also reviewed.
A Simulation Study of Deep Belief Network Combined with the Self-Organizing Mechanism of Adaptive Resonance Theory (2010)

Computer simulation study of brain neuronal networks is an active academic field. Deep Belief Network (DBN) introduces an effective way of training deep neural networks and the Adaptive Resonance Theory (ART) puts forward a two-layer competitive network emulating human cognitive processes. In our study, we implement a DBN with the mechanism of ART which benefits from DBN's multi-layer structure and ART's self-organizing stable learning mechanism. Our preliminary results show that the optimal number of layers is relevant to the data learned. The correct reconstruction rate decreases slowly with respect to the volume of data stored.
Absolute requirement of macrophages for the development and activation of beta-cell cytotoxic CD8+ T-cells in T-cell receptor transgenic NOD mice. (1999)

The development of autoimmune diabetes in NOD mice results from selective destruction of beta-cells by a T-cell-dependent autoimmune process. However, the mechanisms that control the generation of beta-cell cytotoxic T-cells in vivo are poorly understood. We recently established 8.3-T-cell receptor (TCR)-beta transgenic NOD mice that show a selective acceleration of the recruitment of CD8+ T-cells into the islets of prediabetic animals, resulting in rapid beta-cell destruction and early onset of diabetes. This study was initiated to determine the role of macrophages in the development and activation of diabetogenic CD8+ T-cells in 8.3-TCR-beta transgenic NOD mice. Inactivation of macrophages in these transgenic mice resulted in the complete prevention of diabetes. When splenic T-cells from macrophage-depleted 8.3-TCR-beta transgenic NOD mice were transfused into severe combined immunodeficiency disease (NOD.scid) mice, none of the recipients developed diabetes up to 10 weeks after transfer, while most of the recipients of T-cells from age-matched control 8.3-TCR-beta transgenic NOD mice became diabetic. When intact NOD islets were transplanted under the renal capsule of macrophage-depleted 8.3-TCR-beta transgenic NOD mice, the majority of the grafted islets remained intact, while most of the islets grafted into age-matched, control 8.3-TCR-beta transgenic NOD mice were destroyed within 3 weeks after transplantation. The depletion of macrophages in these mice resulted in a decrease in the Th1 immune response along with an increase in the Th2 immune response because of significant decreases in the expression of macrophage-derived cytokines, particularly interleukin-12, and a decrease in beta-cell-specific T-cell activation, as shown by significant decreases in the expression of Fas ligand (FasL), CD40 ligand (CD40L), and perforin, as compared with control mice. We conclude that macrophages are absolutely required for the development and activation of beta-cell cytotoxic CD8+ T-cells in 8.3-TCR-beta transgenic NOD mice.
Transition-State Mimetics for HIV Protease Inhibitors:  Stereocontrolled Synthesis of Hydroxyethylene and Hydroxyethylamine Isosteres by Ester-Derived Titanium Enolate Syn and Anti-Aldol Reactions (1998)

Stereocontrolled syntheses of hydroxyethylene dipeptide isostere and aminoalkyl epoxides for hydroxyethylamine isosteres are described. The stereochemistry of both stereogenic centers of the aminoalkyl epoxides 10 and 15 as well as the gamma-lactone 17 was assembled by our recently developed highly selective ester-derived titanium enolate aldol reactions. The Ti-enolate of 6 reacted with (benzyloxy)acetaldehyde and cinnamaldehyde to provide the syn-aldol product 7 and anti-aldol product 12, respectively. Removal of the chiral template followed by Curtius rearrangement of the resulting acid provided the desired amine functionality. The present syntheses represent practical and enantioselective entry to a range of other dipeptide isosteres, which are not limited to amino acid derived substituents.
PEST sequences are signals for rapid intracellular proteolysis. (1990)

Many features of a protein can enhance its degradation within cells. Unlike thermal lability or oxidizability which increase the likelihood of damage, PEST sequences are built-in signals for destruction. These stretches of polypeptide chain rich in proline (P), glutamate (E), serine (S) and threonine (T) are invariably found in rapidly degraded enzymes, transcriptional factors and components of receptor signalling pathways. They are, by contrast, rarely present among long-lived cellular proteins. In this brief essay, I review the properties of PEST sequences, recent experimental support for the idea that they are indeed proteolytic signals, and possible pathways for catabolism of PEST proteins.
Automatic organization for digital photographs with geographic coordinates (2004)

We describe PhotoCompas, a system that utilizes the time and location information embedded in digital photographs to automatically organize a personal photo collection PhotoCompas produces browseable location and event hierarchies for the collection. These hierarchies are created using algorithms that interleave time and location to produce an organization that mimics the way people think about their photo collections. In addition, our algorithm annotates the generated hierarchy with geographical names. We tested our approach in case studies of three real--world collections and verified that the results are meaningful and useful for the collection owners.
Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors (2017)

The RNA interference pathway is an evolutionary conserved post-transcriptional gene regulation mechanism that is exclusively triggered by double-stranded RNA inducers. RNAi-based methods and technologies have facilitated the discovery of many basic science findings and spurred the development of novel RNA therapeutics. Transient induction of RNAi via transfection of synthetic small interfering RNAs can trigger the selective knockdown of a target mRNA. For durable silencing of gene expression, either artificial short hairpin RNA or microRNA encoding transgene constructs were developed. These miRNAs are based on the molecules that induce the natural RNAi pathway in mammals and humans: the endogenously expressed miRNAs. Significant efforts focused on the construction and delivery of miRNA cassettes in order to solve basic biology questions or to design new therapy strategies. Several viral vectors have been developed, which are particularly useful for the delivery of miRNA expression cassettes to specific target cells. Each vector system has its own unique set of distinct properties. Thus, depending on the specific application, a particular vector may be most suitable. This field was previously reviewed for different viral vector systems, and now the recent progress in the field of miRNA-based gene-silencing approaches using lentiviral vectors is reported. The focus is on the unique properties and respective limitations of the available vector systems for miRNA delivery.
25 nm chromium oxide lines by scanning tunneling lithography in air (1994)

An ambient scanning tunneling microscope is used to oxidize a thin Cr film to different oxidation states depending on the exposure conditions. These oxidation states have shown very different chemical and physical properties and can be used as positive or negative masks for lithography. Chromium oxide lines down to 25 nm have been formed.
Structural Abnormalities in the Brains of Human Subjects Who Use Methamphetamine (2004)

We visualize, for the first time, the profile of structural deficits in the human brain associated with chronic methamphetamine (MA) abuse. Studies of human subjects who have used MA chronically have revealed deficits in dopaminergic and serotonergic systems and cerebral metabolic abnormalities. Using magnetic resonance imaging (MRI) and new computational brain-mapping techniques, we determined the pattern of structural brain alterations associated with chronic MA abuse in human subjects and related these deficits to cognitive impairment. We used high-resolution MRI and surface-based computational image analyses to map regional abnormalities in the cortex, hippocampus, white matter, and ventricles in 22 human subjects who used MA and 21 age-matched, healthy controls. Cortical maps revealed severe gray-matter deficits in the cingulate, limbic, and paralimbic cortices of MA abusers (averaging 11.3% below control; p < 0.05). On average, MA abusers had 7.8% smaller hippocampal volumes than control subjects (p < 0.01; left, p = 0.01; right, p < 0.05) and significant white-matter hypertrophy (7.0%; p < 0.01). Hippocampal deficits were mapped and correlated with memory performance on a word-recall test (p < 0.05). MRI-based maps suggest that chronic methamphetamine abuse causes a selective pattern of cerebral deterioration that contributes to impaired memory performance. MA may selectively damage the medial temporal lobe and, consistent with metabolic studies, the cingulate-limbic cortex, inducing neuroadaptation, neuropil reduction, or cell death. Prominent white-matter hypertrophy may result from altered myelination and adaptive glial changes, including gliosis secondary to neuronal damage. These brain substrates may help account for the symptoms of MA abuse, providing therapeutic targets for drug-induced brain injury.
The protein coded by the X‐adrenoleukodystrophy gene is a peroxisomal integral membrane protein (1994)

The gene for adrenoleukodystrophy (X-ALD), a peroxisomal disease characterized by excessive accumulation of very long-chain (VLC) fatty acids (> C22:0), has recently been identified by positional cloning, and it is predicted to encode a protein (ALD-P) of 745 amino acids [(1993) Nature 361, 726]. Using Western blot analysis of subcellular organelles purified by isopycnic density gradient centrifugation from X-ALD and control fibroblasts, we show that the monoclonal antibodies directed against ALD-P cross-react with a 75 kDa protein in intact peroxisomes and that ALD-P is an integral component of the peroxisomal membrane. Moreover, no signal for ALD-P was detected in peroxisomes from X-ALD patients with deletion of the ALD gene.
Extracellular Matrix Gene Regulation (2004)

Extracellular matrix metabolism plays a central role in development of skeletal tissues and in most orthopaedic diseases and trauma such as fracture or osteotomy repair, arthritis, cartilage repair, and congenital skeletal deformity. During development or disease, specific genes must be expressed in order to make or repair appropriate extracellular matrix. For example, specific gene expression patterns are characteristic of bone and cartilage. The precise expression pattern depends on a balance of positive and negative transcription factors, proteins that control the synthesis of mRNA from the specific gene. In cartilage, a number of studies indicate that Sox transcription factors are critical positive regulators in genes such as COL2A1, COL9A2, COL11A2, aggrecan, and CD-RAP. In addition, negative regulators are also essential to fine tune gene regulation in chondrocytes and to turn off gene expression in noncartilaginous tissues. Negative transcription factors in cartilage include partial differentialEF-1, snail/slug, CYRBP1, NT2, and C/EBP. Runx2 and osterix are critical transcription factors for osteogenesis but also have some influence on chondrogenesis. The availability of cis-regulatory sites in specific genes combined with the availability of transcription factors in the nucleus determines the level of gene expression.
Status Epilepticus in Immature Rats (1976)

The role of glucose metabolism in alleviating the complications of status epilepticus (SE) was investigated in developing rats. Pretreatment with glucose reduced mortality from SE by 90% in rats under 1 week of age, 80% in 10-day-old rats, 50% in 15- to 20-day-olds, and not at all in adults. In 4-day-old animals, brain DNA synthesis during seizures, and in survivors, brain weight, DNA, RNA, protein, and cholesterol contents at 7 days of age were reduced less in glucose-treated than in saline-treated littermates. In the saline group, seizures caused a progressive fall in brain glucose level but no fall in blood glucose level, suggesting that glucose transport from blood to brain could not keep pace with glycolytic demands. In glucose-treated rats, blood and brain glucose concentrations remained elevated throughout the convulsive period. There was no reduction of brain adenosine triphosphate levels in either group. Thus, the protection by glucose appears to be related to its roles as a carbon source rather than an energy source. It is concluded that in immature animals, depletion of brain glucose can occur in the absence of hypoglycemia, and may be an important and potentially treatable complication of status epilepticus.
Somatic signaling mediated by fs(1)Yb is essential for germline stem cell maintenance during Drosophila oogenesis (1999)

Drosophila oogenesis starts when a germline stem cell divides asymmetrically to generate a daughter germline stem cell and a cystoblast that will develop into a mature egg. We show that the fs(1)Yb gene is essential for the maintenance of germline stem cells during oogenesis. We delineate fs(1)Yb within a 6.4 kb genomic region by transgenic rescue experiments. fs(1)Yb encodes a 4.1 kb RNA that is present in the third instar larval, pupal and adult stages, consistent with its role in regulating germline stem cells during oogenesis. Germline clonal analysis shows that all fs(1)Yb mutations are soma-dependent. In the adult ovary, fs(1)Yb is specifically expressed in the terminal filament cells, suggesting that fs(1)Yb acts in these signaling cells to maintain germline stem cells. fs(1)Yb encodes a novel hydrophilic protein with no potential signal peptide or transmembrane domains, suggesting that this protein is not itself a signal but a key component of the signaling machinery for germline stem cell maintenance.
Synthesis and Alkali-cation Complexing Properties of 12-Crown-4 Derivatives (1982)

Abstract Benzyloxymethyl-12-crown-4, a precursor of hydroxymethyl-12-crown-4, is prepared in an excellent yield by the reaction of 3-benzyloxy-1,2-propanediol with 1,8-dichloro-3,6-dioxaoctane in the heterogeneous t-BuOLi/t-BuOH/LiBr·2H2O reaction system. The hydrogenolysis in the presence of p-toluenesulfonic acid leads to a good yield of hydroxymethyl-12-crown-4. The sandwich-type 2:1 complexation with Na+ of 12-crown-4 and hydroxymethyl-12-crown-4 derivatives was discussed on the basis of the stability constants and the solvent extraction in the CH2Cl2–water system.
Nasal carriage of Staphylococcus aureus: the key to preventing staphylococcal disease (1996)

Postoperative infections (Pis) are serious complications of thoracic surgery. To gain insight\\ninto the nature and the scope of the problem, an 18 month prospective surveillance was\\nconducted at the department of thoracic surgery of the University Hospital Rotterdam,\\nDijkzigt. Pis were classified according to CDC criteria. One hundred and ninety-four out of\\n983 patients (19.7%) developed one or more Pis and in these 194 patients, 268 Pis were\\ndiagnosed. The incidence of Pis was 2.0 per 100 days of postoperative stay. The mean\\npostoperative length of stay (LOS) of the 194 patients with Pis was 14.1 days longer than\\nthose without Pis. Deep surgical wound infections (DSWls) were associated with the longest\\nprolongation of the median postoperative LOS in the hospital (30 days longer). Although\\nlower than DSWls, incisional surgical wound infections also had a significant prolongation of\\nstay (median 10 days longer). Staphylococcus aureus was the most important pathogen\\nassociated with surgical wound infections (SWls). Phage typing of 29 strains causing SWI\\nshowed only two identical pairs, so only a minority of infections could be explained by crossinfection.\\nOlder age, and more complicated procedures (e.g. cardiac valve operations) were\\nindependent, statistically significant risk factors for the development of Pis. Since there is a\\nprogressive trend towards operating on older patients and performing more complicated\\nprocedures, the incidence of Pis is expected to increase. Therefore it will become increasingly\\nimportant to develop new strategies to prevent these serious complications.
A Simple and Rapid Protocol to Non-enzymatically Dissociate Fresh Human Tissues for the Analysis of Infiltrating Lymphocytes (2014)

The ability of malignant cells to evade the immune system, characterized by tumor escape from both innate and adaptive immune responses, is now accepted as an important hallmark of cancer. Our research on breast cancer focuses on the active role that tumor infiltrating lymphocytes play in tumor progression and patient outcome. Toward this goal, we developed a methodology for the rapid isolation of intact lymphoid cells from normal and abnormal tissues in an effort to evaluate them proximate to their native state. Homogenates prepared using a mechanical dissociator show both increased viability and cell recovery while preserving surface receptor expression compared to enzyme-digested tissues. Furthermore, enzymatic digestion of the remaining insoluble material did not recover additional CD45(+) cells indicating that quantitative and qualitative measurements in the primary homogenate likely genuinely reflect infiltrating subpopulations in the tissue fragment. The lymphoid cells in these homogenates can be easily characterized using immunological (phenotype, proliferation, etc.) or molecular (DNA, RNA and/or protein) approaches. CD45(+) cells can also be used for subpopulation purification, in vitro expansion or cryopreservation. An additional benefit of this approach is that the primary tissue supernatant from the homogenates can be used to characterize and compare cytokines, chemokines, immunoglobulins and antigens present in normal and malignant tissues. This protocol functions extremely well for human breast tissues and should be applicable to a wide variety of normal and abnormal tissues.
Immediate and long-term atrial sensing stability in single-lead VDD pacing depends on right atrial dimensions (2001)

According to our data, in VDD single-lead systems the amplitude of the atrial signal is stable over time in every physical activity. High RAD and low RAVD values may select patients with poor atrial sensing stability. Anyway, taking into account that no atrial oversensing was observed, atrial sensitivity setting at the highest value should be recommended.
A ligand-binding pocket in the dengue virus envelope glycoprotein (2003)

Dengue virus is an emerging global health threat. Its major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. A crystal structure of the soluble ectodomain of E from dengue virus type 2 reveals a hydrophobic pocket lined by residues that influence the pH threshold for fusion. The pocket, which accepts a hydrophobic ligand, opens and closes through a conformational shift in a beta-hairpin at the interface between two domains. These features point to a structural pathway for the fusion-activating transition and suggest a strategy for finding small-molecule inhibitors of dengue and other flaviviruses.
Pan-neurotrophin 1: a genetically engineered neurotrophic factor displaying multiple specificities in peripheral neurons in vitro and in vivo. (1995)

Pan-neurotrophin 1 (PNT-1) is a synthetic trophic factor engineered by combining active domains of the neurotrophins nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin 3 (NT-3) into an NT-3 backbone. This molecule was produced in transiently transfected COS cells or in baculovirus-infected insect cells transfected COS cells or in baculovirus-infected insect cells and subsequently purified to homogeneity. Saturation binding in embryonic spinal sensory neurons demonstrated a greater number of high-affinity binding sites for PNT-1 than for its parental molecule NT-3. PNT-1 was shown to efficiently block the chemical crosslinking of NGF, BDNF, and NT-3 to their cognate Trk receptors and to the low-affintiy NGF receptor expressed on neuronal and nonneuronal cells. PNT-1 stimulated survival and proliferation of MG87 fibroblasts expressing either TrkA, TrkB, or TrkC. PNT-1 also promoted survival of a greater number of embryonic dorsal root ganglion neurons than any of the other neurotrophins alone, and its effects were equivalent to a combination of NGF, BDNF, and NT-3. Analysis of receptor-specific neurotrophic activities demonstrated that PNT-1 efficiently rescued TrkA mRNA-containing sympathetic neurons and TrkB and TrkC mRNA-containing sensory neurons from the dorsal root and nodose ganglia. Finally, PNT-1 showed robust retrograde transport to DRG neurons in vivo after injection into the sciatic nerve. Radiolabeled PNT-1 accumulated in small-, medium-, and large-sized neurons. Coinjection with different unlabeled neurotrophins inhibited PNT-1 transport in distinct subpopulations of neurons of different sizes, suggesting that this molecule affects sensory neurons of different modalities. These results indicate that PNT-1 is a potent and multispecific neurotrophic factor that may be useful in the treatment of peripheral neurophathies and nerve damage.