gebhart/patrepeval huggingface dataset:
[Biological characteristics of human umbilical cord-derived mesenchymal stem cells and their differentiation into chondrogenic and osteogenic cells]. (2011)

The human MSCs could be isolated from human umbilical cord Wharton's jelly, and it was easy to propagate these MSCs. An in vitro method for isolation and purification of hUCMSCs from human umbilical cord has been established. The cultured cells were composed of only undifferentiated cells and their biological properties were stable. The hUCMSCs are expected to be a new type of stem cells of tissue engineering.
A Heterocyclic Peptide Nanotube (2003)

An open-ended hollow tubular structure is designed based on hydrogen-bond-directed self-assembly of a chimeric cyclic peptide subunit comprised of alternating alpha- and epsilon-amino acids. The design features a novel 1,4-disubstituted-1,2,3-triazole epsilon-amino acid and its utility as a peptide backbone substitute. The N-Fmoc-protected epsilon-amino acid was synthesized in high yield and optical purity in three steps from readily available starting materials and was employed in solid-phase peptide synthesis to afford the desired cyclic peptide structure. The cyclic peptide self-assembly has been studied in solution by (1)H NMR and mass spectrometry and the resulting tubular ensemble characterized in the solid state by X-ray crystallography.
The Agrobacterium Ti Plasmids (2014)

This chapter summarizes the latest information about Ti-encoded functions, with emphasis on the mechanistic studies of proteins associated with pathogenesis and intercellular signaling. The ability to transfer T-DNA across kingdom boundaries is a hallmark feature of the Agrobacterium tumefaciens infection process. Moreover, the presence of overdrive is correlated with increased production of single-stranded T-DNA, the T-strand, which corresponds to the translocation-competent form of the T-DNA. A. tumefaciens strains in the vicinity of the transformed plant cells can then import the opines by mechanisms described for use as sources of carbon and energy and, in some cases, nitrogen. The converse model, that VirA interacts directly with phenolic signals, is supported by two genetic lines of study. First, virA genes from different strains of A. tumefaciens, when introduced into an isogenic background, encode VirA proteins that sense different types of inducers. Second, a recent study reported the reconstitution of the VirA/VirG two-component system in Escherichia coli. VirE1 interacts with an N-terminal domain and at least one internal domain of VirE2. Finally, VirD4 recently was shown to assemble at the poles of A. tumefaciens. One of the most striking features of the Ti plasmids is the evolution of an extensive regulatory network that serves to link the activities of the five conserved gene sets. Studies on the regulatory circuitries governing Ti plasmid gene expression will lead to a refined, mechanistic understanding of the paradigmatic regulatory factors VirA and VirG, OccR and AccR, and TraR.
Analysis of Variance (1965)

第１部 １８８８年—１９０８年（幼年時代の空想；青年期の苦痛；「ジュリエット」自叙伝的実験；禁じられた愛；芸術の慰安；意志に対する感情） 第２部 １９０８年—１９１５年（ロンドンと二重生活；『ドイツの宿』の小説；孤独と危険；ミドルトン・マリと幼年時代のテーマ；夢に対する現実；役割演技） 第３部 １９１５—１９１８年（弟の死；「前奏曲」；小説としてのガーシントン；「私はフランス語が話せない」；悪夢の結婚） 第４部 １９１８年—１９２３年（「落着きを失った男」；母、父と「亡き大佐の娘たち」；愛よりもっと胸のおどる—正直；「入江のほとり」；死に悩まされる；追伸）
Light-Induced Rescue of Breathing after Spinal Cord Injury (2008)

Paralysis is a major consequence of spinal cord injury (SCI). After cervical SCI, respiratory deficits can result through interruption of descending presynaptic inputs to respiratory motor neurons in the spinal cord. Expression of channelrhodopsin-2 (ChR2) and photostimulation in neurons affects neuronal excitability and produces action potentials without any kind of presynaptic inputs. We hypothesized that after transducing spinal neurons in and around the phrenic motor pool to express ChR2, photostimulation would restore respiratory motor function in cervical SCI adult animals. Here we show that light activation of ChR2-expressing animals was sufficient to bring about recovery of respiratory diaphragmatic motor activity. Furthermore, robust rhythmic activity persisted long after photostimulation had ceased. This recovery was accomplished through a form of respiratory plasticity and spinal adaptation which is NMDA receptor dependent. These data suggest a novel, minimally invasive therapeutic avenue to exercise denervated circuitry and/or restore motor function after SCI.
Purification and Characterization of Exo-β- d -Glucosaminidase from a Cellulolytic Fungus, Trichoderma reesei PC-3-7 (1998)

Chitosan-degrading activities induced by glucosamine (GlcN) or N-acetylglucosamine (GlcNAc) were found in a culture filtrate of Trichoderma reesei PC-3-7. One of the chitosan-degrading enzymes was purified to homogeneity by precipitation with ammonium sulfate followed by anion-exchange and hydrophobic-interaction chromatographies. The enzyme was monomeric, and its molecular mass was 93 kDa. The optimum pH and temperature of the enzyme were 4.0 and 50 degrees C, respectively. The activity was stable in the pH range 6.0 to 9.0 and at a temperature below 50 degrees C. Reaction product analysis from the viscosimetric assay and thin-layer chromatography and H nuclear magnetic resonance spectroscopy clearly indicated that the enzyme was an exo-type chitosanase, exo-beta-d-glucosaminidase, that releases GlcN from the nonreducing end of the chitosan chain. H nuclear magnetic resonance spectroscopy also showed that the exo-beta-d-glucosaminidase produced a beta-form of GlcN, demonstrating that the enzyme is a retaining glycanase. Time-dependent liberation of the reducing sugar from partially acetylated chitosan with exo-beta-d-glucosaminidase and the partially purified exo-beta-d-N-acetylglucosaminidase from T. reesei PC-3-7 suggested that the exo-beta-d-glucosaminidase cleaves the glycosidic link of either GlcN-beta(1-->4)-GlcN or GlcN-beta(1-->4)-GlcNAc.
Human immunodeficiency virus type 1 infection of human CD4-transgenic rabbits (1995)

Investigations of human immunodeficiency virus (HIV) infection of man have benefited from the study of relevant animal models of the infection and disease. However, the ultimate models use primate species which are either endangered, not generally available, or expensive to maintain. A transgenic rabbit specifically and stably expressing human CD4 protein on T lymphocytes was assessed as a new laboratory animal model for HIV-1 infection. In vitro studies demonstrate that lymphocytes derived from the transgenic rabbits are more susceptible to HIV-1IIIB infection than those from normal rabbits. In vivo infection of huCD4-transgenic rabbits using HIV-1IIIB-infected autologous lymphocytes was demonstrated by virus isolation, detection of HIV-1-specific DNA in peripheral blood lymphocytes and seroconversion to various HIV-1 proteins. Viral DNA was detected in the tissues of one rabbit sacrificed 7 weeks post-infection and virus was isolated from lymph node. Although these transgenic rabbits are less sensitive to HIV-1 infection than man, such a small and inexpensive animal model may be a useful tool.
Identification and characterization of circulating human transitional B cells (2005)

Murine B-cell development begins in bone marrow and results in the generation of immature transitional B cells that transit to the spleen to complete their maturation. It remains unclear whether the same developmental pathway takes place in humans. Using markers characteristic of human bone marrow immature B cells, we have identified a population of circulating human B cells with a phenotype most similar to mouse transitional type I (T1) B cells, although these human counterparts express CD5. These cells die rapidly in culture, and B-cell activation factor member of the tumor necrosis factor (TNF) family (BAFF) does not effect their survival regardless of B-cell receptor (BCR) stimulation. In contrast, bone marrow stromal cells or interleukin-4 (IL-4) significantly enhanced their survival. In the presence of T-cell signals provided by IL-4 or CD40 ligation, BCR stimulation can induce progression into cell cycle. Interestingly, circulating B cells that phenotypically and functionally resemble murine T2 B cells are found in cord blood and adult peripheral blood, suggesting that B-cell maturation may not be restricted to the spleen. Notably, increased proportions of T1 B cells were found in blood of patients with systemic lupus erythematosus (SLE), although bone marrow production and selection appeared to be normal.
Beginning or end? Telomere structure, genetics and biology (1992)

The word telomere derives from the Greek word telos meaning 'end', roughly translating as 'the thing at the end' when the end is that of a chromosome. Telomeres belie their apparent simplicity of structure by being involved in a wide range of diverse biological phenomena. Much of our understanding of telomere behaviour comes from studies in lower eukaryotes such as ciliates and yeast, the subject of many recent reviews. Here we concentrate on the mammalian telomere, recent progress in its study, and how recent evidence for an involvement of telomeres in the regulation of gene expression and DNA replication in yeast points to new aspects of mammalian telomere function yet to be explored.
Normal flow patterns of intracranial and spinal cerebrospinal fluid defined with phase-contrast cine MR imaging. (1991)

A phase-contrast cine magnetic resonance (MR) imaging technique was used to study normal dynamics of cerebrospinal fluid (CSF) in 10 healthy volunteers and four patients with normal MR images. This pulse sequence yielded 16 quantitative flow-encoded images per cardiac cycle (peripheral gating). Flow encoding depicted craniocaudal flow as high signal intensity and caudo-cranial flow as low signal intensity. Sagittal and axial images of the head, cervical spine, and lumbar spine were obtained, and strategic sites were analyzed for quantitative CSF flow. The onset of CSF systole in the subarachnoid space was synchronous with the onset of systole in the carotid artery. CSF systole and diastole at the foramen of Monro and aqueduct were essentially simultaneous. The systolic and diastolic components were different in the subarachnoid space, where systole occupied approximately 40% and diastole 60% of the cardiac cycle, compared with the ventricular system, where they were equal. This difference results in systole in the intracranial and spinal subarachnoid spaces preceding that in the ventricular system; the same is true for diastole. The fourth ventricle and cisterna magna serve as mixing chambers. The high-velocity flow in the cervical spine and essentially no flow in the distal lumbar sac indicate that a portion of the capacitance necessary in this essentially closed system resides in the distal spinal canal.
Sequential proton NMR assignments of kistrin, a potent platelet aggregation inhibitor and glycoprotein IIb-IIIa antagonist (1992)

Sequence-specific nuclear magnetic resonances assignments have been obtained for the protons of kistrin. Kistrin is a small naturally occurring snake venom protein that inhibits platelet aggregation by blocking the interaction of fibrinogen with the membrane-bound glycoprotein IIb-IIIa (GP IIb-IIIa), a receptor from the integrin family. Kistrin has an Arg-Gly-Asp sequence which is believed to form an adhesion recognition sequence that is essential for activity. Therefore, the interaction between kistrin and GP IIb-IIIa may provide important information on the motif used by integrins to recognize their target proteins which bear RGD sequences. Kistrin consists of 68 residues and contains six intramolecular disulfide bonds. Although one-third of the amide protons are protected from exchange with the solvent, there appears to be little or no regular secondary structure. The large number of NOE's between residues separated by two and three positions in the sequence indicates that the protein contains a large number of tightly packed loops. Along with the sequential assignments, this paper also discusses the construction and use of computerized data bases for manipulating NMR results. A strategy for computer-assisted sequential resonance using these data bases is also presented.
Genome Engineering of Virulent Lactococcal Phages Using CRISPR-Cas9 (2017)

Phages are biological entities found in every ecosystem. Although much has been learned about them in past decades, significant knowledge gaps remain. Manipulating virulent phage genomes is challenging. To date, no efficient gene-editing tools exist for engineering virulent lactococcal phages. Lactococcus lactis is a bacterium extensively used as a starter culture in various milk fermentation processes, and its phage sensitivity poses a constant risk to the cheese industry. The lactococcal phage p2 is one of the best-studied models for these virulent phages. Despite its importance, almost half of its genes have no functional assignment. CRISPR-Cas9 genome editing technology, which is derived from a natural prokaryotic defense mechanism, offers new strategies for phage research. Here, the well-known Streptococcus pyogenes CRISPR-Cas9 was used in a heterologous host to modify the genome of a strictly lytic phage. Implementation of our adapted CRISPR-Cas9 tool in the prototype phage-sensitive host L. lactis MG1363 allowed us to modify the genome of phage p2. A simple, reproducible technique to generate precise mutations that allow the study of lytic phage genes and their encoded proteins in vivo is described.
Data Clustering using Memristor Networks (2015)

Memristors have emerged as a promising candidate for critical applications such as non-volatile memory as well as non-Von Neumann computing architectures based on neuromorphic and machine learning systems. In this study, we demonstrate that memristors can be used to perform principal component analysis (PCA), an important technique for machine learning and data feature learning. The conductance changes of memristors in response to voltage pulses are studied and modeled with an internal state variable to trace the analog behavior of the device. Unsupervised, online learning is achieved in a memristor crossbar using Sanger's learning rule, a derivative of Hebb's rule, to obtain the principal components. The details of weights evolution during training is investigated over learning epochs as a function of training parameters. The effects of device non-uniformity on the PCA network performance are further analyzed. We show that the memristor-based PCA network is capable of linearly separating distinct classes from sensory data with high clarification success of 97.6% even in the presence of large device variations.
Pluribus—An operational fault-tolerant multiprocessor (1978)

The authors describe the Pluribus multiprocessor system, outline several techniques used to achieve fault-tolerance, describe their field experience to date, and mention some potential applications. The Pluribus system places the major responsibility for recovery from failures on the software. Failing hardware modules are removed from the system, spare modules are substituted where available, and appropriate initialization is performed. In applications where the goal is maximum availability rather than totally fault-free operation, this approach represents a considerable savings in complexity and cost over traditional implementations. The software-based reliability approach has been extended to provide enror-handling and recovery mechanisms for the system software structures as well. A number of Pluribus systems have been built and are currently in operation. Experience with these systems has given us confidence in their performance and maintainability, and leads us to suggest other applications that might benefit from this approach.
Building Atomic, Crash-Consistent Data Stores with Disaggregated Persistent Memory (2019)

Byte-addressable persistent memories (PM) has finally made their way into production. An important and pressing problem that follows is how to deploy them in existing datacenters. One viable approach is to attach PM as self-contained devices to the network as disaggregated persistent memory, or DPM. DPM requires no changes to existing servers in datacenters; without the need to include a processor, DPM devices are cheap to build; and by sharing DPM across compute servers, they offer great elasticity and efficient resource packing. This paper explores different ways to organize DPM and to build data stores with DPM. Specifically, we propose three architectures of DPM: 1) compute nodes directly access DPM (DPM-Direct); 2) compute nodes send requests to a coordinator server, which then accesses DPM to complete a request (DPM-Central); and 3) compute nodes directly access DPM for data operations and communicate with a global metadata server for the control plane (DPM-Sep). Based on these architectures, we built three atomic, crash-consistent data stores. We evaluated their performance, scalability, and CPU cost with micro-benchmarks and YCSB. Our evaluation results show that DPM-Direct has great small-size read but poor write performance; DPM-Central has the best write performance when the scale of the cluster is small but performs poorly when the scale increases; and DPM-Sep performs well overall.
Protograph-based Raptor-like LDPC codes with low thresholds (2012)

This paper presents a new construction of punctured-node protograph-based Raptor-like (PN-PBRL) codes that is suitable for long-blocklength applications. As with the Raptor codes, additional parity bits can be easily produced by exclusive-OR operations on the precoded bits, providing extensive rate compatibility. The new construction provides low iterative decoding thresholds that are within 0.45 dB of the capacity for all code rates studied, and the construction is suitable for long blocklengths. Comparing at the same information block size of k = 16368 bits, the PN-PBRL codes are as good as the best known AR4JA codes in the waterfall region. The PN-PBRL codes also perform comparably to DVB-S2 LDPC codes even though the DVBi-S2 codes have longer blocklength and outer BCH codes.
Transcriptional targeting of herpes simplex virus for cell-specific replication (1997)

Tissue- or cell-specific targeting of vectors is critical to the success of gene therapy. We describe a novel approach to virus-mediated gene therapy, where viral replication and associated cytotoxicity are limited to a specific cell type by the regulated expression of an essential immediate-early viral gene product. This is illustrated with a herpes simplex virus type 1 (HSV-1) vector (G92A) whose growth is restricted to albumin-expressing cells. G92A was constructed by inserting an albumin enhancer/promoter-ICP4 transgene into the thymidine kinase gene of mutant HSV-1 d120, deleted for both copies of the ICP4 gene. This vector also contains the Escherichia coli lacZ gene under control of the thymidine kinase promoter, a viral early promoter, to permit easy detection of infected cells containing replicating vector. In the adult, albumin is expressed uniquely in the liver and in hepatocellular carcinoma and is transcriptionally regulated. The plaquing efficiency of G92A is > 10(3) times higher on human hepatoma cells than on non-albumin-expressing human cells. The growth kinetics of G92A in albumin-expressing cells is delayed compared with that of wild-type HSV-1, likely due to aberrant expression of ICP4 protein. Cells undergoing a productive infection expressed detectable levels of ICP4 protein, as well as the reporter gene product beta-galactosidase. Confining a productive, cytotoxic viral infection to a specific cell type should be useful for tumor therapy and the ablation of specific cell types for the generation of animal models of disease.
Molecular Genetics of Human Blue Cone Monochromacy (1989)

Blue cone monochromacy is a rare X-linked disorder of color vision characterized by the absence of both red and green cone sensitivities. In 12 of 12 families carrying this trait, alterations are observed in the red and green visual pigment gene cluster. The alterations fall into two classes. One class arose from the wild type by a two-step pathway consisting of unequal homologous recombination and point mutation. The second class arose by nonhomologous deletion of genomic DNA adjacent to the red and green pigment gene cluster. These deletions define a 579-base pair region that is located 4 kilobases upstream of the red pigment gene and 43 kilobases upstream of the nearest green pigment gene; this 579-base pair region is essential for the activity of both pigment genes.
Migraine: New Molecular Mechanisms (2005)

Migraine is an episodic headache disorder affecting more than 10% of the general population. Migraine arises from a primary brain dysfunction that leads to activation and sensitization of the trigeminovascular system. A major incompletely understood issue in the neurobiology of migraine concerns the molecular and cellular mechanisms that underlie the primary brain dysfunction and lead to activation and sensitization of the trigeminovascular system, thus generating and maintaining migraine pain. Here the author reviews recent discoveries that have advanced our understanding of these mechanisms toward a unifying pathophysiological hypothesis, in which cortical spreading depression (CSD), the phenomenon underlying migraine aura, assumes a key role. In particular, the author discusses the main recent findings in the genetics and neurobiology of familial hemiplegic migraine and the insights they provide into the molecular and cellular mechanisms that may lead to the increased susceptibility of CSD in migraineurs.
Pulsatile ocular blood flow study: decreases in exudative age related macular degeneration (2001)

These data show that the POBF and PA in the patients with exudative AMD are lower than in the patients with non-exudative AMD and normal subjects. Decreased choroidal blood flow may have a role in the development of choroidal neovascularisation in AMD.
User-Driven Frequency Scaling (2006)

We propose and evaluate user-driven frequency scaling (UDFS) for improved power management on processors that support dynamic voltage and frequency scaling (DVFS), e.g, those used in current laptop and desktop computers. UDFS dynamically adapts CPU frequency to the individual user and the workload through a simple user feedback mechanism, unlike currently-used DVFS methods which rely only on CPU utilization. Our UDFS algorithms dramatically reduce typical operating frequencies while maintaining performance at satisfactory levels for each user. We evaluated our techniques through user studies conducted on a Pentium M laptop running Windows applications. The UDFS scheme reduces measured system power by 22.1%, averaged across all our users and applications, compared to the Windows XP DVFS scheme